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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >FLEXIBILITY AND MOBILITY IN MESOPHILIC AND THERMOPHILIC HOMOLOGOUS PROTEINS FROM MOLECULAR DYNAMICS AND FOLDUNFOLD METHOD
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FLEXIBILITY AND MOBILITY IN MESOPHILIC AND THERMOPHILIC HOMOLOGOUS PROTEINS FROM MOLECULAR DYNAMICS AND FOLDUNFOLD METHOD

机译：分子动力学和Foldunfold方法对中，热同质蛋白质的柔性和流动性

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To function properly protein molecules require both flexibility and rigidity, therefore fast and accurate prediction of protein rigidity/flexibility is one of the important problems in protein science. In this work we used two theoretical approaches to determine flexible regions in four homologous pairs of proteins from thermophilic and mesophilic organisms. Protein pairs chosen in this study were selected to represent four typical folding classes. Our first approach, FoldUnfold, uses amino acid sequence and statistical information on the density of contacts of amino acids in tertiary structures of known globular proteins. The main advantages of such knowledge-based methodology are its computational speed and ability to make predictions in the absence of three-dimensional (3D) structure of a protein. The second approach uses a graph theory-based rigid cluster decomposition termed FIRST, applied together with Molecular Dynamics (MD) simulations of proteins with known structure. While MD simulationsare time-consuming, they are the most direct way of studying physical properties of proteins, including their rigidity/flexibility. Flexible regions predicted by both methods in this work were in good agreement with each other. We also showed that high mobility of a site is not necessarily indicative of its high flexibility and vice versa. In our simulations thermophile proteins were less flexible than their mesophilic homologues. Longer flexible loops were found in mesophilic proteins of all classes.
机译：要使蛋白质分子正常运行，就需要柔韧性和刚性，因此，快速，准确地预测蛋白质刚性/柔韧性是蛋白质科学中的重要问题之一。在这项工作中，我们使用了两种理论方法来确定嗜热和嗜温生物中四对同源蛋白质中的柔性区域。选择在这项研究中选择的蛋白质对代表四种典型的折叠类别。我们的第一种方法FoldUnfold使用氨基酸序列和有关已知球状蛋白质三级结构中氨基酸接触密度的统计信息。这种基于知识的方法的主要优点是其计算速度和在没有蛋白质的三维（3D）结构的情况下进行预测的能力。第二种方法使用称为FIRST的基于图论的刚性簇分解，并结合具有已知结构的蛋白质的分子动力学（MD）模拟。 MD模拟虽然很费时，但却是研究蛋白质物理特性（包括其刚度/柔韧性）的最直接方法。两种方法在这项工作中预测的柔性区域彼此之间具有很好的一致性。我们还表明，网站的高移动性并不一定表明它具有高度的灵活性，反之亦然。在我们的模拟中，嗜热蛋白的柔性不如其嗜温同源蛋白。在所有种类的嗜温蛋白中发现了更长的柔性环。

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