NMR parameters for conformational

We first describe the NMR parameters for the duplex to strand transition of the synthetic DNA poly(dA-dT) (18) with occasional reference to poly(dA-dU) (24) and poly(dA- brdU) and the corresponding synthetic RNA poly(A-U) (24). This is followed by a comparison of the NMR parameters of the synthetic DNA in the presence of 1 M Na ion and 1 M tetramethylammonium ion in an attempt to investigate the effect of counterion on the conformation and stability of DNA. We next outline structural and dynamical aspects of the complexes of poly(dA-dT) with the mutagen proflavine (25) and the anti-tumor agent daunomycin (26) which intercalate between base pairs and the peptide antibiotic netropsin (27) which binds in the groove of DNA. 

The research below focusses on the NMR parameters for poly(dA-dT) in 1 M tetramethylammonium chloride (TMA+) relative to their value in the same concentration of sodium chloride. The methyl groups shield the charged nitrogen in the TMA+ ion and it was of interest to determine whether conformational changes occur in the synthetic DNA when the counterion was changed from Na+ to TMA+. 

A comparison of the NMR parameters for (T>4-butadiene)M(CO)s (where M is Fe or Ru), carried out by von Philipsbom and co-workers (54, 55), provides an excellent example of the potential of a complete spectral analysis (Fig. 6). Values for the vicinal C—H and H—H couplings have been extracted and used to deduce the conformation of the complexed ligand. The authors conclude that the carbon skeleton is coplanar, that the... 

Finally, it can be concluded that the chemical shift contour maps are very useful for predicting the dihedral angles , if/) of polypeptides and proteins in the solid state through the shifts of the amide carbonyl carbons of the Gly, L-Ala, n-Leu, L-Val and L-Asp residues. From the above-mentioned results, it has been demonstrated that the NMR chemical shift is a very powerful NMR parameter for obtaining the conformational characterization of solid polypeptides and proteins, and it is greatly enhanced by combining with chemical shift calculations. It has been described elsewhere... 

Despite the extremely wide use of multi-dimensional NMR techniques for conformational studies of biological macromolecules, at present, only a small part of the information contained in the NMR spectrum can be used for structure determination [118,119]. The reason is that there are no well-established correlations between NMR chemical shifts and the structural parameters [118] and only a few useful correlations besides Karplus relations [120,121] for nuclear spin-spin coupling constants. As a consequence, a great deal of important information about the system is not available without turning to quantum chemical approaches for the theoretical interpretation. 

The NMR parameters for the determination of conformation have all been introduced in Sect. 2. To translate them into conformation of biomolecules, two protocols have survived and are applied in general. One is the dis-... 

The conformational description suggested in this Viork is succinct and unequivocal. The use of the notation for analysis of NMR parameters for each bond (eg, J has been developed in a recent review... 

Fig. 1 Solid-state NMR structure analysis relies on the 19F-labelled peptides being uniformly embedded in a macroscopically oriented membrane sample, (a) The angle (0) of the 19F-labelled group (e.g. a CF3-moiety) on the peptide backbone (shown here as a cylinder) relative to the static magnetic field is directly reflected in the NMR parameter measured (e.g. DD, see Fig. 2c). (b) The value of the experimental NMR parameter varies along the peptide sequence with a periodicity that is characteristic for distinct peptide conformations, (c) From such wave plot the alignment of the peptide with respect to the lipid bilayer normal (n) can then be evaluated in terms of its tilt angle (x) and azimuthal rotation (p). Whole-body wobbling can be described by an order parameter, S rtlo. (d) The combined data from several individual 19F-labelled peptide analogues thus yields a 3D structural model of the peptide and how it is oriented in the lipid bilayer...

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