ArticleJournal of chemical theory and computation2019
Insights into Membrane Protein-Lipid Interactions from Free Energy Calculations.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Is the Bilayer Insertion of the Peptide KALP23 Under Kinetic or Thermodynamic Control?The Journal of membrane biology · 2026Article
- Sketching microprotein portraits.Protein science : a publication of the Protein Society · 2026Review
- Article
- Advanced Computational Methods in Protein Simulations: A Case Study of Enhanced Sampling Applied to Membrane Transporters.Advances in experimental medicine and biology · 2026Review
- Ligand-Binding Free Energy Simulations of Membrane Proteins.Advances in experimental medicine and biology · 2026Review
- Mechanisms of KCNQ1 gating modulation by KCNE1/3 for cell-specific function.Cell research · 2025Article
- Effects of Membrane Cholesterol on the Structure and Function of Selected Class A GPCRs─Challenges and Future Perspectives.Biochemistry · 2025Review
- Cardiolipin acyl chain composition tailors the conformation of mammalian ATP synthase dimers.Communications chemistry · 2025Article
- Article
- The Influence of Phosphoinositide Lipids in the Molecular Biology of Membrane Proteins: Recent Insights from Simulations.Journal of molecular biology · 2025Review
- Free Energy, Rates, and Mechanism of Transmembrane Dimerization in Lipid Bilayers from Dynamically Unbiased Molecular Dynamics Simulations.The journal of physical chemistry. B · 2025Article
- A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptor α1.Nature communications · 2024Article
- Functional diversity among cardiolipin binding sites on the mitochondrial ADP/ATP carrier.The EMBO journal · 2024Article
- Improved Highly Mobile Membrane Mimetic Model for Investigating Protein-Cholesterol Interactions.Journal of chemical information and modeling · 2024Article
- Integrating electromagnetic cancer stress with immunotherapy: a therapeutic paradigm.Frontiers in oncology · 2024Article
- Alchemical Free Energy Calculations on Membrane-Associated Proteins.Journal of chemical theory and computation · 2023Review
- The energetics and ion coupling of cholesterol transport through Patched1.Science advances · 2023Article
- Molecular Biophysics of Class A G Protein Coupled Receptors-Lipids Interactome at a Glance-Highlights from the ABiomolecules · 2023Review
- Conserved cardiolipin-mitochondrial ADP/ATP carrier interactions assume distinct structural and functional roles that are clinically relevant.bioRxiv : the preprint server for biology · 2023Article
- UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape.Membranes · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Integral membrane proteins are regulated by specific interactions with lipids from the surrounding bilayer. The structures of protein-lipid complexes can be determined through a combination of experimental and computational approaches, but the energetic basis of these interactions is difficult to resolve. Molecular dynamics simulations provide the primary computational technique to estimate the free energies of these interactions. We demonstrate that the energetics of protein-lipid interactions may be reliably and reproducibly calculated using three simulation-based approaches: potential of mean force calculations, alchemical free energy perturbation, and well-tempered metadynamics. We employ these techniques within the framework of a coarse-grained force field and apply them to both bacterial and mammalian membrane protein-lipid systems. We demonstrate good agreement between the different techniques, providing a robust framework for their automated implementation within a pipeline for annotation of newly determined membrane protein structures.
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Registered trials
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.