Abstract
BackgroundDevelopment of the mathematical models that adequately describe biochemical reactions and molecular-genetic mechanisms is one of the most important tasks in modern bioinformatics. Because the enzyme adenylosuccinate synthetase (AdSS) has long been extensively studied, a wealth of kinetic data has been accumulated.ResultsWe describe a mathematical model for the reaction catalyzed by AdSS. The model's parameters were fitted to experimental data obtained from published literature. The advantage of our model is that it includes relationships between the reaction rate, the concentrations of three substrates (GTP, IMP and ASP), the effects of five inhibitors (GMP, GDP, AMP, ASUC and SUCC), and the influence of Mg2+ ions.ConclusionOur model describes the reaction catalyzed by AdSS as a fully random process. The model structure implies that each of the inhibitors included in it is only competitive to one of the substrates. The model was tested for adequacy using experimental data published elsewhere. The values obtained for the parameters are as follows: Vmax = 1.35·10-3 mM/min, KmGTP = 0.023 mM, KmIMP = 0.02 mM, KmASP = 0.3 mM, KiGMP = 0.024 mM, KiGDP = 8·10-3 mM, KiAMP = 0.01 mM, KiASUC = 7.5·10-3 mM, KiSUCC = 8 mM, KmMg = 0.08 mM.
Highlights
Development of the mathematical models that adequately describe biochemical reactions and molecular-genetic mechanisms is one of the most important tasks in modern bioinformatics
guanosine 5'-diphosphate (GDP) is a competitive inhibitor of guanosine 5'-triphosphate (GTP), which in part explains a gradual decrease in the rate of ASUC formation in solutions if the GTP concentration is not reduced. deoxyadenylic acid (dAMP), CMP, and uridine 5'-monophosphate (UMP) can
We report a more complete model, which describes the reaction catalyzed by adenylosuccinate synthetase and includes the concentrations of three substrates (GTP, inosine 5'-monophosphate (IMP), and ASP), the effects of five inhibitors (GMP, GDP, adenosine 5'monophosphate (AMP), ASUC, and SUCC), and the influence of Mg2+ ions
Summary
Development of the mathematical models that adequately describe biochemical reactions and molecular-genetic mechanisms is one of the most important tasks in modern bioinformatics. Some of the genes that encode these enzymes are arranged into operons (purF, purHD, purMN, purEK, guaBA, purB), while others are located in single cistrons (purT, purl, purC, purA, guaC). Expression of these operons is regulated by regulatory proteins (PurR, DnaA, CRP) and various low-molecular-weight compounds [13]. The enzyme adenylosuccinate synthetase (AdSS; GDPforming IMP: L-aspartate ligase, EC 6.3.4.4), which is the product of the purA gene, catalyzes the conversion of IMP to ASUC in the presence of Mg2+: IMP + GTP + ASP → GDP + PI + ASUC. AMP is a competitive inhibitor of IMP; ASUC, of IMP; dGMP, of IMP; GMP, of GTP. GDP is a competitive inhibitor of GTP, which in part explains a gradual decrease in the rate of ASUC formation in solutions if the GTP concentration is not reduced. dAMP, CMP, and UMP can (page number not for citation purposes)
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