ArticleJournal of chemical theory and computation2020
Capturing Choline-Aromatics Cation-π Interactions in the MARTINI Force Field.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 53 citations in OpenAlex.
- Amphipathic β‑Sheet-Forming Octapeptide Self-Assembly Using the Martini Potential Family.ACS omega · 2026Article
- Tunable electrostatic interactions of lipid-coated quantum dots with biological membranes.bioRxiv : the preprint server for biology · 2026Article
- Characterization of Membrane Binding and Protein-Lipid Interactions at the Atomic Level with an Accelerated HMMM Model.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior.ACS central science · 2025Article
- Review
- Influence of branched ligand architectures on nanoparticle interactions with lipid bilayers.Nanoscale · 2025Article
- Long-Chain Lipids Facilitate Insertion of Large Nanoparticles into Membranes of Small Unilamellar Vesicles.Langmuir : the ACS journal of surfaces and colloids · 2024Article
- Ligand Lipophilicity Determines Molecular Mechanisms of Nanoparticle Adsorption to Lipid Bilayers.ACS nano · 2024Article
- Molecular Dynamics Simulations in Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- An implementation of the Martini coarse-grained force field in OpenMM.Biophysical journal · 2023Article
- Article
- Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid-membrane contacts.PLoS computational biology · 2023Article
- Martini 3 Coarse-Grained Force Field for Carbohydrates.Journal of chemical theory and computation · 2022Article
- Molecular mechanism of CD44 homodimerization modulated by palmitoylation and membrane environments.Biophysical journal · 2022Article
- Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?Bioscience reports · 2022Article
- The Bak core dimer focuses triacylglycerides in the membrane.Biophysical journal · 2022Article
- Regulation of a pentameric ligand-gated ion channel by a semiconserved cationic lipid-binding site.The Journal of biological chemistry · 2021Article
- A Data-Driven Dimensionality Reduction Approach to Compare and Classify Lipid Force Fields.The journal of physical chemistry. B · 2021Article
- Article
- Martini 3: a general purpose force field for coarse-grained molecular dynamics.Nature methods · 2021Article
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cation-π interactions play an important role in biomolecular recognition, including interactions between membrane phosphatidylcholine lipids and aromatic amino acids of peripheral proteins. While molecular mechanics coarse grain (CG) force fields are particularly well suited to simulate membrane proteins in general, they are not parameterized to explicitly reproduce cation-π interactions. We here propose a modification of the polarizable MARTINI coarse grain (CG) model enabling it to model membrane binding events of peripheral proteins whose aromatic amino acid interactions with choline headgroups are crucial for their membrane binding. For this purpose, we first collected and curated a dataset of eight peripheral proteins from different families. We find that the MARTINI CG model expectedly underestimates aromatics-choline interactions and is unable to reproduce membrane binding of the peripheral proteins in our dataset. Adjustments of the relevant interactions in the polarizable MARTINI force field yield significant improvements in the observed binding events. The orientation of each membrane-bound protein is comparable to reference data from all-atom simulations and experimental binding data. We also use negative controls to ensure that choline-aromatics interactions are not overestimated. We finally check that membrane properties, transmembrane proteins, and membrane translocation potential of mean force (PMF) of aromatic amino acid side-chain analogues are not affected by the new parameter set. This new version "MARTINI 2.3P" is a significant improvement over its predecessors and is suitable for modeling membrane proteins including peripheral membrane binding of peptides and proteins.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.