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

We report an approach to determining membrane peptides and membrane 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^α, C^β, and C' chemical shifts were selected from the ensemble. The ¹³C^α chemical shifts alone were sufficient for the selection with backbone rmsd's 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 side chain 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.