Team:UChile OpenBio-CeBiB/Model/Procedure

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Methodology


To achieve each one of the previous proposals, we will follow this methodology:

Equations

For this model, it is firstly necessary to determine the reactions involved in the Calvin cycle, which are available in databases. If you would like to see the equations, click the below.

  • Carbon Dioxide

$${d[CO_2] \over dt} = 0 .$$

  • Erythrose 4-Phosphate

$${d[E4P] \over dt} = {{V_{max}^{F6P \rightarrow E4P} \cdot [F6P]} \over {K_m^{F6P \rightarrow E4P} + [F6P]}} - {{V_{max}^{E4P \rightarrow Sed17P2} \cdot [E4P]} \over {K_m^{E4P \rightarrow Sed17P2} + [E4P]}} - k_{deg}^{E4P}[E4P] .$$

  • Sedoheptulose 1,7-Bisphosphatase

$${d[Sed1,7P2] \over dt} = {{V_{max}^{E4P \rightarrow Sed17P2} \cdot [E4P]} \over {K_m^{E4P \rightarrow Sed17P2} + [E4P]}} - {{V_{max}^{Sed17P2 \rightarrow Sed7P} \cdot [Sed1,7P2]} \over {K_m^{Sed17P2 \rightarrow Sed7P} + [Sed1,7P2]}} - k_{deg}^{Sed17P2}[Sed1,7P2] .$$

  • Sedoheptulose 7-Phosphate

$${d[Sed7P] \over dt} = {{V_{max}^{Sed17P2 \rightarrow Sed7P} \cdot [Sed1,7P2]} \over {K_m^{Sed17P2 \rightarrow Sed7P} + [Sed1,7P2]}} - {{V_{max}^{Sed7P \rightarrow R5P} \cdot [Sed7P]} \over {K_m^{Sed7P \rightarrow R5P} + [Sed7P]}} - k_{deg}^{Sed7P} [Sed7P] .$$

  • Ribose 5-Phosphate

$${d[R5P] \over dt} = {{V_{max}^{Sed7P \rightarrow R5P} \cdot [Sed7P]} \over {K_m^{Sed7P \rightarrow R5P} + [Sed7P]}} - {{V_{max}^{R5P \rightarrow Rul5P} \cdot [R5P]} \over {K_m^{R5P \rightarrow Rul5P} + [R5P]}} - k_{deg}^{R5}[R5P] .$$

  • Ribulose 5-Phosphate

$${d[Rul5P] \over dt} = {{V_{max}^{R5P \rightarrow Rul5P} \cdot [R5P]} \over {K_m^{R5P \rightarrow Rul5P} + [R5P]}} - {{V_{max}^{Rul5P \rightarrow Rul15P2} \cdot [Rul5P]} \over {K_m^{Rul5P \rightarrow Rul15P2} + [Rul5P]}} - k_{deg}^{Rul5P}[Rul5P] .$$

  • Ribulose 1,5-Bisphosphate

$${d[Rul1,5P2] \over dt} = {{V_{max}^{Rul5P \rightarrow Rul15P2} \cdot [Rul5P]} \over {K_m^{Rul5P \rightarrow Rul15P2} + [Rul5P]}} - {{ K_{cat,c} \cdot [CO_2] \cdot [Rul1,5P2] } \over { K_c \cdot {1 + { [CO_2] \over [K_c] } + { [O_2] \over [K_O] } } \cdot {[Rul15P2] + K_{aa}} } } - k_{deg}^{Rul15P2}[Rul1,5P2] .$$

  • Glycerate 3-phosphate

$${d[Gl3P] \over dt} = {{ K_{cat,c} \cdot [CO_2] \cdot [Rul1,5P2] } \over { K_c \cdot {1 + { [CO_2] \over [K_c] } + { [O_2] \over [K_O] } } \cdot {[Rul15P2] + K_{aa}} } } - {{V_{max}^{Gl3P \rightarrow Gl13P2} \cdot [Gl3P]} \over {K_m^{Gl3P \rightarrow Gl13P2} + [Gl3P]}} - k_{deg}^{Gl3P}[Gl3P] .$$

  • Glycerate 1,3-Bisphosphate

$${d[Gl1,3P2] \over dt} = {{V_{max}^{Gl3P \rightarrow Gl13P2} \cdot [Gl3P]} \over {K_m^{Gl3P \rightarrow Gl13P2} + [Gl3P]}} - {{V_{max}^{Gl13P2 \rightarrow GlAl3P} \cdot [Gl1,3P2]} \over {K_m^{Gl13P2 \rightarrow GlAl3P} + [Gl1,3P2]}} - k_{deg}^{Gl13P2}[Gl1,3P2] .$$

  • Glyceraldehyde 3-Phosphate

$${d[GlAl3P] \over dt} = {{V_{max}^{Gl13P2 \rightarrow GlAl3P} \cdot [Gl1,3P2]} \over {K_m^{Gl13P2 \rightarrow GlAl3P} + [Gl1,3P2]}} - {{V_{max}^{GlAl3P \rightarrow F16P2} \cdot [GlAl3P]} \over {K_m^{GlAl3P \rightarrow F16P2} + [GlAl3P]}} - k_{deg}^{GlAl3P}[GlAl3P] .$$

  • Fructose 1,6-Bisphosphatase

$${d[F1,6P2] \over dt} = {{V_{max}^{GlAl3P \rightarrow F16P2} \cdot [GlAl3P]} \over {K_m^{GlAl3P \rightarrow F16P2} + [GlAl3P]}} - {{V_{max}^{F16P2 \rightarrow F6P} \cdot [F1,6P2]} \over {K_m^{F16P2 \rightarrow F6P} + [F1,6P2]}} - k_{deg}^{F16P2}[F1,6P2] .$$

  • Fructose 6-Phosphate

$${d[F6P] \over dt} = {{V_{max}^{F16P2 \rightarrow F6P} \cdot [F1,6P2]]} \over {K_m^{F16P2 \rightarrow F6P} + [F1,6P2]}} - {{V_{max}^{F6P \rightarrow E4P} \cdot [F6P]} \over {K_m^{F6P \rightarrow E4P} + [F6P]}} - k_{deg}^{F6P}[F6P] .$$

  • RNA(FBP/SBP)

$${d[RNA(FBP/SBP)] \over dt} = k_{transc}^{FBP/SBP}[DNA] - k_{deg}^{RNA(FBP/SBP)}[RNA(FBP/SBP)].$$

  • FBP/SBP

$${d[FBP/SBP] \over dt} = k_{trans}^{FBP/SBP}[RNA(FBP/SBP)] - k_{deg}^{FBP/SBP}[FBP/SBP].$$

  • Glucose 6-Phospate

$${d[G6P] \over dt} = {{V_{max}^{F6P \rightarrow G6P} \cdot [F6P]} \over {K_m^{F6P \rightarrow G6P} + [F6P}} - {{V_{max}^{G6P \rightarrow G1P} \cdot [G6P]} \over {K_m^{G6P \rightarrow G1P} + [G6P]}} - k_{deg}^{G6P}[G6P] .$$

  • Glucose 1-Phospate

$${d[G1P] \over dt} = {{V_{max}^{G6P \rightarrow G1P} \cdot [G6P]} \over {K_m^{G6P \rightarrow G1P} + [G6P]}} - {{V_{max}^{G1P \rightarrow ADPG} \cdot [G1P]} \over {K_m^{G1P \rightarrow ADPG} + [G1P]}} - {{V_{max}^{G1P \rightarrow UDPG} \cdot [G1P]} \over {K_m^{G1P \rightarrow UDPG} + [G1P]}} - k_{deg}^{G1P}[G1P] .$$

  • ADP-Glucose

$${d[ADPG] \over dt} = {{V_{max}^{G1P \rightarrow ADPG} \cdot [G1P]} \over {K_m^{G1P \rightarrow ADPG} + [G1P]}} - {{V_{max}^{ADPG \rightarrow Aml} \cdot [ADPG]} \over {K_m^{ADPG \rightarrow Aml} + [ADPG]}} - k_{deg}^{ADPG}[ADPG] .$$

  • UDP-Glucose

$${d[UDPG] \over dt} = {{V_{max}^{G1P \rightarrow UDPG} \cdot [G1P]} \over {K_m^{G1P \rightarrow UDPG} + [G1P]}} - {{V_{max}^{UDPG \rightarrow Aml} \cdot [UDPG]} \over {K_m^{UDPG \rightarrow Aml} + [UDPG]}} - k_{deg}^{UDPG}[UDPG] .$$

  • Amylose

$${d[Aml] \over dt} = {{V_{max}^{ADPG \rightarrow Aml} \cdot [ADPG]} \over {K_m^{ADPG \rightarrow Aml} + [ADPG]}} + {{V_{max}^{UDPG\rightarrow Aml} \cdot [UDPG]} \over {K_m^{UDPG \rightarrow Aml} + [UDPG]}} - {{V_{max}^{Aml \rightarrow Starch} \cdot [Aml]} \over {K_m^{Aml \rightarrow Starch]} + [Aml]}} - K_{deg}[Aml] .$$

  • Starch

$${d[Starch] \over dt} = {{V_{max}^{Aml \rightarrow Starch} \cdot [Aml]} \over {K_m^{Aml \rightarrow Starch} + [Aml]}} - k_{deg}^{Starch}[Starch] .$$

  • GDP-Glucose

$${d[GDPG] \over dt} = {{V_{max}^{G1P \rightarrow GDPG} \cdot [G1P]} \over {K_m^{G1P \rightarrow GDPG} + [G1P]}} - {{V_{max}^{GDPG \rightarrow G1P} \cdot [GDPG]} \over {K_m^{GDPG \rightarrow G1P]} + [GDPG]}} - K_{deg}[GDPG] .$$

  • RNA (ΔSTA1)

$${d[RNA_{ΔSTA1}] \over dt} = {{K1 \cdot K_{metE}} \over {K_{metE} + [B12]}}[DNA] - k_{union}^{STA1}[RNA_{STA1}][ΔRNA_{STA1}] + k_{disunion}^{dsRNA_{STA1}}[dsRNA_{STA1}] - k_{deg}^{RNA_{ΔSTA1}}[RNA_{ΔSTA1}] .$$

  • RNA (STA1)

$${d[RNA_{STA1}] \over dt} = k_{trans}^{RNA_{STA1}}[DNA] - k_{union}^{STA1}[RNA_{STA1}][ΔRNA_{STA1}] + k_{disunion}^{dsRNA_{STA1}}[dsRNA_{STA1}] - k_{deg}^{RNA_{STA1}}[RNA_{STA1}] .$$

  • Union RNA STA1-ΔSTA1

$${d[dsRNA_{STA1}] \over dt} = k_{union}^{STA1}[RNA_{STA1}][ΔRNA_{STA1}] - k_{disunion}^{dsRNA_{STA1}}[dsRNA_{STA1}] - k_{deg}^{dsRNA_{STA1}}[dsRNA_{STA1}] .$$

  • STA1

$${d[STA1] \over dt} = k_{trans}^{STA1}[RNA_{STA1}] - k_{deg}^{STA1}[STA1] .$$

  • RNA (ΔSTA6)

$${d[RNA_{ΔSTA6}] \over dt} = {{K2 \cdot K_{metE}} \over {K_{metE} + [B12]}}[DNA] - k_{union}^{STA6}[RNA_{STA6}][ΔRNA_{STA6}] + k_{disunion}^{dsRNA_{STA6}}[dsRNA_{STA6}] - k_{deg}^{RNA_{ΔSTA6}}[RNA_{ΔSTA6}] .$$

  • RNA (STA6)

$${d[RNA_{STA6}] \over dt} = k_{trans}^{RNA_{STA6}}[DNA] - k_{union}^{STA6}[RNA_{STA6}][ΔRNA_{STA6}] + k_{disunion}^{dsRNA_{STA6}}[dsRNA_{STA6}] - k_{deg}^{RNA_{STA6}}[RNA_{STA6}] .$$

  • Union RNA STA6-ΔSTA6

$${d[dsRNA_{STA6}] \over dt} = k_{union}^{STA6}[RNA_{STA6}][ΔRNA_{STA6}] - k_{disunion}^{dsRNA_{STA6}}[dsRNA_{STA6}] - k_{deg}^{dsRNA_{STA6}}[dsRNA_{STA6}] .$$

  • STA6

$${d[STA6] \over dt} = k_{trans}^{STA6}[RNA_{STA6}] - k_{deg}^{STA6}[STA6] .$$

  • RNA (ΔGBS2)

$${d[RNA_{ΔGBS2}] \over dt} = {{K3 \cdot K_{metE}} \over {K_{metE} + [B12]}}[DNA] - k_{union}^{GBS2}[RNA_{GBS2}][ΔRNA_{GBS2}] + k_{disunion}^{dsRNA_{GBS2}}[dsRNA_{GBS2}] - k_{deg}^{RNA_{ΔGBS2}}[RNA_{ΔGBS2}] .$$

  • RNA (GBS2)

$${d[RNA_{GBS2}] \over dt} = k_{trans}^{RNA_{GBS2}}[DNA] - k_{union}^{GBS2}[RNA_{GBS2}][ΔRNA_{GBS2}] + k_{disunion}^{dsRNA_{GBS2}}[dsRNA_{GBS2}] - k_{deg}^{RNA_{GBS2}}[RNA_{GBS2}] .$$

  • Union RNA GBS2-ΔGBS2

$${d[dsRNA_{GBS2}] \over dt} = k_{union}^{GBS2}[RNA_{GBS2}][ΔRNA_{GBS2}] - k_{disunion}^{dsRNA_{GBS2}}[dsRNA_{GBS2}] - k_{deg}^{dsRNA_{GBS2}}[dsRNA_{GBS2}] .$$

  • GBS2

$${d[GBS2] \over dt} = k_{trans}^{GBS2}[RNA_{GBS2}] - k_{deg}^{GBS2}[GBS2] .$$



Parameter search

The kinetic characterization of the reactions must be done through the search of parameters in scientific publications and other databases.

Due to the existence of various information regarding the same constant, an approximation to a single value can be done by assigning them a weight considering the similarity of the corresponding organism and environmental conditions. If you would like to see the criterias, click below.

Table 1: Criterias

Microorganism Weighting
Same microorganism Infinity
Microalgae x1,000,000
Plant (with chloroplast and cytoplasm/nucleus, same pH and temperature) x100,000
Plant (with chloroplast and cytoplasm/nucleus, high differences of pH or temperatura) x90,000
Plant (with chloroplast and cytoplasm/nucleus, high differences of pH or temperatura) x80,000
Fungus(with chloroplast, same pH and temperature) x1000
Fungus (wiht chloroplast, high differences of pH or temperatura) x800
Fungus (with chloroplast, high differences of pH and temperatura) x600
Fungus (with cytoplasm/nucleus, same pH and temperature) x10,000
Fungus (with cytoplasm/nucleus, high differences of pH or temperature) 8,000
Fungus (with cytoplasm/nucleus, high differences of pH and temperature) x6,000
Cyanobacteria (with chloroplast, same pH and temperature) x10,000
Cyanobacteria (with chloroplast, high differences of pH or temperature) x8,000
Cyanobacteria (with chloroplast, high differences of pH and temperature) x6,000
Cyanobacteria (with cytoplasm/nucleus, same pH and temperature) x1000
Cyanobacteria (with cytoplasm/nucleus, high differences of pH or temperature) x800
Cyanobacteria (with cytoplasm/nucleus, high differences of pH and temperature) x600
Animal/Protozoa (with chloroplast, same pH and temperature) x100
Animal/Protozoa (with chloroplast, high differences of pH and temperature) x80
Animal/Protozoa (with chloroplast, high differences of pH and temperature) x60
Animal/Protozoa (with cytoplasm/nucleus, same pH and temperature) x1,000
Animal/Protozoa (with cytoplasm/nucleus, high differences of pH or temperature) x800
Animal/Protozoa ((with cytoplasm/nucleus, high differences of pH and temperature) x600
Bacteria no-cyano (with cytolpasm/nucleus or chloroplast, same pH and temperature) x80
Bacteria no-cyano (with cytolpasm/nucleus or chloroplast, high differences of pH or temperature) x60
Bacteria no-cyano (with cytolpasm/nucleus or chloroplast, high differences of pH and temperature) x10
Archeae (with cytoplasm/nucleus or chloroplast, same pH and temperature) x10
Archeae (with cytoplasm/nucleus or chloroplast, high differences of pH or temperature) x8
Archeae (with cytoplasm/nucleus or chloroplast, high differences of pH and temperature) x6
Mutant strain 0.7 of wildtype strain



If you would like to see the used parameters, click below.

Table 2: Parameters

Symbol Description Value Reference
$$K_m^{F6P \rightarrow E4P}$$ Michaelis-Menten constant for conversion of Fructose 6-Phosphate to Erythrose 4-Phosphate. 3.05[mM] Weighting of Brenda database values.
$$v_{max}^{F6P \rightarrow E4P}$$ Maximun rate for conversion of Fructose 6-Phosphate to Erythrose 4-Phosphate. 165.24[mM] Weighting of Brenda database values.
$$K_m^{E4P \rightarrow Sed17P2}$$ Michaelis-Menten constant for conversion of Erythrose 4-Phosphate to Sedoheptulose 1,7-Biphosphatase. 0.33[mM] Weighting of Brenda database values.
$$V_{max}^{E4P \rightarrow Sed17P2}$$ Maximun rate for conversion of Erythrose 4-Phosphate to Sedoheptulose 1,7-Biphosphatase. 26.27[mM/s] Weighting of Brenda database values.
$$k_{deg}^{E4P}$$ Degradation rate of Erythrose 4-Phosphate. 5.5e-6[1/s] Estimated.
$$K_{deg}^{Sed17P2}$$ Degradation rate of Sedoheptulose 1,7-Biphosphatase. 5.5e-6[1/s] Estimated.
$$K_m^{Sed7P \rightarrow R5P}$$ Michaelis-Menten constant for conversion of Sedoheptulose 7-Phosphate to Ribose 5-Phosphate. 4[mM] Weighting of Brenda database values.
$$V_{max}^{Sed7P \rightarrow R5P}$$ Maximun rate for conversion of Sedoheptulose 7-Phosphate to Ribose 5-Phosphate. 10[mM/s] Weighting of Brenda database values.
$$k_{deg}^{Sed7P}$$ Degradation rate of Sedoheptulose 7-Phosphate. 5.5e-6[1/s] Estimated.
$$K_m^{R5P \rightarrow Rul5P}$$ Michaelis-Menten constant for conversion of Ribose 5-Phosphate to Ribulose 5-Phosphate. 0.72[mM] Weighting of Brenda database values.
$$V_{max}^{R5P \rightarrow Rul5P}$$ Maximun rate for conversion of Ribose 5-Phosphate to Ribulose 5-Phosphate. 2.76e3[mM/s] Weighting of Brenda database values.
$$k_{deg}^{R5P}$$ Degradation rate of Ribose 5-Phosphate. 5.5e-6[1/s] Estimated.
$$K_m^{Rul5P \rightarrow Rul1,5P2}$$ Michaelis-Menten constant for conversion of Ribulose 5-Phosphate to Ribulose 1,5-Bisphosphate. 0.06[mM] Weighting of Brenda database values.
$$V_{max}^{Rul5P \rightarrow Rul1,5P2}$$ Maximun rate for conversion of Ribulose 5-Phosphate to Ribulose 1,5-Bisphosphate. 5.35[mM/s] Weighting of Brenda database values.
$$k_{deg}^{Rul15P2}$$ Degradation rate of Ribulose 1,5-Bisphosphate. 5.5e-6[1/s] Estimated.
$$K_m^{Rul1,5P2 \rightarrow Gl3P}$$ Michaelis-Menten constant for conversion of Ribulose 1,5-Bisphosphate to Glycerate 3-Phosphate. 0.03[mM] Weighting of Brenda database values.
$$V_{max}^{Rul15P2 \rightarrow Gl3P}$$ Maximun rate for conversion of Ribulose 1,5-Bisphosphate to Glycerate 3-Phosphate. 9.01[mM/s] Weighting of Brenda database values.
$$k_{deg}^{Rul15P2}$$ Degradation rate of Ribulose 1,5-Bisphosphate. 5.5e-[1/s] Estimated.
$$K_m^{ Gl3P \rightarrow Gl13P2}$$ Michaelis-Menten constant for conversion of Glycerate 3-Phosphate to Glycerate 1,3-Biphosphate. 0.40[mM] Weighting of Brenda database values.
$$V_{max}^{ Gl3P \rightarrow Gl13P2}$$ Maximun rate for conversion of Glycerate 3-Phosphate to Glycerate 1,3-Biphosphate. 113.77[mM/s] Weighting of Brenda database values.
$$K_{deg}^{Gl3P}$$ Degradation rate of Glycerate 3-Phosphate. 5.5e-6[1/s] Estimated.
$$K_m^{ Gl13P2 \rightarrow GlAl3P}$$ Michaelis-Menten constant for conversion of Glycerate 1,3-Biphosphate to Glyceraldehyde 3-Phosphate 0.40[mM] Weighting of Brenda database values.
$$V_{max}^{ Gl13P2 \rightarrow GlAl3P}$$ Maximun rate for conversion of Glycerate 1,3-Biphosphate to Glyceraldehyde 3-Phosphate. 113.77[mM/s] Weighting of Brenda database values.
$$k_{deg}^{Gl13P2}$$ Degradation rate of Glycerate 1,3-Biphosphate. 5.5e-6[1/s] Estimated.
$$K_m^{ GlAl3P \rightarrow F16P2}$$ Michaelis-Menten constant for conversion of Glyceraldehyde 3-Phosphate to Fructose 1,6-Biphosphate. 9.50[mM] Weighting of Brenda database values.
$$V_{max}^{ GlAl3P \rightarrow F16P2}$$ Maximun rate for conversion of Glyceraldehyde 3-Phosphate to Fructose 1,6-Biphosphate. 27.93[mM/s] Weighting of Brenda database values.
$$k_{deg}^{GlAl3P}$$ Degradation rate of Glyceraldehyde 3-Phosphate. 5.5e-6[1/s] Estimated.
$$k_{deg}^{F16P2}$$ Degradation rate of Fructose 1,6-Biphosphate./td> 5.5e-6[1/s] Estimated.
$$K_m^{F6P \rightarrow G6P}$$ Michaelis-Menten constant for conversion of Fructose 6-Phosphate to Glucose 6-Phosphate. 0.16[mM] Weighting of Brenda database values.
$$V_{max}^{F6P \rightarrow G6P}$$ Maximun rate for conversion of Fructose 6-Phosphate to Glucose 6-Phosphate. 86.12[mM/s] Weighting of Brenda database values.
$$k_{deg}^{F6P}$$ Degradation rate of Fructose 6-Phosphate. 5.5e-6[1/s] Estimated.
$$K_m^{G6P \rightarrow F6P}$$ Michaelis-Menten constant for conversion of Glucose 6-Phosphate to Fructose 6-Phosphate. 1[mM] Weighting of Brenda database values.
$$V_{max}^{G6P \rightarrow F6P}$$ Maximun rate for conversion of Glucose 6-Phosphate to Fructose 6-Phosphate. 1[mM/s] Weighting of Brenda database values.
$$k_{Transc}^{FBP/SBP}$$ Transcription rate of FBP/SBP. 0.032[1/s] Estimated.
$$k_{deg}^{RNA_{FBP/SBP}}$$ Degradation rate of RNA_{FBP/SBP} 4.17e-4[1/s] Estimated.
$$k_{transl}^{FBP/SBP}$$ Translation rate of FBP/SBP. 0.032[1/s] Estimated.
$$k_{deg}^{FBP/SBP}$$ Degradation rate of FBP/SBP. 6.17e-6[1/s] Estimated.
$$K_m^{G6P \rightarrow G1P}$$ Michaelis-Menten constant for conversion of Glucose 6-Phosphate to Glucose 1-Phosphate. 8.64[mM] Weighting of Brenda database values.
$$V_{max}^{G6P \rightarrow G1P}$$ Maximun rate for conversion of Glucose 6-Phosphate to Glucose 1-Phosphate. 10[mM/s] Weighting of Brenda database values.
$$k_{deg}^{G6P}$$ Degradation rate of Glucose 6-Phosphate. 5.5e-6[1/s] Estimated.
$$K_m^{G1P \rightarrow UDPG}$$ Michaelis-Menten constant for conversion of Glucose 6-Phosphate to UDP-Glucose. 0.21[mM] Weighting of Brenda database values.
$$V_{max}^{G1P \rightarrow UDPG}$$ Maximun rate for conversion of Glucose 6-Phosphate to UDP-Glucose. 14.81[mM/s] Weighting of Brenda database values.
$$k_{deg}^{G1P}$$ Degradation rate of Glucose 1-Phosphate. 5.5e-6[1/s] Estimated.
$$K_m^{ADPG \rightarrow Aml}$$ Michaelis-Menten constant for conversion of ADP-Glucose to Amylose. 1,36[mM] Weighting of Brenda database values.
$$V_{max}^{ADPG \rightarrow Aml}$$ Maximun rate for conversion of ADP-Glucose to Amylose. 53.29[mM/s] Weighting of Brenda database values.
$$k_{deg}^{ADPG}$$ Degradation rate of ADP-Glucose. 5.5e-6[1/s] Estimated.
$$K_m^{Aml \rightarrow Starch}$$ Michaelis-Menten constant for conversion of Amylose to Starch. 1.96[mM] Weighting of Brenda database values.
$$V_{max}^{Aml \rightarrow Starch}$$ Maximun rate for conversion of Amylose to Starch. 99.01[mM/s] Weighting of Brenda database values.
$$k_{deg}^{ADPG}$$ Degradation rate of ADP-Glucose. 5.5e-6[1/s] Estimated.
$$k_{deg}^{Aml}$$ Degradation rate of Amylose. 5.5e-6[1/s] Estimated.
$$k_{deg}^{UDPG}$$ Degradation rate of UDP-Glucose. 5.5e-6[1/s] Estimated.
$$k_{deg}^{Starch}$$ Degradation rate of Starch. 5.5e-6[1/s] Estimated.
$$k_{Transc}^{\Delta STA1}$$ Transcription rate of anti STA1. 0.04[1/s] Estimated.
$$K_met$$ metE promoter constant. 1[1/s] Arbitrary.
$$k_{link}^{STA1}$$ Link rate of complementary RNA regarding STA1 1e+8[1/mMs] Estimated.
$$k_{deg}^{RNA_{\Delta STA1}}$$ Degradation rate of RNA anti STA1. 4.17e-4[1/s] Estimated.
$$k_{deg}^{dsSTA1}$$ Degradation rate of dsSTA1. 4.17e-4[1/s] Estimated.
$$k_{Transl}^{STA1}$$ Translation rate of STA1. 0.04[1/s] Estimated.
$$k_{deg}^{STA1}$$ Degradation rate of STA1. 6.17e-6[1/s] Estimated.
$$k_{Transc}^{\Delta STA6}$$ Transcription rate of anti STA6. 0.04[1/s] Estimated.
$$k_{link}^{STA6}$$ Link rate of complementary RNA regarding STA6. 1e+8[mMs] Estimated.
$$k_{deg}^{RNA_{\Delta STA6}}$$ Degradation rate of anti STA6 4.17e-4[1/s] Estimated.
$$k_{deg}^{dsSTA6}$$ Degradation rate of dsSTA6. 4.17e-4[1/s] Estimated.
$$k_{Transl}^{STA6}$$ Translation rate of STA6. 0.04[1/s] Estimated.
$$k_{deg}^{STA6}$$ Degradation rate of STA6. 6.17e-4[1/s] Estimated.
$$k_{Transc}^{\Delta GBS2}$$ Transcription rate of anti GBS2. 0.038[1/s] Estimated.
$$k_{link}^{GBS2}$$ Link rate of complementary RNA regarding GBS2. 1e+8[1/mMs] Estimated.
$$k_{deg}^{RNA_{\Delta GBS2}}$$ Degradation rate of RNA anti GBS2. 4.17e-4[1/s] Estimated.
$$k_{deg}^{dsGBS2}$$ Degradation rate of dsGBS2. 4.17e-4[1/s] Estimated.
$$k_{Transl}^{GBS2}$$ Translation rate of GBS2. 0.04[1/s] Estimated.
$$k_{deg}^{GBS2}$$ Degradation rate of GBS2. 6.17e-6[1/s] Estimated.
$$K_o$$ Apparent Michaelis constant for O2 0.48[mM] Reference [1]
$$K_c$$ Apparent Michaelis constant for CO2 0.014[mM] Reference [1]
$$k_{cat,c}$$ Turn-over rate for carboxylation. 1.5[mM] Reference [1]
$$k_{aa}$$ Apparent Michaelis constant for RuBP. 0.03[mM] Reference [1]
$$K_m^{FBP/SBP}$$ Michaelis-Menten constant for conversion of Fructose 1,6-Biphosphatase to Fructose 6-Phosphate and Sedoheptulose 1,7-Biphosphatase to Sedoheptulose 7-Phosphate. 0.16[mM/s] Referente [2].
$$V_{max}^{F16P2 \rightarrow F6P}$$ Maximum rate for the conversion of Fructose 1,6-Biphosphatase to Fructose 6-Phosphate and Sedoheptulose 1,7-Biphosphatase to Sedoheptulose 7-Phosphate. 7.35[mM/s] Reference [2].
$$K_m^{STA}$$ Michaelis-Menten constant for STA1 and STA6. 0.17[mM] Weighting of Brenda database values.
$$V_{max}^{STA}$$ Maximum rate for STA1 and STA6. 1800[mM/s] Weighting of Brenda database values.
$$K_m^{GBS2}$$ Michaelis-Menten constant for GBS2. 15.66[mM] Weighting of Brenda database values.
$$V_{max}^{GBS2}$$ Maximum rate for GBS2. 50[mM/s] Weighting of Brenda database values.



Matlab simulation

Afterwards, all the collected data was entered into Matlab and a contrast between the wild-type metabolism and the modified version was studied.

Sensitivity analysis

We aim to know the relevant parameters of our model, and for that we vary each parameter while the rest remain constant. From this analysis, we obtained a set of graphs with the behavior of the model for each parameter value.


After the model

The objective of the model is maximize glucose availability by carbon fixation through adjustment of environmental conditions.

Optimization

After we determinated the relevant parameters of the model, we expect to find the best parameters values to minimize and maximize Starch production.

Model fitting

Meeasurements of various physical and chemical magnitudes must be made to adjust the model, and establish a probability of a parameter to belong in a certain range. The fitting will be made by the least-square method.




References

[1]: G. Tcherkez. 2013. Modelling the reaction mechanism of ribulose-1,5-bisphosphate carboxylase/oxygenase and consequences for kinetic parameters.(36):1586-1596.
[2]: L. Feng, Y. Sun, H. Deng, D. Li, J. Wan, X. Wang, W. Wang, X. Liao, Y. Ren, X. Hu. 2013. Structural and biochemical characterization of fructose-1,6/sedoheptulose-1,7-biphosphatase from the cyanobacterium Synechocystis strain 6803. doi:10.1111.