Temperature weighted histogram analysis method, replica exchange, and transition paths.
We analyzed the data from a replica exchange molecular dynamics simulation using the weighted histogram analysis method to combine data from all of the temperature replicas (T-WHAM) to obtain the room-temperature potential of mean force of the G-peptide (the C-terminal beta-hairpin of the B1 domain of protein G) in regions of conformational space not sampled at room temperature. We were able to determine the potential of mean force in the transition region between a minor alpha-helical population and the major beta-hairpin population and identify a possible transition path between them along which the peptide retains a significant amount of secondary structure. This observation provides new insights into a possible mechanism of formation of beta-sheet secondary structures in proteins. We developed a novel Bayesian statistical uncertainty estimation method for any quantity derived from WHAM and used it to validate the calculated potential of mean force. The feasibility of estimating regions of the potential of mean force with unfavorable free energy at room temperature by T-WHAM analysis of replica exchange simulations was further tested on a system that can be solved analytically and presented some of the same challenges found in more complex chemical systems.
Gallicchio
Emilio
E
Department of Chemistry and Chemical Biology, and BioMaPS Institute of Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854, USA.
Andrec
Michael
M
Felts
Anthony K
AK
Levy
Ronald M
RM
D000465:Algorithms; D020816:Amino Acid Motifs; D001499:Bayes Theorem; D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D016013:Likelihood Functions; D008968:Molecular Conformation; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
D010455:Peptides; D011506:Proteins