Re: [ccp4bb] Organic solvents for ligand solubilisation
Dear Klaus, We've had a lot of luck with ethylene glycol and isopropanol, using them successfully in cases where DMSO affects diffraction. Best wishes Richard = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE1 9HN Tel: 0116 2297100 Web: http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/research Elite Without Being Elitist Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011 Follow us on Twitter http://twitter.com/uniofleicester On 23 May 2013, at 14:36, Klaus Fütterer wrote: Dear CCP4BB followers, We are currently trying to obtain ligand-bound complexes for one of our proteins by soaking and/or co-crystallisation. We have had prior success for this protein, but using a different class of ligands. The new ligand (in DMSO) remains in solution (more or less) when mixed with the reservoir/cryoprotectant, and the diffraction pattern survives the soaking nicely. Annoyingly though, all we see are density peaks that match the size of DMSO and become more pronounced when increasing [DMSO] (to help solubilisation of the ligand). Soaking times varied between minutes to 16 hours. Kd was measured ( ~ 10 uM) in the solution state. We have tried pyridine (which keeps the ligand in solution, but kills diffraction in an instant), and DMF (which doesn't keep the ligand in solution when mixing with cryoprotectant). I am wondering whether the community has suggestions for alternative organic solvents that have been used to solubilise hydrophobic ligands, and are reasonably gentle to the protein crystal. Thank you. Klaus === Klaus Fütterer, Ph.D. Reader in Structural Biology Undergraduate Admissions School of Biosciences P: +44-(0)-121-414 5895 University of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: k.futte...@bham.ac.ukmailto:k.futte...@bham.ac.uk Birmingham, B15 2TT, UK W: http://tinyurl.com/futterer-lab ===
[ccp4bb] Measure Cell option in imosflm
Does anyone know how to access the 'Measure Cell' function in iMosflm? This function in ipmosflm allowed you to click on a pair of spots, then input the number of diffraction orders, to output a rough measure of the cell length. Any help appreciated! Thanks Richard = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE1 9HN Tel: 0116 2297100 Web: http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/research Elite Without Being Elitist Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011 Follow us on Twitter http://twitter.com/uniofleicester
[ccp4bb] Two MRC-funded PhD studentships in Leicester
Two MRC-funded PhD studentships are available in the laboratory of Richard Bayliss at the University of Leicester starting in October 2013. The Department of Biochemistry provides an outstanding environment in research training in structural biology and structure-based drug design and state-of-the-art facilities for X-ray crystallography, NMR spectroscopy and biophysics. 1) MRC Cancer Theme Award Title: Targetting centrosome declustering in haematological cancers Co-supervisors: Prof. Andrew Fry (Biochemistry) and Prof. Martin Dyer (Cancer Studies) Further details: http://www2.le.ac.uk/study/research/funding/mrc-cancer-research 2) MRC Industrial CASE Award Title: Fragment-based approaches to allosteric kinase inhibitors and protein-protein interaction inhibitors Co-supervisor: Dr Andy Merritt at MRC-Technology Centre for Therapeutics Discovery Further details: http://www2.le.ac.uk/study/research/funding/mrc-casestudentship Note that these studentships are available only to British students or those with strong UK links and residency, as per MRC guidelines. Applications must be made online, preferably by February 22nd. = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE1 9HN Tel: 0116 2297100 Web: http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/research Elite Without Being Elitist Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011 Follow us on Twitter http://twitter.com/uniofleicester
Re: [ccp4bb] Structure example request for large domain movement in crystallo soaking
Dear Wenhe, One example we have is the protein kinase Nek2. We co-crystallised with ADP and then soaked in the inhibitors. The activation loop was free to move around and adopt a number of different conformations (e.g. to DFG-out conformation). References: Westwood I, Cheary D-M, Baxter JE, Richards MW, van Montfort R, Fry AM, Bayliss R (2009) Insights into the conformational variability and regulation of human Nek2 kinase. J. Mol. Biol. 386(2):476-85 Whelligan DK, Solanki S, Taylor D, Thomson DW, Cheung K-MJ, Boxall K, Mas-Droux C, Barillari C, Burns S, Grummitt CG, Collins I, van Monfort RLM, Aherne W, Bayliss R, Hoelder S (2010) Aminopyrazine inhibitors binding to an unusual inactive conformation of the mitotic kinase Nek2: SAR and structural characterization. J. Med. Chem. 53(21):7682-98. Solanki S, Innocenti P, Mas-Droux C, Boxall K, Barillari C, van Montfort RLM, Aherne GW, Bayliss R, and Hoelder S (2011) Benzimidazole Inhibitors Induce a DFG-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (Nek2) without Binding to the Back Pocket and Reveal a Nonlinear Structure−Activity Relationship. J. Med. Chem. 54: 1626-1639 Cheers Richard = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE1 9HN Tel: 0116 2297100 Web: http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/research Elite Without Being Elitist Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011 Follow us on Twitter http://twitter.com/uniofleicester On 9 Oct 2012, at 14:33, WENHE ZHONG wrote: Dear CCP4 members, Recently, I got a ligand soaking structure to clearly show a large domain (~100 amino acids) movement compared to the no soaking structure. Although there are some reported examples of this enzyme to suggest the flexibility of this large domain which is relevant to substrate binding. But it is the first time I can see it happen in crystal soaking procedure. In this case, I am pleased by this result. My question is, do you have any other example like mine, where domain (or loop) movement is observed in crystal during ligand soaking procedure? It would be very helpful for me to relate my result to other similar examples. Thank you very much. King regards, Wenhe
[ccp4bb] Job advert: Research Fellow at the University of Leicester, Structural Studies of Protein-Drug Interactions
A position is available in the Centre for Translational Therapeutics (CTT) within the College of Medicine, Biological Sciences and Psychology for a talented postdoctoral structural biologist to work on a collaborative in-house structural biology projects, with an emphasis on structure-based drug discovery and development. The CTT is headed by Prof. Andrew Tobin and aims to facilitate early phase drug discovery within the College. The scientist will be based in the Department of Biochemistry and will work alongside the groups of Prof. Mark Carr (NMR spectroscopy) and Dr Richard Bayliss (X-ray crystallography), who have strong track records in structure-based drug discovery. The scientist will determine the structures of proteins that are targeted by CTT and characterise their interactions with candidate compounds. The proposed work will involve close interactions with other postdoctoral scientists within the CTT, research groups across the College and medicinal chemistry collaborators. The CTT and Department of Biochemistry are superbly equipped for inhibitor discovery using mobility-shift, label-free and thermal shift assays, as well as for all aspects of NMR spectroscopy and X-ray crystallography based structural biology, with excellent supporting facilities for recombinant protein expression and purification. The successful postdoctoral research fellow will have a proven track record in structural biology, with significant experience in X-ray crystallography and/or NMR-based approaches. A willingness to apply either approach to solve protein structures would be desirable. A strong interest in knowledge-based drug discovery is essential. The ability and willingness to travel to meetings with collaborators and to use off-campus research facilities is essential. Good communication and presentation skills are also a pre-requisite. Salary Grade 8 - £39,257 to £44,166 per annum. Available immediately for an initial period of 1 year, with the expectation of extension for a further 2 years Informal enquiries may be made to Dr Richard Bayliss, Tel +44 (0)116 229 7100, E.mail richard.bayl...@le.ac.uk; or Prof. Mark Carr, Tel: +44 (0)116 229 7075, E.mail: md...@le.ac.uk; or Prof. Andrew Tobin, Tel: +44 (0)116 252 2935, Email: t...@le.ac.uk Applications must be made through the University jobs page, on which further details are available (http://www2.le.ac.uk/offices/jobs/opportunities/jobsearch - reference MBP00666) The closing date for this post is midnight on 19th August 2012. = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE1 9HN Tel: 0116 2297100 Web: http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/research Elite Without Being Elitist Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011 Follow us on Twitter http://twitter.com/uniofleicester
[ccp4bb] FW: 3-year MRCT-funded postdoc position in structure-based drug discovery in Leicester
A position is available in the Department of Biochemistry for a talented postdoctoral structural biologist to work on a new 3 year collaborative project with MRC Technology focussed on protein structure-based drug discovery and development. The scientist will work in the groups of Prof. Mark Carr and Dr Richard Bayliss, with a combination of NMR spectroscopy and X-ray crystallography used to determine the structures of proteins targeted by MRC Technology drug discovery programmes and to characterise their interactions with candidate drugs. The proposed work will involve close interactions with experienced research scientists at MRC Technology. The Department of Biochemistry is superbly equipped for all aspects of NMR spectroscopy and X-ray crystallography based structural biology, with excellent supporting facilities for recombinant protein expression and purification. The research fellow position will be supported by a dedicated, part-time (60%) protein biochemistry research assistant. The successful postdoctoral research fellow will have a proven track record in either NMR spectroscopy or X-ray crystallography based structural biology, with some experience in NMR-based approaches desirable. A clear willingness and desire to apply either approach to solve protein structures is essential. A strong interest in knowledge-based drug discovery is also essential for the position. The ability and willingness to travel to meetings with collaborators and to use off-campus research facilities is essential. Good communication and presentation skills are also a pre-requisite. Informal enquiries may be made to Prof. Mark Carr, Tel: +44 (0)116 229 7075, E.mail: md...@le.ac.uk, or to Dr Richard Bayliss, Tel +44 (0)116 229 7100, E.mail rb...@le.ac.uk. Applications must be made through the University vacancies website, reference MBP00560. http://www2.le.ac.uk/offices/personnel/job-vacancies/?newms=jjid=73578newlang=1 Closing date for applications is midnight on 11th March 2012 = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE2 9HN Tel: 0116 2297100 Web: http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/
[ccp4bb] CR-UK funded postdoc vacancy in mitotic regulation, based in Leicester
We are looking for an ambitious and highly-motivated postdoctoral research associate who has expertise in protein crystallography to join the team of Dr Richard Bayliss within the Department of Biochemistry. The position is funded by a 5-year Cancer Research UK Programme Grant, which provides a generous allowance for equipment, running costs and research support. Research in the Bayliss lab is focussed on the structural mechanisms by which cell division is regulated, and on the structure-based design of chemotherapeutics. The group has built an international reputation for excellence in these fields, and has published 10 papers in peer-reviewed journals in the past 3 years. The main objective of this new position will be to elucidate the regulatory mechanisms of separase, the protease that triggers chromosome segregation. This is a high-impact project that will address a long-standing, unresolved question in mitosis and which is supported by several years of pilot work. The researcher will also contribute to the other aspects of the programme, such as the pathways of regulation by protein kinases (Aurora-A, Neks) and the early prophase checkpoint (CHFR). Dr Bayliss’s research group is located in the state-of-the-art Henry Wellcome Building with access to excellent facilities for biochemical studies, structural biology, cell culture (including large-scale insect and mammalian cell expression), microscopy and computer analysis. The position is available from January for three years in the first instance, renewable for a further two years depending on progress. The appointment will be made within the salary range £30,870 - £35,788. Prospective candidates should hold a degree and Ph.D in biochemistry, or related discipline, and have proven expertise in X-ray crystallography through the publication of at least one first author paper in a major international journal. Informal enquiries can be directed to Dr Bayliss via email (richard.bayl...@le.ac.uk). Applications must be made through the Job Vacancies page of the University website, job reference MBP00499. The closing date for this post is midnight on 6th December 2011. = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE2 9HN Tel: 0116 2297100 Web: http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/
[ccp4bb] Postdoc vacancy in Leicester on kinase structure-based design/mechanism
A postdoctoral research post is available to undertake translational structural biology work on a kinase target within my research group in the Department of Biochemistry. My group is located in the state-of-the-art Henry Wellcome Building with access to excellent facilities for biochemical studies, structural biology, cell culture, microscopy and computer analysis. The position is funded by Cancer Research UK and is available immediately for one year in the first instance, renewable for a further year depending on progress. Prospective candidates should hold a degree and Ph.D in biochemistry, or related discipline, and have expertise in X-ray crystallography. Applicants with experience in high-throughput crystallography applied to structure-based drug design would be at an advantage. My team has an established track record in the study of protein kinases and in the development of kinase chemical inhibitors in drug discovery. See the group website for further information (http://web.me.com/baylisslab). Informal enquiries can be directed to me via email (rb...@le.ac.uk). The closing date for this post is midnight on 18th October 2011. For further details, and to apply for the job, use the University vacancy search site (http://www2.le.ac.uk/offices/jobs/opportunities/jobsearch), reference is MBP00426. = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE2 9HN Tel: 0116 2297100 Web: http://web.me.com/baylisslab/
