Creating your myosin model

You will construct two models in this chapter. These models are provided as sample models with model names tutorial MH-3-state model and tutorial energy aware MH-3.

Creating a new model

1. Go to the Cell Models page

Click on the Cell Models link from the navigation bar in your dashboard.

2. Create a new model

Click on the Create a new model button in your Cell Model page. Then a model editor page appears.

Defining your myosin head model

Defining myosin head states

To create your myosin head model, you must define states of the myosin head. Here let us create a 3-state model composed of one no binding state (P_XB) and two binding states (XB_PreR and XB_PostR). XB_PreR is a state just after the myosin head binds with the actin filament. XB_PostR is a state after the myosin rotates its head.

You can add a myosin head state by clicking Add State in the menu bar on your model editor page.

Click on the tentative state name S0 to define the state P_XB.

Click on the Select a type button to determine the type of P_XB.

Select Nobinding from the radio buttons, and click on the Initial State check box. Checking the Initial State check box indicates that XB Modeler initializes states of all myosin heads with this state.

Click on the Close button.

Click on again the tentative state name S0 to replace its name.

Input a new state name P_XB in the text box.

Click on the Rename button to finish renaming.

Then you have finished the definition of the no binding state P_XB.

Next, click Add State again to create the binding state XB_PreR. Then the new state box S1 appears on the same place as the previous state box.

Drag the state box S1 to an appropriate place.

Click on the state name S1, and then click on the Select a type button. After that, click on the Binding radio button to define the state XB_PreR as a binding state. Then click on the Close button.

Click on the state name S1 again, and then input the state name XB_PreR in the text box, and then click on the Rename button.

Now you have finished defining the state XB_PreR.

Finally, click Add State again to add the binding state XB_PosR. Then the new state box S2 appears. Drag the state box S2 to an appropriate place.

Click on the state name S2, and then click on the Select a type button. After that, click on the Binding radio button to define the state XB_PostR as a binding state, and then click on the Close button.

Click on the state name S2 again, and then input the state name XB_PostR in the text box, and then click on the Rename button.

Now you have finished defining all the three states.