ArticleThe journal of physical chemistry. B2014
Partitioning of amino acids into a model membrane: capturing the interface.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- ReVesicle: Curation and Equilibration of Lipid Vesicles for Mesoscale Simulations.Journal of chemical theory and computation · 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
- CaThe journal of physical chemistry. B · 2025Article
- Regulation of Rho guanine nucleotide exchange factor 3 by phosphorylation in the PH domain.iScience · 2025Article
- Identifying and quantifying membrane interactions of the protein human cis-prenyltransferase.Protein science : a publication of the Protein Society · 2025Article
- Charge, Hydrophobicity, and Lipid Type Drive Antimicrobial Peptides' Unique Perturbation Ensembles.Biochemistry · 2025Article
- Membrane-bound model of the ternary complex between factor VIIa/tissue factor and factor X.Blood advances · 2025Article
- Split Membrane: A New Model to Accelerate All-Atom MD Simulation of Phospholipid Bilayers.Journal of chemical information and modeling · 2025Article
- Beyond Fang's fury: a computational study of the enzyme-membrane interaction and catalytic pathway of the snake venom phospholipase AChemical science · 2025Article
- Atomistic characterization of β2-glycoprotein I domain V interaction with anionic membranes.Journal of thrombosis and haemostasis : JTH · 2024Article
- Improved Highly Mobile Membrane Mimetic Model for Investigating Protein-Cholesterol Interactions.Journal of chemical information and modeling · 2024Article
- Lactadherin's Multistate Binding Predicts Stable Membrane-Bound Conformations of Factors V and VIII's C Domains.Biochemistry · 2023Article
- Molecular View into Preferential Binding of the Factor VII Gla Domain to Phosphatidic Acid.Biochemistry · 2022Article
- Towards a Quantitative Understanding of Protein-Lipid Bilayer Interactions at the Single Molecule Level: Opportunities and Challenges.The Journal of membrane biology · 2021Review
- Capturing Choline-Aromatics Cation-π Interactions in the MARTINI Force Field.Journal of chemical theory and computation · 2020Article
- Computer simulations of protein-membrane systems.Progress in molecular biology and translational science · 2020Article
- Coaction of Electrostatic and Hydrophobic Interactions: Dynamic Constraints on Disordered TrkA Juxtamembrane Domain.The journal of physical chemistry. B · 2019Article
- A network of phosphatidylinositol 4,5-bisphosphate binding sites regulates gating of the CaProceedings of the National Academy of Sciences of the United States of America · 2019Article
- 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
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4 authors.
Funding
Abstract
Energetics of protein side chain partitioning between aqueous solution and cellular membranes is of fundamental importance for correctly capturing the membrane binding and specific protein-lipid interactions of peripheral membrane proteins. We recently reported a highly mobile membrane mimetic (HMMM) model that accelerates lipid dynamics by modeling the membrane interior partially as a fluid organic solvent while retaining a literal description of the lipid head groups and the beginning of the tails. While the HMMM has been successfully applied to study spontaneous insertion of a number of peripheral proteins into membranes, a quantitative characterization of the energetics of membrane-protein interactions in HMMM membranes has not been performed. We report here the free energy profiles for partitioning of 10 protein side chain analogues into a HMMM membrane. In the interfacial and headgroup regions of the membrane, the side chain free energy profiles show excellent agreement with profiles previously reported for conventional membranes with full-tail lipids. In regions where the organic solvent is prevalent, the increased dipole and fluidity of the solvent generally result in a less accurate description, most notably overstabilization of aromatic and polar amino acids. As an additional measure of the ability of the HMMM model to describe membrane-protein interactions, the water-to-membrane interface transfer energies were analyzed and found to be in agreement with the previously reported experimental and computational hydrophobicity scales. We discuss strengths and weaknesses of HMMM in describing protein-membrane interactions as well as further development of model membranes.
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