可溶蛋白和膜结合蛋白残基关键结构特征的二级结构依赖性系统分析

IF 3.5 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Mohammed H. AL Mughram , Noah B. Herrington , Claudio Catalano , Glen E. Kellogg
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引用次数: 2

摘要

三维蛋白质结构知识是大多数现代药物发现工作的组成部分。最近的进展突出了3D蛋白质结构测定的新技术,以及无法通过实验收集结构数据的蛋白质结构预测。我们已经进行了一项主要的努力,利用现有的蛋白质结构来收集、表征和编目原子间的相互作用,这些相互作用通过将亲水相互作用环境映射为3D空间中的地图来定义和组成3D结构。这项工作是在逐个残留物的基础上进行的,我们已经看到了环境特征、残留物溶剂可及表面积及其二级结构之间关系的证据。在这个图形回顾中,我们应用我们早期研究的原理,并将范围扩大到可溶性和膜蛋白中所有常见的氨基酸残基类型。此分析的关键是将Ramachandran图解析为8 × 8的棋盘,以定义二级结构箱。我们的分析产生了许多定量发现:1)膜蛋白中的疏水残基(丙氨酸、异亮氨酸、亮氨酸、苯丙氨酸和缬氨酸)的比例比可溶性蛋白中的比例增加;2)与可溶性蛋白相比,膜蛋白中疏水残基的疏水相互作用显著增加;3)更高的埋藏和更有利的极性相互作用的极性残基现在倾向于膜蛋白的内部。这些观察结果和支持数据应该为当前不同环境下蛋白质残基的研究提供基准,并可能指导未来蛋白质结构预测的工作。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Systematized analysis of secondary structure dependence of key structural features of residues in soluble and membrane-bound proteins

Systematized analysis of secondary structure dependence of key structural features of residues in soluble and membrane-bound proteins

Knowledge of three-dimensional protein structure is integral to most modern drug discovery efforts. Recent advancements have highlighted new techniques for 3D protein structure determination and, where structural data cannot be collected experimentally, prediction of protein structure. We have undertaken a major effort to use existing protein structures to collect, characterize, and catalogue the inter-atomic interactions that define and compose 3D structure by mapping hydropathic interaction environments as maps in 3D space. This work has been performed on a residue-by-residue basis, where we have seen evidence for relationships between environment character, residue solvent-accessible surface areas and their secondary structures. In this graphical review, we apply principles from our earlier studies and expand the scope to all common amino acid residue types in both soluble and membrane proteins. Key to this analysis is parsing the Ramachandran plot to an 8-by-8 chessboard to define secondary structure bins. Our analysis yielded a number of quantitative discoveries: 1) increased fraction of hydrophobic residues (alanine, isoleucine, leucine, phenylalanine and valine) in membrane proteins compared to their fractions in soluble proteins; 2) less burial coupled with significant increases in favorable hydrophobic interactions for hydrophobic residues in membrane proteins compared to soluble proteins; and 3) higher burial and more favorable polar interactions for polar residues now preferring the interior of membrane proteins. These observations and the supporting data should provide benchmarks for current studies of protein residues in different environments and may be able to guide future protein structure prediction efforts.

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来源期刊
Journal of Structural Biology: X
Journal of Structural Biology: X Biochemistry, Genetics and Molecular Biology-Structural Biology
CiteScore
6.50
自引率
0.00%
发文量
20
审稿时长
62 days
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