how to obtain Keff for metabolic enzymes

SBRG / ecolime

Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression

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how to obtain Keff for metabolic enzymes #20

Open weif000 opened 4 years ago

weif000 commented 4 years ago

Hi，I want to build other organism genome-model of metabolism and expression (ME-model). I don’t know how to obtain accurate effective turnover rate (Keff) for metabolic enzymes. When you reconstructed E.coli ME-model, how did you get the Keff for each enzyme. Thank you!

coltonlloyd commented 4 years ago

Hello,

Most of the keffs for metabolic enzymes were currently found using a machine learning-based approach outlined in (https://www.nature.com/articles/s41467-018-07652-6). However, depending on the organism, it may not be a horrible assumption to assume that homologous enzymes have similar turnover rates (at least within an order of magnitude).

Colton