User:Wayne Decatur/Generate Unfolded Structures

This describes how to unfold whole or parts of chains in solved structures using Pymol.

This came up because Adriana Zeledon wanted to generate structures derived from her structure of interest where parts were unfolded or folded differently. I thought this could very useful for illustrative or conceptualizing purposes for many users. For maybe simulating denaturing, conformational changes, or other dynamic processes.

Please note this will generate a distorted structure that is just for representational purposes and is not thermodynamically stable. To translate or rotate a chain or parts relative the rest of the structure see my page on moving parts or components of structures using Pymol.

Add information on breaking disulfides first and reforming others. You may wish to break the disulfides to unfold the protein more than you could obtain if you did not:

• Either pick the two atoms (pk1 and pk1, they will be called in the list to the side in Pymol) by going into 3 button Editing mode and selecting the bond between the two atoms and hitting Ctrl-right-click or choose pk1 first by hitting Ctrl-middle-click as you touch the atom and then selecting the next and doing the same.
• Once the two atoms are chosen, break the bond by entering 'unbond pk1,pk2'.
• [1gxv] is a good structure to with which to try this.

Pages with supporting information:

• Modeling and Editing Structures Page at Pymol Wiki
• Posting about using Sculpting in Pymol to manipulate structures

Add link to bottom part of my Morphing page because might want to let Morphing server generate structures transitioning between the folded and modified states for making an animation.