From chemistry-request@server.ccl.net Thu Jul 20 11:19:18 2000 Received: from mail-nord.nord.univ-mrs.fr (mail-nord.nord.univ-mrs.fr [194.214.97.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA07645 for ; Thu, 20 Jul 2000 11:19:17 -0400 Received: from [194.214.94.10] ([194.214.94.10]) by mail-nord.nord.univ-mrs.fr (8.9.3/8.9.3) with ESMTP id QAA07756 for ; Thu, 20 Jul 2000 16:25:03 +0200 Mime-Version: 1.0 X-Sender: sampieri@mail-nord.nord.univ-mrs.fr Message-Id: Date: Thu, 20 Jul 2000 17:19:03 +0200 To: CHEMISTRY@server.ccl.net From: Francois Sampieri Subject: Building complex multimeric models Content-Type: text/plain; charset="us-ascii" ; format="flowed" 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 sampieri.f@jean-roche.univ-mrs.fr Laboratoire de Biochimie IFR Jean Roche Faculte de Medecine Nord MARSEILLE FRANCE