IMR Press / FBL / Volume 14 / Issue 8 / DOI: 10.2741/3415

Frontiers in Bioscience-Landmark (FBL) is published by IMR Press from Volume 26 Issue 5 (2021). Previous articles were published by another publisher on a subscription basis, and they are hosted by IMR Press on imrpress.com as a courtesy and upon agreement with Frontiers in Bioscience.

Open Access Article
Two-state protein folding kinetics through all-atom molecular dynamics based sampling
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1 van't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands

Academic Editor: Dirk Zahn

Front. Biosci. (Landmark Ed) 2009, 14(8), 2801–2828; https://doi.org/10.2741/3415
Published: 1 January 2009
(This article belongs to the Special Issue Atomistic simulations in biosciences: models and methods)
Abstract

This review focuses on advanced computational techniques that employ all atom molecular dynamics to study the folding of small two state proteins. As protein folding is a rare event process, special sampling techniques are required to overcome high folding free energy barriers. Several biased sampling methods enable computation of the free energy landscape. Trajectory based sampling methods can assess the kinetics and the dynamical folding mechanisms. Proper sampling is only the first step, and further analysis is required to obtain the folding mechanisms reaction coordinate. Only a combination of several simulation techniques can solve the sampling problems connected with all-atom protein folding, and allow computation of experimental observables that can validate the force fields and simulation techniques. Several of the involved issues are illustrated with folding of small protein (fragments) such as beta hairpins and the Trp-cage mini protein.

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