Three‐body expansion of the fragment molecular orbital method combined with density‐functional tight‐binding

The three‐body fragment molecular orbital (FMO3) method is formulated for density‐functional tight‐binding (DFTB). The energy, analytic gradient, and Hessian are derived in the gas phase, and the energy and analytic gradient are also derived for polarizable continuum model. The accuracy of FMO3‐DFTB is evaluated for five proteins, sodium cation in explicit solvent, and three isomers of polyalanine. It is shown that FMO3‐DFTB is considerably more accurate than FMO2‐DFTB. Molecular dynamics simulations for sodium cation in water are performed for 100 ps, yielding radial distribution functions and coordination numbers. © 2017 Wiley Periodicals, Inc.     

Toward deformation densities for intramolecular interactions without radical reference states using the fragment,atom, localized,delocalized, and interatomic (FALDI) charge density decomposition scheme

A novel approach for calculating deformation densities is presented, which enables to calculate the deformation density resulting from a change between two chemical states, typically conformers, without the need for radical fragments. The Fragment, Atom, Localized, Delocalized, and Interatomic (FALDI) charge density decomposition scheme is introduced, which is applicable to static electron densities (FALDI‐ED), conformational deformation densities (FALDI‐DD) as well as orthodox fragment‐based deformation densities. The formation of an intramolecular NH⋅⋅⋅N interaction in protonated ethylene diamine is used as a case study where the FALDI‐based conformational deformation densities (with atomic or fragment resolution) are compared with an orthodox EDA‐based approach. Atomic and fragment deformation densities revealed in real‐space details that (i) pointed at the origin of density changes associated with the intramolecular H‐bond formation and (ii) fully support the IUPAC H‐bond representation. The FALDI scheme is equally applicable to intra‐ and intermolecular interactions. © 2017 Wiley Periodicals, Inc.     

固态纳米孔对蛋白质易位的实验研究

蛋白质因其多样性和功能性,是生物体内一类非常重要的分子.通常蛋白质的表征需要借助荧光或者酶的标记.而纳米孔技术,得益于免标记、单分子检测等优势,为蛋白质的表征提供了新方向.我们使用固态纳米孔完成了单个蛋白质分子及蛋白质-蛋白质结合物的检测.可以发现,外部电压和电解质溶液的酸碱度会直接影响蛋白质分子表面带电量,从而加快或延迟其在孔内的易位时间.抗原、抗体本质上都是蛋白质,两者之间具有高度特异性.通过比较抗体溶液在添加特异性抗原前后的易位事件,实现了单个蛋白质分子和蛋白质-蛋白质结合物的区分.未来,纳米孔技术有望应用于多蛋白质分子的辨识、蛋白质分子相互作用机制等方面的研究.     

A New Competitive Inhibitory Monoclonal Antibody to Carboxypcptidase A (CPA)

Catalyticantibodiesareanewclassofbiocatalysts,andhavebeenusedtocatalyzemanytypesofchemicalreactionsuccessfully'.Atpresent,itisdifficulttousecatalyticantibodiestocatalyzethehydrolysisofamidebond.Howtodesignandpreparethecatalyticantibodiesthatcaneffectivelycatalyzethehydrolysisofamidebondhasbeenanunsolvedproblem.Butthehydrolysisandsynthesisofamidebondareveryimportantchemicalandbiologicalreactions.Therefore,toproducethecatalyticantibodieswhichcancatalyzethehydrolysisofamidebondisasignificantresea…     

临床诊断试剂及其诊断方法研究进展

本文结合作者工作,综述了现代临床化学所用诊断试剂,以及诊断方法学研究的某些进展与发展趋向。     

补体C1q压电免疫传感器的研究

研制了一种可重复使用的压电免疫传感器用于检测补体C1q.比较了聚乙烯亚胺粘附、戊二醛交联法,物理吸附法以及蛋白A法三种固定化抗体蛋白的方法.使用蛋白A法,补体C1q在所测浓度范围内有良好的线性关系.使用过的晶片用0.1 mol/L柠檬酸盐缓冲溶液(pH 3.0)解吸,可重复使用4次.     

Sol-gel entrapment of monoclonal anti-atrazine antibodies

We report the successful doping of a sol-gel matrix with an antibody, retaining its ability to bind free antigen from an aqueous solution. The particular system described is monoclonal anti-atrazine mouse antibody which was entrapped in SiO₂ sol-gel matrices, prepared from tetramethoxysilane by several methods. Atrazine was selected as a model compound for this study, within the framework of the development of immunochemical-based methods for monitoring pesticide residues and other organo-synthetic environmental contaminants. Nanogram quantities of atrazine were applied on SiO₂ sol-gel columns doped with this antibody, and the amount of eluted antigen was determined by Enzyme Linked ImmunoSorbent Assay (ELISA). Under appropriate sol-gel-forming conditions, high amounts of atrazine were bound to the sol-gels, ranging between 60% and 91% of the amount applied to the column. The combination of the properties of the sol-gel matrix (e.g., stability, inertness, high porosity, high surface area and optical clarity), together with the selectivity and sensitivity of the antibodies, enable extension of this feasibility study to development of a novel group of immunosensors which could be used for purification, concentration and monitoring of a variety of residues from different sources.Contribution from the Agricultural Research Organization (ARO), Bet Dagan, Israel. No., 1697-E, 1995 series.     

Revised mechanism of carboxylation of ribulose‐1,5‐biphosphate by rubisco from large scale quantum chemical calculations

Here, we describe a computational approach for studying enzymes that catalyze complex multi‐step reactions and apply it to Ribulose 1,5‐bisphosphate carboxylase–oxygenase (Rubisco), the enzyme that fixes atmospheric carbon dioxide within photosynthesis. In the 5‐step carboxylase reaction, the substrate Ribulose‐1,5‐bisphosphate (RuBP) first binds Rubisco and undergoes enolization before binding the second substrate, CO₂. Hydration of the RuBP.CO₂ complex is followed by C C bond scission and stereospecific protonation. However, details of the roles and protonation states of active‐site residues, and sources of protons and water, remain highly speculative. Large‐scale computations on active‐site models provide a means to better understand this complex chemical mechanism. The computational protocol comprises a combination of hybrid semi‐empirical quantum mechanics and molecular mechanics within constrained molecular dynamics simulations, together with constrained gradient minimization calculations using density functional theory. Alternative pathways for hydration of the RuBP.CO₂ complex and associated active‐site protonation networks and proton and water sources were investigated. The main findings from analysis of the resulting energetics advocate major revision to existing mechanisms such that: hydration takes place anti to the CO₂; both hydration and C C bond scission require early protonation of CO₂ in the RuBP.CO₂ complex; C C bond scission and stereospecific protonation reactions are concerted and, effectively, there is only one stable intermediate, the C3‐gemdiolate complex. Our main conclusions for interpreting enzyme kinetic results are that the gemdiolate may represent the elusive Michaelis–Menten‐like complex corresponding to the empirical K_m (=K_c) with turnover to product via bond scission concerted with stereospecific protonation consistent with the observed catalytic rate. © 2018 Wiley Periodicals, Inc.     

The Synthesis of N-Morphine Hapten and Production of Monoclonal Antibody

The drug overdose and addiction is a serious international problem. Therefore developing a rapid, accurate, convenient and cheap method for detecting morphine in urea is useful and necessary, especially for investigation of epidemiology, identification of medical jurisprudence and determination of drug addict etc. There are many compounds that are similar to morphine in chemical structure and tend to have cross-reaction with the anti-morphine antibody. In order to reduce the cross reaction a…     

可溶性人源含硒抗体酶GPx的研究

对噬菌体展示人单链抗体库进行筛选,得到与半抗原S-二硝基苯取代的谷胱甘肽二丁酯特异结合的单链抗体3B10。用计算机模拟分析了单链抗体的空间结构,发现抗原结合的CDR3区位于抗体的表面,推测其可能进一步参加硒化反。利用突变引物,在大肠杆菌中表达了可溶性抗体蛋白,并用化学方法将催化必需基团硒代半胱氨酸（Sec）组装到3B10抗原结合部位,获得了具有谷胱甘肽过氧化酶活力的人源抗体酶。动力学研究结果表明,抗体酶和天然酶一样,符合乒乓反应机制。