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

Overview

MeSH Major

  • Gramicidin
  • Molecular Dynamics Simulation

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 ).

publication date

  • June 9, 2011

Research

keywords

  • Academic Article

Identity

Language

  • eng

PubMed Central ID

  • PMC3114435

Digital Object Identifier (DOI)

  • 10.1021/jp200906y

PubMed ID

  • 21574558

Additional Document Info

start page

  • 7427

end page

  • 32

volume

  • 115

number

  • 22