DYNAMIC AND STRUCTURAL ELUCIDATION OF GRAMICIDIN A

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Presented here is a proposal for the continuation of a project on the gramicidin A cation channel designed to explain the detailed conductance data by the elucidation of the channel's structure and dynamics with atomic resolution. The structural aspects of the effort result from the solid state NMR determination of covalent bond orientations within the polypeptide with respect to a common axis, the magnetic field direction. From the bond orientations of adjacent groups the torsion angles are determined defining the relative orientation of these groups. Because the covalent structure is known a determination of the torsion angles (a total of 52 gramicidin) will result in an atomic resolution structure determination. Described here is such a complete structure determination. The dynamic characterization is composed of two parts; first a spatial characterization of the motion, defining the axis about which the motion occurs, the type of motion whether it is diffusional or discontinuous as in hops between potential energy minima of conformational substates, and finally the range or amplitude of the motion. Only when this spatial model for the motion is complete can an accurate determination of the frequency be made from the NMR relaxation data. A detailed description of the local dynamics for each of the 37 structural units in gramicidin connected by the 52 torsion angles is sought in this proposal. The transport function of the channel appears from computational studies to be dependent on the flexibility of the backbone. The first experimental evidence for these local motions has been achieved in the first two years of support under this grant (Nicholson et al., 1989) where a set of conformational substates for a single peptide linkage in the gramicidin backbone has been observed. The structure of this channel has not been achieved by diffraction techniques. Presented in the Progress Report of this research program is the determination of the first pair of torsion angles in the gramicidin backbone. When the structure and dynamics have been elucidated unique correlations between structure, dynamics and function will be achieve for this cation channel.