Epitope Structure of the Carbohydrate Recognition Domain of Asialoglycoprotein Receptor to a Monoclonal Antibody Revealed by High-Resolution Proteolytic Excision Mass Spectrometry

Recent studies suggest that the H1 subunit of the carbohydrate recognition domain (H1CRD) of the asialoglycoprotein receptor is used as an entry site into hepatocytes by hepatitis A and B viruses and Marburg virus. Thus, molecules binding specifically to the CRD might exert inhibition towards these diseases by blocking the virus entry site. We report here the identification of the epitope structure of H1CRD to a monoclonal antibody by proteolytic epitope excision of the immune complex and high-resolution MALDI-FTICR mass spectrometry. As a prerequisite of the epitope determination, the primary structure of the H1CRD antigen was characterised by ESI-FTICR-MS of the intact protein and by LC-MS/MS of tryptic digest mixtures. Molecular mass determination and proteolytic fragments provided the identification of two intramolecular disulfide bridges (seven Cys residues), and a Cys-mercaptoethanol adduct formed by treatment with β-mercaptoethanol during protein extraction. The H1CRD antigen binds to the monoclonal antibody in both native and Cys-alkylated form. For identification of the epitope, the antibody was immobilized on N-hydroxysuccinimide (NHS)-activated Sepharose. Epitope excision and epitope extraction with trypsin and FTICR-MS of affinity-bound peptides provided the identification of two specific epitope peptides (5–16) and (17–23) that showed high affinity to the antibody. Affinity studies of the synthetic epitope peptides revealed independent binding of each peptide to the antibody.     

乙型肝炎病毒表面抗原三维结构的同源模建及功能预测

结合生物信息学方法及分子模拟手段, 通过同源模建方法构建了乙型肝炎病毒表面抗原(HBsAg)Pres12的三维空间结构, 并结合生物实验在分子水平上探讨了乙型肝炎病毒表面抗原Pres12作为抗乙型肝炎病毒重要靶标的机理. 研究结果表明, HBsAg三维空间结构是由构型性的Pres1和线性的Pres2组成, 此结构由疏水氨基酸形成3个α-螺旋结构及Loop结构域, 并且N端由Pres1中残基构成了一个开裂, 形成了HBsAg可能的活性部位. 静电势分析结果证实, N端可能的活性部位具有较大的静电势分布, 因而具有与受体细胞蛋白相互作用的能力, 这为HBV病毒抑制剂药物分子的设计提供了有益帮助.     

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。     

A ten-residue fragment of an antibody (mini-antibody) directed against lysozyme as ligand in immunoaffinity chromatography

The interaction between an antibody molecule and a protein antigen is an example of "natural" protein modelling. Amino acids of the antigen-binding site consisting of three hypervariable segments (L1, L2, L3) of the light (L) and three (H1, H2, H3) of the heavy (H) chain of an antibody molecule interact with amino acids present in an epitope of a protein. A ten-residue peptide was synthesized with an amino acid sequence analogous to the hypervariable L3 segment of a monoclonal antibody directed against lysozyme. The peptide was immobilized on CH-Sepharose 4B and the affinity adsorbent was used to purify lysozyme added to a detergent extract of insect cells infected with a recombinant baculovirus. This methodology may also be applicable to other antigen-antibody combinations, in immunoaffinity chromatography for selective purification of a protein or in an immunosensor for detection of a protein.     

Preparation of gold colloid monolayer by immunological identification

The design and initial characterization of the self-assembled gold colloid monolayer by a sandwich structure via the immunological identification are reported. The 13 nm gold colloid nanoparticles and the silicon or quartz substrates have been modified with the mouse polyclonal antibody against hepatitis B virus surface antigen (PAb) and the mouse monoclonal antibody against hepatitis B virus surface antigen (MAb), respectively. They can be linked by a special reaction with their corresponding hepatitis B virus surface antigen (Antigen) as a sandwich structure. Thus, the density of gold nanoparticles self-assembled on the substrate can be readily controlled by the amount of the antigen added. The resulting substrates have been characterized by atomic force microscopy (AFM) and surface-enhanced Raman scattering (SERS) spectroscopy when the gold nanoparticles were modified with SERS-active probe molecules of 4-mercaptobenzoic acid (MBA) after silver enhancement. These data show that the gold nanoparticles are separately fixed onto the substrate and form a uniform monolayer, which possess a set of features that make them very attractive for both basic and applied uses, including roughness, high stability, and biocompatibility.     

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.     

Predicting Fixation Tendencies of the H3N2 Influenza Virus by Free Energy Calculation

Influenza virus evolves to escape from immune system antibodies that bind to it. We used free energy calculations with Einstein crystals as reference states to calculate the difference of antibody binding free energy (ΔΔG) induced by amino acid substitution at each position in epitope B of the H3N2 influenza hemagglutinin, the key target for antibody. A substitution with positive ΔΔG value decreases the antibody binding constant. On average an uncharged to charged amino acid substitution generates the highest ΔΔG values. Also on average, substitutions between small amino acids generate ΔΔG values near to zero. The 21 sites in epitope B have varying expected free energy differences for a random substitution. Historical amino acid substitutions in epitope B for the A/Aichi/2/1968 strain of influenza A show that most fixed and temporarily circulating substitutions generate positive ΔΔG values. We propose that the observed pattern of H3N2 virus evolution is affected by the free energy landscape, the mapping from the free energy landscape to virus fitness landscape, and random genetic drift of the virus. Monte Carlo simulations of virus evolution are presented to support this view.     

功能化荧光素掺杂二氧化硅纳米粒子用于免疫层析试验

A simple but effective approach was developed to synthesize amino functionalized fluorescein isothiocyanate-doped silica nanoparticles based upon polycondensation of tetraethoxysilane. Organic dye molecule (fluorescein isothiocyanate) coupled with a silane coupling agent, 3-aminopropyltriethoxysilane, was incorporated into silica sphere through controlled hydrolysis and polymerization of tetraethoxysilane. The dye was connected with silica sphere through 3-aminopropyltriethoxysilane, which avoided the leakage of the dye. The cohydrolysis and polymerization of tetraethoxysilane and 3-aminopropyltriethoxysilane outside the surface of the silica sphere formed another thin silica shell with the functionalized amino groups on the surface. With amino groups on the surface, the nanoparticle surface was affluent in positive charges. The amino-functionalized nanoparticles were linked with mouse monoclonal antibody against hepatitis B virus surface antigen through electrostatic interaction to form fluorescence probes, which were tested by immunochromatographic assay using immunochromatography test strip. It was indicated that the fluorescence probe was suitable for immunoassay.     

乙肝疫苗注入后婴儿血液吞噬细胞吞噬功能变化的临床观察

为探讨乙开型肝炎表面抗原（ｈｅｐａｔｉｔｉｓ Ｂ ｓｕｒｆａｃｅ ａｎｔｉｇｅｎ,ＨＢｓＡｇ）阳性母亲的婴儿乙肝疫苗注入后早期机体免疫反应的特点,采用化我法测定了吞噬细胞的吞噬功能;用双抗原夹心法测定了抗－ＨＢｓ抗体。结果表明,（１）乙肝疫苗注入前两组间吞噬细胞的吞噬功能无明显差异,疫苗注入后３个月和６个月时实组外周血吞噬细胞的吞噬功能明显下降（Ｐ〈０．０５）。两组间同时间点相比,１个月和３个月都     

EXPRESSION AND SECRETION OF preS CONTAINING HEPATITIS B SURFACE ANTIGEN IN VACCINIA VIRUS SYSTEM

The expression and secretion of preS containing hepatitis B surface antigen in vaccinia virus system was investigated. The human TK~- 143 cells were infected with the recombinant vaccinia viruses vTMS-1 or vTLS-1. Cells infected with vTMS-1, which contains the preS2+S gene, produced preS2 containing middle HBsAg proteins. Similarly, cells produced preS1 containing large HBsAg proteins upon infection with vTLS-1, which carries the preS1+preS2+S gene. The expression products could be secreted and form 22 nm particles. They reacted specifically with anti-preS1 and/or anti-preS2 monoclonal antibodies, and exhibited pHSA-receptor (for polymerized human serum albumin) activity. In addition, the major S components of hepatitis B surface antigen were also present in the products expressed by vTMS-1 and vTLS-1.     

表面等离子体子共振生物传感器用于乙肝表面抗原的测定

运用自行研制的表面等离子体子共振（SPR）生物传感器，采用自组装成膜技 术并以戊二醛作偶联剂，在传感片表面修饰HBsAg单克隆抗体，将其用于乙肝表面 抗原（HBsAg)的检测。实验结果表明SPR生物传感器对HBsAg的检出限为0.06ng/mL 。与传统的酶联免疫吸附试验（ELISA）相比，SPR生物传感器的检出灵敏度明显高 于ELISA法。用该SPR生物传感器对HBsAg质控血清与纯化的HBsAg溶液进行比较检测 ，结果表明该SPR生物传感器对HBsAg具有好的特异选择性。     

Synthesis,molecular modeling of N-acyl benzoazetinones and their docking simulation on fungal modeled target

A series of stable N-acyl benzoazetinones have been synthesized in moderate to good yields (58–85%) from easily available substrates such as 2-(N-acyl) amino benzoic acids through intramolecular amidation under mild conditions. These geometry-optimized benzoazetinones were docked in the model target of P450, class CYP53A15, a benzoate 4-monooxygenase abundantly found in the genome of ascomycetes and Basidiomycetes classes of pathogenic fungi. Low per residue root-mean-square deviation (RMSD) of modeled structure of the enzyme indicated similar topology as template (4D6Z.pdb). Observed score judges site-specific docking, and the interaction of quantum mechanically optimized benzoazetinone derivatives with the target enzyme. These results suggest that 3i is the best antifungal agent. The specific hydrophobic substituent in the benzoazetinones contributed to the stability of ligand–target complex. Overall, the study provided insight into the specificity of the site-specific interactions, thereby, facilitating the possibility of development of broad-spectrum antifungal agents against opportunistic and infectious fungi.     

200例乙型肝炎病毒感染者对乙肝预防认知情况调查

为了解乙型肝炎病毒（HBV）新感染人群对乙肝预防的认知情况,对2000年7月－12月在本院就诊的200例HBV感染者做了调查,发现未注射疫苗的人群,94．5％是因对乙肝预防认知程度差所致,其中地区、职业、文化程度的差异是影响认知程度的重要因素。因此,加大对预防工作的投入,加强宣传教育,特别是在我省专州地县、偏远山区,是控制HBV感染的首要途径。     

Characterization of a discontinuous epitope of the HIV envelope protein gp120 recognized by a human monoclonal antibody using chemical modification and mass spectrometric analysis

A subset of the neutralizing anti-HIV antibodies recognize epitopes on the envelope protein gp120 of the human immunodeficiency virus. These epitopes are exposed during conformational changes when gp120 binds to its primary receptor CD4. Based on chemical modification of lysine and arginine residues followed by mass spectrometric analysis, we determined the epitope on gp120 recognized by the human monoclonal antibody 559/64-D, which was previously found to be specific for the CD4 binding domain. Twenty-four lysine and arginine residues in recombinant full-length glycosylated gp120 were characterized; the relative reactivities of two lysine residues and five arginine residues were affected by the binding of 559/64-D. The data show that the epitope is discontinuous and is located in the proximity of the CD4-binding site. Additionally, the reactivities of a residue that is located in the secondary receptor binding region and several residues distant from the CD4 binding site were also altered by Ab binding. These data suggest that binding of 559/64-D induced conformational changes which result in altered surface exposure of specific amino acids distant from the CD4-binding site. Consequently, binding of 559/64-D to gp120 affects not only the CD4-binding site, which is recognized as the epitope, but appears to have a global effect on surface exposed residues of the full-length glycosylated gp120.     

Computational identification of epitopes in the glycoproteins of novel bunyavirus (SFTS virus) recognized by a human monoclonal antibody (MAb 4-5)

In this work, we have developed a new approach to predict the epitopes of antigens that are recognized by a specific antibody. Our method is based on the “multiple copy simultaneous search” (MCSS) approach which identifies optimal locations of small chemical functional groups on the surfaces of the antibody, and identifying sequence patterns of peptides that can bind to the surface of the antibody. The identified sequence patterns are then used to search the amino-acid sequence of the antigen protein. The approach was validated by reproducing the binding epitope of HIV gp120 envelop glycoprotein for the human neutralizing antibody as revealed in the available crystal structure. Our method was then applied to predict the epitopes of two glycoproteins of a newly discovered bunyavirus recognized by an antibody named MAb 4-5. These predicted epitopes can be verified by experimental methods. We also discuss the involvement of different amino acids in the antigen–antibody recognition based on the distributions of MCSS minima of different functional groups.     

Mapping of viral epitopes with conformationally specific monoclonal antibodies using biosensor technology.

An automated biosensor system (BIAcore) designed for measuring molecular interactions in real time and without labelling any of the reactants was used for mapping the epitopes of tobacco mosaic virus protein using conformationally specific monoclonal antibodies (MAbs). Some of the MAbs used as capturing antibody on the sensor chip allowed a conformational change to occur in the viral protein. As a result, MAbs specific for the quaternary structure of polymerized viral protein were able to bind to monomeric viral subunits. Compared with classical solid-phase enzyme immunoassay, the biosensor technology possesses several advantages for epitope mapping of viral proteins.     

用分子对接方法研究HIV-1整合酶与病毒DNA的结合模式

用分子对接方法研究了HIV-1整合酶(Integrase, IN)二聚体与3’ 端加工(3’ Processing, 3’-P)前的8 bp及27 bp病毒DNA的相互作用, 并获得IN与27 bp病毒DNA的特异性结合模式. 模拟结果表明, IN有特异性DNA结合区和非特异性DNA结合区; IN二聚体B链的K14, R20, K156, K159, K160, K186, K188, R199和A链的K219, W243, K244, R262, R263是IN结合病毒DNA的关键残基; 并从结构上解释了能使IN发挥活性的病毒DNA的最小长度是15 bp. 通过分析结合能发现, IN与DNA稳定结合的主要因素是非极性相互作用, 而关键残基与病毒DNA相互识别主要依赖于极性相互作用. 模拟结果与实验数据较吻合.     

Antigen�Cantibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation

Effective interactions between amino acid residues in antigen?Cantibody complex of influenza virus hemagglutinin (HA) protein can be evaluated in terms of the inter-fragment interaction energy (IFIE) analysis with the fragment molecular orbital (FMO) method, in which each fragment contains the side chain of corresponding amino acid residue. We have carried out the FMO-MP2 (second-order Moeller?CPlesset) calculation for the complex of HA antigen and Fab antibody of influenza virus H3N2 A/Aichi/2/68 and obtained the IFIE values between each amino acid residue in HA and the whole antibody as the sums over the residues contained in the latter. Combining this IFIE data with experimental data for hemadsorption activity of HA mutants, we succeeded in theoretically explaining the mutations in HA observed after the emergence of influenza virus H3N2 A/Aichi/2/68 in an earlier study, except for those of THR83. In the present study, we employ an alternative way of fragment division in the FMO calculation at the carbonyl C site of the peptide bond instead of the C_?? site used in the previous work, which provides revised IFIE values consistent with all the historical mutation data in the antigenic region E of HA including the case of THR83 in the present prediction scheme for probable mutations in HA.     

Scoring protein–protein docked structures based on the balance and tightness of binding

One main issue in protein-protein docking is to filter or score the putative docked structures. Unlike many popular scoring functions that are based on geometric and energetic complementarity, we present a set of scoring functions that are based on the consideration of local balance and tightness of binding of the docked structures. These scoring functions include the force and moment acting on one component (ligand) imposed by the other (receptor) and the second order spatial derivatives of protein-protein interaction potential. The scoring functions were applied to the docked structures of 19 test targets including enzyme/inhibitor, antibody/antigen and other classes of protein complexes. The results indicate that these scoring functions are also discriminative for the near-native conformation. For some cases, such as antibody/antigen, they show more discriminative efficiency than some other scoring functions, such as desolvation free energy (deltaG(des)) based on pairwise atom-atom contact energy (ACE). The correlation analyses between present scoring functions and the energetic functions also show that there is no clear correlation between them; therefore, the present scoring functions are not essentially the same as energy functions.     

Use of nitrocellulose films for affinity-directed mass spectrometry for the analysis of antibody/antigen interactions

Combination of affinity extraction procedures with mass spectrometric analyses is termed affinity-directed mass spectrometry, a technique that has gained broad interest in immunology and is extended here with several improvements from methods used in previous studies. A monoclonal antibody was immobilized on a nitrocellulose (NC) membrane, allowing the corresponding antigen to be selectively captured from a complex solution for analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). This method was also used to rapidly determine the approximate binding region responsible for the antibody/antigen interaction. The tryptic fragments of antigen protein in buffer were applied to the antibody immobilized on NC film and allowed to interact. The NC film was then washed to remove salts and other unbound components, and subjected to analysis by MALDI-TOFMS. Using interferon-alpha(2a) and anti-interferon-alpha(2a) monoclonal antibody IgG as a model system, we successfully extracted the antigen protein and determined the approximate binding region for the antigen/antibody interaction (i.e., the tryptic fragment responsible).