054824
constant: true
value: 4.1164
type: Parameter

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

515469
stoichiometry: 1.0
species: 054789
type: SpeciesReference

515493
stoichiometry: 1.0
species: 054798
type: SpeciesReference

515543
stoichiometry: 1.0
species: 054792
type: SpeciesReference

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

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

515397
stoichiometry: 1.0
species: 054790
type: SpeciesReference

BIOMD0000000305
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
species: 054795
parameter: 054833
rule: 054814
species: 054790
parameter: 054830
parameter: 054819
created:
  W3 CDTF: Fri Sep 29 23:36:52 BST 2006
modified:
  W3 CDTF: Fri Nov 04 14:34:25 GMT 2011
parameter: 054839
parameter: 054836
reaction: 054802
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
species: 054796
length unit: length
volume units: volume
is: MODEL6623628741
time units: 447703
type: SBMLModel
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

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

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

054837
constant: false
value: NaN
type: Parameter

515567
stoichiometry: 1.0
species: 054799
type: SpeciesReference

054795
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
type: Species

054789
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
type: Species

515312
unit: 515325
name: micromole
type: SBMLUnitsDef

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

515530
stoichiometry: 1.0
species: 054790
type: SpeciesReference

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

515615
stoichiometry: 1.0
species: 054795
type: SpeciesReference

515421
stoichiometry: 1.0
species: 054793
type: SpeciesReference

515349
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE
type: SBMLUnit

054801
is: SBO:0000409
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: 054788
type: Species

515409
stoichiometry: 1.0
species: 054792
type: SpeciesReference

054821
constant: true
value: 0.0
type: Parameter

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

054836
constant: false
value: NaN
type: Parameter

515325
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE
type: SBMLUnit

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

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

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

515591
stoichiometry: 1.0
species: 054792
type: SpeciesReference

515627
stoichiometry: 1.0
species: 054801
type: SpeciesReference

054793
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
type: Species
initial concentration: 0.0

substance
unit: 515300
name: molecules
type: SBMLUnitsDef

515481
stoichiometry: 1.0
species: 054795
type: SpeciesReference

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

515555
stoichiometry: 1.0
species: 054793
type: SpeciesReference

054802
product: 515433
fast: false
reactant: 515385
type: Reaction
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

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

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

515457
stoichiometry: 1.0
species: 054792
type: SpeciesReference

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

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

515361
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

515337
unit: 515361
unit: 515349
name: uM
type: SBMLUnitsDef

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

515300
exponent: 1.0
scale: 0
multipler: 1.0
kind: ITEM
type: SBMLUnit

515603
stoichiometry: 1.0
species: 054789
type: SpeciesReference

volume
unit: 515373
name: litre
type: SBMLUnitsDef

515433
stoichiometry: 1.0
species: 054796
type: SpeciesReference

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

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

515385
stoichiometry: 1.0
species: 054789
type: SpeciesReference

054798
is: SBO:0000409
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: 054788
type: Species

515517
stoichiometry: 1.0
species: 054789
type: SpeciesReference

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