Simulation of oriented NMR spectra: Combining molecular dynamics and chemical shift tensor calculations

Solid state NMR is widely used to study the orientation and other structural features of proteins and peptides in lipid bilayers. Using data obtained by PISEMA (Polarization Inversion Spin Exchange at Magic Angle) experiments, periodic spectral patterns arise from well-aligned alpha-helical molecules. Significant problems in the interpretation of PISEMA spectra may arise for systems that do not form perfectly defined secondary structures, like alpha-helices, or the signal pattern is disturbed by molecular motion. Here, we present a new method that combines molecular dynamics simulation with tensorial orientational constraints (MDOC) and chemical shift tensor calculations for the simulation and interpretation of PISEMA-like spectra. The calculations include the spectra arising from non alpha-helical molecules and molecules with non-uniform intrinsic mobility. In a first step, dipolar or quadrupolar interaction tensors drive molecular rotations and reorientations to obtain the proper mean values as observed in corresponding NMR experiments. In a second step, the coordinate snapshots of the MDOC simulations are geometry optimized with the isotropic N-15 chemical shifts as constraints using Bond Polarization Theory (BPT) to provide reliable N-15 CS tensor data. The averaged dipolar H-1-N-15 couplings and the delta(zz) tensor components can then be combined to simulate PISEMA patterns. We apply this method to the ss-helical peptide gramicidin A (gA) and demonstrate that this method enables the assignment of most PISEMA resonances. In addition, MDOC simulations provide local order parameters for the calculated sites. These local order parameters reveal large differences in backbone mobility between L- and D-amino acids of gA.

Automated summary

Solid state NMR is widely used for studying protein and peptide structures in lipid bilayers. This study presents a new method combining molecular dynamics simulation with tensorial orientational constraints (MDOC) and chemical shift tensor calculations for the simulation and interpretation of PISEMA-like spectra. The results demonstrate that this method enables successful assignment of PISEMA resonances and provides insights into the differences in backbone mobility between L- and D-amino acids.