Disulfide bonds, their stereospecific environment and conservation in protein structures
Disulfide bonds, their stereospecific environment and conservation in protein structures
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DOI：
10.1093/protein/gzh093
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发表时间：
2004-11-01
影响因子：
2.4
通讯作者：
Chakrabarti, P
中科院分区：
文献类型：
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作者：
Bhattacharyya, R;Pal, D;Chakrabarti, P
我们研究了选自蛋白质数据库的 247 条多肽链中 572 个二硫键环境中非键相互作用的特异性。肽氧原子相互作用的优选几何形状是沿着半胱氨酸的硫原子处的两个共价键的背面。对于芳香族残基，避免了将硫孤对电子之一引导到芳香族π系统的几何结构；通常优选硫化物平面垂直于或倾斜于芳族平面且位于其边缘之上的取向。 S...芳香族相互作用的重要性体现在其在同源蛋白质家族成员之间的高度保守性。这些相互作用在为天然折叠提供额外的整体稳定性并减少二硫键的可及性并从而防止交换反应的同时，还设定了保守芳环的方向以进行进一步的相互作用和与另一个分子的结合。二硫键的构象特征和相互作用模式对于分子设计和蛋白质工程实验应该有用。
We studied the specificity of the non-bonded interaction in the environment of 572 disulfide bonds in 247 polypeptide chains selected from the Protein Data Bank. The preferred geometry of interaction of peptide oxygen atoms is along the back of the two covalent bonds at the sulfur atom of half cystine. With aromatic residues the geometries that direct one of the sulfur lone pair of electrons into the aromatic pi-system are avoided; an orientation in which the sulfide plane is normal or inclined to the aromatic plane and on top of its edge is normally preferred. The importance of the S...aromatic interaction is manifested in the high degree of its conservation across members in homologous protein families. These interactions, while providing extra overall stability to the native fold and reducing the accessibility of the disulfide bond and thereby preventing exchange reactions, also set the orientation of the conserved aromatic rings for further interactions and binding to another molecule. The conformational features and the mode of interactions of disulfide bridges should be useful for molecular design and protein engineering experiments.