PROTEIN STRUCTURES AND COMPLEXES - WHAT THEY REVEAL ABOUT THE INTERACTIONS THAT STABILIZE THEM

The rapid increase in the number of high-quality protein structures pr ovides an expanding knowledge resource about interactions involved in stabilizing protein three-dimensional structures and the complexes the y form with other molecules. In this paper we first review the results of some recent analyses of protein structure, including restrictions on local conformation, and a study of the geometry of hydrogen bonds. Then we consider how such empirical data can be used as a test bed for energy calculations, by using the observed spatial distributions of s ide chain/atom interactions to assess three different methods for mode lling atomic interactions in proteins. We have also derived a new empi rical solvation potential which aims to reproduce the hydrophobic effe ct. To conclude we address the problem of molecular recognition and co nsider what we can deduce about the interactions involved in the bindi ng of peptides to proteins.