Efremov R G, Vergoten G
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow.
J Protein Chem. 1996 Jan;15(1):63-76. doi: 10.1007/BF01886812.
The hydrophobic organization of the intramembrane alpha-helical bundle in bacteriorhodopsin (BRh) was assessed based on a new approach to characterization of spatial hydrophobic properties of transmembrane (TM) alpha-helical peptides. The method employs two independent techniques: Monte Carlo simulations of nonpolar solvent around TM peptides and analysis of molecular hydrophobicity potential on their surfaces. The results obtained by the two methods agree with each other and permit precise hydrophobicity mapping of TM peptides. Superimposition of such data on the experimentally derived spatial model of the membrane moiety together with 2D maps of hydrophobic hydrophilic contacts provide considerable insight into the hydrophobic organization of BRh. The helix bundle is stabilized to a large extent by hydrophobic interactions between helices--neighbors in the sequence of BRh, by long-range interactions in helix pairs C-E, C-F, and C-G, and by nonpolar contracts between retinal and helices C, D, E, F. Unlike globular proteins, no polar contacts between residues distantly separated in the sequence of BRh were found in the bundle. One of the most striking results of this study is the finding that the hydrophobic organization of BRh is significantly different from those in bacterial photoreaction centers. Thus, TM alpha-helices in BRh expose their most nonpolar sides to the bilayer as well as to the neighboring helices and to the interior of the bundle. Some of them contact lipids with their relatively hydrophilic surfaces. No correlation was found between disposition of the most hydrophobic and the most variable sides of the TM helices.
基于一种表征跨膜（TM）α-螺旋肽空间疏水特性的新方法，评估了细菌视紫红质（BRh）中膜内α-螺旋束的疏水结构。该方法采用两种独立技术：对TM肽周围非极性溶剂进行蒙特卡罗模拟，以及分析其表面的分子疏水势。两种方法得到的结果相互吻合，能够精确绘制TM肽的疏水图谱。将这些数据与实验得出的膜部分空间模型以及疏水-亲水接触的二维图谱叠加在一起，能让我们深入了解BRh的疏水结构。螺旋束在很大程度上通过BRh序列中相邻螺旋之间的疏水相互作用、螺旋对C-E、C-F和C-G之间的长程相互作用以及视黄醛与螺旋C、D、E、F之间的非极性接触得以稳定。与球状蛋白质不同，在该束中未发现BRh序列中远距离分隔的残基之间存在极性接触。这项研究最显著的结果之一是发现BRh的疏水结构与细菌光反应中心的疏水结构有显著差异。因此，BRh中的TMα-螺旋将其最非极性的一面暴露给双层膜、相邻螺旋以及螺旋束内部。其中一些螺旋以其相对亲水的表面与脂质接触。未发现TM螺旋最疏水的一面和最可变的一面的排布之间存在相关性。
