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Structure paper

TitleAntibody-directed evolution reveals a mechanism for enhanced neutralization at the HIV-1 fusion peptide site.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 7593, Year 2023
Publish dateNov 21, 2023
AuthorsBailey B Banach / Sergei Pletnev / Adam S Olia / Kai Xu / Baoshan Zhang / Reda Rawi / Tatsiana Bylund / Nicole A Doria-Rose / Thuy Duong Nguyen / Ahmed S Fahad / Myungjin Lee / Bob C Lin / Tracy Liu / Mark K Louder / Bharat Madan / Krisha McKee / Sijy O'Dell / Mallika Sastry / Arne Schön / Natalie Bui / Chen-Hsiang Shen / Jacy R Wolfe / Gwo-Yu Chuang / John R Mascola / Peter D Kwong / Brandon J DeKosky /
PubMed AbstractThe HIV-1 fusion peptide (FP) represents a promising vaccine target, but global FP sequence diversity among circulating strains has limited anti-FP antibodies to ~60% neutralization breadth. Here we ...The HIV-1 fusion peptide (FP) represents a promising vaccine target, but global FP sequence diversity among circulating strains has limited anti-FP antibodies to ~60% neutralization breadth. Here we evolve the FP-targeting antibody VRC34.01 in vitro to enhance FP-neutralization using site saturation mutagenesis and yeast display. Successive rounds of directed evolution by iterative selection of antibodies for binding to resistant HIV-1 strains establish a variant, VRC34.01_mm28, as a best-in-class antibody with 10-fold enhanced potency compared to the template antibody and ~80% breadth on a cross-clade 208-strain neutralization panel. Structural analyses demonstrate that the improved paratope expands the FP binding groove to accommodate diverse FP sequences of different lengths while also recognizing the HIV-1 Env backbone. These data reveal critical antibody features for enhanced neutralization breadth and potency against the FP site of vulnerability and accelerate clinical development of broad HIV-1 FP-targeting vaccines and therapeutics.
External linksNat Commun / PubMed:37989731 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.49 - 2.7 Å
Structure data

28617

8euu

EMDB-28617, PDB-8euu:
Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01 FAB
Method: EM (single particle) / Resolution: 2.7 Å

28618

8euv

EMDB-28618, PDB-8euv:
Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-COMBO1 FAB
Method: EM (single particle) / Resolution: 2.6 Å

28619

8euw

EMDB-28619, PDB-8euw:
Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-MM28 FAB
Method: EM (single particle) / Resolution: 2.7 Å

PDB-8eli:
Broadly neutralizing antibody VRC34-combo.1 in complex with HIV fusion peptide (residue 512-519)
Method: X-RAY DIFFRACTION / Resolution: 1.49 Å

PDB-8f7z:
VRC34.01_mm28 bound to fusion peptide
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

Chemicals

ChemComp-HOH:
WATER / Water

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

Source
  • human immunodeficiency virus 1
  • homo sapiens (human)
  • hiv-1 06tg.ht008 (virus)
KeywordsIMMUNE SYSTEM / HIV / VRC34 / Fusion peptide / broadly neutralizing / VIRAL PROTEIN/ IMMUNE SYSTEM / broadly neutralizing antibody / HIV-1 / glycoprotein / viral protein / FP-targeting vaccines / VIRAL PROTEIN- IMMUNE SYSTEM complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex / FP-NEUTRALIZING ANTIBODY

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