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Binding Sites, Antibody (1):
Recent article
Binding Sites, Antibody
Abstract
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Abstract
We used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed hea...
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PMID: 21835983
PDF is available here.
PDF is available here.
Abstract
Abstract
We cloned 576 new HIV antibodies from four unrelated individuals. All four individuals produced expanded clones of potent broadly neutralizing CD4-binding-site antibodies that mimic binding to CD4. Despite extensive hypermutation, the new antibodies shared a consensus sequence of 68 immunoglobulin H...
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PMID: 21764753
PDF is available here.
PDF is available here.
Abstract
Three pairs of specific primers were designed to amplify F2-1, F2-2, and XF2-2 truncated capsid protein genes of porcine circovirus type 2 (PCV-2). Amplified sequences were subcloned to pET-32a(+) vectors and expressed in Rosetta (DE3) Escherichia coli by induction of isopropy-β-D-thiogalactoside (I...
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PMID: 21461197
PDF is available here.
PDF is available here.
Abstract
We here demonstrate paramagnetic relaxation-enhanced (PRE) NMR spectroscopy to be a powerful tool unraveling structural information about epitope-orientation in a groove spanned by the complementary determining regions. In particular, we utilize the spin label TOAC, which is fused to the peptidic ep...
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PMID: 20476792
PDF is available here.
PDF is available here.
Journal of Immunological Methods (359)1-2 2010
Abstract
We show that antibody-expressing clones can be simultaneously cultured and analysed rapidly in antigen-coated ELISA plate wells yielding high binding signals and saving valuable selection time, while also eliminating the necessity for antibody extraction. The utilisation of the 'on-plate' technique...
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PMID: 20493872
PDF is available here.
PDF is available here.
Abstract
The development of Goodpasture's disease may be considered an autoimmune "conformeropathy" that involves perturbation of the quaternary structure of the alpha345NC1 hexamer, inducing a pathogenic conformational change in the alpha3NC1 and alpha5NC1 subunits, which in turn elicits an autoimmune respo...
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PMID: 20660402
PDF is available here.
PDF is available here.
Abstract
We used knowledge of HIV-1 envelope structure to develop antigenically resurfaced glycoproteins specific for the structurally conserved site of initial CD4 receptor binding. These probes were used to identify sera with NAbs to the CD4-binding site (CD4bs) and to isolate individual B cells from such...
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PMID: 20616233
PDF is available here.
PDF is available here.
Abstract
We determined the crystal structure of VRC01 in complex with a human immunodeficiency virus HIV-1 gp120 core. VRC01 partially mimics CD4 interaction with gp120. A shift from the CD4-defined orientation, however, focuses VRC01 onto the vulnerable site of initial CD4 attachment, allowing it to overcom...
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PMID: 20616231
PDF is available here.
PDF is available here.
Abstract
We have demonstrated the motor terminal to be a vulnerable site. Here we show both in vivo and ex vivo, that nodes of Ranvier in intramuscular motor nerve bundles are also targeted by anti-GD1a antibody in a gradient-dependent manner, with greatest vulnerability at distal nodes. Complement depositio...
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PMID: 20513658
PDF is available here.
PDF is available here.
Infection and Immunity (78)7 2010
Abstract
We isolated human IgG from normal human sera (NHS) using lipooligosaccharide (LOS) from gonococcal strain JW31R as an affinity ligand. We provided evidence that the oligosaccharide (OS) moiety of LOS was immunogenic in humans and that NHS contains functional antibodies that bind to the branched OS....
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PMID: 20479085
PDF is available here.
PDF is available here.
Journal of Neuroimmunology (223)1-2 2010
Abstract
We selected a novel set of human anti-amyloid-beta peptide 1-42 (Abeta1-42) recombinant monoclonal antibodies in a single chain fragment variable (scFv) and a single-domain (VH) format. We demonstrated that these antibody fragments recognize in a specific manner amyloid-beta deposits in APP/Tg mouse...
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PMID: 20451261
PDF is available here.
PDF is available here.
Analytical Biochemistry (402)2 2010
Abstract
A critical assumption in utilizing labeled antibodies is that the conjugation reaction has no deleterious effects on antibody avidity. This study demonstrates that this assumption need not hold true and presents a methodology to quantitatively determine the degree of inactivation and...
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PMID: 20362543
PDF is available here.
PDF is available here.
Abstract
We illustrate a novel approach, named SnugDock, to predict high-resolution antibody-antigen complex structures by simultaneously structurally optimizing the antibody-antigen rigid-body positions, the relative orientation of the antibody light and heavy chains, and the conformations of the six comple...
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PMID: 20098500
PDF is available here.
PDF is available here.
Ukrainskij biokhimicheskij zhurnal/Ukrayins'kij biokhimichnij zhurnal/Ukrainian biochemical journal (82)1 2010
Abstract
The presence of polyreactive immunoglobulins in sera may substantially influence on the accuracy of antibody affinity determination. In order to obtain precise values of antibody affinity one should apply one of two following ways. First, one should block polyreactive immunoglobulins with high conce...
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PMID: 20684229
PDF is available here.
PDF is available here.
Thrombosis and Haemostasis (103)1 2010
Abstract
We characterised, for the first time, a unique anti-FVIII monoclonal antibody, mAb216, that enhanced FVIII coagulant activity. The mAb216 shortened the activated partial thromboplastin time and specifically increased FVIII activity by approximately 1.5-fold dose-dependently. FXa generation and throm...
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PMID: 20062922
PDF is available here.
PDF is available here.
Abstract
We further demonstrated that using a cysteine/cystine redox pair (rather than cysteine alone) can not only effectively remove glutathione at the engineered cysteines, but also generate homogeneously cysteinylated species, which resulted in one main peak in both CEX-HPLC and imaged cIEF assays for an...
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PMID: 20068389
PDF is available here.
PDF is available here.
Abstract
We exploited a previously reported promiscuous binding interaction between a single-chain, variable fragment antibody protein and a family of cyanine dyes to create new protein-dye fluoromodules that exhibit enhanced photostability while retaining high affinity protein-dye binding. Modifications to...
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PMID: 19737016
PDF is available here.
PDF is available here.
Biochemistry (Washington) (48)37 2009
Abstract
We have developed a strategy in which otherwise posttranslationally modified amino acids are genetically encoded in Escherichia coli in response to unique nonsense or frameshift codons. Here, we illustrate the utility of this approach through the characterization of the doubly tyrosine-sulfated anti...
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PMID: 19715291
PDF is available here.
PDF is available here.
Abstract
We combined two lectin-affinity chromatography techniques, Concanavalin A and Lens culinaris agglutinin, to enrich the non-fucosylated species from therapeutic material using the anti-Her2/neu model antibody. Oligosaccharide analysis by matrix-assisted laser desorption/ionization-time of flight MS f...
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PMID: 19721240
PDF is available here.
PDF is available here.
Biochemical Journal (422)2 2009
Abstract
We validated the use of DX-2300 for specific KLK1 inhibition by measuring the inhibition of KLK1-like activity in human urine, saliva and bronchoalveolar lavage fluid, which are known to contain active KLK1. In human tracheobronchial epithelial cells grown at the air/liquid interface, DX-2300 blocke...
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PMID: 19527222
PDF is available here.
PDF is available here.
Abstract
A membrane-based electrochemical nanobiosensor sensitive toward whole viral particles is fabricated by forming a submicrometer thick nanoporous alumina membrane over a platinum disk electrode. Antibody probe molecules are physically adsorbed onto the walls of the membrane nanochannels. The sensing s...
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PMID: 19663392
PDF is available here.
PDF is available here.
Abstract
We present a procedure for quantifying single protein molecules affixed to a surface by counting bound antibodies. We systematically investigate many of the parameters that have prevented the robust single-molecule detection of surface-immobilized proteins. We find that a chemically adsorbed bovine...
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PMID: 19601620
PDF is available here.
PDF is available here.
Abstract
Biochemistry (Washington) (48)33 2009
Abstract
We formed disulfide bonds between Cys residues whose location in a peptide template representing the entire V3(CONSENSUS) epitope recognized by the broadly neutralizing 447-52D antibody was changed systematically. In a previous study [Mor, A., et al. (2009) Biochemistry 48, 3288-3303] we showed that...
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PMID: 19552398
PDF is available here.
PDF is available here.
Journal of Immunology (183)5 2009
Abstract
We previously compared functional profiles of the poxviral complement inhibitors of smallpox, vaccinia, and monkeypox known as SPICE, VCP (or VICE), and MOPICE, respectively. SPICE was the most potent regulator of human complement and attached to cells via glycosaminoglycans. The major goals of the...
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PMID: 19667083
PDF is available here.
PDF is available here.
Abstract
We explore the binding of antibodies to membrane components of the vesicle assembly through the use of quartz crystal microbalance with dissipation monitoring (QCM-D). The technique provides a quantitative, label-free avenue to study binding processes at membrane surfaces. However, converting the si...
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PMID: 19580260
PDF is available here.
PDF is available here.
Abstract
A fully synthetic anticancer vaccine 2 has been prepared via bioconjugation of unimolecular pentavalent construct 1-containing five prostate and breast cancer associated carbohydrate antigens, Globo-H, GM2, STn, TF and Tn-to maleimide-modified carrier protein KLH. An improved conjugation protocol ha...
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PMID: 19518111
PDF is available here.
PDF is available here.
Journal of General Virology (90)Pt 7 2009
Abstract
We analysed the antigenic structure of influenza A virus NP by introducing site-specific mutations at amino acid positions presumed to be relevant for the differentiation of strain differences by anti-NP monoclonal antibodies. Mutant proteins were expressed in a prokaryotic system and analysed by pe...
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PMID: 19297605
PDF is available here.
PDF is available here.
Journal of Neuroimmunology (211)1-2 2009
Abstract
We examined the antibody binding epitope using human and mouse mutant AQP4.
We constructed human and mouse amino acid substitution AQP4 mutants and compared the reactivity with wild-form of human, mouse and rat AQP4.
The decreased intensity of AQP4-Ab staining with mo...
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PMID: 19410301
PDF is available here.
PDF is available here.
Analytical Biochemistry (390)2 2009
Abstract
This article describes the simultaneous Biacore analysis of human anti-human antibodies (HAHAs) with respect to the binding region and the isotype by a combination of 11 single measurements per sample. The multiplexing single assay setup made efficient use of the four parallel flow cells on one bios...
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PMID: 19379704
PDF is available here.
PDF is available here.
Thrombosis and Haemostasis (101)5 2009
Abstract
We examined the FVIII peptide sequence regions recognised by anti-FVIII Ab in the plasma of six congenital and one acquired haemophilia patients with high inhibitor titers (24.4-2000 BU/ml). We used indirect ELISA and overlapping synthetic peptides, 20 residues long, spanning the sequence of the A a...
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PMID: 19404535
PDF is available here.
PDF is available here.
Abstract
We describe an antibody with an antigen binding site that binds two distinct proteins with high affinity. We isolated a variant of Herceptin, a therapeutic monoclonal antibody that binds the human epidermal growth factor receptor 2 (HER2), on the basis of its ability to simultaneously interact with...
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PMID: 19299620
PDF is available here.
PDF is available here.
Abstract
Binding sites of five monoclonal antibodies were obtained by reinforceable method of overlapping recombinant prion protein and synthetic peptide. Overlapping peptides of PrP core were expressed in Escherichia coli by insertion of serial PCR amplicons of ovine PrP gene fragments into pET32a. The expr...
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PMID: 19621573
PDF is available here.
PDF is available here.
Abstract
Proteins and peptides are comprised of both sequence-specific and conformation-specific epitopes. Sequence-specific epitopes are delineated by a peptide approach and other robust methods like competition assays, gene expression assays, synthetic peptide library based assays, etc. Available methods fo...
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PMID: 19117199
PDF is available here.
PDF is available here.
Abstract
We report the development and implementation of RosettaAntibody, a protocol for homology modeling of antibody variable regions. The protocol combines comparative modeling of canonical complementarity determining region (CDR) loop conformations and de novo loop modeling of CDR H3 conformation with si...
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PMID: 19062174
PDF is available here.
PDF is available here.
Journal of Immunology (182)3 2009
Abstract
We cloned a novel chicken FcR, designated gallus gallus FcR (ggFcR), which was shown to bind selectively chicken IgY. The receptor consists of four extracellular C2-set Ig domains, followed by a transmembrane region containing arginine as a positively charged amino acid and a short cytoplasmic tail....
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PMID: 19155501
PDF is available here.
PDF is available here.
Journal of Immunology (182)3 2009
Abstract
We hypothesized that these anti-endothelial Abs promote thrombosis through interference with clearance of dying cells. We show that healthy endothelial cell monolayers effectively remove apoptotic endothelial cells, but this clearance is markedly inhibited by serum or IgG from patients with antiphos...
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PMID: 19155525
PDF is available here.
PDF is available here.
Journal of Immunology (182)3 2009
Abstract
We previously reported that some human antiphospholipid Abs (aPL) in patients with the antiphospholipid syndrome (APS) bind to the homologous enzymatic domains of thrombin and the activated coagulation factor X (FXa). Moreover, some of the reactive Abs are prothrombotic and interfere with inactivati...
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PMID: 19155517
PDF is available here.
PDF is available here.
Journal of Immunology (182)2 2009
Abstract
CD80 expressed on the surface of APCs provides a positive costimulatory signal to naive CD4+ T cells via CD28 during activation. However, CD80 is also expressed on the surface of activated CD4+ T cells, and cross-linking CD80 on the surface of CD4+ T cells activated in the presence of Th1-promoting...
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PMID: 19124719
PDF is available here.
PDF is available here.
BMC Immunology (10)1 2009
Abstract
In this paper, we panned peptide displaying phage libraries against a pool of CHIPS specific affinity-purified polyclonal human IgG. The selected peptides could be divided into two groups of sequences. The first group was the most dominant with 36 of the 48 sequenced clones represented. Binding to h...
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PMID: 19284584
PDF is available here.
PDF is available here.
Abstract
Ruptured atherosclerotic plaques, lined with activated platelets, constitute an attractive target for magnetic resonance imaging (MRI). This study evaluated whether microparticles of iron oxide (MPIO) targeting ligand-induced binding sites (LIBS) on the activated conformation of glycoprotein IIb/III...
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PMID: 18515970
PDF is available here.
PDF is available here.
Immunobiology (214)1 2009
Abstract
We generated a panel of five monoclonal antibodies (mAbs) which specifically recognized the HIV-1 gp41 6-HB formed by the NHR-peptide N36 and CHR-peptide C34 mixture, but did not react with the isolated peptides N36 and C34. These mAbs did not block the HIV-1 Env-mediated cell-cell fusion at physiol...
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PMID: 19159827
PDF is available here.
PDF is available here.
Journal of Immunology (182)1 2009
Abstract
We therefore hypothesized that CTCF may be crucial for the contraction of the Ig loci, but no CTCF sites have been described in any V loci. Using ChIP-chip, we demonstrated many CTCF sites in the V(H) and V(kappa) regions. However, CTCF enrichment in the Igh locus, but not the Igkappa locus, was lar...
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PMID: 19109133
PDF is available here.
PDF is available here.
Journal of Immunology (182)1 2009
Abstract
We developed a murine model wherein anti-MHC class I Abs or control (C1.18.4/anti-keratin) were administered intrabronchially into native lungs. Animals receiving anti-MHC class I, but not control Abs, developed marked cellular infiltration around vessels and bronchiole of lung by day 15, followed b...
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PMID: 19109162
PDF is available here.
PDF is available here.
Journal of Immunology (182)1 2009
Abstract
We previously identified two structurally different peptides that are both effective mimotopes: a 7-mer cyclic peptide (Rp15-C) bearing the antigenic motif (a/sNPS) that matches 170(ANPS)173 of the extracellular loop of CD20, and a 12-mer linear peptide (Rp5-L) containing the antigenic motif (WPxWLE...
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PMID: 19109173
PDF is available here.
PDF is available here.
Journal of Immunology (182)1 2009
Abstract
We developed a mAb, IIC1, that recognized MD-2 both free and when bound to TLR4. MD-2 was found on the surface of freshly isolated monocytes, on a subpopulation of CD19(+) B-cells and on CD15(+) neutrophils. LPS transiently reduced the MD-2 levels on monocytes, which is most likely due to endocytosi...
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PMID: 19109192
PDF is available here.
PDF is available here.
Journal of Immunology (181)12 2008
Abstract
We hypothesized that this interaction was nonessential for PS-specific IgG responses to Pn. We now demonstrate that ICOS(-/-), relative to wild-type, mice elicit a normal PS-specific IgG isotype response to Pn, despite marked inhibition of both the primary and secondary IgG anti-protein (i.e., PspA,...
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PMID: 19050242
PDF is available here.
PDF is available here.
Journal of Immunology (181)12 2008
Abstract
We have described that murine IgG1 Abs can be separated according to their ability to elicit in vivo anaphylaxis in a fraction of anaphylactic and other of non-anaphylactic molecules. Furthermore, we showed that the N-linked oligosaccharide chain is essential for the structural conformation of the a...
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PMID: 19050247
PDF is available here.
PDF is available here.
Sarcoidosis, vasculitis, and diffuse lung diseases : official journal of WASOG / World Association of Sarcoidosis and Other Granulomatous Disorders (25)2 2008
Abstract
We used bioinformatic tools allowing the identification of antigenic peptides in whole microbial genomes to analyze the interaction between the expressed HLA-DR gene allelic variants and the HLA-DR immunome of all pathogenic bacteria in a population of 149 sarcoidosis affected subjects and 447 contr...
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PMID: 19382529
PDF is available here.
PDF is available here.
Gene Therapy (15)24 2008
Abstract
We report on the ability of single-chain variable fragment (scFv) incorporated into the viral envelope to alter the tropism of herpes simplex virus (HSV) 1716. Using recombinant viruses expressing fusion proteins comprising cell-surface antigen-specific scFvs N terminus linked to amino acids 274-393...
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PMID: 18701918
PDF is available here.
PDF is available here.
Growth Factors (26)6 2009
Abstract
We conclude that dissociation kinetics coupled with SS-SPRIA unequivocally provides considerable insight into the study of ligand–ligate interactions and epitope analysis....
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PMID: 19012067
PDF is available here.
PDF is available here.
Abstract
The Candida albicans adhesin, Als3p, was identified as a potential cognate antigen for previously described human antibody fragments [single-chain variable fragment (scFv)] based on similarity of the binding pattern of the scFv to the distribution of this protein on the hyphal surface. Although all...
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PMID: 18662314
PDF is available here.
PDF is available here.
Journal of Immunology (181)9 2008
Abstract
We report the design of an Ab repertoire enriched in Abs binding to small charged carbohydrates and the construction of a human Fab phagemid library, "FAB-CCHO." This library combines L chain Ig sequences from human donors and H chain synthetic diversity constructed in key Ag contact sites in CDRs 1...
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PMID: 18941211
PDF is available here.
PDF is available here.
Journal of Immunology (181)9 2008
Abstract
We present an automated procedure for identifying CDRs and B cell epitopes using consensus structural regions that interact with the antigens in all known antibody-protein complexes. Consequently, we provide the first comprehensive analysis of all CDR-epitope complexes of known three-dimensional str...
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PMID: 18941213
PDF is available here.
PDF is available here.
Analytical Biochemistry (381)2 2008
Abstract
We report a method to build ultrasensitive carbon nanotube-based biosensors using immune binding reaction. Here carbon nanotube-field effect transistors (CNT-FETs) were functionalized with antibody-binding fragments as a receptor, and the binding event of target immunoglobulin G (IgG) onto the fragm...
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PMID: 18640089
PDF is available here.
PDF is available here.
EMBO Journal (27)19 2008
Abstract
We present crystallographic, kinetic and thermodynamic analyses of the binding site of such an antibody and that of its primary immunoglobulin ancestor. These show that these germline V-genes encode key side chain contacts with the viral antigen and thereby dictate key structural features of the hyp...
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PMID: 18772881
PDF is available here.
PDF is available here.
Abstract
We extended these observations by defining annexin A2 as an endothelial beta(2)GPI binding site. We also observed that annexin A2 plays a critical role in endothelial cell activation induced by anti-beta(2)GPI antibodies, and others have described direct endothelial activation by anti-annexin A2 ant...
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PMID: 18827060
PDF is available here.
PDF is available here.
Abstract
The phospholipid binding protein, annexin A5 (AnxA5), has potent anticoagulant properties that result from its forming 2-dimensional crystals over phospholipids, blocking the availability of the phospholipids for critical coagulation enzyme reactions. This article reviews the evidence that antiphosp...
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PMID: 18827057
PDF is available here.
PDF is available here.