ArticleProceedings of the National Academy of Sciences of the United States of America2003
Structural basis of peptide-carbohydrate mimicry in an antibody-combining site.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- Increasing the Affinity of an O-Antigen Polysaccharide Binding Site in Shigella flexneri Bacteriophage Sf6 Tailspike Protein.Chemistry (Weinheim an der Bergstrasse, Germany) · 2020Article
- Structural Basis of GD2 Ganglioside and Mimetic Peptide Recognition by 14G2a Antibody.Molecular & cellular proteomics : MCP · 2015Article
- Genetically encoded fragment-based discovery of glycopeptide ligands for carbohydrate-binding proteins.Journal of the American Chemical Society · 2015Article
- Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff.Journal of computational chemistry · 2014Article
- Yeast killer toxin-like candidacidal Ab6 antibodies elicited through the manipulation of the idiotypic cascade.PloS one · 2014Article
- Structural analysis of a protective epitope of the Francisella tularensis O-polysaccharide.Biochemistry · 2012Article
- Exploring peptide mimics for the production of antibodies against discontinuous protein epitopes.Molecular immunology · 2010Article
- Development, characterization, and immunotherapeutic use of peptide mimics of the Thomsen-Friedenreich carbohydrate antigen.Neoplasia (New York, N.Y.) · 2009Article
- Isothermal titration calorimetry reveals differential binding thermodynamics of variable region-identical antibodies differing in constant region for a univalent ligand.The Journal of biological chemistry · 2008Article
- Immunological evidence for functional rather than structural mimicry by a Shigella flexneri Y polysaccharide-mimetic peptide.Clinical and vaccine immunology : CVI · 2008Article
- A peptide inhibitor of HIV-1 neutralizing antibody 2G12 is not a structural mimic of the natural carbohydrate epitope on gp120.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2008Article
- The epitope space of the human proteome.Protein science : a publication of the Protein Society · 2008Article
- The membrane-proximal external region of the human immunodeficiency virus type 1 envelope: dominant site of antibody neutralization and target for vaccine design.Microbiology and molecular biology reviews : MMBR · 2008Review
- Structure-based dissection of the natural product cyclopentapeptide chitinase inhibitor argifin.Chemistry & biology · 2008Article
- Structure of antibody-neutralized murine norovirus and unexpected differences from viruslike particles.Journal of virology · 2008Article
- Hydrophobic interactions are the driving force for the binding of peptide mimotopes and Staphylococcal protein A to recombinant human IgG1.European biophysics journal : EBJ · 2007Article
- Structure of a high-affinity "mimotope" peptide bound to HIV-1-neutralizing antibody b12 explains its inability to elicit gp120 cross-reactive antibodies.Journal of molecular biology · 2007Article
- Specific and randomly derived immunoactive peptide mimotopes of mycobacterial antigens.Clinical and vaccine immunology : CVI · 2006Article
- Insight into a conserved lifestyle: protein-carbohydrate adhesion strategies of vector-borne pathogens.Infection and immunity · 2005Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The structure of a complex between the Fab fragment of the antibody (SYA/J6) specific for the cell surface O-antigen polysaccharide of the pathogen Shigella flexneri Y and an octapeptide (Met-Asp-Trp-Asn-Met-His-Ala-Ala), a functional mimic of the O-antigen, has been determined at 1.8-A resolution. Comparison of the structure with that of the complex with the pentasaccharide antigen [-->2)-alpha-L-Rha-(1-->2)-alpha-L-Rha-(1-->3)-alpha-L-Rha-(1-->3)-beta-D-GlcNAc-(1-->2)-alpha-L-Rha-(1-->] reveals the molecular recognition process by which a peptide mimics a carbohydrate in binding to an antibody. The binding modes of the two ligands differ considerably. Octapeptide binding complements the shape of the combining site groove much better than pentasaccharide binding. Moreover, the peptide makes a much greater number of contacts (126), which are mostly van der Waals interactions, with the Fab than the saccharide (74). An unusual feature is also the involvement of 12 water molecules in mediating hydrogen bonds between residues within the peptide or of the peptide and Fab. Despite better shape complementarity and greater number of contacts, the octapeptide binds with an affinity (KA = 2.5 x 10(5) M-1, measured by calorimetry) only approximately 2-fold tighter than the pentasaccharide. The structural results are relevant to the design of peptide mimetics with improved affinity for use as vaccines.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.