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蛋白质中的螺旋结构

Helix geometry in proteins.

作者信息

Barlow D J, Thornton J M

机构信息

Department of Crystallography, Birkbeck College London, U.K.

出版信息

J Mol Biol. 1988 Jun 5;201(3):601-19. doi: 10.1016/0022-2836(88)90641-9.

Abstract

In this report we describe a general survey of all helices found in 57 of the known protein crystal structures, together with a detailed analysis of 48 alpha-helices found in 16 of the structures that are determined to high resolution. The survey of all helices reveals a total of 291 alpha-helices, 71 3(10)-helices and no examples of pi-helices. The conformations of the observed helices are significantly different from the "ideal" linear structures. The mean phi, psi angles for the alpha- and 3(10)-helices found in proteins are, respectively, (-62 degrees, -41 degrees) and (-71 degrees, -18 degrees). A computer program, HBEND, is used to characterize and to quantify the different types of helix distortion. alpha-Helices are classified as regular or irregular, linear, curved or kinked. Of the 48 alpha-helices analysed, only 15% are considered to be linear; 17% are kinked, and 58% are curved. The curvature of helices is caused by differences in the peptide hydrogen bonding on opposite faces of the helix, reflecting carbonyl-solvent/side-chain interactions for the exposed residues, and packing constraints for residues involved in the hydrophobic core. Kinked helices arise either as a result of included proline residues, or because of conflicting requirements for the optimal packing of the helix side-chains. In alpha-helices where there are kinks caused by proline residues, we show that the angle of kink is relatively constant (approximately 26 degrees), and that there is minimal disruption of the helix hydrogen bonding. The proline residues responsible for the kinks are highly conserved, suggesting that these distortions may be structurally/functionally important.

摘要

在本报告中,我们描述了对已知57种蛋白质晶体结构中所有螺旋的全面调查,并对其中16种高分辨率结构中发现的48个α螺旋进行了详细分析。对所有螺旋的调查发现共有291个α螺旋、71个3(10)螺旋,没有发现π螺旋的例子。观察到的螺旋构象与“理想”线性结构有显著差异。蛋白质中发现的α螺旋和3(10)螺旋的平均φ、ψ角分别为(-62度,-41度)和(-71度,-18度)。使用计算机程序HBEND来表征和量化不同类型的螺旋畸变。α螺旋被分类为规则或不规则、线性、弯曲或扭结。在分析的48个α螺旋中,只有15%被认为是线性的;17%是扭结的,58%是弯曲的。螺旋的曲率是由螺旋相对面上肽氢键的差异引起的,反映了暴露残基的羰基-溶剂/侧链相互作用以及疏水核心中残基的堆积限制。扭结螺旋的出现要么是由于包含脯氨酸残基,要么是由于螺旋侧链最佳堆积的相互冲突要求。在由脯氨酸残基引起扭结的α螺旋中,我们表明扭结角度相对恒定(约26度),并且螺旋氢键的破坏最小。导致扭结的脯氨酸残基高度保守,表明这些畸变可能在结构/功能上很重要。

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