Medical Illustration > ATP Synthase

ATP Synthase

This illustration communicates the 3D structure of ATP Synthase, a membrane protein that produces adenosine triphosphate (ATP).  It was created using X-ray crystallography and NMR spectroscopy data made available through the Protein Databank. The illustration colour-codes the ATP synthase protein by function and chain.

The data was imported into  Chimera and then exported into Adobe Photoshop to finalize the illustration. This illustration was an experiment in emulating the illustration style of David Goodsell’s  “Molecule of the Month”  illustrations on the Protein Databank’s website. I used a tutorial written by Dr. Bonnie Scott that detailed a method of achieving this illustration style.

ATP Synpthase

Process Work

Process Images
ATP Synthase Process Images. These three images were exported from Chimera and combined in Adobe Photoshop to create the final illustration above.




The Conformational Changes of ATP Synthase: An experiment in data-derived 3D animation


This animation was my first experimentation with 3D animation, created in Maxon Cinema 4D. The animation shows 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:

  1. “open” (ADP and phospate (P) enter the active site).
  2. “loose” (the protein closes around the ADP and P binding them loosely).
  3. “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.