We describe a minimalistic model of a protein undergoing folding into its native (ground) state. This HP protein model is composed of a lattice polymer with two types of monomers: hydrophobic (H) and polar (P). The specific sequence of the two types of monomers is often chosen to mimic real proteins. We explain how these kinds of minimalistic models are well suited to study fundamental phenomena of complex biological processes such as protein folding. We then show how Monte Carlo simulations and, in particular, Wang-Landau sampling, together with a properly chosen trial move set, provide a powerful computational means to investigate the rough energy landscape and native state(s) of this intriguingly simple system. We include the computer code which can be used to reproduce the results we discuss or as a template for further research.
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April 2019
COMPUTATIONAL PHYSICS|
April 01 2019
Statistical physics meets biochemistry: Wang-Landau sampling of the HP model of protein folding
Alfred C.K. Farris;
Alfred C.K. Farris
a)
Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia
, Athens, Georgia 30602
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Thomas Wüst;
Thomas Wüst
Scientific IT Services
, ETH Zürich, 8092 Zürich, Switzerland
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David P. Landau
David P. Landau
Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia
, Athens, Georgia 30602
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a)
Electronic mail: alfred.farris@uga.edu
Am. J. Phys. 87, 310–316 (2019)
Article history
Received:
December 11 2018
Accepted:
January 04 2019
Citation
Alfred C.K. Farris, Thomas Wüst, David P. Landau; Statistical physics meets biochemistry: Wang-Landau sampling of the HP model of protein folding. Am. J. Phys. 1 April 2019; 87 (4): 310–316. https://doi.org/10.1119/1.5093292
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