Mechanisms of Protein-Ligand association and its modulation by protein mutations

Abstract

Protein-ligand interactions are essential for nearly all biological processes, and yet the biophysical mechanism that enables potential binding partners to associate before specic binding occurs remains poorly understood. Fundamental questions include which factors inuence the formation of protein-ligand encounter complexes, and whether designated association pathways exist. In this article we introduce a computational approach to systematically analyze the complete ensemble of association pathways and to thus investigate these questions. This approach is employed here to study the binding of a phosphate ion to the Escherichia coli Phosphate Binding Protein. Various mutants of the protein are considered and their eects on binding free energy proles, association rates and association pathway distributions are quantied. The results reveal the existence of two anion attractors, i.e. regions that initially attract negatively charged particles and allow them to be eciently screened for phosphate which is specically bound subsequently. Point mutations that aect the charge on these attractors modulate their attraction strength and speed up association to a factor of 10 of the diusion limit and thus change the association pathways of the phosphate ligand. It is demonstrated that a phosphate that pre-binds to such an attractor neutralizes its attraction eect to the environment, making the simultaneous association of a second phosphate ion unlikely. Our study suggests ways how structural properties can be used to tune molecular association kinetics so as to optimize the eciency of binding, and highlights the importance of kinetic properties.