An approach to conformational analysis of peptides and proteins in solution based on a combination of nuclear magnetic resonance spectroscopy and conformational energy calculations.

Abstract

Simple criteria, based on the combined use of nmr spectral parameters and potential energy maps, are proposed for the conformational analysis of polypeptides and proteins. Experimentally determined coupling constants (3)J(NC) for the N-C(alpha) bond are consistent with the Karplus-Bystrov relationship. It is proposed therefore that (3)J(NC) can be used to distinguish (a) between right-and left-handed alpha-helices, (b) between alpha-helical, beta-pleated sheet, and randomly coiled forms of peptides. The average (3)J(NC) for the random coil is predicted. The criteria proposed are valid for both L- and D-amino acids. Correlation between the Karplus-Bystrov relationship for (3)J(NC) and the peptide conformational potential energy map limits the possible values of the N-C(alpha) dihedral angle varphi of each amino acid residue in a polypeptide and protein, and therefore presents a method of conformational analysis in solution superior to the use of either nmr or conformational maps alone. Nmr studies of hydrogen bonding or neighboring-group diamagnetic anisotropy reduce the number of possibilities consistent with the above criteria. A suggestion for evaluating the dihedral angle is presented. These criteria are useful provided the coupling constant is not obscured by line broadening.