Biochemistry (Moscow) (v.82, #13)

The ribosome as an allosterically regulated molecular machine by T. M. Makarova; A. A. Bogdanov (1557-1571).
The ribosome as a complex molecular machine undergoes significant conformational rearrangements during the synthesis of polypeptide chains of proteins. In this review, information obtained using various experimental methods on the internal consistency of such rearrangements is discussed. It is demonstrated that allosteric regulation involves all the main stages of the operation of the ribosome and connects functional elements remote by tens and even hundreds of angstroms. Data obtained using Förster resonance energy transfer (FRET) show that translocation is controlled in general by internal mechanisms of the ribosome, and not by the position of the ligands. Chemical probing data revealed the relationship of such remote sites as the decoding, peptidyl transferase, and GTPase centers of the ribosome. Nevertheless, despite the large amount of experimental data accumulated to date, many details and mechanisms of these phenomena are still not under- stood. Analysis of these data demonstrates that the development of new approaches is necessary for deciphering the mech- anisms of allosteric regulation of the operation of the ribosome.
Keywords: ribosome; allostery; allosteric regulation; tRNA; rRNA

Properties of bacterial and archaeal branched-chain amino acid aminotransferases by E. Yu. Bezsudnova; K. M. Boyko; V. O. Popov (1572-1591).
Branched-chain amino acid aminotransferases (BCATs) catalyze reversible stereoselective transamination of branched-chain amino acids (BCAAs) L-leucine, L-isoleucine, and L-valine. BCATs are the key enzymes of BCAA metab- olism in all organisms. The catalysis proceeds through the ping-pong mechanism with the assistance of the cofactor pyri- doxal 5′-phosphate (PLP). BCATs differ from other (S)-selective transaminases (TAs) in 3D-structure and organization of the PLP-binding domain. Unlike other (S)-selective TAs, BCATs belong to the PLP fold type IV and are characterized by the proton transfer on the re-face of PLP, in contrast to the si-specificity of proton transfer in fold type I (S)-selective TAs. Moreover, BCATs are the only (S)-selective enzymes within fold type IV TAs. Dual substrate recognition in BCATs is imple- mented via the “lock and key” mechanism without side-chain rearrangements of the active site residues. Another feature of the active site organization in BCATs is the binding of the substrate α-COOH group on the P-side of the active site near the PLP phosphate group. Close localization of two charged groups seems to increase the effectiveness of external aldimine for- mation in BCAT catalysis. In this review, the structure-function features and the substrate specificity of bacterial and archaeal BCATs are analyzed. These BCATs differ from eukaryotic ones in the wide substrate specificity, optimal tempera- ture, and reactivity toward pyruvate as the second substrate. The prospects of biotechnological application of BCATs in stereoselective synthesis are discussed.
Keywords: branched-chain amino acid aminotransferases (BCATs); pyridoxal 5′-phosphate catalysis; bacterial and archaeal enzymes; substrate specificity; 3D structure; dual substrate recognition; characteristic sequence motifs

Features of protein−protein interactions in the cyanobacterial photoprotection mechanism by N. N. Sluchanko; Y. B. Slonimskiy; E. G. Maksimov (1592-1614).
Photoprotective mechanisms of cyanobacteria are characterized by several features associated with the structure of their water-soluble antenna complexes–the phycobilisomes (PBs). During energy transfer from PBs to chlorophyll of photosystem reaction centers, the “energy funnel” principle is realized, which regulates energy flux due to the specialized interaction of the PBs core with a quenching molecule capable of effectively dissipating electron excitation energy into heat. The role of the quencher is performed by ketocarotenoid within the photoactive orange carotenoid protein (OCP), which is also a sensor for light flux. At a high level of insolation, OCP is reversibly photoactivated, and this is accompanied by a sig- nificant change in its structure and spectral characteristics. Such conformational changes open the possibility for pro- tein–protein interactions between OCP and the PBs core (i.e., activation of photoprotection mechanisms) or the fluores- cence recovery protein. Even though OCP was discovered in 1981, little was known about the conformation of its active form until recently, as well as about the properties of homologs of its N and C domains. Studies carried out during recent years have made a breakthrough in understanding of the structural-functional organization of OCP and have enabled discovery of new aspects of the regulation of photoprotection processes in cyanobacteria. This review focuses on aspects of protein–pro- tein interactions between the main participants of photoprotection reactions and on certain properties of representatives of newly discovered families of OCP homologs.
Keywords: orange carotenoid protein; carotenoids; photoprotection; fluorescence; energy transfer; photosynthesis, phyco-bilisomes

Enteroviruses: Classification, diseases they cause, and approaches to development of antiviral drugs by O. S. Nikonov; E. S. Chernykh; M. B. Garber; E. Yu. Nikonova (1615-1631).
The genus Enterovirus combines a portion of small (+)ssRNA-containing viruses and is divided into 10 species of true enteroviruses and three species of rhinoviruses. These viruses are causative agents of the widest spectrum of severe and deadly epidemic diseases of higher vertebrates, including humans. Their ubiquitous distribution and high pathogenici- ty motivate active search to counteract enterovirus infections. There are no sufficiently effective drugs targeted against enteroviral diseases, thus treatment is reduced to supportive and symptomatic measures. This makes it extremely urgent to develop drugs that directly affect enteroviruses and hinder their development and spread in infected organisms. In this review, we cover the classification of enteroviruses, mention the most common enterovirus infections and their clinical man- ifestations, and consider the current state of development of anti-enteroviral drugs. One of the most promising targets for such antiviral drugs is the viral Internal Ribosome Entry Site (IRES). The classification of these elements of the viral mRNA translation system is also examined.
Keywords: IRES; enteroviruses; Picornaviridae; translation initiation; drug design; taxonomy

Adsorption of bacteriophages on bacterial cells by A. V. Letarov; E. E. Kulikov (1632-1658).
The biological functions of bacteriophage virions come down to the solution of three basic problems: to provide protection of viral nucleic acid from the factors of extracellular environment, to recognize a host suitable for phage replication, and to provide the delivery of nucleic acid through bacterial cell envelopes. This review considers the main regularities of phage–cell interaction at the initial stages of infection of tailed bacteriophages, from the reversible binding with receptors on the surface to the beginning of phage DNA entry. Data on the structure and functions of the phage adsorption apparatus, the main quantitative characteristics of the adsorption process, and the mechanisms of adaptation of phages and their hosts to each other effective at the stage of adsorption are presented.
Keywords: bacteriophages; bacteriophage adsorption; bacteriophage adsorption kinetics; bacteriophage receptors; receptor-binding proteins; modulation of bacteriophage adsorption

Hevein-like antimicrobial peptides of plants by A. A. Slavokhotova; A. A. Shelenkov; Ya. A. Andreev; T. I. Odintsova (1659-1674).
Plant antimicrobial peptides represent one of the evolutionarily oldest innate immunity components providing the first line of host defense to pathogen attacks. This review is dedicated to a small, currently actively studied family of hevein-like peptides that can be found in various monocot and dicot plants. The review thoroughly describes all known pep- tides belonging to this family including data on their structures, functions, and antimicrobial activity. The main features allowing to assign these peptides to a separate family are given, and the specific characteristics of each peptide are described. Further, the mode of action for hevein-like peptides, their role in plant immune system, and the applications of these mol- ecules in biotechnology and medicine are considered.
Keywords: hevein-like peptides; antimicrobial peptides; plant immunity

Amyloid properties of titin by E. I. Yakupova; I. M. Vikhlyantsev; M. Y. Lobanov; O. V. Galzitskaya; A. G. Bobylev (1675-1685).
This review considers data on structural and functional features of titin, on the role of this protein in determination of mechanical properties of sarcomeres, and on specific features of regulation of the stiffness and elasticity of its molecules, amyloid aggregation of this protein in vitro, and possibilities of formation of intramolecular amyloid structure in vivo. Molecular mechanisms are described of protection of titin against aggregation in muscle cells. Based on the data analysis, it is supposed that titin and the formed by it elastic filaments have features of amyloid.
Keywords: amyloids; amyloidoses; titin; functional amyloids

Abstract—8-Oxo-7,8-dihydroguanine (8-oxo-G) is a key biomarker of oxidative damage to DNA in cells, and its genotox- icity is well-studied. In recent years, it has been confirmed experimentally that free 8-oxo-G and molecules containing it are not merely inert products of DNA repair or degradation, but they are actively involved in intracellular signaling. In this review, data are systematized indicating that free 8-oxo-G and oxidized (containing 8-oxo-G) extracellular DNA function in the body as mediators of stress signaling and initiate inflammatory and immune responses to maintain homeostasis under the action of external pathogens, whereas exogenous 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dGuo) exhibits pro- nounced antiinflammatory and antioxidant properties. This review describes known action mechanisms of oxidized guanine and 8-oxo-G-containing molecules. Prospects for their use as a therapeutic target are considered, as well as a pharmaceu- tical agent for treatment of a wide range of diseases whose pathogenesis is significantly contributed to by inflammation and oxidative stress.
Keywords: exogenous 8-oxo-7,8-dihydro-2′-deoxyguanosine; free 8-oxo-7,8-dihydroguanine; oxidized extracellular DNA; inflammation; small GTPases

Three-finger proteins from the Ly6/uPAR family: Functional diversity within one structural motif by N. A. Vasilyeva; E. V. Loktyushov; M. L. Bychkov; Z. O. Shenkarev; E. N. Lyukmanova (1702-1715).
The discovery in higher animals of proteins from the Ly6/uPAR family, which have structural homology with snake “three-finger” neurotoxins, has generated great interest in these molecules and their role in the functioning of the organism. These proteins have been found in the nervous, immune, endocrine, and reproductive systems of mammals. There are two types of the Ly6/uPAR proteins: those associated with the cell membrane by GPI-anchor and secreted ones. For some of them (Lynx1, SLURP-1, SLURP-2, Lypd6), as well as for snake α-neurotoxins, the target of action is nico- tinic acetylcholine receptors, which are widely represented in the central and peripheral nervous systems, and in many other tissues, including epithelial cells and the immune system. However, the targets of most proteins from the Ly6/uPAR family and the mechanism of their action remain unknown. This review presents data on the structural and functional properties of the Ly6/uPAR proteins, which reveal a variety of functions within a single structural motif.
Keywords: three-finger proteins; nicotinic acetylcholine receptor; Ly6/uPAR; Lynx1; Lypd6; SLURP

Novel HIV-1 non-nucleoside reverse transcriptase inhibitors: A combinatorial approach by V. T. Valuev-Elliston; S. N. Kochetkov (1716-1743).
Highly active antiretroviral therapy (HAART) is one of the most effective means for fighting against HIV-infec- tion. HAART primarily targets HIV-1 reverse transcriptase (RT), and 14 of 28 compounds approved by the FDA as anti- HIV drugs act on this enzyme. HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) hold a special place among HIV RT inhibitors owing to their high specificity and unique mode of action. Nonetheless, these drugs show a tendency to decrease their efficacy due to high HIV-1 variability and formation of resistant virus strains tolerant to clinically applied HIV NNRTIs. A combinatorial approach based on varying substituents within various fragments of the parent molecule that results in development of highly potent compounds is one of the approaches aimed at designing novel HIV NNRTIs. Generation of HIV NNRTIs based on pyrimidine derivatives explicitly exemplifies this approach, which is discussed in this review.
Keywords: HIV; HIV reverse transcriptase; inhibitors; NNRTIs

Mathematical modeling of bioassays by D. V. Sotnikov; A. V. Zherdev; B. B. Dzantiev (1744-1766).
The high affinity and specificity of biological receptors determine the demand for and the intensive development of analytical systems based on use of these receptors. Therefore, theoretical concepts of the mechanisms of these systems, quantitative parameters of their reactions, and relationships between their characteristics and ligand–receptor interactions have become extremely important. Many mathematical models describing different bioassay formats have been proposed. However, there is almost no information on the comparative characteristics of these models, their assumptions, and predic- tive insights. In this review we suggested a set of criteria to classify various bioassays and reviewed classical and contempo- rary publications on these bioassays with special emphasis on immunochemical analysis systems as the most common and in-demand techniques. The possibilities of analytical and numerical modeling are discussed, as well as estimations of the minimum concentrations that may be detected in bioassays and recommendations for the choice of assay conditions.
Keywords: bioassay; immunoassay; analytical modeling; numerical modeling; theoretical detection limit