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Zhefu Li
Tsinghua
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bfdf613b
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bfdf613b
authored
7 months ago
by
Zhefu Li
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<h2>
Ordinary Differential Equation of the signal transduction of the yeast MAPK pathway
</h2>
<h2>
Ordinary Differential Equation of the signal transduction of the yeast MAPK pathway
</h2>
<h3>
Model Description
</h3>
<h3>
Model Description
</h3>
<p>
In our project, we express the mus
k ket
one receptor (GPCR) on the yeast cell membrane. After a
<p>
In our project, we express the mus
c
one receptor (GPCR) on the yeast cell membrane. After a
certain concentration of mus
k ket
one diffuses into the intestine and binds to the receptor, it
certain concentration of mus
c
one 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
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
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
can undergo oligomerization and other behaviors, recruiting Ste11, Ste7, and Fus3 near the plasma
...
@@ -467,15 +467,15 @@
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@@ -467,15 +467,15 @@
LahA, which expresses lactate dehydrogenase LDH, catalyzing the conversion of pyruvate to lactate.
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
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
the signaling transduction pathway by writing out chemical reactions and converting them into
ordinary differential equations, in order to obtain the quantitative relationship between mus
k
ordinary differential equations, in order to obtain the quantitative relationship between mus
cone
ketone
activation and lactate secretion. The model includes the following main processes:
</p>
activation and lactate secretion. The model includes the following main processes:
</p>
<ol>
<ol>
<li><strong>
Activation of Mus
k Ket
one Receptor
</strong>
: The mus
k ket
one receptor Ste2, derived from
<li><strong>
Activation of Mus
c
one Receptor
</strong>
: The mus
c
one receptor Ste2, derived from
mouse olfactory epithelium, is a G protein-coupled receptor (GPCR) that is expressed on the cell
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
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
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 mus
k
cell membrane, without discussing the scenario of their separation. After binding with mus
cone,
ketone,
Gpa1 will release Ste4-Ste18.
</li>
Gpa1 will release Ste4-Ste18.
</li>
<li><strong>
Formation of Scaffold
</strong>
: The released Ste4-Ste18 can bind to Ste5, and the Ste5
<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
protein can undergo dimerization, oligomerization, and other behaviors, forming a scaffold near
the cell membrane and recruiting proteins related to the cascade phosphorylation.
</li>
the cell membrane and recruiting proteins related to the cascade phosphorylation.
</li>
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@@ -490,7 +490,7 @@
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@@ -490,7 +490,7 @@
</ol>
</ol>
<h3>
Basic Assumptions
</h3>
<h3>
Basic Assumptions
</h3>
<ol>
<ol>
<li>
Since the model only simulates the signal transduction shortly after mus
k ket
one activation, it
<li>
Since the model only simulates the signal transduction shortly after mus
c
one activation, it
does not consider protein synthesis and degradation, assuming that the concentrations of each
does not consider protein synthesis and degradation, assuming that the concentrations of each
protein remain stable during this time.
</li>
protein remain stable during this time.
</li>
<li>
It is assumed that all proteins involved in the cascade reaction have the same dephosphorylation
<li>
It is assumed that all proteins involved in the cascade reaction have the same dephosphorylation
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@@ -500,7 +500,7 @@
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@@ -500,7 +500,7 @@
</ol>
</ol>
<h3>
Model Equations
</h3>
<h3>
Model Equations
</h3>
<h4>
Activation of
M
us
k Ket
one Receptor
</h4>
<h4>
Activation of
m
us
c
one Receptor
</h4>
<strong>
Reactions
</strong>
:
<strong>
Reactions
</strong>
:
<div>
<div>
<p>
<p>
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@@ -518,13 +518,14 @@
...
@@ -518,13 +518,14 @@
</div>
</div>
<h2>
Explanation
</h2>
<h2>
Explanation
</h2>
<p>
<p>
After Ste2 binds with mus
k ket
one, it interacts with the G protein, causing the exchange of GDP
After Ste2 binds with mus
c
one, 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
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.
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
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.
the pheromone, this section uses Pheromone to represent the molecules that activate the receptor.
</p>
</p>
<h2>
Ordinary Differential Equations
</h2>
<h2>
Ordinary Differential Equations
</h2>
<div>
<div>
<p>
<p>
...
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