{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:41:07Z","timestamp":1760708467978},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1490,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Metabolic engineering aims at modulating the capabilities of metabolic networks by changing the activity of biochemical reactions. The existing constraint-based approaches for metabolic engineering have proven useful, but are limited only to reactions catalogued in various pathway databases.<\/jats:p>\n               <jats:p>Results: We consider the alternative of designing synthetic strategies which can be used not only to characterize the maximum theoretically possible product yield but also to engineer networks with optimal conversion capability by using a suitable biochemically feasible reaction called \u2018stoichiometric capacitance\u2019. In addition, we provide a theoretical solution for decomposing a given stoichiometric capacitance over a set of known enzymatic reactions. We determine the stoichiometric capacitance for genome-scale metabolic networks of 10 organisms from different kingdoms of life and examine its implications for the alterations in flux variability patterns. Our empirical findings suggest that the theoretical capacity of metabolic networks comes at a cost of dramatic system's changes.<\/jats:p>\n               <jats:p>Contact: \u00a0larhlimi@mpimp-golm.mpg.de, or nikoloski@mpimp-golm.mpg.de<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary tables are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts381","type":"journal-article","created":{"date-parts":[[2012,9,7]],"date-time":"2012-09-07T20:35:22Z","timestamp":1347050122000},"page":"i502-i508","source":"Crossref","is-referenced-by-count":6,"title":["Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks"],"prefix":"10.1093","volume":"28","author":[{"given":"Abdelhalim","family":"Larhlimi","sequence":"first","affiliation":[{"name":"1 Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany"},{"name":"2 Bioinformatics, Max-Planck Institute for Molecular Plant Physiology, Am M\u00fchlenberg 1, D-14476 Potsdam, Germany"}]},{"given":"Georg","family":"Basler","sequence":"additional","affiliation":[{"name":"3 Systems Biology and Mathematical Modelling, Max-Planck Institute for Molecular Plant Physiology, Am M\u00fchlenberg 1, D-14476 Potsdam, Germany"}]},{"given":"Sergio","family":"Grimbs","sequence":"additional","affiliation":[{"name":"1 Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany"}]},{"given":"Joachim","family":"Selbig","sequence":"additional","affiliation":[{"name":"1 Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany"},{"name":"2 Bioinformatics, Max-Planck Institute for Molecular Plant Physiology, Am M\u00fchlenberg 1, D-14476 Potsdam, Germany"}]},{"given":"Zoran","family":"Nikoloski","sequence":"additional","affiliation":[{"name":"3 Systems Biology and Mathematical Modelling, Max-Planck Institute for Molecular Plant Physiology, Am M\u00fchlenberg 1, D-14476 Potsdam, Germany"}]}],"member":"286","published-online":{"date-parts":[[2012,9,3]]},"reference":[{"key":"2023012513065531100_B1","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1016\/j.biosystems.2012.04.007","article-title":"Optimizing metabolic pathways by screening for feasible synthetic reactions","volume":"109","author":"Basler","year":"2012","journal-title":"Biosystems"},{"key":"2023012513065531100_B2","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1471-2180-5-8","article-title":"Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation","volume":"5","author":"Becker","year":"2005","journal-title":"BMC Microbiol."},{"key":"2023012513065531100_B3","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1002\/bit.10803","article-title":"OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization","volume":"84","author":"Burgard","year":"2003","journal-title":"Biotechnol. 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