ERK as a Model for Systems Biology of Enzyme Kinetics in Cells

Abstract

A key step towards a chemical picture of enzyme catalysis was taken in 1913, when Leonor Michaelis and Maud Menten published their studies of sucrose hydrolysis by invertase. Based on a novel experimental design and a mathematical model, their work offered a quantitative view of biochemical kinetics well before the protein nature of enzymes was established and complexes with substrates could be detected. Michaelis-Menten kinetics provides a solid framework for enzyme kinetics in vitro, but what about kinetics in cells, where enzymes can be highly regulated and participate in a multitude of interactions? We discuss this question using the Extracellular Signal Regulated Kinase (ERK) as a model of an important enzyme for which we have crystal structures, quantitative in vitro assays, and a vast list of binding partners. Despite great progress, we still cannot quantitatively predict how the rates of ERK-dependent reactions respond to genetic and pharmacological perturbations. Achieving this goal, which is important from both fundamental and practical standpoints, requires measuring the rates of enzyme reactions in their native environment and interpreting these measurements using simple but realistic mathematical models, the two elements which served as the cornerstones for the seminal 1913 paper.

Paradoxical Results in Perturbation-Based Signaling Network Reconstruction

“…Approaches that are more sophisticated are called upon, in order to address the pitfalls of perturbation techniques, which may, by themselves, lead to false conclusions. Seriously erroneous conclusions may derive from considering only discrete classes of connections while ignoring the intricate nonlinear mechanisms underlying processes such as phosphorylation (17,46,47).…”

“…This comprises a set of phosphorylation/dephosphorylation covalent modification cycles found in all eukaryotes (11)(12)(13)(14)(15)(16)(17), and is involved in the regulation of proliferation, gene expression, differentiation, mitosis, cell survival, apoptosis, and other processes (18). Our rationale for testing our ideas on an in vitro system is that, if a method fails there, there is no justification for believing that it will work in a more complicated in vivo context.…”

Mapping the binding interface of ERK and transcriptional repressor Capicua using photocrosslinking

“…Both of these effects rely on the extracellular signal-regulated kinase (ERK), an enzyme that is phosphorylated and activated in response to signaling by RTKs and mediates their transcriptional effects in a wide range of developmental contexts (10). In addition to being regulated by ERK signaling, Cic can control the levels of ERK phosphorylation in vivo (11).…”

MAP Kinase Modules: The Excursion Model and the Steps that Count

“…Signal-to-output studies in cells (17,18), as well as potential mathematical models (12,(19)(20)(21), have been reviewed. Here we review more recent data and attempt to integrate conclusions from diverse approaches.…”