Fujiwara Kazuo, Ebisawa Shinichi, Watanabe Yuka, Toda Hiromi, Ikeguchi Masamichi
Department of Bioinformatics, Soka University, Hachioji, Tokyo, 192-8577, Japan.
Proteins. 2014 Jul;82(7):1484-93. doi: 10.1002/prot.24518. Epub 2014 Feb 18.
β-Sheet twisting is thought to be mainly determined by interstrand hydrogen bonds with little contribution from side chains, but some proteins have large, flat β-sheets, suggesting that side chains influence β-structures. We therefore investigated the relationship between amino acid composition and twists or bends of β-strands. We calculated and statistically analyzed the twist and bend angles of short frames of β-strands in known protein structures. The most frequent twist angles were strongly negatively correlated with the proportion of hydrophilic amino acid residues. The majority of hydrophilic residues (except serine and threonine) were found in the edge regions of β-strands, suggesting that the side chains of these residues likely do not affect β-strand structure. In contrast, the majority of serine, threonine, and asparagine side-chains in β-strands made contacts with a nitrogen atom of the main chain, suggesting that these residues suppress β-strand twisting.
β-折叠扭转被认为主要由链间氢键决定,侧链贡献较小,但一些蛋白质具有大的扁平β-折叠,这表明侧链会影响β-结构。因此,我们研究了氨基酸组成与β-链的扭转或弯曲之间的关系。我们计算并统计分析了已知蛋白质结构中β-链短片段的扭转角和弯曲角。最常见的扭转角与亲水性氨基酸残基的比例呈强烈负相关。大多数亲水性残基(丝氨酸和苏氨酸除外)位于β-链的边缘区域,这表明这些残基的侧链可能不会影响β-链结构。相反,β-链中大多数丝氨酸、苏氨酸和天冬酰胺侧链与主链的氮原子有接触,这表明这些残基会抑制β-链的扭转。