Apparent Substrate Binding Research Articles

Abstract 17158: Effects of Human Monoclonal Antibodies on ADAMTS13 in Immune Thrombotic Thrombocytopenic Purpura

Introduction: Immune thrombotic thrombocytopenic purpura (iTTP) is caused by antibody-mediated deficiency of the metalloprotease ADAMTS13, which cleaves VWF. Myocardial infarction and ischemic strokes are common and often fatal sequelae of iTTP. Inhibitory anti-ADAMTS13 antibodies appear to affect catalytic turnover more than apparent substrate binding affinity (PMID 37023370). Exploring how antibodies affect VWF cleavage by ADAMTS13 in physiologic conditions is needed to better understand the pathophysiology of iTTP. Hypothesis: Anti-ADAMTS13 antibodies may influence ADAMTS13 function by affecting catalytic turnover and/or apparent substrate binding affinity differently in physiologic conditions than in standard assay conditions. Aims: Characterize how single chain fragments of the variable loop (scFv’s) previously identified from a phage display library derived from several iTTP patients’ antibodies affect ADAMTS13-mediated VWF cleavage in conditions that more closely represent plasma and see if/how they differ from scFv-mediated effects in standard conditions. Methods: ADAMTS13 in normal human plasma was titrated with increasing concentrations of the substrate FRETS-VWF73 to derive maximum velocity ( V max ) and apparent Michaelis constant ( K M,app ) in standard assay conditions (pH 6.0) and conditions closer to physiologic (pH 7.0). The same parameters were derived in the presence of saturating concentrations of scFv’s. Results: Compared to VWF cleavage by ADAMTS13 in the absence of scFv, the inhibitory scFv4-20 decreased V max at both pH 6.0 and pH 7.0; K M,app decreased at pH 6.0 and increased at pH 7.0. The stimulatory scFv3-3 and scFv4-41 increased V max at each pH, while K M,app in the presence of each scFv decreased only at pH 7.0. Conclusions: Anti-ADAMTS13 antibody-mediated effects on VWF cleavage differ when comparing standard and more physiologic pH conditions, guiding future investigative directions into iTTP pathophysiology.

Thermodynamic Effects of Antibodies on VWF73 Cleavage By ADAMTS13

Background and objective: Immune thrombotic thrombocytopenic purpura (iTTP) is an antibody-mediated life-threatening disease, caused by severe deficiency a plasma metalloprotease ADAMTS13 that impairs the cleavage of ultra-large von Willebrand factor (VWF). This leads to catastrophic microvascular thrombosis and angiopathic hemolysis. Exploring the mechanism of antibodies that inhibit ADAMTS13 under physiologic conditions and standard assay conditions for diagnosis of iTTP (pH 6.0) may help better understand the pathophysiology of iTTP. Our previous study suggests that an inhibitory anti-ADAMTS13 antibody may affect catalytic turnover of the enzyme more than its apparent substrate binding affinity. Here, we describe a rigorous method to quantitatively determine thermodynamic linkage between antibody binding and substrate binding affinity under various conditions. We used well-characterized single chain fragments of the variable loop (scFv's) identified from a phage display library derived from several iTTP patients, and compare the apparent Michaelis constant ( K M,app,) and the maximal enzyme velocity ( V max) of ADAMTS13-mediated VWF cleavage in conditions that more closely represent plasma and in standard conditions. We also describe the stimulatory effect of a newly characterized scFv that targets the C-terminus of ADAMTS13. Methods: Single chain fragments of the variable region (scFv4-20, scFv3-3 and scFv4-41), isolated by phage display from a human anti-ADAMTS13 antibody library derived from iTTP patients, were expressed and purified. ADAMTS13 in normal human plasma was titrated with increasing concentrations of the fluorescently labeled surrogate substrate FRETS-VWF73 to derive V maxand K M,appin the standard assay conditions (pH 6.0) and the conditions closer to physiologic pH (pH 7.0). The same parameters were derived in the presence of saturating concentrations of scFv's. Reaction quotient (Q), which defines thermodynamic linkage between an allosteric effector and substrate, is derived from the ratio of K M,app when saturating scFv is present and K M,app without antibodies. Results: The V max of VWF73 cleavage by ADAMTS13 was lower at pH 7.0 than at pH 6.0 (5.23 ± 0.15 ΔFU/sec vs 7.48 ± 0.42 ΔFU/sec, respectively), and K M,app at pH 6.0 (2.54 ± 0.26 µM) was higher than at pH 7.0 (1.48 ± 0.11 µM) in the absence of scFv. Saturating inhibitory scFv4-20 decreased V max at both pH 6.0 and pH 7.0 (4.45 ± 0.16 ΔFU/sec and 1.00 ± 0.14 ΔFU/sec, respectively); K M,app was relatively unaffected at pH 6.0 (2.70 ± 0.07 µM, Q 1.06) and decreased at pH 7.0 (1.08 ± 0.27 µM, Q 0.73). Saturating scFv3-3 and scFv4-41 increased V max at both pH 6.0 (9.86 ± 0.46 ΔFU/sec and 10.05 ± 0.67 ΔFU/sec, respectively) and 7.0 (9.09 ± 0.25 ΔFU/sec and 10.26 ± 0.34 ΔFU/sec, respectively); while in the presence of scFv3-3 and scFv4-41, K M,app decreased slightly at pH 6.0 (2.20 ± 0.08 µM, Q 0.87; and 2.36 ± 0.26 µM, Q 0.93, respectively) and more dramatically at pH 7.0 (1.08 ± 0.05 µM, Q 0.73; and 1.16 ± 0.07 µM, Q 0.78, respectively). (Figure 1). Conclusions: These results indicate that anti-ADAMTS13 IgG-mediated effects on VWF cleavage may differ when comparing the standard and more physiologic pH conditions. At pH 7.0, both inhibitory and stimulatory scFvs exert a stronger effect on V max of VWF73 cleavage by ADAMTS13 than at pH 6.0. The scFv4-41, which was not previously characterized, had a stimulatory effect on ADAMTS13 very similar to the previously characterized scFv3-3. The K M,app decreases with the increasing of pH from 6.0 to 7.0, while the presence of saturated scFvs investigated in the study appears to increase apparent substrate binding affinity in conditions close to physiologic. The change of enzyme kinetics of VWF73 cleavage by ADAMTS13 in presence of saturated antibodies adds the understanding of iTTP pathophysiology and guide future investigative directions. Key words: Immune thrombotic thrombocytopenic purpura; ADAMTS13, inhibitory and stimulatory antibody

α‐hydroxytropolones Inhibit RNase H1 Noncompetitively Despite Binding in the Active Site

Human immunodeficiency virus (HIV) and Hepatitis B virus (HBV) ribonucleases H (RNase H) are type 1 RNases H that are promising drug targets because inhibiting their activity blocks viral replication. RNases H cleave RNA in RNA/DNA hybrids. Eukaryotic RNase H1 is an essential protein and probable off‐target enzyme for viral RNase H inhibitors. α‐hydroxytropolones (αHTs) comprise an anti‐RNase H inhibitor class that can inhibit the HIV, HBV, and human RNases H1. These compounds work by binding the RNase H active site by chelating the catalytic divalent metal cofactors. We hypothesized that a better understanding of RNase H1 inhibition will help development of compounds selective for the viral RNases H. To this end, we expressed and purified recombinant human RNase H1 and determined its inhibition mechanism(s) in steady‐state kinetics by two αHTs, 110 and 404 (Fig. 1). Inhibition was not competitive with a 12‐mer RNA/DNA substrate, but the turnover rate was reduced despite inhibitor binding to the active site (Fig. 2). 110 and 404displayed inhibition constants of 9 μM and 3 μM in saturating substrate concentrations, respectively, and these values were elevated 2‐3‐fold in very low substrate. Saturating 110and 404concentrations modestly reduced the apparent substrate binding constant (KM) from 90 nM to ~30 nM, while reducing the turnover rate (kcat = 0.17 s‐1) ~20‐fold. We found that 110enhanced affinity of RNase H1 for substrate by 4‐fold using a fluorescence polarization (FP) substrate binding assay with Ca2+ instead of Mg2+ to prevent RNA cleavage. 404, on the other hand, competed with substrate in binding assays, raising the substrate's KD~7‐fold from 24 nM without compound to ~150 nM. Induced fit docking studies in the Schrödinger suite suggest 110 binds to the active site metals as expected, while the substrate is still capable of binding via RNase H1’s high‐affinity auxiliary RNA/DNA hybrid binding domain (HBD) and substrate binding groove within the RNase H domain. 110 made favorable contacts with both enzyme and substrate, stabilizing an ESI complex. 404, on the other hand, occupies much of the substrate binding groove as well as the active site due to its larger structure. This would explain why 404 competes with substrate binding, while 110enhances substrate binding. The reason the KM decreased with 404 despite its competitive behavior in substrate binding assays is not clear. However, we hypothesize that 404locally competes with the substrate for the RNase H1 active site and the substrate binding groove within the RNase H domain without interfering with the HBD:substrate interface. This could lower the overall ES affinity. However, we speculate that if substrate release is slow relative to RNA hydrolysis and product release, the compound could behave uncompetitively in kinetics assays by inhibiting the breakdown of the ES complex through catalysis, only permitting enzyme‐substrate dissociation via the putatively slow substrate release pathway. Thus, these results illustrate that non‐competitive steady‐state kinetics may be observed without an allosteric inhibitor binding site. This may be common to active‐site inhibitors of enzymes with auxiliary substrate binding domains.

Halogen Substitution Influences Ketamine Metabolism by Cytochrome P450 2B6: In Vitro and Computational Approaches.

Ketamine is analgesic at anesthetic and subanesthetic doses, and it has been used recently to treat depression. Biotransformation mediates ketamine effects, influencing both systemic elimination and bioactivation. CYP2B6 is the major catalyst of hepatic ketamine N-demethylation and metabolism at clinically relevant concentrations. Numerous CYP2B6 substrates contain halogens. CYP2B6 readily forms halogen-protein (particularly Cl-π) bonds, which influence substrate selectivity and active site orientation. Ketamine is chlorinated, but little is known about the metabolism of halogenated analogs. This investigation evaluated halogen substitution effects on CYP2B6-catalyzed ketamine analogs N-demethylation in vitro and modeled interactions with CYP2B6 using various computational approaches. Ortho phenyl ring halogen substituent changes caused substantial (18-fold) differences in Km, on the order of Br (bromoketamine, 10 μM) < Cl < F < H (deschloroketamine, 184 μM). In contrast, Vmax varied minimally (83-103 pmol/min/pmol CYP). Thus, apparent substrate binding affinity was the major consequence of halogen substitution and the major determinant of N-demethylation. Docking poses of ketamine and analogs were similar, sharing a π-stack with F297. Libdock scores were deschloroketamine < bromoketamine < ketamine < fluoroketamine. A Bayesian log Km model generated with Assay Central had a ROC of 0.86. The probability of activity at 15 μM for ketamine and analogs was predicted with this model. Deschloroketamine scores corresponded to the experimental Km, but the model was unable to predict activity with fluoroketamine. The binding pocket of CYP2B6 also suggested a hydrophobic component to substrate docking, on the basis of a strong linear correlation ( R2 = 0.92) between lipophilicity ( Alog P) and metabolism (log Km) of ketamine and analogs. This property may be the simplest design criteria to use when considering similar compounds and CYP2B6 affinity.

Structure–function analysis of the LytM domain of EnvC, an activator of cell wall remodelling at the Escherichia coli division site

Proteins with LytM (Peptidase_M23) domains are broadly distributed in bacteria and have been implicated in a variety of important processes, including cell division and cell-shape determination. Most LytM-like proteins that have been structurally and/or biochemically characterized are metallo-endopeptidases that cleave cross-links in the peptidoglycan (PG) cell wall matrix. Notable exceptions are the Escherichia coli cell division proteins EnvC and NlpD. These LytM factors are not hydrolases themselves, but instead serve as activators that stimulate PG cleavage by target enzymes called amidases to promote cell separation. Here we report the structure of the LytM domain from EnvC, the first structure of a LytM factor implicated in the regulation of PG hydrolysis. As expected, the fold is highly similar to that of other LytM proteins. However, consistent with its role as a regulator, the active-site region is degenerate and lacks a catalytic metal ion. Importantly, genetic analysis indicates that residues in and around this degenerate active site are critical for amidase activation in vivo and in vitro. Thus, in the regulatory LytM factors, the apparent substrate binding pocket conserved in active metallo-endopeptidases has been adapted to control PG hydrolysis by another set of enzymes.

Molecular modeling of different substrate-binding modes and their role in penicillin acylase catalysis

Molecular modeling was addressed to understand different substrate-binding modes and clarify the role of two positively charged residues of the penicillin G acylase active site - βR263 and αR145 - in binding of negatively charged substrates. Although the electrostatic contribution to productive substrate binding was dominated by βR263 rather than αR145, it was found that productive binding was not the only possible mode of substrate placement in the active site. Two extra binding modes - nonproductive and preproductive - were located by means of molecular docking and dynamics with binding affinities comparable with the productive one. A unique feature of nonproductive and preproductive complexes was that the substrate's acyl group did not penetrate the hydrophobic pocket, but occupied a patch on the protein interface spanning from βR263 to αR145. Nonproductive and preproductive complexes competed with each other and productive binding mode, giving rise to increased apparent substrate binding. Preproductive complex revealed an ability to switch to a productive one during molecular dynamics simulations, and conformational plasticity of the penicillin G acylase active site was shown to be crucial for that. Nonproductive binding observed at molecular modeling corresponded well with experimentally observed substrate inhibition in penicillin acylase catalysis. By combining estimated free energies of substrate binding in each mode, and accounting for two possible conformations of the penicillin G acylase active site (closed and open) quantitative agreement with experimentally measured K(M) values was achieved. Calculated near-attack conformation frequencies from corresponding molecular dynamics simulations were in a quantitative correlation with experimental k(cat) values and demonstrated adequate application of molecular modeling methods.

Human and Rat ABC Transporter Efflux of Bisphenol A and Bisphenol A Glucuronide: Interspecies Comparison and Implications for Pharmacokinetic Assessment

Significant interspecies differences exist between human and rodent with respect to absorption, distribution, and excretion of bisphenol A (BPA) and its primary metabolite, BPA-glucuronide (BPA-G). ATP-Binding Cassette (ABC) transporter enzymes play important roles in these physiological processes, and their enzyme localization (apical vs. basolateral) in the plasma membrane allows for different cellular efflux pathways. In this study, we utilized an ATPase assay to evaluate BPA and BPA-G as potential substrates for the human and rat ABC transporters: P-glycoprotein (MDR1), multidrug resistance-associated proteins (MRPs), and breast cancer-resistant protein (BCRP). Based on high ATPase activity, BPA is likely a substrate for rat mdr1b but not for human MDR1 or rat mdr1a. Results indicate that BPA is a potential substrate for rat mrp2 and human MRP2, BCRP, and MRP3. The metabolite BPA-G demonstrated the highest apparent substrate binding affinity for rat mrp2 and human MRP3 but appeared to be a nonsubstrate or potential inhibitor for human MRP2, MDR1, and BCRP and for rat mdr1a, mdr1b, and bcrp. Analysis of ABC transporter amino acid sequences revealed key differences in putative binding site composition that may explain substrate specificity. Collectively, these results suggest that in both rat and human, apical transporters efflux BPA into the bile and/or intestinal lumen. BPA-G would follow a similar pathway in rat; however, in human, due to the basolateral location of MRP3, BPA-G would likely enter systemic and portal blood supplies. These differences between human and rodent ABC transporters may have significant implications for interspecies extrapolation used in risk assessment.

Molecular Evolution, Functional Variation, and Proposed Nomenclature of the Gene Family That Includes Sphingomyelinase D in Sicariid Spider Venoms

The venom enzyme sphingomyelinase D (SMase D) in the spider family Sicariidae (brown or fiddleback spiders [Loxosceles] and six-eyed sand spiders [Sicarius]) causes dermonecrosis in mammals. SMase D is in a gene family with multiple venom-expressed members that vary in functional specificity. We analyze molecular evolution of this family and variation in SMase D activity among crude venoms using a data set that represents the phylogenetic breadth of Loxosceles and Sicarius. We isolated a total of 190 nonredundant nucleotide sequences encoding 168 nonredundant amino acid sequences of SMase D homologs from 21 species. Bayesian phylogenies support two major clades that we name alpha and beta, within which we define seven and three subclades, respectively. Sequences in the alpha clade are exclusively from New World Loxosceles and Loxosceles rufescens and include published genes for which expression products have SMase D and dermonecrotic activity. The beta clade includes paralogs from New World Loxosceles that have no, or reduced, SMase D and no dermonecrotic activity and also paralogs from Sicarius and African Loxosceles of unknown activity. Gene duplications are frequent, consistent with a birth-and-death model, and there is evidence of purifying selection with episodic positive directional selection. Despite having venom-expressed SMase D homologs, venoms from New World Sicarius have reduced, or no, detectable SMase D activity, and Loxosceles in the Southern African spinulosa group have low SMase D activity. Sequence conservation mapping shows >98% conservation of proposed catalytic residues of the active site and around a plug motif at the opposite end of the TIM barrel, but alpha and beta clades differ in conservation of key residues surrounding the apparent substrate binding pocket. Based on these combined results, we propose an inclusive nomenclature for the gene family, renaming it SicTox, and discuss emerging patterns of functional diversification.

Role of Phe-114 in substrate specificity of Candida tenuis xylose reductase (AKR2B5)

The 2.2 Å X-ray crystal structure of Candida tenuis xylose reductase (AKR2B5) bound with NADP+ reveals that Phe-114 contributes to the substrate binding pocket of the enzyme. In the related human aldose reductase (AKR1B1), this phenylalanine is replaced by a tryptophan. The side chain of Trp was previously implicated in forming a hydrogen bond with bound substrate or inhibitor. The apparent Michaelis constant of AKR2B5 for xylose (Km≈90 mM) is 60 times that of AKR1B1, perhaps because critical enzyme–substrate interactions of Trp are not available to Phe-114. We, therefore, prepared a Phe-114→Trp mutant (F114W) of AKR2B5, to mimic the aldose reductase relationship in xylose reductase. Detailed analysis of the kinetic consequences in purified F114W revealed that the Km values for xylose and xylitol at pH 7.0 and 25°C were increased 5.1- and 4.4-fold, respectively, in the mutant compared with the wild-type. Turnover numbers (kcat) of F114W for xylose reduction and xylitol oxidation were half those of the wild-type. Apparent dissociation constants of NADH (KiNADH=44 µM) and NAD+ (KiNAD+=177 µM) were increased 1.6- and 1.4-fold in comparison with values of KiNADH and KiNAD+ for the wild-type, respectively. Catalytic efficiencies (kcat/Km) for NADH-dependent reduction of different aldehydes were between 3.1- and 31.5-fold lower than the corresponding kcat/Km values of the wild-type. Therefore, replacement of Phe-114 with Trp weakens rather than strengthens apparent substrate binding by AKR2B5, suggesting that xylose reductase exploits residue 114 in a different manner from aldose reductase.

Trehalose phosphorylase from Pleurotus ostreatus: Characterization and stabilization by covalent modification, and application for the synthesis of α,α-trehalose

Trehalose phosphorylase from the basidiomycete Pleurotus ostreatus (PoTPase) was isolated from fungal fruit bodies through approximately 500-fold purification with a yield of 44%. Combined analyses by SDS-PAGE and gelfiltration show that PoTPase is a functional monomer of approximately 55 kDa molecular mass. PoTPase catalyzes the phosphorolysis of alpha,alpha-trehalose, yielding alpha-d-glucose 1-phosphate (alphaGlc 1-P) and alpha-d-glucose as the products. The optimum pH of PoTPase for alpha,alpha-trehalose phosphorolysis and synthesis is 6.8 and 6.2, respectively. Apparent substrate binding affinities (K(m)) were determined at pH 6.8 and 30 degrees C: alpha,alpha-trehalose (79 mM); phosphate (3.5 mM); d-glucose (40 mM); alphaGlc 1-P (4.1mM). A series of structural analogues of d-glucose were tested as glucosyl acceptors for the enzymatic reaction with alphaGlc 1-P, and robust activity with d-mannose (3%), 2-deoxy d-glucose (8%), 2-fluoro d-glucose (15%) and 2-keto-d-glucose (50%) was detected. Arsenate replaces, with 30% relative activity, phosphate in the conversion of alpha,alpha-trehalose, and vanadate strongly inhibits the enzyme activity (K(i) approximately 4 microM). PoTPase has a half-life (t(0.5)) of approximately 1 h at 30 degrees C in the absence of stabilizing compounds such as alpha,alpha-trehalose (300 mM; t(0.5)=11.5 h), glycerol (20%, w/v; t(0.5)=6.5h) or polyethylenglycol (PEG) 4000 (26%, w/v; t(0.5)=70 h). Covalent modification of PoTPase with activated derivatives of PEG 5000 increases the stability by up to 600-fold. Sucrose was converted to alpha,alpha-trehalose in approximately 60% yield using a coupled enzyme system composed of sucrose phosphorylase from Leuconostoc mesenteroides, glucose isomerase from Streptomyces murinus and the appropriately stabilized PoTPase.

Probing the substrate binding site of Candida tenuis xylose reductase (AKR2B5) with site-directed mutagenesis

Little is known about how substrates bind to CtXR (Candida tenuis xylose reductase; AKR2B5) and other members of the AKR (aldo-keto reductase) protein superfamily. Modelling of xylose into the active site of CtXR suggested that Trp23, Asp50 and Asn309 are the main components of pentose-specific substrate-binding recognition. Kinetic consequences of site-directed substitutions of these residues are reported. The mutants W23F and W23Y catalysed NADH-dependent reduction of xylose with only 4 and 1% of the wild-type efficiency (kcat/K(m)) respectively, but improved the wild-type selectivity for utilization of ketones, relative to xylose, by factors of 156 and 471 respectively. Comparison of multiple sequence alignment with reported specificities of AKR members emphasizes a conserved role of Trp23 in determining aldehyde-versus-ketone substrate selectivity. D50A showed 31 and 18% of the wild-type catalytic-centre activities for xylose reduction and xylitol oxidation respectively, consistent with a decrease in the rates of the chemical steps caused by the mutation, but no change in the apparent substrate binding constants and the pattern of substrate specificities. The 30-fold preference of the wild-type for D-galactose compared with 2-deoxy-D-galactose was lost completely in N309A and N309D mutants. Comparison of the 2.4 A (1 A=0.1 nm) X-ray crystal structure of mutant N309D bound to NAD+ with the previous structure of the wild-type holoenzyme reveals no major structural perturbations. The results suggest that replacement of Asn309 with alanine or aspartic acid disrupts the function of the original side chain in donating a hydrogen atom for bonding with the substrate C-2(R) hydroxy group, thus causing a loss of transition-state stabilization energy of 8-9 kJ/mol.

Binding energy and specificity in the catalytic mechanism of yeast aldose reductases

Derivatives of D-xylose and D-glucose, in which the hydroxy groups at C-5, and C-5 and C-6 were replaced by fluorine, hydrogen and azide, were synthesized and used as substrates of the NAD(P)H-dependent aldehyde reduction catalysed by aldose reductases isolated from the yeasts Candida tenuis, C. intermedia and Cryptococcus flavus. Steady-state kinetic analysis showed that, in comparison with the parent aldoses, the derivatives were reduced with up to 3000-fold increased catalytic efficiencies (kcat/Km), reflecting apparent substrate binding constants (Km) decreased to as little as 1/250 and, for D-glucose derivatives, up to 5.5-fold increased maximum initial rates (kcat). The effects on Km mirror the relative proportion of free aldehyde that is available in aqueous solution for binding to the binary complex enzyme-NAD(P)H. The effects on kcat reflect non-productive binding of the pyranose ring of sugars; this occurs preferentially with the NADPH-dependent enzymes. No transition-state stabilization energy seems to be derived from hydrogen-bonding interactions between enzyme-NAD(P)H and positions C-5 and C-6 of the aldose. In contrast, unfavourable interactions with the C-6 group are used together with non-productive binding to bring about specificity (6-10 kJ/mol) in a series of D-aldoses and to prevent the reaction with poor substrates such as D-glucose. Azide introduced at C-5 or C-6 destabilizes the transition state of reduction of the corresponding hydrogen-substituted aldoses by approx. 4-9 kJ/mol. The total transition state stabilization energy derived from hydrogen bonds between hydroxy groups of the substrate and enzyme-NAD(P)H is similar for all yeast aldose reductases (yALRs), at approx. 12-17 kJ/mol. Three out of four yALRs manage on only hydrophobic enzyme-substrate interactions to achieve optimal kcat, whereas the NAD(P)H-dependent enzyme from C. intermedia requires additional, probably hydrogen-bonding, interactions with the substrate for efficient turnover.

Binding energy and specificity in the catalytic mechanism of yeast aldose reductases

Derivatives of d-xylose and d-glucose, in which the hydroxy groups at C-5, and C-5 and C-6 were replaced by fluorine, hydrogen and azide, were synthesized and used as substrates of the NAD(P)H-dependent aldehyde reduction catalysed by aldose reductases isolated from the yeasts Candida tenuis, C. intermedia and Cryptococcus flavus. Steady-state kinetic analysis showed that, in comparison with the parent aldoses, the derivatives were reduced with up to 3000-fold increased catalytic efficiencies (k(cat)/K(m)), reflecting apparent substrate binding constants (K(m)) decreased to as little as 1/250 and, for d-glucose derivatives, up to 5.5-fold increased maximum initial rates (k(cat)). The effects on K(m) mirror the relative proportion of free aldehyde that is available in aqueous solution for binding to the binary complex enzyme-NAD(P)H. The effects on k(cat) reflect non-productive binding of the pyranose ring of sugars; this occurs preferentially with the NADPH-dependent enzymes. No transition-state stabilization energy seems to be derived from hydrogen-bonding interactions between enzyme-NAD(P)H and positions C-5 and C-6 of the aldose. In contrast, unfavourable interactions with the C-6 group are used together with non-productive binding to bring about specificity (6-10 kJ/mol) in a series of d-aldoses and to prevent the reaction with poor substrates such as d-glucose. Azide introduced at C-5 or C-6 destabilizes the transition state of reduction of the corresponding hydrogen-substituted aldoses by approx. 4-9 kJ/mol. The total transition state stabilization energy derived from hydrogen bonds between hydroxy groups of the substrate and enzyme-NAD(P)H is similar for all yeast aldose reductases (yALRs), at approx. 12-17 kJ/mol. Three out of four yALRs manage on only hydrophobic enzyme-substrate interactions to achieve optimal k(cat), whereas the NAD(P)H-dependent enzyme from C. intermedia requires additional, probably hydrogen-bonding, interactions with the substrate for efficient turnover.

Regulation of Substrate Recognition by the MiaA tRNA Prenyltransferase Modification Enzyme of Escherichia coliK-12

We purified polyhistidine (His6)-tagged and native Escherichia coli MiaA tRNA prenyltransferase, which uses dimethylallyl diphosphate (DMAPP) to isopentenylate A residues adjacent to the anticodons of most tRNA species that read codons starting with U residues. Kinetic and binding studies of purified MiaA were performed with several substrates, including synthetic wild-type tRNAPhe, the anticodon stem-loop (ACSLPhe) of tRNAPhe, and bulk tRNA isolated from a miaA mutant. Gel filtration shift and steady-state kinetic determinations showed that affinity-purified MiaA had the same properties as native MiaA and was completely active for tRNAPhe binding. MiaA had a Kmapp (tRNA substrates) approximately 3 nM, which is orders of magnitude lower than that of other purified tRNA modification enzymes, a Kmapp (DMAPP) = 632 nM, and a kcatapp = 0.44 s-1. MiaA activity was minimally affected by other modifications or nonsubstrate tRNA species present in bulk tRNA isolated from a miaA mutant. MiaA modified ACSLPhe with a kcatapp/Kmapp substrate specificity about 17-fold lower than that for intact tRNAPhe, mostly due to a decrease in apparent substrate binding affinity. Quantitative Western immunoblotting showed that MiaA is an abundant protein in exponentially growing bacteria (660 monomers per cell; 1.0 microM concentration) and is present in a catalytic excess. However, MiaA activity was strongly competitively inhibited for DMAPP by ATP and ADP (Kiapp = 0.06 microM), suggesting that MiaA activity is inhibited substantially in vivo and that DMAPP may bind to a conserved P-loop motif in this class of prenyltransferases. Band shift, filter binding, and gel filtration shift experiments support a model in which MiaA tRNA substrates are recognized by binding tightly to MiaA multimers possibly in a positively cooperative way (Kdapp approximately 0.07 microM).

Wild-type and mutant D-xylose isomerase from Actinoplanes missouriensis: metal-ion dissociation constants, kinetic parameters of deuterated and non-deuterated substrates and solvent-isotope effects.

The metal-ion dissociation constants (Mg2+, Mn2+) of wild-type and mutant D-xylose isomerases from Actinoplanes missouriensis have been determined by titrating the metal-ion-free enzymes with Mg2+ and Mn2+ respectively. Substitution of amino acids co-ordinated to metal-ion 1 (E181D, D245N) dramatically affects the dissociation constants, pH-activity profiles and apparent substrate binding. Mutagenesis of groups ligated to metal-ion 2 is less drastic except for that of Asp-255: a decrease in metal-ion affinity, a change in metal-ion preference and an improved apparent substrate binding (at pH values above the optimum), especially in the presence of Mn2+, are observed for the D255N enzyme. Similar effects, except for a slightly increased metal-ion affinity, are obtained by mutagenesis of the adjacent Glu-186 to Gln and the unconserved Ala-25 to Lys. Moreover, the striking acidic-pH shifts observed for the D255N and E186Q enzymes support the crucial role of the water molecule, Wa-690, Asp-255 and the adjacent Glu-186 in proton transfer from 2-OH to O-1 of the open and extended aldose substrate. Mutations of other important groups scarcely affect the metal-ion dissociation constants and pH-activity profiles, although pronounced effects on the kinetic parameters may be observed.

A 13C nuclear-magnetic-resonance study of CO2-HCO3-exchange catalyzed by human carbonic anhydrase C at chemical equilibrium.

The effects of human carbonic anhydrase C on the 13C nuclear magnetic resonance spectra of equilibrium mixtures of 13CO2 and NaH13CO3 were measured at 67.89 MHz. Enzyme-catalyzed CO2-HCO-3 exchange rates were estimated from the linewidths of the resonances. The results show that: (a) the maximal exchange rates are larger than the maximal turnover rates; (b) the exchange is equally rapid with 1H2O or with 2H2O as solvents; (c) the exchange is equally rapid in the presence or in the absence of added buffers; (d) the apparent substrate binding is weaker than predicted if steady-state Km values are assumed to represent substrate dissociation constants. The main conclusion concerning the catalytic mechanism of the enzyme is that the proton-transfer processes which limit turnover rates in the steady state are not directly involved in CO2-HCO-3 exchange. In addition, the results suggest that CO2-HCO-3 interconversion takes place by a nucleophilic mechanism, such as a reversible reaction of zinc-coordinated OH- with CO2.

The activity of bovine carbonic anhydrase in imidazole buffers

Abstract The variation of activity with substrate concentration has been measured for bovine carbonic anhydrase (carbonate hydro-lyase, EC 4.2.1.1) at several hydrogen-ion concentrations between pH 6.2 and pH 7.7 in imidazole buffers containing a constant concentration of 1 anion. A simple kinetic picture emerges. In the hydration reaction K m does not vary between pH 6.7 and pH 7.7. ν max varies as if dependent on the ionisation of one group with a p K near 6.9, only the basic form being active. In the dehydration reaction in the range pH 6.2–7.45 the rate is proportional to the bicarbonate concentration: there is thus no apparent substrate binding. The rate varies with pH as though it depends on the ionisation of one group with p K near 6.9 only the acid form being active. The kinetic parameters for hydration and dehydration reactions obey the requirement for a reversible enzyme reaction throughout the range of hydrogen-ion concentration in which measurements on both reactions were made. It is suggested that the apparent binding of bicarbonate as substrate reported by other workers was due to an anionic inhibition of the enzyme by this ion in the dilute phosphate buffers they employed.