The effect of backbone on the small-world properties of protein contact maps

Physical Biology
L BartoliR Casadio

Abstract

In the last years, small-world behavior has been extensively described for proteins, when they are represented by the undirected graph defined by the inter-residue protein contacts. By adopting this representation it was possible to compute the average clustering coefficient (C) and characteristic path length (L) of protein structures, and their values were found to be similar to those of graphs characterized by small-world topology. In this comment, we analyze a large set of non-redundant protein structures (1753) and show that by randomly mimicking the protein collapse, the covalent structure of the protein chain significantly contributes to the small-world behavior of the inter-residue contact graphs. When protein graphs are generated, imposing constraints similar to those induced by the backbone connectivity, their characteristic path lengths and clustering coefficients are indistinguishable from those computed using the real contact maps showing that L and C values cannot be used for 'protein fingerprinting'. Moreover we verified that these results are independent of the selected protein representations, residue composition and protein secondary structures.

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Citations

Jun 27, 2009·PloS One·Tijana MilenkovićNatasa Przulj
Sep 22, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Pietro Di LenaRita Casadio
Oct 17, 2015·Journal of Biomolecular Structure & Dynamics·Lorenzo LiviAlireza Sadeghian
Dec 3, 2013·Journal of Chemical Information and Modeling·Setareh TasdighianAlessandro Giuliani
Jul 29, 2016·Scientific Reports·Giulia MenichettiDaniel Remondini
Dec 6, 2018·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Rabie SaidiEngelbert Mephu Nguifo
Dec 16, 2009·Journal of Physics. Condensed Matter : an Institute of Physics Journal·H E StanleyL Xu
Mar 15, 2011·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Sheeba Jem Irudayam, Richard H Henchman
Jul 9, 2010·Bioinformatics·Pietro Di LenaRita Casadio
Jan 21, 2016·The FEBS Journal·Valquiria P SouzaSandro R Marana
Sep 29, 2011·Theory in Biosciences = Theorie in Den Biowissenschaften·Susan Khor
Dec 19, 2020·Current Opinion in Structural Biology·Pourya HoseiniAmarda Shehu
Nov 29, 2012·Chemical Reviews·L Di PaolaA Giuliani

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