PMID: 9539729May 16, 1998Paper

Brownian dynamics simulations of protein folding: access to milliseconds time scale and beyond

Proceedings of the National Academy of Sciences of the United States of America
A RojnuckarinS Subramaniam

Abstract

Protein folding occurs on a time scale ranging from milliseconds to minutes for a majority of proteins. Computer simulation of protein folding, from a random configuration to the native structure, is nontrivial owing to the large disparity between the simulation and folding time scales. As an effort to overcome this limitation, simple models with idealized protein subdomains, e.g., the diffusion-collision model of Karplus and Weaver, have gained some popularity. We present here new results for the folding of a four-helix bundle within the framework of the diffusion-collision model. Even with such simplifying assumptions, a direct application of standard Brownian dynamics methods would consume 10,000 processor-years on current supercomputers. We circumvent this difficulty by invoking a special Brownian dynamics simulation. The method features the calculation of the mean passage time of an event from the flux overpopulation method and the sampling of events that lead to productive collisions even if their probability is extremely small (because of large free-energy barriers that separate them from the higher probability events). Using these developments, we demonstrate that a coarse-grained model of the four-helix bundle can be s...Continue Reading

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Citations

Jan 9, 2010·BMC Bioinformatics·Shubhra Ghosh DastidarChandra S Verma
Dec 2, 2008·Biological & Pharmaceutical Bulletin·Akifumi OdaOhgi Takahashi
Feb 27, 2010·PloS One·Venkataramanan SoundararajanRam Sasisekharan
Feb 8, 2013·The Journal of Chemical Physics·Joshua L Adelman, Michael Grabe
Nov 7, 2007·Proceedings of the National Academy of Sciences of the United States of America·Bin W ZhangDaniel M Zuckerman
Sep 5, 2002·Proteins·Cornelius G Hunter, Shankar Subramaniam
Sep 21, 2010·Biochimica Et Biophysica Acta·Konstantin KleninWolfgang Wenzel
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Oct 12, 2010·Current Opinion in Pharmacology·Matthew C Zwier, Lillian T Chong
Apr 29, 2016·PLoS Computational Biology·Tatiana MaximovaAmarda Shehu
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Dec 2, 1998·Nature·H Wang, G Oster
Aug 19, 2009·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Fernando A EscobedoJuan C Araque
Jul 17, 2020·The Journal of Chemical Physics·Daniel J Sharpe, David J Wales
Jan 31, 2019·Journal of Computational Chemistry·Laura J S Lopes, Tony Lelièvre
Nov 5, 2019·The Journal of Chemical Physics·Yuguang Yang, Bo Li
Mar 20, 2021·Biophysical Journal·Sagar KaniaEdmund Webb
Aug 19, 2007·The Journal of Physical Chemistry. B·David CurcóCarlos Aleman
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Jun 11, 2011·Journal of Chemical Theory and Computation·Divesh Bhatt, Daniel M Zuckerman
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Nov 18, 2015·Journal of Chemical Theory and Computation·Igor Omelyan, Andriy Kovalenko
Jan 10, 2012·Journal of Chemical Theory and Computation·Igor P Omelyan, Andriy Kovalenko
Jan 1, 2020·Multiscale Modeling & Simulation : a SIAM Interdisciplinary Journal·David Aristoff, Daniel M Zuckerman

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