Coarse-Grained Strategy for Modeling Protein Stability in Concentrated Solutions III: Directional Protein Interactions

Published

June 1, 2007

Author(s)

Jason K. Cheung, Vincent K. Shen, Jeffrey R. Errington, Thomas M. Truskett

Abstract

We introduce an extension to the coarse-grained modeling strategy described in parts I and II of this investigation to account for the possibility of non-uniform spatial distributions of hydrophobic residues on the solvent-exposed surfaces of native proteins in solution. We then explore, within the framework of this modeling strategy, how patchy protein surfaces can modify the intrinsic (i.e., infinite dilution) thermodynamic stability of the native state, the solvent-mediated protein-protein interactions, and the self-assembly/aggregation behaviors of proteins in solution. We do so by contrasting the simulated behaviors of three model proteins that share the same overall sequence hydrophobicity, but exhibit folded configurations with different solvent-exposed hydrophobic residue distributions. Finally, we discuss how the simulation results relate to the experimental solution behaviors of several native proteins with strongly directional interactions.

Citation

Biophysical Journal

Volume

92

Issue

12

Pub Type

Journals

Keywords

coarse-grained model, heteropolymer collapse, hydrophobic interactions, protein-protein interactions, self-assembly

Citation

Cheung, J. , Shen, V. , Errington, J. and Truskett, T. (2007), Coarse-Grained Strategy for Modeling Protein Stability in Concentrated Solutions III: Directional Protein Interactions, Biophysical Journal (Accessed October 7, 2025)