Approximate treatment of the conformational characteristics of a cyclic nonapeptide, cyclolinopeptide a.
Possible conformations for a cyclic nonapeptide that are consistent with conformation-dependent information obtained from an NMR investigation of the peptide in solution are presented. These several conformations are deduced from the myriad of possible conformations by eliminating from consideration all cyclic species having one or more residues in a conformation that does not correspond to the vicinal coupling constants observed by NMR between the amide and alpha-protons. A Karplus-like relation connecting the dihedral angle [unk]' and the vicinal coupling J(Nalpha) between N-H and C(alpha)-H(alpha) is used to test this correspondence. A further reduction in the number of cyclic conformations under consideration is made possible by rejecting the conformations that have a high intramolecular conformational energy. The intramolecular conformational energy of the cyclic nonapeptide is estimated by summing the independent residue energies. These have been calculated by others with approximate potential functions to account for the intrinsic torsional potentials and the nonbonded steric (6-12 potential) and electrostatic (monopole-monopole) interactions solely dependent upon one or both of the residue rotations, [unk] and Psi, about the N-C(alpha) and C(alpha)-C bonds, respectively.
Tonelli
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