受损腺嘌呤与氨基酸残基堆积复合物的ABEEM极化力场

Development of the ABEEM polarizable force field of stacking damaged adenine and amino acid residues

修复酶能特异性识别受损DNA,碱基与氨基酸残基间的堆叠作用是特异性识别的重要因素,遗憾的是目前没有精准的模型进行模拟.本文工作的最大贡献是在ABEEM极化力场基础上添加堆叠作用函数,调节相关π键位点参数,精准模拟受损腺嘌呤与氨基酸残基间的堆积作用.选取4种受损腺嘌呤与4种芳香族氨基酸残基堆积二聚体作为模型分子.以从头算的几何结构、电荷及堆叠能为基准,调节ABEEM极化力场参数,建立模型.ABEEM极化力场的模拟结果与从头算结果具有高度的一致性,可应用于DNA与酶作用体系的动力学模拟.为修复酶特异性识别受损DNA提供理论基础.

The repair enzyme can identify damaged DNA specifically,the stack effect between bases and amino acid residues is one of the most important factors,it is a pity that there is no precise model for simulation.The greatest contribution of this work is based on the ABEEM polarizable force field to add stack effect function,fit the parameters ofπbond sites,and simulate the stack effect of damaged adenine and amino acid residues accurately.This article selects four kinds of damaged adenine and four kinds of aromatic amino acid residues dimer as molecular model.Taking ab initio geometric structure,charge distribution and stack energy as benchmark,fit the ABEEM polarizable force field parameters.The results of ABEEM polarizable force field and ab initio have high consistency.Hence,the ABEEM polarizable force field can be applied to the dynamic simulations of DNA and enzyme system.It can provide theoretical basis for repair enzyme to identify damaged DNA specifically.