Skip Navigation


Bioinformatics Advance Access originally published online on May 22, 2007
Bioinformatics 2007 23(14):1760-1767; doi:10.1093/bioinformatics/btm257
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Supplementary data
Right arrow All Versions of this Article:
23/14/1760    most recent
btm257v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (2)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Bagler, G.
Right arrow Articles by Sinha, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bagler, G.
Right arrow Articles by Sinha, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Assortative mixing in Protein Contact Networks and protein folding kinetics

Ganesh Bagler and Somdatta Sinha *

Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.

*To whom correspondence should be addressed.


  Abstract

Motivation: Starting from linear chains of amino acids, the spontaneous folding of proteins into their elaborate 3D structures is one of the remarkable examples of biological self-organization. We investigated native state structures of 30 single-domain, two-state proteins, from complex networks perspective, to understand the role of topological parameters in proteins’ folding kinetics, at two length scales—as ‘Protein Contact Networks (PCNs)’ and their corresponding ‘Long-range Interaction Networks (LINs)’ constructed by ignoring the short-range interactions.

Results: Our results show that, both PCNs and LINs exhibit the exceptional topological property of ‘assortative mixing’ that is absent in all other biological and technological networks studied so far. We show that the degree distribution of these contact networks is partly responsible for the observed assortativity. The coefficient of assortativity also shows a positive correlation with the rate of protein folding at both short- and long-contact scale, whereas, the clustering coefficients of only the LINs exhibit a negative correlation. The results indicate that the general topological parameters of these naturally evolved protein networks can effectively represent the structural and functional properties required for fast information transfer among the residues facilitating biochemical/kinetic functions, such as, allostery, stability and the rate of folding.

Contact: sinha{at}ccmb.res.in

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alfonso Valencia

Received on February 5, 2007; revised on May 8, 2007; accepted on May 8, 2007

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.