Biomedical subjects

N J Clayden

Publications and source records attributed to N J Clayden.

7 recordsLinked to original sources

PubMed1992

13C-CP/MAS NMR studies of the cyclomalto-oligosaccharide (cyclodextrin) hydrates.

The 13C-CP/MAS NMR spectra of cyclomaltohexaose (alpha-cyclodextrin) hexahydrate, cyclomaltoheptaose (beta-cyclodextrin) "undecahydrate", cyclomalto-octaose (gamma-cyclodextrin) "octadecahydrate", and of the same materials at lower levels of hydration are compared with solution NMR data, structures obtained from single crystal diffraction studies, and with previous reports of the 13C-CP/MAS NMR spectra. The chemical shifts of the C-1 and C-4 resonances can be correlated with the conformation about the (1----4) linkage. The chemical shifts of the C-6 resonances are also sensitive to hydrogen-bonding interactions, as shown by the spectral changes on loss of water from the structures. The results suggest that, for resonances of carbon atoms close to a centre of significant conformational change, chemical shifts may be predicted on the basis of conformation alone, but for the resonances of more distant atoms, changes in chemical shift due to conformational change may be masked by the effects of alterations in the local environment.

Carbohydrate Sequence↗

PubMed1985

Comparison of the solution and crystal structures of mitochondrial cytochrome c. Analysis of paramagnetic shifts in the nuclear magnetic resonance spectrum of ferricytochrome c.

The two accompanying papers describe the assignment of methyl-containing spin-systems in the 1H nuclear magnetic resonance spectra of tuna ferricytochrome c and tuna ferrocytochrome c. At present, 104 resonances from 208 C-H protons are assigned in both oxidation states. In this paper, the difference in chemical shift of a resonance between the two oxidation states is used together with a dipolar model of the unpaired electron spin of ferricytochrome c to compare the structure of cytochrome c in solution with three high-resolution structures of cytochrome c obtained by X-ray diffraction in single crystals. The overall protein fold and the positions of most of the haem-packing residues are shown to be invariant between the crystal and solution. However, three regions of the protein, at the C terminus, around the haem propionic acid groups and at the haem crevice near thioether-2, are found to undergo conformational changes on the removal of crystal packing constraints.

Amino Acid Sequence↗

PubMed1982

Dynamics of erabutoxin b as studied by nuclear magnetic resonance. Relaxation studies of methyl proton resonances.

Longitudinal and transverse relaxation times were measured for well-resolved and assigned methyl proton resonances of erabutoxin b at 270 MHz, 300 MHz and 500 MHz. Both longitudinal and transverse magnetization decay curves are non-exponential due to cross-relaxation and cross-correlation effects. The longitudinal and transverse relaxation rates were obtained from the initial slope of both magnetization decay curves. The correlation times for the isotropic tumbling motion of the protein were determined to be 2.82 ns at 300 K and 1.62 ns at 330 K from the analysis of the relaxation data of some alpha protons. Using these values, the relaxation data of methyl protons were fitted to various theoretical models. Most of the methyl resonances could be fitted well to a model which allowed methyl rotation (in the range 0.01-0.05 ns) and an external contribution from protons assumed to be in positions derived from X-ray coordinates. The data for a few methyl groups, however, could not be fitted in this way. For these a smaller number of external protons than predicted by the X-ray coordinates was assumed. Additionally, a larger amplitude motion had to be introduced into the model for particular residues. This additional motion requires concerted protein motion close to these residues, since the X-ray structure suggests that steric hindrance would prevent local motion. These results are consistent with the idea of a flexible and dynamic structure for proteins.

Elapid Venoms↗

PubMed1982

Metal coordination centres of class II cytochromes c.

The class II cytochromes Rhodospirillum molischianum cytochrome c', Rhodopseudomonas palustris cytochrome C556 and Agrobacterium tumefaciens (B2a) cytochrome c556 have been investigated with a variety of spectroscopic techniques. The cytochrome c' was found to be high-spin and the two cytochromes c556 were found to be mainly low-spin and sx-coordinate with the fifth and sixth ligands being histidine and methionine. The implications of the different types of iron coordination are discussed.

Cytochrome c Group↗

PubMed1982

Individual assignments of the amide proton resonances involved in the triple-stranded antiparallel pleated beta-sheet structure of a long neurotoxin, Laticauda semifasciata III from Laticauda semifasciata.

THe characteristic feature of the crystal structure of erabutoxin b, a short neurotoxin from Laticauda semifasciata, and alpha-cobratoxin, a long neurotoxin from Naja naja siamensis, is the presence of a triple-stranded antiparallel pleated beta-sheet structure formed by the central and the third peptide loops. In the present study, we have studied the assignment of slowly exchangeable amide protons of Laticauda semifasciata III from L. semifasciata, using nuclear Overhauser effects (NOE) and spin-decoupling methods. The results show that nearly all of the slowly exchangeable amide protons are to be assigned to the back-bone amide protons, involved in the triple-stranded antiparallel pleated beta-sheet structure, indicating that this sheet is stable in 2H2O solution. In contrast, the amide protons in short neurotoxins are readily exchangeable under the same experimental condition, suggesting that long neurotoxins have a more rigid sheet structure than short ones. This rigidity may come from the hydrophobic and hydrogen bond interaction between the central loop and the tail, which is not present in short neurotoxins. Since the functionally important residues are located on this beta-sheet, the different kinetic properties of the neurotoxins are well correlated with the difference in the rigidity of the beta-sheet.

Amines↗

PubMed1982

Two-dimensional NMR spectroscopy of siomycin A. Proton--carbon-13 chemical shift correlation.

A trial application of a recent two-dimensional nuclear magnetic resonance experiment to the polypeptide antibiotic siomycin A is described. Proton--carbon-13 chemical shift correlation measures the proton and carbon-13 chemical shift for each directly bonded CH group in a molecule, in a single experiment. The resultant map of correlated chemical shifts enables the carbon-13 spectrum to be assigned directly from the known proton shifts, and allows individual proton signals to be identified without problems of overlap. The signal-to-noise ratio available from such techniques should enable their application to aqueous protein solutions using currently available high-field spectrometers.

Anti-Bacterial Agents↗

PubMed1981

A proton-magnetic-resonance study on the molecular conformation and structure-function relationship of a long neurotoxin, laticauda semifasciata III from Laticauda semifasciata.

The 300-MHz and 500-MHz NMR spectra of a long neurotoxin laticauda semifasciata III (LS III) from Laticauda semifasciata have ben analysed. Comparison with the NMR spectra of alpha-cobratoxin from Naja naja siamensis, a homologous long neurotoxin to laticauda semifasciata III, allowed the assignment of all the aromatic protein resonances to specific amino acid residues. All the methyl proton resonances have been assigned to specific types of amino acid residues. The pH dependences of the aromatic and methyl proton chemical shifts were analyzed by the non-linear least-square method to give the pKa values and protonation shifts. The interproton nuclear Overhauser effect enhancements were measured in order to elucidate the spatial proximity of the methyl-bearing residues and aromatic residues. On the basis of these NMR data and using the crystal structure of alpha-cobratoxin by Walkinshaw et al., more than half of the methyl proton resonances have been assigned to specific amino acid residues. A hydrophobic core comprising the first loop, the central loop and the tail part of the molecule has been defined. This hydrophobic core may be common to all long neurotoxins and may protect the three-stranded antiparallel pleated beta-sheet structure, thus making the backbone structure of long neurotoxins more rigid than that of short neurotoxins. The positively charged surface of laticauda semifasciata III, which is responsible for binding to the acetylcholine receptor protein, is confirmed as the concave surface formed by the central and the third loop. The arrangement of the amino acid residues on this surface is similar to that of all other neurotoxins. Accordingly, the slow on-off rates of association of long neurotoxins with receptor is considered to arise from the rigid backbone structure. A small conformation change is thought to be associated with binding to the receptor protein.

Amino Acid Sequence↗