Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitrokcatmeasurements

Abstract

Turnover numbers, also known askcatvalues, are fundamental properties of enzymes. However,kcatdata are scarce and measured in vitro, thus may not faithfully represent the in vivo situation. A basic question that awaits elucidation is: how representative arekcatvalues for the maximal catalytic rates of enzymes in vivo? Here, we harness omics data to calculatekmaxvivo, the observed maximal catalytic rate of an enzyme inside cells. Comparison withkcatvalues fromEscherichia coli, yields a correlation ofr2= 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 betweenkmaxvivoandkcatvalues. 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.