How to determine the efficiency of intermediate transfer in an interacting enzyme system?

Complex formation between malate dehydrogenase and isocitrate dehydrogenase from Bacillus subtilis is regulated by tricarboxylic acid cycle metabolites

In Bacillus subtilis, recent in vivo studies revealed that particular enzymes of the tricarboxylic acid cycle form complexes that allow an efficient transfer of metabolites. Remarkably, a complex of the malate dehydrogenase (Mdh) (EC 1.1.1.37) with isocitrate dehydrogenase (Icd) (EC 1.1.1.42) was identified, although both enzymes do not catalyze subsequent reactions. In the present study, the interactions between these enzymes were characterized in vitro by surface plasmon resonance in the absence and presence of their substrates and cofactors. These analyses revealed a weak but specific interaction between Mdh and Icd, which was specifically stimulated by a mixture of substrates and cofactors of Icd: isocitrate, NADP(+) and Mg(2+). Wild-type Icd converted these substrates too fast, preventing any valid quantitative analysis of the interaction with Mdh. Therefore, binding of the IcdS104P mutant to Mdh was quantified because the mutation reduced the enzymatic activity by 174-fold but did not affect the stimulatory effect of substrates and cofactors on Icd-Mdh complex formation. The analysis of the unstimulated Mdh-IcdS104P interaction revealed kinetic constants of k(a) = 2.0 ± 0.2 × 10(2) m(-1) ·s(-1) and k(d) = 1.0 ± 0.1 × 10(-3) ·s(-1) and a K(D) value of 5.0 ± 0.1 μm. Addition of isocitrate, NADP(+) and Mg(2+) stimulated the affinity of IcdS104P to Mdh by 33-fold (K(D) = 0.15 ± 0.01 μm, k(a) = 1.7 ± 0.7 × 10(3) m(-1) ·s(-1), k(d) = 2.6 ± 0.6 × 10(-4) ·s(-1)). Analyses of the enzymatic activities of wild-type Icd and Mdh showed that Icd activity doubles in the presence of Mdh, whereas Mdh activity was slightly reduced by Icd. In summary, these data indicate substrate control of complex formation in the tricarboxylic acid cycle metabolon assembly and maintenance of the α-ketoglutarate supply for amino acid anabolism in vivo.

Yeast mitochondrial interactosome model: metabolon membrane proteins complex involved in the channeling of ADP/ATP

The existence of a mitochondrial interactosome (MI) has been currently well established in mammalian cells but the exact composition of this super-complex is not precisely known, and its organization seems to be different from that in yeast. One major difference is the absence of mitochondrial creatine kinase (MtCK) in yeast, unlike that described in the organization model of MI, especially in cardiac, skeletal muscle and brain cells. The aim of this review is to provide a detailed description of different partner proteins involved in the synergistic ADP/ATP transport across the mitochondrial membranes in the yeast Saccharomyces cerevisiae and to propose a new mitochondrial interactosome model. The ADP/ATP (Aacp) and inorganic phosphate (PiC) carriers as well as the VDAC (or mitochondrial porin) catalyze the import and export of ADP, ATP and Pi across the mitochondrial membranes. Aacp and PiC, which appear to be associated with the ATP synthase, consist of two nanomotors (F₀, F₁) under specific conditions and form ATP synthasome. Identification and characterization of such a complex were described for the first time by Pedersen and co-workers in 2003.

Discrete event, multi-level simulation of metabolite channeling

Typically differential equations are employed to simulate cellular dynamics. To develop a valid continuous model based on differential equations requires accurate parameter estimations; an accuracy which is often difficult to achieve, due to the lack of data. In addition, processes in metabolic pathways, e.g. metabolite channeling, seem to be of a rather qualitative and discrete nature. With respect to the available data and to the perception of the underlying system, a discrete rather than a continuous approach to modeling and simulation seems more adequate. A discrete approach does not necessarily imply a more abstract view on the system. If we move from macro to micro and multi-level modeling, aspects of subsystems and their interactions, which have been only implicitly represented, become an explicit part of the model. To start exploring discrete event phenomena within metabolite channeling we choose the tryptophan synthase. Based on a continuous macro model, a discrete event, multi-level model is developed which allows us to analyze the interrelation between structural and functional characteristics of the enzymes.

Electrostatic channeling of substrates between enzyme active sites: comparison of simulation and experiment

Recent simulation work has indicated that channeling of charged substrates between the active sites of bifunctional enzymes or bienzyme complexes can be significantly enhanced by favorable interactions with the electrostatic field of the enzymes. The results of such simulations are expressed in terms of transfer efficiencies, which describe the probability that substrate leaving the active site of the first enzyme will reach the active site of the second enzyme before escaping out into bulk solution. The experimental indicators of channeling, on the other hand, are factors such as a decrease in the transient (lag) time for appearance of the final product of the coupled enzyme reaction or a decrease in the susceptibility of the overall reaction rate to the presence of competing enzymes or competitive inhibitors. The work reported here aims to establish a connection between the transfer efficiencies obtained from simulation, with the above-mentioned experimental observables. This is accomplished by extending previously reported analytical approaches to combine the simulated transfer efficiency with the Michaelis-Menten kinetic parameters Km and Vmax of the enzymes involved; expressions are derived to allow both transient times and steady state rates to be calculated. These results are applied to the two systems that have been studied both theoretically and experimentally. In the first case, that of the bifunctional enzyme dihydrofolate reductase-thymidylate synthase (DHFR-TS), the experimentally observed decrease in transient times is found to be consistent with a transfer efficiency of >/=80%. In the second case, that of a citrate synthase-malate dehydrogenase fusion protein, a transfer efficiency of 73% is consistent with the experimental transient time measurements. Separate and independent analysis of the effects of adding the competing enzyme aspartate aminotransferase gives a transfer efficiency of 69%, in excellent agreement with the transient time results. The transfer efficiencies thus obtained from experimental results are in both cases in good agreement with those obtained from simulations that include electrostatic interactions. One important discrepancy between simulation and experiment, is however, found in the reported effects of adding a competitive inhibitor in the DHFR-TS system: qualitatively different results are expected from the theoretical analysis. A possible reason for this apparent contradiction is discussed.

Metabolic consequences of enzyme interactions

The fact that enzyme complexes, stable, quasi-stable, and dynamic, exist in cells can no longer be ignored. Experimental evidence done with a variety of techniques has demonstrated these interactions in vitro and in vivo. There is scarcely a single known metabolic pathway in which no interactions of any of its enzymes exist (see reference 27 for a list of these). Such interactions are not only ubiquitous throughout metabolism, but they exist in all cell types, procaryote and eucaryote. In many of these systems the advantages of and regulatory power of enzyme-enzyme or enzyme-structural protein interactions has been amply demonstrated. The more difficult task is to assess accurately quantitative aspects of a system that varies between the solid, gel, and aqueous state. It is clear that the metabolic paradigm of soluble randomly dispersed metabolic elements in cells must be replaced, and new theoretical and experimental approaches introduced into this vital area of biological research.

Enzyme-enzyme interactions and their metabolic role

There are continuing reports on the existence of complexes of sequential metabolic enzymes. New techniques for their detection have been described and include affinity electrophoresis and the use of anti-idiotypic antibodies. Channeling of substrates has been reported for several systems as well as direct substrate transfer through dynamic enzyme associations. Kinetic parameters of metabolic control of organized systems have been formulated and tested in several systems. These recent results are expanding our understanding of metabolic processes and their control.

Transient-time analysis of substrate-channelling in interacting enzyme systems

The kinetics of dynamically interacting enzyme systems is examined, in the light of increasing evidence attesting to the widespread occurrence of this mode of organization in vivo. The transient time, a key phenomenological parameter for the coupled reaction, is expressed as a function of the lifetime of the intermediate substrate. The relationships between the transient time and the pseudo-first-order rate constants for the coupled reaction by the complexed and uncomplexed enzyme species are indicative of the mechanism of intermediate transfer ('channelling'). In a dynamically interacting enzyme system these kinetic parameters are composite functions of those for the processes catalysed by the complex and by the separated enzymes. The mathematical paradigm can be extended to a linear sequence of N coupled reactions catalysed by dynamically (pair-wise) interacting enzymes.

The perfection of substrate-channelling in interacting enzyme systems: energetics and evolution

Some implications of substrate channelling in interacting enzyme systems are considered, with regard to the energetics and evolution of enzyme action. The transient time, a key analytical parameter relating to the phenomenon of channelling, is the basis of our kinetic study. Bounds on the kinetics of multienzyme complexes are established using (apparent) rate constants emanating from the transient-time formulation of coupled reactions. From a transition state representation of the rate process, it is shown how dynamically and statically organized enzyme systems lead to the modification of current ideas on the evolutionary optimization of the energy profile of enzyme catalysis in situ.

Complex of brain D-phosphoglycerate mutase and gamma enolase and its reactivation by D-glycerate 2,3-bisphosphate

The dissociabilities of dimeric gamma enolase, alpha enolase, and phosphoglycerate mutase of brain origin were tested using fluorescein isothiocyanate attached covalently to these enzymes. The dissociation constant of dimeric gamma enolase is lower (Kd = 0.03 microM) than that of the alpha enolase (Kd = 3 microM), while dimeric mutase seems to be nondissociable in the concentration range 0.1-10 microM, at pH 7.3 in 50 mM imidazole buffer at 20 degrees C. Interaction of neuron-specific gamma enolase with D-phosphoglycerate mutase was detected with the same fluorescence-labeling technique as well as by a kinetic analysis. The determined dissociation constant of the enolase-mutase complex was found to be in the range 5-40 microM, independent of the technique used. A mixed type of inhibition in the binding of D-glycerate-2-P and mutase to the D-glycerate-2-P binding site on enolase was observed in the absence of D-glycerate-2,3-P2. However, the inhibition of the enolase activity by brain D-phosphoglycerate mutase in the D-glycerate-2-P----phosphoenolpyruvate transformation is almost fully reverted by D-glycerate-2,3-P2, probably via the proper coordination of the active centers in the ternary complex of enolase, D-phosphoglycerate mutase, and their common intermediate, D-glycerate-2-P. The mechanism of intermediate transfer by consecutive enzyme pairs in a nondivergent metabolite flux (around the transformation of D-glycerate-2-P) is examined and conclusions of the present experiments are compared with the results of an extended analysis performed earlier with a divergent metabolite flux (around the transformation of multiusage triosephosphates, D-glyceraldehyde-3-P, and dihydroxyacetone phosphate).