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Issue 2, 2010
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Random network behaviour of protein structures

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Abstract

Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus imperative that, apart from the protein backbone, other tunable degrees of freedom be accountable. Here, we focus on side-chain interactions, which non-covalently link amino acids in folded proteins to form a network structure. At a coarse-grained level, we show that the network conforms remarkably well to realizations of random graphs and displays associated percolation behavior. Thus, within the rigid framework of the protein backbone that restricts the structure space, the side-chain interactions exhibit an element of randomness, which account for the functional flexibility and diversity shown by proteins. However, at a finer level, the network exhibits deviations from these random graphs which, as we demonstrate for a few specific examples, reflect the intrinsic uniqueness in the structure and stability, and perhaps specificity in the functioning of biological proteins.

Graphical abstract: Random network behaviour of protein structures

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Publication details

The article was received on 12 Feb 2009, accepted on 25 Sep 2009 and first published on 16 Nov 2009


Article type: Paper
DOI: 10.1039/B903019K
Mol. BioSyst., 2010,6, 391-398

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    Random network behaviour of protein structures

    K. V. Brinda, S. Vishveshwara and S. Vishveshwara, Mol. BioSyst., 2010, 6, 391
    DOI: 10.1039/B903019K

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