Analysis and prediction of protein β-sheet structures by a combinatorial approach

Abstract

Analysis of β-sheet sandwiches (for example immunoglobulin domains) suggests an algorithm that successfully predicts the tertiary fold of these proteins from their sequence and secondary structure. We propose tertiary structures for β2- microglobulin and an HLA-B7 antigen fragment. Topological rules are presented that markedly reduce the number of folds for proteins in which a-helices pack against a parallel β-sheet.