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Structure paper

TitleTrapping the HIV-1 V3 loop in a helical conformation enables broad neutralization.
Journal, issue, pagesNat Struct Mol Biol, Vol. 30, Issue 9, Page 1323-1336, Year 2023
Publish dateAug 21, 2023
AuthorsMatthias Glögl / Nikolas Friedrich / Gabriele Cerutti / Thomas Lemmin / Young D Kwon / Jason Gorman / Liridona Maliqi / Peer R E Mittl / Maria C Hesselman / Daniel Schmidt / Jacqueline Weber / Caio Foulkes / Adam S Dingens / Tatsiana Bylund / Adam S Olia / Raffaello Verardi / Thomas Reinberg / Nicolas S Baumann / Peter Rusert / Birgit Dreier / Lawrence Shapiro / Peter D Kwong / Andreas Plückthun / Alexandra Trkola /
PubMed AbstractThe third variable (V3) loop on the human immunodeficiency virus 1 (HIV-1) envelope glycoprotein trimer is indispensable for virus cell entry. Conformational masking of V3 within the trimer allows ...The third variable (V3) loop on the human immunodeficiency virus 1 (HIV-1) envelope glycoprotein trimer is indispensable for virus cell entry. Conformational masking of V3 within the trimer allows efficient neutralization via V3 only by rare, broadly neutralizing glycan-dependent antibodies targeting the closed prefusion trimer but not by abundant antibodies that access the V3 crown on open trimers after CD4 attachment. Here, we report on a distinct category of V3-specific inhibitors based on designed ankyrin repeat protein (DARPin) technology that reinstitute the CD4-bound state as a key neutralization target with up to >90% breadth. Broadly neutralizing DARPins (bnDs) bound V3 solely on open envelope and recognized a four-turn amphipathic α-helix in the carboxy-terminal half of V3 (amino acids 314-324), which we termed 'αV3C'. The bnD contact surface on αV3C was as conserved as the CD4 binding site. Molecular dynamics and escape mutation analyses underscored the functional relevance of αV3C, highlighting the potential of αV3C-based inhibitors and, more generally, of postattachment inhibition of HIV-1.
External linksNat Struct Mol Biol / PubMed:37605043 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.17 - 3.87 Å
Structure data

26157

7txd

EMDB-26157, PDB-7txd:
Cryo-EM structure of BG505 SOSIP HIV-1 Env trimer in complex with CD4 receptor (D1D2) and broadly neutralizing darpin bnD.9
Method: EM (single particle) / Resolution: 3.87 Å

PDB-7z7c:
Broadly neutralizing DARPin bnD.8 in complex with the HIV-1 envelope variable loop 3 peptide V3 (BF520)
Method: X-RAY DIFFRACTION / Resolution: 1.22 Å

PDB-8aed:
Broadly neutralizing DARPin bnD.9 in complex with the HIV-1 envelope variable loop 3 peptide V3 (BG505)
Method: X-RAY DIFFRACTION / Resolution: 1.17 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-GLY:
GLYCINE / Glycine

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-HOH:
WATER / Water

ChemComp-ACT:
ACETATE ION / Acetate

ChemComp-MG:
Unknown entry

ChemComp-CIT:
CITRIC ACID / Citric acid

Source
  • human immunodeficiency virus 1
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsVIRAL PROTEIN / HIV / Env / Broadly Neutralizing / Darpin / CD4 / DE NOVO PROTEIN

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