A patch–antipatch representation of specific protein interactions

Abstract

Protein interactions in solution are manifested in macroscopically measurable thermodynamic properties such as the osmotic second virial coefficient. These interactions are typically characterized by a sensitivity to electrostatic parameters such as pH and ionic strength, and by strong short-range attraction with a pronounced orientational dependence. We describe here a model that embodies all these features, yet is sufficiently compact to allow its use in simulations of dynamic and equilibrium properties. The model treats protein molecules as spheres with relatively weak isotropic contributions to intermolecular interactions. In addition, a discrete number of “patch–antipatch” pairs on the surfaces account for highly specific interactions that can arise from geometric complementarity of corresponding areas on the actual molecular surface. Implementation of the model is illustrated for interactions in solution of bovine chymotrypsinogen, based on structural information from crystallographic data. The general trends seen in virial coefficient measurements are captured by the model, despite anomalous features that are thought to result from the importance of the specific interactions.