Dynamic pressure method for kla measurement in large-scale bioreactors

A dynamic method is proposed for k(l)a measurement in aerated and agitated reactors, in which a change in the total pressure in the reactor by approximately 20% leads to a simultaneous change in the oxygen concentration in all the bubbles in the dispersion. This procedure suppresses the influence of nonideal mixing of the gas phase on the k(l)a value. Other dynamic methods so far used do not possess this advantage. They are based on a step change in oxygen concentration in the entering gas, where the interfacial nitrogen transport and the finite rate of the concentration change propagation into the individual bubbles in the dispersion can cause an error in the reported k(l)a values of more than hundreds of percent. The reliability of the pressure method is tested by comparison both with the standard dynamic method, in which pure oxygen is absorbed in a liquid from which all other gas components were previously removed, and with the steady-state sulphite method. The signal of the oxygen probe used in the experiments must be independent of the pressure. A test for this in dependence is described. The pressure method is also suitable for large-scale reactors since the necessary pressure changes are sufficiently small and, morever, air can be used.     

Effect of ajmaline on transient outward current in rat ventricular myocytes

The mechanism of ajmaline-induced inhibition of the transient outward current (I(to)) has been investigated in right ventricular myocytes of rat using the whole cell patch clamp technique. Ajmaline decreased the amplitude and the time integral of I(to) in a concentration-dependent, but frequency- and use-independent manner. In contrast to the single exponential time course of I(to)-inactivation in control conditions (tau(i) = 37.1 +/- 2.7 ms), the apparent inactivation was fitted by a sum of two exponentials under the effect of ajmaline with concentration-dependent fast and slow components (tau(f) = 11.7 +/- 0.8 ms, tau(s) = 57.6 +/- 2.7 ms at 10 micromol/l) suggesting block development primarily in the open channel state. An improved expression enabling to calculate the association and dissociation rate constants from the concentration dependence of tau(f) and tau(s) was derived and resulted in k(on) = 4.57 x 10(6) +/- 0.32 x 10(6) mol(-1).l.s(-1) and k(off) = 20.12 +/- 5.99 s(-1). The value of K(d) = 4.4 micromol/l calculated as k(off) / k(on) was considerably lower than IC(50) = 25.9 +/- 2.9 micromol/l evaluated from the concentration dependence of the integrals of I(to). Simulations on a simple model combining Hodgkin-Huxley type gating kinetics and drug-channel interaction entirely in open channel state agreed well with the experimental data including the difference between the K(d) and IC(50). According to the model, the fraction of blocked channels increases upon depolarization and declines if depolarization is prolonged. The repolarizing step induces recovery from block with time constant of 52 ms. We conclude that in the rat right ventricular myocytes, ajmaline is an open channel blocker with fast recovery from the block at resting voltage.     

Locating the rate-determining step(s) for three-step hydrolase-catalyzed reactions with DYNAFIT

Hydrolytic reactions of oligopeptide 4-nitroanilides catalyzed by human-alpha-thrombin, human activated protein C and human factor Xa were studied at pH 8.0-8.4 and 25.0+/-0.1 degrees C by the progress curve method and individual rate constants were calculated mostly within 10% internal error using DYNAFITV. A systematic strategy has been developed for fitting a three-step consecutive mechanism to eighteen hundred to six thousand time-course data points polled from two to four independent kinetic experiments. Enzyme and substrate concentrations were also calculated. Individual rate constants well reproduce published values obtained under comparable conditions and the Michaelis-Menten kinetic parameters calculated from these elementary rate constants are also within reasonable limits of published values. For comparison, the integrated Michaelis-Menten equation was also fitted to data from twelve sets. Both the k(cat) and k(cat)/K(m) values are within 15% agreement with those calculated using the elementary rate constants obtained with DYNAFITV. Rate constants for the second and third consecutive steps are within 3-4 fold indicating that both determine the overall rate. The Factor Xa-catalyzed hydrolysis of N-alpha-Z-D-Arg-Gly-Arg-pNA.2HCl at pH 8.4 in a series of buffers containing increasing fractions of deuterium at 25.0+/-0.1 degrees C shows a very strong dependence of k(3) and a moderate dependence of k(2) on D content in the buffer: the fractionation factors are: 0.49+/-0.03 for K(1,) 0.70+/-0.05 for k(2), and (0.32+/-0.03)(2) for k(3).     

Numerical modeling and uncertainties in rate coefficients for methane utilization and TCE cometabolism by a methane-oxidizing mixed culture

The rates of methane utilization and trichloroethylene (TCE) cometabolism by a methanotrophic mixed culture were characterized in batch and pseudo-steady-state studies. Procedures for determination of the rate coefficients and their uncertainties by fitting a numerical model to experimental data are described. The model consisted of a system of differential equations for the rates of Monod kinetics, cell growth on methane and inactivation due to TCE transformation product toxicity, gas/liquid mass transfer of methane and TCE, and the rate of passive losses of TCE. The maximum specific rate of methane utilization (k(CH(4) )) was determined by fitting the numerical model to batch experimental data, with the initial concentration of active methane-oxidizing cells (X(0) (a)) also used as a model fitting parameter. The best estimate of k(CH(4) ) was 2.2 g CH(4)/g cells-d with excess copper available, with a single-parameter 95% confidence interval of 2.0-2.4 mg/mg-d. The joint 95% confidence region for k(CH(4) ) and X(0) (a) is presented graphically. The half-velocity coefficient (K(S,CH(4) )) was 0.07 mg CH(4)/L with excess copper available and 0.47 mg CH(4)/L under copper limitation, with 95% confidence intervals of 0.02-0.11 and 0.35-0.59 mg/L, respectively. Unique values of the TCE rate coefficients k(TCE) and K(S,TCE) could not be determined because they were found to be highly correlated in the model fitting analysis. However, the ratio k(TCE)/K(S,TCE) and the TCE transformation capacity (T(C)) were well defined, with values of 0.35 L/mg-day and 0.21 g TCE/g active cells, respectively, for cells transforming TCE in the absence of methane or supplemental formate. The single-parameter 95% confidence intervals for k(TCE)/K(S,TCE) and T(C) were 0.27-0.43 L/mg-d and 0.18-0.24 g TCE/g active cells, respectively. The joint 95% confidence regions for k(TCE)/K(S,TCE) and T(C) are presented graphically. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 320-331, 1997.     

Critical assessment of the steady-state Na2SO3 feeding method for kla measurement in fermentors

Important aspects of k(l)a measurement in agitated aerated vessels are briefly characterized from the standpoint of reliability of the measured data. It seems that most of the k(l)a data, based on a number of variants of the steady-state and dynamic methods in noncoalescent liquids, do not have a clear physical meaning, because they are affected by the differences between the actual driving force and the driving force assumed by the model used for its evaluation. A reliability test is given for the Na(2)SO(3) feeding steady-state method (FSM), by comparing the results of air and pure oxygen absorption in a noncoalescent liquid (0.5M Na(2)SO(4) solution) with the results obtained by the independent pressure step dynamic method (RDM). The RDM is one of a few variants of the dynamic method which gives correct k(l)a data unaffected by nonideal mixing of the gas phase in the reactor. It was found that the FSM yields correct k(l)a values only when pure oxygen is used for absorption. When air is absorbed, the FSM gives k(l)a values in the region of k(l)a > 0.1 s(-1) substantially (to 55%) lower than those for pure oxygen absorption.     

Pseudo-enzymatic hydrolysis of 4-nitrophenyl myristate by human serum albumin

Most of the esterase properties of human serum albumin (HSA) are the result of multiple irreversible chemical modifications rather than turnover. The HSA-catalyzed hydrolysis of 4-nitrophenyl myristate (NphOMy) is consistent with the minimum three-step mechanism involving the acyl-enzyme intermediate HSA-OMy: Under all the experimental conditions, values of K(s) (= k(-1)/k(+1)), k(+2), and k(+2)/K(s) determined under conditions where [HSA] ≥ 5 × [NphOMy] and [NphOMy] ≥ 5 × [HSA] match very well each other. The deacylation process is rate limiting in catalysis (i.e., k(+3) < k(+2)) and k(-2)~k(-3)~0 s(-1). The pH dependence of k(+2)/K(s), k(+2), and K(s) reflects the acidic pK(a)-shift of one ionizing group from 8.9 ± 0.2 in NphOMy-free HSA to 6.8 ± 0.3 in the HSA:NphOMy adduct. The HSA-catalyzed hydrolysis of NphOMy is inhibited competitively by diazepam, indicating that Tyr411 is the active-site nucleophile.     

Influence of body size and environmental temperature on carbon dioxide production by forest centipedes from southwestern North America

We conducted a laboratory study to evaluate the mass and temperature dependence of carbon dioxide production by three dominant centipede species--Arctogeophilus umbraticus McNeill, Gonibius glyptocephalus Chamberlin, and Oabius sp.--from a montane forest in southwestern North America. We found that CO2 production (Q, microl/h) of resting, nonfasted individuals was related to body mass (M, mg live) and environmental temperature (T, K) as Q=e18.32M0.82e-0.49/kT, where e is the base of the natural logarithm and k is Boltzmann's constant (8.62x10(-5) eV/K). Our results indicated that the mass and temperature dependence of centipede metabolism is comparable with that of other arthropods. They also supported previous claims that centipede metabolic rate, for a given mass and temperature, is relatively low compared with other arthropods. Suggestions are given for using resulting metabolic rate equations in conjunction with data on abundance, body size, and environmental temperature to assess energy flux by centipede populations.     

Kinetic and thermodynamic studies of the cross-bridge cycle in rabbit psoas muscle fibers.

The effect of temperature on elementary steps of the cross-bridge cycle was investigated with sinusoidal analysis technique in skinned rabbit psoas fibers. We studied the effect of MgATP on exponential process (C) to characterize the MgATP binding step and cross-bridge detachment step at six different temperatures in the range 5-30 degrees C. Similarly, we studied the effect of MgADP on exponential process (C) to characterize the MgADP binding step. We also studied the effect of phosphate (Pi) on exponential process (B) to characterize the force generation step and Pi-release step. From the results of these studies, we deduced the temperature dependence of the kinetic constants of the elementary steps and their thermodynamic properties. We found that the MgADP association constant (K0) and the MgATP association constant (K1) significantly decreased when the temperature was increased from 5 to 20 degrees C, implying that nucleotide binding became weaker at higher temperatures. K0 and K1 did not change much in the 20-30 degree C range. The association constant of Pi to cross-bridges (K5) did not change much with temperature. We found that Q10 for the cross-bridge detachment step (k2) was 2.6, and for its reversal step (k-2) was 3.0. We found that Q10 for the force generation step (Pi-isomerization step, k4) was 6.8, and its reversal step (k-4) was 1.6. The equilibrium constant of the detachment step (K2) was not affected much by temperature, whereas the equilibrium constant of the force generation step (K4) increased significantly with temperature increase. Thus, the force generation step consists of an endothermic reaction. The rate constant of the rate-limiting step (k6) did not change much with temperature, whereas the ATP hydrolysis rate increased significantly with temperature increase. We found that the force generation step accompanies a large entropy increase and a small free energy change; hence, this step is an entropy-driven reaction. These observations are consistent with the hypothesis that the hydrophobic interaction between residues of actin and myosin underlies the mechanism of force generation. We conclude that the force generation step is the most temperature-sensitive step among elementary steps of the cross-bridge cycle, which explains increased isometric tension at high temperatures in rabbit psoas fibers.     

Reaction velocities in vivo: standardization of kinetic "constants" by correction for blood flow

1. The results of kinetic studies in vitro are difficult to apply to metabolic reactions in vivo. 2. In living vertebrates reaction rates are usually first-order and for a particular reaction the rate "constant", k, varies with the several thousand-fold variations in metabolic rate. 3. Therefore, in the kinetic equation (formula: see text) since K varies with metabolic rate, Vmax and/or Km will aslo vary. 4. However, reaction rates for a series of different substrates were similar in animals varying widely in metabolic rate if corrections were made for differences in blood flow. 5. The observation that metabolic rate (reaction rate) is directly dependent on blood flow (Coulson et al., 1977) allowed derivation of new kinetic constants which were valid in vivo. 6. Introduction of a flow term into the observed first-order equations yields an "affinity constant", K, or a "flow constant", KF, somewhat analogous to Km, which allows one to predict reaction rates in animals of different metabolic rates. 7. The defining equations are (formula: see text) where V = reaction velocity in mmol/hr/kg tissue, [S] = millimolar substrate concentration in the blood, k = In 2/tau (tau the half-life) and F = blood flow in 1/hr/kg tissue. 8. Thus, K = k/F = 1/KF. The KF's for the initial step in the degradation of 17 amino acids in rats, dogs, lizards, turtles and alligators were similar, demonstrating the similarity of enzyme affinities in different species.     

Determination of transference numbers from membrane potential data

A system composed of two ionic solutions, solution () and solution (), which are isotonic and separated by a membrane permeable to the solvent and to at most two of the ionic components present in the solutions, is considered. The variations of the difference of electric potential between solution () and solution (), in the steady state and for zero electric current, corresponding to variations in the composition of e.g. solution (), are found to depend only on the properties of the membrane phase at the boundary with solution (). This result is deducible under loose assumptions as to the dependence of the properties of transport and absorption of the permeant components in the membrane on their activities in solution. It can therefore be particularly useful for the study of systems, like biological membranes, whose structural and chemical composition is so poorly known that any assumption about that dependence is hardly justifiable.     

Dependence of mu-conotoxin block of sodium channels on ionic strength but not on the permeating [Na+]: implications for the distinctive mechanistic interactions between Na+ and K+ channel pore-blocking toxins and their molecular targets

Mu-conotoxins (mu-CTXs) are Na+ channel-blocking, 22-amino acid peptides produced by the sea snail Conus geographus. Although K+ channel pore-blocking toxins show specific interactions with permeant ions and strong dependence on the ionic strength (mu), no such dependence has been reported for mu-CTX and Na+ channels. Such properties would offer insight into the binding and blocking mechanism of mu-CTX as well as functional and structural properties of the Na+ channel pore. Here we studied the effects of mu and permeant ion concentration ([Na+]) on mu-CTX block of rat skeletal muscle (mu1, Nav1.4) Na+ channels. Mu-CTX sensitivity of wild-type and E758Q channels increased significantly (by approximately 20-fold) when mu was lowered by substituting external Na+ with equimolar sucrose (from 140 to 35 mm Na+); however, toxin block was unaltered (p > 0.05) when mu was maintained by replacement of [Na+] with N-methyl-d-glucamine (NMG+), suggesting that the enhanced sensitivity at low mu was not due to reduction in [Na+]. Single-channel recordings identified the association rate constant, k(on), as the primary determinant of the changes in affinity (k(on) increased 40- and 333-fold for mu-CTX D2N/R13Q and D12N/R13Q, respectively, when symmetric 200 mm Na+ was reduced to 50 mm). In contrast, dissociation rates changed <2-fold for the same derivatives under the same conditions. Experiments with additional mu-CTX derivatives identified toxin residues Arg-1, Arg-13, and Lys-16 as important contributors to the sensitivity to external mu. Taken together, our findings indicate that mu-CTX block of Na+ channels depends critically on mu but not specifically on [Na+], contrasting with the known behavior of pore-blocking K+ channel toxins. These findings suggest that different degrees of ion interaction, underlying the fundamental conduction mechanisms of Na+ and K+ channels, are mirrored in ion interactions with pore-blocking toxins.     

Temperature dependence of nucleotide association and kinetic characterization of myo1b

Myo1b is a widely expressed myosin-I isoform that concentrates on endosomal and ruffling membranes and is thought to play roles in membrane trafficking and dynamics. It is one of the best characterized myosin-I isoforms and appears to have unique biochemical properties tuned for tension sensing or tension maintenance. We determined the key biochemical rate constants that define the actomyo1b ATPase cycle at 37 degrees C and measured the temperature dependence of ATP binding, ADP release, and the transition from a nucleotide-inaccessible state to a nucleotide-accessible state (k(alpha)). The rate of ATP binding is highly temperature sensitive, with an Arrhenius activation energy 2-3-fold greater than other characterized myosins (e.g., myosin-II and myosin-V). ATP hydrolysis is fast, and phosphate release is slow and rate limiting with an actin dependence that is nearly identical to the steady-state ATPase parameters (Vmax and K(ATPase)). ADP release is not as temperature dependent as ATP binding. The rates and temperature dependence of ADP release are similar to k(alpha) suggesting that a similar structural change is responsible for both transitions. We calculate a duty ratio of 0.08 based on the biochemical kinetics. However, this duty ratio is likely to be highly sensitive to strain.     

Proton inventories constitute reliable tools in investigating enzymatic mechanisms: application on a novel thermo-stable extracellular protease from a halo-alkalophilic Bacillus sp

A novel protease designated protease-A-17N-1, was purified from the halo-alkalophilic Bacillus sp. 17N-1, and found active in media containing dithiothreitol and EDTAK(2). This enzyme maintained significant activity from pH 6.00 to 9.00, showed optimum k(cat)/K(m) value at pH 7.50 and 33 degrees C. It was observed that only specific inhibitors of cysteine proteinases inhibited its activity. The pH-(k(cat)/K(m)) profile of protease-A-17N-1 was described by three pK(a)s in the acid limb, and one in the alkaline limb. Both are more likely due t3o the protonic dissociation of an acidic residue, and the development and subsequent deprotonation of an ion-pair, respectively, in its catalytic site, characteristic for cysteine proteinases. Moreover, both the obtained estimates of rate constant k(1) and the ratio k(2)/k(-1) at 25 degrees C, from the temperature-(k(cat)/K(m)) profile of protease-A-17N-1, were found similar to those estimated from the proton inventories of the same parameter, verifying the reliability of the latter methodology. Besides, the bowed-downward proton inventories of k(cat)/K(m), as well as the large inverse SIE observed for this parameter, in combination with its dependence versus temperature, were showed unambiguously that k(cat)/K(m) = k(1). Such results suggest that the novel enzyme is more likely to be a cysteine proteinase functioning via a general acid-base mechanism.     

Evidence for dynamics in proteins as a mechanism for ligand dissociation

Signal transduction, regulatory processes and pharmaceutical responses are highly dependent upon ligand residence times. Gaining insight into how physical factors influence residence times (1/k(off)) should enhance our ability to manipulate biological interactions. We report experiments that yield structural insight into k(off) involving a series of eight 2,4-diaminopyrimidine inhibitors of dihydrofolate reductase whose binding affinities vary by six orders of magnitude. NMR relaxation-dispersion experiments revealed a common set of residues near the binding site that undergo a concerted millisecond-timescale switching event to a previously unidentified conformation. The rate of switching from ground to excited conformations correlates exponentially with the binding affinity K(i) and k(off), suggesting that protein dynamics serves as a mechanical initiator of ligand dissociation within this series and potentially for other macromolecule-ligand systems. Although the forward rate of conformational exchange, k(conf,forward), is faster than k(off), the use of the ligand series allowed for connections to be drawn between kinetic events on different timescales.     

A new colorimetric assay for methionyl aminopeptidases: examination of the binding of a new class of pseudopeptide analog inhibitors

A direct and convenient spectrophotometric assay has been developed for methionine aminopeptidases (MetAPs). The method employs the hydrolysis of a substrate that is a methionyl analogue of p-nitroaniline (L-Met-p-NA), which releases the chromogenic product p-nitroaniline. This chromogenic product can be monitored continuously using a UV-Vis spectrophotometer set at 405 nm. The assay was tested with the type I MetAP from Escherichia coli (EcMetAP-I) and the type II MetAP from Pyrococcus furiosus (PfMetAP-II). Using L-Met-p-NA, the kinetic constants k(cat) and K(m) were determined for EcMetAP-I and PfMetAP-II and were compared with those obtained with a "standard" high-performance liquid chromatography (HPLC) discontinuous assay. The assay has also been used to determine the temperature dependence of the kinetic constant k(cat) for PfMetAP-II as well as to screen two novel pseudopeptide inhibitors of MetAPs. The results demonstrate that L-Met-p-NA provides a fast, convenient, and effective substrate for both type I and type II MetAPs and that this substrate can be used to quickly screen inhibitors of MetAPs.     

Mechanistic origins of the substrate selectivity of serine proteases

Serine proteases catalyze the hydrolysis of amide bonds of their protein and peptide substrates through a mechanism involving the intermediacy of an acyl-enzyme. While the rate constant for formation of this intermediate, k(2), shows a dramatic dependence on peptide chain length, the rate constant for the intermediate's hydrolysis is relatively insensitive to chain length. To probe the mechanistic origins of this phenomenon, we determined temperature dependencies and solvent isotope effects for the alpha-chymotrypsin-catalyzed hydrolysis of Suc-Phe-pNA (K(s) = 1 mM, k(2) = 0.04 s(-)(1), and k(3) = 11 s(-)(1)), Suc-Ala-Phe-pNA (K(s) = 4 mM, k(2) = 0.9 s(-)(1), and k(3) = 42 s(-)(1)), and Suc-Ala-Ala-Pro-Phe-pNA (K(s) = 0.1 mM, k(2) = 98 s(-)(1), and k(3) = 71 s(-)(1)). We found that while the van't Hoff plots for K(s) and the Eyring plots for k(3) are linear for all three reactions, the Eyring plots for k(2) are convex, indicating that the process governed by k(2) is complex, possibly involving a coupling between active site chemistry and protein conformational isomerization. This interpretation is strengthened by solvent isotope effects on k(2) that are largely temperature-independent. Furthermore, the dependence of k(2) on peptide length is manifested entirely in the enthalpy of activation, suggesting a mechanism of catalysis by distortion. Taken together, this analysis of acylation suggests that extended substrates which can engage in subsite interactions are able to efficiently trigger the coupling mechanism between chemistry and a conformational isomerization that distorts the substrate and thereby promotes nucleophilic attack.     

Photoreactivation and dark repair in UV-treated microorganisms: effect of temperature

Because of the lack of readily available information about the influence of temperature on microorganism reactivation processes subsequent to inactivation with UV radiation, a series of batch reactivation studies were performed at 5, 10, 15, 20, 25, and 30 degrees C. A special effort was made to model the reactivation process to enable the effect of the temperature variable to be quantified. Because an earlier-proposed kinetic model (K. Kashimada, N. Kamiko, K. Yamamoto, and S. Ohgaki, Water Sci. Technol. 33:261-269, 1996), a first-order saturation type, does not adequately fit the data obtained in experiments of reactivation in conditions of light and darkness, a modification of that model is proposed. The new model, which actually coincides with the classical logistic equation, incorporates two kinetic parameters: the maximum survival ratio (Sm) and the second-order reactivation rate constant (k2). In order to interpret correctly the reactivation occurring in conditions of darkness, a new term for the decay is added to the logistic equation. The new model accurately fits the data obtained in reactivation experiments, permitting the interpretation of the kinetic parameters Sm, k2, and M (for only repair in darkness), where M is mortality, a zero-order decay rate constant, and their relationship with various environmental conditions, such as microbial type, light, and temperature. The parameters Sm and k2 (and M for reactivation in conditions of darkness) show exponential dependence on the reactivating temperature, and it is possible to predict their values and hence the reactivation curve from the equations proposed in this work.     

Relationship of membrane physical properties to alcohol dependence in mice selected for genetic differences in alcohol withdrawal

Genetic selection based on severity of withdrawal seizures following inhalation of ethanol vapor has produced two lines of mice, WSR (withdrawal seizure resistant) and WSP (withdrawal seizure prone), that differ markedly in withdrawal signs. In the present study, we report that these mice also differed in the severity of withdrawal seizures following consumption of an ethanol-containing liquid diet but did not differ in ethanol intake. In contrast to ethanol withdrawal seizures, the lines displayed similar sensitivity to electrical- or pentylenetetrazole-induced seizures. These results suggest that the lines differ in the development of physical dependence on ethanol rather than seizure sensitivity per se. Because decreased synaptic membrane fluidity has been associated with ethanol dependence, we used fluorescence polarization of diphenylhexatriene and trimethylammonium-diphenylhexatriene to evaluate membrane fluidity in WSP and WSR mice fed lab chow, an ethanol-containing liquid diet, or an isocaloric sucrose-containing liquid diet. Fluidity of brain synaptic membranes was identical for WSP and WSR mice fed lab chow. The control liquid diet did not alter membrane fluidity, and the ethanol diet decreased fluidity equally for WSP and WSR mice. Thus, the genetic difference in development of ethanol dependence found in these lines was not reflected in the physical properties of brain membranes.     

Detailed dissection of a new mechanism for glycoside cleavage: alpha-1,4-glucan lyase

The unusual enzyme, Gracilariopsis alpha-1,4-glucan lyase of the sequence-related glycoside hydrolase family 31, cleaves the glycosidic bond of alpha-1,4-glucans via a beta-elimination reaction involving a covalent glycosyl-enzyme intermediate (Lee, S. S., Yu, S., and Withers, S. G. (2002) J. Am. Chem. Soc. 124, 4948-4949). The classical bell-shaped pH dependence of k(cat)/K(m) indicates two ionizable groups in the active site with apparent pK(a) values of 3.05 and 6.66. Br?nsted relationships of log k(cat) versus pK(a) and log(k(cat)/K(m)) versus pK(a) for a series of aryl glucosides both show a linear monotonic dependence on leaving group pK(a) with low beta(lg) values of 0.32 and 0.33, respectively. The combination of these low beta(lg) values with large secondary deuterium kinetic isotope effects (k(H)/k(D) = 1.16 - 1.19) on the first step indicate a glycosylation step with substantial glycosidic bond cleavage and proton donation to the leaving group oxygen at the transition state. Developed oxocarbenium ion character of the transition state is also suggested by the potent inhibition afforded by acarbose and 1-deoxynojirimycin (K(i) = 20 and 130 nM, respectively) and by the substantial rate reduction afforded by adjacent fluorine substitution. For only one substrate, 5-fluoro-alpha-D-glucopyranosyl fluoride, was the second elimination step shown to be rate-limiting. The large alpha-secondary deuterium kinetic isotope effect (k(H)/k(D) = 1.23) at C-1 and the small primary deuterium kinetic isotope effect (k(H)/k(D) = 1.92) at C-2 confirm an E2 mechanism with strong E1 character for this second step. This considerable structural and mechanistic similarity with retaining alpha-glucosidases is clear evidence for the evolution of an enzyme mechanism within the family.     

Role of electrostatics in the interaction between cytochrome f and plastocyanin of the cyanobacterium Phormidium laminosum

The role of charged residues on the surface of plastocyanin from the cyanobacterium Phormidium laminosum in the reaction with soluble cytochrome f in vitro was studied using site-directed mutagenesis. The charge on each of five residues on the eastern face of plastocyanin was neutralized and/or inverted, and the effect of the mutation on midpoint potentials was determined. The dependence of the overall rate constant of reaction, k(2), on ionic strength was investigated using stopped-flow spectrophotometry. Removing negative charges (D44A or D45A) accelerated the reaction and increased the dependence on ionic strength, whereas removing positive charges slowed it down. Two mutations (K46A, K53A) each almost completely abolished any influence of ionic strength on k(2), and three mutations (R93A, R93Q, R93E) each converted electrostatic attraction into repulsion. At low ionic strength, wild type and all mutants showed an inhibition which might be due to changes in the interaction radius as a consequence of ionic strength dependence of the Debye length or to effects on the rate constant of electron transfer, k(et). The study shows that the electrostatics of the interaction between plastocyanin and cytochrome f of P. laminosum in vitro are not optimized for k(2). Whereas electrostatics are the major contributor to k(2) in plants [Kannt, A., et al. (1996) Biochim. Biophys. Acta 1277, 115-126], this role is taken by nonpolar interactions in the cyanobacterium, leading to a remarkably high rate at infinite ionic strength (3.2 x 10(7) M(-1) s(-1)).