Evidence map›Paper›PMID 26628363›Full record

ArticleCell reports2015

The Binding Interface between Human APOBEC3F and HIV-1 Vif Elucidated by Genetic and Computational Approaches.

Christopher Richards, John S Albin, Özlem Demir, Nadine M Shaban, Elizabeth M Luengas, Allison M Land, Brett D Anderson, John R Holten, John S Anderson, Daniel A Harki and 2 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.

0numbers the graph read from it
0cells of the map it votes in
28citing papers in PubMed
3.0field-weighted citation impact, top 8% of its field
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

28 citing papers in PubMed, 38 citations in OpenAlex.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Article
  6. Review
  7. Article
  8. Article
  9. Article
  10. Article
  11. Structural perspectives on HIV-1 Vif and APOBEC3 restriction factor interactions.Protein science : a publication of the Protein Society · 2020
    Review
  12. Review
  13. Structural basis of antagonism of human APOBEC3F by HIV-1 Vif.Nature structural & molecular biology · 2019
    Article
  14. Article
  15. Article
  16. Article
  17. CRL4The EMBO journal · 2018
    Article
  18. Article
  19. Article
  20. Review
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

12 authors at 3 institutions in 1 country.

Christopher RichardsDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
John S AlbinDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
Özlem DemirDepartment of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
Nadine M ShabanDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
Elizabeth M LuengasDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
Allison M LandDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
Brett D AndersonDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
John R HoltenDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
John S AndersonDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
Daniel A HarkiMasonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
Rommie E AmaroDepartment of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
Reuben S HarrisDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address: rsh@umn.edu.
University of Minnesota · USUniversity of Minnesota Medical Center · USUniversity of California, San Diego · US

Funding

National Biomedical Computation Resource - Competitive Revision SupplementP41GM103426 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI AMARO, ROMMIE E · 2012 to 2019
$14.0M
MEDICAL SCIENTIST TRAINING PROGRAMT32GM008244 · NIGMS · UNIVERSITY OF MINNESOTA TWIN CITIES · PI SHIMIZU, YOJI · 1988 to 2024
$13.6M
Structural Characterization of APOBECS's Atomic interactionsP01GM091743 · NIGMS · UNIVERSITY OF MINNESOTA · PI HARRIS, REUBEN S · 2011 to 2015
$10.1M
IMMUNOLOGY TRAINING PROGRAMT32AI007313 · NIAID · UNIVERSITY OF MINNESOTA TWIN CITIES · PI Carla Rothlin · 1989 to 2026
$5.7M
APOBEC3 Proteins in HIV RestrictionR37AI064046 · NIAID · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI HARRIS, REUBEN S · 2015 to 2024
$4.2M
Minnesota Training Program in VirologyT32AI083196 · NIAID · UNIVERSITY OF MINNESOTA · PI Louis M Mansky · 2010 to 2026
$3.2M
APOBEC proteins and uracil in retrovirus restrictionR01AI064046 · NIAID · UNIVERSITY OF MINNESOTA TWIN CITIES · PI HARRIS, REUBEN S · 2005 to 2014
$3.0M
A Structural Systems Biology Approach to Drug DiscoveryDP2OD007237 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI AMARO, ROMMIE E · 2010 to 2015
$2.9M
Determining the Role of APOBEC3 Proteins in HIV-1 Drug ResistanceF30DA026310 · NIDA · UNIVERSITY OF MINNESOTA · PI ALBIN, JOHN S. · 2009 to 2012
$181k
Dual Mechanisms for APOBEC3 Suppression by HIV-1 VifF31AI116305 · NIAID · UNIVERSITY OF MINNESOTA · PI ANDERSON, BRETT D · 2015 to 2016
$62k
Howard Hughes Medical InstituteNIAID NIH HHS F31 AI116305NIAID NIH HHS R01 AI064046NIAID NIH HHS R37 AI064046NIAID NIH HHS T32 AI007313NIAID NIH HHS T32 AI083196NIAID NIH HHS T32 AI83196NIDA NIH HHS F30 DA026310NIGMS NIH HHS P01 GM091743NIGMS NIH HHS P41 GM103426NIGMS NIH HHS T32 GM008244NIH HHS DP2 OD007237NIH HHS DP2-OD007237
6 · The paper itself

Abstract

APOBEC3 family DNA cytosine deaminases provide overlapping defenses against pathogen infections. However, most viruses have elaborate evasion mechanisms such as the HIV-1 Vif protein, which subverts cellular CBF-β and a polyubiquitin ligase complex to neutralize these enzymes. Despite advances in APOBEC3 and Vif biology, a full understanding of this direct host-pathogen conflict has been elusive. We combine virus adaptation and computational studies to interrogate the APOBEC3F-Vif interface and build a robust structural model. A recurring compensatory amino acid substitution from adaptation experiments provided an initial docking constraint, and microsecond molecular dynamic simulations optimized interface contacts. Virus infectivity experiments validated a long-lasting electrostatic interaction between APOBEC3F E289 and HIV-1 Vif R15. Taken together with mutagenesis results, we propose a wobble model to explain how HIV-1 Vif has evolved to bind different APOBEC3 enzymes and, more generally, how pathogens may evolve to escape innate host defenses.

Indexed as

Amino Acid SequenceBinding SitesCell LineCytosine DeaminaseHIV-1HumansImmunity, InnateMolecular Dynamics SimulationMutagenesis, Site-DirectedProtein Structure, TertiaryStatic Electricityvif Gene Products, Human Immunodeficiency VirusAPOBEC3F protein, humanCytosine Deaminasevif Gene Products, Human Immunodeficiency Virusvif protein, Human immunodeficiency virus 1APOBEC3FAPOBEC3F-Vif interfaceHIV-1pathogen-host interactionVif

Identifiers

PMID26628363
PMCPMC4684092
OpenAlexW2180221164

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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.