Biomedical subjects

A E Torda

Publications and source records attributed to A E Torda.

6 recordsLinked to original sources

PubMed1991

On deriving spatial protein structure from NMR or X-ray diffraction data.

During the last decade it has become possible to derive the spatial structure of small proteins in solution using multidimensional NMR spectroscopy measurements and interpreting the data in terms of a chemical atomic model. The NMR experiments generate a set of interproton distance constraints, which is subsequently used to generate spatial structures that satisfy the experimental data. Correspondingly, crystallographic least-squares and molecular dynamics refinement is routinely applied to obtain a protein structure that is compatible with the observed structure factor amplitudes. The quality of the structure obtained will depend on the number and quality of the experimental data and on the searching power of the refinement method and protocol. The potential energy annealing conformational search (PEACS) algorithm is shown to be an improvement over standard molecular dynamics search methods. The use of time-dependent distance or structure factor restraints in molecular dynamics refinement yields a much better representation of experimental information than the fixed, static restraints which have generally been used until now. Conventional structure refinement methods lead to a too static and rigid picture of a protein in solution or in the crystalline state.

Algorithms↗

PubMed1990

Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat.

A penalty function is introduced into molecular dynamics simulations that improves on current methods for enforcing nuclear magnetic resonance-based distance restraints. Rather than treating nuclear Overhauser effects as static distance bounds, they are considered as quantities that must be satisfied on average over the course of a simulation trajectory. The efficacy of the method is demonstrated on the previously determined structure of tendamistat. The molecular dynamics simulations show that the time-averaged constraints increase the mobility allowed to molecules, produce better agreement with distance bounds, improve searching properties and give a better estimate of the conformational space occupied by the molecule in solution.

Magnetic Resonance Spectroscopy↗

PubMed1989

Proton nmr relaxation study of the dynamics of anthopleurin-A in solution.

Spin-spin and spin-lattice 1H-nmr relaxation times of the sea anemone polypeptide anthopleurin-A were measured at frequencies of 200, 300, 400, and 500 MHz. Relaxation times were fitted iteratively by least squares regression to the isotropic tumbling model, Woessner's model for anisotropic motion, and Lipari and Szabo's "model-independent" model. Data for aromatic and aliphatic methine protons could not be fitted satisfactority using the isotropic model. Good fits were obtained, however, using the model-independent approach, indicating that high-frequency internal motions of the polypeptide backbone were significant. In addition, a range of tau c values from 2.2 to 3.2 ns was obtained for various methine protons, suggesting that overall rotational reorientation of the molecule was anisotropic. Methyl group relaxation data were fitted satisfactorily by Woessner's model. Some assessment has been made of the effect of experimental errors on the quality of fit to the data, as well as of the contribution of experimental values at certain frequencies to definition of the spectral density function.

Animals↗

PubMed1988

Backbone folding of the polypeptide cardiac stimulant anthopleurin-A determined by nuclear magnetic resonance, distance geometry and molecular dynamics.

The solution conformation of the cardiac stimulatory sea anemone polypeptide anthopleurin-A has been characterised using distance geometry and restrained molecular dynamics calculations. A set of 253 approximate interproton distance restraints and 14 peptide backbone torsion angle restraints derived from two-dimensional 1H-NMR spectra at 500 MHz were used as input for these calculations. 13 structures generated by either metric matrix or variable target function distance geometry calculations were refined using energy minimisation and restrained molecular dynamics. The resulting structures contain a region of twisted antiparellel beta-sheet to which two separate regions of unordered chain are linked by three disulphide bonds. Two loops, one including Pro-41 and the other encompassing residues 10-18, are poorly defined by the NOE data.

Animals↗

PubMed1987

Amide proton exchange rates in cardioactive sea anemone polypeptides.

Amide hydrogen exchange rates have been measured using high-resolution 1H nuclear magnetic resonance (NMR) spectroscopy at 300 MHz for three homologous cardioactive polypeptides, anthopleurin-A from Anthopleura xanthogrammica and Anemonia sulcata toxins I and II. There are approximately 15 slowly exchanging hydrogens in each polypeptide, but the slowest exchange rates are found in ATX II, with ATX I and AP-A having rates similar to one another. The exchange rates correlate with the thermal stability of these molecules, but not with the potency and species specificity of their biological activities. The data for AP-A are interpreted in terms of a recent structural model for this polypeptide.

Amides↗

PubMed1985

High-resolution proton nuclear magnetic resonance studies of human gastrin.

High-resolution 1H nuclear magnetic resonance (NMR) spectroscopy at 300 MHz has been used to study the behavior of human gastrin in aqueous solution. A large number of resonances have been assigned by analysis of one- and two-dimensional NMR spectra and the effects of pH and by comparison with the spectrum of des-less than Glu1-gastrin. In gastrin, the ratio of cis to trans conformations around the Gly-2 to Pro-3 peptide bond is 3:7. This is reflected in splitting of the resonances of several neighboring residues and of a residue distant in the sequence, Tyr-12. The pKa of Tyr-12 is 10.7. Sulfation of this residue perturbs the resonances of Tyr-12 and Gly-13 but has very little effect on the rest of the spectrum. A study of the temperature dependence shows that several perturbed resonances move toward their expected positions as the temperature is raised but with a linear dependence on temperature, consistent with a redistribution of populations among accessible local conformations rather than a cooperative conformational change. Addition of Na+ or Ca2+ causes only minor changes in the spectrum. The paramagnetic metal ion Co2+ produces a number of spectral changes, reflecting strong binding to at least one site involving the Glu residues and weaker binding to Asp-16.

Binding Sites↗