Evidence map›Paper›PMID 28107435›Full record

ArticlePloS one2017

Peptide Targeted by Human Antibodies Associated with HIV Vaccine-Associated Protection Assumes a Dynamic α-Helical Structure.

Mohammed S Aiyegbo, Evgeny Shmelkov, Lorenzo Dominguez, Michael Goger, Shibani Battacharya, Allan C deCamp, Peter B Gilbert, Phillip W Berman, Timothy Cardozo

Abstract read
In one paragraph

Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing 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

13 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

9 authors.

Mohammed S AiyegboDepartment of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America.
Evgeny ShmelkovDepartment of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America.
Lorenzo DominguezDepartment of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America.
Michael GogerThe New York Structural Biology Center, New York, New York, United States of America.
Shibani BattacharyaThe New York Structural Biology Center, New York, New York, United States of America.
Allan C deCampVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.
Peter B GilbertVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.
Phillip W BermanDepartment of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.
Timothy CardozoDepartment of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America.

Funding

SDMC: HIV Vaccine Trials NetworkUM1AI068635 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI Peter B. Gilbert, Yunda Huang · 2011 to 2026
$385.9M
900 MHz NMR Spectrometer for Structural BiologyP41GM066354 · NIGMS · NEW YORK STRUCTURAL BIOLOGY CENTER · PI COWBURN, DAVID · 2002 to 2006
$4.7M
Combined cocaine and HIV vaccineDP1DA036478 · NIDA · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI CARDOZO, TIMOTHY J · 2013 to 2017
$4.7M
Structure-Based Characterization of gp120 Non-V3 Variable Loop EpitopesR01AI084119 · NIAID · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI CARDOZO, TIMOTHY J, KONG, XIANGPENG · 2009 to 2014
$3.2M
EXTRAMURAL RESEARCH FACILITIES CONSTRUCTIONC06RR015495 · NCRR · NEW YORK STRUCTURAL BIOLOGY CENTER · PI RIFKIND, RICHARD A · 2000 to 2000
$2.0M
Epitope optimization for heterologous prime-boost HIV vaccinesR21AI106501 · NIAID · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI CARDOZO, TIMOTHY J · 2016 to 2017
$539k
NCRR NIH HHS C06 RR015495NIAID NIH HHS R01 AI084119NIAID NIH HHS R21 AI106501NIAID NIH HHS UM1 AI068635NIDA NIH HHS DP1 DA036478NIGMS NIH HHS P41 GM066354
6 · The paper itself

Abstract

The only evidence of vaccine-induced protection from HIV acquisition in humans was obtained in the RV144 HIV vaccine clinical trial. One immune correlate of risk in RV144 was observed to be higher titers of vaccine-induced antibodies (Abs) reacting with a 23-mer non-glycosylated peptide with the same amino acid sequence as a segment in the second variable (V2) loop of the MN strain of HIV. We used NMR to analyze the dynamic 3D structure of this peptide. Distance restraints between spatially proximate inter-residue protons were calculated from NOE cross peak intensities and used to constrain a thorough search of all possible conformations of the peptide. α-helical folding was strongly preferred by part of the peptide. A high-throughput structure prediction of this segment in all circulating HIV strains demonstrated that α-helical conformations are preferred by this segment almost universally across all subtypes. Notably, α-helical conformations of this segment of the V2 loop cluster cross-subtype-conserved amino acids on one face of the helix and the variable amino acid positions on the other in a semblance of an amphipathic α-helix. Accordingly, some Abs that protected against HIV in RV144 may have targeted a specific, conserved α-helical peptide epitope in the V2 loop of HIV's surface envelope glycoprotein.

Indexed as

Protein Conformation, alpha-HelicalAIDS VaccinesAmino Acid SequenceAntibodies, NeutralizingConserved SequenceHIV-1HIV AntibodiesHIV Envelope Protein gp120HumansMagnetic Resonance SpectroscopyModels, MolecularPeptide FragmentsProtein FoldingAIDS VaccinesAntibodies, Neutralizinggp120 protein, Human immunodeficiency virus 1HIV AntibodiesHIV Envelope Protein gp120Peptide Fragments

Identifiers

PMID28107435
PMCPMC5249078

What OpenQuestion holds

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Registered trials

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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.