Paper Citing NAMD - Abstract
Hansen, Sara K.; Vestergaard, Mikkel; Thogersen, Lea; Schiott, Birgit; Nielsen, Niels Chr.; Vosegaard, Thomas
Lipid Dynamics Studied by Calculation of P-31 Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5119-5129, MAY 15 2014
We present a method to calculate P-31 solid-state NMR spectra based on the dynamic input from extended molecular dynamics (MD) simulations. The dynamic information confered by MD simulations is much more comprehensive than the information provided by traditional NMR dynamics models based on, for example, order parameters. Therefore, valuable insight into the dynamics of biomolecules may be achieved by the present method. We have applied this method to study the dynamics of lipid bilayers containing the antimicrobial peptide alamethicin, and we show that the calculated P-31 spectra obtained with input from MD simulations are in agreement with experiments under a large range of different sample conditions, including vesicles and oriented samples with and without peptides. We find that the changes in the P-31 spectra upon addition of peptide stem from lipids with reduced diffusion due to peptide lipid interactions.
