[ccp4bb] CECAM Workshop: Protein assemblies at the interface of functionalised materials
A better understanding of the self-assembly of highly ordered peptide nanostructures is vital as not only does it help to uncover the pathogenesis of various neurodegenerative diseases but it also provides new clues for a bottom-up design and fabrication of nanoscale devices and sensors for use in biomedicine. One of the primary challenges that is faced when designing these nanoscale devices and sensors is the ability to tune the interface in order to optimise the self-assembly of the peptides near the device interface for the desired application. Therefore obtaining a molecular scale understanding of the interactions between peptides and the desired interface is of utmost importance. Computer simulations have proven to be a very powerful tool in providing insight into these interactions and therefore will continue to play a significant part in the further development and design of these systems. Due to the broad range of applications driven by this science, this field continues to become more and more interdisciplinary including medics, biologists, chemists, physicists, material scientists and engineers. This CECAM workshop will bring together the pre-eminent scientists in the various fields to discuss the open questions from the experimental and computational angles of attempting to gain a new level of understanding of how functionalised interfaces interact with the aggregation of proteins. The workshop will be held 17-19 September 2014 in Lausanne, Switzerland. If you are interested in participating in this workshop, please visit the workshop website (http://www.cecam.org/workshop-1040.html) to find details as to how to apply.
Re: [ccp4bb] 2 ligands/monomer
Dear Wei, The enzyme ribonucleotide reductase can, depending on organism and class, bind ATP as a substrate in the active site (c), as an allosteric regulator of substrate specificity at another site (s) and as an overall activity regulator at a third site (a)! It can also bind dATP at the second and third sites, but not as a substrate. It cannot bind to sites (c) and (s) at the same time although it could potentially bind to sites (s) and (a) simultaneously. Here is a review that you might find useful: http://www.ncbi.nlm.nih.gov/pubmed/22050358 Best wishes Derek On 4 Mar 2014, at 04:48, Wei Shi wei.shi...@gmail.com wrote: Dear all, Does anyone happen to know examples of 2 ligands bind to a single protein / each monomer protein in 2 different ligand binding pockets? I know the following example: (1). phosphofructokinase, which binds ATP as both a ligand and a feedback inhibitor in different sites (2). 2 cAMP bound to each E. coli CAP monomer in the crystal structure. Does any of you know other examples? Thank you so much! Best, Wei
[ccp4bb] *abstract deadline 10th March* 3rd annual CCP-BioSim conference - Frontiers of Biomolecular Simulation - University of Edinburgh - 21st-23rd May 2014
Quick reminder that the deadline for abstracts for the CCPBioSim annual conference is next Monday. Cheers Martyn Dear Colleagues, The third annual CCP-BioSim conference will be held at the John McIntyre conference centre, Edinburgh First, from Wednesday 21st to Friday 23rd May 2014. The aim of the event is to bring together computational and experimental scientists with an interest in developing and applying biomolecular simulation techniques to their work. The deadline for submission of abstracts for a contributed oral or poster presentation is March the 10th. Further information regarding registration, schedule, abstract submission and other matters is available at: http://www.ccpbiosim.ac.uk/?q=annualconfs/conf2014 Confirmed Invited Speakers * Alexandre Bonvin, Bijvoet Center for Biomolecular Research, Utrecht, Netherlands * Cecilia Clementi, Rice University, Department of Chemistry, USA * Michael Gilson, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, USA * Bert de Groot, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany * Frauke Gräter, Heidelberg Institute of Theoretical Studies, Germany * Gerhard Hummer, Max Planck Institute of Biophysics, Frankfurt am Main, Germany * Michael Mazanetz, Evotec UK Ltd. , UK * Irina Tikhonova, School of Pharmacy, Queen's University Belfast, UK -- Dr. Julien Michel, Royal Society University Research Fellow Room 263 School of Chemistry University of Edinburgh West Mains Road Edinburgh, EH9 3JJ United Kingdom phone: +44 (0)131 650 4797tel:%2B44%20%280%29131%20650%204797 http://www.julienmichel.net/ - -- Scanned by iCritical.
Re: [ccp4bb] 2 ligands/monomer
Hi, Another example is the Shiga-like toxin B-subunit pentamer (i.e. the cell-surface binding component of this A-B toxin), which binds 3 Gb3 trisaccharides per monomer: http://pdbe.org/1bos http://www.ncbi.nlm.nih.gov/pubmed/9485303 Best wishes, Randy Read On 4 Mar 2014, at 10:41, Derek Logan derek.lo...@biochemistry.lu.se wrote: Dear Wei, The enzyme ribonucleotide reductase can, depending on organism and class, bind ATP as a substrate in the active site (c), as an allosteric regulator of substrate specificity at another site (s) and as an overall activity regulator at a third site (a)! It can also bind dATP at the second and third sites, but not as a substrate. It cannot bind to sites (c) and (s) at the same time although it could potentially bind to sites (s) and (a) simultaneously. Here is a review that you might find useful: http://www.ncbi.nlm.nih.gov/pubmed/22050358 Best wishes Derek On 4 Mar 2014, at 04:48, Wei Shi wei.shi...@gmail.com wrote: Dear all, Does anyone happen to know examples of 2 ligands bind to a single protein / each monomer protein in 2 different ligand binding pockets? I know the following example: (1). phosphofructokinase, which binds ATP as both a ligand and a feedback inhibitor in different sites (2). 2 cAMP bound to each E. coli CAP monomer in the crystal structure. Does any of you know other examples? Thank you so much! Best, Wei -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] 2 ligands/monomer
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Wei, if you are not restricted to 2 ligands, you can also look at human serum albumin, http://pdb.org/pdb/101/motm.do?momID=37 Best regards, Tim On 03/04/2014 04:48 AM, Wei Shi wrote: Dear all, Does anyone happen to know examples of 2 ligands bind to a single protein / each monomer protein in 2 different ligand binding pockets? I know the following example: (1). phosphofructokinase, which binds ATP as both a ligand and a feedback inhibitor in different sites (2). 2 cAMP bound to each E. coli CAP monomer in the crystal structure. Does any of you know other examples? Thank you so much! Best, Wei - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTFcxPUxlJ7aRr7hoRAmHJAKDXg9AN95L6yVNSHjpMtSyyb/aDAgCghvb+ x8f+PjbkG5hbiu8JUpTeNUo= =CdAI -END PGP SIGNATURE-
[ccp4bb] Fwd: Akta Service
Original Message Subject: Akta Service Date: Tue, 04 Mar 2014 10:44:09 + From: sa...@holmesanalytical.co.uk To: CCP4BB@JISCMAIL.AC.UK Dear Sirs, please excuse our intrusion - During our search for Akta users within the UK we have come across your details and specifically the subject of service provisions on FPLC instruments. We at Holmes Analytical are a company who specialise in the service of these instruments and support many customers in the UK including the MIB in Manchester, Syngenta and Cancer Research. If you would like to know more about our company, please just ask - again, apologies for the intrusion Kind regards James James Bull Mobile:07429 592254 Office:0044 845 430 8466 Fax:0044 1233 221600 Email:sa...@holmesanalytical.co.uk www.holmesanalytical.co.uk Please visit our site to see our latest refurbished instruments. Registered in England Number:3699871 Vat Registration Number:703 1837 60 Confidentiality caution disclaimer: This message, together with any attachment, is intended only for the use of the individual or entity to which it is addressed, and may contain information that is legally privileged and confidential. If you are not the intended recipient, please be informed that any dissemination, distribution or copying of this message, or any attachment, is strictly prohibited. kindly note that email communications are not secured and therefore are susceptible to alteration. Holmes Analytical Limited will not accept legal responsibility for the contents of this message. If you have received this message in error please advise the sender by reply email, and delete the message. Thank you for your co-operation.
Re: [ccp4bb] Fwd: Akta Service
Dear James There is no excuse for this intrusion, please refrain from making this another digital goat marked. cheers Preben On 3/4/14 2:51 PM, James Bull wrote: Original Message Subject: Akta Service Date: Tue, 04 Mar 2014 10:44:09 + From: sa...@holmesanalytical.co.uk To: CCP4BB@JISCMAIL.AC.UK Dear Sirs, please excuse our intrusion - During our search for Akta users within the UK we have come across your details and specifically the subject of service provisions on FPLC instruments. We at Holmes Analytical are a company who specialise in the service of these instruments and support many customers in the UK including the MIB in Manchester, Syngenta and Cancer Research. If you would like to know more about our company, please just ask - again, apologies for the intrusion Kind regards James James Bull Mobile:07429 592254 Office:0044 845 430 8466 Fax:0044 1233 221600 Email:sa...@holmesanalytical.co.uk www.holmesanalytical.co.uk Please visit our site to see our latest refurbished instruments. Registered in England Number:3699871 Vat Registration Number:703 1837 60 Confidentiality caution disclaimer: This message, together with any attachment, is intended only for the use of the individual or entity to which it is addressed, and may contain information that is legally privileged and confidential. If you are not the intended recipient, please be informed that any dissemination, distribution or copying of this message, or any attachment, is strictly prohibited. kindly note that email communications are not secured and therefore are susceptible to alteration. Holmes Analytical Limited will not accept legal responsibility for the contents of this message. If you have received this message in error please advise the sender by reply email, and delete the message. Thank you for your co-operation. -- J. Preben Morth, Ph.D Group Leader Membrane Transport Group Nordic EMBL Partnership Centre for Molecular Medicine Norway (NCMM) University of Oslo P.O.Box 1137 Blindern 0318 Oslo, Norway Tel: +47 2284 0794
[ccp4bb] Postdoctoral position in membrane protein structural biology and pharmacology
--- Postdoctoral position in membrane protein structural biology and pharmacology --- The laboratory of Hiro Furukawa at Cold Spring Harbor Laboratory (CSHL) is seeking an enthusiastic postdoc with dynamic interests in solving problems in neurological diseases and cancer using biochemical and biophysical techniques. We conduct x-ray crystallography on transmembrane proteins to understand basic mechanisms of ion and substrate transport and on fragments of water soluble domains to answer specific pharmacological questions. We use diverse techniques to address protein functions including electrophysiology, imaging, calorimetry, and phage-display. We also attempt to understand critical protein-protein interactions in signal transduction cascades in neurons and cancer cells using a combination of proteomics, electron microscopy, and x-ray crystallography. Other projects involve structure-based protein engineering of therapeutic antibodies. We have a state-of-the-art equipment to conduct membrane protein biochemistry and crystallography such as Mosquito LCP, frequent access to synchrotron light sources including NSLS and APS, and excellent facility for phage-display, proteomics, and microscopy. CSHL offers a unique scientific environment to interact with scientists within the institute as well as from outside at the prestigious CSHL courses and meetings (including the famous 2-week course, “X-ray Methods in Structural Biology”). Highly interactive and educative nature of CSHL has traditionally created many successful independent scientists with unique and innovative visions. A qualified candidate should hold or soon expected to hold (within ~1yr) Ph.D. in the area of crystallography, electron microscopy, and biochemistry and have experiences in basic molecular biology, biochemistry, and protein expression. Experience in x-ray crystallography or electron microscopy is desired but not necessary. Please see the lab website (http://www.cshl.edu/public/SCIENCE/furukawa.html - will be updated soon) for further information and send CV with a brief research statement as well as 2-3 contacts for references to furuk...@cshl.edu. Thanks.
Re: [ccp4bb] saving map isovalue surface to file?
USCF Chimera can save maps as a VRML and other formats. You can use 3D animation software to change formats from VRML to anything else. Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 Original message Date: Tue, 4 Mar 2014 10:38:13 -0800 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Alastair Fyfe af...@ucsc.edu) Subject: [ccp4bb] saving map isovalue surface to file? To: CCP4BB@JISCMAIL.AC.UK Is there an easy way to save a map isovalue surface to a file in a standard triangulated mesh format such as ply? This could be done with vtk or similar libraries, but, if there's already a script- accessible coot or pymol command, it would be helpful. Pymol can do this for molecular surfaces, but I haven't found a reference for maps. thanks, Alastair Fyfe
[ccp4bb] Mildred Dresselhaus Guest Professorship 2014
We are calling for applications for the Mildred Dresselhaus Guest Professorship 2014. The award has been established by The Hamburg Centre for Ultrafast Imaging (CUI), the new cluster of excellence at the Universität Hamburg, Germany, to promote outstanding female scientists. The CUI aims to observe and understand molecular processes at the atomic length and time scales, and includes the development of structure determination using ultrafast electron pulses and X-ray free-electron laser pulses. In 2014 the guest professorship will be awarded for the second time to a successful senior scientist and a younger scientist with high potential. The awardees are invited to work in Hamburg within CUI for a period of up to six months in 2014. We provide excellent research conditions to attract world-leading researchers to Hamburg with the aim of starting new and intensifying existing collaborations. Our current awardees are: Prof. Dr. Tamar Seideman, Northwestern University, USA and Prof. Dr. Rosario Gonzalez-Ferez, Universidad de Granada, Spain. Please feel invited to submit your nomination of a suitable candidate or your own application (letter of motivation, scientific CV including the five most important publications, list of invited talks, teaching experience as well as research interests as one single PDF file) to wiebke.kirchei...@cui.uni-hamburg.de by April 15, 2014. For more details, see also http://www.cui.uni-hamburg.de/en/opportunities/mildred- dresselhaus-guest-professorship-programme/ or contact Ms. Kircheisen directly.
Re: [ccp4bb] 2 ligands/monomer
Thank you all so much! Best, Wei On Tue, Mar 4, 2014 at 7:51 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Wei, if you are not restricted to 2 ligands, you can also look at human serum albumin, http://pdb.org/pdb/101/motm.do?momID=37 Best regards, Tim On 03/04/2014 04:48 AM, Wei Shi wrote: Dear all, Does anyone happen to know examples of 2 ligands bind to a single protein / each monomer protein in 2 different ligand binding pockets? I know the following example: (1). phosphofructokinase, which binds ATP as both a ligand and a feedback inhibitor in different sites (2). 2 cAMP bound to each E. coli CAP monomer in the crystal structure. Does any of you know other examples? Thank you so much! Best, Wei - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTFcxPUxlJ7aRr7hoRAmHJAKDXg9AN95L6yVNSHjpMtSyyb/aDAgCghvb+ x8f+PjbkG5hbiu8JUpTeNUo= =CdAI -END PGP SIGNATURE-
[ccp4bb] Peptide solubility issues
Hi all, Slightly off topic - but I'm having trouble solubilizing some peptides for SPR and hoped someone on the BB might have some other suggestions. The peptides are intra-chain S-S cross-linked 12mers with pIs of ~3. 10 residues are hydrophobic and 2 are acidic. Peptides have been tested with and without N- and C-terminal modifications (amidation/acetylation). I have tried: ddH2O raising (and lowering) pH (tested up to 8.5) with different buffers Including DMF as a co-solvent (I'm avoiding DMSO because of a methionine present in the peptide) - peptide still visibly precipitates out at 100uM in 5% DMF (also a 1mM stock in 50% DMF shows significant amounts of ppt) Adding a trace amount of detergent (0.005% Tween 20) I'm guessing I could try other co-solvents such as ethanol or initially solubilizing peptide in dilute NaOH before bringing the pH down with addition of a buffer (though I'm concerned about alkaline hydrolysis). Anyway, I'd rather have some insight from people before I waste any further peptide. Thanks for any suggestions.
