Rate-determining processes and the number of simultaneously active sites of d-glyceraldehyde 3-phosphate dehydrogenase

Transient kinetic studies of the reversible oxidative phosphorylation of d-glyceraldehyde 3-phosphate catalysed by d-glyceraldehyde 3-phosphate dehydrogenase show that all four sites of the tetrameric lobster enzyme are simultaneously active, apparently with equal reactivity. The rate-determining step of the oxidative phosphorylation is NADH release at high pH and phosphorolysis of the acyl-enzyme at low pH. For the reverse reaction the rate-determining step is a process associated with NADH binding, probably a conformation change, at high pH and d-glyceraldehyde 3-phosphate release at low pH. NADH has previously been shown to be a competitive inhibitor of the enzyme with respect to d-glyceraldehyde 3-phosphate and vice versa. This is consistent with the mechanism deduced from transient experiments given the additional proviso that 1-arseno-3-phosphoglycerate has a half-life of about 1min or longer at pH7. The dissociation constants of d-glyceraldehyde 3-phosphate and 1,3-diphosphoglycerate to the NAD+-bound enzyme are too large to measure but are nevertheless consistent with the low Km values of these substrates.

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KINETIC STUDIES OF PROTON TRANSFER FROM PHENOLS TO TRINITROBENZYL ANION

Canadian Journal of Chemistry ◽

10.1139/v66-021 ◽

1966 ◽

Vol 44 (2) ◽

pp. 119-124 ◽

Cited By ~ 15

Author(s):

J. A. Blake ◽

M. J. B. Evans ◽

K. E. Russell

Keyword(s):

Proton Transfer ◽

Rate Constants ◽

Dissociation Constants ◽

Kinetic Studies ◽

Sodium Cation ◽

Rate Determining Step ◽

Rate Of Reaction ◽

Hammett Relationship ◽

Measurable Concentration ◽

Acetic Acids

The rates of reaction of various phenols with the 2,4,6-trinitrobenzyl anion in the solvent ethanol have been determined by a spectrophotometric method. The rate constants at −40 °C are related to the dissociation constants of the phenols in water at 25 °C and the value of α in the Brönsted relation is 0.84 ± 0.07; α drops to 0.44 ± 0.05 if the results for the substituted acetic acids (1) are included. The rate constants for the phenols are also correlated by the Hammett relationship, the ρ value at −40 °C being 1.82 ± 0.2. The activation energies range from 9.4 to 10.9 kcal/mole.The rate of reaction of trinitrobenzyl anion with 3-methylphenol at −30 °C is reduced by a factor of 12 if the phenol is deuterated at the OH group and the solvent is deuteroethanol. The large isotope effect confirms that the rate-determining step involves proton transfer from the OH group of the phenol. Substitution of lithium or potassium cations for the sodium cation does not affect the rate constant at −10 °C.In the reaction with 3-methylphenol, a measurable concentration of trinitrobenzyl anion remains at equilibrium and the equilibrium constant for the reaction is 1.3 ± 0.2 at 25 °C. The heat and entropy changes are approximately −6.5 kcal/mole and −21 e.u./mole respectively.

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Rat small-intestinal β-galactosidases. Kinetic studies with three separated fractions

Biochemical Journal ◽

10.1042/bj1100143 ◽

1968 ◽

Vol 110 (1) ◽

pp. 143-150 ◽

Cited By ~ 35

Author(s):

Nils-Georg Asp ◽

Arne Dahlqvist

Keyword(s):

Active Sites ◽

Kinetic Studies ◽

Competitive Inhibitor ◽

Small Intestinal Mucosa ◽

Lactase Activity ◽

Freezing And Thawing ◽

Ph Optimum ◽

Measurable Rate ◽

Small Intestinal ◽

Hydrolysis Of

1. Three fractions of β-galactosidase activity from the rat small-intestinal mucosa were separated chromatographically. Two of these fractions had an acid pH optimum at 3–4, and the third one had a more neutral pH optimum at 5·7. 2. The two ‘acid’ β-galactosidase fractions had considerably lower Km values for hetero β-galactosides than for lactose. The Vmax. values were similar for all the substrates used (lactose, phenyl β-galactoside, o-nitrophenyl β-galactoside, p-nitrophenyl β-galactoside and 6-bromo-2-naphthyl β-galactoside). No difference could be detected between the two ‘acid’ fractions with respect to their enzymic properties (pH optimum, Km for the different substrates, Ki for lactose as an inhibitor of the hydrolysis of hetero β-galactosides, Ki for phenyl β-galactoside as an inhibitor of the hydrolysis of lactose, and relative Vmax. for the hydrolysis of different substrates). These two fractions probably represent different forms of the same enzyme. 3. The ‘neutral’ fraction had similar Km values for all the substrates hydrolysed, but with lactose as substrate the Vmax. was much higher than with the hetero β-galactosides. This fraction did not split phenyl β-galactoside or 6-bromo-2-naphthyl β-galactoside at a measurable rate. 4. Lactose was a competitive inhibitor of the hetero β-galactosidase activities of all the three fractions, and Ki for lactose as an inhibitor in each case was the same as Km for the lactase activity. Phenyl β-galactoside was a competitive inhibitor of the lactase activity of all the three fractions. These facts strongly indicate that in all the three fractions lactose is hydrolysed by the same active sites as the hetero β-galactosides. 5. Human serum albumin stabilized the separated enzymes against inactivation by freezing and thawing.

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Understanding the reaction mechanism of the regioselective piperidinolysis of aryl 1-(2,4-dinitronaphthyl) ethers in DMSO: Kinetic and DFT studies

Progress in Reaction Kinetics and Mechanism ◽

10.1177/14686783211027446 ◽

2021 ◽

Vol 46 ◽

pp. 146867832110274

Author(s):

Yasmen M Moghazy ◽

Nagwa MM Hamada ◽

Magda F Fathalla ◽

Yasser R Elmarassi ◽

Ezzat A Hamed ◽

...

Keyword(s):

Carbon Atom ◽

Density Functional ◽

Function Analysis ◽

Density Functional Theory Method ◽

Activation Parameters ◽

Kinetic Studies ◽

Nucleophilic Attack ◽

Common Mechanism ◽

Slow Step ◽

Rate Determining Step

Reactions of aryl 1-(2,4-dinitronaphthyl) ethers with piperidine in dimethyl sulfoxide at 25oC resulted in substitution of the aryloxy group at the ipso carbon atom. The reaction was measured spectrophotochemically and the kinetic studies suggested that the titled reaction is accurately third order. The mechanism is began by fast nucleophilic attack of piperidine on C1 to form zwitterion intermediate (I) followed by deprotonation of zwitterion intermediate (I) to the Meisenheimer ion (II) in a slow step, that is, SB catalysis. The regular variation of activation parameters suggested that the reaction proceeded through a common mechanism. The Hammett equation using reaction constant σo values and Brønsted coefficient value showed that the reaction is poorly dependent on aryloxy substituent and the reaction was significantly associative and Meisenheimer intermediate-like. The mechanism of piperidinolysis has been theoretically investigated using density functional theory method using B3LYP/6-311G(d,p) computational level. The combination between experimental and computational studies predicts what mechanism is followed either through uncatalyzed or catalyzed reaction pathways, that is, SB and SB-GA. The global parameters of the reactants, the proposed activated complexes, and the local Fukui function analysis explained that C1 carbon atom is the most electrophilic center of ether. Also, kinetics and theoretical calculation of activation energies indicated that the mechanism of the piperidinolysis passed through a two-step mechanism and the proton transfer process was the rate determining step.

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Theoretical insight on the treatment of β-hexachlorocyclohexane waste through alkaline dehydrochlorination

Scientific Reports ◽

10.1038/s41598-021-88060-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Alicia Bescós ◽

Clara I. Herrerías ◽

Zoel Hormigón ◽

José Antonio Mayoral ◽

Luis Salvatella

Keyword(s):

Density Functional ◽

Kinetic Studies ◽

Alkaline Treatment ◽

Functional Study ◽

Reaction Intermediates ◽

Preferential Formation ◽

Reaction Intermediate ◽

Rate Determining Step ◽

Dehydrochlorination Reaction ◽

Theoretical Results

AbstractThe occurrence of 4.8–7.2 million tons of hexachlorocyclohexane (HCH) isomers stocked in dumpsites around the world constitutes a huge environmental and economical challenge because of their toxicity and persistence. Alkaline treatment of an HCH mixture in a dehydrochlorination reaction is hampered by the low reactivity of the β-HCH isomer (HCl elimination unavoidably occurring through syn H–C–C–Cl arrangements). More intriguingly, the preferential formation of 1,2,4-trichlorobenzene in the β-HCH dehydrochlorination reaction (despite the larger thermodynamical stability of the 1,3,5-isomer) has remained unexplained up to now, though several kinetic studies had been reported. In this paper, we firstly show a detailed Density Functional study on all paths for the hydroxide anion-induced elimination of β-HCH through a three-stage reaction mechanism (involving two types of reaction intermediates). We have now demonstrated that the first reaction intermediate can follow several alternative paths, the preferred route involving abstraction of the most acidic allylic hydrogen which leads to a second reaction intermediate yielding only 1,2,4-trichlorobenzene as the final reaction product. Our theoretical results allow explaining the available experimental data on the β-HCH dehydrochlorination reaction (rate-determining step, regioselectivity, instability of some reaction intermediates).

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Serum Cholinesterase Variants: Examination of Several Differential Inhibitors, Salts, and Buffers Used to Measure Enzyme Activity

Clinical Chemistry ◽

10.1093/clinchem/17.3.183 ◽

1971 ◽

Vol 17 (3) ◽

pp. 183-191 ◽

Cited By ~ 30

Author(s):

Philip J Garry

Keyword(s):

Enzyme Activity ◽

Sodium Fluoride ◽

Phosphate Buffer ◽

Divalent Cations ◽

Kinetic Studies ◽

Competitive Inhibitor ◽

Serum Cholinesterase ◽

Low Concentrations

Abstract Dibucaine, used as a differential inhibitor with acetyl-, propionyl-, and butyrylthiocholine as substrate, clearly identified the "usual" and "atypical" serum cholinesterases. Succinylcholine was also used successfully as a differential inhibitor with butyrylthiocholine as substrate. Sodium fluoride, used as a differential inhibitor, gave conflicting results, depending on whether Tris or phosphate buffer was used in the assay. Mono- and divalent cations (NaCl, KCl, MgCl2, CaCl2, and BaCl2) activated the "usual" and inhibited the "atypical" enzyme at low concentrations. The "usual" enzyme had the same activity in 0.05 mol of Tris or phosphate buffer per liter, while the heterozygous and "atypical" enzymes showed 12 and 42% inhibition, respectively, when assayed in the phosphate buffer. Kinetic studies showed the phosphate acted as a competitive inhibitor of "atypical" enzyme. Km values, determined for "usual" and "atypical" enzymes, were 0.057 and 0.226 mmol/liter, respectively, with butyrylthiocholine as substrate.

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Expression patterns of two carbonic anhydrase genes, Na+/K+-ATPase and V-type H+-ATPase, in the freshwater crayfish, Cherax quadricarinatus, exposed to low pH and high pH

Australian Journal of Zoology ◽

10.1071/zo16048 ◽

2017 ◽

Vol 65 (1) ◽

pp. 50 ◽

Cited By ~ 3

Author(s):

Muhammad Yousuf Ali ◽

Ana Pavasovic ◽

Peter B. Mather ◽

Peter J. Prentis

Keyword(s):

Carbonic Anhydrase ◽

Expression Patterns ◽

Maximum Level ◽

Low Ph ◽

Freshwater Crayfish ◽

Α Subunit ◽

Cherax Quadricarinatus ◽

High Ph ◽

Internal Ph ◽

Ph Conditions

Carbonic anhydrase (CA), Na+/K+-ATPase (NKA) and Vacuolar-type H+-ATPase (HAT) play vital roles in osmoregulation and pH balance in decapod crustaceans. As variable pH levels have a significant impact on the physiology of crustaceans, it is crucial to understand the mechanisms by which an animal maintains its internal pH. We examined expression patterns of cytoplasmic (CAc) and membrane-associated form (CAg) of CA, NKA α subunit and HAT subunit a in gills of freshwater crayfish, Cherax quadricarinatus, at three pH levels – 6.2, 7.2 (control) and 8.2 – over 24 h. Expression levels of CAc were significantly increased at low pH and decreased at high pH conditions 24 h after transfer. Expression increased at low pH after 12 h, and reached its maximum level by 24 h. CAg showed a significant increase in expression at 6 h after transfer at low pH. Expression of NKA significantly increased at 6 h after transfer to pH 6.2 and remained elevated for up to 24 h. Expression for HAT and NKA showed similar patterns, where expression significantly increased 6 h after transfer to low pH and remained significantly elevated throughout the experiment. Overall, CAc, CAg, NKA and HAT gene expression is induced at low pH conditions in freshwater crayfish.

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α-Retaining glucosyl transfer catalysed by trehalose phosphorylase from Schizophyllum commune: mechanistic evidence obtained from steady-state kinetic studies with substrate analogues and inhibitors

Biochemical Journal ◽

10.1042/bj3600727 ◽

2001 ◽

Vol 360 (3) ◽

pp. 727-736 ◽

Cited By ~ 9

Author(s):

Bernd NIDETZKY ◽

Christian EIS

Keyword(s):

Steady State ◽

Transition State ◽

Schizophyllum Commune ◽

Catalytic Efficiency ◽

Kinetic Studies ◽

Competitive Inhibitor ◽

Chemical Mechanism ◽

Steady State Kinetic ◽

State Kinetic ◽

Trehalose Phosphorylase

Fungal trehalose phosphorylase is classified as a family 4 glucosyltransferase that catalyses the reversible phosphorolysis of α,α-trehalose with net retention of anomeric configuration. Glucosyl transfer to and from phosphate takes place by the partly rate-limiting interconversion of ternary enzyme–substrate complexes formed from binary enzyme–phosphate and enzyme–α-d-glucopyranosyl phosphate adducts respectively. To advance a model of the chemical mechanism of trehalose phosphorylase, we performed a steady-state kinetic study with the purified enzyme from the basidiomycete fungus Schizophyllum commune by using alternative substrates, inhibitors and combinations thereof in pairs as specific probes of substrate-binding recognition and transition-state structure. Orthovanadate is a competitive inhibitor against phosphate and α-d-glucopyranosyl phosphate, and binds 3×104-fold tighter (Ki≈ 1μM) than phosphate. Structural alterations of d-glucose at C-2 and O-5 are tolerated by the enzyme at subsite +1. They lead to parallel effects of approximately the same magnitude (slope = 1.14; r2 = 0.98) on the reciprocal catalytic efficiency for reverse glucosyl transfer [log (Km/kcat)] and the apparent affinity of orthovanadate determined in the presence of the respective glucosyl acceptor (log Ki). An adduct of orthovanadate and the nucleophile/leaving group bound at subsite +1 is therefore the true inhibitor and displays partial transition state analogy. Isofagomine binds to subsite −1 in the enzyme–phosphate complex with a dissociation constant of 56μM and inhibits trehalose phosphorylase at least 20-fold better than 1-deoxynojirimycin. The specificity of the reversible azasugars inhibitors would be explained if a positive charge developed on C-1 rather than O-5 in the proposed glucosyl cation-like transition state of the reaction. The results are discussed in the context of α-retaining glucosyltransferase mechanisms that occur with and without a β-glucosyl enzyme intermediate.

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Photolabelling of Salmonella typhimurium LT2 sialidase. Identification of a peptide with a predicted structural similarity to the active sites of influenza-virus sialidases

Biochemical Journal ◽

10.1042/bj2850957 ◽

1992 ◽

Vol 285 (3) ◽

pp. 957-964 ◽

Cited By ~ 5

Author(s):

T G Warner ◽

R Harris ◽

R McDowell ◽

E R Vimr

Keyword(s):

Salmonella Typhimurium ◽

Active Site ◽

Influenza A ◽

Active Sites ◽

Enzyme Inhibitors ◽

Structural Similarity ◽

Competitive Inhibitor ◽

Beta Sheets ◽

Sialidase Inhibitor ◽

Active Site Cavity

The sialidase from Salmonella typhimurium LT2 was characterized by using photoaffinity-labelling techniques. The well-known sialidase inhibitor 5-acetamido-2,6-anhydro-3,5-dideoxy-D-glycero-D-galacto-non- 2-enonic acid (Neu5Ac2en) was modified to contain an amino group at C-9, which permitted the incorporation of 4-azidosalicylic acid in amide linkage at this position. Labelling of the purified protein with the radioactive (125I) photoprobe was determined to be highly specific for a region within the active-site cavity. This conclusion was based on the observation that the competitive inhibitor Neu5Ac2en in the photolysis mixture prevented labelling of the protein. In contrast, compounds with structural and chemical features similar to the probe and Neu5Ac2en, but which were not competitive enzyme inhibitors, did not affect the photolabelling of the protein. The peptide interacting with the probe was identified by CNBr treatment of the labelled protein, followed by N-terminal sequence analysis. Inspection of the primary structure of the protein, predicted from the cloned structural gene for the sialidase [Hoyer, Hamilton, Steenbergen & Vimr (1992) Mol. Microbiol. 6, 873-884] revealed that the label was incorporated into a 9.6 kDa fragment situated within the terminal third of the molecule near the C-terminal end. Secondary-structural predictions using the Garnier-Robson algorithm [Garnier, Osguthorpe & Robson (1978) J. Mol. Biol. 120, 97-120] of the labelled peptide revealed a structural similarity to the active site of influenza-A- and Sendai-HN-virus sialidases with a repetitive series of alternating beta-sheets connected with loops.

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A method for the preparation of low-pH dodecyl sulphate/polyacrylamide-gradient gels

Biochemical Journal ◽

10.1042/bj1931013 ◽

1981 ◽

Vol 193 (3) ◽

pp. 1013-1015 ◽

Cited By ~ 18

Author(s):

G D Jones ◽

M T Wilson ◽

V M Darley-Usmar

Keyword(s):

Cytochrome Oxidase ◽

Low Ph ◽

High Ph ◽

Gel System

1. A low-pH lithium dodecyl sulphate/polyacrylamide-gradient slab-gel system, suitable for electrophoresis, is described, and the migration properties of standard proteins are compared on this and conventional high-pH gels. 2. Cytochrome oxidase may be partially resolved into its component polypeptides. The order of migration of these is, however, dependent on the pH of the gel system.

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