{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:07:15Z","timestamp":1772172435573,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006356","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,8,17]],"date-time":"2018-08-17T00:00:00Z","timestamp":1534464000000}}],"reference-count":52,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2018,8,7]],"date-time":"2018-08-07T00:00:00Z","timestamp":1533600000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Galletti Chair Funds"},{"name":"Genentech Foundation Scholars Program"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006356","type":"journal-article","created":{"date-parts":[[2018,8,7]],"date-time":"2018-08-07T13:29:15Z","timestamp":1533648555000},"page":"e1006356","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9403-509X","authenticated-orcid":true,"given":"James T.","family":"Yurkovich","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Miguel A.","family":"Alcantar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zachary B.","family":"Haiman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2357-6785","authenticated-orcid":true,"given":"Bernhard O.","family":"Palsson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2018,8,7]]},"reference":[{"issue":"4","key":"ref1","first-page":"220","article-title":"Anaerobic storage of red blood cells","volume":"8","author":"T Yoshida","year":"2010","journal-title":"Blood Transfusion"},{"issue":"13","key":"ref2","doi-asserted-by":"crossref","first-page":"4034","DOI":"10.1182\/blood-2005-04-1622","article-title":"The energy-less red blood cell is lost: erythrocyte enzyme abnormalities of glycolysis","volume":"106","author":"R van Wijk","year":"2005","journal-title":"Blood"},{"issue":"1","key":"ref3","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1051\/mmnp\/201611106","article-title":"Blood Cell Dynamics: Half of a Century of Modelling","volume":"11","author":"L Pujo-Menjouet","year":"2016","journal-title":"Mathematical Modelling of Natural Phenomena"},{"issue":"7","key":"ref4","doi-asserted-by":"crossref","first-page":"737","DOI":"10.15252\/msb.20145243","article-title":"Minimal metabolic pathway structure is consistent with associated biomolecular interactions","volume":"10","author":"A Bordbar","year":"2014","journal-title":"Molecular Systems Biology"},{"issue":"5","key":"ref5","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1016\/j.cell.2015.05.019","article-title":"Using Genome-scale Models to Predict Biological Capabilities","volume":"161","author":"EJ O\u2019Brien","year":"2015","journal-title":"Cell"},{"issue":"48","key":"ref6","doi-asserted-by":"crossref","first-page":"19556","DOI":"10.1074\/jbc.M117.804914","article-title":"Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks","volume":"292","author":"JT Yurkovich","year":"2017","journal-title":"Journal of Biological Chemistry"},{"issue":"3","key":"ref7","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1016\/S0006-3495(02)73903-9","article-title":"Dynamic flux balance analysis of diauxic growth in Escherichia coli","volume":"83","author":"R Mahadevan","year":"2002","journal-title":"Biophysical journal"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1016\/j.jtbi.2014.10.035","article-title":"Dynamic optimization of metabolic networks coupled with gene expression","volume":"365","author":"S Waldherr","year":"2015","journal-title":"Journal of theoretical biology"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"46249","DOI":"10.1038\/srep46249","article-title":"Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics","volume":"7","author":"A Bordbar","year":"2017","journal-title":"Scientific Reports"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/msb.2008.8","article-title":"Formulating genome-scale kinetic models in the post-genome era","volume":"4","author":"N Jamshidi","year":"2008","journal-title":"Mol Syst Biol"},{"issue":"11","key":"ref11","doi-asserted-by":"crossref","first-page":"e79195","DOI":"10.1371\/journal.pone.0079195","article-title":"Systematic construction of kinetic models from genome-scale metabolic networks","volume":"8","author":"NJ Stanford","year":"2013","journal-title":"PLoS One"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.copbio.2015.08.019","article-title":"Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes","volume":"36","author":"L Miskovic","year":"2015","journal-title":"Curr Opin Biotechnol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.coisb.2017.01.007","article-title":"Integration of metabolic, regulatory and signaling networks towards analysis of perturbation and dynamic responses","volume":"2","author":"A Chiappino-Pepe","year":"2017","journal-title":"Current Opinion in Systems Biology"},{"issue":"4","key":"ref14","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/S0022-5193(89)80233-4","article-title":"Metabolic dynamics in the human red cell. Part I\u2014A comprehensive kinetic model","volume":"141","author":"A Joshi","year":"1989","journal-title":"J Theor Biol"},{"issue":"4","key":"ref15","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1016\/S0022-5193(89)80234-6","article-title":"Metabolic dynamics in the human red cell. Part II\u2014Interactions with the environment","volume":"141","author":"A Joshi","year":"1989","journal-title":"J Theor Biol"},{"issue":"1","key":"ref16","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/S0022-5193(05)80012-8","article-title":"Metabolic dynamics in the human red cell. Part III\u2014Metabolic reaction rates","volume":"142","author":"A Joshi","year":"1990","journal-title":"J Theor Biol"},{"issue":"1","key":"ref17","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/S0022-5193(05)80013-X","article-title":"Metabolic dynamics in the human red cell. Part IV\u2014Data prediction and some model computations","volume":"142","author":"A Joshi","year":"1990","journal-title":"J Theor Biol"},{"issue":"3","key":"ref18","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1042\/bj3420597","article-title":"Model of 2, 3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations1: computer simulation and Metabolic Control Analysis","volume":"342","author":"PJ Mulquiney","year":"1999","journal-title":"Biochemical Journal"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/1742-4682-2-18","article-title":"Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition","volume":"2","author":"Y Nakayama","year":"2005","journal-title":"Theor Biol Med Model"},{"issue":"4","key":"ref20","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.cels.2015.10.003","article-title":"Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics","volume":"1","author":"A Bordbar","year":"2015","journal-title":"Cell Systems"},{"issue":"2","key":"ref21","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/j.bpj.2009.09.064","article-title":"Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models","volume":"98","author":"N Jamshidi","year":"2010","journal-title":"Biophysical Journal"},{"issue":"1","key":"ref22","article-title":"Evaluation of rate law approximations in bottom-up kinetic models of metabolism","volume":"10","author":"B Du","year":"2016","journal-title":"BMC Systems Biology"},{"key":"ref23","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511736179","article-title":"Systems Biology: Simulation of Dynamic Network States","author":"BO Palsson","year":"2011"},{"issue":"2","key":"ref24","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1002\/j.1538-7305.1938.tb00429.x","article-title":"Variable equalizers","volume":"17","author":"HW Bode","year":"1938","journal-title":"The Bell System Technical Journal"},{"issue":"4","key":"ref25","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1109\/37.526916","article-title":"Phase-root locus and relative stability","volume":"16","author":"TJ Cavicehi","year":"1996","journal-title":"IEEE Control Systems Magazine"},{"issue":"7558","key":"ref26","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1038\/nature14405","article-title":"Structures of human phosphofructokinase-1 and atomic basis of cancer-associated mutations","volume":"523","author":"BA Webb","year":"2015","journal-title":"Nature"},{"issue":"13","key":"ref27","doi-asserted-by":"crossref","first-page":"3239","DOI":"10.1016\/S0021-9258(18)95956-9","article-title":"Adenosine triphosphate conservation in metabolic regulation rat liver citrate cleavage enzyme","volume":"242","author":"DE Atkinson","year":"1967","journal-title":"Journal of Biological Chemistry"},{"issue":"11","key":"ref28","doi-asserted-by":"crossref","first-page":"4041","DOI":"10.1021\/bi00851a035","article-title":"Interaction between energy charge and metabolite modulation in the regulation of enzymes of amphibolic sequences. Phosphofructokinase and pyruvate dehydrogenase","volume":"7","author":"L Shen","year":"1968","journal-title":"Biochemistry"},{"key":"ref29","article-title":"Biochemistry (Chapters 1-34)","author":"JM Berg","year":"2002"},{"issue":"8","key":"ref30","doi-asserted-by":"crossref","DOI":"10.1515\/hsz-2013-0130","article-title":"Structure and allosteric regulation of eukaryotic 6-phosphofructokinases","volume":"394","author":"T Sch\u00f6neberg","year":"2013","journal-title":"Biological Chemistry"},{"issue":"1","key":"ref31","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1111\/j.1365-2141.2005.05527.x","article-title":"Red cell pyruvate kinase deficiency: molecular and clinical aspects","volume":"130","author":"A Zanella","year":"2005","journal-title":"British Journal of Haematology"},{"issue":"1","key":"ref32","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/S0022-2836(65)80285-6","article-title":"On the nature of allosteric transitions: A plausible model","volume":"12","author":"J Monod","year":"1965","journal-title":"Journal of Molecular Biology"},{"issue":"4","key":"ref33","first-page":"H1562","article-title":"Theoretical model of metabolic blood flow regulation: roles of ATP release by red blood cells and conducted responses","volume":"295","author":"JC Arciero","year":"2008","journal-title":"AJP: Heart and Circulatory Physiology"},{"issue":"43","key":"ref34","doi-asserted-by":"crossref","first-page":"16432","DOI":"10.1073\/pnas.0805779105","article-title":"Dynamics of shear-induced ATP release from red blood cells","volume":"105","author":"J Wan","year":"2008","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"1","key":"ref35","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1002\/ddr.10194","article-title":"Critical ATP parameters associated with blood and mammalian cells: Relevant measurement techniques","volume":"59","author":"EH Abraham","year":"2003","journal-title":"Drug Development Research"},{"issue":"39","key":"ref36","doi-asserted-by":"crossref","first-page":"8264","DOI":"10.1021\/bi201284u","article-title":"The original Michaelis constant: translation of the 1913 Michaelis-Menten paper","volume":"50","author":"L Michaelis","year":"2011","journal-title":"Biochemistry"},{"issue":"1","key":"ref37","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/S0968-0004(00)01699-6","article-title":"PFK-2\/FBPase-2: maker and breaker of the essential biofactor fructose-2,6-bisphosphate","volume":"26","author":"DA Okar","year":"2001","journal-title":"Trends Biochem Sci"},{"issue":"1","key":"ref38","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/S0021-9258(19)45782-7","article-title":"Studies on factors influencing enzyme responses to adenylate energy charge","volume":"247","author":"DL Purich","year":"1972","journal-title":"J Biol Chem"},{"issue":"2","key":"ref39","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1109\/TAC.1981.1102603","article-title":"Feedback and optimal sensitivity: Model reference transformations, multiplicative seminorms, and approximate inverses","volume":"26","author":"G Zames","year":"1981","journal-title":"IEEE Transactions on Automatic Control"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1038\/msb4100186","article-title":"The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks","volume":"3","author":"S Grimbs","year":"2007","journal-title":"Mol Syst Biol"},{"issue":"9","key":"ref41","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1002\/biot.201300091","article-title":"Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints","volume":"8","author":"A Chakrabarti","year":"2013","journal-title":"Biotechnol J"},{"issue":"2","key":"ref42","doi-asserted-by":"crossref","first-page":"e1005396","DOI":"10.1371\/journal.pcbi.1005396","article-title":"Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli","volume":"13","author":"P Millard","year":"2017","journal-title":"PLOS Computational Biology"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.ymben.2014.03.007","article-title":"Kinetic models in industrial biotechnology\u2014Improving cell factory performance","volume":"24","author":"J Almquist","year":"2014","journal-title":"Metabolic Engineering"},{"issue":"9","key":"ref44","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1002\/biot.201400522","article-title":"Constructing kinetic models of metabolism at genome-scales: A review","volume":"10","author":"S Srinivasan","year":"2015","journal-title":"Biotechnol J"},{"issue":"8","key":"ref45","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1110\/ps.03259908","article-title":"Allostery and cooperativity revisited","volume":"17","author":"Q Cui","year":"2008","journal-title":"Protein Sci"},{"key":"ref46","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-662-44562-4","article-title":"Analysis of Kinetic Reaction Mechanisms","author":"T Tur\u00e1nyi","year":"2014"},{"key":"ref47","unstructured":"Wolfram Research Inc. Mathematica 11.1; 2017. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.wolfram.com\" xlink:type=\"simple\">http:\/\/www.wolfram.com<\/ext-link>."},{"issue":"4","key":"ref48","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1042\/bj0580622","article-title":"A Study of the Metabolism of Phosphorus in Mammalian Red Cells","volume":"58","author":"TAJ Prankerd","year":"1954","journal-title":"Biochemical Journal"},{"issue":"2","key":"ref49","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1042\/bj3050405","article-title":"Kinetics of the cooperative binding of glucose to dimeric yeast hexokinase PI","volume":"305","author":"JG Hoggett","year":"1995","journal-title":"Biochemical journal"},{"issue":"D1","key":"ref50","doi-asserted-by":"crossref","first-page":"D770","DOI":"10.1093\/nar\/gkr874","article-title":"eQuilibrator\u2014the biochemical thermodynamics calculator","volume":"40","author":"A Flamholz","year":"2011","journal-title":"Nucleic Acids Research"},{"key":"ref51","unstructured":"Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, et al. Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0. ArXiv e-prints. 2017;."},{"issue":"4","key":"ref52","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1021\/ac60052a025","article-title":"Simplified Statistics for Small Numbers of Observations","volume":"23","author":"RB Dean","year":"1951","journal-title":"Analytical Chemistry"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006356","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,8,17]],"date-time":"2018-08-17T00:00:00Z","timestamp":1534464000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006356","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,28]],"date-time":"2022-08-28T18:04:43Z","timestamp":1661709883000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006356"}},"subtitle":[],"editor":[{"given":"Jens","family":"Nielsen","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,8,7]]},"references-count":52,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2018,8,7]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006356","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/227058","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,8,7]]}}}