SIMFIT: a microcomputer software-toolkit for modelistic studies in biochemistry

Mitochondrial cytopathies present a tissue specificity characterized by the fact that even if a mitochondrial DNA mutation is present in all tissues, only some will be affected and induce a pathology. Several mechanisms have been proposed to explain this phenomenon such as the appearance of a sporadic mutation in a given stem cell during embryogenesis or mitotic segregation, giving different degrees of heteroplasmy in tissues. However, these mechanisms cannot be the only ones involved in tissue specificity. In this paper, we propose an additional mechanism contributing to tissue specificity. It is based on the metabolic expression of the defect in oxidative phosphorylation (OXPHOS) complexes that can present a biochemical threshold. The value of this threshold for a given OXPHOS complex can vary according to the tissue; thus different tissues will display different sensitivities to a defect in an OXPHOS complex. To verify this hypothesis and to illustrate the pathological consequences of the variation in biochemical thresholds, we studied their values for seven OXPHOS complexes in mitochondria isolated from five different rat tissues. Two types of behavior in the threshold curves can be distinguished corresponding to two modes of OXPHOS response to a deficiency. We propose a classification of tissues according to their type of OX-PHOS response to a complex deficiency and therefore to their threshold values.Mitochondrial pathologies are a heterogeneous group of metabolic disorders characterized by abnormalities of the mitochondrial ultrastructure as well as of oxidative phosphorylation functioning (1-4). During these last years, the study of mitochondrial DNA (mtDNA) has shown, in a certain number of cases, some precise mutation sites associated with a better clinical definition of the related pathologies (5-20). In addition, it has been shown that defects in oxidative phosphorylations (OXPHOS) 1 are able to affect any tissue, thus leading to the concept of mitochondrial cytopathies (21). This underlies the problem of the variability of the phenotypic expression of an mtDNA mutation. Indeed, an OXPHOS deficit due to such a mutation will not necessarily lead to a pathology. Moreover, mitochondrial cytopathies present a tissue specificity characterized by the fact that even if a mutation is present in all tissues, only some will be affected, leading to the pathology (4,(22)(23)(24)(25).A first mechanism proposed to explain this tissue specificity is based on the random segregation of wild type and mutant mtDNAs during embryogenesis, giving different levels of heteroplasmy in tissues (4,7,26,27). In this case, only tissues with a high proportion of mutated mtDNA would be affected. However, in patients where the mitochondrial mutation is homoplasmic (25, 28) and in the case of nuclear mutations giving a uniform deficiency in all tissues, this mechanism can no longer explain the tissue specificity. For this reason, we propose another mechanism based on the threshold effect in the expression of a defect. This effect ...

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“…1A) are superimposable as are the threshold curves (Fig. 1B), thus validating the fitting procedure (51,53).…”

Section: Resultssupporting

confidence: 73%

“…This method uses a non-linear regression that fits the respiratory rate inhibition curve. Non-linear fitting was done using the program Simfit (53).…”

Section: Titration Curvesmentioning

confidence: 99%

Threshold Effect and Tissue Specificity

Rossignol

Malgat

Mazat

et al. 1999

Journal of Biological Chemistry

248

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“…9 based on a non-linear regression that fits the respiratory rate inhibition curve. The 'Simfit' program was used for nonlinear fitting (21). Using the parameters obtained by this fitting procedure and the model equations, we drew the inhibition curve of the isolated step activity with the program TK Solver Plus (Universal Technical Systems, Rockford, IL).…”

Section: Animals-malementioning

confidence: 99%

Mobilization of Adenine Nucleotide Translocators as Molecular Bases of the Biochemical Threshold Effect Observed in Mitochondrial Diseases

Faustin

Rossignol

Rocher

et al. 2004

Journal of Biological Chemistry

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The existence of a biochemical threshold effect in the metabolic expression of oxidative phosphorylation deficiencies has considerable implications for the understanding of mitochondrial bioenergetics and the study of mitochondrial diseases. However, the molecular bases of this phenomenon remain unclear. We report here a new mechanism to explain this threshold effect, based on a reserve of enzymes not initially participating in the respiratory rate that can be activated either to respond to a flux increase or to compensate for a defect induced by a mutation. We show that this mobilization occurs through 1) the assembly of inactive adenine nucleotide translocator isoform 1 subunits into oligomeric active carriers or 2) conformational changes in the adenine nucleotide translocator isoform 1 in a permeability transition pore-like structure. We discuss how these transitions are sensitive to the steady state of oxidative phosphorylation functioning or tissue and analyze their consequences on the threshold effect.

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“…This was done by simulating the AK reaction according to eqn (7) (see below) plus a first-order hydrolysis of aspp with SCAMP [6] and SIMFIT [31]. The aspp concentrations were then fitted using SIMFIT with the equilibrium constant, the aspp hydrolysis rate and the inhibition constant of AK by aspp as the variable parameters, and all other parameters for AK fixed at the values described in the Results section.…”

Section: Ak Equilibrium-constant Measurementmentioning

confidence: 99%

“…The experimental data were fitted to the theoretical equations by non-linear least squares using several different programs : SIMFIT [31], Kaleidagraph 3.0.2 (Abelbeck software) and the Excel V solver (Microsoft). For each enzyme, the empirical rate equations used for the determination of the different kinetic parameters (V max , K m and K i ) were developed and chosen as the experiments progressed ; they are presented in the Results section.…”

Section: Kinetic Analysismentioning

confidence: 99%

An integrated study of threonine-pathway enzyme kinetics in Escherichia coli

Chassagnole

Raïs

QUENTIN³

et al. 2001

Biochemical Journal

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We have determined the kinetic parameters of the individual steps of the threonine pathway from aspartate in Escherichia coli under a single set of experimental conditions chosen to be physiologically relevant. Our aim was to summarize the kinetic behaviour of each enzyme in a single tractable equation that takes into account the effect of the products as competitive inhibitors of the substrates in the forward reaction and also, when appropriate (e.g. near-equilibrium reactions), as substrates of the reverse reactions. Co-operative feedback inhibition by threonine and lysine was also included as necessary. We derived the simplest rate equations that describe the salient features of the enzymes in the physiological range of metabolite concentrations in order to incorporate them ultimately into a complete model of the threonine pathway, able to predict quantitatively the behaviour of the pathway under natural or engineered conditions.

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SIMFIT: a microcomputer software-toolkit for modelistic studies in biochemistry

Cited by 19 publications

References 13 publications

Threshold Effect and Tissue Specificity

Threshold Effect and Tissue Specificity

Mobilization of Adenine Nucleotide Translocators as Molecular Bases of the Biochemical Threshold Effect Observed in Mitochondrial Diseases

An integrated study of threonine-pathway enzyme kinetics in Escherichia coli

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