Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs

BMC Bioinformatics

Research Article

Dhananjay Bhattacharyya¹  Rahul Banerjee²  Sankar Basu² 

[1] Biophysics Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, 700 064, Kolkata, India;Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, 700 064, Kolkata, India;

关键词: Random Graph;    Large Graph;    Contact Network;    Side Chain Atom;    Diagonal Edge;   

DOI  :  10.1186/1471-2105-12-195

 received in 2010-10-20, accepted in 2011-05-24,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundMapping protein primary sequences to their three dimensional folds referred to as the 'second genetic code' remains an unsolved scientific problem. A crucial part of the problem concerns the geometrical specificity in side chain association leading to densely packed protein cores, a hallmark of correctly folded native structures. Thus, any model of packing within proteins should constitute an indispensable component of protein folding and design.ResultsIn this study an attempt has been made to find, characterize and classify recurring patterns in the packing of side chain atoms within a protein which sustains its native fold. The interaction of side chain atoms within the protein core has been represented as a contact network based on the surface complementarity and overlap between associating side chain surfaces. Some network topologies definitely appear to be preferred and they have been termed 'packing motifs', analogous to super secondary structures in proteins. Study of the distribution of these motifs reveals the ubiquitous presence of typical smaller graphs, which appear to get linked or coalesce to give larger graphs, reminiscent of the nucleation-condensation model in protein folding. One such frequently occurring motif, also envisaged as the unit of clustering, the three residue clique was invariably found in regions of dense packing. Finally, topological measures based on surface contact networks appeared to be effective in discriminating sequences native to a specific fold amongst a set of decoys.ConclusionsOut of innumerable topological possibilities, only a finite number of specific packing motifs are actually realized in proteins. This small number of motifs could serve as a basis set in the construction of larger networks. Of these, the triplet clique exhibits distinct preference both in terms of composition and geometry.

【 授权许可】

Unknown   
© Basu et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.