Structural basis of peptide–carbohydrate mimicry in an antibody-combining site

Vyas, Nand K.; Vyas, M.N.; Chervenak, Mary C.; Bundle, David R.; Pinto, B. Mario; Quiocho, Florante A.

doi:10.1073/pnas.2431286100

Cited by 70 publications

(60 citation statements)

References 35 publications

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“…The . A constituent pentasaccharide of the O-antigen binds with comparable affinity to the same binding site of the antibody (18). The functional oligosaccharide analog of P1 is unknown; therefore, we are unable to compare the affinity of the oligosaccharide epitope to that of its mimetic peptide P1.…”

Section: Resultsmentioning

confidence: 99%

“…The favorable entropic contribution in P1 binding is somewhat unique compared with some other antibody-peptide interactions. For example, in another system, binding of peptides to mAbs CB4-1 and SYA/J6 is mostly enthalpy-driven and is significantly compensated by unfavorable entropic effects (17,18). However, it is interesting to note that binding of a pentasaccharide and other oligosaccharides corresponding to O-polysaccharide to SYA/J6 is associated with favorable entropy (T⌬S ϭ 2.3-5.9), and hydrophobic interactions make significant contributions to binding (20).…”

Section: Relative Contributions Of Enthalpy and Entropy To The Bindinmentioning

confidence: 99%

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Isothermal Titration Calorimetry Reveals Differential Binding Thermodynamics of Variable Region-identical Antibodies Differing in Constant Region for a Univalent Ligand

Dam

Torres

Brewer

et al. 2008

Journal of Biological Chemistry

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The classical view of immunoglobulin molecules posits two functional domains defined by the variable (V) and constant (C) regions, which are responsible for antigen binding and antibody effector functions, respectively. These two domains are thought to function independently. However, several lines of evidence strongly suggest that C region domains can affect the specificity and affinity of an antibody for its antigen (Ag), independent of avidity-type effects. In this study, we used isothermal titration calorimetry to investigate the thermodynamic properties of the interactions of four V region-identical monoclonal antibodies with a univalent peptide antigen. Comparison of the binding of IgG1, IgG2a, IgG2b, and IgG3 with a 12-mer peptide mimetic of Cryptococcus neoformans polysaccharide revealed a stoichiometry of 1.9 -2.0 with significant differences in thermodynamic binding parameters. Binding of this peptide to the antibodies was dominated by favorable entropy. The interaction of these antibodies with biotinylated peptides manifested greater enthalpy than for native peptides indicating that biotin labeling affected the types of Ag-Ab complexes formed. Our results provide unambiguous thermodynamic evidence for the notion that the C region can affect the interaction of the V region with an Ag.

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Section: Resultsmentioning

confidence: 99%

Section: Relative Contributions Of Enthalpy and Entropy To The Bindinmentioning

confidence: 99%

Isothermal Titration Calorimetry Reveals Differential Binding Thermodynamics of Variable Region-identical Antibodies Differing in Constant Region for a Univalent Ligand

Dam

Torres

Brewer

et al. 2008

Journal of Biological Chemistry

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“…However, structures of both peptide and carbohydrate with the cognate antibody are not available. Comparison of crystal structures of an anticarbohydrate antibody against the O-antigen polysaccharide of S. flexneri Y (SYA/J6) with an octapeptide ligand and a synthetic pentasaccharide antigen revealed that peptide and pentasaccharide both bind to an overlapping site on SYA/J6, but the antibody-peptide contacts and the thermodynamics of binding are very different from those of the pentasaccharide (28). Similar to our results, peptide ligands for concanavalin A (ConA) bind at sites different from those used by carbohydrate ligands (27).…”

Section: Discussionmentioning

confidence: 99%

“…However, very little is actually known about the molecular mechanisms of carbohydratepeptide cross-reactivity. Only two comparative structural analyses of carbohydrate and peptide ligands in complex with carbohydrate-binding proteins are available: the lectin concanavalin A specific for Man(α1-6) Man(α1-3) Man trimannose cores in mannose-containing carbohydrates, and the MAb SYA/J6, directed against the O-antigen polysaccharide of Shigella flexneri Y (27,28). These two studies have suggested that structural mimicry is not a major mechanism by which carbohydrate-binding proteins interact with peptides.…”

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confidence: 99%

A peptide inhibitor of HIV‐1 neutralizing antibody 2G12 is not a structural mimic of the natural carbohydrate epitope on gp120

Menéndez

Calarese

Stanfield³

et al. 2008

FASEB j.

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MAb 2G12 neutralizes HIV-1 by binding with high affinity to a cluster of high-mannose oligosaccharides on the envelope glycoprotein, gp120. Screening of phage-displayed peptide libraries with 2G12 identified peptides that bind specifically, with K d s ranging from 0.4 to 200 μM. The crystal structure of a 21-mer peptide ligand in complex with 2G12 Fab was determined at 2.8 Å resolution. Comparison of this structure with previous structures of 2G12-carbohydrate complexes revealed striking differences in the mechanism of 2G12 binding to peptide vs. carbohydrate. The peptide occupies a site different from, but adjacent to, the primary carbohydrate-binding site on 2G12, and makes only slightly fewer contacts to the Fab than Man 9 GlcNAc 2 (51 vs. 56, respectively). However, only two antibody contacts with the peptide are hydrogen bonds in contrast to six with Man 9 GlcNAc 2 , and only three of the antibody residues that interact with Man 9 GlcNAc 2 also contact the peptide. Thus, this mechanism of peptide binding to 2G12 does not support structural mimicry of the native carbohydrate epitope on gp120, since it neither replicates the oligosaccharide footprint on the antibody nor most of the contact residues. Moreover, 2G12.1 peptide is not an immunogenic mimic of the 2G12 epitope, since antisera produced against it did not bind gp120.-Menendez, A., Calarese, D. A., Stanfield, R. L., Chow, K. C., Scanlan, C. N., Kunert, R., Katinger, H., Burton, D. R., Wilson, I. A., Scott, J. K. A peptide inhibitor of HIV-1 neutralizing antibody 2G12 is not a structural mimic of the natural carbohydrate epitope on gp120. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptHuman monoclonal antibody (MAb) 2G12 efficiently neutralizes a broad range of HIV-1 primary isolates in vitro (1-3) and protects from in vivo viral challenge in macaques in combination with other antibodies (4-6). MAb 2G12 binds with high affinity to a unique, conserved epitope on the HIV-1 envelope that is formed by a cluster of N-linked, high-mannose glycan groups on the "silent" face of gp120 (7-10). Crystal structures of 2G12 Fab alone, and in complex with oligosaccharides Man 9 GlcNAc 2 and Manα1-2Man, revealed that two Fab monomers assemble into an interlocked, domain-swapped dimer, that forms an extensive, multivalent binding surface (11). Four Man 9 GlcNAc 2 moieties were observed bound to the Fab dimer in the crystal structure, occupying the two canonical antigen-binding sites, and two novel ones located at the assembled interface of the two interlocked V H domains. Since the identification of its epitope, MAb 2G12 has received significant attention as a template for HIV-1 vaccine development. Considerable effort has been directed at characterizing its oligosaccharide-binding profile (12)(13)(14)(15), and the generation of novel antigens in the form of synthetic oligomannoses (13,16,17) or short, synthetic glycopeptides (18-20). In an attempt to generate immunogens that elicit 2G12-like antibodies, we chose to isolate peptides t...

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“…Finally, several strategies may be easily applied to improve the properties of these peptides and to engineer further refined, second-generation mimics that would more closely resemble the natural Ag. Recent studies convincingly demonstrate the feasibility of reaching this goal by design, i.e., based on detailed structural analysis of the interactions of the nominal Ag and its mimics with the Ab-combining site (33).…”

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confidence: 98%

Peptide Mimics of the Group B Meningococcal Capsule Induce Bactericidal and Protective Antibodies after Immunization

Passo¹,

Romeo²,

Pernice³

et al. 2007

The Journal of Immunology

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Neisseria meningitidis serogroup B (MenB) is a leading cause of sepsis and meningitis in children. No vaccine is available for the prevention of these infections because the group B capsular polysaccharide (CP) (MenB CP) is unable to stimulate an immune response, due to its similarity with human polysialic acid. Because the MenB CP bears both human cross-reactive and non-cross-reactive determinants, we developed immunogenic peptide mimics of the latter epitopes. Peptides were selected from phage display libraries for their ability to bind to a protective anti-MenB CP mAb. One of these peptides (designated 9M) induced marked elevations in serum bactericidal activity, but not polysialic acid cross-reacting Abs, after gene priming followed by carrier-conjugate boosting. Moreover, the occurrence of bacteremia was prevented in infant rats by administration of immune sera before MenB challenge. 9M is a promising lead candidate for the development of an effective and affordable anti-MenB vaccine.

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Structural basis of peptide–carbohydrate mimicry in an antibody-combining site

Cited by 70 publications

References 35 publications

Isothermal Titration Calorimetry Reveals Differential Binding Thermodynamics of Variable Region-identical Antibodies Differing in Constant Region for a Univalent Ligand

Isothermal Titration Calorimetry Reveals Differential Binding Thermodynamics of Variable Region-identical Antibodies Differing in Constant Region for a Univalent Ligand

A peptide inhibitor of HIV‐1 neutralizing antibody 2G12 is not a structural mimic of the natural carbohydrate epitope on gp120

Peptide Mimics of the Group B Meningococcal Capsule Induce Bactericidal and Protective Antibodies after Immunization

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