Chemical Chaperones Increasing Expression Level of Soluble Single-chain Fv Antibody（scFv2F3）

IntroductionGlutathione peroxidase(GPX, EC 1·11·1·9) is aselenoenzyme that protects the biomembrane and othercellular components againstoxidative damage[1—3]. Itisclosely related with several diseases[4—7]. Because ofthe disadvantages of native GPX,     

Novel Selenium-containing Human Single-chain Variable Fragment with Glutathione Peroxidase Activity from Computer-aided Molecular Design

In order to enhance the glutathione peroxidase(GPX) catalytic activity of the selenium-containing single-chain variable fragments(Se-scFv), a novel human scFv was designed on the basis of the structure of human antibody and optimized via bioinformatics methods such as homologous sequence analysis, three-dimensional(3D) model building, binding-site analysis and docking. The DNA sequence of the new human scFv was synthesized and cloned into the expression vector pET22b(+), then the scFv protein was expressed in soluble form in Escherichia coli BL21(DE3) and purified by Ni2+-immobilized metal affinity chromatography(IMAC). The serine residue of scFv in the active site was converted into selenocysteine(Sec) with the chemical modification method, thus, the human Se-scFv with GPX activity was obtained. The GPX activity of the Se-scFv protein was characterized. Compared with other Se-scFv, the new human Se-scFv showed similar efficiency for catalyzing the reduction of hydrogen peroxide by glutathione. It exhibited pH and temperature dependent catalytic activity and a typical ping-pong kinetic mecha- nism.     

Routes to covalent catalysis by reactive selection for nascent protein nucleophiles

Reactivity-based selection strategies have been used to enrich combinatorial libraries for encoded biocatalysts having revised substrate specificity or altered catalytic activity. This approach can also assist in artificial evolution of enzyme catalysis from protein templates without bias for predefined catalytic sites. The prevalence of covalent intermediates in enzymatic mechanisms suggests the universal utility of the covalent complex as the basis for selection. Covalent selection by phosphonate ester exchange was applied to a phage display library of antibody variable fragments (scFv) to sample the scope and mechanism of chemical reactivity in a naive molecular library. Selected scFv segregated into structurally related covalent and noncovalent binders. Clones that reacted covalently utilized tyrosine residues exclusively as the nucleophile. Two motifs were identified by structural analysis, recruiting distinct Tyr residues of the light chain. Most clones employed Tyr32 in CDR-L1, whereas a unique clone (A.17) reacted at Tyr36 in FR-L2. Enhanced phosphonylation kinetics and modest amidase activity of A.17 suggested a primitive catalytic site. Covalent selection may thus provide access to protein molecules that approximate an early apparatus for covalent catalysis.     

Stepwise Versus Concerted Mechanisms in General‐Base Catalysis by Serine Proteases

General‐base catalysis in serine proteases still poses mechanistic challenges despite decades of research. Whether proton transfer from the catalytic Ser to His and nucleophilic attack on the substrate are concerted or stepwise is still under debate, even for the classical Asp‐His‐Ser catalytic triad. To address these key catalytic steps, the transformation of the Michaelis complex to tetrahedral complex in the covalent inhibition of two prototype serine proteases was studied: chymotrypsin (with the catalytic triad) inhibition by a peptidyl trifluoromethane and GlpG rhomboid (with Ser‐His dyad) inhibition by an isocoumarin derivative. The sampled MD trajectories of averaged pK_a values of catalytic residues were QM calculated by the MD‐QM/SCRF(VS) method on molecular clusters simulating the active site. Differences between concerted and stepwise mechanisms are controlled by the dynamically changing pK_a values of the catalytic residues as a function of their progressively reduced water exposure, caused by the incoming ligand.     

力场/溶剂水模型对EGFRvⅢ抗原-MR1(scFv)抗体复合物的MM-PBSA计算精度的影响与实验验证

以表皮生长因子Ⅲ型突变体(EGFRvⅢ)抗原多肽与其抗体(MR1)及其人源化突变体的复合物结构为出发点,采用分子动力学中的6种常用力场及3种常用溶剂水模型,分别对上述抗原-抗体复合物进行100ns的分子动力学模拟与分子力学和连续介质模型计算自由能(MM-PBSA),并在实验上利用等温滴定量热(ITC)仪测定了抗原和抗体相互作用的热力学参数.通过在结构变化、能量变化及野生型与突变体比较等几个方面进行综合分析,给出了最佳的计算模型.对不同力场及水模型计算精度等相关问题进行了探讨.     

A phage-displayed chicken single-chain antibody fused to alkaline phosphatase detects Fusarium pathogens and their presence in cereal grains

Fusarium and its poisonous mycotoxins are distributed worldwide and are of particular interest in agriculture and food safety. A simple analytical method to detect pathogens is essential for forecasting diseases and controlling mycotoxins. This article describes a proposed method for convenient and sensitive detection of Fusarium pathogens that uses the fusion of single-chain variable fragment (scFv) and alkaline phosphatase (AP). A highly reactive scFv antibody specific to soluble cell wall-bound proteins (SCWPs) of F. verticillioides was selected from an immunized chicken phagemid library by phage display. The antibody was verified to bind on the surface of ungerminated conidiospores and mycelia of F. verticillioides. The scFv–AP fusion was constructed, and soluble expression in bacteria was confirmed. Both the antibody properties and enzymatic activity were retained, and the antigen-binding capacity of the fusion was enhanced by the addition of a linker. Surface plasmon resonance measurements confirmed that the fusion displayed 4-fold higher affinity compared with the fusion's parental scFv antibody. Immunoblot analyses showed that the fusion had good binding capacity to the components from SCWPs of F. verticillioides, and enzyme-linked immunosorbent assays revealed that the detection limit of the fungus was below 10⁻² μg mL⁻¹, superior to the scFv antibody. The fusion protein was able to detect fungal concentrations as low as 10⁻³ mg g⁻¹ of maize grains in both naturally and artificially contaminated samples. Thus, the fusion can be applied in rapid and simple diagnosis of Fusarium contamination in field and stored grain or in food.     

二乙氧基硫代磷酸酯类有机磷农药单链抗体的制备及广谱特异性

从分泌抗二乙氧基硫代磷酸酯类有机磷农药(DPPs)单克隆抗体(MAb)的杂交瘤细胞系(12C2)中提取了总RNA, 经RT-PCR反转录成cDNA, 设计带linker引物, 采用重叠延伸PCR制备单链抗体(scFv)基因, 将其克隆到噬菌体载体p3MH中, 构建成噬菌体单链抗体表达载体, 转化大肠杆菌表达出噬菌体表面展示scFv, 对经过Phage-ELISA鉴定的阳性克隆进行噬菌体外壳蛋白基因geneⅢ的去除, 用IPTG诱导其可溶性表达, 对表达产物进行SDS-PAGE, Western-Blot及ELISA鉴定, 并与亲本MAb进行性能对比. 结果表明, 可溶性表达的scFv分子量为27000; scFv与DPPs的交叉反应率比其亲本MAb提高了1.3~3.5倍, 表明其广谱特异性有所提高. 由于scFv与MAb相比具有诸多优点, 因此本研究为有机磷农药多残留检测方法的建立提供了一种更广谱、 更灵敏的新型识别分子.     

Catalytic Reduction of Cyclic Ethers with Hydrosilanes

Catalytic reductive transformations of ethers as a synthetic building block are an important class of chemical reactions because a range of essential chemical feedstocks and fuels in contemporary life can be prepared through the key step of ethereal C?O bond cleavage of cellulosic biomass. Although conventional stoichiometric and catalytic methods for sp²‐ and sp³‐C?O bond cleavage of linear ethers and alcohols with hydrosilanes are well established, silylative ring opening of cyclic ethers has been less highlighted in this context. This review outlines catalytic systems for the silylative reduction of a range of cyclic ethers, including epoxides and sugars, leading to the corresponding alcohols and/or hydrocarbons. The chemical reactivity and selectivity of these ring‐opening catalytic processes are discussed with respect to the type of substrates; the representative catalytic working modes are also described.     

NiO-Fe2O3/MD催化剂的制备及其在城市生活垃圾气化中的应用

以改性白云石(Modified Dolomite, MD)为载体,利用沉积沉淀法制备了负载型NiO-Fe₂O₃/MD催化剂,并利用XRD、SEM、TEM、BET等手段对催化剂进行了表征和分析.同时,利用双固定床反应器对NiO-Fe₂O₃/MD催化剂在城市生活垃圾气化中的催化活性和使用寿命进行了评价,并与NiO/MD催化剂进行了比较.实验结果表明,NiO-Fe₂O₃/MD催化剂为核壳式涂层结构,表面活性颗粒粒径约为37 nm,比表面积62.48 m²/g.催化剂活性测试显示,NiO-Fe₂O₃/MD催化剂用于城市生活垃圾气化具有极高的催化活性,能够显著提高产品燃气品质及燃气中的H₂含量,减少焦油的产生;相对于NiO/MD催化剂,其抗失活能力强,使用寿命长.     

An affinity improved single-chain antibody from phage display of a library derived from monoclonal antibodies detects fumonisins by immunoassay

Fumonisin B analogs, particularly FB₁, FB₂, and FB₃, are major mycotoxins found in cereals. Single-chain fragment variable (scFv) antibodies represent a promising alternative immunoassay system. A phage-displayed antibody library derived from four monoclonal antibodies (mAbs) generated against FB₁ was used to screen high binding affinity scFv antibodies; the best candidate was designated H2. Surface plasmon resonance measurements confirmed that the H2 scFv displayed a 82-fold higher binding affinity than its parent mAb. Direct competitive enzyme-linked immunosorbent assay demonstrated that the H2 antibody could competitively bind to free FB₁, FB₂, and FB₃, with an IC₅₀ of 0.11, 0.04, and 0.10 μM, respectively; it had no cross-reactivity to deoxynivalenol, nivalenol and aflatoxin. Validation assays with naturally contaminated samples revealed a linear relationship between the H2 antibody-based assay results and chemical analysis results, that could be expressed as y = 1.7072x + 5.5606 (R² = 0.8883). Homology modeling of H2 revealed a favorable binding structure highly complementary to the three fumonisins. Molecular docking analyses suggested that the preferential binding of the H2 scFv to FB₂ was due to the presence of a hydrogen radical in its R1 position, leading to a proper electrostatic matching and hydrophobic interaction. The H2 scFv antibody can be used for the rapid, accurate, and specific detection of fumonisin contamination in agricultural samples.     

Catalytic mechanism of an abzyme displaying a beta-lactamase-like activity

A catalytic IgG (Ab2) displaying a beta-lactamase-like activity was previously obtained by using the antiidiotypic pathway: the particularity of this antibody is that it is a true antiidiotype of the beta-lactamase active site. We have previously demonstrated that this IgG has retained some of the structural information displayed by the beta-lactamase active site, evident from data that polyclonal anti-Ab2 antibodies (Ab3) recognize beta-lactamase. In this article, we investigated the catalytic mechanism of the abzyme compared to that of the enzyme. The experimental data allow us to hypothesize the catalytic residues required for catalysis.     

Elucidating the intermolecular interactions within a desolvated protein-ligand complex. An experimental and computational study

The first detailed study of the intermolecular hydrogens bonds (H-bonds) within a desolvated, noncovalent protein-ligand complex is reported. Using both experimental and computational methods, the intermolecular H-bonds stabilizing protonated and deprotonated ions of a complex composed of a single chain fragment (scFv) of a monoclonal antibody and its native trisaccharide ligand, alphaGal[alphaAbe] alphaMan (1), are characterized. Using the blackbody infrared radiative dissociation-functional group replacement (BIRD/FGR) technique, three H-bond donor-acceptor pairs within the gaseous (scFv + 1)n+ ions are identified and quantified. Additional sites of interaction on the protein and ligand, for which the binding partner could not be elucidated, are also identified. Comparison of the gas-phase interaction maps with the crystal structure suggests that at least two of the specific H-bonds are conserved upon transfer of the complex from solution to the gas phase by electrospray ionization. However, new (nonspecific) interactions can also form in the gas phase. Notably, the nature and strength of the intermolecular interactions can vary significantly with charge state, and striking differences in the structures of the (scFv + 1)n+ and (scFv + 1)n- ions are evident. Intermolecular H-bonds are also identified from molecular dynamics (MD) simulations performed at the +8 and -8 charge states. Agreement is found for a majority of intermolecular interactions predicted for the (scFv + 1)8+ ion by the MD simulation and BIRD/FGR method; the agreement is less favorable in the case of the (scFv + 1)8- ion. However, both the computational and experimental results point to structural differences between the +8 and -8 ions. The computational results also provide insights into the structural changes that accompany the loss of interfacial waters from the complex.     

脂肪酰胺水解酶催化三联体膦酰化失活的机理：一个模型体系的理论研究

甲基花生四烯基氟代膦酸酯(MAFP)是脂肪酰胺水解酶(FAAH)的一个抑制剂. FAAH的丝氨酸241(Ser241)-丝氨酸217(Ser217)-赖氨酸142(Lys142)催化三联体被MAFP膦酰化后将导致FAAH失活. 本文采用B3LYP/6-311G(d,p)和MP2/6-311G(d,p)方法及一个简化的计算模型体系对这个膦酰化抑制反应进行理论研究. 考虑了两种反应途径. Path A涉及FAAH的催化三联体的所有残基, 是一个分步的加成-消除过程, 形成两性离子的三角双锥中间体, 其中第一步反应是决速步骤. 在这个反应途径中, Ser217和Lys142对亲核试剂Ser241起到碱催化活化的作用, 而Ser217充作Lys142和Ser241之间的桥梁. 此外, 溶剂中的一个水分子作为Lys142和MAFP间的“氢桥”具有关键的作用, 通过给出和接收质子促进了长距离的质子转移. Path B是催化三联体中的残基Lys142被突变为丙氨酸以后的膦酰化反应, 也是一个分步过程. 水的本体溶剂效应通过极化连续介质模型(PCM)估算. 计算结果显示膦酰化反应的Path A是优势途径, 在水溶液中其决速步骤的活化能垒为64.9 kJ·mol-1. FAAH催化三联体中残基Lys142的变异会降低膦酰化反应的速率, 这与实验结果相一致.     

A human single-chain antibody specific for integrin alpha3beta1 capable of cell internalization and delivery of antitumor agents

Selective antitumor chemotherapy can be achieved by using antibody-drug conjugates that recognize surface proteins upregulated in cancer cells. One such receptor is integrin alpha3beta1, which is overexpressed on malignant melanoma, prostate carcinoma, and glioma cells. We previously identified a human single-chain Fv antibody (scFv), denoted Pan10, specific for integrin alpha3beta1 that is internalized by human pancreatic cancer cells. Herein, we describe the chemical introduction of reactive thiol groups onto Pan10, the specific conjugation of the modified scFv to maleimide-derivatized analogs of the potent cytotoxic agent duocarmycin SA, and the properties of the resultant conjugates. Our findings provide evidence that Pan10-drug conjugates maintain the internalizing capacity of the parent scFv and are cytotoxic at nanomolar concentrations. Our Pan10-drug conjugates may be promising candidates for targeted chemotherapy of malignant diseases associated with overexpression of integrin alpha3beta1.     

无铝V-β分子筛的合成、表征及催化性能研究

采用水热晶化法在SiO2-V2O5-(TEA)2O-NH4F-H2O体系中合成了无铝V-β分子筛,运用XRD,IR,UV-Vis漫反射,TG/DTA和SEM等技术表征了样品的物理化学特性,证明样品具有BEA拓扑结构,结晶良好,且钒原子进入了分子筛骨架. 探讨了反应混合物组成对V-β分子筛晶化的影响,在以H2O2为氧化剂的苯酚羟基化反应中,考察了V-β分子筛的催化氧化性能.     

具有谷胱甘肽过氧化物酶活性的含硒人源单链抗体的制备

以谷胱甘肽(GSH)为靶抗原, 从噬菌体展示人源单链抗体库中筛选人源单链抗体(scFv). 经3轮筛选后, 用ELISA方法检测出5个(2, 11, 16, 24, 32 )可以和GSH结合的克隆. PCR产物的电泳和测序结果表明, 只有3个克隆(11, 16, 24)具有完整的scFv编码基因. 选取和GSH结合力高的克隆11的scFv 编码基因组装到表达载体pPELB上, 在大肠杆菌Rosetta中进行可溶性表达, 用Ni2+螯合亲和层析纯化scFv-11, 免疫点印迹结果证实该抗体能与GSH特异结合. 通过化学突变将scFv-11的丝氨酸转变成硒代半胱氨酸(Sec)后, 获得了具有谷胱甘肽过氧化物酶(GPX)活力的含硒(Se)人源单链抗体(Se-scFv-11), 其活力为351 U/μmol.     

催化抗体的催化效率优化和展望

综述了改进催化抗体催化效率的可能方法 ,包括较好的半抗原、广泛的筛选、工程化及选择优化等     

Intricate role of water in proton transport through cytochrome c oxidase

Cytochrome c oxidase (CytcO), the final electron acceptor in the respiratory chain, catalyzes the reduction of O(2) to H(2)O while simultaneously pumping protons across the inner mitochondrial or bacterial membrane to maintain a transmembrane electrochemical gradient that drives, for example, ATP synthesis. In this work mutations that were predicted to alter proton translocation and enzyme activity in preliminary computational studies are characterized with extensive experimental and computational analysis. The mutations were introduced in the D pathway, one of two proton-uptake pathways, in CytcO from Rhodobacter sphaeroides . Serine residues 200 and 201, which are hydrogen-bonded to crystallographically resolved water molecules halfway up the D pathway, were replaced by more bulky hydrophobic residues (Ser200Ile, Ser200Val/Ser201Val, and Ser200Val/Ser201Tyr) to query the effects of changing the local structure on enzyme activity as well as proton uptake, release, and intermediate transitions. In addition, the effects of these mutations on internal proton transfer were investigated by blocking proton uptake at the pathway entrance (Asp132Asn replacement in addition to the above-mentioned mutations). Even though the overall activities of all mutant CytcO's were lowered, both the Ser200Ile and Ser200Val/Ser201Val variants maintained the ability to pump protons. The lowered activities were shown to be due to slowed oxidation kinetics during the P(R) → F and F → O transitions (P(R) is the "peroxy" intermediate formed at the catalytic site upon reaction of the four-electron-reduced CytcO with O(2), F is the oxoferryl intermediate, and O is the fully oxidized CytcO). Furthermore, the P(R) → F transition is shown to be essentially pH independent up to pH 12 (i.e., the apparent pK(a) of Glu286 is increased from 9.4 by at least 3 pK(a) units) in the Ser200Val/Ser201Val mutant. Explicit simulations of proton transport in the mutated enzymes revealed that the solvation dynamics can cause intriguing energetic consequences and hence provide mechanistic insights that would never be detected in static structures or simulations of the system with fixed protonation states (i.e., lacking explicit proton transport). The results are discussed in terms of the proton-pumping mechanism of CytcO.     

量子点与人源抗谷胱甘肽单链抗体的连接与表征

用已构建的表达载体pPELB-B3, 在大肠杆菌Rosetta中可溶性表达人源抗谷胱甘肽(GSH)单链抗体B3(scFv-B3), 经Ni2+螯合亲和层析纯化后, 用点印迹法验证了其与GSH结合的特异性. 将水相合成的半导体纳米粒子(半导体量子点, QDs)在N-羟基琥珀酰亚胺(NHS)和1-乙基-3-(3-二甲基氨基丙基)碳酰二亚胺盐酸盐(EDC)的作用下, 与scFvs连接. 光谱分析和膜印迹结果表明, scFvs成功地共价连接到QDs表面, 所得的QD-scFvs复合物能够较好地识别GSH. 荧光显微镜观察QD-scFvs与人乳腺癌细胞MCF-7的作用结果, 初步判断QD-scFvs能够跨膜进入细胞.     

Controlling the Catalytic Properties of Copper-Containing Oxide Catalysts

The results of a systematic study of the formation of Cu–Zn, Cu–Zn–Al, Cu–Zn–Cr, Cu–Zn–Si, Cu–Cr, and Cu–Si oxide catalysts with a widely varied ratio between their components are generalized within the chemical approach developed by G.K. Boreskov to establish the quantitative relation between their chemical composition and catalytic activity. Simultaneously, their catalytic properties, such as selectivity and activity, are measured under the same conditions in the methanol synthesis and dehydrogenation and water gas shift reactions, whose common feature is a reductive reaction medium. The activity of Cu–Zn–Al–Cr— Si-oxide catalysts in all the studied reactions is governed by the Cu⁰ nanoparticles formed on their surface in the process of reductive activation. Nanoparticles of different catalysts have similar sizes (3–8 nm). However, the ratios between the catalytic activities per unit of the copper surface area for catalysts with various structures of their oxide support (spinel, wurtzite, zincsilite, or silica type) are appreciably different in each reaction. The relation between the chemical composition of a catalyst and its catalytic activity in a certain reaction is established by the chemical composition of its precursor representing a hydroxo compound, i.e., the nature of the selected cations and the quantitative ratio between them. The decomposition of hydroxo compounds to oxides (and the further activation of oxides) should be performed at medium temperatures, providing the incomplete elimination of ОН^– and CO₃^2- anions, i.e., the formation of anion-modified oxides. The structure of the latter and the type of interaction between Cu⁰ nanoparticles and an oxide support are governed by the structure of the hydroxo precursor compound.