摘要
非键作用是自然界中广泛存在的分子间作用,参与到生命体中最基本的蛋白质与核酸的相互作用等过程。该过程以氨基酸侧链与碱基的相互作用为主,因此准确预测氨基酸侧链与碱基等生物分子的相互作用具有十分重要的科学意义。选用量子力学方法计算了15个含氨基酸侧链的带正电堆积复合物的相互作用能,并与CCSD(T)/CBS方法计算结果进行比较。计算结果表明,SCS-CCSD/CBS方法的均方根偏差为0.06 kcal/mol,线性相关系数为0.999 8;SCS-MI-CCSD/CBS方法的均方根偏差为0.11 kcal/mol,线性相关系数为0.999 9;MP2.5/CBS方法的均方根偏差为0.13 kcal/mol,线性相关系数为0.999 3,验证了上述方法的可靠性。而后进一步使用MP2.5/CBS方法计算精氨酸、组氨酸和赖氨酸侧链与中性分子形成堆积复合物在不同距离下的相互作用能,进而构建并完善了带正电氨基酸分子与中性分子间非键作用强度的标准数据。
Noncovalent interaction exists in nature widely,especially it plays an important role during the interaction of protein and nucleic acid in organisms,which actually is the interaction between the side chain of amino acids and bases.Therefore,the accurate prediction of the interaction between the side chain of amino acids and bases is extremely important in life science.Correlated Quantum Mechanics(QM) methods are used to calculate the interaction energy of 15 dimers of amino acid with positive charge and compared with those calculated at the level of CCSD(T)/CBS.It shows that the Root Mean Squared Error(RMSE) of SCS-CCSD/CBS method is 0.06 kcal/mol,and the linear correlation coefficient is 0.999 8.The RMSE of SCS-MI-CCSD/CBS method is 0.11 kcal/mol,and the linear correlation coefficient is 0.999 9.The RMSE of MP2.5/CBS method is 0.13 kcal/mol,and the linear correlation coefficient is 0.999 3.These results prove the reliability of the correlated QM methods,and then,MP2.5/CBS method is applied to calculate the interaction energies for the stacking dimers including arginine,histidine and lysine side chains with neutral molecules at different intermolecular distances,which could be used as the benchmark value of the noncovalent interaction for positively charged stacking dimers.
作者
王一博
孙瑞鸿
王长生
王磊
WANG Yibo;SUN Ruihong;WANG Changsheng;WANG Lei(School of Chemistry and Chemical Engineering,Liaoning Normal University,Dalian 116029 Liaoning China)
出处
《化学研究》
CAS
2024年第1期61-67,共7页
Chemical Research
基金
国家自然科学基金(21773102)
辽宁省教育厅青年项目(LQ2020024)。
关键词
非键作用
量子力学方法
堆积复合物
氨基酸侧链
noncovalent interaction
quantum mechanics method
stacking dimer
side chain of amino
