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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >STATISTICAL AND VISUAL MORPH MOVIE ANALYSIS OF CRYSTALLOGRAPHIC MUTANT SELECTION BIAS IN PROTEIN MUTATION RESOURCE DATA
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STATISTICAL AND VISUAL MORPH MOVIE ANALYSIS OF CRYSTALLOGRAPHIC MUTANT SELECTION BIAS IN PROTEIN MUTATION RESOURCE DATA

机译：蛋白质突变源数据中晶体突变选择偏向的统计和视觉形态分析

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Structural studies of the effects of non-silent mutations on protein conformational change are an important key in deciphering the language that relates protein amino acid primary structure to tertiary structure. Elsewhere, we presented the Protein Mutant Resource (PMR) database, a set of online tools that systematically identified groups of related mutant structures in the Protein DataBank (PDB), accurately inferred mutant classifications in the Gene Ontology using an innovative, statistically rigorous data-mining algorithm with more general applicability, and illustrated the relationship of these mutant structures via an intuitive user interface. Here, we perform a comprehensive statistical analysis of the effect of PMR mutations on protein tertiary structure. We find that, although the PMR does contain spectacular examples of conformational change, in general there is a counter-intuitive inverse relationship between conformational change (measured as C-alpha displacement or RMS of the core structure) and the number of mutations in a structure. That is, point mutations by structural biologists present in the PDB contrast naturally evolved mutations. We compare the frequency of mutations in the PMR/PDB datasets against the accepted PAM250 natural amino acid mutation frequency to confirm these observations. We generated morph movies from PMR structure pairs using technology previously developed for the Macromolecular Motions Database (http://molmovdb.org), allowing bioinformaticians, geneticists, protein engineers, and rational drug designers to analyze visually the mechanisms of protein conformational change and distinguish between conformational change due to motions (e.g., ligand binding) and mutations. The PMR morph movies and statistics can be freely viewed from the PMR website, http://pmr.sdsc.edu.
机译：非沉默突变对蛋白质构象变化影响的结构研究是解密将蛋白质氨基酸一级结构与三级结构相关的语言的重要关键。在其他地方，我们介绍了蛋白质突变体资源（PMR）数据库，这是一套在线工具，可以系统地识别Protein DataBank（PDB）中的相关突变体结构组，并使用创新的，统计严格的数据准确地推断出Gene Ontology中的突变体分类，挖掘算法具有更广泛的适用性，并通过直观的用户界面说明了这些突变体结构的关系。在这里，我们对PMR突变对蛋白质三级结构的影响进行了全面的统计分析。我们发现，尽管PMR确实包含构象变化的引人注目的示例，但通常在构象变化（以核心结构的C-α位移或RMS衡量）与结构中的突变数量之间存在反直觉的逆关系。 。也就是说，PDB中存在的结构生物学家的点突变与自然进化的突变形成对比。我们将PMR / PDB数据集中的突变频率与公认的PAM250天然氨基酸突变频率进行比较，以确认这些观察结果。我们使用先前为大分子运动数据库（http://molmovdb.org）开发的技术，从PMR结构对中生成了变形电影，从而使生物信息学家，遗传学家，蛋白质工程师和理性的药物设计师可以直观地分析蛋白质构象变化的机制并加以区分在由于运动（例如，配体结合）和突变引起的构象变化之间。可以从PMR网站http://pmr.sdsc.edu免费查看PMR变形电影和统计信息。

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