Why are MD simulated protein folding times wrong?


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.

Publication DOI: https://doi.org/10.1007/978-1-4419-5913-3_36
Divisions: College of Engineering & Physical Sciences > Systems analytics research institute (SARI)
Additional Information: The original publication is available at www.springerlink.com
Uncontrolled Keywords: molecular dynamics,MSM,protein folding,simulation models,VPAL,Biochemistry, Genetics and Molecular Biology(all),Medicine(all)
ISBN: 9781441959126
Last Modified: 02 Jan 2024 18:34
Date Deposited: 01 Nov 2010 13:18
Full Text Link: http://www.spri ... 8-1-4419-5912-6
Related URLs: http://www.scop ... tnerID=8YFLogxK (Scopus URL)
PURE Output Type: Chapter
Published Date: 2010-10-06
Authors: Nerukh, Dmitry (ORCID Profile 0000-0001-9005-9919)


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