Understanding protein structure from a percolation perspective

Dhruba Deb, Saraswathi Vishveshwara, Smitha Vishveshwara

Research output: Contribution to journalArticle

Abstract

Underlying the unique structures and diverse functions of proteins are a vast range of amino-acid sequences and a highly limited number of folds taken up by the polypeptide backbone. By investigating the role of noncovalent connections at the backbone level and at the detailed side-chain level, we show that these unique structures emerge from interplay between random and selected features. Primarily, the protein structure network formed by these connections shows simple (bond) and higher order (clique) percolation behavior distinctly reminiscent of random network models. However, the clique percolation specific to the side-chain interaction network bears signatures unique to proteins characterized by a larger degree of connectivity than in random networks. These studies reflect some salient features of the manner in which amino acid sequences select the unique structure of proteins from the pool of a limited number of available folds.

Original languageEnglish (US)
Pages (from-to)1787-1794
Number of pages8
JournalBiophysical journal
Volume97
Issue number6
DOIs
StatePublished - Sep 16 2009

ASJC Scopus subject areas

  • Biophysics

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