[Chimera-users] Re: Questions about phosphorylating residues on proteins

Thank you so much, This is all very helpful, I really appreciate it. Thank you, Andy Bui

On Oct 16, 2023, at 9:23 AM, Elaine Meng wrote:

Dear Andy, There are a few different ways you could do it... what is easiest depends on whether you are familiar with text-editing PDB format or using the Build Structure tool in Chimera.

(A) using Build Structure: add/modify atoms to the sidechain manually in a stepwise process and change residue name using Build Structure (in Chimera menu under Tools... Structure Editing, use the Modify Structure part). https://www.google.com/url?q=https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html&source=gmail-imap&ust=1698078229000000&usg=AOvVaw02XySkDhpB2P80DulRSHCs https://www.google.com/url?q=https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html%23modify&source=gmail-imap&ust=1698078229000000&usg=AOvVaw1vmgy0z-1rpgRdnTTLK5ce

- OR -

(B) text-editing PDB files: open a separate PDB file with the modified residue (phosphoserine, phosphothreonine, or phosphotyrosine), superimpose on existing residue backbone atoms, save modified residue PDB "relative to" your protein, then manually with text-editor substitute in the coordinates of the newly saved PDB of the modified residue into the PDB of the original structure. May also need to renumber atoms, edit residue name, etc. https://www.google.com/url?q=https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html%23pdb&source=gmail-imap&ust=1698078229000000&usg=AOvVaw12ydEeUfEx95-viIo0UL7m

- OR -

(C) install the SwissSideChain plugin to Chimera and then use it to "mutate" serine to SEP or SEP2, threonine to TPO or TPO2, tyrosine to PTR or PTR2 (see second link below for explanation of residue names). The plugin creates a new command "swapnaa" for doing the mutation.

Plugin and installation: https://www.google.com/url?q=https://swisssidechain.ch/visualization/chimera.php&source=gmail-imap&ust=1698078229000000&usg=AOvVaw2-BQxt6ipZkTeFKQIk4GfR

List of non-natural amino acids available via this plugin: https://www.google.com/url?q=https://www.swisssidechain.ch/browse/family/table.php?family%3Dall&source=gmail-imap&ust=1698078229000000&usg=AOvVaw2Hb2FaGZvxwV4XRUh8PG2N

Methods (A) and (B) are also available in our newer program, ChimeraX, but it does not have a SwissSideChain plugin: https://www.google.com/url?q=https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html%23modify&source=gmail-imap&ust=1698078229000000&usg=AOvVaw1I1mnwdoAFxibQCcmcV9_S https://www.google.com/url?q=https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html%23pdb&source=gmail-imap&ust=1698078229000000&usg=AOvVaw2hzg-E1O-Fy-A5haIVn1dg

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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On Oct 15, 2023, at 9:16 PM, Hoang-Long Bui via Chimera-users wrote: Hello, My name is Andy and I am a student researcher at San Jose State University with the Grazioli Research Group. I am trying to research a section of a protein using your software and was wondering if I could phosphorylate certain residues of the protein, and how. Thank you! Andy Bui