Team:ESBS-Strasbourg/Project/visual

• Animation
• Molecular Structure of the System
• Molecular Structure of 1 unit
• System description
• Assembly
• Tagged protein
• Mechanical description
• Workstation

All animation were modeled in blender 2.54 beta. Blender is a open source program for 3D animation.
(http://www.blender.org/)
The two videos cover the assembly of the ClpXP system and the degradation of the tagged protein. It is important to note that protein proportions a molecular structure are not entirely respected in the animation. Also the change of the phytochrome B conformation from the Pf state into the Pfr state is symbolized by a change of color. However, the hexametric structure of ClpX and the heptametrical structure of ClpP were schematically shown. Picture 1 and Picture 2 give a better understanding between the molecular structure and the schematic animation. Picture 1 (Molecular Structure of the System) describes the modeled system in detail. Picture 2 (Tagged protein) describes the protein in detail.

 

The left shows the molecular structure of the ClpX hexamere fused to the phytochrome B and the
schematic image in the animation

This shows the molecular structure of the trimetric unit of the ClpX fused to phytochrome B
and the schematic image in the animation.

This picture shows a detailed information about the animated ClpXP system. Phytochrome B in the inactive state and the ClpP are in a bright petrol color. The ClpX unit is shown in a dark petrol color. The conformation change of the phytochrome B from the Pf to the Pfr state is shown with a color change.

In this video the assembly of the ClpXP system in the inactive state is shown. First joining of the two trimetric subunit interconnected with a linker is shown. After the ClpX hexamere is created to the two units of the ClpP joins and built a multi protein complex.

This picture shows the test protein GFP colored green with the PIF3/6 fused to the N-terminus of the protein colored violet and at the C-terminus the DAS tag colored yellow. The gray part is the fused 20 amino acid linker. In the little square at the right bottom of the image you can see the schematic image found in the animation.

This video shows the working system. In the beginning the Phytochrome B is not in its active Pfr state and so the tagged protein GFP is not degraded. After a short red light impulse the conformation of the phytochrome B changes to its active state. Now the six tagged GFP proteins can interact over the PIF- Phytochrome B system with the ClpX, which lead them to the ClpP. The ClpP is the catalytic core of the protease.

click to enlarge

This image shows how the work in blender 2.54beta looks like. It was taken during the modeling and animation of the mechanics video.