Prediction of the structural motifs of sandwich proteins.

Abstract

We investigate the supersecondary structure of a large group of proteins, the so-called sandwich proteins. The analysis of a large number of such proteins has led us to propose a set of rules that can be used to predict the possible arrangements of strands in the two beta-sheets forming a given sandwich structure. These rules imply the existence of certain invariant supersecondary substructures common to all sandwich proteins. Furthermore, they dramatically restrict the number of permissible arrangements. For example, whereas for proteins consisting of three strands in each beta-sheet 180 possible strand arrangements exist a priori, our rules imply that only 15 of them are permissible. Five of these predicted arrangements describe all currently known sandwich proteins with six strands.