Structure, catalytic mechanism, and membrane interaction of the mTOR activator Rheb
by
Mohammad Taghi Mazhab Jafari
A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy
Department of Medical Biophysics University of Toronto
© Copyright by Mohammad Taghi Mazhab Jafari 2014
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Structure, catalytic mechanism, and membrane interaction of the
mTOR activator Rheb
Mohammad Taghi Mazhab Jafari
Doctor of Philosophy
Department of Medical Biophysics University of Toronto
2014
Abstract
The activator of mammalian target of rapamycin complex 1 (mTORC1), Ras homolog enriched in brain
(Rheb), is a membrane-associated protein belonging to the Ras subfamily of small GTPases. Rheb’s
slow GTPase activity is stimulated by the GTPase activating protein (GAP) domain of tuberous sclerosis
complex 1 and 2 (TSC1/2). Rheb hyperactivation, through its overexpression or loss of TSC1/2 GAP
function, results in hyperactivated mTORC1 signaling culminating in tumourigenesis. The molecular
details of Rheb GTP hydrolysis and the effect of membrane association on Rheb structure, dynamics and
its GTPase function are currently not fully understood. The studies presented in this thesis focus on two
key determinants of Rheb function i) the mechanism of Rheb GTP hydrolysis and ii) the structural and
functional consequence of Rheb-bilayer membrane interaction. Through studies of fluorescent
nucleotides, we revealed that the conserved G2-box residue Tyr35 auto-inhibits GTP hydrolysis in
Rheb. We demonstrated that a non-canonical catalytic residue, Asp65, in the switch II region of Rheb,
contributed more to the GTP hydrolysis rate than Gln64, which corresponds to the canonical Ras Gln61.
This non-canonical auto-inhibited mechanism of GTP hydrolysis was required for optimal mTORC1
regulation. These structural insights were then used to guide the design of novel gain- and loss-of
function mutants by substitutions of the ultra-conserved G3-box Gly63 of Rheb. Finally, using solution
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NMR spectroscopy, we monitored the Rheb GTPase cycle and characterized its nucleotide-dependent
membrane orientations on nanodisc-based phospholipid bilayers. Rheb was shown to sample two
orientations in which its C-terminal helix was semi-perpendicular or semi-parallel with respect to the
bilayer plane. The semi-parallel orientation, where switch II residues critical for mTORC1
communication are accessible, was favored in the GTP bound conformation, suggesting that membrane-
tethering modulates Rheb function. These structural insights into the catalytic machinery of Rheb and its
membrane interface suggest new approaches to modulate these key determinants of Rheb function
through small molecules towards development of therapeutic avenues for Rheb-mediated pathogenesis
such as tuberous sclerosis or cancer.
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Acknowledgments
First and foremost, I would like to thank my supervisor Dr. Mitsu Ikura for his guidance, support, and
understanding. I could have not accomplished any portion of this research without his supervision. His
passion for science was a continuous source of inspiration for me over the years. I learned key aspects of
successful research from him, including critical thinking.
I am grateful to my supervisory committee members; Dr. Lewis Kay and Dr. Vuk Stambolic. Their
expert inputs were critical to the success of this thesis. Thank you for your advise, supervision and
encouragement, which kept me on the right path.
I am also thankful to my collaborators, Vanessa De Palma and Jason Ho from Dr. Stambolic lab for the
cell biology experiments.
I had the honor of working with and learning from many excellent current and former members of
Ikura’s lab including; Dr. Christopher Marshall, Dr. Peter Stathopulos, Dr. Genevieve Seabrook, Dr.
Noboru Ishiyama, Le Zheng, Dr. Feng Wang, Carol Liu, and Dr. Fernando Amador. I would like to
specially thank Chris, who was involved in all aspects of my projects and gave valuable inputs and
suggestions.
Finally, I would like to thank my family; my parents Mohammad Mazhab-Jafari and Ziba Fadavi and
my brother Hamed Mazhab-Jafari for all their sacrifice that provided me with the opportunity to carry
out this research. Words cannot express my grateful feelings for you.
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Table of Contents
Acknowledgements……………………………………………………………………………………….iv
Table of Contents………………………………………………………………………………………...v
List of Tables…………………………………………………………………………………………….x
List of Figures…………………………………………………………………………………………...xi
List of Appendices……………………………………………………………………………………...xiv
List of Abbreviations…………………………………………………………………………………...xv
Chapter 1: Introduction and Thesis Overview………………………………………………………...1
1.1 General introduction to small GTPase proteins……………………………………………………….2
1.2 Introduction to Rheb………………………………………………………………..............................3
1.3 Biophysical and biochemical properties of Rheb…………………………………..............................6
1.4 Pathogenesis of Rheb………………………………………………………………………………….9
1.5 Thesis Overview and Rationale……………………………………………………………………...11
1.6 Attributions…………………………………………………………………………………………..12
1.7 References……………………………………………………………………………………………12
Chapter 2: Fluorescent-tagged Nucleotides Alter the Native GTPase Cycle…………………….…17
2.1 Abstract………………………………………………………………………………………………18
2.2 Introduction………………………………………………………………………..............................19
2.3 Results………………………………………………………………………………………………..20
2.3.1 The effect of mant on the intrinsic rate of nucleotide hydrolysis………………………….20
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2.3.2 The effect of mant on the rate of GAP-catalyzed nucleotide hydrolysis…………………..23
2.3.3 The effect of mant on the GEF-mediated nucleotide exchange…………………………....25
2.4 Discussion……………………………………………………………………………………………28
2.4.1 Intrinsic hydrolysis of GTP and mantGTP………………………………………………...28
2.4.2 GAP-catalyzed GTP hydrolysis by HRas and Rheb…………………………………….…30
2.4.3 GEF-accelerated nucleotide exchange of HRas and RhoA………………………………..31
2.5 Experimental Procedures…………………………………………………………………………….32
2.5.1 Protein preparation…………………………………………………………………………32
2.5.2 NMR-based GTPase, GAP and GEF assays……………………………………………….33
2.5.3 Fluorescence-based GTPase assay…………………………………………………………34
2.6 References……………………………………………………………………………………………34
Chapter 3: Mechanism of GTP hydrolysis by Rheb……………………………………………..…...36
3.1 Abstract…………………………………………………………………………………………..…..37
3.2 Introduction………………………………………………………………………………………..…38
3.3 Results………………………………………………………………………………………………..39
3.3.1 Rheb Tyr35 inhibits intrinsic GTPase activity……………………………………………..39
3.3.2 Structural basis for the Tyr35 auto-inhibitory function……………………………………40
3.3.3 Identification of a catalytic residue for GTP hydrolysis…………………………………...42
3.3.4 Involvement of Rheb’s Asp65 and Tyr35 in TSC2GAP-mediated GTP hydrolysis…......47
3.3.5 Thermodynamic basis for the Tyr35 auto-inhibitory function…………………………….49
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3.3.6 Regulation of mTORC1 by growth factors involves the non-canonical catalytic and
autoinhibitory mechanisms…………………………………………………………….………...54
3.4 Discussion……………………………………………………………………………………….…...57
3.5 Experimental Procedures……………………………………………………………………….……60
3.5.1 Protein preparation………………………………………………………………….……...60
3.5.2 Crystallization and data collection………………………………………………….……...61
3.5.3 Structure determination and refinement…………………………………………….……...61
3.5.4 NMR-based GTPase assays…………………………………………………………….…62
3.5.5 Thermodynamic measurements……………………………………………………….…..63
3.5.6 Cell-based phosphorylation assay……………………………………………………..…...63
3.5.7 Nucleotide binding in vivo…………………………………………………………………64
3.6 References……………………………………………………………………………………………65
Chapter 4: Structure-guided design of novel active and inactive Rheb mutants using single site
modifications……………………………………………………………………………………………68
4.1 Abstract……………………………………………………………………………………………....69
4.2 Introduction…………………………………………………………………………………………..70
4.3 Results and Discussion……………………………………………………………………………....72
4.4 Experimental Procedures…………………………………………………………………………….78
4.4.1 Protein Preparation…………………………………………………………………………78
4.4.2 NMR-based Real-time GTPase assay……………………………………………………...78
4.4.3 Crystallization and Data Collection………………………………………………………..79
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4.4.4 Structure Determination and Refinement………………………………………………….79
4.4.5 Cell-based Phosphorylation Assays………………………………………………………..80
4.5 References……………………………………………………………………………………………82
Chapter 5: Structural and Functional consequence of Rheb-membrane interaction……………...84
5.1 Abstract………………………………………………………………………………………………85
5.2 Introduction…………………………………………………………………………………………..86
5.3 Results and Discussion………………………………………………………………………………88
5.4 Experimental Procedures……………………………………………………………………….……99
5.4.1 Protein preparations………………………………………………………………….…….99
5.4.2 Preparation of Rheb-nanodisc complex…………………………………………………..100
5.4.3 NMR- measurements……………………………………………………………………..101
5.4.4 Real-time NMR-based GTPase assay………………………………………………….…103
5.4.5 Molecular docking simulation……………………………………………………………103
5.5 References……………………………………………………………………………………….….106
Chapter 6: Conclusions and Future directions……………...………………………………………108
6.1 Conclusions…………………………………………………………………………………………109
6.2 Future Directions…………………………………………………………………………………...110
6.2.1 Engineering GTPase probes by structure-guided mutations of G3-box glycine………....110
6.2.2 Drugging Rheb……………………………………………………………………………111
6.2.3 Probing membrane-dependent regulation of KRas-effector interaction………………….111
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6.3 Closing Remarks……………………………………………………………………………………112
6.4 References…………………………………………………………………………………………..114
Appendix A……………………………………………………………………………………………..116
Appendix B……………………………………………………………………………………………..118
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List of Tables
Table 2.1 The rates of intrinsic and GAP mediated nucleotide hydrolysis for three small GTPase
proteins…………………………………………………………………………………………………..23
Table 2.2: The rates of GEF mediated nucleotide exchange for HRas and RhoA proteins……………..27
Table 3.1 Summary of thermodynamic activation parameters…………………………………………..54
Table 3.2 Data collection and refinement statistics……………………………………………………...62
Table 4.1 Data collection and refinement statistics……………………………………………………...81
Table 5.1 Resonance assignment of Rheb HVR………………………………………………….…....101
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List of Figures
Figure 1.1 Sequence alignment of Rheb with other small GTPase proteins investigated in this thesis......3
Figure 1.2 Schematic illustration of Rheb in the mTORC1 signaling pathway…………………………..5
Figure 1.3 Overall structure of active Rheb and comparison with that of HRas……………………….....8
Figure 2.1 Effect of mant-substituted GTP on the intrinsic nucleotide hydrolysis of Ras, Rheb and
RhoA……………………………………………………………………………………………………..19
Figure 2.2 Comparison of the real-time NMR and fluorescence-substituted nucleotide-based GTPase
assays…………………………………………………………………………………………………….21
Figure 2.3 Perturbation of the native structure of GTPase proteins by mant-tagged nucleotides……….22
Figure 2.4 Effects of mant-substituted GTP on GAP-mediated nucleotide hydrolysis by HRas and
Rheb……………………………………………………………………………………………………...24
Figure 2.5 Effects of mant-substituted nucleotides on GEF-mediated nucleotide exchange for HRas and
RhoA……………………………………………………………………………………………………..26
Figure 2.6 Complementary assays of the effects of mant-substituted nucleotides on GEF-mediated
nucleotide exchange for HRas and RhoA………………………………………………………………..27
Figure 2.7 mantGTP-induced chemical shift perturbations in Ras, Rheb and RhoA……………………29
Figure 2.8 Rheb Gln64 is not involved in the rapid hydrolysis of mantGTP……………………………30
Figure 3.1 Rapid hydrolysis of mantGTP by Rheb is related to autoinhibitory role of Tyr35…………..40
Figure 3.2 Structure and dynamics of Rheb Y35A……………………………………………………....41
Figure 3.3 Mutagenic analysis of potential catalytic residues in Rheb Y35A…………………………...43
Figure 3.4 Role of Asp65 in intrinsic and GAP-mediated GTP hydrolysis by Rheb……………………45
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Figure 3.5 Effect on Rheb GTPase activity of mutations of acidic and electronegative residues in switch
II………………………………………………………………………………………………………….46
Figure 3.6. Structure-function analysis of the position of putative catalytic residues and the conserved
switch I Tyrosine in small GTPases……………………………………………………………………...48
Figure 3.7 Perturbation of Rheb HSQC spectrum by Tyr35 mutation…………………………………..50
Figure 3.8 Minimal chemical shift perturbation associated with mutation of Rheb Asp65…………….51
Figure 3.9 Tyr35 hydroxyl is required for TSC2GAP-assisted GTP hydrolysis………………………...52
Figure 3.10 Effect of Tyr35 and Asp65 mutations on the thermodynamic activation parameters for GTP
hydrolysis by Rheb………………………………………………………………………………………53
Figure 3.11 Mutations of Rheb catalytic and autoinhibitory residues impact Rheb’s activation level and
mTORC1 phosphorylation of p70 S6K…………………………………………………………………55
Figure 3.12 Effects of Y35A and D65A mutations in Rheb on mTORC1 activity……………………...56
Figure 3.13 Schematic model of intrinsic and TSC2GAP-stimulated GTP hydrolysis by Rheb………..59
Figure 4.1) Manipulation of the GTPase cycle of Rheb and mTOR signaling through substitutions of
Gly63…………………………………………………………………………………………………….71
Figure 4.2 Conservation of the G3-box glycine and structural basis for the functional properties of Rheb
Gly63Ala/Val mutants…………………………………………………………………………………..73
Figure 4.3 Electron densities of the catalytic sites of wild-type Rheb and its Gly63 mutations………..74
Figure 4.4 Intrinsic nucleotide hydrolysis and exchange of Rap1A GTPase and its Gly60 mutations…77
Figure 5.1 Tethering Rheb to a bilayer membrane inhibits nucleotide exchange and activation……….87
Figure 5.2 Preparation of Rheb-nanodisc complex……………………………………………………...89
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Figure 5.3 Backbone 15N relaxation data for Rheb-GDP 1-181 in free (black) and nanodisc-bound (red)
states……………………………………………………………………………………………………...91
Figure 5.4 Backbone 15N relaxation data for Rheb-GMPPNP 1-181 in free (black) and nanodisc-bound
(red) states………………………………………………………………………………………………..92
Figure 5.5 Identification of the Rheb-membrane interface and its modulation by the bound nucleotide.93
Figure 5.6 Residues affected by PRE localized on the HADDOCK models…………………………….94
Figure 5.7 Cluster analysis of final HADDOCK solutions………………………………………………95
Figure 5.8 Subtle changes in surface electrostatics upon nucleotide exchange………………………….97
Figure 5.9 Formation of a Rheb-PDEδ complex is compatible with Rheb-nanodisc model 2, but not
model 1…………………………………………………………………………………………………..98
Figure 6.1 Backbone and side chain assignments of free KRas4B in complex with GMPPNP…….…113
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List of Appendices
Appendix A……………………………………………………………………………………………..116
Appendix B…………………………………………………………………………………………….118
xv
List of Abbreviations
4E-BP (eIF)4E-binding proteins
Arf ADP ribosylation factor
BMRB Biological Magnetic Resonance Bank
CNS Crystallography & NMR System
Coot Crystallographic Object-Oriented Toolkit
DH-PH Dbl homology-Pleckstrin-homology
DOPC 1,2-dioleoyl-sn-glycero-3-phosphocholine
DOPS 1,2-dioleoyl-sn-glycero-3-phospho-L-serine
DTT Dithiothreitol
ER Endoplasmic reticulum
EDTA Ethylenediaminetetraacetic acid
FKBP FK506-binding protein
FRET Fluorescence resonance energy transfer
FTI Farnesyltransferase Inhibitors
GAP GTPase activating protein
GDI Guanine Dissociation Inhibitor
GEF Guanine Exchange Factor
GMPPNP 5'-Guanylyl imidodiphosphate
H2Ocat Catalytic water
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HADDOCK High Ambiguity Driven biomolecular DOCKing
HVR Hyper Variable Region
IPTG Isopropyl β-D-1-thiogalactopyranoside
LAM lymphangioleiomyomatosis
LC3 Light Chain 3
Mant 2'(3')-O-(N-Methylanthraniloyl)
MCF-7 Michigan Cancer Foundation-7
MD Molecular Dynamics
MSP Membrane Scaffold Protein
mTORC1 mammalina Target of Rapamycin Complex 1
NBS Nucleotide Binding Site
NMR Nuclear Magnetic Resonance
NOE Nuclear Overhauser effect
PAM Associated with Myc
PDB Protein Data Bank
PDE phosphodiesterase
PE-DTPA(Ga3+) 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-
diethylenetriaminepentaacetic acid (gadolinium salt)
PE-MCC 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-
maleimidomethyl)cyclohexane-carboxamide]
PI3K Phosphatidylinositol 3-kinases
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POPC 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
PRAK p38-regulated/activated kinase
PRE Paramagnetic Relaxation Enhancement
Ran Ras-related nuclear
Ras Rat sarcoma
RBD Ras Binding Domain
Rheb Ras homolog enriched in brain
RhebL1 Ras homolog enriched in brain-like 1
Rho Ras homolog
RMSD Root Mean Square Deviation
S6K S6 Kinase
PAGE polyacrylamide gel electrophoresis
SDS sodium dodecyl sulfate
SOS Son of Sevenless
SRP signal recognition particle
TCEP tris(2-carboxyethyl)phosphine
TRIS tris(hydroxymethyl)aminomethane
UV Ultraviolet
WT Wild Type
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CHAPTER 1
Introduction and Thesis Overview
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1.1 General introduction to small GTPase proteins:
The Rat sarcoma (Ras) superfamily of small GTPases are ~21 kDa globular protein-nucleotide
complexes that control diverse signaling networks affecting cell growth, proliferation and
differentiation, intracellular trafficking, cellular morphology, mobility, chemotaxis and apoptosis
(Wittinghofer and Vetter 2011; Cherfils and Zeghouf 2013). Deregulation of GTPase signaling has
immense implications on human health and can result in life-threatening diseases such as cancer. The
superfamily was originally divided into five subfamilies, based on cellular function and sequence
similarities (Wennerberg et al. 2005). These include Ras, Ras homolog (Rho), Ras related in brain
(Rab), ADP ribosylation factor (Arf), and Ras-related nuclear (Ran) subfamilies. A more recent
phylogenetic analysis has identified additional small GTPases that are yet to be classified into a specific
subfamily (Rojas et al. 2012). The superfamily members contain five conserved sequence motifs,
identified as the G1 to G5 boxes, which are required for interactions with nucleotides, effectors, and
regulators (Figure 1.1). The G1, G2 and G3 boxes reside within functionally important and dynamic
regions of GTPase proteins. The G1 box forms a loop/helix structural motif termed the P-loop, which is
responsible for phosphate binding, whereas G2 and G3 are found within switch I and II, respectively,
which are responsible for interaction with effectors and regulators of GTPases (Wittinghofer and Vetter
2011). Additionally, most members of the superfamily are targeted to intracellular membrane
compartments through post-translational modifications whereby hydrophobic moieties are covalently
attached to either the N- or C-terminus (Ahearn et al. 2012). A universal feature of the small GTPases is
their ability to bind guanine nucleotides, specifically, guanosine di-(GDP) and tri-(GTP) phosphates, and
cycle between GDP- and GTP-bound states. When bound to GTP they adopt a conformation that allows
recognition and activation of downstream effector proteins. Hydrolysis of the γ-phosphate of GTP
converts the GTPases to a GDP-bound inactive state, where they can no longer functionally interact with
their effectors. The GTPase can then be reactivated by exchange of GDP for a new molecule of GTP,
driven in part by the higher concentrations of GTP in eukaryotic cells (Traut 1994). The rate of this
cycle depends in part on intrinsic properties of each GTPase, including their relative affinities for GDP
and GTP and the efficiency of their nucleotide hydrolyzing machinery (Li and Zhang 2004). However
the rate of the GTPase cycle is tightly linked to internal and external stimuli of the cell that are
transmitted to the small GTPase by the action of upstream regulators, such as guanine exchange factors
(GEF), which accelerate the intrinsic nucleotide exchange, and GTPase activating proteins (GAP),
which accelerate the intrinsic GTP hydrolysis.
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Figure 1.1 Sequence alignment of Rheb with other small GTPase proteins investigated in this thesis. Alignment of Rheb is shown with its close homologues K- and H-Ras isoforms and Rap1A, as well as the more distant homologue RhoA, from the Rho subfamily. Conserved amino acids are highlighted in green, those conserved in more than half of the alignment are shown in yellow, and semi-conserved amino acids in cyan. G1 to G5 boxes are indicated with solid bars and the P-loop, switch I and switch II regions are indicated in red. The hyper variable region (HVR) is indicated with a green bar, and the CaaX (C is Cys, a is aliphatic aa, X is any aa) box is highlighted with a rectangle.
The Ras superfamily is an excellent example of achieving functional diversity within a similar structural
framework. Therefore, detailed understanding of the structural and dynamic properties of these switch
proteins is critical to the understanding of their function in cells and can aid in therapeutic intervention
for patients suffering from diseases associated with aberrant GTPase function.
1.2 Introduction to Rheb:
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The main focus of this thesis is an important disease-related member of the Ras subfamily called Ras
homolog enriched in brain (Rheb). Rheb was originally discovered in a screen for genes induced in
hippocampal granule cells of Rat by seizures and by N-methyl-aspartate (NMDA)-dependent synaptic
activity (Yamagata et al. 1994). Sequence analysis identified Rheb as a member of the Ras superfamily
of small GTP binding proteins with the highest similarity to Rap1A and H-Ras GTPases. Subsequently,
the gene encoding human Rheb was identified on chromosome 7 (Gromov et al. 1995; Mizuki et al.
1996), and a second Rheb-like 1 (RhebL1) gene was later identified on chromosome 12 (Patel et al.
2003). Rheb is expressed ubiquitously with higher expression levels in skeletal and cardiac muscle
whereas RhebL1 is primarily expressed in the brain. Rheb homologs have been found in yeast, slime
mold, fungi, fruit fly and zebra fish (Reuther and Der 2000). Rheb was shown to bind to and hydrolyze
GTP with a rate slower than that of H-Ras (Marshall et al. 2009). Like its close homolog H-Ras, Rheb
was shown to be farnesylated in cells (Clark et al. 1997) suggesting membrane association. Rheb was
originally described to interact with Raf-1 kinase and antagonize Ras signaling and transformation
(Clark et al. 1997; Yee and Worley 1997). Later it was shown that Rheb affinity for Raf-1 is 1000-fold
lower than that of Ras (Karassek et al.), thus Raf might not be a physiological effector. Loss of the Rheb
ortholog Rhb1 in fission yeast mimics the nitrogen-starvation induced phenotype and growth arrest
(Mach et al. 2000), and Drosophila Rheb is required for cell growth and cell cycle progression (Patel et
al. 2003). In 2003, several independent groups showed that Rheb is involved in the target of rapamycin
complex 1 (TORC1) signaling pathway (Figure 1.2) in Drosophila melanogaster and mammalian cells
(Garami et al. 2003; Saucedo et al. 2003; Stocker et al. 2003). Rheb was found to promote cellular
growth in a mTOR- (mammalian TOR) dependent manner in response to insulin and nutrient
availability. This activity required phosphorylation and activation of the TOR substrate p70 S6 Kinase,
driving protein translation and cell growth (Ruvinsky and Meyuhas 2006). Another major Rheb-
regulated target of mTORC1 was identified as eukaryotic initiation factor (eIF)4E-binding proteins (4E-
BPs), involved in cap-dependent translation (Beretta et al. 1996; Bommareddy et al. 2009). The
molecular mechanism by which Rheb activates mTORC1 is not yet fully understood and is still a matter
of debate (Bai et al. 2007; Sun et al. 2008; Wang et al. 2008; Sato et al. 2009). It is however clear that
Rheb activates mTORC1 kinase activity in a GTP-dependent manner (Sancak et al. 2007), but
paradoxically both GDP- and GTP-bound states of Rheb were reported to interact with mTORC1 (Long
et al. 2005). Biochemical and genetic studies placed Rheb downstream of the tumor suppressors
tuberous sclerosis complex 1 and 2 (TSC 1/2) in both Drosophila and mammalian cells (Garami et al.
5
2003; Inoki et al. 2003; Tee et al. 2003; Zhang et al. 2003). Rheb was shown to be a direct target of
TSC2 GTPase activating domain (GAP) activity both in vitro and in vivo (Inoki et al. 2003). The
isolated TSC2 GAP domain was later shown to accelerate the slow intrinsic GTP hydrolysis rate of
Figure 1.2 Schematic illustration of Rheb in the mTORC1 signaling pathway. Rheb-GTP stimulates the kinase activity of mammalian target of rapamycin complex 1 (mTORC1) that phosphorylates its substrates including 4E-BP1 and p70S6K1 promoting protein biosynthesis and cell cycle progression. Rheb intrinsic GTP hydrolysis rate is accelerated via the GAP activity of TSC1/2, which is regulated in response to the availability of growth factors, and energy stress.
Rheb in vitro (Scrima et al. 2008; Marshall et al. 2009). The GAP function of TSC 1/2 is tightly
regulated by upstream signaling via phosphorylation events in response to internal and external
6
nutritional and energy status of the cell (Huang and Manning 2008). Hence, Rheb acts as a switch to
regulate cellular growth and cell cycle progression in response to nutrient availability, energy status and
hypoxia, via bridging TSC 1/2 to mTORC1 activity. Interestingly, it was recently recognized that under
certain stress conditions such as UV irradiation and cellular intoxication, Rheb can switch from a pro-
growth signaling molecule to a pro-apoptotic one using both canonical (mTORC1-dependent) and non-
canonical (mTORC1-independent) signaling networks (Ehrkamp et al. 2013). Some of the interesting
non-canonical and membrane-dependent interactions reported for Rheb include; interaction with
mitochondrial autophagic receptor Nix and the autophagosomal protein LC3-II in promoting mitophagy
(Melser et al. 2013); regulation of FKBP38 interaction with anti-apoptotic proteins Bcl-2 and Bcl-XL
(Ma et al. 2010); an inhibitory interaction between Rheb and Bnip3 in hypoxia-mediated inhibition of
mTORC1 signaling (Li et al. 2007); and sequestration of farnesylated Rheb by cAMP hydrolyzing
enzyme phosphodiesterase 4D (PDE4D) (Kim et al. 2010), and the proposed solubilizing factor for
farnesylated Ras-subfamily proteins, PDEδ (Ismail et al. 2011).
Currently, there is no consensus on the identity of the protein, if any, that plays the role of a Rheb GEF.
There is debate whether the translationally controlled tumor protein (TCTP) is the physiological GEF for
this small GTPase (Hsu et al. 2007; Rehmann et al. 2008; Wang et al. 2008; Dong et al. 2009).
Interestingly, recent studies have proposed other potential GEFs for Rheb including; the E3 ubiquitin
ligase Protein Associated with Myc (PAM) (Maeurer et al. 2009) and deacetylated soluble αβ-tubulin
(Lee et al. 2013). In both cases, it remains to be determined whether the newly identified candidates
possess direct GEF-function toward Rheb in vitro using purified recombinant proteins.
1.3 Biophysical and biochemical properties of Rheb:
Rheb is a 184-amino acid GTPase, containing 6 conserved sequence elements that are hallmarks of the
Ras subfamily. These include G1 to G5 boxes, as descried above plus a C-terminal CaaX box (where C
is cysteine, a is aliphatic amino acid, and X is any amino acid). Rheb is post-translationally modified via
farnesylation, cleavage of the aaX tripeptide and carboxymethylation of the C-terminal cysteine by the
concerted actions of farnesyltransferase, Ras converting enzyme 1 (Rce1) and isoprenylcysteine
carboxyl methyltransferase (Icmt) enzymes, respectively (Seabra 1998). These modifications target
Rheb to intracellular membrane compartments such as the ER, Golgi apparatus, and lysosome
7
(Takahashi et al. 2005; Buerger et al. 2006). Inhibition of Rheb farnesylation, via mutation of the CaaX
box Cys residue or treatment with farnesyltransferase inhibitors (FTIs), drastically reduces Rheb’s
ability to stimulate mTORC1 activity in cells (Buerger et al. 2006; Finlay et al. 2007). Although Rheb
shares 34% sequence identity with H-Ras and harbors many conserved sequence elements through G1-
G5 boxes, two key sequence variations were observed upon its discovery. In Ras, codons 12 and 13
encode two conserved Glycine residues, mutations of which result in oncogenic Ras molecules that are
constitutively GTP bound (Figure 1.3) (Prior et al. 2012). The structural basis for the Gly12 and Gly13
mutation-mediated oncogenic transformation in Ras is well characterized (Krengel et al. 1990). For
example, H-Ras G12V, a high frequency mutation in various tumor types, sterically blocks the canonical
catalytic residue, Gln61 (H-Ras numbering), from the nucleotide binding site, impairing GTP
hydrolysis. Gln61 is positioned at the N-terminus of switch II and it is shown to stimulate the GTP
hydrolysis reaction by interacting with a water molecule positioned in-line with the γ-phosphate of GTP
(aka, the catalytic water, H2Ocat). In Rheb the corresponding codons (15 and 16) encode Arginine and
Serine residues, respectively. However, the slow GTP hydrolysis by Rheb is not due to the presence of
these residues at codons 15 and 16. In cells over-expressing Rheb, R15G and S16G mutations did not
affect its activation state (Im et al. 2002), suggesting that Arg15 and Ser16 did not affect the Rheb-GTP
levels, where the function of TSC2GAP is limiting.
Compared to Ras, Rheb exists in a high activation state in cells (Im et al. 2002). Initial characterization
of Rheb’s intrinsic GTP hydrolysis rate suggested Rheb possesses a slower GTP hydrolysis rate than
Ras (Aspuria and Tamanoi 2004). This was confirmed by the use of the novel real-time NMR-based
GTPase assay that accurately measured the nucleotide hydrolysis rate of Rheb to be 10 times slower
than that of H-Ras (Marshall et al. 2009). A potential structural explanation for this low GTPase activity
was found eleven years after Rheb was first discovered. Crystal structures of Rheb were solved in both
an inactive GDP-bound state (PDB: 1XTQ) and active states bound to GTP (PDB: 1XTS) and
GMPPNP-bound, a non-hydrolyzable analog of GTP (PDB: 1XTR) (Yu et al. 2005). The overall fold is
typical of Ras subfamily members, namely a six-stranded β-sheet and five α-helices forming a globular
20 kDa protein (Figure 1.3). However, two important structural differences were observed in the switch
I and II regions of the GMPPNP-bound state compared to that observed in H-Ras. In Rheb, switch I
forms a lid that covers the phosphate groups of the nucleotide and simultaneously creates a pore to the
8
bulk solvent, which is occupied by the H2Ocat. This lid is formed by the H-bonding interaction between
the hydroxyl group of the conserved Tyr35 in switch I of Rheb and the γ-phosphate (Figure 1.3).
Figure 1.3 Overall structure of active Rheb and comparison with that of H-Ras. Crystal structure of Rheb bound to GMPPNP (PDB: 1XTR) is shown in green. The nucleotide is shown with stick. The inset
9
shows the positions of key residues within the nucleotide binding site of Rheb and H-Ras (cyan) (PDB: 5P21). The H2O
cat is presented with spheres. The backbones of Tyr35, Gln61 and Gln64 are not shown.
In H-Ras, the equivalent tyrosine (Tyr32) is in an open conformation that does not interact with the γ-
phosphate, thus exposing the nucleotide phosphate groups to the solvent (Figure 1.3). This
conformational divergence could aid in differential recognition of interactors by Ras versus Rheb. For
example, the open conformation of Ras Tyr32 allows p120 RasGAP to insert an Arginine (aka the
Arginine finger) into the nucleotide binding site to stimulate GTP hydrolysis (Scheffzek et al. 1997).
The second difference involves the conformation of switch II. Whereas the H-Ras switch II harbors a
10-residue curved alpha helix and is relatively detached from the globular G-domain, in Rheb switch II
is mainly unstructured and forms tight contacts with the G-domain (Figure 1.3). The structural
consequence of this conformation is a net removal of the switch II residues from the nucleotide binding
site of Rheb compared to that of H-Ras. The point of divergence begin after the conserved DxxG motif
at the N-terminus of switch II, a conserved curved loop structure responsible for Mg2+ and H2Ocat
coordination. This unique switch II configuration flips the Gln64 (corresponding to H-Ras Gln61) side
chain away from the nucleotide binding pocket and traps it within a hydrophobic pocket underneath
switch II formed by Leu12, Phe70, Pro71, Tyr74, and Ile99. A salt bridge between Glu66 in switch II
and Lys91 of the α3 helix stabilizes switch II away from the nucleotide binding site. Further stabilization
is achieved by polar interaction between the Lys102 of α3 helix and the backbone carbonyl of Glu66.
This switch II conformation of Rheb provides additional space that accommodates the Arg15 side chain
that is not available in the H-Ras structure. Hence, the structural analysis indicated that although Rheb
possesses a glutamine residue corresponding to H-Ras Gln61, this residue does not participate in GTP
hydrolysis. This was later confirmed via NMR-based GTPase assay, demonstrating that the Q64L
mutation in Rheb has minor effects on both intrinsic and TSC2GAP-mediated GTP hydrolysis (Marshall
et al. 2009).
1.4 Pathogenesis of Rheb:
Rheb is involved in the pathogenesis of the tuberous sclerosis disease, which is an autosomal dominant
genetic disorder with a prevalence of ~1 in 8,000 (Napolioni and Curatolo 2008). Mutations in tsc1 and
tsc2 genes that disrupt TSC1/2 GAP function in tuberous sclerosis and lymphangioleiomyomatosis
(LAM) diseases result in high levels of Rheb-GTP that constitutively activate mTORC1. Tuberous
sclerosis disease is characterized by multiple benign tumor formation in multiple organ systems. The
10
symptoms include autism, developmental delay, hematuria (blood in urine), cardiac arrhythmia and skin
disfigurement.
Additionally, numerous studies have suggested Rheb to be directly involved in tumorgenesis.
Constitutively activated Rheb mutants have been shown to induce oncogenic transformation in cell
culture (Jiang and Vogt 2008) and it has been well established that transcriptional- and translational-
mediated elevation of Rheb expression contributes to its hyperactivation (Norsted Gregory et al. 2010;
Cao et al. 2013). Elevated levels of Rheb result in high activation levels due to limiting GAP function of
TSC1/2. The highly GTP-loaded Rheb constitutively signals to mTORC1 to promote cellular growth
and cell cycle progression. The elevated expression of Rheb has been found in fibroadenoma (Eom et al.
2008), shown to be critical and sufficient for skin epithelial carcinogenesis (Lu et al. 2010), and to cause
prostate cancer (Nardella et al. 2008; Kobayashi et al. 2010) and lymphomagenesis (Mavrakis et al.
2008). An increase in Rheb activation state has also been demonstrated to drive 17-beta estradiol (E(2))-
dependent proliferation of the MCF-7 breast cell line (Yu and Henske 2006).
Where mutations of Gly12, Gly13 and Gln61 result in oncogenic transformation of Ras, Rheb has not
been associated with any particular oncogenic mutation. However, recent high-thoughput cancer
genome sequencing analyses of tumor samples from patients with various tumour types including lung,
breast, urinary tract, endometrium, colon, kidney and stomach has revealed multiple missense mutations
throughout the Rheb gene (COSMIC database). The mutations map to the important structural regions in
Rheb including the P-loop, switch I and II. Residues with the highest frequency mutations are Tyr35 (to
Asn) (Lawrence et al. 2014) and Glu139 (to Lys, Glu, and Asp). Tyr35 is in the middle of switch I (G2
box) and, as noted above, covers the nucleotide-binding pocket from the bulk solvent. Glu139 is at the
C-terminus of α5 near a site of post-translational modification (Ser130 at the N-terminus of α5). Rheb
nucleotide loading is inhibited by phosphorylation of Ser130 by p38-regulated/activated kinase (PRAK)
(Zheng et al. 2011). The functional properties of these Rheb mutants are yet to be characterized to
determine weather they drive tumorgenesis.
To target deregulated mTORC1 signaling, several therapeutic strategies are being investigated. First is
the direct inhibition of mTORC1 via small molecules. Rapamycin and its synthetic analogs (Rapalogs),
also known as the first-generation mTOR inhibitors, inhibit phosphorylation of a subset of mTORC1
11
substrates (Kang et al. 2013). Rapmycin directly blocks substrate recruitment by forming a complex
with FK506-binding protein 12 (FKBP12) and binding to the FKBP12–rapamycin-binding (FRB)
domain of mTORC1, close to the kinase catalytic site (Choi et al. 1996; Yang et al. 2013). Clinical trials
have shown that rapalogs are cytostatic and tend to be stabilizers of diseases rather than causing disease
regression (Wander et al. 2011). In addition, rapalog-mediated inhibition of mTORC1 fails to suppress a
negative feedback loop that results in phosphorylation-mediated activation of AKT (Wan et al. 2007).
More recently, ATP-binding site inhibitors, also known as second-generation mTOR inhibitors, were
developed, which directly compete with ATP binding and inhibit the kinase activity of both mTORC1
and mTORC2 for all substrates (Zaytseva et al. 2012). However, they display cytotoxic effects and are
only partially effective in K-Ras driven tumors (Zaytseva et al. 2012). An alternate strategy involves
prevention of Rheb association with bilayer membranes through the use of FTIs, which block
farnesylation of Rheb and its ability to signal to mTORC1 in the cells, but suffer from non-specificity
(Mavrakis et al. 2008). Interestingly, a cytotoxic biphenyl compound, 4,4′-biphenol was shown to
interact with Rheb switch II region, block mTORC1 signaling and induce cell death (Schopel et al.
2013). However the affinity of the compound was low (Kd in millimolar range), indicating the
requirement for structure-guided optimization of the compound.
1.5 Thesis Overview and Rationale:
From the above discussion it is clear that two key physiological properties of Rheb are directly linked to
human diseases: (a) its GTP hydrolysis rate and (b) its membrane association. The studies presented in
this thesis are basic research aimed at gaining an atomic-resolution understanding of Rheb’s catalytic
mechanism and its interaction with phospholipid bilayers. The information gained, could aid in the i)
mechanistic understanding of disease-associated mutations in Rheb, ii) development of small molecules
that specifically target the disease-associated Rheb mutant states, iii) development of novel probes to
study the biology of the mTORC1 pathway, and iv) characterization of the Rheb-membrane interface
and its implication for Rheb signaling.
The catalytic mechanism of Rheb GTP hydrolysis is described in Chapters 2, 3 and 4, representing three
published manuscripts. When I commenced my Ph. D. studies, Dr. Marshall published a novel method
for quantitatively measuring the rate of the GTPase cycle using native nucleotides via real-time NMR-
based GTPase assay (Marshall et al. 2009). Hence, in my first study (chapter 2), I examined the effect of
12
widely used fluorescent nucleotide analogs, 2'(3')-O-(N-Methylanthraniloyl)-(mant)-GDP and mant-
GTP in modulating the kinetics of the GTPase cycle. Chapter 3 describes a structure-function study of
the non-canonical GTP catalytic mechanism of Rheb that was initially revealed by studies of Rheb
hydrolysis of the mant-nucleotide. Chapter 4 describes the structure-guided development of novel gain-
of-function and loss-of-function mutants of Rheb using the knowledge gained from its nucleotide
catalytic mechanism.
The Rheb-membrane interaction is described in Chapter 5, representing our published work on a novel
NMR-based method for studying GTPase-membrane interaction at atomic resolution using nanodisc-
based lipid bilayers. These methods demonstrated effects of membrane binding on Rheb’s GTPase
cycle, as well as determining the orientation of Rheb with respect to the lipid bilayer in both GDP- and
GTP- bound states.
Chapter 6 includes concluding remarks and future directions, including (i) potential applications of the
gain- and loss-of-function Rheb mutants generated via structure-guided design, and (ii) the feasibility of
applying nanodisc-GTPase methodology to other disease-related GTPases, such as K-Ras, and its
complexes with different Ras Binding Domains (RBDs).
1.6 Attributions:
The cell-based assays of nucleotide binding (Chapter 3) and mTORC1 phosphorylation (Chapter 3 and
4) were performed by our collaborators, Vanessa Di Palma and Jason Ho, from Dr. Vuk Stambolic’s
Lab (Department of Medical Biophysics, Campbell Family Cancer Research Institute, Ontario Cancer
Institute, Princess Margaret Cancer Centre, University Health Network, University of Toronto).
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CHAPTER 2
Real-time NMR assays on Rheb, Ras, and RhoA GTPase cycles
This chapter has been reformatted from the original publication: Mazhab-Jafari MT, Marshall CB, Smith M, Gasmi-Seabrook GM, Stambolic V, Rottapel R, Neel BG, Ikura M. Real-time NMR study of three small GTPases reveals that fluorescent 2'(3')-O-(N-methylanthraniloyl)-tagged nucleotides alter hydrolysis and exchange kinetics. J Biol Chem. 2010 Feb 19;285(8):5132-6. A link to the published paper can be found at:
http://www.jbc.org/content/285/8/5132.long
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2.1 Abstract
The Ras family of small GTPases control diverse signaling pathways through a conserved ‘switch’
mechanism, which is turned on by binding of GTP and turned off by GTP hydrolysis to GDP. Full
understanding of GTPase ‘switch’ functions requires reliable, quantitative assays for nucleotide binding
and hydrolysis. Fluorescently labeled guanine nucleotides, such as 2'(3')-O-(N-Methylanthraniloyl)-
(mant)-substituted GTP and GDP analogs, have been widely used to investigate the molecular properties
of small GTPases, including Ras and Rho. Using a recently-developed NMR method, we show that the
kinetics of nucleotide hydrolysis and exchange by three small GTPases, alone and in the presence of
their cognate GTPase activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs), are
affected by the presence of the fluorescent mant moiety. Intrinsic hydrolysis of mantGTP by Rheb is
~10-times faster than that of GTP, whereas it is 3.4-times slower with RhoA. On the other hand, the
mant tag inhibits TSC2GAP-catalyzed GTP hydrolysis by Rheb but promotes p120 RasGAP-catalyzed
GTP hydrolysis by HRas. GEF catalyzed nucleotide exchange for both HRas and RhoA were inhibited
by mant-substituted nucleotides, and the degree of inhibition depends highly on the GTPase and whether
the assay measures association of mantGTP with, or dissociation of mantGDP from the GTPase. These
results indicate that the mant moiety has significant and unpredictable effects on GTPase reaction
kinetics and underscore the importance of validating its use in each assay.
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2.2 Introduction:
The Ras superfamily of small GTPases plays vital roles in the integrated network of cellular signaling.
They are “turned on” by binding to GTP and adopting a conformation that allows modulation of their
downstream effectors. The proteins are then “turned off” by hydrolysis of the γ-phosphate of GTP and
conversion to GDP (Figure 2.1a). The relative amounts of activated GTP-bound and inactive GDP-
bound forms of GTPases are tightly regulated by GAPs, which catalyze nucleotide hydrolysis, and
GEFs, which promote nucleotide exchange. Mutation or unregulated expression of the small GTPase
proteins or their respective GAPs and GEFs can deregulate the GTPase cycle and lead to diseases such
as cancer, neurodegeneration and mental disabilities (Ahmadian et al. 1996).
Figure 2.1 Effect of mant-substituted GTP on the intrinsic nucleotide hydrolysis of Ras, Rheb and RhoA. a) Nucleotide dependent conformational changes in GTPases. Nucleotide hydrolysis and exchange are correlated with conformational changes that are readily probed in two dimensional 1H-15N HSQC spectra (PDB: 1XTS green, 1XTQ cyan). b) The chemical structure of mantGTP (ChemSketch (Spessard 1998)) is shown with the mant moiety at the 3’ position of the ribose ring. In solution, this moiety exhibits slow chemical exchange between the 2’ and 3’ positions of the ribose ring, producing an equilibrium ratio of 4:6 (Neal et al. 1990). c) The time course of intrinsic GTP (black) and mantGTP (green) hydrolysis by HRas, Rheb and RhoA probed via real time solution NMR spectroscopy. All the proteins were fully loaded with GTP or mantGTP before the start of the assay, as assessed by 1H-15N HSQC. The rates are displayed with a histogram for each curve in inserted panel c. See appendix A for description of equations.
A B
C
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Although several methods for monitoring GTP hydrolysis and nucleotide exchange of small GTPase
proteins have been developed (Ahmadian et al. 1996; Zhang and Zheng 1998; Albert and Gallwitz 2000;
Futai et al. 2004), the assay most widely used to monitor kinetics employs the fluorescently labeled
guanosine nucleotide analogs 2'(3')-O-(N-Methylanthraniloyl) - GTP/GDP (mantGTP / mantGDP),
which are sensitive to the hydrophobic environment of proteins (Figure 2.1b). Because of high
sensitivity and selectivity, mantGTP and mantGDP have been widely used in the field (Sondermann et
al. 2004; Mou et al. 2005; Gureasko et al. 2008), however, the use of these nucleotide analogs is
justified only if they report reaction kinetics and thermodynamics that are consistent with the natural
ligands GTP and GDP. Previously, some inconsistencies between native GTP and mantGTP were
observed in nucleotide hydrolysis assays of Ras and RhoA with their cognate GAPs (Moore et al. 1993;
Eberth et al. 2005). However, these fluorescent probes have never been fully assessed due to the lack of
appropriate methodology.
Recently we developed an NMR-based real-time assay to monitor the rate of GTP hydrolysis of Ras
homolog enriched in brain (Rheb), enabling us to monitor GTPase reactions using native GTP and GDP
(Figure 2.2b) (Marshall et al. 2009). We have demonstrated that the real-time NMR methodology can be
successfully used to assay nucleotide exchange in RhoA (Gasmi-Seabrook et al. 2010). This
methodology requires no chemical modification of the protein or the nucleotide, which can perturb the
native structure of the protein (Figure 2.3), and has the ability to sense subtle changes in the rate of
catalysis in real-time fashion. In this study we employed the NMR methodology to examine how the
fluorescent adduct on mantGTP and mantGDP affects the kinetics of nucleotide hydrolysis and
exchange of three small GTPases (HRas, Rheb and RhoA) alone and in the presence of their GAPs or
GEFs.
2.3 Results:
2.3.1 The effect of mant on the intrinsic rate of nucleotide hydrolysis:Mant-substituted nucleotides have
been used extensively to investigate many aspects of G-protein signaling, including the kinetics and
mechanisms of RasGAP-mediated GTP hydrolysis (Moore et al. 1993; Ahmadian et al. 1997; Ahmadian
et al. 2002; Phillips et al. 2003) and Cdc25SOS-mediated nucleotide exchange (Sondermann et al. 2004;
Gureasko et al. 2008). We first used NMR methodology to examine whether the addition of the mant
21
moiety alters the intrinsic hydrolysis rate of the GTPase domain of HRas (1-171) (Figure 2.1c) and
found that it had little effect (Table 2.1), consistent with previous reports (Remmers et al. 1994).
Figure 2.2 Comparison of the real-time NMR and fluorescence-substituted nucleotide-based GTPase assays. a) Fluorescence assay. Left panel: The emission spectra of Rheb-mantGTP (black) and Rheb-mantGDP (red) illustrating the decline in the fluorescence intensity accompanied by a red shift upon nucleotide hydrolysis. Right panel: The time-dependent intrinsic hydrolysis of mantGTP by Rheb monitored by fluorescence and fitted to a one-phase exponential decay. b) GTP hydrolysis by Rheb observed using NMR. Snapshots of 1H-15N HSQC spectra collected over the time course of hydrolysis. The green box indicates the resonance specific to Gly13 of Rheb-GTP and the red box corresponds to that of Rheb-GDP.
A
B
22
Figure 2.3 Perturbation of the native structure of GTPase proteins by mant-tagged nucleotides. Selected regions of 1H-15N HSQC spectra from HRas, Rheb, and RhoA bound to GTP (green) or mantGTP (red) are shown. Dashed boxes indicate resonances that exhibit chemical shift changes between GTP and mantGTP.
23
Table 2.1 The rates of intrinsic and GAP mediated nucleotide hydrolysis for three small GTPase proteins. All rates are reported in min-1.
1: A molar ratio of 1/2,500 HRasGAP to HRas was used. 2: A molar ratio of 1/2.2 TSC2GAP to Rheb was used.
Next, we analyzed GTP hydrolysis by Ras homolog enriched in brain (Rheb), which shares ~33%
sequence identity with HRas. Surprisingly, the hydrolysis rate of mantGTP by Rheb (3.2×10-3 min-1)
was >10 times faster than that of native GTP when both reactions were monitored by NMR (Figure
2.1c). The rate constant obtained with mantGTP by NMR was identical to the value obtained using
fluorescence spectroscopy (Figure 2.1c and 2.2a), demonstrating that the results are independent of the
detection method. Using mantGTP to compare the activity of different GTPases, the intrinsic GTPase
activity of Rheb would appear ~2 times lower than that of HRas, whereas it is actually ~32 times lower
with native GTP, demonstrating that reliance on mantGTP would overlook this biologically important
difference.
As a third case, the effect of the mant substitution on the GTPase activity of RhoA, which shares ~31%
sequence identity with HRas and Rheb, was investigated and found to be opposite to that observed with
Rheb (Figure 2.1c). The half-life of mantGTP bound to RhoA was ~155 min, 3.5 fold longer than that of
native GTP (~45 min) (Table 2.1). Taken together, the results show that mant-substituted nucleotides
can substantially alter the kinetics of nucleotide hydrolysis by small GTPases in a manner that could not
have been predicted a priori.
2.3.2 The effect of mant on the rate of GAP-catalyzed nucleotide hydrolysis:Having established that
mant can have a substantial effect on intrinsic GTPase reaction rates, we investigated the effect of
1 21
24
mantGTP on GAP-accelerated GTPase reactions. First, we used the GAP domain of the human p120-
RasGAP. GTP was hydrolyzed with a rate of 2.6×10-2 min-1 by HRas in the presence of a 1/2,500 molar
ratio of RasGAP, whereas mantGTP was turned over ~5 times faster (Figure 2.4a and Table 2.1).
Indeed, Moore et al. (Moore et al. 1993) previously noted that in the presence of RasGAP, p21N-Ras
hydrolyzes mantGTP more rapidly than native GTP, although the cleavage of the two nucleotides were
not monitored by the same method.
Figure 2.4 Effects of mant-substituted GTP on GAP-mediated nucleotide hydrolysis by HRas and Rheb. a) Time course of RasGAP-mediated nucleotide hydrolysis of HRas with GTP (black) and mantGTP (green). A molar ratio of 1:2,500 RasGAP to HRas was used. b) Time course of TSC2GAP-mediated hydrolysis of GTP (black) and mantGTP (green) bound to Rheb. A molar ratio of 1:2.2 TSC2GAP to Rheb was used for both assays. Rates extracted from each curve are displayed with an inserted histogram. Each experiment was performed in duplicate, and each curve represents a single representative experiment. We then examined how mantGTP might affect GAP-mediated GTP hydrolysis of a second, unrelated
GAP with a distinct mechanism of action, by studying Rheb and its well-characterized GAP, TSC2GAP
A
B
25
(Marshall et al. 2009). At a TSC2GAP to Rheb ratio of 1/2.2, GTP was hydrolyzed at a rate of 1.9×10-2
min-1 whereas mantGTP was hydrolyzed ~2.5 fold more slowly (Figure 2.4b and Table 2.1). Comparing
Rheb’s intrinsic rate of mantGTP hydrolysis to the GAP-catalyzed rate, TSC2GAP only produced a two-
fold enhancement (Table 2.1). This contrasts sharply with the ~50 fold stimulation of Rheb GTPase
activity by TSC2GAP when native GTP is used in the assay. Hence, exclusive use of mantGTP would
lead to a gross underestimation of the GAP activity of TSC2 towards Rheb, underscoring the utility of
the NMR-based methodology.
2.3.3 The effect of mant on the GEF-mediated nucleotide exchange:We examined how mant-substituted
nucleotides affect the DH-PHPRG-mediated nucleotide exchange of RhoA (Figure 2.5a) using a
procedure described elsewhere (Gasmi-Seabrook et al. 2010). In the NMR GEF assay with hydrolysable
nucleotides, the readout (i.e, GDP- and GTP-specific protein cross-peaks) is determined by both
exchange and intrinsic nucleotide hydrolysis. This is evident in the case of Ras and RhoA (Figure 2.5)
which do not become 100% saturated with GTP or mantGTP. Hence the observed data was fit to an
equation that considers exchange and hydrolysis (see appendix A), to derive the true exchange rate. We
have shown that this derived rate agrees well with the rate determined for the non-hydrolysable GTPγS
(Gasmi-Seabrook et al. 2010). In an assay of nucleotide association with RhoA, mantGTP exhibits a
30% lower exchange rate (4.9×10-2 min-1) compared to native GTP (7.0×10-2 min-1) (Table 2.2). In the
literature, both the incorporation (Hutchinson and Eccleston 2000; Derewenda et al. 2004; Oleksy et al.
2004) and dissociation (Tan et al. 2002; Hemsath and Ahmadian 2005) of the mant-substituted
nucleotide have been employed to study the function of RhoA and its interaction with GEFs. Hence, we
also performed the ‘dissociation’ assay, initially loading RhoA with GDP or mantGDP, and monitoring
exchange to GTP. In this reaction the rate of DH-PHPRG mediated nucleotide dissociation was
approximately six times slower for mantGDP than for GDP (Figure 2.6a and 6c).
Previous studies have used mantGDP extensively to probe the Son of Sevenless (Cdc25SOS) catalyzed
nucleotide exchange of Ras GTPase. Generally, Ras is preloaded with mantGDP and the decay in
fluorescent intensity is monitored as this fluorescent nucleotide is displaced by unlabeled GTP (Margarit
et al. 2003; Sondermann et al. 2004; Ford et al. 2005; Ford et al. 2006; Freedman et al. 2006; Gureasko
et al. 2008). Here, using an NMR-based protocol similar to that described for RhoA, we show (Figure
2.5b and Table 2.2) that the rate of Cdc25SOS-catalyzed mantGDP dissociation (7.2×10-3 min-1) is
26
approximately 30% slower compared with that of native GDP. GEF assays using association of mant-
tagged nucleotide with Ras have also been reported (Sacco et al. 2006), thus we used NMR to compare
the Cdc25SOS-catalyzed association of mantGTP and GTP. We found that the rate of association of
mantGTP with HRas is ~3-fold slower than that of GTP (Figure 2.6b and 6d).
Figure 2.5 Effects of mant-substituted nucleotides on GEF-mediated nucleotide exchange for HRas and RhoA. a) Time course of DH-PHPRG mediated nucleotide exchange of RhoA-GDP to GTP (black) and mantGTP (green). A molar ratio of 1/30,000 RhoA to DH-PHPRG was used for both assays. b) Time course of CDC25SOS mediated nucleotide exchange of HRas-GDP (black) and HRas-mantGDP (green) to GTP with 1/30,000 HRas to CDC25SOS molar ratio. Observed data (continuous lines) were fitted to an equation that considers both exchange and hydrolysis to extract the true exchange rate kex in each experiment (see appendix A). Using this rate, exponential decay curves (dashed lines) were generated to approximate nucleotide exchange in the absence of hydrolysis. The corrected rates are displayed with an inserted histogram for each curve. Each experiment was performed in duplicate, and each curve represents a single representative experiment.
A
B
27
Table 2.2 The rates of GEF mediated nucleotide exchange for HRas and RhoA proteins. These exchange rates are reported in min-1 and determined by fitting data to an equation that considers both exchange and hydrolysis.
1: A ratio of 1/30,000 GEF to GTPase was used with 10 molar excess of nucleotide relative to GTPase.
A B
C D
28
Figure 2.6 Complementary assays of the effects of mant-substituted nucleotides on GEF-mediated nucleotide exchange for HRas and RhoA. a) The DH-PHPRG mediated nucleotide exchange of RhoA-GDP to GTP (black) and mantGDP to GTP (green). A molar ratio of 1/30,000 RhoA to DH-PHPRG was used for both assays. b) The CDC25SOS-mediated nucleotide exchange of HRas-GDP to GTP (black) or mantGTP (green). A molar ratio of 1/30,000 HRas to CDC25SOS was used for both assays. Observed data (circles and triangles) were fitted to an equation that considers both exchange and hydrolysis to extract the true exchange rate, which was used to plot exponential decay curves (gray and green lines) (see Appendix A). These rates are displayed with a histogram for each curve in panels c and d.
2.4 Discussion:
Fluorescently-labeled guanosine nucleotides have been used extensively to study nucleotide hydrolysis
and exchange of GTPases. However, covalent modification of the nucleotide with a bulky fluorophore
raises concerns about how this reporter moiety may perturb enzymatic activity. The NMR methodology
recently developed by our group (Marshall et al. 2009) does not require any chemical modification of
GTP or GDP because it makes direct observation of protein resonances that depend on nucleotide-
induced changes in chemical environment of protein (Figure 2.2b). In this study, we employed this
NMR method to compare native versus mant-labeled nucleotides in the kinetics of intrinsic GTPase
reactions, GAP-mediated nucleotide hydrolysis, and GEF-mediated nucleotide exchange reactions of
three small GTPases, HRas, Rheb, and RhoA. Our results clearly demonstrate that mant-labeled
nucleotides had substantial effects on the kinetics of these reactions and that these effects were
remarkably different and unpredictable with each GTPase, GAP, and GEF.
2.4.1 Intrinsic hydrolysis of GTP and mantGTP:HRas exhibited a small decrease in the intrinsic
hydrolysis rate of mantGTP versus native GTP, however Rheb and RhoA were affected more drastically
by this fluorescent tag. Remarkably, mant had opposite effects on Rheb and RhoA; Rheb hydrolyzed
mantGTP ~10 fold faster than native GTP, whereas RhoA hydrolyzed this analog 3 fold more slowly
than GTP. Thus, the effects of mant are specific to the structure and catalytic mechanism of each
GTPase rather than the inherent lability of the nucleotide. With all three GTPases, the mant-adduct
perturbed proximal residues in the P-loop, switch I and G-5 box, but also induced long range
perturbations in several regions including switch II (Figure 2.7). The catalytic Gln of RhoA is found in
switch II, thus distortion of the structure of this loop could inhibit the hydrolysis of mantGTP.
Interestingly, the analogous Gln in Rheb is in an orientation that does not contribute to catalysis (Yu et
al. 2005; Marshall et al. 2009). To understand the rapid hydrolysis of mantGTP by Rheb, we asked
29
Figure 2.7 mantGTP-induced chemical shift perturbations in Ras, Rheb and RhoA. Residues exhibiting chemical shift perturbations induced by binding of mantGTP (versus GTP) are mapped onto
A
B
C
30
the structures of a) Ras(PDB:5P21), b) Rheb(PDB:1XTS) and c) RhoA(PDB:1KMQ). Magenta colored residues correspond to small chemical shift changes (i.e., peaks partially overlap) whereas residues exhibiting large chemical shift changes or severe line broadening are colored red. Unassigned residues including prolines are indicated with dark gray. The nucleotide is shown in spheres with carbon, oxygen, nitrogen, and phosphate shown in green, red, blue, and orange respectively. The magnesium ion is shown with cyan sphere. The predicted position of the mant-moiety, which exists in equilibrium between the 2’ and 3’ hydroxyl groups of the ribose ring, is indicated in each structure by a red circle. Switch I residues of all three GTPases are broadened beyond detection in both the GTP- and mantGTP-bound states, however chemical shift perturbations would be expected based on the structure of Ras in complex with mant-dGppNHp(PDB:1GNP), in which the mant moiety faces the switch I region of Ras. whether the mant-induced perturbation of switch II might favor a catalytically competent conformation
of Gln64. However the Q64L mutation had no effect on hydrolysis of mantGTP, indicating that this
reaction occurs through more complex mechanism (Figure 2.8).
Figure 2.8 Rheb Gln64 is not involved in the rapid hydrolysis of mantGTP. The time course of mantGTP hydrolysis by wild type Rheb (black) and RhebQ64L mutant (green) probed via real time solution NMR spectroscopy. The proteins were fully loaded with mantGTP before the start of the assay, as assessed by 1H-15N HSQC.
2.4.2 GAP-catalyzed GTP hydrolysis by HRas and Rheb:p120-RasGAP-catalyzed hydrolysis of
mantGTP by HRas was ~5 fold faster than that of native GTP whereas TSC2GAP-mediated hydrolysis
of mantGTP by Rheb was slower by a factor of ~2.5 relative to unmodified GTP. Considering the rapid
intrinsic GTPase activity of Rheb towards mantGTP, it is apparent that TSC2GAP activity is severely
inhibited by mant. These results demonstrate the unpredictable effects of mant-tagged nucleotides on
intrinsic and GAP-mediated GTPase activities and highlight the utility of the NMR approach.
31
Previous studies using a phosphate release assay showed that the Km of p120 RasGAP-mediated
hydrolysis of p21 N-Ras-mantGTP is lower than that of the p21 N-Ras-GTP complex (Moore et al.
1993). This result suggests that mant may increase the affinity of the HRas-nucleotide complex for
RasGAP, thus increasing the rate of nucleotide hydrolysis. Conversely, we propose that for Rheb the
mant moiety probably hinders docking of the TSC2GAP domain to Rheb. Note that TSC2 and p120
RasGAP are not homologous, have different folds and function through distinct catalytic mechanisms.
Further structural insights are required to address the mechanistic basis for the ‘mant effect’ on GAP-
mediated nucleotide hydrolysis for both HRas and Rheb.
2.4.3 GEF-accelerated nucleotide exchange of HRas and RhoA:Using the aforementioned NMR-based
approach (Gasmi-Seabrook et al. 2010), we performed GEF assays to measure both association and
dissociation of mant-tagged nucleotides, as fluorescence-based experiments have been reported both
ways in the literature (Hutchinson and Eccleston 2000; Tan et al. 2002; Margarit et al. 2003; Derewenda
et al. 2004; Oleksy et al. 2004; Sondermann et al. 2004; Ford et al. 2005; Hemsath and Ahmadian 2005;
Ford et al. 2006; Freedman et al. 2006; Sacco et al. 2006; Gureasko et al. 2008). Comparing
dissociation, Cdc25SOS-mediated nucleotide exchange was 30% slower when starting with mantGDP-
bound HRas (mantGDP to GTP) than with GDP-bound HRas (GDP to GTP). Measuring association
under the same conditions, the GDP to mantGTP exchange was ~3 times slower than GDP to GTP
exchange. Similarly, DH-PHPRG-mediated nucleotide exchange was 30% slower for the GDP to
mantGTP than the GDP to GTP exchange in the association assay and ~6 fold slower for the mantGDP
to GTP than GDP to GTP exchange in the dissociation assay. In the crystal structure of HRas-mant
dGppNHp (Scheidig et al. 1995), mant is near residue Tyr32 in switch I, which would introduce steric
clashes at the primary contact point between the GTPase and Cdc25SOS and could interfere with
nucleotide exchange. Assuming the mant moiety of the nucleotide is similarly positioned on the switch I
region of RhoA, it would also hinder DH-PHPRG binding to RhoA (Derewenda et al. 2004). Furthermore,
mant-induced structural perturbations of the GEF binding sites in the GTPase switch regions may inhibit
interactions with GEFs. The exchange kinetics reported by mant are more reliable when the dissociation
assay is used for the Ras-CDC25SOS system and the association assay is used for the RhoA-DH-PHPRG
system. Note that these are the conventional fluorescence methods for each protein, nevertheless the less
accurate alternative approaches are still in use. Finally, the reduced sensitivity of mantGDP-bound
GTPases to the action of GEFs suggests an avenue for design of GTPase inhibitors.
32
In conclusion, we have demonstrated that mant-labeled nucleotides can alter the intrinsic GTPase
activity of Rheb, RhoA, the GAP-catalyzed GTP hydrolysis of HRas-RasGAP and Rheb-TSC2GAP, as
well as the DH-PHPRG and CDC25SOS-mediated nucleotide exchange of RhoA and HRas, respectively.
These results reveal that the fluorescent probes could yield biochemically inaccurate data and potentially
lead to misleading conclusions. The significant and unpredictable effects of the mant tag clearly indicate
that mant-tagged nucleotides should be used with caution and should be validated for each GTPase
system studied. At the same time, these findings provide clues as to how one could inhibit or activate
specific signaling pathways using small organic molecules, which may mimic the effects of the mant-tag
on small GTPases. This study also extends the utility and value of the NMR-based assays for both
GTPase and GEF reactions for three small GTPases, suggesting that it will be broadly applicable to the
GTPase superfamily.
2.5 Experimental procedures:
2.5.1 Protein preparation: Murine Rheb (residues 1-169), human HRas (residues 1-171) and murine
RhoA (residues 1-181) were prepared according to previous protocols (Scheidig et al. 1995; Derewenda
et al. 2004; Marshall et al. 2009). In brief, the three proteins were expressed in Escherichia coli (BL21),
grown in minimal media supplemented with 15NH4Cl at 15oC with 0.25 mM IPTG. Rheb, HRas and
RhoA were expressed using pGEX2T, pET15b and pET28 vectors, respectively. All purified proteins
were exchanged into NMR buffer (25 mM sodium phosphate pH 7.0, 100 mM NaCl, 5 mM MgCl2 and
1mM DTT) in a PD MidiTrapTM G-25 column (GE healthcare). Small GTPase-proteins expressed in E.
coli co-purified primarily as complexes with GDP. Tuberous sclerosis 2 (TSC2) GAP domain (residues
1525-1742: hereafter termed TSC2GAP) and the DH-PH fragment of PDZ-RhoGEF (residues 713-
1081: hereafter termed DH-PHPRG) were prepared using pGEX2T and pGEX4T1 vectors, respectively
(Derewenda et al. 2004; Marshall et al. 2009). Catalytic domain constructs of the Son of Sevenless
(SOS, Cdc25 residues 566-1049: hereafter referred to as Cdc25SOS) and the GTPase activating domain
of human GTPase activating protein p120GAP (residues 715-1047: hereafter referred to as RasGAP)
were prepared as His-tagged proteins from the pET15b vector. All proteins were cleaved from their tags
via thrombin.
33
2.5.2 NMR-based GTPase, GAP and GEF assays: HRas and Rheb were loaded with GTP or mantGTP
by incubation with a 10 fold excess of nucleotide in the presence of 10mM EDTA. RhoA was loaded
with GTP or mantGTP in the presence 0.5 M urea and 10 mM EDTA. A 1H-15N HSQC (Heteronuclear
Single Quantum Coherence) spectrum was collected to confirm full nucleotide loading, and the mixture
was then passed through a de-salting column (PD MidiTrapTM G-25 (GE healthcare)) equilibrated with
NMR buffer, to produce a 1:1 complex of GTPase and the nucleotide.
All NMR experiments were run on a Bruker AVANCE II 800 MHz spectrometer equipped with a 5mm
TCI CryoProbe. Sensitivity enhanced 1H-15N HSQCs with 2 scans (5 min) were run in succession to
monitor the intrinsic GTP hydrolysis activity of GTPases (0.1-0.3 mM) at 20oC. The spectra were
processed with NMRPipe (Delaglio et al. 1995) and the peak heights were analyzed with Sparky
(Goddard and Kneller) via Gaussian line fitting. Residues from switch I&II, P-loop, β3 & β4 and the α3
helix that exhibit distinct well-resolved peaks in each nucleotide-bound state were used as reporters of
the reaction rates for each of the three GTPases, as described previously for Rheb (Marshall et al. 2009).
For the intrinsic nucleotide hydrolysis, the fraction of GTPase protein in the GDP-bound state was
calculated for each reporter residue using the equation 1 for Ras and Rheb relying on both GDP and
GTP peaks (see appendix A). In the case of RhoA the active state exhibited broadened and split peaks
that complicate peak integration, hence we monitored (equation 2; appendix A) the appearance of GDP
peaks. Data fitting was done using PRISM (GraphPad software).
To assay GAP-mediated nucleotide hydrolysis, RasGAP or TSC2GAP was added to GTP-loaded HRas
or Rheb at a GAP to GTPase molar ratio of 1/2,500 or 1/2.2, respectively. The hydrolysis rate was
determined by fitting the data to equation 1 in appendix A.
For GEF assays, DH-PHPRG or Cdc25SOS were added at a molar ratio of 1/30,000 GEF to RhoA or Ras,
in the presence of a 10 fold molar excess of GTP or mantGTP. All the experiments were performed in
duplicate with 0.1 mM GTPase. The observed rates of nucleotide exchange assays performed with
hydrolysable nucleotides are affected by intrinsic hydrolysis. Thus the observed data were fitted to an
equation that considers both exchange and hydrolysis (see appendix A) to extract the true exchange rate.
34
Using this rate, an exponential decay curve was generated to approximate nucleotide exchange in the
absence of hydrolysis.
2.5.3 Fluorescence-based GTPase assay:Emission spectra of 5 µM Rheb-mantGTP and Rheb-mantGDP
(380-525 nm) were collected at 20oC on a Shimadzu RF-5301PC spectrofluorophotometer with
excitation at 370 nm. Fluorescence emission intensity at 436 nm was monitored during the hydrolysis
reaction with excitation at 370 nm. Ten measurements were collected per minute and the average and
standard deviation were reported.
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Sondermann H, Soisson SM, Boykevisch S, Yang SS, Bar-Sagi D, Kuriyan J. 2004. Structural analysis of autoinhibition in the Ras activator Son of sevenless. Cell 119: 393-405.
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Tan YC, Wu H, Wang WN, Zheng Y, Wang ZX. 2002. Characterization of the interactions between the small GTPase RhoA and its guanine nucleotide exchange factors. Anal Biochem 310: 156-162.
Yu Y, Li S, Xu X, Li Y, Guan K, Arnold E, Ding J. 2005. Structural basis for the unique biological function of small GTPase RHEB. J Biol Chem 280: 17093-17100.
Zhang B, Zheng Y. 1998. Regulation of RhoA GTP hydrolysis by the GTPase-activating proteins p190, p50RhoGAP, Bcr, and 3BP-1. Biochemistry 37: 5249-5257.
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CHAPTER 3
Identification of critical amino acids in Rheb GTP hydrolysis
This chapter has been reformatted from the original publication: Mazhab-Jafari MT, Marshall CB, Ishiyama N, Ho J, Di Palma V, Stambolic V, Ikura M. An autoinhibited noncanonical mechanism of GTP hydrolysis by Rheb maintains mTORC1 homeostasis. Structure. 2012 Sep 5;20(9):1528-39. A link to the published paper can be found at:
http://www.sciencedirect.com/science/article/pii/S096921261200247X
37
3.1 Abstract:
Rheb, an activator of mammalian target of rapamycin (mTOR), displays low intrinsic GTPase activity
favoring the biologically activated, GTP-bound state. We identified a Rheb mutation (Y35A) that
increases its intrinsic nucleotide hydrolysis activity ~10-fold, and solved structures of both its active and
inactive forms, revealing an unexpected mechanism of GTP hydrolysis involving Asp65 in switch II and
Thr38 in switch I. In the wild-type protein, this non-canonical mechanism is markedly inhibited by
Tyr35, which constrains the active site conformation, restricting the access of the catalytic Asp65 to the
nucleotide-binding pocket. Rheb-Y35A mimics the enthalpic and entropic changes associated with GTP
hydrolysis elicited by the GTPase activating protein (GAP) TSC2, and is insensitive to further TSC2
stimulation. Overexpression of Rheb-Y35A impaired the regulation of mTORC1 signaling by growth
factor availability. We demonstrate that the opposing functions of Tyr35 in the intrinsic and GAP-
stimulated GTP catalysis are critical for optimal mTORC1 regulation.
38
3.2 Introduction:
Small GTPases act as molecular switches to regulate diverse cellular functions. When bound to
guanosine trisphosphate (GTP), they adopt an ‘on’ conformation that elicits a biological response. GTP
hydrolysis is accompanied by a conformational change into a GDP-bound ‘off’ conformation. Cycling
between the active and inactive states of each GTPase is a result of the intrinsic nucleotide hydrolysis
and exchange rates, and regulatory proteins that catalyze these processes. GTPase activating proteins
(GAPs) stimulate GTP hydrolysis, whereas guanine nucleotide exchange factors (GEFs) mediate the
displacement of GDP, allowing a new GTP molecule to bind (Bos et al. 2007). GTPase proteins possess
either complete or partial catalytic machinery for hydrolysis of GTP. In most cases, an electronegative
group is used for stabilization/polarization of the hydrolytic water for in-line nucleophilic attack of the
γ-phosphate (Maegley et al. 1996; Li and Zhang 2004). In most Ras and Rho subfamily GTPases, this is
achieved by the carboxamide oxygen of a conserved Gln in a dynamic loop called switch II. Ras and
Rho GAPs work by stabilizing this Gln in a catalytic conformation, while an Arg residue referred to as
an “Arginine finger” neutralizes the developing negative charge on the α- and β-phosphates of GTP
(Scheffzek et al. 1997). In other systems, such as Rap-RapGAP, a catalytic asparagine is provided in
trans by the GAP (Scrima et al. 2008).
Ras homolog enriched in brain (Rheb) is a key regulator of the mTOR complex 1 (mTORC1) signaling
pathway (Inoki et al. 2003; Dunlop et al. 2009). Rheb-GTP promotes phosphorylation of mTORC1
targets, resulting in enhanced protein translation and cellular growth (Garami et al. 2003). Rheb has an
unusually slow intrinsic GTPase activity, which is regulated by the GAP activity of tuberous sclerosis
complex 2 (TSC2), a tumor suppressor frequently inactivated in human patients with the tumor
predisposition syndrome tuberous sclerosis (Garami et al. 2003; Tee et al. 2003). Rheb overexpression
has been observed in certain cancer cell lines (Im et al. 2002; Eom et al. 2008; Nardella et al. 2008) and
constitutively activated Rheb mutants can induce oncogenic transformation in cell culture (Jiang and
Vogt 2008). The low intrinsic GTPase activity of Rheb has been attributed to the catalytically
incompetent conformation of Gln64 (Yu et al. 2005), which is homologous to Ras Gln61, but does not
participate in GTP hydrolysis (Li et al. 2004; Marshall et al. 2009). TSC2GAP is thought to utilize
Asn1643 to promote GTP hydrolysis by substituting for Gln64 in an “Asn thumb”-type mechanism
(Inoki et al. 2003; Marshall et al. 2009) similar to that of RapGAP (Scrima et al. 2008).
39
Here, utilizing site-directed mutagenesis, crystallography and real-time NMR-based GTPase assays, we
discovered that Rheb Tyr35, a residue that is highly conserved across the small GTPase superfamily
(Wennerberg et al. 2005), maintains the high activation state of Rheb by inhibiting intrinsic GTP
hydrolysis. Mutation of this residue substantially accelerated intrinsic nucleotide hydrolysis through a
catalytic mechanism that did not require Gln64, but also conferred resistance to the activity of TSC2.
Crystal structures of RhebY35A led us to identify the backbone carbonyl of Thr38 and side chain of
Asp65 as candidate residues that contribute to the intrinsic GTPase activity. Mutagenesis studies
confirm that Asp65 contributes significantly to the intrinsic GTPase activity of both wild-type Rheb and
the Y35A mutant. Further, Asp65 was absolutely essential for the sensitivity of Rheb to the GAP
activity of TSC2, whereas Gln64 was dispensable. Consistent with the in vitro data, expression of Rheb
Y35A and D65A mutants in mammalian cells affected transduction of growth factor signals to
mTORC1. Taken together, our observations reveal an efficient non-canonical mechanism of GTP
hydrolysis by Rheb, and suggest that autoinhibition of catalysis maintains Rheb in its highly activated
state upon growth factor stimulation, which is necessary for the proper signal transduction to mTORC1.
3.3 Results:
3.3.1 Rheb Tyr35 inhibits intrinsic GTPase activity: We previously showed that fluorescent-tagged
nucleotides can alter the hydrolysis and exchange rates governing the GTPase cycle (Mazhab-Jafari et
al. 2010). The most striking example we observed was that 2'-/3'-O-(N'- Methylanthraniloyl) (mant)GTP
was hydrolyzed by Rheb ~10-fold faster than GTP. This is not an intrinsic property of the modified
nucleotide as the mant moiety inhibited GTP hydrolysis by RhoA and did not affect hydrolysis by Ras.
The rate of mantGTP hydrolysis by Rheb is similar to that of Ras (Figure 3.1a), indicating that Rheb has
a latent capacity for efficient catalysis. Interestingly however, the rapid hydrolysis of mantGTP was
independent of Rheb Gln64 (Mazhab-Jafari et al. 2010). The position of the fluorophore in a structure of
Ras bound to a non-hydrolyzable analog of mantGTP (Scheidig et al. 1995) suggested it may interact
with the phenol ring of Tyr35 in switch I of Rheb. Remarkably, mutation of Tyr35 to Ala recapitulated
the mant effect, increasing the rate of GTP hydrolysis by an order of magnitude (Figure 3.1b).
Furthermore, the mant tag had no further effect on the catalytic activity of Rheb Y35A, suggesting that
the mutation and the fluorophore stimulate hydrolysis through the same mechanism (Figure 3.1b). These
observations indicate that Tyr35 auto-inhibits the intrinsic GTPase activity of Rheb.
40
Figure 3.1 Rapid hydrolysis of mantGTP by Rheb is related to autoinhibitory role of Tyr35. a) Hydrolysis of GTP or mantGTP by Rheb (black and green, respectively) and Ras (red and blue, respectively). Reaction rates derived by curve fitting are presented in the insets. b) Hydrolysis of GTP by wild-type Rheb (black), and GTP and mantGTP by Rheb Y35A (green and red respectively).
3.3.2 Structural basis for the Tyr35 auto-inhibitory function: We crystallized GDP-bound Rheb
Y35A in the presence of excess GMPPNP (a non-hydrolyzable analog of GTP) and to our surprise, the
asymmetric unit contained two molecules of Rheb, one bound to GDP and one to GMPPNP (Figure
3.2a-c). The overall protein fold is very similar to WT Rheb (Yu et al. 2005) (backbone RMSD of 0.44
Å) with a few key differences. The nucleotide-binding pocket is completely solvent exposed in the
GMPPNP-bound structure of Rheb Y35A, whereas in the WT protein the triphosphate group of the
41
Figure 3.2 Structure and dynamics of Rheb Y35A. (a) Asymmetric unit and electron density of nucleotide substrates. The asymmetric unit of the RhebY35A crystal containing one GDP-bound (cyan) and one GMPPNP-bound (green) Rheb molecule is shown in the center. 2Fo-Fc electron density maps at 1.5σ of the nucleotide binding site with GMPPNP (left) fitted into one Rheb Y35A molecule and GDP (right) in the second molecule of the crystal asymmetric unit. (b) Ribbon model of GMPPNP-bound Rheb Y35A. (c) Ribbon model of GDP-bound Rheb Y35A in the same orientation as b. Panels d, e, f and g show overlays of GMPPNP- or GDP-bound Rheb Y35A (colored as above) and WT Rheb in
42
complex with GMPPNP(1XTR) (magenta) or GDP(1XTQ) (gray), as indicated. d) Mutation of Tyr35 affects the position of the catalytic water (spheres) and γ-phosphate with respect to the carbonyl of Thr38. e) Minor conformational change of Ala35 in the Rheb mutant upon GTP hydrolysis. The Ala35 Cα and Cβ translocation distances from the GMPPNP-bound form to the GDP-bound form are shown. f) Major conformational rearrangement of WT Rheb Tyr35 upon GTP hydrolysis, with translocations indicated as in e. g) Position of switch II residues relative to the nucleotide binding site in the activated form of WT Rheb versus that of the Y35A mutant. The backbone of N-terminal switch II residues Gly63-Ser68 and side chains of Asp65 and Glu66 are shown. Two conformations were observed for the Asp65 side chain. h) 1H-15N HSQC spectra illustrating cross-peaks from switch II residues in WT Rheb (black) and Rheb Y35A (red) in complex with GTP. The panel showing Ser68 is illustrated at a higher contour level for clarity. The reduction in height of the peak from the mutant relative to the wild-type peak is indicated as a percentage at the bottom of each panel in which it is measurable. The full spectra are shown in figure 3.7a. nucleotide is shielded from the solvent by the phenol ring of Tyr35, which forms a hydrogen bond with
the γ-phosphate. In addition, the γ-phosphate is 0.5 Å closer to Thr38 in the absence of Tyr35 (Figure
3.2d), which in the WT structure “pulls” the γ-phosphate toward the middle of switch I. Interestingly,
the hydrolytic water is closer to the backbone carbonyl of Thr38 in the mutant (2.7 Å versus 3.8 Å in the
WT protein) (Figure 3.2d), placing it in a more electron-rich environment that may enhance its
polarization for an in-line nucleophilic attack to the γ-phosphate. It has been proposed that the
corresponding backbone carbonyl of Ras (Thr35) contributes to the stabilization/activation of the
catalytic water during intrinsic GTP hydrolysis (Frech et al. 1994; Buhrman et al. 2010). Comparison of
our structure with that of wild-type Rheb indicates that Tyr35 pulls the γ-phosphate and catalytic water
away from the Thr38 carbonyl, thus reducing its catalytic contribution.
Switch I of Rheb Y35A does not undergo any substantial conformational change upon nucleotide
hydrolysis, whereas this region of the WT protein exhibits a large structural change mediated by an
interaction between Tyr35 and the γ-phosphate (Yu et al. 2005) (Figure 3.2e&f). It was hypothesized
that a similar nucleotide-dependent rearrangement of Rap Tyr32 would be energetically unfavourable to
the GTPase reaction (Cherfils et al. 1997), consistent with our observation that nucleotide hydrolysis is
accelerated by a mutation that disrupts this conformational change.
3.3.3 Identification of a catalytic residue for GTP hydrolysis: Previous work has shown that Gln64,
corresponding to the catalytic Gln61 of Ras, is not involved in GTP hydrolysis by WT Rheb (Inoki et al.
2003; Li et al. 2004; Marshall et al. 2009). Likewise, Gln64 remains in a non-catalytic conformation in
the structure of Rheb Y35A (Figure 3.3a) and is not required for the accelerated hydrolysis of GTP by
43
Figure 3.3 Mutagenic analysis of potential catalytic residues in Rheb Y35A. a) Position in the structure of GMPPNP-bound Rheb Y35A of potential catalytic residues selected for mutagenesis,. b-e) Intrinsic GTPase assays for hydrolysis of GTP or mantGTP by WT Rheb and mutants as indicated: Hydrolysis of (b) GTP by Rheb Y35A and the double mutant Y35A, S16A, (c) mantGTP by WT Rheb and Rheb D36A, (d) GTP by Rheb Y35A and the double mutant Y35A, Q64L, (e) GTP by Rheb Y35A and the double mutant Y35A, R15G. Hydrolysis of mantGTP by Rheb Y35A is shown in Figure 3.1b, and hydrolysis of GTP by additional Rheb mutants is shown in Figures 3.4, 3.5 and 3.9. f) Multiple conformations of Arg15, Asp65, and Ser68 in the structure of Rheb Y35A in complex with GMPPNP.
44
The 2Fo-Fc electron density map at 1.0σ is shown for the three aforementioned residues with double-headed arrows indicating the movement of the side chains. Rheb Y35A (Figure 3.3d and 3.5a). Since the catalytic residues of other small GTPase superfamily
members are found in the N-terminus of switch II, we examined this region for residues with
electronegative side chains that may contribute to the hydrolytic reaction. Immediately downstream of
Gln64 are two residues with acidic side chains, Asp65 and Glu66 (Figure 3.2g). The crystal structure of
Rheb Y35A shows that the backbone of the N-terminal loop of switch II of this mutant is displaced by
an average of 1 Å toward the nucleotide binding pocket relative to the wild type, which brings the side-
chain carboxylate of Asp65 closer to the nucleotide by 1 Å (average Asp65Oδ1,2WT- average
Asp65Oδ1,2Y35A) (Figure 3.2g). Mutation of Asp65 to Ala reduced the intrinsic hydrolysis of Rheb Y35A
by more than 60% and that of wild type by 30% (Figure 3.4a), as did the conservative substitution of
Asp65 by Asn (Figure 3.5b). On the other hand, mutations of Glu66 had no effect on intrinsic GTPase
activity (Figure 3.5c), consistent with its perpendicular orientation away from the nucleotide (Figure
3.2g). We also tested all other residues found within 10 Å of the hydrolytic water in the Rheb Y35A
structure that could potentially provide (i) a negative charge to activate this water molecule, or (ii) a
positive charge to stabilize the β- and γ-phosphates in the transition state for hydrolysis (Figure 3.3).
There was no change in the rate of intrinsic nucleotide hydrolysis associated with R15G, S16A, or D36A
mutations (Figure 3.3b, c, e). The only other charged residues within 10 Å of the hydrolytic water are
Lys19 and Asp60 of the highly conserved G1 and G3 box motifs, respectively. The Rheb K19A mutant
failed to express, presumably due to impaired nucleotide binding, and D60A was highly unstable and
could not be loaded with GTP, consistent with the role of this residue in Mg++ coordination (Yu et al.
2005). These data strongly suggest that Asp65 is the sole candidate for a catalytic residue in Rheb.
Notably, carboxylates are more potent nucleophiles than carboxamides, and consistently, the Q61E
substitution increased the GTPase activity of Ras (Frech et al. 1994).
In the structure of wild-type Rheb, the carboxylate of Asp65 is 12 Å (average Asp65Oδ1,2) from the γ-
phosphate in a single conformation, whereas the electron density of Rheb Y35A indicates that Asp65
exists in two conformations, 11.0 and 12.0 Å from the γ-phosphate, respectively (Figure 3.3f). By
comparison, the catalytic carboxamide of Ras (Gln61Oε) has been found at distances varying from 4.7 to
12.2 Å from the γ-phosphate (median distance of 8.1Å) (Figure 3.6a) in available crystallographic
snapshots, consistent with the dynamic nature of switch II determined by NMR studies (Ito et al. 1997).
45
Figure 3.4 Role of Asp65 in intrinsic and GAP-mediated GTP hydrolysis by Rheb. a) Hydrolysis of GTP by wild-type Rheb (black), the mutants D65A and Y35A (blue and green, respectively), as well as the double mutant Y35A-D65A (red). Reaction rates derived by curve fitting are presented in the insets. b) Sensitivity of WT Rheb and Asp65 mutants to TSC2GAP-stimulated GTP hydrolysis. WT, WT+GAP, D65A+GAP, D65E+GAP, and D65N+GAP are shown with black, blue, green, yellow, and red respectively.
Thus, despite its established role as a catalytic residue (Frech et al. 1994), Gln61 is rarely found in a
catalytically competent conformation in Ras crystal structures, presumably because this state is transient
and energetically unfavorable (Grant et al. 2009; Fraser et al. 2011). Similarly, our Y35A structure and
46
the previous wild-type Rheb structure (Yu et al. 2005) both appear to be energetically stable states, with
the conformations of Asp65 stabilized primarily by ionic and polar interactions with the Arg15 and
Ser68 side chains, which are also found in two alternate conformations in our structure (Figure 3.3f).
Interestingly, comparison of WT and Y35A 1H-15N heteronuclear single quantum coherence (HSQC)
spectra revealed increased line broadening for residues in the P-loop and the N-terminus of switch II of
GTP-bound Rheb Y35A (Figure 3.2h & 3.7a), suggesting elevated dynamics in µs-ms time scale. This
47
Figure 3.5 Effect on Rheb GTPase activity of mutations of acidic and electronegative residues in switch II. a) Intrinsic GTPase assays for hydrolysis of mantGTP by WT Rheb (black), Rheb D65A (green), and Rheb Q64L (red). b) Intrinsic GTPase assays for hydrolysis of GTP by WT Rheb (black) and Rheb D65N (green). c) Mutation of Glu66 impairs TSC2 GAP-catalyzed but not intrinsic GTPase activity of Rheb. Intrinsic GTP hydrolysis by WT and E66A Rheb are shown in black and green, respectively. TSC2GAP-mediated GTP hydrolysis by Rheb WT and E66A are shown in blue and red, respectively. Note that the GTPase activity of Rheb E66A is modestly stimulated by TSC2GAP, but this mutant exhibits reduced sensitivity to GAP activity. could allow the N-terminus of switch II to sample alternate conformations closer to the nucleotide and
the catalytic water. The elevated dynamics of the N-terminal region of switch II and its proximity to the
nucleotide binding site in Rheb Y35A is consistent with the greater impact on catalysis of Asp65
mutations in the Y35A mutant than in wild-type Rheb (Figure 3.4a). Hence, in addition to affecting the
orientation of the nucleotide and hydrolytic water, Tyr35 may reduce the intrinsic GTPase activity of
Rheb by restricting the dynamics of switch II and displacing it from the nucleotide binding site. Relative
to Ras, the catalytic Gln residues of Rho subfamily GTPases were found closer to the γ-phosphate
(median distance of 5.5Å) (Figure 3.6a and c), which may contribute to their faster intrinsic nucleotide
hydrolysis rate (Mazhab-Jafari et al. 2010). On the other hand Gln63, which was recently proposed to be
a non-canonical catalytic residue of Rap in GAP1IP4BP-mediated GTP hydrolysis (Sot et al. 2010), is
found with a median distance of 11.8Å from the γ-phosphate in structures of free Rap (Figure 3.6a),
consistent with the slow nucleotide hydrolysis of this GTPase.
In Ras, Gly12, Gly13 and Gln61 are the major sites of oncogenic mutations. Mutation of Ras Gly12 to
any other residue hinders GTP hydrolysis by sterically occluding access of the catalytic residue Gln61 to
the hydrolytic water and nucleotide (Krengel et al. 1990). However, Rheb has an Arg in this position
and its mutation to Gly (R15G) does not increase the catalytic activity of Rheb Y35A (Figure 3.3e) or
WT (Yamagata et al. 1994; Im et al. 2002; Li et al. 2004; Marshall et al. 2009). The distinctive impact of
P-loop residues on the activities of Ras and Rheb lends further support to the different molecular
mechanisms of action of these two closely related GTPase homologs.
3.3.4 Involvement of Rheb’s Asp65 and Tyr35 in TSC2GAP-mediated GTP hydrolysis: Mutation of
the solvent exposed residue Asp65 to Ala (D65A) did not perturb the structure of Rheb, on the basis of
minimal and localized chemical shift perturbations in the 1H 15N HSQC spectra that were mainly
confined to switch II (Figure 3.8), but totally abolished the susceptibility of Rheb to the GAP activity of
48
Figure 3.6 Structure-function analysis of the position of putative catalytic residues and the conserved switch I Tyrosine in small GTPases. a) Crystallographic ensemble of interatomic distances between the γ-phosphate of GTP (or analogue) and the proposed catalytic residues of Ras, Rheb, Rho, and Rap GTPases. Histogram of distances measured from the γ-phosphate (Pγ) to Ras Gln61Oε (blue), Rheb average Asp65Oδ1,2 (red), Rho Gln63Oε (green), and Rap Gln63Oε (purple) from crystal structures of free protein in complex with GTP and non-hydrolyzable GTP analogs. All available PDB-archived structures of Ras with wild-type GTPase activity where Q61 is resolved were included, [PDB code] (distance in Å): [5P21] (6.1), [6Q21] (6.3, 7.0, 6.8, 7.6), [1QRA] (7.8, 6.7), [1CTQ] (6.7), [1GNP] (9.7),
49
[3K8Y] (5.9), [3K9N] (11.7), [1P2S] (6.3), [1P2V] (6.7), [1PLK] (4.7), [2CL0] (12.2), [2CL7] (10.4), [2CLC] (10.3), [121P] (8.1), [3PIR] (9.0), [3PIT] (9.8), [3I3S] (7.2). Some structures contain more than one Ras molecule in the asymmetric unit, in which case the distance was measured for each molecule separately. 1GNP and 3K9N are structures of WT-Ras in complex with mantGMPPNP and Ras Y32F in complex with GMPPNP, respectively, both of which have the same intrinsic nucleotide hydrolysis rate as WT Ras (Yamasaki et al. 1994; Mazhab-Jafari et al. 2010). 2CL0, 2CLC and 2CL7 are structures of Ras bearing a fluorescent tag on switch I (with Y32C mutation) in complex with GMPPNP or GTP (Klink et al. 2006). 3PIR, 3PIT, and 3I3S are structures of Ras D41E and T50I, mutations that are solvent exposed and far away from switch II. For Rheb, distances were measured for WT Rheb-GMPPNP [1XTR] (12.0), WT Rheb-GTP [1XTS] (12.1) and two separate measurements were made for Rheb Y35A-GMPPNP, in which Asp65 exists in two conformations (11.0, 12.0). The distances for Rho subfamily GTPases (Rac1, TC10/RhoQ, RhoC, Rac3, Cdc42) were measured using the following structures: [1MH1] (5.7), [2ATX] (6.8, 7.4), [2GCO] (5.7, 5.7), [2GCP] (5.6), [2IC5] (4.8), [2QRZ] (4.4, 3.8). 1MH1 is structure of Rac1 M1P-F78S double mutant, both of which are far away from nucleotide binding site. Finally, the distances for Rap were from structures of Rap2A: [2RAP] (12.7), [3RAP] (10.4, 12.2). b) Curves showing the intrinsic GTP hydrolysis rate of WT RhoA (black) and the Y34A mutant (green). c) The positions of the Tyr34, Gln63 and the non-hydrolyzable nucleotide GTPγS in RhoA G14V mutant (PDB code: 1A2B). d) Curves showing the intrinsic GTP hydrolysis rate of WT Ras (black) and the Y32A mutant (green). e) The positions of the Tyr32, Gln61 and the non-hydrolyzable nucleotide GMPPNP in Ras (PBD code: 5P21). TSC2 (Figure 3.4b). Furthermore, even conservative mutations of Asp65 (D65E/N) rendered Rheb
totally insensitive to the activity of TSC2 GAP. The strict requirement for the geometry and charge of
this side chain suggest that it might be a critical catalytic residue for the GAP-mediated hydrolysis
reaction. We also tested the sensitivity of the GTPase activity of Rheb Y35A to the action of TSC2GAP
and found that the GTPase activity of this mutant was not further stimulated by the addition of the GAP
domain of TSC2 (Figure 3.9a). An analagous mutation (Y32A), impaired the sensitivity of Rap GTPase
to the function of RapGAP (Brinkmann et al. 2002; Scrima et al. 2008), however a conservative
mutation (Y32F) was tolerated. Interestingly, the Y35F mutation was sufficient to render Rheb
insensitive to the function of the TSC2GAP (Figure 3.9b), highlighting differences in the details of
molecular recognition in these two homologous systems.
3.3.5 Thermodynamic basis for the Tyr35 auto-inhibitory function: To better understand the energetic
basis of Tyr35 auto-inhibition, we analyzed the thermodynamics of the GTP hydrolysis reaction using
an Arrhenius plot (Figure 3.10). This powerful technique allows one to extract energetic parameters,
such as enthalpy, entropy and free energy, from the highly unstable and low populated transition state of
an enzymatic reaction. The increased catalytic activity of Rheb Y35A was associated with a large
reduction in the activation enthalpy for GTP hydrolysis (Figure 3.10, Table 3.1). However, the
50
Figure 3.7 Perturbation of Rheb HSQC spectrum by Tyr35 mutation. a) HSQC spectrum of Rheb Y35A-GTP (red) overlaid with WT Rheb-GTP (black). Resonances that are present in the wild-type
51
spectrum but exhibit large chemical shift changes or severe broadening in the spectrum of the mutant are circled. Resonances showing minor chemical shift changes due to the mutation are indicated by double headed arrows. Note that in the GTP-bound form there are no extra peaks in the Y35A mutant, indicating that most circled peaks correspond to resonances broadened beyond detection in the mutant. b) HSQC spectrum of Y35A-GDP (red) overlaid with WT Rheb-GDP (black). Resonances that are unique to the wild-type spectrum are circled and those unique to the mutant spectrum are highlighted by squares. Note that in the GDP-bound form, the total number of observable resonances remains constant between WT Rheb and the Y35A mutant (circles ≈ squares), indicating that most of these resonances undergo long range chemical shift changes.
activation entropy was also reduced (unfavorable contribution), resulting in a modest decrease in the
overall activation free energy of the nucleotide hydrolysis reaction in the mutant. Because there is a
build-up of negative charge on the β-γ bridging oxygen during GTP hydrolysis (Cepus et al. 1998; Du et
al. 2000; Allin et al. 2001), the proximity of the electron rich phenol ring of Rheb Tyr35 could
destabilize the transition state, which is consistent with the reduction in activation enthalpy associated
with mutation of this residue. Interestingly, the Arg fingers of Ras- and Rho-GAPs accelerate nucleotide
hydrolysis of their cognate GTPases by providing positive charge in a position equivalent to that of
Rheb Tyr35. Another contribution to the enthalpic term may come from the strengthened hydrogen bond
between the Thr38 carbonyl in the mutant and the repositioned catalytic water, which may be more
reactive toward the γ-phosphate (Frech et al. 1994).
52
Figure 3.8 Minimal chemical shift perturbation associated with mutation of Rheb Asp65. HSQC spectrum of Rheb D65A-GTP (red) overlaid with WT Rheb-GTP (black). Resonances that are strongly perturbed by the mutation (severe broadening or large chemical shift change) are circled and those showing minor chemical shift changes are indicated by double headed arrows.
The larger negative value of ∆S‡ for Rheb Y35A indicates that formation of the transition state requires
the mutant to undergo a larger increase in “order” than the wild-type protein. In the crystal structure of
WT Rheb-GMPPNP, a hydrogen bond between the hydroxyl of Tyr35 and the γ-phosphate of GMPPNP
stabilizes switch I, contributing to the order of the ground state. Disruption of this contact by mutation of
Tyr35 increases the disorder in switch I, as illustrated by partial spectral broadening of peaks from
residues 27-30 of GTP-bound Rheb Y35A (Figure 3.7). Thus assembly of the ordered transition state
from the more flexible Rheb Y35A ground state would be more entropically unfavourable. The
conservative mutation Y35F increased intrinsic hydrolysis almost as much as Y35A with similar
thermodynamic effects (Figure 3.10, Table 3.1), suggesting that the H-bond between the hydroxyl of
Tyr35 and the γ-phosphate is critical for the auto-inhibition of Rheb’s GTPase activity. It is very
interesting to note that the thermodynamic landscape of intrinsic GTP hydrolysis in the Y35A mutant
53
Figure 3.9 Tyr35 hydroxyl is required for TSC2GAP-assisted GTP hydrolysis. a) Intrinsic and GAP-catalyzed GTP hydrolysis by Rheb Y35A. b) Intrinsic and GAP-catalyzed GTP hydrolysis by Rheb Y35F. In both graphs the GTPase activity of mutant Rheb with and without TSC2GAP are shown in black and green, respectively, and the TSC2GAP-catalyzed GTP hydrolysis by WT Rheb is shown in blue.
(reduced activation enthalpy with an entropic penalty) is similar to that reported for TSC2GAP-mediated
GTP hydrolysis in WT Rheb (Marshall et al. 2009), suggesting that TSC2GAP may promote hydrolysis
in part by disrupting the electrostatic contact between Tyr35 and the γ-phosphate. Consistent with this
hypothesis, the increased rate of GTP hydrolysis by the Rheb Y35A/F mutants is not further accelerated
by the addition of the GAP (Figure 3.9). The larger reduction of the activation enthalpy by TSC2GAP-
mediated catalysis compared to Y35A mutation suggests the GAP provides additional stimulatory
electrostatic contributions to GTP hydrolysis, perhaps via complementation of the intrinsic catalytic
machinery by the Asn thumb. On the other hand the larger unfavorable reduction in entropy of the GAP-
mediated reaction could be due to complex formation between Rheb and the GAP domain of TSC2.
Figure 3.10 Effect of Tyr35 and Asp65 mutations on the thermodynamic activation parameters for GTP hydrolysis by Rheb. Arrhenius plots for intrinsic GTP hydrolysis by Rheb WT (black), Y35A (green), Y35F (brown), Y35A-D65A (blue) and D65A (red). Each data point represents a rate
54
determined from a representative GTPase assay consisting of 25 time points performed at a given temperature. Error bars represent standard error associated with derivation of the rate by curve fitting. Mutation of Asp65 substantially impairs the stimulatory effect of the Y35A mutation on intrinsic
hydrolysis, hence we measured the thermodynamic parameters of the transition state for the Rheb
double mutant Y35A-D65A (Table 3.1). Mutation of Asp65 increased the activation enthalpy (∆H‡ ) of
Rheb Y35A, indicating that the negatively charged carboxylic acid side chain of Asp65 stabilizes the
transition state since the enthalpic term originates primarily from electrostatic interactions (Kötting and
Gerwert 2004). In Ras, the enthalpic contribution to hydrolysis was attributed to the charge shift from
the γ- toward the β-phosphate (Kötting and Gerwert 2004). We propose that electrostatic interactions
between Rheb Asp65 and the nucleotide similarly shift charge in the transition state to promote
hydrolysis. Interestingly, Tyr35 reduces the enthalpic contribution of Asp65 to GTP hydrolysis,
∆∆H‡(Y35A-Y35A,D65A) > ∆∆H‡(WT-D65A) (Table 3.1), which is consistent with our kinetic data (Figure 3.4a).
Table 3.1 Summary of thermodynamic activation parameters. [free energy of activation (∆G‡), activation enthalpy (∆H‡), and activation entropy (T∆S‡) in kJ/mol] calculated for GTP hydrolysis by Rheb WT and mutants. T is set to 298 K in the equation; ∆G‡ = ∆H‡ - T ∆S‡.
Protein
WT Y35A Y35F Y35A-D65A
D65A TSC2GAP*
∆H‡
86.0 52.3 52.7 55.6 87.0 41.3
T∆S‡
-13.5 -43 -43.3 -41.6 -13.3 -51.8
∆G‡
99.5 95.3 96.0 97.2 100.3 93.1
*: Values from (Marshall et al. 2009).
3.3.6 Regulation of mTORC1 by growth factors involves the non-canonical catalytic and autoinhibitory
mechanisms: To investigate the role of Rheb’s newly discovered catalytic machinery, and its auto-
inhibition, in the activation of mTORC1, HeLa cells were transfected with wild-type Rheb or the Y35A
or D65A mutants. Phosphorylation of p70 S6K Thr389, a measure of mTORC1 signaling throughput
(Figure 3.11a), was monitored by immunoblotting, upon growth factor starvation, as well as 15 min and
6 h after growth factor stimulation (Figure 3.11b & Figure 3.12). Following growth factor stimulation,
when the TSC1/2 complex is down-regulated (Benvenuto et al. 2000; Chong-Kopera et al. 2006),
mutation of Rheb Tyr35 to Ala reduced the activation of mTORC1, as evidenced by slightly lower p70
55
S6K phosphorylation despite higher Rheb Y35A expression compared to Rheb WT, an effect made
more apparent with longer stimulation (Figure 3.11b & 3.12). Remarkably, in the absence of stimuli
upon serum starvation, Rheb Y35A led to a significant increase in mTORC1 activity (Figure 3.11b), as
did the expression of the GAP-resistant mutant Rheb D65A (Figure 3.11b). Mutation of Asp65 (but not
Tyr35) perturbed the chemical shift of the neighboring switch II residue Tyr67 (Figure 3.7a & 3.8),
previously shown to be critical for activation of mTORC1 (Long et al. 2007), which may affect the
ability of Rheb D65A to fully activate mTORC1. This may explain the fact that under conditions of
growth factor stimulation, Rheb D65A induced less S6K phosphorylation than the wild type protein,
despite its reduced intrinsic GTPase activity (Figure 3.11b).
Figure 3.11 Mutations of Rheb catalytic and autoinhibitory residues impact Rheb’s activation level and mTORC1 phosphorylation of p70 S6K. a) Signaling pathway by which growth factors
56
stimulate mTORC1 phosphorylation of p70 S6K. b) Normalized values of p70 S6K phosphorylation for cells starved (-) or stimulated (+) with serum and insulin for 15 min (left) or 6 h (right) are shown as bar graphs. More details in experimental procedures. Representative Western blots are shown in Figure 3.12. c) Rheb nucleotide loading monitored in HEK293 cells with 32P-labeling experiment as described in experimental procedures.
Guanine nucleotide loading of WT Rheb and the mutants in vivo was determined by their
immunoprecipitation from HEK293 cells metabolically labeled with 32P-orthophosphate and nucleotide
resolution by thin layer chromatography (Figure 3.11c). Consistent with its increased GTPase activity,
Rheb Y35A displayed reduced loading of GTP, whereas Rheb D65A showed modestly increased GTP
loading. Reflected in the elevated loading of WT Rheb with GTP (Figure 3.11c), the overabundance of
transfected Rheb proteins likely negates the effects of endogenous TSC2 on the overexpressed Rheb
57
Figure 3.12 Effects of Y35A and D65A mutations in Rheb on mTORC1 activity. Western blots detecting p70 S6K phosphorylated at Thr389, total p70 S6K, and Myc-tagged Rheb in HeLa cells transfected with wild-type Rheb, or D65A or Y35A mutants, or empty vector, in the absence (-) or presence (+) of serum and insulin for a) 15min and b) 6 h. More details in experimental procedures. mutants in this cell line. While the lower GTP loading of Rheb Y35A indicates higher intrinsic
hydrolysis rate than that of the wt protein, modestly increased GTP loading of D65A signifies the auto-
inhibitory effects of Tyr35 on Asp65’s contribution to intrinsic catalysis, consistent with their in vitro
behavior (Figure 3.4a).
3.4 Discussion:
GTPases are versatile molecular switches that utilize surprisingly diverse mechanisms to mediate the
interconversion between the active and inactive states. The study presented here illustrates how Rheb
evolved a GTP hydrolysis mechanism drastically different from its close homolog H-Ras. Rheb employs
an autoinhibitory mechanism to maintain a high activation state in cells essential for the proper
maintenance of mTORC1 signaling and cellular growth.
The novel auto-inhibitory mechanism functions via an interaction between Rheb Tyr35-OH and the γ-
phosphate of GTP, which hinders GTP hydrolysis. Interestingly, our investigation of this inhibitory
mechanism led to the elucidation of an unusual Rheb catalytic mechanism involving Asp65, which is
one position downstream of the canonical catalytic Gln, equivalent to Ras Gln61 and Rho Gln63. In the
canonical mechanism, the catalytic water is activated/stabilized by interaction with an electronegative
group, the carboxamide oxygen of a glutamine, provided either in cis or trans (Bos et al. 2007).
Although an equivalent residue (Gln64) is present in the sequence of Rheb switch II, our work
demonstrates that the catalytic function is carried out by the adjacent Asp65.
A Tyr residue in switch I is highly conserved amongst the GTPase superfamily, however the functional
role of this residue varies. For example, in RhoA, Tyr34 stimulates intrinsic hydrolysis, presumably by
stabilizing the catalytic conformation of Gln63 in switch II, whereas Ras Tyr32 is solvent exposed and
does not impact the intrinsic hydrolysis (Figure 3.6). In Rheb, Tyr35 counters the contribution of Asp65
to catalysis by restricting the dynamics of switch II and reducing its access to the catalytic site (Figure
3.13). Severe peak broadening was observed for the amides of Gly63, Gln64, Asp65 and Glu66 in the 1H-15N HSQC spectrum of the Y35A mutant (Figure 3.2h), presumably the result of disrupting the H-
bond network from Tyr35 to the amide of Gly63 through the catalytic water and the γ-phosphate (Figure
58
3.2d). Moreover, Tyr35 restricts the position of the hydrolytic water and reduces its polarization by the
carbonyl of Thr38, which is thought to promote hydrolysis (Frech et al. 1994; Buhrman et al. 2010). The
residual catalytic activity found in Rheb D65A may reflect the stimulatory effect of the Thr38 backbone
carbonyl in polarization and/or stabilization of the hydrolytic water. Upon mutation of Tyr35, Asp65
adopts two conformations, one of which is more proximal (relative to the WT) to the nucleotide binding
site and appears better positioned for hydrolysis (Figure 3.2g), consistent with our finding that mutation
of Asp65 has a greater impact on the catalytic activity of Rheb Y35A than that of WT (Figure 3.4a). On
the basis of the multiple crystallographic conformations of Asp65, and the NMR peak broadening, we
propose that in both wild-type and Y35A Rheb, switch II exists in an ensemble of conformations, some
of which allow Asp65 to adopt a catalytic conformation closer to the nucleotide.
Structural evidence implicating Asp as a catalytic residue exists for at least one other member of the
GTPase superfamily, the signal recognition particle (SRP) Ffh/FtsY (Focia et al. 2004), which is a large
dimeric prokaryotic GTPase that is highly divergent from the Ras family. Nevertheless, to our
knowledge, a catalytic Asp has not been previously reported within the Ras subfamily. On the other
hand, the inhibitory role for a switch I Tyr we discovered in Rheb may be relevant in inhibiting the
intrinsic hydrolytic machinery in certain other GTPases, such as Ran (Brucker et al. 2010).
Our structural analysis of Rheb also shed further light on the mechanism of TSC2GAP-mediated
hydrolysis of GTP. We propose that while providing an Asn thumb as a means of accelerating catalysis,
TSC2GAP may also stimulate the GTPase activity of Rheb by relieving autoinhibition and aligning
Rheb’s newly identified catalytic machinery (Figure 3.13c). Interaction of TSC2 with Rheb switch I may
disrupt the electrostatic contact between Tyr35 and the γ-phosphate, reducing the auto-inhibitory effect
of this residue on GTP hydrolysis, explaining the functional and thermodynamic similarities between
WT Rheb in the presence of the TSC2GAP and the Rheb Y35A mutant alone. A common theme in
GAP-stimulated GTP hydrolysis is repositioning of the N-terminus of switch II relative to the nucleotide
binding site to allow for efficient catalysis. For example, the RanGAP Asn thumb serves to properly
orient the catalytic Gln69 of Ran (Seewald et al. 2002; Bos et al. 2007). Similarly, GAPIP4BP has been
proposed to promote Rap GTP hydrolysis by repositioning a non-canonical catalytic glutamine residue,
Gln63, located two positions C-terminal to the position corresponding to Ras Gln61 (Sot et al. 2010). In
the case of Rheb, we propose that Rheb-TSC2GAP interaction stabilizes Asp65 closer to the γ-
59
phosphate to catalyze GTP hydrolysis in synergy with the Asn thumb (Asn1643) provided by
TSC2GAP. The delineation of the precise details of TSC2-mediated catalysis will require a more
detailed structural analysis of the Rheb:TSC2GAP complex that is hindered by the transient nature of
their interaction observed by us and others (Scrima et al. 2008; Marshall et al. 2009), preventing us from
distinguishing impaired binding from impaired catalysis.
60
Figure 3.13 Schematic model of intrinsic and TSC2GAP-stimulated GTP hydrolysis by Rheb. a) In wild-type Rheb, Tyr35 displaces the hydrolytic water away from the backbone carbonyl of Thr38, reducing the polarization and reactivity of this water molecule. Further, Tyr35 reduces the electrostatic contribution of Asp65 to the GTP hydrolysis reaction by displacing this residue away from the nucleotide and the catalytic water. b) Mutation of Tyr35 allows Asp65 and Thr38 to assemble a more efficient catalytic site. c) Interaction of the GAP domain of TSC2 with Rheb may reduce the inhibitory effects of Tyr35, allowing Asp65 to promote catalysis in synergy with the Asn thumb (Asn1643) provided in trans by TSC2GAP. The Tyr35-mediated auto-inhibition of Rheb’s GTPase reaction is necessary to maintain the appropriate
level of activation of this small GTPase, and thus mTORC1 signaling, in response to growth factors.
When growth factors are available, TSC2GAP activity becomes limiting, and Tyr35 inhibits GTP
hydrolysis, resulting in mTORC1 up-regulation. In the absence of stimulation, Rheb Tyr35 is required
for productive TSC2GAP-mediated acceleration of GTP hydrolysis to shut down mTORC1 signaling.
Indeed, overexpression of Rheb Y35A substantially uncouples mTOR signaling from growth factors. In
cells overexpressing wild-type Rheb, mTOR signaling was strongly responsive to the availability of
serum and insulin, whereas this response was significantly dampened in cells overexpressing the Y35A
mutant.
To our knowledge this is the first example of a distinct mechanism of intrinsic nucleotide hydrolysis
within the Ras subfamily, which may be relevant to some other Ras superfamily GTPases, particularly
those that lack the canonical catalytic Gln in switch II (e.g., Rap GTPases). This study provides a view
into an unusual mechanism of GTP hydrolysis by Rheb and an intriguing autoinhibitory interaction that
blocks this GTPase reaction.
3.5 Experimental Procedures:
3.5.1 Protein preparation: Mus musculus Rheb (residues 1-169) WT and mutants and Tuberous
sclerosis 2 (TSC2) GAP domain (residues 1525-1742) were prepared according to previous protocols
(Mazhab-Jafari et al. 2010). In brief, the proteins were expressed in Escherichia coli (BL21) using
pGEX2T vector, grown in minimal media supplemented with either 14NH4Cl or 15NH4Cl at 15oC with
0.25 mM IPTG. Mutagenesis was performed with Quikchange site-directed mutagenesis. Small GTPase-
proteins expressed in E. coli co-purified mainly as complexes with GDP nucleotide. Rheb and TSC2
proteins were initially purified using glutathione Sepharose, cleaved from the GST tag by thrombin, and
further purified via Superdex 75 size exclusion chromatography. Human H-Ras (residues 1-171) and
61
murine RhoA (residues 1-181) were expressed using pET15b and pET28, respectively, and purified by
Ni-NTA followed by Superdex 75 after removal of the His tag with thrombin.
3.5.2 Crystallization and data collection: Crystals of Rheb (residues 1-169) Y35A mutant were
grown at room temperature with seeding using the hanging drop vapor diffusion method. The protein
solution contained 20mM Tris hydrochloride pH 8.0, 100 mM NaCl, 5 mM MgCl2 and 0.02% NaN3
w/v. The protein was concentrated to 870 µM, and GMPPNP was added to a final concentration of 3.8
mM. The solution was allowed to sit at room temperature for 4h for nucleotide exchange and then
placed at 4oC overnight. Crystallization experiments were set at room temperature by mixing equal
volumes of the protein solution with the well solution (100 mM Tris hydrochloride pH 8.5, 200 mM
Sodium acetate trihydrate and 30% w/v Polyethylene glycol 4,000). Seed crystals (grown at 4oC from a
360 µM protein solution containing 1.56 mM GMPPNP and a well solution of 100 mM Tris
hydrochloride pH 8.5, 200 mM Sodium acetate trihydrate and 30% w/v Polyethylene glycol 4,000) were
added in serial dilution to hanging drops to promote crystal growth. Resulting crystals were soaked in a
cryoprotective solution containing 25% PEG 400 and flash frozen in liquid Nitrogen. The diffraction
data were collected using an R-Axis IV++, Rigaku RUH3R rotating anode generator equipped with
Osmic optics and an X-stream cryosystem for data collection at a temperature of 100K with a
wavelength of 1.54 Å and processed using HKL2000 (Otwinowski and Minor 1997).
3.5.3 Structure determination and refinement: The phase problem was solved by molecular
replacement method using the structure of WT Rheb (PDB code: 1XTR) as a search model. Successive
rounds of refinements and manual model building were performed to construct the final model. Phenix
was used for both phase determination and structure refinement (Adams et al. 2010), while manual
model building was performed in Coot (Emsley and Cowtan 2004). During the course of refinement,
density for the nucleotides could be clearly seen in difference electron density maps, which allowed us
to manually position GMPPNP bound to one Rheb molecule and GDP bound to the other Rheb molecule
in the asymmetric unit. The refinement statistic can be found in Table 3.2. The structure is released with
the PDB ID code 3SEA.
62
Table 3.2 Data collection and refinement statistics.
Rheb-Y35A Data collection Space group P 2 21 21 Cell dimensions a, b, c (Å) 57.2, 69.9, 79.2 α, β, γ (°) 90, 90, 90 Resolution (Å) 46.4-2.0 (2.07-2.0) * Rsym 9.3 (41.2) I / σI 20.7 (4.6) Completeness (%) 99.7 (100) Redundancy 7.0 (6.6) Refinement Resolution (Å) 26.9-2.0 No. reflections 21742 Rwork / Rfree 16.2 / 21.4 No. atoms Protein 2766 Ligand / Mg2+ion 62 / 2 Water 252 B-factors Protein 26.3 Ligand / Mg2+ ion 21.6 / 24.2 Water 30.3 R.m.s. deviations Bond lengths (Å) 0.007 Bond angles (°) 1.14 Ramachandran statistics Most favorable regions (%) 96.7 Allowed regions (%) 3.3 Disallowed regions (%) 0
*Data set was collected from one crystal. *Values in parentheses are for highest-resolution shell.
3.5.4 NMR-based GTPase assays: Rheb WT and mutants were loaded with GTP or mantGTP
by incubation with a 10-20-fold molar excess of nucleotide in the presence of 10mM EDTA. Full
nucleotide loading was confirmed by collecting a sensitivity-enhanced 1H-15N HSQC (Heteronuclear
Single Quantum Coherence) spectrum, and the mixture was then passed through a de-salting column
(PD MidiTrapTM G-25 (GE healthcare)) equilibrated with NMR buffer (20 mM sodium phosphate pH
7.0, 100 mM NaCl, 5 mM MgCl2 1mM DTT and 5% D2O), to produce a 1:1 complex of GTPase and the
nucleotide for the kinetic measurements. Nucleotide loading of Ras was achieved by the same method,
63
however in the case of RhoA, 0.5 M urea was included to facilitate the EDTA-mediated nucleotide
exchange and was removed by the de-salting column (Mazhab-Jafari et al. 2010).
NMR experiments were run on a Bruker AVANCE II 800 MHz spectrometer equipped with a 5mm TCI
CryoProbeTM or a 600 MHz spectrometer equipped with TCI 1.7 mm MicroCryoProbeTM. Sensitivity
enhanced 1H-15N HSQCs with 4 scans (10 min) were run in succession for monitoring the GTP
hydrolysis reactions at a temperature of 20oC using GTPase concentrations of 0.1-0.3 mM. The spectra
were then processed with NMRPipe (Delaglio et al. 1995) and GDP- and GTP-specific peak heights
were analyzed via Gaussian line fitting using Sparky (Goddard and Kneller). Residues from switch I&II,
P-loop, β3 & β4 and the α3 helix that exhibit distinct well-resolved resonances in each nucleotide-bound
form were used as reporters of the reaction rates, as described previously (Marshall et al. 2009; Mazhab-
Jafari et al. 2010). The fraction of GTPase protein in the GDP-bound state was calculated for each
reporter residue using the following equation: IGDP/(IGDP+IGTP), where I represents intensity, and plotted
against time. In the case of RhoA, the decay of IGDP peaks were used in the rate calculation, as described
previously (Gasmi-Seabrook et al. 2010; Mazhab-Jafari et al. 2010). Data fitting was done using PRISM
(GraphPad software). To assay GAP-mediated nucleotide hydrolysis, TSC2GAP was added to GTP-
loaded Rheb at a GAP to GTPase molar ratio of 1:2.
3.5.5 Thermodynamic measurements: All assays for thermodynamic measurements of WT,
Y35A, Y35F, Y35A-D65A, and D65A Rheb were run on 600 MHz spectrometer at a protein
concentration of 0.5 mM in 20mM HEPES pH 8.0, 100mM NaCl, 5mM MgCl2, 2mM DTT and 10%
D2O with 4 scans. The GTPase assays were run at four temperatures (287, 292, 296, and 301.5 K) and
Arrhenius plots were constructed by plotting ln(k) as a function of 1/T (K), where k is the rate of GTP
hydrolysis in sec-1. Activation energy (Ea) and activation entropy (∆S‡) values were calculated from the
slope and Y-intercept, respectively, as described previously. The activation enthalpy (∆H‡ = Ea – RT)
and the free energy of activation (∆G‡ = ∆H‡ - T ∆S‡) were then calculated with T set to 298 K. The
∆G‡ values are reported in kJ/mol.
3.5.6 Cell-based phosphorylation assay: All chemicals were purchased from Sigma unless stated
otherwise. Antibodies against p70 S6 Kinase and p70 S6 Kinase phosphorylated at Thr389 were from
Cell Signaling Technology and Anti-Myc 9E10 is described previously (Buerger et al. 2006). Murine
64
Rheb cDNA was obtained from Open Biosystems and subcloned into pcDNA3.1 myc-His. The Rheb
mutations were generated by site-directed mutagenesis (Agilent).
HeLaBT cells were cultured in Dulbecco's modified Eagle's medium containing 10% foetal calf serum
(DMEM/10%FCS) and transfected using the calcium phosphate precipitation method. 24h after
transfection, the media was replaced with serum-free DMEM. 48h after transfection, cells were either
further starved, or stimulated for 15 minutes or 6 h with DMEM/10% FCS and 10µg/mL insulin. Cells
were then lysed in CHAPS lysis buffer (40mM Hepes, pH 7.5, 0.3% CHAPS, 120mM NaCl, imM
EDTA, 10mM pyrophosphate, 50mM NaF, 1mM Na2VO3, 20mM β-glycerophosphate, and protease
inhibitors). Total protein in lysates was quantified using Bradford reagent (Bio-Rad), and equalized.
Samples were then boiled in SDS-PAGE sample buffer, separated by SDS-PAGE, and transferred to
PVDF membranes. After blocking in 5% bovine serum albumin in TBS-T (50mM Tris-HCl, pH 7.5,
150mM NaCl and 0.1% Tween 20), membranes were probed with the indicated antibodies and
visualized with HRP-conjugated secondary antibodies using the ECL system (Amersham).
The band intensities of p70 S6K P-Thr389, total S6K and Myc-Rheb for each lysate were measured
using ImageJ software (NIH). Normalized p70 S6K P-Thr389 values were determined using the
formula [(p70 S6K P-Thr389) / (total S6K)] / (Myc-Rheb) and the value for Rheb WT under growth
factor stimulated condition was set to 100 for each time point after starvation/stimulation. The
background intensity was used as estimation for the error in the intensity measurements and propagated
appropriately throughout division.
3.5.7 Nucleotide binding in vivo: Labeling was done according to previous protocols (Wolthuis et al.
1997) with the following modification. HEK293 cells were seeded in a 6-well plate and transfected with
2.5ug of DNA using the calcium-phosphate method. The following morning, cells were washed and
maintained in DMEM containing 10% FBS and 6 hours later, their media replaced with phosphate- and
serum-free DMEM and the cells incubated for 1hr. Cells were labeled with 250uCi/ml of [32P]
orthophosphoric acid (Perkin Elmer) overnight. Cells were washed with cold PBS and lysed in 750ul of
50mM Tris pH 7.4, 140mM NaCl, 1mM KCl, 2mM MgCl2, 1% Triton X-100, protease inhibitor
cocktail. Lysates were precleared with 20ul of protein A sepharose for 20 minutes. Myc-Rheb was
immunoprecipitated with 1ug of anti-myc antibody (Cell Signaling) for 2hrs and 20ul of protein A
65
sepharose for 30 minutes. Immunoprecipitates were washed 4 times in lysis buffer containing 500mM
NaCl and twice in lysis buffer with 0.1% Triton X-100. Nucleotides were eluted in 20ul of 2mM
EDTA, 2mM DTT, 0.2% SDS, 1mM GDP, 1mM GTP at 68oC for 15 minutes. Eluted nucleotides were
separated by spotting 10ul on PEI cellulose TLC plates and resolved in 0.75M KH2PO4 pH 3.4. Air
dried TLC plates were exposed using a phosphorimager and GTP/GDP ratios calculated using
ImageQuant 5.2 software.
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Marshall CB, Ho J, Buerger C, Plevin MJ, Li GY, Li Z, Ikura M, Stambolic V. 2009. Characterization of the intrinsic and TSC2-GAP-regulated GTPase activity of Rheb by real-time NMR. Sci Signal 2: ra3.
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CHAPTER 4
Structure-guided design of a constitutively active mutant of Rheb
This chapter has been reformatted from the original publication: Mohammad T. Mazhab-Jafari, Christopher B. Marshall, Jason Ho, Noboru Ishiyama, Vuk Stambolic, and Mitsuhiko Ikura. Structure-guided mutation of the conserved G3-box glycine in Rheb generates a constitutively activated regulator of mTOR. J Biol Chem. In Press. doi: 10.1074/jbc.C113.543736 A link to the published paper can be found at:
http://www.jbc.org/content/289/18/12195.long
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4.1 Abstract:
Constitutively activated variants of small GTPases, which provide valuable functional probes of their
role in cellular signaling pathways, can often be generated by mutating the canonical catalytic residue
(e.g., RasQ61L) to impair GTP hydrolysis. However, this general approach is ineffective for a
substantial fraction of the small GTPase family in which this residue is not conserved (e.g., Rap) or not
catalytic (e.g., Rheb). Using a novel engineering approach, we have manipulated nucleotide binding
through structure-guided substitutions of an ultra-conserved glycine residue in the G3-box motif
(DxxG). Substitution of Rheb Gly63 with alanine impaired both intrinsic and TSC2 GTPase activating
protein (GAP)-mediated GTP hydrolysis by displacing the hydrolytic water molecule, while introduction
of a bulkier valine sidechain selectively blocked GTP binding by steric occlusion of the γ-phosphate.
Rheb G63A stimulated phosphorylation of the mTORC1 substrate p70S6 kinase more strongly than
wild-type, thus offering a new tool for mTOR signaling.
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4.2 Introduction:
The Ras-superfamily comprises 167 members, which share a common fold and function as ‘switches’ to
regulate diverse cellular signaling pathways (Wittinghofer and Vetter 2011). Small GTPases cycle
between an activated guanosine triphosphate (GTP)-bound state that interacts with and activates
downstream effector proteins to drive signaling, and an inactive guanosine diphosphate (GDP)-bound
state. Thus GTPases are inactivated by hydrolysis of the γ-phosphate of GTP, and can be reactivated by
exchange of GDP for a new molecule of GTP, processes that occur slowly, but are catalyzed by the
upstream regulators GTPase activating proteins (GAPs) and guanine nucleotide exchange factors
(GEFs), respectively. Mutations that impair GTP hydrolysis perturb this cycle and generate
hyperactivated variants (e.g., Ras G12V and Q61L) that are often associated with disease processes.
Nevertheless, constitutively activated and inactive GTPase mutants are indispensible research tools for
probing the function of GTPases, and dissecting the signaling pathways they regulate. The strategy most
widely used to generate activated GTPases employs point mutations of a solvent-exposed glutamine
residue in the G3-box motif (Der et al. 1986) in switch II (five G-boxes comprise conserved sequence
elements for nucleotide binding and effector recognition). This glutamine is conserved in 73% of
human GTPases (Wennerberg et al. 2005) and has been demonstrated to be a key catalytic residue in
several cases. Structural and enzymatic studies of Ras have shown that the carboxamide oxygen of this
glutamine sidechain (Gln61) catalyzes GTP hydrolysis by increasing the nucleophilicity of a hydrolytic
water molecule (H2Ocat) positioned in-line with the γ-phosphate (Frech et al. 1994). Although this
mechanism is conserved amongst many GTPases, this residue is substituted in one quarter of small
GTPases, and in some Ras superfamily members, this glutamine is present but non-catalytic. These
GTPases have lower catalytic activity, which may proceed through alternate mechanisms. In Ras
homolog enriched in brain (Rheb), the G3-box glutamine residue (Gln64) is found in a non-catalytic
conformation, and its mutation has no impact on intrinsic hydrolysis and only modestly reduces GAP-
mediated hydrolysis (Li et al. 2004; Yu et al. 2005; Marshall et al. 2009). Mutations of Ras Gly12
impair GTP hydrolysis because the presence of a sidechain restricts the proper alignment of the catalytic
residue, however Rheb already has a bulky residue (Arg15) in this position and its mutation has little
effect on hydrolysis (Marshall et al. 2009). Thus, despite the modest impact of the Q64L mutation, it
remains well used for lack of a more robust activated Rheb variant (Li et al. 2004; Jiang and Vogt 2008;
Mavrakis et al. 2008; Zhou et al. 2009). In mutagenic analyses of residues potentially mediating Rheb’s
non-canonical catalytic mechanism, mutation of Asp65 had the greatest impact on catalytic activity
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(Mazhab-Jafari et al. 2012), however the reduction in intrinsic GTPase activity was limited to a modest
~30% (D65A). Tuberous sclerosis complex 2 (TSC2) possesses a GAP activity that accelerates the
intrinsic GTP hydrolysis of wild-type Rheb (Inoki et al. 2003; Marshall et al. 2009). Mutation of Rheb
Asp65 also impaired sensitivity to TSC2 GAP, but Rheb D65A did not fully activate mTORC1, possibly
due to weakened interaction (Mazhab-Jafari et al. 2012). Therefore we sought to develop novel
strategies to control the GTPase cycle of Rheb and other GTPase proteins that lack the canonical
catalytic machinery.
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Figure 4.1 Manipulation of the GTPase cycle of Rheb and mTOR signaling through substitutions of Gly63. a), Schematic illustration of the mTORC1 signaling pathway. b), Hydrolysis of GTP by wild-type Rheb and G63A in the presence and absence of the TSC2 GAP domain, monitored by real-time NMR. c), Intrinsic nucleotide exchange (GDP to GTP) of wild-type Rheb, G63A and G63V. Reaction rates are in min-1. (d-e) Rheb G63A mutation increases activation of mTORC1 signaling under starvation. (d) HeLa and (e) TSC2-deficient MEF cells were transfected with wild-type Rheb, G63A or empty vector, and starved or stimulated with insulin prior to lysis. Each experiment was performed in duplicate with one representative blot shown. 4.3 Results and Discussion:
The hydrolytic H2Ocat has been observed in almost all high-resolution GTPase structures. It is
coordinated by hydrogen bonds with the γ-phosphate of GTP and a common set of highly conserved
residues including the backbone carbonyl of a threonine in the G2 box, and the backbone amide of a
glycine in the G3 box. The threonine (Thr35 in Ras) is in the C-terminal part of switch I and is 90%
identical amongst human GTPases (Wennerberg et al. 2005), whereas the glycine (Gly60 in Ras, 93%
identity) (Wennerberg et al. 2005) is in the N-terminal part switch II. The curved-loop configuration of
the G3-box DxxG motif (where x stands for any amino acid) allows the aspartic acid to coordinate a
Mg2+ ion required for nucleotide binding (John et al. 1993), and positions the Cα of the glycine next to
H2Ocat and proximal to the γ-phosphate (Wittinghofer and Vetter 2011). On the basis of this structure,
we hypothesized that by substituting various residues for glycine, we could introduce side-chain steric
clashes to selectively perturb binding of the H2Ocat and/or the γ-phosphate. Displacing the H2O
cat would
impair GTP hydrolysis, yielding an activated variant, whereas blocking γ-phosphate binding would yield
an inactive mutant that can only accommodate GDP. We first applied this novel engineering approach to
the mTOR activator Rheb (Figure 4.1a), examining how mutations of Gly63 affect its non-canonical
GTPase cycle.
Real-time NMR-based GTPase assays (Marshall et al. 2009) demonstrated that mutation of Gly63 to
alanine substantially reduced Rheb’s intrinsic GTP hydrolysis rate by ~4.5 fold, (Figure 4.1b),
consistent with our notion that the introduction of a methyl side chain could destabilize the H2Ocat. Most
remarkably, no TSC2 GAP activity could be detected for the Rheb-G63A mutant (Figure 4.1b), which
was predicted since GAP-catalyzed hydrolysis utilizes the same H2Ocat, stimulating the reaction by
stabilizing and complementing the intrinsic catalytic machinery. Finally, to investigate whether the
mutation affects intrinsic nucleotide exchange of GDP for GTP, we carried out real-time NMR exchange
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assays. Rheb-G63A exchanged >10 times faster than the wild-type protein (Figure 4.1c), and although
this effect was not anticipated a priori, it would further drive this mutant towards the activated state.
Figure 4.2 Conservation of the G3-box glycine and structural basis for the functional properties of Rheb Gly63Ala/Val mutants. a) Alignment of the G3-boxes of selected small GTPase protein sequences illustrating conservation of the glycine residue. GTPases lacking the catalytic glutamine residue were selected. b-c) Overall fold of b) wild-type Rheb-GTP, c) Rheb G63A-GTP, and d) Rheb G63V-GDP, with each nucleotide binding site enlarged (right). The nucleotide is represented with
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spheres (left) or balls-and-sticks (right) and the glycine, alanine, and valine are shown in yellow. For clarity Tyr35 is not shown.
Conversely, mutation of Gly63 to valine resulted in a Rheb variant that failed to bind GTP (Figure 4.1c),
consistent with steric interference between the bulkier side chain and the γ-phosphate. As expected,
Rheb G63V remained fully GDP-bound and inactive. Therefore, we have identified a single, highly
conserved residue whose mutation can result in two diametrically opposed effects on activation.
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Figure 4.3 Electron densities of the catalytic sites of wild-type Rheb and its Gly63 mutations. 2Fo-Fc electron density maps of the nucleotide and residue 63 at 1.0σ are shown for a) WT Rheb-GTP b), G63A Rheb-GTP and c), G63V Rheb-GDP. The 2Fo-Fc electron density map of the hydrolytic water is shown at 1.0σ in a, but is absent in b and c. The predicted position of the γ-phosphate, based on global alignment of WT Rheb-GTP with G63V Rheb-GDP, is indicated in C (semi-transparent). The insets in each panel are chemical schematics illustrating the relative positions of the γ-phosphate, the G3-box glycine (the mutated alanine and valine), the hydrolytic water, and the nucleophilic GTPase reaction.
Rheb activates the mammalian target of rapamycin complex 1 (mTORC1), which regulates protein
biosynthesis, cell growth, proliferation and autophagy (Saucedo et al. 2003; Stocker et al. 2003; Kim et
al. 2011). Consistent with our biochemical data (Figure 4.1b), overexpression of Rheb G63A in HeLa
cells stimulated phosphorylation of the mTORC1 kinase substrate p70 S6K more strongly than wild-
type Rheb in the absence of serum, when TSC2 is active (Figure 4.1d). Upon serum stimulation, which
inactivates TSC2, p70 S6K is highly phosphorylated and its phosphorylation cannot be further enhanced
by expression of wild-type or G63A Rheb, suggesting that under this condition, p70 S6K
phosphorylation is limited by mTORC1 rather than the availability of endogenous Rheb-GTP (Figure
4.1d). Similarly, high level of p70 S6K phosphorylation in TSC2-null MEFs cannot be further enhanced
by expression of wild-type or G63A Rheb (Figure 4.1e). Although Rheb G63V expressed well in E. coli,
in mammalian cells its expression was ~90% lower than the wild type, thus we could not reliably probe
the effects of this mutation on mTORC1 signaling. Reduced expression of nucleotide-free Rheb mutants
has been reported previously (Li et al. 2004). The inability to bind GTP, which is much more abundant
than GDP in mammalian cells (Traut 1994), might explain the poor expression of G63V, despite the
stability of its GDP-bound form.
To validate that these mutations of the ultra-conserved G3-box glycine (Figure 4.2a) exert their effects
through the anticipated mechanisms, we solved the crystal structures of wild-type Rheb and the G63A
mutant bound to GTP, and the Rheb G63V mutant bound to GDP (Figure 4.2b-d and 4.3a-c). The
overall fold was not substantially affected by the mutations (all atoms RMSD WT-GTP vs. G63A-GTP
= 0.23 Å and WT-GDP(Yu et al. 2005) vs. G63V-GDP = 0.74 Å), however, the electron density of the
nucleotide-binding pocket confirmed the positioning of the Ala63 side chain in the H2Ocat-γ-phosphate
binding cavity of the mutant (Figure 4.2c and 4.3b). Whereas the electron density of the H2Ocat is clearly
visible in the WT structure, no corresponding density is observed in the G63A mutant structure (Figure
4.3a and b). Hence we hypothesize that the reduced residency of the hydrolytic H2Ocat decreases the
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ability of the G63A mutant to hydrolyze GTP, in full agreement with the biochemical observations. In
the structure of Rheb G63V in complex with GDP, the bulkier valine side chain occupies additional
space within the nucleotide-binding pocket. Val63 Cγ was positioned less than 2 Å from the γ-phosphate
location determined in the GTP-bound wild-type structure (Figure 4.2d and 4.3c). Thus enthalpic costs
and steric clashes prevent the γ-phosphate from approaching the methyl protons, explaining the lack of
GTP binding and nucleotide exchange for Rheb G63V.
Previously, an analogous substitution (G60A) in Ras was biochemically and structurally characterized.
This G60A mutation reduced the intrinsic GTP hydrolysis rate of Ras as well, however this was
mediated by a distinct mechanism involving substantial distortions of both switch regions that displace
the catalytic glutamine away from the nucleotide binding site by ~5-8 Ǻ (Ford et al. 2005). This
conformation resembled that of nucleotide-free Ras in complex with its exchange factor Son of
Sevenless (SOS) (Sung et al. 1996; Boriack-Sjodin et al. 1998; Ford et al. 2005), and consequently Ras
G60A was shown to exert a dominant negative effect in cells by forming a stable non-productive
complex with SOS that sequesters this GEF (Sung et al. 1996; Ford et al. 2005). In contrast, the switch I
and II regions of Rheb retain the wild-type conformation in the G63A mutant structure (all atoms RMSD
of 0.22 and 0.35 Ǻ for switch I and II, respectively). Thus the in vivo phenotypes of G3-box glycine
mutants are GTPase specific, and must be characterized. Nevertheless, the ability to generate gain-of-
function mutants for some non-canonical GTPases is especially valuable for developing probes. We
therefore investigated the effect of substituting Gly60 in Rap1A (37% sequence identity with Rheb), a
small GTPase for which no mutation impairing GTP hydrolysis is available because the canonical
catalytic glutamine is replaced by a threonine. The G60A mutation reduced the GTP hydrolysis rate of
Rap1A by 3 fold (Figure 4.4a), which is remarkable considering that no other mutation has been
reported to inactivate Rap GTPase activity. In the case of Rap1A, however, the G60V mutation did not
perturb nucleotide exchange activity (Figure 4.4b), suggesting that the valine side chain adopts a
different conformation from that of Rheb G63V. Hence the structural and functional properties of G3-
box Glycine mutations should be investigated for each GTPase. Intriguingly, a few examples of G3-box
Gly residue mutations have been listed in the catalogue of somatic mutations in cancer (COSMIC)
database (K-Ras G60A/V/D, H-Ras G60S, and Rheb G63W). While these mutations were identified in
colon, thyroid and hematopoietic cancers, it remains to be determined whether they are oncogenic
‘driver’ mutations.
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Herein this report, we have successfully demonstrated a structure-guided approach whereby mutating a
single residue in the conserved G3 box can control nucleotide binding thereby locking Rheb in an
activated (G63A-GTP) or an inactive (G63V-GDP) conformation. In serum-starved HeLa cells, the
G63A mutant strongly activated the downstream effector mTORC1, thus enhancing p70 S6K
phosphorylation, whereas the inability to bind GTP rendered G63V unstable in these cells. The crystal
structures of the two Rheb mutants provided the structural basis for the unique features of each mutant.
To our knowledge this is the first report of a mutation that severely impairs GTP hydrolysis of GTPases
with non-canonical catalytic mechanisms. This diverse group of GTPases includes several members
from four of the five GTPase subfamilies: Ras, Rab, Rho, and Arf (Figure 4.2a), thus this strategy
should be a valuable biological tool for probing the functions of these unique proteins.
Figure 4.4 Intrinsic nucleotide hydrolysis and exchange of Rap1A GTPase and its Gly60 mutations. a) GTP hydrolysis by wild-type Rap1A (black) and the G60A mutant (green). b) GDP to
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GTP exchange monitored for wild-type Rap1A (black), and the G60A (green) and G60V (blue) mutants. Reaction rates derived by curve fitting are shown with the same color codes (in min-1). 4.4 Experimental Procedures:
4.4.1 Protein Preparation: Mus musculus Rheb (residues 1–169) WT and G63A and G63V mutants and
TSC2 GAP domain (residues 1,525–1,742) were expressed as glutathione-S-transferase (GST) fusions
from the pGEX2T in Escherichia coli (BL21 strain) vector as described previously (Marshall et al.
2012). Briefly, bacteria were grown in minimal M9 media supplemented with either 14NH4Cl or 15NH4Cl
at 37 oC to OD600 = 0.6, and protein expression was initiated with 0.25 mM IPTG at 15 oC. Mutations
were introduced using QuikChange site-directed mutagenesis (Stratagene). The proteins were affinity
purified using glutathione Sepharose, cleaved from the GST tag by thrombin, and further purified using
Superdex 75 (GE Healthcare) size exclusion chromatography. Human Rap1A (residues 1–167) was
expressed using pET28 vector and purified using Ni-NTA resin, followed by removal of the His tag with
thrombin and further purification by Superdex 75 size exclusion chromatography. Small GTPase
proteins expressed in E. coli co-purified with guanine nucleotide.
4.4.2 NMR-based Real-time GTPase assay: For GTP hydrolysis assays, the small GTPase proteins were
loaded with GTP in the presence of EDTA and 10-fold excess GTP, and following addition of MgCl2
excess reagents were removed by passage through a desalting column (PD MidiTrap G-25; GE
Healthcare) equilibrated with NMR buffer (20 mM Tris pH 7.4, 100 mM NaCl, 5 mM MgCl2, and 1 mM
Tris (2-carboxyethyl) phosphine hydrochloride (TCEP)). The final protein concentration used in NMR
experiments was 0.3 mM. The proteins were fully GTP loaded at the start of each assay, as judged by 1H-15N heteronuclear single-quantum coherence (HSQC) spectrum. Prior to nucleotide exchange assays,
the GTPase proteins were incubated at room temperature for a minimum of a week and monitored by 1H-15N HSQC spectra to ensure that E. coli-derived GTP had hydrolyzed, and then exchange reactions
were initiated by addition of 1.5 mM GTP (5-fold molar excess). For GAP assays, TSC2 GAP domain
was added to the GTP-loaded Rheb (WT or mutant) at a molar ratio of 1:2.
All NMR spectra were acquired on Bruker AVANCE II 800 MHz spectrometer equipped with a 5 mm
TCI CryoProbe or a 600 MHz spectrometer with a TCI 1.7 mm MicroCryoProbe. 1H-15N HSQC spectra
with sensitivity enhancement were collected in succession with 4 scans (10 min acquisition time) to
monitor the GTPase reaction at 293.2 K. Spectral processing was carried out with NMRPipe(Delaglio et
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al. 1995) and the nucleotide sensitive peaks were integrated via Gaussian line fitting using SPARKY
(Goddard and Kneller). Residues exhibiting distinct and well-resolved peaks for each nucleotide-bound
state were monitored as reporters of the reaction rates, as described previously (Marshall et al. 2009).
For each pair of reporter resonances, the fraction of protein in the GDP-bound state was calculated as
IGDP/(IGDP+IGTP), where I represents intensity, plotted against time and fit to one-phase exponential
decay (instead of equation 4 of appendix A, since Kex >> Khyd) or association functions for nucleotide
exchange and hydrolysis, respectively. The error was estimated as described previously (Marshall et al.
2009). Because resonance assignments are not available for Rap1A GTPase the fraction of protein in the
GDP-bound state was calculated as IGDPavg/(IGDP
avg+IGTPavg), where IGDP
avg and IGTPavg represent the
average intensities of GDP- and GTP-specific peaks. The error was then estimated from spectral noise
and propagated accordingly. Data fitting was performed with PRISM (GraphPad software).
4.4.3 Crystallization and Data Collection: Crystals of Rheb (residues 1–169) WT, G63A, and G63V
mutants were grown with seeding using the hanging drop vapor diffusion method at room temperature.
The protein solution contained 0.8 mM protein, 20 mM Tris hydrochloride (Tris-HCl) [pH 8.0], 200 mM
NaCl, 5 mM MgCl2, and 0.02% NaN3 w/v. The protein solution was mixed with an equal volume of the
well solution (100 mM Tris-HCl [pH 8.5], 200 mM sodium acetate trihydrate, and 30% w/v
Polyethylene Glycol 4000). Crystals of Rheb WT and G63A mutant were soaked in a solution
containing 20 mM GTP and 25% Polyethylene Glycol 400 for 2 hours at room temperature to allow
nucleotide exchange whereas G63V crystals were soaked in 25% Polyethylene Glycol 400 alone.
Crystals were then flash frozen in liquid nitrogen. Diffraction data (WT and G63A) were collected at
100K on a Rigaku FR-E super-bright rotating anode generator equipped with Rigaku Saturn A200 CCD
detector, Osmic VariMAx HF optics and an Oxford cryosystem with a wavelength of 1.54 Ǻ at
Structural Genomics Consortium, Toronto, and processed with HKL2000 (Otwinowski and Minor
1997). Rheb WT-GTP and G63A-GTP diffracted to a resolution of 2.2 and 2.40 Ǻ, respectively. The
diffraction data for Rheb G63V-GDP was collected at 100K with Cu Kα radiation on a Bruker Microstar
X8 Proteum SMART CCD system with a wavelength of 1.54 Ǻ to a resolution of 2.25 Ǻ, and processed
with PROTEUM suite of programs.
4.4.4 Structure Determination and Refinement: The structures of GTP-bound murine Rheb-WT and –
G63A were solved by molecular replacement using the structure of human Rheb-WT in GTP-bound
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conformation [PDB: 1XTS] as the initial search model, whereas the structure of murine Rheb-G63V in
complex with GDP was solved using the structure of human Rheb in GDP-bound conformation [PDB:
1XTQ]. The final models were generated after successive rounds of refinements using PHENIX (Adams
et al. 2010) accompanied by manual model building with Coot (Emsley and Cowtan 2004). During the
course of refinement, densities for the nucleotides and the hydrolytic water molecules (in the case of
Rheb-WT) were clearly visible in difference electron density maps, which enabled us to manually
position the molecules. WT and mutant proteins were crystallized with two Rheb molecules in the
asymmetric unit, with one of the molecule’s switch I and II regions being involved in the crystal
packing. All the structures discussed in the manuscript are from the Rheb molecules where the switch I
and II are not involved in crystal packing, except for the GDP-bound Rheb-G63V, where the electron
density of switch II was weak in the absence of crystal contact but well resolved upon crystal contact
formation. It worth to note that switch II in GDP-bound Rheb-G63V adopted similar conformation as to
the GDP-bound Rheb-WT (PDB: 1XTQ). The data collection and refinement statistics can be found in
table 4.1. The structures has been deposited in the protein data bank with the following PDB codes:
4O25, 4O2L, and 4O2R for Rheb WT, G63A, and G63V, respectively.
4.4.5 Cell-based Phosphorylation Assays: Antibodies against p70 S6 Kinase and its Thr389-
phosphorylated form were from Cell Signaling Technology and the M2-FLAG antibody was from
Sigma. Murine Rheb cDNA (Open Biosystems) was subcloned into FLAG-tagged pcDNA5. The mutant
Rheb construct was generated via site-directed mutagenesis (Agilent). Myc-p70 S6K was cloned in to
pcDNA3.1. The p70 S6K phosphorylation assays were performed according to a previously described
protocol (Mazhab-Jafari et al. 2012) with the following modifications. In brief, 3 x 105 HeLa H1 and 2.7
x 106 TSC2 -/- MEF cells, cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal calf
serum (DMEM/10% FCS), were co-transfected with FLAG-Rheb-WT or –G63A and myc-S6K at a ratio
of 20:1 using Effectene (Qiagen) and 5:1 using GenJet reagent (SignaGen) for HeLa H1 and MEF cells,
respectively. Twenty-four hours post-transfection, the media were exchanged with serum-free DMEM.
Forty-eight hours post-transfection, cells were either further starved or stimulated with 100 nM insulin
for 15 minutes prior to harvesting. FLAG-Rheb and myc-S6K were immunoprecipitated from
normalized lysates with anti-Flag and anti-myc antibodies and Protein A/G Mix PureProteome magnetic
beads (Millipore) for western blot analysis.
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Table 4.1 Data collection and refinement statistics. Statistic information regarding the crystal structures of Rheb WT and G63A mutant in GTP bound form and G63V mutant in GDP bound form is presented.
Rheb-WT-GTP Rheb-G63A-GTP Rheb-G63V-GDP
Data collection Space group P 2 21 21 P 2 21 21 P 21 21 2 Cell dimensions a, b, c (Å) 57.7, 70.5, 79.8 57.6, 70.2, 79.7 70.3, 79.2, 57.3 α, β, γ (°) 90, 90, 90 90, 90, 90 90, 90, 90 Resolution (Å) 50.0-2.20 (2.24-2.20)* 50.0-2.40 (2.44-2.40)* 50-2.25 (2.35-2.25)* Rsym 0.127 (0.549) 0.155 (0.574) 0.073 (0.344) I / σI 15 (4.1) 14.9 (3.8) 12.3 (3.4) Completeness (%) 99.0 (98.6) 100 (100) 99.9 (100) Redundancy 7.0 (7.1) 7.7 (7.8) 13 (8.0) Refinement Resolution (Å) 39.9-2.2 38.9-2.4 28.7-2.25 No. reflections 15674 12371 14672 Rwork / Rfree 20.3 / 25.6 19.5 / 24.3 20.6 / 25.9 No. atoms Protein 2738 2736 2742 Ligand / Mg2+ion 62 / 2 62 / 2 54 / 2 Water 130 119 125 B-factors Protein 25.2 30.7 21.9 Ligand/ion 26.4 33.3 17.8 Water 28.1 34.3 23.1 R.m.s. deviations Bond lengths (Å) 1.04 1.11 1.13 Bond angles (°) 0.007 0.008 0.008 Ramachandran statistics Most Favorable region (%) 94.8 95.1 94.6 Allowed region (%) 5.2 4.9 5.4 Disallowed region (%) 0 0 0
*Data set was collected from one crystal. *Values in parentheses are for highest-resolution shell.
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4.5 References: Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ,
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CHAPTER 5
Structural and Functional consequences of Rheb-membrane interaction
This chapter has been reformatted from the original publication: Mazhab-Jafari MT, Marshall CB, Stathopulos PB, Kobashigawa Y, Stambolic V, Kay LE, Inagaki F, Ikura M. Membrane-dependent modulation of the mTOR activator Rheb: NMR observations of a GTPase tethered to a lipid-bilayer nanodisc. J Am Chem Soc. 2013 Mar 6;135(9):3367-70. A link to the published paper can be found at:
http://pubs.acs.org/doi/abs/10.1021/ja312508w
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5.1 Abstract:
Like most Ras superfamily proteins, the GTPase domain of Ras homolog enriched in brain (Rheb) is
tethered to cellular membranes through a prenylated cysteine in a flexible C-terminal region, however
little is known about how Rheb or other GTPases interact with the membrane or how this environment
may affect their GTPase functions. We used NMR methods to characterize Rheb tethered to nanodiscs,
monodisperse protein-encapsulated lipid bilayers with a diameter of 10 nm. Membrane conjugation
markedly reduced the rate of intrinsic nucleotide exchange, while GTP hydrolysis was unchanged. NMR
measurements revealed that the GTPase domain interacts transiently with the surface of the bilayer in
two distinct preferred orientations, which are determined by the bound nucleotide. We propose models
of membrane-dependent signal regulation by Rheb that shed light on previously unexplained in vivo
properties of this GTPase. The study presented provides a general approach for direct experimental
investigation of membrane-dependent properties of other Ras-superfamily GTPases.
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5.2 Introduction:
Most Ras superfamily small GTPase proteins are targeted by prenylation to cellular membranes, where
they function as switches in a variety of signaling networks. Following prenylation of a CaaX-box
Cysteine residue (C; a is an aliphatic residue; X is the C-terminal amino acid) in the C-terminal
hypervariable region (HVR) (Brunsveld et al. 2009), the aaX peptide is cleaved by C-terminal
prenylprotein peptidases, and Cys is carboxymethylated. Blockage of these post-translational
modifications prevents GTPase-mediated signal transduction, highlighting the critical role of membrane
localization. Hence, farnesyltransferase inhibitors have been developed to inhibit the biological activity
of oncogenic Ras mutants (Berndt et al. 2011). While fluorescence-studies and molecular dynamic (MD)
simulations have provided insight into small GTPase interactions with bilayer membranes (Gorfe et al.
2007a; Gorfe et al. 2007b; Abankwa et al. 2008b; Gureasko et al. 2008), atomic scale pictures of small
GTPases on membranes are lacking due to the inherent challenges imposed by bilayer-membrane
systems to high-resolution structural biology techniques.
Recent advances in the assembly of stable nano-scale bilayer membranes have made it possible to study
structure, dynamics, and functions of peripheral and membrane-integrated proteins at the atomic level.
Here, we used nanodiscs (Ritchie TK 2009), which are 5 by 10 nm discoidal lipoprotein complexes
comprised of a bilayer of 120-160 lipid molecules bounded and stabilized by two copies of an
engineered variant of Apo-lipoprotein A(Denisov et al. 2004), to enable nuclear magnetic resonance
(NMR)-based characterization of the structure, dynamics, and function of membrane-tethered Rheb.
Rheb is targeted to endomembrane compartments including Golgi, endoplasmic reticulum and
lysosomes via farnesylation of its sole Cys residue (Cys181), processing that is required for its activation
of mTORC1 (Buerger et al. 2006). To mimic processed Rheb, a truncated construct (residues 1-181) was
covalently linked through Cys181 to a maleimide-conjugated lipid (Gureasko et al. 2008) incorporated
into assembled nanodiscs (Figure 5.1a&b) or vesicles, a strategy previously described in studies of H-
Ras on unilamellar vesicles (Gureasko et al. 2008). Relative to vesicles, for which diameters of 20-500
nm are typical, the smaller size of nanodiscs results in rapid tumbling, enabling high-resolution NMR
studies of membrane-anchored Rheb and NMR-based real-time assays (Marshall et al. 2009) of the
GTPase cycle of Rheb on the bilayer membrane.
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Figure 5.1 Tethering Rheb to a bilayer membrane inhibits nucleotide exchange and activation. a) Lipids used for nanodisc assembly (full names in text). Reaction between Rheb Cys181 and the maleimide-moiety of PE-MCC was used to tether Rheb to the nanodisc bilayer. Drawn with ChemSketch (Advanced Chemistry Development, Inc.) b) Schematic diagram of the Rheb-nanodisc complex. c,d) Nucleotide hydrolysis and exchange reactions were monitored using NMR-based real-time GTPase assays of Rheb free in solution or tethered to nanodisc membrane bilayers. c) Intrinsic GTP hydrolysis by free and nanodisc-bound Rheb are shown in black and green, respectively. GTP hydrolysis by free and nanodisc-bound Rheb in the presence of extract of HEK-293 cells overexpressing TSC1/TSC2 are shown in red and blue, respectively. d) Intrinsic nucleotide exchange for free and
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nanodisc-bound Rheb are shown in black and green, respectively. I(GDP) and I(GTP) are intensities of several peaks in HSQC spectra that are specific to Rheb-GDP and -GTP, respectively. The higher plateau of the green curve reflects the greater impact of GTP hydrolysis when nucleotide exchange is slow. 5.3 Results and Discussion:
Tethering Rheb to the nanodisc did not alter the rate of intrinsic GTP hydrolysis or the GTPase
activating protein (GAP) TSC2-catalyzed GTP hydrolysis rates by Rheb (Figure 5.1c); however, the
intrinsic nucleotide exchange rate was significantly reduced upon membrane association (Figure 5.1d),
indicating that membrane conjugation directly impacts the GTPase cycle of Rheb. To investigate the
structural and dynamical properties of the interactions between the membrane and the GTPase domain
of tethered Rheb, we used chemical shift perturbation (CSP) analysis, 15N R1, 15N R2, steady state 1H-15N NOE backbone relaxation measurements, and paramagnetic relaxation enhancement (PRE)
experiments.
Conjugation of Rheb to the membrane did not detectably perturb the chemical shifts of resonances in the 1H-15N HSQC spectrum, with the exception of Cys181 (Figure 5.2), suggesting that the GTPase domain
(1-169) and the HVR (170-180) of Rheb do not tightly associate with the bilayer. The overall rotational
correlation time (τM) was calculated from 15N R1, 15N R2, and steady state 1H-15N NOE (Farrow NA
1995) for GDP- and GMPPNP- (non-hydrolyzable analog of GTP) bound Rheb conjugated to the
nanodisc and free in solution. Overall tumbling-times (τM) for Rheb-GDP were calculated to be 17.0±0.2
ns in solution and 35.4±1.3 ns when conjugated to the nanodiscs (20 °C). A protein rigidly associated
with the >100 kDa Rheb-nanodisc complex would have an expected τM >60 ns (based on Stoke’s law
assuming a spherical protein-nanodisc complex), thus the intermediate τM value indicates that the
GTPase domain of Rheb-GDP exhibits a high degree of freedom (dynamics) despite being tethered to
the membrane. The τM values for Rheb-GMPPNP in solution and conjugated to nanodiscs were 17.0±0.5
ns and 32.6±1.4 ns, respectively, similar to what was observed for Rheb-GDP. These results further
establish the transient nature of Rheb’s interactions with the membrane.
The most significant local changes in dynamics upon membrane binding were at the C-terminal HVR,
where the backbone ps-ns motions were partially quenched, independent of the bound nucleotide (Figure
5.3 and 5.4). Within the GTPase domain, the only significant change in local dynamics upon membrane
conjugation was an increase in the µs-ms time-scale motions in the α3 helix (R2 and R1×R2 of residues
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Figure 5.2 Preparation of Rheb-nanodisc complex. a) Superdex S200 chromatograms of nanodiscs before and after conjugation with Rheb. SDS-PAGE analysis of the fraction containing Rheb-tethered nanodiscs (*) indicates a ~1:1 ratio of Rheb to MSP. b) 15N1H-HSQC spectra of 0.3 mM free (black) and 0.6 mM nanodisc-conjugated (red) Rheb-GDP. The only peak (Cys181) exhibiting appreciable chemical shift change upon membrane conjugation is shown with a dashed rectangle. Resonances with low S/N in free Rheb that are broadened beyond detection upon membrane conjugation are shown with dashed circles. c) Linewidths of free (black) versus nanodisc-conjugated (red) Rheb. The region illustrated is indicated by a solid rectangle in b and is shown at the same contour level in c.
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90-95) of Rheb-GDP, which was not observed for the GMPPNP-bound form (Figure 5.3&5.4). The α3
helix forms ionic contacts with switch II in Rheb, and in the homolog H-Ras, α3 is allosterically coupled
to the nucleotide binding site (NBS) (Fraser et al. 2011), thus the effect of membrane conjugation on the
rate of nucleotide exchange may involve modulation of the NBS by perturbation of α3 dynamics.
Another factor that might impair nucleotide exchange is occlusion of the NBS by the membrane surface,
thus we explored this possibility more fully by performing PRE experiments as detailed below.
The PRE effect can be powerful for identifying transient interactions, such as those between Rheb and
the bilayer plane, and for determining “preferred conformations” of a protein such as membrane-
associated Rheb. Rheb-tethered nanodiscs were prepared with the incorporation of lipids (5%) in which
the head group was conjugated to the paramagnetic ion gadolinium (Gd3+) (see Methods). Intensities of
Rheb resonances were compared in the presence and absence of Gd3+ to identify specific residues that
interact with the membrane (Figure 5.5a). For Rheb-GDP the residues broadened by the paramagnetic
ion (defined as >50% decrease in peak intensity) were distributed throughout the GTPase domain (30
peaks), including the N-terminus, β2-β3 loop, C-terminus of switch II, C-terminus of α3 and, as
expected, the HVR (11 peaks). Mapping these regions to the Rheb-GDP structure illuminates a patch
surrounding residue 171, which links the GTPase domain to the HVR, which is prenylated in cells
(Figure 5.5b) (Clark et al. 1997). The unusually slow rate of GTP hydrolysis by Rheb (Marshall et al.
2009) allowed us to extend this PRE approach to Rheb bound to native GTP. The perturbed residues (24
in the GTPase-domain and 11 in the HVR) form a pattern similar to that seen for Rheb-GDP, however
the C-terminus of switch II was less broadened in the GTP-bound form, as was the C-terminus of α3,
albeit with smaller differences here (Figure 5.5b). To generate atomic-resolution models of the Rheb-
membrane complex, we performed simulations with High Ambiguity Driven biomolecular DOCKing
(HADDOCK) (Dominguez et al. 2003) using our experimentally derived PRE-restraints (as described in
experimental procedures).
We generated 3000 models of Rheb docked to the membrane surface and the 300 models with lowest
HADDOCK scores (a weighted sum of energy terms related to the interface and the individual
components comprising the complex) were selected for cluster analysis. These models were grouped
into clusters based on the orientation of Rheb relative to the membrane surface (i.e., RMSD following
translation in the plane of the nanodisc and rotation about the normal axis, see experimental procedures).
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Figure 5.3 Backbone 15N relaxation data for Rheb-GDP 1-181 in free (black) and nanodisc-bound (red) states. From top to bottom, transverse (15N R2) relaxations, longitudinal (15N R1) relaxations, R1×R2 products, and the {1H} 15N steady state NOE (Isaturated/Iunsaturated), each plotted against the residue number. The α3-helix, which exhibits increased R2 and R1R2, is highlighted in red.
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Figure 5.4 Backbone 15N relaxation data for Rheb-GMPPNP 1-181 in free (black) and nanodisc-bound (red) states. From top to bottom, transverse relaxations (R2), longitudinal (15N R1) relaxations, R1×R2 products, and the {1H} 15N steady state NOE, each plotted against the residue number. Notably, mapping the PRE-affected residues on the structure of Rheb (Figure 5.5b and 5.6)
illustrates that a single Rheb orientation cannot simultaneously satisfy all of the PRE-derived restraints,
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and indeed, two major clusters of solutions were identified for the GDP-bound form (Figure 5.6a and
5.7a). Cluster 1 (backbone RMSD cutoff = 8 Å) was oriented such that the α6 helix (residues 153-171)
was semi-perpendicular (58˚ relative to the bilayer plane for the cluster center, i.e., model with the
lowest RMSD to all other models within the cluster), while cluster 2 (backbone RMSD cutoff = 8 Å)
was semi-parallel (6˚ relative to the bilayer plane). Cluster 1 represented ~52% of the final solutions for
Rheb·GDP docked to nanodiscs, while cluster 2 represented ~17% of the solutions. The remainder of the
solutions formed small clusters, each of which comprised < 10% of total solutions, or did not cluster. In
both cluster 1 and 2 models, the NBS, comprising the P-loop, switch I, G4 (residues 118-123), and G5
(residues 149-151) boxes were facing away from the membrane bilayer and were > 10 Å away (Figure
5.6a), consistent with the lack of broadening of these resonances, while the N-terminus, β2-β3 loop, and
HVR were each within 10 Å of the bilayer plane. The major difference between the models in clusters 1
Figure 5.5 Identification of the Rheb-membrane interface and its modulation by the bound nucleotide. a) Paramagnetic relaxation enhancement (PRE) of Rheb H(15N) peak intensities induced by Gd3+-conjugated lipids incorporated into nanodiscs. PRE effects detected for each residue of Rheb-GDP (black) and Rheb-GTP (red) presented as a ratio of H(15N) resonance intensities of Rheb conjugated to nanodiscs in the presence (I*) or absence (Io) of Gd3+. Error bars based on spectral noise. b) PRE-affected residues mapped on Rheb G-domain. Residues that exhibited > 50% and > 80% peak broadening in the presence of Gd3+ are shown as orange and red surfaces, respectively, for Rheb-GDP (left) and -GTP (right), and two interfaces are identified. c) PRE-driven HADDOCK models of Rheb-nanodisc complexes. Cluster center models of GDP- (left) and GTP- (right) bound Rheb in the semi-perpendicular and semi-parallel orientations. The non-transparent models reflect the favored conformation in each nucleotide bound state. The axis of Rheb α6 helix is shown with a brown arrow.
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PDB 1XTQ and 1XTS (Yu et al. 2005) were used in the calculations, and results were deposited as 2M4A and 2M4B for GDP- and GTP-bound states, respectively. versus 2 was the re-orientation of the G-domain with respect to the bilayer due to rotation about residue
171. This re-orientation causes the C-terminal regions of switch II and α3 to sample positions proximal
to the bilayer plane (<5 Å) in cluster 1, and distal from the bilayer plane (>10 Å) in cluster 2. The re-
orientation also brought α5 and β6 (residues 132-148) to within 10 Å of the bilayer in cluster 2.
Likewise, two major clusters of models were identified for docking of ‘activated’ Rheb-GTP to the
nanodisc (Figure 5.6b and 5.7b), with orientations similar to those determined for Rheb-GDP (i.e.,
cluster 1 exhibited a semi-perpendicular orientation with an α6 angle of 54˚, and cluster 2 was semi-
parallel with an α6 angle of 3˚). Interestingly, relative to its GDP-counterpart, clusters 1 and 2 were
more equally populated for Rheb-GTP, where 39 and 35 % of total models were found in clusters 1 and
2, respectively. The relative cluster sizes were independent of the overall number of models calculated
and were consistently reproducible. It is intriguing that on the basis of FRET analysis and MD
simulations, remarkably similar semi-perpendicular and semi-parallel orientations have been proposed
for H-Ras-GDP and -GTP interactions with the membrane, respectively (Gorfe et al. 2007b; Abankwa et
al. 2008b).
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Figure 5.6 Residues affected by PRE localized on the HADDOCK models. The cluster center models of Rheb-nanodisc complexes are shown as follows; a) Rheb-GDP in orientation 1 (left) and 2 (right), b) Rheb-GTP in orientation 1 (left) and 2 (right). Residues exhibiting I*/Io < 0.5 and < 0.2 as described in Figure 2a are colored orange and red, respectively for Rheb-GDP and -GTP. The orange text indicates that the highlighted region is at the back of the page.
Our calculations show that the measured PRE restraints are consistent with an equilibrium between two
distinguishable Rheb configurations, and that both of these conformers are populated by each of the
GDP- and GTP-bound states, as illustrated in Figure 5.5c. The C-terminus of switch II of Rheb-GTP
(residues 74-79) is significantly less perturbed by the PRE-tagged lipid than that of Rheb-GDP (Figure
5.5a), whereas the magnitude and distribution of the PRE effects are otherwise similar for both states;
thus, the population of each clustered orientation is largely dictated by the nucleotide-specific PRE
differences in switch II.
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Figure 5.7 Cluster analysis of final HADDOCK solutions. The final 300 complex structures, represented with empty black circles are displayed in a plot of HADDOCK score versus rmsd to the global mean structure (defined as the structure with lowest rmsd to all other 299 structures) for a) Rheb-GDP-nanodisc and b) Rheb-GTP-nanodisc simulations. Complex structures belonging to cluster 1 (semi-perpendicular orientation, as described in the main text) and cluster 2 (semi-parallel orientation) are highlighted with green and magenta, respectively. The average HADDOCK score and rmsd (± standard deviation) of the 30 complex structures with lowest HADDOCK scores in each cluster is plotted as a filled black rectangle. The low τM value we determined for membrane-tethered Rheb indicates considerable mobility on the
membrane, most likely reflecting the fact that both semi-perpendicular and semi-parallel orientations are
sampled during transient interactions between Rheb and the membrane surface. However, the semi-
perpendicular configuration 1 appears to be less favoured in the GTP-bound state, due to subtle
redistribution of surface electrostatics. The surface of the switch II-α3 region that forms the membrane
interface in orientation 1 becomes less positively charged in the GTP-bound structure (Figure 5.8),
which may diminish interactions with exposed negative charges in the phosphocholine
bilayer(Semchyschyn and Macdonald 2004). Concomitantly, the α5-β6 of interface 2 becomes more
positive in the GTP-bound structure, stabilizing the semi-parallel orientation (Figure 5.8). Consistent
with this notion, a GDP/GTP-dependent shift in the equilibrium between perpendicular and parallel
orientations has been described for H-Ras-membrane interactions by MD simulations (Gorfe et al.
2007b; Abankwa et al. 2008b). The NBS is not sterically occluded by the membrane surface in either
perpendicular or parallel orientations; thus, we suggest that the mechanism by which membrane
association impairs nucleotide exchange likely involves allosteric effects mediated via the membrane
interaction, propagated from helix α3. The lower kinetic rate indicates a higher activation energy for the
rate-limiting step in the intrinsic exchange reaction, suggesting that the proposed allosteric effect might
stabilize the NBS in the GDP-bound state.
Avruch and colleagues previously performed a comprehensive Ala-mutation scan of surface accessible
residues in Rheb and analyzed their effects on cellular mTORC1 signaling (Long et al. 2007). Ectopic
expression of Rheb with mutations in the C-terminal region of switch II that did not impair GTP
binding, nevertheless abolished the rescue of mTORC1 signaling in nutrient starved cells, and relative to
wild-type Rheb, significantly reduced mTORC1 output in replenished cells with endogenous Rheb
knocked down. This phenotype is similar to that observed with the nucleotide-deficient Rheb mutant
D60I, but appears to be mediated by a different mechanism (Tabancay et al. 2003). Our data show that
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Figure 5.8 Subtle changes in surface electrostatics upon nucleotide exchange. The lowest energy annealed structures of Rheb (residues 1-181) before docking simulations. Rheb-GDP and -GTP are shown on the left and right of each panel, respectively. Panels a and b represent the electrostatic surfaces of the switch II-α3 (interface 1) and α5-β6 (interface 2) motifs, respectively. In the electrostatic surface, red, blue and gray represent negative, positive and neutral (hydrophobic) surfaces. The surface electrostatics were generated using the macromolecular electrostatics calculation program Adaptive Poisson-Boltzmann Solver (APBS) (Baker et al. 2001), and visualized via PyMOL.
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the C-terminal residues of switch II form part of the Rheb-membrane interface in cluster 1 of the GDP
and GTP-bound states, but become solvent exposed in cluster 2. In light of these observations, we
propose that the membrane acts as a regulatory platform in Rheb-mTORC1 communication in cells, in
synergy with the GTPase cycle of Rheb. In our proposed model, the nucleotide-dependent re-orientation
of Rheb regulates communication with mTORC1 in cells by GTP-mediated exposure of switch II. A
similar mode of GTPase-effector regulation has been suggested for H-Ras interactions with the Ras
binding domain (RBD) of C-Raf and Phosphatidylinositol 3-kinases γ (PI3Kγ) (Abankwa et al. 2008a).
However, as the Rheb-binding domain in mTOR has not been defined, the precise molecular details of
mTORC1 regulation by the C-terminal switch II segment of Rheb in vivo remain to be fully elucidated.
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Figure 5.9 Formation of a Rheb-PDEδ complex is compatible with Rheb-nanodisc model 2, but not model 1. Cluster center structures for models 1 and 2 from Rheb-GDP docking simulations are shown in green in a and b, respectively. The Rheb and PDEδ components of the Rheb-PDEδ complex (PDB: 3T5G) are shown in orange and blue, respectively, and were aligned with the G-domain of Rheb (residues 4-171). The nucleotide, Mg2+ ion, and all atoms of POPC are represented as spheres.
Interestingly, a recent structure of Rheb in complex with PDEδ, a nucleotide-independent guanine
dissociation inhibitor (GDI)-like protein (Ismail et al. 2011), reveals that PDEδ captures the farnesyl tail
of Rheb in a deep pocket, and makes additional contacts (~20% of the total buried surface area) with the
N-terminal β1 strand, and to a lesser extent, the C-terminal loop of switch II. Thus, overlaying the Rheb-
PDEδ structure with Rheb-nanodisc models 1 and 2, it is evident that steric clashes between PDEδ and
the membrane bilayer would preclude the Rheb-PDEδ complex from adopting a model 1 orientation,
and likewise block PDEδ from binding this state of Rheb (Figure 5.9a). However, because of the
transient nature of the Rheb-membrane interaction, other orientations sampled by the G-domain of Rheb
including model 2 would allow the β1 strand and the C-terminal loop of switch II to interact with PDEδ
(Figure 5.9b). Formation of this complex would then restrict G-domain interactions with the membrane
and may initiate solubilization of Rheb, involving extraction of the farnesyl moiety from the bilayer into
the hydrophobic pocket of PDEδ.
To our knowledge, the present study is the first experimental work to directly probe membrane-
dependent regulation of the structure and function of a GTPase at atomic resolution, and provides a
general approach for direct experimental studies on membrane-dependent regulation of other GTPases.
5.4 Experimental procedures:
5.4.1 Protein preparations: Mus musculus Rheb (residues 1-181) was prepared according to previous
protocols (Marshall et al. 2009). In brief, the protein was expressed in Escherichia coli (BL21) using a
pGEX2T vector and grown in minimal media supplemented with 15NH4Cl and induced at 15oC with
0.25 mM IPTG. The protein was initially purified using glutathione Sepharose, cleaved from the GST
tag by thrombin, with subsequent purification using Superdex 75 size exclusion chromatography in
buffer A (20mM Tris pH 7.4, 100mM NaCl, 5mM MgCl2, 1mM TCEP). Rheb typically yields ~20
mg/L of culture, and like other members of the small GTPase superfamily, it co-purified with
endogenous guanine nucleotide. Membrane scaffold protein 1D1 (MSP1D1) (Ritchie TK 2009) was
prepared as described previously (Kobashigawa et al. 2011), with the following modifications. The
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protein was expressed in Escherichia coli (BL21) with pGBHPS–MSP in 2× TY media using a LEXTM
bioreactor system at 37 ˚C with 1 mM IPTG for 1 h followed by further 2.5h incubation at 28 ˚C. MSP
was purified using His-tagged affinity purification followed by HRV3C protease-mediated His-tag
cleavage and subsequent size exclusion chromatography using Superdex 75, with a typical yield of 40
mg/L of culture.
5.4.2 Preparation of Rheb-nanodisc complex: All lipids were purchased from Avanti Polar Lipids,
Inc. Nanodiscs were prepared according to previous protocols (Kobashigawa et al. 2011) with the
following modifications. 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and the thiol-reactive lipid
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]
(PE-MCC), were mixed with a molar ratio of 20:1 in a chloroform-ethyl alcohol solution. For PRE
experiments, 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid
(gadolinium salt) (PE-DTPA (Gd3+)) was added to the lipids at a molar ratio of 20 DOPC : 1 PE-MCC :
1 PE-DTPA (Gd3+). The organic solvents were then removed using gentle nitrogen flow followed by
vacuum, and the dried lipid film was solubilized in aqueous buffer containing detergent (20mM Tris pH
7.4, 100mM NaCl, and 100mM sodium cholate). This mixture was subjected to three freeze/thaw cycles,
vortexed until clarified, then MSP1D1 was added at a 1:40 molar ratio relative to the lipids
(Kobashigawa et al. 2011). Following 1 h incubation with mild rotation at 20 °C, sodium cholate was
removed from the MSP-lipid mixture with Bio-Beads SM-2 Adsorbents (Bio-RAD) using a batch
method with 2h incubation at room temperature with mild rotation. The nanodisc particles were then
purified via size exclusion chromatography using a 26-60 Superdex 200 column equilibrated with buffer
A without TCEP. The particle size were analyzed with dynamic light scattering (DLS) and corresponded
with a 10nm diameter particle. Rheb 1-181 was passed through a 10-30 Superdex S75 column
equilibrated with buffer A without TCEP at 4oC to remove reducing agent, and was immediately added
to the nanodisc preparation at a 2:1 molar ratio (one Rheb molecule for each face of the nanodisc). The
conjugation reaction was allowed to proceed for 16h at room temperature, then the mixture was passed
through a Superdex 200 column equilibrated with buffer A to separate free Rheb from nanodisc-bound
Rheb. The concentration of the nanodisc-Rheb complex was estimated by SDS-PAGE and size
exclusion chromatography analysis.
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5.4.3 NMR- measurements: NMR measurements were carried out on either a Bruker AVANCE II 800
MHz spectrometer equipped with a 5 mm TCI CryoProbeTM or a 600 MHz spectrometer equipped with
TCI 1.7 mm MicroCryoProbeTM. The spectra were acquired at a temperature of 20o C using samples
containing 0.3mM free Rheb or 0.6mM nanodisc-conjugated Rheb. Backbone assignment of Rheb G-
domain (residues 1-169) has been previously carried out and the HVR (residues 171-181) were assigned
using HNCACB and CbCa(co)NH experiments (Table 5.1).
Table 5.1) Resonance assignment of Rheb HVR.
Residue
ID
Residue
#
Atom
type
chemical
shift
Asp 171 N 121.793
Asp 171 H 8.334
Gly 172 N 108.277
Gly 172 H 8.199
Ala 173 N 123.686
Ala 173 H 7.975
Ala 174 N 122.079
Ala 174 H 8.157
Ser 175 N 114.197
Ser 175 H 8.172
Gln 176 N 121.812
Gln 176 H 8.272
Gly 177 N 109.788
Gly 177 H 8.441
Lys 178 N 120.904
Lys 178 H 8.2
Ser 179 N 117.489
Ser 179 H 8.484
Ser 180 N 118.296
Ser 180 H 8.475
Cys 181 N 124.733
Cys 181 H 8.194
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To monitor GTPase reactions in real-time, sensitivity enhanced 1H-15N heteronuclear single quantum
coherence (HSQC) spectra with 8 scans (18 min) each were collected in succession as previously
described(Marshall et al. 2009). For analysis of chemical shift perturbation and PRE experiments, 32
scans (72min) were used. No GDP resonances were observable above the spectral noise in the 32-scan 15N1H-HSQC of a GTP-loaded Rheb sample indicating that any hydrolysis occurring during data
collection was not appreciable. For PRE measurements, the resonance intensities of 15N Rheb on PE-
DTPA (Gd3+)-containing nanodiscs were compared to those of a control sample prepared without PE-
DTPA (Gd3+). No PE-DTPA-chelated diamagnetic ion is available to serve as a control, however the
absence of any detectable chemical shift differences in the Rheb spectrum in the absence or presence of
5% (mole fraction to total lipid) PE-DTPA suggests that PE-DTPA-free nanodiscs provide an
appropriate control to monitor the PRE-effect. The cross-peak intensities were measured using
Sparky(Goddard and Kneller) and Gaussian line fitting. The difference in concentration between the
PRE and the control samples was less than 10%, as judged by the size exclusion chromatogram and
SDS-PAGE. This difference in concentration was corrected by normalization of the calculated intensity
ratios against the highest observed I*/Io (where I* is the resonance intensities of Rheb conjugated to
nanodiscs incorporating 5% Gd3+-conjugated PE-DTPA, and Io is that in the paramagnetic ion-free
nanodiscs) for each GDP and GTP plot. Residues in the β1-α1 and β4-α3 loops, which are in close
proximity to each other and close to the nucleotide binding pocket, exhibited the least PRE and were
therefore used as an internal standard for the normalization, for GDP and GTP, respectively. For
comparing GDP and GTP plots, this normalization process was evaluated using the PRE-effect on
Cys181, which is covalently linked to the surface of the membrane, and thus would be expected to
exhibit similar PRE, independent of the bound nucleotide. Indeed, Cys181 was similarly broadened in
GDP- and GTP-bound samples (96.0% and 95.5 %, respectively). For relaxation experiments, the 15N
longitudinal and transverse relaxation rates R1 and R2, as well as the {1H} 15N steady-state NOEs were
measured using 0.3mM samples of free 15N Rheb-GDP and -GMPPNP (∆182-184) and samples of
0.6mM 15N Rheb-GDP and -GMPPNP (∆182-184) conjugated to 0.3 mM nanodiscs. Rheb was pre-
loaded with GMPPNP in the presence of EDTA- and alkaline phosphatase, as described
previously(Marshall et al. 2009), prior to nanodisc conjugation. Backbone relaxation measurements
were performed at 800MHz. Recycle delays of 3.0, 2.5, and 4.0 sec were used for 15N R1, 15N R2, and
{ 1H} 15N steady state NOE acquisitions, respectively. The relaxation delays (15N R1 experiments:10,
180, 900, 265, 700, 1400, 350, 1100, 265, and 10 ms, and R2 experiments: 15.84, 63.36, 31.68, 95.04,
103
47.52, 84.20, 110.9, 63.36, and 15.84 ms) were varied in non-sequential order (as listed) to avoid
systematic stability-related fluctuations in peak intensities, and duplicate delay times were used to
ensure sample stability and estimate errors in fitting curves. Sample stability was monitored by
intermediate HSQCs between T1, T2, and {1H} 15N steady state NOE measurements. 15N R1 and 15N R2
experiments were run with 16 scans, and 64 scans were acquired for {1H} 15N steady state NOEs. The
overall rotational correlation time (τM) was calculated as previously detailed (Farrow NA 1995). In brief,
the values of the spectral density functions J(0.870ωH), J(ωN), and J(0) were determined from the mean
of R1, R2 and {1H} 15N steady state NOEs using equations 12-14 from Farrow et al (Farrow NA 1995),
in which no prior assumption is made on the structure of the molecule. Of the values of 15N R1, 15N R2,
and {1H} 15N steady state NOEs determined for each peak, the top and bottom 10% were excluded from
the calculation. The value of the spectral density function at zero frequency was then used to derive the
(τM) using the form of the spectral density function derived from model-free formalism (equation 4 in
Farrow et al (Farrow NA 1995)) assuming limited (large order parameter, S2) and fast (<10ps) internal
motions. The variations in the trimmed means of R1, R2, and {1H} 15N steady state NOEs were used in
error calculations.
5.4.4 Real-time NMR-based GTPase assay: Assays of Rheb GTPase function were carried out as
described previously (Marshall et al. 2009). In brief, nucleotide exchange reactions were initiated by
adding a 5-fold molar excess of GTP to a GDP-loaded 15N Rheb sample, and monitored via successive
8-scan 15N 1H HSQC spectra (18min). TSC2GAP-catalyzed reactions were initiated by adding extracts
of HEK-293 cells over-expressing full length TSC1 and TSC2 as described previously (Marshall et al.
2012). The reactions were initiated with cell extracts prepared by mechanical lysis. Expression of TSC2
in these lysates was confirmed by Western blots. The hydrolysis data were fitted to a one phase
association function. Since the intrinsic hydrolysis was unchanged upon membrane association, a simple
one phase exponential decay function was used to fit the intrinsic exchange data.
5.4.5 Molecular docking simulation: All docking simulations were performed with gpc supercomputer
at the SciNet (Chris Loken 2010) HPC Consortium using High Ambiguity Driven biomolecular
DOCKing (HADDOCK) sofware version 2.1 (Dominguez et al. 2003; de Vries et al. 2007). The
structures of GDP- and GTP-bound of Mus musculus Rheb (residues 1-181) were annealed in CNS
using the RECOORD scripts (Nederveen et al. 2005) from starting extended polypeptide chains using
104
distance, hydrogen bond, and torsion angle restraints derived from the crystal structures of human Rheb
GDP and GTP (1XTQ and 1XTS, respectively)(Yu et al. 2005), which share 99% sequence identity. No
restraints were given for 1-MP-2 and 172-DGAASQGKSSC-181 residues during the annealing protocol
so that these Rheb termini sampled a large conformational variability in the final ensemble of structures
consistent with our {1H} - 15N steady state NOEs. The G-domains (residues 4-171) of the 20 lowest
energy annealed structures were all within 0.1 Å backbone rmsd of the template crystal structures. Each
of the 20 lowest-energy structures for Rheb-GDP and Rheb-GTP were used as starting models in
HADDOCK. The coordinate file for a nanodisc model (Segrest et al. 1999) contained 80 1-palmitoyl-2-
oleoyl-sn-glycero-3-phosphocholine (POPC) lipids per leaflet (i.e. 160 total), encompassed by 2 MSP
polypeptide chains. The acyl chain of POPC is shorter than that of DOPC by two C atoms, but they
share the same headgroup, thus their bilayer surfaces would be virtually identical.
HADDOCK ambiguous restraints were generated using the PRE-measurements on nanodisc-tethered
Rheb. Because the lateral diffusion rate of DOPC at room temperature (~8.2×103 nm2/ms) (Andrey
Filippov 2003) is high relative to T2 relaxation times of Rheb on nanodiscs (~30 ms), an assumption
was made that the PRE tag uniformly sampled all positions on the nanodisc surface (78 nm2) during the
time course of the measurement. Thus, ambiguous restraints were generated between PRE-affected
residues on Rheb (e.g. Gly51) and “any” lipid headgroup atom on the nanodisc surface (e.g. G51 to
lipid-1[N1 or C13 or C14 or C15 or P1 or O11 …] or lipid-2[N1 or C13 or C14 or C15 or P1 or O11 …] or …). Residues in Rheb
with peaks displaying >80% broadening were defined in HADDOCK as ‘active’ residues and those
broadened between 50% and 80% were defined as passive residues. For the Rheb-GDP-nanodisc
complex the active residues were 1, 3, 6, 51, 77, 110, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181,
and the passive residues were 5, 7, 47, 48, 49, 53, 55, 74, 75, 76, 78, 106, 107, 108, 132, 114, 141, 143,
144, 145, 154, 162, 164, 169, 171. For the Rheb-GTP-nanodisc the active residues were 1, 3, 6, 48, 51,
110, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, and the passive residues were 5, 7, 49, 53, 54,
108, 109, 114, 115, 132, 140, 141, 143, 144, 145, 154, 162, 166, 171. The ambiguous restraints were
assigned a distance range of 2-10 Å from any atom of any lipid headgroup. Although Gd3+ is known to
affect nuclear spin magnetization within a 20 Å radius (Otting 2010), the upper limit of 10 Å was
selected because i) each lipid head group on the membrane surface is only partially occupied by Gd3+-
conjugated lipid which comprises 5% of the total lipids, and ii) active residues were stringently defined
(i.e. >80% broadening) in HADDOCK. An upper limit of 2 Å was selected for Cys181 of Rheb, since it
105
was covalently linked to the membrane surface. The CNS topology and the parameter files for the
nucleotides and POPC lipids were initially generated using the HIC-UP server (Kleywegt et al. 2003)
and modified according to the data listed for these small molecules in the Automated Topology Builder
(ATB) and Repository (Malde AK 2011). The docking protocol consisted of a 3000 rigid-body docking
stage, where the top 300 ranked structures based on the HADDOCK score were refined using semi-
flexible simulated annealing. The docking protocol was executed using the default HADDOCK script
parameters except an additional Powell energy minimization step was performed on the lipid
headgroups prior to the semi-flexible refinement stage.
Pairwise backbone rmsd values were tabulated for the Rheb G-domain (residues 4-171) after alignment
of the nanodiscs on the same plane and a translational and 360o rotational (in 5˚ increments) rmsd
minimization search confined only to movements within the 2D plane of the membrane surface in order
to structurally align the Rheb molecules relative to the large lateral dimension of the nanodisc. The
Rheb-nanodisc position in each solution was kept constant during pairwise rmsd calculation. Cluster
analysis was then performed on the pairwise rmsd values using a previously described algorithm (Xavier
Daura 1999), setting an rmsd cutoff of 8 Å and cluster size cutoff of 30 structures. The HADDOCK
scores of all 300 structures were plotted against rmsd relative to the global mean structure, defined as the
solution with the lowest average pairwise rmsd to all other 299 solutions (Figure 5.7). To estimate the
orientation angles, a vector was defined along the α6-helix of Rheb’s G-domain, and the minimum angle
between the long axis of α6 and the nanodisc membrane surface was measured for each complex. All
structural manipulations and measurements in three-dimensional space were performed using
Crystallography & NMR System (CNS) (Brunger et al. 1998). The top 20% HADDOCK-scored
complex structures of each cluster, as well as the cluster center models for each nucleotide-bound state,
have been deposited in PDB/BMRB (PDB codes 2M4A (GDP) and 2M4B (GTP); BMRB accession
numbers 18996 (GDP) and 18997 (GTP)).
106
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Andrey Filippov GO, and Göran Lindblom. 2003. Influence of Cholesterol and Water Content on Phospholipid Lateral Diffusion in Bilayers. Langmuir 19: 6397–6400.
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. 2001. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98: 10037-10041.
Berndt N, Hamilton AD, Sebti SM. 2011. Targeting protein prenylation for cancer therapy. Nat Rev Cancer 11: 775-791.
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Brunsveld L, Waldmann H, Huster D. 2009. Membrane binding of lipidated Ras peptides and proteins--the structural point of view. Biochim Biophys Acta 1788: 273-288.
Buerger C, DeVries B, Stambolic V. 2006. Localization of Rheb to the endomembrane is critical for its signaling function. Biochem Biophys Res Commun 344: 869-880.
Chris Loken DG, Leslie Groer, Richard Peltier, Neil Bunn, Michael Craig, Teresa Henriques, Jillian Dempsey, Ching-Hsing Yu, Joseph Chen, L Jonathan Dursi, Jason Chong, Scott Northrup, Jaime Pinto, Neil Knecht and Ramses Van Zon. 2010. SciNet: Lessons Learned from Building a Power-efficient Top-20 System and Data Centre. J Phys: Conf Ser 256: 012026.
Clark GJ, Kinch MS, Rogers-Graham K, Sebti SM, Hamilton AD, Der CJ. 1997. The Ras-related protein Rheb is farnesylated and antagonizes Ras signaling and transformation. J Biol Chem 272: 10608-10615.
de Vries SJ, van Dijk AD, Krzeminski M, van Dijk M, Thureau A, Hsu V, Wassenaar T, Bonvin AM. 2007. HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins 69: 726-733.
Denisov IG, Grinkova YV, Lazarides AA, Sligar SG. 2004. Directed self-assembly of monodisperse phospholipid bilayer Nanodiscs with controlled size. J Am Chem Soc 126: 3477-3487.
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Farrow NA ZO, Szabo A, Torchia DA, Kay LE. 1995. Spectral density function mapping using 15N relaxation data exclusively. J Biomol NMR 6: 153-162.
Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T. 2011. Accessing protein conformational ensembles using room-temperature X-ray crystallography. Proc Natl Acad Sci U S A 108: 16247-16252.
Goddard TD, Kneller D. SPARKY 3. in University of California, San Francisco. Gorfe AA, Babakhani A, McCammon JA. 2007a. H-ras protein in a bilayer: interaction and structure
perturbation. J Am Chem Soc 129: 12280-12286. Gorfe AA, Hanzal-Bayer M, Abankwa D, Hancock JF, McCammon JA. 2007b. Structure and dynamics
of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer. J Med Chem 50: 674-684.
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Ismail SA, Chen YX, Rusinova A, Chandra A, Bierbaum M, Gremer L, Triola G, Waldmann H, Bastiaens PI, Wittinghofer A. 2011. Arl2-GTP and Arl3-GTP regulate a GDI-like transport system for farnesylated cargo. Nat Chem Biol 7: 942-949.
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Long X, Lin Y, Ortiz-Vega S, Busch S, Avruch J. 2007. The Rheb switch 2 segment is critical for signaling to target of rapamycin complex 1. J Biol Chem 282: 18542-18551.
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of Membrane Proteins in Phospholipid Bilayer Nanodiscs. Methods Enzymol 464: 211-231. Segrest JP, Jones MK, Klon AE, Sheldahl CJ, Hellinger M, De Loof H, Harvey SC. 1999. A detailed
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Tabancay AP, Jr., Gau CL, Machado IM, Uhlmann EJ, Gutmann DH, Guo L, Tamanoi F. 2003. Identification of dominant negative mutants of Rheb GTPase and their use to implicate the involvement of human Rheb in the activation of p70S6K. J Biol Chem 278: 39921-39930.
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Chapter 6
Conclusions and Future directions
109
6.1 Conclusions: In our studies of the widely used mant-conjugated nucleotides, we demonstrated how perturbation of
exchange and hydrolysis reaction rates due to the fluorescent tag can lead to potential misinterpretations
of enzymatic functions of three small GTPases, H-Ras, Rheb, and RhoA. The effects of the mant moiety
on the reaction kinetics were unpredictable for each GTPase tested, demonstrating the importance of the
NMR-based GTPase assay, which is ‘label-free’ and enables determination of kinetic parameters of the
GTPase reactions with native nucleotide. This work was published in J. Biol. Chem (Mazhab-Jafari et al.
2010).
The fluorescent mant-GTP analog unexpectedly enhanced Rheb’s intrinsic nucleotide hydrolysis rate by
~10 fold, through a mechanism that is independent of Gln64 (which corresponds to the Ras catalytic
residue Gln61). Through our studies to understand the mechanism of rapid hydrolysis of mant-GTP by
Rheb, we identified and characterized a non-canonical nucleotide hydrolysis mechanism involving
Tyr35 in switch I and Asp65 in switch II. Tyr35 played a dual role in Rheb nucleotide catalysis. On one
hand it auto-inhibited the intrinsic nucleotide hydrolysis by stabilizing a switch II conformation in which
Asp65 was further away form the nucleotide through an H-bonding network from the side-chain
hydroxyl of Tyr35 to the backbone amide of Gly63. Mutation of Tyr35 to Ala increased GTP hydrolysis
10-fold. On the other hand, Tyr35 was necessary to facilitate productive TSC2GAP-mediated
nucleotide hydrolysis by Rheb. Indeed, we showed that Tyr35 was necessary for mTORC1 homeostasis
in cells, as its mutation decoupled mTORC1 signaling from regulation by serum. We also showed that
Asp65 contributed significantly to GTP hydrolysis in Rheb, implicating this residue as a potential
catalytic residue in this GTPase. This work was published in Structure (Mazhab-Jafari et al. 2012).
Our structural analyses of the Rheb Y35A mutant showed that the catalytic water molecule H2Ocat is
coordinated by the amide of Gly63 in the conserved G3 box at the N-terminus of switch II. We utilized
this observation in a novel protein engineering strategy to generate GDP- and GTP-locked Rheb variants
by mutations of the single ultra-conversed residue Gly63. Replacing the Hα with a larger methyl group
(G63A mutation) displaced the H2Ocat, resulting in severely reduced intrinsic GTP hydrolysis and
resistance to the GAP activity of TSC2. However, introducing a bulkier side chain (G63V mutation)
sterically occluded the space occupied by the γ-phosphate of GTP in the WT protein, resulting in an
inactive Rheb mutant that could only accommodate GDP. We demonstrated that Rheb G63A over-
110
expression results in elevated mTORC1 signaling in cells. This work was published in J. Biol. Chem (In
Press, doi: 10.1074/jbc.C113.543736).
In the final study of this thesis, we sought to characterize Rheb’s interactions with membranes, and
investigate how this affects its GTPase functions. This is an important study, since Rheb requires
farnesylation and membrane association to carry out its physiological functions in cells, however very
little is known about the details of Rheb-membrane interactions. These challenging NMR studies were
enabled by the use of nanodiscs, 5 by 10 nm discoidal lipoprotein complexes, as a model membrane
system. Rheb was covalently conjugated through its sole C-terminal cysteine to a maleimide-conjugated
lipid incorporated into nanodiscs. The GTPase domain of Rheb loosely associates with the surface of the
bilayer and we defined two preferred specific orientations, which are dependent on the bound
nucleotide. Using real-time NMR-based GTPase assays, we showed that membrane conjugation of Rheb
directly impacts the GTPase cycle. This work, published in J. Am. Chem. Soc. (Mazhab-Jafari et al.
2013), revealed previously unknown biological properties of Rheb, and sets the stage for future studies
of other membrane-associated GTPases of the Ras super-family.
6.2 Future Directions:
6.2.1 Engineering GTPase probes by structure-guided mutations of the G3-box glycine: Our protein
engineering study showed that manipulation of the conserved G3-box glycine in Rheb by mutations can
be used to control the GTPase cycle, and led to the development of the gain-of-function mutant Rheb
G63A, which is constitutively GTP-bound. This mutant, which is resistant to intrinsic and TSC2GAP-
mediated nucleotide hydrolysis reactions, should provide a valuable probe to identify potential novel
Rheb protein-protein interactions in cells, which appear to be transient and difficult to detect. In the last
few years, there have been a number of controversial reports of Rheb protein:protein interactions that
could not be reproduced by other groups such as FKPB38 (Wang et al. 2008; Uhlenbrock et al. 2009)
and TCTP (Rehmann et al. 2008; Wang et al. 2008). Paradoxically, mTOR was reported to interact more
tightly with inactive Rheb-GDP than –GTP (Long et al. 2005), but was only activated by Rheb-GTP
(Sancak et al. 2007). More reliable activated and inactivated Rheb mutants may contribute to a better
understanding of its structure and function. Furthermore, the G63V mutant, although it expressed at
lower concentrations in eukaryotic cells, may be useful to identify potential GEFs for Rheb, since it
cannot bind GTP, and thus may engage in longer-lived interactions with GEFs. Indeed, we have
111
promising preliminary data in a recent collaboration with Dr. Anne-Claude Gingras to identify proteins
that are associated with Rheb WT, G63A, and G63V mutants stably expressed in cells using the
proximity-dependent biotin identification (BioID) method (Roux et al. 2012). In addition, the high
degree of conservation of this G3-box residue across the Ras superfamily of GTPases, both at the level
of the sequence and tertiary structure, suggests that analogous mutations may serve as probes for other
GTPases. This would be particularly valuable for those GTPases in which the canonical catalytic Gln
(i.e. Ras Q61) is not conserved, and thus catalytically impaired hyperactivated mutants are not available.
However, it will be important to characterize whether mutations of the G3-box glycine confer the
expected biochemical properties and phenotype for each GTPase. For example, in Ras, G60A mutation
reduces the GTP hydrolysis rate, however this mutant acts as a dominant negative mutant in cells by
sequestering SOS (Ford et al. 2005).
6.2.2 Towards small molecule inhibitors of Rheb: Traditionally small GTPases were thought to be
undruggable because GTP binds with very high affinity (Kd ~ nM) and is abundant in the cell, and these
proteins generally lack other defined binding site on the surface of the protein. However, recent
structure-guided studies have produced promising results in targeting H- and K-Ras with small molecule
compounds (Maurer et al. 2012; Sun et al. 2012; Ostrem et al. 2013; Hunter et al. 2014; Shima et al.
2013; Lim et al. 2014). Our studies suggest at least two strategies for targeting Rheb with small
molecules that stabilize its inactive form. (i) The NBS is in an open conformation in the GDP-bound
state due to the lack of a Try35-γ-phosphate interaction. Since we showed that positioning of bulky
valine side chain in close proximity to Gly63 can inhibit GTP binding, a small molecule that specifically
binds Rheb-GDP and occupies this space close to Gly63 may block GTP binding to WT Rheb by
occluding the γ-phosphate binding site. (ii) Since we found that Rheb-GDP adopts a specific orientation
with respect to the membrane surface that masks switch II from the solvent, one can analyze the protein-
membrane interface to develop a small compound with a hydrophobic side chain that inserts into the
bilayer and a head group that specifically binds Rheb-GDP at the membrane interface. This type of
molecule may stabilize a Rheb orientation in which switch II is masked from the solvent, and diminish
Rheb’s ability to signal to mTORC1.
6.2.3 Probing membrane-dependent regulation of K-Ras-effector interaction: The methods we
developed to analyze Rheb GTPase interactions with membranes at high resolution using nanodisc-
112
based lipid bilayers can be extended to other members of the Ras superfamily that are targeted to
biological membrane compartments in cells to carry out their physiological functions. Hence, we have
begun preliminary analysis of K-Ras4B (Figure 6.1) conjugated to nanodiscs, using a protocol described
in detail in appendix B. The K isoform of Ras displays the highest frequency of somatic mutations in
cancer (Prior et al. 2012). Thus understanding its physiological and oncogenic properties as well as
interactions with its effectors on membrane bilayers is crucial to rational design of small molecular
inhibitors for therapeutic interventions.
These nanodisc methodologies have enabled preliminary investigations of biophysical properties of K-
Ras on bilayer membranes including; i) orientation with respect to the bilayer plane and its modulation
by the bound nucleotide (GDP versus GMPPNP), ii) structural and dynamical effects of membrane
binding on the K-Ras G-domain, iii) examination of the interactions between K-Ras and Ras binding
domains (RBDs) on the membrane, iv) effects of oncogenic mutations on Ras-membrane orientation and
interaction with RBDs, and v) effect of membrane association on the K-Ras GTPase cycle.
6.3 Closing Remarks:
Since the discovery of Rheb two decades ago, intense studies of its physiological and pathological roles
have been carried out and an understanding of the role of this small GTPase in different cellular
signaling pathways is emerging, however many questions remain. Far fewer structure-function studies of
Rheb have been carried out, relative to those of Ras. The structural and functional works presented in
this thesis, revealed the structural basis of autoinhibition of Rheb GTPase activity that contributes to its
high activation state in cells, which can become pathogenic upon limiting TSC2 GAP activity. Using
this knowledge, we have also developed novel probes for dissecting the signaling pathways that Rheb
regulates. These probes can also be applied to studies of other GTPases with non-canonical GTP
hydrolysis mechanisms (i.e., no functional catalytic Gln corresponding to Ras Gln61). Furthermore, our
structural and functional work on the bilayer membranes have revealed potential mechanisms of
membrane-dependent regulation of Rheb function in cells, and this high-resolution methodology can be
extended to the studies of other membrane associated GTPases. The structural and functional knowledge
of Rheb catalytic function and membrane association, which are two pillars of Rheb function, can aid in
development of novel therapeutic strategies that combat Rheb-mediated pathogenesis.
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Figure 6.1) Backbone and side chain assignments of free K-Ras4B in complex with GMPPNP. a) Assignment of K-Ras4B residues 1-185. 60% of the G-domain and all of the HVR were assigned. b) Chemical shift assignment of K-Ras4B Ile δ-CH3 (aided by assignment transfer from of H-Ras-GDP, courtesy of Dr. Sharon Campbell, see appendix B for more details). 6.4 References: Ford B, Skowronek K, Boykevisch S, Bar-Sagi D, Nassar N. 2005. Structure of the G60A mutant of
Ras: implications for the dominant negative effect. J Biol Chem 280: 25697-25705. Hunter JC, Gurbani D, Ficarro SB, Carrasco MA, Lim SM, Choi HG, Xie T, Marto JA, Chen Z, Gray
NS et al. 2014. In situ selectivity profiling and crystal structure of SML-8-73-1, an active site inhibitor of oncogenic K-Ras G12C. Proc Natl Acad Sci U S A 111: 8895-8900.
Lim SM, Westover KD, Ficarro SB, Harrison RA, Choi HG, Pacold ME, Carrasco M, Hunter J, Kim ND, Xie T et al. 2014. Therapeutic targeting of oncogenic K-Ras by a covalent catalytic site inhibitor. Angew Chem Int Ed Engl 53: 199-204.
Long X, Lin Y, Ortiz-Vega S, Yonezawa K, Avruch J. 2005. Rheb binds and regulates the mTOR kinase. Curr Biol 15: 702-713.
Maurer T, Garrenton LS, Oh A, Pitts K, Anderson DJ, Skelton NJ, Fauber BP, Pan B, Malek S, Stokoe D et al. 2012. Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity. Proc Natl Acad Sci U S A 109: 5299-5304.
Mazhab-Jafari MT, Marshall CB, Ishiyama N, Ho J, Di Palma V, Stambolic V, Ikura M. 2012. An autoinhibited noncanonical mechanism of GTP hydrolysis by Rheb maintains mTORC1 homeostasis. Structure 20: 1528-1539.
Mazhab-Jafari MT, Marshall CB, Smith M, Gasmi-Seabrook GM, Stambolic V, Rottapel R, Neel BG, Ikura M. 2010. Real-time NMR study of three small GTPases reveals that fluorescent 2'(3')-O-(N-methylanthraniloyl)-tagged nucleotides alter hydrolysis and exchange kinetics. J Biol Chem 285: 5132-5136.
Mazhab-Jafari MT, Marshall CB, Stathopulos PB, Kobashigawa Y, Stambolic V, Kay LE, Inagaki F, Ikura M. 2013. Membrane-dependent modulation of the mTOR activator Rheb: NMR observations of a GTPase tethered to a lipid-bilayer nanodisc. J Am Chem Soc 135: 3367-3370.
Ostrem JM, Peters U, Sos ML, Wells JA, Shokat KM. 2013. K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions. Nature 503: 548-551.
Prior IA, Lewis PD, Mattos C. 2012. A comprehensive survey of Ras mutations in cancer. Cancer Res 72: 2457-2467.
Rehmann H, Bruning M, Berghaus C, Schwarten M, Kohler K, Stocker H, Stoll R, Zwartkruis FJ, Wittinghofer A. 2008. Biochemical characterisation of TCTP questions its function as a guanine nucleotide exchange factor for Rheb. FEBS Lett 582: 3005-3010.
Roux KJ, Kim DI, Raida M, Burke B. 2012. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J Cell Biol 196: 801-810.
Sancak Y, Thoreen CC, Peterson TR, Lindquist RA, Kang SA, Spooner E, Carr SA, Sabatini DM. 2007. PRAS40 is an insulin-regulated inhibitor of the mTORC1 protein kinase. Mol Cell 25: 903-915.
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Shima F, Yoshikawa Y, Ye M, Araki M, Matsumoto S, Liao J, Hu L, Sugimoto T, Ijiri Y, Takeda A et al. 2013. In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction. Proc Natl Acad Sci U S A 110: 8182-8187.
Sun Q, Burke JP, Phan J, Burns MC, Olejniczak ET, Waterson AG, Lee T, Rossanese OW, Fesik SW. 2012. Discovery of small molecules that bind to K-Ras and inhibit Sos-mediated activation. Angew Chem Int Ed Engl 51: 6140-6143.
Uhlenbrock K, Weiwad M, Wetzker R, Fischer G, Wittinghofer A, Rubio I. 2009. Reassessment of the role of FKBP38 in the Rheb/mTORC1 pathway. FEBS Lett 583: 965-970.
Wang X, Fonseca BD, Tang H, Liu R, Elia A, Clemens MJ, Bommer UA, Proud CG. 2008. Re-evaluating the roles of proposed modulators of mammalian target of rapamycin complex 1 (mTORC1) signaling. J Biol Chem 283: 30482-30492.
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APPENDIX A Formula used for data fitting of intrinsic- and GAP-mediated nucleotide hydrolysis:
Intrinsic- and GAP- mediated nucleotide hydrolysis data were fitted to one phase exponential
association to determine the rates according to:
[I *
GDP/(I*GDP+I*GTP)] (t) = 1 - exp (-khy × t) equation 1
I*
GDP = Peak heights of Ras or Rheb bound to GDP or mantGDP I*
GTP = Peak heights of Ras or Rheb bound to GTP or mantGTP khy = nucleotide hydrolysis rate In the case of RhoA, due to line broadening of the activated (GTP-bound) state, we used the following
one phase exponential association formula using the increasing intensities of the resonances related to
the inactive (GDP-bound) conformation of the GTPase:
[I *
GDP/I*f
GDP] (t) = 1 - exp (-khy × t) equation 2 I*f
GDP = Peak heights of the GDP or mantGDP after complete GTP or mantGTP hydrolysis.
Determination of the true nucleotide exchange rate kex in the presence of intrinsic hydrolysis.
When nucleotide exchange assays are performed with hydrolysable nucleotides (e.g., GTP, mantGTP),
the observed exchange rate (plotted by continuous lines in figures 2.5 and 2.6) is determined by a
combination of the GEF-mediated exchange rate and the intrinsic hydrolysis of the nucleotide bound to
the small GTPase (Ras or RhoA). If the rate of intrinsic nucleotide hydrolysis is known, the observed
data can be fitted to equation 4 to obtain the true exchange rate kex. This model makes the assumption
that all of the GTPase protein is bound to either GTP or GDP in solution, due to nM affinities for the
nucleotide. The true exchange rate can be used to plot a one phase exponential decay curve
approximating exchange in the absence of hydrolysis (dashed lines in figures 2.5 and 2.6).
d [I*GDP/(I
*GDP+I*GTP)] / d t = - kex [I
*GDP/(I
*GDP+I*GTP)] + khy [1 – (I*GDP/(I
*GDP+I*GTP))]equation 3
I*
GDP/(I*GDP+I*GTP) (t=0) = 1
[I *
GDP/(I*GDP+I*GTP)](t)= 1 – [kex /(kex +khy) - kex /(kex + khy) exp –(kex + khy) t] equation 4
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kex = nucleotide exchange rate
As mentioned above, GTP-bound RhoA exhibited line broadening and split peaks that
complicated peak integration hence we used the resonances of the GDP-bound state to calculate the
exchange rate.
d [I*GDP/I
*0GDP] / d t = - kex [I
*GDP/I
*0GDP] + khy [1 – (I*GDP/I
*0GDP)] equation 5
I*
GDP/I*0
GDP (t=0) = 1 [I *
GDP/I*0
GDP](t)= 1 – [kex /(kex +khy) - kex /(kex + khy) exp –(kex + khy) t] equation 6 I*0
GDP = Peak heights of the GDP or mantGDP before the addition of GEF and excess GTP or mantGTP nucleotide.
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APPENDIX B Preparation of K-Ras4B-nanodisc complex: A construct encoding K-ras4b (amino acids 1-185, C51S, C80S, C118S) was synthesized (Genscript)
and ligated into pET-28 vector. The buried Ser51 and Ser80 were back mutated to native Cys residues
via site directed mutagenesis to improve expression. The protein expression was induced in E. Coli
BL21 (DE3) at an OD600 of 0.6 and a temperature of 15 Co in M9 media supplemented with 15NH3. 70
mg/L of 2-Ketobutyric acid-4-13C was added to the media one hour prior to IPTG-meditated induction
of expression to label the Cδ position of the isoleucine residues with 13C isotope (Tugarinov et al. 2006).
K-Ras4B was then purified using standard His-tag affinity purification methods, as described for H-Ras
in chapter 2.
The nanodisc assembly was carried out as described in detail in chapter 5, with the exception of a
different lipid composition (75% DOPC, 20% DOPS, 5% PE-MCC, mol ratio) to mimic the mammalian
plasma membrane. For PRE experiments, 2.5% (final mol ratio) of 1,2-distearoyl-sn-glycero-3-
phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt) was used in the assembly
of nanodiscs. All lipids were from Avanti Polar Lipids. The GTPase-nanodisc conjugation reaction and
size exclusion chromatography were performed as described for Rheb-nanodisc conjugation, in chapter
5, except that K-Ras4B constructs were incubated with 100 units of bovine thrombin (per 20 mg of
KRas at a concentration of 1mM) for 2h at room temperatures to ensure complete cleavage of the His-
tag prior to the conjugation reaction. The cleavage reaction was confirmed via mass spectroscopy.
Nucleotide exchange was carried out prior to nanodisc conjugation in the presence of GMPPNP, EDTA
and calf intestinal alkaline phosphatase, (Cip) followed by passage through S75 size exclusion
chromatography. Unlabeled RBDs [A-Raf, RalGDS, and PLCε1-2, prepared as described previously
(Smith and Ikura 2014)] were added to the uniformly 15N- Ile13Cδ-labeled K-Ras-nanodisc conjugate
at an excess of 1:1.2 KRas:RBD to ensure saturation. To analyze interactions of the RBDs with the
bilayer, similar experiments were also performed with uniformly 15N- Ile13Cδ-labeled RBDs and
unlabeled K-Ras-nanodisc conjugate. Assignment of K-Ras Ile side chains were transferred from the H-
Ras-GMPPNP T35S mutant (BMRB entry: 17610) and H-Ras-GDP (courtesy of Dr. Sharon Campbell).
The assignment was then completed via site directed mutagenesis of residues with low confidence
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assignment transfer. Five mutants were prepares including; Ile21Leu, Ile36Leu, Ile100Leu, Ile139Leu,
and Ile163Leu.
1H-15N HSQC, 1H-15N TROSY-HSQC, and 1H-13C HMQC spectra were collected at 298.2 Ko on a
Bruker AVANCE II 800 MHz spectrometer equipped with a 5 mm TCI CryoProbe and a 600 MHz
spectrometer with a TCI 1.7 mm MicroCryoProbe, for nanodisc-bound and free samples, respectively.
Spectra were processed and analyzed as described in chapter 5.
References:
Smith, M. J. and M. Ikura (2014). "Integrated RAS signaling defined by parallel NMR detection of effectors and regulators." Nat Chem Biol.
Tugarinov, V., V. Kanelis and L. E. Kay (2006). "Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy." Nat Protoc 1(2): 749-54.
