1GZL

Crystal structure of C14linkmid/IQN17: a cross-linked inhibitor of HIV-1 entry bound to the gp41 hydrophobic pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Short Constrained Peptides that Inhibit HIV-1 Entry

Sia, S.K.Carr, P.A.Cochran, A.G.Malashkevich, V.M.Kim, P.S.

(2002) Proc.Natl.Acad.Sci.USA 99: 14664

  • DOI: 10.1073/pnas.232566599

  • PubMed Abstract: 
  • Peptides corresponding to the C-terminal heptad repeat of HIV-1 gp41 (C-peptides) are potent inhibitors of HIV-1 entry into cells. Their mechanism of inhibition involves binding in a helical conformation to the central coiled coil of HIV-1 gp41 in a ...

    Peptides corresponding to the C-terminal heptad repeat of HIV-1 gp41 (C-peptides) are potent inhibitors of HIV-1 entry into cells. Their mechanism of inhibition involves binding in a helical conformation to the central coiled coil of HIV-1 gp41 in a dominant-negative manner. Short C-peptides, however, have low binding affinity for gp41 and poor inhibitory activity, which creates an obstacle to the development of small drug-like C-peptides. To improve the inhibitory potency of short C-peptides that target the hydrophobic pocket region of gp41, we use two strategies to stabilize the C-peptide helix: chemical crosslinking and substitution with unnatural helix-favoring amino acids. In this study, the short linear peptide shows no significant inhibitory activity, but a constrained peptide (C14linkmid) inhibits cell-cell fusion at micromolar potency. Structural studies confirm that the constrained peptides bind to the gp41 hydrophobic pocket. Calorimetry reveals that, of the peptides analyzed, the most potent are those that best balance the changes in binding enthalpy and entropy, and surprisingly not those with the highest helical propensity as measured by circular dichroism spectroscopy. Our study reveals the thermodynamic basis of inhibition of an HIV C-peptide, demonstrates the utility of constraining methods for a short antiviral peptide inhibitor, and has implications for the future design of constrained peptides.


    Organizational Affiliation

    Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, USA. sia@fas.harvard.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GENERAL CONTROL PROTEIN GCN4-PIQI
A, B
46Human immunodeficiency virus type 1 group M subtype BSaccharomyces cerevisiae (strain ATCC 204508 / S288c)
This entity is chimeric
Mutation(s): 0 
Gene Names: env, GCN4 (AAS3, ARG9)
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04578
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P03069
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ENVELOPE GLYCOPROTEIN GP41
C, D
12Human immunodeficiency virus type 1 group M subtype BMutation(s): 2 
Gene Names: env
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04578
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
N2P
Query on N2P

Download SDF File 
Download CCD File 
C, D
PENTANE-1,5-DIAMINE
C5 H14 N2
VHRGRCVQAFMJIZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.208 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 38.358α = 90.00
b = 38.358β = 90.00
c = 169.695γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-10
    Type: Initial release
  • Version 1.1: 2015-12-02
    Type: Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Version format compliance