From owner-structural-nmr@net.bio.net Sun Jul 05 23:00:00 1998 Path: biosci!biosci!not-for-mail From: jbaleja@biba.med.tufts.edu (Jim Baleja) Newsgroups: bionet.structural-nmr Subject: postdoc_in_Boston Date: 6 Jul 1998 14:12:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 47 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <199807062036.QAA20155@biba.med.tufts.edu> NNTP-Posting-Host: net.bio.net Post-doc position available at Tufts University School of Medicine The project is on the investigation of protein-lipid interactions by blood coagulation proteins. The model system is the C-terminal domain of Factor VIII. [Gilbert, G. E. and Baleja, J. D., Membrane-binding peptide from the C2 domain of Factor VIII forms an amphipathic structure as determined by NMR spectroscopy, Biochemistry 34, 3022-3031 (1995).] [Veeraraghavan, S., Gilbert, G.D. & Baleja, J.D. Structure and topology of the membrane binding C2 domain of factor VIII in the presence of dodecylphosphocholine micelles. Biochem. J. 332, 549-555 (1998).] [Freedman, S. J., Blostein, M. D., Baleja, J. D., Jacobs, M., Furie, B. C., and Furie, B., Identification of the phospholipid binding site in the vitamin K-dependent blood coagulation protein Factor IX, J. Biol. Chem. 271, 16227-36 (1996).] The successful candidate will have experience in NMR techniques and protein purification. Good communication skills are an asset. Spectrometers at 300, 500, and 600 MHz field strengths and Silicon Graphics workstations will be available. The primary emphasis is on the study of the C2 domain using NMR spectroscopy (at Tufts). The fellow is also expected to become familiar with Hematology by interacting with Drs. Bruce and Barbara Furie and their research groups at the Beth-Israel Deaconess Medical Center, through which the position will be administered. There also will be opportunities to work in the laboratory of Dr. Gary Gilbert at the West Roxbury VA Medical Center (in Boston). This position is available starting immediately and the initial committment period is one year. If interested, please reply to me by E-mail or mail. If C.V.'s are sent by E-mail, they should in plain text only (not encoded) and include a list of references. Sincerely, Jim Baleja E-mail : jbaleja@biba.med.tufts.edu Mail : Dept. of Biochemistry 136 Harrison Ave. Tufts University Boston, MA 02111 --------------------------------------------------------------- Jim Baleja Tel. (617) 636-6872 Department of Biochemistry FAX (617) 636-2409 Tufts University School of Medicine E-mail: 136 Harrison Ave. jbaleja@biba.med.tufts.edu Boston, MA 02111 --------------------------------------------------------------- From owner-structural-nmr@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Athan Kuliopulos Newsgroups: bionet.structural-nmr Subject: Two Signal Transduction Postdoc Positions Avail-Boston Date: 7 Jul 1998 10:18:18 -0700 Organization: NEMC Lines: 61 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <35A22865.F8C011F8@opal.tufts.edu> Reply-To: "Kuliopoulos@HemOnc"@NEMC.nemc.org NNTP-Posting-Host: net.bio.net Two Postdoctoral Positions Available Molecular Cardiology Research Institute Tufts University School of Medicine-NEMC Boston, MA We have an immediate opening for two Postdoctoral Fellows to work in the field of molecular signaling and peptide-protein recognition. The projects focus on the human thrombin receptor. The thrombin receptor is activated by thrombin cleavage of the receptor exodomain and exposure of an N-terminal tethered ligand that binds to the body of the receptor. Receptor activation precipitates complex signaling events culminating in platelet aggregation, wound healing, and cellular proliferation. Since chronic activation of the receptor may lead to coronary artery disease, stroke, and other vascular diseases, preventing thrombin receptor activation is of pharmacologic interest. 1) Macromolecular Structural Studies of the Resting and Activated States of Thrombin Receptor Extracellular Domains. NMR structural studies of the thrombin receptor exodomain in activated and resting forms are currently in progress and a preliminary structure has been generated for the activated exodomain. Future projects include solving the structure of the exodomain complexed with extracellular loops. Insight into the molecular interactions between the exodomain and the body of the receptor should provide leads for the development of novel anti-thrombin receptor agents in collaboration with a pharmaceutical company. The NMR facility is located in the Medical School Biochemistry Department and current instrumentation include a new Bruker 600 MHz and updated 500 MHz magnets along with several SGI workstations. Our lab has close collaborations with NMR spectroscopists who provide additional technical expertise. 2) Thrombin-Cell Surface Protein Interactions; Development of Cell Surface-Specific Anti-Thrombotic Agents. During coagulation, the physiologic concentration of thrombin exceeds that of its thrombin receptor substrate. Therefore, thrombin has a difficult task of discriminating among the various cell surface proteins to find the receptor and cleave it in the millisecond time range. We are interested in exploring this unusual mechanism of substrate-assisted domain cleavage by thrombin and using this information to develop a novel class of cell surface anti-thrombin agents. The laboratory is located within the Molecular Cardiology Research Institute, a modern, state-of-the-art facility with a staff of 40 investigators including technical support. Qualifications for this position are a Ph.D. degree. Candidates with training in NMR who would like to acquire expertise in molecular biology are encouraged to apply. Interested candidates should e-mail a description of their research interests, a CV, and names of three references to: Athan Kuliopulos, MD., Ph.D. Assistant Professor of Medicine and Biochemistry Molecular Cardiology Research Institute Tufts-NEMC Box 832 750 Washington Street Boston, MA 02111 617-636-8482 617-636-4833 (fax) akuliopu@opal.tufts.edu From owner-structural-nmr@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Tim Hubbard Newsgroups: bionet.structural-nmr Subject: Call for prediction targets for CASP3 Date: 7 Jul 1998 10:19:18 -0700 Organization: The Sanger Centre Lines: 268 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <35A218D3.23F1B96F@sanger.ac.uk> Reply-To: th@sanger.ac.uk NNTP-Posting-Host: net.bio.net Call for prediction targets for CASP3 ===================================== This is a call to X-ray crystallographers and NMR spectroscopists for targets for CASP3, the third experiment in critical assessment of techniques for protein structure prediction. In 1994 the first protein structure prediction experiment was held to evaluate prediction methods through blind prediction. Details of about 33 protein sequences, which were expected to be solved before the end of 1994, were submitted by experimentalists and this allowed 135 blind predictions to be made by 35 different groups. The results of the experiment are published in the November 1995 issue of Proteins: Structure, Function, and Genetics, volume 23, No 3. A second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (December 1996) was a culmination of the second 9 month long, community wide experiment. Before that meeting, 42 structural targets provided by crystallographers and NMR spectroscopists were made available to the prediction community. Prior to the public release of structures, more than 900 predictions by approximately 70 research groups world wide were collected, and led to the most objective assessment of prediction methods so far. The results are published in a special issue of Proteins: Structure, Function and Genetics, Suppl.1, 1997. The third experiment is now running and will culminate in a meeting in December 1998. As before, the goal is to obtain an in-depth and objective assessment of our current abilities and inabilities in this area. To this end, participants will predict as much as possible about a set of soon to be known structures in advance of the meeting. Sessions will be devoted to presentation of the results and comparison with experiment, and to the description of the methods used. As before, for the experiment to succeed, it is essential that we obtain the help of the experimental community. Therefore, we would like to invite Protein crystallographers and NMR spectroscopists who expect to solve a structure before 1st October 1998 to submit the sequence so that attempts can be made to predict it before it is publically announced. Each prediction will be given a deadline prior to the date on which the first information about the structure is to be made public. Targets of all sizes and types are required. Small structures (less than 100 residues) are needed to test some of the ab initio structure prediction methods. Proteins with folds related to those of known structures are needed to test fold identification methods. Proteins with sequences homologous to that of one or more known structures are needed to test comparative modeling methods. We would like to collect as many targets are possible. All that is requested is: - the sequence or a sequence accession number of the protein - an estimate of the likely date of public release (and updates if the work procedes faster or slower) - a commitment to make the coordinates available to the independent assessors not latter than 1st October should the structure be solved by then. Any coordinates provided will be treated with strict confidentiality as requested and used only to evalute the accuracy of predictions. For further information and on-line forms and documents see: http://predictioncenter.llnl.gov/casp3/ A Target protein submission form is also attached to this message and can be mailed to casp3@predictioncenter.llnl.gov John Moult CARB, University of Maryland, USA Tim Hubbard Sanger Centre, Hinxton, UK Jan Pedersen Acadia Pharmaceuticals, Denmark Krzysztof Fidelis Lawrence Livermore National Laboratory, USA CASP3 organising committee ---- Instructions for completing this form ------------------------------------- (0) Please only use this form if you are unable to complete the WWW version at http://predictioncenter.llnl.gov/casp3/ (1) Save this page as a text file (2) Complete all sections (3) send by email to casp3@predictioncenter.llnl.gov (4) if you have filled out the form correctly, you should receive an email acknowledgement (though not necessarily immediately) cut here ------------------------------------------------------------------------- CASP3: Third Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction Target submission form ====================== This is the text version of the Prediction target submission form for the Third Critical Assessment of Techniques for Protein Structure Prediction Experiment (CASP3). Introduction ============ Protein crystallographers and NMR spectroscopists are asked to provide details of structures they expect to have solved before 1st September 1998 using this form. Targets of all sizes and types are required. Small structures (less than 100 residues) are needed to test some of the ab initio structure prediction methods. Proteins with folds related to those of known structures are needed to test fold recognition methods. Proteins with sequences homologous to that of one or more known structures are needed to test comparative modelling methods. To be useful to the predictors, a period of at least a month is required before any details of the structure will be released. Please notify us immediately when the details are going to be made public, so that we can ask the predictors to stop work in a timely manner. This can be done by sending a mail to casp3@predictioncenter.llnl.gov In order for the predictions to be assessed in time for the meeting in December, we will need a set of co-ordinates by the beginning of September at the latest. If necessary, these can be for limited distribution until the meeting. A. Scientific information ========================= 1. [ ] Protein Name 2. [ ] Organism Name 3. [ ] Number of amino acids (does not need to be exact) Please provide accession number and the name of the database of the protein (4. and 5.) or the actual sequence (6.) (both if possible). 4. [ ] Accession number 5. Sequence Database [ ] Swiss-prot [ ] PIR [ ] Genbank [ ] EMBL [ ] Other [ ] 6. Amino acid sequence One letter code (ACEDFTK) is preferred, but three letter code (ala cys glu asp) can also be processed. 7. Are there homologous sequences of known structure to this protein Yes [ ] No [ ] 8. Current state of the experimental work Please describe briefly where things are at, addressing as many of the following points as you wish to/are relevant/can. The more information, the easier it is for a modeler to decide whether to predict your structure. Protein supply? Crystals? Diffraction quality? Molecular replacement in progress? Molecular replacement solution in hand? Heavy atom derivative search in progress? Heavy atom derivatives in hand? 9. Do you already have an interpretable map? Yes [ ] No [ ] 10. [ ] Estimated date of chain tracing completion. In order to assess the predictions before the meeting, this date should be before 1st September 1998. 11. [ ] Estimated date of public release of structure 12. If you have any other useful information about this sequence family please enter it below B. Administrative information ============================= 13. [ ] Name 14. Mailing address: [ ] Institution [ ] Street/P.O. Box [ ] City [ ] State/Province [ ] ZIP/Postal code [ ] Country 15. [ ] Tel 16. [ ] Fax 17. [ ] Email 18. How did you hear about this prediction experiment? [ ] Nature Add [ ] Poster [ ] Newsgroup [ ] Email [ ] Other [ ] 19. Do you wish to remain anonymous until the structure is publically announced? Yes [ ] No [ ] ------------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!biosci!not-for-mail From: "Axel T. Brunger" Newsgroups: bionet.structural-nmr Subject: position in computational NMR reserch Date: 8 Jul 1998 15:28:55 -0700 Organization: Howard Hughes Medical Institute Lines: 45 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <35A3F09B.63DE@laplace.csb.yale.edu> NNTP-Posting-Host: net.bio.net We are seeking an NMR spectroscopist with an interest in computational = methods development. A full time position is available at Yale = University for development and support of NMR related aspects of the = program "Crystallography & NMR System" (CNS). The successful candidate = will be involved in computational research and software development in = structure determination by solution NMR. There will be opportunities = for collaborations with NMR groups at Yale University and Dr. Marius = Clore=B9s group at the National Institutes of Health. A Ph.D. in a = field related to NMR spectroscopy is required. Several years of = postdoctoral experience are preferred. Competitive salary and benefits = will be offered. Candidates should send a resume and three letters of reference to = Professor Axel T. Br=FCnger, Yale University, Department of Molecular = Biophysics and Biochemistry, P.O. Box 208114, 434 Bass Center, 266 = Whitney Avenue, New Haven, CT 06520-8114. -- = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D | Axel T. Brunger Dept. Molecular Biophysics and Biochemistry| | Professor/Investigator Bass Center, 266 Whitney Avenue | | Office: 203-432-6143 Howard Hughes Medical Institute/Yale Univ. | | FAX: 203-432-6946 New Haven, CT 06520, USA. | | http://atb.csb.yale.edu | | mailto:brunger@laplace.csb.yale.edu | =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From owner-structural-nmr@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Mary Donlan Newsgroups: bionet.structural-nmr Subject: X-PLOR 98.0 is released Date: 8 Jul 1998 15:52:03 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <3.0.32.19980708154537.00c12c04@146.202.6.217> NNTP-Posting-Host: net.bio.net Dear X-PLOR users: MSI would like to announce the release of X-PLOR 98.0. This new release offers substantial new capabilities for both X-ray crystallographic and NMR Structure refinement including: -Maximum Likelihood methods for X-ray Structure Refinement -Optimized Torsion Angle Dynamic (TAD) Methods -Validated scripts for TAD with NMR distance restraints -Ambiguous Restraints for Iterative Assignment (ARIA) technology -Novel technology for NOE refinement. All of these enhancements are geared towards helping you determine better quality structures faster. Interfaces to X-PLOR 98.0 are also available as part of InsightII (Xsight for crystallography and NMR X-PLOR for NMR) as well as Quanta for X-ray refinement. As this new release indicates and as our continued development plans will show, MSI is committed to maintaining X-PLOR's leadership status through MSI's ongoing development and support of X-PLOR. If you are interested in obtaining additional information on X-PLOR 98.0, please email me at med@msi.com or at solutions@msi.com or visit our web site at http://www.msi.com. ******************************************** Mary E. Donlan, Ph.D Sr. Product Manager, Structural Biology Molecular Simulations Inc. 9685 Scranton Road San Diego, CA 92121 Phone: (619) 546-5532 Fax: (619) 458-0136 med@msi.com From owner-structural-nmr@net.bio.net Thu Jul 09 23:00:00 1998 Path: biosci!biosci!not-for-mail From: rwgk@laplace.csb.yale.edu Newsgroups: bionet.structural-nmr Subject: System Manager/Scientific Programmer Position Date: 9 Jul 1998 23:35:21 -0700 Organization: Deja News - The Leader in Internet Discussion Lines: 37 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <6o3q8b$5pe$1@nnrp1.dejanews.com> NNTP-Posting-Host: net.bio.net System Manager/Scientific Programmer Position The Howard Hughes Medical Institute (HHMI) is currently seeking a System Manager/Scientific Programmer for our facility at Yale University. The candidate will work in a structural-biology research group with state-of-the-art facilities for X-ray crystallography and NMR spectroscopy. Responsibilities involve system administration of our network of Unix workstations and Windows 95/NT PCs. Extensive Unix experience is essential. Practical experience with FORTRAN, C, Java or Perl is highly desirable. We expect these responsibilities to occupy about 1/2 of the candidate's time. The remainder is available for scientific research. This position is an excellent opportunity for a recent Ph.D. graduate with a strong computational background and has a significantly higher compensation than regular post-doctoral appointments, including an excellent benefits package. Yale University is located in New Haven, which is in convenient driving distance to New York and Boston. Please forward your resume to: Axel T. Brunger Howard Hughes Medical Institute Yale University Room 434A Bass Center 266 Whitney Avenue New Haven, CT 06520-8114 mailto:brunger@laplace.csb.yale.edu HHMI is an equal opportunity employer. From owner-structural-nmr@net.bio.net Thu Jul 09 23:00:00 1998 Path: biosci!biosci!not-for-mail From: "Stefan Berger" Newsgroups: bionet.structural-nmr Subject: 150 And More Date: 10 Jul 1998 09:30:42 -0700 Organization: University Leipzig Lines: 21 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <199807090640.IAA11332@server1.rz.uni-leipzig.de> NNTP-Posting-Host: net.bio.net For those of you, who enjoyed "100 and More basic NMR experiments", there is now the possibility to enjoy even more the fully revised and considerably enlarged edition "150 and More", which has been published last week by Wiley-VCH, ISBN 3-527-29512-7. The price in Germany is 88 DM and any further information on contents and first bugs can be inspected on my home page. stb ------------------------------------------------- Prof. Dr. Stefan Berger Institut fuer Analytische Chemie Universitaet Leipzig Linn=E9str.3 04103 Leipzig Tel: +49 341 9736101 Fax: +49 341 9711833 or 9736115 e-mail: stberger@rz.uni-leipzig.de home page: http://www.uni-leipzig.de/~nmr/STB/stb.html ----------------------------------------------- From owner-structural-nmr@net.bio.net Thu Jul 16 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Robert Fraczkiewicz Newsgroups: bionet.structural-nmr Subject: New web interface to solvent accessible surface area calculations Date: 17 Jul 1998 09:59:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <35A695C7.F3C89A6D@keep.out.com> NNTP-Posting-Host: net.bio.net Dear Colleagues, We would like to announce the release of beta version of GETAREA 1.0, the new free WWW service for calculating the solvent accessible surface area of molecules. Users wanting to calculate SASA of proteins will merely supply the name of their local file containing atomic coordinates in PDB format. There is an otpion to calculate solvation energy and inclusion of molecules other than proteins. The relevant URL is: http://www.scsb.utmb.edu/getarea/area_form.html Note: the current release is for testing purposes only. Surely there are still some undiscovered bugs. Please help us disclose them by submitting test inputs. All remarks and suggestions should be directed to robert@nmr.utmb.edu or werner@newton.utmb.edu Thank you in advance, Robert Fraczkiewicz Sealy Center for Structural Biology University of Texas Medical Branch Galveston, TX 77555 From owner-structural-nmr@net.bio.net Thu Jul 16 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Thomas Haselhorst Newsgroups: bionet.structural-nmr Subject: dissociation constant rate (k_off) ?? Date: 17 Jul 1998 09:46:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <35AF0497.41C6@chemie.mu-luebeck.de> NNTP-Posting-Host: net.bio.net Dear netters, I want to measure the dissociation constant rate, especially k_off for my protein-ligand complex. I know that they are several ways. Who has experience in this kind of measurements and could suggest me the best method and pulsesequence ?? Thank in advance Thomas ************************************************************************ Thomas Haselhorst e-mail : thomas@chemie.mu-luebeck.de Institute of Chemistry Medical University of Luebeck Tel. x49 451 500 4239 Ratzeburger Allee 160 Fax. x49 451 500 4241 23538 Luebeck, Germany ************************************************************************ From owner-structural-nmr@net.bio.net Thu Jul 16 23:00:00 1998 Path: biosci!biosci!not-for-mail From: CS Raman Newsgroups: bionet.structural-nmr Subject: Upcoming Meetings Date: 17 Jul 1998 09:59:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <199807171655.QAA12300@hemebase.bio.uci.edu> NNTP-Posting-Host: net.bio.net NMR TECHNOLOGY: Developments and Applications October 29-30, 1998 =95 Baltimore, Maryland Advances in MASS SPECTROMETRY for Genomic and Biomolecular Research=20 January 7-8, 1999 =95 Orlando, Florida For more information please contact Cambridge Healthtech Institute 1037 Chestnut St. Newton Upper Falls, MA 02464 PH: 617-630-1300 Fax: 617-630-1325 Email: chi@healthtech.com ___________________________________________________________________ C.S.Raman Tel: (949) 824-4322 University of California Fax: (949) 824-3280 Dept. MB & B, SH530 email: craman@uci.edu 3205 Bio Sci II Irvine, CA 92697-3900 ------------------------------------------------------------------- Any fool can know. The point is to understand. --Albert Einstein ___________________________________________________________________ From owner-structural-nmr@net.bio.net Thu Jul 16 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Brian Cutting Newsgroups: bionet.structural-nmr Subject: Commercially availible RNA/DNA Date: 17 Jul 1998 09:56:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello, We are in search of commercially availible RNA/DNA samples. Does anyone know of a company that sells labeled or unlabeled samples with an approximate size of 10-20 units? Particularly useful would be a sample with a known structure, assignment, and coupling network. Sincerely, Brian Cutting From owner-structural-nmr@net.bio.net Thu Jul 16 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Oliver Zerbe Newsgroups: bionet.structural-nmr Subject: deuterated CHAPS Date: 17 Jul 1998 09:55:51 -0700 Organization: Department of Pharmacy, ETH Zuerich Lines: 20 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <6okuf2$lna@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net Dear friends, does anyone know a supplier for deuterated CHAPS. Suprisingly, we have not been able to get an offer from the "usual" companies. Any tips are highly appreciated, Oliver -- Dr. Oliver Zerbe Dept. Pharmazie ETH-Zuerich Winterthurerstr. 190 CH-8057 Zuerich Tel.: 0041-1-635 60 81/ 635 6080 Fax: 0041-1-635 68 84 mailto:oliver.zerbe@pharma.ethz.ch WWW: http://www.pharma.ethz.ch/~oz From owner-structural-nmr@net.bio.net Mon Jul 20 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Oliver Zerbe Newsgroups: bionet.structural-nmr Subject: deuterated CHAPS Date: 21 Jul 1998 09:22:13 -0700 Organization: Department of Pharmacy, ETH Zuerich Lines: 23 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <6p2d9i$9np@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net dear friends, from replies I have received I am more and more convinced that you cannot buy perdeuterated CHAPS. It also probably is a very time-consuming and expensive task to synthesize it in perdeuterated form. It is still worth trying to use it in isotope-edited or in heteronulcear correlated spectra where is is filtered out. Thanks to replies from C.Weber, M.Ottiger and C. Sanders. Oliver Zerbe -- Dr. Oliver Zerbe Dept. Pharmazie ETH-Zuerich Winterthurerstr. 190 CH-8057 Zuerich Tel.: 0041-1-635 60 81/ 635 6080 Fax: 0041-1-635 68 84 mailto:oliver.zerbe@pharma.ethz.ch WWW: http://www.pharma.ethz.ch/~oz From owner-structural-nmr@net.bio.net Mon Jul 20 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Peter Guentert Newsgroups: bionet.structural-nmr Subject: DYANA version 1.5 is available Date: 21 Jul 1998 00:17:54 -0700 Organization: Institute for Molecular Biology and Biophysics, ETH Zurich Lines: 28 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <35B43674.3F52E6C6@mol.biol.ethz.ch> References: <35A695C7.F3C89A6D@keep.out.com> NNTP-Posting-Host: net.bio.net DYANA 1.5 ========= The new version 1.5 of the program package DYANA for NMR structure calculation of biological macromolecules is available. DYANA is a highly efficient and easy-to-use tool for NMR structure calculation. The new version 1.5 includes many new features, improvements, and bug fixes. For further details, please see the DYANA home page at http://www.mol.biol.ethz.ch/dyana DYANA 1.5 is available to academic and commercial users (see "How to obtain DYANA" on the DYANA home page), and users of an earlier version can get a free update to DYANA 1.5. -- ---------------------------------------------------------------------- Dr. Peter Guentert phone +41 1 633 34 54 Institute for Molecular Biology and Biophysics fax +41 1 633 11 51 ETH-Hoenggerberg, HPM G22 guentert@mol.biol.ethz.ch CH-8093 Zurich (Switzerland) http://www.mol.biol.ethz.ch/~guentert ---------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Dave Scott Newsgroups: bionet.structural-nmr Subject: DNA deuterium exchange Date: 22 Jul 1998 10:39:09 -0700 Organization: University of York Lines: 23 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <35B5B904.4B00@york.ac.uk> Reply-To: djs17@york.ac.uk NNTP-Posting-Host: net.bio.net Question: If I place DNA into deuterium oxide, by how much (percentagewise) will the molecular weight increase? Thanks in advance DJS. -- ******************************* * Dr. David Scott * * Dept Biology * * University of York * * YORK * * YO1 5DD * * * * United Kingdom * * * * phone +44 1904 432868 * * fax +44 1904 432860 * ******************************* From owner-structural-nmr@net.bio.net Wed Jul 22 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Pornthep Sompornpisut Newsgroups: bionet.structural-nmr Subject: an effect of glycerol Date: 23 Jul 1998 10:16:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <1.5.4.32.19980723135515.00686ae0@pioneer.netserv.chula.ac.th> NNTP-Posting-Host: net.bio.net Dear All, I am going to perform 2D NMR such as DQFCOSY, NOESY and TOCSY with water suppression for a 2 mM non-enriched protein sample on 400 MHz NMR spectrometer. The protein sample is an enzyme of which the stability is about 10-12 hrs under room temperature. The sample solution has also 20% of glycerol. Therefore I am not sure whether this amount of glycerol could effect the NMR spectra or not? So I am afraid about the problem from the stability of the enzyme and the vicosity of the solution. I would appreciate receiving any suggestions how to check the quality of the NMR spectra and how good the spectra should be? Is there any caution during acquiring the NMR spectra? Thank you very much Cheers Pornthep From owner-structural-nmr@net.bio.net Wed Jul 22 23:00:00 1998 Path: biosci!biosci!not-for-mail From: sudha@biba.med.tufts.edu (Sudha Veeraraghavan) Newsgroups: bionet.structural-nmr Subject: Re: an effect of glycerol Date: 23 Jul 1998 15:31:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <199807232041.QAA20351@biba.med.tufts.edu> NNTP-Posting-Host: net.bio.net Dear Pornthep You will find, by taking a quick 1D spectrum that viscosity has made the lines very broad. In addition, unless you have perdeuterated glycerol there will be several sharp and strong peaks from glycerol that will obliterate the methylene region of the protein spectrum. Have you tried other ways to stabilize the protein.. say change in salt, pH, ionic strength, temperature, DTT, etc.? Good luck, Sudha !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ************************************************************************* Sudha Veeraraghavan, Ph.D. E-Mail: sudha@biba.med.tufts.edu Department of Biochemistry School of Medicine Phone : (617) 636-6873 136 Harrison Ave. Boston, MA 02111 Fax : (617) 636-6409 ************************************************************************** !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! From owner-structural-nmr@net.bio.net Wed Jul 22 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Philip Coughlin Newsgroups: bionet.structural-nmr Subject: NMR protein standard Date: 23 Jul 1998 12:46:03 -0700 Organization: Martek Biosciences Lines: 21 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <35B78D34.41B48E4E@clark.net> Reply-To: sibs@clark.net NNTP-Posting-Host: net.bio.net Dear Colleague, Martek Biosciences is pleased to announce the availability of isotopically enriched HUMAN UBIQUITIN with a Ser-(His)6 tag at the C-terminus. Expressed in transformed E.Coli , grown in our Celtone media and purified by Ni 2+ resin and RP-HPLC. This protein is ideal as your NMR protein standard. Ubiquitin is available NOW in two labeled forms: 15N (Molecular weight 9596.75) and 13C15N (MW 9992.75) We can also prepare 13C, and 2H13C15N material. Dr. Philip E. Coughlin Senior Chemist Stable Isotope Group Martek Biosciences 6480 Dobbin Road Columbia MD 21045 USA From owner-structural-nmr@net.bio.net Wed Jul 29 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Istvan Pelczer Newsgroups: bionet.structural-nmr Subject: probehead Date: 29 Jul 1998 20:14:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, We are looking for a replacement 5mm H,C probehead for a narrow bore JEOL 270 MHz spectrometer. I shall appreciate any hint or offer. Thanks a lot, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry, Frick Lab., ph# (609) 258 2342 Washington Road fax# (609) 258 6746 Princeton, NJ 08544, USA