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Computational Prediction of Heme-Binding Residues by Exploiting Residue Interaction Network

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  • Rong Liu
  • Jianjun Hu

Abstract

Computational identification of heme-binding residues is beneficial for predicting and designing novel heme proteins. Here we proposed a novel method for heme-binding residue prediction by exploiting topological properties of these residues in the residue interaction networks derived from three-dimensional structures. Comprehensive analysis showed that key residues located in heme-binding regions are generally associated with the nodes with higher degree, closeness and betweenness, but lower clustering coefficient in the network. HemeNet, a support vector machine (SVM) based predictor, was developed to identify heme-binding residues by combining topological features with existing sequence and structural features. The results showed that incorporation of network-based features significantly improved the prediction performance. We also compared the residue interaction networks of heme proteins before and after heme binding and found that the topological features can well characterize the heme-binding sites of apo structures as well as those of holo structures, which led to reliable performance improvement as we applied HemeNet to predicting the binding residues of proteins in the heme-free state. HemeNet web server is freely accessible at http://mleg.cse.sc.edu/hemeNet/.

Suggested Citation

  • Rong Liu & Jianjun Hu, 2011. "Computational Prediction of Heme-Binding Residues by Exploiting Residue Interaction Network," PLOS ONE, Public Library of Science, vol. 6(10), pages 1-11, October.
  • Handle: RePEc:plo:pone00:0025560
    DOI: 10.1371/journal.pone.0025560
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    References listed on IDEAS

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    1. Michele Vendruscolo & Emanuele Paci & Christopher M. Dobson & Martin Karplus, 2001. "Three key residues form a critical contact network in a protein folding transition state," Nature, Nature, vol. 409(6820), pages 641-645, February.
    2. Bagler, Ganesh & Sinha, Somdatta, 2005. "Network properties of protein structures," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 346(1), pages 27-33.
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