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- W2895589968 abstract "The membrane alignment of helical amphiphilic peptides in oriented phospholipid bilayers can be obtained as ensemble and time averages from solid state 2H NMR by fitting the quadrupolar splittings to ideal α-helices. At the same time, molecular dynamics (MD) simulations can provide atomistic insight into peptide–membrane systems. Here, we evaluate the potential of MD simulations to complement the experimental NMR data that is available on three exemplary systems: the natural antimicrobial peptide PGLa and the two designer-made peptides MSI-103 and KIA14, whose sequences were derived from PGLa. Each peptide was simulated for 1 μs in a DMPC lipid bilayer. We calculated from the MD simulations the local angles which define the side chain geometry with respect to the peptide helix. The peptide orientation was then calculated (i) directly from the simulation, (ii) from back-calculated MD-derived NMR splittings, and (iii) from experimental 2H NMR splittings. Our findings are that (1) the membrane orientation and secondary structure of the peptides found in the NMR analysis are generally well reproduced by the simulations; (2) the geometry of the side chains with respect to the helix backbone can deviate significantly from the ideal structure depending on the specific residue, but on average all side chains have the same orientation; and (3) for all of our peptides, the azimuthal rotation angle found from the MD-derived splittings is about 15° smaller than the experimental value." @default.
- W2895589968 created "2018-10-12" @default.
- W2895589968 creator A5026196545 @default.
- W2895589968 creator A5037635585 @default.
- W2895589968 creator A5047628202 @default.
- W2895589968 creator A5071855862 @default.
- W2895589968 creator A5072002304 @default.
- W2895589968 date "2018-10-05" @default.
- W2895589968 modified "2023-10-17" @default.
- W2895589968 title "Best of Two Worlds? How MD Simulations of Amphiphilic Helical Peptides in Membranes Can Complement Data from Oriented Solid-State NMR" @default.
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- W2895589968 doi "https://doi.org/10.1021/acs.jctc.8b00283" @default.
- W2895589968 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/30289704" @default.