Structural and sequence features of two residue turns in beta-hairpins
Structural and sequence features of two residue turns in beta-hairpins
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DOI：
10.1002/prot.24526
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发表时间：
2014-09-01
影响因子：
2.9
通讯作者：
Lee, Sun-Gu
中科院分区：
文献类型：
--
作者：
Madan, Bharat;Seo, Sung Yong;Lee, Sun-Gu
β -发夹中的β -转被认为是蛋白质折叠的重要位点。特别是，两个残基β -匝，在β -发夹中最丰富的连接元件，已经成为工程蛋白稳定性和折叠的主要目标。在这项研究中，我们试图用一个大数据集来研究和更新β -发夹中两个残基匝的结构和序列特性。为此，从2394个非同源蛋白链中提取3977个β -turn进行分析。首先，确定了两种残轮类型的分布、二面角和扭转，并与已有数据进行了比较。转弯类型的发生趋势和大部分转弯类型的结构特征与以往的结果相似，但首次发现了β -发夹的II型转弯。其次，基于双残基匝的氨基酸位置势设计了匝型序列基序，并对其分布进行了分析。从这项研究中，我们可以识别出两种残基β转类型的代码样序列基序。最后，分析了β -发夹中β -链的结构和序列特性，发现β -链没有特定的回合类型序列和结构模式。本研究的分析结果有望为β -发夹弯结构和序列的工程设计提供参考。
Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue beta-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 nonhomologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences.