An independent method for the analysis of protein folding kinetics from all-atom molecular dynamics simulations.
We propose a method for extracting useful kinetic information from all-atom molecular dynamics simulations of protein folding. By calculating the time correlation functions between the evolution of different structural properties during the course of the simulation we can determine the endpoint of the reaction and the mechanism by which it occurs. As a test of our method we use thermal denaturation simulations on a 76 residue protein, ubiquitin. The method we present should be used in combination with current techniques for analyzing molecular dynamics trajectories.
Marianayagam
Neelan J
NJ
Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK. neelanm@yahoo.com
Brown
Andrew G
AG
Jackson
Sophie E
SE
D003198:Computer Simulation; D006358:Hot Temperature; D007700:Kinetics; D008958:Models, Molecular; D008968:Molecular Conformation; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D012984:Software; D013696:Temperature; D013997:Time Factors