[ccp4bb] Postdoctoral Position in synthesis of glucopyranonucleosides
Dear all, please follow the link http://www.hecra.gr/vacancies/21_6.pdf for a posdoctoral position in Organic Synthesis at the Department of Biochemistry and Biotechnology, University of Thessaly. Demetres -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
Re: [ccp4bb] estimate of effective concentration
Dear Filip, I believe that you may find interesting methods, insights and principles to get you going in the following paper: Wu et al. Transforming binding affinities from three dimensions to two with application to cadherin clustering. Nature. 2011 Jul 27;475(7357):510-3 doi: 10.1038/nature10183 best regards Savvas Savvas Savvides Unit for Structural Biology, L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Tel/SMS/texting +32 (0)472 928 519 Skype: savvas.savvides_skype http://www.LProBE.ugent.be/xray.html On 21 Jun 2012, at 01:08, Filip Van Petegem wrote: Dear crystallographers, I have a question concerning effective concentration. Say you have a crystal structure whereby two loops, each part of a different domain but within the same molecule happen to be juxtaposed and can form an interaction. The loops have some degree of flexibility, but are ordered when interacting. The domains on which they are attached have a rigid configuration due to the remainder of the structure. The interaction is potentially very weak and mainly driven by the fact that the effective concentration is extremely high. The question: how can one obtain a rough estimate of the effective concentration of these two juxtaposed loops? The simple straightforward answer would be to just divide number (1 each) by volume (some box drawn around the loops), and convert this to molar. That's easy. However, this is over-simplified and really an underestimate of 'effective' concentration, because these loops cannot rotate freely when attached to the domains. Hence, there are constraints that allow them to interact more readily compared to the isolated loops within the same box. So I'm looking for a model that also takes limited conformational freedom into account. If anybody has any pointers to some reference text or paper that has performed such an analysis, I would be very interested. Regards, Filip -- Filip Van Petegem, PhD Associate Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
[ccp4bb] INVITATION: Murnau Conference 2012 on Structural Biology of Molecular Transport
Dear colleagues, this is to remind you that the Murnau Conference 2012 on Structural Biology of Molecular Transport will be taking place from 17-20 October. Online registration is NOW OPEN on a first come-first served basis (http://www.murnauconference.de/2012/registration.html). We would be delighted to meet you at the conference. Please also spread the information amongst your colleagues to help us attract a broad audience and an interesting cross-section of the community. If you want the conference poster (PDF file) for your notice boards, please let us know. Murnau Conference 2012 on Structural Biology of Molecular Transport October 17-20, 2012 - Murnau/Germany SESSIONS I Channels and Transporters I: Transport through Membrane II RNA, Nuclear and ER Transport / Nucleocytoplasmic Transport III Endosomal / Synaptic Transport IV Cytoskeleton and Cellular Motility V Channels and Transporters II: Molecular Machines PLENARY SPEAKERS Marc Baldus (Utrecht) Tamir Gonen (Seattle) Reinhard Jahn (Göttingen) Hartmut Michel (Frankfurt) You Min Chook (Dallas) Poul Nissen (Arhus) Tom Pollard (New Haven) Jim Rothman (Yale) Mike Rosen (Dallas) Helen Saibil (London) Irmi Sinning (Heidelberg) Daniela Stock (Darlinghurst) Gerhard Wagner (Harvard) BACKGROUND INFO The Murnau Conference is an international meeting covering current issues in the wide field of modern structural biology. A clear goal of the conference, which will take place this year for the 4th time, is to bring together the most eminent scientists in the field with young researchers in a casual atmosphere in the heart of Europe. The first three meetings in the series took place in 2005 (Structural Biology of Molecular Recognition), 2007 (Structural Biology of Disease Mechanisms) and 2010 (Structural Biology of the Modern RNA World). Murnau is a picturesque small town located directly at lake Staffelsee in the Bavarian alpine upland between Munich and Garmisch-Partenkirchen. There will be an exciting social program including a typical Bavarian evening in a fashionable microbrewery and ample time for stimulating discussions with participants from all over the world. Please contact us in case of further questions. With best regards, Prof. Dr. Dirk Heinz in the name of the organization committee www.murnauconference.de murnauconference2...@gmail.com Murnau Conference 2012 -Office- Christine Bentz GF/W (Scientific Director's Office) Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig, Germany christine.be...@helmholtz-hzi.de +49 (0)531-6181-1003 Protect the environment - please don't print this e-mail unless you really need to Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir'in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477
Re: [ccp4bb] help regarding structure solution
Dear Raaij, We have not done mass-spec on the band from SDS-PAGE to confirm if it is our desired protein or any other contaminant. So, cant say for sure. Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” --- On Thu, 21/6/12, Mark J van Raaij mjvanra...@cnb.csic.es wrote: From: Mark J van Raaij mjvanra...@cnb.csic.es Subject: Re: [ccp4bb] help regarding structure solution To: sonali dhindwal sonali11dhind...@yahoo.co.in Date: Thursday, 21 June, 2012, 11:33 AM you didn't answer the most important question - are you 100% sure the protein in the crystal is not a contaminant? Unfortunately, these things happen... Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 21 Jun 2012, at 06:47, sonali dhindwal wrote: Dear All, Thanks a lot for your replies. Glad to found so much help. Clemens, cell parameters are, 38.0020 78.0240 56.3800 90. 102.2770 90., in P21 spacegroup. Raaij, Savvas, we have checked for the twining and no twining was detected. Nat, DEN is a good suggestion, i will definitely try it today. Roger, Molrep didn't fail but as i mentioned in the mail, it do give solution. Molrep gives contrast even 10 or more but no good electron density map yet. Free R and figure of merit becomes 52% and 42% respectively in Refmac with all the solutions. But none of the solution fits in the electron density. And phaser didn't give any solution. We checked in pointless also, it was suggesting the same spacegroup. Matthew, Yes, we don't have the same crystal now. Garib, I will run the balbes server, and will let you know then. Robert, I tried using your server, and found few hits. Will run those templates for molecular replacement. Peter, We didnt had MBP tag in the protein. But your idea of doing limited proteolysis sounds good, and will definitely try that. Thanks again to all, for their kind and valuable help. I will write after trying all the things as suggested. Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” --- On Thu, 21/6/12, Peter Hsu hsuu...@u.washington.edu wrote: From: Peter Hsu hsuu...@u.washington.edu Subject: Re: [ccp4bb] help regarding structure solution To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, 21 June, 2012, 5:08 AM Hi Sonali, Did you use MBP as your purification tag? That's around 45-50kDa if I remember right. If not, I've had a decent amount of luck using in situ proteolysis to get crystals of degraded fragments. Try a limited proteolysis first overnight at 4C at varying concentrations of trypsin, see which one gives a nice stable band after overnight. Use that same concentration to add to your protein stock before setting up drops and then try another screen. I always use freshly prepared trypsin stock instead of frozen solutions to make sure that the freeze thaw doesn't reduce activity of the trypsin and that batch to batch is reproducible. Best of luck, Peter
[ccp4bb] Expressed protein hinders cell lysis?
Greetings, everyone. We need to ask your advice on an issue with one of our proteins expressed in E. coli Rosetta cells. This yeast-derived protein has a very low yield compared to others we work with, and we think it is because the cells are hard to lyse: even after 3 cycles in a cell cracker the solution barely changes colour. We have no problems lysing Rosetta cells expressing other yeast-derived soluble proteins, and we usually obtain enough for our crystallisation screens. For the aforementioned protein we have already tried using STAR cells, varying the contents of the lysis buffer, sonicating, or adding FeSO4 to the solution (we think the protein binds Fe or Mn because it is yellow), but to no avail. Searching the ccp4bb archive and other resources did not help, so we would like to ask 2 questions to the community in order to focus our efforts better: 1. How can a recombinant protein make a cell harder to lyse? 2. Do you have any suggestions to avoid this effect? We appreciate any input, and will be sure to post a summary for future reference once this issue is solved. Sincerely, -- J. Valencia S. PhD student CGR-NU
Re: [ccp4bb] Expressed protein hinders cell lysis?
Hi, I often see no real change in change in solution appearance after sonication mediated lysis, with proteins which yield low amounts or no soluble protein in E. coli. I've had a look at the solution post lysis under the microscope and the cells are infact lysed, it's just the presence of high levels of inclusion bodies means the solution remains turbid. Check your pre and post lysis solution under the microscope to see if you see the same thing. Cheers, Rhys From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of J. Valencia S. [valen...@gene.nagoya-u.ac.jp] Sent: 21 June 2012 13:44 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Expressed protein hinders cell lysis? Greetings, everyone. We need to ask your advice on an issue with one of our proteins expressed in E. coli Rosetta cells. This yeast-derived protein has a very low yield compared to others we work with, and we think it is because the cells are hard to lyse: even after 3 cycles in a cell cracker the solution barely changes colour. We have no problems lysing Rosetta cells expressing other yeast-derived soluble proteins, and we usually obtain enough for our crystallisation screens. For the aforementioned protein we have already tried using STAR cells, varying the contents of the lysis buffer, sonicating, or adding FeSO4 to the solution (we think the protein binds Fe or Mn because it is yellow), but to no avail. Searching the ccp4bb archive and other resources did not help, so we would like to ask 2 questions to the community in order to focus our efforts better: 1. How can a recombinant protein make a cell harder to lyse? 2. Do you have any suggestions to avoid this effect? We appreciate any input, and will be sure to post a summary for future reference once this issue is solved. Sincerely, -- J. Valencia S. PhD student CGR-NU
[ccp4bb] Detergent and protein oligomerization
Hi Everyone, Sorry for the non-CCP4 post. I have a very basic question about detergents, critical micelle concentration and behavior on gel filtration. A 33kDa membrane protein was purified by gel filtration in a buffer containing 0.4%(w/v) beta-NG (CMC: 6.5mM) and 0.046%(w/v)LDAO (CMC: 0.14mM). So the concentrations of beta-NG and LDAO in the gel-filtration buffer are ~2X and ~14X that of the CMCs of the respective detergents. The elution volume of the protein peak (plus detergent) on Superdex200 corresponds to a molecular mass of 100kDa. I think that the 100kDa mass above includes contributions from both the protein as well as the detergent micelles. If this is correct, is it then accurate to try to glean the oligomerization state of the protein (and conclude that it is a trimer or tetramer) without taking into account detergent micellar mass and its influence on elution volume? How should one interpret the 100kDa mass estimate from the gel filtration? Thanks. Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
[ccp4bb] CCP-BioSim workshop on QM/MM methods for modelling enzyme-catalysed reactions
CCP-BioSim workshop on QM/MM methods for modelling enzyme-catalysed reactions School of Chemistry, University of Bristol, UK Tuesday July 17th 2012 This practical workshop will introduce combined quantum mechanics/molecular mechanics (QM/MM) methods and their application to modelling enzyme-catalysed reactions. It will involve hands-on use of QM/MM methods, in particular using the CHARMM program, and their application to modelling a reaction within an enzyme. No prior experience of simulations or QM/MM methods is required; the workshop is suitable for non-specialists. Registration is free to academic researchers and students. Places are limited. Lunch will be provided. Registration is via: https://eventbooking.stfc.ac.uk/news-events/ccpbiosim-training-workshop-qmmm-methods-for-modelling-enzyme-catalysed-reactions Cheers Martyn P.S. Sorry for the non-CCP4 post -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] Detergent and protein oligomerization
First of all, isn't the choice either dimer or trimer, and second, as a protein-detergent complex (PDC), it would be very unlikely that a trimer of 99 kD would run at 100 kD, although all is fair in love, war, and membrane proteins. JPK On Thu, Jun 21, 2012 at 10:50 AM, Raji Edayathumangalam r...@brandeis.eduwrote: Hi Everyone, Sorry for the non-CCP4 post. I have a very basic question about detergents, critical micelle concentration and behavior on gel filtration. A 33kDa membrane protein was purified by gel filtration in a buffer containing 0.4%(w/v) beta-NG (CMC: 6.5mM) and 0.046%(w/v)LDAO (CMC: 0.14mM). So the concentrations of beta-NG and LDAO in the gel-filtration buffer are ~2X and ~14X that of the CMCs of the respective detergents. The elution volume of the protein peak (plus detergent) on Superdex200 corresponds to a molecular mass of 100kDa. I think that the 100kDa mass above includes contributions from both the protein as well as the detergent micelles. If this is correct, is it then accurate to try to glean the oligomerization state of the protein (and conclude that it is a trimer or tetramer) without taking into account detergent micellar mass and its influence on elution volume? How should one interpret the 100kDa mass estimate from the gel filtration? Thanks. Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Detergent and protein oligomerization
Dear Raji, The best way to find out is to run a SEC-MALLS (Size Exclusion Chomatography - Multi-Angle Laser Light Scattering) experiment. Best, Isabel - Dr. Isabel De Moraes, MRSC Membrane Protein Laboratory Facility Co-ordinator Membrane Protein Laboratory Diamond Light Source Ltd, Chilton, Didcot, Oxfordshire, OX11 ODE, UK Tel (direct): 01235 778664 -- From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob Keller [j-kell...@fsm.northwestern.edu] Sent: 21 June 2012 17:11 To: ccp4bb Subject: Re: [ccp4bb] Detergent and protein oligomerization First of all, isn't the choice either dimer or trimer, and second, as a protein-detergent complex (PDC), it would be very unlikely that a trimer of 99 kD would run at 100 kD, although all is fair in love, war, and membrane proteins. JPK On Thu, Jun 21, 2012 at 10:50 AM, Raji Edayathumangalam r...@brandeis.edumailto:r...@brandeis.edu wrote: Hi Everyone, Sorry for the non-CCP4 post. I have a very basic question about detergents, critical micelle concentration and behavior on gel filtration. A 33kDa membrane protein was purified by gel filtration in a buffer containing 0.4%(w/v) beta-NG (CMC: 6.5mM) and 0.046%(w/v)LDAO (CMC: 0.14mM). So the concentrations of beta-NG and LDAO in the gel-filtration buffer are ~2X and ~14X that of the CMCs of the respective detergents. The elution volume of the protein peak (plus detergent) on Superdex200 corresponds to a molecular mass of 100kDa. I think that the 100kDa mass above includes contributions from both the protein as well as the detergent micelles. If this is correct, is it then accurate to try to glean the oligomerization state of the protein (and conclude that it is a trimer or tetramer) without taking into account detergent micellar mass and its influence on elution volume? How should one interpret the 100kDa mass estimate from the gel filtration? Thanks. Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu ***
Re: [ccp4bb] Detergent and protein oligomerization
There is something even better than SEC-MALS--solving the structure! JPK On Thu, Jun 21, 2012 at 11:16 AM, isabel.de-mor...@diamond.ac.uk wrote: Dear Raji, The best way to find out is to run a SEC-MALLS (Size Exclusion Chomatography - Multi-Angle Laser Light Scattering) experiment. Best, Isabel - Dr. Isabel De Moraes, MRSC Membrane Protein Laboratory Facility Co-ordinator Membrane Protein Laboratory Diamond Light Source Ltd, Chilton, Didcot, Oxfordshire, OX11 ODE, UK Tel (direct): 01235 778664 -- From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob Keller [j-kell...@fsm.northwestern.edu] Sent: 21 June 2012 17:11 To: ccp4bb Subject: Re: [ccp4bb] Detergent and protein oligomerization First of all, isn't the choice either dimer or trimer, and second, as a protein-detergent complex (PDC), it would be very unlikely that a trimer of 99 kD would run at 100 kD, although all is fair in love, war, and membrane proteins. JPK On Thu, Jun 21, 2012 at 10:50 AM, Raji Edayathumangalam r...@brandeis.edu mailto:r...@brandeis.edu wrote: Hi Everyone, Sorry for the non-CCP4 post. I have a very basic question about detergents, critical micelle concentration and behavior on gel filtration. A 33kDa membrane protein was purified by gel filtration in a buffer containing 0.4%(w/v) beta-NG (CMC: 6.5mM) and 0.046%(w/v)LDAO (CMC: 0.14mM). So the concentrations of beta-NG and LDAO in the gel-filtration buffer are ~2X and ~14X that of the CMCs of the respective detergents. The elution volume of the protein peak (plus detergent) on Superdex200 corresponds to a molecular mass of 100kDa. I think that the 100kDa mass above includes contributions from both the protein as well as the detergent micelles. If this is correct, is it then accurate to try to glean the oligomerization state of the protein (and conclude that it is a trimer or tetramer) without taking into account detergent micellar mass and its influence on elution volume? How should one interpret the 100kDa mass estimate from the gel filtration? Thanks. Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu *** -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Expressed protein hinders cell lysis?
can you specify what your cell cracker is. Thanks, Jürgen On Jun 21, 2012, at 9:50 AM, Kelly Daughtry wrote: If it is inclusion bodies, I generally see a milky solution after lysis. Have you centrifuged post-lysis and then run an SDS-PAGE? Kelly *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 *** On Thu, Jun 21, 2012 at 9:33 AM, RHYS GRINTER r.grinte...@research.gla.ac.ukmailto:r.grinte...@research.gla.ac.uk wrote: Hi, I often see no real change in change in solution appearance after sonication mediated lysis, with proteins which yield low amounts or no soluble protein in E. coli. I've had a look at the solution post lysis under the microscope and the cells are infact lysed, it's just the presence of high levels of inclusion bodies means the solution remains turbid. Check your pre and post lysis solution under the microscope to see if you see the same thing. Cheers, Rhys From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of J. Valencia S. [valen...@gene.nagoya-u.ac.jpmailto:valen...@gene.nagoya-u.ac.jp] Sent: 21 June 2012 13:44 To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Expressed protein hinders cell lysis? Greetings, everyone. We need to ask your advice on an issue with one of our proteins expressed in E. coli Rosetta cells. This yeast-derived protein has a very low yield compared to others we work with, and we think it is because the cells are hard to lyse: even after 3 cycles in a cell cracker the solution barely changes colour. We have no problems lysing Rosetta cells expressing other yeast-derived soluble proteins, and we usually obtain enough for our crystallisation screens. For the aforementioned protein we have already tried using STAR cells, varying the contents of the lysis buffer, sonicating, or adding FeSO4 to the solution (we think the protein binds Fe or Mn because it is yellow), but to no avail. Searching the ccp4bb archive and other resources did not help, so we would like to ask 2 questions to the community in order to focus our efforts better: 1. How can a recombinant protein make a cell harder to lyse? 2. Do you have any suggestions to avoid this effect? We appreciate any input, and will be sure to post a summary for future reference once this issue is solved. Sincerely, -- J. Valencia S. PhD student CGR-NU .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
[ccp4bb] Software and servers in Uppsala
Hi all, In the past couple of years, Mark Harris in Uppsala has developed a bunch of programs and servers that are useful for crystallographers, structural biologists and structural bioinformaticians. Some of his programs are listed here: http://xray.bmc.uu.se/markh/programs.html My favourite is O on a stick for Macs. If you download a tarball from an EDS entry, you can unzip it and drop it on the O on a stick icon on your desktop and O will start up and execute a bunch of macros. Within seconds you have the PDB entry and the EDS maps on your screen, ready for scrutiny! Mark's servers are listed here: http://xray.bmc.uu.se/markh/servers.html Several of these provide a user-friendly interface to some of my old programs: - Australis allows you to do a quick and dirty superposition of two protein structures, and it will show the result in Jmol as well as allow you to download the superimposed coordinates, structure-based sequence alignment, etc. Australis is driven by LSQMAN. - Borealis does essentially the same as Australis, but for nucleic acid structures instead of proteins (try out the default example, 1HR2 versus 1U9S). Borealis is also driven by LSQMAN. - Spasm is a server to run SPASM (unsurprisingly, perhaps) which allows you to detect small motifs (that you provide) in existing PDB entries. Use the default example to find out how it works. - Spana runs a program that I've never even published, SPANA - it does the same as SPASM, but for nucleic acid motifs and structures. Use the default example to find out what it can do. - CavitySearch can be used to find cavities and tunnels in proteins. It can use either VOIDOO or MAMA (implementing Delaney's method). You can download the results and view the cavity(ies) with the AstexViewer. Try 1CEL chain A, looking for the biggest cavity using Delaney's method - this shows how a tunnel in a structure can be visualised. See also: http://xray.bmc.uu.se/usf/vis_tunnel.html - Morphtician allows you to do simple morphs between protein chains in the same or different structures. It uses LSQMAN under the hood. Interpolated coordinates can be downloaded and the morphing visualised in Jmol. See also: http://xray.bmc.uu.se/usf/mol_morph.html - ValLiGURL has been around for a few years. Note: since Mark is no longer employed at Uppsala University, these programs and servers come with no warranty or support. --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
[ccp4bb] Practical Membrane Protein Course in Brazil
Dear All, The Laboratório Nacional de Biociências (Campinas-Brazil) and The Membrane Protein Laboratory (MPL) at Diamond Light Source are organising a Practical course in Structure and Function of Membrane Proteins. The goal of the course is to introduce PhD students and post-docs to the basic principles of membranes proteins and the methods for production, structure solving and analyses of these proteins. The course will run at The Laboratório Nacional de Biociências, Campinas-Brazil The official language is english. The course suits attendees who are entirely new to the field as well as those who wish to acquire an in-depth understanding of the methodology. The course will be limited to 20 people from Universities and Research Institutes from MERCOSUL. Deadline for application: 30th June, 2012 For more information: www2.lnbio.org.br/membraneproteinscourse Best Wishes, Isabel - Dr. Isabel De Moraes, MRSC Membrane Protein Laboratory Facility Co-ordinator Membrane Protein Laboratory Diamond Light Source Ltd, Chilton, Didcot, Oxfordshire, OX11 ODE, UK Tel (direct): 01235 778664 --
Re: [ccp4bb] Expressed protein hinders cell lysis?
I'm not convinced you are not getting lysis but if you want to try something different use a BeadBeater. They are gentle and very efficient. Roger Rowlett On Jun 21, 2012 8:54 AM, J. Valencia S. valen...@gene.nagoya-u.ac.jp wrote: Greetings, everyone. We need to ask your advice on an issue with one of our proteins expressed in E. coli Rosetta cells. This yeast-derived protein has a very low yield compared to others we work with, and we think it is because the cells are hard to lyse: even after 3 cycles in a cell cracker the solution barely changes colour. We have no problems lysing Rosetta cells expressing other yeast-derived soluble proteins, and we usually obtain enough for our crystallisation screens. For the aforementioned protein we have already tried using STAR cells, varying the contents of the lysis buffer, sonicating, or adding FeSO4 to the solution (we think the protein binds Fe or Mn because it is yellow), but to no avail. Searching the ccp4bb archive and other resources did not help, so we would like to ask 2 questions to the community in order to focus our efforts better: 1. How can a recombinant protein make a cell harder to lyse? 2. Do you have any suggestions to avoid this effect? We appreciate any input, and will be sure to post a summary for future reference once this issue is solved. Sincerely, -- J. Valencia S. PhD student CGR-NU
[ccp4bb] Building coot from scratch
Dear All I'm trying build_from_scratch my coot and it doesn't work... the following error appears, and I really don't know how to fix it: Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 7039 (6.9K) [text/plain] Saving to: `build-notes' 100%[=] 7,039 26.4K/s in 0.3s 2012-06-21 17:10:09 (26.4 KB/s) - `build-notes' saved [7039/7039] WARNING: timestamping does nothing in combination with -O. See the manual for details. WARNING: timestamping does nothing in combination with -O. See the manual for details. WARNING: timestamping does nothing in combination with -O. See the manual for details. If i try has root, an different error appears: Resolving coot.googlecode.com... 74.125.134.82, 2001:4860:800a::52 Connecting to coot.googlecode.com|74.125.134.82|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 111873 (109K) [text/plain] Saving to: `build-it-gtk2-simple' 100%[=] 111,873 223K/s in 0.5s 2012-06-21 17:17:04 (223 KB/s) - `build-it-gtk2-simple' saved [111873/111873] .: 7: build-it-gtk2-simple: not found anyone know how to fix? thank you all Andre
Re: [ccp4bb] Building coot from scratch
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello Andre,
what you see is not an error message, it is only a warning message. It
is actually the last message before the remaining output is redirected
to into the ${LOGS} directory.
Paul set up a wrapper wrap-build-it for me:
#!/bin/bash
OS=$(uname)
HOST=$(hostname)
AUTOBUILD_BUILD=$HOME/public_html/coot_deb/autobuild/building
AUTOBUILD_INSTALL=$HOME/public_html/coot_deb/autobuild/${OS}-${HOST}
AUTOBUILD_INSTALLED=$HOME/public_html/coot_deb/autobuild/${OS}-${HOST}
LOGS=$HOME/public_html/coot_deb/build-logs/${OS}-${HOST}
NIGHTLY_DEST_DIR=$HOME/public_html/coot_deb/binaries/nightlies/pre-release
STABLE_DEST_DIR=$HOME/public_html/coot_deb/binaries/stable
. build-it-gtk2-simple python
when you place it into $HOME/public_html/coot_deb together with
build-it-gtk2-simple, call it as
bash wrap-build-it
that seems to work reasonably well - we have not fixed all testing
issues, but at least the resulting binary tree works for me.
Good luck,
Tim
On 06/21/2012 10:17 PM, Andre Godoy wrote:
Dear All
I'm trying build_from_scratch my coot and it doesn't work... the
following error appears, and I really don't know how to fix it:
Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected.
HTTP request sent, awaiting response... 200 OK Length: 7039 (6.9K)
[text/plain] Saving to: `build-notes'
100%[=]
7,039 26.4K/s in 0.3s
2012-06-21 17:10:09 (26.4 KB/s) - `build-notes' saved [7039/7039]
WARNING: timestamping does nothing in combination with -O. See the
manual for details.
WARNING: timestamping does nothing in combination with -O. See the
manual for details.
WARNING: timestamping does nothing in combination with -O. See the
manual for details.
If i try has root, an different error appears:
Resolving coot.googlecode.com... 74.125.134.82, 2001:4860:800a::52
Connecting to coot.googlecode.com|74.125.134.82|:80... connected.
HTTP request sent, awaiting response... 200 OK Length: 111873
(109K) [text/plain] Saving to: `build-it-gtk2-simple'
100%[=]
111,873 223K/s in 0.5s
2012-06-21 17:17:04 (223 KB/s) - `build-it-gtk2-simple' saved
[111873/111873]
.: 7: build-it-gtk2-simple: not found
anyone know how to fix?
thank you all
Andre
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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Re: [ccp4bb] help regarding structure solution
Hi Sonali, You could try wide-search MR: https://portal.sbgrid.org/d/apps/wsmr/ Best of luck, val On 20 June 2012 19:13, sonali dhindwal sonali11dhind...@yahoo.co.in wrote: Dear All, I am working on a protein for last so many years and for which i have got crystal now in a tray which i kept 1 years ago. It diffracts well and resolution is 2.2A, which is good. I indexed in HKL2000, mosflm and automar and it shows P21 space group in all data reduction packages. But when I tried using molrep or phaser then I do not get any solution. The sequence of my protein is having 46% identity with other available crystal structure. Also when I tried to get matthews coffecient, it calculates its molecular mass less ( about 35 kDa) than which should be (original 54kDa) with solvent content 47%. I have also run the silver staining gel of the protein which contained crystal that shows about 45 kD protein band which is 10 less than the original. Also I tried to run gel on crystal but it did not give anything as it was a small crystal. I have tried all combinations of the search model and tried to break available pdb many ways to make different search models but have not got any good solution. Molrep gives contrast even 10 or more but no good electron density map yet. Free R and figure of merit becomes 52% and 42% respectively in Refmac with all the solutions. I will highly appreciate all the suggestions for this kind of problem. Thanks and regards -- Sonali
[ccp4bb] FW: [PyMOL] Structural biologist job
FYI for the on-pymol readers. BR -Original Message- From: H. Adam Steinberg [mailto:a...@steinbergs.us] Sent: Tuesday, June 12, 2012 4:22 AM To: pymol-us...@lists.sourceforge.net Subject: [PyMOL] Structural biologist job Hi all, A friend of mine is looking to hire a structural biologist. With the tight job market I though I would try and get this out to as many people as possible. I am looking to hire a PhD structural biologist to join the team I manage at Myriad Genetic Laboratories in Salt Lake City, Utah. Please forward/post/pin-up the attached pdf if you can think of anybody who might be interested, or if you can think of someone that might know someone who might be interested. Myriad Genetics is a great company to work for, with all the perks of a biotech company (employee stock option purchase plan, 401k company match, full benefits, etc). Myriad Genetics is nestled in the foothills of the Rocky Mountains with over 1,100 employees and growing. Salt Lake City is a great place to live both for the outdoorsy person, as well as the cultural arts type person. It s also a great place to raise a family. Please email all job inquiries to Dr. Julie Eggington at jeggi...@myriad.com. Thank you. Julie Myriad Genetics - Clinical Variant Specialist unofficial job posting 2012.pdf JOB OPENING: Clinical Variant Specialist Requires Ph.D. in Biochemistry or related field, with emphasis in structural biology. Location: Myriad Genetic Laboratories, Inc. Salt Lake City, UT. Full time position NOTE: This is an early, unofficial job posting. Official job postings are found at www.myriad.com Overview: Myriad Genetic Laboratories is a leading molecular diagnostic company based in Salt Lake City, Utah. Myriad offers predictive medicine tests that identify hereditary breast and ovarian cancer, hereditary colorectal and uterine cancer, and other hereditary cancer syndromes. DNA sequencing allows Myriad to detect these syndromes by identifying disease causing mutations in specific genes. However, not all genetic variants which are identified in DNA testing are disease causing. Initially, some variants are classified as Genetic Variant of Uncertain Significance until research shows whether or not the genetic variant is disease causing or benign. It is the role of Myriad's Variant Specialist Team to collect and analyze data so that these Genetic Variants of Uncertain Significance can be correctly classified in a clinical setting. The Variant Specialist Team is looking to hire an expert in structural biology. Unlike traditional Scientist I/II positions in biotechnology, the Clinical Variant Specialist is not likely to pursue lab bench work, but will apply his/her skills to reviewing literature and using molecular modeling and bio-informatics approaches to assist in better understanding the effects of genetic mutations. The Clinical Variant Specialist will work within a larger group of cross-disciplinary scientists and statisticians. Additionally, the Clinical Variant Specialist will work with clinician customers to assist in scientific understanding and in the coordination of research studies. Excellent communication skills are required. Attendance at professional meetings and publication opportunities are fostered. The clinical Variant Specialist will also work on a variety of projects across different non-science divisions within Myriad as a representative of the Variant Specialist Team. Qualifications: -Ph.D. in Biochemistry or a related field required, with emphasis in structural biology -Excellent written and verbal communication skills -Candidates with postdoctoral research experience or equivalent are preferred -Candidates with experience in protein-nucleic acid interactions and/or experience in cancer causing biological pathways are preferred How to apply: -Applications are to be formally made through http://www.myriad.com/careers/ when the position officially posts (likely in July 2012). The position may have a different title at time of posting. Dr. Julie Eggington is seeking resumes early to screen candidates as soon as possible starting in June 2012. To facilitate this, please email resumes and enquiries to Dr. Julie Eggington at jeggi...@myriad.com with Clinical Variant Specialist Job Opening in the subject line. About Myriad: Myriad Genetics, Inc. (Nasdaq: MYGN) is a leading molecular diagnostic company dedicated to making a difference in patient s lives through the discovery and commercialization of transformative tests to assess a person s risk of developing disease, guide treatment decisions and assess risk of disease progression and recurrence. With fiscal year 2011 revenue of over $400 million and more than 1,100 employees, Myriad is working on strategic directives, including new test introductions, companion diagnostics, and international expansion, to take advantage of significant
[ccp4bb] Capping peptide
Hi all I m just finishing the refinement of several peptide:protein complex structures and have become unstuck at modifying the N and C terminal ends (of the synthetic peptides) with the generic acetyl and amide capping groups respectively. Could some one please explain to me the most straight forward way of accomplishing this. regards Chris
