Weak nonbonded S•••X (X=O, N, and S) interactions in proteins. Statistical and theoretical studies.
Weak nonbonded S•••X (X=O, N, and S) interactions in proteins. Statistical and theoretical studies.
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DOI：
10.1246/bcsj.75.1611
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发表时间：
2002-07-01
影响因子：
4
通讯作者：
Tomoda, S
中科院分区：
文献类型：
--
作者：
Iwaoka, M;Takemoto, S;Tomoda, S
胱氨酸（SSC基团）和甲硫氨酸（CSC基团）的含硫官能团通常被认为是折叠蛋白质结构中的疏水部分或弱氢键受体。然而，本研究中进行的数据库分析以及理论计算为二价硫原子（S）和附近的极性非氢原子（X）之间存在特定的非键相互作用提供了强有力的证据。关闭S. X（X = O、N、S、C等）从蛋白质数据库（PDB_SELECT）中选择604个高分辨率异质X射线结构，对原子接触进行统计分析。S...在SSC和CSC组中发现的O相互作用显示出基于方向偏好的pi（C=O）-> sigma*（S）轨道相互作用的特定特征。在α-螺旋中最常观察到相互作用。应用二阶Moller-Plesset微扰理论（MP2）的从头计算表明，电子关联的主要重要性。计算得到SSC和CSC基团的总稳定化能分别为3.2和2.5 kcal/mol，其中包括共存的CH基团的贡献。O氢键。另一方面，S…结果表明，CSC基团的N相互作用表现为π（N）-> sigma*（S）轨道相互作用和NH-N相互作用. S氢键，和S…SSC基团的S相互作用表现出n（S）-> sigma*（S）轨道相互作用的结构特征。S... C（pi）相互作用应该是相当弱和长程的。
Sulfur-containing functional groups of cystine (an SSC group) and methionine (a CSC group) are usually considered as hydrophobic moieties or weak hydrogen-bond acceptors in folded protein structures. However, database analysis as well as theoretical calculations carried out in this study have provided strong evidence for the presence of specific non-bonded interactions between the divalent sulfur atoms (S) and nearby polar non-hydrogen atoms (X). Close S...X (X = O, N, S, C, etc.) atomic contacts were statistically analyzed in 604 high-resolution heterogeneous X-ray structures selected from a protein databank (PDB_SELECT). The S...O interactions found for both SSC and CSC groups showed a specific character as a pi(C=O) --> sigma*(S) orbital interaction based on the directional preferences. The interactions were most frequently observed in alpha-helices. Ab initio calculations applying the second order Moller-Plesset perturbation theory (MP2) suggested the primary importance of electron correlations. The total stabilization energies were calculated to be similar to3.2 and similar to2.5 kcal/mol for SSC and CSC groups, respectively, including the contribution from a coexisting CH...O hydrogen bond. On the other hand, the S...N interactions observed for a CSC group exhibited structural characters as a pi(N) --> sigma*(S) orbital interaction and an NH...S hydrogen bond, and the S...S interactions for an SSC group showed a structural character as an n(S) --> sigma*(S) orbital interaction. The S...C(pi) interactions should be rather weak and long-range.