2M8O

NMR assignment and structure of a peptide derived from the membrane proximal external region of HIV-1 gp41 in DPC


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and Immunogenicity of a Peptide Vaccine, Including the Complete HIV-1 gp41 2F5 Epitope: IMPLICATIONS FOR ANTIBODY RECOGNITION MECHANISM AND IMMUNOGEN DESIGN.

Serrano, S.Araujo, A.Apellaniz, B.Bryson, S.Carravilla, P.de la Arada, I.Huarte, N.Rujas, E.Pai, E.F.Arrondo, J.L.Domene, C.Jimenez, M.A.Nieva, J.L.

(2014) J Biol Chem 289: 6565-6580

  • DOI: https://doi.org/10.1074/jbc.M113.527747
  • Primary Citation of Related Structures:  
    2M8M, 2M8O

  • PubMed Abstract: 

    The membrane-proximal external region (MPER) of gp41 harbors the epitope recognized by the broadly neutralizing anti-HIV 2F5 antibody, a research focus in HIV-1 vaccine development. In this work, we analyze the structure and immunogenic properties of MPERp, a peptide vaccine that includes the following: (i) the complete sequence protected from proteolysis by the 2F5 paratope; (ii) downstream residues postulated to establish weak contacts with the CDR-H3 loop of the antibody, which are believed to be crucial for neutralization; and (iii) an aromatic rich anchor to the membrane interface. MPERp structures solved in dodecylphosphocholine micelles and 25% 1,1,1,3,3,3-hexafluoro-2-propanol (v/v) confirmed folding of the complete 2F5 epitope within continuous kinked helices. Infrared spectroscopy (IR) measurements demonstrated the retention of main helical conformations in immunogenic formulations based on alum, Freund's adjuvant, or two different types of liposomes. Binding to membrane-inserted MPERp, IR, molecular dynamics simulations, and characterization of the immune responses further suggested that packed helical bundles partially inserted into the lipid bilayer, rather than monomeric helices adsorbed to the membrane interface, could encompass effective MPER peptide vaccines. Together, our data constitute a proof-of-concept to support MPER-based peptides in combination with liposomes as stand-alone immunogens and suggest new approaches for structure-aided MPER vaccine development.


  • Organizational Affiliation

    Institute of Physical Chemistry "Rocasolano," Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Serrano 119, E-28006 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein gp4128Human immunodeficiency virus type 1 (SC ISOLATE)Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05878 (Human immunodeficiency virus type 1 group M subtype B (isolate SC))
Explore P05878 
Go to UniProtKB:  P05878
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05878
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-02-26
    Changes: Database references
  • Version 1.2: 2014-05-14
    Changes: Database references
  • Version 1.3: 2023-06-14
    Changes: Data collection, Database references, Other