ArticleThe journal of physical chemistry. B2017
Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents.
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 19 papers.
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Who cites it
19 citing papers in PubMed, 31 citations in OpenAlex.
- 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
- Differences and Similarities in Protein and Nucleic Acid Structures and Their Biological Interactions.Current issues in molecular biology · 2025Review
- CaThe journal of physical chemistry. B · 2025Article
- Cholesterol-targeting Wnt-β-catenin signaling inhibitors for colorectal cancer.Nature chemical biology · 2025Article
- Molecular dynamics simulations of biological membranes and membrane-associated phenomena across scales.Current opinion in structural biology · 2025Review
- Restricted Surface Diffusion of Cytochromes on Bioenergetic Membranes with Anionic Lipids.Membranes · 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
- Atomistic characterization of β2-glycoprotein I domain V interaction with anionic membranes.Journal of thrombosis and haemostasis : JTH · 2024Article
- Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM.PLoS computational biology · 2024Article
- Improved Highly Mobile Membrane Mimetic Model for Investigating Protein-Cholesterol Interactions.Journal of chemical information and modeling · 2024Article
- Membrane binding and lipid-protein interaction of the C2 domain from coagulation factor V.Current research in structural biology · 2024Article
- Molecular View into Preferential Binding of the Factor VII Gla Domain to Phosphatidic Acid.Biochemistry · 2022Article
- PIPBiophysical journal · 2021Article
- Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.Biophysical journal · 2020Article
- Computer simulations of protein-membrane systems.Progress in molecular biology and translational science · 2020Article
- 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
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The mechanics of the protein-lipid interactions of transmembrane proteins are difficult to capture with conventional atomic molecular dynamics, due to the slow lateral diffusion of lipids restricting sampling to states near the initial membrane configuration. The highly mobile membrane mimetic (HMMM) model accelerates lipid dynamics by modeling the acyl tails nearest to the membrane center as a fluid organic solvent while maintaining an atomic description of the lipid headgroups and short acyl tails. The HMMM has been applied to many peripheral protein systems; however, the organic solvent used to date caused deformations in transmembrane proteins by intercalating into the protein and disrupting interactions between individual side chains. We ameliorate the effect of the solvent on transmembrane protein structure through the development of two new in silico Lennard-Jones solvents. The parameters for the new solvents were determined through an extensive parameter search in order to match the bulk properties of alkanes in a highly simplified model. Using these new solvents, we substantially improve the insertion free energy profiles of 10 protein side chain analogues across the entire bilayer. In addition, we reduce the intercalation of solvent into transmembrane systems, resulting in native-like transmembrane protein structures from five different topological classes within a HMMM bilayer. The parametrization of the solvents, in addition to their computed physical properties, is discussed. By combining high lipid lateral diffusion with intact transmembrane proteins, we foresee the developed solvents being useful to efficiently identify membrane composition inhomogeneities and lipid binding caused by the presence of membrane proteins.
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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.