Gramicidin A Backbone and Side Chain Dynamics Evaluated by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Experiments. II: Nuclear Magnetic Resonance Experiments
by Vostrikov, V. V.; Gu, H.; Ingolfsson, H. I.; Hinton, J. F.; Andersen, O. S.; Roux, B.; Koeppe, R. E.
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 N-15 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 N-15 NMR spectra for labeled gA samples incorporated in sodium dodecylsulfate (SDS) micelles, we determined T-1, T-2 and heteronuclear NOE values for backbone and indole (NH)-N-15 groups. The results indicate that the SDS-incorporated g,A 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).