Cataloging topologies of protein folding patterns

Abstract

Comparing and classifying protein folding patterns allows organizing the known structures, structure search and retrieval, and investigation of general principles of protein architecture. We have been developing a concise tableau representation of protein folding patterns, based on the order and contact patterns of elements of secondary structure: helices and strands of sheet (Lesk, 1995; Kamat and Lesk, 2007; Konagurthu et al., 2008). The tableaux provide a database, derived from the world-wide protein data bank, mineable in studies of protein architecture, including: (i) determination of statistical properties of secondary structure contacts in an unbiased set of protein domains, (ii) investigations of the range of, and relationships among, protein topologies, (iii) investigation of the relationship between local structure of proteins and the complete folding topology, (iv) potential for fold identification from amino acid sequence, and (v) the basis for a complete enumeration of possible protein folding patterns, which can be compared with the corpus of known structures.