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- W2057697922 abstract "Gramicidin A (gA) channels make an ideal system to test molecular dynamics (MD) of membrane proteins (and ion permeation). In addition to being one of the most highly studied membrane “proteins”, gA channels are tiny, relatively speaking, allowing for long MD runs and calculations of potential of mean force in tractable time. The structure of gA has been determined by solid-state Nuclear Magnetic Resonance (NMR) and solution-state NMR. The structures are in overall agreement, but differ slightly in backbone pitch and in a few amino acid (AA) side chains orientations. Most of these differences have been understood using MD simulations of gA channels in planar bilayers (Allen et al., J Am Chem Soc. 125:9868-77, 2003). Because the AA backbone lines the pore and tryptophan side chains are in close proximity to the permeating ion, the average structure and extent of fluctuations of all atoms in the peptide will greatly influence ion permeation. This raises the question of how well molecular mechanical force fields used in potential of mean force studies of ion permeation can reproduce experimental backbone and side chain structure and dynamics. To examine this we measured the gA channel backbone dynamics using solution state 15N-NMR on gA dimers in sodium dodecyl sulfate (SDS) micelles, in parallel with fully atomistic MD simulations on a gA dimer within an explicit SDS micelle. The methods enable us to examine the robustness of the MD simulations done under different conditions (different tryptophan force fields, with/without CMAP corrections), as well as their ability to predict the NMR observables." @default.
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- W2057697922 date "2009-02-01" @default.
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- W2057697922 title "Evaluating Gramicidin A Channel Backbone Dynamics by Molecular Dynamics and Nuclear Magnetic Resonance" @default.
- W2057697922 doi "https://doi.org/10.1016/j.bpj.2008.12.688" @default.
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