Dual Character of Reactive Oxygen, Nitrogen, and Halogen Species: Endogenous Sources, Interconversions and Neutralization.

Oxidative stress resulting from accumulation of reactive oxygen, nitrogen, and halogen species (ROS, RNS, and RHS, respectively) causes the damage of cells and biomolecules. However, over the long evolutionary time, living organisms have developed the mechanisms for adaptation to oxidative stress conditions including the activity of the antioxidant system (AOS), which maintains low intracellular levels of RONS (ROS and RNS) and RHS. Moreover, living organisms have adapted to use low concentrations of these electrophiles for the regulation of cell functions through the reversible post-translational chemical modifications of redox-sensitive amino acid residues in intracellular effectors of signal transduction pathways (protein kinases and protein phosphatases), transcription factors, etc. An important fine-tuning mechanism that ensures involvement of RONS and RHS in the regulation of physiological processes is interconversion between different reactive species. This review focuses on the complex networks of interacting RONS and RHS types and their endogenous sources, such as NOX family of NADPH oxidases, complexes I and III of the mitochondrial electron transport chain, NO synthases, cytochrome P450-containing monooxygenase system, xanthine oxidoreductase, and myeloperoxidases. We highlight that kinetic parameters of reactions involving RONS and RHS determine the effects of these reactive species on cell functions. We also describe the functioning of enzymatic and non-enzymatic AOS components and the mechanisms of RONS and RHS scavenging under physiological conditions. We believe that analysis of interactions between RONS and relationships between different endogenous sources of these compounds will contribute to better understanding of their role in the maintenance of cell redox homeostasis as well as initiation and progression of diseases.

ROS and RNS signalling: adaptive redox switches through oxidative/nitrosative protein modifications.

Over the last decade, a dual character of cell response to oxidative stress, eustress versus distress, has become increasingly recognized. A growing body of evidence indicates that under physiological conditions, low concentrations of reactive oxygen and nitrogen species (RONS) maintained by the activity of endogenous antioxidant system (AOS) allow reversible oxidative/nitrosative modifications of key redox-sensitive residues in regulatory proteins. The reversibility of redox modifications such as Cys S-sulphenylation/S-glutathionylation/S-nitrosylation/S-persulphidation and disulphide bond formation, or Tyr nitration, which occur through electrophilic attack of RONS to nucleophilic groups in amino acid residues provides redox switches in the activities of signalling proteins. Key requirement for the involvement of the redox modifications in RONS signalling including ROS-MAPK, ROS-PI3K/Akt, and RNS-TNF-α/NF-kB signalling is their specificity provided by a residue microenvironment and reaction kinetics. Glutathione, glutathione peroxidases, peroxiredoxins, thioredoxin, glutathione reductases, and glutaredoxins modulate RONS level and cell signalling, while some of the modulators (glutathione, glutathione peroxidases and peroxiredoxins) are themselves targets for redox modifications. Additionally, gene expression, activities of transcription factors, and epigenetic pathways are also under redox regulation. The present review focuses on RONS sources (NADPH-oxidases, mitochondrial electron-transportation chain (ETC), nitric oxide synthase (NOS), etc.), and their cross-talks, which influence reversible redox modifications of proteins as physiological phenomenon attained by living cells during the evolution to control cell signalling in the oxygen-enriched environment. We discussed recent advances in investigation of mechanisms of protein redox modifications and adaptive redox switches such as MAPK/PI3K/PTEN, Nrf2/Keap1, and NF-κB/IκB, powerful regulators of numerous physiological processes, also implicated in various diseases.

Alpha-fetoprotein: a renaissance.

Alpha-fetoprotein (AFP) is a major mammalian embryo-specific and tumor-associated protein that is also present in small quantities in adults at normal conditions. Discovery of the phenomenon of AFP biosynthesis in carcinogenesis by G. Abelev and Yu. Tatarinov 50 years ago, in 1963, provoked intensive studies of this protein. AFPs of some mammalian species were isolated, purified and physico-chemically and immunochemically characterized. Despite the significant success in study of AFP, its three-dimensional structure, mechanisms of receptor binding along with a structure of the receptor itself and, what is the most important, its biological role in embryo- and carcinogenesis remain still obscure. Due to difficulties linked with methodological limitations, research of AFP was to some extent extinguished by the 1990 s. However, over the last decade a growing number of investigations of AFP and its usage as a tumor-specific biomarker have been observed. This was caused by the use of new technologies, primarily, computer-based and genetic engineering approaches in studying of this very important oncodevelopmental protein. Our review summarizes efforts of different scientific groups throughout the world in studying AFP for 50 years with emphasis on detailed description of recent achievements in this field.

Correlation between biological activity and conformational dynamics properties of tetra- and pentapeptides derived from fetoplacental proteins.

In this work, using molecular dynamics simulation, we study conformational and dynamic properties of biologically active penta- and tetrapeptides derived from fetoplacental proteins such as alpha-fetoprotein, pregnancy specific ß1-glycoprotein, and carcinoembryonic antigen. Existence of correlation between flexibility of peptide backbone and biological activity of the investigated peptides was shown. It was also demonstrated that flexibility of peptide backbone depends not only on its length, but also on the presence of reactive functional groups in amino acid side chains that participate in intramolecular interactions. Peptides that demonstrate similar biological effects in regulation of proliferation of lymphocytes and expression of differentiation antigens on their surface (LDSYQCT, PYECE, YECE, and YVCE) are characterized by rigidity of their peptide backbone. Increased backbone flexibility in peptides PYQCE, YQCE, SYKCE, YQCT, YQCS, YVCS, YACS, and YACE is correlated with decreased biological activity. Conformational mobility of amino acid residues does not depend on physicochemical properties only, but also on intramolecular interactions. So, evolutionary restrictions should exist to maintain such interactions in the environment of functionally important sites.

Influence of intramolecular interactions on conformational and dynamic properties of analogs of heptapeptide AFP(14-20).

Conformational and dynamic properties of proteins and peptides play an important role in their functioning. However, mechanisms that underlie this influence have not been fully elucidated. In the present work we computationally constructed analogs of heptapeptide AFP(14-20) (LDSYQCT) - one of the biologically active sites of human α-fetoprotein (AFP) - to study their conformational and dynamic properties using molecular dynamics simulation. Analogs were obtained by point substitutions of amino acid residues taking into account differences in their physicochemical properties and also on the basis of analysis of amino acid substitutions in the AFP(14-20)-like motifs revealed in different physiologically active proteins. It is shown that changes in conformational mobility of amino acid residues of analogs are due to disruption or arising of intramolecular interactions that, in turn, determine existence of steric restrictions during rotation around covalent bonds of the peptide backbone. Substitution of an amino acid by another one with significant difference in physicochemical properties may not lead to remarkable changes in conformational and dynamic properties of the peptide if intramolecular interactions remain unchanged.

Dynamic proteomics in modeling of the living cell. Protein-protein interactions.

This review is devoted to describing, summarizing, and analyzing of dynamic proteomics data obtained over the last few years and concerning the role of protein-protein interactions in modeling of the living cell. Principles of modern high-throughput experimental methods for investigation of protein-protein interactions are described. Systems biology approaches based on integrative view on cellular processes are used to analyze organization of protein interaction networks. It is proposed that finding of some proteins in different protein complexes can be explained by their multi-modular and polyfunctional properties; the different protein modules can be located in the nodes of protein interaction networks. Mathematical and computational approaches to modeling of the living cell with emphasis on molecular dynamics simulation are provided. The role of the network analysis in fundamental medicine is also briefly reviewed.

[A molecular dynamics simulation study of human alpha-fetoprotein-derived peptide and its analogues. Influence of dielectric constant].

A comparative study of the conformation dynamics of a series of heptapeptides: the human alpha-fetoprotein fragment LDSYQCT and its seven analogues has been conducted. The effect of the dielectric constant of medium on the dynamics of heptapeptide conformation is considered. It is shown that electrostatic interactions have a marked effect on several accessible conformations and the dynamics of the behavior of amino acid residues.

Cell adhesion proteins and alpha-fetoprotein. Similar structural motifs as prerequisites for common functions.

This review summarizes and analyzes data on structural and functional relationships between cell adhesion proteins and alpha-fetoprotein (AFP), which play an important role in embryo- and carcinogenesis and act in synergism with growth factors. These two groups of proteins are mosaic, multimodular, and polyfunctional, and each of their modules can function independently through binding with its specific membrane receptor. Most cell adhesion proteins contain modules similar to epidermal growth factor (EGF) and also their repeats, which determine the involvement of these proteins in regulation of cell proliferation, differentiation, and apoptosis. These EGF-like modules are found to include short motifs similar to the fragment LDSYQCT of human AFP. Both direct and inverted AFP-like motifs are linked through a consensus octapeptide motif CXXGY/FXGX. Such AFP-like motifs of cell adhesion proteins and the tripeptide RGD found in AFP may be structural prerequisites for common functions of these groups of nonhomologous and unrelated proteins.

Conformational dynamics of human alpha-fetoprotein-derived heptapeptide LDSYQCT analogs.

Conformational dynamics of a biologically active fragment of alpha-fetoprotein, the heptapeptide LDSYQCT, and its analogs obtained by site-directed substitutions of amino acid residues were studied. The conformational dynamics of the peptide were conservative under the substitutions Y17F, Y17S, and D15E. Substitutions C19A and S16V resulted only in local changes in the dynamic behavior of the peptide. Chemical modification of cysteine (C19) or dimerization of the peptide by producing a disulfide bond between cysteine residues of two parallel peptide chains, as well as the substitutions C19G, C19S, Q18E, and D15N changed a set of possible conformations and dynamic behavior of all amino acid residues. The most significant changes were caused by substitution of uncharged amino acid residues by charged ones, and vice versa.

Structural and functional mapping of alpha-fetoprotein.

Alpha-fetoprotein (AFP) is a major mammalian oncofetal protein, which is also present in small quantities in adults. It is a member of the albuminoid gene superfamily, which consists of AFP, serum albumin, vitamin D binding protein, and alpha-albumin (afamin). Although physicochemical and immunological properties of AFP have been well-studied, its biological role in embryo- and carcinogenesis and in adult organisms as well as mechanisms underlying its functioning remain unclear. During the recent decades, the biological role of AFP has been evaluated by identification of its functionally important sites. Comparison of primary structure of AFP and some physiologically active proteins revealed similarity of some polypeptide regions. This has been used for prediction of AFP functions (i.e., its multifunctionality). Localization of functionally important sites followed by determination of their amino acid composition and type of biological activity has provided valuable information for structural-functional mapping of AFP. Some peptide fragments of AFP have been synthesized and tested for biological activity. This review summarizes data on structural-functional interrelationships. We also describe functionally important AFP sites found by various groups during the last decade of structural-functional mapping of AFP with experimentally confirmed and putative biologically active sites.

[Relationship between structure and function of alpha-fetoprotein: conformational status and biological activity].

Alpha-fetoprotein (AFP) is the major mammalian fetal protein and the recognized tumor marker. This review summarizes data on structure and function of AFP with emphasis on human AFP, which is intensively investigated. During the last decade multiple functionally important sites of human AFP have been revealed or predicted by searching of similarity between primary structures of AFP and other proteins or their DNA sequences. A number of peptides derived from human AFP have been studied by different teams of investigators. These peptides were obtained by limited proteolysis of AFP or synthesized using solid phase chemistry. Study of biological (physiological) activities of these peptides allows determining biologically active sites of alpha-fetoprotein and constructing its structural and functional map. Biomodulating properties of these peptides make them a potential basis for design of drugs for different purposes including using in anticancer therapy. Conformational changes in AFP molecule have been intensively studied for the last few years and sufficient conformational mobility of AFP with the ability to form molten globule form (MGF) despite its stability in solution has been demonstrated. Native molecule of AFP may contain cryptic biologically active sites, which are not available for ligand binding. These sites become open and available for interaction after changes in conformation of AFP molecule. Study of conformational changes of AFP under different conditions allows understanding molecular mechanisms of its functioning. This review describes and analyses data obtained, mainly, during the last few years on study of conformational states of alpha-fetoprotein and relationship between conformational changes of AFP and its biological activity. Biochemical, biophysical and functional characterislics of some well-studied peptide fragments of AFP and their structural and functional mapping are presented.

[Affinity chromatography of mouse and rat alpha-fetoproteins on immobilized diethylstilbestrol]. / Affinnaia khromatografiia al'fa-fetoproteinov myshi i krysy na immobilizovannom diétilstil'bestrole.

Alpha-fetoproteins (AFP) from amniotic fluid of mouse and rat demonstrate high affinity and specificity during their binding with immobilized diethylstilbestrol, which allows to isolate these two proteins by one step using the method of affinity chromatography on Sepharose with immobilized diethylstilbestrol. Meanwhile the yield of mouse AFP was 42%, and rat AFP--75%. The preliminary incubation of the amniotic fluid of rat and mouse with free estradiol results in abrupt fall of AFP outcome, which may testify to the binding of estradiol and diethylstilbestrol by the same receptor sites on AFP molecule.

Human alpha-fetoprotein and its purification by chromatography on immobilized estrogens.

Human alpha-fetoprotein (AFP) was isolated from human abortive tissue by biospecific chromatography on immobilized estrogens. The most effective sorbents were: estrone-0-3-hemisuccinyl-hexamethylenediamine-Sepharose CL 4B and diethylstilbestrol-diasoanisole-sulfonyl-oxyethyl-Sepharose CL 4B. As elution solution the most optimum was 10% buffered aqueous butanol. Taking into consideration the data obtained, one can conclude that AFP in human biological fluids is bound to immobilized estrogens. Butanol extraction deestrogenizes AFP, and as a result human AFP acquires affinity to immobilized estrogens. During rechromatography on immobilized diethylstilbestrol, it was possible to obtain AFP preparations of about 95% purity. The present results provide the opportunity to work out new methodological approaches to human AFP isolation using biospecific chromatography on immobilized estrogens.

[Competitive affinity chromatography of human alpha fetoprotein on immobilized diethylstilbestrol]. / Konkurentnaia affinnaia khromatografiia al'fa-fetoproteina cheloveka na immobilizovannom diétilstil'bestrole.

Human alpha-fetoprotein (AFP) was isolated by affinity chromatography method on immobilized diethylstilbestrol from butanol extract of abortive material. Elution from the column was performed with 10% aqueous buffered butanol solution, pH 8.6. During one procedure human AFP-preparation containing about 10% of AFP and about 90% of albumin was obtained, with the yield about 60%. The preliminary incubation of extract of the abortive material with estrone raised AFP yield up to 85% with the increase of AFP content in the preparation up to 35%, and preincubation with estriol and estradiol caused the increase of the yield up to 88-92%, and AFP content in the preparation was 50% and 65%, respectively. The preincubation of human AFP with diethylstilbestrol lowers the yield of this protein, which testified to the possible binding of human AFP with free diethylstilbestrol; testosterone, hydrocortisone and desoxycorticosterone caused the increase of the yield of AFP. So the competitive variant of the affinity chromatography on immobilized diethylstilbestrol makes it possible to raise human AFP preparation purity and yield by decreasing the competition between AFP, and not binding free steroid hormones, ad albumin for immobilized diethylstilbestrol.

[Affinity chromatography of human alpha-fetoprotein on immobilized estrogens]. / Affinnaia khromatografiia al'fa-fetoproteina cheloveka na immobilizovannykh éstrogenakh.

Human alpha-fetoprotein was isolated from abortive material with the help of affinity chromatography on immobilized estrogens. After butanol extraction from the abortive material human AFP obtained the ability for affinity binding with immobilized estrogens. The addition of estrogens to the extract of isolated AFP preparation and incubation with them did not lower AFP binding with immobilized estrogens during the experiments, using affinity chromatography. A 10% buffered aqueous butanol solution was most optimal for elution. The data obtained can suggest that AFP in biological fluids is bound to estrogens, and butanol extraction deestrogenizes human AFP. The mechanism of AFP binding to estrogens in vivo is, evidently, carried out with the help of specific unknown carrier, as AFP does not bind free estrogens.