ArticleProtein engineering, design & selection : PEDS2019
Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism.
Article in Protein engineering, design & selection : PEDS, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 26 citations in OpenAlex.
- Affinity of drug candidates binding to SARS-CoV-2 PLpro assessed using a generalized-ensemble method.Scientific reports · 2026Article
- A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape.Biophysics and physicobiology · 2025Article
- The transition state for coupled folding and binding of a disordered DNA binding domain resembles the unbound state.Nucleic acids research · 2024Article
- Molecular Mechanisms of Functional Modulation of Transcriptional Coactivator PC4 via Phosphorylation on Its Intrinsically Disordered Region.ACS omega · 2023Article
- Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics.Biophysics and physicobiology · 2023Article
- Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule.Scientific reports · 2022Article
- Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities.Scientific reports · 2021Article
- myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling.Biophysics and physicobiology · 2020Article
- GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics.Biophysics and physicobiology · 2020Article
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9 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The free-energy landscape of interaction between a medium-sized peptide, endothelin 1 (ET1), and its receptor, human endothelin type B receptor (hETB), was computed using multidimensional virtual-system coupled molecular dynamics, which controls the system's motions by introducing multiple reaction coordinates. The hETB embedded in lipid bilayer was immersed in explicit solvent. All molecules were expressed as all-atom models. The resultant free-energy landscape had five ranges with decreasing ET1-hETB distance: completely dissociative, outside-gate, gate, binding pocket, and genuine-bound ranges. In the completely dissociative range, no ET1-hETB interaction appeared. In the outside-gate range, an ET1-hETB attractive interaction was the fly-casting mechanism. In the gate range, the ET1 orientational variety decreased rapidly. In the binding pocket range, ET1 was in a narrow pathway with a steep free-energy slope. In the genuine-bound range, ET1 was in a stable free-energy basin. A G-protein-coupled receptor (GPCR) might capture its ligand from a distant place.
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