Team:LCG-UNAM-Mexico:WTM
From 2009.igem.org
(Difference between revisions)
(→WILD-TYPE MOLECULAR MODEL) |
(→WILD-TYPE MOLECULAR MODEL) |
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<br>It has been shown that T7 genes are expressed in overlapped polycistronic mRNAs. | <br>It has been shown that T7 genes are expressed in overlapped polycistronic mRNAs. | ||
<br>Transcription of T7 polycistronic mRNAs occurs only if its coding DNA segment is available in the cell, for example early phage mRNAs are present before late mRNAs given that DNA responsible for them is inserted at early stages. | <br>Transcription of T7 polycistronic mRNAs occurs only if its coding DNA segment is available in the cell, for example early phage mRNAs are present before late mRNAs given that DNA responsible for them is inserted at early stages. | ||
+ | <br>We define a set of transcription rates for every polycistronic mRNA taking into account constant bacterial or T7 RNA polymerase elongation rates and the length of the polycistronic mRNA, these transcription rates would be our rate limiting steps. | ||
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* Translation of phage's mRNAs into proteins | * Translation of phage's mRNAs into proteins | ||
<br>In this model, translation is simulated assuming an environment of unlimited amino acids and ribosomes. We also assume that the rate at which ribosomes incorporate amino acids is constant over all T7 mRNA. | <br>In this model, translation is simulated assuming an environment of unlimited amino acids and ribosomes. We also assume that the rate at which ribosomes incorporate amino acids is constant over all T7 mRNA. | ||
- | <br> | + | <br> As it has been done for transcription here we define a set of translation rates for every protein taking into account a constant ribosome elongation rate and the length of the protein, these translation rates would be our rate limiting steps. |
- | + | ||
* T7 DNA replication | * T7 DNA replication | ||
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* Procapsid Assembly | * Procapsid Assembly | ||
<br>This phenomenon is simulated in almost the same way as Drew Endy et al. 1996 using mass action kinetics. | <br>This phenomenon is simulated in almost the same way as Drew Endy et al. 1996 using mass action kinetics. | ||
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* DNA packaging and final assembly | * DNA packaging and final assembly | ||
- | <br>Both processes are modeled using mass action kinetics as well. | + | <br>Both processes are modeled using mass action kinetics as well. This last step requires complete procapsids, T7 DNA, and enough of each structural protein to complete the phage. The simulation assumes that packaging of DNA into the procapsid is the rate-limiting step for T7 progeny formation. |
Revision as of 02:06, 18 October 2009