Toward cell circuitry: Topological analysis of enzyme reaction networks via reaction route graphs |
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Authors: | Ravindra Datta Saurabh A Vilekar James P Dittami |
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Institution: | a Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609, United States b Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01609, United States |
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Abstract: | The first step toward developing complete cell circuitry is to build quantitative networks for enzyme reactions. The conventional King-Altman-Hill (KAH) algorithm for topological analysis of enzyme networks, adapted from electrical networks, is based on “Reaction Graphs” that, unlike electrical circuits, are not quantitative, being straightforward renderings of conventional schematics of reaction mechanisms. Therefore, we propose the use of “Reaction Route (RR) Graphs” instead, as a more suitable graph-theoretical representation for topological analysis of enzyme reaction networks. The RR Graphs are drawn such that they are not only useful for visualizing the various reaction routes or pathways, but unlike Reaction Graphs possess network properties consistent with requisite kinetic, mass balance, and thermodynamic constraints. Therefore, they are better than the conventional Reaction Graphs for topological representation and analysis of enzyme reactions, both via the KAH methodology as well as via numerical matrix inversion. The difference between the two is highlighted based on the example of a single enzyme reaction network for the conversion of 7,8-dihydrofolate and NADPH into 5,6,7,8-tetrahydrofolate and NADP+, catalyzed by the enzyme dihydrofolate reductase. |
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Keywords: | King-Altman-Hill method Reaction graphs Reaction route graphs Enzyme kinetics Quasi-steady-state kinetics |
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