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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >COVARIATION ANALYSIS OF LOCAL AMINO ACID SEQUENCES IN RECURRENT PROTEIN LOCAL STRUCTURES
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COVARIATION ANALYSIS OF LOCAL AMINO ACID SEQUENCES IN RECURRENT PROTEIN LOCAL STRUCTURES

机译：递归蛋白质局部结构中局部氨基酸序列的比较分析

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Local structural information is supposed to be frequently encoded in local amino acid sequences. Previous research only indicated that some local structure positions have specific residue preferences in some particular local structures. However, correlated pairwise replacements for interacting residues in recurrent local structural motifs from unrelated proteins have not been studied systematically. We introduced a new method fusing statistical covariation analysis and local structure-based alignment. Systematic analysis of structure-based multiple alignments of recurrent local structures from unrelated proteins in representative subset of Protein Databank indicates that covarying residue pairs with statistical significance exist in local structural motifs, in particular β-turns and helix caps. These residue pairs are mostly linked through polar functional groups with direct or indirect hydrogen bonding. Hydrophobic interaction is also a major factor in constraining pairwise amino acid residue replacement in recurrent local structures. We also found correlated residue pairs that are not clearly linked with through-space interactions. The physical constrains underlying these covariations are less clear. Overall, covarying residue pairs with statistical significance exist in local structures from unrelated proteins. The existence of sequence covariations in local structural motifs from unrelated proteins indicates that many relics of local relations are still retained in the tertiary structures after protein folding. It supports the notion that some local structural information is encoded in local sequences and the local structural codes could play important roles in determining native state protein folding topology.
机译：假定局部结构信息经常在局部氨基酸序列中编码。先前的研究仅表明，某些局部结构位置在某些特定局部结构中具有特定的残基偏好。但是，尚未系统研究相关联的成对替代物，用于从不相关的蛋白质中复发性局部结构基序中相互作用的残基。我们介绍了一种融合统计协方差分析和基于局部结构的比对的新方法。系统分析基于蛋白质数据库代表性子集中不相关蛋白质的递归局部结构的基于结构的多重比对，表明具有统计学意义的同变残基对存在于局部结构基序中，尤其是β-turns和helix caps。这些残基对主要通过极性官能团通过直接或间接氢键连接。疏水相互作用也是限制循环局部结构中成对氨基酸残基置换的主要因素。我们还发现了相关的残基对，这些残基对与穿越空间的相互作用没有明确联系。这些协变量所基于的物理约束尚不清楚。总的来说，具有无关紧要的残基对具有统计意义，存在于无关蛋白质的局部结构中。来自不相关蛋白质的局部结构基序中序列共变的存在表明，蛋白质折叠后，许多局部关系的文物仍保留在三级结构中。它支持以下观点：一些局部结构信息以局部序列编码，并且局部结构代码可以在确定天然蛋白折叠拓扑结构中发挥重要作用。

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