Search for the most stable folds of protein chains: II. Computation of stable architectures of β-proteins using a self-consistent molecular field theory

Abstract

In a preceding paper we presented a novel approach to computation of 3-D folds of protein chains from their amino acid sequences. This approach is a physically correct generalization of the ‘threading’ methods. It is based on a self-consistent molecular field theory and on a physical theory of protein folding patterns, which make it possible to examine all the variety of ‘potentially stable’ folding patterns and all the variety of the chain conformations within each of them and to determine the thermodynamically stable structure. In this paper, we apply this approach to single out stable folding patterns and conformations for the chains of β-sandwich proteins and show that the similarity of the calculated and observed structures is usually rather close.