Abstract

Understanding protein sequence-structure relationship is a key to solving many problems of molecular biology, such as annotation of genome sequences, protein structure prediction, protein-protein interaction, and protein evolution, among others. These problems are convenient to consider on the level of super-secondary structures, which define arrangement of strands and helices in 3D structures. In this presentation, first, the strict rule which describe how structure elements – beta-strands come together into super-secondary structures of sandwich-like proteins will be presented. Then the main sequence regularities (a specific set of residues at particular positions), which dictate the folding of amino acid sequence will be described. Residues at certain positions constitute the characteristic residue pattern of specific super-secondary structures. The pattern can be viewed as an amino acid ‘tag’ that brands a sequence as having a particular super-secondary structure.

References

Alexander Kister and Israel Gelfand, (2009) PNAS , 106, 18996-19000 Alexander Kister (2012) in “Protein super-secondary structures” Ed. A. Kister in “Methods in Molecular Biology’ series Humana Press (in press)