Combining Bioinformatics and Biophysics to Understand Protein-Protein and Protein-Ligand Interactions.

Abstract

INTRODUCTION. The increasing numbers of proteins whose three-dimensional structures have been determined will have major impact on the ability to exploit genomic data. Sequence alignments will become more meaningful, protein structure prediction will become more accurate, and the prediction of protein function will become increasingly refined and precise. Such developments will require that sequence, structure, and physical chemical information be fully integrated and correlated with biological data in as much detail as possible. We have been developing a series of computational tools with the goal of detecting relationships among amino acid sequence, protein structure and protein function. In this context, recent computational advances in using structure to improve sequence alignments, in homology model building and in the calculation of binding affinities will be summarized as will their combined use, with specific application to understanding the principles of protein-protein and protein-ligand interactions. METHODS. Our basic approach involves calculating protein folding and binding free energies as well as contributions of individual amino acids to these free energies, and correlating these energetic contributions with sequence patterns and with physical and chemical properties of the protein. With regard to binding, we are particularly interested in delineating features that may dictate specificity vs. affinity and in predicting binding specificity from sequence alone. Binding free energies are described in terms of electrostatic and hydrophobic interactions. The former are calculated using finite difference Poisson-Boltzmann methods while the latter are generally calculated from free energy-surface area relationships. RESULTS AND DISCUSSIONS. Our approach to the calculation of binding free energies is validated by its ability to select the correct conformation of protein-protein complexes from a large number of alternative complex geometries. The factors that determine binding free energies will be discussed with particular emphasis on understanding how protein interfaces are designed, in a structural sense, to exploit different combinations of electrostatic and hydrophobic interactions to achieve both affinity and specificity. This information is derived in part by calculating binding free energies for different interfaces and correlating these with structural features on the interface and with sequence patterns. In addition, we have created a database of all protein-protein interfaces of known structure. This allows us to carry out statistical analysis of different interfaces which, when combined with binding free energy calculations, provides a