Chakrabarti P, Chakrabarti S
Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VII-M, Calcutta, 700 054, India. pinak/2boseinst.ernet.in
J Mol Biol. 1998 Dec 11;284(4):867-73. doi: 10.1006/jmbi.1998.2199.
Despite proline being assumed to be a helix-breaker, a large number of alpha-helices are found to contain Pro in globular as well as membrane proteins. Proline has no free NH group and therefore cannot form the conventional intra-helical NH.O=C hydrogen bond. An analysis of known protein structures has shown that the Cdelta protons are involved in C--H...O hydrogen bonds, usually two, with the carbonyl groups in the preceding turn of the helix (four and three residues away). These interactions satisfy the hydrogen bond forming potential of the carbonyl groups, which would otherwise, in the case of membrane-bound helices, be unfavorably exposed to hydrophobic surroundings. Depending on the type (based on the location of the carbonyl group, usually three, four or five residues preceding Pro) of C--H...O interactions, the kink in the helix may be of different magnitude. The puckering (UP or DOWN) of the pyrrolidine ring of Pro residues is controlled by the type of the C--H...O bond present, and the form that provides a better hydrogen bond geometry is preferred.
尽管脯氨酸被认为是一种螺旋破坏剂，但在球状蛋白和膜蛋白中发现大量α螺旋含有脯氨酸。脯氨酸没有游离的NH基团，因此不能形成传统的螺旋内NH…O=C氢键。对已知蛋白质结构的分析表明，Cδ质子参与C-H…O氢键，通常与螺旋前一圈（相隔四个和三个残基）的羰基形成两个氢键。这些相互作用满足了羰基形成氢键的潜力，否则对于膜结合螺旋来说，羰基会不利地暴露在疏水环境中。根据C-H…O相互作用的类型（基于羰基的位置，通常在脯氨酸之前三个、四个或五个残基），螺旋中的扭结可能具有不同的幅度。脯氨酸残基吡咯烷环的褶皱（向上或向下）由存在的C-H…O键的类型控制，提供更好氢键几何形状的形式更受青睐。
