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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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Article information


Submitted
12 Feb 2009
Accepted
25 Sep 2009
First published
16 Nov 2009

Mol. BioSyst., 2010,6, 391-398
Article type
Paper

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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