ß-ß-heptapeptidheptapeptidee

CC

C

MD: rmsd 0.14 MD: rmsd 0.14 ÅÅ

NMR structure(31 Helix)

Reversibly folds on 10 -20 ns time scale (X. Daura et al.)

• 7 residues, in methanol (less atoms): 3000 at

~ 0.2 - 1 ns / hour (GROMACS)~ 0.2 - 1 ns / hour (GROMACS)

ß-ß-heptapeptidheptapeptidee

i) -amino-acids (additional backbone carbon)ii) Stable 2nd structure.iii) Non-degradable peptide mimetics

(e.g. highly selective somatastatin analogue)

D. Seebach, B. Jaun + coworkersorganic chem ETH-Zurich

-Heptapeptide (M) 31-helix in MeOH at 298 K

(left-handed)

Daura, X., Bernhard, J., Seebach, D., van Gunsteren, W. F. and Mark, A. E. (1998)

J. Mol. Biol. 280, 925-932.

ß-ß-heptapeptidheptapeptidee

unfold fold fold unfoldunfold

-Heptapeptide, 340 K

ß-ß-heptapeptidheptapeptideeStarting structure

-Heptapeptide, 360 K

Protocol for MD:Protocol for MD:• ß-heptatpetide 7 residues in 986 methanol molecules (~3000 atoms)

• GROMOS96 force field (van Gunsteren and co-workers)

• GROMACS software (www.gromacs.org)

• twin-range cutoff (1.0/1.4nm) for vdW and Elec.

• Reaction Field for long-range Elec.

• NP1atmT and NV300KT ensembles.

• Temp= 275.3, 286.4, 297.8, 322.1, 348.6, 399.6K

• Berendsen Thermostat, τT=0.1ps and τP=1.0ps

• run on 8 processors for 1ns/hour.

ß-heptapeptide: Conventional ß-heptapeptide: Conventional MDMD

Time (ns)

Folded = rmsd from NMR Model < 0.7 Folded = rmsd from NMR Model < 0.7 ÅÅ

ß-heptapeptide: Conventional ß-heptapeptide: Conventional MDMD

Folded = rmsd from NMR Model < 0.7 Folded = rmsd from NMR Model < 0.7 ÅÅ

ß-heptapeptide: Conventional ß-heptapeptide: Conventional MDMD

ß-heptapeptide: Replica ß-heptapeptide: Replica ExchangeExchange

Replica ExchangeReplica Exchange

Methodology

Protocol for the REMD:Protocol for the REMD:

• 20 structures selected as initial structures for the REMD 20 structures selected as initial structures for the REMD (more than 1ns spaced and rmsd from NMR > 0.3 nm)(more than 1ns spaced and rmsd from NMR > 0.3 nm)

• 200 ps of equilibration of each replica at its initial temperature200 ps of equilibration of each replica at its initial temperature

• T= T= 275.3, 280.8, 286.8, 292.0, 297.8, 303.7, 309.7, 315.8, 322.1, 328.1, 335.0, 275.3, 280.8, 286.8, 292.0, 297.8, 303.7, 309.7, 315.8, 322.1, 328.1, 335.0, 341.6, 348.4, 355.4, 362.3, 369.5, 376.8, 384.2, 391.8, 399.6341.6, 348.4, 355.4, 362.3, 369.5, 376.8, 384.2, 391.8, 399.6

• V = Cste = V (NPT at 300K)V = Cste = V (NPT at 300K)

• exchange trials every 0.1, 0.5, 2.0 and 5.0 psexchange trials every 0.1, 0.5, 2.0 and 5.0 ps

• 50 ns at 400 K to unfold it and generate random structures50 ns at 400 K to unfold it and generate random structures

• ß-heptatpetide 7 residues in 986 methanol molecules (3000 atoms)ß-heptatpetide 7 residues in 986 methanol molecules (3000 atoms)

• T controled by a Berendsen bath, τT controled by a Berendsen bath, τTT=0.1ps.=0.1ps.

ß-heptapeptide: Replica ß-heptapeptide: Replica ExchangeExchange

RMSD from the NMR model (CRMSD from the NMR model (C res. 2-6) res. 2-6)

Exchange trial every 2.0 psExchange trial every 2.0 ps

ß-heptapeptide: Replica ß-heptapeptide: Replica ExchangeExchange

RMSD from the NMR model (CRMSD from the NMR model (C res. 2-6) res. 2-6)

0.5ps0.5ps 2.0ps2.0ps 5.0ps5.0ps

Time of Equilibration Increasing Time of Equilibration Increasing with Time Interval Between Exchange Trialwith Time Interval Between Exchange Trial

Ratio of Folded Peptide at each temperature Ratio of Folded Peptide at each temperature Criterion: folded = rmsd Criterion: folded = rmsd 0.7 0.7ÅÅ

ß-heptapeptide: Replica ß-heptapeptide: Replica ExchangeExchange

Folded Peptide ratios as a function of the interval between exchanges Folded Peptide ratios as a function of the interval between exchanges

ß-heptapeptide: Replica ß-heptapeptide: Replica ExchangeExchange

The replicas explore temperatures at different rates.The replicas explore temperatures at different rates.

Temperature Exploration Temperature Exploration

0.5ps0.5ps

2.0ps2.0ps

5.0ps5.0ps

ß-heptapeptide: Replica ß-heptapeptide: Replica ExchangeExchange

Simulations convergedSimulations converged

Folded Peptide ratios as function of the interval between exchanges Folded Peptide ratios as function of the interval between exchanges

ß-heptapeptide: Replica ß-heptapeptide: Replica ExchangeExchange

Folded Peptide ratios: REMD vs. Standard MD Folded Peptide ratios: REMD vs. Standard MD

ß-heptapeptide: Replica ß-heptapeptide: Replica ExchangeExchange

PfPufPf

TkG B −=−=Δ

1log

Folding free energy: REMD vs. Brute Force MD Folding free energy: REMD vs. Brute Force MD

ß-heptapeptide: Replica ß-heptapeptide: Replica ExchangeExchange

72 9 3 2 40 13 9 2 55 9 4 4 28 14 7 3 23 8 5 3

1 2 3 41 2 3 4 1 2 3 41 2 3 4 1 2 3 41 2 3 4 1 2 3 41 2 3 4 1 2 3 41 2 3 4 1 2 3 41 2 3 4

50 15 9 3

60 10 3 2 70 6 3 2 31 12 7 3 26 10 8 5 8 7 4 448 17 8 3

69 13 7 2 61 11 8 2 43 10 7 3 29 8 7 4 13 5 5 565 12 7 2

NPT

NVT

REMD

275275 286286 298298 322322 348348 399399

Cluster #

T (K)

Conformational exploration: REMD vs. Brute Force MD Conformational exploration: REMD vs. Brute Force MD

72 9 3 2 40 13 9 2 55 9 4 4 28 14 7 3 23 8 5 350 15 9 3

60 10 3 2 70 6 3 2 31 12 7 3 26 10 8 5 8 7 4 448 17 8 3

69 13 7 2 61 11 8 2 43 10 7 3 29 8 7 4 13 5 5 565 12 7 2

Cluster Analysis: use of the 4 more populated clusters (% of the total ensemble)Cluster Analysis: use of the 4 more populated clusters (% of the total ensemble)

REMD simulations reproduce conformational ensemblesREMD simulations reproduce conformational ensembles

ß-heptapeptide: Replica ß-heptapeptide: Replica ExchangeExchange

REMD simulation: REMD simulation: 1) accurately reproduces 1) accurately reproduces

- thermodynamics - thermodynamics (folding free energy)(folding free energy)- conformational - conformational (clusters)(clusters)

MD data for foldingMD data for folding

2) faster than MD2) faster than MDsimulation timesimulation time REMD: 20*15nsREMD: 20*15ns = = 300ns300ns

BFMD: 2*200+400+3*800BFMD: 2*200+400+3*800 == 3200ns3200ns

one Tempone Temp REMD: 20*15ns REMD: 20*15ns = 300ns = 300nsBFMD: 1*800ns BFMD: 1*800ns = 800ns = 800ns

real timereal time REMD: 15ns / 1 CPU = 7.5 daysREMD: 15ns / 1 CPU = 7.5 daysBFMD: 800ns / 8 CPUs BFMD: 800ns / 8 CPUs = = 34 days34 days

Efficiency: REMD vs. Brute Force MD Efficiency: REMD vs. Brute Force MD

ß-heptapeptide: Replica ß-heptapeptide: Replica ExchangeExchange