Dynamic structure of the polytheonamide B channel studied by normal mode analysis

Polytheonamide B is a linear 48-residue peptide with alternating D- and L-amino acids. It forms a single beta(6.3)-helix structure and acts as a cation-selective ion channel. We performed normal mode analysis to investigate the dynamical properties of the polytheonamide B channel. We calculated root-mean-square (RMS) displacements of all backbone atoms, RMS fluctuations of the backbone dihedral angles phi and psi, and correlation factors for the C-alpha atom and for dihedral angle fluctuations. The analysis revealed that polytheonamide B has elastic rod properties in very low-frequency modes and that the librational motions of backbone amide planes have the modes with relatively low frequencies, which is relevant to the function of polytheonamide B. The librational motions occur almost independently and are weakly anti-correlated with those of the neighbouring hydrogen-bonded amide planes. Backbone fluctuations show that polytheonamide B is roughly uniformly flexible over the entire helix. We also compared our results with those of gramicidin A, an analogue of polytheonamide B and found some common features in the dynamics of the 'channel wall'. It was suggested that polytheonamide B utilises similar mechanisms to gramicidin A for conducting cations across the membrane.