[ccp4bb] Structural Biology job vacancy
Structural Biologist â Crysalin Limited, Upper Heyford, Oxfordshire Crysalin Limited is a venture capital backed structural biology company recently spun out of the University of Oxfordâs Biophysics Laboratory. It is based upon the pioneering work of Professor Martin Noble and Dr. John Sinclair. Crysalin is developing novel protein nanoassemblies to address the problems of the crystallization step in structure based drug design. The successful candidate will join a small group of motivated industrial professionals at our Upper Heyford facility focussed on this developing this technology. Candidates will have significant experience of the x-ray crystallography process from crystal manipulation to structural refinement. Specifically the ideal candidate will have demonstrated experience in crystal mounting, data collection, structural solution and refinement. The following additional technical skills would be of value: molecular biology, protein purification, protein design and engineering, electron microscopy and atomic force microscopy. The ideal candidate will be self-motivated, have experience in team working environments and have proven presentation and interpersonal skills. Crysalin offers an opportunity to work at the cutting edge of structural biology research with expert groups both at the University of Oxford and at Crysalin. A competitive salary and options package will be provided. Please reply with a C.V. to Ceri Lewis , Crysalin Limited, 77 Heyford Park, Upper Heyford , Oxfordshire, OX25 5HD or Email- recruitm...@crysalin.com.
[ccp4bb] about partial plroteolysis
hello CCp4ers: Sorry about the off-topic question. My protein is a kinase which the predicted kinase domain is from 32aa to 319aa. But the protein sequence after partial proteolysis is from 52aa. what should I do? Are there any reasonable expanation? Thanks in advance! Xinghua Qin -- Xinghua Qin Room 4022, Center for Life Sciences, China Agricultural University, No.2, Yuan Ming Yuan West Road, Haidian District， Beijing，China，100193 Tel: +86-10-62732672
Re: [ccp4bb] off topic: problematic protein
I would think thing here is that this protein actually associates to those lipid nanodiscs...(around the disc) and Na cholate CMC is around 10 mM. so, yes you can solubilise proteins that bind lipids, the question is does this protein bind lipids or not? or is it just scrambled or whatever, doesnt like to be overexpressed etc??? or sticky because it is part of a larger complex naturally and not stable alone, for instance. which i wouldn't know of course. regards, Tommi On Apr 20, 2011, at 1:08 AM, Arthur Glasfeld wrote: I recently followed a protocol from Stephen Sligar's lab for the purification of his nanodisc protein, which has strong hydrophobic character as it associates with phospholipids. His protocol includes washes with 1% Triton X-100 and then with 50 mM cholate (both at pH 8 in the presence of 300 mM NaCl). Worked great, and I saw stuff coming off the column in both washes. The reference is: Bayburt et al. (2002) Nano Letters, vol. 2, pp 853-856. http://pubs.acs.org/doi/abs/10.1021/nl025623k Good luck, Arthur Arthur Glasfeld Department of Chemistry Reed College 3203 SE Woodstock Blvd. Portland, OR 97202 USA On Apr 19, 2011, at 12:48 PM, Savvas Savvides wrote: Dear colleagues We are working on a large bacterial protein (featuring a large number of repeats) that appears to copurify with a lot of other proteins after Ni-affinity chromatography and gel-filtration. We have tried adjusting the ionic strength of these runs and have gone to as high as 5M NaCl but only saw marginal improvements. It appears that the protein likes to stick to a lot of stuff, and in fact the number of repeats in a given construct appears to correlate with the extent of contaminants in our purification steps. We have admittedly never seen anything like this among the so many different, and often challenging, proteins, we have worked on in our group over the last few years. We are now thinking of trying detergents in the buffers (at non- micellar concentrations), in conjunction with playing a bit with the pH to see if such an approach provides a 'stripping' effect. Interestingly, the protein has a calculated pI of 3.5 ! As the options for handling this protein are indeed quite numerous, we would be grateful for any additional input and possible tips/ tricks. I will prompty post a summary of the thread. Best regards Savvas et al. 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 Tommi Kajander, Ph.D. Structural Biology and Biophysics Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki Finland p. +358-9-19158903 tommi.kajan...@helsinki.fi
[ccp4bb] Fwd: IUCr 2011 - AUGUST 22 - 30
Dear allI've been asked to distribute this in the best way I can - I can thinkof no better way than to distribute it to ccp4bb...Begin forwarded message:From: "IUCR" iucr2...@pacifico-meetings.comDate: 20 April 2011 09:27:45 GMT+01:00To: "'IUCR'" iucr2...@pacifico-meetings.comSubject: IUCr 2011 - AUGUST 22 - 30Dear Chairs of IUCr Commissions,We would appreciate if you could please distribute this email among the members and consultans of your commission, asking them to distribute this information in the best way they could.Important Annoucement:The deadline for sending contributions to theXXII Congress and General Assembly has been extended to the28th ofApril.For further information, please check our web pagehttp://www.iucr2011madrid.es/Looking forward to welcoming you in Madrid from August 22ndto 30th.Best regards.The Local Organizing CommitteeIUCr 2011 TECHNICAL SECRETARIAT:GRUPO PACIFICOPaseo General Martínez Campos, 44, 1º28010 Madrid - SPAINTel. (34) 913.836.000 ext. 127Fax. (34) 913.023.926iucr2...@pacificio-meetings.comwww.iucr2011madrid.es Harry--Dr Harry Powell, MRC Laboratory of MolecularBiology, MRC Centre, Hills Road, Cambridge,CB2 0QHhttp://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011
Re: [ccp4bb] about partial plroteolysis
On Wed, 2011-04-20 at 14:27 +0800, xinghua qin wrote: But the protein sequence after partial proteolysis is from 52aa. what should I do? Are there any reasonable expanation? The protease cut your protein at position 52 sounds reasonable enough to me -- Hurry up before we all come back to our senses! Julian, King of Lemurs
[ccp4bb] insert a cleavage site between scondary structures
Dear ALL; One of our proteins will gain activities after cleavage between secondary structures(probably at three sites). In the intact structure, the N-terminal and C-terminal domains beside this cleavage site have extensive contacts. So far we are stilling looking for the enzymes that cut this protein in human, probably at disease situation. However, when we made the truncates, both the N-ter and C-ter domains become soluble aggregates even during expression at 20 degree, whereas the whole enzyme can be solubly expressed in E.coli. Now we are trying to design an artificial cleavage site, say TEV or thrombin site, to at least prove the idea at the biochemistry level. There are some short loops between strands and helices. Can anyone suggest a good way of adding in the cleavage site without changing the native structures? Thanks a lot. Jerry McCully
[ccp4bb] PDBe annotates its 10,000th structure
In June 1999, staff of the Macromolecular Structure Database (MSD; nowadays known as the Protein Data Bank in Europe, http://pdbe.org/) at the European Bioinformatics Institute (EMBL-EBI; http://www.ebi.ac.uk/) began annotating PDB entries. Now, eleven years later, PDBe has annotated its 10,000th structure, 2YF6 (http://pdbe.org/2yf6). This structure is of a chicken MHC/peptide complex and was determined in the group of Susan Lea at the University of Oxford. You can read more about this milestone in the Wellcome Trust blog at http://wellcometrust.wordpress.com/2011/04/20/1th-structure-curated-by-the-protein-data-bank-in-europe/ This month's episode of Quips is also dedicated to 2YF6 - see http://www.ebi.ac.uk/pdbe-apps/quips?story=MHCstory For some early history of MSD/PDBe, see http://www.riethoven.org/BioInformer/newsletter/archives/6/msd.html We are grateful to all the structural biologists who have deposited their structures with PDBe and look forward to annotating the next 10,000 entries! --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] 250 years of Bayes' Theorem: Link
This link should be helpful to many folks here: http://blog.revolutionanalytics.com/2011/04/250-years-of-bayes-theorem.html
[ccp4bb] Rcullis and phasing power
sirs: I am running BP3 in crank on SeMet data SAD and getting a solution, but we need a number like Rcullis which is nowhere to be found, and comes from Mlphare. What is best to report? thanks kas -- Kenneth A. Satyshur, M.S.,Ph.D. Associate Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207 attachment: satyshur.vcf
