Evidence map›Paper›PMID 30770829›Full record

ArticleNature communications2019

Capturing the inherent structural dynamics of the HIV-1 envelope glycoprotein fusion peptide.

Sonu Kumar, Anita Sarkar, Pavel Pugach, Rogier W Sanders, John P Moore, Andrew B Ward, Ian A Wilson

Abstract read
In one paragraph

Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.

0numbers the graph read from it
0cells of the map it votes in
23citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

23 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Sonu KumarDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.ORCID http://orcid.org/0000-0003-0423-2880
Anita SarkarDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.ORCID http://orcid.org/0000-0001-5602-8406
Pavel PugachDepartment of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA.
Rogier W SandersDepartment of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA.
John P MooreDepartment of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA.ORCID http://orcid.org/0000-0002-9902-6096
Andrew B WardDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.ORCID http://orcid.org/0000-0001-7153-3769
Ian A WilsonDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA. wilson@scripps.edu.ORCID http://orcid.org/0000-0002-6469-2419

Funding

Support Component D/Vaccine Discovery, Concept to ClinicUM1AI100663 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI BAROUCH, DAN H. · 2012 to 2018
$131.5M
Structural studies of native-like SOSIP trimersP01AI110657 · NIAID · WEILL MEDICAL COLL OF CORNELL UNIV · PI MOORE, JOHN P · 2015 to 2024
$35.4M
NIAID NIH HHS P01 AI110657NIAID NIH HHS UM1 AI100663
6 · The paper itself

Abstract

The N-terminal fusion peptide (FP) of the human immunodeficiency virus (HIV)-1 envelope glycoprotein (Env) gp41 subunit plays a critical role in cell entry. However, capturing the structural flexibility in the unbound FP is challenging in the native Env trimer. Here, FP conformational isomerism is observed in two crystal structures of a soluble clade B transmitted/founder virus B41 SOSIP.664 Env with broadly neutralizing antibodies (bNAbs) PGT124 and 35O22 to aid in crystallization and that are not specific for binding to the FP. Large rearrangements in the FP and fusion peptide proximal region occur around M530, which remains anchored in the tryptophan clasp (gp41 W623, W628, W631) in the B41 Env prefusion state. Further, we redesigned the FP at position 518 to reinstate the bNAb VRC34.01 epitope. These findings provide further structural evidence for the dynamic nature of the FP and how a bNAb epitope can be restored during vaccine design.

Indexed as

Antibodies, NeutralizingEpitopesHIV-1HIV AntibodiesHIV Envelope Protein gp41HumansProtein Structure, SecondaryProtein Structure, TertiaryViral ProteinsAntibodies, NeutralizingEpitopesHIV AntibodiesHIV Envelope Protein gp41Viral Proteins

Identifiers

PMID30770829
PMCPMC6377653

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.