From 2009.igem.org

Blue Light Receptor: Modeling

Biological Model

Mathematical Model

*Parameter values (Vanillin Sensor)*
Name	Value	Comments	Reference
Degradation Rates
d_mRNA	2.3105E-3 s^-1		[3]
d_Proteins	1.9254E-5 s^-1		[4]
Transcription Rates
k_YcgF	0.0154 s^-1	Rate is faster than transcription rate of YcgE	[1]
k_YcgE	0.00848 s^-1	estimate	[1]
Translation Rates
k_YcgF	0.167s^-1	Rate is faster than transcription rate of YcgE	[5]
k_YcgE	0.167 s^-1	estimate	[5]
Dimerization Parameters
k_dimerization	8.0E-11 (s W/m^2)^-1	Rate of dimerization of YcgF	[1]
k_dissociation	0.0058 s^-1	Rate of dissociation of the YcgF complex	[2]
YcgF/YcgE Interaction
k_bind	100 (s molecule)^-1	Rate of binding of YcgF dimer to YcgE	[1]
k_unbind	1 s^-1	Rate of dissociation of the YcgF/YcgE complex	[1]

Simulation

The amount of produced RIBOKEY is positively correlated on the incident blue radiation. The build up of key in the begin period of is due to the relative slow build up of the active state of YcgF protein in compared to the build up of YcgE.

References

[1] Natalia Tschowri, Susan Busse and Regine Hengge, "The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli"

[2] Y. Nakasone et al., "Transient Dimerization and Conformational Change of a BLUF Protein: YcgF", Journal of the American Chemical Society, Apr. 2006

[3] J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, Jul. 2002, pp. 9697–9702

[4] K. Nath et al., “Protein degradation in Escherichia Coli,” The Journal of Biological Chemistry, vol. 246, Nov. 1971, pp. 6956-6967

[5] S.L. Gotta et al., “rRNA Transcription Rate in Escherichia Coli,” Journal of Bacteriology, vol. 173, Oct. 1991, pp. 6647-6649

Team:KULeuven/Modeling/Blue Light Receptor