title: Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements.
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 kmax(vivo), the observed maximal catalytic rate of an enzyme inside cells. Comparison with kcat values from Escherichia coli, yields a correlation ofr(2)= 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 kmax(vivo) 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.
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;
authors.forename: Dan
authors.initials: D
authors.lastname: Davidi
authors.affiliation: Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland;
authors.forename: Elad
authors.initials: E
authors.lastname: Noor
authors.affiliation: Institut für Biochemie, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany;
authors.forename: Wolfram
authors.initials: W
authors.lastname: Liebermeister
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
authors.forename: Arren
authors.initials: A
authors.lastname: Bar-Even
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720;
authors.forename: Avi
authors.initials: A
authors.lastname: Flamholz
authors.affiliation: Theoretical Biophysics, Humboldt-Universität zu Berlin, 10115 Berlin, Germany;
authors.forename: Katja
authors.initials: K
authors.lastname: Tummler
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;
authors.forename: Uri
authors.initials: U
authors.lastname: Barenholz
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;
authors.forename: Miki
authors.initials: M
authors.lastname: Goldenfeld
authors.affiliation: Department of Computer Science, Technion, Haifa 32000, Israel.
authors.forename: Tomer
authors.initials: T
authors.lastname: Shlomi
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel; ron.milo@weizmann.ac.il.
authors.forename: Ron
authors.initials: R
authors.lastname: Milo
mesh_terms: D002384:Catalysis; D004798:Enzymes / Q000378:metabolism*
chemical_list: D004798:Enzymes
keywords: flux balance analysis; kcat; kinetic constants; proteomics; turnover number