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Physics-Based Modeling of Side Chain—Side Chain Interactions in the UNRES Force Field

  • Mariusz Makowski
Chapter
Part of the Springer Series on Bio- and Neurosystems book series (SSBN, volume 8)

Abstract

Work on a development of a new model of side-chain—side-chain interactions for side-chains of amino acids, to be used in the UNRES force-field and in other large-scale simulations, has been described in this chapter. In the presented model a polar/charged side chain consists of two sites of interaction, nonpolar and polar. General expressions for the effective energy of interaction between amino acids are given depending on the kind of interacting pair. Results of tests with the new UNRES force-field parameters have also been shown together with an extension of the force-field for the phosphorylated amino-acids in this chapter. The results of the studies on the influence of particle size on the free-energy profile of hydrophobic interactions, and the temperature dependence of the potential of mean force for side chain—side chain interactions are also presented.

Keywords

Amino acid side chains Model of side-chain—side-chain interactions Potential of mean force Phosphorylated amino-acids Hydrophobic interactions Temperature dependence Molecular dynamics Umbrella sampling 

Notes

Acknowledgements

This research was conducted by using the resources of (a) our 818-processor Beowulf cluster at the Baker Laboratory of Chemistry and Chemical Biology, Cornell University, (b) the National Science Foundation Terascale Computing System at the Pittsburgh Supercomputer Center, (c) 45-processor Beowulf cluster at the Faculty of Chemistry, University of Gdańsk, (d) the Informatics Center of the Metropolitan Academic Network (IC MAN) in Gdańsk. This work was supported by grants from the U.S. National Institutes of Health (GM-14312), the U.S. National Science Foundation (MCB05-41633), the Polish Ministry of Science and Education (N N204 152836), and the Polish National Science Centre (UMO-2013/10/E/ST4/00755).

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Authors and Affiliations

  1. 1.Faculty of ChemistryUniversity of GdańskGdańskPoland

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