Characterization of the steric defense of the HIV-1 gp41 N-trimer region

Debra M Eckert, Yu Shi, Sunghwan Kim, Brett D Welch, Eunchai Kang, Emily S Poff, Michael S Kay

Research output: Contribution to journalArticlepeer-review

28 Citations (Scopus)


During viral entry, HIV gp41 adopts a transient conformation called the "prehairpin intermediate" in which a highly conserved therapeutic target, the N-trimer, is exposed. Despite extensive discovery efforts, potent and broadly neutralizing antibodies that target the N-trimer are elusive. We previously demonstrated the N-trimer is protected by a steric block that prevents large proteins, such as antibodies, from accessing it. Here we further characterize the steric block and identify its source. To study the N-trimer steric accessibility, we produced two sets of C-peptide inhibitors (a potent inhibitor targeting the N-trimer) fused to cargo proteins of increasing size facing either the virus or cell side of the prehairpin intermediate. Both bulky inhibitor sets show a steric block, but the effect is more pronounced with virus-side cargo. Additionally, both sets maintain their potencies in a modified entry assay that removes possible sources of target cell steric hindrance. These results implicate a viral source, likely gp120, as the primary component of the steric block. In addition, we studied the steric accessibility of the "pocket" region of the N-trimer, a highly attractive drug and vaccine target. We demonstrated a pocket-specific antibody, D5, is more potent as an scFv than as a full-length IgG, suggesting the N-trimer steric restriction extends to the pocket. This characterization will facilitate the design of sterically restricted antigens that mimic the steric environment of the N-trimer in the prehairpin intermediate and are capable of inducing potent and broadly neutralizing antibodies that circumvent the N-trimer steric block.

Original languageEnglish
Pages (from-to)2091-100
Number of pages10
JournalProtein science : a publication of the Protein Society
Issue number12
Publication statusPublished - Dec 2008


  • HIV Envelope Protein gp41/chemistry
  • Humans
  • Kinetics
  • Membrane Fusion
  • Peptide Fragments/antagonists & inhibitors
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Domains and Motifs
  • Protein Stability
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Recombinant Fusion Proteins/chemistry
  • Surface Plasmon Resonance


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