Universal Architectural Concepts Underlying Protein Folding Patterns

Abstract

What is the architectural "basis set" of the observed universe of protein structures? Using information-theoretic inference, we answer this question with a dictionary of 1,493 substructures-called concepts-typically at a subdomain level, based on an unbiased subset of known protein structures. Each concept represents a topologically conserved assembly of helices and strands that make contact. Any protein structure can be dissected into instances of concepts from this dictionary. We dissected the Protein Data Bank and completely inventoried all the concept instances. This yields many insights, including correlations between concepts and catalytic activities or binding sites, useful for ration..