Subject: Building complex multimeric models

From: Francois Sampieri <[email-masked]>
Date: Thu, 20 Jul 2000 17:19:03 +0200

Hi all,

I had to construct a model of a protein complex derived from 
experimental 3D structures. I believed that it could be obtained 
without special skills.

The templates were:

1- A protein P made up of two well separated domains covalently 
attached: A and B, such:
                   A-B

2- A non-covalent complex between 3 protein subunits C, D, and E:
                 C==D==E

My purpose was to split the protein P into its two domains and to 
covalently attach each domain to the C and E units with a polypetidyl 
arm:

           A       and       B
          /                   \
         C                     E

to eventually obtain, in the presence of D, a new complex:

                  A=B
                 /   \
                C==D==E

with A=B bound non-covalently.

I worked with InsightII-Biopolymer from MSI, and I succeded in 
splitting the starting protein model into its two separate domains, 
then building the arms (I'm so proud of that  ;-), but a problem 
arose when I attempted to bind these arms to their respective C/E 
unit, since when creating the covalent bond between, say the A-arm 
and C, the whole C==D==E complex went into a very embarrassing 
orientation in the space, due to the rigid geometry of the bond 
created. Seems as if there is only one way to make a new bond in 
InsightII.
I tried lots of methods without success and now I wonder if this 
could be possible with this program.

Unless I missed some hidden tricks in InsightII, my question is: is 
there any other program (running on a SGI O2; IRIX 6.5) capable of 
building bonds with 'soft' (not rigid) geometry?
Thus, it would de possible to build the complex with the actual 
conformations and orientations of A-B and of C==D==E bound to the 
polypeptide arms, then energy-minimize the arms to make them to 
conform to the standard geometry.
A program with only building capabilities would be satisfactory, 
provided that it should be able to create pdb files and handle more 
than 15.000 atoms.

I hope I'have not been too obscure.

Thanks and best wishes to all!

Francois

Francois Sampieri
[email-masked]
Laboratoire de Biochimie
IFR Jean Roche
Faculte de Medecine Nord
MARSEILLE
FRANCE