Team:NYMU-Taipei/Model
FRET Ratio Model
Background
This model aims to find out how much FRET protein should be added into our screening system.
Methods
Chemical equilibrium is used to determine the fluorescence level and the minimal FRET protein activity required to produce the fluorescence that can be detected. This model assumes the portion of active protein in all protein is constant.
Results
Conclusion
The optimal ratio of the amount of one FRET protein to that of the other is the following:
The figures in the table indicates the optimal ratio of the protein on the top over the protein on the left.
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FRET Efficiency Model
Background
The efficiency of FRET is inversely proportional to the sixth power of the distance between donor and acceptor, making FRET extremely sensitive to small changes in distance. Therefore, simulating structure of protein-protein interactions is important. This model aims to predict the FRET efficiency in order to determine which molecules and which terminals should be used.
Methods
pyDockWEB is used for structural prediction of protein-protein interactions and the prediction of distances between donor and acceptor. Förster theory is used determine the FRET efficiency.
Results
Conclusion
The FRET efficiency is given by the following table.
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mCherry Expression Model
[1]
Background
This project constructs a plasmid that connects DKK1 promoter to mCherry. The gene expression rate of DKK1 promoter is affected by testosterone activity and affects the expression level of mCherry. The expression level of mCherry should be greater than a threshold so that its fluorescence can be detected by devices. In order to achieve this threshold, sufficient amount of testosterone should be added into our screening system; this is the sensitivity of our screening system. This model aims to find out the sensitivity of our screening system.
Methods
This model simulates the kinetics of transcription signal the expression of DKK1 promoter. The process of protein synthesis is simulated with differential equations, assuming the synthesis of mCherry follows the central dogma of molecular biology. Signaling pathways of the androgen receptor is modeled based on chemical equilibrium of each transcription factor and intermediate. Fluorescence decay is not considered in this model because ……..
Results
[DKK1] = 5 + 0.006 [DHT]^2
where [DKK1] indicate activity in ng/ml and [DHT] indicates activity in nM.
Conclusion
[mCherry] = c_1 + c_2 [Testosterone]^2
where square brackets indicate activity in M, and c_1 and c_2 are constants to be determined.
Note: This model is accurate only when [DHT] is less than 50 nM.
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References
- Meehan KL1, Sadar MD. (2003). "Androgens and androgen receptor in prostate and ovarian malignancies." Front Biosci. 2003 May 1;8:d780-800.
- Jiménez-García B, Pons C, Fernández-Recio J. (2013). "pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring." Bioinformatics. 2013 Jul 1;29(13):1698-9. doi: 10.1093/bioinformatics/btt262. Epub 2013 May 9.