The Conformational Changes of ATP Synthase


This animation is my first experimentation with 3D animation. It was created in Maxon Cinema 4D. It is showing the conformational changes of the ATP synthase f1 complex (blue). The beta subunits of the f1 complex (dark blue) cycle through three conformational changes known as open (ADP and phospate (P) enter the active site), loose( the protein closes around the ADP and P binding them loosely), and tight (binding the ADP and P to produce ATP). I loaded Protein Databank (PDB) files into Cinema 4D through the use of the embedded Python Molecular Viewer (ePMV).

The f1 complex contains 3 beta subunits. The PDB file I used for the f1 complex (pdb entry 1COW) shows each of the beta subunits in a different conformation (open, loose, or tight). I used this page on the Swiss Institute of Bioinformatics site as a reference description of the 1COW PDB file. To create the conformational change animations I primarily used this tutorial on the ePMV website that describes how to use PDB files to make conformational change animations using a morph server. I edited out the individual beta chains from the 1COW pdb file and used the morph server to genterate new .pdb files that represent likely intermediates between the two conformational states. I used the ePMV data player and Cinema4D’s “metaballs” to create the conformation change animation.

I first rendered some test animations to make sure the morphing .pdb files were working:

I used this animation by Said Sannuga of the Medical Research Council in the UK to judge the accuracy of my conformational changes in relation the the rotation of the axle subunit.

In the future I will use Adobe After Effects to add text descriptions to the animation and pauses at each confomational change to describe what is hapening at each step. I would also like to add the movement of protons arcross the membrane throught ATP Synthase’s proton channel (orange). The animation also needs to be revisited to get more accurate contact between the axle (yellow) and f1 alpha and beta subunits(blue).