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Imaging Spatial Reorganization of a MAPK Signaling Pathway Using the Tobacco Transient Expression System
Published on: March 20, 2016
Spatio-temporal correlations can drastically change the response of a MAPK pathway
Koichi Takahashi1, Sorin Tanase-Nicola, Pieter Rein ten Wolde
1Advanced Sciences Institute, RIKEN, 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan. ktakahashi@riken.jp
Abstract:
Multisite covalent modification of proteins is omnipresent in eukaryotic cells. A well-known example is the mitogen-activated protein kinase (MAPK) cascade where, in each layer of the cascade, a protein is phosphorylated at two sites. It has long been known that the response of a MAPK pathway strongly depends on whether the enzymes that modify the protein act processively or distributively. A distributive mechanism, in which the enzyme molecules have to release the substrate molecules in between the modification of the two sites, can generate an ultrasensitive response and lead to hysteresis and bistability. We study by Green's Function Reaction Dynamics (GFRD), a stochastic scheme that makes it possible to simulate biochemical networks at the particle level in time and space, a dual phosphorylation cycle in which the enzymes act according to a distributive mechanism. We find that the response of this network can differ dramatically from that predicted by a mean-field analysis based on the chemical rate equations. In particular, rapid rebindings of the enzyme molecules to the substrate molecules after modification of the first site can markedly speed up the response and lead to loss of ultrasensitivity and bistability. In essence, rapid enzyme-substrate rebindings can turn a distributive mechanism into a processive mechanism. We argue that slow ADP release by the enzymes can protect the system against these rapid rebindings, thus enabling ultrasensitivity and bistability.
Insights
Enzyme action in dual phosphorylation cycles can be processive or distributive. Rapid enzyme-substrate rebindings can unexpectedly convert distributive mechanisms into processive ones, altering cellular responses.
Area of Science:
- Biochemistry
- Systems Biology
- Biophysics
Background:
- Multisite protein modification is crucial in eukaryotic cells, exemplified by mitogen-activated protein kinase (MAPK) cascades.
- Enzyme mechanism (processive vs. distributive) significantly impacts MAPK pathway response, with distributive mechanisms potentially causing ultrasensitivity, hysteresis, and bistability.
Purpose of the Study:
- To investigate the stochastic dynamics of a dual phosphorylation cycle with distributive enzyme mechanisms using Green's Function Reaction Dynamics (GFRD).
- To compare particle-level simulations with mean-field predictions for understanding ultrasensitivity and bistability in these systems.
Main Methods:
- Utilized Green's Function Reaction Dynamics (GFRD), a particle-level stochastic simulation scheme.
- Analyzed a dual phosphorylation cycle model where enzymes operate distributively.
Main Results:
- GFRD simulations revealed that the network's response can deviate significantly from mean-field predictions.
- Rapid enzyme-substrate rebindings after initial modification can accelerate the response, diminishing ultrasensitivity and bistability.
- These rapid rebindings effectively transform a distributive mechanism into a processive one.
Conclusions:
- Stochastic effects, particularly rapid rebindings, are critical in determining the behavior of distributive enzyme mechanisms in dual phosphorylation cycles.
- Slow ADP release by enzymes may be a regulatory mechanism to prevent rapid rebindings, thereby preserving ultrasensitivity and bistability.
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