Statistical radii associated with amino acids to determine the contact map: fixing the structure of a type I cohesin domain in the Clostridium thermocellum cellulosome
Statistical radii associated with amino acids to determine the contact map: fixing the structure of a type I cohesin domain in the Clostridium thermocellum cellulosome
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DOI：
10.1088/1478-3975/12/4/046002
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发表时间：
2015-07-01
期刊：
影响因子：
2
通讯作者：
Cieplak, Marek
中科院分区：
文献类型：
--
作者：
Chwastyk, Mateusz;Bernaola, Adolfo Poma;Cieplak, Marek
我们建议通过考虑哪些氨基酸残基对应形成天然接触来改进和简化蛋白质精制程序。我们首先考虑 CATH 数据库中的 11 330 个蛋白质，以确定与给定类型氨基酸相关的接触的统计分布。分布是在接触的 α-C 原子之间的距离上设置的。基于这些数据，我们确定了可以放置在 α-C 原子上的有效球体的典型半径，以便重建接触长度的分布。这是通过检查与其他氨基酸上的重原子相关的扩大的范德华球的重叠来完成的。由此产生的接触可用于识别在基于结构的模型的时间演化过程中可能出现的非天然接触。在这里，半径用于指导重建 I 型粘连蛋白结构域中九个缺失的侧链，蛋白质数据库代码为 1AOH。我们首先识别可能缺失的接触点，然后通过标准细化工具雕刻相应的侧链，以实现与预期接触图的一致性。通过确定全原子构象能解决了细化中的一个歧义。
We propose to improve and simplify protein refinement procedures through consideration of which pairs of amino acid residues should form native contacts. We first consider 11 330 proteins from the CATH database to determine statistical distributions of contacts associated with a given type of amino acid. The distributions are set across the distances between the alpha-C atoms that are in contact. Based on this data, we determine typical radii of effective spheres that can be placed on the alpha-C atoms in order to reconstruct the distribution of the contact lengths. This is done by checking for overlaps with enlarged van der Waals spheres associated with heavy atoms on other amino acids.The resulting contacts can be used to identify non-native contacts that may arise during the time evolution of structure-based models. Here, the radii are used to guide reconstruction of nine missing side chains in a type I cohesin domain with the Protein Data Bank code 1AOH. We first identify the likely missing contacts and then sculpt the corresponding side chains by standard refinement tools to achieve consistency with the expected contact map. One ambiguity in refinement is resolved by determining all-atom conformational energies.