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Curr Biol. 2020 Mar 9;30(5):877-882.e6. doi: 10.1016/j.cub.2019.12.052. Epub 2020 Feb 13.

Inference of Multisite Phosphorylation Rate Constants and Their Modulation by Pathogenic Mutations.

Author information

1
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
2
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Engineering Quad, Princeton University, Princeton, NJ 08544, USA.
3
Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford OX2 6GG, UK.
4
Department of Mathematics, James College, Campus West, University of York, York YO10 5DD, UK.
5
Department of Epidemiology and Biostatistics, Imperial College London, Medical School Building, St Mary's Campus, Norfolk Place, London W2 1PG, UK; Department of Mathematics, South Kensington Campus, Imperial College London, London SW7 2AZ, UK.
6
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA; Flatiron Institute, Simons Foundation, New York, NY 10010, USA. Electronic address: stas@princeton.edu.
7
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA. Electronic address: wuhr@princeton.edu.

Abstract

Multisite protein phosphorylation plays a critical role in cell regulation [1-3]. It is widely appreciated that the functional capabilities of multisite phosphorylation depend on the order and kinetics of phosphorylation steps, but kinetic aspects of multisite phosphorylation remain poorly understood [4-6]. Here, we focus on what appears to be the simplest scenario, when a protein is phosphorylated on only two sites in a strict, well-defined order. This scenario describes the activation of ERK, a highly conserved cell-signaling enzyme. We use Bayesian parameter inference in a structurally identifiable kinetic model to dissect dual phosphorylation of ERK by MEK, a kinase that is mutated in a large number of human diseases [7-12]. Our results reveal how enzyme processivity and efficiencies of individual phosphorylation steps are altered by pathogenic mutations. The presented approach, which connects specific mutations to kinetic parameters of multisite phosphorylation mechanisms, provides a systematic framework for closing the gap between studies with purified enzymes and their effects in the living organism.

KEYWORDS:

Bayesian parameter inference; ERK; MAPK pathway; MEK; kinase; kinetic parameters; multisite protein phosphorylation; pathogenic mutations; phosphorylation; structurally identifiable kinetic model

PMID:
32059766
PMCID:
PMC7085240
[Available on 2021-03-09]
DOI:
10.1016/j.cub.2019.12.052

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