ArticlePloS one2012
Insights into the structure, correlated motions, and electrostatic properties of two HIV-1 gp120 V3 loops.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 21 citations in OpenAlex.
- Novel small synthetic HIV-1 V3 crown variants: CCR5 targeting ligands.Journal of biochemistry · 2022Article
- Molecular Mechanism for Attractant Signaling to DHMA by E. coli Tsr.Biophysical journal · 2020Article
- Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding.Computational and structural biotechnology journal · 2020Article
- Elucidating the multi-targeted anti-amyloid activity and enhanced islet amyloid polypeptide binding ofComputers & chemical engineering · 2018Article
- All-atom virus simulations.Current opinion in virology · 2018Review
- The Transmission and Evolution of HIV-1 Quasispecies within One Couple: a Follow-up Study based on Next-Generation Sequencing.Scientific reports · 2018Article
- Computational study of HIV gp120 as a target for polyanionic entry inhibitors: Exploiting the V3 loop region.PloS one · 2018Article
- Elucidating a key anti-HIV-1 and cancer-associated axis: the structure of CCL5 (Rantes) in complex with CCR5.Scientific reports · 2014Article
- Elucidating a key component of cancer metastasis: CXCL12 (SDF-1α) binding to CXCR4.Journal of chemical information and modeling · 2014Article
- Molecular recognition of CCR5 by an HIV-1 gp120 V3 loop.PloS one · 2014Article
- Molecular recognition of CXCR4 by a dual tropic HIV-1 gp120 V3 loop.Biophysical journal · 2013Article
- The influence of N-linked glycans on the molecular dynamics of the HIV-1 gp120 V3 loop.PloS one · 2013Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The V3 loop of the glycoprotein 120 (gp120) is a contact point for cell entry of HIV-1 leading to infection. Despite sequence variability and lack of specific structure, the highly flexible V3 loop possesses a well-defined role in recognizing and selecting cell-bound coreceptors CCR5 and CXCR4 through a mechanism of charge complementarity. We have performed two independent molecular dynamics (MD) simulations to gain insights into the dynamic character of two V3 loops with slightly different sequences, but significantly different starting crystallographic structures. We have identified highly populated trajectory-specific salt bridges between oppositely charged stem residues Arg9 and Glu25 or Asp29. The two trajectories share nearly identical correlated motions within the simulations, despite their different overall structures. High occupancy salt bridges play a key role in the major cross-correlated motions in both trajectories, and may be responsible for transient structural stability in preparation for coreceptor binding. In addition, the two V3 loops visit conformations with similarities in spatial distributions of electrostatic potentials, despite their inherent flexibility, which may play a role in coreceptor recognition. It is plausible that cooperativity between overall electrostatic potential, charged residue interactions, and correlated motions could be associated with a coreceptor selection and binding.
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