Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide.
Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide.
J Phys Chem B. 2011 Jun 13;
Authors: Ikeda K, Kameda T, Harada E, Akutsu H, Fujiwara T
We report an approach to determining membrane-peptides and -protein complex structures by magic-angle-spinning solid-state NMR and molecular dynamics simulation. First, an ensemble of low energy structures of mastoparan-X, a wasp venom peptide, in lipid bilayers was generated by replica-exchange molecular dynamics (REMD) simulation with the implicit membrane/solvent model. Next, peptide structures compatible with experimental 13C?, C? and C' chemical shifts were selected from the ensemble. The 13C? chemical shifts alone were sufficient for the selection with backbone RMSDs of ~0.8 Å from the experimentally determined structure. The dipolar couplings between the peptide protons and lipid 2H/31P nuclei were obtained from the 13C-observed 2H/31P-selective 1H-demagnetization experiments for selecting the backbone and sidechain structures relative to the membrane. The simulated structure agreed with the experimental one in the depth and orientation. The REMD simulation can be used for supplementing the limited structural constraints obtainable from the solid-state NMR spectra.
PMID: 21668001 [PubMed - as supplied by publisher]
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PubMed