[BiO BB] Generate Quaternary structure of protein from monomer

vidya kothekar vidyakothekar at yahoo.com
Mon Mar 7 12:51:21 EST 2005

Dear Subhash
I find people are having some confusion regarding
crystal packing, and symmetry elements associated with
it and multimeric structure of the proteins. 

Crystal symmetry and packing you can talk if the
crystal structure is solved and symmetry groups are
observed. Obtaining coordinates of different chains is
no problem. There are plenty of programs and tools
available with the graphics software or Work stations
as O. Even if these are not available, one can write
the program very easily and generate the coordinates
using PDB coordinates of the monomers using text book
level information for the transformation.

However, the arrangement of the subunits in the
quarternary structure of a protein is a complicated
task. It is even more complecated in case of modelled
protein or for proteins for which part of the
structure is solved. It is true that, if it is not
done then it is very difficult to predict the active

In reality there is no method. The problem is first
one should identify constituents of the multimeric
structures as same chain, chemically modified chins
etc. It is possible to use series of experimental
techniques to get tentative guess for protein-protein
interaction. Later one can use combination of
experiment and theory to arrive at the multimeric

In case one has a good template and one is convinced
that the modelled proteins and the template for which
the X-ray structure is available have the same
function and also have same packing, one can
extrapolate the results on template and use graphic
software or O or write a small program
Good luck.

--- Subhash Agarwal <smagarwal at yahoo.com> wrote:

> Hi all
> As James and Boris have written that the solution
> they
> are able to provide depends on the knowledge of the
> user with regards to progam O and understanding of
> crystallography. So i would like to say that neither
> i
> have used program O before nor i am
> cryatallographer.
> So making things difficult for me.
> While Dr.Nagasuma Chandra writes that i need to be
> sure that whether my model has the same quaternary
> arrangement as my template or not. Sir in this
> regard
> i would like to say that the sequence (Query) i have
> picked for modelling has known function
> (experimentally characterised) and for the same the
> template are avaliable and therfore i started
> working
> on this protein. 
> My need to generate the quaternary structure is due
> to
> reason that i need to observe the active site in the
> generated model. Also u state that " it is
> relatively
> simple to apply the translational and rotational
> matrices to obtain a multimer". Can u tell me how
> will
> u suggest me to do this.
> Moreover if any of u feels that should mail pdb of
> generated model and the PDB id of template used,
> that
> can also be done by me.
> Also i am thankful to everybody as u r trying to
> help
> me by responding. Please continue to provide
> support.
> Thanks
> Subhash Agarwal 
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