Antiperoxidase antibodies enhance refolding of horseradish peroxidase

The effect of monoclonal antibodies on protein folding was studied using horseradish peroxidase refolding from guanidine hydrochloride as a model process. Among the five antiperoxidase clones tested, one was found to increase the yield of catalytically active peroxidase after guanidine treatment. The same clone also increased the activity of the native peroxidase by a factor of 2-2.5. While peroxidase refolding under standard conditions resulted in the recovery of only 7-8% of the initial catalytic activity, antibody-assisted refolding increased the yield to 50-100% (or 20-40% from the activity of native enzyme with antibodies). Kinetics of autorefolding and antibody-assisted refolding differed significantly. In the course of autorefolding the catalytic activity was recovered within the first 2.5 min and did not change further within a 2.5- to 60-min interval, whereas in the course of antibody-assisted refolding maximal catalytic activity was attained only in 60 min. The yield of active peroxidase for the antibody-assisted refolding depended linearly on the antibody concentration. The observed effect was strongly specific. Other antiperoxidase clones tested as well as nonspecific antithyroglobulin antibody affected neither kinetics, no the yield of peroxidase refolding.

[Analysis of kinetic parameters of gas phase bioreactors]

The dependence of toluene elimination capacity on its load was obtained in five small-scale reactors filled with glass beads carrying biocatalyst cells. With increase in operation time the calculated maximal elimination capacity was shown to increase along with biomass density in the biocatalyst bed. Fivefold increase in trickling intensity did not affect the reactor performance. A simplified mathematical model for evaluation of minimal required biocatalyst bed volume at certain loading was developed based on experimental dependence of elimination capacity vs. loading.

[Five-years' experience in the use of extracorporeal shockwave lithotripsy at the Central Kiev Clinic Hospital]

The article focuses on the main aspects of treatment of urolithiasis with the aid of extracorporeal lithotripsy at the Central Kiev City Clinical Hospital with particular regard to the therapeutic policy of in-patient managing of patients. An analysis has been performed together with substantiation of connection between physical parameters of the focal zone and efficiency of lithotripsy, which attempts will, we believe, promote the accuracy of prognostication of the course of treatment.

Enzymatic oxidation of cadmium and lead metals photodeposited on cadmium sulfide

Cadmium and lead metals deposited on CdS particles are shown to act as substrates--electron donors for enzymes, hydrogenase from Thiocapsa roseopersicina (HG), NAD-dependent hydrogenase from Alcaligenes eutrophus (NLH), and ferredoxin:NADP oxidoreductase (FNR) from Chlorella in the formation of hydrogen, NADH and NADPH, respectively. Adsorption of the enzyme on the surface of the metallized CdS particle is required for enzymatic oxidation of metal. The maximum rates for the formation of hydrogen and NADH catalyzed by hydrogenase and NAD-dependent hydrogenase with metals as electron donors are comparable with the rates obtained for these enzymes using soluble substrates. Kinetic analysis of the enzymatic oxidation of cadmium metal has revealed that the rate decreases mainly due to the formation of a solid product, which is supposed to be Cd(OH)2. The deceleration of lead oxidation catalyzed by hydrogenase proceeds at the expense of the inhibitory effect of the formed Pb2+. The enzymatic oxidation of electrochemically prepared cadmium metal is also shown. Based on these results, a new mechanism of action of the enzymes involved in anaerobic biocorrosion is proposed. By this mechanism, the enzyme accelerates the process of metal dissolution through a mediatorless catalysis of the reduction of the enzyme substrate.

[Development of microbiological technology of air deodoration in laboratory-industrial conditions using a pilot plant]

Laboratory tests were performed to select a complex of bacterial strains capable of effective deodoration of waste air produced by an animal formulated feed works under elevated temperature with the presence of numerous organic pollutants. The complex included species from the general Nocardia, Rhodococcus, and Comamonas. The biocatalyst was tested in a real industrial process with the use of a pilot plant for microbiological deodoration of waste air. The test lasted for over six months and confirmed the efficiency of the development method of deodoration.

[The estimation of the degree of surgical risk in patients with prostatic adenoma]

Based on the authors' personal experience of surgical treatment of prostate adenoma an assessment has been carried out of general status and degree of operation-related risk using a simplified "acute physiologic scale" the total score of which is the sum 13 of easily identifiable vital physiologic or biochemical parameters. The assessment is performed by 4-score scheme, with prognosis of lethality being given depending on values obtained. Radical adenomectomy was found out to be indicated in those patients in whom the total score did not exceed 5; electroresection (transurethral or transvesical) can be recommended in those patients having the total score under 11. The score above 11 necessitates cystostomy (including the trochar one) or else indwelling catheter is supposed to be inserted.

Conserved supersecondary structural motif in NAD-dependent dehydrogenases

L- and D-specific nicotinamide adenine dinucleotide (NAD)-dependent dehydrogenases map to the same structural protein superfamily as defined by the Structural Classification of Proteins (SCOP) and are based on the Rossmann fold type domains. A detailed classification of these domains is proposed using a novel diagnostic parameter of the rms per aligned pair. The catalytic domain in D-specific dehydrogenases shows a strong structural homology to the coenzyme binding domain. A topologically conserved part within the dehydrogenase superfamily reveals a supersecondary structural motif comprising the 5-stranded left-handedly twisted parallel beta-sheet with one complete and one partial Rossmann fold units and two alpha-helices, the long helix, adjacent to and running roughly parallel with the beta-sheet plane and the helix connecting two Rossmann folds.

[Preparation and characteristics of antibodies to a sulfur-containing hapten, mimicking the transition state in lactamization reactions]

A sulfur-containing hapten was proposed to be an analogue of the tetrahedral transition state of lactamization reactions. The dynamics of the immune response to this hapten upon using different immunization schemes was studied. Sixty-one clones of mouse anti-hapten antibodies were obtained. Three clones efficiently bound not only the transition state analogue (the hapten) but also potential substrates of lactamization reactions. Antibody-induced changes in the optical absorption spectra of substrate solutions were studied for a substrate with stabilized active conformation (2-aminomethylbenzoate) and an unmodified substrate (gamma-aminobutyric acid), which demonstrated that the catalytic antibodies obtained significantly accelerated the lactam ring formation.

Effect of pH on kinetic parameters of NAD+-dependent formate dehydrogenase

To define in detail the molecular mechanism of NAD+-dependent formate dehydrogenase, the pH dependences of various kinetic and spectroscopic parameters have been studied: Vmax, Km (NAD+), Km (formate), inhibition constants for structural analogues of substrate (NO3-) and product (CNS-, CNO-, N3-), CD and fluorescence properties. The value of Vmax, rate-limiting hydride transfer, is nearly constant throughout the entire pH range of enzyme stability (6.0-11.2) but decreases below 6. The K(m) values for both substrates remain constant within the pH range 6-10. At pH values below 6 (for the coenzyme) and above 10 (for both substrate and coenzyme) the Km values increase. In the acidic range this change is attributed to the ionization of two carboxy groups (pK approx. 5.5-6.0) located at the NAD+-binding site of the enzyme active centre. The pH transition in the basic region (pK 10.5 +/- 0.2) has a conformational origin and affects the enzyme's affinity for substrates and anion inhibitors. A similar transition has been observed for formate dehydrogenases from yeast Candida boidinii and Hansenula polymorpha. The results complement the conclusions about the catalytic mechanism deduced from the crystal structure of the enzyme.

Site-directed mutagenesis of the formate dehydrogenase active centre: role of the His332-Gln313 pair in enzyme catalysis

Gln313 and His332 residues in the active centre of NAD(+)-dependent formate dehydrogenase (EC 1.2.1.2, FDH) from the bacterium Pseudomonas sp. 101 are conserved in all FDHs and are equivalent to the glutamate-histidine pair in active sites of D-specific 2-hydroxyacid dehydrogenases. Two mutants of formate dehydrogenase from Pseudomonas sp. 101, Gln313Glu and His332Phe, have been obtained and characterised. The Gln313Glu mutation shifts the pK of the group controlling formate binding from less than 5.5 in wild-type enzyme to 7.6 thus indicating that Gln313 is essential for the broad pH affinity profile towards substrate. His332Phe mutation leads to a complete loss of enzyme activity. The His332Phe mutant is still able to bind coenzyme but not substrate or analogues. The role of histidine in the active centre of FDH is discussed. The protonation state of His332 is not critical for catalysis but vital for substrate binding. A partial positive charge on the histidine imidazole, required for substrate binding, is provided via tight H-bond to the Gln313 carboxamide.

NAD(+)-dependent formate dehydrogenase

Images

High resolution structures of holo and apo formate dehydrogenase

Three-dimensional crystal structures of holo (ternary complex enzyme-NAD-azide) and apo NAD-dependent dimeric formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 have been refined to R factors of 11.7% and 14.8% at 2.05 and 1.80 A resolution, respectively. The estimated root-mean-square error in atomic co-ordinates is 0.11 A for holo and 0.18 A for apo. X-ray data were collected from single crystals using an imaging plate scanner and synchrotron radiation. In both crystal forms there is a dimer in the asymmetric unit. Both structures show essentially 2-fold molecular symmetry. NAD binding causes movement of the catalytic domain and ordering of the C terminus, where a new helix appears. This completes formation of the enzyme active centre in holo FDH. NAD is bound in the cleft separating the domains and mainly interacts with residues from the co-enzyme binding domain. In apo FDH these residues are held in essentially the same conformation by water molecules occupying the NAD binding region. An azide molecule is located near the point of catalysis, the C4 atom of the nicotinamide moiety of NAD, and overlaps with the proposed formate binding site. There is an extensive channel running from the active site to the protein surface and this is supposed to be used by substrate to reach the active centre after NAD has already bound. The structure of the active site and a hypothetical catalytic mechanism are discussed. Sequence homology of FDH with other NAD-dependent formate dehydrogenases and some D-specific dehydrogenases is discussed on the basis of the FDH three-dimensional structure.

Metal as a novel type of the enzyme substrate. Metallic cadmium photogenerated in the system CdS-formate as a substrate of the NAD-dependent hydrogenase

The process of NAD+ photoreduction under the coupled action of CdS semiconductor and NAD-dependent hydrogenase from hydrogen-oxidizing bacterium Alcaligenes eutrophus may be divided into light and dark stages. At the first stage, illumination of the system leads to the photooxidation of the sacrificial electron donor and results in the reduction of the semiconductor surface. At the second dark stage NAD+ is reduced to NADH in the presence of hydrogenase. Atoms of metallic Cd(0) are shown to be the true substrate of the enzymatic reaction. The prerequisite for the electron transfer from Cd(0) to hydrogenase is enzyme adsorption on the semiconductor surface. The redox center of the hydrogenase reacting with Cd(0) atoms resides on the flavin-containing heterodimer of the protein. The activity of the hydrogenase immobilized on CdS in the reaction of NAD+ reduction by metallic Cd is close to the enzyme activity with the physiological substrates in solution. Thus, the first example of a metal being the substrate of the enzymatic process is presented.

Photogeneration of NADH under coupled action of CdS semiconductor and hydrogenase from Alcaligenes eutrophus without exogenous mediators

Photoreduction of NAD has been accomplished by a system consisting of the NAD-dependent hydrogenase from Alcaligenes eutrophus immobilized on CdS particles with formate as artificial electron donor. Enzymatically active NADH is formed under illumination of this system by visible light. Accumulation of the coenzyme dimer (NAD)2 was not detected. NAD photoreduction is supposed to proceed via the direct electron transfer from the semiconductor to the enzyme electron transport chain. However, NADH formation as a result of hydrogenase interaction with anion-radicals (CO2.-) formed in the course of formate photooxidation cannot at present be excluded.

Crystal structure of NAD-dependent formate dehydrogenase

The ternary complex of NAD-dependent formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 (enzyme-NAD-azide) has been crystallised in the space group P2(1)2(1)2(1) with cell dimensions a = 11.60 nm, b = 11.33 nm, c = 6.34 nm. There is 1 dimeric molecule/asymmetric unit. An electron density map was calculated using phases from multiple isomorphous replacement at 0.30 nm resolution. Four heavy atom derivatives were used. The map was improved by solvent flattening and molecular averaging. The atomic model, including 2 x 393 amino acid residues, was refined by the CORELS and PROLSQ packages using data between 1.0 nm and 0.30 nm excluding structure factors less than 1 sigma. The current R factor is 27.1% and the root mean square deviation from ideal bond lengths is 4.2 pm. The FDH subunit is folded into a globular two-domain (coenzyme and catalytic) structure and the active centre and NAD binding site are situated at the domain interface. The beta sheet in the FDH coenzyme binding domain contains an additional beta strand compared to other dehydrogenases. The difference in quaternary structure between FDH and the other dehydrogenases means that FDH constitutes a new subfamily of NAD-dependent dehydrogenases: namely the P-oriented dimer. The FDH nucleotide binding region of the structure is aligned with the three dimensional structures of four other dehydrogenases and the conserved residues are discussed. The amino acid residues which contribute to the active centre and which make contact with NAD have been identified.

[NAD-dependent formate dehydrogenase of methylotrophic bacteria Pseudomonas sp. 101. III. Comparative analysis]

The comparative analysis of the primary and tertiary structures of NAD-dependent bacterial formate dehydrogenase (FDH) from methylotrophic bacterium Pseudomonas sp. 101 and a number of structurally characterized NAD-dependent dehydrogenases were performed. FDH has a highly conservative fold of the coenzyme binding domain. Position of the symmetry axis in the FDH molecule relative to the beta-sheets of its coenzyme binding domain with the respective sequences of the other NAD-dependent enzymes was performed on the basis of the spatial homology between these structures. Only one of the three amino acid residues previously thought to be conserved in the coenzyme binding domains of NAD-dependent dehydrogenases is preserved in the FDH molecule (Asp-221). Two glycine residues found in all previously studied dehydrogenases are substituted in FDH by Ala-198 and Pro-256, respectively. Position of the essential thiol of FDH (Cys-255) in the protein structure was established. It is suggested that Cys-255 is situated on or near polypeptide locus taking part in the conformational changes of the protein in the course of the catalysis.

[NAD-dependent formate dehydrogenase from methylotrophic bacteria Pseudomonas sp. 101. I. Amino acid sequence]

The primary structure of NAD-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 is determined. The enzyme is composed of two identical subunits, each comprising 393 amino acid residues, and has a molecular weight of 43.1 kD. To elucidate the protein's amino acid sequence, four types of digestion were used: cyanogen bromide cleavage at methionine residues, endoproteinase Lys-C digestion at lysine residues, endoproteinase Glu-C cleavage at glutamic acid residues, and tryptic digestion. The peptides obtained were purified to homogeneity and characterized.

Mapping of the immunodominant regions of the NAD-dependent formate dehydrogenase

A panel of 4 monoclonal antibodies and 7 polyclonal antisera against NAD-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 has been obtained. The reactivity of the 37 overlapping proteolytic peptides with the monoclonal antibodies and polyclonal antisera has been studied with ELISA test. The data obtained were interpreted residing on the structural model of the formate dehydrogenase at 3 A resolution. The immunodominant regions in the formate dehydrogenase molecule and the epitopes for the monoclonal antibodies were elucidated.

Effect of redox potential on the catalytic properties of the NAD-dependent hydrogenase from Alcaligenes eutrophus Z1

The effect of redox potential on the catalytic activities of the soluble hydrogenase from the hydrogen bacterium Alcaligenes eutrophus Z1 was studied. Several transitions were observed on the enzyme catalytic activity vs potential profiles. The coenzyme-dependent activities of the hydrogenase, its diaphorase activity and activity toward NAD, are controlled by the Em -300 mV, while the process of hydrogen evolution from reduced methyl viologen is governed by the midpoint redox potential of -435 mV. This value of Em was independent of pH in the range 5 to 8. The redox potential of the medium appears to be one of the major factors determining the hydrogenase activation, inactivation, and catalytic properties. It is suggested that a change in the redox state of the enzyme electron transport chain is followed by structural rearrangements within the protein affecting both the hydrogenase catalytic activity and stability. The probable mechanism of enzyme activity regulation is discussed.

Redox-dependent inactivation of the NAD-dependent hydrogenase from Alcaligenes eutrophus Z1

A novel inactivation mechanism of the NAD-dependent hydrogenase from Alcaligenes eutrophus Z1 comprising redox-dependent steps is described. The model of the hydrogenase inactivation process is proposed which implies that the enzyme may exist in several forms which differ in their stability and spectral properties. One of these forms, existing within a limited (approximately -200 +/- 30 mV) potential range, undergoes a rapid and irreversible inactivation. The dissociation of the FMN prosthetic group from the apohydrogenase appears to be the main reason for the enzyme inactivation. The rationale for the enzyme stabilization under real operational conditions based on the chemical modification of the hydrogenase molecule is suggested.

Effect of redox potential on the activation of the NAD-dependent hydrogenase from Alcaligenes eutrophus Z1

A formal kinetic treatment of the autocatalytic activation cycle of the NAD-dependent hydrogenase from Alcaligenes eutrophus Z1 is presented. The value for the enzyme first-order activation rate constant is estimated to be (2.0 +/- 0.6) s-1 (pH 7.8, 25 degrees C). The effect of the redox potential on the activation properties of the NAD-dependent hydrogenase is studied. Hydrogenase activation is controlled by a midpoint redox potential of approximately -100 mV (pH 7.8). Once activated the enzyme is not immediately transformed back into an inactive state on rapid reoxidation and is able to preserve its catalytic properties for at least 3-4 h of intense oxigenation. Several lines of evidence show that the reductive activation of the NAD-dependent hydrogenase is accompanied by a structural reorganization of the protein. A possible origin of the -100 mV transition is discussed. A model for the activation process of the NAD-dependent hydrogenase is suggested.