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      Permanent link:
      http://www.ias.ac.in/article/fulltext/pram/071/02/0369-0378

    • Keywords

       

      Protein structure; network; contact map; fold recognition; EF-hand; ubiquitin-like.

    • Abstract

       

      Proteins are important biomolecules, which perform diverse structural and functional roles in living systems. Starting from a linear chain of amino acids, proteins fold to different secondary structures, which then fold through short- and long-range interactions to give rise to the final three-dimensional shapes useful to carry out the biophysical and biochemical functions. Proteins are defined as having a common `fold' if they have major secondary structural elements with same topological connections. It is known that folding mechanisms are largely determined by a protein's topology rather than its interatomic interactions. The native state protein structures can, thus, be modelled, using a graph-theoretical approach, as coarse-grained networks of amino acid residues as `nodes' and the inter-residue interactions/contacts as `links'. Using the network representation of protein structures and their 2D contact maps, we have identified the conserved contact patterns (groups of contacts) representing two typical folds – the EF-hand and the ubiquitin-like folds. Our results suggest that this direct and computationally simple methodology can be used to infer about the presence of specific folds from the protein's contact map alone.

    • Author Affiliations

       

      Pankaj Barah1 Somdatta Sinha1

      1. Mathematical Modelling and Computational Biology Group, Centre for Cellular and Molecular Biology (CSIR), Uppal Road, Hyderabad 500 007, India
  • Pramana – Journal of Physics | News

    • Proceedings of the International Workshop/Conference on Computational Condensed Matter Physics and Materials Science
      (IWCCMP-2015)

      Posted on November 27, 2015

      Guest Editors: Anurag Srivastava, C. S. Praveen,
      H. S. Tewari

© 2017 Indian Academy of Sciences, Bengaluru.