Proteins: the hard sphere, structure and energetics

Abstract

The Ramachandran map was derived by treating atoms as hard spheres and restricting allowed conformations so as to avoid steric overlap between non-bonded atoms. The high packing density characteristic of most solids and reflected in individual protein molecules can be anticipated in terms of hard sphere atoms. The constraints of high packing density and avoidance of steric overlap have been used to develop algorithms which attempt to predict sets of sequences consistent with a given protein main-chain architecture. However hard sphere models cannot predict the energetics of specific interactions within the protein-aqueous solvent system. Accurate and detailed measurements of such interactions coupled with high resolution structural information are essential in understanding the relationship between protein sequence and structure. We describe some recent results of such studies in the ribonuclease-S system.