0000000000011424
AUTHOR
Inara Kampenusa
Relationships between metabolic fluxes and enzyme amino acid composition
AbstractMetabolic fluxes are a key parameter of metabolic pathways being closely related to the kinetic properties of enzymes and could be conditional on their sequence characteristics. This study examines possible relationships between the metabolic fluxes and the amino acid (AA) composition (AAC) for enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway. Metabolic fluxes were quantified by the COPASI tool using the kinetic models of Hynne and Teusink at 25 mM, 50 mM, and 100 mM of external glucose or employing literature data for cognate kinetic or stoichiometric models. The enzyme sequences were taken from the UniProtKB, and the AAC computed by the ExPASy/ProtParam tool. Mul…
Distinctive attributes for predicted secondary structures at terminal sequences of non-classically secreted proteins from proteobacteria
Abstract C- and N-terminal sequences (64 amino acid residues each) of 89 non-classically secreted type I, type III and type IV proteins (Swiss-Prot/TrEMBL) from proteobacteria were transformed into predicted secondary structures. Multivariate analysis of variance (MANOVA) confirmed the significance of location (C- or N-termini) and secretion type as essential factors in respect of quantitative representations of structured (a-helices, b-strands) and unstructured (coils) elements. The profiles of secondary structures were transcripted using unequal property values for helices, strands and coils and corresponding numerical vectors (independent variables) were subjected to multiple discriminan…
Relationship between Metabolic Fluxes and Sequence-Derived Properties of Enzymes
Metabolic fluxes are key parameters of metabolic pathways being closely related to the kinetic properties of enzymes, thereby could be dependent on. This study examines possible relationships between the metabolic fluxes and the physical-chemical/structural features of enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway. Metabolic fluxes were quantified by the COPASI tool using the kinetic models of Hynne and Teusink at varied concentrations of external glucose. The enzyme sequences were taken from the UniProtKB and the average amino acid (AA) properties were computed using the set of Georgiev’s uncorrelated scales that satisfy the VARIMAX criterion and specific AA indices th…
Relationships between kinetic constants and the amino acid composition of enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway
The kinetic models of metabolic pathways represent a system of biochemical reactions in terms of metabolic fluxes and enzyme kinetics. Therefore, the apparent differences of metabolic fluxes might reflect distinctive kinetic characteristics, as well as sequence-dependent properties of the employed enzymes. This study aims to examine possible linkages between kinetic constants and the amino acid (AA) composition (AAC) for enzymes from the yeast Saccharomyces cerevisiae glycolytic pathway. The values of Michaelis-Menten constant (K M), turnover number (k cat), and specificity constant (k sp = k cat/K M) were taken from BRENDA (15, 17, and 16 values, respectively) and protein sequences of nine…