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Fridlyand et al. 1995

Fridlyand L, Kaplan A, Reinhold L (1995) Quantitative evaluation of the role of a putative CO2-scavenging entity in the cyanobacterial CO2-concentrating mechanism. Biosystems 1996;37(3):229-38.

This paper assesses the contribution of a postulated CO2-scavenging system to the efficient operation of the CO2-concentrating mechanism (CCM) in cyanobacteria. A quantitative model for the CCM is presented which incorporates an energy-dependent carbonic anhydrase-like entity located at or near the inner surface of the plasma membrane. This entity, which converts CO2 to HCO3- against the thermodynamic potential, scavenges CO2 leaking outward from the carboxysomes, and, further, converts CO2 entering from the medium to HCO3-, thus maintaining an inward diffusion gradient along which CO2 enters passively. The model resembles our earlier models in postulating that CO2 and HCO3- are not at equilibrium throughout the greater part of the cell, and that CO2 is generated in high concentration at carbonic anhydrase sites within the carboxysomes. The model further takes into account the concentric thylakoid membranes which surround the carboxysomes, and events in the periplasmic space and the unstirred layer surrounding the cell. Implications of the predicted steady state fluxes of CO2 and HCO3-, and of their steady state concentrations in various cellular compartments, are discussed. The plasma membrane carbonic anhydrase-like activity lowers the photosynthetic Km for external Ci, as well as decreasing the inorganic C 'leak', but it may not save on energy expenditure.


model:Fridlyand et al. (1995)

Fridlyand L, Kaplan A, Reinhold L (1995) Quantitative evaluation of the role of a putative CO2-scavenging entity in the cyanobacterial CO2-concentrating mechanism. Biosystems 1996;37(3):229-38.


publication:Fridlyand et al. (1995)
Contains:
Initial expression: 1
Simulation type: fixed
Details
Initial expression: 3910
Simulation type: reaction
Details
Initial expression: 259
Simulation type: reaction
Details
Initial expression: 1
Simulation type: fixed
Details
Initial expression: 8870
Simulation type: reaction
Details
Initial expression: 3.7
Simulation type: reaction
Details
Initial expression: 1
Simulation type: fixed
Details
Initial expression: 8920
Simulation type: reaction
Details
Initial expression: 3.5
Simulation type: reaction
Details
Initial expression: 1
Simulation type: fixed
Details
Initial expression: 142
Simulation type: reaction
Details
Initial expression: 3.4
Simulation type: reaction
Details
Initial expression: 1
Simulation type: fixed
Details
Initial expression: 143
Simulation type: fixed
Details
Initial expression: 3.3
Simulation type: fixed
Details
Equation: CO2_cyt_ocyt -> HCO3_m_ocyt
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_cmax*CO2_cyt_ocyt)/(K_mc + CO2_cyt_ocyt)
Kinetic rate constant Value
V_cmax 3.5 * V_p
K_mc 0.4
Details
Equation: HCO3_m_carb -> CO2_carb
Function: Function for Fridlyand 1 (irreversible)
Reaction rate: (V_ba*K_ca*HCO3_m_carb)/(K_ba*K_ca+K_ca*HCO3_m_carb+K_ba*CO2_carb)
Kinetic rate constant Value
V_ba 1.18*V_ca
K_ca 30311
K_ba 1800
Details
Equation: HCO3_m_ocyt -> CO2_cyt_ocyt
Function: light-dependend Mass Action (irreversible)
Reaction rate: K_3*HCO3_m_ocyt*V_e
Kinetic rate constant Value
K_3 2.63e-3
V_e 1.0
Details
Equation: HCO3_m_icyt -> CO2_cyt_icyt
Function: light-dependend Mass Action (irreversible)
Reaction rate: K_3*HCO3_m_icyt*V_cvolume
Kinetic rate constant Value
K_3 2.63e-3
V_cvolume 1.0
Details
Equation: CO2_liq -> CO2_pps
Function: Diffusion3 (irreversible)
Reaction rate: (4*pi*D_C*r_5*r_6*(CO2_liq-CO2_pps))/(r_6-r_5)
Kinetic rate constant Value
pi 3.14159265359
D_C 1.88e+3
r_5 1.87
r_6 3.54
Details
Equation: HCO3_m_ocyt -> HCO3_m_pps
Function: Diffusion2 (irreversible)
Reaction rate: P_pH*A_r_4*(HCO3_m_ocyt - HCO3_m_pps)
Kinetic rate constant Value
P_pH 0.3e-2
A_r_4 4*pi*r_4^2
Details
Equation: HCO3_m_icyt -> HCO3_m_carb
Function: Diffusion (irreversible)
Reaction rate: ("N"*4*pi*D_xH*r_1*r_2*(HCO3_m_icyt - HCO3_m_carb))/(r_2-r_1)
Kinetic rate constant Value
N 6
pi 3.14159265359
D_xH 0.09*D_xC
r_1 0.01
r_2 0.2
Details
Equation: HCO3_m_liq -> HCO3_m_pps
Function: Diffusion3 (irreversible)
Reaction rate: (4*pi*D_H*r_5*r_6*(HCO3_m_liq-HCO3_m_pps))/(r_6-r_5)
Kinetic rate constant Value
pi 3.14159265359
D_H 1.15e+3
r_5 1.87
r_6 3.54
Details
Equation: CO2_carb ->
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_p*CO2_carb)/(K_c + CO2_carb)
Kinetic rate constant Value
V_p 8e-12
K_c 250
Details
Equation: HCO3_m_ocyt -> HCO3_m_pps
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_t*HCO3_m_ocyt)/(K_r + HCO3_m_ocyt)
Kinetic rate constant Value
V_t 1.6e-11
K_r 200000
Details
Equation: HCO3_m_pps -> HCO3_m_ocyt
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_t*HCO3_m_pps)/(K_t + HCO3_m_pps)
Kinetic rate constant Value
V_t 1.6e-11
K_t 80
Details
Equation: CO2_carb -> HCO3_m_carb
Function: Function for Fridlyand 1 (irreversible)
Reaction rate: (V_ca*K_ba*CO2_carb)/(K_ca*K_ba+K_ba*CO2_carb+K_ca*HCO3_m_carb)
Kinetic rate constant Value
V_ca 0.0000000008
K_ca 30311
K_ba 1800
Details
Equation: CO2_cyt_ocyt -> HCO3_m_ocyt
Function: light-dependend Mass Action (irreversible)
Reaction rate: K_4*CO2_cyt_ocyt*V_e
Kinetic rate constant Value
K_4 37.2e-3
V_e 1.0
Details
Equation: CO2_cyt_icyt -> HCO3_m_icyt
Function: light-dependend Mass Action (irreversible)
Reaction rate: K_4*CO2_cyt_icyt*V_cvolume
Kinetic rate constant Value
K_4 37.2e-3
V_cvolume 1.0
Details
Equation: HCO3_m_ocyt -> HCO3_m_icyt
Function: Diffusion2 (irreversible)
Reaction rate: P_tH*A_r_3*(HCO3_m_ocyt - HCO3_m_icyt)
Kinetic rate constant Value
P_tH P_b / 100
A_r_3 4*pi*r_3^2
Details
Equation: CO2_cyt_icyt -> CO2_cyt_ocyt
Function: Diffusion2 (irreversible)
Reaction rate: P_cc*A_r_3*(CO2_cyt_icyt - CO2_cyt_ocyt)
Kinetic rate constant Value
P_cc 0.01
A_r_3 4*pi*r_3^2
Details
Equation: CO2_carb -> CO2_cyt_icyt
Function: Diffusion (irreversible)
Reaction rate: ("N"*4*pi*D_xC*r_1*r_2*(CO2_carb - CO2_cyt_icyt))/(r_2-r_1)
Kinetic rate constant Value
N 6
pi 3.14159265359
D_xC D_H / 80
r_1 0.01
r_2 0.2
Details
Equation: CO2_pps -> CO2_cyt_ocyt
Function: Diffusion2 (irreversible)
Reaction rate: P_b*A_r_4*(CO2_pps - CO2_cyt_ocyt)
Kinetic rate constant Value
P_b 3.5e+3
A_r_4 4*pi*r_4^2
Details

Constant quantities

Initial expression: 1.88e+3
Simulation type: fixed
Initial expression: 1.15e+3
Simulation type: fixed
Initial expression: 2.63e-3
Simulation type: fixed
Initial expression: 37.2e-3
Simulation type: fixed
Initial expression: 1800
Simulation type: fixed
Initial expression: 250
Simulation type: fixed
Initial expression: 30311
Simulation type: fixed
Initial expression: 0.4
Simulation type: fixed
Initial expression: 200000
Simulation type: fixed
Initial expression: 80
Simulation type: fixed
Initial expression: 6
Simulation type: fixed
Initial expression: 3.5e+3
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.3e-2
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.2
Simulation type: fixed
Initial expression: 1.73
Simulation type: fixed
Initial expression: 1.77
Simulation type: fixed
Initial expression: 1.87
Simulation type: fixed
Initial expression: 3.54
Simulation type: fixed
Initial expression: 0.0000000008
Simulation type: fixed
Initial expression: 1.0
Simulation type: fixed
Initial expression: 1.0
Simulation type: fixed
Initial expression: 8e-12
Simulation type: fixed
Initial expression: 1.6e-11
Simulation type: fixed
Initial expression: 3.14159265359
Simulation type: fixed
Initial expression: 0
Simulation type: fixed

Assigned quantities

Initial expression: 4*pi*r_4^2
Simulation type: assignment
Initial expression: 4*pi*r_3^2
Simulation type: assignment
Initial expression: P_b / 100
Simulation type: assignment
Initial expression: D_H / 80
Simulation type: assignment
Initial expression: 0.09*D_xC
Simulation type: assignment
Initial expression: 1.18*V_ca
Simulation type: assignment
Initial expression: 3.5 * V_p
Simulation type: assignment
Initial expression: (V_t*HCO3_m_pps)/(K_t + HCO3_m_pps)
Simulation type: assignment
Initial expression: K_3*HCO3_m_ocyt*V_e
Simulation type: assignment
Initial expression: P_b*A_r_4*(CO2_pps - CO2_cyt_ocyt)
Simulation type: assignment
Initial expression: (V_p*CO2_carb)/(K_c + CO2_carb)
Simulation type: assignment
Initial expression: (V_ba*K_ca*HCO3_m_carb)/(K_ba*K_ca+K_ca*HCO3_m_carb+K_ba*CO2_carb)
Simulation type: assignment
Initial expression: (V_ca*K_ba*CO2_carb)/(K_ca*K_ba+K_ba*CO2_carb+K_ca*HCO3_m_carb)
Simulation type: assignment
Initial expression: (6*4*pi*D_xC*r_1*r_2*(CO2_carb - CO2_cyt_icyt))/(r_2-r_1)
Simulation type: assignment
Name Value
carb 1
icyt 1
ocyt 1
pps 1
liq 1
HCO3_m_carb 3910
CO2_carb 259
HCO3_m_icyt 8870
CO2_cyt_icyt 3.7
HCO3_m_ocyt 8920
CO2_cyt_ocyt 3.5
HCO3_m_pps 142
CO2_pps 3.4
HCO3_m_liq 143
CO2_liq 3.3

Constant quantities

Name Value
D_C 1.88e+3
D_H 1.15e+3
K_3 2.63e-3
K_4 37.2e-3
K_ba 1800
K_c 250
K_ca 30311
K_mc 0.4
K_r 200000
K_t 80
N 6
P_b 3.5e+3
P_cc 0.01
P_pH 0.3e-2
r_1 0.01
r_2 0.2
r_3 1.73
r_4 1.77
r_5 1.87
r_6 3.54
V_ca 0.0000000008
V_cvolume 1.0
V_e 1.0
V_p 8e-12
V_t 1.6e-11
pi 3.14159265359
zero 0

Assigned quantities

Name Value
A_r_4 4*pi*r_4^2
A_r_3 4*pi*r_3^2
P_tH P_b / 100
D_xC D_H / 80
D_xH 0.09*D_xC
V_ba 1.18*V_ca
V_cmax 3.5 * V_p
v9 (V_t*HCO3_m_pps)/(K_t + HCO3_m_pps)
v5 K_3*HCO3_m_ocyt*V_e
v15 P_b*A_r_4*(CO2_pps - CO2_cyt_ocyt)
v8 (V_p*CO2_carb)/(K_c + CO2_carb)
v1 (V_ba*K_ca*HCO3_m_carb)/(K_ba*K_ca+K_ca*HCO3_m_carb+K_ba*CO2_carb)
v2 (V_ca*K_ba*CO2_carb)/(K_ca*K_ba+K_ba*CO2_carb+K_ca*HCO3_m_carb)
v11 (6*4*pi*D_xC*r_1*r_2*(CO2_carb - CO2_cyt_icyt))/(r_2-r_1)
Name Value
start_time 0  
end_time 300  
time_offset 0  
step 1000  

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