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首页> 外文期刊>Journal of Molecular Biology >Statistical analysis of interface similarity in crystals of homologous proteins.
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Statistical analysis of interface similarity in crystals of homologous proteins.

机译：同源蛋白晶体界面相似性的统计分析。

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Many proteins function as homo-oligomers and are regulated via their oligomeric state. For some proteins, the stoichiometry of homo-oligomeric states under various conditions has been studied using gel filtration or analytical ultracentrifugation experiments. The interfaces involved in these assemblies may be identified using cross-linking and mass spectrometry, solution-state NMR, and other experiments. However, for most proteins, the actual interfaces that are involved in oligomerization are inferred from X-ray crystallographic structures using assumptions about interface surface areas and physical properties. Examination of interfaces across different Protein Data Bank (PDB) entries in a protein family reveals several important features. First, similarities in space group, asymmetric unit size, and cell dimensions and angles (within 1%) do not guarantee that two crystals are actually the same crystal form, containing similar relative orientations and interactions within the crystal. Conversely, two crystals in different space groups may be quite similar in terms of all the interfaces within each crystal. Second, NMR structures and an existing benchmark of PDB crystallographic entries consisting of 126 dimers as well as larger structures and 132 monomers were used to determine whether the existence or lack of common interfaces across multiple crystal forms can be used to predict whether a protein is an oligomer or not. Monomeric proteins tend to have common interfaces across only a minority of crystal forms, whereas higher-order structures exhibit common interfaces across a majority of available crystal forms. The data can be used to estimate the probability that an interface is biological if two or more crystal forms are available. Finally, the Protein Interfaces, Surfaces, and Assemblies (PISA) database available from the European Bioinformatics Institute is more consistent in identifying interfaces observed in many crystal forms compared with the PDB and the European Bioinformatics Institute's ProteinQuaternary Server (PQS). The PDB, in particular, is missing highly likely biological interfaces in its biological unit files for about 10% of PDB entries.
机译：许多蛋白质起着同源寡聚体的作用，并通过其寡聚态受到调控。对于某些蛋白质，已经使用凝胶过滤或分析超速离心实验研究了在各种条件下的均聚状态的化学计量。这些组件中涉及的界面可以使用交联和质谱，溶液态NMR和其他实验进行鉴定。但是，对于大多数蛋白质，使用有关界面表面积和物理性质的假设，从X射线晶体学结构可以推断参与寡聚化的实际界面。检查蛋白质家族中不同蛋白质数据库（PDB）条目之间的接口揭示了几个重要功能。首先，空间群，不对称单位大小以及晶胞尺寸和角度（在1％以内）的相似性不能保证两个晶体实际上是相同的晶体形式，在晶体内包含相似的相对取向和相互作用。相反，就每个晶体内的所有界面而言，不同空间组中的两个晶体可能非常相似。其次，使用NMR结构和由126个二聚体以及更大的结构和132个单体组成的PDB晶体学条目的现有基准，来确定是否存在跨多种晶型的公共界面来预测蛋白质是否为是否低聚物。单体蛋白倾向于仅在少数晶型上具有公共界面，而高阶结构则在大多数可用晶型上具有公共界面。如果可以使用两种或多种晶体形式，则该数据可用于估计界面是生物的可能性。最后，与PDB和欧洲生物信息学协会的ProteinQuaternary Server（PQS）相比，欧洲生物信息学研究所的Protein Interfaces，Surfaces和Assemblys（PISA）数据库在识别以多种晶体形式观察到的界面方面更加一致。尤其是，PDB在其生物单位文件中丢失了大约10％的PDB条目中极有可能的生物学接口。

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