A study on the flexibility of enzyme active sites

BMC Bioinformatics

Research

Yi-Zhong Weng¹  Yu-Feng Huang¹  Chih-Wei Lin¹  Darby Tien-Hao Chang² 

[1] Department of Computer Science and Information Engineering, National Taiwan University, 106, Taipei, Taiwan;Department of Electrical Engineering, National Cheng Kung University, 701, Tainan, Taiwan;

关键词: Structure Alignment;    Catalytic Residue;    Enzyme Active Site;    Protein Data Bank Structure;    Zinc Site;   

DOI  :  10.1186/1471-2105-12-S1-S32

来源: Springer

【 摘 要 】

BackgroundA common assumption about enzyme active sites is that their structures are highly conserved to specifically distinguish between closely similar compounds. However, with the discovery of distinct enzymes with similar reaction chemistries, more and more studies discussing the structural flexibility of the active site have been conducted.ResultsMost of the existing works on the flexibility of active sites focuses on a set of pre-selected active sites that were already known to be flexible. This study, on the other hand, proposes an analysis framework composed of a new data collecting strategy, a local structure alignment tool and several physicochemical measures derived from the alignments. The method proposed to identify flexible active sites is highly automated and robust so that more extensive studies will be feasible in the future. The experimental results show the proposed method is (a) consistent with previous works based on manually identified flexible active sites and (b) capable of identifying potentially new flexible active sites.ConclusionsThis proposed analysis framework and the former analyses on flexibility have their own advantages and disadvantage, depending on the cause of the flexibility. In this regard, this study proposes an alternative that complements previous studies and helps to construct a more comprehensive view of the flexibility of enzyme active sites.

【 授权许可】

Unknown   
© Weng et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.