SARS冠状病毒E蛋白的结构研究及功能预测

结合生物信息学方法及分子模拟手段,选择较高准确度的方法,预测了SARSE蛋白的分子结构并探讨其潜在的生物学活性和功能.研究结果表明,SARSE蛋白跨膜区25个疏水的氨基酸形成α-螺旋结构,包埋于病毒外壳磷脂双分子层中;N端10个氨基酸残基位于膜外;C端41个残基则附着于磷脂双分子膜内侧.同时发现,C端由9个氨基酸组成的劈裂是一个可能的活性部位.对分子进行进一步静电势分析证实,E蛋白C端可能的活性部位具有较大的静电势,可能的活性残基具有最大电荷密度,故有较强的结合受体或与其它蛋白相互作用的能力.     

杜鹃花科植物有毒成分的电子结构及构效关系

本文应用INDO方法, 对由杜鹃花科植物中提取分离的九个化合物进行了量子化学计算, 得到了分子轨道波函数等多种电子结构信息, 并计算了这些化合物活性部位的分子静电势, 得到了静电势图。用分子图形技术与药理性质相同的其它生物碱类毒素进行了空间结构比较。研究了它们的电子结构特征和活性部位, 讨论了作用机理及电子结构与毒性之间的关系。     

红细胞标记抗体的化学发光免疫分析

用红细胞代替辣根过氧化物酶作为双抗体夹心免疫分析中第二抗体的标记物, 建立了一种红细胞标记抗体的免疫化学发光测定乙型肝炎病毒表面抗原的新方法. 在免疫反应完成后, 结合了抗原-抗体免疫复合物的致敏红细胞在低渗溶液中溶血, 释放出血红蛋白. 基于血红蛋白对鲁米诺-H2O2体系化学发光具有催化作用的原理, 采用化学发光法测定血红蛋白含量. 测得的血红蛋白发光强度与待测抗原浓度呈线性关系. 采用这种方法可检测出0.5 ng/mL的乙型肝炎病毒表面抗原. 将该方法与酶联免疫吸附分析(ELISA)结合起来对乙型肝炎患者血清乙肝病毒表面抗原(HBsAg)进行检测, 两者符合率均为97%, 表明本法具有良好的灵敏度和特异性, 可用于临床标本测试.     

黄酮类化合物的密度泛函理论研究

在混合密度泛函B3LYP理论下,用6-31G*基函数研究了几种典型黄酮类化合物分子的几何结构、电子结构和分子的静电势,讨论了电子结构和分子活性部位的关系.     

adr亚型乙型肝炎病毒表面抗原基因在大肠杆菌中的表达

利用adr亚型乙型肝炎病毒(HBV)DNA克隆株,组建表面抗原(HBsAg)基因表达质粒。用竞争性抑制放射免疫分析方法和聚丙烯酰胺——SDS凝胶电泳检测表达产物,获得了含HBsAg的杂合多肽。     

合并血浆中病毒标记检测临界值的确定分析

确保合并血浆检测结果的判定准确可靠,能够有效保证合并血浆的病毒安全性,对合并血浆乙型肝炎病毒表面抗原、丙型肝炎病毒抗体、人类免疫缺陷病毒抗体检测时不同厂家检测试剂的临界值进行确定。(1)使用双抗体夹心酶联免疫法对合并血浆HBsAg和HIV-1/HIV-2抗体的检测临界值进行确定。(2)使用酶联免疫法检测合并血浆HCV抗体的临界值进行确定。经检测和计算,两个厂家检测试剂的检测临界值系数分别为乙型肝炎病毒表面抗原23.398%和26.845%、丙型肝炎病毒抗体9.012%和16.481%、人类免疫缺陷病毒抗体20.025%和23.424%。     

7313、7321系列农药的构效关系研究

对7313、7321系列农药利用MOPAC程序包PM3方法进行量子化学计算,讨论了它们的活性部位及构效关系,发现形成6员稠合环结构有利于分子产生药效,N(7)、S(9)、N(11)、C(12)等原子分别与受体的自由基相作用,是该类农药产生共同生物活性的化学基础。     

静电势方法研究分子间的电子转移 II: 在光电转移模拟体系中的应用

用从头算和静电势方法研究了光电转换模拟体系C~6H~7N+C~6H~8N^+中的分子间电荷转移。通过计算分子间的静电势分布, 确定了电子在分子间运动所需穿透势垒的特性, 对电子穿透几率及穿透弛时间等参数作了理论预测并研究了外接基团的影响。在分子间距d=0.35nm时, 穿透几率P=2.94x10^-^4, 穿透弛豫时间τ=3.4x10^-^1^0s, 在此情况下, 由模型分子组成的截面积为10x1mm^2的多层分子膜, 在光照条件下可能产生的理论光电流为0.28A。     

静电势方法研究分子间的电子转移 II: 在光电转移模拟体系中的应用

用从头算和静电势方法研究了光电转换模拟体系C~6H~7N+C~6H~8N^+中的分子间电荷转移。通过计算分子间的静电势分布, 确定了电子在分子间运动所需穿透势垒的特性, 对电子穿透几率及穿透弛时间等参数作了理论预测并研究了外接基团的影响。在分子间距d=0.35nm时, 穿透几率P=2.94x10^-^4, 穿透弛豫时间τ=3.4x10^-^1^0s, 在此情况下, 由模型分子组成的截面积为10x1mm^2的多层分子膜, 在光照条件下可能产生的理论光电流为0.28A。     

单环共轭多烯的结构与芳香性研究

基于先进的量化计算软件Gaussian和波函数分析软件Multiwfn,研究结构化学课程中七种单环共轭多烯和环碳18的结构,形成“有图有真相”的立体直观的分子空间结构,形象化展示了各个分子的几何结构、分子尺寸、静电势、芳香性等。将课本知识与先进的量化软件结合起来,在量子化学层次上拓展有关芳香性的认识,引导学生加深对课本知识的理解,同时开拓学生的视野和知识层次。     

一种乙肝病毒表面抗原和其单克隆抗体相互作用的SERS研究

利用银纳米粒子的表面增强拉曼散射（SERS）效应，研究了乙肝病毒表面抗原 （HBsAg)和其鼠源单克隆抗体（单抗，Ab-HBsAg)的相互作用。SERS光谱结果表明 ，Ab-HBsAg分子主要通过位于非抗原结合部位的去质子化羧基（COO）^-实现与银 纳米粒子的结合。HBsAg与Ab-HBsAg相互作用形成免疫复合物后，HBsAg分子上的色 氨酸（Trp)残基特征振动完全消失，表明Trp残基位于HBsAg抗原分子的活性区，是 HBsAg与Ab-HBsAg相互作用的重要位点。     

Exploring the conformation,charge density distribution and the electrostatic properties of galanthamine molecule in the active site of AChE using DFT and AIM theory

Quantum chemical calculations and charge density analysis were carried out to understand the geometry, charge density distribution and the electrostatic properties of isolated galanthamine molecule (form I) and for the same lifted out from the active site (form II) of AChE. The optimized geometry of isolated galanthamine was obtained from a hybrid density functional theory (B3LYP/6‐311G**) calculation. A docking analysis on galanthamine with AChE was performed, and the lowest docked energy structure was selected from the active site of AChE for the further study. A single point energy quantum chemical calculation (B3LYP/6‐311G**) was carried out for the lowest energy structure, which was lifted from the galanthamine–AChE complex from molecular docking analysis. The structural comparison between (I) and (II) helps to understand the conformational modification of the galanthamine molecule in the active site. When the molecule present in the active site, the molecular geometry is seen to be significantly altered, specifically, large changes were observed in the outer core of the molecule while the inner core geometry is intact. The bond topological and electrostatic properties of (I) and (II) were calculated. The dipole moment of the galanthamine molecule also increases from 2.09 to 2.67 D in the process. A large negative electrostatic potential region is found at the vicinity of oxygen and nitrogen atoms of the molecule, which predominantly involve strong hydrophobic and electrostatic interactions with the amino acid residues TRP84, PHE330, GLY118, TYR70, and SER122 present in the active site of AChE. © 2013 Wiley Periodicals, Inc.     

Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins

The electrostatic potential plays a key role in many biological processes like determining the affinity of a ligand to a given protein target, and they are responsible for the catalytic activity of many enzymes. Understanding the effect that amino acid mutations will have on the electrostatic potential of a protein, will allow a thorough understanding of which residues are the most important in a protein. MutantElec, is a friendly web application for in silico generation of site‐directed mutagenesis of proteins and the comparison of electrostatic potential between the wild type protein and the mutant(s), based on the three‐dimensional structure of the protein. The effect of the mutation is evaluated using different approach to the traditional surface map. MutantElec provides a graphical display of the results that allows the visualization of changes occurring at close distance from the mutation and thus uncovers the local and global impact of a specific change. © 2017 Wiley Periodicals, Inc.     

Translational Enhancer of Tobacco mosaic virus Enhancing Expression of Hepatitis B Surface Antigen in Transgenic Panax ginseng C. A. Meyer Callus

The 5＇-nontranslated leader（omega sequence） of Tobacco mosaic virus（TMV） was used as a translational enhancer sequence in the expression of the hepatitis B surface antigen（HBsAg） gene in transgenic ginseng callus cultures. The adr subtype HBsAg gene was placed under the control of the Cauliflower mosaic virus（CaMV） 35S promoter linking to the TMV leader sequence. The antisense omega sequence was used in a control construct. The resulting constructs cloned in the binary vector pBI121 were used to transform the ginseng callus tissue via the Agrobacterium-mediated procedure. The integration and expression of the HBsAg gene were evaluated by PCR and western blot, respectively. Enzyme-linked immunoassays（ELISA） using a monoclonal antibody directed against human serum-derived HBsAg revealed a three to four-fold enhanced expression of HBsAg in ginseng cells conferred by the TMV omega element.     

酮醇酸还原异构酶(KARI)与其抑制剂间相互作用的分子模拟研究

采用MCCE, Autodock及密度泛函方法对酮醇酸还原异构酶(KARI)与其抑制剂间相互作用进行了研究. 计算结果表明, KARI活性位点中的Mg^2＋在活性位点残基的离子化状态、活性位点的静电性质以及与抑制剂结合等方面起重要的作用; 同时, 抑制剂在结合方式、前线轨道布居及静电势等方面与酶促反应中间体(HOIV)具有一定程度的相似性; 可电离的羧基是当前发现的靶向KARI抑制剂一个重要的结构特征, 进一步推广可认为潜在的抑制剂应该拥有可电离成负电荷的功能团. 在药物设计中考虑到以上结论, 将有利于发现和改造靶向KARI的抑制剂.     

某些海生毒素(TTX、STX)对钠离子通道的作用研究

研究了河豚毒素（TTX）和石房蛤毒素（STX）及其衍生物的电子结构和分子构型．结果表明TTX中的胍基和半缩醛内酯环以及STX中的两个胍基均形成具有一个碳正电中心的两个高极性平面构型，三角形三个顶点的氮和氧原子分别带有大量负电荷．TTX和STX具有相似的电子结构和空间结构．对于TTX和STX及其衍生物的作用机理以及分子构型与毒性之间的关系也进行了讨论．     

Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path

The structure and dynamics of the hepatitis delta virus ribozyme (HDVr) are studies using molecular dynamics simulations at several stages along its catalytic reaction path, including reactant, activated precursor, transition state mimic and product states, departing from an initial structure based on the C75U mutant crystal structure (PDB: 1VC7). Results of five 350 ns molecular dynamics simulations reveal a spontaneous rotation of U-1 that leads to an in-line conformation and support the role of protonated C75 as the general acid in the transition state. Our results provide rationale for the interpretation of several important experimental results, and make experimentally testable predictions regarding the roles of key active site residues that are not obvious from any available crystal structures.     

Photochemically inactivated hepatitis B virus promotes upregulation of Th1-type cytokines

Photochemical virus inactivation technology is widely used to improve the safety of blood products. However, the process by which this inactivation occurs and the resulting immunogenicity of treated viruses remain to be elucidated. This study aimed to explore the effects of two photochemical inactivation methods (methylene and riboflavin, MP and RP) on hepatitis B virus (HBV) immunogenicity. Inactivated HBV were incubated with PBMC from six healthy donors. Culture supernatants were collected at 0, 24 and 72 h for the analysis of HBsAg and HBeAg expression using ELISA. Cytokine expression was analyzed at 72 h using ELISA. Costimulatory and cell adhesion molecule mRNA expression was analyzed at 24 h by RT–PCR. No significant changes in HBsAg and HBeAg were detected following MP. However, the secretion of TNF‐α and IFN‐γ was upregulated. Expression of CD80, CD86, ICAM2 and LFA3 mRNA was also upregulated. In contrast, although RP did not significantly alter HBsAg expression, a reduction in HBeAg expression was observed. Furthermore, no upregulation of cytokines and intracellular molecule expression was observed following RP. These data indicate that the immunogenicity of HBV is retained following MP, and the inactivation of HBV could upregulate the Th1‐type cellular immune responses, which may play significant roles in the antiviral process.     

In silico design novel (5-imidazol-2-yl-4-phenylpyrimidin-2-yl)[2-(2-pyridylamino)ethyl]amine derivatives as inhibitors for glycogen synthase kinase 3 based on 3D-QSAR,molecular docking and molecular dynamics simulation

Glycogen Synthase Kinase 3 (GSK-3) is a member of cellular kinase with various functions, such as glucose regulation, cellular differentiation, neuronal function and cell apoptosis. It has been proved as an important therapeutic target in type 2 diabetes mellitus and Alzheimer's disease. To better understand their structure–activity relationships and mechanism of action, an integrated computational study, including three dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, and molecular dynamics (MD), was performed on 79 (5-Imidazol-2-yl-4-phenylpyrimidin-2-yl)[2-(2-pyridylamino)ethyl]amine GSK-3 inhibitors. In this paper, we constructed 3D-QSAR using comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) method. The results showed that the CoMFA model (q ² = 0.743, r² = 0.980) and the CoMSIA model (q² = 0.813, r² = 0.976) had stable and reliable predictive ability. The electrostatic and H-bond donor fields play important roles in the models. The contour maps of the model visually showed the relationship between the activity of compounds and their three-dimensional structure. Molecular docking was used to identify the key amino acid residues at the active site of GSK-3 and explore its binding mode with ligands. Based on 3D-QSAR models, contour maps and the binding feature between GSK-3 and inhibitor, we designed 10 novel compounds with good potential activity and ADME/T profile. Molecular dynamics simulation results validated that Ile62, Val70 and Lys85 located in the active site play a key role for GSK-3 complexed with inhibitors. These results might provide important information for designing GSK-3 inhibitors with high activity.