Advanced Interactive Simulations: UNILIPID membrane protein insertion

We will use UnityMol and Biospring for this tutorial.

Start up the OMPT-UNILIPID-v1 exercise using the graphical interface. UnityMol will open, Biospring will start up in the background, and the visualization will connect to the running simulation. More instructions are provided in the video walkthrough.

The protein is shown as a colored surface inside placeholders for the implicit membrane. Two projections of the protein insertion are shown to immediately see the orientation normal to the membrane.

When you manipulate the simulation, be gentle, otherwise the simulation will crash and you need to start over. The main task is to:

• insert the protein in various ways into the membrane and observe the arrangements it prefers
• compare in particular insertion depths and angles
• try to pull the protein out of the membrane, or put it flat in the middle of the bilayer and observe what happens

• on the right hand side you have a python console. You can quit each tutorial by typing q() plus enter.
• you can modulate the applied force with the f(value) shortcut, where value is something in the range from roughly 0.1 to 6.0. You can check for the current value with fp().
• if you want to save the coordinates of the current scene, use s(), which writes snap.pdb in the current directory (it is indicated in the console upon saving)
• if you do not need the console, you can hide it with the arrow in a blue circle
• on the left hand side you have the main graphical menu. you can control the visualization, trajectory player speed and a few other settings, such as visual effects
• the menu can also be hidden with it’s attached arrow in a blue circle, when you don’t need it

You’ll learn:

• Work with a rigid body protein model and an implicit membrane
• Use advanced plotting functionalities
• Use multiple scene projections for a comprehensive overview

Click like 👍 on the video if you’re excited to get started!