From owner-structural-nmr@net.bio.net Fri Mar 05 22:00:00 1999 Path: biosci!biosci!not-for-mail From: Istvan Pelczer Newsgroups: bionet.structural-nmr Subject: Re: OH of threonine Date: 5 Mar 1999 17:19:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Approved: raman@bragg.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Herve, Take a look at the BioMagResBank database (www.bmrb.wisc.edu); in the statistics there are data for Thr-OH, so there should be submissions with such parameter included (I have not checked in particular). All the best, 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 Book Review Editor for "The NMR Newsletter" http://www.nmrnewsletter.com On Tue, 2 Mar 1999, Herve DARBON wrote: > Hi, > > Does anyone have detected an hydroxy proton of threonine and if yes at > which chemical shift? > > Thanks for your help > > -- > Herve Darbon > > ------------------------------------------------------------------- > www: http://afmb.cnrs-mrs.fr/nmr/ > ------------------------------------------------------------------- > E-Mail: herve@afmb.cnrs-mrs.fr > ------------------------------------------------------------------- > Phone: (33)491-16-45-35 > Fax: (33)491-16-45-36 > Mail: CNRS > Laboratoire AFMB > 31 chemin Joseph-Aiguier > F-13402 MARSEILLES cedex 20 > France From owner-structural-nmr@net.bio.net Fri Mar 05 22:00:00 1999 Path: biosci!biosci!not-for-mail From: Herve DARBON Newsgroups: bionet.structural-nmr Subject: OH of threonine Date: 5 Mar 1999 16:37:26 -0800 Organization: UPR 9039 CNRS Lines: 24 Sender: daemon@net.bio.net Approved: raman@bragg.bio.uci.edu Distribution: world Message-ID: <36DBF3C1.B3A5F1E4@afmb.cnrs-mrs.fr> Reply-To: herve@afmb.cnrs-mrs.fr NNTP-Posting-Host: net.bio.net Hi, Does anyone have detected an hydroxy proton of threonine and if yes at which chemical shift? Thanks for your help -- Herve Darbon ------------------------------------------------------------------- www: http://afmb.cnrs-mrs.fr/nmr/ ------------------------------------------------------------------- E-Mail: herve@afmb.cnrs-mrs.fr ------------------------------------------------------------------- Phone: (33)491-16-45-35 Fax: (33)491-16-45-36 Mail: CNRS Laboratoire AFMB 31 chemin Joseph-Aiguier F-13402 MARSEILLES cedex 20 France From owner-structural-nmr@net.bio.net Mon Mar 08 22:00:00 1999 Path: biosci!biosci!not-for-mail From: Honggao Yan Newsgroups: bionet.structural-nmr Subject: Protein NMR Postdoctoral Associate Date: 9 Mar 1999 09:10:36 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Approved: raman@bragg.bio.uci.edu Distribution: world Message-ID: <36E5494F.3681299F@pilot.msu.edu> NNTP-Posting-Host: net.bio.net A postdoctoral position is available to study the structures and dynamics of the enzymes in the shikimate and folate biosynthetic pathways. Since the shikimate and folate biosynthetic pathways are unique to microbial and plant worlds, the two pathways are ideal targets for development of antimicrobial agents and herbicides. The long-term goals of the projects are to elucidate the structure-function relationships of these proteins that account for their catalytic mechanisms and to design specific inhibitors that may become new antimicrobial agents. A variety of techniques is employed in these projects, including recombinant DNA, biochemical, and biophysical methods. The main structural technique is multidimensional NMR spectroscopy. These projects are of great biomedical significance, especially in light of rapidly increasing antibiotic resistance in recent years that has rendered the current antibiotics ineffective for treating many microbial infections and caused a worldwide health care crisis. Our laboratory is well equipped for protein NMR spectroscopy. Instrumentation includes three computer workstations (one from SGI and two from Sun) and 500 MHz and 600 MHz Varian NMR spectrometers. The 600 MHz Varian Inova NMR spectrometer is equipped with four rf channels and tri-axis pulsed field gradients and is dedicated to biomolecular NMR studies. The initial appointment for the position will be two years and is renewable upon mutual agreement. The applicants should have experience with multidimensional NMR spectroscopy. If interested, please send a CV along with telephone numbers and email addresses of three references to the address below. Email responses are encouraged. Dr. Honggao Yan Department of Biochemistry Michigan State University East Lansing, MI 48824 Tel: (517) 353-8786 Fax: (517) 353-9334 Email: yanh@pilot.msu.edu From owner-structural-nmr@net.bio.net Wed Mar 17 22:00:00 1999 Path: biosci!biosci!not-for-mail From: John Tomaszewski Newsgroups: bionet.structural-nmr Subject: JR-HMQC for LBHBs Date: 17 Mar 1999 22:56:39 -0800 Organization: University of Washington Lines: 24 Sender: daemon@net.bio.net Approved: raman@bragg.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi all, I have a LBHB (1H-18ppm x 15N-~180ppm, but I'll need to see down to ~250ppm) that I want to look at in 2D. So far the only 1D sequence that allows me to see it is a basic jump-return (the linewidth is on the order of the coupling constant, ~100Hz, and watergate or presat seem to wipe the signal out). From the literature it seems that a JR-HMQC sequence is favored for viewing them (LBHBs) in 2D. I wrote up a JR-HMQC sequence (from Bax et al. J. Mag. Reson. 1990, 86 p.304-318) for a Bruker DRX, but as simple as it is, I can't get it to work. Does anyone have a working JR-HMQC or other sequence for this purpose? Any help would be appreciated. Sincerely, John T. ******************************************************************** ** ** ** ** * ** DEPARTMENT OF CHEMISTRY ** ** ** ** ** * ** tomasz@protein.chem.washington.edu ** ** ** ** ** * ** (206) 616-2993 ** ** ***** ***** JOHN TOMASZEWSKI ** ******************************************************************** From owner-structural-nmr@net.bio.net Wed Mar 17 22:00:00 1999 Path: biosci!biosci!not-for-mail From: Istvan Pelczer Newsgroups: bionet.structural-nmr Subject: Re: JR-HMQC for LBHBs Date: 18 Mar 1999 06:55:45 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Approved: raman@bragg.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear John, Did you consider a regular HMQC or HSQC setting the carrier to, or above, the chemical shift of the proton at ca. 18ppm, and use soft-enough proton pulses which have their sinc-profile zero crossing at the water resonance? Around the 180 pulses you might be fine using gradients. All the best, 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 Book Review Editor for "The NMR Newsletter" http://www.nmrnewsletter.com On Tue, 16 Mar 1999, John Tomaszewski wrote: > Hi all, > I have a LBHB (1H-18ppm x 15N-~180ppm, but I'll need to see > down to ~250ppm) that I want to look at in 2D. So far the only 1D > sequence that allows me to see it is a basic jump-return (the > linewidth is on the order of the coupling constant, ~100Hz, and > watergate or presat seem to wipe the signal out). From the > literature it seems that a JR-HMQC sequence is favored for viewing > them (LBHBs) in 2D. I wrote up a JR-HMQC sequence (from Bax et al. J. > Mag. Reson. 1990, 86 p.304-318) for a Bruker DRX, but as simple as it > is, I can't get it to work. > Does anyone have a working JR-HMQC or other sequence for this > purpose? Any help would be appreciated. > > Sincerely, > > John T. > > ******************************************************************** > ** ** ** ** * ** DEPARTMENT OF CHEMISTRY ** > ** ** ** ** * ** tomasz@protein.chem.washington.edu ** > ** ** ** ** * ** (206) 616-2993 ** > ** ***** ***** JOHN TOMASZEWSKI ** > ******************************************************************** > > From owner-structural-nmr@net.bio.net Wed Mar 17 22:00:00 1999 Path: biosci!biosci!not-for-mail From: Mark Girvin Newsgroups: bionet.structural-nmr Subject: Re: JR-HMQC for LBHBs Date: 18 Mar 1999 06:55:09 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 95 Sender: daemon@net.bio.net Approved: raman@bragg.bio.uci.edu Distribution: world Message-ID: <3.0.32.19990318084913.0089c6e0@icar.bioc.aecom.yu.edu> NNTP-Posting-Host: net.bio.net Dear John, The pulse program listed below seems to work well for us on a DRX600 (used for similar reasons, e.g. Li et al, Nat. Struct Biol 1999 in press). - Mark ====== At 05:41 PM 3/16/99 -0800, you wrote: >Hi all, > I have a LBHB (1H-18ppm x 15N-~180ppm, but I'll need to see >down to ~250ppm) that I want to look at in 2D. So far the only 1D >sequence that allows me to see it is a basic jump-return (the >linewidth is on the order of the coupling constant, ~100Hz, and >watergate or presat seem to wipe the signal out). From the >literature it seems that a JR-HMQC sequence is favored for viewing >them (LBHBs) in 2D. I wrote up a JR-HMQC sequence (from Bax et al. J. >Mag. Reson. 1990, 86 p.304-318) for a Bruker DRX, but as simple as it >is, I can't get it to work. > Does anyone have a working JR-HMQC or other sequence for this >purpose? Any help would be appreciated. ================= ;hnqc_jr.mg ;2D HMQC, solvent suppression via j-r ;f1: 1H, f2: 13C/15N ;Process as States-TPPI ;d2 1/(2*J) ;d20 j-r delay "d11=100m" "d12=10u" "d13=5u" "d14=20u" ;uncomment below to run 1D 15N-edited version: ;#define ONE_D #include 1 ze 2 d11 do:f2 3 d14 4 4u d12 pl1:f1 d1 d13 d12 (p1 ph11):f1 d20 (p1 ph12):f1 d2 pl3:f2 p3:f2 ph3 d0 (p1 ph11):f1 d20 d20 (p1 ph12):f1 d0 p3:f2 ph4 d13 d2 pl13:f2 go=2 ph31 cpds3:f2 #ifdef ONE_D d11 do:f2 wr #0 #else d11 do:f2 wr #0 if #0 ip3 zd lo to 3 times 2 d14 id0 lo to 4 times l4 #endif exit ph1=0 ph2=0 ph3=0 2 ph4=0 0 2 2 ph11=0 ph12=2 ph31=0 2 2 0 ================= _______________________________________________________________ Mark Girvin Biochemistry Department girvin@aecom.yu.edu Albert Einstein College of Medicine Tel:(718) 430-2025/2021 1300 Morris Park Ave. FAX:(718) 430-8565 Bronx, NY 10461 http://www.bioc.aecom.yu.edu/labs/girvlab/ _______________________________________________________________ From owner-structural-nmr@net.bio.net Sun Mar 21 22:00:00 1999 Path: biosci!biosci!not-for-mail From: John Tomaszewski Newsgroups: bionet.structural-nmr Subject: Re: JR-HMQC for LBHBs Date: 22 Mar 1999 11:40:24 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Approved: raman@bragg.bio.uci.edu Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net On Thu, 18 Mar 1999, Mark Girvin wrote: ->The pulse program listed below seems to work well for us on a DRX600 (used ->for similar reasons, e.g. Li et al, Nat. Struct Biol 1999 in press). Thanks Mark for the pulse sequence, it works fine. So far though I still haven't been able to tune it to see the LBHB. This sample is very problematic. It behaves as a molten globule, such that with no inhibitor in place proton and/or site exchange prevent me from seeing the LBHB at all. With the inhibitor, it's visible via J-R, but line broadening in the sample suggests the formation of soluble aggregates. This seems to increase the relaxation to the point where correlations can't be seen. The JR delay is easy to tune, and I can see that it's right where I want it, but I thought that perhaps reducing the correlation delay might help. So far though, no go. I'll drop you a note if I solve this. Thanks, John T. ******************************************************************** ** ** ** ** * ** DEPARTMENT OF CHEMISTRY ** ** ** ** ** * ** tomasz@protein.chem.washington.edu ** ** ** ** ** * ** (206) 616-2993 ** ** ***** ***** JOHN TOMASZEWSKI ** ******************************************************************** From owner-structural-nmr@net.bio.net Wed Mar 24 22:00:00 1999 Path: biosci!biosci!not-for-mail From: "Graham E Jackson" Newsgroups: bionet.structural-nmr Subject: water suppression Date: 25 Mar 1999 13:55:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Approved: raman@bragg.bio.uci.edu Distribution: world Message-ID: <7ddg50$ggi$1@mserv2.dl.ac.uk> NNTP-Posting-Host: net.bio.net Does anyone have a pulse sequence for water suppression of urine samples on a Varian Unity machine? I'm particularly interested in using a 1D noesy sequence with presaturation. Also are there any tricks I should know about eg adding 0.5M NH4Cl when using CPMG sequence. Thanks Graham Graham E Jackson Associate Professor Department of Chemistry University of Cape Town Cape Town South Africa Fax: (027 21) 6897499 Tel: (027 21) 6502531 E-mail: jackson@psipsy.uct.ac.za http://www.uct.ac.za/depts/cem/academic/gjackson.htm From owner-structural-nmr@net.bio.net Wed Mar 24 22:00:00 1999 Path: biosci!biosci!not-for-mail From: "Andrew Hinck" Newsgroups: bionet.structural-nmr Subject: Position Available in San Antonio Date: 25 Mar 1999 13:57:20 -0800 Organization: U. Texas Health Sci. Ctr. at San Antonio Lines: 42 Sender: daemon@net.bio.net Approved: raman@bragg.bio.uci.edu Distribution: world Message-ID: <7dbu9b$qo$3@cosmos.uthscsa.edu> NNTP-Posting-Host: net.bio.net A SENIOR RESEARCH ASSISTANT POSITION is available starting IMMEDIATELY to examine structure/function relationships of biomedically relavant macromolecules, including cytokines, cytokine receptors, and transcription factors. Individuals having experience in bacterial and eukaryotic protein expression, protein purification, and use of radioisotopes in binding assays are desired. Molecular and cellular biologists with an interest in working in the area of structural biology are especially encouraged to apply. Subjects of study include components of the transforming growth fator-beta (TGF-beta) signaling pathway: TGF-beta and the TGF-beta type I and type II transmembrane signaling receptors, the SMAD family of proteins, and transciption factors such as FAST-1 and FAST-2. The laboratory is part of the core high field NMR facility in the Center for Biomolecular Structure Analysis. This facility includes state of the art instrumentation for high field (600 MHz) NMR and computational (DEC-alpha/Silicon Graphics) facilities located in a brand new research building on the University of Texas Health Science Center at San Antonio (UTHSCSA) campus. The Center also includes state of the art instrumentation for other aspects of biomolecular structure analysis, including X-ray crystallography (MSC R-axis IV, RU-300, X-stream), analytical ultracentrifugation (Beckman XL-I), and mass spectrometry (Finnagan LCQ). Ample shared facilities are also available on the Health Science Center campus including automated fluorescent DNA sequencing, protein sequencing, amino acid analysis, and peptide synthesis. UTHSCSA is located 8 miles north of downtown San Antonio and just south of the scenic Texas Hill Country. The University has over 900 full-time faculty, and a student enrollment of approximately 3000. Resources include 1.65 million square feet of research and research support facilities and a nationally recognized library. Visit http://biochem.uthscsa.edu to learn more about the Department, the University, and San Antonio. Applicants should have a M.S. or Ph.D. degree in cell biology, molecular biology, biochemistry, or a related field. Please send a cover letter, c.v., and contact information for three references to: Dr. Andrew Hinck Department of Biochemistry/AH 5.206 7703 Floyd Curl Drive San Antonio, TX 78284-7760 (210) 567-8780 From owner-structural-nmr@net.bio.net Sun Mar 28 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Giuseppe Bifulco Newsgroups: bionet.structural-nmr Subject: PS-HMBC with gradients Date: 29 Mar 1999 12:47:56 -0800 Organization: C.D.S. Centro di Servizi Didattico Scientifico Lines: 9 Sender: daemon@net.bio.net Approved: raman@bragg.bio.uci.edu Distribution: world Message-ID: <36FFE161.3B7E@unina.it> NNTP-Posting-Host: net.bio.net Hello, can anybody suggest a phase sensitive HMBC pulse sequence with gradients? Thanks in advance Giuseppe Bifulco From owner-structural-nmr@net.bio.net Mon Mar 29 23:00:00 1999 Path: biosci!biosci!not-for-mail From: "A. Maudsley" Newsgroups: bionet.structural-nmr Subject: isotope effect question Date: 30 Mar 1999 09:30:28 -0800 Organization: UCSF, ITS Lines: 19 Sender: daemon@net.bio.net Approved: raman@bragg.bio.uci.edu Distribution: world Message-ID: <7dqv1h$oho@itssrv1.ucsf.edu> NNTP-Posting-Host: net.bio.net Can anyone point me to any publications (or personal experiences) describing the isotope effect on proton chemical shifts, due to _exchangeable_ protons being substituted with Deuterium. This shift is observable even several bond lengths away. Specifically, I want to calculate the changes in chemical shifts in low molecular weight organic compounds due to measurement in D2O compared to H2O. Thanks Andrew Maudsley UCSF Email: maudsle@itsa.ucsf.edu