ArticleThe journal of physical chemistry. B2017
Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- Free energy of collagen-mimetic peptide dimerization and implications for fibrillization.Biophysical journal · 2026Article
- Mechanistic Insights into Human Defensin Antimicrobial Activity from Membrane Simulations.The Journal of membrane biology · 2026Article
- Molecular dynamics reveals how calcium drives hetero- versus homotrimerization of type I collagen.Biophysical journal · 2026Article
- Multiscale Simulation Approaches to Probe Lipid Interactions of G Protein-Coupled Receptors.Methods in molecular biology (Clifton, N.J.) · 2026Article
- STIM1 transmembrane helix dimerization captured by AI-guided transition path sampling.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Single-molecule tweezers decode hidden dimerization patterns of membrane proteins within lipid bilayers.Nature communications · 2025Article
- 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
- Characterization of hyperactive mutations in the renal potassium channel ROMK uncovers unique effects on channel biogenesis and ion conductance.Molecular biology of the cell · 2024Article
- Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane.Journal of chemical theory and computation · 2024Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- Mechanism of hydrophobic gating in the acetylcholine receptor channel pore.The Journal of general physiology · 2024Article
- A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes.Journal of chemical theory and computation · 2023Article
- The role of structural heterogeneity in the homodimerization of transmembrane proteins.The Journal of chemical physics · 2023Article
- Umbrella Sampling Simulations of Cardiac Thin Filament Reveal Thermodynamic Consequences of Troponin I Inhibitory Peptide Mutations.Journal of chemical information and modeling · 2023Article
- Molecular mechanism of CD44 homodimerization modulated by palmitoylation and membrane environments.Biophysical journal · 2022Article
- On Computing Equilibrium Binding Constants for Protein-Protein Association in Membranes.Journal of chemical theory and computation · 2022Article
- Effects of cholesterol and PIP2 on interactions between glycophorin A and Band 3 in lipid bilayers.Biophysical journal · 2022Article
- From Bench to Biomolecular Simulation: Phospholipid Modulation of Potassium Channels.Journal of molecular biology · 2021Review
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5 authors.
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Abstract
Potential of mean force (PMF) calculations are used to characterize the free energy landscape of protein-lipid and protein-protein association within membranes. Coarse-grained simulations allow binding free energies to be determined with reasonable statistical error. This accuracy relies on defining a good collective variable to describe the binding and unbinding transitions, and upon criteria for assessing the convergence of the simulation toward representative equilibrium sampling. As examples, we calculate protein-lipid binding PMFs for ANT/cardiolipin and Kir2.2/PIP
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