Protein folding kinetics and thermodynamics from atomistic simulations

van der Spoel, DavidUppsala universitet,Beräknings- och systembiologi (författare)

Determining protein folding kinetics and thermodynamics from all-atom molecular dynamics (MD) simulations without using experimental data represents a formidable scientific challenge because simulations can easily get trapped in local minima on rough free energy landscapes. This necessitates the computation of multiple simulation trajectories, which can be independent from each other or coupled in some manner, as, for example, in the replica exchange MD method. Here we present results obtained with a new analysis tool that allows the deduction of faithful kinetics data from a heterogeneous ensemble of simulation trajectories. The method is demonstrated on the decapeptide Chignolin for which we predict folding and unfolding time constants of 1.0±0.3 and 2.6±0.4 μs, respectively. We also derive the energetics of folding, and calculate a realistic melting curve for Chignolin.

NATURVETENSKAP Biologi Bioinformatik och systembiologi hsv//swe
NATURAL SCIENCES Biological Sciences Bioinformatics and Systems Biology hsv//eng
Computer Simulation
Kinetics
Models; Chemical
Models; Molecular
Protein Folding
Proteins/*chemistry/*ultrastructure
Quantum Theory
Research Support; Non-U.S. Gov't
Thermodynamics

Seibert, M MarvinUppsala universitet,Molekylär biofysik(Swepub:uu)masei255 (författare)
Uppsala universitetBeräknings- och systembiologi (creator_code:org_t)

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