应用ABEEM极化力场研究核酸碱基和氨基酸侧链的相互作用  

Study on the interaction between nucleic acid base and amino acid side chain by ABEEM polarizable force field

作　　者：卢丽男[1] 杨忠志[1] 赵东霞[1] LU Linan;YANG Zhongzhi;ZHAO Dongxia(School of Chemistry and Chemical Engineering,Liaoning Normal University,Dalian 116029,China)

机构地区：[1]辽宁师范大学化学化工学院,辽宁大连116029

出　　处：《辽宁师范大学学报（自然科学版）》2023年第1期56-63,共8页Journal of Liaoning Normal University:Natural Science Edition

基　　金：国家自然科学基金资助项目(22273033)。

摘　　要：对ABEEM极化力场(ABEEM PFF)对核酸碱基、氨基酸侧链以及它们之间的相互作用进行研究.ABEEM PFF将体系的电荷密度分解到了原子区域、σ键区域、π键区域和孤对电子区域,各个区域的电荷可以随着体系结构的变化以及周围环境不同而浮动,很好体现了体系极化效应.在碱基和氨基酸之间的相互作用中氢键起到了很重要的关键作用.ABEEMPFF通过氢键拟合函数对氢键相互作用区域进行特殊的考虑和处理.研究结果表明,应用ABEEM电荷模型计算得到4个碱基模型、5个氨基酸侧链模型和20个相互作用模型的电荷分布以及偶极矩,计算结果与量子力学方法(QM)相媲美.应用ABEEMPFF对29个模型分子进行结构的优化得到稳定结构,与QM计算的结果以及实验的构象有很好的一致性.应用ABEEMPFF和QM方法计算20个碱基和氨基酸相互作用模型的相互作用能,计算结果表明带电的氨基酸侧链与碱基的相互作用能大于不带电氨基酸侧链.氨基酸侧链与碱基的相互作用能的顺序为:Lys>Asp/Glu>Arg>Asn/Gln>Ser/Thr.ABEEMPFF研究碱基和氨基酸侧链的相互作用,为研究和揭示蛋白质和核酸的相互识别机理奠定了良好的基础.ABEEM polarizable force field(ABEEM PFF)is developed to study the nucleic acid bases,the side chain of amino acids and their interactions.ABEEM PFF decomposes the molecular charge density into atomic region,σbond region,πbond region,and lone pair electron region.The charge in each region can fluctuate with the change of the system structure and the surrounding environment,which well reflects the polarization effect of the system.Hydrogen bond plays an important role in the interaction between bases and amino acids.ABEEM PFF takes special consideration and treatment of hydrogen bond interaction region through hydrogen bond fitting function.The results show that the charge distribution and dipole moment of 4 base models,5 amino acid side chain models and 20 interaction models calculated by ABEEM charge method are comparable to those calculated by quantum mechanical(QM)method.The ABEEM PFF are used to optimize the structure of 29 model molecules,and to obtain stable structures,which is in good agreement with the QM method calculation results and the experimental structures.The ABEEM PFF and QM method are used to calculate the interaction energies of the 20 base and amino acid complexes.The results show that the interaction ability of charged amino acid side chain with base is greater than that of uncharged amino acid side chain.The order of interaction ability between amino acid side chain and base is Lys>Asp/Glu>Arg>Asn/Gln>Ser/Thr.ABEEM PFF studies the interaction between base and amino acid side chain,which lays a good foundation for studying and revealing the mutual recognition mechanism of protein and nucleic acid.

关 键 词：ABEEM极化力场 电荷分布 氢键 碱基和氨基酸侧链相互作用 

分 类 号：O641[理学—物理化学]