Hi Carl, I have never attempted docking two proteins as you describe using XPLOR. One thing that you may want to try is to use MODULE - http://www.nmr.chem.uu.nl/education/module/module_doc/practical.html - or some other rigid-body RDC refinement tool just to see if you can get the correct orientation of the two proteins; i.e., a reasonable fit to your RDC data independent of trying to fit the chemical shifts as well. Maybe this can be done in XPLOR as well to just orient the domains (use RDCs only and make sure the domain are far enough apart so as not to clash.) This will not give any indication of the binding surfaces, but the chemical shift information that you have should allow with the final docking if the RDC data alone produces a good fit. If you have cross-linking data or paramagnetic distance restraints those would also be a great help.
We recently used MODULE followed by XPLOR refinement to determine the orientation of two domains in a phosphatase, see the supporting information in: http://www.sciencedirect.com/science/article/pii/S0960894X13006471 Of course we know the relative position of the domains since there are two connections between the cap and core domains. The core domain consists of residues 1 - 19 and 108 - 246, the cap domain is residues 20 - 107. Hope this helps, Keith Keith L. Constantine, Ph. D. Sr. Research Investigator II Mechanistic Biochemistry Bristol Myers Squibb Research and Development P.O. Box 4000 Princeton, NJ 08543-4000 Tel: (609)-252-6926 Fax: (609)-252-6012 e-mail: keith.constant...@bms.com >-----Original Message----- >From: xplor-nih-boun...@dcb.cit.nih.gov [mailto:xplor-nih- >boun...@dcb.cit.nih.gov] On Behalf Of Carl Diehl >Sent: Thursday, October 24, 2013 8:16 AM >To: xplor-...@nmr.cit.nih.gov >Subject: [Xplor-nih] Docking structures using RDCs > >Hello > >I have been trying to get the script for docking 2 protein using >chemical shifts and RDCs to work. >One of my proteins contain Zn2+ ions and I've been able to generate psf- >files for this structure with some help from this mailing list and by >modifying topology and parameter files. >After running the dock_tor_rigid.py and comparing experimental RDCs to >RDCs calculated from the complex, there is very little correlation. Is >the alignment tensor allowed to vary in this protocol or is fixed from >the start and throughout the protocol? > >Both of the protein structures in the complex are NMR-structures, solved >without RDC-refinement, where the correlation between my experimental >RDCs and those calculated from the structures are weak. Based on >chemical shifts we know that there is no major structural rearrangement >upon complex formation, so experimental RDCs should agree with the >uncomplexed structures. > >I tried refining my structures vs the experimental RDCs by using the >refine.py script from the gb1_rdc example and removing NOE, dihedral and >hydrogen-bond restraints. >I don't know if this is the best procedure however, for getting better >agreement with RDCs, since you remove restraints which keep the >secondary structure together. > >Based on this refinement, I could get a better agreement with RDCs for >the structure lacking Zn2+. However the same procedure doesn't work for >the structure containing Zn2+, which blows up during refinement. > >For the non-Zn2+ structure I use the following command to generate the >input structure (from gb1_rdc/refine.py): >protocol.initParams("protein") >protocol.loadPDB("../1a5ra_cns.pdb") >xplor.simulation.deleteAtoms("not known") >protocol.fixupCovalentGeom(maxIters=100,useVDW=1) > >For the Zn2+-structure I use the following commands, which works in the >dock_tor_rigid.py script: >command("param @TOPPAR:parallhdg_new.pro @../param19.ion end") >command("structure @../1tota_cns_zn_t2a.psf end") >command("coor @../1tota_cns_zn_t2a.pdb") >command("coor copy end") >xplor.simulation.deleteAtoms("not known") >protocol.fixupCovalentGeom(maxIters=1000,useVDW=1) > >Is there a difference in how RDCs are used in the gb1_rdc/refine.py vs >the dock_tor_rigid.py script? >Also, what is the difference in how the parameters are setup? >The syntax is different, and I can't readily discern what is different. > >In the dock_tor_rigid.py script I initialize both structures using the >following commands: >command("param @TOPPAR:parallhdg_new.pro @param19.ion >@TOPPAR:par_axis_3.pro end") >command("structure @1a5ra_cns.psf @1tota_cns_zn_t2a.psf >@TOPPAR:axis_500.psf end") >command("coor @1tota_cns_zn_t2a.pdb") >command("coor @1a5ra_cns.pdb") >command("coor @TOPPAR:axis_xyzo_3.pdb") >command("coor copy end") > >Best Regards >Carl Diehl >NNF CPR > > > >_______________________________________________ >Xplor-nih mailing list >Xplor-nih@cake.cit.nih.gov >http://cake.cit.nih.gov/mailman/listinfo/xplor-nih This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited. _______________________________________________ Xplor-nih mailing list Xplor-nih@cake.cit.nih.gov http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
