Biomedical subjects
Publications and source records attributed to G Damaschun.
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Spermine-DNA complexes have been examined by small-angle and wide-angle X-ray scattering as well as by circular dichroism studies. Condensed complexes are building up below a critical ionic strength. We have found that at one and the same ionic strength condensed complexes having two different supramolecular structures (Type I and Type II) can coexist. The structure of the condensates depends on the method of condensate formation. Phase transitions between these structures can be induced by thermal treatment. We conclude from these facts that with polyamine-DNA condensates metastable structures are of importance.
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The holo-enzyme of the pyruvate decarboxylase EC 4.1.1.1 isolated from brewer's yeast was studied by small-angle X-ray scattering. The point-group symmetry 222 deduced from electron microscopic investigations was confirmed for molecules in solution. The best approximation of the overall shape of the enzyme was reached by an homogeneous triaxial ellipsoid, with the half-axes of a = 2.47 nm, b = 5.08 nm and c = 8.0 nm. The ellipsoid is halved vertical to the a-axis, and both halves are turned from each other by about 30 degrees. As an explanation of the existence of four binding sites for Mg2+ and thiamine pyrophosphate on the dimeric molecule the hypothesis of a gene duplication is discussed.
The spatial structure of rat liver polysomes in dilute solution has been studied by the small-angle X-ray scattering technique. The distance between the mass centres of neighbouring ribosomes on the mRNA molecule is 35 nm, and the distance from next-but-one neighbour, about 55 nm. The spatial arrangement of the ribosomes on the polysome is compact; stretched configurations can be ruled out. The best model is a solenoid with six ribosomes per turn and a pitch of about 33 nm. The greatest diameter of a polysome with eight ribosomes is 130 nm, the radius of gyration 34 nm.
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Circular dichroism measurements with DNA-spermine complexes at 0.075 M NaCl and at 0.15 M NaCl reveal +psi (type I) and -psi (type II) CD spectra respectively. From small-angle X-ray scattering studies it could be shown that type I has a long-range order, short-range order supramolecular structure, while type II is of long-range disorder, short-range disorder structure. The secondary structure of the DNA in both types of condensates is B-like as concluded from wide-angle X-ray scattering diagrams of the condensates and from a comparison with the wide-angle X-ray curves of DNA and RNA in solution.
The phosphofructokinase (E.C. 2.7.1.11) from baker's yeast was examined by means of small angle X-ray scattering in 0.1 M K-phosphate buffer, pH 7. A quaternary structure model was obtained from the comparison of the model scattering curve with the experimental one. The eight subunits of the yeast phosphofructokinase are arranged in a D2-symmetry. The proposed scattering equivalent model corresponds to a structural description with a resolution of 2.5 nm. Models with a C8-symmetry and D4-symmetry can be ruled out.
Ethanol precipitated DNA shows a CD spectrum of the +psi-type which is similar to that of DNA in the A-form. DNA condensed with cetyl-trimethylammonium-bromide shows, depending on the condensation velocity, a CD spectrum of the -psi-type, or a CD spectrum only slightly modified from that of DNA in solution. The first spectrum is similar to that of DNA in the C-form, and the second one, to that of DNA in the B-form. Using large-angle X-ray scattering of the three DNA condensates and comparing them with the scattering curves calculated from the atom coordinates for the A-, B-, and C-form of DNA it is shown that the secondary structure of the DNA belongs in all three cases to the B-family. It follows from this result that the secondary structure of DNA alone does not determine the type of CD spectrum. The CD spectrum of condensed DNA is essentially determined by the supramolecular structures of the partially crystalline DNA condensates. These supramolecular structures can be demonstrated by the small-angle X-ray diagrams. The condensation of DNA by ethanol and cetyl-trimethylammonium-bromide proceeds in the form of a partial crystallization of the DNA.
It is demonstrated by means of small-angle X-ray scattering that 11 S globulin of sunflower (Helianthus annuus L.) consists of six subunits. The point group symmetry of the quaternary structure is 23 (D3). It is postulated that this symmetry is typical for the group of 11 S seed proteins.
In general, saturation curves for ligand binding by proteins are described by the Adair-equation. The approach to ligand binding with methods of statistical mechanics leads not only to expressions for the Adair-constants, but gives also the possibility of describing the effect of protein-protein interactions on the binding of ligands by proteins. Under the assumption of the superposition-approximation for the potential of mean force between proteins in a solution, which contains also ligand molecules, the variations of the second and third virial coefficient with ligand activity are calculated for several simple model-pontentials. Finally the pair potential of hemoglobin molecules known from X-ray measurements will be approximated by such a simple square-well potential. With that the effect of hemoglobin density on oxygenation will be estimated. One finds for our model system that at relatively high protein density a further increase in density should be accompanied by a decrease in affinity (hindrance of saturation) and an increasing steepness of the slope of the saturation curve.
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The diffuse wide angle x-ray scattering (WAXS) of polyglutamic acid (PGA) in solution was studied using an x-ray diffractometer with small aperture of the primary beam. The scattering curve was recorded at an angular interval from (article: see text). The experimental scattering intensity of PGA with alpha-helical CD spectrum showed a maximum at 14.4 nm-1. Unordered PGA in solution yielded no maximum at this scattering angle. The studies have proved that the scattering theory can be applied to globular proteins in solution as well as to chain molecules in solution in this angular interval. The differences between the calculated scattering curves and the experimental curves indicate minor movements of the side chains of PGA in solutions and slight structuring of the solvent at the surface of the polypeptide chain.
The X-ray scattering diagram from single chromatin subunit particles is registered within a scattering vector intervall from s = 0 to s = 1 1/A. Preliminary results concerning the dimensions and the structure of the nucleosome core particle are communicated.
The following model is proposed for the structure of deoxyribonucleic acid (DNA) in chromatin: The DNA in a nucleosome is folded seven times to and fro on the surface of a cylindrical protein nucleus. There exist 3.5 DNA hairpins. The seven arms of the hairpins contain twenty DNA base pairs each. The six loops of the DNA hairpins contain ten DNA base pairs each. Consistently with the experiment, the model gives X-ray small-angle diffraction reflexes at 10.5 nm, 5.5 nm, 3.6 nm. The X-ray larg-angle diagram can also be interpreted by the model. Folding crystallization is the mechanism of supramolecular selfassembly giving condensation of DNA in the chromatin.
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It is shown by means of circular dichroism studies of variously condensed forms of DNA that the specific supramolecular structure of DNA determines the type of CD spectra. DNA, condensed (crystallized) slowly in the presence of cetyltrimethyl ammonium bromide yields a spectrum very similar to that of DNA in solution in the B-form. The condensates appear in the phase-contrast microscope as spherulitic crystallites. Rapidly condensed DNA in the presence of cetyltrimethyl ammonium bromide shows a spectrum of the psi-type with large negative ellipticites. The influence of condensation velocity upon the supramolecular structure of DNA gives evidence that the various condensation forms of DNA are not thermodynamical equilibrium conformations.