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BIOMD0000000305 - Kolomeisky2003_MyosinV_Processivity

 

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Reference Publication
Publication ID: 12609867
Kolomeisky AB, Fisher ME.
A simple kinetic model describes the processivity of myosin-v.
Biophys. J. 2003 Mar; 84(3): 1642-1650
Department of Chemistry, Rice University, Houston, Texas 77005-1892, USA. tolya@rice.edu  [more]
Model
Original Model: BIOMD0000000305.xml.origin
Submitter: Nicolas Le Novère
Submission ID: MODEL6623628741
Submission Date: 29 Sep 2006 22:36:52 UTC
Last Modification Date: 07 Apr 2014 01:49:47 UTC
Creation Date: 29 Sep 2006 22:36:52 UTC
Encoders:  Lukas Endler
set #1
bqbiol:hasTaxon Taxonomy Eukaryota
bqbiol:isVersionOf Gene Ontology regulation of actin filament length
Gene Ontology microfilament motor activity
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 k0 0, u0 1, k' 0 and w0 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 libSBML 3.4.1)

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 12609867 Submission Date: 29 Sep 2006 22:36:52 UTC Last Modification Date: 07 Apr 2014 01:49:47 UTC Creation Date: 29 Sep 2006 22:36:52 UTC
Mathematical expressions
Reactions
Fw_1st_step Fw_2nd_step Bw_1st_step Bw_2nd_step
Rules
Assignment Rule (variable: S_tot) Assignment Rule (variable: V) Assignment Rule (variable: V_ave) Assignment Rule (variable: tau)
Physical entities
Compartments Species
compartment_ S0 ATP S1
Pi_ ADP fwd_step1
fwd_step2 back_step1 back_step2
Global parameters
k_1 th_1 Force d
kT k_2 th_2 k_3
th_3 k_4 th_4 S_tot
V V_ave tau  
Reactions (4)
 
 Fw_1st_step [S0] + [ATP] → [S1] + [Pi_] + [fwd_step1];  
 
 Fw_2nd_step [S1] → [S0] + [ADP] + [fwd_step2];  
 
 Bw_1st_step [S0] + [ATP] → [S1] + [Pi_] + [back_step1];  
 
 Bw_2nd_step [S1] → [S0] + [ADP] + [back_step2];  
 
Rules (4)
 
 Assignment Rule (name: S_tot) S_tot = S0+S1
 
 Assignment Rule (name: V) V = d*((Fw_1st_step+Fw_2nd_step)/2-(Bw_1st_step+Bw_2nd_step)/2)/S_tot
 
 Assignment Rule (name: V_ave) V_ave = d*((fwd_step1+fwd_step2)/2-(back_step1+back_step2)/2)/(S_tot*time)
 
 Assignment Rule (name: tau) tau = (k_1*ATP*exp((-th_1)*Force*d/kT)+k_2*exp((-th_2)*Force*d/kT)+k_3*ATP*exp(th_3*Force*d/kT)+k_4*exp(th_4*Force*d/kT))/(k_1*ATP*exp((-th_1)*Force*d/kT)*k_2*exp((-th_2)*Force*d/kT)+k_3*ATP*exp(th_3*Force*d/kT)*k_4*exp(th_4*Force*d/kT))
 
  Spatial dimensions: 3.0  Compartment size: 1.0E-15
 
 S0
Compartment: compartment_
Initial amount: 10.0
 
 ATP
Compartment: compartment_
Initial concentration: 20.0  (Units: umole)
 
 S1
Compartment: compartment_
Initial amount: 0.0
 
 Pi_
Compartment: compartment_
Initial concentration: 0.0  (Units: umole)
 
 ADP
Compartment: compartment_
Initial concentration: 0.0  (Units: umole)
 
 fwd_step1
Compartment: compartment_
Initial amount: 0.0
 
 fwd_step2
Compartment: compartment_
Initial amount: 0.0
 
 back_step1
Compartment: compartment_
Initial amount: 0.0
 
 back_step2
Compartment: compartment_
Initial amount: 0.0
 
Global Parameters (15)
 
 k_1
Value: 0.7
Constant
 
 th_1
Value: -0.01
Constant
 
   Force
Constant
 
 d
Value: 36.0
Constant
 
   kT
Value: 4.1164
Constant
 
 k_2
Value: 12.0
Constant
 
 th_2
Value: 0.045
Constant
 
 k_3
Value: 5.0E-6
Constant
 
 th_3
Value: 0.58
Constant
 
 k_4
Value: 6.0E-6
Constant
 
 th_4
Value: 0.385
Constant
 
  S_tot
Value: NaN
 
   V
Value: NaN
 
   V_ave
Value: NaN
 
  tau
Value: NaN
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000305

Curator's comment: (updated: 27 Jan 2011 05:29:55 GMT)

Reproduction of figure 3 of the original publication. Copasi 4.6 was used to perform a parameter scan over the given range of applied force with 100 intervals. At each point a time course simulation was calculated for 100 sec to retrieve a equilibrated value of the velocity.

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