Biomedical subjects

G A Kochetov

Publications and source records attributed to G A Kochetov.

At least 19 recordsLinked to original sources

PubMed2006

Two methods for determination of transketolase activity.

Two new optical methods for transketolase activity assay using only one substrate, xylulose 5-phosphate or glycol aldehyde, have been developed. For transketolase activity assay in the first method, it is necessary to add auxiliary enzyme, glyceraldehyde phosphate dehydrogenase. It is not needed in the second method. The range of transketolase concentration in the activity assay is 0.036-0.144 U/ml for the first method and 1.8-6.8 U/ml for the second one.

Glyceraldehyde 3-Phosphate↗

PubMed2005

Effect of transketolase substrates on holoenzyme reconstitution and stability.

The influence of transketolase substrates on the interaction of apotransketolase with its coenzyme thiamine diphosphate (TDP) and on the stability of the reconstituted holoenzyme was studied. Donor substrates increased the affinity of the coenzyme for transketolase, whereas acceptor substrate did not. In the presence of magnesium ions, the active centers of transketolase initially identical in TDP binding lose their equivalence in the presence of donor substrates. The stability of transketolase depended on the cation type used during its reconstitution--the holoenzyme reconstituted in the presence of calcium ions was more stable than the holoenzyme produced in the presence of magnesium ions. In the presence of donor substrate, the holoenzyme stability increased without depending on the cation used during the reconstitution. Donor substrate did not influence the interaction of apotransketolase with the inactive analog of the coenzyme N3'-pyridyl thiamine diphosphate and did not stabilize the transketolase complex with this analog. The findings suggest that the effect of the substrate on the interaction of the coenzyme with apotransketolase and on stability of the reconstituted holoenzyme is caused by generation of 2-(alpha,beta-dihydroxyethyl)thiamine diphosphate (an intermediate product of the transketolase reaction), which has higher affinity for apotransketolase than TDP.

Calcium↗

PubMed2005

Binding of the coenzyme and formation of the transketolase active center.

Transketolase (TK) is a homodimer, the simplest representative of thiamine diphosphate (ThDP)-dependent enzymes. It was first ThDP-dependent enzymes the crystal structure of which has been solved and revealed the general fold for this class of enzymes and the interactions of the non-covalently bound coenzyme ThDP with the protein component. Transketolase is a convenient model to study the structure(s) of the active center and the mechanism of action of ThDP-dependent enzymes. This review summarizes the results of studies on the kinetics of the interaction of ThDP with TK from Saccharomyces cerevisiae as well as the generation of the catalytically active form of the coenzyme within the holoenzyme and formation of the enzyme's active center.

Animals↗

PubMed2004

Optical characteristics of thiamine in model systems and in holoenzyme.

The optical properties of thiamine diphosphate-dependent enzymes change significantly on their interaction with cofactors (thiamine, bivalent metal ions) and substrates. These changes are connected with structural alterations of the active site and the mechanism of its functioning, and in some cases they reflect changes in the optical properties of the coenzyme itself within the protein. The use of optical characteristics, especially together with model systems, appeared to be a rather promising approach for investigation of the active site of thiamine diphosphate-dependent enzymes and the mechanism of its functioning. So, it seemed to be useful to summarize the literature data concerning the optical characteristics of thiamine (thiamine diphosphate) in model systems and the efficiency of their application for study of thiamine diphosphate-dependent enzymes.

Circular Dichroism↗

PubMed2003

Induced absorption band of holotransketolase and its interpretation.

It has long been known that formation of a catalytically active holotransketolase from the apoenzyme and thiamine diphosphate (ThDP) is accompanied by appearance, in both the absorption and CD spectra, of a new band. Binding and subsequent conversion of transketolase substrates bring about changes in the intensity of this band. The observation of these changes allows the investigator to monitor the coenzyme-to-apoenzyme binding and the conversion of the substrates during the transketolase reaction and thus to kinetically characterize its individual steps. As regards the new absorption band induced by ThDP binding, its nature, until recently, remained unknown. The reason for its appearance was considered to be either the formation of a charge transfer complex between ThDP and tryptophan (phenylalanine) residue or stacking interaction between the residues of aromatic amino acids. They are thought to be brought together as a result of conformational changes of the apoenzyme during its interaction with the coenzyme. However none of these hypotheses had been substantiated experimentally. According to our hypothesis, the induced absorption band is that of the imino form of ThDP resulting from three contributing features of the ThDP binding site of transketolase: the relative hydrophobicity of this site, hydrogen bonding of the N1;-atom of the ThDP aminopyrimidine ring to Glu418, and base stacking interactions between the aminopyrimidine ring of ThDP and Phe445.

Binding Sites↗

PubMed2001

One-substrate transketolase-catalyzed reaction.

Apart from catalyzing the common two-substrate reaction with ketose as donor substrate and aldose as acceptor substrate, transketolase is also able to catalyze a one-substrate reaction utilizing only ketose (xylulose 5-phosphate) as substrate. The products of this one-substrate reaction were glyceraldehyde 3-phosphate and erythrulose. No free glycolaldehyde (a product of xylulose 5-phosphate splitting in the transketolase reaction) was revealed.

Circular Dichroism↗

PubMed2001

Cleaving of ketosubstrates by transketolase and the nature of the products formed.

The interaction of transketolase ketosubstrates with the holoenzyme has been studied. On addition of ketosubstrates cleaving both irreversibly (hydroxypyruvate) and reversibly (xylulose 5-phosphate), identical changes in the CD spectrum at 300-360 nm are observed. The changes in this spectral region, as previously shown, are due to the formation of the catalytically active holoenzyme from the apoenzyme and the coenzyme, and the cleavage of ketosubstrates by transketolase. The identity of the changes in transketolase CD spectrum caused by the addition of reversibly or irreversibly cleaving substrates indicates that in the both cases the changes are due to the formation of an intermediate product of the transketolase reaction--a glycolaldehyde residue covalently bound to the coenzyme within the holoenzyme molecule. Usually, in the course of the transferase reaction, the glycolaldehyde residue is transferred to an aldose (acceptor substrate), resulting in the recycling of the holoenzyme free of the glycolaldehyde residue. The removal of the glycolaldehyde residue from the holoenzyme appears to proceed even in the absence of an aldose. However, the glycolaldehyde cannot be found the free state because it condenses with another glycolaldehyde residue formed in the course of the cleavage of another ketosubstrate molecule yielding erythrulose.

Circular Dichroism↗

PubMed2001

Functional flexibility of the transketolase molecule.

Transketolase is the simplest representative of the thiamine diphosphate-dependent enzymes. It was the first of these enzymes for which X-ray analysis was performed. Based on the data of X-ray studies and using the mutagenesis technique, the nature of functional groups of the enzyme involved in the interaction with substrates and cofactors and in the coenzyme activation was defined. Thus, considerable achievements have been made in studying the structure of transketolase. However, there is relatively little information on the conformational flexibility of the enzyme molecule while it is functioning, i.e., during its interaction with cofactors and substrates and in the course of intermediate product formation. This review summarizes mainly the results obtained in the author's group, as well as those rare data on this subject that could be found in literature.

Binding Sites↗

PubMed2000

Influence of transketolase substrates on its conformation.

Dynamics stimulation of the holotransketolase molecule revealed that the enzyme's conformation in crystal was different from that in solution. It was shown also that dissolved holotransketolase can bind aldose (the acceptor substrate) even in the absence of ketose (the donor substrate). The holotransketolase conformation did not change upon aldose binding unlike in the case of ketose binding/cleavage. Therefore the conformation of a catalytic complex of holotransketolase with an intermediate-i.e., a glycolaldehyde residue formed upon binding and subsequent cleavage of ketose-differed, at least in solution, from the conformation of both the free and aldose-complexed holotransketolase. Some structural peculiarities of the holotransketolase with the intermediate were established by means of molecular dynamics stimulation.

Acetaldehyde↗

PubMed2000

Acceptor substrate inhibits transketolase competitively with respect to donor substrate.

Two substrates of the transketolase reaction are known to bind with the enzyme according to a ping-pong mechanism [1]. It is shown in this work that high concentrations of ribose-5-phosphate (acceptor substrate) compete with xylulose-5-phosphate (donor substrate), suppressing the transketolase activity (Ki = 3.8 mM). However, interacting with the donor-substrate binding site on the protein molecule, the acceptor substrate, unlike the donor substrate, does not cause any change in the active site of the enzyme. The data are interesting in terms of studying the regulatory mechanism of the transketolase activity and the structure of the enzyme-substrate complex.

Catalytic Domain↗

PubMed1999

Inhibition of transketolase by p-hydroxyphenylpyruvate.

The effect of p-hydroxyphenylpyruvate, a natural analogue of transketolase substrate, on the catalytic activity of the enzyme was investigated. p-Hydroxyphenylpyruvate proved to be a reversible and competitive inhibitor of transketolase with respect to substrate; it was also able to displace thiamine diphosphate from holotransketolase. The data suggest that p-hydroxyphenylpyruvate participates in the regulation of tyrosine biosynthesis by influencing the catalytic activity of transketolase.

Binding, Competitive↗

PubMed1998

Cooperativity and flexibility of active sites in homodimeric transketolase.

Here we summarize evidence for non-equivalence of two structurally similar active sites in transketolase and other thiamine-dependent enzymes. This non-equivalence takes place when the enzymes interact with various ligands (inhibitors, cations, coenzyme and substrates). Data on different strains in the structure of the holotransketolase subunits are also given. The above results are discussed within the framework of a concept of permanent alternative site oscillation of the transketolase molecule in the presence and in the absence of substrate as a manifestation of a 'flip-flop' mechanism.

Animals↗

PubMed1998

Kinetic investigation of cooperativity in coenzyme binding by transketolase active sites.

The two-step mechanism of coenzyme (thiamine diphosphate, ThDP) binding with two initially identical active sites of apotransketolase has been examined with a kinetic model. Cooperativity between sites in the primary ThDP binding and in the following conformational transition has been analyzed. The only reliable difference between sites is shown to be the tenfold difference in the backward rate constants of the conformational transition; this means that the cooperative interaction between sites takes place only after termination of both steps of ThDP binding in both sites.

Apoenzymes↗

PubMed1997

Kinetic mechanism of active site non-equivalence in transketolase.

The two-step mechanism of coenzyme (TDP) binding to apotransketolase has been examined by kinetic modeling, and the rate and equilibrium constants for each binding step for two active sites have been determined. The dissociation constants for the primary fast binding step and the forward rate constants for the secondary slow binding step have been shown to be similar for two active sites. The backward rate constants for the secondary binding step are different for two active sites, providing the kinetic mechanism of their non-equivalence in TDP binding.

Binding Sites↗

PubMed1997

Determination of constants of substrate primary binding with baker's yeast transketolase by kinetic modelling.

A kinetic model of bisubstrate reaction catalyzed by baker's yeast transketolase is proposed. The model considers individual stages of substrates reversible primary binding. The model corresponds to the observed kinetics of product accumulation within a wide range of initial substrate concentrations. Kinetic parameters for the best simulation of the experimental data are defined. The equilibrium constants of the primary binding of both the initial and produced ketose and also the initial aldose were unequivocally determined by varying the initial substrate concentrations. The dissociation constants of the primary enzyme-substrate complex for the initial ketose (xylulose 5-phosphate) and the reaction product (sedoheptulose 7-phosphate) were found to differ by more than by two orders of magnitude. The result is discussed in the context of the hypothesis of flip-flop functioning of the transketolase active sites.

Binding Sites↗

PubMed1996

Interaction of dihydroxyethylthiamine pyrophosphate with transketolase.

Deprotonated form of dihydroxyethylthiamine pyrophosphate (DHETPP) is an intermediate product of the transketolase reaction. We have shown that when added to the reaction medium DHETPP can act as a substrate of the holoenzyme. The rate of the enzymatic reaction is quite close to that observed with ordinary substrates of transketolase. This fact suggests that the interaction of DHETPP with the holotransketolase and its deprotonation are not rate-limiting steps of the transketolase reaction.

Apoenzymes↗

PubMed1995

The presence of a hydroxyl group at the C-1 atom of the transketolase substrate molecule is necessary for the enzyme to perform the transferase reaction.

Transketolase catalyzes the transfer of an aldehyde residue from keto sugars to aldo sugars. The intermediate product is dihydroxyethylthiamine pyrophosphate (DHETPP). In the absence of an acceptor substrate, the reaction is stopped at this stage and DHETPP does not undergo subsequent transformations. Pyruvate decarboxylase catalyses pyruvate decarboxylation to yield free aldehyde. The intermediate product is hydroxyethylthiamine pyrophosphate (HETPP). It differs from DHETPP only in that it has no hydroxyl at the C-2 atom of the aldehyde residue. We have shown that transketolase can bind HETPP and split the aldehyde residue from it. This fact suggests that the path of the reaction is determined by the absence (in HETPP) or presence (in DHETPP) of a hydroxyl group. In the former case the reaction will yield free aldehyde, in the latter the aldehyde residue will be transferred onto an acceptor substrate.

Apoenzymes↗

PubMed1995

[Some properties of multiple forms of transketolase from baker's yeast].

It has been shown that transketolase A does not differ from the enzyme earlier described in the literature by a number of properties (lack of intersubunit disulfide bonds, identical number of sulfhydryl groups, two values of Km for thiamine pyrophosphate and identity of their absolute values). Transketolase C subunits are linked together by disulfide bonds; their total number in the enzyme molecule is five (transketolase C-1) or six (transketolase C-2). The Km values of transketolase C-1 for thiamine pyrophosphate are commensurate with those of transketolase A. Transketolase C-2 has only one Km value for thiamine pyrophosphate which is close to one of the two Km values for transketolase A. The maximal rate values for transketolases C-1 and C-2 with dihydroxyacetone as substrate differ by more than one order of magnitude.

Disulfides↗