[Chimera-users] How to predict/model the structure of two known structure proteins

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 21 14:01:37 PST 2015


Dear Hoang,
Yes, but there are a few steps.  You would need to:

(1) use a text-editor to make a plain text fasta-format file of the fusion protein sequence, if you don’t already have such a file.  Fasta format description:
<http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml>
Make the name of your file end with “.fasta"

(2) open the fasta file in Chimera.  Then from sequence window menu: Info… Blast Protein to search the PDB for matching structures.  In the Blast Protein results, find the two structure proteins and choose both lines (click, ctrl-click in the results dialog), then click the “Show in MAV” and “Load Structure” buttons at the bottom of the dialog.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/blast.html>

(3) now you will have a new sequence alignment window with 3 sequences in it: the fusion protein and the two protein structures, and in the main Chimera window, the two structures.

(4) In Chimera, delete any extra protein chains.  In other words, if there are extra copies of those structures, just delete them so that you have only one copy to use as the template.  Make sure that the remaining copy of each is associated with its sequence in the alignment (sequence alignment window menu: Structures… Associations…)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#assocpanel>

(5) position the two structures so that the termini are in a somewhat reasonable place relative to each other to template the fusion protein.  You can “freeze” one in place by deactivating it and move just the other with the mouse as described here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>

6) from the sequence alignment window menu choose:  Structure… Modeller (homology) to show the Modeller dialog.  Choose the query as the target and both structures as the template, etc. as in the modeling tutorials.  You may also want to turn on “Use thorough optimization” in the Advanced Options section. I don’t know which homology-modeling tutorial you have been using, but here is one:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html#modeller>

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

On Jan 21, 2015, at 2:16 AM, Phan Trong Hoang <hoang at ipk-gatersleben.de> wrote:

> Dear UCSF developers,
> I am Hoang, working in IPK in Germany. I am following your series online tutorials about how to use UCSF Chimera. This program is very useful for me. However, I did not see your video showing how to predict/model the structure of a fusion protein that is made by combination of two known structure proteins in PDB (for example gi|534286646|pdb|4KRN| and gi|390136394|pdb|4DDF|A).
> Is this function available in your software? If yes can you show me how to manipulate with it.
> I would like appreciate it very much
> Thank you for your attention and I am looking forward to hearing from you.
> Best regards
> Hoang Phan




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