Parameter

Value

Reasoning

Temp

Variable (default value of 37 Celsius)

The experiment can be carried out under various temperatures. Temperature affects the rate of intein splicing.

ppt

Variable (default value of 1000)

Parts per trillion of estrogen in the water you are testing.

rfp_copies

15 copies/cell

Number of rfp containing plasmids per cell.

int_copies

2984 copies/cell

Number of intein containing plasmids per cell.

estrogen_out

ppt * 5.6e-02 nM

Concentration of estrogen outside the cell.

estrogen_in

0 nM

Concentration of estrogen inside the cell. Since e. coli is a prokaryote assume it is 0 nM.

t7_intein

0 nM

Assume initial concentration of T7-Intein complex is 0 nM.

t7_estrogen_u

0 nM

Assume initial concentration of T7-Intein complex bound to estrogen is 0 nM.

t7_estrogen_s

0 nM

Assume initial concentration of spliced out Intein-Estrogen complex is 0 nM.

t7_nc

0 nM

Assume initial concentration of T7 polymerase is 0 nM.

plas_int

int_copies * 1.0e-03 nM

Concentration of T7-Intein plasmids.

plas_rfp

rfp_copies * 1.0e-03 nM

Concentration of T7-RFP plasmids.

t7_rfp

0 nM

Assume initial concentration of T7 bound to plasmid 2 is 0 nM.

mrna_rfp

0 nM

Assume initial concentration of mRNA RFP is 0 nM.

prot_rfp

0 nM

Assume initial concentration of protein RFP is 0 nM.

mrna_int

0 nM

Assume initial concentration of mRNA intein is 0 nM.

prot_yfp

0 nM

Assume initial concentration of protein YFP is 0 nM.

k_e

1.7e-02 s^-1

Rate at which estrogen diffuses through membrane. The diffusion coefficient of a steroid hormone in an aqueous phase = 10^-13 m²/s and the surface area of a bacteria is 6 * 10^-12 m². Thus (10^-13 m²/s) / (6 * 10 ^-12 m²) = 1.7e-02 s^-1

k_e_t7_on

1.3e-03 nM^-1s^-1

Rate at which estrogen binds to the intein. The intein is the human estrogen receptor, so the value is from the literature.

k_e_t7_off

1.2e-03 s^-1

Rate at which estrogen dissociates from the intein. Based on literature value of human estrogen receptor.

k_splice

7.1e-04 s^-1

Rate at which intein splices out. Based on literature values of other inteins’ splicing kinetics.

k_t7_rfp_on

3.3e-01 nM^-1s^-1

Rate at which T7 binds to the RFP plasmid. Value obtained from literature.

k_t7_rfp_off

1.0e-01 s^-1

Rate at which T7 dissociates from the RFP plasmid. Value obtained from literature.

k_rna_rfp

8.8e-01 nM s^-1

Rate at which mRNA is synthesized from RFP plasmid. From iGEM team PKU ’09.

k_rna_deg_rfp

4.3e-03 s^-1

Rate at which mRNA RFP degrades. From iGEM team PKU ’09.

k_prot_rfp

9.0e03 s^-1

Rate at which RFP protein is made. From iGEM team PKU ’09.

k_prot_deg_rfp

8.3e-04 s^-1

Rate at which RFP protein degrades. From iGEM team PKU ’09.

k_rna_int

2.6e-02 nM s^-1

Rate at which mRNA is synthesized from T7-Intein plasmid. From iGEM team PKU ’09.

k_rna_deg_int

4.3e-03 s^-1

Rate at which mRNA of T7-Intein degrades. From iGEM team PKU ’09.

k_prot_int

2.2e-03 s^-1

Rate at which T7-Intein is made from mRNA. From iGEM team PKU ’09.

k_prot_deg_int

9.7e-04

Rate at which T7 polymerase is degraded. From iGEM team PKU ’09.