ArticleJournal of chemical theory and computation2014
Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix-Helix Association.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Effect of Disulfide Bridge on the Binding of SARS-CoV-2 Fusion Peptide to Cell Membrane: A Coarse-Grained Study.ACS omega · 2022Article
- Applications of Molecular Dynamics Simulation in Protein Study.Membranes · 2022Review
- Computational Models for the Study of Protein Aggregation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications.International journal of molecular sciences · 2019Review
- Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.Chemical reviews · 2019Review
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- Article
- Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.Journal of chemical theory and computation · 2017Article
- Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.Biochimica et biophysica acta · 2016Review
- Model parameters for simulation of physiological lipids.Journal of computational chemistry · 2016Article
- Enhanced Sampling of Coarse-Grained Transmembrane-Peptide Structure Formation from Hydrogen-Bond Replica Exchange.The Journal of membrane biology · 2015Article
- Recent advances in transferable coarse-grained modeling of proteins.Advances in protein chemistry and structural biology · 2014Review
- Review
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Authors and funding
5 authors.
Funding
Abstract
An extension of the recently developed PRIMO coarse-grained force field to membrane environments, PRIMO-M, is described. The membrane environment is modeled with the heterogeneous dielectric generalized Born (HDGB) methodology that simply replaces the standard generalized Born model in PRIMO without further parametrization. The resulting model was validated by comparing amino acid insertion free energy profiles and application in molecular dynamics simulations of membrane proteins and membrane-interacting peptides. Membrane proteins with 148-661 amino acids show stable root-mean-squared-deviations (RMSD) between 2 and 4 Å for most systems. Transmembrane helical peptides maintain helical shape and exhibit tilt angles in good agreement with experimental or other simulation data. The association of two glycophorin A (GpA) helices was simulated using replica exchange molecular dynamics simulations yielding the correct dimer structure with a crossing angle in agreement with previous studies. Finally, conformational sampling of the influenza fusion peptide also generates structures in agreement with previous studies. Overall, these findings suggest that PRIMO-M can be used to study membrane bound peptides and proteins and validates the transferable nature of the PRIMO coarse-grained force field.
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