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

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 3JNC for the N-Ca bond are consistent with the Karplus-Bystrov relationship. It is proposed therefore that 3JNC can be used to distinguish (a) between rightand left-handed a-helices, (b) between a-helical, p-pleated sheet, and randomly coiled forms of peptides. The average 3JNC 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 3JNC and the peptide conformational potential energy map limits the possible values of the N-Ca dihedral angle 4 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.Simple accurate rules for determining details of the conformation of proteins and peptides would be of great help in understanding their chemistry. X-ray diffraction provides the type of information needed to derive such rules for materials in the crystalline form but cannot be used for those solutes which crystallize poorly or for determining the conformation of molecules in solution. Methods capable of revealing the subtle changes in conformation brought about by a change in solution environment or temperature are also needed.The requirements obviously demand a combination of techniques which give information not only on the overall size and shape of the molecule but also on local structural features. Nuclear magnetic resonance (nmr) which has the intrinsic potential of revealing something of the spatial arrangement of the immediate neighbors of any magnetic nucleus in the molecule, at present seems to be the most promising spectroscopic technique available.The difficulty in the use of nmr stems from the numbers of overlapping resonances. Although advances in resolution and sensitivity have been made re-239

Proton NMR studies on thyrotropin releasing factor

“…Let us first consider the peptide backbone: the dihedral angle corresponding to the C,H-NH coupling constant JC,H-NH (7.5-8 Hz) for histidine has been derived on the basis of Bystov et al [ 131 calculations and empirical curves, and from Gibbons et al [7] and Ramachandran et al [6] work on peptide conformations. To choose between the three possibilities offered for Cp, -ISO", -90" and +60°, Dreiding models have been made.…”

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