Pramana

, 71:369 | Cite as

Analysis of protein folds using protein contact networks

Article

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.

Keywords

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

PACS Nos

89.75.-k 87.14.Ee 05.65.+b 

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Copyright information

© Indian Academy of Sciences 2008

Authors and Affiliations

  1. 1.Mathematical Modelling and Computational Biology GroupCentre for Cellular and Molecular Biology (CSIR)HyderabadIndia

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