Predicting and interpreting EPR spectra of POPC lipid bilayers with transmembrane α-helical peptides from all-atom Molecular Dynamics simulations

Catte, Andrea and Oganesyan, Vasily (2025) Predicting and interpreting EPR spectra of POPC lipid bilayers with transmembrane α-helical peptides from all-atom Molecular Dynamics simulations. Physical Chemistry Chemical Physics. ISSN 1463-9076

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Abstract

This study reports a large-scale all-atom MD simulation of POPC lipid bilayers in the presence of different concentrations of the transmembrane peptide acetyl-K2(LA)12K2-amide ((LA)12) and doped with 5-PC paramagnetic spin probes used in EPR studies. We apply a combined MD-EPR simulation methodology for the prediction of EPR spectra directly and completely from MD trajectories. This approach serves three major purposes. Firstly, comparing predicted EPR spectra with experimental ones, which are highly sensitive to motions, provides an ultimate test bed for the force fields currently employed for modeling lipid bilayer systems with embedded proteins or peptides. Secondly, simulations of EPR spectra directly from the atomistic MD models simplify the interpretation of the EPR line shapes and their changes induced by the presence of peptides in the lipid bilayer. These changes are directly linked to the dynamics and order of spin probes and POPC host molecules. Lastly and importantly, we demonstrate how the MD-EPR methodology can be employed to test the validity and limitations of the widely used approach for the estimation of the order parameter of lipids directly from the EPR experimental line shapes.

Item Type:	Article
Faculty \ School:	Faculty of Science > School of Chemistry, Pharmacy and Pharmacology
UEA Research Groups:	Faculty of Science > Research Groups > Centre for Photonics and Quantum Science Faculty of Science > Research Groups > Chemistry of Light and Energy Faculty of Science > Research Groups > Chemistry of Life Processes Faculty of Science > Research Centres > Centre for Molecular and Structural Biochemistry
Depositing User:	LivePure Connector
Date Deposited:	17 Feb 2025 10:30
Last Modified:	22 Feb 2025 01:19
URI:	https://ueaeprints.uea.ac.uk/id/eprint/98512
DOI:	10.1039/D4CP04802D

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