Team:Tsinghua/Modeling

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====DNA protein complex’s binding and separating is a dynamical process ====
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====DNA protein complex’s binding and dissociation is a dynamical process ====
*[[Image:Eqn1.gif]]
*[[Image:Eqn1.gif]]
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parameters:
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'''k'''<sub>on</sub> =0.021/sec binding rate of dimers to DNA
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'''k'''<sub>off1</sub> =0.04/sec  unbinding rate of cI dimer from Or1
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'''k'''<sub>off1</sub> =1.026/sec unbinding rate of cI dimer from Or2
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'''k'''<sub>off1</sub> =5.197/sec unbinding rate of cI dimer from Or3
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Note:we get these values from ref(1). In (1) authers estimate these values from experimentally measured protein diffusion coefficient in ''e.coli'' and Gibbs free energy
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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.
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====The replication and degration of plasmid====
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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.
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Revision as of 23:54, 6 August 2009

Home The Team The Project Protocols Parts Modeling Notebook Brainstorming

Contents

Introduction

Phage production in E.coli

Naked Plasmid Vector Production

One of our team's sub project is the use nakes plasmid binded with a specified protein as the vector of gene therapy DNA. The normal replication process of plasmid will be changed due to the binding of specified protein(in our model,lambda repressor). 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.

Reaction kinetics

Dimmer formation and dissociation between λ cI repressor protein

  • Eqn8.gif

parameters:

kdon =0.05/(M*sec) (Burz et al. (1994); Shea and Ackers (1985) )
kdoff =0.5/sec

Notes:

DNA protein complex’s binding and dissociation is a dynamical process

  • Eqn1.gif


parameters:

kon =0.021/sec binding rate of dimers to DNA
                      
koff1 =0.04/sec  unbinding rate of cI dimer from Or1
koff1 =1.026/sec unbinding rate of cI dimer from Or2
koff1 =5.197/sec unbinding rate of cI dimer from Or3

Note:we get these values from ref(1). In (1) authers estimate these values from experimentally measured protein diffusion coefficient in e.coli and Gibbs free energy

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 reff means the actual replicating rate of plasmid taken the binding protein into consideration.

  • Eqn3.gif


The transcription of λ cI repressor, notice that λ cI repressor is coded in the plasmid, so the copy number of plasmid will affect the amount of λ cI repressor.

  • Eqn4.gif

The translation of λ repressor

  • Eqn5.gif


Plasmid-protein complex affect plasmid replication

If a replication is already initiated but when the replication forks meet a lamda protein on the way, this replication will be aborted. So only when replication forks pass the protein binding point without lamda protein there, the replication processes are effective. This is a simplified model on how plasmid-protein complex affect plasmid replication, we will try to find out some more detailed mechanisms in the future. The probability of a plasmid to become a protein-DNA complex is:

  • Eqn6.gif

Because of the DNA-protein complex, the effective replication rate of plasmid is

  • Eqn7.gif

The amount of plasmid protein complex for a set of parameters

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