User:Wayne Decatur/Generate Unfolded Structures

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Theoretical Structure Will Result: The protein structure that will result from manipulations suggested on this page will be theoretical, and hence should be interpreted with caution.

This describes how to unfold whole or parts of chains in solved structures using Pymol. This maintains the covalent bonds. Also below is how to alter disulfide bonds in a structure using PyMOL.


Contents

2024 automated or scripted way to 'unfold' a range of residues in a protein structure

I provide a Jupyter notebook file and an environment where it will actively work to let PyMOL do this is largely automated way after setting a few settings. The notebook will produce a modified PDB file with the specified span of amino acids adjusted to have phi, psi and omega angles representing an unfolded state. I'll come back to the specifics on how to get started doing that after mentioning where can find more details and a script for doing that in the standard PyMOL GUI-based software. For the details on that and a script you can edit and run with your favorite protein structure directly in PyMOL, see my answer here to the question on Biostars entitled 'How can I linearize certain residues within an existing protein structure to create a dumbbell-shaped structure?'.

Importantly, you can do with an PDB that has a protein chain by specifying the PDB id code and chain and region without needing to install anything on your system. It works for entries in the Protein Data Bank if you have the PDB id code and the chain designation. Go here and press the 'launch binder' badge (or alternatively just click here to launch) and then when the Jupyter session comes up, choose from the available notebooks, 'Demo of Unfolding Region of Protein Chain via PyMOL'. Then step through running the notebook. I suggest step through first running it with the settings there to see how it works and then change the settings to what you want for the next run. It uses PyMOL headlessly in the session to do the adjustments of the torsional angles. It should be adjustable with some hand editing to use custom, private/un-released PDB files uploaded to the session, too. (You can drag and drop from your local system into the file browser panel that appears in the left side of the JupyterLab interface in the session.) Download the modified PDB file from the temporary session.

Below is the older way of doing this with Auto-Sculpting in PyMOL...

Older way with Auto-Sculpting in 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 that while maintaining covalent bonds, this process 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.

To enable yourself to 'drag' a chain in a structure however you want:

See the movie guides with step by step instructions at Sculpting protein conformations.

  • Load the structure into Pymol with all the consoles open.
  • Toggle in the bottom right corner the text next to 'Selecting' until 'Residues' comes up. ('Selecting' currently shows as 'Picking' in Mac Pymol1.3r1.)
  • put the mouse into 3-button editing mode either using 'Mouse' menu in upper console or toggle it by clicking text next to 'Mouse mode'. (On Max currently doing this causes the 'Picking' setting to look like it changes to atoms but holding down control key on the Mac and dragging with left click still drags chain around elastic and over time it settles to a form where bonds still constrained to proper length. )
  • Click on Auto-Sculpting in the Sculpting menu that is under the Build menu.
  • Use control-left-click-and-drag to click on the chain of interest and drag to move the chain where you want it to go and it will move towards your mouse like it is trying to catch up but is in viscous solution.
  • When things are where you want for that part of the chain, quickly click 'Deactivate' under the Sculpting menu. The chain will freeze where it is.
  • If you view in cartoons you will see that the secondary structure assignments are maintained from before you modified the structure. To recalculate the secondary structure based on the new one enter in the command line 'dss [object-name/pdb-code]'
  • Save your modified structure.


Disulfide bonds are covalent bonds that will remain maintained when you do the above process; however this may not be the behavior you wish for some or all of these bonds. You may wish to break the disulfides to unfold the protein more than you could obtain if you did not using the above process.

Breaking disulfide bonds with Pymol:

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

If you want to form new disulfide bonds after you modified the structure:

  • Use the 'bond' command to link the gamma sulfur atoms of the resides of interest. For example, if we were joining residues 37 and 82, 'bond 37/sg,82/sg'
  • Then enter the command 'unpick' to hide the 'bond baton' that gets displayed.

Morphing

To make clear the changes that took place to get to the modified structure, you may want to submit the original and modified structures to the Yale Morph Server and let it generate the steps needed to go from one structure to the other and make an animation with this collection of structures. You may wish to look at the Morphs page or Eric Martz's page on the lac repressor morphs or my page on a complex morph that I did for more information on creating morphs.

Pages with supporting information

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur, Eric Martz

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