Convergent Evolution in the Assembly of Polyubiquitin Degradation Signals by the Shigella flexneri IpaH9.8 Ligase

The human pathogen Shigella flexneri subverts host function and defenses by deploying a cohort of effector proteins via a type III secretion system. The IpaH family of 10 such effectors mimics ubiquitin ligases but bears no sequence or structural homology to their eukaryotic counterpoints. Using rates of ¹²⁵I-polyubiquitin chain formation as a functional read out, IpaH9.8 displays V-type positive cooperativity with respect to varying concentrations of its Ubc5B∼¹²⁵I-ubiquitin thioester co-substrate in the nanomolar range ([S]_½ = 140 ± 32 nm; n = 1.8 ± 0.1) and cooperative substrate inhibition at micromolar concentrations ([S]_½ = 740 ± 240 nm; n = 1.7 ± 0.2), requiring ordered binding to two functionally distinct sites per subunit. The isosteric substrate analog Ubc5BC85S-ubiquitin oxyester acts as a competitive inhibitor of wild-type Ubc5B∼¹²⁵I-ubiquitin thioester (K_i = 117 ± 29 nm), whereas a Ubc5BC85A product analog shows noncompetitive inhibition (K_i = 2.2 ± 0.5 μm), consistent with the two-site model. Re-evaluation of a related IpaH3 crystal structure (PDB entry 3CVR) identifies a symmetric dimer consistent with the observed cooperativity. Genetic disruption of the predicted IpaH9.8 dimer interface reduces the solution molecular weight and significantly ablates the k_cat but not [S]_½ for polyubiquitin chain formation. Other studies demonstrate that cooperativity requires the N-terminal leucine-rich repeat-targeting domain and is transduced through Phe³⁹⁵. Additionally, these mechanistic features are conserved in a distantly related SspH2 Salmonella enterica ligase. Kinetic parallels between IpaH9.8 and the recently revised mechanism for E6AP/UBE3A (Ronchi, V. P., Klein, J. M., and Haas, A. L. (2013) E6AP/UBE3A ubiquitin ligase harbors two E2∼ubiquitin binding sites. J. Biol. Chem. 288, 10349–10360) suggest convergent evolution of the catalytic mechanisms for prokaryotic and eukaryotic ligases.     

Concentration and flux of solutes from snow and forest floor during snowmelt in the West-Central Adirondack region of New York

Decreases in pH and increases in the concentration of Al and NO ₃ ^– have been observed in surface waters draining acid-sensitive regions in the northeastern U.S. during spring snowmelt. To assess the source of this acidity, we evaluated solute concentrations in snowpack, and in meltwater collected from snow and forest floor lysimeters in the west-central Adirondack Mountains of New York during the spring snowmelt period, 29 March through 15 April 1984.During the initial phase of snowmelt, ions were preferentially leached from the snowpack resulting in elevated concentrations in snowmelt water (e.g. H⁺ = 140 eq.l^–1; NO ₄ ^2– = 123 eq.l^–1; SO ₃ ^– = 160 eq.l^–1). Solute concentrations decreased dramatically within a few days of the initial melt (< 50 eq.l^–1). The concentrations of SO ₄ ^2– and NO ₃ ^– in snowpack and snowmelt water were similar, whereas NO^– ₃ in the forest floor leachate was at least two times the concentration of SO ₄ ^2– .Study results suggest that the forest floor was a sink for snowmelt inputs of alkalinity, and a net source of H⁺, NO ₃ ^– , dissolved organic carbon, K⁺ and Al inputs to the mineral soil. The forest floor was relatively conservative with respect to snowmelt inputs of Ca²⁺, SO ₄ ^2– and Cl^–. These results indicate that mineralization of N, followed by nitrification in the forest floor may be an important process contributing to elevated concentrations of H⁺ and NO ₃ ^– in streams during the snowmelt period.     

Augmentation of H2 photoproduction in Rhodopseudomonas palustris by N-heterocyclic aromatic compounds

Increases of 23- (5.6 mmol acetylene reduced mg dry wt^–1) and 16- (4 mmol acetylene reduced mg dry wt^–1) fold in nitrogenase activity and 12- (671 l H₂ mg dry wt^–1 h^–1) and 6- (349 l mg dry wt^–1 h^–1) fold in H₂ photoproduction in Rhodopseudomonas palustris JA1 over 24 h were achieved with pyrazine 2-carboxylate (3 mM) and 3-picoline (3 mM), respectively, and were higher than earlier reports of enhancement (1.5 to 5- fold) in biological H₂ production using various alternative methods.     

Substitution of D-Trp32 in NPY Destabilizes the Binding Transition State to the Y1 Receptor Site in SK-N-MC Cell Membranes

The retention rate of the spin label 3-isothiocyanto methyl-2,2,5,5-tetramethyl-1-pyrrolidinyl oxyl spin label (proxyl) attached to the porcine N-acetyl-NPY peptide and the porcine N-acetyl-D-Trp³²-NPY peptide at Lys⁴ was investigated using SK-N-MC neuroblastoma cell membranes containing the Y1 receptor. The release rate of the spin labeled peptides was monitored by electron spin resonance and the K_D was determined by a direct radiolabeled NPY displacement binding assay. The analyses show that for the porcine [Ac-Tyr¹N⁴-proxyl]-NPY, the K_D was 8 × 10^–10 M and k_off was 2.7 × 10^–4 sec^–1 yielding a value for k_on of 3.3 × 10⁵ sec^–1 M^–1. The [Ac-Tyr¹, N⁴-proxyl,-D-Trp³²]-NPY antagonist ligand had a value of K_D equal to 1.35 × 10^–7 M and k_off was 1.7 × 10^–4 sec^–1 leading to a value for k_on of 1.2 × 10³ sec^–1 M^–1. The difference in the k_on rates of two orders of magnitude is interpreted as demonstrating the N-acetyl-N⁴ proxyl-D-Trp³²-NPY ligand binding transition state to be of higher energy then for the unmodified NPY amino acid sequence.     

Seasonal variation of nitrogen transformations in the pelagial of selected nearshore waters of the Baltic Sea with emphasis on the particulate pool

Physical and chemical conditions, particulate matter and N-uptake were characterized at two sampling sites at the eastern German coast of the Baltic Sea (Pomeranian Bay) over the annual period of 1997 (February–November). The inshore sampling sites (5 m water depth) differed with respect to the potential influences of river run-off and salt water exchange (mean values of salinity: 7.05 and 8.72 PSU), respectively. The mean org-C_diss/org-C_part-ratios (4.9 and 12.6) fell in the same order of magnitude (1.0–12.6) as values of neighboring inshore waters, and increasing values reflect an enhancement of the trophic level. Beside differences of nitrogen concentrations (dissolved inorganic nitrogen: 1.8–23.8 and 0.9–9.9 mol l^–1), particulate nitrogen (4.30–41.01 and 2.69–9.08 mol l^–1) and absolute uptake of N-nutrients (mean sum of NH₄ ⁺, urea, NO₃ ^– uptake rates: 0.141 and 0.087 mol l^–1 h^–1), specific uptake of ¹⁵N-labelled nutrients (NH₄ ⁺, urea, NO₃ ^–) as well as the relationships between the measured variables characterize distinguishable inshore systems. The high variability at the shallow sampling sites prevents, however a simple resolution of the seasonal courses. Light dose could be identified as a potential key in order to describe long-term variations of N-uptake at the station with higher organic matter concentration (station KW), but phytoplankton development is better reflected in the seasonal course of N-uptake at the other station. Specific nitrogen uptake rates (NH₄ ⁺: 0.0009–0.0353 h^–1, urea: 0.0001–0.0137 h^–1, NO₃ ^–: 0.000004–0.0009 h^–1) and relative nitrogen preferences indicate extraordinary importance of reduced nitrogenous nutrients (NH₄ ⁺, urea) at both stations throughout the year.     

n-3 PUFA productivity in chemostat cultures of microalgae

Eicosapentaenoic (EPA) and docosahexaenoic (DHA) acid productivities from chemostat cultures of an isolate of Isochrysis galbana have been studied. The productivities reached in the interval of dilution rates between 0.0295 h^–1 and 0.0355 h^–1 were 1.5mg·1^–1·h^–1 for lipids, 300 g·1^–1·h^–1 for EPA and 130g1·1^–1·h^–1 for DHA. Furthermore, light attenuation by mutual shading, and agitation speed influences on growth and fatty acid composition were analysed. A model relating steady-state dilution rates to internal average light intensity has been proposed, the parameter values of which obtained by non-linear regression were: maximum specific growth rate (_max)=0.0426 h^–1; the affinity of cells to light (I_k) = 10.92 W·m^–2; the exponent (n) = 5.13; regression coefficient (r ²)=0.9999. Correspondence to: E. Molina Grima     

Lipolytic and adenyl-cyclase-stimulating activity of glucagon1–6: comparison with glucagon derivatives chemically modified in the 7–29 sequence

Glucagon_1–6 has a maximum lipolytic activity (L_max) in the rat adipocyte which is 66% of that of glucagon. The N-guanidyl derivative, modified at Lys₁₂ , has about the same L_max as glucagon_1–6. Modifying the carboxyl groups of glucagon with glycinamide or removing the COON-terminal residues with cyanogen bromide reduces L_max to less than 25% of the level of glucagon. The potency of each of these analogs (A₅₀) in M is as follows: glucagon 6×10^–3; glucagon^1–6 2 ×10^–2; N-guanidyl glucagon 9×10^–3; glycinamide glucagon 10^–2; cyanogen bromide peptide of glucagon 2 ×10^–1. The ability of all of the glucagon analogs to stimulate adenyl cyclase was somewhat less than their tipolytic activities with the exception of the glycin-amide derivative and the cyanogen bromide peptide, which were slightly more active in stimulating adenyl cyclase than in lipolysis. Glucagon_1–6 is much more potent in stimulating adipocyte than liver adenyl cyclase.     

Energetics of cyclodextrin-induced dissociation of insulin

The energetics of dissociation of bovine insulin in aqueous solution have been investigated by sensitive dilution microcalorimetry. Cyclodextrins increase dissociation of insulin oligomers in a manner consistent with their interaction with protein side chains. For example, assuming monomer-dimer equilibrium, in the absence of cyclo-dextrins the calorimetric dilution data (25 °C, pH 2.5) indicate a dimer dissociation constant (K_diss) of about 12 µM and an endothermic dissociation enthalpy (H_diss) of +41 kJ mol^–1. Addition of methyl--cyclodextrin (up to 200 mm) makes dissociation significantly more endothermic (H_diss = 79 kJ mol^–1) and reduces the apparent dimer dissociation constant by more than two orders of magnitude (K_diss 1.7 mm). Qualitatively similar results are observed with -cyclodextrin and other -cyclodextrin derivatives. Cyclodextrin-induced insulin dissociation is also observed at pH 7.4.     

Fatty acid-binding to erythrocyte ghost membranes and transmembrane movement

Summary Palmitate binding to human erythrocyte ghost membranes has been investigated with ghost preparations suspended in 0.2% albumin solutions. Free unbound palmitate in the extracellular water phase was measured in equilibrium studies using albumin-filled acid loaded ghosts as small semipermeable bags. The apparent dissociation constant of binding to the membrane is 13.5 nM and the binding capacity 19 nmoles per 7.2 × 109 cells.The 0°C exchange efflux kinetics of palmitate from albumin-filled ghosts is described by a model, which provides estimates of the rate constant of membrane transfer, k₃ = 0.024 s^–1, independent of the molar ratio of palmitate to albumin () and of a mean dissociation rate constant of the palmitate-albumin complex, k₁ = 0.0015 s^–1 at 0.2, allowing for a heterogeneity of the palmitate binding to albumin.The values of a third kinetically determined dependent model constant, Q, the ratio of palmitate bound to the membrane inner surface to palmitate on intracellular albumin, are not different from the Q values obtained by equilibrium experiments.The temperature dependences of k₁ and k₃ in the interval 0°C to 15°C give activation energies of 96 and 103 kJ/mole, respectively. The 0°C exchange efflux increases about 2 fold in response to a rise of pH from 6 to 9. The results suggest a carrier mediated palmitate flux at low with a V_max about 2 pmoles min^–1 cm^–2 at 0°C pH 7.3.     

Free energy dependence of the direct charge recombination from the primary and secondary quinones in reaction centers from Rhodobacter sphaeroides

The direct charge recombination rates from the primary quinone, k _AD (D⁺Q _A ^– DQ_A) and the secondary quinone, k _BD (D⁺Q _B ^– DQ_B), in reaction centers from Rhodobacter sphaeroides were measured as a function of the free energy differences for the processes, G _AD ⁰ and G _BD ⁰ , respectively. Measurements were performed at 21 °C on a series of mutant reaction centers that have a wide range of dimer midpoint potentials and consequently a large variation in G _AD ⁰ and G _BD ⁰ . As –G _AD ⁰ varied from 0.43 to 0.78 eV, k _AD varied from 4.6 to 28.6 s^–1. The corresponding values for the wild type are 0.52 eV and 8.9 s^–1. Observation of the direct charge recombination rate k _BD was achieved by substitution of the primary quinone with naphthoquinones in samples in which ubiquinone was present at the secondary quinone site, resulting specifically in an increase in the free energy of the D⁺Q _A ^– state relative to the D⁺Q_AQ _B ^– state. As –G _BD ⁰ varied from 0.37 to 0.67 eV, k _BD varied from 0.03 to 1.4 s^–1. The corresponding values for the wild type are 0.46 eV and 0.2 s^–1. A fit of the two sets of data to the Marcus theory for electron transfer yielded significantly different reorganization energies of 0.82 and 1.3 eV for k _AD and k _BD, respectively. In contrast, the fitted values for the coupling matrix element, or equivalently the maximum possible rate, were comparable (25 s^–1) for the two charge recombination processes. These results are in accord with Q_B having more interactions with dipoles, from both the surrounding protein and bound water molecules, than Q_A and with the primary determinant of the maximal rate being the quinone-donor distance.     

Binding of phosphate in sediment accumulation areas of the eastern Gulf of Finland,Baltic Sea

The relationships between P and components binding P were studied by analysing the concentrations of N, P, Fe, Mn, Ca and Al in sediments and pore water along the estuarine transect of the River Neva in August 1995. The high sediment organic matter concentration resulted in low surface redox potential and high pore-water o-P concentration, whereas the abundance of amphipods resulted in high surface redox potentials and low pore-water o-P concentration. However, despite the variation in sediment organic matter and the abundance of amphipods, very reduced conditions and slightly variable concentrations of Tot-P (0.7–1.1 mg g^–1 DW) were observed in the 10–15 cm sediment depth along the estuarine gradient, indicating that the pools of mobile P were largely depleted within the depth of 0–15 cm. Multiple regression analysis demonstrated that organic matter and Tot-Fe concentration of the sediment were closely related to the variation in Tot-P concentration of the sediments (r ² = 0.817, n=32). In addition, the high total Fe:P ratio suggested that there is enough Fe to bind P in sediments along the estuarine gradient. However, low Fe_diss concentrations in the pore water of reduced sediment (redox-potential <–50 mV) indicated efficient precipitation of FeS (FeS and FeS₂), incapable to efficiently bind P. Consequently, the low Fe_diss:o-P ratio (< 1) recorded in pore water in late summer implied that Fe³⁺ oxides formed by diffusing Fe_diss in the oxic zone of the sediments were insufficient to bind the diffusing o-P completely. The measured high o-P concentrations in the near-bottom water are consistent with this conclusion. However, there was enough Fe_diss in pore water to form Fe³⁺ oxides to bind upwards diffusing P in the oxic sediment layer of the innermost Neva estuary and the areas bioturbated by abundant amphipods.     

Dialysis cultures with immobilized hybridoma cells for effective production of monoclonal antibodies

An industrial scale reactor concept for continuous cultivation of immobilized animal cells (e.g. hybridoma cells) in a radial-flow fixed bed is presented, where low molecular weight metabolites are removed via dialysis membrane and high molecular products (e.g. monoclonal antibodies) are enriched. In a new nutrient-split feeding strategy concentrated medium is fed directly to the fixed bed unit, whereas a buffer solution is used as dialysis fluid. This feeding strategy was investigated in a laboratory scale reactor with hybridoma cells for production of monoclonal antibodies. A steady state monoclonal antibody concentration of 478 mg l^-1 was reached, appr. 15 times more compared to the concentration reached in chemostat cultures with suspended cells. Glucose and glutamine were used up to 98%. The experiments were described successfully with a kinetic model for immobilized growing cells. Conclusions were drawn for scale-up and design of the large scale system.Abbreviations: c_Glc – glucose concentration, mmol l^-1; c_Gln – glutamine concentration, mmol l^-1; c_Amm – ammonia concentration, mmol l^-1; c_Lac – lactate concentration, mmol l^-1; c_MAb – MAb concentration, mg l^-1; D – dilution rate, d^-1; D_i – dilution rate in the inner chamber of the membrane dialysis reactor, d^-1; D₀ – dilution rate in the outer chamber of the membrane dialysis reactor, d^-1; q*_FB,Glc – volume specific glucose uptake rate related to the fixed bed volume, mmol l_FB ^-1 h^-1; q*_FB,Gln – volume specific glutamine uptake rate related to the fixed bed volume, mmol l_FB ^-1 h^-1.     

Medium optimization for a methanol utilizing bacterium based on chemostat theory

Summary In the productions of biomass and vitamin B₁₂ using methanol as the sole carbon source, it is necessary to use a medium in which methanol is the growth limiting substrate. Other inorganic salts should be in slight excess so that the yield of cells and the intracellular content of vitamin B₁₂ do not vary. From basic principles of chemostat culture, a medium was optimized for Pseudomonas AM-1 a methanol utilizing bacterium, for the concentrations of various inorganic salts. This was done in a series of chemostat cultures at a dilution rate of 0.1 h^–1. Optimum amounts of NH₄ ⁺, PO₄ ^3- and Mg²⁺ were estimated from the minimum concentration of the salt at which methanol became growth limiting. The optimum concentrations of Ca²⁺, Fe²⁺, Mn²⁺, and Zn²⁺ as a group were determined in the same way. Cu²⁺, Mo⁶⁺, Co²⁺ and B³⁺ are required at concentrations of g/l and they were not studied as these very low level can be introduced as contaminants from other salts. The optimum medium composition (in g/l) was as follows: (NH₄)₂SO₄, 1.0; H₃PO₄, 75×10^–3; MgSO₄ · 7H₂O, 30×10^–3; CaCl₂ · 2H₂O, 3.3×10^–3; FeSO₄ · 7H₂O, 1.3×10^–3, MnSO₄ · 4H₂O, 0.13×10^–3; ZnSO₄ · 7H₂O, 0.13×10^–3; CuSO₄ · 5H₂O, 40×10^–6; Na₂MoO₄, 40×10^–6; CoCl₂ · 6H₂O, 40×10^–6; H₃BO₃, 30×10^–6 and methanol 4.     

Binding of chloride and a disulfonic stilbene transport inhibitor to red cell band 3

Summary The effect of chloride on 4,4-dibenzamido-2,2-disulfonic stilbene (DBDS) binding to band 3 in unsealed red cell ghost membranes was studied in buffer [NaCl (0 to 500mm) + Na citrate] at constant ionic strength (160 or 600mm). pH 7.4, 25°C. In the presence of chloride, DBDS binds to a single class of sites on band 3. At 160mm ionic strength, the dissociation constant of DBDS increases linearly with chloride concentration in the range [Cl]=450mm. The observed rate of DBDS binding to ghost membranes, as measured by fluorescence stopped-flow kinetic experiments, increases with chloride concentration at both 160 and 600mm ionic strength. The equilibrium and kinetic results have been incorporated into the following model of the DBDS-band 3 interaction: The equilibrium and rate constants of the model at 600mm ionic strength areK ₁=0.67±0.16 m,k ₂=1.6±0.7 sec^–1,k _–2=0.17±0.09 sec^–1,K ₁=6.3±1.7 m,k ₂=9±4 sec^–1 andk _–2=7±3 sec^–1. The apparent dissociation constants of chloride from band 3,K _Cl, are 40±4mm (160mm ionic strength) and 11±3mm (600mm ionic strength). Our results indicate that chloride and DBDS have distinct, interacting binding sites on band 3.     

Determination of the inherent kinetics of immobilized glucose oxidase using a diffusion cell

The enzyme glucose oxidase (GO) was covalently immobilized onto a poly(vinyl alcohol) hydrogel, cross-linked with glutardialdehyde and a polyazonium salt. To compare the kinetic parameters of immobilized GO with the known kinetic parameters of soluble GO, the diffusion cell method was used.Between two compartments, containing solutions with different glucose concentrations, a GO-containing hydrogel membrane was placed. Simultaneous diffusion through and enzymatic reaction in the membrane occurred. In this way diffusional effects of the membrane could be eliminated from the effective kinetic parameters to yield the inherent kinetic parameters.It appeared that the enzymatic reaction is independent of the oxygen concentration at oxygen concentrations 0.22 mol m^–3 (Michaelis constant for oxygen < 0.22 mol m^–3). Further, the Michaelis constant for glucose does not change dramatically after immobilizing the enzyme. The maximal reaction rate is depending on the enzyme concentration. As the enzyme concentration in the membrane is not exactly known (mainly due to leakage of enzyme out of the membrane during membrane preparation), only an estimation of the turnover number can be made.The diffusion cell method is easy to carry out. Still, some recommendations can be made on the performance.List of Symbols _g , _0x partition coefficient of glucose and oxygen, respectively - thickness of the wetted membrane (m) - A _m surface area of membrane (m^–2) - C constant (mol² m^–3) - c _g , c _0x concentration of glucose and oxygen, respectively (mol m^–3) - c _g,0 c _g, glucose concentration at the filter-paper/membrane interface next to compartment A and B, respectively (mol m^–3) - c _{g, A} c _{g, B} glucose concentration in compartment A and B, respectively (mol m^–3) - c _GO glucose oxidase concentration (mol m^–3) - D _eff effective diffusion coefficient (m² s^–1) - D _m , D _sl diffusion coefficient in, respectively, the membrane and the solution layer (m² s^–1) - d _dl , d _df , d _sl thickness of, respectively, the diffusion layer, the filter-paper and the solution layer (m) - h _B initial slope of concentration versus time curve of compartment B (mol m^–3 s^–1) - J flux (mol m^–2 s^–1) - J ₀ flux in the membrane at membrane/filter-paper interface next to compartment A and B, respectively (mol m^–2 s^–1) - J _A , J _B flux leaving compartment A and entering compartment B, respectively (mol m^–2 s^–1) - J _m flux through the membrane (mol m^–2 s^–1) - k total mass transfer coefficient (m s^–1) - k ₁ , k ₂ rate constant of a particular reaction step (m³ mol^–1 s^–1) - k_–1, k_–2 rate constant of a particular reaction step (s^–1) - k _cat (intrinsic) catalytic constant of turnover number (s^–1) - k _cat ^* inherent catalytic constant, determined by inserting D _m (s^–1) - k _cat ^** inherent catalytic constant, determined by inserting D _eff (s^–1) - k _m (g) (intrinsic) Michaelis constant for glucose (mol m^–3) - k _m (o) (intrinsic) Michaelis constant for oxygen (mol m^–3) - k _m ^* (g) inherent Michaelis constant for glucose (mol m^–3) - k _m ^* (o) inherent Michaelis constant for oxygen (mol m^–3) - m _GO number of moles of GO present (mol) - P _m permeability of glucose in the mebrane (m s^–1) - P _eff effective permeability (m s^–1) - V volume (m³) - v ₀ initial reaction velocity (mol m^–3 s^–1) - V _max ^** inherent maximal reaction velocity, determined by inserting D_eff (mol m^–3 s^–1) - x distance (m)     

Optimum temperature policy for batch reactors performing biochemical reactions in the presence of enzyme deactivation

A necessary condition is found for the optimum temperature policy which leads to the minimum reaction time for a given final conversion of substrate in a well stirred, enzymatic batch reactor performing an enzyme-catalyzed reaction following Michaelis-Menten kinetics in the presence of first order enzyme decay. The reasoning, which is based on Euler's classical approach to variational calculus, is relevant for the predesign steps because it indicates in a simple fashion which temperature program should be followed in order to obtain the maximum advantage of existing enzyme using the type of reactor usually elected by technologists in the fine biochemistry field. In order to highlight the relevance and applicability of the work reported here, the case of optimality under isothermal operating conditions is considered and a practical example is worked out.List of Symbols C _E mol.m^–3 concentration of active enzyme - C _E ^* dimensionless counterpart of C_E - C _E,0 mol.m^–3 initial concentration of active enzyme - C _E,b mol.m^–3 final concentration of active enzyme - C _E,opt ^* optimal dimensionless counterpart of C_E - C _smol.m^–3 concentration of substrate - C _S ^Emphasis>/* dimensionless counterpart of C_S - C _S,0mol.m^–3 initial concentration of substrate - C _S,bmol.m^–3 final concentration of substrate - E enzyme in active form - E ₃ ^* dimensionless counterpart of E_a,3 - E _a,1J.mol^–1 activation energy associated with k₁ - E _a,3J.mol^–1 activation energy associated with k₃ - E _d enzyme in deactivated form - ES enzyme/substrate complex - k ₁ s^–1 kinetic constant associated with the enzyme-catalyzed transformation of substrate - k _1,0 s^–1 preexponential factor associated with k₁ - k ₂ mol^–1.m³s^–1 kinetic constant associated with the binding of substrate to the enzyme - k _–2 s^–1 kinetic constant associated with the dissociation of the enzyme/substrate complex - K _2,0 mol.m^–3 constant value of K₂ - K _2,0 ^* dimensionless counterpart of K_2,0 - k ₃ s^–1 kinetic constant associated with the deactivation of enzyme - k _3,0 s^–1 preexponential factor associated with k₃ - k _3,0 ^* dimensionless counterpart of k_3,0 - P product - R J.K^–1.mol^–1 ideal gas constant - S substrate - t s time since start-up of reaction - T K absolute temperature - T ^* dimensionless absolute temperature - T _i,opt ^* optimal dimensionless isothermal temperature of operation - T _opt ^* optimal dimensionless temperature of operation - t _b s time of a batch - t _b ^* dimensionless counterpart of t_b - t _b,min ^* minimum value of the dimensionless counterpart of t_b Greek Symbols dimensionless counterpart of C_E,0 - dimensionless counterpart of C_E,b - dummmy variable of integration - dummy variable of integration - auxiliary dimensionless variable - ^* dimensionless variation of k₁ with temperature - _i ^* dimensionless value of k₁ under isothermal conditions - _opt ^* optimal dimensionless variation of k₁ with temperature     

Optimal temperature and concentration profiles in a cascade of CSTR's performing Michaelis-Menten reactions with first order enzyme deactivation

A necessary condition is found for the intermediate temperatures and substrate concentrations in a series of CSTR's performing an enzyme-catalyzed reaction which leads to the minimum overall volume of the cascade for given initial and final temperatures and substrate concentrations. The reaction is assumed to occur in a single phase under steady state conditions. The common case of Michaelis-Menten kinetics coupled with first order deactivation of the enzyme is considered. This analysis shows that intermediate stream temperatures play as important a role as intermediate substrate concentrations when optimizing in the presence of nonisothermal conditions. The general procedure is applied to a practical example involving a series of two reactors with reasonable values for the relevant five operating parameters. These parameters are defined as dimensionless ratios involving activation energies (or enthalpy changes of reaction), preexponential factors, and initial temperature and substrate concentration. For negligible rate of deactivation, the qptimality condition corresponds to having the ratio of any two consecutive concentrations as a single-parameter increasing function of the previous ratio of consecutive concentrations.List of Symbols C _E,0 mol.m^–3 Initial concentration of active enzyme - C _E,i mol.m^–3 Concentration of active enzyme at the outlet of the i-th reactor - C _S,0 mol.m^–3 Initial concentration of substrate - C _S,i mol.m^–3 Concentration of substrate at the outlet of the i-th reactor - Da _i Damköhler number associated with the i-th reactor ((V _i.k_v,0.C_E,0)/(Q.C_S,0)) - Da _min Minimum value of the overall Damköhler number - Da _tot Overall Damköhler number - E _d J.mol^–1 Activation energy of the step of deactivation of the enzyme - E _m J.mol^–1 Standard enthalpy change of the step of binding of substrate to the enzyme - E _v J.mol^–1 Activation energy of the step of enzymatic transformation of substrate - i Integer variable - j Dummy integer variable - k Dummy integer variable - k _d,i s^–1 Kinetic constant associated with the deactivation of enzyme in the i-th reactor (k _d,o·exp{–E _d/(R.T _i}) - k _d,0 s^–1 Preexponential factor of the kinetic constant associated with the deactivation of the enzyme - K _m,i mol.m^–3 Equilibrium constant associated with the binding of substrate to the enzyme in the i-th reactor, (k _m,o·exp{–E _m}(R.T _i}) - K _m,0 mol.m^–3 Preexponential factor of the Michaelis-Menten constant associated with the binding of substrate to the enzyme - k _v,i s^–1 Kinetic constant associated with the transformation of the substrate by the enzyme in the i-th reactor (k _v,o·exp{–E _v/(R.T _i})) - k _v,0 s^–1 Preexponential factor of the kinetic constant associated with the transformation of the substrate by the enzyme - N Number of reactors in the series - Q m³.s^–1 Volumetric flow rate of reacting liquid through the reactor network - R J.K^–1.mol^–1 Ideal gas constant - T _i K Absolute temperature at the outlet of the i-th reactor - T ₀ K Initial absolute temperature - V _i m³ Volume of the i-th reactor - v _max mol.m^–3.s^–1 Maximum rate of reaction under saturation conditions of substrate - x _i Normalized concentration of substrate (C_S,i/C_{S, 0}) - x _i,opt Optimum value of the normalized concentration of substrate - y _i Dimensionless temperature (exp{–T ₀/T _i}) - y _i,opt Optimum value of the dimensionless temperature Greek Symbols Dimensionless preexponential factor associated with the Michaelis-Menten constant (K _m,0/C_s,0) - Dimensionless activation energy of the step of enzymatic transformation of substrate (E _v/R.T₀)) - Dimensionless standard enthalpy change of the step of binding of substrate to the enzyme (E _m/(R.T₀)) - Dimensionless activation energy of the step of deactivation of the enzyme (E _d/(R.T₀)) - Dimensionless deactivation preexponential factor ((k _d,0.C_S,0)/(k_v,0.C_E,0)     

Growth simulation ofHansenula polymorpha

Summary Using the model presented in part I, the measured time and spacial variations of process variables were simulated with satisfactory accuracy. Especially the experimentally found minima of the longitudinal dissolved oxygen concentration profiles in the substrate limiting growth range, which are caused by the transition from oxygen transfer limited to substrate limited growth along the tower, can be simulated with great accuracy.Symbols L length - M mass - T time - K temperature - M_M mole mass - a Specific gas/liquid interfacial area with regard to the liquid volume in the tower (L^–1) - DS_R Substrate feed rate (ML^–3T^–1) - K_O Saturation constant of Monod kinetics with regard to oxygen (ML^–3) - K_S Saturation constant of Monod kinetics with regard to the substrate (ML^–3) - K_ST Constant - K_L Mass transfer coefficient (LT^–1) - k_La Volumetric mass transfer coefficient (T^–1) - k_La^E Volumetric mass transfer coefficient at the entrance (T^–1) - k_La Volumetric mass transfer coefficient at large distances from the entrance (T^–1) - k_La ₀ Volumetric mass transfer coefficient in the absence of substrate (ethanol) (T^–1) - L_R Gas-liquid layer height in the tower (L) - L_R Height of the loop (L) - - O_B Dissolved oxygen concentration in the loop liquid (ML^–3) - O_F Dissolved oxygen concentration in the tower liquid (ML^–3) - O _F ^* Saturation value of O_F (ML^–3) - OTR Oxygen transfer rate (ML^–3T^–1) - P Pressure - Oxygen transfer rate (ML^–3T) - S_B Substrate concentration in the loop liquid (ML^–3) - S_D Substrate concentration at which k_La=2 k_La ₀ (ML^–3) - S_F Substrate concentration in the tower liquid (ML^–3) - T Absolute temperature - t Time (T) - u_Go Superficial gas velocity in the tower - V_R Reactor volume (L³) - V_G Volumetric gas flow rate in the tower (L³T^–1) - V_B Volumetric liquid flow rate in the loop (L³T^–1) - V_F Volumetric liquid flow rate in the tower (L³T^–3) - V_u Liquid recycling rate (L³T^–1) - X_B Biomass concentration in the loop liquid (ML^–3) - X_F Biomass concentration in the tower liquid (ML^–3) - x Longitudinal coordinate in the tower (L) - x^* Longitudinal coordinate in the loop (L) - x_OG O₂ mole fraction in the gas phase - Y_X/O Yield coefficient of biomass with regard to oxygen - Y_X/S Yield coefficient of biomass with regard to substrate - z=x/L_R Dimensionless longitudinal coordinate in the tower - z^*=x^*/L_B Dimensionless longitudinal coordinate in the loop - Constant (L_R is the distance from the aerator on which k_L a is space dependent) - Liquid recirculation ratio - _G Mean relative gas holdup in the tower - _exp Experimentally determined (T^–1) - _max Maximum specific growth rate (T^–1) - _F Liquid density (ML^–3) - A At the exit - E At the inlet     

Synthetic model and bioactive peptides as potential substrates for enteropeptidase

Enteropeptidase (enterokinase EC 3.4.21.9), catalyzing trypsinogen activation, exhibits unique properties for high efficiency hydrolysis of the polypeptide chain after the N-terminal tetraaspartyl-lysyl sequence. This makes it a convenient tool for the processing of fusion proteins containing this sequence. We found the enteropeptidase-catalysing degradation of some bioactive peptides: cattle hemoglobin beta-chain fragments Hb (2–8) (LTAEEKA) and Hb (1–9) (MLTAEEKAA), human angiotensin II (DRVYIHPF) (AT). Model peptideswith truncated linker WDDRG and WDDKG also were shown to be susceptible to enteropeptidase action. Kinetic parameters ofenteropeptidase hydrolysis for these substrates were determined.K _m values for all substrates with truncated linker (10^-3 M) are an order of magnitude higher thancorresponding values for typical enteropeptidase artificial peptide or fusion protein substrates with full enteropeptidase linker –DDDDK– (K _m 10^-4 M). k _cat values for AT, Hb (2–8), WDDRG and WDDKG are 30–40 min^-1. But one additional amino acid residue at both N- and C-terminus of Hb (2–8) results in a drastic increase of hydrolysis efficiency: k _cat value for Hb (1–9) is 1510 min^-1. Recent study demonstrates the possibility of undesirable cleavage of target peptides or proteins containing the above-mentioned truncated linker sequences; further, the ability of enteropeptidase to hydrolyse specifically several biologically active peptides in vitro along with its unique natural substrate trypsinogen was demonstrated.     

New solution method for equations of reaction and mass transfer in biocatalyst particles

Summary For numerical solution of the reaction-mass transfer equations for immobilised biocatalysts it may be better to start integration at the particle surface and proceed inwards: calculations are targetted on the region to which practically interesting changes are often confined (because concentrations are effectively zero in the interior); and during iterative solution wrong initial estimates may be rejected after detecting anomalies early in the integration.Symbols C_b substrate concentration in bulk (mol m^–3) - c dimensionless substrate concentration (C/C_b) (-) - D_e effective diffusion coefficient (m²s^–1) - Da Damkohler number (V.r_o ²/D_e.K_s) (-) - K_s substrate concentration kinetic coefficient (mol m^–3) - k_e external mass transfer coefficient (ms^–1) - r_o bead radius (m) - Sh Sherwood number (k_e.r_o/D_e) (-) - V maximum rate per unit volume in beads (mol m^–3s^–1) - x dimensionless distance from bead centre (r/r_o) (-) - dimensionless kinetic coefficient (K_s/C_b) (-) - _o effectiveness factor (-)