From owner-structural-nmr@net.bio.net Wed Jan 01 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news-xfer.netaxs.com!netnews.upenn.edu!dellwo From: dellwo@spruce.chem.upenn.edu (Martin J. Dellwo) Newsgroups: bionet.structural-nmr Subject: Re: 3D NMR processing on Felix950 Date: 2 Jan 1997 18:19:56 GMT Organization: Department of Chemistry, University of Pennsylvania Lines: 32 Message-ID: <5agu8c$3fb@netnews.upenn.edu> References: <32CAA3AA.41C6@tracer.chem.uh.edu> Reply-To: dellwo@spruce.chem.upenn.edu NNTP-Posting-Host: spruce.chem.upenn.edu In article <32CAA3AA.41C6@tracer.chem.uh.edu>, Hong Yu Liu wrote: > I acquired the NOESY-HMQC data on a bruker600 AMX instrument with the >following TD: t3 X t2 X t1: 1024 X 32 X 256. > I used the conversion program supplied by felix X32 New to convert the >bruker format to felix format. It seems to went through fine ( at least >no complaining messages). > Matrix dimension: D1 X D2 X D3: 512 X 32 X 256 > > Acquisition Data > acquisition type: Quartets > 1st incremented: t2 > # of t2 exps: 32 > # of t1 exps: 256 It is highly unlikely that '1st incremented' was t2 and not t1. You probably should run it with t1 as the '1st incremented', and matrix dimensions d1xd2xd2:512x256x32 Also, since you used the x32_new to convert the data, you should verify that the transform used is the 'dft' command, with the correct decimation factor. If your traces looked ok after processing D1, than this was probably the case. I do not use the EZ transforms, so I can't tell you if the remaining parameters were correct (specifically, I can't tell you if 'acquisition type: Quartets' is correct). -- Martin J. Dellwo (215) 898-4886 dellwo@spruce.chem.upenn.edu Department of Chemistry, University of Pennsylvania http://cherry.chem.upenn.edu/~dellwo/ From owner-structural-nmr@net.bio.net Thu Jan 02 22:00:00 1997 Path: biosci!SPRUCE.CHEM.UPENN.EDU!tan From: tan@SPRUCE.CHEM.UPENN.EDU (Wee "Derrick" Tan) Newsgroups: bionet.structural-nmr Subject: ROESY-HSQC Date: 3 Jan 1997 13:52:34 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701032104.QAA14159@spruce.chem.upenn.edu> NNTP-Posting-Host: net.bio.net Dear NMR specialists, Does any one of you have the pulse sequence for a 3D ROESY-HSQC or HMQC encoded for the Bruker system? I will appreciated it very much if anyone of you can provide me with one. Thanks in advance. -- Derrick Tan University of Pennsylvania Phone : (215) 898-4886 Department of Chemistry Fax : (215) 573-2123 231 S. 34th St. Email : tan@osage.chem.upenn.edu Philadelphia, PA 19104 Homepage : http://cherry.chem.upenn.edu/~tan/ From owner-structural-nmr@net.bio.net Thu Jan 02 22:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!newsxfer3.itd.umich.edu!portc01.blue.aol.com!newsstand.cit.cornell.edu!news.acsu.buffalo.edu!acsu.buffalo.edu!marcus From: marcus@acsu.buffalo.edu (Emil Marcus) Newsgroups: bionet.structural-nmr Subject: BRUKER to VARIAN conversion Date: 3 Jan 1997 18:53:22 GMT Organization: State University of New York at Buffalo Lines: 12 Distribution: world Message-ID: <5ajkj2$7d4@prometheus.acsu.buffalo.edu> NNTP-Posting-Host: autarch.acsu.buffalo.edu NNTP-Posting-User: marcus Dear NMR specialists: I would be grateful if you could help me find computer programs that are capable to convert BRUKER (raw data) files into VARIAN files, to be used with VNMR, which is VARIAN's own spectra processing program. Emil Emil Marcus University at Buffalo marcus@acsu.buffalo.edu From owner-structural-nmr@net.bio.net Sat Jan 04 22:00:00 1997 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Linear Prediction vs. First Point Scaling Date: 5 Jan 1997 09:30:58 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <32CFB108.14A3@plaza.snu.ac.kr> NNTP-Posting-Host: net.bio.net Dear Ji Hyun, It is the position of the first point in time which decides (at the first place) if there is need for correction. Linear prediction in usuual circumstances does not change digitization, therefore if your experiment was set up with first point at half dwell time then this will be retained after LP replacement of some of the first points with no correction required. An alternative is (giving up advantageous aliasing properties in the frequency domain) to detect "first point" at a full dwell time, then back calculate the true first point (t1=0) using LP. In this case 0.5 correction is needed in an ideal case. Both alternatives were presented in the literature from Ad Bax's lab, and you can find some description and references in our reviews on data processing in multidimensional NMR (Pelczer & Szalma, Chem. Rev., 91(1991)1507, or in an upcoming book from Humana Press, edited by D. G. Reid: Pelczer & Carter, Data Processing in Multidimensional NMR, Chapter for the book: Protein NMR Protocols, in the series: Methods in Molecular Biology). It is another issue if the first point(s) are distorted by either hardware or errors by LP. Then correction by other than the theoretical value may be required. All the best, and good luck with processing, 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 On Sun, 5 Jan 1997, Lee, Ji Hyun wrote: > To my knowledge, if we don't half dwell time delay during data > acqusition, first point is scaled with some factor, which is to > eliminate ridges. > After I predict some first points of time domain data with the linear > precdiction method and replace the experimental data with them, which is > right : I should scale the first point as above or I don't need to do > such a thing after linear prediction? > > Happy New Year. > > Pharmacy, Seoul National University > > From owner-structural-nmr@net.bio.net Mon Jan 06 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!news.sprintlink.net!news-peer.sprintlink.net!news.mindspring.com!usenet From: Wave@mindspring.com (Pieter Ibelings) Newsgroups: bionet.structural-nmr Subject: PTS160 Generators Still Available 4Sale Date: 7 Jan 1997 04:44:41 GMT Organization: www.mindspring.com/~wave Lines: 32 Message-ID: <5askbp$1qf@camel2.mindspring.com> NNTP-Posting-Host: user-168-121-20-253.dialup.mindspring.com Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.8 (x86 32bit) ** RE. PTS160 Generators Still Available 4Sale.** I still have a couple of PTS 160 Synthesizers for sale. I am asking $650 plus shipping for these real clean units. These are very clean with some minor scratches.I guarantee that they are in full working condition at time of receipt. All the units have the TCXO, GPIB, BCD, Rack mount, 1Hz resolution and option X27??? These are surplus units from GE Medical Systems. All reasonable forms of payment are available (money orders or checks). If you want to send us a PO, we can send you the unit and then you can send us the check within a reasonable ammount of time. A friend of mine is taking care of the sales and he can be reached at the address and phone below. Please give him a call if you are ready to order and tell him that I refered you. If you require any additional information please do not hesitate to send me some e-mail. Thanks Pieter wave@mindspring.com ******************************** Video Audio Repair Service Inc. William E. Flake Jr. (Bill) 6658 B Hillandale Drv. Lithonia, GA 30058 Phone (770) 482-2989 Tue-Fri 10:00am to 7:30pm From owner-structural-nmr@net.bio.net Mon Jan 06 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!news-peer.gsl.net!news.gsl.net!news-stkh.gsl.net!news.gsl.net!sn.no!nntp.uio.no!nntp-trd.UNINETT.no!daresbury!not-for-mail From: Marc-Andre.Delsuc@cbs.univ-montp1.fr (Marc-Andre Delsuc) Newsgroups: bionet.structural-nmr Subject: Re: NMR to Matlab Date: 7 Jan 1997 14:29:19 -0000 Lines: 35 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5atmjv$2um@mserv1.dl.ac.uk> X-Sender: mad@tome.cbs.univ-montp1.fr Original-To: str-nmr@dl.ac.uk >Dear NMR-experts, >can anybody help me with a program that converts 2D spectra (Bruker and >Felix format) in >Matlab-matrices and/or vice versa? >Thanks a lot. >Andr=E9 > >------------------------------------------------------------------ >Andre Pampel >University of Leipzig >Faculty of Physics and Geosciences >Linnestrasse 5 >04103 Leipzig >Germany >------------------------------------------------------------------ You may want to try the Gifa package. It is a complete NMR processing progra= m running on all kind of Unix machines (including Linux). It permits to read Varian and Bruker files, and is able to read and write Matlab matrices (ascii format). check at : http://www.cbs.univ-montp1.fr/GIFA/ Good luck ! Marc-Andr=E9 _________________________________________________________________________ Marc-Andre' Delsuc Centre de Biochimie Structurale Marc-Andre.Delsuc@cbs.univ-montp1.fr Faculte de Pharmacie tel : (33) (0) 467 04 34 36 15 av, Charles Flahault fax : (33) (0) 467 52 96 23 34060 Montpellier cedex www : http://www.cbs.univ-montp1.fr FRANCE From owner-structural-nmr@net.bio.net Mon Jan 06 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!feed1.news.erols.com!cwix!uunet!in1.uu.net!160.45.4.4!fu-berlin.de!news-ber1.dfn.de!news-lei1.dfn.de!news.uni-leipzig.de!news From: André Pampel Newsgroups: bionet.structural-nmr Subject: NMR to Matlab Date: Tue, 07 Jan 1997 08:42:23 -0800 Organization: Uni Leipzig Lines: 15 Message-ID: <32D27CEF.F98@rz.uni-leipzig.de> NNTP-Posting-Host: fun.exphysik.uni-leipzig.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.01Gold (Win16; I) Dear NMR-experts, can anybody help me with a program that converts 2D spectra (Bruker and Felix format) in Matlab-matrices and/or vice versa? Thanks a lot. André ------------------------------------------------------------------ Andre Pampel University of Leipzig Faculty of Physics and Geosciences Linnestrasse 5 04103 Leipzig Germany ------------------------------------------------------------------ From owner-structural-nmr@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!uknet!usenet1.news.uk.psi.net!uknet!EU.net!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!portc02.blue.aol.com!audrey01.news.aol.com!not-for-mail From: harrisonat@aol.com (HarrisonAT) Newsgroups: bionet.structural-nmr Subject: Nalorac ENC Symposium Date: 9 Jan 1997 23:05:25 GMT Organization: AOL http://www.aol.com Lines: 20 Message-ID: <19970109230300.SAA22079@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com ADVANCES IN NMR APPLICATIONS SYMPOSIUM You are invited to attend the 5th Annual ADVANCES IN NMR APPLICATIONS SYMPOSIUM featuring the latest developments in experimental techniques to be held prior to ENC at the Omni Rosen Hotel, Ballroom D & E, 9840 International Drive, (located next to the Clarion Plaza Hotel, site of the 38th ENC) on Sunday, March 23, 2:30 to 6:00 p.m. The agenda includes a presentation of recent results by leading NMR experimentalists concerning applications of pulsed field gradient and classical NMR techniques with both large and small molecular systems. The results obtained will be of interest to all liquid state NMR Spectroscopists. Request a detailed program or RSVP by contacting Chris Tierney, Nalorac s ENC Coordinator. at NALORAC, 841-A Arnold Drive, Martinez, CA 94553 Phone: (510) 229-3501 Fax: (510) 229-1651, Email: christierney@nalorac.com From owner-structural-nmr@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!agate!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!mindspring!news.mindspring.com!usenet From: Wave@mindspring.com (Pieter Ibelings) Newsgroups: bionet.structural-nmr Subject: PTS160 Synthesizers for sale. See pictures @ Date: 9 Jan 1997 04:09:05 GMT Organization: www.mindspring.com/~wave Lines: 36 Message-ID: <5b1r11$9dk@camel5.mindspring.com> NNTP-Posting-Host: user-168-121-20-253.dialup.mindspring.com Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.8 (x86 32bit) ** RE. PTS160 Generators Still Available 4Sale.** Pictures available at: http://www.mindspring.com/~wave/sale.html I still have a couple of PTS 160 Synthesizers for sale. I am asking $650 plus shipping for these real clean units. These are very clean with some minor scratches.I guarantee that they are in full working condition at time of receipt. All the units have the TCXO, GPIB, BCD, Rack mount, 1Hz resolution and option X27??? These are surplus units from GE Medical Systems. All reasonable forms of payment are available (money orders or checks). If you want to send us a PO, we can send you the unit and then you can send us the check within a reasonable ammount of time. A friend of mine is taking care of the sales and he can be reached at the address and phone below. Please give him a call if you are ready to order and tell him that I refered you. If you require any additional information please do not hesitate to send me some e-mail. Thanks Pieter wave@mindspring.com ******************************** Video Audio Repair Service Inc. William E. Flake Jr. (Bill) 6658 B Hillandale Drv. Lithonia, GA 30058 Phone (770) 482-2989 Tue-Fri 10:00am to 7:30pm From owner-structural-nmr@net.bio.net Sun Jan 12 22:00:00 1997 Path: biosci!Roche.COM!alfred.ross From: alfred.ross@Roche.COM (Alfred Ross) Newsgroups: bionet.structural-nmr Subject: Deuteration of Glucose Date: 13 Jan 1997 07:46:14 -0800 Organization: Roche Basel AG Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <32DA5891.41C6@roche.com> NNTP-Posting-Host: net.bio.net Dear netters, does anybody know a reference/recipe how to perform deuteration of glucose. Tanks a lot from Alfred -- ************************************* Dr. Alfred Ross NMR-Spectroscopist e-mail: alfred.ross@roche.com ******* Phone: CH-(0)61-6887029 * * Fax: CH-(0)61-6887408 * ROCHE * * * Mail: F. Hoffmann-LaRoche AG ******* (A. Ross - PRPI) Postfach CH-4070 Basel ************************************* From owner-structural-nmr@net.bio.net Sun Jan 12 22:00:00 1997 Path: biosci!SODIUM.BAS.ROCHE.COM!rossa From: rossa@SODIUM.BAS.ROCHE.COM ("Alfred.Ross@Roche.com") Newsgroups: bionet.structural-nmr Subject: Deuteration of Glucose Date: 13 Jan 1997 07:58:35 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <9701131647.ZM29386@sodium.bas.roche.com> NNTP-Posting-Host: net.bio.net Dear netters, does anybody know a reference/recipe about the deuteration of glucose. Thanks in advance Alfred -- ************************************* Dr. Alfred Ross NMR-Spectroscopist e-mail: alfred.ross@roche.com ******* Phone: CH-(0)61-6887029 * * Fax: CH-(0)61-6887408 * ROCHE * * * Mail: F. Hoffmann-LaRoche AG ******* (A. Ross - PRPS) Postfach CH-4070 Basel ************************************* From owner-structural-nmr@net.bio.net Sun Jan 12 22:00:00 1997 Path: biosci!biosci!not-for-mail From: Bridget.Mabbutt@mq.edu.au Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance Subject: NMR postdoc position Date: 12 Jan 1997 16:51:43 -0800 Organization: Macquarie University Lines: 53 Sender: daemon@net.bio.net Distribution: world Message-ID: <32D5B5B8.2BC0@mq.edu.au> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.structural-nmr:1679 sci.techniques.mag-resonance:1926 The following position will shortly be advertised: MUCAB Protein Structure Group School of Chemistry Macquarie University, Sydney, Australia Protein NMR Spectroscopist Salary: Research Associate ($38,092 - 40,889, subject to approval) A two-year postdoctoral position is available immediately to determine the NMR structure of various proteins within the Protein Structure Group at Macquarie University, Sydney. The successful applicant will primarily work to define a protein fold thought to be representative of a new family of cell-cell adhesion molecules. Spectra obtained to date on this surface glycoprotein (MW=15kDa) are of very high quality (Zachara et al., Eur. J. Biochem. 238, 511-518, 1996) and milligram quantities of the 15N-labelled recombinant protein are routinely prepared in this laboratory. The Protein Structure Group is focussed on several proteins involved in cellular adhesion and regulation. It is staffed by a multidisciplinary team encompassing molecular biology, protein expression and NMR structure determination. We are a component of the Macquarie University Centre for Analytical Biotechnology, and are closely associated with the Australian Proteome Analysis Facility, which together form the major centre for protein research in the Sydney region. The Group is also part of IBiS (Initiative in Biomolecular Structure), a multidisciplinary forum addressing NMR, crystallography and computer techniques in structural biology. A new 600 MHz NMR spectrometer will be installed in the School of Chemistry in 1997. In the interim, generous access to a DMX-600 spectrometer (with pulse-field gradient capability) is available nearby at the University of New South Wales. Other resources include state-of-the art protein purification and analysis equipment, and a cluster of dedicated Silicon Graphics workstations. Applicants should have a Ph.D. in Chemistry, Biochemistry or related field. Experience in the recording and analysis of heteronuclear multidimensional NMR spectra of proteins is essential, as is familiarity with UNIX and NMR processing packages. Appointment is available immediately, initially until December 1997, and is renewable subject to grant funding. Applications will close early February 1997. For further information concerning applications contact: Dr Bridget Mabbutt, School of Chemistry, email: bridget.mabbutt@mq.edu.au, telephone: (61 2) 9850 8282, fax: (61 2) 9850 8313 From owner-structural-nmr@net.bio.net Tue Jan 14 22:00:00 1997 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!u-psud.fr!usenet From: Mark Blight Newsgroups: bionet.structural-nmr Subject: Help needed with Flame Spec Date: Wed, 15 Jan 1997 19:39:29 +0100 Organization: Universite Paris-Sud, France. Lines: 54 Message-ID: <32DD2461.786B@igmors.u-psud.fr> NNTP-Posting-Host: bmec2.igmors.u-psud.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 2.0 (Macintosh; I; 68K) Hello, I am a molecular biologist by training and so am a bit rusty on some of the= apparatus and = techniques that can be used for more chemical type studies. However, I am interested in determining the "purity" of a complex mixture (= a plant extract) = with respect to other contaminating mixtures from, for example, other plant= species. I also = need to process many samples with great rapidity and so organic extraction = and HPLC etc = are probably too slow. I was wondering if the absorption spectra (like for = stellar objects) of = a reference sample could be compared to an unknown and additional absorptio= n bands = subtracted to help identify the possible contaminant by comparison to a dat= abank of = potential contaminating substances (or mixtures). Like I said, I'm not very= familiar with = the techniques that might be employed or the equipment. So, would I need a = flame = spectrometer (or is that a photometer?) to generate the absorption spectra?= And can anyone = with more experience give me an idea if this might work? Thanks for any suggestions, Please reply by e-mail. Mark _______________________________________ Dr. Mark A. Blight, Institut de G=E9n=E9tique et Microbiologie, CNRS URA 1354, B=E2timent 409, Universit=E9 de Paris XI, 91405 Orsay cedex, France. Tel: +33 1 69 15 66 99 Fax: + 33 1 69 15 78 08 e-mail: BLIGHT@IGMORS.U-PSUD.FR _______________________________________ From owner-structural-nmr@net.bio.net Thu Jan 16 22:00:00 1997 Path: biosci!CASPUR.IT!r.ragno From: r.ragno@CASPUR.IT (Gianluca Sbardella) Newsgroups: bionet.structural-nmr Subject: Is OrgChem still "alive" ??? Date: 16 Jan 1997 23:41:39 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: Gianluca Sbardella NNTP-Posting-Host: net.bio.net Dear Netters, I'm sending this question to a few different mail lists: my apologies for any repetitiion!!! The question is this: Does anybody know if ORGCHEM (Organic Chemistry Mail List) IS STILL ALIVE? Thank you all in advance, Gianluca Sbardella *************************************************************** * * * Dr. Gianluca Sbardella E-mail: r.ragno@caspur.it * * Dip. Studi Farmaceutici * * Universita' "La Sapienza" Phone: 39-6-49913814 * * P.le A. Moro, 5 Fax: 39-6-491491 * * 00185 Roma * * ITALY * * * *************************************************************** From owner-structural-nmr@net.bio.net Sun Jan 19 22:00:00 1997 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!arclight.uoregon.edu!feed1.news.erols.com!howland.erols.net!news2.digex.net!news5.digex.net!news1.cstone.net!Skuzzy.cstone.net!not-for-mail From: Dave Dolak Newsgroups: bionet.structural-nmr Subject: NMR & aggregation Date: Mon, 20 Jan 1997 10:55:21 -0500 Organization: Protein Solutions, Inc. Lines: 12 Message-ID: <32E39569.17AD@cstone.net> Reply-To: crystal@cstone.net NNTP-Posting-Host: dialin92.cstone.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) How detrimental is a small amount of large aggregation during NMR analysis? I've heard some people say that it can be very detrimental while others argue that it is not that important to eliminate. Which is it? Can there be some aggregation that doesn't matter but above some 'threshold' it can interfere? I'd like to better understand what limits there are on the presence of aggregates for successful NMR analysis. Thanks, Dave Dolak Protein Solutions, Inc. 70651.3674@compuserve.com From owner-structural-nmr@net.bio.net Sun Jan 19 22:00:00 1997 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: NMR & aggregation Date: 20 Jan 1997 09:39:26 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 47 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <32E39569.17AD@cstone.net> NNTP-Posting-Host: net.bio.net Dear Dave, I am sure there will be people with more experience and more quantitative advise than what I can offer here, but let me put down my two cents... I believe aggregation is most of a problem if it is uncontrolled. The primary result is broadening lines, e.g., faster relaxation, enhanced spin diffusion, etc. Dynamic characterization of the structure can give misleading information, too. Symmetry of the aggregates can be a issue, as well. I don't think there is a general "threshold" to be set; should you have a chance, work with monomers at low enough concentration (as low as 0.2-0.5 mM/L can be used with modern high-field instruments -- however, this is the edge of capabilities). However, every sample is an individual, and practical compromises have to be considered. A reasonable spectrum is better than no spectrum; just be careful with the conclusions... Good luck, and 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 On Mon, 20 Jan 1997, Dave Dolak wrote: > How detrimental is a small amount of large aggregation during NMR > analysis? I've heard some people say that it can be very detrimental > while others argue that it is not that important to eliminate. Which is > it? Can there be some aggregation that doesn't matter but above some > 'threshold' it can interfere? > > I'd like to better understand what limits there are on the presence of > aggregates for successful NMR analysis. > Thanks, > Dave Dolak > Protein Solutions, Inc. > 70651.3674@compuserve.com > > From owner-structural-nmr@net.bio.net Mon Jan 20 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: Isabelle Phan Newsgroups: bionet.structural-nmr Subject: Re: NMR & aggregation Date: Tue, 21 Jan 1997 12:06:08 +0000 Organization: Oxford Centre for Molecular Sciences Lines: 20 Message-ID: <32E4B130.794BDF32@bioch.ox.ac.uk> References: <32E39569.17AD@cstone.net> NNTP-Posting-Host: nmrh.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; SunOS 4.1.3 sun4m) Dear Dave, As a follow up of Istvan Pelczer's post: Shurr et al., J.Magn.Reson., B105, 211-224, discuss the theoretical effect of aggregation on relaxation measurements. They seem to say that 20% aggregation leads already to significant errors when extracting dynamic parameters from relaxation data. On my own sample, I found that a fourfold dilution to about .5mM led to a 30% drop in the apparent correlation time (see current issue of J. Biomol. NMR). Cheers, Isabelle -- ____________________________________________________________________ Dr. Isabelle Phan phan@bioch.ox.ac.uk Oxford Centre for Molecular Sciences http://www.ocms.ox.ac.uk/ University of Oxford voice: 44-1865-275773 OXFORD OX1 3QU, U.K. fax: 44-1865-275253 From owner-structural-nmr@net.bio.net Mon Jan 20 22:00:00 1997 Path: biosci!PINES.MED.UTORONTO.CA!vincent From: vincent@PINES.MED.UTORONTO.CA (Sebastien Vincent) Newsgroups: bionet.structural-nmr Subject: Re: Aggregation and HSQC Linewidths Date: 21 Jan 1997 14:45:55 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701212243.RAA11934@pines.med.utoronto.ca> NNTP-Posting-Host: net.bio.net > In practice, when working with a new protein, we usually do not know much > about the aggregation parameters (unless we have done some fairly > sophisticated sedimentation analysis). Martin, you can know a lot if you get a nitrogen-15 labelled sample in an NMR tube and record 15N T2 (see ) relaxation data. This gives, in 1 or 2 days, a way to obtain the overall correlation time, and this is part of an answer (Note: If you have time and want to be sure, you can also record 15N T1 and 15N1H NOE mexperiments). For a ref., see Farrow et al, Biochem. 33 (1994) 5984-6003. In the case of aggregation, you can expect a certain correlation time for a monomer, and acertainly more for a monomer. > what amide proton line widths should we be looking > for to satisfy ourselves that standard triple resonance experiments will > work and structure determination will be feasible for a new protein? A rule of thumb is that if your overall correlation time is lower than 15ns, you're in good shape. If more, think deuteration or get another cDNA... Sebastien (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) (::) Sebastien Vincent University of Toronto vincent@redfield.med.utoronto.ca Department of Medical Genetics, Voice: ++(416) 978-0642 1, King's College Circle, Fax: ++(416) 978-6885 Toronto, Ontario, CANADA M5S 1A8 www: http://abragam.med.utoronto.ca/~vincent/ "Half the world population has never made a phone call." (M. Murphy, 12.96) From owner-structural-nmr@net.bio.net Mon Jan 20 22:00:00 1997 Path: biosci!INDIANA.EDU!mastone From: mastone@INDIANA.EDU (Martin J. Stone) Newsgroups: bionet.structural-nmr Subject: Aggregation and HSQC Linewidths Date: 21 Jan 1997 12:40:21 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 45 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701212040.PAA01633@belize.ucs.indiana.edu> NNTP-Posting-Host: net.bio.net It seems to me that the effect aggregation has on an NMR spectrum will depend on: - the average size of the aggregated species - the distribution of sizes of aggregated species - the exchange rates between various aggregated and non-aggregated species etc. I would like to change the direction of the discussion slightly. In practice, when working with a new protein, we usually do not know much about the aggregation parameters (unless we have done some fairly sophisticated sedimentation analysis). Therefore, if we see lousy spectra, we are left wondering whether they could potentially be improved by changes in sample conditions that overcome aggregation. In practice, we tend to try many different variations of temperature, pH, salt conditions, cosolvents, sample concentration, etc. until we find a spectrum that is good enough, and then we assume we have overcome the aggregation effects in the spectrum. So my question is this: HOW GOOD IS GOOD ENOUGH?? ...or more specifically, what amide proton line widths should we be looking for to satisfy ourselves that standard triple resonance experiments will work and structure determination will be feasible for a new protein? I would appreciate some leading references (or some personal anecdotes) that would help to address this question. thanks Martin ======================================= Martin J. Stone, Assistant Professor of Biochemistry, Department of Chemistry, Indiana University, Bloomington, IN 47405. Tel. (812)855-6779 Fax. (812)855-8300 email. mastone@indiana.edu www: http://pooh.chem.indiana.edu/ From owner-structural-nmr@net.bio.net Mon Jan 20 22:00:00 1997 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!news-peer.gsl.net!news.gsl.net!howland.erols.net!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.idt.net!news.cerf.net!ihnp4.ucsd.edu!scripps.edu!obelix!weber From: weber@obelix.scripps (Christoph Weber) Newsgroups: bionet.structural-nmr Subject: Re: NMR & aggregation Date: 21 Jan 1997 19:53:41 GMT Organization: The Scripps Research Institute Lines: 35 Message-ID: <5c36s5$ivd@riscsm.scripps.edu> References: <32E39569.17AD@cstone.net> Reply-To: weber@scripps.edu NNTP-Posting-Host: obelix.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Keywords: protein In article <32E39569.17AD@cstone.net>, Dave Dolak writes: > How detrimental is a small amount of large aggregation during NMR > analysis? I've heard some people say that it can be very detrimental > while others argue that it is not that important to eliminate. Which is > it? Can there be some aggregation that doesn't matter but above some > 'threshold' it can interfere? The problem is that 'aggregation' is a very broad term and in most instances cannot be defined and/or measured in a sufficiently precise way. If there are aggregates that show up in gel electrophoresis, then they should and can be eliminated. However, in most cases we conclude that there is some 'aggregation' from circumstantial evidence, like overly broad lines in the NMR spectrum. Since we don't even know what we're talking about really, it is impossible to say at the outset how much is to much. There are cases where we know what to expect. Camelized Ig VH domains come to mind, for example, where there may be residual dimerization. Having a precise idea of what 'aggregation' we are looking at can make our job much easier. As Istvan says, what really matters in the end is whether you can get NMR data of sufficiemt quality to do your analysis and whether you can circumvent additional problems, such as intermolecular NOEs. Everything else is rather moot. Christoph | Dr. Christoph Weber Sen. Research Associate | Dept.of Molecular Biology, MB9 619-784-9869 (phone) | The Scripps Research Institute 619-784-2857 (FAX) | La Jolla CA 92037-1027 weber@scripps.edu | http://www.scripps.edu/~chazin/people/cw.html From owner-structural-nmr@net.bio.net Mon Jan 20 22:00:00 1997 Path: biosci!MAILBOX.SYR.EDU!lpappala From: lpappala@MAILBOX.SYR.EDU (Lucia Pappalardo) Newsgroups: bionet.structural-nmr Subject: Bruker pulse sequences Date: 21 Jan 1997 06:43:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: Lucia Pappalardo NNTP-Posting-Host: net.bio.net Dear Netters, I am looking for the pulse program of a 3D TOCSY/NOE w/ water suppression using gradients suitable for an Avance Bruker DRX-500 w/ 3-axis gradient probehead. Thanks in advance Lucia From owner-structural-nmr@net.bio.net Tue Jan 21 22:00:00 1997 Path: biosci!MRIRIS.ROCKEFELLER.EDU!cowburn From: cowburn@MRIRIS.ROCKEFELLER.EDU ("David Cowburn") Newsgroups: bionet.structural-nmr Subject: Aggregation phenomena, relaxation etc. Date: 22 Jan 1997 06:23:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <9701220922.ZM5658@mriris.rockefeller.edu> Reply-To: cowburn@rockvax.rockefeller.edu NNTP-Posting-Host: net.bio.net The ongoing discussion covers two slightly seperate issues concerned with the same physical phenomena. One issue is how to optimise sample conditions for narrow linewidths, and at what point is deviation from the expected values a problem. Our own experience is that screening a range of conditions using unlabelled or N15 labeled material is vital, and direct measurement of aggregation state is critical. Light scattering and low angle X-ray scattering are difficult to do well and precisely; sedimentation equilibrium is very valuable, but time consuming to do; amide hydrogen T2's and diffusion measurments using gradients are empirically more useful to us. As to what conditions are unsuitable, if the target is of sufficient significance, then you have to judge whether the critical experiments (e.g. CBCANH) can be done at all, and if so, in what time. The second issue is what are the effects of nonspecific aggregation on relaxation and spectral properties, generally. We have recently dealt with such a system, and a paper will appear very shortly. == Fushman, David; Cahill, Sean M.; Cowburn, David (1997) "The main chain dynamics of the dynamin pleckstrin homology (PH) domain in solution: Analysis of 15N relaxation with monomer/dimer equilibration." J. Mol. Biol.,266, 173-194. == The JMB issue containing the paper should appear about Feb 1. While each protein system will have its own peculiarities, this paper deals generally with the problem of nonspecific aggregation at the approx. 1mM dissociation constant level, with relatively rapid exchange. With the relaxation equations modified for these conditions, the analysis can be done, and the variations of tau(c) rationalised. For this paper, sedimentation equilibrium experiments were done, at NMR concentrations. -- David Cowburn, The Rockefeller University, 1230 York Avenue, NY, NY 10021, USA. Tel 212.327.8270. Fax 212.327.7566 http://mriris.rockefeller.edu/ From owner-structural-nmr@net.bio.net Tue Jan 21 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Paul Driscoll Newsgroups: bionet.structural-nmr Subject: aggregation or viscosity? Date: 22 Jan 1997 11:57:50 -0000 Organization: Dept. Biochem. & Mol. Biol., UCL Lines: 64 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5c4vbu$ahh@mserv1.dl.ac.uk> Original-To: nmr@biochemistry.ucl.ac.uk, str-nmr@dl.ac.uk I would like to put my oar in on this discussion about protein aggregation. We have been working for some time now on protein systems which demonstrate a concentration-dependent rotational correlation time (based on 15N nuclear relaxation measurements). The obvious explanation for this phenomenon is a fast exchange oligomerisation equilibria (e.g. dimerisation or higher order association) that is enhanced at higher protein concentration. I believe there are well documented examples of this behaviour in the literature. I have been wondering if there are other factors to be concerned about. (Ignoring analytical ultracentrifugation for the moment...) In principle, estimates of molecular size or whether a protein is truly monomeric in solution could be obtained by measurement of rotational correlation times (tau_c) and comparison with calculations based on the Stokes-Einstein equation or more sophisticated hydrodynamic models (e.g. Beads, HYDRO, etc). At the end of the day one needs to know the viscosity of the solvent to go into these calculations. My quandry is: what defines the viscosity for this purpose in a heterogeneous protein/solvent/buffer mixture? Is it safe to use the book value of the viscosity for the solvent (H2O,D2O) or should one be concerned that at least the buffer and no doubt the protein itself change in some manner the structure of the solvent and alter the (macroscopic) viscosity? Or is tau_c dependent more on local 'microscopic' protein-solvent interactions? I have thought a lot about this but can't decide if these 'viscosity' factors are important. We tend to use deuterated TRIS/HCl as a buffer, rather than phosphate. Also we often have 50mM-100mM salt present. Does that mean we should invest time and money in measuring the viscosity of the buffer explicitly to see if there are systematic effects on protein tau_c values arising from this condition? Maybe. Anyone done anything like this before? Perhaps the right conclusion is that the simple hydrodynamic models are too simple - the solvation sphere of a protein is likely a complex thing, different layers with graded characteristics, and there could be specific salt effects of certain cations and anions (maybe TRIS has some peculiarities in this regard?) which make a mockery of these calculations. Against this view there are clearly proteins which behave as ideal monomers, completely fitting the hydrodynamic models (e.g. ubiquitin), which suggests that when one does not obtain sensible tau_c values for other proteins then one either has (specific or non-specific) aggregation, a 'floppy' or 'expanded' structure, an unusually high degree of protein solvation, or there is something screwy with the solvent viscosity. Perhaps others have some comments to make that would help eliminate this last possibility. Cheers, Paul P.S. A small plea. When people report tau_c values for proteins, I strongly believe they should state the CALIBRATED temperature of the sample in the spectrometer. Over recent times I have beome aware that the reported probe temperature on the spectrometer console can be significantly different from the actual sample temperature (perhaps one should even take into account the RF heating effects of the pulse sequences). I wonder whether the scatter one observes in a graph of reported tau_c vs. molecular weight is exaggerated by this type of discrepency. --------------------------------------------------------------------- Paul Driscoll | Office (answer)phone: (44)-171 380 7035 Dept. Biochem. & Mol. Biol. | Department fax: (44)-171 380 7193 University College London | driscoll@biochem.ucl.ac.uk From owner-structural-nmr@net.bio.net Tue Jan 21 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 22 Jan 1997 02:00:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701221000.CAA27307@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. 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Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-structural-nmr@net.bio.net Tue Jan 21 22:00:00 1997 Path: biosci!biosci!not-for-mail From: Reto Koradi Newsgroups: bionet.structural-nmr,bionet.software,bionet.molec-model,bionet.molbio.proteins,comp.graphics.visualization,comp.sys.sgi.apps Subject: ANNOUNCE: MOLMOL 2.3 Date: 21 Jan 1997 21:38:56 -0800 Organization: Swiss Federal Institute of Technology (ETHZ) Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <32E49735.2575@mol.biol.ethz.ch> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.structural-nmr:1694 bionet.software:17661 bionet.molec-model:1333 bionet.molbio.proteins:9787 comp.graphics.visualization:9259 comp.sys.sgi.apps:14250 Release 2.3 of MOLMOL, a program for display and analysis of macromolecular structures, is now available free of charge. Information about the program and links to download sites can be found at: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ The program was developed as a joint project between BRUKER/Spectrospin and the group of Prof. Wuthrich at the Institute for Molecular Biology and Biophysics at the ETH Zurich. It runs on various UNIX workstations, the ftp sites hold source code and binaries for Silicon Graphics, Sun, IBM, Digital and Linux. -- Reto Koradi (kor@mol.biol.ethz.ch, http://www.mol.biol.ethz.ch/~kor) From owner-structural-nmr@net.bio.net Tue Jan 21 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Paul Driscoll Newsgroups: bionet.structural-nmr Subject: Re: Aggregation phenomena, relaxation etc. Date: 22 Jan 1997 17:58:04 -0000 Organization: Dept. Biochem. & Mol. Biol., UCL Lines: 32 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5c5kfc$8bm@mserv1.dl.ac.uk> References: <97122145331.~INN-VSNa00197.bionet-news@dl.ac.uk> Original-To: str-nmr@dl.ac.uk, David Cowburn Dear David, Janet Thornton showed me a pre-print of your paper. It's excellent stuff, and we enjoyed reading it. However, in your post you did not comment on what defines viscosity in the 'Stokes-Einstein' sense. Do you take a view on this? Cheers, Paul --------------------------------------------------------------------- Paul Driscoll | Office (answer)phone: (44)-171 380 7035 Dept. Biochem. & Mol. Biol. | Department fax: (44)-171 380 7193 University College London | driscoll@biochem.ucl.ac.uk > > The second issue is what are the effects of nonspecific aggregation on > relaxation and spectral properties, generally. We have recently dealt with > such a system, and a paper will appear very shortly. == Fushman, David; > Cahill, Sean M.; Cowburn, David (1997) "The main chain dynamics of the dynamin > pleckstrin homology (PH) domain in solution: Analysis of 15N relaxation with > monomer/dimer equilibration." J. Mol. Biol.,266, 173-194. == The JMB issue > containing the paper should appear about Feb 1. > > While each protein system will have its own peculiarities, this paper deals > generally with the problem of nonspecific aggregation at the approx. 1mM > dissociation constant level, with relatively rapid exchange. With the > relaxation equations modified for these conditions, the analysis can be done, > and the variations of tau(c) rationalised. For this paper, sedimentation > equilibrium experiments were done, at NMR concentrations. > From owner-structural-nmr@net.bio.net Tue Jan 21 22:00:00 1997 Path: biosci!daresbury!bioftp.unibas.ch!ubaclu.unibas.ch!ubaclu.unibas.ch!nntp Newsgroups: bionet.structural-nmr Subject: aggregation /viscosity Message-ID: <1997Jan22.181549.47295@yogi.urz.unibas.ch> From: andrei Date: 22 Jan 97 18:15:49 MET Organization: Biozentrum - U. Basel Nntp-Posting-Host: skivacation.bioz.unibas.ch X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) MIME-Version: 1.0 X-URL: news:bionet.structural-nmr Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Lines: 22 Everyone in this discussion has focused on rotational diffusion (e.g. tau_c), which probably depends on billions of things. An alternative way to measure viscosity/aggregation is to look at translational diffusion see : Alteri ... Byrd, "Association of biomolecular systems via pulsed field gradient NMR self-diffusion measurements" Since this method uses 1D's I would imagine its a lot simpler than 3 relaxation measurments and worries about R2ex and te. P.S. Does anyone have experience with urea or other denaturants to reduce aggregation (i.e. enough urea to break up aggregates but not to unfold protein). I know urea isn't very physiological but then neither are MPD, PEG, Ammonium Sulfate ... Anyone know of any other methods to reduce aggregation (i.e. Chaps has been suggested) From owner-structural-nmr@net.bio.net Tue Jan 21 22:00:00 1997 Path: biosci!NMRSGI2.NCIFCRF.GOV!rabyrd From: rabyrd@NMRSGI2.NCIFCRF.GOV (R. Andrew Byrd) Newsgroups: bionet.structural-nmr Subject: Aggregation and Diffusion Date: 22 Jan 1997 08:21:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 86 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701221618.LAA24839@nmrsgi2.ncifcrf.gov> NNTP-Posting-Host: net.bio.net In light of recent postings to the newsgroup concerning aggregation, and various discussions, we would like to point out some elements of our recent work that we used to address this problem. Specifically, Martin Stone mentioned that unless one does some sophisticated sedimentation analyses, then the aggregation state is unknown. He also pointed out the difficulties of knowing which direction to move in while measuring lots of parameters, pH, temperature, salts, buffers, etc. and to know what the endpoint is. Furthermore, the monitoring of parameters in an unlabeled protein [...holding off on labels until you feel you have the right conditions...] can be misleading if there are things contributing to linewidth other than aggregation, e.g. exchange with solvent or internal conformations, paramagnetic metals contaminating the solvent. Consequently, we felt it was important to monitor the bulk behaviour of the particle under exactly the same conditions as would be used for NMR experiments. The approach is to use translational diffusion measurements made in standard pfg NMR probes. We demonstrated that with even moderate gradients [up to 30-40 G/cm] it is possible to measure the diffusion constants of particles corresponding to molecular weights of 40-45 kDa. For larger particles, it is simple to see that they are greater than 45 kDa, in which case you know the answer about using NMR! The concepts behind the measurement of Ds are well established in the literature. Our approach was to adapt the work of Gibbs and Johnson such that one can use current high-resolution NMR probes and include one technique for water suppression. There are various improvements and different ways to achieve this, so I will only point you to the one approach which we published: Altieri, Hinton, and Byrd; JACS 117:7566-7567 (1995) A quantitative analysis of the Ds is not required, since that will depend on temperature, buffer viscosity, and possibly other factors. However, a comparative measurement can provide a clear answer to dimerization or higher oligimerization. The case of higher oligomerization causes a numerical instability in the analysis of the diffusion data (multi- component exponential fit where the difference in size is only a factor of 2 or 3). However, if high signal-to-noise ratios are obtained and one analyzes the residual plot [observed - fit values], then it is possible to discern if the model of a single species in solution fits reasonably. The presence of systematic errors in the residual plot is an indication of non-compliance. This characteristic should change when the conditions shift toward a single species, be it monomer, dimer, etc. Nevertheless, as a RELATIVE measure, the Ds is still valid, and it is reasonable to monitor the transition towards a monomeric or stable dimeric state via the measured 'apparent' Ds. One final point, I have stated that the analysis of exchange is complicated...this stems from the combination of multiple exponential functions which differ in their respective time constants by only, roughly, the order of aggregation. As pointed out by Paul Driscoll and others, this is a complex issue. I am less comfortable with comments which indicate that as long as you can measure NOEs all is well, since the effective buildup rate is dependent on the effective correlation time. Any quantitative analysis of the NOE buildup rates must also take these aggregation and exchange effects into account. Finally, I would also like to point interested readers to the work of Cynthia Larive's group and to Glen King's group (JBNMR 6:321-328 (1995)). Amanda Altieri Andy Byrd altieri@ncifcrf.gov rabyrd@ncifcrf.gov ------------------ Dr. R. Andrew Byrd Macromolecular NMR/MSL/ABL TEL: 301-846-1407 FAX: 301-846-6195 From owner-structural-nmr@net.bio.net Tue Jan 21 22:00:00 1997 Path: biosci!MOLE.BIO.CAM.AC.UK!mjh2 From: mjh2@MOLE.BIO.CAM.AC.UK (Mark J Howard) Newsgroups: bionet.structural-nmr Subject: Re: aggregation or viscosity? Date: 22 Jan 1997 06:51:59 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 70 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Just a few thoughts regarding Paul Driscoll's recent communication to bionet.str-nmr: > At the end of the day one needs to know the > viscosity of the solvent to go into these calculations. My quandry is: > what defines the viscosity for this purpose in a heterogeneous > protein/solvent/buffer mixture? Is it safe to use the book value of the > viscosity for the solvent (H2O,D2O) or should one be concerned that at > least the buffer and no doubt the protein itself change in some manner > the structure of the solvent and alter the (macroscopic) viscosity? Or > is tau_c dependent more on local 'microscopic' protein-solvent > interactions? It is funny you should say this but I have encountered several instances where text books and papers convince the reader that protein solutions used in NMR are non-viscous due to the low sample concentration. I have seen several examples where this is not the case, and I am sure I am not the only one. These effects have been observed regardless of high or low salt concentration. With this in mind, if the protein concentrations you are using are over 1mM, then there is every possibility that the viscosity of H2O/D2O will be different from what you are actually dealing with. However, there can be some debate over the dependence of tau_c on the macroscopic viscosity or 'local' viscosity. I have heard of good (as in narrow lines and fully resolable) protein spectra being obtained from almost gel-like samples, this appears to back up a 'local' rather than global viscosity. On the point of measuring viscosity, there are digital viscometers about, but when I last looked into this in 1992 I was told they only measured quite viscous mixtures and could not resolve viscosity differences much below 10 times the viscosity of water but perhaps that has changed now. The better method is to us an Oswald Viscometer (I remember my physical chemistry practical well!). These contraptions are very accurate, but you must obtain the correct viscometer for the range of viscosity you intend measuring. You should still be able to get Oswald viscometers which measure viscous differences of dilute solutions and water. I think I may know a possible source if you are interested. > P.S. A small plea. When people report tau_c values for proteins, I > strongly believe they should state the CALIBRATED temperature of the > sample in the spectrometer. Over recent times I have beome aware that > the reported probe temperature on the spectrometer console can be > significantly different from the actual sample temperature (perhaps one > should even take into account the RF heating effects of the pulse > sequences). I wonder whether the scatter one observes in a graph of > reported tau_c vs. molecular weight is exaggerated by this type of > discrepency. I could not agree more. I personally feel that not enough experimental details are given in many papers, especially important physical parameters including the corrected temperature. ******************************************************** Dr. Mark Howard Protein NMR Spectroscopy | Dept. of Biochemistry | University of Cambridge || | Tennis Court Road | || | | Cambridge, UK. || | ||| | | CB2 1QW ____|||||___/\__||||||||___|_|_ Tel: (01223) 333662 Fax: (01223) 333661 E-mail: mjh2@mole.bio.cam.ac.uk ******************************************************** From owner-structural-nmr@net.bio.net Wed Jan 22 22:00:00 1997 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!news-xfer.netaxs.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!howland.erols.net!usenet.kornet.nm.kr!newsfeed.dacom.co.kr!arclight.uoregon.edu!newsfeed.uk.ibm.net!news-m01.ny.us.ibm.net!newsfeed.de.ibm.net!02-newsfeed.univie.ac.at!03-newsfeed.univie.ac.at!fstgal00.tu-graz.ac.at!balu.kfunigraz.ac.at!balu!sengst From: Helmut Sengstschmid Newsgroups: bionet.structural-nmr Subject: control of pH Date: Thu, 23 Jan 1997 17:01:47 +0100 Organization: Karl-Franzens-Universitaet Graz, Austria Lines: 31 Message-ID: NNTP-Posting-Host: balu.kfunigraz.ac.at Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: sengst@balu Good evening! I have not been in the field of peptide/protein NMR for long and so I lack a lot of practical experience. Recently I had the problem of measuring the pH of a protein solution. What is the best way to do that? Do you use these small electrodes to fit into the NMR tube? Furthermore if you want to measure a spectrum at a given pH (e.g. pH 5.0) what is the best way to get there? Do you use buffers (if yes, which) or do you just add a few drops of HCl? Furthermore this whole issue gets complicated if you add some other compounds like SDS (for simulating membranes) that may change the pH quite severely and that cannot be used in combination with certain buffers (e.g. SDS precipitates with phosphate). Thanks for your replies, Helmut Sengstschmid ----------------------------- DI Helmut Sengstschmid Institut fuer Organische Chemie Karl Franzens Universitaet Heinrichstr. 28 A-8010 Graz Austria Tel.: ++43 / 316 / 380 53 44 Fax: ++43 / 316 / 38 33 40 E-Mail: sengst@kfunigraz.ac.at From owner-structural-nmr@net.bio.net Wed Jan 22 22:00:00 1997 Path: biosci!UGA.CC.UGA.EDU!JLEE From: JLEE@UGA.CC.UGA.EDU Newsgroups: bionet.structural-nmr Subject: protein solution viscosity Date: 23 Jan 1997 06:55:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <970123.095503.EST.JLEE@UGA.CC.UGA.EDU> NNTP-Posting-Host: net.bio.net The question of what solution (solvent) viscosity to use is adequately discussed in H.K.Schackmann's book "Ultracentrifugation in Biochemistry". In this field the solvent viscosity is taken since the macromolecules seldom encounter one another. John Lee Department of Biochemistry University of Georgia Athens GA 30602-7229 USA Phone 706-542-1764 FAX 706-542-1738 From owner-structural-nmr@net.bio.net Thu Jan 23 22:00:00 1997 Path: biosci!BIBA.MED.TUFTS.EDU!sudha From: sudha@BIBA.MED.TUFTS.EDU (Sudha Veeraraghavan) Newsgroups: bionet.structural-nmr Subject: handling proteins Date: 23 Jan 1997 20:15:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701240411.XAA21042@biba.med.tufts.edu> NNTP-Posting-Host: net.bio.net Helmut, The first thing you would want to do is to get the book edited by G.C.K. Roberts called "NMR of Macromolecules - A Practical Approach" (IRL Press, 1993). In this book, the second chapter, written by W. Primrose, details painstakingly techniques and methodologies in handling protein samples for NMR. To directly answer your questions: Yes, you need to have a buffer that is suitable for your purposes and one that will has a pKa in the range of pH you wish to keep your sample at. Yes, you will need to use a pH electrode thin enough to insert into the NMR tube - so you can measure the pH in the NMR tube. You may also pH the sample before transferring it into the NMR tube. Adjusting the pH is a bit tricky. One has to be very careful doing this. In my experience with pHing proteins, HCl and NaOH are two reagents best not used. Using a dual buffer system, e.g., phosphate-citrate or phosphate-acetate, reduces loss of sample to precipitation. 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 Thu Jan 23 22:00:00 1997 Newsgroups: bionet.structural-nmr Path: biosci!rutgers!utcsri!utnut!utinfo!bloch.med.utoronto.ca!not-for-mail From: gardner@bloch.med.utoronto.ca (Kevin Gardner) Subject: Re: aggregation /viscosity X-Nntp-Posting-Host: bloch.med.utoronto.ca Message-ID: Lines: 42 Sender: nntp@utcc.utoronto.ca (News) Organization: UTCC Campus Access X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] References: <1997Jan22.181549.47295@yogi.urz.unibas.ch> Date: Thu, 23 Jan 1997 14:31:21 GMT andrei (alexandrescu@ubaclu.unibas.ch) wrote: : P.S. Does anyone have experience with urea or other denaturants to : reduce aggregation (i.e. enough urea to break up aggregates but not to : unfold protein). I know urea isn't very physiological but then neither : are MPD, PEG, Ammonium Sulfate ... : : Anyone know of any other methods to reduce aggregation (i.e. Chaps has : been suggested) Aside from the facetious suggestion of raising temperature :), I've got two others from a couple of papers: 1. trifluoroethanol (TFE), used up to 15% v/v to break apart a troponin C dimer: "Calcium-induced dimerization of troponin C: mode of interaction and use of TFE as a denaturant of quaternary structure" Slupsky, C.M. et al Biochemistry 34(1995): 7365-7375. 2. partial proteolysis to remove non-specifically aggregating segments --- this was demonstrated nicely in a figure from Mike Summers' group's determination of the HIV capsid protein structure (I believe Gitti, R.K. et al. Science 273(1996): 231-235?). By adding a small amt of protease to a protein solution and recording 1D 1H spectra over time a marked improvement was observed. One last note in defense of small-angle X-ray scattering: I've found this to be a wonderfully complementary approach to NMR as one can/should use a protein sample at the same concentrations for these techniques. I agree that there is a problem with the relatively limited number of sites that with scattering setups --- Cheers, Kevin -- ************************************************************************* Kevin Gardner gardner@bloch.med.utoronto.ca University of Toronto http://abragam.med.utoronto.ca/~gardner Dept. of Medical Genetics & Microbiology phone: 416-978-0642/FAX: -6885 From owner-structural-nmr@net.bio.net Thu Jan 23 22:00:00 1997 Path: biosci!daresbury!bioftp.unibas.ch!ubaclu.unibas.ch!ubaclu.unibas.ch!nntp Newsgroups: bionet.structural-nmr Subject: Re: control of pH Message-ID: <1997Jan24.130323.47303@yogi.urz.unibas.ch> From: Andrei Alexandrescu Date: 24 Jan 97 13:03:22 MET References: Organization: Biozentrum, U-Basel Nntp-Posting-Host: secsy.bioz.unibas.ch X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) MIME-Version: 1.0 X-URL: news:Pine.SGI.3.93.970123165712.14842A-100000@balu Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Lines: 32 (1) The G.C.K. Roberts book "NMR of Macromolecules" is very good, and has a good introduction to sample preparation. (2) This is probably heresy (please no e-mail) but personally, I'm not a big fan of buffers. I think protein solution at 1-2 mM concentrations are usually quite good buffers already. Unless you have a 1-sample NMR project you also have to consider what to do with the buffer if you want to concentrate the sample, change the pH, add Ca2+, etc... Buffers also have some detrimental NMR effects (described in Roberts book). I will grant, however, that some proteins do behave pretty badly without buffers, so I guess it depends on the protein. The biologists who gave you the protein will probably have suggestions (e.g. PBS). Unless I was given the world's only 4 mg sample of quadruple labeled preciouslin that took 5 years to purify, however, I would be inclined to collect a spectrum of the protein without added buffers. (3) While using electrodes that fit in an NMR tube is an option, its not the only one! In MY HANDS these rather expensive electrodes seem to have a high proclivity to snap into little pieces. You also have to consider how to mix the sample in the NMR tube. I prefer electrodes that fit in an Eppendorf tube. You can pH the sample in the Eppendorf, and transfer it to the NMR tube. You have to be careful, however, with "newly cleaned" NMR tubes since they may have been cleaned with something acidic. Its a good idea to take the sample back out of the NMR tube and check its pH again after the initial transfer. For changing pH, with HCl or DCl, dilution helps (e.g. dilute to 1M or less). For really small pH changes you can touch the tip of your pippete to a kimwipe or other absorbant tissue to decrease the size of the drop (assuming your kimwipes are not a major source of impurities). From owner-structural-nmr@net.bio.net Thu Jan 23 22:00:00 1997 Path: biosci!SNEEZY.FHIS.NET!barry From: barry@SNEEZY.FHIS.NET ("Barry Schweitzer") Newsgroups: bionet.structural-nmr Subject: Re: aggregation /viscosity Date: 24 Jan 1997 06:05:29 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: <9701240903.ZM4981@sneezy.fhis.net> NNTP-Posting-Host: net.bio.net On Jan 23, 2:31pm, Kevin Gardner wrote: > Subject: Re: aggregation /viscosity > andrei (alexandrescu@ubaclu.unibas.ch) wrote: > : P.S. Does anyone have experience with urea or other denaturants to > : reduce aggregation (i.e. enough urea to break up aggregates but not to > : unfold protein). I know urea isn't very physiological but then neither > : are MPD, PEG, Ammonium Sulfate ... > : > : Anyone know of any other methods to reduce aggregation (i.e. Chaps has > : been suggested) > You might want to check out the paper from Jim Baleja's group (Biochemistry (1995) 34, 12126-12137). They use a cocktail of urea and guanidinium to keep a Ca2+ bound gla domain (otherwise known as the Rock of Gilbralter) soluble. If you're lucky, your protein will retain its structure in this solution (which is definitely not physiological!), but lose its tendency to aggregate. It is somewhat problematic to knock down the large urea and guanidine peaks, but we have found that it can be done using either a WET sequence or excitation sculpting. Good luck! Barry -- Barry Schweitzer, Ph.D. Director Division of Molecular & Structural Biology Walt Disney Memorial Cancer Institute at Florida Hospital 12722 Research Parkway Orlando, FL 32826 Phone: (407) 380-9977 FAX: (407) 380-9978 email: barry@sneezy.fhis.net From owner-structural-nmr@net.bio.net Thu Jan 23 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Paul Driscoll Newsgroups: bionet.structural-nmr Subject: Re: control of pH Date: 24 Jan 1997 15:10:48 -0000 Organization: Dept. Biochem. & Mol. Biol., UCL Lines: 32 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5cajdo$cgn@mserv1.dl.ac.uk> References: <97124123520.~INN-QBPa00197.bionet-news@dl.ac.uk> Original-To: str-nmr@dl.ac.uk, Andrei Alexandrescu Andrei Alexandrescu wrote: > (2) This is probably heresy (please no e-mail) but personally, I'm not a > big fan of buffers. I think protein solution at 1-2 mM concentrations > are usually quite good buffers already. Unless you have a 1-sample NMR > project you also have to consider what to do with the buffer if you want > to concentrate the sample, change the pH, add Ca2+, etc... Buffers also > have some detrimental NMR effects (described in Roberts book). I will > grant, however, that some proteins do behave pretty badly without > buffers, so I guess it depends on the protein. The biologists who gave > you the protein will probably have suggestions (e.g. PBS). Unless I was > given the world's only 4 mg sample of quadruple labeled preciouslin that > took 5 years to purify, however, I would be inclined to collect a > spectrum of the protein without added buffers. > Surely this is wrong. Proteins are only buffers themselves in that they adsorb or give up protons on acidic and basic residue sidechains. The consequences of this are that for a sample coming to equilibrium during an experiment (e.g. by slow and small amounts of precipitation) or titration of a ligand the pH changes slightly, and the chemical shifts of some side chain and even backbone NH signals are thereby likely to change. This can cause severe problems in further analysis of the spectra. I would always recommend the use of a 10-20mM exogeneous buffer if possible. Believe me, it can eliminate a lot of hassle later on. Paul --------------------------------------------------------------------- Paul Driscoll | Office (answer)phone: (44)-171 380 7035 Dept. Biochem. & Mol. Biol. | Department fax: (44)-171 380 7193 University College London | driscoll@biochem.ucl.ac.uk From owner-structural-nmr@net.bio.net Thu Jan 23 22:00:00 1997 Path: biosci!sfu.ca!dnaugler From: dnaugler@sfu.ca (David Naugler) Newsgroups: bionet.structural-nmr Subject: Re: control of pH Date: 24 Jan 1997 08:07:52 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701241608.QAA03555@beaufort.sfu.ca> References: <1997Jan24.130323.47303@yogi.urz.unibas.ch> NNTP-Posting-Host: net.bio.net From Andrei Alexandrescu > (2) This is probably heresy (please no e-mail) but personally, I'm not a > big fan of buffers. I think protein solution at 1-2 mM concentrations > are usually quite good buffers already. Unless you have a 1-sample NMR > project you also have to consider what to do with the buffer if you want > to concentrate the sample, change the pH, add Ca2+, etc... Buffers also > have some detrimental NMR effects (described in Roberts book). I will > grant, however, that some proteins do behave pretty badly without > buffers, so I guess it depends on the protein. The biologists who gave > you the protein will probably have suggestions (e.g. PBS). Unless I was > given the world's only 4 mg sample of quadruple labeled preciouslin that > took 5 years to purify, however, I would be inclined to collect a > spectrum of the protein without added buffers. Although this topic is beyond my current level of expertise, I am inclined to accept this point of view based on my own experience. In work with an intractable peptide, a fragment of an integral membrane protein, I found that I could prepare an acceptable NMR sample by repeated dialysis against distilled water. The peptide has a tendency to aggregate above a pH 4.1. The lyophilized peptide can then be prepared as an NMR sample at pH 6.49 with SDS. In the case of a soluble protein rather than a protein subunit, SDS would not be necessary. I would think that a proper NMR sample could be prepared by the dialysis of any buffer compounds. Because of the presence of basic and acidic residues such a prepation should be self buffering and have a stable pH at least stable enough for good NMR. David Naugler Institute of Molecular Biology and Biochemistry Simon Fraser University From owner-structural-nmr@net.bio.net Thu Jan 23 22:00:00 1997 Path: biosci!A.CHEM.UPENN.EDU!eshapiro From: eshapiro@A.CHEM.UPENN.EDU ("Erik M. Shapiro") Newsgroups: bionet.structural-nmr Subject: Subscribe Date: 24 Jan 1997 13:33:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Subscribe. From owner-structural-nmr@net.bio.net Thu Jan 23 22:00:00 1997 Path: biosci!MSI.COM!mjf From: mjf@MSI.COM (Mark J Forster) Newsgroups: bionet.structural-nmr Subject: unsubscribe Date: 24 Jan 1997 13:46:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701242146.NAA26873@iris70.msi.com> NNTP-Posting-Host: net.bio.net unsubscribe From owner-structural-nmr@net.bio.net Thu Jan 23 22:00:00 1997 Path: biosci!charnwood.gb.astra.com!"/I=JM/G=Mark/S=Dixon/OU=Physical and Metabolic Sciences/" From: "/I=JM/G=Mark/S=Dixon/OU=Physical and Metabolic Sciences/"@charnwood.gb.astra.com (Mark Dixon, Tel +44 1509 644 062) Newsgroups: bionet.structural-nmr Subject: 4D in H2O Date: 24 Jan 1997 11:03:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <"91546142107991.41123.MRX*"@MHS> NNTP-Posting-Host: net.bio.net Dear Protein Spectroscopists, I have searched the literature for variants of the 4D 13C/13C HMQC-NOESY-HMQC with gradients, and I have hit upon a bit of a problem. All of the sequences I have found operate in a D2O solution, whereas I have _one_ sample in 90% H2O/10% D2O, which is not amenable to solvent exchange. Can anyone tell me why it is not possible to run this experiment in predominantly H2O ? I am prepared to consider the various tricks for water suppression, but I cannot see why the water should be a problem. Thank you for your consideration, J. Mark Dixon ASTRA CHARNWOOD mark.j.m.dixon@charnwood.gb.astra.com From owner-structural-nmr@net.bio.net Fri Jan 24 22:00:00 1997 Path: biosci!CARIBE.CHEM.UKY.EDU!cammers From: cammers@CARIBE.CHEM.UKY.EDU (Arthur Cammers) Newsgroups: bionet.structural-nmr Subject: (none) Date: 24 Jan 1997 20:08:37 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 63 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I would like to invite all who are close enough for a day trip to the University of Kentucky's Symposium on chemistry and molecular biology; the topic this year is "The Role of Combinatorial Chemistry in Drug Design." Attendence is free of charge. We will have a series of four seminars on april 8th starting at 8:30 a.m.-1:00 p.m. Check out the webpage. http://www.chem.uky.edu/seminars/naff97.html For those of you who are not www capable below are the speakers and short point-wise outlines of their talks. ------------------------------------------------- -Arno Spatola (University of Louisville) Title: "Combinatorial Chemistry: The End of Rational Drug Design? Lessons from Macrocyclic Libraries" - basic combinatorial methods - a Brief Historical Overview - a "Realistic" View of the Methods-not a Panacea - Why so much Industrial Attention? - Parallel synthesis vs. mixtures - The deconvolution problem - Combinatorial Chemistry at the University of Louisville ----- ------- -Kim Janda (Scripps Institute and CombiChem) Title: "From Combinatorics to Soluble Polymer Supported Synthesis" - Encoded Combinatorial Chemistry - Recursive Deconvolution - Liquid Phase Combinatorial Synthesis of peptides, - Peptidomimetics, and Small Molecules - Multipolymeric Reactions - Combizymes - Combinatorial Polymer Synthesis ----- ------- -Jon Ellman (University of California at Berkeley) Title: "Design, Synthesis, and Evaluation of Small Molecule Libraries" - General Philosophy for the Design of Combinatorial Schemes - Prudent Selection of Classes of Compounds for Combinatorial Approaches. - Heuristic Bioactivity of Known Drugs as Starting Points in Combinatorial approaches. - Synthetic Approaches to Maximize Molecular Diversity ----- ------- -Dr. Mario Geysen (Glaxo Wellcome Pharmaceuticals) - Dr. Geysen is credited as inventor of combinatorial synthesis. Title: "Combinatorial Chemistry: A New Paradigm for Drug Discovery." - Combinatorial Chemistry at Glaxo Wellcome. ------------------------------------------------------------------------- Arthur Cammers-Goodwin Assistant Professor of Chemistry Department of Chemistry-Organic Division University of Kentucky acgood1@pop.uky.edu http://www.chem.uky.edu/research/cammers/cammerscv.html From owner-structural-nmr@net.bio.net Sat Jan 25 22:00:00 1997 Path: biosci!MAILBOX.UQ.OZ.AU!L.Miranda From: L.Miranda@MAILBOX.UQ.OZ.AU (Leslie Miranda) Newsgroups: bionet.structural-nmr Subject: (none) Date: 25 Jan 1997 21:52:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net subscribe Les Miranda From owner-structural-nmr@net.bio.net Sun Jan 26 22:00:00 1997 Path: biosci!Merck.Com!yves_aubin From: yves_aubin@Merck.Com (Yves Aubin) Newsgroups: bionet.structural-nmr Subject: Shielding Date: 27 Jan 1997 14:50:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701272104.QAA16919@igw2> NNTP-Posting-Host: net.bio.net Dear netters, Several months ago, there was an inquiry from Istvan about shielding monitors from the stray fields of NMR magnets. In the solution I proposed (a homebuilt shield made of plywood and M6 shielding material) I mentionned the name of the company from where we got the material but not the person who helped us. I guess I wanted to shield this person from too many phone calls... In fact, I apologize because I should have acknowledged his help in choosing the right material for our needs. This person is named Vahe Ohanian. Vahe is an engineer at BCL Magnetics and was very helpful in helping me getting a good shielding material for an affordable price (compare to NUmetal). Talking with him recently, he was telling me that he is testing a new software that will enable him to model magnetic fields and allow him to do better suggestions regarding shielding design and shielding material. He told me that he would be keen in helping people in those issues. Is coordinates are: Vahe Ohanian BCL-Magnetics 5045 North Service Rd Burlington, ON, Canada, L7L 5H6 phone: (905) 335-2530 FAX: (905) 335-8474 email: magnetic@world.com I thought that it would be useful to the NMR community to know someone who knows about magnetic shielding. Hope this helps! Yves Yves Aubin Ph.D. Merck Frosst Canada Inc. P.O. Box1005 Pointe-Claire--Dorval QC, H9R 4P8 tel: (514) 428-3931 fax: (514) 428-8615 email: yves_aubin@merck.com From owner-structural-nmr@net.bio.net Sun Jan 26 22:00:00 1997 Path: biosci!rutgers!news.sgi.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!news.sprintlink.net!news-peer.sprintlink.net!howland.erols.net!surfnet.nl!highway.leidenuniv.nl!usenet From: Aart Spilt Newsgroups: bionet.structural-nmr,sci.materials,sci.med,sci.med.physics,sci.med.radiology Subject: Monel Date: Mon, 27 Jan 1997 11:23:12 +0100 Organization: Leiden University, The Netherlands Lines: 9 Message-ID: <32EC8210.2388@lkeb.medfac.leidenuniv.nl> NNTP-Posting-Host: 913azl63.azl.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win95; I; 16bit) Xref: biosci bionet.structural-nmr:1718 sci.materials:21123 sci.med:148763 sci.med.physics:5110 sci.med.radiology:8283 Hello, I'm trying to find out anything about the magnetic characteristics of Monel. It is an Alloy of Ni, C, Mn Fe, S, Si and Cu. Please give me all the information you have. I will be very thankful with every kind of information. Aart Spilt From owner-structural-nmr@net.bio.net Sun Jan 26 22:00:00 1997 Path: biosci!SHIELDING.USI.UTAH.EDU!facelli From: facelli@SHIELDING.USI.UTAH.EDU (Julio Facelli) Newsgroups: bionet.structural-nmr Subject: unsubscribe Date: 27 Jan 1997 08:03:49 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701271602.JAA03629@shielding.usi.utah.edu> NNTP-Posting-Host: net.bio.net unsubscribe ________________________________________________________________________________ Julio C. Facelli, PhD. Director Center for High Performance Computing (CHPC) 66 SSB, The University of Utah Salt Lake City, Utah 84112, USA. Phone (801)-581-7529 Fax (801)-585-5366 e-mail facelli@shielding.usi.utah.edu ________________________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Jan 27 22:00:00 1997 Path: biosci!rutgers!gatech!www.nntp.primenet.com!nntp.primenet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!portc02.blue.aol.com!newstf02.news.aol.com!audrey01.news.aol.com!not-for-mail From: harrisonat@aol.com (HarrisonAT) Newsgroups: bionet.structural-nmr Subject: Nalorac Symposium Date: 28 Jan 1997 22:49:05 GMT Organization: AOL http://www.aol.com Lines: 55 Message-ID: <19970128224900.RAA26848@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com ADVANCES IN NMR APPLICATIONS SYMPOSIUM - AGENDA You are invited to attend the 5th Annual ADVANCES IN NMR APPLICATIONS SYMPOSIUM featuring the latest developments in experimental techniques to be held prior to ENC at the Omni Rosen Hotel, Ballroom D & E, 9840 International Drive, (located next to the Clarion Plaza Hotel, site of the 38th ENC) on Sunday, March 23, 1:15 to 6:00 p.m. The Role of NMR in the Study of Drug Metabolism. John Shockcor, John Lindon and Jeremy Nicholson, Glaxo Wellcome Carbon 13, A Renaissance? Andy Roberts, Duncan Farrant and Philip Sidebottom, Glaxo Wellcome Liquid Phase Combinatorial Chemistry and Characterization of Intermediates by Routine Solution State NMR. Ron Kim, Mahua Manna, Steve Hutchins and Kevin Chapman, Merck & Company Experimental Aspects of Advanced Diffusion Measurements with PFG NMR. Donghui Wu, Aidi Chem and Charles S. Johnson, Jr., University of North Carolina Evaluation of HTS Probes and Preliminary Results for Biomacromolecular, Metabolite and Natural Product Compounds. R. Andrew Byrd and Siddhartha Sarma, NCI-FCRDC John Shockcor, Glaxo Wellcome Gary Martin, Pharmacia & Upjohn, Inc. Ron Crouch and Toby Zens, Nalorac Corporation Structure Determination of Proteins in the 30 kD Range and New Methods for Determining Long Range Order. G. Marius Clore, National Institutes of Health High Field Offers More Than High Resolution and Sensitivity. Ad Bax, National Institutes of Health Quadruple Resonance Probes - New Tools for Biological NMR. Arthur Pardi, University of Colorado Gershon Wolfe and Brian Marsden, Nalorac Corporation Advances in Solution State NMR Probe Performance. Toby Zens and Gershon Wolfe, Nalorac Corporation Application of 1H/31P/X Triple Resonance Experiments in Organometallic Chemistry. Emilio Bunel, E.I. DuPont 1H/13C/29Si Triple Resonance Heteronuclear 3D NMR of Organosilicon Compounds at Natural Abundance. Peter Rinaldi, University of Akron Please RSVP by contacting Chris Tierney, Nalorac s ENC Coordinator at NALORAC, 841-A Arnold Drive, Martinez, CA 94553. Phone: (510) 229-3501 Fax: (510) 229-1651, Email: christierney@nalorac.com From owner-structural-nmr@net.bio.net Mon Jan 27 22:00:00 1997 Path: biosci!lhc.nlm.nih.gov!biosci!Merck.Com!yves_aubin From: yves_aubin@Merck.Com (Yves Aubin) Newsgroups: bionet.structural-nmr Subject: Shielding Date: 27 Jan 1997 14:50:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701272104.QAA16919@igw2> NNTP-Posting-Host: net.bio.net Dear netters, Several months ago, there was an inquiry from Istvan about shielding monitors from the stray fields of NMR magnets. In the solution I proposed (a homebuilt shield made of plywood and M6 shielding material) I mentionned the name of the company from where we got the material but not the person who helped us. I guess I wanted to shield this person from too many phone calls... In fact, I apologize because I should have acknowledged his help in choosing the right material for our needs. This person is named Vahe Ohanian. Vahe is an engineer at BCL Magnetics and was very helpful in helping me getting a good shielding material for an affordable price (compare to NUmetal). Talking with him recently, he was telling me that he is testing a new software that will enable him to model magnetic fields and allow him to do better suggestions regarding shielding design and shielding material. He told me that he would be keen in helping people in those issues. Is coordinates are: Vahe Ohanian BCL-Magnetics 5045 North Service Rd Burlington, ON, Canada, L7L 5H6 phone: (905) 335-2530 FAX: (905) 335-8474 email: magnetic@world.com I thought that it would be useful to the NMR community to know someone who knows about magnetic shielding. Hope this helps! Yves Yves Aubin Ph.D. Merck Frosst Canada Inc. P.O. Box1005 Pointe-Claire--Dorval QC, H9R 4P8 tel: (514) 428-3931 fax: (514) 428-8615 email: yves_aubin@merck.com From owner-structural-nmr@net.bio.net Mon Jan 27 22:00:00 1997 Path: biosci!rutgers!gatech!arclight.uoregon.edu!news.sprintlink.net!news-peer.sprintlink.net!howland.erols.net!newspump.sol.net!ddsw1!news.mcs.net!not-for-mail From: W R Shefte Newsgroups: bionet.structural-nmr,sci.materials,sci.med,sci.med.physics,sci.med.radiology Subject: Re: Monel Date: Tue, 28 Jan 1997 14:10:48 -0600 Organization: Thermal Processing Solutions, Inc. Lines: 14 Message-ID: <32EE5D48.737A@mcs.net> References: <32EC8210.2388@lkeb.medfac.leidenuniv.nl> NNTP-Posting-Host: tpsi.pr.mcs.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (WinNT; I) Xref: biosci bionet.structural-nmr:1722 sci.materials:21161 sci.med:148918 sci.med.physics:5112 sci.med.radiology:8294 Aart Spilt wrote: > > Hello, > > I'm trying to find out anything about the magnetic characteristics of > Monel. It is an Alloy of Ni, C, Mn Fe, S, Si and Cu. Please give me all > the information you have. > > I will be very thankful with every kind of information. > > Aart Spilt Call Huntington (INCO) Alloys in Huntington WV....(800)334-4626 may work...otherwise check directory assistance... They are a mfg of monel inconel and incoly........ From owner-structural-nmr@net.bio.net Mon Jan 27 22:00:00 1997 Path: biosci!agate!howland.erols.net!worldnet.att.net!newsadm From: Stella Pankey Newsgroups: bionet.structural-nmr,sci.materials,sci.med,sci.med.physics,sci.med.radiology Subject: Re: Monel Date: 28 Jan 1997 00:36:30 GMT Organization: AT&T WorldNet Services Lines: 6 Message-ID: <5cjhme$2ub@mtinsc05.worldnet.att.net> References: <32EC8210.2388@lkeb.medfac.leidenuniv.nl> NNTP-Posting-Host: 207.146.160.99 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22ATT (Windows; U; 16bit) Xref: biosci bionet.structural-nmr:1721 sci.materials:21132 sci.med:148793 sci.med.physics:5111 sci.med.radiology:8290 I don't know where you live, but have you tried calling a steel distributor? I am certain a major steel distributor-( look thru the industrial yellow pages) can help you. From owner-structural-nmr@net.bio.net Tue Jan 28 22:00:00 1997 Path: biosci!agate!news.Stanford.EDU!newshub.internex.net!masters0.news.internex.net!usenet From: "Woodrow W. Conover" Newsgroups: bionet.structural-nmr Subject: Re: (none) Date: 29 Jan 1997 18:09:34 GMT Organization: Acorn NMR Lines: 42 Message-ID: <01bc0e0f$c834e7e0$3de29fce@almond> References: NNTP-Posting-Host: 206.159.226.61 X-Newsreader: Microsoft Internet News 4.70.1160 When the NMR shims behave differently with a change in the sample it is possible that the sample has some solid materials in the solution. It is not unusal for the solid material to be iron particles which can really mess up the shimming. Examine the sample with a magnifying glass under a strong light and see if you have some solid stuff in the solution. If the solution is clean, it could be a defective NMR tube but this would be very unusal. I suggest: 1. Go back to a known sample and confirm that it is working okay. If it is not then something happened to the NMR system (wrong shim values, bad shim power supply, broken NMR probe and etc). 2. Clean the NMR tube and filter the sample through glass wool into the cleaned NMR tube. Make sure there is about the sample volume of sample as in the known good sample, because end effects of a short sample can make shimming difficult. 3. If this fails try another tube. woody@acornnmr.com Arthur Cammers wrote in article ... > I was shimming the magnet (300MHz widebore) the other day with an > unknown in the probe. The unknown I ran just before I put this one in the > probe gave me beautiful line shapes with widths at half height of ~0.5Hz, > 1H. > With this sample maximizing the lock signal with the spinning > shimming parameters did not optimize the peak shape. I suspect a bad > tube. Is this behavior a sign of a untrue nmr tube? Could someone else > with experience with this aberrant shimming behavior please comment? > Thanks. > > > Arthur Cammers-Goodwin > Assistant Professor of Chemistry > Department of Chemistry-Organic Division > University of Kentucky > acgood1@pop.uky.edu > http://www.chem.uky.edu/research/cammers/cammerscv.html > > From owner-structural-nmr@net.bio.net Tue Jan 28 22:00:00 1997 Path: biosci!CARIBE.CHEM.UKY.EDU!cammers From: cammers@CARIBE.CHEM.UKY.EDU (Arthur Cammers) Newsgroups: bionet.structural-nmr Subject: (none) Date: 29 Jan 1997 08:23:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I was shimming the magnet (300MHz widebore) the other day with an unknown in the probe. The unknown I ran just before I put this one in the probe gave me beautiful line shapes with widths at half height of ~0.5Hz, 1H. With this sample maximizing the lock signal with the spinning shimming parameters did not optimize the peak shape. I suspect a bad tube. Is this behavior a sign of a untrue nmr tube? Could someone else with experience with this aberrant shimming behavior please comment? Thanks. Arthur Cammers-Goodwin Assistant Professor of Chemistry Department of Chemistry-Organic Division University of Kentucky acgood1@pop.uky.edu http://www.chem.uky.edu/research/cammers/cammerscv.html From owner-structural-nmr@net.bio.net Wed Jan 29 22:00:00 1997 Path: biosci!agate!howland.erols.net!feed1.news.erols.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.mindspring.com!uunet!in1.uu.net!138.133.17.7!amgen!usenet From: Thomas J Hoeffel Newsgroups: bionet.structural-nmr Subject: position available Date: Wed, 29 Jan 1997 16:35:33 -0800 Organization: Amgen Lines: 36 Message-ID: <32EFECD5.2781@amgen.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 6.2 IP22) Amgen, the world's largest biotechnology company, seeks the computational/analytical talents of an experienced UNIX System Administrator to support our Research Staff. In collaboration with current system administration staff the incumbent will be responsible for administration of the installed UNIX systems in Research with a focus on SGI systems and scientific applications in a graphical environment. In addition the incumbent will be responsible for recommending additonal equipment purchases, participating in Disaster Recovery Planning/Testing and assisting the strategic planning for the use of computers in Research. This position requires a BS/MS degree in the Life Sciences or Computer Science or the equivalent plus a minimum of three years of UNIX System Administration experience with a minimum of two years of IRIX experience. Familiarity with the Research Computing Environment and the ability to work in multi-disciplinary teams is a must. Additional experience with other UNIX systems (HP, SUN, DEC Alpha) is highly desirable, experience with Macintosh and/or Wintel PC's as well as VMS would be valuable. We value and encourage the diverse perspectives essential to the process of discovery. At Amgen, your accomplishments will be rewarded, our generous compensation and benefits package includes a retirement and savings plan, an on-site fitness center and three weeks vacation. For immediate consideration, mail your resume to: Amgen, Staffing Job Code: T10139, P.O. Box 2569, Thousand Oaks, CA 91319-2569. E-mail: jobs@amgen.com. Please consult our on line Job Bulletin Board at http//amgen.bio.com for information on other career opportunities available at Amgen. Principals only, please. EEO/AA Employer M/F/D/V -- *** Disclaimer: These are the opinions of the poster not Amgen Inc.*** From owner-structural-nmr@net.bio.net Wed Jan 29 22:00:00 1997 Path: biosci!OTTER.BIOCHEM.UBC.CA!mcintosh From: mcintosh@OTTER.BIOCHEM.UBC.CA (Lawrence McIntosh) Newsgroups: bionet.structural-nmr Subject: color printers Date: 29 Jan 1997 17:28:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello: I am interested in purchasing a color printer to make (ideally inexpensive and "routine") color prints of NMR spectra, structures, etc. Certainly a Codonex dye sublimination printer is the Cadillac, but not cheap. Does anyone have experience with color laser printers or "bubble-jet" printers in terms of computers (SGI or Sun), NMR programs (Felix, NMRdraw), and structure programs (postscript, hpgl, etc)? Thanks!! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Lawrence McIntosh 2146 Health Sciences Mall Departments of Biochemistry and Chemistry University of British Columbia Vancouver, BC, Canada V6T 1Z3 mcintosh@otter.biochem.ubc.ca ph: (604) 822-3341 fax: (604) 822-5227 http://www.biochem.ubc.ca/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-structural-nmr@net.bio.net Wed Jan 29 22:00:00 1997 Path: biosci!MANGO.UOREGON.EDU!strain From: strain@MANGO.UOREGON.EDU (Michael Strain) Newsgroups: bionet.structural-nmr Subject: Re: Tube Problem? Date: 30 Jan 1997 09:55:59 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 93 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net A few years ago Wilmad sent out test "turbines", a length of heavy-wall precision glass tubing into which a 5mm NMR tube could be inserted and spun by hand. Good tubes would spin easily for many seconds after an initial twist. Tubes with poor camber or concentricity would not spin well. I don't know if these test turbines are still available. Another way to check for a bad tube is using the real-time swept tuning display available on some spectrometers with the sample in the magnet. With the sample spinning, the tuning dip should be quite stable, moving side-to-side only a little. I have seen tubes so bad that the dip moved about like a prairie cyclone. Besides yielding poor NMR performance, such tubes also have the potential to damage the coil insert in the probe. --Mike ----------------------------------------------------------------------- Michael Strain strain@mango.uoregon.edu Institute of Molecular Biology desk/voice-mail: 541-346-4605 and Department of Chemistry lab: 541-346-4036 University of Oregon FAX: 541-346-5891 Eugene, OR 97403 NMR instrument rooms: 600MHz, 6-5161; 500MHz, 6-4621; 300MHz, 6-4616 ----------------------------------------------------------------------- On 30 Jan 1997, Mark J Howard wrote: > > > > > > I was shimming the magnet (300MHz widebore) the other day with an > > unknown in the probe. The unknown I ran just before I put this one in the > > probe gave me beautiful line shapes with widths at half height of ~0.5Hz, > > 1H. > > With this sample maximizing the lock signal with the spinning > > shimming parameters did not optimize the peak shape. I suspect a bad > > tube. Is this behavior a sign of a untrue nmr tube? Could someone else > > with experience with this aberrant shimming behavior please comment? > > Thanks. > > I would agree with Woodrow Conover and acertain whether the fault > definately lies with the sample or spectrometer. As an alternative to > using glass wool to filter your sample, you can get microfilters from > Millipore or Whatman which will filter down past 0.2um. There are > filters specially designed for coping with small sample volumes without > excessive loss due to liquid absorption into the filter. > > On the point of faulty NMR tubes, I have seen this before. I had a > protein sample which just would not shim well and as a result the line > shape and presaturation was terrible. I checked the spectrometer with a > sample that I knew was ok. So I transfered the original to a second tube > and all my problems were cured. I did take a very close look at the > 'faulty'NMR tube and I found a very small (~0.2mm) scratch on the outside > surface of the tube just at the position where the probe coils would be, > so I put the problem down to that. However, I then had problems with the > rest of the tubes that came boxed with the original problem tube. They > all would not shim well etc.., but when samples were placed in tubes from > another batch or I knew were ok, they were fine. I made sure nothing > had been accidently introduced during the washing process before they were > used, but they still were not shimming well. I could not see any > visible fault on the other tubes unlike the one that originally caused > the problem. In the end, I sent the box back to the manufacturer and got > a new box sent free so I put the experience down to a bad batch of > tubes. So if you do suspect a tube of being faulty, it may be wise to > isolate all tubes from the same box and try a tube you know to be sound if > the problem occurs with tubes from the same batch. > > > Mark Howard > > ******************************************************** > Dr. Mark Howard > Protein NMR Spectroscopy | > Dept. of Biochemistry | > University of Cambridge || | > Tennis Court Road | || | | > Cambridge, UK. || | ||| | | > CB2 1QW ____|||||___/\__||||||||___|_|_ > > Tel: (01223) 333662 Fax: (01223) 333661 > E-mail: mjh2@mole.bio.cam.ac.uk > ******************************************************** > > > > > > From owner-structural-nmr@net.bio.net Wed Jan 29 22:00:00 1997 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: color printers/NMR programs Date: 30 Jan 1997 05:48:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net This comment is not about color printers in particular, only a note on the sideline about NMR programs mentioned by Lawrence ("...NMR programs (Felix, NMRdraw)..."). Beside Felix and nmrPipe/nmrDraw I can truly recommed NMRView for visualization and spectrum analysis, which complements the other two and takes direct input from each. In addition, it generates plots both in postscript and hpgl format now. It is a free software. Whoever is interested please, take a look at: http://www.ges.com/nmrview/ or contact Bruce Johnson (bruce_johnson@merck.com). 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 From owner-structural-nmr@net.bio.net Wed Jan 29 22:00:00 1997 Path: biosci!rutgers!gatech!news.sprintlink.net!news-peer.sprintlink.net!arclight.uoregon.edu!news.bbnplanet.com!su-news-hub1.bbnplanet.com!csn!nntp-xfer-1.csn.net!csn!nntp-xfer-2.csn.net!tali.UCHSC.edu!chris From: "Joel Guthridge, Ph.D." Newsgroups: bionet.structural-nmr Subject: Isotopic labeling of proteins produced in Pichia Date: Thu, 30 Jan 1997 09:43:35 -0700 Organization: Div. of Rheumatology, Univ. of Colorado Health Sci. Ctr. Lines: 13 Message-ID: <32F0CFB7.23AC@uchsc.edu> Reply-To: Joel.Guthridge@uchsc.edu NNTP-Posting-Host: handel.uchsc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Does anyone have some information on isotopic labeling of proteins produced in Pichia? I'm looking for both some protocols to use as starting points and information on sources of labeled reagents that will work well in the methanol induction of protein expression in Pichia. Thanks, Joel Guthridge Div. of Rheumatology, Univ. of Colorado Health Sci. Ctr. Denver, CO email: Joel.Guthridge@uchsc.edu From owner-structural-nmr@net.bio.net Wed Jan 29 22:00:00 1997 Path: biosci!rutgers!gatech!arclight.uoregon.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.maxwell.syr.edu!newsfeeds.sol.net!nntp.uio.no!news.kth.se!tybalt.admin.kth.se!celsiustech.se!seunet!news2.swip.net!mailgate.astra.com!usenet From: Gunnar Gronberg Newsgroups: bionet.structural-nmr Subject: Position available Date: Thu, 30 Jan 1997 11:36:03 -0800 Organization: Astra Draco AB Lines: 40 Message-ID: <32F0F823.2AEC@draco.se.astra.com> NNTP-Posting-Host: dpggg.draco.se.astra.com Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 2.0 (Win16; I) NMR Specialist Department of Medicinal Chemistry ASTRA DRACO Lund, Sweden The Department of Medicinal Chemistry is involved in the creation of new drugs. New chemical compounds are synthesised and their structures characterised. Properties essential to the biological effects are investigated and optimised. The department consits of a number of organic chemistry groups orientated towards projects in different phases of development together with special competence in the areas of Combinatorial Chemistry, Radio-chemistry, NMR, Computational Chemistry and Information Technology/System Management. The NMR facilitiy consists three high resolution spectrometers: 300, 400 and 500 MHz (Varian). The Department of Medicinal Chemistry invites applications for a position as an NMR Chemist to perform structural/conformational as well as physical chemistry related NMR investigations of drug molecules and their interactions with target molecules and pharmaceutical preparations. The primary interactions will be with Medicinal Chemists and Computational Chemists but also with other disciplines within ASTRA DRACO. Other responsibilities include maintenance of the NMR systems, development of automation routines as well as training and consultation with chemists. Candidates are expected to posses a PhD in Physical Chemistry or Organic Chemistry with NMR experience from peptides, bio membranes, protein ligand interactions, diffusion measurements etc. Experience of UNIX administration, pulse programming and maintenance of NMR systems are important qualifications. Further information is available directly from: Gunnar Grönberg +46 46 33 70 65 email: gunnar.gronberg@draco.se.astra.com http://www.astra.com Please submit application, curriculum vitae and letters of recommendation before February 10, 1996 to: Personalavdelningen, Lena Ask, Astra Draco AB, Box 34, 221 00 Lund, Sweden From owner-structural-nmr@net.bio.net Wed Jan 29 22:00:00 1997 Path: biosci!agate!howland.erols.net!surfnet.nl!swidir.switch.ch!scsing.switch.ch!elna.ethz.ch!usenet From: Reto Koradi Newsgroups: bionet.structural-nmr Subject: Re: color printers Date: Thu, 30 Jan 1997 11:18:00 +0100 Organization: Swiss Federal Institute of Technology (ETHZ) Lines: 36 Message-ID: <32F07558.4346@mol.biol.ethz.ch> References: NNTP-Posting-Host: odin.ethz.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; SunOS 5.4 sun4d) To: Lawrence McIntosh Lawrence McIntosh wrote: > Does anyone have experience with color laser > printers or "bubble-jet" printers in terms > of computers (SGI or Sun), NMR programs (Felix, NMRdraw), > and structure programs (postscript, hpgl, etc)? We frequently use Canon color laser printers (CLC 500), and they are excellent. But these are large units, suited for central printing facilities. We also have an Apple Color LaserWriter 12/600 PS available. The output quality is fine, but it happens that it refuses to print PostScript files that other printers accept. It also completely broke down once. These color laser printers are getting cheaper, you can probably get something in that class for around $6000. Tektronix has an excellent reputation for their color printers, in a similar price class. About ink jet printers, I haven't seen any recently. But I'm told that they have improved quite dramatically, and have very good output quality. They're typically slow. Good brands there are Epson and HP. With all color printers, you should not only look at the price for buying it, but also the costs per page. Ink jet printers need frequent ink refills, and might need special paper for good results. Laser printers eat toners. All these things tend to be quite expensive. The more expensive (laser) printers will probably come with PostScript support, and that's what most programs produce. Ink jet printers normally don't understand PostScript, or only as an added option. You can either go the free (Ghostscript) way, or pay for commercial solutions, like Impressario by SGI. -- Reto Koradi (kor@mol.biol.ethz.ch, http://www.mol.biol.ethz.ch/~kor) From owner-structural-nmr@net.bio.net Wed Jan 29 22:00:00 1997 Path: biosci!MOLE.BIO.CAM.AC.UK!mjh2 From: mjh2@MOLE.BIO.CAM.AC.UK (Mark J Howard) Newsgroups: bionet.structural-nmr Subject: Tube Problem? Date: 30 Jan 1997 00:08:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 61 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net > I was shimming the magnet (300MHz widebore) the other day with an > unknown in the probe. The unknown I ran just before I put this one in the > probe gave me beautiful line shapes with widths at half height of ~0.5Hz, > 1H. > With this sample maximizing the lock signal with the spinning > shimming parameters did not optimize the peak shape. I suspect a bad > tube. Is this behavior a sign of a untrue nmr tube? Could someone else > with experience with this aberrant shimming behavior please comment? > Thanks. I would agree with Woodrow Conover and acertain whether the fault definately lies with the sample or spectrometer. As an alternative to using glass wool to filter your sample, you can get microfilters from Millipore or Whatman which will filter down past 0.2um. There are filters specially designed for coping with small sample volumes without excessive loss due to liquid absorption into the filter. On the point of faulty NMR tubes, I have seen this before. I had a protein sample which just would not shim well and as a result the line shape and presaturation was terrible. I checked the spectrometer with a sample that I knew was ok. So I transfered the original to a second tube and all my problems were cured. I did take a very close look at the 'faulty'NMR tube and I found a very small (~0.2mm) scratch on the outside surface of the tube just at the position where the probe coils would be, so I put the problem down to that. However, I then had problems with the rest of the tubes that came boxed with the original problem tube. They all would not shim well etc.., but when samples were placed in tubes from another batch or I knew were ok, they were fine. I made sure nothing had been accidently introduced during the washing process before they were used, but they still were not shimming well. I could not see any visible fault on the other tubes unlike the one that originally caused the problem. In the end, I sent the box back to the manufacturer and got a new box sent free so I put the experience down to a bad batch of tubes. So if you do suspect a tube of being faulty, it may be wise to isolate all tubes from the same box and try a tube you know to be sound if the problem occurs with tubes from the same batch. Mark Howard ******************************************************** Dr. Mark Howard Protein NMR Spectroscopy | Dept. of Biochemistry | University of Cambridge || | Tennis Court Road | || | | Cambridge, UK. || | ||| | | CB2 1QW ____|||||___/\__||||||||___|_|_ Tel: (01223) 333662 Fax: (01223) 333661 E-mail: mjh2@mole.bio.cam.ac.uk ******************************************************** From owner-structural-nmr@net.bio.net Thu Jan 30 22:00:00 1997 Path: biosci!agate!newsgate.cuhk.edu.hk!news.glink.net.hk!uunet!in2.uu.net!192.89.123.24!nntp.inet.fi!news.csc.fi!ousrvr3.oulu.fi!ernst.oulu.fi!not-for-mail From: eha@ernst.oulu.fi (Esa Haapaniemi) Newsgroups: bionet.structural-nmr Subject: Re: color printers Date: 31 Jan 1997 12:50:26 GMT Organization: University of Oulu Lines: 20 Distribution: world Message-ID: <5cspqi$48j@ousrvr3.oulu.fi> References: NNTP-Posting-Host: ernst.oulu.fi Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Lawrence McIntosh (mcintosh@OTTER.BIOCHEM.UBC.CA) wrote: : Does anyone have experience with color laser : printers or "bubble-jet" printers in terms : of computers (SGI or Sun), NMR programs (Felix, NMRdraw), : and structure programs (postscript, hpgl, etc)? Yes and no. We have used several B&W and colour printers here, but normally they are connected to PCs. Worst problem with getting them to work on workstations is the need of drivers. So in our department files are moved to PC and printed from there (in need). With that we can use all kinds of possible printers/plotters/diaprinters/... BTW Epson is currently working on 1400 dpi colour bubblejet that should be out on March. The Pro model should handle postscript and network printing and might be suitable for workstations as well. Esa Haapaniemi University of Oulu Department of Chemistry Finland From owner-structural-nmr@net.bio.net Thu Jan 30 22:00:00 1997 Path: biosci!SCRIPPS.EDU!georges From: georges@SCRIPPS.EDU (Georges Mer) Newsgroups: bionet.structural-nmr Subject: subscribe Date: 30 Jan 1997 18:15:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <32F154E9.41C67EA6@scripps.edu> NNTP-Posting-Host: net.bio.net subscribe From owner-structural-nmr@net.bio.net Fri Jan 31 22:00:00 1997 Path: biosci!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!warwick!lyra.csx.cam.ac.uk!bioc.cam.ac.uk!wb104 From: wb104@bioc.cam.ac.uk (Wayne Boucher) Newsgroups: bionet.structural-nmr,sci.techniques.mag-resonance Subject: Azara 2.0 release Date: 1 Feb 1997 10:33:27 GMT Organization: Somewhere in the University of Cambridge Lines: 15 Distribution: world Message-ID: <5cv65n$lro@lyra.csx.cam.ac.uk> NNTP-Posting-Host: giza.bioc.cam.ac.uk Xref: biosci bionet.structural-nmr:1739 sci.techniques.mag-resonance:1966 Azara (v2.0) is a suite of programs to process and view NMR data, including 1D, 2D and 3D maximum entropy processing (in an ND data set). The distribution can be obtained via anonymous ftp at ftp.bio.cam.ac.uk in the directory pub/azara, or via the Web at www.bio.cam.ac.uk/azara. The distribution comes with either the source code plus executables or with just the executables (compiled for Silicon Graphics machines). Several of the programs have been designed so that they may be used in conjunction with Per Kraulis' program Ansig. In particular, the data structures are consistent between Ansig and Azara. The programs were developed initially at, and now in conjunction with, the Department of Biochemistry at the University of Cambridge.