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I N Serdiuk

Publications and source records attributed to I N Serdiuk.

11 recordsLinked to original sources
PubMed1996

[Partially unfolded state of lysozyme with a developed secondary structure in dimethylsulfoxide].

The conformation of a chicken egg lysozyme molecule (dimensions, stoichiometry of its associates, and the degree of helicity) in DMSO was studied by small-angle neutron scattering, dynamic light scattering, and optical rotatory dispersion in the visible region of the spectrum. At high DMSO concentrations (70%), the protein was shown to exist as a dimer. The monomer molecules in the dimer adopt a partially unfolded conformation, with dimensions substantially greater than those in the native state and a high content of secondary structure (the degree of helicity is close to that of native lysozyme). This approach provides a unique possibility to assess the compactness of molecules in associates, which may be very useful in studying protein self-organization.

Animals↗
PubMedDate not supplied

[Changes in mechanical characteristics of immobilized crystals and films of globular proteins during substitution of D2O for H2O].

The influence of substitution of the isotopic composition of the medium on the mechanical properties of immobilized crystals and films from bovine pancreatic ribonuclease and hen egg white lysozyme was investigated. The order of magnitude of the observed effects indicates that the contribution of the electrostatic interaction to the observed isotopic effect may be considered inessential. The absence of aggregation in the H2O and D2O medium under experimental conditions is demonstrated by the method of the low angle dispersion of X-rays. The observed effects of D2O on the mechanical behavior of crystals and films of proteins may be accounted for by the strengthening of molecular interactions in the samples.

Animals↗
PubMedDate not supplied

[Internal structure of ribosomes using different types of emission].

A review is made of the experimental results obtained by the author and co-workers on the study of the structural organization of the RNA and the protein in ribosomes by the method of joint use of light, X-ray and neutron scattering and by the method of contrast variation in neutron scattering. Two rules are formulated for the folding of the ribonucleoprotein strand in ribosomes: (1) in each ribosomal subparticle the RNA is concentrated predominantly closer to the center of the particle whereas the protein has a more peripherical localization; (2) the compact ("crystallic") packing of hydrated RNA helices is an essential feature of the nucleus (nuclei) organization of the particles. An analysis of the experimental data on neutron scattering by ribosomal proteins has been done and the globulin conformation in solution of some of these proteins has been established. The widespread concept according to which the majority of ribosomal proteins on the ribosome and in solution are enlongated expanded structures is disputed. It is suggested that all, or almost all, ribosomal proteins are usual globular proteins recognizing the specific sequence of RNA on the periphery of the particles, and , hence, that the formation of functional centrers on the ribosome is, in principle, analogous to the formation of functional centers of other complex proteins with a quaternary structure.

Escherichia coli↗
PubMedDate not supplied

[Quaternary structure of the ribosomal 30S subparticle: the model and its experimental verification].

In considering the structure of the ribosomal 30S subparticle from Escherichia coli we have assumed that : 1) all or almost all the proteins in the 30S subparticle are compact and globular as has been shown for isolated proteins S4, S7, S8, S15 and S16 in solution [Serdyuk I. N., Zaccai G. and Spirin A. S. (1978) FEBS Letters, 94, 349-352]; 2) RNA within the 30S subparticle has the same specific V-like or Y-like shape demonstrated for the isolated 16S RNA in a compact conformation [Vasiliev V. D., Selivanova O. M. and Koteliansky V. E. (1978) FEBS Letters, 95, 273-276]. On the basis of this assumption and numerous data published on the mutual localization of ribosomal proteins, we have constructed a model of the quaternary structure of the ribosomal 30S subparticle. We have tested the model by comparing the theoretically calculated curves of neutron and X-ray scattering at different contrasts with the corresponding experimental scattering curves of the E. coli 30S subparticles and have found that they coincide. The calculated scattering curves of several previously published three-dimensional diagrams of protein topography in the 30S subparticle do not agree with experiment.

Escherichia coli↗
PubMedDate not supplied

[Isolation and physical study of the 13S fragment of 16S RNA and its complex with ribosomal protein S4].

A fragment of E. coli 16S RNA has been obtained by its hydrolysis with pancreatic RNAase A coupled to Sepharose 4B. This fragment has a molecular weight of 170 000 and a sedimentation coefficient of 13S. It does not aggregate in solution and binds with the ribosomal protein S4. The 13S fragment and it complex with the protein S4 have been studied by different physical methods in the first place, by neutron scattering. It has been shown that this fragment is compact in solution. The radii of gyration of the fragment (50 +/- 3 A) and of the protein S4 within the complex (17 +/- 3 A) coincide, within limits of experimental error, with the radii of gyration for the free RNA fragment (47 +/- 2 A) and the free ribosomal protein S4 in solution (18 +/- 2 A). Hence, the conclusion is made that the compactness of the 13S fragment of the 16S RNA and the ribosomal protein S4 does not change at the complex formation. The compact 13S fragment of the 16S RNA is shown to be contrast matched in the H2O/D2O mixture containing 70% D2O which corresponds to its partial specific volume v equal to 0.537 cm3/g.

Chemical Phenomena↗
PubMedDate not supplied

[Structure and density of ribosomal RNA and its complexes with proteins in a solution].

X-ray and neutron scattering, as well as velocity sedimentation, were used to study the shape and dimensions (compactness) of isolated ribosomal (16S and 23S) RNA's and their complexes with ribosomal proteins. The neutron scattering of ribosomal particles in 42% 2H2O where the protein component is contrast-matched, were taken as a standard of comparison characterizing the dimensions and shape of the 16S and 23S RNA in situ. This comparison allowed the following conclusions: (1) The shape of the isolated 16S RNA at a sufficient Mg2+ concentration (e. g., in the reconstruction buffer) is similar to that of the 16S RNA in situ, but its compactness is somewhat less. (2) The 16S RNA in the complex with protein S4 has a shape and compactness similar to those of the isolated 16S RNA. (3) The 16S RNA in the complex with four core proteins, namely S4, S7, S8 and S15, has a shape and compactness similar to those of the isolated 16S RNA. (4). The six ribosomal proteins, S4, S7, S8, S15, S16, and S17, are necessary and sufficient for the 16S RNA to acquire a compactness similar to that in situ.

Bacterial Proteins↗
PubMedDate not supplied

[Roughness of the globular protein surface].

The area and volume of the approximating ellipsoids taken from low resolution X-ray data have been calculated for 65 globular proteins. It has been shown that the dependence of these values on the protein molecular mass (M) coincides with those for even isometric bodies. This indicates that the asymmetry of globular proteins does not grow with the increase of their sizes. At the same time the 0.73 slope of the log-log dependence of the accessible surface area (A(s)) on the protein molecular mass differing from the value of 0.67 for even isometric bodies was observed (Miller S. et al., J. Mol. Biol. 1987. V.196. P.641). This can be explained by peculiarities of the protein surface. The method of molecule shape recovery by spherical harmonics has shown that the domain organization of protein molecule cannot explain the observed difference. Therefore the more detailed analysis of protein surface structure would be necessary.

Models, Molecular↗