ArticleJournal of the American Chemical Society2011
In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions.
Article in Journal of the American Chemical Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Guidelines for Comparing Circular Dichroism Spectroscopy and Molecular Dynamics Simulations for Biomolecules.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Membrane Protein Folding and Biogenesis: Insights from Single-Molecule Force Spectroscopy.Chemical reviews · 2026Review
- Membrane insertion and dimerization of glycophorin-A mutations studied by free energy simulations.Biophysical journal · 2026Article
- In Silico Prediction and Validation of the Permeability of Small Molecules Across the Blood-Brain Barrier.International journal of molecular sciences · 2026Article
- Spatially regulated mRNA translation enables functional membrane protein integration in synthetic cells.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Physics-based evolution of transmembrane helices reveals mechanisms of cholesterol attraction.Nature communications · 2025Article
- Unidirectional Transmembrane Photoinduced Electron Transfer with Artificial Metallopeptides.Artificial photosynthesis (Washington, D.C.) · 2025Article
- The difference between MelP5 and melittin membrane poration.Scientific reports · 2025Article
- Transmembrane Parkinson's disease mutation of PINK1 leads to altered mitochondrial anchoring.The Journal of biological chemistry · 2025Article
- Melittin can permeabilize membranes via large transient pores.Nature communications · 2024Article
- Antibacterial and Antiviral Properties of Chenopodin-Derived Synthetic Peptides.Antibiotics (Basel, Switzerland) · 2024Article
- A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood-brain barrier endothelium.Journal of computer-aided molecular design · 2023Article
- Three-stage model of helical membrane protein folding: Role of membrane-water interface as the intermediate stage vestibule for TM helices during their in membrano assembly.Biochemical and biophysical research communications · 2022Article
- Integrated Design of a Membrane-Lytic Peptide-Based Intravenous Nanotherapeutic Suppresses Triple-Negative Breast Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Untangling the complexity of membrane protein folding.Current opinion in structural biology · 2022Review
- Vectorial insertion of a β-helical peptide into membrane: a theoretical study on polytheonamide B.Biophysical journal · 2021Article
- Cotranslational recruitment of ribosomes in protocells recreates a translocon-independent mechanism of proteorhodopsin biogenesis.iScience · 2021Article
- Article
- Towards a Quantitative Understanding of Protein-Lipid Bilayer Interactions at the Single Molecule Level: Opportunities and Challenges.The Journal of membrane biology · 2021Review
- Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition.The Journal of membrane biology · 2021Article
3 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
Nascent transmembrane (TM) polypeptide segments are recognized and inserted into the lipid bilayer by the cellular translocon machinery. The recognition rules, described by a biological hydrophobicity scale, correlate strongly with physical hydrophobicity scales that describe the free energy of insertion of TM helices from water. However, the exact relationship between the physical and biological scales is unknown, because solubility problems limit our ability to measure experimentally the direct partitioning of hydrophobic peptides across lipid membranes. Here we use microsecond molecular dynamics (MD) simulations in which monomeric polyleucine segments of different lengths are allowed to partition spontaneously into and out of lipid bilayers. This approach directly reveals all states populated at equilibrium. For the hydrophobic peptides studied here, only surface-bound and transmembrane-inserted helices are found. The free energy of insertion is directly obtained from the relative occupancy of these states. A water-soluble state was not observed, consistent with the general insolubility of hydrophobic peptides. The approach further allows determination of the partitioning pathways and kinetics. Surprisingly, the transfer free energy appears to be independent of temperature, which implies that surface-to-bilayer peptide insertion is a zero-entropy process. We find that the partitioning free energy of the polyleucine segments correlates strongly with values from translocon experiments but reveals a systematic shift favoring shorter peptides, suggesting that translocon-to-bilayer partitioning is not equivalent but related to spontaneous surface-to-bilayer partitioning.
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