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

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

^* Department of Chemical Engineering, and Institute for Theoretical Chemistry, The University of Texas at Austin, Austin, Texas; Physical and Chemical Properties Division, National Institute of Standards and Technology, Gaithersburg, Maryland; and Department of Chemical and Biological Engineering, The State University of New York at Buffalo, Buffalo, New York

Correspondence: Address reprint requests to T. M. Truskett, Tel.: 512-471-6308; E-mail: truskett{at}che.utexas.edu.

We extend our coarse-grained modeling strategy described in parts I and II of this investigation to account for nonuniform spatial distributions of hydrophobic residues on the solvent-exposed surfaces of native proteins. Within this framework, we explore how patchy surfaces can influence the solvent-mediated protein-protein interactions, and the unfolding and self-assembly behaviors of proteins in solution. In particular, we compare the equilibrium unfolding and self-assembly trends for three model proteins that share the same overall sequence hydrophobicity, but exhibit folded configurations with different solvent-exposed native-state surface morphologies. Our model provides new insights into how directional interactions can affect native-state protein stability in solution. We find that strongly-directional attractions between native molecules with patchy surfaces can help stabilize the folded conformation through the formation of self-assembled clusters. In contrast, native proteins with more uniform surfaces are destabilized by protein-protein attractions involving the denatured state. Finally, we discuss how the simulation results provide insights into the experimental solution behaviors of several proteins that display directional interactions in their native states.