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krab

krab

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v_1

R00 = A00

v_10

F01 = F02

v_11

F02 = F03

v_12

F03 = F04

v_13

F04 = F05

v_14

F05 = O00

v_15

O00 = O01

v_16

O01 = O02

v_17

O02 = O03

v_18

O03 = O04

v_19

O04 = O05

v_2

A00 = P00

v_20

O05 = E00

v_21

E00 = E01

v_22

E01 = E02

v_23

E02 = E03

v_24

E03 = E04

v_25

E04 = E05

v_26

E05 = R00

v_3

P00 = P01

v_4

P01 = P02

v_5

P02 = P03

v_6

P03 = P04

v_7

P04 = P05

v_8

P05 = F00

v_9

F00 = F01

Parameters

Global parameters

Fixed species

Initial values

Functions and Rules

Assignment rules

kb24 = kb18*(rE03^((phiE03-1)/2))

kf12 = kf18*(rF03^((phiF03+1)/2))

rF03 = 2.718281828^(96485*(EmaccF-Emcyta)/(8.314*298.15))/(kf18/kb18)

kb04 = kb16

kf06 = kf18*(rP03^((phiP03+1)/2))

kf13 = kf19*(rF04^((phiF04+1)/2))

kf24 = kf18*(rE03^((phiE03+1)/2))

kf04 = kf16

kf26 = kf20

kf22 = kf16

rP04 = rtotal/(rP03*rF03*rE03*rF04*rE04)

rP03 = 2.718281828^(96485*(EmaccP-Emcyta)/(8.314*298.15))/(kf18/kb18)

kb03 = kb15

rE03 = 2.718281828^(96485*(EmaccE-Emcyta)/(8.314*298.15))/(kf18/kb18)

kf14 = kf20

kb12 = kb18*(rF03^((phiF03-1)/2))

kf07 = kf19*(rP04^((phiP04+1)/2))

kf10 = kf16

kb13 = kb19*(rF04^((phiF04-1)/2))

kf08 = kf20

kf21 = kf15

kb11 = kb17

kb09 = kb15

kb10 = kb16

kb05 = kb17

rF04 = (10^pKaF)/(kf19/kb19)

kf11 = kf17

kb22 = kb16

kb21 = kb15

kf09 = kf15

kb26 = kb20

kb14 = kb20

kb08 = kb20

kb07 = kb19*(rP04^((phiP04-1)/2))

kb23 = kb17

kf03 = kf15

kf25 = kf19*(rE04^((phiE04+1)/2))

kf05 = kf17

kf23 = kf17

rE04 = (10^pKaE)/(kf19/kb19)

kb06 = kb18*(rP03^((phiP03-1)/2))

kb25 = kb19*(rE04^((phiE04-1)/2))

Function definitions

Events

Constraints

Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.


Species:

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Explaining the enigmatic K(M) for oxygen in cytochrome c oxidase: a kinetic model.

  • K Krab
  • H Kempe
  • M Wikström
Biochim. Biophys. Acta 2011; 1807 (3): 348-358
Abstract
We present a mathematical model for the functioning of proton-pumping cytochrome c oxidase, consisting of cyclic conversions between 26 enzyme states. The model is based on the mechanism of oxygen reduction and linked proton translocation postulated by Wikström and Verkhovsky (2007). It enables the calculation of the steady-state turnover rates and enzyme-state populations as functions of the cytochrome c reduction state, oxygen concentration, membrane potential, and pH on either side of the inner mitochondrial membrane. We use the model to explain the enigmatic decrease in oxygen affinity of the enzyme that has been observed in mitochondria when the proton-motive force is increased. The importance of the 26 transitions in the mechanism of cytochrome oxidase for the functional properties of cytochrome oxidase is compared through Metabolic Control Analysis. The control of the K(M) value is distributed mainly between the steps in the mechanism that involve electrogenic proton movements, with both positive and negative contributions. Positive contributions derive from the same steps that control enzyme turnover rate in the model. Limitations and possible further applications of the model are discussed.

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