Rajashankar K R, Ramakumar S
Department of Physics, Indian Institute of Science, Bangalore, India.
Protein Sci. 1996 May;5(5):932-46. doi: 10.1002/pro.5560050515.
The i + 5-->i hydrogen bonded turn conformation (pi-turn) with the fifth residue adopting alpha L conformation is frequently found at the C-terminus of helices in proteins and hence is speculated to be a "helix termination signal." An analysis of the occurrence of i + 5-->i hydrogen bonded turn conformation at any general position in proteins (not specifically at the helix C-terminus), using coordinates of 228 protein crystal structures determined by X-ray crystallography to better than 2.5 A resolution is reported in this paper. Of 486 detected pi-turn conformations, 367 have the (i + 4)th residue in alpha L conformation, generally occurring at the C-terminus of alpha-helices, consistent with previous observations. However, a significant number (111) of pi-turn conformations occur with (i + 4)th residue in alpha R conformation also, generally occurring in alpha-helices as distortions either at the terminii or at the middle, a novel finding. These two sets of pi-turn conformations are referred to by the names pi alpha L and pi alpha R-turns, respectively, depending upon whether the (i + 4)th residue adopts alpha L or alpha R conformations. Four pi-turns, named pi alpha L'-turns, were noticed to be mirror images of pi alpha L-turns, and four more pi-turns, which have the (i + 4)th residue in beta conformation and denoted as pi beta-turns, occur as a part of hairpin bend connecting twisted beta-strands. Consecutive pi-turns occur, but only with pi alpha R-turns. The preference for amino acid residues is different in pi alpha L and pi alpha R-turns. However, both show a preference for Pro after the C-termini. Hydrophilic residues are preferred at positions i + 1, i + 2, and i + 3 of pi alpha L-turns, whereas positions i and i + 5 prefer hydrophobic residues. Residue i + 4 in pi alpha L-turns is mainly Gly and less often Asn. Although pi alpha R-turns generally occur as distortions in helices, their amino acid preference is different from that of helices. Poor helix formers, such as His, Tyr, and Asn, also were found to be preferred for pi alpha R-turns, whereas good helix former Ala is not preferred. pi-Turns in peptides provide a picture of the pi-turn at atomic resolution. Only nine peptide-based pi-turns are reported so far, and all of them belong to pi alpha L-turn type with an achiral residue in position i + 4. The results are of importance for structure prediction, modeling, and de novo design of proteins.
第五个残基采用αL构象的i + 5→i氢键转角构象（π转角）在蛋白质螺旋的C末端经常出现，因此被推测为一种“螺旋终止信号”。本文报道了一项分析，利用X射线晶体学测定的分辨率优于2.5 Å的228个蛋白质晶体结构坐标，研究i + 5→i氢键转角构象在蛋白质任何一般位置（并非专门在螺旋C末端）的出现情况。在检测到的486个π转角构象中，367个的（i + 4）位残基处于αL构象，通常出现在α螺旋的C末端，这与之前的观察结果一致。然而，也有相当数量（111个）的π转角构象的（i + 4）位残基处于αR构象，通常出现在α螺旋的末端或中间作为扭曲，这是一个新发现。根据（i + 4）位残基采用αL还是αR构象，这两组π转角构象分别被称为παL和παR转角。注意到有四个π转角，称为παL'转角，是παL转角的镜像，还有另外四个π转角，其（i + 4）位残基处于β构象，记为πβ转角，作为连接扭曲β链的发夹弯的一部分出现。连续的π转角会出现，但仅与παR转角一起出现。παL和παR转角中对氨基酸残基的偏好不同。然而，两者在C末端之后都偏好脯氨酸。在παL转角的i + 1、i + 2和i + 3位，亲水残基更受青睐，而i和i + 5位则偏好疏水残基。παL转角中的i + 4位残基主要是甘氨酸，天冬酰胺较少。尽管παR转角通常作为螺旋中的扭曲出现，但其氨基酸偏好与螺旋不同。发现组氨酸、酪氨酸和天冬酰胺等不良螺旋形成残基在παR转角中也更受青睐，而良好的螺旋形成残基丙氨酸则不受青睐。肽中的π转角提供了原子分辨率下的π转角图像。到目前为止，仅报道了九个基于肽的π转角，并且它们都属于παL转角类型，在i + 4位有一个非手性残基。这些结果对蛋白质的结构预测、建模和从头设计具有重要意义。
