The role of Tyr102 residue in the functioning of bacterial NAD+-dependent formate dehydrogenase of Pseudomonas sp. 101.

Once you have missed the first button …, you'll never manage to button up Johann Wolfgang von Goethe Formate oxidation is a final step of methanol oxidation in methylotrophic prokaryotes and is important for detoxification of formate in other organisms. The structural mechanism of the formate dehydrogenase (FDH) of Pseudomonas sp. 101 has been studied for about 30 years. In the active center of FDH, the oxidation of formic acid into carbon dioxide in a NAD+-dependent way takes place. Residues that form the active center of that enzyme, as well as those that form the so-called substrate channel, are engaged in the catalytic cycle. Our study allowed to characterize a new residue, Tyr102, involved in the work of the enzyme. This residue is located in the outer neck of the substrate channel (at the beginning of the path of the substrate to the active center) and acts as a "button" which connects two enzyme domains into an active, "buttoned up" conformation. Our study of the kinetic parameters of mutant enzymes has shown that Tyr102Phe substitution leads to an approximately 80-fold increase of the Michaelis constant relative to the native enzyme, unlike Phe311Trp and Phe311Tyr substitution of neighboring residue Phe311. Our analysis of the Tyr102Phe mutant in the open conformation by X-ray crystallography has shown that its overall fold remains almost the same as that of the native enzyme. Molecular dynamics simulations of the ternary complexes of the native FDH enzyme and its Tyr102Phe mutant showed that Tyr102Phe substitution results in the loss of an interdomain hydrogen bond between the Tyr102 and Gln313 residues, which, in turn, destabilizes the closed conformation and affects the isolation of the FDH active site from water molecules. Our structural investigations have shown that Tyr102Phe replacement also leads to the destruction of interdomain contacts of Phe102 with Phe311, Pro312 residues, and decreases the stability of the Leu103-Val127 beta bridge. Phylogenetic analysis also confirmed the importance of the Tyr102 residue for enzymes from the FDH family, in which it is absolutely conserved.

[Inverse correlation between GC-content of bacterial genomes and the level of preterminal codons usage in them].

The purpose of this work was to find the character of the dependence between the GC-content of the gene and the level of preterminal codons usage inside it. 84 codon usage tables were used as the material (each of them contains average frequencies of codon usage for all encoding districts belonging to one bacterial specie). We also used nucleotide sequences encoding for active centers of bacterial adenylate cyclases. Inverse correlation between the GC-content (G+C) and the total level of preterminal codons usage (PCU) was observed (R = - 0.97). For nucleotide sequences encoding for active centers from adenylate cyclases class I the coefficient of correlation between G+C and PCU is -0.75. For sequences encoding for active centers from adenylate cyclases class III the coefficient of correlation between G+C and PCU is -0.91. Preterminal codons are mostly GC-deficient relative to their synonymous nonpreterminal codons and in absolute terms. The cause of the inverse correlation between G+C and the level of preterminal codons usage is an increase in their frequencies of usage due to mutational AT-pressure and the decrease of their frequencies of usage due to mutational GC-pressure. The evidence of the frequent fixation of nonsense mutations in GC-deficient bacteria was found. The practical conclusion is the following: the higher is the GC-content of gene or genome, the lower is the probability of nonsense mutation inside it.

[Mutational pressure in genomes of alphaherpesviruses infecting human].

Genomes of the herpes simplex viruses are extremely enriched with GC. Elevated G+C level in genomes of the simplex viruses is a result of their long-term evolution under the influence of the mutational pressure. We counted the rates of nucleotide substitutions from gene coding major capsid protein (MCP) (G+C = 0.68, 3GC = 0.89) of human simplex virus 1 (HSV-1) to the MCP gene (G+C = 0.70, 3GC = 0.91) of HSV-2 (the first pair of genes) and from the same MCP gene of HSV-1 to the homologous gene (G+C = 0.73, 3GC = 0.99) from cercopithecine herpes virus 16 (the second pair of genes). The rates of transitions from A-T to G-C base pairs increases 2.17-, 3.09-, and 1.27-fold in the first, second, and third codon positions, respectively, if compared those rates between the second and first pair of genes (the growth of GC-richness is only 3%). This effect is due to an approximately 90% GC-richness of the third codon positions in all those genes. Transitions caused by the strong mutational pressure (from A-T to G-C base pairs) have a low probability to occur in the third positions, but high probability to occur in the first and second positions. For MCP gene of human herpes 3, the probability of the occurrence of transition caused by mutational pressure in the third codon position is 2.36 times higher than in MCP gene of HSV1, and 3 times higher than in MCP gene of HSV2. These data could provide an explanation of rarely occurring relapses of herpes Zoster infection and frequently occurring relapses of herpes simplex infection.

Phase transition in a strongly nonideal deuterium plasma generated by quasi-isentropical compression at megabar pressures.

High-explosive driven generators of cylindrical and plane shock waves in D2 and H2 were used for the generation of warm and dense strongly nonideal matter with an intense interparticle interaction and Fermi statistics. Highly resolved flash x-ray diagnostics were used to measure the adiabatic plasma compressibility. The thermodynamic measurements demonstrated the 20% increase of density at megabar pressure, just in the density range, where the electrical measurements indicated a sharp--5 orders of magnitude--increase of electrical conductivity due to pressure ionization in strongly coupled plasmas.