Linking structural features of protein complexes and biological function

Gopichandran Sowmya, Edmond J. Breen, Shoba Ranganathan

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions.

LanguageEnglish
Pages1486-1494
Number of pages9
JournalProtein Science
Volume24
Issue number9
DOIs
Publication statusPublished - 1 Sep 2015

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Proteins
Solvation
Nonparametric Statistics
Genomics
Binding energy
Catalysis
Free energy
Hydrogen
Immunity
Hydrogen bonds
Salts
Databases

Cite this

Sowmya, Gopichandran ; Breen, Edmond J. ; Ranganathan, Shoba. / Linking structural features of protein complexes and biological function. In: Protein Science. 2015 ; Vol. 24, No. 9. pp. 1486-1494.
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Linking structural features of protein complexes and biological function. / Sowmya, Gopichandran; Breen, Edmond J.; Ranganathan, Shoba.

In: Protein Science, Vol. 24, No. 9, 01.09.2015, p. 1486-1494.

Research output: Contribution to journalArticleResearchpeer-review

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