The Experts below are selected from a list of 1680 Experts worldwide ranked by ideXlab platform

Robert J Woods - One of the best experts on this subject based on the ideXlab platform.

  • Computational Screening of the Human TF-Glycome Provides a Structural Definition for the Specificity of Anti-Tumor Antibody JAA-F11
    2016
    Co-Authors: Matthew B Tessier, Oliver C Grant, Snehal Jadey, Andrew M Gulick, John Glushka, Susan L Deutscher, Jamie Heimburg-molinaro, David Smith, Kate Rittenhouse-olson, Robert J Woods
    Abstract:

    Recombinant antibodies are of profound clinical significance; yet, anti-carbohydrate antibodies are prone to undesirable cross-reactivity with structurally related-glycans. Here we introduce a new technology called Computational Carbohydrate Grafting (CCG), which enables a virtual library of glycans to be assessed for protein binding specificity, and employ it to define the scope and structural origin of the binding specificity of Antibody JAA-F11 for glycans containing the Thomsen-Friedenreich (TF) human tumor antigen. A virtual library of the entire human glycome (GLibrary-3D) was constructed, from which 1,182 TF-containing human glycans were identified and assessed for their ability to fit into the Antibody Combining Site. The glycans were categorized into putative binders, or non-binders, on the basis of steric clashes with the Antibody surface. The analysis employed a structure of the immune complex, generated by docking the TF-disaccharide (Galb1-3GalNAca) into a crystal structure of the JAA-F11 antigen binding fragment, which was shown to be consistent with saturation transfer difference (STD) NMR data. The specificities predicted by CCG were fully consistent with data from experimental glycan array screening, and confirmed that the Antibody is selective for the TF-antigen and certain extended core-2 type mucins. Additionally, the CCG analysis identified a limited number of related putative binding motifs, an

  • computational screening of the human tf glycome provides a structural definition for the specificity of anti tumor Antibody jaa f11
    PLOS ONE, 2013
    Co-Authors: Matthew B Tessier, Oliver C Grant, Jamie Heimburgmolinaro, David F Smith, Snehal Jadey, Andrew M Gulick, John Glushka, Susan L Deutscher, Kate Rittenhouseolson, Robert J Woods
    Abstract:

    Recombinant antibodies are of profound clinical significance; yet, anti-carbohydrate antibodies are prone to undesirable cross-reactivity with structurally related-glycans. Here we introduce a new technology called Computational Carbohydrate Grafting (CCG), which enables a virtual library of glycans to be assessed for protein binding specificity, and employ it to define the scope and structural origin of the binding specificity of Antibody JAA-F11 for glycans containing the Thomsen-Friedenreich (TF) human tumor antigen. A virtual library of the entire human glycome (GLibrary-3D) was constructed, from which 1,182 TF-containing human glycans were identified and assessed for their ability to fit into the Antibody Combining Site. The glycans were categorized into putative binders, or non-binders, on the basis of steric clashes with the Antibody surface. The analysis employed a structure of the immune complex, generated by docking the TF-disaccharide (Galβ1-3GalNAcα) into a crystal structure of the JAA-F11 antigen binding fragment, which was shown to be consistent with saturation transfer difference (STD) NMR data. The specificities predicted by CCG were fully consistent with data from experimental glycan array screening, and confirmed that the Antibody is selective for the TF-antigen and certain extended core-2 type mucins. Additionally, the CCG analysis identified a limited number of related putative binding motifs, and provided a structural basis for interpreting the specificity. CCG can be utilized to facilitate clinical applications through the determination of the three-dimensional interaction of glycans with proteins, thus augmenting drug and vaccine development techniques that seek to optimize the specificity and affinity of neutralizing proteins, which target glycans associated with diseases including cancer and HIV.

Alexander H Lucas - One of the best experts on this subject based on the ideXlab platform.

  • molecular ontogeny of the human Antibody repertoire to the haemophilus influenzae type b polysaccharide expression of canonical variable regions and their variants in vaccinated infants
    Clinical Immunology, 2003
    Co-Authors: Alexander H Lucas, Gary R Mclean, Donald C Reason, Adam P Oconnor, Mistique C Felton, Karen D Moulton
    Abstract:

    A structurally conserved Antibody Combining Site, encoded by the IGH V3-23 and kappa A2 variable (V) region gene segments, predominates the adult immune response to the Haemophilus influenzae type b (Hib) capsular polysaccharide (PS). This Site has been elevated to canonical status based upon its relative molecular uniformity and prevalence in adults. To date, no studies have examined the primary structure of Hib PS-specific antibodies in young infants, who are the primary targets of Hib vaccination. In this study we show that canonical Hib PS-specific heavy (H) and light (L) chain V regions are present in 4-month-old infants following two vaccinations with Hib PS-protein conjugates. The infant V regions contain sequence polymorphisms that resemble those found in adult antibodies, as well as polymorphisms at position 95a of the A2 L chain not previously observed in adults. In vitro studies of Fab fragments and recombinant IgG2 antibodies using these V regions identify sequence polymorphisms that impact Hib PS binding affinity and bactericidal activity. These results demonstrate the establishment of canonical V regions in early ontogeny and provide a structural explanation of how canonical antibodies in the infant can vary in their affinity and protective activity against Hib.

  • igh v3 23 01 and its allele v3 23 03 differ in their capacity to form the canonical human Antibody Combining Site specific for the capsular polysaccharide of haemophilus influenzae type b
    Immunogenetics, 2003
    Co-Authors: Leyu Liu, Alexander H Lucas
    Abstract:

    The IGH V3-23*01 gene is used in the formation of the canonical Combining Site which dominates the human Antibody repertoire to the Haemophilus influenzae type b (Hib) polysaccharide (PS). An allele of the human IGH V3-23*01 gene, known as V3-23*03, differs from V3-23*01 in nine bases, eight of which are located in the second complementarity determining region. These eight differences encode five amino acid substitutions. In this study we investigated whether the V3-23*03 sequence polymorphism affected Hib PS binding. We constructed two Fab fragments that had the canonical Hib PS Combining Site VH-VL configuration but that had either V3-23*01 or V3-23*03. Radioantigen binding assay showed that on a concentration basis the V3-23*03 Fab was 20-fold more effective in binding Hib PS than the V3-23*01 Fab. The V3-23*03 Fab was 4-fold more effective than the V3-23*01 Fab in mediating facilitated bactericidal activity against Hib organisms. These findings identify a functional consequence of V3-23 allelism, and suggest that utilization of the V3-23*03 gene in the human Hib PS repertoire would generate canonical antibodies with higher affinity and protective efficacy than canonical antibodies utilizing V3-23*01. Thus, IGH V gene allelic variation has the potential to impact the generation of protective immunity to Hib.

Yoji Arata - One of the best experts on this subject based on the ideXlab platform.

  • application of 13c nmr spectroscopy to paratope mapping for larger antigen fab complexes
    FEBS Letters, 1994
    Co-Authors: Hahyung Kim, Koichi Kato, Sumie Yamato, Takako Igarashi, Chigusa Matsunaga, Hiroshi Ohtsuka, Atsuko Higuchi, Noriko Nomura, Hiroshi Noguchi, Yoji Arata
    Abstract:

    Abstract For the purpose of engineering the Antibody Combining Site, mapping residues that are involved in antigen binding provide us with valuable information. By use of13C NMR spectroscopy with selectively13C-labeled Fv fragments, we have established a general strategy to identify the residues that are perturbed upon binding of small antigen (hapten) molecules [(1990) Biochemistry 30, 6604–6610]. In the present paper, we demonstrate that this strategy can be extended to molecular structural analyses of the complexes of an Fab fragment and a larger antigen molecule such asPseudomonas aeruginosa exotoxin A with a molecular mass of 67 kDa.

  • of 13c nmr spectroscopy to paratope mapping for larger antigen fab complexes
    1994
    Co-Authors: Hahyung Kim, Koichi Kato, Sumie Yamato, Takako Igarashi, Chigusa Matsunaga, Hiroshi Ohtsuka, Atsuko Higuchi, Noriko Nomura, Hiroshi Noguchi, Yoji Arata
    Abstract:

    Abstract For the purpose of engineering the Antibody Combining Site, mapping residues that are involved in antigen binding provide us with valuable information. By use of t3C NMR spectroscopy with selectively ~3C-labeled Fv fragments, we have established a general strategy to identify the residues that are perturbed upon binding of small antigen (hapten) molecules [(1990) Biochemistry 30, 6604--6610]. In the present paper, we demonstrate that this strategy can be extended to molecular structural analyses of the complexes of an Fab fragment and a larger antigen molecule such as Pseudomonas aeruginosa exotoxin A with a molecular mass of 67 kDa, Key words: Antigen-binding Site; Antigen-Antibody interaction; Fab; 13C NMR; Immunoglobulin G; Mouse; Exotoxin A (Pseudomonas aeruginosa) 1. Introduction Since hybridoma technology was established, mono- clonal antibodies have been widely used as immuno- chemical tools, diagnostic reagents, and therapeutics. Recently, genetically engineered antibodies have been produced in order to improve specific reactivity with target antigens, to reduce antigenicity for human ther- apy, and to control the expression of effector functions [1]. The antigen Combining Site in the Antibody molecule is particularly attractive as a target for Antibody engi- neering including the design of catalytic antibodies. With the knowledge of the structure of the antigen Combining Site, one could make an improved Antibody with a higher binding affinity by a conventional method such as Site- directed mutagenesis. Hence, the mapping of residues involved in

  • dynamical structure of the Antibody Combining Site as studied by proton nitrogen 15 shift correlation nmr spectroscopy
    Biochemistry, 1992
    Co-Authors: Hideo Takahashi, Ichio Shimada, Erika Suzuki, Yoji Arata
    Abstract:

    The Fv fragment, which is a smallest antigen-binding unit of immunoglobulin, has been used for a 1H-15N shift correlation NMR study of the dynamical structure of the Antibody Combining Site. Fv has been prepared by clostripain digestion of a mouse anti-dansyl IgG2a monoclonal Antibody that lacks the entire CH1 domain. We have previously reported that of the six hypervariable regions, three each from the heavy chain (H1, H2, and H3) and the light chain (L1, L2, and L3), H3 is primarily responsible for the antigen binding in the anti-dansyl Fv fragment. The backbone amide nitrogens of all non-proline amino acid residues in H3 have been multiply labeled with 15N. [15N]T2 relaxation times and hydrogen-deuterium exchange rates of the amide groups of the main chain were measured in the absence and presence of epsilon-dansyl-L-lysine (DNS-Lys). It has been shown that (1) in the absence of DNS-Lys H3 displays a significant degree of internal motion and (2) antigen binding induces a significant change in the dynamical structure of H3.

John Glushka - One of the best experts on this subject based on the ideXlab platform.

  • a combined computational experimental approach to define the structural origin of Antibody recognition of sialyl tn a tumor associated carbohydrate antigen
    Scientific Reports, 2018
    Co-Authors: Ron Amon, Oliver C Grant, John Glushka, Shani Leviatan Benarye, Spandana Makeneni, Anita K Nivedha, Tal Marshanski, Christoffer Norn, Sarel J Fleishman, Xi Chen
    Abstract:

    Anti-carbohydrate monoclonal antibodies (mAbs) hold great promise as cancer therapeutics and diagnostics. However, their specificity can be mixed, and detailed characterization is problematic, because Antibody-glycan complexes are challenging to crystallize. Here, we developed a generalizable approach employing high-throughput techniques for characterizing the structure and specificity of such mAbs, and applied it to the mAb TKH2 developed against the tumor-associated carbohydrate antigen sialyl-Tn (STn). The mAb specificity was defined by apparent KD values determined by quantitative glycan microarray screening. Key residues in the Antibody Combining Site were identified by Site-directed mutagenesis, and the glycan-antigen contact surface was defined using saturation transfer difference NMR (STD-NMR). These features were then employed as metrics for selecting the optimal 3D-model of the Antibody-glycan complex, out of thousands plausible options generated by automated docking and molecular dynamics simulation. STn-specificity was further validated by computationally screening of the selected Antibody 3D-model against the human sialyl-Tn-glycome. This computational-experimental approach would allow rational design of potent antibodies targeting carbohydrates.

  • Computational Screening of the Human TF-Glycome Provides a Structural Definition for the Specificity of Anti-Tumor Antibody JAA-F11
    2016
    Co-Authors: Matthew B Tessier, Oliver C Grant, Snehal Jadey, Andrew M Gulick, John Glushka, Susan L Deutscher, Jamie Heimburg-molinaro, David Smith, Kate Rittenhouse-olson, Robert J Woods
    Abstract:

    Recombinant antibodies are of profound clinical significance; yet, anti-carbohydrate antibodies are prone to undesirable cross-reactivity with structurally related-glycans. Here we introduce a new technology called Computational Carbohydrate Grafting (CCG), which enables a virtual library of glycans to be assessed for protein binding specificity, and employ it to define the scope and structural origin of the binding specificity of Antibody JAA-F11 for glycans containing the Thomsen-Friedenreich (TF) human tumor antigen. A virtual library of the entire human glycome (GLibrary-3D) was constructed, from which 1,182 TF-containing human glycans were identified and assessed for their ability to fit into the Antibody Combining Site. The glycans were categorized into putative binders, or non-binders, on the basis of steric clashes with the Antibody surface. The analysis employed a structure of the immune complex, generated by docking the TF-disaccharide (Galb1-3GalNAca) into a crystal structure of the JAA-F11 antigen binding fragment, which was shown to be consistent with saturation transfer difference (STD) NMR data. The specificities predicted by CCG were fully consistent with data from experimental glycan array screening, and confirmed that the Antibody is selective for the TF-antigen and certain extended core-2 type mucins. Additionally, the CCG analysis identified a limited number of related putative binding motifs, an

  • computational screening of the human tf glycome provides a structural definition for the specificity of anti tumor Antibody jaa f11
    PLOS ONE, 2013
    Co-Authors: Matthew B Tessier, Oliver C Grant, Jamie Heimburgmolinaro, David F Smith, Snehal Jadey, Andrew M Gulick, John Glushka, Susan L Deutscher, Kate Rittenhouseolson, Robert J Woods
    Abstract:

    Recombinant antibodies are of profound clinical significance; yet, anti-carbohydrate antibodies are prone to undesirable cross-reactivity with structurally related-glycans. Here we introduce a new technology called Computational Carbohydrate Grafting (CCG), which enables a virtual library of glycans to be assessed for protein binding specificity, and employ it to define the scope and structural origin of the binding specificity of Antibody JAA-F11 for glycans containing the Thomsen-Friedenreich (TF) human tumor antigen. A virtual library of the entire human glycome (GLibrary-3D) was constructed, from which 1,182 TF-containing human glycans were identified and assessed for their ability to fit into the Antibody Combining Site. The glycans were categorized into putative binders, or non-binders, on the basis of steric clashes with the Antibody surface. The analysis employed a structure of the immune complex, generated by docking the TF-disaccharide (Galβ1-3GalNAcα) into a crystal structure of the JAA-F11 antigen binding fragment, which was shown to be consistent with saturation transfer difference (STD) NMR data. The specificities predicted by CCG were fully consistent with data from experimental glycan array screening, and confirmed that the Antibody is selective for the TF-antigen and certain extended core-2 type mucins. Additionally, the CCG analysis identified a limited number of related putative binding motifs, and provided a structural basis for interpreting the specificity. CCG can be utilized to facilitate clinical applications through the determination of the three-dimensional interaction of glycans with proteins, thus augmenting drug and vaccine development techniques that seek to optimize the specificity and affinity of neutralizing proteins, which target glycans associated with diseases including cancer and HIV.

Oliver C Grant - One of the best experts on this subject based on the ideXlab platform.

  • a combined computational experimental approach to define the structural origin of Antibody recognition of sialyl tn a tumor associated carbohydrate antigen
    Scientific Reports, 2018
    Co-Authors: Ron Amon, Oliver C Grant, John Glushka, Shani Leviatan Benarye, Spandana Makeneni, Anita K Nivedha, Tal Marshanski, Christoffer Norn, Sarel J Fleishman, Xi Chen
    Abstract:

    Anti-carbohydrate monoclonal antibodies (mAbs) hold great promise as cancer therapeutics and diagnostics. However, their specificity can be mixed, and detailed characterization is problematic, because Antibody-glycan complexes are challenging to crystallize. Here, we developed a generalizable approach employing high-throughput techniques for characterizing the structure and specificity of such mAbs, and applied it to the mAb TKH2 developed against the tumor-associated carbohydrate antigen sialyl-Tn (STn). The mAb specificity was defined by apparent KD values determined by quantitative glycan microarray screening. Key residues in the Antibody Combining Site were identified by Site-directed mutagenesis, and the glycan-antigen contact surface was defined using saturation transfer difference NMR (STD-NMR). These features were then employed as metrics for selecting the optimal 3D-model of the Antibody-glycan complex, out of thousands plausible options generated by automated docking and molecular dynamics simulation. STn-specificity was further validated by computationally screening of the selected Antibody 3D-model against the human sialyl-Tn-glycome. This computational-experimental approach would allow rational design of potent antibodies targeting carbohydrates.

  • Computational Screening of the Human TF-Glycome Provides a Structural Definition for the Specificity of Anti-Tumor Antibody JAA-F11
    2016
    Co-Authors: Matthew B Tessier, Oliver C Grant, Snehal Jadey, Andrew M Gulick, John Glushka, Susan L Deutscher, Jamie Heimburg-molinaro, David Smith, Kate Rittenhouse-olson, Robert J Woods
    Abstract:

    Recombinant antibodies are of profound clinical significance; yet, anti-carbohydrate antibodies are prone to undesirable cross-reactivity with structurally related-glycans. Here we introduce a new technology called Computational Carbohydrate Grafting (CCG), which enables a virtual library of glycans to be assessed for protein binding specificity, and employ it to define the scope and structural origin of the binding specificity of Antibody JAA-F11 for glycans containing the Thomsen-Friedenreich (TF) human tumor antigen. A virtual library of the entire human glycome (GLibrary-3D) was constructed, from which 1,182 TF-containing human glycans were identified and assessed for their ability to fit into the Antibody Combining Site. The glycans were categorized into putative binders, or non-binders, on the basis of steric clashes with the Antibody surface. The analysis employed a structure of the immune complex, generated by docking the TF-disaccharide (Galb1-3GalNAca) into a crystal structure of the JAA-F11 antigen binding fragment, which was shown to be consistent with saturation transfer difference (STD) NMR data. The specificities predicted by CCG were fully consistent with data from experimental glycan array screening, and confirmed that the Antibody is selective for the TF-antigen and certain extended core-2 type mucins. Additionally, the CCG analysis identified a limited number of related putative binding motifs, an

  • computational screening of the human tf glycome provides a structural definition for the specificity of anti tumor Antibody jaa f11
    PLOS ONE, 2013
    Co-Authors: Matthew B Tessier, Oliver C Grant, Jamie Heimburgmolinaro, David F Smith, Snehal Jadey, Andrew M Gulick, John Glushka, Susan L Deutscher, Kate Rittenhouseolson, Robert J Woods
    Abstract:

    Recombinant antibodies are of profound clinical significance; yet, anti-carbohydrate antibodies are prone to undesirable cross-reactivity with structurally related-glycans. Here we introduce a new technology called Computational Carbohydrate Grafting (CCG), which enables a virtual library of glycans to be assessed for protein binding specificity, and employ it to define the scope and structural origin of the binding specificity of Antibody JAA-F11 for glycans containing the Thomsen-Friedenreich (TF) human tumor antigen. A virtual library of the entire human glycome (GLibrary-3D) was constructed, from which 1,182 TF-containing human glycans were identified and assessed for their ability to fit into the Antibody Combining Site. The glycans were categorized into putative binders, or non-binders, on the basis of steric clashes with the Antibody surface. The analysis employed a structure of the immune complex, generated by docking the TF-disaccharide (Galβ1-3GalNAcα) into a crystal structure of the JAA-F11 antigen binding fragment, which was shown to be consistent with saturation transfer difference (STD) NMR data. The specificities predicted by CCG were fully consistent with data from experimental glycan array screening, and confirmed that the Antibody is selective for the TF-antigen and certain extended core-2 type mucins. Additionally, the CCG analysis identified a limited number of related putative binding motifs, and provided a structural basis for interpreting the specificity. CCG can be utilized to facilitate clinical applications through the determination of the three-dimensional interaction of glycans with proteins, thus augmenting drug and vaccine development techniques that seek to optimize the specificity and affinity of neutralizing proteins, which target glycans associated with diseases including cancer and HIV.