基于能量的分块方法用于多肽构象动力学的研究
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- 英文论文题名：The Conformational Dynamics of Polypeptides with the Generalized Energy-Based Fragmentation Approach
- 论文作者：张蕾 ; 李伟 ; 方涛 ; 黎书华
- 英文论文作者：Lei Zhang ; Wei Li ; Tao Fang ; Shuhua Li ; School of Chemistry and Chemical Engineering ; Nanjing University
- 年：2016
- 作者机构：南京大学化学化工学院;
- 论文关键词：基于能量的分块方法 ; 从头算分子动力学 ; 气相多肽 ; 构象动力学
- 会议召开时间：2016-07-01
- 会议录名称：中国化学会第30届学术年会摘要集-第十八分会：电子结构理论方法的发展与应用
- 语种：中文
- 分类号：O621.13
- 学会代码：ZGHY
- 会议名称：中国化学会第30届学术年会-第十八分会 ; 电子结构理论方法的发展与应用
- 会议地点：中国辽宁大连
- 主办单位：中国化学会
- 学会名称：中国化学会
- 页数：1
- 文件大小：178k
- 原文格式：D
- 会议级别：全国
摘要
近十年来对气相多肽的构象研究成为一个热门领域。与溶液中的多肽相比,气相多肽为研究多肽蛋白分子内非共价相互作用提供单一的环境。我们采用基于能量的分块(GEBF)方法在不同温度下,对3_(10)-helical acetyl(ala)_(18)NH_2和DNA聚合酶β片段(含有11个残基,记为polβ)进行气相蛋动力学的从头算分子动力学(AIMD)模拟。研究结果表明:由于能够较好地描述分子间的非共价相互作用,基于GEBF-M06-2X的AIMD模拟可以合理描述这两种气相多肽的构象动力学,而采用AMBER99和CHARMM22分子力场、半经验方法的紧束缚方法(DFTB)及包含经验色散校正的DFTB(DFTB-D)方法得到完全不同的结果。因此,我们期望使用基于GEBF-M06-2X的AIMD模拟,可以应用到气相多肽的快速或超快构象动力学研究,并且可以用来拟合和改进经典分子力学的力场参数。
The conformational study of unsolvated polypeptides has become an active field in the last decade.By comparing with the polypeptides in solutions, unsolvated polypeptides provides a clean condition for studying the influences of intramolecular noncovalent interactions in polypeptides.The ab initio molecular dynamics(AIMD) simulations with the generalized energy-based fragmentation(GEBF) method are employed for the conformational dynamics of an unsolvated large polyalanine, 3_(10)-helical acetyl(ala)_(18)NH_2 and a part of a real peptide, DNA polymerased β(including 11 residues; denoted as pol β) at various temperatures.Our results show that the GEBF-M06-2X based simulations may provide reasonable results for the conformational changes of the two unsolvated polypeptides due to the description of intramolecular noncovalent interactions.However, the AMBER99 and CHARMM22 force fields, the semiempirical density-functional tight-binding(DFTB), and DFTB with empirical dispersion(DFTB-D) simulations give quite different results.The GEBF-M06-2X-based AIMD simulations are expected to be applied to the fast or ultrafast conformational dynamics of large unsolvated polypeptides and to be employed for improving the empirical force fields.
The conformational study of unsolvated polypeptides has become an active field in the last decade.By comparing with the polypeptides in solutions, unsolvated polypeptides provides a clean condition for studying the influences of intramolecular noncovalent interactions in polypeptides.The ab initio molecular dynamics(AIMD) simulations with the generalized energy-based fragmentation(GEBF) method are employed for the conformational dynamics of an unsolvated large polyalanine, 3_(10)-helical acetyl(ala)_(18)NH_2 and a part of a real peptide, DNA polymerased β(including 11 residues; denoted as pol β) at various temperatures.Our results show that the GEBF-M06-2X based simulations may provide reasonable results for the conformational changes of the two unsolvated polypeptides due to the description of intramolecular noncovalent interactions.However, the AMBER99 and CHARMM22 force fields, the semiempirical density-functional tight-binding(DFTB), and DFTB with empirical dispersion(DFTB-D) simulations give quite different results.The GEBF-M06-2X-based AIMD simulations are expected to be applied to the fast or ultrafast conformational dynamics of large unsolvated polypeptides and to be employed for improving the empirical force fields.
引文
[1]Li,W.;Li,S.;Jiang,Y.J.Phys.Chem.A 2007,111:2193
[2]Li,S.;Li,W.;Ma,J.Acc.Chem.Res.2014,47:2712
[3]Zhang,L.;Li,W.;Fang T.;Li,S.Theor.Chem.Acc.,2016,135:34.
[2]Li,S.;Li,W.;Ma,J.Acc.Chem.Res.2014,47:2712
[3]Zhang,L.;Li,W.;Fang T.;Li,S.Theor.Chem.Acc.,2016,135:34.