Functional mapping of conserved, surface-exposed charges of antibody variable domains

Surface-exposed charges can affect protein structure, stability and solubility as well as the kinetics of both the folding process and interaction with binding partners. We have investigated the influence on kinetic interaction parameters of 14 conserved, surface-exposed charges located away from the paratope in the variable domains of two antibodies of different specificity. We found that conserved, surface-exposed, charged framework residues are asymmetrically distributed on opposite faces of both VH and VL domains. Some of the charges play a critical role in protein folding and stability. While electrostatic forces within or close to the binding interface can be used to optimize the association rate, we confirmed the predicted minor effects of charge modifications remote from the binding site. They had no effect on the dissociation rate parameter. Our study demonstrates the role of residues remote from the interaction site in the recognition function as well as the limited effect of surface charge modifications in antibody fragments on kinetic interaction parameters.     

抗黄曲霉毒素B1单链抗体的筛选和鉴定

目的】从Tomlinson（I）噬菌体抗体库中筛选人源化抗黄曲霉毒素B1单链抗体蛋白（scFv）并进行鉴定。【方法】分别采用甘氨酸洗脱、胰蛋白酶洗脱、游离AFB1竞争洗脱和AFB1竞争洗脱加胰蛋白酶处理4种方法对噬菌体抗体进行特异性洗脱。将筛选到的噬菌体阳性克隆转化到大肠杆菌 (Escherichia.coli ) HB2151,IPTG诱导表达scFv。ELISA检测和基因序列测定。【结果】比较四种洗脱方法,发现用AFB1竞争加胰蛋白酶洗脱筛选到阳性克隆的的概率最高,把此方法得到的阳性噬菌体克隆转化大肠杆菌HB2151表达,竞争性ELISA检测得到2个能特异性结合游离的AFB1阳性克隆。间接性ELISA测定相对亲和力分别为0.4 μg/mL和0.7 μg/mL 。测序证实scFv属于人类免疫球蛋白可变区。【结论】利用噬菌体展示技术获得高特异性抗黄曲霉毒素B1的人源化单链抗体,本实验方法可以为其它抗半抗原重组抗体的筛选提供一定的借鉴意义。     

The three-dimensional structure of the antigen-binding fragment of a monoclonal antibody to human interleukin-2 in two crystal forms at 2.2 and 2.9 Å resolution

The three-dimensional structure of the antigen-binding fragment of a monoclonal antibody to human interleukin-2 was determined in two crystal forms by the X-ray method of molecular replacement at 2.2 and 2.9 Å resolutions. The spatial structure of the protein and the stereochemistry of its antigen-binding site were analyzed.     

Comparison of an antibody model with an X-ray structure: The variable fragment of BR96

A model of the BR96 antibody variable regions is compared to two X-ray structures of a BR96–carbohydrate complex, independently determined after the model was built and analyzed. The comparison illustrates the opportunities and limitations of antibody modeling. Encouraging results were obtained for the prediction of single CDR loop conformations and for the outline of the BR96 antigen binding site. The comparison of CDR loop conformations in the two X-ray structures provides a realistic reference frame for the CDR loop predictions. CDR loop prediction accuracy is lower when not only conformational, but also positional criteria are taken into account.     

Serum antibody responses to Wolbachia surface protein in patients with human lymphatic filariasis

Wolbachia surface protein (WSP), which is the most abundantly expressed protein of Wolbachia from the human filarial parasite Brugia malayi, was chosen for the present study. B‐cell epitope prediction of the WSP protein sequence indicates a high antigenicity, surface probability and hydrophilicity by DNA STAR software analysis. ProPred analysis suggests the presence of HLA class II binding regions in the WSP protein that contribute to T‐cell responses and isotype reactivity. In order to validate these findings, the gene coding for endosymbiont WSP was PCR‐amplified from the genomic DNA of the human filarial parasite Brugia malayi and cloned in T‐7 expression vector pRSET‐A. Western blot and ELISA at the total IgG level with recombiant WSP indicated a significantly elevated reactivity in CP compared to MF, EN and NEN individuals. Isotype ELISA also suggested an elevated reactivity in CP patients at the IgG1 level. In contrast, WSP‐specific IgG4 levels were found to be elevated in MF patients compared to CP and EN. Besides this, WSP‐specific IgE levels indicated an elevated reactivity in CP and MF patients compared to normals. Observations from ELISA supported the in silico predictions that indicate the presence of B‐ and T‐cell epitopes. Hence, a combinatorial approach of in silico predictions and wet‐lab studies provides interesting insights into the role of Wolbachia proteins in filarial pathogenesis.     

Crystal structure of an RNA polymerase ribozyme in complex with an antibody fragment

All models of the RNA world era invoke the presence of ribozymes that can catalyse RNA polymerization. The class I ligase ribozyme selected in vitro 15 years ago from a pool of random RNA sequences catalyses formation of a 3',5'-phosphodiester linkage analogous to a single step of RNA polymerization. Recently, the three-dimensional structure of the ligase was solved in complex with U1A RNA-binding protein and independently in complex with an antibody fragment. The RNA adopts a tripod arrangement and appears to use a two-metal ion mechanism similar to protein polymerases. Here, we discuss structural implications for engineering a true polymerase ribozyme and describe the use of the antibody framework both as a portable chaperone for crystallization of other RNAs and as a platform for exploring steps in evolution from the RNA world to the RNA-protein world.     

Bacterial aspects associated with the expression of a single-chain antibody fragment in Escherichia coli

The bacterial expression of a single-chain antibody fragment, designated L6 sFv, was examined. Periplasmic targeting resulted in the production of a correctly folded protein that bound tumor antigen. However, immediately after induction at either 30°C or 37°C there was a significant loss in bacterial viability, which was followed by a loss in absorbance. The loss in absorbance correlated with cell lysis and release of the L6 sFv into the culture supernatant. The kinetics of appearance of L6 sFv in the supernatant paralleled that of periplasmic \-lactamase and confirmed an initial loss of cell-wall integrity prior to cell lysis. Bacteria incubated at 30°C produced approximately threefold more correctly folded antibody fragment because of an increase in the number of cells/A ₆₆₀ at the lower incubation temperature. More than 95% of the L6 sFv, made at either incubation temperature, was incorrectly folded. Osmotic-shock procedures did not release L6 sFv. However, in situ subtilisin susceptibility experiments with bacterial spheroplasts confirmed a periplasmic location. French press disruption resulted in the release of correctly but not incorrectly folded material. Membrane fractionation revealed that the incorrectly folded L6 sFv remained associated with both the inner and outer membrane. These results demonstrate that, in this system, antibody fragment expression resulted initially in cell death, which was followed by release of protein into the culture supernatant and eventually cell lysis. It is also suggested that membrane association in the periplasmic space may impede proper folding.     

Effect of protein structure on deamidation rate in the Fc fragment of an IgG1 monoclonal antibody

The effects of secondary structure on asparagine (N) deamidation in a 22 amino acid sequence (369‐GFYPSDIAVEWESNGQPENNYK‐390) of the crystallizable (Fc) fragment of a human monoclonal antibody (Fc IgG1) were investigated using high‐resolution ultra performance liquid chromatography with tandem mass spectrometry (UPLC/MS). Samples containing either the intact Fc IgG (～50 kD) (“intact protein”), or corresponding synthetic peptides (“peptide”) were stored in Tris buffer at 37°C and pH 7.5 for up to forty days, then subjected to UPLC/MS analysis with high energy MS1 fragmentation. The peptide deamidated only at N₃₈₂ to form the isoaspartate (isoD₃₈₂) and aspartate (D₃₈₂) products in the ratio of ～4:1, with a half‐life of ～3.4 days. The succinimide intermediate (Su₃₈₂) was also detected; deamidation was not observed for the other two sites (N₃₈₇ and N₃₈₈) in peptide samples. The intact protein showed a 30‐fold slower overall deamidation half‐life of ～108 days to produce the isoD₃₈₂ and D₃₈₇ products, together with minor amounts of D₃₈₂. Surprisingly, the D₃₈₂ and isoD₃₈₇ products were not detected in intact protein samples and, as in the peptide samples, deamidation was not detected at N₃₈₈. The results indicate that higher order structure influences both the rate of N‐deamidation and the product distribution.     

Functional proteomic analysis of GS-NS0 murine myeloma cell lines with varying recombinant monoclonal antibody production rate

We previously compared changes in individual protein abundance between the proteomes of GS-NS0 cell lines with varying rates of cell-specific recombinant monoclonal antibody production (qMab). Here we extend analyses of our proteomic dataset to statistically determine if particular cell lines have distinct functional capabilities that facilitate production of secreted recombinant Mab. We categorized 79 proteins identified by mass spectrometry according to their biological function or location in the cell and statistically compared the relative abundance of proteins in each category between GS-NS0 cell lines with varying qMab. We found that the relative abundance of proteins in ER chaperone, non-ER chaperone, cytoskeletal, cell signaling, metabolic, and mitochondrial categories were significantly increased with qMab. As the GS-NS0 cell line with highest qMab also had an increased intracellular abundance of unassembled Mab heavy chain (HC), we tested the hypothesis that the increased ER chaperone content was caused by induction of an unfolded protein response (UPR) signaling pathway. Immunoblot analyses revealed that spliced X-box binding protein 1 (XBP1), a marker for UPR induction, was not detectable in the GS-NS0 cells with elevated qMab, although it was induced by chemical inhibitors of protein folding. These data suggest that qMab is functionally related to the abundance of specific categories of proteins that together facilitate recombinant protein production. We infer that individual cells within parental populations are more functionally equipped for high-level recombinant protein production than others and that this bias could be used to select cells that are more likely to achieve high qMab.     

Actin surface structure revealed by antibody imprints: evaluation of phage-display analysis of anti-actin antibodies

Phage-display peptide library analysis of an anti-F actin polyclonal antibody identified 12 amino acid residues of actin that appear, in its X-ray crystal structure, to be grouped together in a surface accessible conformational epitope. Phage epitope mapping was carried out by isolating immune complexes containing members of the J404 nonapeptide phage-display library formed in diluted antiserum and isolated on a protein A affinity matrix. Immunoreactive clones were grown as plaques, replica plated onto nitrocellulose, and labeled with anti-actin immune serum. One hundred and forty-four positively staining clones identified in this way were sequenced. Of these, 54 displayed peptides with sequence similarities. When the most abundantly selected sequence, KQTWQQLWD, was produced as a synthetic peptide and derivatized to ovalbumin, the complex was strongly recognized by the antiserum on Western blots and inhibited the binding of the antibody to immobilized F-actin by 60%. A scrambled version of this sequence WQDK WLQTQ, when coupled to ovalbumin, was not recognized by the antiserum and minimally inhibited binding of antiserum to immobilized F-actin by 10%. KQTWQQLWD contained four residues that corresponded, in frame, to a highly conserved six residue region of the chicken beta-actin sequence 351TFQQMW356 (identical residues are shown in bold). Examination of the rabbit skeletal muscle X-ray crystal structure suggested that within a 15 A radius of W356, nine additional residues were arranged on the actin surface in such a way that they could be mimicked by several of the selected phage sequences with root-mean-square deviation fits of 2.1-2.5 A. We conclude that phage-display analysis can provide information about the relative location of amino acids on the surfaces of proteins using antibody imprints of the protein surface structure.     

待孕夫妇乙肝表面抗原及乙肝表面抗体阳性情况分析

目的 分析与探讨待孕夫妇乙肝表面抗原及乙肝表面抗体检测结果,并研究其对临床孕前检查的影响及评价。方法 随机选取2015‒2017年度在我院进行孕前检查的夫妇2440对（4 880例）为研究对象,按照年度将待孕夫妇分为两组,每组2 440例,两组均加强孕前检查中的乙肝表面抗原（HBsAg）及乙肝表面抗体（HBsAb）的检测。A组为2015年3月‒2016年2月在我院进行乙肝表面抗原及乙肝表面抗体检查的待孕夫妇;B组为2016年3月‒2017年2月在我院进行乙肝表面抗原及乙肝表面抗体检查的待孕夫妇。比较两组待孕夫妇乙肝表面抗原及乙肝表面抗体检测的阳性结果。结果 B组HBsAg阳性率、HBsAb阳性率明显高于A组（6.43% vs 4.63%;62.99% vs 58.44%）,差异有统计学意义（P＜0.05）。B组、A组男性HBsAg阳性率明显高于同组女性（59.87% vs 40.13%;60.18% vs 39.82%）,HBsAb阳性率低于同组女性（46.52% vs 53.48%;47.41% vs 52.59%）,差异均有统计学意义（P＜0.05）。B组、A组高中及以上学历HBsAg阳性率明显低于同组高中以下学历（38.85% vs 61.95%;38.05% vs 61.15%）,高中及以上学历HBsAb阳性率高于同组高中以下学历（53.15% vs 46.84%;51.75% vs 48.25%）,差异均有统计学意义（P＜0.05）结论 目前夫妇乙肝感染仍处于增高趋势,对于进行孕前检查的待孕夫妇加强乙肝表面抗原及乙肝表面抗体的检测,有助于疾病的早期诊断、干预及治疗,能够减少乙肝传播,可有效降低新生儿乙肝发病率,促进优生优育,提高出生人口整体素质。     

Crystal structure of the disulfide-stabilized Fv fragment of anticancer antibody B1: Conformational influence of an engineered disulfide bond

A recombinant Fv construct of the B1 monoclonal antibody that recognizes the Lewis^Y-related carbohydrate epitope on human carcinoma cells has been prepared. The Fv is composed of the polypeptide chains of the V_H and V_L domains expressed independently and isolated as inclusion bodies. The Fv is prepared by combining and refolding equimolar amounts of guanidine chloride solubilized inclusion bodies. The Fv is stabilized by an engineered interchain disulfide bridge between residues V_L100 and V_H44. This construct has a similar binding affinity as that of the single-chain construct (Benhar and Pastan, Clin. Cancer Res. 1:1023–1029, 1995). The B1 disulfide-stabilized Fv (B1dsFv) crystallizes in space group P6₁22 with the unit cell parameters a = b = 80.1 Å, and c = 138.1 Å. The crystal structure of the B1dsFv has been determined at 2.1-Å resolution using the molecular replacement technique. The final structure has a crystallographic R-value of 0.187 with a root mean square deviation in bond distance of 0.014 Å and in bond angle of 2.74°. Comparisons of the B1dsFv structure with known structures of Fv regions of other immunoglobulin fragments shows closely related secondary and tertiary structures. The antigen combining site of B1dsFv is a deep depression 10-Å wide and 17-Å long with the walls of the depression composed of residues, many of which are tyrosines, from complementarity determining regions L1, L3, H1, H2, and H3. Model building studies indicate that the Lewis^Y tetrasaccharide, Fuc–Gal–Nag–Fuc, can be accommodated in the antigen combining site in a manner consistent with the epitope predicted in earlier biochemical studies (Pastan, Lovelace, Gallo, Rutherford, Magnani, and Willingham, Cancer Res. 51:3781–3787, 1991). Thus, the engineered disulfide bridge appears to cause little, if any, distortion in the Fv structure, making it an effective substitute for the B1 Fab. Proteins 31:128–138, 1998. Published 1998 Wiley-Liss, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.

     

Context-dependent mutations predominate in an engineered high-affinity single chain antibody fragment

A mutational analysis of the femtomolar-affinity anti-fluorescein antibody 4M5.3, compared to its wild-type progenitor, 4-4-20, indicates both context-dependent and -independent mutations are responsible for the 1800-fold affinity improvement. 4M5.3 was engineered from 4-4-20 by directed evolution and contains 14 mutations. The seven mutations identified as present in each of 10 final round affinity maturation clones were studied here. Affinities of the 4-4-20 single mutant addition and 4M5.3 single site reversion mutants were compared. These experiments identified four mutations, of these seven, that were context-dependent in their contribution to higher affinity. A simplified mutant containing only these seven mutations was created to analyze complete double mutant cycles of selected sets of mutations. Specific mutational sets studied included the ligand contact mutations, the heavy chain CDR3 mutations, the heavy chain CDR3 mutations plus the neighboring residue at site H108, and the early and late acquired mutations on the directed evolution pathway. The heavy chain CDR3 mutational set and the ligand-contacting mutations were shown to provide -1.4 and -2.0 kcal/mol, respectively, of the total -3.5 kcal/mol change in free energy of binding of the seven-site consensus mutant. The mutations acquired late in the directed evolution rounds provided much of the change in free energy without the earlier acquired mutations (-3.1 kcal/mol of the total -3.5 kcal/mol). Prior structural data and electrostatic calculations presented several hypotheses for the higher affinity contributions, some of which are supported by these mutational data.     

Construction of recombinant monoclonal antibodies from a chicken hybridoma line secreting specific antibody

The chicken is a useful animal for the development of the specificantibodies against the mammalian conserved proteins. We generated twotypes of recombinant chicken monoclonal antibodies (mAbs), using a phagedisplay technique from a chicken hybridoma HUC2-13 which secreted themAb to the N-terminal of the mammalian prion protein (PrP). Althoughthe mAb HUC2-13 is a useful antibody for the prion research, thehybridoma produces a low level of antibody production. In order to producea large amount of the mAb, we have constructed a single chain fragmentvariable region (scF_V) mAb by using the variable heavy(V_H) and light (V_L)genes which were amplified by using the two primer pairs and theflexible linker. The two phage display mAbs (HUC2p3 and HUC2p5)expressed on a M13 filamentous phage and their soluble type mAbs(HUC2s3 and HUC2s5) were reacted with the PrP peptide antigen in theELISA. In the Western blot analysis, the mAbs HUC2p3 and HUC2s3 wereas reactive to PrP^c from mouse brains as the mAb HUC2-13 was. The nucleotide sequences of V_H and V_L genes from HUC2-13 and the two cloneswere identical except for only one residue. These results indicate that themethods presented here provide an effective tool for the improvement ofthe low levels of antibody production in the chicken hybridoma system.     

人CLEC-2胞外段CRD重组蛋白纯化与多克隆抗体的制备和活性鉴定

人C型凝集素样受体(human C-type lectin-like receptor-2, hCLEC-2)是新克隆的Ⅱ型跨膜受体分子,研究表明,它在病毒感染,血小板活化、聚集,肿瘤转移和信号转导等方面发挥重要作用．通过制备针对其胞外段糖类识别结构域(CRD)的抗体来进一步研究该蛋白质的生物学功能及相关信号通路．构建了pET23b-CRD重组表达质粒,将其转化到大肠杆菌BL21中,用于hCLEC-2-CRD-His融合蛋白的表达,经聚丙烯酰胺凝胶电泳检测表明,融合重组蛋白成功获得了高效表达,分子质量在18 ku左右．经鉴定,发现hCLEC-2-CRD-His表达于包涵体中．为获得高纯度的可溶性蛋白,将包涵体溶于6 mol/L盐酸胍,并用镍柱进行纯化．纯化后的蛋白质经过透析、再折叠后作为抗原,免疫家兔制备抗血清,抗血清经蛋白G亲合层析纯化后用Western blot等方法进行鉴定,结果显示该抗体能特异性地检测到GFP-hCLEC-2和GFP-CRD．通过使用该抗体,进一步发现,在用PMA和IL-4诱导单核细胞THP-1分化的过程中,内源性hCLEC-2蛋白水平下调,初步揭示了hCLEC-2的表达和单核细胞的分化存在一定的联系．因此,该抗体的成功制备将为进一步研究CLEC-2的生物学功能提供有利的条件．     

Expression of a single-chain Fv antibody fragment specific for the Hepatitis B surface antigen in transgenic tobacco plants

An anti-Hepatitis B virus surface antigen (HBsAg) single chain Fv (scFv) antibody fragment was expressed in Nicotiana tabacum transgenic plants. The 6-histidine tagged scFv was targeted to either the cytosol, apoplast, and vacuole, or for retention in the endoplasmic reticulum. Expression of active scFv was detected by ELISA in fresh leaf material from F1 transgenic plant lines representative of the genetic constructs targeting the antibody fragment to the apoplastic fluid (AF-12, 0.031% of the total soluble protein), vacuole (V-20, 0.032% of the total soluble protein), and endoplasmic reticulum (ER-52, 0.22% of the total soluble protein). No scFv was detected by ELISA or western blot in the plants transformed with the cytosol construct. The biologically active scFv was easily purified (to 94–95% purity) from ER-52 and AF-12 plant material using immobilized metal ion affinity chromatography. Recovery estimated from the ER-52 plant line indicates that 15–20g of pure active scFv can be obtained per gram of fresh leaf material, on a laboratory scale.     

烟草细胞中高效表达的药用蛋白可以提高血清的半衰期

小分子治疗蛋白, 如干扰素α2b(IFNα2)和人生长激素(hGH), 由于其对血清蛋白酶的易感性及分子小, 可被肾迅速清除, 因而一般在血清中的半衰期都很短。化学衍生处理虽可以克服这些问题, 但却要以降低蛋白的生物活性为代价。本研究建立了一种新方法, 使干扰素α2b (IFNα2)和人类生长激素(hGH)在烟草细胞中高效表达为阿拉伯半乳糖聚糖糖蛋白嵌合体(AGP)。这样不仅提高了药用蛋白的产量, 而且提高了其血清半衰期。这种嵌合糖蛋白的分泌量比没有糖基化时高500~1800 倍。重要的是, 与未糖基化的干扰素和人生长激素相比, 这种嵌合糖蛋白的体内血半衰期提高13倍, 生物活性仍保持与未糖基化时相似。这种嵌合糖蛋白注射到小鼠体内未引起免疫性反应。