Temporal analysis of metabolic systems and its application to metabolite channelling

Understanding differential aspects of microdiffusion (channeling) in the Coenzyme Q and Cytochrome c regions of the mitochondrial respiratory system

Over the past decades, models of the organization of mitochondrial respiratory system have been controversial. The goal of this perspective is to assess this "conflict of models" by focusing on specific kinetic evidence in the two distinct segments of Coenzyme Q- and Cytochrome c-mediated electron transfer. Respiratory supercomplexes provide kinetic advantage by allowing a restricted diffusion of Coenzyme Q and Cytochrome c, and short-range interaction with their partner enzymes. In particular, electron transfer from NADH is compartmentalized by channeling of Coenzyme Q within supercomplexes, whereas succinate oxidation proceeds separately using the free Coenzyme Q pool. Previous evidence favoring Coenzyme Q random diffusion in the NADH-dependent electron transfer is due to downstream flux interference and misinterpretation of results. Indeed, electron transfer by complexes III and IV via Cytochrome c is less strictly dependent on substrate channeling in mammalian mitochondria. We briefly describe these differences and their physiological implications.

Mechanisms of dysfunction of the nitric oxide pathway in vascular diseases

Vascular nitric oxide (NO) is involved in many physiologic and pathophysiologic processes throughout the body. Many vascular diseases have a reduction in the activity of endothelium-derived NO as an important component involved in the initiation and/or progression of the disease. It is now known that there are multiple mechanisms for this reduction in NO activity with one or more mechanisms operating depending on the specific condition or stage of a disease. In other instances, the therapy for certain diseases is responsible for the reduction in NO activity and contributes to the acceleration of vascular disease. This review details the known mechanisms of dysfunction of the NO pathway leading to vascular diseases, which provides the rationale for why certain therapies can improve while other therapies adversely affect vascular health.

Relationship between the catalytic sites of human bifunctional IMP synthase

BACKGROUND AND AIMS

The bifunctional enzyme, IMP synthase, contains 5-aminoimidazole-4-carboxamide ribotide (AICAR) transformylase and IMP cyclohydrolase activities and catalyses the ninth and tenth reactions of the pathway for de novo biosynthesis of purine nucleotides (AICAR-->FAICAR-->IMP). The spatial relationship between the two active sites on IMP synthase has been investigated along with the possibility that the intermediate, FAICAR, may be channelled between the two sites.

METHODS

The two catalytic activities and the overall reaction (AICAR-->FAICAR-->IMP) were assayed using 3H-labelled AICAR or FAICAR with isolation of the reaction products by thin-layer chromatography.

RESULTS

Inhibition constants for the interactions of six purine nucleoside 5'-monophosphate derivatives with AICAR transformylase and IMP cyclohydrolase were 24- to 820-fold higher for the transformylase. N-ethylmaleimide inactivated IMP cyclohydrolase but not AICAR transformylase. The rate of IMP synthesis from AICAR was consistent with a high local concentration of FAICAR at the cyclohydrolase site but addition of exogenous unlabelled FAICAR reduced the amount of [3H]AICAR formed from [3H]AICAR indicating that the channelling of FAICAR was not absolute.

CONCLUSION

The AICAR transformylase and IMP cyclohydrolase active sites of IMP synthase are distinct but sufficiently close for the FAICAR produced by a transformylase site to be preferentially utilized as a substrate by a cyclohydrolase site on the same molecule if dimeric, bifunctional IMP synthase.

Why and when channelling can decrease pool size at constant net flux in a simple dynamic channel

Cornish-Bowden and Cárdenas (Cornish-Bowden, A. and Cárdenas M.L. (1993) Eur. J. Biochem. 213, 87-92) have suggested that simulation results peviously published by us (Mendes, P., Kell, D.B. and Westerhoff, H.V. (1992) Eur. J. Biochem. 204, 255-266) which had demonstrated that large reductions of intermediate pool sizes could be accompanied by increasing channel flux in a model metabolic pathway, were an artefact of changes in the pathway's overall flux of the order of 0.0075%, or of inappropriate alterations of enzyme activities. They also asserted to prove that the "channelling of an intermediate cannot affect its free concentration at constant net flux". We consider the co-response of the intermediate metabolite concentration ('pool') and the channel flux to changes in kinetic (or thermodynamic) parameters. Both by analytical proofs and by numerical examples we show that this co-response can be positive, negative or null, depending on the parameter change. In particular, we prove that there is always a number of ways of changing parameters such that the intermediate metabolite concentration decreases with increasing channel flux, whether the total flux varies or is constant. We also show that increased stability of the (dynamic) enzyme-intermediate-enzyme complex, as well as a single parameter change that similarly displays no cross-over effects, can lead to decreased intermediate metabolite concentration and increased channel flux at constant total flux. In general, a non-zero co-response of the intermediate metabolite concentration ('pool') and the channel flux to changes in kinetic (or other) parameters is the rule rather than the exception. More specifically: (i) The algebraic analysis ('general proof') given in Cornish-Bowden and Cárdenas (1993) contains the constraint that the elasticities of various steps to the modulation parameters which were used to vary the channel flux at constant net flux were unity. This is an unfortunate and unnecessary constraint which, when lifted, means that the concentration of the pool in the general case can indeed change at constant net flux. A 'simplified proof' given in Cornish-Bowden and Cárdenas (1993) also fails, due in addition to the consequent failure to include mass conservation relations for some of the enzymes. (ii) In the systems studied by Cornish-Bowden and Cárdenas (1993), flux is properly to be considered as a variable (since it varies during the transition to the steady state), and not a parameter, and as such cannot per se affect the magnitude of other variables in the steady state. (iii) By relaxing the constraint referred to in (i), above, and by making dual modulations (i.e., of more than one parameter at once) which are different from those carried out in Cornish-Bowden and Cárdenas (1993) we find many instances in which channelling (described by a parameter p) does significantly affect the concentration of the pool intermediate C at constant total flux. (iv) In the same pathways, but in which the flux is held constant by setting it via a zero-order flux-generating reaction, the addition of a channel is also able to significantly to modulate the size of the pool at constant total flux. Our results show that the effectiveness of channelling in decreasing a pool, even at constant flux, is very much a reality.