ArticleStructure (London, England : 1993)2015
Computational Refinement and Validation Protocol for Proteins with Large Variable Regions Applied to Model HIV Env Spike in CD4 and 17b Bound State.
Article in Structure (London, England : 1993), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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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.
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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.
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Who cites it
21 citing papers in PubMed, 33 citations in OpenAlex.
- Graph neural network integrated with pretrained protein language model for predicting human-virus protein-protein interactions.Briefings in bioinformatics · 2025Article
- HIV-1-envelope trimer transitions from prefusion-closed to CD4-bound-open conformations through an occluded-intermediate state.Computational and structural biotechnology journal · 2024Article
- The combination of three CD4-induced antibodies targeting highly conserved Env regions with a small CD4-mimetic achieves potent ADCC activity.Journal of virology · 2024Article
- Three families of CD4-induced antibodies are associated with the capacity of plasma from people living with HIV to mediate ADCC in the presence of CD4-mimetics.Journal of virology · 2024Article
- HIV-1-envelope trimer transitions from prefusion-closed to CD4-bound-open conformations through an occluded-intermediate state.bioRxiv : the preprint server for biology · 2024Article
- The combination of three CD4-induced antibodies targeting highly conserved Env regions with a small CD4-mimetic achieves potent ADCC activity.bioRxiv : the preprint server for biology · 2024Article
- Three families of CD4-induced antibodies are associated with the capacity of plasma from people living with HIV to mediate ADCC in presence of CD4-mimetics.medRxiv : the preprint server for health sciences · 2024Article
- Structure-Based Identification of Natural-Product-Derived Compounds with Potential to Inhibit HIV-1 Entry.Molecules (Basel, Switzerland) · 2023Article
- Modeling of CCR5 Recognition by HIV-1 gp120: How the Viral Protein Exploits the Conformational Plasticity of the Coreceptor.Viruses · 2021Article
- Stabilizing the HIV-1 envelope glycoprotein State 2A conformation.Journal of virology · 2021Article
- Probing intrinsic dynamics and conformational transition of HIV gp120 by molecular dynamics simulation.RSC advances · 2020Article
- Specific Substitutions in Region V2 of gp120Pathogens (Basel, Switzerland) · 2020Article
- Effects of CD4 Binding on Conformational Dynamics, Molecular Motions, and Thermodynamics of HIV-1 gp120.International journal of molecular sciences · 2019Article
- Article
- Recent advances in retroviruses via cryo-electron microscopy.Retrovirology · 2018Review
- Computational study of HIV gp120 as a target for polyanionic entry inhibitors: Exploiting the V3 loop region.PloS one · 2018Article
- HIV-1 subtype CRF01_AE and B differ in utilization of low levels of CCR5, Maraviroc susceptibility and potential N-glycosylation sites.Virology · 2017Article
- Survivors Remorse: antibody-mediated protection against HIV-1.Immunological reviews · 2017Review
- Cryo-EM structure of a CD4-bound open HIV-1 envelope trimer reveals structural rearrangements of the gp120 V1V2 loop.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Molecular basis for epitope recognition by non-neutralizing anti-gp41 antibody F240.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Envelope glycoprotein gp120 of HIV-1 possesses several variable regions; their precise structure has been difficult to establish. We report a new model of gp120, in complex with antibodies CD4 and 17b, complete with its variable regions. The model was produced by a computational protocol that uses cryo-electron microscopy (EM) maps, atomic-resolution structures of the core, and information on binding interactions. Our model has excellent fit with EMD: 5020, is stereochemically and energetically favorable, and has the expected binding interfaces. Comparison of the ternary arrangement of the loops in this model with those bound to PGT122 and PGV04 suggested a possible motion of the V1V2 away from the CCR5 binding site and toward CD4. Our study also revealed that the CD4-bound state of the V1V2 loop is not optimal for gp120 bound with several neutralizing antibodies.
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Registered trials
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.