ReviewThe Journal of membrane biology2011
Arginine in membranes: the connection between molecular dynamics simulations and translocon-mediated insertion experiments.
Review in The Journal of membrane biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed, 111 citations in OpenAlex.
- Membrane-Traversing Peptides: Mechanistic Landscapes, Assays, and Applications.Chemical reviews · 2026Review
- Thermodynamics of arginine interactions with organic phosphates.Biophysical journal · 2025Article
- An ultra-rare missense variant in the KIF1B gene linked to autoinflammatory Menière's disease.NPJ genomic medicine · 2025Article
- Not All Bacterial Outer-Membrane Proteins Are β-Barrels.microPublication biology · 2025Article
- Discovery and Mechanism of Action of a Novel Antimicrobial Peptide from an Earthworm.Microbiology spectrum · 2023Article
- Amphiphilic Gold Nanoparticles: A Biomimetic Tool to Gain Mechanistic Insights into Peptide-Lipid Interactions.Membranes · 2022Review
- Differential Pathomechanisms of Desmoglein 1 Transmembrane Domain Mutations in Skin Disease.The Journal of investigative dermatology · 2022Article
- Characterization of the Features of Water Inside the SecY Translocon.The Journal of membrane biology · 2021Review
- Thermodynamics and Mechanism of the Membrane Permeation of Hv1 Channel Blockers.The Journal of membrane biology · 2021Article
- Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network.Frontiers in molecular biosciences · 2021Article
- Using Simulation to Understand the Role of Titration on the Stability of a Peptide-Lipid Bilayer Complex.Langmuir : the ACS journal of surfaces and colloids · 2020Article
- A dynamic anchor domain in slc13 transporters controls metabolite transport.The Journal of biological chemistry · 2020Article
- How We Came to Understand the "Tumultuous Chemical Heterogeneity" of the Lipid Bilayer Membrane.The Journal of membrane biology · 2020Review
- Influence of Lipid Saturation, Hydrophobic Length and Cholesterol on Double-Arginine-Containing Helical Peptides in Bilayer Membranes.Chembiochem : a European journal of chemical biology · 2019Article
- Membrane Protein Integration and Topogenesis at the ER.The protein journal · 2019Review
- The desmosome is a mesoscale lipid raft-like membrane domain.Molecular biology of the cell · 2019Article
- Macromolecular-clustered facial amphiphilic antimicrobials.Nature communications · 2018Article
- The importance of the membrane interface as the reference state for membrane protein stability.Biochimica et biophysica acta. Biomembranes · 2018Article
- Article
- Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method.The Journal of membrane biology · 2018Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
Several laboratories have carried out molecular dynamics (MD) simulations of arginine interactions with lipid bilayers and found that the energetic cost of placing arginine in lipid bilayers is an order of magnitude greater than observed in molecular biology experiments in which Arg-containing transmembrane helices are inserted across the endoplasmic reticulum membrane by the Sec61 translocon. We attempt here to reconcile the results of the two approaches. We first present MD simulations of guanidinium groups alone in lipid bilayers, and then, to mimic the molecular biology experiments, we present simulations of hydrophobic helices containing single Arg residues at different positions along the helix. We discuss the simulation results in the context of molecular biology results and show that the energetic discrepancy is reduced, but not eliminated, by considering free energy differences between Arg at the interface and at the center of the model helices. The reduction occurs because Arg snorkeling to the interface prevents Arg from residing in the bilayer center where the energetic cost of desolvation is highest. We then show that the problem with MD simulations is that they measure water-to-bilayer free energies, whereas the molecular biology experiments measure the energetics of partitioning from translocon to bilayer, which raises the fundamental question of the relationship between water-to-bilayer and water-to-translocon partitioning. We present two thermodynamic scenarios as a foundation for reconciliation of the simulation and molecular biology results. The simplest scenario is that translocon-to-bilayer partitioning is independent of water-to-bilayer partitioning; there is no thermodynamic cycle connecting the two paths.
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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.