Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan.
BMC Bioinformatics. 2011 Feb 15;12 Suppl 1(Suppl 1):S32. doi: 10.1186/1471-2105-12-S1-S32.
A 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.
Most 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.
This 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.
人们普遍认为酶的活性部位的结构高度保守，以特异性区分密切相似的化合物。然而，随着具有相似反应化学特性的不同酶的发现，越来越多的研究探讨了活性部位的结构灵活性。
大多数关于活性部位灵活性的现有研究都集中在一组预先选择的已知具有灵活性的活性部位上。另一方面，本研究提出了一个由新的数据收集策略、局部结构对齐工具和从对齐中得出的几个物理化学度量组成的分析框架。用于识别灵活活性部位的方法高度自动化且稳健，因此未来可以进行更广泛的研究。实验结果表明，所提出的方法（a）与基于手动识别的灵活活性部位的先前工作一致，（b）能够识别潜在的新的灵活活性部位。
该分析框架和以前关于灵活性的分析具有各自的优点和缺点，这取决于灵活性的原因。在这方面，本研究提出了一种替代方案，补充了以前的研究，有助于构建酶活性部位灵活性的更全面观点。
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