MODEL4151491057
type: SBMLModel
parameter: metaid_0000073
parameter: metaid_0000024
rule: metaid_0000196
rule: metaid_0000170
notes: This is the model described in the article: A biophysical model of the mitochondrial respiratory system and oxidative phosphorylation. Beard DA. PLoS Comput Biol. 2005 Sep;1(4):e36. Pubmed ID: 16163394 , doi: 10.1371/journal.pcbi.0010036 . Abstract: A computational model for the mitochondrial respiratory chain that appropriately balances mass, charge, and free energy transduction is introduced and analyzed based on a previously published set of data measured on isolated cardiac mitochondria. The basic components included in the model are the reactions at complexes I, III, and IV of the electron transport system, ATP synthesis at F1F0 ATPase, substrate transporters including adenine nucleotide translocase and the phosphate-hydrogen co-transporter, and cation fluxes across the inner membrane including fluxes through the K+/H+ antiporter and passive H+ and K+ permeation. Estimation of 16 adjustable parameter values is based on fitting model simulations to nine independent data curves. The identified model is further validated by comparison to additional datasets measured from mitochondria isolated from rat heart and liver and observed at low oxygen concentration. To obtain reasonable fits to the available data, it is necessary to incorporate inorganic-phosphate-dependent activation of the dehydrogenase activity and the electron transport system. Specifically, it is shown that a model incorporating phosphate-dependent activation of complex III is able to reasonably reproduce the observed data. The resulting validated and verified model provides a foundation for building larger and more complex systems models and investigating complex physiological and pathophysiological interactions in cardiac energetics. This model was taken from the CellML repository and automatically converted to SBML. The original model was: Beard, 2005 version 03 The original CellML model was created and curated by: Geoffrey Nunns The University of Auckland, Bioengineering Research Group This model…
rule: metaid_0000154
rule: metaid_0000181
parameter: metaid_0000104
units def: metaid_0000013
parameter: metaid_0000127
parameter: metaid_0000061
is described by: http://identifiers.org/pubmed/16163394
rule: metaid_0000174
parameter: metaid_0000074
parameter: metaid_0000108
parameter: metaid_0000097
parameter: metaid_0000048
rule: metaid_0000147
rule: metaid_0000185
rule: metaid_0000145
rule: metaid_0000143
rule: metaid_0000180
parameter: metaid_0000031
units def: metaid_0000014
parameter: metaid_0000034
parameter: metaid_0000115
units def: metaid_0000020
parameter: metaid_0000128
parameter: metaid_0000062
parameter: metaid_0000080
rule: metaid_0000163
parameter: metaid_0000085
parameter: metaid_0000119
parameter: metaid_0000098
parameter: metaid_0000101
rule: metaid_0000184
units def: metaid_0000005
parameter: metaid_0000071
rule: metaid_0000142
parameter: metaid_0000032
rule: metaid_0000169
parameter: metaid_0000035
parameter: metaid_0000055
units def: metaid_0000021
parameter: metaid_0000116
parameter: metaid_0000058
rule: metaid_0000162
parameter: metaid_0000086
parameter: metaid_0000102
units def: metaid_0000015
parameter: metaid_0000125
parameter: metaid_0000072
parameter: metaid_0000023
parameter: metaid_0000043
parameter: metaid_0000095
parameter: metaid_0000046
rule: metaid_0000193
units def: metaid_0000010
parameter: metaid_0000059
rule: metaid_0000151
rule: metaid_0000138
units def: metaid_0000016
parameter: metaid_0000110
rule: metaid_0000178
parameter: metaid_0000113
rule: metaid_0000159
units def: metaid_0000022
parameter: metaid_0000126
parameter: metaid_0000060
rule: metaid_0000197
rule: metaid_0000171
parameter: metaid_0000083
parameter: metaid_0000044
parameter: metaid_0000096
parameter: metaid_0000047
rule: metaid_0000157
units def: metaid_0000007
parameter: metaid_0000030
rule: metaid_0000137

metaid_0000073
type: Parameter
constant: true
value: 1.2E-4
name: k_O2

metaid_0000024
type: Parameter
constant: true
value: 0.005
name: Mg_tot

metaid_0000104
type: Parameter
constant: false
value: NaN
name: H2PIx

metaid_0000013
type: SBMLUnitsDef
unit: 045034
name: millivolt

045034
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: VOLT

metaid_0000127
type: Parameter
constant: false
value: 0.0
name: ATP_i

metaid_0000061
type: Parameter
constant: true
value: 0.36923
name: x_C1

metaid_0000074
type: Parameter
constant: true
value: 4.253
name: r_buff

metaid_0000108
type: Parameter
constant: false
value: NaN
name: J_KH

metaid_0000097
type: Parameter
constant: false
value: NaN
name: ADP_fi

metaid_0000048
type: Parameter
constant: true
value: 5.99
name: gamma

metaid_0000031
type: Parameter
constant: true
value: -32.53
name: dG_C3o

metaid_0000014
type: SBMLUnitsDef
unit: 045070
unit: 045058
unit: 045046
name: kilojoule_per_mole_per_millivolt

045070
type: SBMLUnit
exponent: -1.0
scale: -3
multipler: 1.0
kind: VOLT

045058
type: SBMLUnit
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scale: 0
multipler: 1.0
kind: MOLE

045046
type: SBMLUnit
exponent: 1.0
scale: 3
multipler: 1.0
kind: JOULE

metaid_0000034
type: Parameter
constant: true
value: 7.1
name: pH_e

metaid_0000115
type: Parameter
constant: false
value: NaN
name: Mg_i

metaid_0000020
type: SBMLUnitsDef
unit: 045239
unit: 045227
unit: 045214
name: mole_per_second_per_l_mito_per_molar_per_molar

045239
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

045227
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

045214
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE

metaid_0000128
type: Parameter
constant: false
value: 0.0
name: ADP_i

metaid_0000062
type: Parameter
constant: true
value: 0.091737
name: x_C3

metaid_0000080
type: Parameter
constant: false
value: NaN
name: dG_C1op

metaid_0000085
type: Parameter
constant: false
value: NaN
name: J_F1

metaid_0000119
type: Parameter
constant: false
value: 0.0015
name: NADH_x

metaid_0000098
type: Parameter
constant: false
value: NaN
name: J_ATP

metaid_0000101
type: Parameter
constant: false
value: NaN
name: J_Pi2

metaid_0000005
type: SBMLUnitsDef
unit: 044866
unit: 044853
unit: 044841
name: M_per_second

044866
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

044853
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

044841
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE

metaid_0000071
type: Parameter
constant: true
value: 0.0
name: x_AK

metaid_0000032
type: Parameter
constant: true
value: -122.94
name: dG_C4o

metaid_0000035
type: Parameter
constant: false
value: NaN
name: H_e

metaid_0000055
type: Parameter
constant: true
value: 6.7668E-4
name: k_Pi2

metaid_0000021
type: SBMLUnitsDef
unit: 045275
unit: 045263
unit: 045251
name: mole_per_l_mito_per_millivolt

045275
type: SBMLUnit
exponent: -1.0
scale: -3
multipler: 1.0
kind: VOLT

045263
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

045251
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE

metaid_0000116
type: Parameter
constant: false
value: 6.30957344480193E-8
name: H_x

metaid_0000058
type: Parameter
constant: true
value: 4.5082E-4
name: k_PiH

metaid_0000086
type: Parameter
constant: false
value: NaN
name: J_ANT

metaid_0000102
type: Parameter
constant: false
value: NaN
name: J_Pi1

metaid_0000015
type: SBMLUnitsDef
unit: 045094
unit: 045082
name: molar_per_cyto

045094
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

045082
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE

metaid_0000125
type: Parameter
constant: false
value: 0.0
name: ADP_mx

metaid_0000072
type: Parameter
constant: true
value: 85.0
name: p_A

metaid_0000023
type: Parameter
constant: true
value: NaN
name: t

metaid_0000043
type: Parameter
constant: true
value: 3.47E-4
name: K_DD

metaid_0000095
type: Parameter
constant: false
value: NaN
name: ATP_fi

metaid_0000046
type: Parameter
constant: false
value: NaN
name: W_x

metaid_0000010
type: SBMLUnitsDef
unit: 044986
unit: 044974
name: micron_per_second

044986
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

044974
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: METRE

metaid_0000059
type: Parameter
constant: true
value: 4.5807
name: r

metaid_0000016
type: SBMLUnitsDef
unit: 045118
unit: 045106
name: molar_per_mito

045118
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

045106
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE

metaid_0000110
type: Parameter
constant: false
value: NaN
name: Q

metaid_0000113
type: Parameter
constant: false
value: NaN
name: ADP_fe

metaid_0000022
type: SBMLUnitsDef
unit: 045300
unit: 045287
name: mole_per_second_per_l_mito_per_molar_per_millivolt

045300
type: SBMLUnit
exponent: -1.0
scale: -3
multipler: 1.0
kind: VOLT

045287
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

metaid_0000126
type: Parameter
constant: false
value: 0.001
name: Pi_x

metaid_0000060
type: Parameter
constant: true
value: 0.09183
name: x_DH

metaid_0000083
type: Parameter
constant: false
value: NaN
name: J_C4

metaid_0000044
type: Parameter
constant: true
value: 0.4331
name: K_AK

metaid_0000096
type: Parameter
constant: false
value: NaN
name: J_MgADPi

metaid_0000047
type: Parameter
constant: false
value: NaN
name: W_i

metaid_0000007
type: SBMLUnitsDef
unit: 044914
unit: 044902
name: M_3

044914
type: SBMLUnit
exponent: -3.0
scale: 0
multipler: 1.0
kind: LITRE

044902
type: SBMLUnit
exponent: 3.0
scale: 0
multipler: 1.0
kind: MOLE

metaid_0000030
type: Parameter
constant: true
value: -69.37
name: dG_C1o

metaid_0000114
type: Parameter
constant: false
value: NaN
name: Mg_e

metaid_0000053
type: Parameter
constant: false
value: NaN
name: K_i

metaid_0000056
type: Parameter
constant: true
value: 1.9172E-4
name: k_Pi3

metaid_0000084
type: Parameter
constant: false
value: NaN
name: dG_C4op

metaid_0000100
type: Parameter
constant: false
value: NaN
name: J_AMP

metaid_0000017
type: SBMLUnitsDef
unit: 045154
unit: 045142
unit: 045130
name: mole_per_second_per_l_cyto

045154
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

045142
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

045130
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE

W3 CDTF: Thu Feb 02 21:34:55 GMT 2012

metaid_0000123
type: Parameter
constant: false
value: 0.01
name: ADP_x

metaid_0000004
type: SBMLUnitsDef
unit: 044829
unit: 044817
name: M

044829
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

044817
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE

metaid_0000070
type: Parameter
constant: true
value: 3.5E-6
name: k_mADP

metaid_0000107
type: Parameter
constant: false
value: NaN
name: J_K

metaid_0000041
type: Parameter
constant: true
value: 5.12861383991365E-7
name: k_dHadp

metaid_0000093
type: Parameter
constant: false
value: NaN
name: ADP_fx

metaid_0000054
type: Parameter
constant: true
value: 1.3413E-4
name: k_Pi1

metaid_0000091
type: Parameter
constant: false
value: NaN
name: ATP_fx

metaid_0000057
type: Parameter
constant: true
value: 0.02531
name: k_Pi4

metaid_0000077
type: Parameter
constant: false
value: NaN
name: dG_H

metaid_0000028
type: Parameter
constant: true
value: 0.096485
name: F

metaid_0000018
type: SBMLUnitsDef
unit: 045190
unit: 045178
unit: 045166
name: mole_per_second_per_l_mito

045190
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

045178
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

045166
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE

metaid_0000111
type: Parameter
constant: false
value: NaN
name: Cox

metaid_0000121
type: Parameter
constant: false
value: 0.001
name: Cred

metaid_0000124
type: Parameter
constant: false
value: 0.0
name: ATP_mx

metaid_0000081
type: Parameter
constant: false
value: NaN
name: J_C3

metaid_0000042
type: Parameter
constant: true
value: 2.4E-5
name: K_DT

metaid_0000094
type: Parameter
constant: false
value: NaN
name: J_MgATPi

metaid_0000045
type: Parameter
constant: true
value: 0.72376
name: W_m

metaid_0000012
type: SBMLUnitsDef
unit: 045022
unit: 045010
name: kilojoule_per_mole

045022
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE

045010
type: SBMLUnit
exponent: 1.0
scale: 3
multipler: 1.0
kind: JOULE

metaid_0000065
type: Parameter
constant: true
value: 0.0079204
name: x_ANT

metaid_0000068
type: Parameter
constant: true
value: 250.0
name: x_Hle

metaid_0000029
type: Parameter
constant: true
value: 3.0
name: n_A

metaid_0000112
type: Parameter
constant: false
value: NaN
name: ADP_me

metaid_0000135
type: Parameter
constant: false
value: 2.6E-5
name: O2

metaid_0000082
type: Parameter
constant: false
value: NaN
name: dG_C3op

metaid_0000038
type: Parameter
constant: true
value: 0.0
name: AMP_e

metaid_0000019
type: SBMLUnitsDef
unit: 045202
name: mole_per_second_per_l_mito_per_molar

045202
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

metaid_0000066
type: Parameter
constant: true
value: 339430.0
name: x_Pi1

metaid_0000069
type: Parameter
constant: true
value: 0.0
name: x_K

metaid_0000006
type: SBMLUnitsDef
unit: 044890
unit: 044878
name: M_2

044890
type: SBMLUnit
exponent: -2.0
scale: 0
multipler: 1.0
kind: LITRE

044878
type: SBMLUnit
exponent: 2.0
scale: 0
multipler: 1.0
kind: MOLE

metaid_0000052
type: Parameter
constant: false
value: NaN
name: H_i

metaid_0000026
type: Parameter
constant: true
value: 0.0013
name: ADP_e

metaid_0000078
type: Parameter
constant: false
value: NaN
name: J_DH

metaid_0000039
type: Parameter
constant: true
value: 1.77827541003892E-7
name: k_dHPi

metaid_0000120
type: Parameter
constant: false
value: 8.0E-4
name: QH2

metaid_0000122
type: Parameter
constant: false
value: 0.0
name: ATP_x

metaid_0000106
type: Parameter
constant: false
value: NaN
name: J_Hle

metaid_0000040
type: Parameter
constant: true
value: 3.31131121482591E-7
name: k_dHatp

metaid_0000092
type: Parameter
constant: false
value: NaN
name: J_MgADPx

metaid_0000090
type: Parameter
constant: false
value: NaN
name: J_MgATPx

metaid_0000011
type: SBMLUnitsDef
unit: 044998
name: per_micron

044998
type: SBMLUnit
exponent: -1.0
scale: -6
multipler: 1.0
kind: METRE

metaid_0000076
type: Parameter
constant: true
value: 327.0
name: x_Pi2

metaid_0000027
type: Parameter
constant: true
value: 2.4734
name: RT

metaid_0000079
type: Parameter
constant: false
value: NaN
name: J_C1

metaid_0000064
type: Parameter
constant: true
value: 150.93
name: x_F1

metaid_0000067
type: Parameter
constant: true
value: 2.9802E7
name: x_KH

metaid_0000008
type: SBMLUnitsDef
unit: 044938
unit: 044926
name: microM

044938
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

044926
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

metaid_0000051
type: Parameter
constant: true
value: 0.00297
name: NADtot

metaid_0000132
type: Parameter
constant: false
value: 0.001
name: Pi_i

metaid_0000134
type: Parameter
constant: true
value: 1.0E-6
name: C_im

metaid_0000037
type: Parameter
constant: true
value: 0.0
name: ATP_e

metaid_0000118
type: Parameter
constant: false
value: 0.005
name: Mg_x

metaid_0000088
type: Parameter
constant: false
value: NaN
name: Psi_i

metaid_0000105
type: Parameter
constant: false
value: NaN
name: J_AKi

metaid_0000075
type: Parameter
constant: true
value: 1000000.0
name: x_MgA

metaid_0000109
type: Parameter
constant: false
value: NaN
name: NAD_x

metaid_0000025
type: Parameter
constant: true
value: 0.001
name: Pi_e

W3 CDTF: Thu Feb 02 21:34:55 GMT 2012

metaid_0000129
type: Parameter
constant: false
value: 0.0
name: AMP_i

metaid_0000063
type: Parameter
constant: true
value: 3.2562E-5
name: x_C4

metaid_0000099
type: Parameter
constant: false
value: NaN
name: J_ADP

metaid_0000009
type: SBMLUnitsDef
unit: 044962
unit: 044950
name: per_M

044962
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

044950
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE

metaid_0000049
type: Parameter
constant: true
value: 0.0027
name: Ctot

metaid_0000130
type: Parameter
constant: false
value: 0.0
name: ATP_mi

metaid_0000133
type: Parameter
constant: false
value: 160.0
name: dPsi

metaid_0000033
type: Parameter
constant: true
value: 36.03
name: dG_F1o

metaid_0000036
type: Parameter
constant: true
value: 0.15
name: K_e

metaid_0000117
type: Parameter
constant: false
value: 0.14
name: K_x

metaid_0000136
type: Compartment
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0

ORG:
  orgname: Auckland Bioengineering Institute, The Auckland University
n:
  given: Geoffrey
  family: Nunns

metaid_0000087
type: Parameter
constant: false
value: NaN
name: Psi_x

W3 CDTF: Thu Feb 02 21:34:55 GMT 2012

metaid_0000103
type: Parameter
constant: false
value: NaN
name: H2PIi

metaid_0000003
type: SBMLUnitsDef
unit: 044805
name: mg_per_mitochondria

044805
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: GRAM

metaid_0000089
type: Parameter
constant: true
value: 1.0E-12
name: mincond

metaid_0000050
type: Parameter
constant: true
value: 0.00135
name: Qtot

metaid_0000131
type: Parameter
constant: false
value: 0.0
name: ADP_mi

W3 CDTF: Thu Feb 02 21:34:55 GMT 2012

W3 CDTF: Wed Mar 25 10:27:18 GMT 2009