Asymmetric recognition of HIV-1 Envelope trimer by V1V2 loop-targeting antibodies

  1. Haoqing Wang
  2. Harry B Gristick
  3. Louise Scharf
  4. Anthony P West
  5. Rachel P Galimidi
  6. Michael S Seaman
  7. Natalia T Freund
  8. Michel C Nussenzweig
  9. Pamela J Bjorkman  Is a corresponding author
  1. California Institute of Technology, United States
  2. 23andMe, United States
  3. Beth Israel Deaconess Medical Center, United States
  4. Tel Aviv University, Israel
  5. The Rockefeller University, United States

Abstract

The HIV-1 envelope (Env) glycoprotein binds to host cell receptors to mediate membrane fusion. The prefusion Env trimer is stabilized by V1V2 loops that interact at the trimer apex. Broadly neutralizing antibodies (bNAbs) against V1V2 loops, exemplified by PG9, bind asymmetrically as a single Fab to the apex of the symmetric Env trimer using a protruding CDRH3 to penetrate the Env glycan shield. Here we characterized a distinct mode of V1V2 epitope recognition by the new bNAb BG1 in which two Fabs bind asymmetrically per Env trimer using a compact CDRH3. Comparisons between cryo-EM structures of Env trimer complexed with BG1 (6.2Å resolution) and PG9 (11.5Å resolution) revealed a new V1V2-targeting strategy by BG1. Analyses of the EM structures provided information relevant to vaccine design including molecular details for different modes of asymmetric recognition of Env trimer and a binding model for BG1 recognition of V1V2 involving glycan flexibility.

Data availability

The following data sets were generated
    1. Haoqing Wang
    2. Harry Gristick
    3. Pamela Bjorkman
    (2017) BG1-Env-8ANC195 complex
    Publicly available at the EMBL_EBI Protein Dtat Bank in Europe (accession no: EMD-8693).
    1. Haoqing Wang
    2. Harry Gristick
    3. Pamela Bjorkm
    (2017) PG9-Env-8ANC195 complex
    Publicly available at the EMBL_EBI Protein Dtat Bank in Europe (accession no: EMDB-8695).
    1. Louise Scharf
    2. Harry Gristick
    3. Pamela Bjorkman
    (2017) BG1 Fab coordinate
    Publicly available at the RCSB Protein Data Bank (accession no: 5VVF).

Article and author information

Author details

  1. Haoqing Wang

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    No competing interests declared.
  2. Harry B Gristick

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    No competing interests declared.
  3. Louise Scharf

    Therapeutics, 23andMe, Mountain View, United States
    Competing interests
    No competing interests declared.
  4. Anthony P West

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    No competing interests declared.
  5. Rachel P Galimidi

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    No competing interests declared.
  6. Michael S Seaman

    Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, United States
    Competing interests
    No competing interests declared.
  7. Natalia T Freund

    Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
    Competing interests
    No competing interests declared.
  8. Michel C Nussenzweig

    Laboratory of Molecular Immunology, The Rockefeller University, New York, United States
    Competing interests
    Michel C Nussenzweig, Senior editor, eLife.
  9. Pamela J Bjorkman

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    For correspondence
    bjorkman@caltech.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2277-3990

Funding

National Institutes of Health (GM082545-06)

  • Pamela J Bjorkman

National Institute of Allergy and Infectious Diseases (HIVRAD P01 AI100148)

  • Michel C Nussenzweig
  • Pamela J Bjorkman

Bill and Melinda Gates Foundation (1040753)

  • Michel C Nussenzweig
  • Pamela J Bjorkman

Comprehensive Antibody-Vaccine Immune Monitoring Consortium (1032144)

  • Michael S Seaman

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Arup K. Chakraborty, Massachusetts Institute of Technology, United States

Publication history

  1. Received: April 1, 2017
  2. Accepted: May 24, 2017
  3. Accepted Manuscript published: May 26, 2017 (version 1)
  4. Version of Record published: June 15, 2017 (version 2)

Copyright

© 2017, Wang et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,856
    Page views
  • 423
    Downloads
  • 31
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Haoqing Wang
  2. Harry B Gristick
  3. Louise Scharf
  4. Anthony P West
  5. Rachel P Galimidi
  6. Michael S Seaman
  7. Natalia T Freund
  8. Michel C Nussenzweig
  9. Pamela J Bjorkman
(2017)
Asymmetric recognition of HIV-1 Envelope trimer by V1V2 loop-targeting antibodies
eLife 6:e27389.
https://doi.org/10.7554/eLife.27389

Further reading

    1. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics
    Claudia C Carcamo et al.
    Research Article Updated

    One-dimensional (1D) target search is a well-characterized phenomenon for many DNA-binding proteins but is poorly understood for chromatin remodelers. Herein, we characterize the 1D scanning properties of SWR1, a conserved yeast chromatin remodeler that performs histone exchange on +1 nucleosomes adjacent to a nucleosome-depleted region (NDR) at gene promoters. We demonstrate that SWR1 has a kinetic binding preference for DNA of NDR length as opposed to gene-body linker length DNA. Using single and dual color single-particle tracking on DNA stretched with optical tweezers, we directly observe SWR1 diffusion on DNA. We found that various factors impact SWR1 scanning, including ATP which promotes diffusion through nucleotide binding rather than ATP hydrolysis. A DNA-binding subunit, Swc2, plays an important role in the overall diffusive behavior of the complex, as the subunit in isolation retains similar, although faster, scanning properties as the whole remodeler. ATP-bound SWR1 slides until it encounters a protein roadblock, of which we tested dCas9 and nucleosomes. The median diffusion coefficient, 0.024 μm2/s, in the regime of helical sliding, would mediate rapid encounter of NDR-flanking nucleosomes at length scales found in cellular chromatin.

    1. Structural Biology and Molecular Biophysics
    Marina Schrecker et al.
    Research Article

    The DNA sliding clamp proliferating cell nuclear antigen (PCNA) is an essential co-factor for many eukaryotic DNA metabolic enzymes. PCNA is loaded around DNA by the ATP-dependent clamp loader replication factor C (RFC), which acts at single-stranded (ss)/double-stranded DNA (dsDNA) junctions harboring a recessed 3’ end (3’ ss/dsDNA junctions) and at DNA nicks. To illuminate the loading mechanism we have investigated the structure of RFC:PCNA bound to ATPγS and 3’ ss/dsDNA junctions or nicked DNA using cryogenic electron microscopy. Unexpectedly, we observe open and closed PCNA conformations in the RFC:PCNA:DNA complex, revealing that PCNA can adopt an open, planar conformation that allows direct insertion of dsDNA, and raising the question of whether PCNA ring closure is mechanistically coupled to ATP hydrolysis. By resolving multiple DNA-bound states of RFC:PCNA we observe that partial melting facilitates lateral insertion into the central channel formed by RFC:PCNA. We also resolve the Rfc1 N-terminal domain and demonstrate that its single BRCT domain participates in coordinating DNA prior to insertion into the central RFC channel, which promotes PCNA loading on the lagging strand of replication forks in vitro. Combined, our data suggest a comprehensive and fundamentally revised model for the RFC-catalyzed loading of PCNA onto DNA.