Re: [ccp4bb] Morphing with mutations
Mario You guys don't be so modests. Implement the "idea" could take me quite some time and you guys does it so easy (at least for me point of view :-) and nice. And is a good oportunity for me to Thanks for your many ideas... Regards Mario Gerard DVD Kleywegt wrote: Quite a beauty... what a nice way to show the effect of the mutation in the binding site. really nice, don't be so modest, mario - he implemented *your* idea!!! :-) --gerard ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell & Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** -- = Mario A. Bianchet Ph.D.| [EMAIL PROTECTED] Instructor | http://juliet.med.jhmi.edu/~bianchet Dept. of Biophysics and Biophysical| Address:725 N.Wolfe st, WBSB 614 Chemistry, Johns Hopkins University| Baltimore, Maryland, 21205, USA School of Medicine | Assistant Professor, (adjunct app.)| Phones: +1 (410) 931-2143(home) Center of Marine Biotechnology,| +1 (410) 614-8221(work) University of Maryland !fax: +1 (410) 955-0637 =
Re: [ccp4bb] Domain swapping..... and unswapping.
Dear Miriam, We have seen this in our study of the FOXP2/DNA complexes (Stroud et al., Structure, 14, 159-16, 2006). Lin Lin Chen, Ph.D. Associate Professor Molecular and Computational Biology University of Southern California 1050 Childs Way, Los Angeles, CA 90089 Phone: 213-821-4277 Fax: 213-740-8631 e-mail: [EMAIL PROTECTED] Web page: http://structure.usc.edu - Original Message - From: Miriam-Rose Ash <[EMAIL PROTECTED]> Date: Friday, October 5, 2007 8:46 am Subject: [ccp4bb] Domain swapping. and unswapping. To: CCP4BB@JISCMAIL.AC.UK > Hey all, > > Sorry for the off-topic post, but I'm just wondering if anyone has > heard of any examples in which a single crystal contained both the > domain-swapped and unswapped forms of a protein? > > Thanks! > Miriam >
Re: [ccp4bb] Domain swapping..... and unswapping.
Dear Miriam I had that case of the 4-helix bundle FAT domain of Focal Adhesion Kinase. It crystallised as a helix-swapped dimer (PDB ID 1k04, 1mol/ASU), as a non-swapped 4helix bundle (1ow7, 3 mol/ASU), and as a hybrid, where 2 mols / ASU were not swapped, and one was swapped (1ow6). With best wishes Stefan Miriam-Rose Ash a écrit : Hey all, Sorry for the off-topic post, but I'm just wondering if anyone has heard of any examples in which a single crystal contained both the domain-swapped and unswapped forms of a protein? Thanks! Miriam -- == Stefan T. Arold, PhD Centre de Biochimie Structurale CNRS UMR 5048 - UM 1 - INSERM UMR 554 29 rue de Navacelles 34090 MONTPELLIER Cedex - France email: [EMAIL PROTECTED] Phone: +33 (0)4.67.41.77.02 Fax: +33 (0)4.67.41.79.13 ==
[ccp4bb] Structural Biology Post-Doctoral Position
Dear CCP4 Users, We have an opening for one federally funded post-doctoral position for a structural biologist or protein biochemist to study bacterial voltage-gated sodium channels. The ideal candidate will be self-motivated, creative, organized, and experienced in crystallography or protein biochemistry. The lab is a structural biology group within the department of Pharmacology at the Vanderbilt University medical center in Nashville, TN. Nashville combines the features of a college town with those of a fairly large city. Urban amenities include restaurants, museums, theatres, music, yet the cost of living is moderate and the city is very livable. Please email questions, CVs, and references to Ben Spiller: [EMAIL PROTECTED]
Re: [ccp4bb] Domain swapping..... and unswapping.
Hi Miriam, If you check PDB ID 1K50 you would see that the asymmetric unit contains two monomers and a domain swapped dimmer. The reference if you want to read the paper is: O`Neill, J.W., Kim, D.E., Johnsen, K., Baker, D., Zhang, K.Y. Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus. Structure v9 pp. 1017-1027, 2001 Regards Myron -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Miriam-Rose Ash Sent: Friday, October 05, 2007 3:41 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Domain swapping. and unswapping. Hey all, Sorry for the off-topic post, but I'm just wondering if anyone has heard of any examples in which a single crystal contained both the domain-swapped and unswapped forms of a protein? Thanks! Miriam Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] Domain swapping..... and unswapping.
We've had a case recently (unpublished) with 4 molecules in the asymmetric unit, two self-contained and two domain-swapped (asymmetrically) ... anything is possible, though in this case the "domains" are really separate proteins expressed as an artificial fusion Phil On 5 Oct 2007, at 15:40, Miriam-Rose Ash wrote: Hey all, Sorry for the off-topic post, but I'm just wondering if anyone has heard of any examples in which a single crystal contained both the domain-swapped and unswapped forms of a protein? Thanks! Miriam
[ccp4bb] Domain swapping..... and unswapping.
Hey all, Sorry for the off-topic post, but I'm just wondering if anyone has heard of any examples in which a single crystal contained both the domain-swapped and unswapped forms of a protein? Thanks! Miriam
[ccp4bb] Beamtime at SLS X06SA
= SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE UNDULATOR BEAMLINE X06SA AT SLS FROM JANUARY-APRIL 2008 = - PILATUS 6M pixel detector available for user operation at High Resolution Diffractometer. Continuous data acquisition (10 frames per second) with 20 bit dynamic range, see http://pilatus.web.psi.ch/ or www.dectris.com for further information - CATS sample changer (http://www.irelec.fr/en/produit.asp?idproduit=38) to be installed in April on HR - diffractometer - Detector upgrade to mar225 CCD on Micro-Diffractometer MD2. This MAD-compatible diffractometer allows for data collection with a beam size down to 5 micrometers. - ACTOR sample changer operational on the Micro-Diffractometer. Adaptor for use of SPINE pucks in preparation. - SLS is able to provide support for travel and accomodation for two users per trip: http://sls.web.psi.ch/view.php/users/experiments/eusupport/index.html - For recent highlights: http://sls.web.psi.ch/view.php/beamlines/px/research/index.html PROPOSAL SUBMISSION DEADLINE: Monday, October 15th 2007. For further information and / or proposal submission: http://sls.web.psi.ch/view.php/users/experiments/proposals/opencalls/PX/index.html Looking forward to seeing you at SLS, Clemens Schulze-Briese -- Dr. Clemens Schulze-Briese - [EMAIL PROTECTED] --- Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://sls.web.psi.ch Phone +41 56 310 4533 - Fax -5292 - Secretary -3178
Re: [ccp4bb] Morphing with mutations
Warren, Quite a beauty... what a nice way to show the effect of the mutation in the binding site. really nice, Mario Warren DeLano wrote: http://delsci.com/morph It's a start... -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Gerard DVD Kleywegt Sent: Wednesday, October 03, 2007 6:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Morphing with mutations What about to do a cartesian morphing with the mutated residue added (or removed) atoms having initial ( or final) coordinates taken from previous common atom? Will work? Coloring may be a factor... but with a manual editing perhaps... you mean, for instance, if you have an Ala->Trp you call the ala 'trp', add all missing 'trp' side-chain atoms and put them on top of the CB, and then morph to the real trp, so the additional side-chain atoms will slowly "explode" out of the CB and towards their final positions? (and for a Trp->Ala mutation you could do the same thing of course, but the extra side-chain atoms would then be "sucked up" by the CB like a black hole) yep, that is a trick that would probably work! if anyone gets it to work, i would be interested in seeing the result and learning details, so i could add it to the lsqman manual or the morphing tutorial --dvd ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell & Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** -- = Mario A. Bianchet Ph.D.| [EMAIL PROTECTED] Instructor | http://juliet.med.jhmi.edu/~bianchet Dept. of Biophysics and Biophysical| Address:725 N.Wolfe st, WBSB 614 Chemistry, Johns Hopkins University| Baltimore, Maryland, 21205, USA School of Medicine | Assistant Professor, (adjunct app.)| Phones: +1 (410) 931-2143(home) Center of Marine Biotechnology,| +1 (410) 614-8221(work) University of Maryland !fax: +1 (410) 955-0637 =
