Electrochemical Regeneration of Oxidoreductases for Cell-free Biocatalytic Redox Reactions

Oxidoreductases represent a highly interesting and versatile class of biocatalysts for specific reduction, oxidation, and oxyfunctionalization reactions. Since oxidoreductases depend on cofactors and coenzymes to supply or withdraw redox equivalents released during the catalytic process, their application in cell-free environments requires external supply with these redox equivalents. Next to enzymatic approaches, a variety of non-enzymatic regeneration strategies have been developed. This review focuses on electrochemical methods for the in situ regeneration of nicotinamide cofactors as well as flavin- and heme-coenzymes, developed for synthetic application. The fields of electrochemical biosensors as well as biofuel cells are not discussed in detail. Electrochemical approaches bear much promise and in some cases are more efficient and more versatile than enzymatic regeneration approaches.     

Redox Reactions between Kaempferol and Illuminated Chloroplasts

Bleaching of kaempferol by illuminated chloroplasts was observed at 380 nanometers. The photobleaching was stimulated by methyl viologen and suppressed by superoxide dismutase indicating the participation of O₂⁻ in the reaction. An electron transfer inhibitor on the oxidizing side of photosystem II, carbonylcyanide m-chlorophenylhydrazone (CCCP), stimulated the photobleaching and 3-(3,4-dichlorophenyl)-1,1-dimethylurea partially suppressed it. The stimulation by CCCP suggests that kaempferol is also bleached on the oxidizing side of photosystem II. The spectrum of kaempferol bleaching in the presence of methyl viologen was the same as that in the presence of CCCP having a maximum in absorbance decrease at around 380 nanometers. When kaempferol was oxidized by KMnO₂ or KO₂, the oxidized minus reduced difference spectra had also a negative peak at about 380 nanometers. The results suggest that kaempferol was oxidized by illuminated chloroplasts.

The rate of kaempferol photooxidation increased as its concentration was increased from 1 to 100 micromolar. The rate of quercetin photooxidation also increased as its concentration was increased from 1 to 100 micromolar. Concentration of quercetin glycosides higher than 10 micromolar was required to detect their photobleaching by illuminated chloroplasts. From these results, it is postulated that flavonols function as antioxidants in chloroplasts.

     

Two Organic Fixatives for Acid Mucopolysaccharides

Cetyl pyridinium chloride, 0.5% in 4% aqueous formaldehyde and 5-aminoacridine hydrochloride, 0.4% in 50% aqueous ethanol, have been tested as fixatives for acid mucopolysaccharides in a variety of tissues. These solutions are superior to 4% aqueous formaldehyde, Carnoy's fluid and basic lead acetate for this purpose and also give good nuclear fixation. Tissues containing these mucopolysaccharides are particularly well defined with the acridine-ethanol fixative.     

Making Biological Materials

1 Chemistry and synthesis 1.1 Production and control of materials These days there can be few people who do not know that proteins are defined by DNA. DNA is made of two strands, each of which has along it, like a string of fairy lights, side branches that meet between the strands and hold them together. It is the sequence of these paired side branches （bases） that stores the information needed to define a protein. Three of the bases in sequence provide the information which, translated by the cell＇ s machinery, codes for a particular amino acid. Amino acids polymerise to make up specific proteins and, eventually, us. In defining an organism, that can weigh several tons, in its sequence of bases, the minute amount of DNA necessary for this task is an amazing example of data compression. When I was at school in Cambridge, shortly after Crick and Watson had worked out the basic structure of DNA for their Nobel prize, an enterprising breakfast cereal company had a cardboard cut-out DNA double spiral on the back of their packets. No doubt if you ate enough breakfasts you could save up for a whole gene. I don＇ t know what bit of protein the DNA coded for - I suspect no one did at the time. I remember another of the big names in genetics, Sydney Brenner （whose son went to our school and who later also got a Nobel prize）,     

Light Induced Polarity of Redox Reactions in Leaves of Elodea canadensis Michx

This paper reports that extracellular reductase activity in leaves of Elodea canadensis, hitherto never associated with polar processes thought to be involved in bicarbonate utilization, also shows a very marked polarity in light. The effect of ferricyanide, applied to the lower side of illuminated leaves, was a depolarization of the membrane electrical potential of up to 110 millivolts, while no depolarization was induced when ferricyanide was applied to the upper side. In the dark ferricyanide induced a depolarization when applied to either the upper or to the lower side of the leaf. Staining with tetrazolium salts, specific indicators for reductase activity, resulted in the formation of a precipitate on the lower side of the leaf when illuminated and on both sides in the dark. The precipitate was only located along the plasmalemma.     

Accelerated Search Kinetics Mediated by Redox Reactions of DNA Repair Enzymes

A charge transport (CT) mechanism has been proposed in several articles to explain the localization of base excision repair (BER) enzymes to lesions on DNA. The CT mechanism relies on redox reactions of iron-sulfur cofactors that modify the enzyme's binding affinity. These redox reactions are mediated by the DNA strand and involve the exchange of electrons between BER enzymes along DNA. We propose a mathematical model that incorporates enzyme binding/unbinding, electron transport, and enzyme diffusion along DNA. Analysis of our model within a range of parameter values suggests that the redox reactions can increase desorption of BER enzymes not already bound to lesions, allowing the enzymes to be recycled—thus accelerating the overall search process. This acceleration mechanism is most effective when enzyme copy numbers and enzyme diffusivity along the DNA are small. Under such conditions, we find that CT BER enzymes find their targets more quickly than simple passive enzymes that simply attach to the DNA without desorbing.     

The Quantitative Determination of Osmium Tetroxide in Fixatives

This rapid spectrophotometric method for determining the OsO₄ concentration in fixative and stock solutions is based on the reduction of OsO₄ by acidified KI to the blue species of OsI₆ =, which is then determined at 649 mµ. The salt K₂OsI₆ has been isolated from the reaction mixture and characterized. Method: A I ml aliquot of the solution, containing up to 3% OsO₄, is diluted to 100 ml with distilled water. To 1 ml of the diluted solution is added, in order: distilled water, 2 ml; 1 M HCI, 1 ml; and 1 M KI, 1 ml. Optical density at 649 mµ is read from 10-120 min thereafter. OsO₄ concentration is calculated from the measured molecular extinction coefficient of OsI₆ =, 4400 liter/mole cm.     

Redox Reactions Induced by Nitrosative Stress Mediate Protein Misfolding and Mitochondrial Dysfunction in Neurodegenerative Diseases

Overstimulation of N-methyl-d-aspartate (NMDA)-type glutamate receptors accounts, at least in part, for excitotoxic neuronal damage, potentially contributing to a wide range of acute and chronic neurologic diseases. Neurodegenerative disorders including Alzheimer’s disease (AD) and Parkinson’s disease (PD), manifest deposits of misfolded or aggregated proteins, and result from synaptic injury and neuronal death. Recent studies have suggested that nitrosative stress due to generation of excessive nitric oxide (NO) can mediate excitotoxicity in part by triggering protein misfolding and aggregation, and mitochondrial fragmentation in the absence of genetic predisposition. S-Nitrosylation, or covalent reaction of NO with specific protein thiol groups, represents a convergent signal pathway contributing to NO-induced protein misfolding and aggregation, compromised dynamics of mitochondrial fission-fusion process, thus leading to neurotoxicity. Here, we review the effect of S-nitrosylation on protein function under excitotoxic conditions, and present evidence suggesting that NO contributes to protein misfolding and aggregation via S-nitrosylating protein-disulfide isomerase or the E3 ubiquitin ligase parkin, and mitochondrial fragmentation through β-amyloid-related S-nitrosylation of dynamin-related protein-1. Moreover, we also discuss that inhibition of excessive NMDA receptor activity by memantine, an uncompetitive/fast off-rate (UFO) drug can ameliorate excessive production of NO, protein misfolding and aggregation, mitochondrial fragmentation, and neurodegeneration.     

New Method for Monitoring the Process of Freeze Drying of Biological Materials

A capacitive sensor was proposed and tested for the monitoring and control of a freeze drying process of a vaccine against the Newcastle disease of birds. The residual moisture of the vaccine was measured by the thermogravimetric method. The vaccine activity was determined by titration in chicken embryos. It was shown that, at the stages of freezing and primary drying, a capacitive sensor measured the fraction of unfrozen liquid phase in a material and allowed one to control the sublimation stage of drying in an optimal way. This prevented the foaming of the material and shortened the total drying time approximately twice. The control range at the sublimation stage of drying expanded up to −70°C. It was found at the final stage of drying that the signal of a capacitive sensor passed through a maximum value. We supposed that this maximum corresponds to the minimum of intramolecular mobility of biological macromolecules and hence to the optimal residual moisture of the material, which ensures long-term preservation of its activity. We also suppose that using the capacitive sensor at the final stage of drying allows one to more precisely detect the time when the residual moisture of dried material reaches the optimal value.KEY WORDS: biological materials, capacitive sensor, freeze drying, optimal residual moistureAt present, most biological materials containing live viruses or bacteria are exposed to lyophilization (i.e., drying from the frozen state); this ensures long-term preservation of their activity. Typically, this process consists of preliminary freezing and subsequent freeze drying. The latter process, in turn, consists of two stages: primary drying and secondary drying. During primary drying or sublimation, frozen water is removed from a biological product under vacuum and at temperatures below 0°C. At this stage, the drying rate is limited because of the foaming of a product that occurs due to its high temperature and the excess amount of liquid phase in it. The secondary drying, or final stage, begins after the end of the sublimation stage and occurs at temperatures above 0°C. The goal of the secondary drying is to bring the residual moisture of a biological product to an optimum level, which provides long-term preservation of its activity. Note that the moisture content both above and below the optimum value reduces the effective life of biological materials (1,2)To increase the shelf life of biological products, the following should be investigated: (1) the influence of the composition of the dried biological product and the residual moisture on the change in its activity over the time (3); (2) it is needed to optimize the sublimation drying process for different types of biological products (4). For the investigation of the of the state of water in the dried biologic drugs and the influence of the humidity of the biological on the change in their activity during shelf life, different physical methods are used such as neutron scattering (5), nuclear magnetic resonance (NMR) (6,7), Raman spectroscopy (8), infrared spectroscopy, differential scanning calorimetry, thermal activity monitor (9), and gravimetric sorption analysis (10). The investigations using these methods allow to find an optimum composition of a protective medium for biologics and to determine its optimal residual moisture.At all stages of the freeze drying, the parameters of the material and the parameters of the drying process (temperature of a material, the shelf temperature, the condenser temperature, the pressure in the sublimation chamber, etc.) are also monitored. According to these data, the mode of the process is selected to conduct him for the minimum time and get the best product quality (11). Usually during the drying process, the temperature is measured in several vials with biologic located on different shelves. The sharp increase of the temperature indicates the end of primary drying and the beginning of the secondary drying. The finish of the sublimation stage is revealed by a sharp decrease of the partial pressure of water vapor in the sublimation chamber (12,13). Note that the partial pressure of water vapor in the sublimation chamber does not characterize the state of the biological product to be dried and it is an indirect parameter. For monitoring and controlling the process of freeze drying, it is important to use the own properties of biological materials. In (14), a resistivity sensor placed in a frozen biological material was proposed to control the primary stage of freeze drying. A disadvantage of this method is that one cannot establish an unambiguous relationship between the amount of liquid phase in the frozen material and the value of resistivity: the resistance of the sensor depends not only on the amount of liquid phase but also on the concentration of dissolved salts. Another disadvantage of the resistivity sensor is that, when the temperature decreases, the resistivity of the material sharply increases to values that are difficult to measure, which makes impossible the control of the sublimation stage with this sensor.In (15,16), the interesting methods for determining the moisture of biological materials during secondary drying were proposed. These methods are based on the measurement of the partial pressure of water vapors in the sublimation chamber by NIR spectroscopy or Raman spectroscopy. Note that this method is indirect and requires laborious calibration to establish a correspondence between the current moisture of the biological material in vials and the pressure of water vapor in the sublimation chamber.It should be noted that one has to carry out a series of long-term experiments to find the optimal residual moisture of a biological product. These experiments result in the lifetimes of biological samples with various residual moistures. As the optimal residual moisture of a biological product, one takes the value that provides the longest term preservation of its activity.However, finding the optimal conditions of freeze drying has traditionally been a process of trial and error and required several experimental runs (17). Note also that the freeze drying process is time-consuming and labor intensive.A promising method for the investigation of the properties of biological materials is dielcometry (18,19). This method is relatively simple and very informative since it gives information about the structure of biological macromolecules and the state and role of water in the biological material, etc. This method was used in (20–22) for monitoring biological materials at the primary stage of freeze drying. In (20), authors had found an anomalous low-frequency dispersion of the dielectric permittivity in the biological under study and explain this phenomenon by the proton transfer among water molecules, connected by hydrogen bonds The dielectric relaxation time turned out to be sensitive to the loss of moisture content in the product, and the authors suggested to use of this phenomenon to determine the end point of the freeze drying process. The authors mounted the electrodes of the capacitive sensor on the outer surface of vials with the material to be dried. This approach allows monitoring the sublimation rate and determining the end of the primary stage of freeze drying. Unfortunately, the sensitivity of the capacitive sensor of this design is not enough for the reliable monitoring of the stage of secondary drying.In this paper, a new design of a capacitive sensor and measurement technique are proposed that enable monitoring all stages of the drying process: the freezing stage, the sublimation stage, and the final stage. During freezing and the sublimation stages, the sensor monitors the amount of liquid phase in the frozen material. This allows an optimal control during the whole sublimation stage which prevents the foaming of the material and significantly reduces the total drying time. The sensor also fixes the end of the sublimation stage and the beginning of the final stage of drying. At this stage, the high sensitivity of the measuring system enables one to discover that there is a certain time interval when the signal of the capacitive sensor passes through a maximum. We believe that this maximum corresponds to the minimum of the molecular mobility of biological macromolecules and the optimal residual moisture of the material to be dried.     

Artificial Electron Carriers for Preparative Biocatalytic Redox Reactions Forming Reversibly Carbon Hydrogen Bonds with Enzymes Present in Strict or Facultative Anaerobes

The application of various artificial electron mediators in combination with redox enzymes present in anaerobically grown cells is described. Examples include viologens of different redox potential, cobalt complexes, anthraquinones, phenoxazines, phenazines and others. The regeneration of the reduced or oxidised mediators by various methods is discussed, with hydrogen gas, carbon monoxide, formate or a cathode as electron donors, and dimethylsulphoxide, quinones, oxygen or an anode as electron acceptors. The enzymes used, usually in the form of resting cells or crude cell extracts of clostridia or Proteus species are mostly reversible. Examples for preparative reductions as well as for dehydrogenations are given.     

大型真菌分子生物学实验材料的保存方法介绍

介绍了几种保存大型真菌分子生物学实验材料的方法 ,用这几种方法所保存的材料提取的基因组核糖体脱氧核糖核酸 (DNA)质量适于系统生物学及其他分子生物学研究之用。     

Plant Defense Response to Fungal Pathogens (II. G-Protein-Mediated Changes in Host Plasma Membrane Redox Reactions)

Elicitor preparations containing the avr5 gene products from races 4 and 2.3 of Cladosporium fulvum, and tomato (Lycopersicon esculentum L.) cells containing the resistance gene Cf5 were used to investigate the involvement of redox processes in the production of active oxygen species associated with the plant response to the fungal elicitors. Here we demonstrate that certain race-specific elicitors of C. fulvum induced an increase in ferricyanide reduction in enriched plasma membrane fractions of tomato cells. The addition of elicitors to plasma membranes also induced increases in NADH oxidase and NADH-dependent cytochrome c reductase activities, whereas ascorbate peroxidase activity was decreased. These results suggest that changes in the host plasma membrane redox processes, transferring electrons from reducing agents to oxygen, could be involved in the increased production of active oxygen species by the race-specific elicitors. Our results also show that the dephosphorylation of enzymes involved in redox reactions is responsible for the race-specific induced redox activity. The effects of guanidine nucleotide analogs and mastoparan on the activation of plasma membrane redox reactions support the role of GTP-binding proteins in the transduction of signals leading to the activation of the defense response mechanisms of tomato against fungal pathogens.     

Hot Biological Catalysis: Isothermal Titration Calorimetry to Characterize Enzymatic Reactions

Isothermal titration calorimetry (ITC) is a well-described technique that measures the heat released or absorbed during a chemical reaction, using it as an intrinsic probe to characterize virtually every chemical process. Nowadays, this technique is extensively applied to determine thermodynamic parameters of biomolecular binding equilibria. In addition, ITC has been demonstrated to be able of directly measuring kinetics and thermodynamic parameters (k_cat, K_M, ΔH) of enzymatic reactions, even though this application is still underexploited. As heat changes spontaneously occur during enzymatic catalysis, ITC does not require any modification or labeling of the system under analysis and can be performed in solution. Moreover, the method needs little amount of material. These properties make ITC an invaluable, powerful and unique tool to study enzyme kinetics in several applications, such as, for example, drug discovery.In this work an experimental ITC-based method to quantify kinetics and thermodynamics of enzymatic reactions is thoroughly described. This method is applied to determine k_cat and K_M of the enzymatic hydrolysis of urea by Canavalia ensiformis (jack bean) urease. Calculation of intrinsic molar enthalpy (ΔH_int) of the reaction is performed. The values thus obtained are consistent with previous data reported in literature, demonstrating the reliability of the methodology.