Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. II: Nuclear magnetic resonance experiments

Motional properties are important for understanding protein function and are accessible to NMR relaxation measurements. The goal of this study is to investigate the internal dynamics occurring in gramicidin A (gA) channels in order to provide benchmark experimental data for comparison with the results of molecular dynamics simulations. We therefore synthesized several ¹⁵N isotope-enriched gA samples, covering all backbone residues as well as the Trp indole side chains for NMR relaxation experiments. On the basis of the ¹⁵N NMR spectra for labeled gA samples incorporated in sodium dodecylsulfate (SDS) micelles, we determined T₁, T₂, and heteronuclear NOE values for backbone and indole ¹⁵NH groups. The results indicate that the SDS-incorporated gA channel is a constrained structure without an especially "floppy" region. The NMR observables, particularly those for backbone groups, are predicted well by the molecular dynamics simulations in the accompanying article (DOI 10.1021/jp200904d).