<abstract xmlns="http://www.w3.org/1999/xhtml">

<p>Biological membranes are complex systems due to their composition and dynamics. Therefore, membrane mimetics are widely used to investigate lipid properties and interactions between molecules and membrane lipids. Using all-atom molecular dynamics simulations, within this study two systems composed of different membrane mimetics are compared: a 1-palmitoyl-2-oleoyl-3-glycero-phosphatidylcholine (POPC) bilayer or a dodecylphosphocholine (DPC) micelle and a nonapeptide (V94-T-K-Y-W-F-Y-R-L102). Previous <sup>1</sup>H-NMR experiments have demonstrated that, in the presence of DPC micelles, this peptide folds as a stable amphipathic helix located in the polar head group region with the tryptophan residue pointing toward the inside of the micelle. The present comparison reveals a hydrophobic surface twice as large for the micelle as for the bilayer and a different arrangement of the acyl chains. The peptide secondary structure is not strongly affected by the membrane mimetics whereas the peptide is more deeply inserted in the bilayer than in the micelle. The contacts between the peptide and the DPC or POPC molecules are analysed and although the distances and lifetimes of these contacts are very different in the micelle and the bilayer, similar specific interactions were found that mainly involved the side chains of the residues R101 and L102.</p>
</abstract>

Biological membranes are complex systems due to their composition and dynamics. Therefore, membrane mimetics are widely used to investigate lipid properties and interactions between molecules and membrane lipids. Using all-atom molecular dynamics simulations, within this study two systems composed of different membrane mimetics are compared: a 1-palmitoyl-2-oleoyl-3-glycero-phosphatidylcholine (POPC) bilayer or a dodecylphosphocholine (DPC) micelle and a nonapeptide (V94-T-K-Y-W-F-Y-R-L102). Previous 1H-NMR experiments have demonstrated that, in the presence of DPC micelles, this peptide folds as a stable amphipathic helix located in the polar head group region with the tryptophan residue pointing toward the inside of the micelle. The present comparison reveals a hydrophobic surface twice as large for the micelle as for the bilayer and a different arrangement of the acyl chains. The peptide secondary structure is not strongly affected by the membrane mimetics whereas the peptide is more deeply inserted in the bilayer than in the micelle. The contacts between the peptide and the DPC or POPC molecules are analysed and although the distances and lifetimes of these contacts are very different in the micelle and the bilayer, similar specific interactions were found that mainly involved the side chains of the residues R101 and L102.

Comparative analysis of a POPC bilayer and a DPC micelle comprising an interfacial anchored peptide using all-atom MD simulations

Department of Medicine, Division of Hematology / Oncology

Department of Biology-Chemistry and Advanced Environmental Research Laboratories

Ovidius University Annals of Chemistry

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Biological membranes are complex systems due to their composition and dynamics. Therefore, membrane mimetics are widely used to investigate lipid properties...

Comparative analysis of a POPC bilayer and a DPC micelle comprising an interfacial anchored peptide using all-atom MD simulations

Published Online: Jan 11, 2024

Page range: 121 - 131

Received: Sep 05, 2023

Accepted: Dec 09, 2023

DOI: https://doi.org/10.2478/auoc-2023-0016

Keywords
membrane, interactions peptide-lipids, secondary structure, dynamics

© 2023 Nahuel Perrot et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Comparative analysis of a POPC bilayer and a DPC micelle comprising an interfacial anchored peptide using all-atom MD simulations

Published Online: Jan 11, 2024

Page range: 121 - 131

Received: Sep 05, 2023

Accepted: Dec 09, 2023

DOI: https://doi.org/10.2478/auoc-2023-0016

Keywordsmembrane, interactions peptide-lipids, secondary structure, dynamics

© 2023 Nahuel Perrot et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Keywords
membrane, interactions peptide-lipids, secondary structure, dynamics