Team:Tsinghua/Modeling
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GuoQiangChen (Talk | contribs) |
GuoQiangChen (Talk | contribs) |
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by data fitting, we would like to know how Q protein regulates Pr' promoter quantitativly | by data fitting, we would like to know how Q protein regulates Pr' promoter quantitativly | ||
- | + | = '''Naked Plasmid Vector Production''' = | |
One of our team's sub project is the use nakes plasmid bound with a specified protein as the vector of gene therapy DNA. The normal replication process of plasmid will be disrupted due to the binding of specified protein(in our model,lambda repressor). If the protein has a high affinity with the plasmid we will have more fraction of plasmid protein complex however with less plasmid substrates. Considering production of the plasmid protein complex, we want to maxize the amounts of plasmid protein complex, so a balance between the amounts of plasmid and protein is needed. In this model, we want to find out the optimized parameters for this plasmid vector production process. | One of our team's sub project is the use nakes plasmid bound with a specified protein as the vector of gene therapy DNA. The normal replication process of plasmid will be disrupted due to the binding of specified protein(in our model,lambda repressor). If the protein has a high affinity with the plasmid we will have more fraction of plasmid protein complex however with less plasmid substrates. Considering production of the plasmid protein complex, we want to maxize the amounts of plasmid protein complex, so a balance between the amounts of plasmid and protein is needed. In this model, we want to find out the optimized parameters for this plasmid vector production process. | ||
<h3>Reaction kinetics </h3> | <h3>Reaction kinetics </h3> | ||
- | + | == Dimmer formation and dissociation between λ rep-fiber == | |
*[[Image:Eqn8.gif]] | *[[Image:Eqn8.gif]] | ||
parameters: | parameters: | ||
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<br> | <br> | ||
- | + | ==DNA protein complex’s binding and dissociation is a dynamical process == | |
*[[Image:Eqn1.gif]] | *[[Image:Eqn1.gif]] | ||
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Gibbs free energy. We give all the three unbinding rate of cI dimer from three kinds of binding sites to find out the best site we want to use in the experiment. | Gibbs free energy. We give all the three unbinding rate of cI dimer from three kinds of binding sites to find out the best site we want to use in the experiment. | ||
- | + | ==The replication and degration of plasmid== | |
The plasmid is considered to replicate in a constant rate (''r'') without the interference of binding protein. Here the parameter ''r<sub>eff</sub>'' means the actual replicating rate of plasmid taken the binding protein into consideration. | The plasmid is considered to replicate in a constant rate (''r'') without the interference of binding protein. Here the parameter ''r<sub>eff</sub>'' means the actual replicating rate of plasmid taken the binding protein into consideration. | ||
<br> | <br> | ||
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The half-life of widetype λ repressor is 60 mins (10), however, with degradation tag, it could be as short as 4 min (11). | The half-life of widetype λ repressor is 60 mins (10), however, with degradation tag, it could be as short as 4 min (11). | ||
- | + | ==REFERRENCE == | |
[1] Burz, D.S., et al., ''Self-assembly of bacteriophage lambda cI repressor: effects of single-site mutations on the monomer-dimer equilibrium.'' Biochemistry, 1994. '''33'''(28): p. 8399-405. | [1] Burz, D.S., et al., ''Self-assembly of bacteriophage lambda cI repressor: effects of single-site mutations on the monomer-dimer equilibrium.'' Biochemistry, 1994. '''33'''(28): p. 8399-405. | ||
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[12] Brendel, V. and A.S. Perelson, Quantitative model of ColE1 plasmid copy number control. J Mol Biol, 1993. 229(4): p. 860-72. | [12] Brendel, V. and A.S. Perelson, Quantitative model of ColE1 plasmid copy number control. J Mol Biol, 1993. 229(4): p. 860-72. | ||
<h3>The amount of plasmid protein complex for a set of parameters </h3> | <h3>The amount of plasmid protein complex for a set of parameters </h3> | ||
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== Headline text == | == Headline text == |
Revision as of 15:51, 14 October 2009
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