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BioMed Research International
Volume 2013 (2013), Article ID 802945, 9 pages
http://dx.doi.org/10.1155/2013/802945
Research Article

On the Structural Context and Identification of Enzyme Catalytic Residues

Department of Medical Informatics, Tzu Chi University, 701 Zhongyang Road, Section 3, Hualien 97004, Taiwan

Received 29 November 2012; Accepted 28 December 2012

Academic Editor: Tun-Wen Pai

Copyright © 2013 Yu-Tung Chien and Shao-Wei Huang. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Enzymes play important roles in most of the biological processes. Although only a small fraction of residues are directly involved in catalytic reactions, these catalytic residues are the most crucial parts in enzymes. The study of the fundamental and unique features of catalytic residues benefits the understanding of enzyme functions and catalytic mechanisms. In this work, we analyze the structural context of catalytic residues based on theoretical and experimental structure flexibility. The results show that catalytic residues have distinct structural features and context. Their neighboring residues, whether sequence or structure neighbors within specific range, are usually structurally more rigid than those of noncatalytic residues. The structural context feature is combined with support vector machine to identify catalytic residues from enzyme structure. The prediction results are better or comparable to those of recent structure-based prediction methods.