Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core

  1. Andrew J Borst
  2. Connor E Weidle
  3. Matthew D Gray
  4. Brandon Frenz
  5. Joost Snijder
  6. M Gordon Joyce
  7. Ivelin S Georgiev
  8. Guillaume BE Stewart-Jones
  9. Peter D Kwong
  10. Andrew T McGuire
  11. Frank DiMaio
  12. Leonidas Stamatatos  Is a corresponding author
  13. Marie Pancera  Is a corresponding author
  14. David Veesler  Is a corresponding author
  1. University of Washington, United States
  2. Fred Hutchinson Cancer Research Center, United States
  3. National Institute of Allergy and Infectious Diseases, National Institutes of Health, United States

Abstract

VRC01 broadly neutralizing antibodies (bnAbs) target the CD4-binding site (CD4BS) of the human immunodeficiency virus-1 (HIV-1) envelope glycoprotein (Env). Unlike mature antibodies, corresponding VRC01 germline precursors poorly bind to Env. Immunogen design has mostly relied on glycan removal from trimeric Env constructs and has had limited success in eliciting mature VRC01 bnAbs. To better understand elicitation of such bnAbs, we characterized the inferred germline precursor of VRC01 in complex with a modified trimeric 426c Env by cryo-electron microscopy and a 426c gp120 core by X-ray crystallography, biolayer interferometry, immunoprecipitation, and glycoproteomics. Our results show VRC01 germline antibodies interacted with a wild-type 426c core lacking variable loops 1-3 in the presence or absence of a glycan at position Asn276, with the latter form binding with higher affinity than the former. Interactions in the presence of an Asn276 oligosaccharide could be enhanced upon carbohydrate shortening, which should be considered for immunogen design.

Data availability

Mass spectrometry data have been deposited to the PRIDE archive under accession number PXD011494. CryoEM maps are available for download from the EMDB under accession numbers EMD-9294 (426cDS-SOSIP D3†-VRC01GL, 3 Fabs, sharpened), EMD-9295 (426cDS-SOSIP D3†-VRC01GL, 3 Fabs, unsharpened), EMD-9304 (426cDS-SOSIP D3†-VRC01GL, 2 fabs, unsharpened), and EMD-9303 (426cDS-SOSIP D3†-VRC01GL, 2 fabs, sharpened). Structures have been deposited to the PDB under accession numbers PDB-6MYY (426cDS-SOSIP D3†-VRC01GL, 3 Fabs]), PDB-6MZJ (426cDS-SOSIP D3†-VRC01GL, 2 fabs), and PDB-6MFT (426c core†-VRC01GL).

The following data sets were generated

Article and author information

Author details

  1. Andrew J Borst

    Department of Biochemistry, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4297-7824
  2. Connor E Weidle

    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Matthew D Gray

    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Brandon Frenz

    Department of Biochemistry, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Joost Snijder

    Department of Biochemistry, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. M Gordon Joyce

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Ivelin S Georgiev

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Guillaume BE Stewart-Jones

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Peter D Kwong

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Andrew T McGuire

    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Frank DiMaio

    Department of Biochemistry, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7524-8938
  12. Leonidas Stamatatos

    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    For correspondence
    lstamata@fredhutch.org
    Competing interests
    The authors declare that no competing interests exist.
  13. Marie Pancera

    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    For correspondence
    mpancera@fredhutch.org
    Competing interests
    The authors declare that no competing interests exist.
  14. David Veesler

    Department of Biochemistry, University of Washington, Seattle, United States
    For correspondence
    dveesler@uw.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6019-8675

Funding

National Institute of General Medical Sciences (R01GM120553)

  • David Veesler

National Institute of Allergy and Infectious Diseases (R01AI081625)

  • Leonidas Stamatatos

Pew Charitable Trusts

  • David Veesler

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

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Metrics

  • 2,923
    views
  • 389
    downloads
  • 32
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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. Andrew J Borst
  2. Connor E Weidle
  3. Matthew D Gray
  4. Brandon Frenz
  5. Joost Snijder
  6. M Gordon Joyce
  7. Ivelin S Georgiev
  8. Guillaume BE Stewart-Jones
  9. Peter D Kwong
  10. Andrew T McGuire
  11. Frank DiMaio
  12. Leonidas Stamatatos
  13. Marie Pancera
  14. David Veesler
(2018)
Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core
eLife 7:e37688.
https://doi.org/10.7554/eLife.37688

Share this article

https://doi.org/10.7554/eLife.37688

Further reading

    1. Structural Biology and Molecular Biophysics
    Johannes Elferich, Lingli Kong ... Nikolaus Grigorieff
    Research Advance

    Images taken by transmission electron microscopes are usually affected by lens aberrations and image defocus, among other factors. These distortions can be modeled in reciprocal space using the contrast transfer function (CTF). Accurate estimation and correction of the CTF is essential for restoring the high-resolution signal in cryogenic electron microscopy (cryoEM). Previously, we described the implementation of algorithms for this task in the cisTEM software package (Grant et al., 2018). Here we show that taking sample characteristics, such as thickness and tilt, into account can improve CTF estimation. This is particularly important when imaging cellular samples, where measurement of sample thickness and geometry derived from accurate modeling of the Thon ring pattern helps judging the quality of the sample. This improved CTF estimation has been implemented in CTFFIND5, a new version of the cisTEM program CTFFIND. We evaluated the accuracy of these estimates using images of tilted aquaporin crystals and eukaryotic cells thinned by focused ion beam milling. We estimate that with micrographs of sufficient quality CTFFIND5 can measure sample tilt with an accuracy of 3° and sample thickness with an accuracy of 5 nm.

    1. Structural Biology and Molecular Biophysics
    Mrityunjay Singh, Dinesh C Indurthi ... Shailendra Asthana
    Research Advance

    Agonists enhance receptor activity by providing net-favorable binding energy to active over resting conformations, with efficiency (η) linking binding energy to gating. Previously, we showed that in nicotinic receptors, η-values are grouped into five structural pairs, correlating efficacy and affinity within each class, uniting binding with allosteric activation (Indurthi and Auerbach, 2023). Here, we use molecular dynamics (MD) simulations to investigate the low-to-high affinity transition (L→H) at the Torpedo α−δ nicotinic acetylcholine receptor neurotransmitter site. Using four agonists spanning three η-classes, the simulations reveal the structural basis of the L→H transition where: the agonist pivots around its cationic center (‘flip’), loop C undergoes staged downward displacement (‘flop’), and a compact, stable high-affinity pocket forms (‘fix’). The η derived from binding energies calculated in silico matched exact values measured experimentally in vitro. Intermediate states of the orthosteric site during receptor activation are apparent only in simulations, but could potentially be observed experimentally via time-resolved structural studies.