title: Why are MD simulated protein folding times wrong?
abstract: The question of significant deviations of protein folding times simulated using molecular dynamics from experimental values is investigated. It is shown that in the framework of Markov State Model (MSM) describing the conformational dynamics of peptides and proteins, the folding time is very sensitive to the simulation model parameters, such as forcefield and temperature. Using two peptides as examples, we show that the deviations in the folding times can reach an order of magnitude for modest variations of the molecular model. We, therefore, conclude that the folding rate values obtained in molecular dynamics simulations have to be treated with care.
authors.affiliation: Unilever Centre for Molecular Sciences Informatics, Department of Chemistry, Cambridge University, Cambridge CB2 1EW, UK. 232@cam.ac.uk
authors.forename: Dmitry
authors.initials: D
authors.lastname: Nerukhdn
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D008390:Markov Chains; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry
chemical_list: D011506:Proteins