1MZI

Solution ensemble structures of HIV-1 gp41 2F5 mAb epitope


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 6400 
  • Conformers Submitted: 81 
  • Selection Criteria: Base set ensemble representative of the conformational space experimentally allowed 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of the epitope of the anti-HIV antibody 2F5 sheds light into its mechanism of neutralization and HIV fusion.

Barbato, G.Bianchi, E.Ingallinella, P.Hurni, W.H.Miller, M.D.Ciliberto, G.Cortese, R.Bazzo, R.Shiver, J.W.Pessi, A.

(2003) J.Mol.Biol. 330: 1101-1115


  • PubMed Abstract: 
  • Inhibition of human immunodeficiency virus (HIV) fusion with the host cell has emerged as a viable therapeutic strategy, and rational design of inhibitors and vaccines, interfering with this process, is a prime target for antiviral research. To advan ...

    Inhibition of human immunodeficiency virus (HIV) fusion with the host cell has emerged as a viable therapeutic strategy, and rational design of inhibitors and vaccines, interfering with this process, is a prime target for antiviral research. To advance our knowledge of the structural biology of HIV fusion, we have studied the membrane-proximal region of the fusogenic envelope subunit gp41, which includes the epitope ELDKWA of the broadly neutralizing human antibody 2F5. The structural evidence available for this region is contradictory, with some studies suggesting an overall helical conformation, while the X-ray structure of the ELDKWAS peptide bound to the antibody shows it folded in a type I beta turn. We used a two-step strategy: Firstly, by a competition binding assay, we identified the proper boundaries of the domain recognized by 2F5, which we found considerably larger than the ELDKWAS hexapeptide. Secondly, we studied the structure of the resulting 13 amino acid residue peptide by collecting NMR data and analyzing them by our previously developed statistical method (NAMFIS). Our study revealed that the increase in binding affinity goes in parallel with stabilization of specific local and global conformational propensities, absent from the shorter epitope. When compounded with the available biological evidence, our structural analysis allows us to propose a specific role for the membrane-proximal region during HIV fusion, in terms of a conformational transition between the turn and the helical structure. At the same time, our hypothesis offers a structural explanation for the mechanism of neutralization of mAb 2F5.


    Related Citations: 
    • Multi-conformational peptide dynamics derived from NMR data: a new search algorithm and its application to antamanide
      Bruschweiler, R.,Blackledge, M.,Ernst, R.R.
      (1991) J.Biomol.NMR 1: 3
    • NMR analysis of molecular flexibility in solution: a new method for the study of complex distributions of rapidly exchanging conformations. Application to a 13-residue peptide with an 8-residue loop
      Cicero, D.O.,Barbato, G.,Bazzo, R.
      (1995) J.Am.Chem.Soc. 117: 1027
    • An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
      Kelley, L.A.,Gardner, S.P.,Sutcliffe, M.J.
      (1996) Protein Eng. 9: 1063


    Organizational Affiliation

    Istituto di Ricerche di Biologia Molecolare P. Angeletti (IRBM), Via Pontina Km 30.600, 00040 Pomezia, Rome, Italy. gaetano_barbato@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2F5 epitope of HIV-1 gp41 fusion protein
A
13Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: env
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04578
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 6400 
  • Conformers Submitted: 81 
  • Selection Criteria: Base set ensemble representative of the conformational space experimentally allowed 
  • Olderado: 1MZI Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-02
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance