Central European Journal of Biology * E-mail: zikmanis@lanet.lv Research Article Institute of Microbiology and Biotechnology, University of Latvia, LV-1010 Riga, Latvia Inara Kampenusa, Peteris Zikmanis* Relationships between metabolic fuxes and enzyme amino acid composition Abbreviations AA - amino acid; AAC - amino acid composition; LOOCV - leave-one-out cross-validation; VIF - variance infation factor. 1. Introduction Cell metabolism is comprised of enzyme-catalyzed biochemical reactions and carrier-mediated transport processes. Taken as a whole, these reactions form interrelated metabolic pathways which are combined into a cellular metabolic network. Metabolic fuxes describe the amount of material chemically converted or transported per time unit and are considered as the key parameters of any metabolic pathway and hence, as the fundamental determinants of cell physiology [1-4]. Changes in metabolic fuxes in response to various types of genetic and environmental perturbations are critical for the metabolic fux control which is a key objective of metabolic engineering [5,6]. On the other hand, enzyme activity is one of the major factors infuencing the magnitude of metabolic fuxes in any cell [6]. According to concepts of systems biology, metabolic fuxes are net sums of underlying enzymatic reaction rates represented by integral outputs of three biological quantities which interact at the level of enzyme kinetics: kinetic parameters, enzyme and reactant concentrations [7]. An integrated view on enzymes suggests them as dynamic assemblies whose variable structures are closely related to catalytic functions [8,9]. It is therefore important to extend our knowledge of enzyme sequence, structure, and function relationships [10], as well as to explore coherencies between enzyme activity profles and metabolic fux distributions in order to understand the physiological dynamics within a cell [2,11]. Amino acid (AA) composition (AAC) is a simplest attribute of proteins among so-called global sequence Cent. Eur. J. Biol. • 8(2) • 2013 • 107-120 DOI: 10.2478/s11535-013-0125-1 107 Received 14 August 2012; Accepted 12 November 2012 Keywords: Saccharomyces cerevisiae • Metabolic fuxes • Glycolytic enzymes • Amino acid composition • Multivariate relationships Abstract: Metabolic fuxes 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 fuxes and the amino acid (AA) composition (AAC) for enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway. Metabolic fuxes were quantifed 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. Multiple linear regressions (89.07% < R2 adjusted < 91.82%; P<0.00001) were found between the values of metabolic fuxes and the selected sets of AA frequencies (5 to 7 for each model). Selected AA differed from the rest by their physicochemical and structural propensities, thus suggesting a distinctive contribution to the properties of enzymes, and hence the metabolic fuxes. The results provide evidence that metabolic fuxes of the yeast glycolysis pathway are closely related to the AAC of relevant enzymes and support the view that catalytic, binding and structural residues are interdependent to ensure the effciency of biocatalysts. © Versita Sp. z o.o. Unauthenticated Download Date | 7/25/18 5:32 PM