ArticleScientific reports2015
Investigation of Inhibition Mechanism of Chemokine Receptor CCR5 by Micro-second Molecular Dynamics Simulations.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Whole-Genome Sequencing of Multidrug-ResistantInternational journal of molecular sciences · 2026Article
- Disclosing Pathogenic Variant Effects on the Structural Dynamics of the VAPB MSP Domain Causing Familial ALS.International journal of molecular sciences · 2025Article
- Targeting HIV-1 conserved regions: An immunoinformatic pathway to vaccine innovation for the Asia.PloS one · 2025Article
- Targeting CCR3 with antagonist SB 328437 sensitizes 5‑fluorouracil‑resistant gastric cancer cells: Experimental evidence and computational insights.Oncology letters · 2024Article
- Pharmacophore-Oriented Identification of Potential Leads as CCR5 Inhibitors to Block HIV Cellular Entry.International journal of molecular sciences · 2022Article
- Dynamic insights into the effects of nonsynonymous polymorphisms (nsSNPs) on loss of TREM2 function.Scientific reports · 2022Article
- Structural Consequence of Non-Synonymous Single-Nucleotide Variants in the N-Terminal Domain of LIS1.International journal of molecular sciences · 2022Article
- Computational study of the structural ensemble of CC chemokine receptor type 5 (CCR5) and its interactions with different ligands.PloS one · 2022Article
- Article
- Mechanistic insights into the deleterious roles of Nasu-Hakola disease associated TREM2 variants.Scientific reports · 2020Article
- A two-stage computational approach to predict novel ligands for a chemosensory receptor.Current research in structural biology · 2020Article
- Structural and Dynamic Characterizations Highlight the Deleterious Role of SULT1A1 R213H Polymorphism in Substrate Binding.International journal of molecular sciences · 2019Article
- Using accelerated molecular dynamics simulation to shed light on the mechanism of activation/deactivation upon mutations for CCR5.RSC advances · 2018Article
- Exploration of binding and inhibition mechanism of a small molecule inhibitor of influenza virus H1N1 hemagglutinin by molecular dynamics simulation.Scientific reports · 2017Article
- Understanding the molecular mechanism for the differential inhibitory activities of compounds against MTH1.Scientific reports · 2017Article
- The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B.Scientific reports · 2016Article
- Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis.Scientific reports · 2016Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chemokine receptor 5 (CCR5) belongs to G protein coupled receptors (GPCRs) and plays an important role in treatment of human immunodeficiency virus (HIV) infection since HIV uses CCR5 protein as a co-receptor. Recently, the crystal structure of CCR5-bound complex with an approved anti-retroviral drug (maroviroc) was resolved. During the crystallization procedure, amino acid residues (i.e., Cys224, Arg225, Asn226 and Glu227) at the third intra-cellular loop were replaced by the rubredoxin for stability reasons. In the current study, we aimed to understand the impact of the incorporated rubredoxin on the conformations of TM domains of the target protein. For this reason, rubredoxin was deleted from the crystal structure and the missing amino acids were engineered. The resultant structure was subjected to long (μs) molecular dynamics (MD) simulations to shed light into the inhibitory mechanism. The derived model structure displayed a significant deviation in the cytoplasmic domain of TM5 and IC3 in the absence of rubredoxin. The principal component analyses (PCA) and MD trajectory analyses revealed important structural and dynamical differences at apo and holo forms of the CCR5.
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