The dynamic nature of gramicidin

Abstract

Publisher Summary This chapter discusses the nature of gramicidin. Gramicidin is a small, hydrophobic polypeptide consisting of fifteen amino acids. An unusual feature of this peptide is the alternating L-,D-configuration of its amino acids. The unusual L-,D-configuration of the amino acids means that gramicidin is unable to adopt the standard types of protein secondary structures such as a-helices, p-sheets, or turns. In addition, its small size allows it to adopt many different conformations in various environments. In the organic solvent methanol, gramicidin exists as four distinct dimer conformations that differed from one another in helical sense and chain orientation. This equilibrium mixture, which can be separated by chromatographic techniques and the individual conformers stabilized in dioxane, was also found to exist in other alcohols. Veatch and his colleagues characterized these by circular dichroism spectroscopy (CD), nuclear magnetic resonance spectroscopy (NMR), and infrared spectroscopy (IR) and proposed models to account for their experimental observations. They suggested that gramicidin could form either parallel or antiparallel, left- or right-handed inter-twined double helices with the two monomers joined together in a β-sheet like hydrogen bonding pattern. Their predictions were later confirmed by Bystrov and Arseniev using 2D-NMR. They found that in ethanol, the short-range proton–proton distances matched those calculated from four models: two parallel left-handed double helices that differ in chain overlap, one left-handed antiparallel double helix, and a right-handed antiparallel double helix.