[ccp4bb] Is there a protein that it could interact with different proteins by the same part?
HI all, We know one protein can interact with different partners by different domains or different parts. Is there a protein that it could interact with different proteins by the same part (maybe the same part but in different conformations?)? Thank you in advance!! yamei
Re: [ccp4bb] Is there a protein that it could interact with different proteins by the same part?
What about polyclonal antibody? I am sure that you find some structures in the PDB. Petr 2011/8/23 Yamei Yu ymyux...@gmail.com: HI all, We know one protein can interact with different partners by different domains or different parts. Is there a protein that it could interact with different proteins by the same part (maybe the same part but in different conformations?)? Thank you in advance!! yamei -- Petr Kolenko kole...@imc.cas.cz http://kolda.webz.cz
Re: [ccp4bb] Is there a protein that it could interact with different proteins by the same part?
On Tue, 2011-08-23 at 09:44 -0400, Yamei Yu wrote: Is there a protein that it could interact with different proteins by the same part (maybe the same part but in different conformations?)? Lysozyme interacts with two antibodies, HyHel-5 and D44.1 via the same epitope but different set of interactions. -- Hurry up before we all come back to our senses! Julian, King of Lemurs
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Re: [ccp4bb] Is there a protein that it could interact with different proteins by the same part?
This is very common among the small GTP-binding proteins of the Ras superfamily. For an interesting analysis (although doubtless there are lots of more recent examples) you might look at: Corbett and Alber, TIBS 26 (12) 710-716 (2001) Evette S. Radisky, Ph.D. Assistant Professor Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yamei Yu Sent: Tuesday, August 23, 2011 9:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Is there a protein that it could interact with different proteins by the same part? HI all, We know one protein can interact with different partners by different domains or different parts. Is there a protein that it could interact with different proteins by the same part (maybe the same part but in different conformations?)? Thank you in advance!! yamei
[ccp4bb] PDRA job opportunity
Dear all, see below for a PDRA opportunity at Imperial college to work on the structural basis of Photosystem II assembly and repair. James http://www.jobs.ac.uk/job/ADC906/research-associate/ Research Associate Imperial College London - Faculty of Natural Sciences, Division of Molecular Biosciences Salary: £31,300 - £39,920 per annum We are seeking to appoint a Research Associate to investigate the roles of assembly factors involved in the assembly and repair of Photosystem II using biochemical and structural biology techniques. The successful applicant will be based within the Nixon group in the Department of Life Sciences at the South Kensington Campus of Imperial College London. The post holder will assist in scientific research into the mechanisms of assembly and repair of Photosystem II. You will be expected to produce independent and original research; submit publications to journals and assist with teaching and administration of the research group. The successful applicant will hold a PhD degree in biochemistry, microbiology, structural biology or a related discipline, or an equivalent level of professional qualifications and experience. You will have experience of experimental design and statistical analysis. You must also be able to demonstrate research experience in a molecular biology/cyanobacterial microbiology environment and experience of standard molecular biology techniques. A successful track record in academic publications is essential. Experience of culturing cyanobacteria, protein purification, synchrotron X-ray data collection, X-ray crystallography and biological NMR are desirable. You must be willing to travel to synchrotrons for X-ray data collection and be able to follow protocols and learn new techniques in a concise and skilled manner. You must also work autonomously and show initiative with research and be able to prioritise work in response to deadlines. The willingness to travel within the UK and abroad to conduct research and attend conferences is essential. You must be prepared to work unsociable hours as the work demands from time to time. You must have strong written communication skills and the ability to write clearly and succinctly for publication. Advanced computer skills, including word-processing, spreadsheets, Internet are also essential. A flexible attitude towards work and the willingness to cooperate as part of a team as well as the ability to work independently and be open-minded and cooperative are essential. You must also have an enthusiastic approach to research, the ability to develop and apply new concepts, techniques and methods and a creative approach to problem solving. You must show initiative, be committed to meeting deadlines, maintaining and enhancing facilities and training others in their use. This is a fixed term position and is funded by the BBSRC for up to three years. Our preferred method of application is online via our website http://www3.imperial.ac.uk/employment (please select Job Search then enter the job title or vacancy reference number including spaces - NS 2011 147 KT into Keywords). Please complete and upload an application form as directed, attaching a curriculum vitae, a cover letter and the name and contact details of two referees. For informal enquiries please contact Professor Peter Nixon: p.ni...@imperial.ac.uk Alternatively, If you are unable to apply online, please contact Richard Bowman by email r.bow...@imperial.ac.uk to request an application form. Closing date: 19 September 2011 Committed to equality and valuing diversity. We are also an Athena Silver SWAN Award winner and a Stonewall Diversity Champion. -- Dr. James W. Murray David Phillips Research Fellow Division of Molecular Biosciences Imperial College, LONDON Tel: +44 (0)20 759 48895
Re: [ccp4bb] Is there a protein that it could interact with different proteins by the same part?
We know one protein can interact with different partners by different domains or different parts. Is there a protein that it could interact with different proteins by the same part (maybe the same part but in different conformations?)? Thank you in advance!! The RNA Polymerase II rpb1 CTD interacts with numerous other proteins - it's disordered in isolation, and adopts different conformations with different binding partners (at least in the available structures).
Re: [ccp4bb] Is there a protein that it could interact with different proteins by the same part?
Calmodulin Poul On 23/08/2011, at 16.55, Pete Meyer wrote: We know one protein can interact with different partners by different domains or different parts. Is there a protein that it could interact with different proteins by the same part (maybe the same part but in different conformations?)? Thank you in advance!! The RNA Polymerase II rpb1 CTD interacts with numerous other proteins - it's disordered in isolation, and adopts different conformations with different binding partners (at least in the available structures).
Re: [ccp4bb] Is there a protein that it could interact with different proteins by the same part?
Look at AP-2 alpha-appendage. And for that matter, the beta appendage too. Alpha appendage binds ~30 different proteins using two sites on one domain. J Biol Chem. 2004 Oct 29;279(44):46191-203. Epub 2004 Aug 2. Dual engagement regulation of protein interactions with the AP-2 adaptor alpha appendage. Mishra SK, Hawryluk MJ, Brett TJ, Keyel PA, Dupin AL, Jha A, Heuser JE, Fremont DH, Traub LM. Structure. 2002 Jun;10(6):797-809. Accessory protein recruitment motifs in clathrin-mediated endocytosis. Brett TJ, Traub LM, Fremont DH. Mol Biol Cell. 2008 Dec;19(12):5309-26. Epub 2008 Oct 8. The AP-2 adaptor beta2 appendage scaffolds alternate cargo endocytosis. Keyel PA, Thieman JR, Roth R, Erkan E, Everett ET, Watkins SC, Heuser JE, Traub LM. -Tom Tom J. Brett, PhD Assistant Professor of Medicine Division of Pulmonary and Critical Care Washington University School of Medicine Campus Box 8052, 660 S. Euclid Saint Louis, MO 63110 http://brettlab.dom.wustl.edu/ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Radisky, Evette S., Ph.D. [radisky.eve...@mayo.edu] Sent: Tuesday, August 23, 2011 9:41 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Is there a protein that it could interact with different proteins by the same part? This is very common among the small GTP-binding proteins of the Ras superfamily. For an interesting analysis (although doubtless there are lots of more recent examples) you might look at: Corbett and Alber, TIBS 26 (12) 710-716 (2001) Evette S. Radisky, Ph.D. Assistant Professor Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yamei Yu Sent: Tuesday, August 23, 2011 9:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Is there a protein that it could interact with different proteins by the same part? HI all, We know one protein can interact with different partners by different domains or different parts. Is there a protein that it could interact with different proteins by the same part (maybe the same part but in different conformations?)? Thank you in advance!! yamei
[ccp4bb] PISA question
Dear CCP4bb, We are trying to get some detailed interface information from an antibody:antigen complex, PDBePISA used to have an option to select atomic level details, now the new web interface only gives residue level information. Is there a way to run PISA (in the CCP4 package) with a different configuration to get the detailed information? Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. **
Re: [ccp4bb] PISA question
Dear Tongqing No there is no such option in CCP4's PISA, but I put this on the list for further developments. Regrettably PDBe changed the interface after I moved out and I cannot help you with that. However, you may ask them to put that option back. Sorry, Eugene. On 23 Aug 2011, at 17:16, Zhou, Tongqing (NIH/VRC) [E] wrote: Dear CCP4bb, We are trying to get some detailed interface information from an antibody:antigen complex, PDBePISA used to have an option to select atomic level details, now the new web interface only gives residue level information. Is there a way to run PISA (in the CCP4 package) with a different configuration to get the detailed information? Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. **
[ccp4bb] How to handle b-factors at low resolution and very incomplete model?
Hi all What's a way to determining a B-factor to set for all residues of a model at low resolution (4A)? How valid is the wilson B at this resolution? (better than nothing?) I'm in the process of fitting whole domains into some rasty experimental density maps and was thinking of doing a rigid body or very restrained ( secondary structure | reference structure | etc ) refinement of the coordinates for helping the fit. Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] How to handle b-factors at low resolution and very incomplete model?
On Tue, 2011-08-23 at 11:30 -0600, Francis E Reyes wrote: What's a way to determining a B-factor to set for all residues of a model at low resolution (4A)? Why not refine the overall B-factor? Even at 4A it should still be legitimate. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] How to handle b-factors at low resolution and very incomplete model?
I distinctly remember reading a paper where B factors were predicted based on the location of the atoms (core vs exposed, main chain vs side chain) and the predicted values were not that far off. I wonder if B factors could actually be restrained at low resolution towards values reasonable/expected/similar to model values, just as how we put in model restraints for coordinate refinement these days, since many of us working at low resolution have at some point or another experienced catastrophe with B factor refinement. I wonder if this has been tested... Engin On 8/23/11 10:30 AM, Francis E Reyes wrote: Hi all What's a way to determining a B-factor to set for all residues of a model at low resolution (4A)? How valid is the wilson B at this resolution? (better than nothing?) I'm in the process of fitting whole domains into some rasty experimental density maps and was thinking of doing a rigid body or very restrained ( secondary structure | reference structure | etc ) refinement of the coordinates for helping the fit. Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder -- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
[ccp4bb] Modeling ligands in binding pockets when the density is weak.
Seems to be a quiet day on the BB, so I propose this question: Suppose you have a ligand in the binding pocket and some mediocre data (3 A or so), the 'core' of the ligand is well defined in 2Fo-Fc map using the model phases of your protein, however there are 'chains/tails' of the ligand which are not. Composite omit or simulated annealing omit maps do not produce density for these 'chains' The question here is how the chains/tails should be modeled (if at all). [1] Model in the core, but remove the atoms for the chains (and conclude the diffraction data do not support interactions with the protein and subsequent experiments are needed (higher resolution data, biochemical data, etc)). or [2] Model in the chains/tails noting that potential hydrogen bond donors/acceptors on the protein are within hydrogen bonding distance to the chains/tails. You do this and subsequent refinement still does not produce the expected density for the chains. or [3] Your solution here. If this situation has been discussed before, please let me know . F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] Modeling ligands in binding pockets when the density is weak.
On Tue, 2011-08-23 at 12:36 -0600, Francis E Reyes wrote: Seems to be a quiet day on the BB So you need an earthquake :) This is similar, imho, to the issue of disordered side chains: https://docs.google.com/spreadsheet/gform?key=0Ahe0ET6Vsx-kdHVNa3VodUtfbVQtZ2pnUFcxQkx6RHchl=en_USgridId=0#chart https://docs.google.com/spreadsheet/viewform?hl=en_USformkey=dHVNa3VodUtfbVQtZ2pnUFcxQkx6RHc6MQ#gid=0 -- Hurry up before we all come back to our senses! Julian, King of Lemurs
Re: [ccp4bb] Modeling ligands in binding pockets when the density is weak.
(3a) You could give GraphENT a shot first and see if you can do magic on visualizing the remaining bits of density. You could also have multiple conformations, try refining with a low occupancy first and see what you get back. (3b) use AFitt Jürgen P.S. I would set the occupancy to zero for those parts which you don't see density but I would never remove them unless you know that your ligands has been degraded. On Aug 23, 2011, at 2:36 PM, Francis E Reyes wrote: Seems to be a quiet day on the BB, so I propose this question: Suppose you have a ligand in the binding pocket and some mediocre data (3 A or so), the 'core' of the ligand is well defined in 2Fo-Fc map using the model phases of your protein, however there are 'chains/tails' of the ligand which are not. Composite omit or simulated annealing omit maps do not produce density for these 'chains' The question here is how the chains/tails should be modeled (if at all). [1] Model in the core, but remove the atoms for the chains (and conclude the diffraction data do not support interactions with the protein and subsequent experiments are needed (higher resolution data, biochemical data, etc)). or [2] Model in the chains/tails noting that potential hydrogen bond donors/acceptors on the protein are within hydrogen bonding distance to the chains/tails. You do this and subsequent refinement still does not produce the expected density for the chains. or [3] Your solution here. If this situation has been discussed before, please let me know . F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
[ccp4bb] Check PDB file for missing atoms
Dear all, Does anyone know a program that will check a PDB file for missing atoms and output a list of the corresponding residues? Many thanks in advance, Tiago *** Tiago Barros, PhD Kuriyan lab - Molecular and Cellular Biology University of California, Berkeley 527 Stanley Hall, QB3 Berkeley, CA 94720-3220 USA tel: + 1 510 643 0164 fax: + 1 510 643 2352 ***
Re: [ccp4bb] Check PDB file for missing atoms
On Tue, 2011-08-23 at 12:19 -0700, Tiago Barros wrote: Does anyone know a program that will check a PDB file for missing atoms and output a list of the corresponding residues? REFMAC reports a (truncated?) list in the log file. Coot can also identify missing atoms. I would be pretty sure there is something like phinix.which_atoms_are_missing or such :) -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Modeling ligands in binding pockets when the density is weak.
On 08/23/11 15:01, Ed Pozharski wrote: On Tue, 2011-08-23 at 12:36 -0600, Francis E Reyes wrote: Seems to be a quiet day on the BB So you need an earthquake :) Had one already, thanks. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Modeling ligands in binding pockets when the density is weak.
David Schuller wrote: On 08/23/11 15:01, Ed Pozharski wrote: On Tue, 2011-08-23 at 12:36 -0600, Francis E Reyes wrote: Seems to be a quiet day on the BB So you need an earthquake :) Had one already, thanks. Apparently sent from the vicinity of U. Maryland and JHSPH, thanks.
Re: [ccp4bb] Check PDB file for missing atoms
Hi Tiago, easy, two steps: 1) Save the lines between *** into a file say called run.py: *** import os,sys from mmtbx.monomer_library import pdb_interpretation from mmtbx import monomer_library import mmtbx.monomer_library.server from cStringIO import StringIO def exercise(args): file_name = args[0] mon_lib_srv = monomer_library.server.server() ener_lib = monomer_library.server.ener_lib() processed = monomer_library.pdb_interpretation.process( mon_lib_srv = mon_lib_srv, ener_lib = ener_lib, file_name = file_name, keep_monomer_mappings = True, log = StringIO()) for monomer_mapping in processed.all_chain_proxies.all_monomer_mappings: ma = monomer_mapping.missing_non_hydrogen_atoms.keys() if(len(ma)0): print monomer_mapping.pdb_residue_id_str, Missing atoms:, ma if (__name__ == __main__): exercise(sys.argv[1:]) *** 2) Run it from the command line as: phenix.python run.py model.pdb and it will list you incomplete residues and missing atoms, just like this: pdbres=ASP A 1 segid=AMissing atoms: ['C', 'OD1', 'CA', 'CG', 'O', 'N', 'OD2'] pdbres=THR A 5 segid=AMissing atoms: ['C', 'CB', 'CA', 'OG1', 'O', 'N', 'CG2'] pdbres=THR A 10 segid=AMissing atoms: ['C', 'CG2', 'OG1', 'O'] pdbres=SER A 12 segid=AMissing atoms: ['CA', 'N'] Let me know if you need any help with this. Pavel. P.S.: You need to have PHENIX installed. On Tue, Aug 23, 2011 at 12:19 PM, Tiago Barros ti...@me.com wrote: Dear all, Does anyone know a program that will check a PDB file for missing atoms and output a list of the corresponding residues? Many thanks in advance, Tiago *** Tiago Barros, PhD Kuriyan lab - Molecular and Cellular Biology University of California, Berkeley 527 Stanley Hall, QB3 Berkeley, CA 94720-3220 USA tel: + 1 510 643 0164 fax: + 1 510 643 2352 ***
Re: [ccp4bb] Check PDB file for missing atoms
According to the PDB Format document, entries with missing atoms should have a parsable REMARK 470. You might want to write some quick code to look for that REMARK. The PDB staff could comment about the accuracy of REMARK 470 in its entries. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Tue, 23 Aug 2011, Pavel Afonine wrote: Hi Ed, On Tue, Aug 23, 2011 at 12:39 PM, Ed Pozharski epozh...@umaryland.edu wrote: I would be pretty sure there is something like phinix.which_atoms_are_missing or such :) good idea! I can turn the script that I just sent into this command so it is available in a couple of days -:) Pavel.
Re: [ccp4bb] Check PDB file for missing atoms
The RCSB PDB Validation server will also report this info for you. Diana ** Diana R. Tomchick Associate Professor Department of Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214B Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tiago Barros [ti...@me.com] Sent: Tuesday, August 23, 2011 2:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Check PDB file for missing atoms Dear all, Does anyone know a program that will check a PDB file for missing atoms and output a list of the corresponding residues? Many thanks in advance, Tiago *** Tiago Barros, PhD Kuriyan lab - Molecular and Cellular Biology University of California, Berkeley 527 Stanley Hall, QB3 Berkeley, CA 94720-3220 USA tel: + 1 510 643 0164 fax: + 1 510 643 2352 *** UT Southwestern Medical Center The future of medicine, today.
