C-H•••π-interactions in proteins
C-H•••π-interactions in proteins
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DOI：
10.1006/jmbi.2000.4473
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发表时间：
2001-03-16
影响因子：
5.6
通讯作者：
Hilgenfeld, R
中科院分区：
文献类型：
--
作者：
Brandl, M;Weiss, MS;Hilgenfeld, R
从蛋白质数据库中提取了1154个非冗余的蛋白质结构，研究了c - h供体和pi -受体基团之间的密切相互作用。共有31,087个相互作用被发现满足我们的选择标准。它们的几何参数表明，这些相互作用可以归类为弱氢键。根据供体分为三组，受者分为四组，定义了一组12个交互类。这些类分别进行了研究，并在每个类中进行了详细描述。最突出的是脂肪族碳氢化合物给体和芳香受体之间的相互作用以及芳香碳氢化合物给体和芳香受体之间的相互作用。大约四分之三的trp -环、一半的Phe和tyrr -环以及四分之一的his -环被发现作为C-H的受体参与。π相互作用。在供体侧，观察到芳香C-H基团的偏好，但也观察到长，延伸的氨基酸残基的脂肪侧链Lys， Arg和Met，以及Pro环。在> - 2.5埃分辨率下测定的174个蛋白质结构中，c -供体与pi -受体质心之间的平均距离明显更长。此外，分布范围也明显更广。这种分辨率依赖性表明，通常用于改进蛋白质结构的力场可能不够。芳香基团作为供体或受体的PI -相互作用主要发生在蛋白质内部。参与基团越亲水，相互作用的位置就越靠近表面。大约40%的碳氢化合物…PI -相互作用发生在氨基酸残基侧链之间，这些氨基酸残基侧链按顺序被9个或更少的残基分开。根据相互作用类别的不同，对二级结构、残基类型和侧链构象的偏好不同。很可能C-H -相互作用对蛋白质的整体稳定性有重要贡献。(C) 2001学术出版社。
A non-redundant set of 1154 protein structures from the Protein Data Bank was examined with respect to close interactions between C-H-donor and pi -acceptor groups. A total of 31,087 interactions were found to satisfy our selection criteria. Their geometric parameters suggest that these interactions can be classified as weak hydrogen bonds.A set of 12 interaction classes were defined based on the division of the donors into three groups and the accepters into four groups. These classes were examined separately, and described in detail in each class. Most prominent were interactions between aliphatic C-H donors and aromatic pi -acceptors and interactions between aromatic C-H donors and aromatic pi -acceptors. About three-quarters of the Trp-rings, half of all Phe and Tyr-rings and a quarter of all His-rings were found to be involved as accepters in C-H... pi -interactions. On the donor side, a preference for aromatic C-H groups was observed, but also for the aliphatic side-chains of the long, extended amino acid residues Lys, Arg and Met, and the Pro ring.The average distance between the C-donor and the center-of-mass of the pi -acceptor was observed to be significantly longer in the 174 protein structures determined at >2.5 Angstrom resolution. Also, the distribution is significantly wider. This resolution dependance suggests that the force fields commonly used for the refinement of protein structures may not be adequate.C-H... pi -interactions involving aromatic groups either as donor or as acceptor groups are found mostly in the interior of the protein. The more hydrophilic the participating groups are, the closer to the surface are the interactions located.About 40% of all C-H... pi -interactions occur between amino acid residue side-chains that are separated by nine or less residues in sequence. Dependent on the interaction class, different preferences for secondary structure, residue type and side-chain conformation were observed.It is likely that the C-H pi -interactions contribute significantly to the overall stability of a protein. (C) 2001 Academic Press.