ArticleThe Journal of membrane biology2018
Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method.
Article in The Journal of membrane biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Melittin can permeabilize membranes via large transient pores.Nature communications · 2024Article
- Insertion and Anchoring of HIV-1 Fusion Peptide into Complex Membrane Mimicking Human T-cell.bioRxiv : the preprint server for biology · 2024Article
- Molecular Dynamics Simulations of Drug-Conjugated Cell-Penetrating Peptides.Pharmaceuticals (Basel, Switzerland) · 2023Article
- A Molecular Dynamics Study of Antimicrobial Peptide Interactions with the Lipopolysaccharides of the Outer Bacterial Membrane.The Journal of membrane biology · 2022Article
- PEO-Biomacromolecules · 2022Article
- Article
- Vectorial insertion of a β-helical peptide into membrane: a theoretical study on polytheonamide B.Biophysical journal · 2021Article
- Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes.Journal of the American Chemical Society · 2021Article
- A Global Review on Short Peptides: Frontiers and Perspectives.Molecules (Basel, Switzerland) · 2021Review
- A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins.Journal of computational chemistry · 2020Article
- Article
- Accelerating Membrane Simulations with Hydrogen Mass Repartitioning.Journal of chemical theory and computation · 2019Article
- How Melittin Inserts into Cell Membrane: Conformational Changes, Inter-Peptide Cooperation, and Disturbance on the Membrane.Molecules (Basel, Switzerland) · 2019Review
- Dropping Out and Other Fates of Transmembrane Segments Inserted by the SecA ATPase.Journal of molecular biology · 2019Article
- The importance of the membrane interface as the reference state for membrane protein stability.Biochimica et biophysica acta. Biomembranes · 2018Article
- Membrane Active Peptides and Their Biophysical Characterization.Biomolecules · 2018Review
- Lipid Membranes and Reactions at Lipid Interfaces: Theory, Experiments, and Applications.The Journal of membrane biology · 2018Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
Abstract
We show that the free energy of inserting hydrophobic peptides into lipid bilayer membranes from surface-aligned to transmembrane inserted states can be reliably calculated using atomistic models. We use two entirely different computational methods: high temperature spontaneous peptide insertion calculations as well as umbrella sampling potential-of-mean-force (PMF) calculations, both yielding the same energetic profiles. The insertion free energies were calculated using two different protein and lipid force fields (OPLS protein/united-atom lipids and CHARMM36 protein/all-atom lipids) and found to be independent of the simulation parameters. In addition, the free energy of insertion is found to be independent of temperature for both force fields. However, we find major difference in the partitioning kinetics between OPLS and CHARMM36, likely due to the difference in roughness of the underlying free energy surfaces. Our results demonstrate not only a reliable method to calculate insertion free energies for peptides, but also represent a rare case where equilibrium simulations and PMF calculations can be directly compared.
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