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Research In the Van Vranken Group
Christopher J. McGeeUniversity of California, Irvine
protein of interest
peptide
Pro-fluorophore
Applications of Combinatorial Libraries to the Discovery of Chemically Reactive Peptide Tags
Medicine is Linked To Understanding Protein Function
40% of our proteins cannot be assigned a likely function
by homology to other organisms
80 % of our drug arsenal Targets proteins
(1,065 drugs out of 1,357)
Genomics
Proteomics
Nature Reviews Drug Discovery. 2006, 5, 992–996
It’s Hard To Understand What You Can’t See
Cell
Direct visualization of the proteome: immunofluorescent labeling (dead Cells) bioorthogonal fluorescent labeling (live cells)
n Dead cells can’t convey dynamic character
Fluorescein
GFP “Tags” Allow Visualization in Living Cells
Green Fluorescent Protein
MSKGEELFTGVVPVLVELDGDVNGQKFSVSGEGEGDATYGKLTLNFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFYKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKMEYNYNSHNVYIMGDKPKNGIKVNFKIRHNIKDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMILLEFVTAARITHGMDELYK
238 Total Amino Acids
Aequorea victoria
Genetic engineering: add gene for GFP to gene for Protein of Interest
Introduce DNA into cell
Cell transcribes/translates protein+GFP, glued together
protein gene GFP gene
RNA
PROTEIN
Cell
t1/2 = ~3 min t1/2 = 20–80 minTsien. Annu. Rev. Biochem. 1998
Nat. Cell Biol. 2008 10, 211–9
H.I.V infected T cells expressing Gag protein fused to GFP
GFP Reveals Location and Speed of HIV Transmission
n This mechanism of HIV-1 transmission could be important to its pathogenicity and may open new avenues for drug targets
n We can see where a protein originated, where it went, how, and how fast
The Large Size of GFP Tags Limits Applicationsn Tags should NOT perturb the native folding, localization, or function of the
POI n Many Human proteins are likely too small to study with fluorescent proteins
Size of GFP238 Amino Acds
rela
tive
freq
uenc
y
Sequence length (from human proteome)
Think this tracking device will impact the Bee’s behavior?
n At best, you can shave 11 residues off the 238 in GFP, and still get fluorescence
pH 7.4 buffer i) pick beads
ii) cleave &sequence
40 。C
n Dimerization and oxidation of Trp’s in peptides generates a highly fluorescent chromopohore
Can this be extended to biologically relevant peptides ?
Sequence-dependent fluorogenes in peptides is too slow for cellular labeling
J. Am. Chem. Soc. 1996, 118, 1225-1226.
J. Am. Chem. Soc. 2004, 126, 550-556.
Our Group Sought Smaller Fluorogenic Tags
Ala-Lys-Pro-Trp-Gly-Gly-Asp-Ala
100 µM
TentaGel-HL-NH2Resin Beads
Bead Interior PEG Grafted to Polystyrene
Amine Functionalize PEG Tails
OBOC Library Beads Contain Trillions of the Same Peptide
1013 Amine Tails
= 320 pmol peptide per single bead
Ala-Lys-Pro-Trp-Gly-Gly-Asp-Ala
Ala-Lys-Pro-Trp-Gly-Gly-Asp-Ala
Ala-Lys-Pro-Trp-Gly-Gly-Asp-Ala
Ala-Lys-Pro-Trp-Gly-Gly-Asp-Ala
Each Bead =
1013 identical peptide molecules
n Fluorogenesis was a bonus
n Arsenic has high affinity for proteins containing proximal cysteines - toxic
n Small vicinal thiols form tighter complexes with trivalent arsenic than cellular thiols -antidote
n Engineer a peptide tag having cysteines with greater arsenic affinity than dithiols
Peptide Tag That Binds Arsenic Containing Fluorescein
Tsien, et al. Science 1998
SH SH
SHSH
ii+1
i+4 i+5
S
S
S
S
FlAsH-EDT2 + 2 EDT
WEAAAREACCRECCARATag Sequence:
Tags are labeled in less than 1 hr with with 1 mM EDT and 1 mM BAL
Peptide Tag Pro-Fluorophore Fluorescentcomplex
Tagpro -flourophore
CCXXCC = Best Motif Out of 10 Peptides Screened
We would begin our search for improved FlAsH tags here –with OBOC libraries
Tsien, et al. JACS 2002
n These binding constants are not relevant – dithiols always used in cellular screening
180067
100
707242
472
92000
150
41
Kdapp(pM)
CCXXCCWDCCPGCCK = T1
original
improved
~240 nM Kd
Best case scenario FlAsH labels 60% of expressed tags
What about :CXCXCXC, CCXCXXC, CXCCXC ….
Mammalian Cell Screens Optimizes Tag System 6 Fold
F.A.C.S Dithiol
Washes
230 million NIH 3T3 CellsXXCCXXCCXX
CCPGCC Confirmed
F.A.C.S Dithiol
Washes
370 million NIH 3T3 CellsXXXCCPGCCXXX
T2= FLNCCPGCCMEP T3= HRWCCPGCCKTF
T1= WDCCPGCCK
Offers 6 fold better contrast than T1
n Still 16 less sensitive than GFPn Still have only looked at only a few motifs (CCXCC)
n Experimentally T2 has shown better contrast and is the preferred tag
FLNCCPGCCMEP•ReAsH Proposed Structure Unsetteling
As1
As2
As1As2
n Flattened arsinesn No interstrand hydrogen bondsn As2 is tilted only 44.3° from
alignment with the xanthene π-system Has an edge to face interaction between Phe and the xanthene ring system
Elements Of 2° Structure One Might Expect
Gräslund Model
Conformational Search for FLNCCPGCCMEP•ReAsH
Hydrogen bond between the Cys4 & Cys8 (i and i+4)
n Phe in close proximity to the xanthene system, consistent with NOE data
As1
As2
Arsenics were pyramidal
Differed from Gräslund model’s peptide backbone
Gräslund Model Our Model
Why am I showing your this ? Later, we’ll model one of our FlAsH Tags
n A cysteine-rich library (Ac-X-X-X-X-X-X-X-X-K-M-TentaGel)
n Bias towards 4 cysteines per peptide
Tetracysteine-Biased OBOC Library May Hold New Tags
Cysteine-Containing OBOC Libraries Are Unprecedented
n Disulfide bonds are often undesired during screening , thus reducing agents must be used
n Free cysteine undergoes side reactions in Edman degradation and cyanogen bromide cleavage, chemistry used in two common methods for direct sequecening
n Cysteine is difficult to distiguinsh from arginine in Edman Sequencing
The problems caused by cysteine during synthesis screening and sequencing leads to nearly complete exclusion of cysteine from OBOC libraries
Hits [FlAsH] Round Relative Reactivity
35 10 nM 1 100 X28 10 nM 28 100 nM 3 10X
Many 1000 nM 4 Average
Screening The First Cys-Biased Library With FlAsH
1.0 mM BAL, 1.0 M BMEMCB pH 7.2, 0.1% TrX-100
FlAsH
FL1Ac-X8-KM-Tentagel~6.5 milion beads
X = 10 different Amino Acids
n In cell labeling, equilibrium is established in less than 1 hour with 1 mM dithiol
High concentration of monothiol was necessary to catalyze equilibrium on beads
WDCCPGCCKM•FlAsH
WDCCPGCCKM
Screening The Library w/ Nanomolar conc. Of FlAsHIsolating a Hit, Alkylating Cysteines, and Cleaving Peptide
MS/MS
How Does MS/MS Afford the Peptide Sequence
Subpopulations of parent ions with a ‘mobile proton’ at a different amide bonds
Spectra of Ac-CYCFCRCCK-Hsl (Nanoflow LC-MS/MS)
De Novo MS/MS Identifies the Sequence of ‘Hit’ Beads
1st Round of 10 nm Hits 2nd Round of 10 nm Hits
Hits With Exactly 4 Cysteines Reveal New Reactive Motifs
CCXCXXCCXCCXXC
CCCXXC
Tsien CCXXCCCCCXXXC
CXCCXC
n 5 New reactive motifs
n Endogenous human proteins with these motifs could lead to off-target labeling and toxicity
C
N
CCWCSSC•ReAsH CYCCLSC•ReAsH
N C
Looking for Elements of 2° New Motifs
n Weak H bond between the N-acetyl carbonyl and the NH of Trp3 (i and i+3)
n H bond between the NH of Tyr2 and carbonyl of Cys7 ( i and i+5)
The three new motifs are not richly structured (nor was CCPGCC) Making it difficult to to guess their apptitude as FlAsH Tags. Of course, we can find out through experimentation
CCCPGC•ReAsH
N
C
Making Sure Tag Reactivity is Reproducible Off of the Bead
Pursue spots that: Give brighter complexes than T2 Cannot bind through CCXXCC
1-7
1-131-12 1-12
2-10 T2
T1
n Solution phase has low [monothiol] in contrast to our bead and cellulose screens
Solution Phase Fluorescence Assay Comparing FlAsH Tags
n Our best hit was only 3 times less fluorescent than the T2 sequence
T2 –state of the art FlAsH tag (optimized)
Our best hit (not optimized)
n We would go on to screen another library with low [monothiol]…. No hits better than 2-10
Best Peptide YCCLCCPCKM-COOH
CCXCXXC, CXCCXC,CCXXCXC, CXXCCXC
Possible Motifs
i and i +3 H bond between Cys2 and Cys5 = b hairpin turn i and i +2 bond hydrogen betweenCys7 and Cys9 = g turn
N
C
Salt Bridge between Lys9 and FlAsH Carboxylate Phe nearing an edge to face interaction with xanthene system
Y C C L C C P C K MC C X C X X C
Modeled CCXCXXC•FlAsH Has Good Attributes For A Tag
Discovering The 2 Best Known FlAsH Tags In One Screen
We successfully identified sequences containing both known FlAsH tag Motifs: CCPGCC and CCKXCC
FB1 & FB2 FB3 FB4 FB5 FB6
FB1 CCCCKCCCKMFB2 CCPCCCYNKMFB6 WDCCPGCCKM
Employing the post screen dithiol wash (mimicking Tsien’s cell screen)
n Dramatic improvements have seemed unlikely n Identification of several different reactive peptides suggests off-target labeling/ toxicity as an obstacle that will remain as long as arsenic is part of the system
Accomplishments from Biarsenical-Tetracysteine Work
n Longest and most diverse OBOC derived peptides ever sequence with MS/MS
n First MS/MS analysis applied to any oligomer containing cysteine
n First method for the synthesis, screening, and sequencing of cysteine-rich OBOC peptide libraries
Accomplishments from Biarsenical-Tetracysteine Work
n Could identify new reactive tags for biarsenicalsn Identifed endogenous human protein targetsn Protocols viable to screen for all important cysteine reactivity – heavy metal sequestering
New Fluorophore-Peptide Complexes From 1,4-Dicarbonyls
ortho-phthalaldehyde can condenses with amines and either a thiol or cyanide anion to generate a fluorescent isoindole in aqueous buffers
OPA derivatives with increased stability and better fluorescence properties
There have been no attempts to find short peptides with the right juxtaposition of lysine and cysteine side chains that can react with OPA derivatives
3-benzoyl-2-quinolinecarboxaldehyde (BQCA) is optimal
Fluorescent Isoindole
n 10 nM hits lost to trapping cycle on nano-LC (C18)
13 100 nM hits sequenced
Screening A Cysteine-Rich Library with BQCA
fused silica emitter
movable metal stagedamaged emitter tip www.newobjective.com/electrospray/index.html
nanoLC MS/MS sequencing trouble shooting
Confirm The Red Fluorescence is Legit
493 (λ max ex)
Fluorophore is a good candidate for argon laser excitation (max output 488 nM)
A SPOT array was screened with 500nM BQCA, 10 mM BuNH2, 5 mM BME
SPOT Screen of 13 Hit Sequences Reveals Best BQCA Tag
1
25
n CXXXXXXXK is prevalent
n CK is prevalant
CK and CXXXXXXXK Do Not Appear Ideal
Relative Fluorescence of Designed Peptides
n Because VWCCACSKM superior in the initial SPOT array comparison, we made a library of variants.
1 V W C C A C S K M2 W C C A C S K M3 V C C A C S K M4 V W C A C S K M5 V W C C C S K M6 V W C C A S K M7 V W C C A C K M8 V W C C A C S M9 V W C C A C S K
10 C C A C S K M11 C A C S K M12 A C S K M13 C S K M14 V W C C A C S K M15 A W C C A C S K M16 V A C C A C S K M17 V W A C A C S K M18 V W C A A C S K M19 V W C C C C S K M20 V W C C A A S K M21 V W C C A C A K M22 V W C C A C S A M23 V W C C A C S K A24 V Y C C A C S K M25 V F C C A C S K M26 V H C C A C S K M27 L W C C A C S K M28 I W C C A C S K M29 V W C C A C T K M30 V W C C A C S R M
Po
int
De
letio
ns
De
letio
ns
Ala
Sca
n
30
Optimized Variant of VWCCACSKM Discovered
2x optimization
original
Adding A Reversible Chelating Group – Enhance Selectivity
Precedence for aryl boronic acids being selective for serine sidechains in presence of cellular sugars (diols)
Built a mass ladder into the library
Post Screen Chemical degredation Avoided
MS/MS Avoided
Screening A Ladder Library with BQCA Boronic Ester
Cys* AlaTyr Trp
n Identified the first peptide tags that react selectively with 1,4-dicarbonyls to give fluorescent isoindoles
n Synthesized a novel boronic ester variant of BQCA, with the capacity to react with four peptide sidechains
n Have shown the simplicity of the traditional ladder method offers a simple alternative to MS/MS
Ac-VWCCACSKM-TentaGel
Accomplishments from BQCA Work
Acknowledgements
Roomates:Mom and DadAmber Reilly
DVV Labmates:Dave Van Vranken*, Gary Juskowiak, Sean Devine, Romas Kudirka,
Denise Dunn, Chris Adams, Avi Khanna, Glenn Eldridge
UW Madison Labmates:Pete Belshaw, Shane Lamos, Casey Krusemark, Alex Shaginian,
Marissa Rosen, Adam Miller
TeachersMs. Bareman (4th Grd) Mr. Jaeyk (7th Grd) Mr. Melter (HS)
GAANN Fellowship, Chem Office, Students, B-field Crew
John Greaves & Shirin Sorooshian
Any Structural Trends Between Motifs ?
CCPGCC CCCPGC
C
C
N
N
(From Peptide 1-13)
Bead Screen Suggests CCCPGC is better than CCPGCC
Modeling suggests CCPGC is better
CCPGCC appears less strained , but both lack hydrogen bonding
+6.3 kcal/mol
Red precipitate in mintues
Solution Phase Studies With BQCA
1 of 2 possibilities