Statistical fluctuations in processes of gene expression regulation: consideration of the problem from point of view of statistical mechanics

The regulation of gene expression is a basic problem of biology. In some cases, the gene activity is regulated by specific binding of regulatory proteins to DNA. In terms of statistical mechanics, this binding is described as the process of adsorption of ligands on the one-dimensional lattice and has a probability nature. As a random physical process, the adsorption of regulatory proteins on DNA introduces a noise to the regulation of gene activity. We derived equations, which make it possible to estimate this noise in the case of the binding of the lac repressor to the operator and showed that these estimates correspond to experimental data. Many ligands are able to bind nonspecifically to DNA. Nonspecific binding is characterized by a lesser equilibrium constant but a greater number of binding sites on the DNA, as compared with specific binding. Relations are presented, which enable one to estimate the probability of the binding of a ligand on a specific site and on nonspecific sites on DNA. The competition between specific and nonspecific binding of regulatory proteins plays a great role in the regulation of gene activity. Similar to the one-dimensional "lattice gas" of particles, ligands adsorbed on DNA produce "one-dimensional" pressure on proteins located at the termini of free regions of DNA. This pressure, an analog of osmotic pressure, may be of importance in processes leading to changes in chromatin structure and activation of gene expression.     

Hydrodynamic parameters of native C-reactive protein molecule in a solution

The hydrodynamic properties of the C-reactive protein in solution (pH 6.8) were studied using quasi-elastic light scattering and size-exclusion liquid chromatography. It was shown that the solution containing the C-reactive protein represents a polydisperse system. The values of the translation diffusion coefficient and the apparent molecular weight of the C-reactive protein in solution at pH 6.8 were determined. The values of the translation diffusion coefficient, molecular weight and the hydration radius obtained suggest that the native pentameric C-reactive protein is the major form of the protein in solution at pH 6.8.     

Role of rapid movement of spin labels in interpreting EPR spectra for spin-labelled macromolecules

The method of spin labeling was used to monitor quick movements of side residues in protein monocrystals. The EPR spectra of monocrystals of spin-labeled lysozyme at different orientations of the tetrahonal crystal relative to the direction of the magnetic field were interpreted using the molecular dynamics method. A simple model was proposed, which enables one to calculate the trajectory of movements of the spin label by the molecular dynamic method over a relatively short period of time. The entire "frozen" protein molecule and a "defrozen" spin-labeled amino acid residue were considered in the framework of the model. To calculate the trajectories in vacuum, a model of spin-labeled lysozyme was constructed, and the parameters of force potentials for the atoms of the protein molecule and the spin label were specified. It follows from the calculations that the protein environment sterically hinders the range of eventual angular reorientations of the reporter NO-group of nitroxyl incorporated into the spin label, thereby affecting the shape of the EPR spectrum. However, the scatter in the positions of the reporter group in the angular space turned out to correspond to the Gauss distribution. Using the atomic coordinates of the spin label, obtained in a chosen time interval by the method of molecular dynamics, and taking into account the distribution of the states of the spin label in the ensemble of spin-labeled macromolecules in the crystal, we simulated the EPR spectra of monocrystals of spin-labeled lysozyme. The theoretical EPR spectra coincide well with the experimental.     

Effect of superlow quantities of hydrogen peroxide on water base of solutions

In was shown previously that cations in superlow concentrations strongly change the integral characteristics of the state of the solution water component. The role of the structure of the water component in this process was examined using a model of hydrogen peroxide transformation in water. The dispersion rates of the transmission factors for nine regions of the IR spectrum were analyzed in hydrogen peroxide solutions of different superlow concentrations having the Makhalanobis criteria maximal and close to the standard, which indicate the integral state of the water component in the presence of this substance.     

Dependence of 'macroscopic fluctuations" on geographic coordinates (from materials of Arctic (2000) and Antarctic (2001) expeditions

The detailed structure of histograms constructed from the results of synchronous measurements of the alpha-activity of 239Pu microsamples, conducted in Pushchino (Moscow Region, Russia) and on board the ship "Academician Fedorov" during the Arctic and Antarctic expeditions (2000 and 2001) was analyzed. It was shown that, if the histograms were constructed over a total period of 15 min and more, the "local zone effect" and the circadian periodicity in the similarity of histogram structure, observed during measurements in Pushchino, are not found in measurements on board the ship near the North Pole (latitude 82 degrees). If the histograms were constructed over a total time of 1 min, a strict periodicity ("stellar day" 23 h 56 min) in the appearance of similar histograms in Pushchino and the Arctic and a strict synchronicity of the appearance of similar histograms of measurements in Pushchino and on board the ship at the same local geographical time were observed. During the Antarctic expedition, the effect of synchronicity of the appearance of similar histograms in Pushchino and on board the ship decreased as the ship moved towards the South Pole and the difference in latitude between the points of measurements increased.     

Interaction of Pb(II) ions with C-phycocyanin from Spirulina platensis: effect of ionic strength

The effect of Pb(II) ions on C-phycocyanin from Spirulina platensis was studied by the method of fluorescence spectroscopy. The efficiency of quenching was analyzed using the Stern-Volmer relation. Isotherms of adsorption were constructed, and the constants of binding of Pb(II) ions to C-phycocyanin in solutions of varying ionic strength were determined by equilibrium dialysis and atomic absorption spectroscopy. The constants of binding of Pb(II) ions to C-phycocyanin in 2, 20, and 50 mM NaN03 solutions were estimated to be 4.79 x 10(5), 3.63 x 10(5) and 2.82 x 10(5), respectively. It was found that the interaction of Pb(II) ions with C-phycocyanin has a cooperative character at all values of ionic strengths studied.     

Fluctuations of pass band coefficients of water and water salt solutions in the spectral infrared region

The effect of superlow concentrations of KCl and CaCl2 solutions, obtained by diluting starting 1 M solutions of these salts 10(9)-10(15) times, on the fluctuations of pass band coefficients of water was studied. It was found that these solutions are substantially distinguished from bidistilled water by a high intensity of fluctuations of spectra in the infrared region. It was also shown that higher concentrations of solutions of these salts (at dilutions less than 10(8) times) have no strong and specific effect on fluctuations of the infrared spectrum: the intensity of fluctuations of the infrared spectra of these solutions practically coincides with that of control water. Possible reasons for this effect are discussed.     

Genetic analysis of inheritance of mei8, sy1 and sy10 mutations,disrupting the correct meiosis in the rye Secale cereale L

It is shown that mutations mei8 (irregular condensation and fragmentation of meiotic chromosomes), sy1 (asynapsis), and sy10 (heterologous synapsis) of rye Secale cereal are nonallelic. In double mutants mei8 sy1 and mei8 sy10 both mutations are expressed simultaneously and independently of each other. A study of joint inheritance of mutations sy1 and sy10 revealed their interaction by means of recessive epistasis: the double mutants has the sy10 phenotype. This means that the sy10 gene controls an earlier stage of synapsis in meiotic prophase than the sy1 gene. Mutation mei8 is inherited independently of sy1 but it is linked to sy10 (recombination frequency 26.8 +/- 3.58%).     

The study of joint inheritance of mutations impairing the structure of meiotic chromosomes in rye Secale cereale L

Genetic analysis has demonstrated that meiotic mutations mei8 (irregular condensation and fragmentation of meiotic chromosomes) and mei10 (chromosome overcompaction) are nonallelic. Mutation mei10 exhibits digenic inheritance (with a segregation ratio of 13:3) in the combinations of crosses studied. It is assumed that the phenotypic expression of mutation mei10 is suppressed by the effect of recessive gene lch1 or lch2 (long chromosomes), both of which have been revealed in one of the parental lines (Mc10). These genes determine weak condensation of meiotic chromosomes. In double mutants mei8 mei10, the mutations are expressed independently of each other. Gene mei10 is linked with gene mei8 (r = 36.8 +/- 5.38%); genes lch1 and lch2 are not linked either with them or with each other. Taking into account the data on the linkage between genes mei10 and sy10 and between mei8 and sy10, the order of genes in the linkage group is shown to the following: mei8-sy10-mei10.     

Genetic structure of the Iranian-speaking population of Azerbaijan from data on frequencies of immunologic and biochemical gene markers

The data on the genetic studies of Iranian-speaking populations from Azerbaijan (Talyshs and Tats) are presented. In these populations gene frequency distributions for the immunological (AB0, MN, Rhesus-D, -C, -E, P, Lewis, and Kell-Chellano) and biochemical (HP, GC, C'3, TF, 6PGD, GLO1, ESD, ACP1, and PGM1) gene markers were determined. Comparison of the genetic structure of the populations examined with the other Iranian-speaking populations (Persians and Kurds from Iran, Ossetins and Tajiks) and Azerbaijanis showed that Iranian-speaking populations from Azerbaijan were more close to Azerbaijanis, than to Iranian-speaking populations inhabiting other world regions.