Using two recently-Using two recently-developed molecular developed molecular
dynamics protocols for dynamics protocols for protein foldingprotein folding
Timothy H. ClickTimothy H. ClickDepartment of Chemistry and Department of Chemistry and
BiochemistryBiochemistryUniversity of OklahomaUniversity of Oklahoma
Norman, OklahomaNorman, Oklahoma
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OutlineOutline
Introduction to MD protocolsIntroduction to MD protocols Previous workPrevious work Simulations of tryptophan zipper 2Simulations of tryptophan zipper 2 Simulation of Simulation of StreptococcalStreptococcal protein G B1 protein G B1
domain (residues 41-56)domain (residues 41-56) ConclusionsConclusions Future directionsFuture directions AcknowledgementsAcknowledgements
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Protein geometry Protein geometry optimizationoptimization
Dill, K.A.; Chan, H.S. Nat. Struct. Biol., 1997, 4, 10-19.
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11stst MD protocol — DIVE MD protocol — DIVE
Disrupted Velocity (DIVE) search Disrupted Velocity (DIVE) search protocolprotocol Velocity reassignment of coordinate historiesVelocity reassignment of coordinate histories
Magnitude rescaling — energy perturbationMagnitude rescaling — energy perturbation Direction changesDirection changes Reassignment every n steps (defined by user)Reassignment every n steps (defined by user)
Heating and cooling cyclesHeating and cooling cycles Conformations sampled near absolute zeroConformations sampled near absolute zero Overall, protocol disrupts equilibriumOverall, protocol disrupts equilibrium Energy barriers overcome or circumventedEnergy barriers overcome or circumvented Several potential energy minima sampledSeveral potential energy minima sampled
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How conformations are How conformations are selectedselected
Disrupted Velocity for trpzip2
-500
-495
-490
-485
-480
-475
-470
-465
-460
-455
-450
0 500 1000 1500 2000 2500 3000 3500 4000
Time (ps)
Po
ten
tia
l e
ne
rgy
(k
ca
l/m
ol)
Disrupted velocity for trpzip2
-500.00
-495.00
-490.00
-485.00
-480.00
-475.00
-470.00
-465.00
-460.00
0 500 1000 1500 2000 2500 3000 3500 4000
Time (ps)
Po
ten
tial
en
erg
y (k
cal/
mo
l)
βlowto
DIP
βlow2to
DIP
β
βlow
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22ndnd MD protocol — DIP MD protocol — DIP
Divergent Path (DIP) search strategyDivergent Path (DIP) search strategy Coordinate histories at same constant Coordinate histories at same constant
temperaturetemperature Simulations involve multiple coordinate historiesSimulations involve multiple coordinate histories Individual coordinate histories randomly Individual coordinate histories randomly
assigned initial velocitiesassigned initial velocities Velocities can be altered allowing for different Velocities can be altered allowing for different
conditionsconditions Constant temperatures maintained by rescaling Constant temperatures maintained by rescaling
velocity magnitudesvelocity magnitudes Broader sampling of potential energy surface Broader sampling of potential energy surface
allowedallowed
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DIP simulationDIP simulation
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DIP simulation (cont’d)DIP simulation (cont’d)<E>= -624.22 ± 8.27
kcal/mol<RMSD> = 1.6 ± 0.5 Å
<E>= -632.42 ± 8.44
kcal/mol<RMSD> = 1.8 ± 0.2 Å
<E>= -587.16 ± 9.50
kcal/mol<RMSD> = 13.2 ± 0.5 Å
<E>= -633.94 ± 7.87
kcal/mol<RMSD> = 1.5 ± 0.2 Å
<E>= -592.02 ± 8.38
kcal/mol<RMSD> = 12.5 ± 0.5 Å
<E>= -600.29 ± 13.05
kcal/mol<RMSD> = 11.3 ± 0.7 Å
nmr
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Protocol proceduresProtocol procedures
Modified Amber force field (Okur,A.; Modified Amber force field (Okur,A.; Strockbine, B.; Hornak, V.; Simmerling, C., Strockbine, B.; Hornak, V.; Simmerling, C., J. J. Comput. Chem.Comput. Chem., , 20032003, 21), 21)
Constraints on atoms covalently bonded to Constraints on atoms covalently bonded to hydrogenhydrogen
Implicit solventImplicit solvent 2 fs time step2 fs time step 4,000,000 steps4,000,000 steps Velocity disruption every 20,000 steps (DIVE)Velocity disruption every 20,000 steps (DIVE) T = 300 ± 20 K (DIP)T = 300 ± 20 K (DIP) 6 independent coordinate histories/simulation6 independent coordinate histories/simulation
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Previous work with Previous work with αα--heliceshelices
Zunnan HuangZunnan Huang 13-residue polyalanine13-residue polyalanine Trp-cage (Trp-cage (αα-helix and 3-helix and 31010-helix-helix
Huang and Zhanyong GuoHuang and Zhanyong Guo Peptide FPeptide F
Timothy H. ClickTimothy H. Click C-peptide of ribonuclease A (residues 1-13)C-peptide of ribonuclease A (residues 1-13)
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Tryptophan zipper 2 Tryptophan zipper 2 (trpzip2)(trpzip2)
De novo 12-residue polypeptideDe novo 12-residue polypeptide Sequence (SSequence (S11WTWENGKWTWKWTWENGKWTWK1212-NH2)-NH2) PDB code 1LE1 (20 NMR models)PDB code 1LE1 (20 NMR models) Stable β-sheet in aqueous solution by cross-Stable β-sheet in aqueous solution by cross-
stranded pairs of four tryptophansstranded pairs of four tryptophans Simulations completed by other groupsSimulations completed by other groups
1 Cochran, A.G.; Skelton, N.J.; Starovasnik, M.A. P. Natl. Acad. Sci. USA, 2001, 98, 5578-5583.
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Trpzip2 DIVE ResultsTrpzip2 DIVE Results
extlowE = -496.59 kcal/mol
RMSD 6.9 Ẳ
βlowE = -494.05 kcal/mol
RMSD 5.0 Ẳ
αlowE = -498.22 kcal/mol
RMSD 6.1 Ẳ
β*E = -489.44 kcal/mol
RMSD 0.9 Ẳ
extlow2E = -499.23 kcal/mol
RMSD 7.0 Ẳ
βlow2E = -497.06 kcal/mol
RMSD 5.7 Ẳ
αlow2E = -498.17 kcal/mol
RMSD 6.1 Ẳ
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Trpzip2 DIP ResultsTrpzip2 DIP Results
ext<E> = -360.82 ± 7.66
kcal/mol<RMSD> 6.5 ± 0.8 Ẳ
β<E> = -381.65 ± 4.55
kcal/mol<RMSD> 0.9 ± 0.1 Ẳ
α<E> = -369.79 ± 9.01
kcal/mol<RMSD> 6.7 ± 0.4 Ẳ
extlow<E> = -375.47 ± 6.28
kcal/mol<RMSD> 7.5 ± 0.1 Ẳ
βlow<E> = -374.14 ± 7.18
kcal/mol<RMSD> 7.0 ± 0.3 Ẳ
αlow<E> = -368.77 ± 7.38
kcal/mol<RMSD> 6.1 ± 0.1 Ẳ
extlow2<E> = -381.44 ± 5.74
kcal/mol<RMSD> 7.4 ± 0.1 Ẳ
βlow2<E> = -378.75 ± 6.04
kcal/mol<RMSD> 7.0 ± 0.3 Ẳ
αlow2<E> = -368.93 ± 7.54
kcal/mol<RMSD> 6.2 ± 0.3 Ẳ
β*<E> = -381.65 ± 5.04
kcal/mol<RMSD> 0.8 ± 0.1 Ẳ
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Trpzip2 Trpzip2 SummarySummary
PES rough at low temperaturesPES rough at low temperatures ββ-hairpin challenging secondary structure-hairpin challenging secondary structure ββ-hairpin as relative global PE -hairpin as relative global PE
conformationconformation αα-helices metastable conformation-helices metastable conformation
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B1 domain of B1 domain of StreptococcalStreptococcal protein Gprotein G
Natural Natural ββ-hairpin stable in aqueous -hairpin stable in aqueous solution.solution. Sequence (GSequence (G4141EWTYDDATKTFTVTEEWTYDDATKTFTVTE5656)) PDB 2GB1 (x-ray crystal structure)PDB 2GB1 (x-ray crystal structure) Stabilization factorsStabilization factors
Hydrophobic coreHydrophobic core Terminal salt bridgeTerminal salt bridge
Several simulationsSeveral simulations
22 Gronenborn, A. M.; Filpula, D. R.; Essig, N. Z.; Achari, A.; Gronenborn, A. M.; Filpula, D. R.; Essig, N. Z.; Achari, A.; Whitlow, M.; Wingfield, P. T.; Clore, G. M. Science, Whitlow, M.; Wingfield, P. T.; Clore, G. M. Science, 19911991, , 253, 657-661.253, 657-661.
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Protein G DIVE resultsProtein G DIVE results
extlowE = -784.40 kcal/mol
RMSD 7.4 Ẳ
βlowE = -774.96 kcal/mol
RMSD 6.8 Ẳ
αlowE = -783.53 kcal/mol
RMSD 8.4 Ẳ
β*E = -770.54 kcal/mol
RMSD 0.9 Ẳ
extlow2E = -785.85 kcal/mol
RMSD 7.3 Ẳ
βlow2E = -781.75 kcal/mol
RMSD 6.4 Ẳ
αlow2E = -785.64 kcal/mol
RMSD 8.4 Ẳ
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Protein G DIP resultsProtein G DIP results
ext<E> = -612.63 ± 9.31
kcal/mol<RMSD> 10.6 ± 0.6 Ẳ
β<E> = -638.42 ± 5.84
kcal/mol<RMSD> 1.6 ± 0.4 Ẳ
α<E> = -646.18 ± 6.90
kcal/mol<RMSD> 8.9 ± 0.2 Ẳ
extlow<E> = -640.60 ± 7.13
kcal/mol<RMSD> 9.1 ± 0.3 Ẳ
βlow<E> = -651.05 ± 6.34
kcal/mol<RMSD> 6.9 ± 1.2 Ẳ
αlow<E> = -646.14 ± 6.01
kcal/mol<RMSD> 9.0 ± 0.3 Ẳ
extlow2<E> = -633.74 ± 7.13
kcal/mol<RMSD> 9.0 ± 0.7 Ẳ
βlow2<E> = -643.91 ± 7.86
kcal/mol<RMSD> 9.0 ± 0.3 Ẳ
αlow2<E> = -650.14 ± 6.33
kcal/mol<RMSD> 9.0 ± 0.2 Ẳ
β*<E> = -644.28 ± 6.08
kcal/mol<RMSD> 1.6 ± 0.2 Ẳ
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Protein G summaryProtein G summary
ββ-hairpin stable at 300 K-hairpin stable at 300 K Helical conformation lower in energyHelical conformation lower in energy
Better energy compensationBetter energy compensation33
Agreement with other simulationAgreement with other simulation44
Various factors may overstabilize Various factors may overstabilize helices (e.g., implicit solvent, salt helices (e.g., implicit solvent, salt bridges)bridges)
33 Muñoz, V.; Thompson, P. A.; Hofrichter, J.; Eaton, W. A. Muñoz, V.; Thompson, P. A.; Hofrichter, J.; Eaton, W. A. NatureNature, , 19971997, 390, 196-199., 390, 196-199.44 Krivov, S. V.; Karplus, M. P. Natl. Acad. Sci., USA, Krivov, S. V.; Karplus, M. P. Natl. Acad. Sci., USA, 20042004, , 101, 14766-14770.101, 14766-14770.
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ConclusionsConclusions
DIVE and DIP locate several PE minimaDIVE and DIP locate several PE minima PES mapped by DIVEPES mapped by DIVE PES of conformations at desired PES of conformations at desired
temperature with DIPtemperature with DIP Conformations in good, if not excellent, Conformations in good, if not excellent,
agreement with experimental agreement with experimental structures using DIP and DIVEstructures using DIP and DIVE
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Future directionsFuture directions
Continue validation of MD protocols with Continue validation of MD protocols with larger larger ββ-sheet-sheet
Further test MD protocols with tertiary Further test MD protocols with tertiary structurestructure
Predict structure of small proteinPredict structure of small protein
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AcknowledgementsAcknowledgements
Ralph A. WheelerRalph A. Wheeler Zunnan Huang and Adam HixsonZunnan Huang and Adam Hixson National Research Service Award 5 F31 National Research Service Award 5 F31
GM067560-03 to THC from the GM067560-03 to THC from the NIH/NIGMSNIH/NIGMS
Oklahoma Center for the Advancement of Oklahoma Center for the Advancement of Science and Technology (OCAST) HR01-Science and Technology (OCAST) HR01-148148
Oklahoma Supercomputing Center for Oklahoma Supercomputing Center for Education and Research (OSCER)Education and Research (OSCER)
NSF/NRAC supercomputer time MCA96-NSF/NRAC supercomputer time MCA96-N019N019