Biochemistry (Moscow) (v.72, #13)

The p53 tumor suppressor plays a pivotal role in multicellular organism by enforcing benefits of the organism over those of an individual cell. The task of p53 is to control the integrity and correctness of all processes in each individual cell and in the organism as a whole. Information about the state of ongoing events in the cell is gathered through multiple signaling pathways that convey signals modifying activities of p53. Changes in the activities depend on the character of damages or deviations from optimum in processes, and the activity of p53 changes depending on the degree of the aberration, which results in either stimulation of repair processes and protective mechanisms, or the cessation of further cell divisions and the induction of programmed cell death. The strategy of p53 ensures genetic identity of cells and prevents the selection of abnormal cells. By accomplishing these strategic tasks, p53 may use a wide spectrum of activities, such as its ability to function as a transcription factor, by inducing or repressing different genes, or as an enzyme, by acting as an exonuclease during DNA reparation, or as an adaptor or a regulatory protein, intervening into functions of numerous signaling pathways. Loss of function of the p53 gene occurs in virtually every case of cancer, and deficiency in p53 is an unavoidable prerequisite to the development of malignancies. The functions of p53 play substantial roles in many other pathologies as well as in the aging process. This review is focused on strategies of the p53 gene, demonstrating individual mechanisms underlying its functions.
Keywords: genetic stability; tumor suppressors; apoptosis; carcinogenesis; aging; cell growth regulation

Noncoding RNAs and chromatin structure by S. A. Lavrov; M. V. Kibanov (1422-1438).
A number of examples of noncoding RNA-connected chromatin modifications in eukaryotes has been recently revealed. Four cases are under detailed consideration in the present review, namely Xist RNA-dependent X-chromosome inactivation in mammals, roX RNA-dependent hyperactivation of X-chromosome in the fruit fly (in both cases the goal is dosage compensation, equalization of transcription level from two X chromosomes in females and one in males), and two examples of RNAi-connected down-regulation of transcription—siRNA-dependent heterochromatin formation in fission yeast and RdDM (RNA-dependent DNA methylation) in plants (FWA gene regulation in Arabidopsis). Although overall quite different, each phenomenon demonstrates some common features of RNA-driven chromatin modification process, including the role of RNA in aiming of chromatin-modifying protein complexes to their targets and subsequent formation of self-maintaining specific chromatin conformation (DNA methylation, changes in histone code, and binding of self-assembling protein complexes).
Keywords: RNA interference; chromatin structure; transcription regulation

Nucleocytoplasmic transport of proteins by A. V. Sorokin; E. R. Kim; L. P. Ovchinnikov (1439-1457).
In eukaryotic cells, the movement of macromolecules between the nucleus and cytoplasm occurs through the nuclear pore complex (NPC)—a large protein complex spanning the nuclear envelope. The nuclear transport of proteins is usually mediated by a family of transport receptors known as karyopherins. Karyopherins bind to their cargoes via recognition of nuclear localization signal (NLS) for nuclear import or nuclear export signal (NES) for export to form a transport complex. Its transport through NPC is facilitated by transient interactions between the karyopherins and NPC components. The interactions of karyopherins with their cargoes are regulated by GTPase Ran. In the current review, we describe the NPC structure, NLS, and NES, as well as the model of classic Ran-dependent transport, with special emphasis on existing alternative mechanisms; we also propose a classification of the basic mechanisms of protein transport regulation.
Keywords: nucleocytoplasmic transport; nuclear pore complex; nucleoporin; exportin; importin; karyopherin; nuclear export signal; nuclear localization signal; Ran

This review summarizes contemporary data on structure and function of photoactive pigment—enzyme complexes of the chlorophyll precursor that undergoes photochemical transformation to chlorophyllide. The properties and functions of the complex and its principal components are considered including the pigment (protochlorophyllide), the hydrogen donor (NADPH), and the photoenzyme protochlorophyllide oxidoreductase (POR) that catalyzes the photochemical production of chlorophyllide. Chemical variants of the chlorophyll precursor are described (protochlorophyllide, protochlorophyll, and their mono- and divinyl forms). The nature and photochemical activity of spectrally distinct native protochlorophyllide forms are discussed. Data are presented on structural organization of the photoenzyme POR, its substrate specificity, localization in etioplasts, and heterogeneity. The significance of different POR forms (PORA, PORB, and PORC) in adaptation of chlorophyll biosynthesis to various illumination conditions is considered. Attention is paid to structural and functional interactions of three main constituents of the photoactive complex and to possible existence of additional components associated with the pigment-enzyme complex. Historical aspects of the problem and the prospects of further investigations are outlined.
Keywords: chlorophyll biosynthesis; photoreduction of protochlorophyllide; protochlorophyllide oxidoreductase; pigment—protein complexes

Cell cytoplasm contains high concentrations of macromolecules occupying a significant part of the cell volume (crowding conditions). According to modern concepts, crowding has a pronounced effect on the rate and equilibrium of biochemical reactions and stimulates the formation of more compact structures. This review considers different aspects of the crowding effect in vivo and in vitro, its role in regulation of cell volume, the effect of crowding on various interactions, such as protein-ligand and protein-protein interactions, as well as on protein denaturation, conformation transitions of macromolecules, and supramolecular structure formation. The influence of crowding arising from the presence of high concentrations of osmolytes on the interactions of the enzymes of glycogenolysis has been demonstrated. It has been established that, in accordance with predictions of crowding theory, trimethylamine N-oxide (TMAO) and betaine highly stimulate the association of phosphorylase kinase (PhK) and its interaction with glycogen. However, high concentrations of proline, betaine, and TMAO completely suppress the formation of PhK complex with phosphorylase b (Phb). The protective effect of osmolyte-induced molecular crowding on Phb denaturation by guanidine hydrochloride is shown. The influence of crowding on the interaction of Phb with allosteric inhibitor FAD has been revealed. The results show that, under crowding conditions, the equilibrium of the isomerization of Phb shifts towards a more compact dimeric state with decreased affinity for FAD.
Keywords: glycogen phosphorylase b ; kinase phosphorylase; molecular crowding; osmolytes; protein association; protein denaturation

Biological activity of hemoprotein nitrosyl complexes by A. N. Osipov; G. G. Borisenko; Yu. A. Vladimirov (1491-1504).
Chemical and biological functions of hemoprotein nitrosyl complexes as well as their photolysis products are discussed in this review. Chemical properties of nitric oxide are discussed, and major chemical reactions such as interaction with thiols, free radicals, and transition metals are considered. Specific attention is paid to the generation of hemoprotein nitrosyl complexes. The mechanisms of nitric oxide reactions with hemoglobin and cytochrome c and physicochemical properties of their nitrosyl complexes are discussed. A review of photochemical reactions of nitrosyl complexes with various ligands is given. Finally, we observe physiological effects of visible radiation on hemoprotein nitrosyl complexes: smooth muscle relaxation and reactivation of mitochondrial respiration.
Keywords: hemoproteins; nitric oxide; laser radiation

Methods for selection of aptamers to protein targets by A. V. Kulbachinskiy (1505-1518).
Aptamers are synthetic single-stranded RNA or DNA molecules capable of specific binding to other target molecules. In this review, the main aptamer properties are considered and methods for selection of aptamers against various protein targets are described. Special attention is given to the methods for directed selection of aptamers, which allow one to obtain ligands with specified properties.
Keywords: aptamers; aptazymes; SELEX; site-directed selection

Prions by I. S. Shkundina; M. D. Ter-Avanesyan (1519-1536).
Prions were originally defined as infectious agents of protein nature, which caused neurodegenerative diseases in animals and humans. The prion concept implies that the infectious agent is a protein in special conformation that can be transmitted to the normal molecules of the same protein through protein-protein interactions. Until the 1990s, the prion phenomenon was associated with the single protein named PrP. Discovery of prions in lower eukaryotes, the yeast Saccharomyces cerevisiae and fungus Podospora anserina, suggests that prions have wider significance. Prions of lower eukaryotes are not related to diseases; their propagation caused by aggregation of prion-like proteins underlies the inheritance of phenotypic traits and most likely has adaptive significance. This review covers prions of mammals and lower eukaryotes, mechanisms of their appearance de novo and maintenance, structure of prion particles, and prospects for the treatment of prion diseases. Recent data concerning the search for new prion-like proteins is included. The paper focuses on the [PSI +] prion of S. cerevisiae, since at present it is the most investigated one. The biological significance of prions is discussed.
Keywords: prion; PrP; neurodegenerative disease; non-chromosomal inheritance; conformational rearrangement