[chimera-dev] Building a multimer model

[Benjamin G.S. Horsman]

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