VCell Tutorial. FRAP with binding
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1 VCell Tutorial FRAP with binding Create a simple biomodel and spatial (PDE) application to simulate a photobleaching experiment with both diffusion and binding.
2 In this tutorial Gain a basic introduction to the Virtual Cell interface Create a simple biomodel with species and reactions Create a compartmental (ODE) application of the model to determine steady state binding conditions. Create a spatial deterministic (PDE) application using analytic equations to create a simple geometry Define initial concentrations that are non-uniform using Boolean expressions Created a timed event in a spatial simulation. View and analyze results of a spatial simulation.
3 To re-open a model, click on the folder that the model was saved in and double-click on the model.
4 Starting from a new model Click on the compartment tool, click the dotted black lines so they turn green and click Add Membrane.
5 Click on the black lines and select Add Compartment.
6 Click the select tool. Click on the label of the first compartment. Next to Structure Name type Cyt. Next to Annotation type Cytosol.
7 Click on the membrane label. Next to Structure Name type NM (which stands for Nuclear Membrane ).
8 Click on the label of the second compartment. Next to Structure Name type Nuc. Next to Annotation type Nucleus.
9 Click the species tool. Click on six different points within the Nuc compartment to create six species.
10 To move a species, click the select tool and click a drag a species to a point.
11 Click on s0. Next to Species Name type r. Next to Annotation type RAN.
12 Click on s1. Next to Species Name type rf. Next to Annotation type RAN_FITC.
13 Click on s2. Next to Species Name type rb. Next to Annotation type RAN_Bound.
14 Click on s3. Next to Species Name type BS. Next to Annotation type Binding Sites.
15 Click on s4. Next to Species Name type rfb. Next to Annotation type RAN_FITC_Bound.
16 Click on s5. Next to Species Name type Laser. Next to Annotation type Light Source.
17 Click the select tool. Click and drag the species so that the order is from left to right r, Laser, rb, rf, BS, rfb.
18 Click the RX connection tool. Click on BS and drag your cursor, which will create a line marked <<REACTANT>>. Drop your cursor anywhere inside the Nuc compartment, which will create a reaction node called r0.
19 Click the select tool and click and drag r0 to move its position within the compartment. Drop your cursor to finalize the position of r0.
20 Using the RX connection tool, drag a line from r to r0.
21 Drag a line from r0 to rb.
22 Click on BS and drag your cursor to another rpoint in the Nuc compartment. This will create a reaction node called r1. Adjust position using the select tool.
23 Using the RX Connection tool, drag a line from rf to r1.
24 Drag a line from r1 to rfb.
25 Drag your cursor from rf to r. A reaction node r2 will be created.
26 Drag your cursor from rfb to rb. A reaction node r3 will be created.
27 Click on the catalyst tool. Click on r2 and drag your cursor, which will create a line marked <<CATALYST>>. Drop your cursor on Laser.
28 Drag a line from Laser to r3.
29 Click the select tool. Click on r0. Next to Reaction Name type RAN binding.
30 In the forward rate constant row, type.02 under the Expression column. Press Enter on your keyboard to finalize. In the reverse rate constant row, type.1 under the Expression column. Press Enter on your keyboard to finalize.
31 Click r1. Next to Reaction Name, type RAN_FITC binding.
32 In the forward rate constant row, type.02 under the Expression column. Press Enter on your keyboard to finalize. In the reverse rate constant row, type.1 under the Expression column. Press Enter on your keyboard to finalize.
33 Click r2. Click the drop down menu next to Kinetic Type. Click General [μm/s].
34 In the reaction rate row, type (Vmax*rf*Laser*((t>1.0)&&(t<1.5))) under the Expression column. Press Enter on your keyboard to finalize. The Boolean expression evaluates to 1 during the time interval from 1.0 to 1.5 secs; at other times, the expression evaluates to 0 so the bleaching reactions only occur during the specificed time interval.
35 In the Vmax row, type 50 under the Expression column. Press Enter on your keyboard to finalize.
36 Next to Reaction Name type bleaching 1.
37 Click r3. Next to Reaction Name type bleaching 2.
38 Click the drop down menu next to Kinetic Type. Click General [μm/s].
39 In the reaction rate row, type (Vmax2*rfB*Laser*((t>1.0)&&(t<1.5))) under the Expression column. Press Enter on your keyboard to finalize.
40 In the Vmax row, type 50 under the Expression column. Press Enter on your keyboard to finalize.
41 Click Applications > Add New > Deterministic.
42 Double click Application0 under the Name column. Type in Compartmental. Press Enter on your keyboard to finalize. This compartmental application will be used to determine the steady-state concentrations for the binding reaction.
43 Double click Compartmental and click Geometry > Structure Mapping. In the Size column for Cyt, NM and Nuc, type in , and respectively. Press Enter on your keyboard to finalize.
44 Click Specifications > Species. In the Initial Condition column for r, rf and BS, type in 5, 5 and 20 respectively. Press Enter on your keyboard to finalize.
45 To save your model, click File > Save As.
46 Click on a folder to select the location for your model to be saved. Type in a name under Please type in a new name: and click Save.
47 Click Simulations and the new simulation icon.
48 Click the edit simulation icon.
49 Click Solver. Type Ending Time = 30.0 Click OK.
50 Click the green play icon to run and save the simulation.
51 Click the results icon when the simulation is completed.
52 Click to exit. Press ctrl on your keyboard and click on different species to view multiple species graphs at once.
53 Right click Compartmental. Click Copy.
54 Right click Copy of Compartmental. Click Rename. Type Spatial. Press Enter on your keyboard to finalize.
55 Double click Spatial and click Geometry > Geometry Definition. Click Add Geometry > New.
56 Click Analytic Equations (2D). Click OK.
57 Double click subdomain0 and type Cyt. Press Enter on your keyboard to finalize.
58 Click Add Subdomain > Analytic.
59 Click the drop down menu next to Select Subdomain Shape:. Click Circle. Under Radius type 10. Click Add New Subdomain.
60 Double click subdomain0 and type Nuc. Press Enter on your keyboard to finalize.
61 Click the black down arrow icon to adjust the Slice View window.
62 Click Edit Domain.
63 Next to Size, type 22 for X and Y. Next to Origin, type -11 for X and Y. Click OK.
64 Your Slice View should now be a circle inside of a square.
65 Use the line tool to drag a line from the structures to their corresponding subdomains Go to Structure Mapping
66 Double click Compartmental > Simulations > results icon.
67 Click the spreadsheet icon.
68 Press Ctrl on your keyboard and select BS, rb, rf and rfb.
69 Press Ctrl on your keyboard and click the final concentrations for BS, rb, rf and rfb. Right click and click Copy.
70 Click Spatial > Specifications > Species. Click on the cell in the r row and Initial Condition column. Right click Paste All.
71 Click Select All and then click OK.
72 In the Laser row and Initial Condition column, type ((x>-2.0)&&(x<2.0)&&(y>-2.0)&&(y<2.0)). Press Enter on your keyboard to finalize.
73 Click Reactions. Click on all boxes in the Enabled column so that they are checked off if they are not already.
74 Click Simulations > edit simulation icon. If an error message appears, click OK.
75 To fix the error message, click Generated Math > Refresh Math. Click OK.
76 Go back to simulations, select Simulation1 and click the edit simulation icon.
77 Click Mesh. Click Lock aspect ratio if it is not checked off already. Type in 51 next to Mesh Size for X.
78 Click Solver. Type 50.0 next to Ending, under Time Bounds. Type 0.5 next to Output Interval. Click OK.
79 Click the green play icon to run and save the simulation.
80 Click the results icon when the simulation is completed.
81 To change the time frame being viewed, type in a value under Time or hold down and drag the slider under Time. The minimum and maximum values correspond to the colors Click here to view different species concentrations
82 Click on either Gray or BlueRed to change the color gradient.
83 Click on the line tool. Click on a point within the data and click on another point. A line will form and connect the two points. Click Plot > Spatial to create a graph of the two points.
84 Click the dot tool. Click on a point within the data and click on another point. Click Plot > Time.
85 Press ctrl on your keyboard and click on multiple species to compare concentrations over time.
86 Next: VCell PIP2 to IP3 Tutorial
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