CHAPTER 2: Combining NMR Spectroscopic Measurements and Molecular Dynamics Simulations to Determine the Orientation of Amphipathic Peptides in Lipid Bilayers
Published:24 Feb 2014
B. S. Perrin Jr., R. W. Pastor, and M. Cotten, in Advances in Biological Solid-State NMR: Proteins and Membrane-Active Peptides, ed. F. Separovic and A. Naito, The Royal Society of Chemistry, 2014, pp. 18-35.
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Determining the orientation of an amphipathic α-helix in a lipid bilayer can be achieved indirectly with oriented sample solid-state NMR or directly by molecular dynamics (MD) simulations. In a peptide plane, both the 1H–15N dipolar coupling (DC) and 15N chemical shift (CS) tensors are sensitive to orientation with respect to the static magnetic field. Two-dimensional separated local field spectra from α-helices display ellipsoidal patterns called PISA wheels. Plotting DNH or CS values from these spectra as a function of residue number produces sinusoidal waves. PISA wheels, dipolar waves and CS waves each give the orientation of the α-helix in the bilayer; however, this is not always accurate. A bias in orientation due to dynamic fluctuations in tilt was demonstrated for transmembrane peptides studied using PISA wheels. Here, the ambiguity associated with the use of dipolar and CS waves is presented for piscidin, an antimicrobial peptide. The dipolar and CS wave-fit analysis resulted in multiple solutions for the peptide orientation and MD was used to identify the more probable value. Since the NMR observables can be affected by peptide dynamics, the effect on the NH bond order parameter is explored and the implications for determination of peptide structures are discussed.