Anbarasu Anand, Anand Sudha, Babu M Madan, Sethumadhavan Rao
School of Bio-Technology, Chemical and Bio-Medical Engineering, VIT University, Vellore 632014, India.
Int J Biol Macromol. 2007 Aug 1;41(3):251-9. doi: 10.1016/j.ijbiomac.2007.02.013. Epub 2007 Mar 7.
We have investigated the roles played by C-Hcdots, three dots, centeredpi interactions in RNA binding proteins. There was an average of 55 C-Hcdots, three dots, centeredpi interactions per protein and also there was an average of one significant C-Hcdots, three dots, centeredpi interaction for every nine residues in the 59 RNA binding proteins studied. Main-chain to side-chain C-Hcdots, three dots, centeredpi interactions is the predominant type of interactions in RNA binding proteins. The donor atom contribution to C-Hcdots, three dots, centeredpi interactions was mainly from Phe, Tyr, Trp, Pro, Gly, Lys, His and Ala residues. The acceptor atom contribution to main-chain to side-chain C-Hcdots, three dots, centeredpi and side-chain to side-chain C-Hcdots, three dots, centeredpi interactions was mainly from Phe and Tyr residues. On the contrary, the acceptor atoms of Trp residues contributed to all the four types of C-Hcdots, three dots, centeredpi interactions. Also, Trp contributed both donor and acceptor atoms in main-chain to side-chain, main-chain to side-chain five-member aromatic ring and side-chain to side-chain C-Hcdots, three dots, centeredpi interactions. The secondary structure preference analysis of C-Hcdots, three dots, centeredpi interacting residues showed that, Arg, Gln, Glu, His, Ile, Leu, Lys, Met, Phe and Tyr preferred to be in helix, while Ala, Asp, Cys, Gly, Trp and Val preferred to be in strand conformation. Long-range C-Hcdots, three dots, centeredpi interactions are the predominant type of interactions in RNA binding proteins. More than 50% of C-Hcdots, three dots, centeredpi interacting residues had a higher conservation score. Significant percentage of C-Hcdots, three dots, centeredpi interacting residues had one or more stabilization centers. Seven percent of the theoretically predicted stabilizing residues were also involved in C-Hcdots, three dots, centeredpi interactions and hence these residues may also contribute additional stability to RNA binding proteins.
我们研究了C-H···π相互作用在RNA结合蛋白中所起的作用。在所研究的59种RNA结合蛋白中，每种蛋白平均有55个C-H···π相互作用，并且每九个残基平均有一个显著的C-H···π相互作用。主链与侧链的C-H···π相互作用是RNA结合蛋白中主要的相互作用类型。对C-H···π相互作用的供体原子贡献主要来自苯丙氨酸（Phe）、酪氨酸（Tyr）、色氨酸（Trp）、脯氨酸（Pro）、甘氨酸（Gly）、赖氨酸（Lys）、组氨酸（His）和丙氨酸（Ala）残基。对主链与侧链的C-H···π相互作用以及侧链与侧链的C-H···π相互作用的受体原子贡献主要来自苯丙氨酸和酪氨酸残基。相反，色氨酸残基的受体原子对所有四种类型的C-H···π相互作用都有贡献。此外，色氨酸在主链与侧链、主链与侧链五元芳香环以及侧链与侧链的C-H···π相互作用中既提供供体原子也提供受体原子。对C-H···π相互作用残基的二级结构偏好分析表明，精氨酸（Arg）、谷氨酰胺（Gln）、谷氨酸（Glu）、组氨酸、异亮氨酸（Ile）、亮氨酸（Leu）、赖氨酸、甲硫氨酸（Met）、苯丙氨酸和酪氨酸倾向于处于螺旋结构中，而丙氨酸、天冬氨酸（Asp）、半胱氨酸（Cys）、甘氨酸、色氨酸和缬氨酸（Val）倾向于处于链状构象。远距离的C-H···π相互作用是RNA结合蛋白中主要的相互作用类型。超过50%的C-H···π相互作用残基具有较高的保守性得分。相当比例的C-H···π相互作用残基有一个或多个稳定中心。理论上预测的稳定残基中有7%也参与了C-H···π相互作用，因此这些残基可能也为RNA结合蛋白提供了额外的稳定性。
