| CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY |
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Characterization of the Topological Features of Catalytic Sites in Protein Coevolution Networks |
| Xiu-Lian Xu**, Jin-Xuan Shi |
| School of Physics Science and Technology, Yangzhou University, Yangzhou 225002, China |
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| Cite this article: |
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Xiu-Lian Xu, Jin-Xuan Shi 2020 Chin. Phys. Lett. 37 068701 |
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Abstract The knowledge of sequence and structural properties of residues in the catalytic sites of enzymes is important for understanding the physiochemical basis of enzymatic catalysis. We reveal new features of the catalytic sites by analyzing the coevolutionary behavior of amino acid sequences. By performing direct coupling analysis of the sequences of homologous proteins, we construct the coevolution networks at the residue level. Based on the analysis of the topological features of the coevolution networks for a dataset including 20 enzymes, we show that there is significant correlation between the catalytic sites and topological features of protein coevolution networks. Residues at the catalytic center often correspond to the nodes with high values of centralities in the networks as characterized by the degree, betweenness, closeness, and Laplacian centrality. The results of this work provide a possible way to extract key coevolutionary information from the sequences of enzymes, which is useful in the prediction of catalytic sites of enzymes.
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Received: 06 February 2020
Published: 26 May 2020
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| PACS: |
87.15.-v
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(Biomolecules: structure and physical properties)
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87.14.E-
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(Proteins)
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89.75.Fb
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(Structures and organization in complex systems)
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89.75.-k
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(Complex systems)
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| Fund: *Supported by the National Natural Science Foundation of China (Grant No. 11305139). |
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