Moscow University Chemistry Bulletin最新文献

DNA glycosylases are enzymes that hydrolyze the N-glycosidic bond of damaged nucleotides, initiating the process of base excision DNA repair. There are at least eight structural classes of these enzymes, differing in both their substrate specificity and the mechanism of catalysis. The review examines the mechanisms of human and bacterial DNA glycosylases that protect the genome from the major types of DNA damage.

Lactate oxidase is a practically important enzyme widely used to detect L-lactate in medical diagnostics and in the food industry. This review summarizes the results of protein engineering of lactate oxidases to clarify the underlying mechanism of action of the enzyme and to improve its performance properties.

Expression of recombinant proteins is important for studying their biological functions. For the primary description of protein properties, the E. coli expression system is most often used. However, in overexpression conditions, the rate of aggregation of target proteins often exceeds the rate of proper folding, resulting in the formation of insoluble inclusion bodies. Inclusion bodies are a clear disadvantage of the E. coli expression system since they prevent the extraction of target recombinant proteins. The use of chaperone-like proteins in vitro while refolding a target protein is one of the solutions to the existing problem. In this study, the MF3 recombinant protein is an example of a chaperone-like protein, which increases the yield of soluble plant chitinase by 92% compared to the yield of this protein using the standard refolding procedure.

This paper reviews the protein engineering of Bst polymerase using various methods. To modify the enzyme, approaches such as the production of chimeric proteins, directed evolution, and directed and random mutagenesis are used. Examples of successful changes in enzyme properties such as catalytic activity, processivity, thermal stability, and resistance to inhibitors are described.

World-wide introduction of high throughput screening (HTS) methods in drug discovery research did not result in the increased number of novel medications on the market. We discuss novel trends in drug discovery that came from the understanding that majority of diseases are multifactorial and that one enzyme has many protein substrates. Hence, new approaches are focused on development of drugs, which (1) trigger survival pathways to return the organism to homeostatic balance, and (2) inhibit enzymes modifying histones or transcription factors not at the active site, but by displacement of protein substrates from the enzyme complexes. A good example for both approaches comes from the development of activators of antioxidant defense. We analyze and illustrate problems of commonly used in vitro HTS assays, and briefly discuss advantages and limitations of small animal models. The novel approaches are complementary to the standard HTS and do not substitute for testing in mammals. Development of transgenic reporter mice to monitor drug effects by means of in vivo imaging is extremely promising to select proper dosage and administration regimes for full-range PK studies.

The combined quantum mechanics/molecular mechanics method is most often used to describe the molecular mechanisms of enzymatic reactions. The review discusses the main methodological issues, gives practical recommendations, and also illustrates the progress of the method over the past 20 years using an important example of the reaction of guanosine triphosphate hydrolysis by a protein complex.

The transition of active Mycolicibacterium smegmatis cells to a dormant state under acidification conditions is accompanied by the intracellular accumulation of tetramethyl ester of coproporphyrin (TMC). At the same time, the dormant forms of mycobacteria develop resistance to a number of damaging factors. The addition of 5-aminolevulinic acid (ALA), a precursor of porphyrin synthesis, into the bacterial culture medium leads to the accumulation of TMC in actively growing cells, which simulates the situation with dormant mycobacteria. Upon threefold increasing the concentration of TMC, the bacteria become sevenfold more resistant to the action of 40 mM hydrogen peroxide and 90-fold more resistant to heating up to 80°C. At the same time, in M. smegmatis cells with an increased concentration of TMC, the activity of dichlorophenolindophenol reductase that is a marker of respiratory chain activity decreases by 18%. The detected inhibition of activity can lead to a decrease in side oxidative reactions in the cell. Therefore, the accumulation of methylated coproporphyrin is possibly one of the mechanisms for the development of mycobacterium resistance at dormancy.

Aptamers are promising for a wide application range in biomedicine and various diagnostic systems due to their unique properties as selective ligands specifically obtained or a selected target using methods of artificial evolution and combinatorial chemistry. Strategies for obtaining aptamers in vitro and using their chemical modifications, as well as approaches to design the initial libraries of compounds based on in silico prestructuring are discussed. Limitations are formulated, and a direction for the development of the field of obtaining new aptamers is proposed.

The main types of oxidative post-translational modifications of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDН) targeting the sulfhydryl group of the catalytic cysteine residue Cys152 are reviewed. The highly reactive sulfhydryl group of Cys152 in the active center of GAPDH undergoes oxidation and S-nitrosylation, leading to inactivation and destabilization of the enzyme. Upon reversible oxidation of the sulfhydryl group to form cysteine-sulfenic acid, the enzyme loses dehydrogenase activity, but gains the ability to catalyze the acyl-phosphatase reaction. Hydrolysis of the product of the dehydrogenase reaction, 1,3-diphosphoglycerate, under the action of oxidized GAPDH leads to uncoupling of oxidation and phosphorylation at this stage of glycolysis. The action of nitric oxide results in S-nitrosylation of Cys152 in GAPDH with the subsequent formation of cysteine-sulfenic acid due to hydrolysis of the S-NO-group. Data are presented on the relationship between S-nitrosylation, oxidation and S-glutathionylation of Cys152 in GAPDH. The role of post-translational modifications of the sulfhydryl group of the catalytic cysteine residue in the regulation of enzyme activity, as well as the mechanisms ensuring the reversibility of such modifications are discussed.

In this review the methods used to study internal rotation (IR) in the ground (S₀) and excited (S₁) electronic states for compounds of the benzoic series C₆H₅–COR, where R = H, F, and CI, are compared. In the (S₀) electronic state, differences in the values of (0–v) transitions of the torsional vibration for the studied compounds are revealed in the methods of analysis of the vibrational structure of the n–π* transition of high-resolution UV absorption spectra and Fourier-transform IR spectra. The reasons for such differences are established. In the excited (S₁) state for benzaldehyde, the method of analyzing the vibrational structure of the n–π* transition of high-resolution UV absorption spectra and the method of analyzing the excitation spectra of the sensitized phosphorescence of this compound in a cooled jet are compared. It is concluded that the method of analyzing the vibrational structure of the n–π* transition of the high-resolution UV absorption spectra of vapors of the investigated compounds is more reliable and accurate when studying the IR in both electronic states.