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首页> 外文期刊>Journal of Molecular Biology >AUTOMATIC ANALYSIS OF PROTEIN CONFORMATIONAL CHANGES BY MULTIPLE LINKAGE CLUSTERING
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AUTOMATIC ANALYSIS OF PROTEIN CONFORMATIONAL CHANGES BY MULTIPLE LINKAGE CLUSTERING

机译：通过多链接簇自动分析蛋白质构象变化

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An automatic algorithm is presented for analyzing protein conformational changes such as those occurring upon substrate binding or in different crystal forms of the same protein. Using, as sole information, the atomic coordinates of a Fair of protein structures, the procedure first generates structure alignments, which optimize the root-mean-square deviation of the backbone atoms. To this end, equivalent secondary structures and/or loops from both proteins are combined by a multiple linkage hierarchic clustering algorithm, which generates several intertwined clustering trees. Automatic analysis of these clustering trees is used to dissect the mechanism of the conformational change. It allows the identification of the static core, representing the collection of secondary structures which undergo no structural changes, as well as other entities which move like rigid bodies. It also permits the description of the movement of secondary structures or loops relative to this core or entities. Using this information, it can be inferred whether a particular conformational change involves shear or hinge motion, or components of both. The algorithm is applied to the analysis of the conformational changes of citrate synthase, lactate dehydrogenase, lactoferrin and beta-glucosyltransferase, representing typical examples of shear- and hinge-type mechanisms, and a varied range in movement size. Tile results are shown to be in excellent agreement with previous analyses, and to provide additional information which gives a more complete and objective picture of the conformational change. Using our automatic algorithm, we find that any conformational change may be viewed as having components of both shear- and hinge-type motion. Determining which of these is most appropriate requires the combination of the information provided by our procedure with detailed knowledge of the protein tertiary structures. (C) 1995 Academic Press Limited [References: 34]
机译：提出了一种自动算法，用于分析蛋白质构象变化，例如那些在底物结合时发生的变化或同一蛋白质的不同晶体形式中发生的变化。作为唯一信息，使用Fair蛋白质结构的原子坐标，该过程首先生成结构比对，该比对可优化骨架原子的均方根偏差。为此，来自两种蛋白质的等效二级结构和/或环通过多重连接层次聚类算法进行组合，该算法会生成多个相互缠绕的聚类树。这些聚类树的自动分析用于剖析构象变化的机制。它可以识别静态核心，表示未发生结构变化的二级结构以及其他像刚体一样移动的实体的集合。它还允许描述二级结构或环路相对于该核心或实体的运动。使用该信息，可以推断出特定的构象变化是涉及剪切运动还是铰链运动，还是两者的组成。该算法用于分析柠檬酸合酶，乳酸脱氢酶，乳铁蛋白和β-葡萄糖基转移酶的构象变化，代表剪切型和铰链型机制的典型实例，以及运动范围的变化范围。瓷砖的结果与以前的分析非常吻合，并提供了更多的信息，这些信息提供了更完整，更客观的构象变化图。使用我们的自动算法，我们发现任何构象变化都可以被视为具有剪切运动和铰链运动的组成部分。要确定其中最合适的方法，需要结合我们程序提供的信息以及对蛋白质三级结构的详细了解。 （C）1995 Academic Press Limited [参考文献：34]

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