From owner-structural-nmr@net.bio.net Sun Mar 01 22:00:00 1998 Path: biosci!biosci!not-for-mail From: sudha@biba.med.tufts.edu (Sudha Veeraraghavan) Newsgroups: bionet.structural-nmr Subject: chemical shifts of SDS Date: 2 Mar 1998 08:29:13 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <9803021022.ZM24417@biba.med.tufts.edu> NNTP-Posting-Host: net.bio.net Dear Andre' One article that gives 13C and 1H chemical shifts of SDS and DPC (dodecylphosphocholine) is: H.W. Van Den Hooven et al. (1996) Eur. J. Biochem. 235, 394-403. --Sudha -- _______________________________________________________________________________ ******************************************************************************* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Sudha Veeraraghavan, Ph.D. Phone: (617) 636-6873 Department of Biochemistry MV605 Fax : (617) 636-6409 Tufts Univ. Sch. Medicine 136 Harrison Ave. E-mail: sudha@biba.med.tufts.edu Boston, MA 02111 sveerara@opal.tufts.edu !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ******************************************************************************* _______________________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Mar 02 22:00:00 1998 Path: biosci!biosci!not-for-mail From: "MR IAN FAIRLAMB" Newsgroups: bionet.structural-nmr Subject: Enquiry Date: 3 Mar 1998 14:51:33 -0800 Organization: Manchester Metropolitan University Lines: 16 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <6dhf4q$2cp@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net Hi there! I don't know if you can help. I am currently studying towards my PhD at the Manchester Met. University, and have started to use 2D NOESY and COSY techniques. Could you tell me if it is possible to calculate %NOE's from 2D NOESY Spectra i.e. can i intergrate the cross peaks. We are a bit short on NMR expertise here, so i would really appreciate if you could help or put me into contact with someone who can. The Machine i am using is a JEOL 270MHz. Thank you Ian Fairlamb From owner-structural-nmr@net.bio.net Sun Mar 15 22:00:00 1998 Path: biosci!biosci!not-for-mail From: CS Raman Newsgroups: bionet.structural-nmr Subject: job Date: 16 Mar 1998 15:06:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 91 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <199803162303.XAA00753@hemebase.bio.uci.edu> NNTP-Posting-Host: net.bio.net From: Sandor Szalma Subject: job@msi Sender: uucp@msi.com To: x-plor@net.bio.net Message-id: <350D6912.2781@msi.com> MIME-version: 1.0 X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 6.2 IP20) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Nntp-Posting-Host: iris108 X-Disclaimer: _ Unless stated otherwise, everything in this message is personal opinion and nothing in it is an official statement of Molecular Simulations Inc. Status: RO JOBS@MSI As the world's premier developer of molecular modeling/simulation software, we serve the leading R&D facilities in the pharmaceutical, biotech, chemical, and engineering fields. We are seeking top-notch, dynamic software engineers, scientists, sales & marketing personnel and a whole host of other talented individuals to join us as we change the world TODAY. MSI's offers a leading-edge environment. Our employees are creating, marketing and supporting sophisticated client-server molecular modeling applications designed to enable scientists to accelerate their R&D processes. At MSI, we work with the latest technologies to create our innovative applications. Invest in your future; working at MSI prepares you in tomorrow's technologies today. We are committed to the ongoing state-of-the-art training and development of our employees. 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From owner-structural-nmr@net.bio.net Sun Mar 15 22:00:00 1998 Path: biosci!biosci!not-for-mail From: David Gorenstein Newsgroups: bionet.structural-nmr Subject: Third Annual Structural Biology Symposium, Galveston, TX Date: 16 Mar 1998 13:52:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 165 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear colleague: I would like to invite you and your colleagues to participate in The Third Annual Structural Biology Symposium organized by the Sealy Center for Structural Biology and the Department of Human Biological Chemistry and Genetics of the University of Texas Medical Branch at Galveston, Texas. The meeting will start on Friday afternoon at 4:00 p.m., April 3, 1998 and ends on Sunday at noon, April 5, 1998. The speakers at the symposium are distinguished researchers in the field of Structural Biology. The program is listed at the end of the e-mail. Please forward the information to other appropriate individuals in your department. Specific informations for registration, poster session and hotel reservations is available at=20 http://www.scsb.utmb.edu/symposium/symp98.html On behalf of the co-chairs, James C. Lee and Robert Fox and the organizing committee I look forward to your participation. =20 Sincerely yours, David Gorenstein Director Sealy Center for Structural Biology Department of Human Biological =09 Chemistry & Genetics THE THIRD ANNUAL STRUCTURAL BIOLOGY SYMPOSIUM April 3-5, 1998 Sealy Center for Structural Biology Department of Human Biological Chemistry & Genetics University of Texas Medical Branch at Galveston REGISTRATIONTimes Book_AntiquaNo registration fee. Return registration form (see WEB site) by Friday, March 20, 1998. RECEPTION, LUNCH AND BANQUETTimes Book_AntiquaReception on =46riday, April 3, is open to everyone. Participant of lunch and banquet, please send a check for $65. Participant of lunch, please send a check for $10. Payable to: UTMB-SCSB by Friday, March 20, 1998. POSTER SESSIONTimes Book_AntiquaSubmit abstract by =46riday, March 20, 1998. The abstract should fit on one page with one inch margin on all sides. A space of 4_ x 6_ has been allocated for each poster presentation. HOTEL RESERVATIONTim= es Book_AntiquaA block of rooms has been reserved for attendees at the beachfront Hotel Galvez. Rate: $89 Single/Double $99 Triple $109 Quadruple (with availability) Call 1-800-392-4285=20 Registration form may be obtained from: Structural Biology Symposium Shirley Broz Department of Human Biological Chemistry & Genetics University of Texas Medical Branch at Galveston 5.138 Medical Research Building Galveston, TX 77555-1055 Phone: (409) 772-2281 FAX: (409) 772-4298 E-mail: SBroz@mspo1.med.utmb.edu ----------------------------------------------------------- David Gorenstein Director, Sealy Center for Structural Biology Charles Marc Pomerat Distinguished Professor of Biological Sciences,=20 Dept. of Human Biological Chemistry and Genetics =20 Dept. of Physiology and Biophysics University of Texas Medical Branch Galveston, TX 77555-1157 Office: (409) 747 6801 Main Office: (409) 747 6800 Voice Mail: (409) 747 6801 =46ax: (409) 747 6850 E-MAIL ADDRESS: david@nmr.utmb.edu http://www.nmr.utmb.edu/ From owner-structural-nmr@net.bio.net Mon Mar 16 22:00:00 1998 Path: biosci!biosci!not-for-mail From: David Gorenstein Newsgroups: bionet.structural-nmr Subject: symposium addendum, speaker list Date: 17 Mar 1998 10:10:21 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 150 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <6ema45$2f5@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net Dear colleague: I would like to invite you and your colleagues to participate in The Third Annual Structural Biology Symposium organized by the Sealy Center for Structural Biology and the Department of Human Biological Chemistry and Genetics of the University of Texas Medical Branch at Galveston, Texas. The meeting will start on Friday afternoon at 4:00 p.m., April 3, 1998 and ends on Sunday at noon, April 5, 1998. The speakers at the symposium are distinguished researchers in the field of Structural Biology. Dr. Wayne A. Hendrickson Columbia University, New York, NY "Structural Biology of the HIV Envelope Glycoprotein gp120" Dr. Wah Chiu Baylor College of Medicine, Houston "Scaffolding-Assisted Assembly Mechanism in Herpesvirus Capsid" Dr. Michael Rossmann Purdue University "Interaction of Rhinoviruses With Their Cellular Receptors" Dr. Juli Feigon University of California Los Angeles "New Views on Nucleic Acid Folding from Structures of Small RNA's" Dr. Michael Summers University of Maryland Baltimore County "NMR Studies of HIV-1 Gag Proteins and Gag-Genome Recognition" Dr. Michael Hecht University of Princeton "De Novo Proteins from Designed Combinatorial Libraries" Dr. Susan S. Taylor University of California San Diego "cAMP-Dependent Protein Kinase: Structural Basis for Function, Regulation and Subcellular Localization" Dr. Homme W. Hellinga Duke University Medical Center "Rational Design of Protein Function" Dr. D. Wayne Bolen University of Texas Medical Branch "Protein Folding in Organisms Adapted to Environmental Stresses: The Medium is the Message" Dr. John Kuriyan The Rockefeller University "The Regulation of Src-Family Tyrosine Kinases" Dr. Vincent J. Hilser University of Texas Medical Branch "Viewing Proteins as Ensembles" Please forward the information to other appropriate individuals in your department. Specific informations for registration, poster session and hotel reservations is available at http://www.scsb.utmb.edu/symposium/symp98.html On behalf of the co-chairs, James C. Lee and Robert Fox and the organizing committee I look forward to your participation. Sincerely yours, David Gorenstein Director Sealy Center for Structural Biology Department of Human Biological Chemistry & Genetics THE THIRD ANNUAL STRUCTURAL BIOLOGY SYMPOSIUM April 3-5, 1998 Sealy Center for Structural Biology Department of Human Biological Chemistry & Genetics University of Texas Medical Branch at Galveston REGISTRATION No registration fee. See registration form (WEB site) RECEPTION, LUNCH AND BANQUET Reception on Friday, April 3, is open to everyone. Participant of lunch and banquet, please send a check for $65. Participant of lunch, please send a check for $10. Payable to: UTMB-SCSB (subject to availability) POSTER SESSION Submit abstract by Friday, March 27, 1998. The abstract should fit on one page with one inch margin on all sides. A space of 4_ x 6_ has been allocated for each poster presentation. HOTEL RESERVATION A block of rooms has been reserved for attendees at the beachfront Hotel Galvez. Rate: $89 Single/Double $99 Triple $109 Quadruple (with availability) Call 1-800-392-4285 Registration form may be obtained from: Structural Biology Symposium Shirley Broz Department of Human Biological Chemistry & Genetics University of Texas Medical Branch at Galveston 5.138 Medical Research Building Galveston, TX 77555-1055 Phone: (409) 772-2281 FAX: (409) 772-4298 E-mail: SBroz@mspo1.med.utmb.edu ----------------------------------------------------------- David Gorenstein Director, Sealy Center for Structural Biology Charles Marc Pomerat Distinguished Professor of Biological Sciences, Dept. of Human Biological Chemistry and Genetics Dept. of Physiology and Biophysics University of Texas Medical Branch Galveston, TX 77555-1157 Office: (409) 747 6801 Main Office: (409) 747 6800 Voice Mail: (409) 747 6801 Fax: (409) 747 6850 E-MAIL ADDRESS: david@nmr.utmb.edu http://www.nmr.utmb.edu/ From owner-structural-nmr@net.bio.net Mon Mar 16 22:00:00 1998 Path: biosci!biosci!not-for-mail From: sudha@biba.med.tufts.edu (Sudha Veeraraghavan) Newsgroups: bionet.structural-nmr Subject: TOCSY Date: 17 Mar 1998 12:42:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <9803171529.ZM865@biba.med.tufts.edu> NNTP-Posting-Host: net.bio.net Dear Hae-Kap Cheong, You said: >I have some difficulties using TOCSY, >J. Magn. Reson. 65, 355-360 (1985) Ad Bax and Donald G. Davis Using the z-filtered TOCSY, which gives symmetric peaks, will make phasing easier. See: Rance, M. (1987) J. Mag. Reson. 74, 557-564. The use of this pulse program is supposed to decrease the s/n some, but the benefits outweigh the small loss of signal intensity. Good luck, Sudha -- _______________________________________________________________________________ ******************************************************************************* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Sudha Veeraraghavan, Ph.D. Phone: (617) 636-6873 Department of Biochemistry MV605 Fax : (617) 636-6409 Tufts Univ. Sch. Medicine 136 Harrison Ave. E-mail: sudha@biba.med.tufts.edu Boston, MA 02111 sveerara@opal.tufts.edu !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ******************************************************************************* _______________________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Mar 16 22:00:00 1998 Path: biosci!biosci!not-for-mail From: "=C1=A4=C7=D8=B0=A9" Newsgroups: bionet.structural-nmr Subject: TOCSY-trim pulses Date: 17 Mar 1998 10:08:44 -0800 Organization: KAIST Lines: 33 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <350E4D79.2A4EB8FE@reflex.kaist.ac.kr> NNTP-Posting-Host: net.bio.net Dear Netter I have some difficulties using TOCSY, J. Magn. Reson. 65, 355-360 (1985) Ad Bax and Donald G. Davis They used trim pulses (spin lock pulses) at the beginning and end of the mixing period (MLEV17). My problem is that, when using the trim pulses, it is difficult to phase the 2D spectrum. (Ad Bax said in the paper, 2D spectrum can be phased easiliy to the absorption mode.) Sometimes it seems that w2 dimension is reverted near the o1. like this |||||||||||| |||||||| ^ o1 where '|'s are diagonal peaks. Someone says that usually trim pulses are ommited in TOCSY and the trim pulses are the cause of phase distorsion. But I can't understand why trim pulse distort the phase. Any comments are appreciated. Thanks in advance. Cheong, Hae-Kap e-mail. haekap@reflex.kaist.ac.kr T. 82-42-865-3417 F. 82-42-865-3419 From owner-structural-nmr@net.bio.net Sun Mar 29 23:00:00 1998 Path: biosci!biosci!not-for-mail From: porn@atc.atccu.chula.ac.th Newsgroups: bionet.structural-nmr Subject: aggregation of the protein sample Date: 29 Mar 1998 19:25:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear All, We have been preparing an enzyme (a molecular weight about 27 kDa) in order for a NMR study. The recombinant protein that we are interested in is overexpressed from E. coli. When we concentrated a few milligramms of the protein in 1.0 ml of the solution (~0.07 millimolar concentration), the sample is already precipitated. Therefore, we added chemical agents that we normally use (glycerol) for preventing sample sedimentation but it does not significantly enhance the solubility of the sample. We will appreciate if there will be any discussions, articles, publications, textbooks etc. concerning the topics on protein aggregation. Tricks or techniques avoiding the aggregation problem are extremely useful information. All comments from any aspects are appreciated. I apologize if the questions do already exist before. Thank you very much for your times and consideration. Yours sincerely **************************************************************** P.Sompornpisut Chemist Lecturer Phone: 66-2-2185221-2 Chemistry Department Fax: 66-2-2521730 Facult. of Science e-mail: porn@atc.atccu.chula.ac.th Chulalongkorn University Thailand **************************************************************** From owner-structural-nmr@net.bio.net Mon Mar 30 23:00:00 1998 Path: biosci!biosci!not-for-mail From: CS Raman Newsgroups: bionet.structural-nmr Subject: Structure Assessment Date: 31 Mar 1998 10:16:36 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 71 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: <199803311814.SAA01178@hemebase.bio.uci.edu> NNTP-Posting-Host: net.bio.net >From pdb-l@pdb.pdb.bnl.gov Tue Mar 31 17:54:52 1998 Received: from mta1.nts.uci.edu (mta1.nts.uci.edu [255.255.255.255]) by hemebase.bio.uci.edu (8.8.8/) with ESMTP id RAA00827; Tue, 31 Mar 1998 17:54:52 GMT Received: (from daemon@localhost) by mta1.nts.uci.edu (8.8.5/8.8.5) id JAA15960 for raman@hemebase.bio.uci.edu.xyzzy; Tue, 31 Mar 1998 09:46:11 -0800 (PST) Received: (from daemon@localhost) by mta1.nts.uci.edu (8.8.5/8.8.5) id JAA15947 for craman@uci.edu.xyzzy; Tue, 31 Mar 1998 09:46:09 -0800 (PST) Received: from elzip.uthscsa.edu (elzip.uthscsa.edu [129.111.1.11]) by mta1.nts.uci.edu (8.8.5/8.8.5) with ESMTP id JAA15830 for ; Tue, 31 Mar 1998 09:45:46 -0800 (PST) Received: from bioc01 (bioc01.uthscsa.edu) by uthscsa.edu (PMDF V5.0-5 #26649) id <01IVBCV5B0FK0059SP@uthscsa.edu> for craman@uci.edu; Tue, 31 Mar 1998 11:49:21 -0600 (CST) Received: from bioc01 (bioc01.uthscsa.edu) by uthscsa.edu (PMDF V5.0-5 #26649) id <01IVBCV33PI4005BTP@uthscsa.edu> for craman@uci.edu; Tue, 31 Mar 1998 11:49:19 -0600 (CST) Received: from pdb.pdb.bnl.gov by bioc01 (4.1/SMI-4.1) id AA05852; Tue, 31 Mar 1998 11:49:28 -0600 (CST) Received: from (localhost [127.0.0.1]) by pdb.pdb.bnl.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id MAA14241; Tue, 31 Mar 1998 12:47:28 -0500 Date: Tue, 31 Mar 1998 12:47:28 -0500 From: "Jurgen F. Doreleijers" Subject: Quality assessment of NMR structures Sender: pdb-l@pdb.pdb.bnl.gov To: Multiple recipients of list Errors-to: owner@pdb.pdb.bnl.gov Errors-to: owner@pdb.pdb.bnl.gov Reply-to: pdb-l@pdb.pdb.bnl.gov Message-id: <351FD9E3.FF6@nmr.chem.ruu.nl> Content-transfer-encoding: 7BIT Precedence: bulk Originator: pdb-l@pdb.pdb.bnl.gov X-Comment: Protein Data Bank list X-Listprocessor-version: 6.0b -- ListProcessor by Anastasios Kotsikonas Status: RO Dear people, If you are interested in our paper on the quality of NMR structures please have a look at: http://www-nmr.chem.ruu.nl/users/jurgen/R2D2/description.html We have studied the geometrical quality indicators such as the Ramachandran map, and the agreement between calculated structures and experimental data for almost a hundred PDB entries. The paper is expected to appear in the June 25th issue of JMB. They did approve of this electronic preprint:-) Hope it helps, Jurgen -- Drs Jurgen F. Doreleijers NMR spectroscopy, Utrecht University, The Netherlands mailto:jurgen@nmr.chem.ruu.nl http://www-nmr.chem.ruu.nl/users/jurgen/jurgen.html ___________________________________________________________________ C.S.Raman Tel: (714) 824-4322 University of California Fax: (714) 824-3280 Dept. MB & B, SH530 email: craman@uci.edu 3205 Bio Sci II Irvine, CA 92697-3900 ------------------------------------------------------------------- In a time of drastic change it is the learners who inherit the future. The learned usually find themselves equipped to live in a world that no longer exists. --Eric Hoffer ___________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Mar 30 23:00:00 1998 Path: biosci!biosci!not-for-mail From: "Peter J. Connolly" Newsgroups: bionet.structural-nmr Subject: TOCSY Date: 31 Mar 1998 09:23:29 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hae-Kap and Sudha: I have also seen these types of phasing problems using MLEV-17 w/trim pulses in TOCSY. They are likely due to cross-relaxaion effects (ROE) that occur both during the mixing sequence and trim pulses. And yes, these problems are reduced in z-filtered experiments. In my hands, these experiments show no reduced sensitivity relative to the MLEV-17 versions, in fact, they usually look significantly better. However, I would suggest the PEP-z-filtered versions which give a S/N improvement of sqrt(2) over the 1987 Rance sequence. (Cavanagah and Rance, J. Mag. Reson., _88_, 72-85, (1990)). This has always worked well for me using DIPSI-2. You could also try the so-called DIPSI-2rc version (Cavanagh and Rance, J. Mag. Reson., _96_, 670-678, (1992)), which uses delays during isotropic mixing to minimize the ROESY further. I`ve found only slight improvements over the normal DIPSI-2, and it is a bit more difficult to get going, but it's definately worth looking at that paper to see how the phasing problem improves as the ROE problem is reduced. This may be too late to help you...but I was off at the ENC.. Good Luck...Peter ------------------------------------------------------------------------------- Peter J. Connolly Ph.D The Rowland Institute for Science 100 Edwin H. Land Blvd. Cambridge MA 02152 617-497-4682 (voice) 617-497-4627 (fax) From owner-structural-nmr@net.bio.net Tue Mar 31 23:00:00 1998 Path: biosci!biosci!not-for-mail From: David Erbe Newsgroups: bionet.structural-nmr Subject: Protein Engineering Position Available Date: 31 Mar 1998 19:41:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Approved: raman@hemebase.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Protein Engineering Position Available Genetics Institute, Inc. Cambridge, MA A motivated Protein Engineer is wanted to join a multidisciplinary group to perform research directed at the discovery of small molecule inhibitors of various immune system targets. This group is housed in a facility equipped with the latest technology for structure based drug discovery including 600MHz NMR, X-ray lab, Computational Chemistry, and Medicinal Chemistry, all supported by dedicated Molecular Biology and Protein Biochemistry groups. Candidates should have interests and experience that include study of recombinant proteins, especially protein structure/function and engineering. Staff Scientist: Requires a Ph.D. In Molecular Biology, Biochemistry, Biophysics or equivalent and 0 - 5 years postdoctoral research. Contact via email: Dave Erbe (derbe@genetics.com)