Amino acid distributions in integral membrane protein structures
Amino acid distributions in integral membrane protein structures
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DOI：
10.1016/s0005-2736(01)00299-1
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发表时间：
2001-05-02
影响因子：
3.4
通讯作者：
Sansom, MSP
中科院分区：
文献类型：
--
作者：
Ulmschneider, MB;Sansom, MSP
膜蛋白结构测定的进展使得能够基于结构而不是序列和预测的拓扑结构来分析膜外与跨膜位置中氨基酸的倾向。使用分辨率优于4埃的29种可用的完整膜蛋白结构，计算跨膜结构域中的氨基酸分布。结果与仅基于相同跨膜α-螺旋序列的分析相比，发现有显著差异，并且还比较了跨膜α-螺旋和β-链之间的残基分布。大的疏水性（Phe、Leu、Ile、瓦尔）残基显示出对β-桶面向脂质的蛋白质表面的明显偏好，但在α-螺旋蛋白质中没有观察到这种偏好：这些残基均匀地分布在蛋白质的内部和表面之间.一个值得注意的例外是丙氨酸，它显示出对α-螺旋膜蛋白内部的轻微偏好。芳香族残基被发现遵循鞍状分布，更喜欢位于脂质/水界面。β-桶蛋白的芳香带比α-螺旋膜蛋白的芳香带间隔更近.尽管发现带电残基经常出现在β-桶的跨膜区域中，但可以显示带电残基通常避免面向双层的表面。实际上，α-螺旋和β-桶蛋白质之间的详细比较显示了残基分布的许多定性差异.这表明，在细菌外膜中稳定β-桶的因子和在所有其他膜中稳定α-螺旋束的因子可能存在细微的差异。(C)2001 Elsevier Science B. V.保留所有权利。
Advances in structure determination of membrane proteins enable analysis of the propensities of amino acids in extramembrane versus transmembrane locations to be performed on the basis of structure rather than of sequence and predicted topology. Using 29 available structures of integral membrane proteins with resolutions better than 4 Angstrom the distributions of amino acids in the transmembrane domains were calculated. The results were compared to analysis based on just the sequences of the same transmembrane alpha -helices and significant differences were found. The distribution of residues between transmembrane alpha -helices and beta -strands was also compared. Large hydrophobic (Phe, Leu, Ile, Val) residues showed a clear preference for the protein surfaces facing the lipids for beta -barrels, but in alpha -helical proteins no such preference was seen: with these residues equally distributed between the interior and the surface of the protein. A notable exception to this was alanine, which showed a slight preference for the interior of alpha -helical membrane proteins. Aromatic residues were found to follow saddle-like distributions preferring to be located in the lipid/water interfaces. The resultant 'aromatic belts' were spaced more closely for beta -barrel than for alpha -helical membrane proteins. Charged residues could be shown to generally avoid surfaces facing the bilayer although they were found to occur frequently in the transmembrane region of beta -barrels. Indeed detailed comparison between alpha -helical and beta -barrel proteins showed many qualitative differences in residue distributions. This suggests that there may be subtle differences in the factors stabilising beta -barrels in bacterial outer membranes and alpha -helix bundles in all other membranes. (C) 2001 Elsevier Science B.V. All rights reserved.