Determination of the structure and dynamics of linear polypeptide gramicidin A at atomic-scale resolution

Abstract

The resonance lines of the ¹H and ¹³C liquid NMR spectra of the linear peptide antibiotic gramicidin A were assigned by performing various 2D NMR experiments such as 2D ¹H–¹³C HSQC, 2D ¹H–¹⁵N HSQC, ¹H–¹³C HMBC, ¹H–¹H COSY, and ¹H–¹H TOCSY. The spatial proximity among various protons and inter-nuclear distances were determined by a 2D ¹H–¹H NOESY NMR experiment. The detailed structure and nuclear spin dynamics of this peptide antibiotic were also determined by extracting the principal components of CSA (chemical shift anisotropy) parameters and spin-lattice relaxation times at the various ¹³C nuclear sites by applying advanced solid-state NMR methodologies. The CSA parameters were determined by employing a ¹³C 2DPASS CP-MAS SSNMR experiment; the site-specific spin-lattice relaxation time was determined by a method designed by Torchia, and the spatial proximity between ¹H and ¹³C nuclei was determined by a ¹H–¹³C PMLG HETCOR experiment. A higher degree of freedom was observed within this linear polypeptide by the spin-lattice relaxation measurements, which can be considered the origin of its antibacterial activity. The principal components of the CSA-parameters are substantially higher for the carbon-13 nuclei residing on the indole ring of the l-tryptophan amino acid residue due to magnetic shielding and deshielding effects and also due to the presence of intramolecular and intermolecular hydrogen bonds. Notably, ¹³C nuclei in the indole rings of l-tryptophan residues exhibited significantly larger values of the principal components of CSA parameters and longer spin-lattice relaxation times. These types of detailed analysis of the structure and dynamics of peptide antibiotics will augment the field of ‘NMR crystallography’ and will also serve as a foundation for formulating a new class of antimicrobial peptides.