Cold and distant: structural features of the nucleoprotein complex of a cold-adapted influenza A virus strain.

Two influenza A nucleoprotein variants (wild-type: G102R; and mutant: G102R and E292G) were studied with regard to macro-molecular interactions in oligomeric form (24-mers). The E292G mutation has been previously shown to provide cold adaptation. Molecular dynamics simulations of these complexes and trajectory analysis showed that the most significant difference between the obtained models was distance between nucleoprotein complex strands. The isolated complexes of two ribonucleoprotein variants were characterized by transmission electron microscopy and differential scanning fluorimetry (DSF). Presence of the E292G substitution was shown by DSF to affect nucleoprotein complex melting temperature. In the filament interface peptide model, it was shown that the peptide corresponding in primary structure to the wild-type NP (SGYDFEREGYS) is prone to temperature-dependent self-association, unlike the peptide corresponding to E292G substitution (SGYDFGREGYS). It was also shown that the SGYDFEREGYS peptide is capable of interacting with a monomeric nucleoprotein (wild type); this interaction's equilibrium dissociation constant is five orders of magnitude lower than for the SGYDFGREGYS peptide. Using small-angle neutron scattering (SANS), the supramolecular structures of isolated complexes of these proteins were studied at temperatures of 15, 32, and 37 °C. SANS data show that the structures of the studied complexes at elevated temperature differ from the rod-like particle model and react differently to temperature changes. The data suggest that the mechanism behind cold adaptation with E292G is associated with a weakening of the interaction between strands of the ribonucleoprotein complex and, as a result, the appearance of inter-chain interface flexibility necessary for complex function at low temperature.Communicated by Ramaswamy H. Sarma.

[Current insights into chromatin structure organization].

This review summarizes current insights into organization of chromatin structure at different levels of DNA compaction. Analysis of available experimental data allowed concluding that only nucleosomal level of structural organization was sufficiently investigated, whereas structure of a 30-nm chromatin fiber remains an open issue. The data on the chromatin structure obtained at the level of the nucleus speak in favor of a biphasic fractal organization of chromatin.

[Spatial distribution of transverse stiffness of relaxed and activated rat soleus myofibers].

The transverse stiffness of isolated glycerinated and demembranized muscle fibers from soleus muscle of Wistar rat were measured in different functional states by atomic force microscopy. It was shown that transverse stiffness of relaxed fibers near the Z-disk projection is approximately twice as high as near the M-line. The transverse stiffness of demembranized fibers is much higher than that of glycerinated fibers for both the Z-disk and M-line. The activation of the fiber resulted in a significant increase in transverse stiffness. However, while the stiffness of activated glycerinated fibers near the Z-disk increased about twofold, demembranized fibers showed a more than fourfold increase in transverse stiffness compared to relaxed fibers. The stiffness of both glycerinated and demembranized fibers near the M-line increased approximately threefold.

[Dynamic properties of recA protein filaments from E. coli and P. aeruginosa investigated by neutron spin-echo].

Bacterial RecA protein is the key enzyme in the processes of homologous recombination, post-replication repair and induction of SOS-repair functions. While a significant amount of data on the structure of RecA protein and its functional analogs has been obtained, there is little information about the molecular dynamics of this protein. In this work we present the results of neutron spin-echo measurements of the relaxation kinetics of filaments formed by RecA proteins from E. coli and P. aeruginosa. The results suggest that the protein filaments exhibit both diffusion and internal relaxation modes, which change during the formation of complexes of these proteins with ATP and single-stranded DNA.

Atomic force microscopy study of peptides homologous to beta-domain of alpha-lactalbumins.

Symmetrical peptide GYDTQAIVENNESTEYG (WT, Wild Type) identical to 35-51 aminoacid residues of human alpha-lactalbumin (HLA) and peptide GYDTQTVVNNNGHTDYG (ID, IDeal symmetry) homologous to beta-domain of mammalian alpha-lactalbumins can form amyloid-like fibrils in conditions required for fibrillogenesis of HLA. The latter peptide can also form fibrils in deionized water. Fibrils formed by these peptides can cause forming of HLA amyloid-like aggregates in physiological conditions. These results provide an evidence for presence of amyloidogenic determinant in beta-domain of alpha-lactalbumin. Thus, symmetry in the primary structure may play the role in fibrillogenesis of proteins.

Fractal nature of chromatin organization in interphase chicken erythrocyte nuclei: DNA structure exhibits biphasic fractal properties.

Arrangement of chromatin in intact chicken erythrocyte nuclei was investigated by small angle neutron scattering. The scattering spectra have revealed that on the scales between 15 nm and 1.5 microm the interior of the nucleus exhibited properties of a mass fractal. The fractal dimension of the protein component of cell nucleus held constant at approximately 2.5, while the DNA organization was biphasic, with the fractal dimension slightly higher than 2 on the scales smaller than 300 nm and approaching 3 on the larger scales.

[Molecular reasons for the regulation of the enzymatic activity of bovine pancreatic deoxyribonuclease I as studied by dynamic light scattering and fluorescent spectroscopy].

The effect of catalytic bivalent and inhibitory monovalent cations on the interactions of bovine pancreatic deoxyribonuclease I with the circle single-stranded DNA of M13 phase was studied. It was found that monovalent cations affect the site of binding to DNA and the active center of the enzyme; in their presence, a break of the formation of the enzyme-substrate complex occurs. The results provide evidence that conformational changes of the protein molecule in all cases are more substantial that it could be expected from X-ray data published earlier.

Analytical model for determination of parameters of helical structures in solution by small angle scattering: comparison of RecA structures by SANS.

The filament structures of the self-polymers of RecA proteins from Escherichia coli and Pseudomonas aeruginosa, their complexes with ATPgammaS, phage M13 single-stranded DNA (ssDNA) and the tertiary complexes RecA::ATPgammaS::ssDNA were compared by small angle neutron scattering. A model was developed that allowed for an analytical solution for small angle scattering on a long helical filament, making it possible to obtain the helical pitch and the mean diameter of the protein filament from the scattering curves. The results suggest that the structure of the filaments formed by these two RecA proteins, and particularly their complexes with ATPgammaS, is conservative.

Fluorescence and excitation Escherichia coli RecA protein spectra analyzed separately for tyrosine and tryptophan residues.

The method for separation of emission (EM) and excitation (EX) spectra of a protein into EM and EX spectra of its tyrosine (Tyr) and tryptophan (Trp) residues was described. The method was applied to analysis of Escherichia coli RecA protein and its complexes with Mg(2+), ATPgammaS or ADP, and single-stranded DNA (ssDNA). RecA consists of a C-terminal domain containing two Trp and two Tyr residues, a major domain with five Tyr residues, and an N-terminal domain without these residues (R. M. Story, I. T. Weber, and T. A. Steitz (1992) Nature (London) 355, 374-376). Because the fluorescence of Tyr residues in the C-terminal domain was shown to be quenched by energy transfer to Trp residues, Trp and Tyr fluorescence of RecA was provided by the C-terminal and the major domains, respectively. Spectral analysis of Trp and Tyr constituents revealed that a relative spatial location of the C-terminal and the major domains in RecA monomers was different for their complexes with either ATPgammaS or ADP, whereas this location did not change upon additional interaction of these complexes with ssDNA. Homogeneous (that is, independent of EX wavelength) and nonhomogeneous (dependent on EX wavelength) types of Tyr and Trp fluorescence quenching were analyzed for RecA and its complexes with nucleotide cofactors and ssDNA. The former was expected to result from singlet-singlet energy transfer from these residues to adenine of ATPgammaS or ADP. By analogy, the latter was suggested to proceed through energy transfer from high vibrational levels of the excited state of Trp and Tyr residues to the adenine. In this case, for correct calculation of the overlap integral, Trp and Tyr donor emission spectra were substituted by the spectral function of convolution of emission and excitation spectra that resulted in a significant increase of the overlap integral and gave an explanation of the nonhomogeneous quenching of Trp residues in the C-terminal domain.

Tryptophan residues in alpha-galactosidase from Trichoderma reesei.

Tryptophan residues in alpha-galactosidase were modified with bromosuccinimide. The fact that galactose, a specific inhibitor of alpha-galactosidase, does not prevent this modification demonstrates that tryptophan residues are not located in galactose binding sites. Analysis of the inactivation kinetics revealed two groups of Trp residues (8.5 and 7.5 residues) with different accessibility for N-bromosuccinimide. We studied specific quenching of alpha-galactosidase fluorescence resulting from modification of an sulfhydryl group in the active site of the enzyme with Hg2+ and Ag+ ions. The specific quenching is due to conformational changes of the enzyme. Forster's radii were determined for various protein--chromophore complexes. Dynamic quenching of alpha-galactosidase fluorescence was investigated. To describe abnormal dynamic quenching in alpha-galactosidase, a modification of the Stern--Volmer equation is suggested.

[Distribution of the tempo-dichlorotriazine spin label in the immunoglobulin molecule]. / Raspredelenie spinovoi metki tempo-dikhlorotriazina po molekule immunoglobulina.

Spin-label 14C-TEMPO-dichlorotriazine distribution in Fab- and Fc-fragments of monoclonal myeloma immunoglobulin IgG (lambda) 1 Bel, in their heavy and light chains, and tryptic fragments of chains was investigated. Radio-active spin label in proteolytic Fab- and Fc-fragments, in heavy and light chains, and in separate peptides was detected. 3 cm and 2 mm band ESR spectra of spin-labeled IgG in water solutions was studied. It was shown that the models of highly anisotropic motion, isotropic motion and slow isotropic motion of spin label around globule or the description of experimental ESR spectra of TEMPO-dichlorotriazine spin-labeled immunoglobulins do not work.

[Analysis of existing models of spin label movement during spin labeling of biological macromolecules]. / Analiz sushchestvuiushchikh modelei dvizheniia spinovoi metki pri spin-mechenii biologicheskikh makromolekul.

The spin-labeled bovine serum albumin and IgG were studied in search of an experimental approach for comparison of different models of rotational mobility of spin label. These models are: the model of isotropic motion of spin label together with the macromolecule (IM); the model of highly anisotropic motion of spin label (HAM); and the model of slow isotropic motion of label around the binding site (SIML). The experimental spectra were measured on a common X-band ESR spectrometer and on the unique 140 GHZ (lambda = 2 mm) ESR spectrometer under the same conditions. Theoretical spectra were computer-calculated according to Freed's theory. We have found, that the results of temperature-viscosity experiments in X-band are contradictory to the model of IM both for the BSA and IgG species. The models of HAM and SIML for the BSA give identical X-band spectra. The bovine serum albumin spectra in the 2 mm region strongly contradict to the assumptions of the HAM model. Also, the SIML model fails to describe the experimental spectra in terms of isotropic motion of the spin label around the binding site. X-band spectra of IgG can not be explained by the SIML model, while the same spectra in the 2 mm region can not be explained by the HAM model.

[Physico-chemical mechanisms of organic acid transport in the apical membrane cells of the proximal kidney tubules in rats. I. Kinetic transport parameters and effect of the lipid phasic state on transport]. / Fiziko-khimicheskie mekhanizmy transporta organicheskikh kislot v vezikulakh apikal'noi membrany kletok proksimal'nykh kanal'tsev pochki krys. I. Kineticheskie parametry transporta i vliianie fazovogo sostoianiia na transport.

The kinetics of the transport of 3H-para-aminohippuric acid (PAH) and the influence of the temperature on the initial rate of transport were studied on the vesicles of a purified fraction of the apical membrane isolated from cells of kidney proximal tubules. The PAH transport is accomplished owing to the facilitate diffusion mechanism. The apparent Michaelis constant at 36 degrees C was equal to 7.0 + 1.0 mM, the maximum rate was 15 nmol/min on 1 mg of protein, the inhibition constant for the PAH transport by probenecid being 0.5 mM. At 22 degrees C the apparent Michaelis constant was drastically increased. When the temperature dependence of the initial rate of PAH transport into vesicles was replotted in the form of the Arrhenius plot, there was a turning-point of the line at 28-30 degrees C. The same turning-point is shown on the Arrhenius plot for temperature dependence of alkaline phosphatase activity (a marker enzyme for the apical membrane). The electron paramagnetic resonance spectra analysis of 5-doxylstearate-labeled apical membrane preparation reveals a thermotropic transition near 21-29 degrees C. It is concluded that the function of the carrier and the activity of alkaline phosphatase depend on the phasic state of membrane lipids; the normal function of membrane proteins is possible under the liquid-crystalline state of the lipid bilayer.

[Spectral division of conformational states of spin-labeled tRNA Phe from Escherichia coli]. / Spektral'noe razdelenie konformatsionnykh sostoianii na spin-mechenoi tRNK Phe iz Escherichia coli.

A spectral division method of two conformational states of spin-labeled macromolecules is presented. The method is suitable in conditions of highly anisotropic motion of spin label and is based on titration of experimental spectra of spin-labeled macromolecule by theoretical ones. Theoretical spectra simulation uses the Freed theory and spin-Hamiltonian parameters, derived from independent experiments. Nomogrammes and formula for calculation of order parameter Sz and correlation time tau c in temperature-viscosity experiment are available. The method was applied to spectral division of two conformational states of spin-labeled tRNAPhe from E. coli and spectral parameters Sz and tau c were obtained for both states. ESR spectra of these conformational states at t degree = 20 degrees differ strongly from one another by order parameter Sz. The first conformer, that is characterised by a greater order parameter has no globular conformational transition (in terms of changes of the hydrodynamic macromolecule radius) between 2 degrees and 20 degrees, but local conformational changes take place in this temperature region.

[Study on the conformational state of Escherichia coli tRNA-Phe in solution by ESR-spectometry without modulation]. / Izuchenie konformatsionnoi situatsii v vodnykh rastvorakh spin-mechenoi tRNA-Phe iz Escherichia coli bezomduliatsionnym metodom EPR.

ESR-spectrometry without modulation of the magnetic field was used for registering the EST spectral line shape (with shape distortion about 0.1 percent) of spin-labeled Escherichia coli tRNAPhe. The analysis of line shape of two different spin-labels in position 8 (S4U) revealed that tRNAPhe in solution always exists as a mixture of at least two conformers, the equilibria between conformers being dependent on pH, concentration of magnesium and the biological state of tRNA (deacylated, aminoacyl- or peptidyl-tRNA). There are no large structural rearrangements upon aminoacylation or peptidylation of tRNA, the observed small changes of spectral line shape are due to the changes in conformational equilibria.

Study on conformational states of Escherichia coli tRNAPhe in solution by a modulation-free ESR-spectrometer.

A modulation free Electron Spin Resonance spectrometer was used for the registration of spectral absorption lines of a spin-labeled Escherichia coli phenylalanine tRNA in solution with low (less than 0.1%) line shape distortion. The analysis of line shape of two different spin-labels introduced into position 8 revealed that phenylalanine tRNA in solution exists as a mixture of two conformers, the equilibria between conformers being dependent on pH, concentration of magnesium and functional state of tRNA (deacylated, aminoacylated or peptidylated). There are no overall structural rearrangements upon aminoacylation or peptidylation of tRNA. The observed small changes of spectral line shape can be assigned to shifts in conformational equilibria.