ArticleBiophysical journal2012
Determination of membrane-insertion free energies by molecular dynamics simulations.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Membrane insertion and dimerization of glycophorin-A mutations studied by free energy simulations.Biophysical journal · 2026Article
- Integrating Docking, Dynamics, and Assays to Predict Antimicrobial Peptide Interactions with Mycolic Acid Membranes inACS measurement science au · 2025Article
- Alchemical Free Energy Calculations on Membrane-Associated Proteins.Journal of chemical theory and computation · 2023Review
- Not sorcery after all: Roles of multiple charged residues in membrane insertion of gasdermin-A3.Frontiers in cell and developmental biology · 2022Article
- Vectorial insertion of a β-helical peptide into membrane: a theoretical study on polytheonamide B.Biophysical journal · 2021Article
- Molecular Dynamics Simulations of Human Beta-Defensin Type 3 Crossing Different Lipid Bilayers.ACS omega · 2021Article
- GeTFEP: A general transfer free energy profile of transmembrane proteins.Protein science : a publication of the Protein Society · 2020Article
- Quantitative Characterization of Protein-Lipid Interactions by Free Energy Simulation between Binary Bilayers.Journal of chemical theory and computation · 2019Article
- The importance of the membrane interface as the reference state for membrane protein stability.Biochimica et biophysica acta. Biomembranes · 2018Article
- Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method.The Journal of membrane biology · 2018Article
- Refining Protein Penetration into the Lipid Bilayer Using Fluorescence Quenching and Molecular Dynamics Simulations: The Case of Diphtheria Toxin Translocation Domain.The Journal of membrane biology · 2018Article
- Article
- Transmembrane helices containing a charged arginine are thermodynamically stable.European biophysics journal : EBJ · 2017Article
- Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins.Bioinformatics (Oxford, England) · 2017Article
- Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents.The journal of physical chemistry. B · 2017Article
- Grafting Charged Species to Membrane-Embedded Scaffolds Dramatically Increases the Rate of Bilayer Flipping.ACS central science · 2017Article
- Article
- Molecular Mechanism of Processive 3' to 5' RNA Translocation in the Active Subunit of the RNA Exosome Complex.Journal of the American Chemical Society · 2016Article
- Outer Membrane Protein Folding and Topology from a Computational Transfer Free Energy Scale.Journal of the American Chemical Society · 2016Article
- IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels.PloS one · 2016Article
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2 authors.
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Abstract
The accurate prediction of membrane-insertion probability for arbitrary protein sequences is a critical challenge to identifying membrane proteins and determining their folded structures. Although algorithms based on sequence statistics have had moderate success, a complete understanding of the energetic factors that drive the insertion of membrane proteins is essential to thoroughly meeting this challenge. In the last few years, numerous attempts to define a free-energy scale for amino-acid insertion have been made, yet disagreement between most experimental and theoretical scales persists. However, for a recently resolved water-to-bilayer scale, it is found that molecular dynamics simulations that carefully mimic the conditions of the experiment can reproduce experimental free energies, even when using the same force field as previous computational studies that were cited as evidence of this disagreement. Therefore, it is suggested that experimental and simulation-based scales can both be accurate and that discrepancies stem from disparities in the microscopic processes being considered rather than methodological errors. Furthermore, these disparities make the development of a single universally applicable membrane-insertion free energy scale difficult.
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