Reversible folding simulation by hybrid Hamiltonian replica exchange.
Reversible foldings of a beta-hairpin peptide, chignolin, by recently invented hybrid Hamiltonian replica exchange molecular dynamics simulations based on Poisson-Boltzmann model in explicit water are demonstrated. Initiated from extended structures the peptide folded and unfolded a couple of times in seven out of eight replica trajectories during 100 nanoseconds simulation. The folded states have the lowest all-atom root mean squared deviation of 1.3 A with respect to the NMR structures. At T=300 K the occurrence of folded states was converged to 62% during 80 ns simulation which agrees well with experimental data. Especially, a detailed structural evolution map was constructed based on 800,000 structural snapshots and from where a unique folding doorway emerges. Compared with 130 ns standard replica exchange simulation using 24 replicas on the same system, the hybrid Hamiltonian replica exchange molecular dynamics simulation presents consistent results.
Xu
Weixin
W
School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
Lai
Tingfeng
T
Yang
Ye
Y
Mu
Yuguang
Y
D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D009154:Mutation; D009842:Oligopeptides / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D020673:Protein Renaturation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors
D009842:Oligopeptides; D011506:Proteins; C506175:chignolin