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.     

模拟酶催化荧光反应测定核酸

痕量核酸对meso-四-(3-N-甲基吡啶基)卟啉合锰(Mn-TMPyP)催化H2O2氧化对-羟基苯乙酸(p-HPA)的荧光反应产生增强作用,且增强程度与核酸浓度之间有良好韵线性关系,据此建立了测定核酸的高灵敏的荧光分析方法。在最佳条件下,测定小牛胸腺DNA和酵母RNA的线性范围分别是2．0-150μg/L和5．0-100μg／L;检出限分别为0．6和1．6μg/L。对50μg／L CT DNA作7次平行测定,相对标准偏差为1．6％。本法已应用于锯缘青蟹样品中核酸含量的测定,所得结果与紫外吸收法一致。     

血红素近轴侧基氢键的ABEEM/MM分子动力学模拟

应用ABEEM/MM浮动电荷力场对鲸鱼肌红蛋白及突变体进行了分子动力学模拟. 结果表明, 血红素近轴侧基不存在稳定的双氢键, 该氢键对轴配体咪唑的取向不起决定性作用, 而咪唑的取向与键联的组氨酸有密切联系. 同时表明, 血红素轴配体的柔性与其邻近的氨基酸和咪唑体积有关.     

超临界水的分子动力学模拟

采用分子动力学(MD)模拟的方法对超临界条件下水的结构及扩散性质进行了研究.模拟结果表明超临界条件下水分子之间的氢键作用明显减弱,分子极性大大降低.扩散性质与常温下相比,其大小约上升了两个数量级.     

微过氧化物酶水溶液的ABEEM/MM动力学模拟

应用原子-键电负性均衡浮动电荷分子力场(ABEEM/MM), 对微过氧化物酶水溶液进行了分子动力学模拟. 研究了水溶液对微过氧化物酶的结构, 血红素的皱裂构象以及轴配体咪唑基的取向的影响. 结果表明, 在水溶液中微过氧化物酶的骨架氨基酸是稳定的, 而血红素的皱裂构象在水分子的作用下趋于平面. 与血红素轴配体咪唑基键连的组氨酸决定着咪唑基的空间取向, 而咪唑基与血红素侧链的丙酸基的静电作用对其取向仅起次要作用.     

H-β和H-MOR分子筛催化甲苯与叔丁醇叔丁基化反应机理:QM/MM研究

本文采用分层计算(own-N-layered integrated molecular orbit+molecular mechanics, ONIOM)和密度泛函理论(DFT)组合的方法,系统地研究了H-β和H-MOR催化甲苯与叔丁醇叔丁基化反应机理.依据结构参数分析和相对自由能结果,考察了沿叔丁基化路径的共吸附复合物和过渡态结构的稳定性,对比研究了分子筛的催化性能.在116T ONIOM2模型中, H-MOR催化甲苯叔丁基化反应的自由能垒更低,证明其催化活性比H-β更好.随着温度从298 K升高为453 K,两种催化剂催化甲苯叔丁基化反应的能垒都降低,说明温度对促进甲苯转化有重要作用.与3-叔丁基甲苯相比, H-β和H-MOR分子筛通过形成更稳定的C4-过渡态结构可以获得非常高的4-叔丁基甲苯选择性.相对反应速率常数的计算结果也表明, 4-叔丁基甲苯为动力学优先生成产物,并且发现H-β对C4位的选择性比H-MOR更高.     

非水介质中酶催化的反应研究新进展

介绍了非水介质中酶催化反应有机合成中的应用及手性化合物的酶促拆分与合 成反应，分析了冷冻干燥保护剂和修饰剂对酶性质的影响，论述了固定化酶在有机 溶剂中的应用，并讨论了影响固定化酶性质的因素。     

抗体催化的氨酰化反应

酰基转移反应在许多生物学或化学过程中都起着十分重要的作用。氨酰tRNA合成酶在蛋白质生物合成中起关键作用。它催化tRNA的终端腺苷上2′,3′-二醇的酯化反应。伯克利化学系的Schultz小组最近提出这样一个问题,能否产生催化这类反应的抗体。这样的抗体也许会加速tRNA与新氨基酸的氨酰化,可用于蛋白质的生物合成研究。他们发现,针对磷酸二酯过渡态类似物产生的一种     

水滑石/氯化锌催化Knoevenagel缩合反应

浸渍法制备水滑石负载氯化锌(LDH/ZnCl2)催化剂,使用傅里叶变换红外光谱(FT-IR)、扫描电镜(SEM)、比表面积(BET)、热重分析(TG)对催化剂进行表征.结果表明:在FT-IR中LDH/ZnCl2出现LDH骨架特征吸收峰和ZnCl2特征吸收峰,SEM图中LDH/ZnCl2的表面比LDH表面粗糙,可以辅证Z...     

基于过氧化物模拟酶催化显色反应的博来霉素比色检测

首次报道了博来霉素(BLM)与亚铁离子相互结合,形成的BLM·Fe(Ⅱ)复合物具有内在的过氧化物模拟酶催化活性,能够催化过氧化氢氧化2,2'-联氮基-双(3-乙基苯并噻唑-6-磺酸)(ABTS)的显色反应,产生深绿色的产物。与天然酶辣根过氧化物酶类似,BLM·Fe(Ⅱ)复合物的催化活性强烈依赖于pH值和温度,相应的最优化条件分别为pH 6.0和30℃。利用BLM·Fe(Ⅱ)复合物催化ABTS的显色反应,建立了一种简便快捷的可视化检测博来霉素的新方法,检出限可达14.1 nmol/L。该检测方法还显示了良好的可重复性和选择性,在临床分析中具有潜在的应用价值。     

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 Methods for Biomolecular Systems

Two are better than one : Quantum mechanics/molecular mechanics (QM/MM) methods are the state‐of‐the‐art computational technique for treating reactive and other “electronic” processes in biomolecular systems. This Review presents the general methodological aspects of the QM/MM approach, its use within optimization and simulation techniques, and its areas of application, always with a biomolecular focus.

     

QM/MM Studies on Cyclodextrin-Alcohol Interaction

The main objective of this study is to provide an insight into the interactions involved during adsorption of the alcohols on β-CD composite nanostructured membrane. Interactions between β-cyclodextrin (β-CD) and alcohols (methanol, ethanol and butanol) are studied using the QM/MM method. Magnitude of interaction energies show that the alcohols are adsorbed on the membrane. In addition, the thermochemical analysis suggests that the formation of these host-guest complexes is enthalpy driven.     

How Photoisomerization Drives Peptide Folding and Unfolding: Insights from QM/MM and MM Dynamics Simulations

Photoswitchable azobenzene cross‐linkers can control the folding and unfolding of peptides by photoisomerization and can thus regulate peptide affinities and enzyme activities. Using quantum mechanics/molecular mechanics (QM/MM) methods and classical MM force fields, we report the first molecular dynamics simulations of the photoinduced folding and unfolding processes in the azobenzene cross‐linked FK‐11 peptide. We find that the interactions between the peptide and the azobenzene cross‐linker are crucial for controlling the evolution of the secondary structure of the peptide and responsible for accelerating the folding and unfolding events. They also modify the photoisomerization mechanism of the azobenzene cross‐linker compared with the situation in vacuo or in solution.     

Developing adaptive QM/MM computer simulations for electrochemistry

We report the development of adaptive QM/MM computer simulations for electrochemistry, providing public access to all sources via the free and open source software development model. We present a modular workflow‐based MD simulation code as a platform for algorithms for partitioning space into different regions, which can be treated at different levels of theory on a per‐timestep basis. Currently implemented algorithms focus on targeting molecules and their solvation layers relevant to electrochemistry. Instead of using built‐in forcefields and quantum mechanical methods, the code features a universal interface, which allows for extension to a range of external forcefield programs and programs for quantum mechanical calculations, thus enabling the user to readily implement interfaces to those programs. The purpose of this article is to describe our codes and illustrate its usage. © 2016 Wiley Periodicals, Inc.     

Chaperoned alchemical free energy simulations: a general method for QM, MM, and QM/MM potentials

A general method for alchemical free energy simulations using QM, MM, and QM/MM potential is developed by introducing "chaperones" to restrain the structures, particularly near the end points. A calculation of the free energy difference between two triazole tautomers in aqueous solution is used to illustrate the method.     

QM/MM study of the taxadiene synthase mechanism

Combined quantum mechanics/molecular mechanics (QM/MM) calculations were used to investigate the reaction mechanism of taxadiene synthase (TXS). TXS catalyzes the cyclization of geranylgeranyl diphosphate (GGPP) to taxadiene (T) and four minor cyclic products. All these products originate from the deprotonation of carbocation intermediates. The reaction profiles for the conversion of GGPP to T as well as to minor products were calculated for different configurations of relevant TXS carbocation complexes. The QM region was treated at the M06-2X/TZVP level, while the CHARMM27 force field was used to describe the MM region. The QM/MM calculations suggest a reaction pathway for the conversion of GGPP to T, which slightly differs from previous proposals regarding the number of reaction steps and the conformation of the carbocations. The QM/MM results also indicate that the formation of minor products via water-assisted deprotonation of the carbocations is highly exothermic, by about −7 to −23 kcal/mol. Curiously, however, the computed barriers and reaction energies indicate that the formation of some of the minor products is more facile than the formation of T. Thus, the present QM/MM calculations provide detailed insights into possible reaction pathways and into the origin of the promiscuity of TXS, but they do not reproduce the product distribution observed experimentally. © 2019 Wiley Periodicals, Inc.