Mathematical Modeling of Mitochondrial Adenine Nucleotide Translocase (original) (raw)
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Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 2002
To understand the transport mechanism of the bovine heart mitochondrial ADP/ATP carrier at the atomic level, we studied the four-dimensional features of the interaction of various purine nucleotides with the adenine nucleotide binding region (ABR) consisting of Arg 151-Asp 167 in the second loop facing the matrix side. After three-dimensional modeling of ABR based on the experimental results, its structural changes on interaction with purine nucleotides were examined by molecular dynamics computation at 300 K. ATP/ADP were translocated to a considerable degree from the matrix side to the inner membrane region accompanied by significant backbone conformational changes, whereas neither appreciable translocation nor a significant conformational change was observed with the untransportable nucleotides AMP/GTP. The results suggested that binding of the terminal phosphate group and the adenine ring of ATP/ADP with Arg 151 and Lys 162 , respectively, and subsequent interaction of a phosphate group(s) other than the terminal phosphate with Lys 162 triggered the expansion and subsequent contraction of the backbone conformation of ABR, leading to the translocation of ATP/ ADP. Based on a simplified molecular dynamic simulation, we propose a dynamic model for the initial recognition process of ATP/ADP with the carrier.
Mathematical model of mitochondrial ionic homeostasis: Three modes of Ca2+ transport
Journal of Theoretical Biology, 2006
Mitochondria play an important role in regulation of Ca 2+ homeostasis in a cell. Here we present a mathematical model of mitochondrial ion transport and use this model to analyse different modes of Ca 2+ uptake by mitochondria. The model includes transport of H + , Ca 2+ , K + , inorganic phosphate and oxidative substrates across the inner mitochondrial membrane harboring permeability transition pore (PTP). The detailed description of ion fluxes is based on the experimental ion kinetics in isolated mitochondria. Using the model we show that the kinetics of Ca 2+ uptake by mitochondria is regulated by the total amount of Ca 2+ in the system and the rate of Ca 2+ infusion. Varying these parameters we find three different modes of ion transport. When the total amount of Ca 2+ is below 140 nmol Ca 2+ /mg protein, all available Ca 2+ is accumulated in the matrix without activation of the PTP. Between 140 and 160 nmol Ca 2+ /mg protein, accumulation of Ca 2+ generates periodic opening and closure of the PTP and oscillations of ion fluxes. Higher levels of Ca 2+ (4160 nmol Ca 2+ /mg protein) result in a permanently open PTP, membrane depolarization and loss of small ions from the matrix. We show that in the intermediate range of Ca 2+ concentrations the rate of Ca 2+ infusion regulates the PTP state, so that slow Ca 2+ infusion does not lead to PTP opening, while fast Ca 2+ infusion results in an oscillatory state. r J uni -the rate of Ca 2+ flux via a mitochondrial Ca 2+ uniporter; J CaH -the rate of Ca 2+ and/or H + fluxes via an electroneutral Ca/2H exchanger; J H,res -the rate of H + flux via the respiratory chain, supported by NADH oxidation; J H,leak -the rate of back-flow of H + ions via ''leakage'' of the mitochondrial membrane; J K -the rate of K + flux via the mitochondrial K + uniporter; J KH -the rate of K + and/or H + fluxes via an electroneutral K/H exchanger; J POH -the rate of inorganic phosphate flux via a mitochondrial P/OH exchanger; J dic -the rate of P 2À and A 2À fluxes via a mitochondrial dicarboxylic acid exchanger; J NADH -the rate of NADH recovery from NAD by matrix dehydrogenases; L Ca , L CaÀP , L CaÀA , L A , L K , L P À , L P 2À , L H -the rates of corresponding ion fluxes via PTP.
A model for adenosine transport and metabolism
Biochemical …, 1992
A model is presented for adenosine transport and metabolism in different steady states. The model considers steadystate equations for metabolic enzymes based on information from the literature on their kinetic behaviour. 2. Assuming that extracellular adenosine and inosine are translocated by three transporters, we have devised rate equations for these nucleoside transporters which are valid when both nucleosides are present. Since the Na+-independent transporter can either incorporate nucleosides into the cell or release them, various conditions have been simulated in which inosine was either incorporated or released. 3. Control analyses are reported which show that the fluxes towards intracellular adenine nucleosides are controlled by ecto-5'-nucleotidase in some circumstances and by the nucleoside transporters in others. The nucleoside transporter is responsible for five fluxes (two Na+ dependent adenosine transport mechanisms, a Na+dependent inosine transport, a Na+-independent adenosine transport and a Na+-independent inosine influx or efflux) but the control is not always positive for all these fluxes. The control patterns of these five fluxes indicate that, in the presence of extracellular adenosine and inosine, the intracellular metabolism of adenine derivatives would be highly dependent on the extracellular and intracellular concentrations of both nucleosides, on the ectoenzymes (5'-nucleotidase and adenosine deaminase) and on the transporter. 4. Predictions of the model were examined. The results indicate that a change in one independent variable (extracellular AMP concentration) makes the system evolve towards a new steady state which is far from the initial one and has a different control pattern. In contrast, simulation of inhibition of the carriers produces only slight modification of the fluxes since the concentrations of the metabolites change to counteract the effect. Thus, for instance, a 50 % inhibition of the three carriers does not affect the flux towards intracellular adenine nucleotides. Finally, our model has confirmed that the evolution of the concentration of extracellular adenosine, when an increase in extracellular AMP is produced, agrees with the behaviour expected for a neurohormone.
Journal of Biological Chemistry, 2003
The ABC transporter Mdl1p, a structural and functional homologue of the transporter associated with antigen processing (TAP) plays an important role in intracellular peptide transport from the mitochondrial matrix of Saccharomyces cerevisiae. To characterize the ATP hydrolysis cycle of Mdl1p, the nucleotide-binding domain (NBD) was overexpressed in Escherichia coli and purified to homogeneity. The isolated NBD was active in ATP binding and hydrolysis with a turnover of 25 ATP per minute and a K m of 0.6 mM and did not show cooperativity in ATPase activity. However, the ATPase activity was non-linearly dependent on protein concentration (Hill coefficient of 1.7), indicating that the functional state is a dimer. Dimeric catalytic transition states could be trapped either by incubation with orthovanadate or beryllium fluoride, or by mutagenesis of the NBD. The nucleotide composition of trapped intermediate states was determined using [␣-32 P]ATP and [␥-32 P]ATP. Three different dimeric intermediate states were isolated, containing either two ATPs, one ATP and one ADP, or two ADPs. Based on these experiments, it was shown that: (i) ATP binding to two NBDs induces dimerization, (ii) in all isolated dimeric states, two nucleotides are present, (iii) phosphate can dissociate from the dimer, (iv) both nucleotides are hydrolyzed, and (v) hydrolysis occurs in a sequential mode. Based on these data, we propose a processive-clamp model for the catalytic cycle in which association and dissociation of the NBDs depends on the status of bound nucleotides.