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Protein Science (2004), 13:358-369. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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Solvent–amino acid interaction energies in three-dimensional-lattice Monte Carlo simulations of a model 27-mer protein: Folding thermodynamics and kinetics

Kai Leonhard1, John M. Prausnitz1,2 and Clayton J. Radke1,3

1 Department of Chemical Engineering, University of California, Berkeley, California 94720-1462, USA
2 Chemical Sciences Division and
3 Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA

(RECEIVED May 9, 2003; FINAL REVISION September 24, 2003; ACCEPTED October 1, 2003)



Abstract

Amino acid residue–solvent interactions are required for lattice Monte Carlo simulations of model proteins in water. In this study, we propose an interaction-energy scale that is based on the interaction scale by Miyazawa and Jernigan. It permits systematic variation of the amino acid–solvent interactions by introducing a contrast parameter for the hydrophobicity, Cs, and a mean attraction parameter for the amino acids, {omega}. Changes in the interaction energies strongly affect many protein properties. We present an optimized energy parameter set for best representing realistic behavior typical for many proteins (fast folding and high cooperativity for single chains). Our optimal parameters feature a much weaker hydrophobicity contrast and mean attraction than does the original interaction scale. The proposed interaction scale is designed for calculating the behavior of proteins in bulk and at interfaces as a function of solvent characteristics, as well as protein size and sequence.

Keywords: Lattice simulation; interaction energies; protein folding; aggregation; solvation

Reprint requests to: Clayton J. Radke, Department of Chemical Engineering, University of California, Berkeley, CA 94720-1462, USA; e-mail: radke{at}cchem.berkeley.edu; fax: (510) 642-4778.

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.03198204.


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