Kinetic modeling of metabolism: Present and future

Maranas, 2016 Foster, 2021, Building kinetic models for metabolic engineering, Curr Opin Biotechnol, 67, 35, 10.1016/j.copbio.2020.11.010 Oberhardt, 2009, Flux balance analysis: interrogating genome-scale metabolic networks, Methods Mol Biol, 500, 61, 10.1007/978-1-59745-525-1_3 Palsson, 2006 Saa, 2017, Formulation, construction and analysis of kinetic models of metabolism: a review of modelling frameworks, Biotechnol Adv, 35, 981, 10.1016/j.biotechadv.2017.09.005 Guldberg Pw, 1964 Savageau, 1969, Biochemical systems analysis: I. Some mathematical properties of the rate law for the component enzymatic reactions, J Theor Biol, 25, 365, 10.1016/S0022-5193(69)80026-3 Hatzimanikatis, 1997, Effects of spatiotemporal variations on metabolic control: approximate analysis using (log)linear kinetic models, Biotechnol Bioeng, 54, 91, 10.1002/(SICI)1097-0290(19970420)54:2<91::AID-BIT1>3.0.CO;2-Q Heijnen, 2005, Approximative kinetic formats used in metabolic network modeling, Biotechnol Bioeng, 91, 534, 10.1002/bit.20558 Visser, 2003, Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics, Metab Eng, 5, 164, 10.1016/S1096-7176(03)00025-9 Saa, 2016, Construction of feasible and accurate kinetic models of metabolism: a Bayesian approach, Sci Rep, 6, 29635, 10.1038/srep29635 Deichmann, 2014, Commemorating the 1913 michaelis-menten paper Die Kinetik der Invertinwirkung: three perspectives, FEBS J, 281, 435, 10.1111/febs.12598 Hofmeyr, 1997, The reversible Hill equation: how to incorporate cooperative enzymes into metabolic models, Comput Appl Biosci, 13, 377 Liebermeister, 2006, Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data, Theor Biol Med Model, 3, 42, 10.1186/1742-4682-3-42 Ederer, 2007, Thermodynamically feasible kinetic models of reaction networks, Biophys J, 92, 1846, 10.1529/biophysj.106.094094 Steuer, 2006, Structural kinetic modeling of metabolic networks, Proc Natl Acad Sci U S A, 103, 11868, 10.1073/pnas.0600013103 Grimbs, 2007, The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks, Mol Syst Biol, 3, 146, 10.1038/msb4100186 Steuer, 2007, From structure to dynamics of metabolic pathways: application to the plant mitochondrial TCA cycle, Bioinformatics, 23, 1378, 10.1093/bioinformatics/btm065 Jamshidi, 2010, Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models, Biophys J, 98, 175, 10.1016/j.bpj.2009.09.064 Bordbar, 2015, Personalized whole-cell kinetic models of metabolism for discovery in genomics and pharmacodynamics, Cell Syst, 1, 283, 10.1016/j.cels.2015.10.003 Haiman, 2020, MASSpy: building, simulating, and visualizing dynamic biological models in Python using mass action kinetics, bioRxiv Tran, 2008, Ensemble modeling of metabolic networks, Biophys J, 95, 5606, 10.1529/biophysj.108.135442 Zomorrodi, 2013, Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks, Biotechnol J, 8, 1090, 10.1002/biot.201200270 Khodayari, 2014, A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data, Metab Eng, 25, 50, 10.1016/j.ymben.2014.05.014 Wang, 2020, Mapping allosteric communications within individual proteins, Nat Commun, 11, 3862, 10.1038/s41467-020-17618-2 Hackett, 2016, Systems-level analysis of mechanisms regulating yeast metabolic flux, Science, 354, 10.1126/science.aaf2786 Schroeder, 2019, KOPTIC: a novel approach for in silico prediction of enzyme kinetics and regulation, bioRxiv Islam, 2018, Dissecting metabolic flux in C4 plants: experimental and theoretical approaches, Phytochemistry Rev, 17, 1253, 10.1007/s11101-018-9579-8 Bar-Even, 2011, Hydrophobicity and charge shape cellular metabolite concentrations, PLoS Comput Biol, 7, 10.1371/journal.pcbi.1002166 Christodoulou, 2018, Reserve flux capacity in the pentose phosphate pathway enables Escherichia coli's rapid response to oxidative stress, Cell Syst, 6, 569, 10.1016/j.cels.2018.04.009 Khodayari, 2016, A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains, Nat Commun, 7, 13806, 10.1038/ncomms13806 Greene, 2017, Acceleration strategies to enhance metabolic ensemble modeling performance, Biophys J, 113, 1150, 10.1016/j.bpj.2017.07.018 St John, 2019, Bayesian inference of metabolic kinetics from genome-scale multiomics data, PLoS Comput Biol, 15, 10.1371/journal.pcbi.1007424 Gopalakrishnan, 2020, K-FIT: an accelerated kinetic parameterization algorithm using steady-state fluxomic data, Metab Eng, 61, 197, 10.1016/j.ymben.2020.03.001 Guo, 2018, Dynamic modeling of subcellular phenylpropanoid metabolism in Arabidopsis lignifying cells, Metab Eng, 49, 36, 10.1016/j.ymben.2018.07.003 Andreozzi, 2016, iSCHRUNK--In silico approach to characterization and reduction of uncertainty in the kinetic models of genome-scale metabolic networks, Metab Eng, 33, 158, 10.1016/j.ymben.2015.10.002 Miskovic, 2010, Production of biofuels and biochemicals: in need of an ORACLE, Trends Biotechnol, 28, 391, 10.1016/j.tibtech.2010.05.003 Hameri, 2019, Statistical inference in ensemble modeling of cellular metabolism, PLoS Comput Biol, 15, 10.1371/journal.pcbi.1007536 Hameri, 2019, Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations, Metab Eng, 52, 29, 10.1016/j.ymben.2018.10.005 Savoglidis, 2016, A method for analysis and design of metabolism using metabolomics data and kinetic models: application on lipidomics using a novel kinetic model of sphingolipid metabolism, Metab Eng, 37, 46, 10.1016/j.ymben.2016.04.002 Foster, 2019, From Escherichia coli mutant 13C labeling data to a core kinetic model: a kinetic model parameterization pipeline, PLoS Comput Biol, 15, 10.1371/journal.pcbi.1007319 Chowdhury, 2015, Improving prediction fidelity of cellular metabolism with kinetic descriptions, Curr Opin Biotechnol, 36, 57, 10.1016/j.copbio.2015.08.011 Ng, 2015, Advances in de novo strain design using integrated systems and synthetic biology tools, Curr Opin Chem Biol, 28, 105, 10.1016/j.cbpa.2015.06.026 Khodayari, 2015, Succinate overproduction: a case study of computational strain design using a comprehensive Escherichia coli kinetic model, Front Bioeng Biotechnol, 2, 10.3389/fbioe.2014.00076 Dash, 2017, Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations, Biotechnol Biofuels, 10, 108, 10.1186/s13068-017-0792-2 Chowdhury, 2014, k-OptForce: integrating kinetics with flux balance analysis for strain design, PLoS Comput Biol, 10, 10.1371/journal.pcbi.1003487 Tokic, 2020, Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies, Biotechnol Biofuels, 13, 33, 10.1186/s13068-020-1665-7 Chen, 2012, Genome-based kinetic modeling of cytosolic glucose metabolism in industrially relevant cell lines: Saccharomyces cerevisiae and Chinese hamster ovary cells, Bioproc Biosyst Eng, 35, 1023, 10.1007/s00449-012-0687-3 Mulukutla, 2015, Multiplicity of steady states in glycolysis and shift of metabolic state in cultured mammalian cells, PloS One, 10, 10.1371/journal.pone.0121561 Farquhar, 1980, A biochemical model of photosynthetic CO2 assimilation in leaves of C 3 species, Planta, 149, 78, 10.1007/BF00386231 Zhu, 2007, Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically increase photosynthetic rate: a numerical simulation using an evolutionary algorithm, Plant Physiol, 145, 513, 10.1104/pp.107.103713 Rohwer, 2001, Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data, Biochem J, 358, 437, 10.1042/bj3580437 Curien, 2009, Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters, Mol Syst Biol, 5, 271, 10.1038/msb.2009.29 Wang, 2014, Complete proteomic-based enzyme reaction and inhibition kinetics reveal how monolignol biosynthetic enzyme families affect metabolic flux and lignin in Populus trichocarpa, Plant Cell, 26, 894, 10.1105/tpc.113.120881 Alsiyabi, 2021, Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants, PloS Comput Biol, 17, 10.1371/journal.pcbi.1008284 Liu, 2014, Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale, BMC Syst Biol, 8, 110, 10.1186/s12918-014-0110-6 Monk, 2017, iML1515, a knowledgebase that computes Escherichia coli traits, Nat Biotechnol, 35, 904, 10.1038/nbt.3956 Orth, 2011, A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011, Mol Syst Biol, 7, 535, 10.1038/msb.2011.65 Edwards, 2000, The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities, Proc Natl Acad Sci USA, 97, 5528, 10.1073/pnas.97.10.5528 Mendoza, 2019, A systematic assessment of current genome-scale metabolic reconstruction tools, Genome Biol, 20, 158, 10.1186/s13059-019-1769-1 Zotter, 2017, Quantifying enzyme activity in living cells, J Biol Chem, 292, 15838, 10.1074/jbc.M117.792119 Ellis, 2001, Macromolecular crowding: obvious but underappreciated, Trends Biochem Sci, 26, 597, 10.1016/S0968-0004(01)01938-7 Agrawal, 2008, Effect of macromolecular crowding on the rate of diffusion-limited enzymatic reaction, Pramana, 71, 359, 10.1007/s12043-008-0169-y