Biochemistry (Moscow) (v.78, #13)

Poly(A)-binding proteins: Structure, domain organization, and activity regulation by I. A. Eliseeva; D. N. Lyabin; L. P. Ovchinnikov (1377-1391).
RNA-binding proteins are of vital importance for mRNA functioning. Among these, poly(A)-binding proteins (PABPs) are of special interest due to their participation in virtually all mRNA-dependent events that is caused by their high affinity for A-rich mRNA sequences. Apart from mRNAs, PABPs interact with many proteins, thus promoting their involvement in cellular events. In the nucleus, PABPs play a role in polyadenylation, determine the length of the poly(A) tail, and may be involved in mRNA export. In the cytoplasm, they participate in regulation of translation initiation and either protect mRNAs from decay through binding to their poly(A) tails or stimulate this decay by promoting mRNA inter-actions with deadenylase complex proteins. This review presents modern notions of the role of PABPs in mRNA-dependent events; peculiarities of regulation of PABP amount in the cell and activities are also discussed.
Keywords: PABPs; mRNA; translation; poly(A) tail; polyadenylation; mRNA decay

Modified nucleotides are universally conserved in all living kingdoms and are present in almost all types of cellular RNAs, including tRNA, rRNA, sn(sno)RNA, and mRNA and in recently discovered regulatory RNAs. Altogether, over 110 chemically distinct RNA modifications have been characterized and localized in RNA by various analytical methods. However, this impressive list of known modified nucleotides is certainly incomplete, mainly due to difficulties in identification and characterization of these particular residues in low abundance cellular RNAs. In DNA, modified residues are formed by both enzymatic reactions (like DNA methylations, for example) and by spontaneous chemical reactions resulting from oxidative damage. In contrast, all modified residues characterized in cellular RNA molecules are formed by specific action of dedicated RNA-modification enzymes, which recognize their RNA substrate with high specificity. These RNA-modification enzymes display a great diversity in terms of the chemical reaction and use various low molecular weight cofactors (or co-substrates) in enzymatic catalysis. Depending on the nature of the target base and of the co-substrate, precise chemical mechanisms are used for appropriate activation of the base and the co-substrate in the enzyme active site. In this review, we give an extended summary of the enzymatic mechanisms involved in formation of different methylated nucleotides in RNA, as well as pseudouridine residues, which are almost universally conserved in all living organisms. Other interesting mechanisms include thiolation of uridine residues by ThiI and the reaction of guanine exchange catalyzed by TGT. The latter implies the reversible cleavage of the N-glycosidic bond in order to replace the initially encoded guanine by an aza-guanosine base. Despite the extensive studies of RNA modification and RNA-modification machinery during the last 20 years, our knowledge on the exact chemical steps involved in catalysis of RNA modification remains very limited. Recent discoveries of radical mechanisms involved in base methylation clearly demonstrate that numerous possibilities are used in Nature for these difficult reactions. Future studies are certainly required for better understanding of the enzymatic mechanisms of RNA modification, and this knowledge is crucial not only for basic research, but also for development of new therapeutic molecules.
Keywords: RNA-modification; methylation; pseudouridine; catalytic mechanisms

Molecular chaperone GroEL/ES: Unfolding and refolding processes by N. A. Ryabova; V. V. Marchenkov; S. Yu. Marchenkova; N. V. Kotova; G. V. Semisotnov (1405-1414).
Molecular chaperones are a special class of heat shock proteins (Hsp) that assist the folding and formation of the quaternary structure of other proteins both in vivo and in vitro. However, some chaperones are complex oligomeric proteins, and one of the intriguing questions is how the chaperones fold. The representatives of the Escherichia coli chaperone system GroEL (Hsp60) and GroES (Hsp10) have been studied most intensively. GroEL consists of 14 identical subunits combined into two interacting ring-like structures of seven subunits each, while the co-chaperone GroES interacting with GroEL consists of seven identical subunits combined into a dome-like oligomeric structure. In spite of their complex quaternary structure, GroEL and GroES fold well both in vivo and in vitro. However, the specific oligomerization of GroEL subunits is dependent on ligands and external conditions. This review analyzes the literature and our own data on the study of unfolding (denaturation) and refolding (renaturation) processes of these molecular chaperones and the effect of ligands and solvent composition. Such analysis seems to be useful for understanding the folding mechanism not only of the GroEL/GroES complex, but also of other oligomeric protein complexes.
Keywords: protein folding, molecular chaperones, GroEL, GroES

AGR2, ERp57/GRP58, and some other human protein disulfide isomerases by S. S. Shishkin; L. S. Eremina; L. I. Kovalev; M. A. Kovaleva (1415-1430).
This review considers the major features of human proteins AGR2 and ERp57/GRP58 and of other members of the protein disulfide isomerase (PDI) family. The ability of both AGR2 and ERp57/GRP58 to catalyze the formation of disulfide bonds in proteins is the parameter most important for assigning them to a PDI family. Moreover, these proteins and also other members of the PDI family have specific structural features (thioredoxin-like domains, special C-terminal motifs characteristic for proteins localized in the endoplasmic reticulum, etc.) that are necessary for their assignment to a PDI family. Data demonstrating the role of these two proteins in carcinogenesis are analyzed. Special attention is given to data indicating the presence of biomarker features in AGR2 and ERp57/GRP58. It is now thought that there is sufficient reason for studies of AGR2 and ERp57/GRP58 for possible use of these proteins in diagnosis of tumors. There are also prospects for studies on AGR2 and ERp57/GRP58 leading to developments in chemotherapy. Thus, we suppose that further studies on different members of the PDI family using modern postgenomic technologies will broaden current concepts about functions of these proteins, and this will be helpful for solution of urgent biomedical problems.
Keywords: protein disulfide isomerases; detection in tumoral cells; markers of cancer

Hydroxylamine derivatives for regulation of spermine and spermidine metabolism by M. A. Khomutov; J. Weisell; M. Hyvönen; T. A. Keinänen; J. Vepsäläinen; L. Alhonen; A. R. Khomutov; S. N. Kochetkov (1431-1446).
The biogenic polyamines spermine, spermidine, and their precursor putrescine are present in micro-to-millimolar concentrations in all cell types and are vitally important for their normal growth. High intracellular content of spermine and spermidine determines the multiplicity of the cellular functions of the polyamines. Many of these functions are not well characterized at the molecular level, ensuring the ongoing development of this field of biochemistry. Tumor cells have elevated polyamine level if compared with normal cells, and this greatly stimulates the search for new opportunities to deplete the intracellular pool of spermine and spermidine resulting in decrease in cell growth and even cell death. O-Substituted hydroxylamines occupy their own place among chemical regulators of the activity of the enzymes of polyamine metabolism. Varying the structure of the alkyl substituent made it possible to obtain within one class of chemical compounds highly effective inhibitors and regulators of the activity of all the enzymes of putrescine, spermine and spermidine metabolism (with the exception of FAD-dependent spermine oxidase and acetylpolyamine oxidase), effectors of the polyamine transport system, and even actively transported in cells “proinhibitor” of ornithine decarboxylase. Some principles for the design of specific inhibitors of these enzymes as well as the peculiarities of cellular effects of corresponding O-substituted hydroxylamines are discussed.
Keywords: polyamines; spermine; spermidine; O-substituted hydroxylamines; ornithine decarboxylase; S-adenosylmethionine decarboxylase; spermidine/spermine-N 1-acetyltransferase; cell culture

Troponin complex is a component of skeletal and cardiac muscle thin filaments. It consists of three subunits — troponin I, T, and C, and it plays a crucial role in muscle activity, connecting changes in intracellular Ca2+ concentration with generation of contraction. In spite of more than 40 years of studies, many aspects of troponin functioning are still not completely understood, and several models describing the mechanism of muscle contraction exist. Being a key factor in the regulation of cardiac muscle contraction, troponin complex is utilized in medicine as a target for some cardiotonic drugs used in the treatment of heart failure. A number of mutations in troponin subunits are associated with development of different types of cardiomyopathy. Moreover, for the last 25 years cardiac isoforms of troponin I and T have been widely used for immunochemical diagnostics of pathologies associated with cardiomyocyte death (myocardial infarction, myocardial trauma, and others). This review summarizes the existing evidence on the structure and function of troponin complex subunits, their role in the regulation of cardiac muscle contraction, and their clinical applications.
Keywords: troponin complex; muscle contraction; phosphorylation; troponin I; troponin T; troponin C

Hypochlorous acid as a precursor of free radicals in living systems by O. M. Panasenko; I. V. Gorudko; A. V. Sokolov (1466-1489).
Hypochlorous acid (HOCl) is produced in the human body by the family of mammalian heme peroxidases, mainly by myeloperoxidase, which is secreted by neutrophils and monocytes at sites of inflammation. This review discusses the reactions that occur between HOCl and the major classes of biologically important molecules (amino acids, proteins, nucleotides, nucleic acids, carbohydrates, lipids, and inorganic substances) to form free radicals. The generation of such free radical intermediates by HOCl and other reactive halogen species is accompanied by the development of halogenative stress, which causes a number of socially important diseases, such as cardiovascular, neurodegenerative, infectious, and other diseases usually associated with inflammatory response and characterized by the appearance of biomarkers of myeloperoxidase and halogenative stress. Investigations aimed at elucidating the mechanisms regulating the activity of enzyme systems that are responsible for the production of reactive halogen species are a crucial step in opening possibilities for control of the development of the body’s inflammatory response.
Keywords: myeloperoxidase; hypochlorous acid; free radicals; reactive halogen species; halogenative stress; biomarker of myeloperoxidase; inflammation

Mitochondrial production of reactive oxygen species by V. G. Grivennikova; A. D. Vinogradov (1490-1511).
Numerous biochemical studies are aimed at elucidating the sources and mechanisms of formation of reactive oxygen species (ROS) because they are involved in cellular, organ-, and tissue-specific physiology. Mitochondria along with other cellular organelles of eukaryotes contribute significantly to ROS formation and utilization. This review is a critical account of the mitochondrial ROS production and methods for their registration. The physiological and pathophysiological significance of the mitochondrially produced ROS are discussed.
Keywords: oxidoreductases; respiratory chain; ROS production; mitochondria

ATP synthases (FoF1-ATPases) of chloroplasts, mitochondria, and bacteria catalyze ATP synthesis or hydrolysis coupled with the transmembrane transfer of protons or sodium ions. Their activity is regulated through their reversible inactivation resulting from a decreased transmembrane potential difference. The inactivation is believed to conserve ATP previously synthesized under conditions of sufficient energy supply against unproductive hydrolysis. This review is focused on the mechanism of nucleotide-dependent regulation of the ATP synthase activity where the so-called noncatalytic nucleotide binding sites are involved. Properties of these sites varying upon free enzyme transition to its membrane-bound form, their dependence on membrane energization, and putative mechanisms of noncatalytic site-mediated regulation of the ATP synthase activity are discussed.
Keywords: noncatalytic sites; F1-ATPase; ATP synthase; activation/inactivation; regulation

Structural studies on photosystem II of cyanobacteria by A. G. Gabdulkhakov; M. V. Dontsova (1524-1538).
Photosynthesis is one of the most important chemical processes in the biosphere responsible for the maintenance of life on Earth. Light energy is converted into energy of chemical bonds in photoreaction centers, which, in particular, include photosystem II (PS II). PS II is a multisubunit pigment-protein complex located in the thylakoid membrane of cyanobacteria, algae and plants. PS II realizes the first stage of solar energy conversion that results in decomposition of water to molecular oxygen, protons, and bound electrons via a series of consecutive reactions. During recent years, considerable progress has been achieved in determination of the spatial structures of PS II from various cyanobacteria. In the present review, we outline the current state of crystallographic studies on PS II.
Keywords: photosystem II; water oxidation; manganese cluster; lipids; plastoquinone; channels

Biocatalytic synthesis of conducting polymers and prospects for its application by G. V. Otrokhov; O. V. Morozova; I. S. Vasil’eva; G. P. Shumakovich; E. A. Zaitseva; M. E. Khlupova; A. I. Yaropolov (1539-1553).
Enzymatic methods of synthesis of conducting polymers, physicochemical properties of the resulting products, and mechanisms of the reactions are considered. The enzymes involved in oxidative polymerization of monomers are briefly characterized. Examples of practical application of enzymatically synthesized conducting polymers are given.
Keywords: conducting polymer; physicochemical properties; enzymatic polymerization; redox mediator; laccase; peroxidase; practical application

Methods for the quantitative estimation of the antiaggregation activity of protein chaperones (first of all, small heat shock proteins) and chemical chaperones including amino acids, carbohydrates, polyamines, and cyclodextrins are discussed. Based on analysis of the plots of light scattering intensity or apparent optical absorption versus time, formulas for calculation of initial rate of aggregation of protein substrate and lag period on kinetic curves of aggregation were derived. Possible determination of the stoichiometry of chaperone-protein substrate complex from the dependence of the initial rate of aggregation on the ratio of protein chaperone/protein substrate concentrations is discussed. To characterize efficiency of the protective action of chemical chaperones, the [L]0.5 value can be used ([L]0.5 is the concentration of a chemical chaperone at which twofold decrease in the initial rate of aggregation occurs). Methods for quantitative estimation of the combined protective action of chaperones are discussed.
Keywords: small heat shock proteins; chemical chaperones; protein aggregation; chaperone-like activity; cyclodextrins