Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements

Dan Davidi, Elad Noor, Wolfram Liebermeister, Arren Bar-Even, Avi Flamholz, Katja Tummler, Uri Barenholz, Miki Goldenfeld, Tomer Shlomi, Ron Milo

Research output: Contribution to journalArticlepeer-review

Abstract

Turnover numbers, also known as kcat values, are fundamental properties of enzymes. However, kcat data are scarce and measured in vitro, thus may not faithfully represent the in vivo situation. A basic question that awaits elucidation is: how representative are kcat values for the maximal catalytic rates of enzymes in vivo? Here, we harness omics data to calculate kvivomax, the observed maximal catalytic rate of an enzyme inside cells. Comparison with kcat values from Escherichia coli, yields a correlation of r2= 0.62 in log scale (p < 10−10), with a root mean square difference of 0.54 (3.5-fold in linear scale), indicating that in vivo and in vitro maximal rates generally concur. By accounting for the degree of saturation of enzymes and the backward flux dictated by thermodynamics, we further refine the correspondence between kvivomax and kcat values. The approach we present here characterizes the quantitative relationship between enzymatic catalysis in vitro and in vivo and offers a high-throughput method for extracting enzyme kinetic constants from omics data.
Original languageEnglish
Pages (from-to)3401–3406
Number of pages6
JournalPNAS
Volume113
Early online date7 Mar 2016
DOIs
StatePublished - 22 Mar 2016

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