Catalysis by mutants of human carbonic anhydrase II: effects of replacing hydrophobic residues 198 and 204

Previous studies shows that the replacement of Phe-198 in carbonic anhydrase III to the corresponding Leu residue found in carbonic anhydrase II caused the appearance of isozyme II-like activity (LoGrasso et al. (1991) Biochemistry 30, 8463-8470). Carbonic anhydrase II is more efficient in the catalysis of CO2 hydration by 500-fold and has an apparent pKa for this catalysis about two pKa units above that of carbonic anhydrase III. Moreover, isozyme II catalyzes the hydrolysis of 4-nitrophenyl acetate, whereas isozyme III shows no appreciable catalysis. The purpose of this work was to test the hypothesis that making the converse replacement Leu-198-->Phe as well as Leu-204-->Glu and the double replacement in carbonic anhydrase II would give the resulting mutants of isozyme II properties of isozyme III. The catalytic activities of these mutants in CO2 hydration and 4-nitrophenyl acetate hydrolysis were smaller by at most 5-fold and the pKa values for these catalyses were identical compared with wild-type isozyme II. The different effects of converse mutants of HCA II and III indicate complexity in structure not evident from their similar backbone conformations.

Finite element simulation of pulsatile flow through arterial stenosis

The problem of blood flow through a stenosis is solved using the incompressible Navier-Stokes equations in a rigid circular tube presenting a partial occlusion. Calculations are based on a Galerkin finite element method. The time marching scheme employs a predictor-corrector technique using a variable time step. Results are obtained for steady and physiological pulsatile flows. Computational experiments analyse the effect of varying the degree of stenosis, the stricture length, the Reynolds number and Womersley number. The method gives results which agree well with previous computations for steady flows and experimental findings for steady and pulsatile flows.

Ribosomal movement impeded at a pseudoknot required for frameshifting

Translational frameshifting sometimes occurs when ribosomes encounter a "shift" site preceding a region of unusual secondary structure, which in at least three cases is known to be a pseudoknot. We provide evidence that ribosomes have a decreased rate of movement through a pseudoknot required for frameshifting. These paused ribosomes are directly situated over the shift sequence. Ribosomal pausing appears to be necessary but not sufficient for frameshifting.

The exuperantia gene is required for Drosophila spermatogenesis as well as anteroposterior polarity of the developing oocyte, and encodes overlapping sex-specific transcripts

The Drosophila gene exuperantia (exu) is a maternal effect gene which is needed for proper localization of the bcd RNA during the formation of oocytes. We have extended the characterization of the exu phenotype and find that the gene functions in the male as well as the female germline. Six of seven exu alleles are male-sterile; mutant defects in spermatogenesis first appear during meiosis. A genetic analysis presented here shows that the exu gene does not encode a zygotic vital function. The isolation of two overlapping deficiencies that delete exu function localizes the gene cytologically to polytene bands 57A4-B1. We describe the molecular cloning and identification of the gene, and show that it encodes overlapping sex-specific transcripts of 2.9 kb in the male and 2.1 kb in the female. We also show that these two transcripts are limited in expression to the germline. We demonstrate that one allele, exuVL57, is a deletion of about 700 bp which results in a loss of both transcripts.

Mechanistic studies on trans-2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (Ent A) in the biosynthesis of the iron chelator enterobactin

The enzyme 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (2,3-diDHB dehydrogenase, hereafter Ent A), the product of the enterobactin biosynthetic gene entA, catalyzes the NAD(+)-dependent oxidation of the dihydroaromatic substrate 2,3-dihydro-2,3-dihydroxybenzoate (2,3-diDHB) to the aromatic catecholic product 2,3-dihydroxybenzoate (2,3-DHB). The catechol 2,3-DHB is one of the key siderophore units of enterobactin, a potent iron chelator secreted by Escherichia coli. To probe the reaction mechanism of this oxidation, a variety of 2,3-diDHB analogues were synthesized and tested as substrates. Specifically, we set out to elucidate both the regio- and stereospecificity of alcohol oxidation as well as the stereochemistry of NAD+ reduction. Of those analogues tested, only those with a C3-hydroxyl group (but not a C2-hydroxyl group) were oxidized to the corresponding ketone products. Reversibility of the Ent A catalyzed reaction was demonstrated with the corresponding NADH-dependent reduction of 3-ketocyclohexane- and cyclohexene-1-carboxylates but not the 2-keto compounds. These results establish that Ent A functions as an alcohol dehydrogenase to specifically oxidize the C3-hydroxyl group of 2,3-diDHB to produce the corresponding 2-hydroxy-3-oxo-4,6-cyclohexadiene-1-carboxylate (Scheme II) as a transient species that undergoes rapid aromatization to give 2,3-DHB. Stereospecificity of the C3 allylic alcohol group oxidation was confirmed to be 3R in a 1R,3R dihydro substrate, 3, and hydride transfer occurs to the si face of enzyme-bound NAD+.

Chemical modification of carbonic anhydrase II with acrolein

We have reacted acrolein with human carbonic anhydrase II using conditions reported to result in maximal formylethylation of exposed histidine and lysine residues (Pocker, Y., and Janjić, N. (1988) J. Biol. Chem. 263, 6169-6176). Pocker and Janjić proposed that the decrease by 95-98% in the steady-state turnover number for the hydration of CO2 caused by this chemical modification is due predominantly to the alkylation of one residue, the imidazole side chain of histidine 64. We measured the rate of 18O exchange between CO2 and water catalyzed by these enzymes at chemical equilibrium using membrane inlet mass spectrometry. The catalyzed rate of interconversion of CO2 and HCO3- at chemical equilibrium was the same for the acrolein-modified and the unmodified carbonic anhydrases, but the rate of release of 18O-labeled water from the active site had decreased by as much as 85% for the acrolein-modified enzyme. The 18O-exchange kinetics catalyzed by the acrolein-modified carbonic anhydrase II was similar to that catalyzed by a mutant human carbonic anhydrase II in which histidine at residue 64 was replaced with alanine. Moreover, modification of this mutant carbonic anhydrase II with acrolein did not alter to a significant extent its 18O-exchange pattern. These results support the proposal of Pocker and Janjić and the suggested role of histidine 64 in carbonic anhydrase II as a proton shuttle residue that transfers a proton from zinc-bound water to buffer in solution.

Hemodynamics in transposition of the great arteries with comparison to ventricular septal defect

This paper uses a mathematical model of the circulations to study the hemodynamics of transposition of the great arteries (TGA) with comparison to ventricular septal defect (VSD). Computer experiments are conducted to determine the influence of the defect conductance and the pulmonary vascular conductance on the pulsatile pressures, flows, and oxygen concentrations of the circulation. In particular, the model is used to determine the waveform of the (possibly bidirectional) shunt through the ventricular and atrial septal defects. The results of the computer experiments consist of two parts. The first set of experiments is devoted to the comparison of VSD and TGA with a ventricular septal defect. The results are theoretical in the sense that most parameters have been fixed at the same levels. In each case TGA is represented by changing the connection of the chambers and reversing the compliance of the two ventricles. In the second set of experiments we attempt to simulate conditions clinically observed in a variety of cases of TGA. In each case we use clinical observations to infer parameters as the input to the model. We find that the model (with appropriate choice of parameters) generally exhibits blood pressure, blood flows and oxygen concentrations similar to the clinical observations. As a byproduct of these computer experiments we predict the effects of changing the pulmonary conductance. The comparison between TGA and VSD shows that as the defect conductance increases, the systemic oxygen concentrations decrease in VSD and increase in TGA. Even at large defect conductance, the two conditions remain distinct, however, since the mixing of the right and left ventricular blood pools is incomplete. This phenomenon of incomplete mixing sets quantitative limits on the benefits that can be achieved by surgical enlargement of the defect. A result of this study that may be useful in the management of TGA patients with a ventricular septal defect is the finding that there is a value of the pulmonary conductance that maximizes the effective flow and hence the systemic oxygen concentrations. The optimal pulmonary conductance is approximately equal to the systemic conductance when the defect is large.

Role of Photosynthetic Reactions in the Activity of Carbonic Anhydrase in Synechococcus sp. (UTEX 2380) in the Light : Inhibitor Studies Using the O-Exchange in C/O-Labeled Bicarbonate

The role of the photosystems in the exchange of (18)O between species of inorganic carbon and water was studied in suspensions of the cyanobacterium Synechococcus sp. (UTEX 2380) using membrane-inlet mass spectrometry. This (18)O exchange is caused by the hydration-dehydration cycle of CO(2) and is catalyzed by carbonic anhydrase. We observed the complex (18)O exchange kinetics including dark-light-dark transients in suspensions of whole cells and found these to be identical to the (18)O exchange kinetics of physiologically fully active spheroplast preparations. There was no enhancement effect of inorganic nitrogen on inorganic carbon accumulation. Membrane preparations exhibited no uptake of inorganic carbon and very little carbonic anhydrase activity, although these membranes were photosynthetically fully competent. DCMU, the inhibitor of photosystem II, eliminated almost entirely the (18)O exchange activity of whole cells in the light. But this effect of DCMU could be reversed by addition of the electron donor couple 3,6-diaminodurene/ascorbate, suggesting the involvement of photosystem I in the events leading to (18)O exchange. Iodoacetamide, an inhibitor of CO(2) fixation, enhanced the (18)O exchange in whole cell suspensions and inhibited neither the uptake of inorganic carbon nor the dehydration of bicarbonate in the light. The proton carrier carbonylcyanide m-chlorophenylhydrazone and the inhibitors diethylstilbestrol and N,N' -dicyclohexyl carbodiimide affecting the membrane potential, totally abolished (18)O exchange in the light. From (18) O-labeled inorganic carbon experiments we conclude that one of the roles of photosystem I is to provide the active uptake of inorganic carbon into the cells, where carbonic anhydrase catalyzes the interconversion between CO(2) and HCO(3) (-) resulting in the (18)O exchange from inorganic carbon to water.

Carbonic Anhydrase and the Uptake of Inorganic Carbon by Synechococcus sp. (UTEX-2380)

We report the changes in the concentrations and (18)O contents of extracellular CO(2) and HCO(3) (-) in suspensions of Synechococcus sp. (UTEX 2380) using membrane inlet mass spectrometry. This marine cyanobacterium is known to have an active uptake mechanism for inorganic carbon. Measuring (18)O exchange between CO(2) and water, we have found the intracellular carbonic anhydrase activity to be equivalent to 20 times the uncatalyzed CO(2) hydration rate in different samples of cells that were grown on bubbled air (low-CO(2) conditions). This activity was only weakly inhibited by ethoxzolamide with an I(50) near 7 to 10 micromolar in lysed cell suspensions. We have shown that even with CO(2)-starved cells there is considerable generation of CO(2) from intracellular stores, a factor that can cause errors in measurement of net CO(2) uptake unless accounted for. It was demonstrated that use of (13)C-labeled inorganic carbon outside the cell can correct for such errors in mass spectrometric measurement. Oxygen-18 depletion experiments show that in the light, CO(2) readily passes across the cell membrane to the sites of intracellular carbonic anhydrase. Although HCO(3) (-) was readily taken up by the cells, these experiments shown that there is no significant efflux of HCO(3) (-) from Synechococcus.

Hemodynamics in congenital heart disease

This paper introduces a very general and flexible model for the study of hemodynamic changes in congenital heart disease. The generality of the model makes it possible to use the same computer program (which is included in an Appendix) to study both the fetal circulation and the adult circulation, as well as such diverse disease states as patent ductus arteriosus, ventricular septal defect, atrial septal defect, tetralogy of Fallot and transposition of the great arteries. In this paper, only patent ductus and ventricular or atrial septal defect are studied, with special emphasis on the influence of increasing pulmonary vascular resistance on the shunt flow. In the case of patent ductus and ventricular septal defect, the computed shunt flow is very time-dependent and the left-to-right shunt becomes first bidirectional and then right-to-left as the pulmonary resistance increases. By contrast, the computed shunt flow of atrial septal defect is nearly time-independent and is also somewhat less sensitive to the pulmonary vascular resistance.

The pH dependence of the hydration of CO2 catalyzed by carbonic anhydrase III from skeletal muscle of the cat. Steady state and equilibrium studies

We have measured the pH dependence of the kinetics of CO2 hydration catalyzed by carbonic anhydrase III from the skeletal muscle of the cat. Two methods were used: an initial velocity study in which the change in absorbance of a pH indicator was measured in a stopped flow spectrophotometer, and an equilibrium study in which the rate of exchange of 18O between CO2 and H2O was measured with a mass spectrometer. We have found that the steady state constants kCO2 cat and KCO2 m are independent of pH within experimental error in the range of pH 5.0 to 8.5; the rate of release from the enzyme of the oxygen abstracted from substrate HCO-3 in the dehydration is also independent of pH in this range. This behavior is very different from that observed for carbonic anhydrase II for which kCO2 cat and the rate of release of substrate oxygen are very pH-dependent. The rate of interconversion of CO2 and HCO-3 at equilibrium catalyzed by carbonic anhydrase III is not altered when the solvent is changed from H2O to 98% D2O and 2% H2O. Thus, the interconversion probably proceeds without proton transfer in its rate-limiting steps, similar to isozymes I and II.

Role of hemoglobin in proton transfer to the active site of carbonic anhydrase

The binding of bovine oxyhemoglobin to bovine carbonic anhydrase with a dissociation constant between 10(-5) and 10(-7) M has been determined by countercurrent distribution using aqueous, biphasic polymer systems. This result provides an explanation for the very efficient proton transfer between hemoglobin and carbonic anhydrase, a transfer which enhances the catalytic activity of carbonic anhydrase as measured by 18O exchange between bicarbonate and water at chemical equilibrium (Silverman, D. N., Tu, C. K., and Wynns, G. C. (1978) J. Biol. Chem, 253, 2563-2567). Two rate constants describing 18O exchange activity of carbonic anhydrase at pH 7.5 show saturation behavior when plotted against hemoglobin concentration consistent with a dissociation constant of 2.5 X 10(-6) M between bovine hemoglobin and carbonic anhydrase. Interpretation of these rate constants in terms of a two-step model for 18O exchange indicates that hemoglobin enhances the rate of exchange from carbonic anhydrase of water containing the oxygen abstracted from bicarbonate, but does not affect the catalytic interconversion of CO2 and HCO3- at chemical equilibrium.

Depletion of 18O from C18O2 in erythrocyte suspensions. The permeability of the erythrocyte membrane to CO2

The depletion of 18O from CO2, caused by the exchange of oxygen between CO2 and water during the hydration-dehydration cycle, is catalyzed by carbonic anhydrase. This depletion process at chemical equilibrium in the presence of erythrocytes is biphasic, exhibiting a very rapid depletion rate immediately following the addition of cells to an isotonic solution containing 18O-enriched CO2, followed by a much slower depletion rate. It is hypothesized that these depletion characteristics are caused by the diffusion of labeled CO2 into erythrocytes where depletion occurs rapidly due to the large intracellular carbonic anhydrase content. Kinetic equations which describe this hypothesis are solved and a rate constant is obtained which represents the depletion of 18O in CO2 caused by the presence of red cells. These are equilibrium experiments with no net uptake or loss of CO2 in the cells. Consequently, depletion processes are not limited in rate by bicarbonate-chloride exchange or proton distribution across the membrane. The purpose of these measurements is to determine whether the rate of 18O depletion in red cell suspensions is determined by carbonic anhydrase activity in the cell or by the diffusion process by which CO2 enters the cell. This goal is achieved by partially inhibiting carbonic anhydrase with acetazolamide. The rate constant representing 18O depletion caused by the presence of red cells is unchanged, even though up to 90% of carbonic anhydrase is inhibited. From this rate constant the permeability constant of the membrane of rat erythrocytes to CO2 at 25 degrees and pH 7.4 is determined to be (7.6 +/- 1.2) X 10(-3) cm s-1 in the presence of 3.2 mM picrate, a passive anion diffusion inhibitor intended to block HCO3 -flux across the membrane. Using no picrate and allowing HCO3-flux to introduce an error in the measurements, the permeability constant is (1.6 +/- 0.4) X 10(-2) cm s-1. The permeability constants measured by this technique include the diffusion barrier to CO2 not only of the red cell membrane but also of a portion of the intracellular medium.

Photosensitivity and heat resistance conferred by BrdU incorporation upon a thymidine kinase-deficient mouse cell line with persistent mitochondrial enzyme activity

The selective incorporation of 5-bromodeoxyuridine (BrdU) into mitochondrial DNA (mit-DNA) in the LM(TK-) ClID cell line, a thymidine kinase-deficient derivative of L fibroblasts with persistent mitochondrial enzyme activity, has been utilized to specifically damage mit-DNA by ‘visible’ light irradiation. (‘Visible light’ indicates the source of light used, although the components most active photochemically on BrdU-substituted DNA are in the near-visible range, 300–340 nm.) (Szybalski & Opara-Kubinski, 1965). LM(TK-) Cl ID cells, which had been grown in the presence of 30 mug/ml BrdU, were irradiated with ‘visible’ light. Analysis of the pre-existing mit-DNA in these cells, which had been long-term labelled with [5-3H]deoxycytidine, showed a progressive decrease, with increasing duration of irradiation, in the proportion of the closed-circular form and an increase in that of the open-circular form of mit-DNA, with the subsequent appearance of fragments of this DNA. Furthermore, there was a decrease during irradiation in the total amount of mit-DNA, which became about 35% of the non-irradiated control after 65 h irradiation. On the other hand, irradiation with ‘visible’ light failed to cause any quantitative or qualitative change, with respect to the non-irradiated control, in mit-DNA from cells grown in the absence of BrdU and long-term labelled with [Me-3h]thymidine. An analysis of the incorporation of [5-3H]deoxycytidine into mit-DNA of BrdU-grown cells, during a 3-h exposure of the cells to the precursor following irradiation, showed a fairly rapid decline of mit-DNA labelling; this became about 50% of the non-irradiated control after 12 h irradiation, decreasing to about 25% in the next 48 h. By contrast, no effect of irradiation was observed on the subsequent pulse-labelling of mit-DNA with [Me-3H]thymidine in cells grown in the absence of BrdU. Furthermore, no change in the size of the extracted nuclear DNA was found in irradiated BrdU-grown cells. The progressive and selective damage and destruction of mit-DNA during irradiation with ‘visible’ light of Cl ID cells correlate fairly well with the kinetics of loss of cell viability occurring under the same conditions, as described in the accompanying paper, strongly suggesting a link between the two phenomena.