Hi Elaine, Your method worked perfectly. Thanks for help! Ben On 4/5/07, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Benjamin, There is probably more than one way to do this in Chimera, but I'd open the protein of interest six times and match it to the six monomers of the related protein. Let's call your protein "A" and the similar protein "B" (for which a hexamer is available or can be easily constructed from matrices in the PDB file). Since you didn't mention the specifics, I didn't try the whole process outlined below (not having a good example to work with), but have used the tools in other contexts.

This is kind of a brute force approach. Someone else may know of a more elegant way...

Making the hexamer of B: If the PDB file doesn't already have a hexamer, it should have matrix information that allows it to be constructed. If BIOMT, use Multiscale Models (under Tools... Higher-Order Structure). Initially, this doesn't copy all the atoms but just makes surfaces for computational expediency. Since you will need copies of all the atoms for matching, using the Multiscale Models GUI: select "All" chains, change their style to anything other than surface (e.g. Show... Ribbons). You can see the model IDs of the copies of B in the Model Panel (under Favorites). If SMTRY, CRYST1, or MTRIX you could use the Unit Cell tool (under Tools... Higher-Order Structure) instead of Multiscale Models. Relevant manual pages: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/ framemulti.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/ unitcell.html

Matching the 6 copies of A to the monomers of B: Options for matching are the "match" command or MatchMaker (GUI under Tools... Structure Comparison, also implemented as a command, "matchmaker"). If you wanted to name specific atoms to use for fitting, you'd use the "match" command. That can be tedious, and I'd try MatchMaker first - if there is some sequence similarity, even fairly low, it usually works quite well. By default, it iterates the fit so that only residues that match well in space are ultimately used to superimpose the proteins. That means the parts that are different should not interfere with a good fit of the parts that are the same. You can adjust several parameters, but for example if B is model 0, chains A-F and copies of A are models 1-6, these commands would use the matchmaker defaults: matchmaker #0:.a #1 pair ss matchmaker #0:.b #2 pair ss matchmaker #0:.c #3 pair ss matchmaker #0:.d #4 pair ss matchmaker #0:.e #5 pair ss matchmaker #0:.f #6 pair ss (pair ss just means to use the specified chains rather than trying all chain combinations between the models) You could specify other parameters with various keywords, for example the stringency to use when iterating the fit, how much weight secondary structure should have vs. the residue types in the sequence, etc. Relevant manual pages: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ matchmaker.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

On Apr 5, 2007, at 12:10 AM, Benjamin G.S. Horsman wrote:

...

Hello,

My name is Benjamin Horsman and I am a student at the University of Toronto. I have what should be a basic (possibly naive) question regarding protein modelling that I was hoping you might be able to answer for me or point my in the right direction. I have been studying the structure of a bacterial protein complex, trying to understand how it interacts with several known binding partners. The complex is known to be a hexameric homomultimer. Recently the structure of the subunit protein was solved. However, only the monomeric form of the protein was determined, and the corresponding PDB file does not contain coordinates for the multimer (i.e., no BIOMT1, BIOMT2, BIOMT3 matrix values). I would like to assemble a model of the hexameric complex for visual inspection and for some docking studies. What would be the best way to accomplish this?

There are several structures in the PDB of hexameric protein complexes composed of subunits with very close structural alignment to my protein of interest, differing in two regions of the protein that are outside of the multimer binding regions. I believe that my protein complex posses very similar or nearly identical geometry to these known complexes. Is there any way to basically insert my protein into this geometry? Can this be done in Chimera? If not, is there any program or web server that allows this to be done? Or are you aware of a better way to get this done?

Thank you for your time. Any help is greatly appreciated.

Benjamin Horsman _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev