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Commit bfdf613b authored by Zhefu Li's avatar Zhefu Li
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<h2>Ordinary Differential Equation of the signal transduction of the yeast MAPK pathway</h2>
<h3>Model Description</h3>
<p>In our project, we express the musk ketone receptor (GPCR) on the yeast cell membrane. After a
certain concentration of musk ketone diffuses into the intestine and binds to the receptor, it
<p>In our project, we express the muscone receptor (GPCR) on the yeast cell membrane. After a
certain concentration of muscone diffuses into the intestine and binds to the receptor, it
activates the receptor, which in turn activates the G protein. The G protein dissociates into α and
βγ subunits, with the βγ subunit releasing and activating Ste20 and the scaffold protein Ste5. Ste5
can undergo oligomerization and other behaviors, recruiting Ste11, Ste7, and Fus3 near the plasma
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LahA, which expresses lactate dehydrogenase LDH, catalyzing the conversion of pyruvate to lactate.
This model simulates the changes in the concentrations and phosphorylation states of molecules in
the signaling transduction pathway by writing out chemical reactions and converting them into
ordinary differential equations, in order to obtain the quantitative relationship between musk
ketone activation and lactate secretion. The model includes the following main processes:</p>
ordinary differential equations, in order to obtain the quantitative relationship between muscone
activation and lactate secretion. The model includes the following main processes:</p>
<ol>
<li><strong>Activation of Musk Ketone Receptor</strong>: The musk ketone receptor Ste2, derived from
<li><strong>Activation of Muscone Receptor</strong>: The muscone receptor Ste2, derived from
mouse olfactory epithelium, is a G protein-coupled receptor (GPCR) that is expressed on the cell
membrane and receives signals. Its domains consist of α, β, and γ, where the Gα subunit is
called Gpa1, and the Gα and Gγ subunits are Ste4 and Ste18, respectively, both anchored in the
cell membrane, without discussing the scenario of their separation. After binding with musk
ketone, Gpa1 will release Ste4-Ste18.</li>
cell membrane, without discussing the scenario of their separation. After binding with muscone,
Gpa1 will release Ste4-Ste18.</li>
<li><strong>Formation of Scaffold</strong>: The released Ste4-Ste18 can bind to Ste5, and the Ste5
protein can undergo dimerization, oligomerization, and other behaviors, forming a scaffold near
the cell membrane and recruiting proteins related to the cascade phosphorylation.</li>
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</ol>
<h3>Basic Assumptions</h3>
<ol>
<li>Since the model only simulates the signal transduction shortly after musk ketone activation, it
<li>Since the model only simulates the signal transduction shortly after muscone activation, it
does not consider protein synthesis and degradation, assuming that the concentrations of each
protein remain stable during this time.</li>
<li>It is assumed that all proteins involved in the cascade reaction have the same dephosphorylation
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</ol>
<h3>Model Equations</h3>
<h4>Activation of Musk Ketone Receptor</h4>
<h4>Activation of muscone Receptor</h4>
<strong>Reactions</strong>:
<div>
<p>
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</div>
<h2>Explanation</h2>
<p>
After Ste2 binds with musk ketone, it interacts with the G protein, causing the exchange of GDP
After Ste2 binds with muscone, it interacts with the G protein, causing the exchange of GDP
bound to the G protein with GTP in the cytoplasm, releasing Ste4 and Ste18. After Gpa1 catalyzes the
conversion of GTP to GDP, it can return to the cytoplasm and rebind, forming a G protein trimer.
Since the original signaling pathway is the yeast pheromone signaling pathway, with the ligand being
the pheromone, this section uses Pheromone to represent the molecules that activate the receptor.
</p>
<h2>Ordinary Differential Equations</h2>
<div>
<p>
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