title: Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. II: nuclear magnetic resonance experiments.
abstract: 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 (15)N 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 (15)N 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 (15)NH 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 ).
authors.affiliation: Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States.
authors.forename: Vitaly V
authors.initials: VV
authors.lastname: Vostrikov
authors.forename: Hong
authors.initials: H
authors.lastname: Gu
authors.forename: Helgi I
authors.initials: HI
authors.lastname: Ingólfsson
authors.forename: James F
authors.initials: JF
authors.lastname: Hinton
authors.forename: Olaf S
authors.initials: OS
authors.lastname: Andersen
authors.forename: Benoît
authors.initials: B
authors.lastname: Roux
authors.forename: Roger E
authors.initials: RE
authors.lastname: Koeppe
mesh_terms: D000595:Amino Acid Sequence; D019281:Dimerization; D006096:Gramicidin / Q000737:chemistry*; D007211:Indoles / Q000737:chemistry; D008823:Micelles; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D012967:Sodium Dodecyl Sulfate / Q000737:chemistry
chemical_list: D007211:Indoles; D008823:Micelles; D006096:Gramicidin; D012967:Sodium Dodecyl Sulfate; C030374:indole