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Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non-enzyme families

¹ Bioinformatics Research Unit, Research and Development Division, Fujirebio, Inc., Hachioji-shi, Tokyo 192-0031, Japan
² Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, Maryland 21702, USA
³ Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Tel Aviv University, Tel Aviv 69978, Israel

(RECEIVED March 28, 2006; FINAL REVISION May 19, 2006; ACCEPTED May 24, 2006)

The representation of protein structures as small-world networks facilitates the search for topological determinants, which may relate to functionally important residues. Here, we aimed to investigate the performance of residue centrality, viewed as a family fold characteristic, in identifying functionally important residues in protein families. Our study is based on 46 families, including 29 enzyme and 17 non-enzyme families. A total of 80% of these central positions corresponded to active site residues or residues in direct contact with these sites. For enzyme families, this percentage increased to 91%, while for non-enzyme families the percentage decreased substantially to 48%. A total of 70% of these central positions are located in catalytic sites in the enzyme families, 64% are in hetero-atom binding sites in those families binding hetero-atoms, and only 16% belong to protein–protein interfaces in families with protein–protein interaction data. These differences reflect the active site shape: enzyme active sites locate in surface clefts, hetero-atom binding residues are in deep cavities, while protein–protein interactions involve a more planar configuration. On the other hand, not all surface cavities or clefts are comprised of central residues. Thus, closeness centrality identifies functionally important residues in enzymes. While here we focus on binding sites, we expect to identify key residues for the integration and transmission of the information to the rest of the protein, reflecting the relationship between fold and function. Residue centrality is more conserved than the protein sequence, emphasizing the robustness of protein structures.

Keywords: network; closeness centrality; characteristic path length; conserved central positions; active sites

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