ArticleJournal of chemical theory and computation2017
An Ensemble-Based Protocol for the Computational Prediction of Helix-Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Improved Method for Predicting GPCR-GPCR Interaction Pairs.Proteins · 2026Article
- Inhibitory effect of truncated isoforms on GPCR dimerization predicted by combinatorial computational strategy.Computational and structural biotechnology journal · 2024Article
- Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints.Journal of molecular biology · 2024Article
- Dynamic Dimerization of Chemokine Receptors and Potential Inhibitory Role of Their Truncated Isoforms Revealed through Combinatorial Prediction.International journal of molecular sciences · 2023Article
- Evolutionary Couplings and Molecular Dynamic Simulations Highlight Details of GPCRs Heterodimers' Interfaces.Molecules (Basel, Switzerland) · 2023Article
- Rapid, accurate, precise and reproducible ligand-protein binding free energy prediction.Interface focus · 2020Review
- Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors.Interface focus · 2020Article
- Computational Nanoscopy of Tight Junctions at the Blood-Brain Barrier Interface.International journal of molecular sciences · 2019Review
- Modulating Hinge Flexibility in the APP Transmembrane Domain Alters γ-Secretase Cleavage.Biophysical journal · 2019Article
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- Probing the Druggablility on the Interface of the Protein-Protein Interaction and Its Allosteric Regulation Mechanism on the Drug Screening for the CXCR4 Homodimer.Frontiers in pharmacology · 2019Article
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Authors and funding
5 authors.
Funding
Abstract
The accurate identification of the specific points of interaction between G protein-coupled receptor (GPCR) oligomers is essential for the design of receptor ligands targeting oligomeric receptor targets. A coarse-grained molecular dynamics computer simulation approach would provide a compelling means of identifying these specific protein-protein interactions and could be applied both for known oligomers of interest and as a high-throughput screen to identify novel oligomeric targets. However, to be effective, this in silico modeling must provide accurate, precise, and reproducible information. This has been achieved recently in numerous biological systems using an ensemble-based all-atom molecular dynamics approach. In this study, we describe an equivalent methodology for ensemble-based coarse-grained simulations. We report the performance of this method when applied to four different GPCRs known to oligomerize using error analysis to determine the ensemble size and individual replica simulation time required. Our measurements of distance between residues shown to be involved in oligomerization of the fifth transmembrane domain from the adenosine A
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