Repository: Freie Universität Berlin, Math Department

Non-Markovian modeling of protein folding

Ayaz, Cihan and Tepper, Lucas and Brünig, Florian N. and Daldrop, Jan O. and Netz, Roland R. (2021) Non-Markovian modeling of protein folding. Proceedings of the National Academy of Sciences, 118 (31). pp. 1-7.

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We extract the folding free energy landscape and the time- dependent friction function, the two ingredients of the gener- alized Langevin equation (GLE), from explicit-water molecular dynamics (MD) simulations of the α-helix forming polypeptide alanine9 for a one-dimensional reaction coordinate based on the sum of the native H-bond distances. Folding and unfolding times from numerical integration of the GLE agree accurately with MD results, which demonstrate the robustness of our GLE-based non-Markovian model. In contrast, Markovian models do not accurately describe the peptide kinetics and in particular, cannot reproduce the folding and unfolding kinetics simultaneously, even if a spatially dependent friction profile is used. Analysis of the GLE demonstrates that memory effects in the friction significantly speed up peptide folding and unfolding kinetics, as predicted by the Grote–Hynes theory, and are the cause of anomalous diffusion in configuration space. Our methods are applicable to any reac- tion coordinate and in principle, also to experimental trajectories from single-molecule experiments. Our results demonstrate that a consistent description of protein-folding dynamics must account for memory friction effects.

Item Type:Article
Subjects:Mathematical and Computer Sciences > Mathematics > Applied Mathematics
Divisions:Department of Mathematics and Computer Science > Institute of Mathematics
ID Code:2613
Deposited By: Monika Drueck
Deposited On:24 Sep 2021 11:20
Last Modified:24 Sep 2021 11:20

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