QM/MM方法的研究

从理论上探讨了QM/MM方法在模拟计算生物大分子体系的运用,实践表明这种方法能提高计算结果的精确性,能有效地降低计算成本.

HIV-1蛋白酶与抑制剂结合中桥接水分子作用的QM/MM研究

对HIV-1蛋白酶与抑制剂2AH和4AH结合的两个复合物体系进行了水溶液环境下量子力学分子力学混合方法(hybrid QM/MM)的1ns分子动力学模拟,用MM-GBSA方法得到桥接水分子W301与HIV-1蛋白酶和抑制剂结合体的结合自由能分别为-24.93 kJ/mol和-20.29 kJ/mol,表明W301在抑制剂和HIV-1蛋白酶结合的过程中起到了不能被忽略的作用。

W301水分子在HIV-1蛋白酶和配体ABT-538结合中作用的QM/MM研究

结晶水分子W301在几乎所有的HIV-1蛋白酶(HIV-1PR)和配体的晶体结构中出现.在HIV-1PR中A链天门冬氨酸残基Asp25质子化状态或B链Asp25质子化状态下,QM/MM模拟后MM-GBSA方法计算得到W301水分子在HIV-1PR/ABT-538结合中的自由能贡献分别为-16.88kJ/mol、-17.63kJ/mol,W301水分子在HIV-1PR/ABT-538的结合中起到了关键的作用.进一步分析发现W301水分子与HIV-1PR和ABT-538分别形成了两个、四个氢键.

烟酰胺酶催化水解脱氨反应的QM/MM分子动力学模拟

采用QM(PM3)/MM分子动力学(MD)方法模拟了烟酰胺酶催化烟酰胺水解脱氨形成烟碱酸的反应过程.计算结果表明,硫的亲核进攻是整个反应的速率控制步骤.当改变Ala155所在Loop区的位置,在亲核进攻时,底物能够自由旋转,可以加速亲核进攻过程并降低整个催化反应的能垒.讨论了氨分子的离去过程和质子传递过程的相关细节.为烟酰胺酶的定点突变以及脱氨酶的设计提供了有益的参考.

Molecular Dynamics and Combined QM/MM Studies on the Deactivation of anti-Tubercular Drug Isoniazid by Arylamine N-Acetyltransferases

Both a molecule dynamic study and a combined quantum mechanics and mole-cule mechanics（QM/MM） study on the acetylating deactivation mechanism of isoniazid were presented.This type of reaction was catalyzed by arylamine N-acetyltransferases（NATs） and the results strongly support a direct acetyl group transfer process rather than a stepwise one.The isoniazid was strictly restrained in proper relative position to accept the acetyl group by a Hydrogen-bond network formed by the residues at the active center.The residues,His110 and Cys70,would be functioned as ＇general base＇ rather than ＇general acid＇.If all the residues（including H2O molecules） were removed from the system,the activation energy will be increased from 145.1 to 243.3 kJ/mol.The calculations met the experimental data with good agreement.

QM/MM and MD Studies of the First Proton Transfer for O2 Activation in the Catalytic Cycle of Cytochrome P450cin

P450 cin(CYP176 A1) isolated from Citrobacter braakii is a biodegradation enzyme that catalyzes the enantiospecific conversion of 1,8-cineole to(1 R)-6β-hydroxycineole. In many P450 family members the mechanism of proton delivery for O2activation is proposed to require a conserved acid-alcohol dyad in the active area, while P450 cin has no such residue with alcohol but asparagine instead. In the present work, the mechanism of the first proton transfer of O2activation in P450 cin has been investigated by molecular dynamics(MD) and hybrid quantum mechanics/molecular mechanics(QM/MM) techniques. The MD simulation suggests there are two hydrogen bonding networks around the active site, one involving Asp241 and the other involving Glu356. According to our MD and QM/MM calculations, this Asp241 channel is proposed to be the energy accessible. MD results show that the hydrogen bonds around the substrate may contribute to regio-and stereo-oxidation of the substrate.

QM/MM Study of the Second Harmonic Generation and Two-photon Absorption Properties of a Fluorescent Proteins-Dreiklang

A new reversibly switchable fluorescent protein（RSFP）, namely Dreiklang, exhibits prominent feature that the wavelengths for switching and fluorescence are decoupled due to its great different structures between bright and dark states. This feature might also induce some nonlinear optic（NLO） properties changing as switching between two states, which might promote new method of biological science. We employ the QM/MM method to simulate the structures of different states, and study their second harmonic generation（SHG） and two-photon absorption（TPA） properties. And we found different states of Dreiklang have different SHG and TPA responses. The SHG and TPA properties of Dreiklang are correlated to particularly geometrical structures of different states, especially the centrosymmetric or nocentrosymmetric π-stacking structures which are formed by chromophore and beside residue Tyr203, so the SHG and TPA responses could be changed as the light induces switching among different states of Dreiklang. This work would prospectively guide the application of Dreiklang on the NLO technology, and help the development of new RSFP with special NLO function.

Quantifying Electronic Effects in QM and QM/MM Biomolecular Modeling with the Fukui Function

Multi-scale quantum-mechanical/molecular-mechanical(QM/MM) and large-scale QM simulation provide valuable insight into enzyme mechanism and structure-property relationships. Analysis of the electron density afforded through these methods can enhance our understanding of how the enzyme environment modulates reactivity at the enzyme active site. From this perspective, tools from conceptual density functional theory to interrogate electron densities can provide added insight into enzyme function. We recently introduced the highly parallelizable Fukui shift analysis(FSA) method, which identifies how frontier states of an active site are altered by the presence of an additional QM residue to identify when QM treatment of a residue is essential as a result of quantum-mechanically affecting the behavior of the active site. We now demonstrate and analyze distance and residue dependence of Fukui function shifts in pairs of residues representing different non-covalent interactions. We also show how the interpretation of the Fukui function as a measure of relative nucleophilicity provides insight into enzymes that carry out S_N2 methyl transfer. The FSA method represents a promising approach for the systematic, unbiased determination of quantum mechanical effects in enzymes and for other complex systems that necessitate multi-scale modeling.

Reaction Mechanism of Actin ATP Hydrolysis Studied by QM/MM Calculations

Actin fibers are an important part of the cytoskeleton,providing vital support for the plasma membrane.This function is driven by its ATPase(ATP:adenosine triphosphate)activity,i.e.,ATP+H_(2)O→ADP+Pi.This seemingly simple reaction has attracted much attention because the hydrolysis of ATP provides energy to support life processes.However,the reaction mechanism of ATP hydrolysis in actin is not clear.In order to gain deep insights into the functions of actin,it is essential to elucidate the reaction mechanism of the actin ATP hydrolysis.In this paper,we have studied the reaction mechanism of the ATP hydrolysis in actin by the combined quantum mechanical and molecular mechanics(QM/MM)calculations.Our results show that 1)bond cleavage of the Pγ—OS of ATP and bond formation between oxygen of the lytic water and Pγatoms take place simultaneously,and this is the rate-limiting step of the hydrolysis;2)the proton on the lytic water transfers to the phosphate to form H_(2)P_(γ)O_(4)−via one bridge water.The energy barrier of the complete reaction is 17.6 kcal/mol(1 kcal=4.184 kJ),which is in high agreement with the experimental value.

QM/MM study on the O_(2)activation reaction of 4-hydroxylphenyl pyruvate dioxygenase reveals a common mechanism forα-ketoglutarate dependent dioxygenase

The dioxygen activation catalyzed by 4-hydorxylphenyl pyruvate dioxygenase(HPPD)were reinvestigated by using hybrid quantum mechanics/molecular mechanics(QM/MM)approaches at the B3LYP/6-311++G(d,p):AMBER level.These studies showed that this reaction consisted of two steps including the dioxygen addition/decarboxylation and hetero O-O bond cleavage,where the first step was found to be rate-determining.The former step initially runs on a septet potential energy surface(PES),then switches to a quintet PES after crossing a septet/quintet minimum energy crossing point(MECP)5-7M2,whereas the rest step runs on the quintet PES.The reliability of our theoretical predictions is supported by the excellent agreement of the calculated free-energy barrier value of 16.9 kcal/mol with available experimental value of 16-17 kcal/mol.The present study challenges the widely accepted view which holds that the O2activation catalyzed byα-keto glutamate(α-KG)dioxygenase mainly runs on the quintet PES and provides new insight into the catalytic mechanism ofα-KG dioxygenase and/or other related Fe(Ⅱ)-dependent oxygenase.

抗原肽与MHC分子相互作用QM/MM分子动力学模拟研究

在MHC I类(major histocompatibility complex class I)分子抗原加工提呈过程中抗原蛋白在抗原提呈细胞(antigen-presenting cells,APC)的胞浆中被蛋白酶体(proteasome)裂解成短肽peptide,由转运相关蛋白(transporter associated with antigen processing,TAP)将蛋白酶体裂解产生的短肽片段从胞浆转运至内质网腔.短肽peptide在内质网中与新生成的MHC I类分子结合,形成peptide-MHC复合体被提呈到APC细胞表面,与T细胞表面抗原受体(T cell receptor,TCR)特异性识别结合,使得CTL细胞开始活化、增殖、分化,进而对肿瘤细胞进行特异性杀伤.目前对CTL细胞如何识别抗原肽-MHC复合物分子及抗原短肽peptide如何与主要组织相容性复合体MHC分子的相互作用识别结合的机理还不是很清楚.传统的预测CTL细胞表位的方法没有考虑受体与配体结合过程中电子结构的变化,电子结构的变化需要用量子力学方法来处理.本文采用QM/MM多尺度生物大分子的分子动力学模拟方法,以天然抗原肽TAX(LLFGYPVYVYU)与HLA-A*0201分子结合的晶体结构为模板,替换抗原肽"锚点"氨基酸,将口袋氨基酸残基的原子极化电荷在空间形成的静电势用电多极矩分量表示.用箱线图分析每个口袋氨基酸分子静电势变化和功能,确定Pocket B的Glu63和Lys66的功能是精细识别氨基酸和一级结合氨基酸,Pocket F的Asp77,Tyr84的功能是精细识别氨基酸,而Asp77,Lys146是一级结合氨基酸,表明QM/MM方法在提取抗原肽与MHC I类分子识别结合特异性信息是可行的,这对了解免疫识别机理和指导肿瘤疫苗的开发都具有指导意义.

How Mutations Affecting the Ligand-receptor Interactions： a Combined MD and QM/MM Calculation on CYP2E1 and Its Two Mutants

Cytochrome P450（CYP） 2El is a dual function monoxygenase with a crucial role in the metabolism of 6% of drugs on the market at present. The enzyme is of tremendous interest for its association with alcohol consumption, diabetes, obesity and fasting. Despite the abundant experimental mutagenesis data, the molecular origin and the structural motifs for the enzymatic activity deficiencies have not been rationalized at the atomic level. In this regard, we have investigated the effects of mutation on the structural and energetic characteristics upon single point mutations in CYP2E1, N219D and $366C. The molecular dynamics（MD） simulation combined with quantum mechanics/molecular mechanics（QM/MM） and noncovalent interaction（NCI） analysis was carried out on CYP2EI and its two mutants. The results highlight the critical role of Phe207, which is responsible for both structural flexibility and energetic variation, shortening the gap between the theory and the experimentally observed results of enzymatic activity decrease, The underlying molecular mechanism of the enzymatic activity deficiencies for mutants may be attributed to the changes of spatial position of Phe207 in the two mutants. This work provides particular explanations to how mutations affect ligand-receptor interactions based on combined MD and QM/MM calculations. Furthermore, the mutational effects on the activity of CYP2E1 obtained in the present study are beneficial to both the experimental and the computational works of CYPs and may allow researchers to achieve desirable changes in enzymatic activity.

Infrared spectroscopy of N-methylacetamide in water from high-level QM/MM calculations

The infrared （IR） spectra of the N-methylacetamide molecule in water are calculated by using the MD simulation with high-level QM]MM corrections. The B3LYP and MP2 levels with 6-31 I＋＋G＊＊ basis set are used for the QM region, respectively, Our results show all IR spectra at the B3LYP level are well consistent with the corresponding MP2 results. A dynamical charge fluctuation is observed for each atom along the simulation trajectories due to the electrostatic polarization （EP） effects from surrounding solvent environment, We find that the QM/MM corrected IR spectra satisfactorily reprodnce the experimental vibrational features of amide 1-11I modes.

Catalytic Mechanism of Cytochrome P450 2D6 for 4-Hydroxylation of Aripiprazole： A QM/MM Study

Drug metabolism is an important issue in drug discovery. Understanding how a drug is metabolized in the body will provide helpful information for lead optimization. Cytochrome P450 2D6 （CYP2D6） is a key enzyme for drug metabolism and responsible for the metabolism of about one third marketed drugs. Aripiprazole is an atypical an- tipsychotic and metabolized by CYP2D6 to its hydroxylated form. In this study, a series of computational methods were performed to understand how CYP2D6 accomplishes the 4-hydroxylation of aripiprazole. Molecular docking and molecular dynamics simulations were first performed to prepare the initial conformations for QM/MM calcula- tions. The results revealed two possible conformations for the drug-CYP2D6 complex. The ONIOM method for QM/MM calculations was then carried out to show detailed reaction pathways for the CYP2D6-catalyzed aripipra- zole hydroxylation reaction, which demonstrated that the dominant reactive channel was electrophilic and involved an initial attack on the n-system of the dichlorophenyl group of aripiprazole to produce cation δ-complex. Further- more, the product complex for each conformation was thermodynamically stable, which is in good agreement with previous reports.

QM/MM在计算DNA与配体评分函数的准确性研究

目的:评估QM/MM方法和Surflex-Dock分子对接程序对DNA-配体复合物模拟的准确性。方法:从蛋白质数据库(Protein Data Bank)下载DNA-配体复合物的三维结构,利用计算机辅助药物设计的分子对接程序Surflex-Dock模拟出147个诱饵化合物(decoys)并计算其结合分数(binding score)。然后将得出的分数与从QM/MM计算的结合能力以Z-score和辨别力(DP)作比较。从而评估Surflex-Dock和QM/MM的准确性。结果:Surflex-Dock的DPi值比QM/MM高,显示Surflex-Dock的辨别力较低。结论:因QM/MM计算速度慢,本研究认为Surflex-Dock可用作快速虚拟筛选,而较准确的QM/MM则适合用于对拥有较高结合分数的化合物进行再评分(rescoring)。

丝组二肽对DNA切割作用的QM-MM研究

运用QM MM方法对丝组二肽切割DNA作用的机理进行了研究 .通过计算得到了丝组二肽与DNA形成多氢键作用的有效分子识别模型及相关分子结构参数 ,从理论上解释了丝组二肽与DNA通过形成五配位磷中间体而使磷酸二酯键发生水解 ,从而使得DNA被切断的作用机理 .

QM/MM自由能模拟3-吲哚乙酸甲基转移(IAMT):催化机理和底物特异性(英文)

3-吲哚乙酸甲基转移(IAMT)催化甲基化植物激素3-吲哚乙酸(IAA)的端位自由羧酸,被认为在叶片发育过程中起到了至关重要的作用.然而,目前对于酶催化机理的详尽过程尚未被研究。在这里本文对拟南芥的甲基转移过程(AtIAMT1)进行结合量子力学和分子力学(QM/MM)的自由能模拟,并确定了其催化机制及IAMTs的底物特异性根源.研究表明,从S腺苷L甲硫氨酸(AdoMet)到3-吲哚乙酸盐(IAA)的甲基转移自由能垒要比从AdoMet到水杨酸盐的自由能垒低很多,这与之前的实验发现以及酶的底物特异性完全一致.这表明,与水杨酸相比,IAA相对高效性的甲基化是由于一部分过渡态构型的稳定性可能通过底物结合反映在反应物里,本文研究支持了之前关于计算模拟可对SABATH系列中酶的底物特异性根源进行深入理解的设想,并且可用来帮助生成可控的并具其他底物特异性的酶的实验研究.

[C_(2)mim][BF_(4)]离子液体^(1)H NMR性质的理论研究

本研究选择1-甲基-3-乙基咪唑四氟硼酸盐(简称[C_(2)mim][BF_(4)])离子液体为研究对象,计算其^(1)H NMR化学位移。首先,我们构建了含有20对阴阳离子的凝聚相体系,采用分子动力学模拟方法获得其凝聚相的平衡态结构。随后,我们等间距的选择5个平衡态结构,用于构建QM/MM模型,详细考察两种QM/MM模型对离子液体^(1)H NMR性质的影响。选取的两种QM/MM模型中的QM分别是一个阳离子、一对阴阳离子。在QM/MM计算中,QM层采用B97-2/pcseg-2模型,MM层采用UFF点电荷模型。我们发现,QM/MM计算结果比仅采用一个阳离子的计算结果与实验值更加的接近。我们考察了MM背景电荷对计算结果的影响,研究表明,当MM层有背景电荷时,其实验值与计算值的偏差为0.30,当MM无背景电荷时,其实验值与计算值的偏差为0.31,表明MM的背景电荷对计算结果的影响较小。

HY分子筛催化异丁烷/丁烯烷基化反应中氢负离子转移过程的模拟

建立了120T HY分子筛模型,应用QM/MM方法,揭示了叔/仲丁基烷氧基团(t-butyl alkoxide/s-butyl alkoxide,TBA/SBA)与异丁烷分子发生氢负离子转移反应的机理,并分析比较了二者的异同。结果表明,碳正离子是氢负离子转移反应的过渡态。与TBA相比,SBA与异丁烷分子发生氢负离子转移反应的能垒高出27.5kJ/mol。这是由于TBA的C—O键长大于SBA,因而C—O键断裂所需能量更低,导致反应能垒更低。C—O键断裂后,TBA生成叔丁基碳正离子,SBA生成仲丁基碳正离子,前者中心碳原子所带电荷大于后者,因而与仲丁基碳正离子相比,叔丁基碳正离子更容易与异丁烷分子形成C—H—C"三中心两电子"结构。

理论计算中溶剂效应模型的构建及应用

目前计算溶剂效应的方法主要有两种:一种是自洽反应场(self-consistent reactionfield,SCRF)理论计算法,该方法从发展初期至今一直应用广泛;另一类是将量子力学(quantum mechan-ics,QM)和分子力学(molecular mechanics,MM)结合起来,分别用量子力学和分子力学来计算化合物及所在溶剂的结构与性质,这种方法近几年发展较快。笔者通过大量的文献论证了加入溶剂效应所得出的计算结果更加接近真实的实验结果这一结论。