Small-world communication of residues and significance for protein dynamics

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Atılgan, Ali Rana and Akan, Pelin and Baysal, Canan (2004) Small-world communication of residues and significance for protein dynamics. Biophysical Journal, 86 (Issue:). pp. 85-91. ISSN 0006-3495 (Print) 1542-0086 (Online)

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Abstract

It is not merely the position of residues that is critically important for a protein’s function and stability, but also their interactions. We illustrate, by using a network construction on a set of 595 nonhomologous proteins, that regular packing is preserved in short-range interactions, but short average path lengths are achieved through some long-range contacts. Thus, lying between the two extremes of regularity and randomness, residues in folded proteins are distributed according to a ‘‘smallworld’’ topology. Using this topology, we show that the core residues have the same local packing arrangements irrespective of protein size. Furthermore, we find that the average shortest path lengths are highly correlated with residue fluctuations, providing a link between the spatial arrangement of the residues and protein dynamics.
Item Type: Article
Additional Information: WoS - Open Access (Bronze, Green Published) / Scopus - Open Access
Subjects: Q Science > QD Chemistry
Divisions: Faculty of Engineering and Natural Sciences > Academic programs > Materials Science & Eng.
Faculty of Engineering and Natural Sciences
Depositing User: Canan Atılgan
Date Deposited: 16 Feb 2007 02:00
Last Modified: 26 Apr 2022 08:05
URI: https://research.sabanciuniv.edu/id/eprint/312

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