Primary catalytic systems of biogenesis and structure-functional evolution of biocatalysers

An important aspect of biological evolution is the development of biocatalyzers. The connection between abiotic and biological catalyzers is discussed, and the role of metal ions as primary catalysts is considered. The evolutionary demand for greater specificity and efficiency may have been fulfilled through the formation of metal-organic complexes and later through enzyme systems. Metal ions are probably responsible for the formation of some of the isoenzymes found in contemporary organisms.     

Cellular and subcellular effects of very heavy ions

The biological effects of irradiation with ions of masses larger than 40 and energies up to 20 MeV per atomic mass unit are reviewed. The objects are viruses, bacterial spores, yeast and mammalian cells. Experimental parameters include loss of colony forming ability, induction of mutants, chromosomal aberrations, cell cycle progression, inhibition of biochemical activities and the formation of strand breaks. Some of the pertinent physical questions--e.g. track structure--are also discussed. It is shown that with very heavy ions the biological effectiveness is no longer unambiguously related to a single parameter like l.e.t. or Z*2/beta 2 but depends strongly on ion energy. This points to the importance of far-reaching delta-electrons. The analysis indicates also that even with very high l.e.t., cells are not killed by the passage of a single particle through their nucleus. Possible implications of the findings for fundamental radiation biology are outlined.     

Self-organization of mitochondrial associates and effects of negative air ions

A convenient model for studying the mechanisms of biological self-organization is described by morphometric investigation of formation of mitochondrion associations in medium containing physiological concentration of potassium ions without nonpolar substances. Association formation was considerably better at 15-18 degrees C during isolation and storage than at 0 degree C. The existence of filamented mitochondria in homogenate was also shown by staining of succinate dehydrogenase. Formation of associations increased in medium pretreated with negative air ions carrying superoxide and is probably due to hydrogen peroxide. The effect of substances influencing the surface charge on association formation was studied.     

Resistance to heavy metal toxicity in organisms under chronic exposure

The rate of changes of heavy metal ions concentrations in the organism or biological system will determine the choice of strategy of realization of heavy metal ions effect and, consequently, the biological effect itself. Which of the possible strategies will dominate, depend on the rate of changes of concentration of heavy metal ions in biological systems, functional activity of organism at the moment of metal action and on metals chemical properties. Keeping this view, the present review deals with the concept of time-based alterations of concentration of heavy metal ions (TACMI) in biological systems. On the basis of TACMI concept formation of organism resistance to metal ions action could be explained. In the event of slow increase of its concentration in organism, it produces induction of metallothioneins, other stress-proteins and relative changes in the whole metabolic system. This, first of all, results in formation of new specific epigenotypes, which provide higher resistance (hormesis effect) not only to metal ions that induced this effect, but also to such stress-factors as high temperature (at least, for micro-algae cells).     

Effects of Organic Matter on Solubilities and Crystal Form of Carbonates

The results of a study of the role of organic compounds in theformation of carlxmate crystals in marine biological systemsare reported. In an increasing concentration of certain organiccompounds which complex calcium ions, the proportion of aragonitedecreases and that of calcite increases. In increasing concentrationsof magnesium ions the proportion of aragonite increases andthat of calcite and vaterite decreases. When the influence oforganic compounds is greater or smaller than that of magnesiumions, only calcite or only aragonite is formed, respectively.Organic compounds forming a strong complex with calcium ionscause the formation of magnesium-rich calcite, and with an increasein temperature and the concentration of magnesium ions, themagnesium carbonate content of precipitated magnesian calciteincreases. When the influence of organic compounds is almostequivalent to that of magnesium ions, in increasing or decreasingtemperatures, the proportion of calcite decreases or increases,respectively, and the proportion of aragonite increases or decreases,respectively. The concentration of magnesium ions in the bodyfluids of marine calcareous organisms seems to differ littlefrom that of other organisms, and seems to be similar to thatof sea water. Only the presence of certain organic compoundsbrings about the formation of the carbonate crystals observedin marine biological systems. The very important role of organicmatter in the formation of crystals found in skeletal carbonatesis emphasized.     

Iron(III) reduction by D-galacturonic acid. Part II. Influence of uranyl(VI), lead(II), nickel(II), and cadmium(II) complexes formation

As a part of our study on iron reduction-mobilization in biological systems, in particular at root-soil interface, the effect of the addition of different metal ions to the iron(III)-D-galacturonic acid system has been investigated. The ions which are found to form particularly stable complexes with the galacturonate ligand strongly increase the yield of the reduction of iron(III) to iron(II). These findings are in agreement with the capability of some metal ions to form stable complexes through interaction both with the carboxylate group and with the ring oxygen atom of the sugar molecule, inducing opening of the ring and formation of a free aldehydic group. The importance of these processes in availability of iron to plant roots is emphasized.     

An extensive numerical simulation of the cephalic furrow formation in Drosophila embryo

Here, we propose a new finite element model of the Drosophila embryo to simulate the cephalic furrow (CF) formation. Two different 3D geometries are introduced to reproduce the embryo. The two of them are parametrised through a novel system of curvilinear coordinates, well adapted for biological structures, which is obtained by three fictive electrostatic potentials. A gradient decomposition method is used to take into account both the active and the passive deformations occurring to the cells. Four simulations of the CF are proposed, which in turn considers singular and coupled aspects of the problem.     

The interaction of calcium ions with glycocholate micelles in aqueous solution.

The formation of soluble complexes of Ca2+ ions and glycocholate has been demonstrated. The dissociation constant is 26 nmol/litre and a maximum of 2 Ca2+ ions are bound to each glycocholate micelle. The formation of this complex is shown to be reversible. Binding is increased by the introduction of phosphatidylcholine into the micelle; it is decreased by a decrease in pH and by increased counter-ion concentration. The biological significance of these effects is discussed.     

金属硫蛋白及其生物学功能

金属硫蛋白(metallothionein, MT) 是一类富含半胱氨酸的低分子质量蛋白质,已鉴定4种亚型：MT-1、MT-2、MT-3和MT-4,基于各亚型功能的相对异质性而使MT呈现其生物学作用的多样性。金属硫蛋白通过与金属离子结合而参与基因表达调控和机体的重金属解毒过程;金属硫蛋白通过抑制多种氧化应激途径而保护细胞免受损伤;金属硫蛋白通过参与细胞的增殖、分化和凋亡的调节而影响肿瘤及其他重大疾病的发生发展。本文在金属硫蛋白的结构和分类的基础上综述其生物学作用及其相关机制。     

A few remarks on 'combined action of DC and AC magnetic fields on ion motion in a macromolecule'

Zhadin and Barnes [2005:26:323-330] concluded that they solved the differential equation describing combined action of DC and AC magnetic fields on thermal motion of ions in a biological macromolecule and, as a result, a diversity of biological phenomena could be explained. It is shown here that biological phenomena cannot be explained based on this model. Adair [2006:27:332-334] gave several arguments for the statement that the interaction of weak magnetic fields with ions trapped in protein cavities cannot produce detectable biological effects through changing the character of the ion orbits. The arguments are analyzed here and some are shown to be questionable or unjustified. We stress the difference between the conclusion made by Adair and that stated in this article.     

Ion leakage through transient water pores in protein-free lipid membranes driven by transmembrane ionic charge imbalance

We have employed atomic-scale molecular dynamics simulations to address ion leakage through transient water pores in protein-free phospholipid membranes. Our results for phospholipid membranes in aqueous solution with NaCl and KCl salts show that the formation of transient water pores and the consequent ion leakage can be induced and be driven by a transmembrane ionic charge imbalance, an inherent feature in living cells. These processes take place if the gradient is large enough to develop a sufficiently significant potential difference across the membrane. The transport of cations and anions through the water pores is then seen; it discharges the transmembrane potential, considerably reduces the size of a water pore, and makes the water pore metastable, leading eventually to its sealing. The ion transport is found to be sensitive to the type of ions. It turns out that Na(+) and Cl(-) ions leak through a membrane at approximately the same ratio despite the fact that Na(+) ions are expected to experience a lower potential barrier for the permeation through the pore. This is because of strong interactions of sodium ions with the carbonyl region of a phospholipid membrane as well as with lipid headgroups forming pore "walls," considerably slowing down the permeation of sodium ions. In contrast, we observed a pronounced selectivity of a phospholipid membrane to the permeation of potassium ions as compared to chloride ions: Potassium ions, being larger than sodium ions, interact only weakly with phospholipid headgroups, so that these interactions are not able to compensate for a large difference in free-energy barriers for permeation of K(+) and Cl(-) ions. These findings are found to be robust to a choice of force-field parameters for ions (tested by Gromacs and Charmm force-fields for ions). What is more, a potassium ion is found to be able to permeate a membrane along an alternate, "water-defect-mediated" pathway without actual formation of a pore. The "water-defect-mediated" leakage involves formation of a single water defect only and is found to be at least one order of magnitude faster than the pore-mediated ion leakage.     

General features of the energetics of complex formation between ligand and nucleic acids

The analysis of the energy contributions of various physical factors to the complex formation between biologically active compounds and nucleic acids in aqueous solution was performed. A comparison of the energy parameters was made for ligand-ligand, intercalator-DNA, MGB-DNA and ligand-RNA groups. It was shown that the energetics of these reactions is of compensatory nature. Physical factors exerting the most pronounced influence on the energy parameters were identified. Correlation of the energy contributions to MGB-DNA complex formation and its biological effect was found.     

Reactions and reactivity of myeloperoxidase-derived oxidants: differential biological effects of hypochlorous and hypothiocyanous acids

Myeloperoxidase (MPO) is recognised to play important roles both in the immune system and during the development of numerous human pathologies. MPO is released by activated neutrophils, monocytes and some tissue macrophages, where it catalyses the conversion of hydrogen peroxide to hypohalous acids (HOX; X = Cl, Br, SCN) in the presence of halide and pseudo-halide ions. The major reactive species produced by MPO under physiological conditions are hypochlorous acid (HOCl) and hypothiocyanous acid (HOSCN), with the ratio of these oxidants critically dependent on the concentration of thiocyanate ions (SCN?). The reactivity and selectivity of HOCl and HOSCN for biological targets are markedly different, indicating that SCN? ions have the potential to modulate both the extent and nature of oxidative damage in vivo. This article reviews recent developments in our understanding of the role of SCN? in modulating the formation of MPO-derived oxidants, particularly in respect to the differences in reaction kinetics and targets of HOCl compared to HOSCN and the ability of these two oxidants to induce damage in biological systems.     

Effect of high hydrostatic pressure on hydration and activity of ribozymes

Formation and stabilization of RNA structure in the cell depends on its interaction with solvent and metal ions. High hydrostatic pressure (HHP) is a convenient tool in an analysis of the role of small molecules in the structure stabilization of biological macromolecules. Analysis of HHP effect and various concentrations of ions showed that water induce formation of the active ribozyme structure. So, it is clear that water is the driving force of conformational changes of nucleic acid.     

Biophysical and biological properties of quadruplex oligodeoxyribonucleotides

Single-stranded guanosine-rich oligodeoxyribonucleotides (GROs) have a propensity to form quadruplex structures that are stabilized by G-quartets. In addition to intense speculation about the role of G-quartet formation in vivo, there is considerable interest in the therapeutic potential of quadruplex oligonucleotides as aptamers or non-antisense antiproliferative agents. We previously have described several GROs that inhibit proliferation and induce apoptosis in cancer cell lines. The activity of these GROs was related to their ability to bind to a specific cellular protein (GRO-binding protein, which has been tentatively identified as nucleolin). In this report, we describe the physical properties and biological activity of a group of 12 quadruplex oligonucleotides whose structures have been characterized previously. This group includes the thrombin-binding aptamer, an anti-HIV oligonucleotide, and several quadruplexes derived from telomere sequences. Thermal denaturation and circular dichroism (CD) spectropolarimetry were utilized to investigate the stability, reversibility and ion dependence of G-quartet formation. The ability of each oligonucleotide to inhibit the proliferation of cancer cells and to compete for binding to the GRO-binding protein was also examined. Our results confirm that G-quartet formation is essential for biological activity of GROs and show that, in some cases, quadruplex structures formed in the presence of potassium ions are significantly more active than those formed in the presence of sodium ions. However, not all quadruplex structures exhibit antiproliferative effects, and the most accurate factor in predicting biological activity was the ability to bind to the GRO-binding protein. Our data also indicate that the CD spectra of quadruplex oligonucleotides may be more complex than previously thought.     

Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules

Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth''s atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.     

Negative air ions as a source of superoxide

The physico-chemical characteristics and possible formation mechanisms of negative air ions are considered. It was found that the products of oxygen and nitrogen negative ionization reduce ferricytochromec and nitroblue tetrazolium, and that these reactions were inhibited by superoxide dismutase. The interaction of negatively ionized oxygen with water led to hydrogen peroxide accumulation, which was inhibited by tetranitromethane or catalase. Nitrogen ionization under these conditions caused the formation of the hydrated electron e _aq ^— and the superoxide anion O ₂ ^— . The data obtained indicate that the biological activity of negative air ions may be dependent on superoxide. The generation of reactive oxygen ions in the gas phase and also at a gas/water interface is described. A scheme for superoxide production under oxygen and nitrogen ionization is proposed.     

Mechanism of copper mediated triple helix formation at neutral pH in Drosophila satellite repeats

The highly repeated Drosophila melanogaster AAGAGAG satellite sequence is present at each chromosome centromere of the fly. We demonstrate here how, under nearly physiological pH conditions, these sequences can form a pyrimidine triple helix containing T.A-T and CCu.G-C base triplets, stabilized by Cu2+ metal ions in amounts mirroring in vivo concentrations. Ultraviolet experiments were used to monitor the triple helix formation at pH 7.2 in presence of Cu2+ ions. Triplex melting is observed at 23 degrees C. Furthermore, a characteristic signature of triple helix formation was obtained by Fourier transform infrared spectroscopy. The stabilization of the C.G-C base triplets at pH 7.2 is shown to occur via interactions of Cu2+ ions on the third strand cytosine N3 atom and on the guanine N7 atom of the polypurine target strand forming CCu.G-C triplets. Under the same neutral pH conditions in absence of Cu2+ ions, the triple helix fails to form. Possible biological implications are discussed.     

The origin of membranes

The physicochemical conditions of the environment in which life arose are discussed, along with the appearance of protocells, their membranous envelope and the subsequent appearance of plasma membranes. The hypothesis that the first cells originated in reservoirs where potassium and magnesium salts (necessary for protein synthesis and thus for the formation of a cellular membrane) dominated, is substantiated. This was followed by adaptation of these cells to an external ocean-like environment, where sodium salts were prevalent. This stage of evolution required a plasma membrane capable of providing ion asymmetry between the cell’s cytoplasm and the external environment. At this stage of evolution in the predecessors of animals, the process of removal of sodium ions and accumulation of potassium ions began functioning in the plasma membrane. The problem of multicellular organisms was solved differently by animals and plants: animals developed a system of the extracellular fluids that provided stable physicochemical conditions on the external surface of the plasma membrane. Sodium ions were the stimulus for the formation of the polar cell, where sodium channels are situated on one side of the plasma membrane, and sodium pumps on the other, allowing the development of the absorption, excretion and breathing functions. The formation of fluids of the internal environment enabled the development of homeostasis and facilitated the biological progress of the animal kingdom.     

Nitrosothiol formation catalyzed by ceruloplasmin. Implication for cytoprotective mechanism in vivo.

Ceruloplasmin (CP) is a major multicopper-containing plasma protein that is not only involved in iron metabolism through its ferroxidase activity but also functions as an antioxidant. However, physiological substrates for CP have not been fully identified nor has the role of CP been fully understood. The reaction of nitric oxide (NO) with CP was investigated in view of nitrosothiol (RS-NO) formation. First, formation of heavy metal- or CP-catalyzed RS-NO was examined with physiologically relevant concentrations of NO and various thiol compounds (RSH) such as glutathione (GSH). Among the various heavy metal ions and copper-containing enzymes and proteins examined, only copper ion (Cu(2+)) and CP showed potent RS-NO (S-nitrosoglutathione)-producing activity. Also, RS-NO-forming catalytic activity was evident for CP added exogenously to RAW264 cells expressing inducible NO synthase in culture, but this was not the case for copper ion. Similarly, CP produced endogenously by HepG2 cells showed potent RS-NO-forming activity in the cell culture. One-electron oxidation of NO appears to be operative for RS-NO production via electron transfer from type 1 copper to a cluster of types 2 and 3 copper in CP. Neurological disorders are associated with aceruloplasminemia; besides RS-NO, S-nitrosoglutathione particularly has been shown to have neuroprotective effect against oxidative stress induced by iron overload. Thus, we suggest that CP plays an important catalytic role in RS-NO formation, which may contribute to its potent antioxidant and cytoprotective activities in vivo in mammalian biological systems.