BIOMD0000000305
type: SBMLModel
parameter: 054831
species: 054801
parameter: 054821
is version of: GO:0000146
compartment: 054788
species: 054789
species: 054799
area units: area
is part of: GO:0030048
reaction: 054806
curated: true
parameter: 054837
units def: volume
substance units: substance
parameter: 054827
reaction: 054803
name: Kolomeisky2003_MyosinV_Processivity
parameter: 054834
parameter: 054824
rule: 054811
rule: 054813
created:
  W3 CDTF: Fri Sep 29 23:36:52 BST 2006
species: 054795
parameter: 054833
rule: 054814
species: 054790
parameter: 054830
parameter: 054819
modified:
  W3 CDTF: Fri Nov 04 14:34:25 GMT 2011
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
parameter: 054839
parameter: 054836
reaction: 054802
species: 054796
length unit: length
volume units: volume
is: MODEL6623628741
time units: 447703
parameter: 054822
rule: 054816
parameter: 054818
occurs in: http://identifiers.org/taxonomy/2759
species: 054793
units def: 515312
species: 054792
parameter: 054828
reaction: 054804
notes: This is the 2 state model of Myosin V movement described in the article: A simple kinetic model describes the processivity of myosin-v. Kolomeisky AB , Fisher ME Biophys. J. 84(3):1642-50 (2003); PubmedID: 12609867 Abstract: Myosin-V is a motor protein responsible for organelle and vesicle transport in cells. Recent single-molecule experiments have shown that it is an efficient processive motor that walks along actin filaments taking steps of mean size close to 36 nm. A theoretical study of myosin-V motility is presented following an approach used successfully to analyze the dynamics of conventional kinesin but also taking some account of step-size variations. Much of the present experimental data for myosin-V can be well described by a two-state chemical kinetic model with three load-dependent rates. In addition, the analysis predicts the variation of the mean velocity and of the randomness-a quantitative measure of the stochastic deviations from uniform, constant-speed motion-with ATP concentration under both resisting and assisting loads, and indicates a substep of size d(0) approximately 13-14 nm (from the ATP-binding state) that appears to accord with independent observations. The model differs slightly from the published version. The ATP and ADP bound forms of myosin are called S0 and S1. The state transition and binding constants are called k_1, k_2, k_3 and k_4 instead of k 0 0 , u 0 1 , k ' 0 and w 0 1 . Similarly the state loading factors are named th_1, th_2, th_3 and th_4 instead of θ + 0 , θ + 1 , θ - 0 and θ - 1 . The species fwd_step1, fwd_step2, back_step1 and back_step2 count the number of state changes of each kind the myosine molecules have taken over time. The model can be evaluated in a deterministic continuous or stochastic discreet fashion. The parameter V holds the (forward) speed at each time point, the V_avg the overall way divided by the simulation time and the amount of myosine molecules. Originally created by libAntimony v1.4 (using libS…
parameter: 054825
units def: substance
species: 054798
units def: 515337
is described by: http://identifiers.org/pubmed/12609867

054831
type: Parameter
is: SBO:0000022
constant: true
value: 6.0E-6

054801
type: Species
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constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: 054788

054788
type: Compartment
is: SBO:0000290
constant: true
size: 1.0E-15
spatial dimensions: 3.0

054821
type: Parameter
constant: true
value: 0.0

054789
type: Species
is: GO:0031475
is: SBO:0000297
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 10.0
in compartment: 054788

054799
type: Species
is: SBO:0000409
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: 054788

054806
type: Reaction
product: 515627
product: 515603
is: SBO:0000180
product: 515615
reversible: false
fast: false
kinetic law: 515639
reactant: 515591

515627
type: SpeciesReference
stoichiometry: 1.0
species: 054801

515603
type: SpeciesReference
stoichiometry: 1.0
species: 054789

515615
type: SpeciesReference
stoichiometry: 1.0
species: 054795

054795
type: Species
in compartment: 054788
initial concentration: 0.0
is: SBO:0000247
is: http://identifiers.org/pubchem.substance/3310
boundary condition: true
is: CHEBI:16761
has only substance units: false
substance units: 515312
constant: false
initial amount: NaN
is: C00008

515312
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name: micromole

515325
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scale: -6
multipler: 1.0
kind: MOLE

515591
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species: 054792

054792
type: Species
constant: false
in compartment: 054788
is: SBO:0000297
has part: CHEBI:16761
initial amount: 0.0
initial concentration: NaN
boundary condition: false
has only substance units: true
has version: GO:0031475

054837
type: Parameter
constant: false
value: NaN

volume
type: SBMLUnitsDef
unit: 515373
name: litre

515373
type: SBMLUnit
exponent: 1.0
scale: 0
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kind: LITRE

substance
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unit: 515300
name: molecules

515300
type: SBMLUnit
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kind: ITEM

054827
type: Parameter
is: SBO:0000380
constant: true
value: 0.045

054803
type: Reaction
product: 515493
reactant: 515457
product: 515481
is: SBO:0000180
reversible: false
kinetic law: 515505
fast: false
product: 515469

515493
type: SpeciesReference
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054798
type: Species
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boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.0
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515457
type: SpeciesReference
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species: 054792

515481
type: SpeciesReference
stoichiometry: 1.0
species: 054795

515469
type: SpeciesReference
stoichiometry: 1.0
species: 054789

054834
type: Parameter
is: SBO:0000360
constant: false
value: NaN

054824
type: Parameter
constant: true
value: 4.1164

054833
type: Parameter
is: SBO:0000380
constant: true
value: 0.385

054790
type: Species
initial concentration: 20.0
is: CHEBI:15422
is: SBO:0000247
in compartment: 054788
boundary condition: true
constant: false
is: C00002
has only substance units: false
initial amount: NaN
substance units: 515312
is: http://identifiers.org/pubchem.substance/3304

054830
type: Parameter
is: SBO:0000380
constant: true
value: 0.58

054819
type: Parameter
is: SBO:0000380
constant: true
value: -0.01

054839
type: Parameter
is: SBO:0000347
constant: false
value: NaN

054836
type: Parameter
constant: false
value: NaN

054802
type: Reaction
product: 515433
fast: false
reactant: 515385
product: 515421
reactant: 515397
has part: http://identifiers.org/ec-code/3.6.4.1
product: 515409
reversible: false
kinetic law: 515445
is: SBO:0000376

515433
type: SpeciesReference
stoichiometry: 1.0
species: 054796

054796
type: Species
is: SBO:0000409
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: 054788

515385
type: SpeciesReference
stoichiometry: 1.0
species: 054789

515421
type: SpeciesReference
stoichiometry: 1.0
species: 054793

054793
type: Species
in compartment: 054788
boundary condition: true
substance units: 515312
constant: false
has only substance units: false
is: C00009
initial amount: NaN
is: SBO:0000247
is: CHEBI:18367
initial concentration: 0.0

515397
type: SpeciesReference
stoichiometry: 1.0
species: 054790

515409
type: SpeciesReference
stoichiometry: 1.0
species: 054792

054822
type: Parameter
is: SBO:0000466
constant: true
value: 36.0

054818
type: Parameter
is: SBO:0000023
constant: true
value: 0.7

054828
type: Parameter
is: SBO:0000023
constant: true
value: 5.0E-6

054804
type: Reaction
fast: false
product: 515567
reactant: 515517
kinetic law: 515579
product: 515555
reversible: false
product: 515543
has part: http://identifiers.org/ec-code/3.6.4.1
reactant: 515530
is: SBO:0000376

515567
type: SpeciesReference
stoichiometry: 1.0
species: 054799

515517
type: SpeciesReference
stoichiometry: 1.0
species: 054789

515555
type: SpeciesReference
stoichiometry: 1.0
species: 054793

515543
type: SpeciesReference
stoichiometry: 1.0
species: 054792

515530
type: SpeciesReference
stoichiometry: 1.0
species: 054790

054825
type: Parameter
is: SBO:0000022
constant: true
value: 12.0

515337
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unit: 515349
name: uM

515361
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515349
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kind: MOLE