kolmeisky1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000305) Biomodels notes: 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.

None

None

None

None

None

None

A simple kinetic model describes the processivity of myosin-v.

  • Anatoly B Kolomeisky
  • Michael E Fisher
Biophys. J. 2003; 84 (3): 1642-1650
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.

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
1.0 item
1e-06 mole
1e-06 mole litre^(-1.0)
1.0 litre
Id Name Spatial dimensions Size
compartment_ 3.0 0.000000000000001
Id Name Initial quantity Compartment Fixed
ADP 0.0 compartment_
ATP 20.0 compartment_
Pi_ 0.0 compartment_
S0 10.0 compartment_
S1 0.0 compartment_
back_step1 0.0 compartment_
back_step2 0.0 compartment_
fwd_step1 0.0 compartment_
fwd_step2 0.0 compartment_

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
Bw_1st_step S0 + ATP > S1 + Pi_ + back_step1

k_3 * S0 * ATP * exp(th_3 * Force * d / kT)
Bw_2nd_step S1 > S0 + ADP + back_step2

k_4 * S1 * exp(th_4 * Force * d / kT)
Fw_1st_step S0 + ATP > S1 + Pi_ + fwd_step1

k_1 * S0 * ATP * exp(-th_1 * Force * d / kT)
Fw_2nd_step S1 > S0 + ADP + fwd_step2

k_2 * S1 * exp(-th_2 * Force * d / kT)

Global parameters

Id Value
Force 0.0
S_tot 0.0
V 0.0
V_ave 0.0
d 36.0
kT 4.1164
k_1 0.7
k_2 12.0
k_3 0.000005
k_4 0.000006
tau 0.0
th_1 -0.01
th_2 0.045
th_3 0.58
th_4 0.385

Local parameters

Id Value Reaction

Assignment rules

Definition
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))
V_ave = d * ((fwd_step1 + fwd_step2) / 2.0 - (back_step1 + back_step2) / 2.0) / (S_tot * time)
V = d * ((Fw_1st_step + Fw_2nd_step) / 2.0 - (Bw_1st_step + Bw_2nd_step) / 2.0) / S_tot
S_tot = S0 + S1

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments