From owner-proteins@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!gatech!news.fsu.edu!usenet From: Jayne Williams Newsgroups: bionet.molbio.proteins Subject: Protein Expression Screening Date: Tue, 02 Jul 1996 08:52:49 -0400 Organization: Institute of Molecular Biophysics Lines: 23 Message-ID: <31D91BA1.41C6@sb.fsu.edu> NNTP-Posting-Host: met.sb.fsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) Hello Everyone, I am a beginner and there is probably a simple answer to my question, yet I have been unsuccessful in finding anything in the literature on this: I have transfected a plasmid (pMAMneo) into CHO cells (Lec-1 line), and will soon induce expression of my protein (Thy-1: a cell surface glycoprotein, 111 aa). I have already verified the presence of the gene by PCR. I'd like to quickly screen for protein expression by comparing SDS-PAGE of cell lysates (induced vs noninduced). My question: how much lysate (very roughly, how many cells) must I load to see my protein on the gel? (Of course, I have no idea at this point what level of expression I will get, so am only looking for a reasonable starting point.) Any suggestions/references very much appreciated. (E-mail replies equally appreciated). Jayne Williams Institute of Molecular Biophysics Williams@sb.fsu.edu From owner-proteins@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!cs.utexas.edu!newshost.convex.com!newsgate.duke.edu!kwatra2.mc.duke.edu!user From: edroush@acpub.duke.edu (Eric Roush) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Expression Screening Date: Tue, 02 Jul 1996 16:51:01 -0400 Organization: rlm:SMoRDFC Lines: 51 Distribution: world Message-ID: References: <31D91BA1.41C6@sb.fsu.edu> NNTP-Posting-Host: kwatra2.mc.duke.edu In article <31D91BA1.41C6@sb.fsu.edu>, Jayne Williams wrote: > Hello Everyone, > > I am a beginner and there is probably a simple answer to my question, > yet I have been unsuccessful in finding anything in the literature on > this: > > I have transfected a plasmid (pMAMneo) into CHO cells (Lec-1 line), and > will soon induce expression of my protein (Thy-1: a cell surface > glycoprotein, 111 aa). I have already verified the presence of the gene > by PCR. > > I'd like to quickly screen for protein expression by comparing SDS-PAGE > of cell lysates (induced vs noninduced). My question: how much lysate > (very roughly, how many cells) must I load to see my protein on the gel? > (Of course, I have no idea at this point what level of expression I will > get, so am only looking for a reasonable starting point.) > > Any suggestions/references very much appreciated. (E-mail replies > equally appreciated). My suggestion would be, if possible, obtain an antibody against Thy-1 and do a Western blot. Using a quick ballpark estimate for your problem, assuming 100,000 molecules/cell, 1 million cells, and a MW of 30,000 for the product (I'd estimate that Thy-1 is around 15,000 given the number of amino acids it has, but there's no way that I am aware of to estimate how much glycosylation has been added to your protein): (100,000 molecules/cell) (1 x 10^6 cells) (30,000 g/mole) ---------------------------------------------------------- (6.02 x 10^23 molecules/mole) gives me roughly 5 ng of your target molecule. I think it's safe to say that you won't see that against a whole cell lysate using standard protein detection techniques. You might be able to see your protein by isolating the plasma membranes and only run those on your gel, which would reduce your background protein levels at least 10-fold, but there would still be no guarantee of identifying your protein of interest. -- Eric Roush Phil Niekro for the HOF! edroush@acpub.duke.edu (Net and Real!) also coache@aol.com Send your net ballot to vinay@baseball.org ------------------------------------------------------ Maddux/Glavine in 1996! It's Time for a Change-Up! From owner-proteins@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!news.ac.net!news.cais.net!news.abs.net!cs.umd.edu!news.umbc.edu!news.ums.edu!umabnet.ab.umd.edu!umabnet.ab.umd.edu!mremingt From: "Mary P. Remington" Newsgroups: bionet.molbio.proteins Subject: Sulfur 35 labeling reagent-Amersham Date: Tue, 2 Jul 1996 11:33:11 -0400 Organization: University of Maryland at Baltimore Lines: 4 Message-ID: NNTP-Posting-Host: umabnet.ab.umd.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone have any experience with Amersham's SLR? We are using it in our lab and the specific activity is much lower than what is expected. Any help with this matter would be greatly appreciated. Regards, Mary From owner-proteins@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!geraldo.cc.utexas.edu!netnews.uthscsa.edu!usenet From: Jeff Seale Newsgroups: bionet.molbio.proteins,bionet.microbiology,bionet.immunology,sci.research,bionet.general Subject: Chaperonin Web page back up Date: Tue, 02 Jul 1996 16:56:50 -0700 Organization: Univ. of Texas Health Science Center @ San Antonio Lines: 12 Message-ID: <31D9B742.53B2@bioc02.uthscsa.edu> NNTP-Posting-Host: horowitz-lab1.uthscsa.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win16; I) Xref: biosci bionet.molbio.proteins:8238 bionet.microbiology:6492 bionet.immunology:9246 sci.research:9181 bionet.general:22608 The Chaperonin Web Page is now back up and running after a network glitch somwhere just down the line from here. The latest addition is a New Paper Alert - located in the Chaperonin Library. You can check it out at: http://bioc09.uthscsa.edu/~seale/Chap/chap.html Leave your comments in the guestbook. And again, if someone would like to help expand the coverage to other families of heat shock proteins, just email me. -Jeff From owner-proteins@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!Norway.EU.net!EU.net!main.Germany.EU.net!Germany.EU.net!howland.reston.ans.net!spool.mu.edu!usenet.eel.ufl.edu!tank.news.pipex.net!pipex!oleane!jussieu.fr!cea.fr!news From: Falson Newsgroups: bionet.molbio.proteins Subject: Re: SDS-PAGE of membrane protein Date: Tue, 02 Jul 1996 18:44:18 +0200 Organization: CEA Lines: 16 Message-ID: <31D951E2.590C@verlaine.saclay.cea.fr> References: <31C5B99F.2117@qms1.life.uiuc.edu> NNTP-Posting-Host: verlaine.saclay.cea.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 2.01 (Win95; I) hi hui-chu chang, I'm working on a calcium transporting ATPase, which is a membrane protein with probably 10 membrane spans. recently, we had this type of problem which was resolved by mixing urea SDS and bMe in a special way : 15 µl of a mixture containing 6.7 % of SDS and 4.6 M of bMercaptoethanol (in fact it corresponds to a 2:1 mix solution of 10%SDS and 14.3M bMe (stock solution)) is mixed to 40 mg of urea (at this point, the urea is not completly dissolved); then 40 µl of sample is added and, after 1 min vortexing at room temperature to dissolve urea, the mix is heated for 70 sec at 100 °C. THe concentration of urea is approx. 8M. If you want, you can see this note in Anal. Biochem. 1996 236, 363-364 . However, it seems when I see what you describes that the problem can come from the reducing agent that you use, I'm afraid it is too old. pierre falson falson@verlaine.saclay.cea.fr From owner-proteins@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!ra.nrl.navy.mil!news.math.psu.edu!news.cse.psu.edu!uwm.edu!news-res.gsl.net!news.gsl.net!sgigate.sgi.com!esiee.fr!jussieu.fr!citi2.fr!federici.cochin.inserm.fr!user From: federici@icgm.cochin.inserm.fr (Federici) Newsgroups: bionet.molbio.proteins Subject: Re: Protein elution from SDS-PAGE gel ?? Date: 3 Jul 1996 10:47:46 GMT Organization: ICGM CNRS UPR415 Lines: 22 Message-ID: References: <4r61f8$9mr@worak.kaist.ac.kr> NNTP-Posting-Host: federici.cochin.inserm.fr X-Newsreader: Yet Another NewsWatcher F2.0 In article (Dans l'article) <4r61f8$9mr@worak.kaist.ac.kr>, "Kernee H. Chang" wrote (écrivait) : > Dear Netters > > I'm trying to elute my glycoprotein from 1.5mm PAGE gel. > > Could you tell me the best method for the case ? > > And also the yield of the protein is important. > > > Thank you very much.... electroelution combined with recuperation on hydroxyapatite is an efficient method. This experiment is carried out on acrylamide gel polymerized into tubes. First of all, prepare a tube containing a gel filling about the third of the total volume; then add 0.5 ml of hydroxyapatite washed by the buffer of electrophoresis (SDS, Na P...); cut the gel containing the band you intend to elute, into small pieces, and put these pieces onto hydroxyapatite. fter electrophoresis, recuperate hydroxyapatite and elute the protein using 0.5M NaP, SDS 0.2%, DTT. From owner-proteins@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!martinlab From: klenchin@macc.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: % of ammonium sulphate - PKC precipitation? Date: 3 Jul 1996 14:28:43 GMT Organization: UW-Madison Lines: 10 Message-ID: <4re02r$h92@news.doit.wisc.edu> NNTP-Posting-Host: martinlab.biochem.wisc.edu X-Newsreader: News Xpress Version 1.0 Beta #4 Xref: biosci bionet.molbio.methds-reagnts:46466 bionet.molbio.proteins:8242 Hi, Could anyone give me rough idea about typical % of saturation of AS solution at which PKC precipitates? The conditions would be ~ 5 mg/ml of total protein, pH 7.5. Thanks, - Dima From owner-proteins@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!cok-mac2.gen.cam.ac.uk!user From: c.okane@gen.cam.ac.uk (cok@mole.bio.cam.ac.uk) Newsgroups: bionet.molbio.proteins Subject: phage promoter + AUG vectors for IVTT? Date: Wed, 03 Jul 1996 13:22:46 +0000 Organization: Dept. of Genetics, University of Cambridge, UK Lines: 15 Message-ID: NNTP-Posting-Host: cok-mac2.gen.cam.ac.uk X-Newsreader: Value-Added NewsWatcher 2.0b19.1+ We'd like to express 35S-labelled protein domains in vitro. They don't have their own ATG initiation codon. Can anyone recommend any vector series with a standard phage promoter (T3, T7, SP6) and an ATG which is known to work efficiently in a system like Promega TNT, followed by a multiple cloning site - preferably there should be three vectors with the polylinker staggered to allow use of all three reading frames with the same restriction sites. Thanks, Cahir c.okane@gen.cam.ac.uk -- Cahir O'Kane, Dept of Genetics, Univ. of Cambridge, UK cok@mole.bio.cam.ac.uk From owner-proteins@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!newshub.csu.net!csulb.edu!drivel.ics.uci.edu!news.service.uci.edu!waldo.path.uci.edu!user From: ytang@uci.edu (yi-quan tang) Newsgroups: bionet.molbio.proteins Subject: need peptide sequencing by ms-ms service Date: 3 Jul 1996 21:45:04 GMT Organization: Pathology, UC Irvine Lines: 2 Message-ID: NNTP-Posting-Host: waldo.path.uci.edu Please let me know which lab. doing this service in USA. Thanks. My e-mail: ytang@uci.edu From owner-proteins@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!NEWSSUN.MED.MIAMI.EDU!vslepak From: vslepak@NEWSSUN.MED.MIAMI.EDU ("Vladlen Z. Slepak") Newsgroups: bionet.molbio.proteins Subject: Postdoctoral position in University of Miami Sc. Med. Date: 3 Jul 1996 15:15:10 -0700 Organization: University of Miami Medical School Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <31DAF01A.6AAF@newssun.med.miami.edu> Reply-To: vslepak@newssun.med.miami.edu NNTP-Posting-Host: net.bio.net POSTDOCTORAL POSITION is available immideately at the UNIVERSITY OF MIAMI SCHOOL OF MEDICINE. Successful candidate will join a new, well-funded and equipped lab studying G protein-mediated signal transduction mechanisms. Projects involve protein isolation from native sources, mutagenesis and heterologous expression of proteins, kinetic analysis of protein-protein interactions using Surface Plasmon Resonance (BIAcore instrument) and other approaches. Background in the area of cellular signaling and expertise in protein-protein interactions and molecular biology is preferred, but is not as essential as strong commitment to career in science and ability to work independently. Future promotion to a more independent, research-track faculty position and obtaining technical support is achievable. Salary is negotiable and commensurate with experience. Send CV and three references to: Dr. V. Z. Slepak, Department of Pharmacology, University of Miami School of Medicine, 1600 N.W. 10th ave. R-189 Miami, Fl 33136. fax: (305) 243-4555, E.mail From owner-proteins@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!Norway.EU.net!nntp.uio.no!news2.interlog.com!news.sprintlink.net!news-fw-12.sprintlink.net!news2.noc.netcom.net!noc.netcom.net!nntp!nandu From: nandu@curagen.com (Krishnan Nandabalan) Newsgroups: bionet.molbio.proteins Subject: Research Scientist- Molecular Biology-Signal Transduction Date: Wed, 3 Jul 96 14:40:16 GMT Organization: CuraGen Corporation Lines: 57 Message-ID: NNTP-Posting-Host: 199.183.38.43 X-NETCOM-Date: Wed Jul 03 12:36:16 PM PDT 1996 X-Newsreader: VersaTerm Link v1.1.1 CuraGen Corporation 322 East Main St. Branford, CT 06405 (203) 481 1104 (203) 481 1102 - Fax CuraGen Corporation is a dynamic and rapidly expanding biotechnology company on a mission to systematically extract from the human genome those disease related genes for which therapeutics can be successfully designed. CuraGen is pioneering a novel systematic approach to developing pharmaceuticals for treating cancer. In pursuit of its interdisciplinary approach, CuraGen has assembled a research team with expertise in molecular biology, biochemistry, statistical mechanics, computational methods, mathematics, nanofabrication, and spectroscopy. Close ties with several major academic laboratories complement our own resources and facilities. We seek creative and motivated individuals with the dedication and ambition to succeed in an entrepreneurial setting. Compensation package includes opportunity for equity participation. Extensive collaborations with Yale University (12 minutes away), Yale Comprehensive Cancer Center and Cornell University provide excellent opportunities for academic collaborations and publication. CuraGen is a recent winner of two coveted Advanced Technology Program awards from the National Institute for Standards and Technology, and also receives funding from the National Cancer Institute and the National Center for Human Genome Research. CuraGen is an EEO/AA employer. TITLE: Research Scientist, Molecular Biology-Signal Transduction CuraGen is seeking to hire a Research Scientist in Molecular Biology-Signal Transduction. Initially, the successful candidate will work closely with senior scientists. There is room for internal advancement. The successful candidate will have an intimate knowledge of the Signal Transduction phenomena and its relevance to disease processes as evidenced by publications and /or patents. In addition the candidate will have experience in more than one of the following: cell-based assays to monitor gene-expression, in vitro assays to monitor protein-protein interactions, RNA isolation, cDNA synthesis, construction of cDNA and genomic libraries, normalization of cDNA libraries etc. Applications with resume and a list of three references should be addressed to Dept. of Functional Genomics, CuraGen Corporation, 322 East Main St., Branford, CT 06405. Fax: (203) 481 1102. Applications with resume and a list of three references should be addressed to Dept. of Functional Genomics, CuraGen Corporation, 322 East Main St., Branford, CT 06405. Fax: (203) 481 1102. Krishnan Nandabalan Senior Research Scientist CuraGen Corporation 322 E. Main St. Branford, CT 06405. Fax: (203) 481 1102 From owner-proteins@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!news-stk-200.sprintlink.net!news.sprintlink.net!news-stk-11.sprintlink.net!coopnews.coop.net!boulder.earthnet.net!usenet From: James Stiehr Newsgroups: bionet.general,bionet.cellbiol,bionet.cellbiol.cytonet,bionet.diagnostics,bionet.immunology,bionet.molbio.methds.reagnts,bionet.molbio.proteins,bionet.neuroscience Subject: Re: FDA TO REGULATE RESEARCH ANTIBODIES Date: Wed, 03 Jul 1996 08:38:29 -0700 Organization: Affinity BioReagents, Inc. Lines: 78 Message-ID: <31DA93F5.464B@bioreagents.com> References: <31D7FA26.377@bioreagents.com> <4ra9jd$ivu@optional.cts.com> NNTP-Posting-Host: slip1.earthnet.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Xref: biosci bionet.general:22615 bionet.cellbiol:5039 bionet.cellbiol.cytonet:593 bionet.diagnostics:950 bionet.immunology:9251 bionet.molbio.proteins:8244 bionet.neuroscience:14768 Bryan Kiehl wrote: > > It is my understanding that the FDA does now require that reagents > that may be used for diagnostic uses (e.g., cancer markers, infectious > disease detection, etc.) are to be regulated. > > However, it also appears the amount of regulation is minimal. They > require that the manufacturer follow good manufacturing practices. > These include proper labeling and documentation during the > manufacturing processes, as well as being able to field customer > complaints and document how you deal with these. The regs also require > that the company submit a notifcation with proposed labeling before > marketing the product. This is then reviewed by the FDA for truth and > accuracy. > > For example, is the reagent is an antibody, then one must identify > what the antibody recognizes and be sure that all claims are accurate. > If this is only a reagent and not a kit, there can be no performance > claims. These reagents are intended for the user to establish the > assay method. The user (e.g., pathologist, laboratory) must "validate" > that the assay using this reagent performs well enough for diagnostic > uses. The end user must also assure continued performance. > > If the manufacturer puts the reagent into kits or claims diagnostic > performance, then he needs to provide data to the FDA. Otherwise, he > mostly needs to just assure that the reagents are made well and > packaged without error. > > For most smaller companies this may seem a burden at first, but > similar regs are being established in Europe under ISO regs. Since many of the companies which provide reagetns are small companies, it becomes a major issue. Look in linscott's directory, you don't see many large companies with the deep pockets necessary to manage these regulations. GMP sounds nice and easy, but if you look at the actual requirements, they are not trivial. If people would like to see it, I would be happy to add it to the web site that has been created for this purpose: http://www.earthnet.net/~affinity/fda. > I also doubt that true research reagents that are never or rarely > used in the clniical realm will ever be regulated. Remember, the FDA > can only come down on a company that sells these reagents to groups > that really do use them for human diagnostics. It is unfortunate that a company cannot decide for itself that it does not want to be a diagnostic company and offer "dual use" products which can be identified as not appropriate for diagnostic use. There are federal consumer laws making it illegal to use a proguct contrary to its labeled use, however, pathologists (and other physicians) have managed to exempt themselves from these laws. Unfortunately, this leaves the supplier responsible for the use of its product. When you consider that most research reagents are sold to universities and ordered through the purchasing dept. to be delivered to "receiving" how can a company know who and how its product is used? What about the situation where today we sell a product that is not clinically relevant, but a paper comes out tomorrow saying it is? In that case, we have developed a market for a "true research reagent' that is discovered to have a new application. We still don't want to be a diagnostic company, yet at that point, according the the regs. we're selling an IVD and must therefore either conform to the regs and incur all of the marginal expenses for that single antibody (most of which only sell $5000-$10,000/year) or remove them from the market. Why can't we all be responsible suppliers and consumers (shades of Rodney King). If FDA, CLIA, suppliers and consumers could all agree to recognize that a product labeled "For In Vitro Experimental Use Only, Not for Diagnostic Use" really should not be used in any kind of clinical setting, then these would not need to be regulated by FDA. If CLIA found pathologists using them in their lab, sanctions could be applied. If FDA found suppliers promoting them for clinical use, appropriate disciplinary action could be taken. Honest companies who supply the research market with important research tools could go about their business either making quality products which their customers are happy with or going out of business if they are not - no harm done to anyone. James Stiehr Affinity Bioreagents, Inc. From owner-proteins@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!spool.mu.edu!torn!ccshst05.uoguelph.ca!ccshst01!wyu From: wyu@uoguelph.ca (Wenjin Yu) Newsgroups: bionet.molbio.proteins Subject: Protein Software Date: 3 Jul 1996 22:15:20 GMT Organization: University of Guelph Lines: 7 Message-ID: <4rerdo$brc@ccshst05.uoguelph.ca> NNTP-Posting-Host: ccshst01.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] Dear friends on the net, I'm wondering if there is a software which can determine and make graphics of 3D structure of a protein based on its amino acid sequence. Thank you in advance for your reply. Wenjin Yu From owner-proteins@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!usc!newshub.cts.com!usenet From: b3748@cts.com (Bryan Kiehl) Newsgroups: bionet.general,bionet.cellbiol,bionet.cellbiol.cytonet,bionet.diagnostics,bionet.immunology,bionet.molbio.methds.reagnts,bionet.molbio.proteins,bionet.neuroscience Subject: Re: FDA TO REGULATE RESEARCH ANTIBODIES Date: Wed, 03 Jul 1996 23:09:01 GMT Organization: CTS Network Services Lines: 21 Message-ID: <4reu4j$b9u@optional.cts.com> References: <31D7FA26.377@bioreagents.com> <4ra9jd$ivu@optional.cts.com> <31DA93F5.464B@bioreagents.com> NNTP-Posting-Host: kiehl.cts.com Xref: biosci bionet.general:22621 bionet.cellbiol:5047 bionet.cellbiol.cytonet:594 bionet.diagnostics:951 bionet.immunology:9257 bionet.molbio.proteins:8248 bionet.neuroscience:14774 We are a small company too, but are in the diagnostics business and not the research business. I do understand the requirements to comply with GMP, but you might be surprised how this might not be so bad. I also wonder whether you will be in trouble with FDA if you receive a letter from the user that absolutely assures that the reagent you sell them will not be used for diagnostic purposes. Does this allow you to sell without FDA clearance? I'm not sure. If there are any FDA types that wish to comment, this might help some people. I also suggest that this may be an appropriate forum to disucss what GMP really does mean. There are alot of opinions, but the acutual practices may not be so terrible. Any comments? Bryan Kiehl GenBio GenBio@msn.com San Diego, CA From owner-proteins@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!swrinde!tank.news.pipex.net!pipex!oleane!jussieu.fr!centre.univ-orleans.fr!univ-tours.fr!univ-tours.fr!MOREAUT From: moreaut@univ-tours.fr Newsgroups: bionet.molbio.proteins Subject: 2nd Announcement: PROLYSIS Web server Date: 3 Jul 1996 14:45:34 GMT Organization: Universite de TOURS - France Lines: 21 Message-ID: <4re12e$k93@ronsar.univ-tours.fr> Reply-To: moreaut@univ-tours.fr NNTP-Posting-Host: balzac.univ-tours.fr PROLYSIS is a Web server intended as a Web resource for proteases and protease inhibitors. This server contains informations of general interest and images, as well as useful links to other Internet resources related to proteases and their inhibitors. Suggestions and/or comments as well as material that can be added in PROLYSIS are welcomed. Please point your browser at: http://prolysis.phys.univ-tours.fr/Prolysis *------------------------------------------------------------------* | Dr. Thierry MOREAU | | Laboratoire d'Enzymologie et Chimie des Proteines | | 2bis, Bd Tonnelle Phone: (33) 47 36 62 06 | | 37032 TOURS cedex Fax: (33) 47 36 60 46 | | FRANCE Email: moreaut@univ-tours.fr | *------------------------------------------------------------------* From owner-proteins@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!GUARANY.CPD.UNB.BR!wagnerf From: wagnerf@GUARANY.CPD.UNB.BR (wagner fontes) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Software Date: 4 Jul 1996 08:09:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4rerdo$brc@ccshst05.uoguelph.ca> NNTP-Posting-Host: net.bio.net Dear Wenjin, If you mean molecular modelling for protein structure, try to look at the SwissModel site at http://expasy.hcuge.ch/www/tools.html or look for Biosym Technologies, who makes Insight, a good software package for modelling. If you mean a software to use in a smaller computer, try RasMol or MolView. Wagner. ****************************************************************************** Wagner Fontes wagnerf@guarany.cpd.unb.br http://www.angelfire.com/pages0/wagnerf/index.html Brazilian Protein Sequencing Center Biochemistry / Protein Chemistry lab University of Brasilia Phone (55 61) 348 2142 Brazil FAX (55 61) 272 4548 ****************************************************************************** On 3 Jul 1996, Wenjin Yu wrote: > Dear friends on the net, > I'm wondering if there is a software which can determine and make > graphics of 3D structure of a protein based on its amino acid sequence. > Thank you in advance for your reply. > > Wenjin Yu > > > From owner-proteins@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!howland.reston.ans.net!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!sdd.hp.com!ihnp4.ucsd.edu!munnari.OZ.AU!news.unimelb.EDU.AU!tracy From: tracy@austin.unimelb.edu.au (Tracy Nero) Newsgroups: bionet.molbio.proteins Subject: Australian Medicinal Chemistry Conference Dec 96 Date: 4 Jul 1996 06:59:38 GMT Organization: Melbourne University, Victoria, Australia Lines: 86 Sender: tracy@gjok@austin.unimelb.edu.au (Tracy Nero) Distribution: world Message-ID: <4rfq4q$pjo@news.unimelb.EDU.AU> NNTP-Posting-Host: tango.austin.unimelb.edu.au Please excuse multiple copies due to cross posting. ROYAL AUSTRALIAN CHEMICAL INSTITUTE MEDICINAL & AGRICULTURAL DIVISION 13TH NATIONAL CONFERENCE "UP AND COMING RESEARCH IN AUSTRALIA" 8-11 DECEMBER, 1996, Monash University, Clayton 3168, Victoria, Australia The conference will cover all aspects of medicinal and agricultural chemistry with a focus on: o students and new researchers o emerging research areas in medicinal and agricultural chemistry o the interaction between medicinal chemists, pharmacologists and industry. Papers are invited for both lecture and poster sessions. The meeting will be held in conjunction with the ASCEPT (Australian Society of Clinical and Experimental Pharmacologists and Toxicologists) and APPS (Australian Physiological and Pharmacological Society) conferences. There will be a joint social mixer and workshop on the initiation of research/industry interactions on sunday evening. Monday morning will feature a joint session on mass screening and combinatorial chemistry, followed in the evening by a joint poster session and wine tasting. Invited Speakers Include: Preliminary Session Topics Include: o Dr George Fleet - glycochemistry, o agrochemistry herbicides,tuberculosis o glycobiology and glycochemistry (Oxford University, UK) o toxins o Dr David Manallack - metalloproteins, o anti-infectives neural networks (Chiroscience, UK) o enzyme inhibitors o Dr Lia Addadi - biomineralization o QSAR methods (Weizman Institute, Israel) o automated methods of o Dr Shiela Unkles - fungal enzymes synthesis and screening (Monash University, Aus) o DNA and drugs o Dr Ron Quinn - mass screening o medicinal chemistry teaching (Griffith University, Aus) o Dr John Bremner - medicinal chemistry teaching (Uni. of Wollongong, Aus) Social Events: o Dr Mohan Venkataraman - DNA drugs o mixer sunday evening (ISIS Pharmaceuticals, USA) o wine tasting and mixer after o Dr Paul Rowland - drug poster session monday evening development (Medeval Ltd., UK) o conference dinner at Kenloch o Dr Damon Ridley - chemical restaurant in the Dandenong Ranges databases (Uni. of Sydney, Aus) (dinner cost for accompanying person $60) o Prof Colin Masters - prions, Alzheimers disease (Uni. of Melbourne, Aus) o Prof William Denny - cancer research (Auckland University, NZ) Student Scholarships: 10 scholarships of $250 will be available to interstate students presenting either a talk or poster Deadlines: Abstract 30th Sept., 1996 Registration 8th Nov., 1996 Registration Costs: On or before 8th Nov After 8th Nov RACI Member $300 $400 non-RACI Member $375 $475 Reciprocal Society Member $300 $400 RACI Student $100 $200 non-RACI Student $140 $240 NOTE 1: Above costs are all in AUSTRALIAN DOLLARS NOTE 2: All social mixers,the conference dinner, workshop, morning & afternoon teas and boxed lunches are included in the registration cost To receive the conference circular and registration form contact: o the conference organiser Dr Mick Gould, Conference Associates Pty Ltd, 13 Jeffrey St, Mt Waverly, Victoria, Australia 3149. Ph: (03) 9887-8003 Fax: (03) 9887-8773 email: ca@netwide.com.au o Dr. Margaret Wong, Department of Applied Chemistry,Swinburne University of Technology, Hawthorn,Victoria, Australia 3122. Ph: (03) 9214-8542 Fax: (03) 9819-0834 email: marg@chem1.chem.swin.edu.au o Web page http://www.chem.swin.edu.au/ma/mconf.html (registration forms will be available from the web site at a later date) From owner-proteins@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!surfnet.nl!ruu.nl!cble46.chem.ruu.nl!user From: f.s.wouters@chem.ruu.nl (fred wouters) Newsgroups: bionet.molbio.proteins Subject: bovine cellines Date: Wed, 03 Jul 1996 16:35:11 +0100 Organization: ruu Lines: 15 Message-ID: NNTP-Posting-Host: cble46.chem.ruu.nl X-Newsreader: Yet Another NewsWatcher 2.1.8 Hi everybody, I'm in posession of an antibody raised against a bovine protein. We were hoping that this antibody was cross-reactive with the same protein in a usefull celline (e.g. 3T3 mouse fibro's) but it doesn't. I have tried other animal cellines but again no results. So my question to the world is: does anyone have a bovine celline from liver, kidney or testis (in order of importance). If so, please send me some lyophilized cellpellets to test them for my protein. please help, I don't fancy making a primary culture At the slaughterhouse thanx in advance Fred Wouters From owner-proteins@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!Norway.EU.net!EU.net!main.Germany.EU.net!Frankfurt.Germany.EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!sdd.hp.com!ihnp4.ucsd.edu!munnari.OZ.AU!metro!metro!seagoon.newcastle.edu.au!usenet From: mdpjr@cc.newcastle.edu.au (Phil Robinson) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: % of ammonium sulphate - PKC precipitation? Date: Fri, 05 Jul 1996 00:29:13 GMT Organization: The University of Newcastle Lines: 19 Message-ID: <4rfrs6$npo@seagoon.newcastle.edu.au> References: <4re02r$h92@news.doit.wisc.edu> NNTP-Posting-Host: jh-rob.newcastle.edu.au X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.molbio.methds-reagnts:46508 bionet.molbio.proteins:8253 I don't know the exact answer, but we use a brain extract that is about 1 mg/ml pH 7.4 and it does NOT come down with 35% AS (while our protein of interest does), and it does come down if we follow this with 80% AS. Maybe this will get you started. We have sometimes purified it from this point. My other comment is that while the protein concentration is clearly critical, so is the source of that protein (species, organ, and whether it is cytosol, peripheral membrane extracts etc). Phil klenchin@macc.wisc.edu (Dima Klenchin) wrote: >Could anyone give me rough idea about typical % of saturation of >AS solution at which PKC precipitates? The conditions would be >~ 5 mg/ml of total protein, pH 7.5. >Thanks, >- Dima From owner-proteins@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!nntp.coast.net!oleane!jussieu.fr!citi2.fr!federici.cochin.inserm.fr!user From: federici@icgm.cochin.inserm.fr (Federici) Newsgroups: bionet.molbio.proteins Subject: E.coli proteins retained on Ni-column Date: 4 Jul 1996 14:04:44 GMT Organization: ICGM CNRS UPR415 Lines: 12 Message-ID: NNTP-Posting-Host: federici.cochin.inserm.fr X-Newsreader: Yet Another NewsWatcher F2.0 To facilitate the purification of a recombinant protein expressed in E.coli, a poly-histidine tag can be added to the N-terminal sequence of the protein. In this way, the protein can be retained on a matrix charged with Ni2+ ions which form complexes with the histidine residues, and therefore, a specific elution can be carried out. But, due to their amino acid content, some E.coli proteins are also bound to the Ni-column, and disturb the purification of the recombinant protein. Has anybody identified E.coli proteins which are retained during purification using a Ni-column? I would also be very interested in references describing this subset of E.coli proteins. From owner-proteins@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!uwm.edu!news-res.gsl.net!news.gsl.net!sgigate.sgi.com!esiee.fr!jussieu.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-hohenheim.de!wpxx02.toxi.uni-wuerzburg.de!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Software Date: 4 Jul 1996 15:25:35 GMT Organization: CC University of Hohenheim (not responsible for contents) Lines: 19 Message-ID: <4rgnpf$1cqa@power5.rz.uni-hohenheim.de> References: <4rerdo$brc@ccshst05.uoguelph.ca> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Wenjin Yu (wyu@uoguelph.ca) wrote: > I'm wondering if there is a software which can determine and make > graphics of 3D structure of a protein based on its amino acid sequence. It's not except if your protein of interest has considerable homology to another protein the structure of which is known. Find out by running BLAST or FASTA of your protein sequence against the NRL_3D database. Universal software of the kind you mention above would mean solving the protein folding problem -- one of the greatest riddles in molecular biology/biochemistry nowadays. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!biosci!not-for-mail From: ketchemr@scripps.edu (Randal R. Ketchem) Newsgroups: bionet.molec-model,bionet.molecules.peptides,bionet.molbio.proteins,sci.chem,bionet.structural-nmr Subject: Research Fellow In NMR Spectroscopy Date: 4 Jul 1996 23:16:33 -0700 Organization: University of Melbourne Lines: 46 Sender: daemon@net.bio.net Distribution: world Message-ID: <4rd3gv$kd6@riscsm.scripps.edu> NNTP-Posting-Host: net.bio.net Keywords: job, NMR Xref: biosci bionet.molec-model:1018 bionet.molecules.peptides:356 bionet.molbio.proteins:8263 sci.chem:59381 bionet.structural-nmr:1362 Date: 7/2/96 7:03 PM From: Frances Separovic Research Fellow In NMR Spectroscopy A research fellowship in NMR spectroscopy is available with the School of Chemistry, University of Melbourne, Australia. The School has a wide range of research interests in structural and solution NMR studies in organic, inorganic and biological chemistry. You, with the help of a Professional Officer, will be responsible for the daily function of the NMR Centre, technique development and training. You will be encouraged to undertake collaborative research. The NMR centre at the School of Chemistry is equipped with 4 Varian NMR spectrometers: an Inova 400, Unity Plus 400, Unity 300 and an Inova 300 for solid-state work plus 2 Sparc workstations for data processing and 20% access to a Bruker DRX 500 NMR spectrometer. Planning to gain access to higher field instruments has a high priority. You will have a relevant post graduate qualification and some experience in most solution state NMR techniques with emphasis on the structural studies of organic molecules and/or biomolecules. Experience with molecular dynamics calculations and computational methods in solution structural refinement of biological macromolecules would be particularly desirable. This appointment will be for three years (Limited Tenure). Salary: $30130 - $40889 pa (Research Fellow Grade 1). For further information, position description and the School Research Booklet contact: Associate Professor Frances Separovic (61-3) 9344 6464; fax (61-3) 9347 5180 e-mail: Frances_Separovic@muwayf.unimelb.edu.au Applications close: 27 July 1996 Reference number: Y0003776 Applications (including the names and facsimile numbers of three referees) should quote the reference number and be sent in duplicate to the Director, Human Resources, The University of Melbourne, Parkville, Victoria, 3052 Australia; fax (61-3) 9344 4694. Applications will not be acknowledged but you will be advised of the outcome. The University of Melbourne is an equal opportunity employer and has a smoke-free workplace policy. THE AUSTRALIAN UNI APPOINTS SAT 6 JULY 1996 LINE AD WITH LOGO From owner-proteins@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!swrinde!tank.news.pipex.net!pipex!oleane!in2p3.fr!swidir.switch.ch!scsing.switch.ch!swsbe6.switch.ch!news.belnet.be!news.vub.ac.be!ben!rwattiez From: rwattiez@ben.vub.ac.be (Wattiez Ruddy) Newsgroups: bionet.molbio.proteins Subject: co-translational modifications of proteins Date: 4 Jul 1996 13:11:40 GMT Organization: Brussels Free Universities (VUB/ULB), Belgium Lines: 12 Message-ID: <4rgfuc$3g0@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] : Iwould like recommendations for a book about co-translational and post-translational modifications of proteins. Thanks From owner-proteins@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-freiburg.de!mibm1.ruf.uni-freiburg.de!krieger From: krieger@mibm1.ruf.uni-freiburg.de (Jens Krieger) Newsgroups: bionet.molbio.proteins Subject: High background with SDS Date: 4 Jul 1996 21:57:18 GMT Organization: Rechenzentrum der Universitaet Freiburg, Germany Lines: 42 Message-ID: <4rhenu$e9d@n.ruf.uni-freiburg.de> NNTP-Posting-Host: mibm1.ruf.uni-freiburg.de X-Newsreader: TIN [version 1.2 PL2] [ Article crossposted from bionet.molbio.methds-reagnts ] [ Author was Jens Krieger (krieger@mibm1.ruf.uni-freiburg.de) ] [ Posted on 4 Jul 1996 21:55:29 GMT ] Hello! I'm staining SDS-PAGE with methylgreen, using the method of Cutting and Roth (73), but I've problems with high background and no seriously fixed proteins. I fix the gels with sulfosalicylic acid (SSA, 10% w/v)) and CaCl2 to build unsoluble calcium-phosphat complexes. So far, so good. With the last step, rinsing with aequos ammonium-molybdat, there should be phospho-molybdat complexes. I think it works so far, because if I stain it with methylgreen (5% in 7% acetic acid) and then destain it with SSA, i will see for a short time very sharp green bands, but there are still a very high background. So I have to destain ti further on, and suddenly....the bands disappear. The background is okay, but without any bands..... Does everyone has an idea, why the bands suddenly disappear? Another destaining reagent, another fixing reagent? (i've tried TCA and normal acetic acid; it doesnt work at any time). Thanks in advance, Jens. -- /~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\ | Jens Krieger "Solange die Alpen noch stehen, | | wird es keine | | Tel.:+49.351.463.5465 Gerechtigkeit geben."| | | | krieger@rcs.urz.tu-dresden.de H.Achternbusch | \ krieger@mibm.ruf.uni-freiburg.de / ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- /~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\ | Jens Krieger "Solange die Alpen noch stehen, | | wird es keine | | Tel.:+49.351.463.5465 Gerechtigkeit geben."| | | | krieger@rcs.urz.tu-dresden.de H.Achternbusch | \ krieger@mibm.ruf.uni-freiburg.de / ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-proteins@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!oslonett.no!sn.no!Norway.EU.net!EU.net!main.Germany.EU.net!Frankfurt.Germany.EU.net!howland.reston.ans.net!newsfeed.internetmci.com!uwm.edu!fnnews.fnal.gov!lakesis.fapesp.br!news.dcc.unicamp.br!bee.uspnet.usp.br!spider.usp.br!zeribajr From: Jose Ribamar dos Santos Ferreira Junior Newsgroups: bionet.molbio.proteins Subject: yeast Glycoproteins! Date: Thu, 4 Jul 1996 09:58:16 -0300 Organization: Universidade de Sao Paulo / Brasil Lines: 12 Message-ID: NNTP-Posting-Host: spider.usp.br Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear, I'm working in a master program at University of Sao Paulo in Brasil. I have a class in wich the main subject is post-translational modifications of proteins and I need to do a project using the class material for proofing that a Saccahromyces cerevisiae protein have a post-translational modification. I would like to know how can I study a protein in order to determine if it's glycosilated and how can I evaluate the sugar subunits of this modification. In fact, I would like to know what experiments for proofing that is enough. Bets Regards From owner-proteins@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!caen!uwm.edu!news-res.gsl.net!news.gsl.net!usenet.eel.ufl.edu!tank.news.pipex.net!pipex!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!gmorley From: gmorley@hgmp.mrc.ac.uk (Mr. G. Morley) Newsgroups: bionet.molbio.proteins Subject: ubiquitin and sds Date: 4 Jul 1996 15:27:49 GMT Organization: MRC Human Genome Resource Centre Lines: 17 Message-ID: <4rgntl$fao@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: tin.hgmp.mrc.ac.uk Dear all, just a quick note to ask about precipitating ubiquitin bound proteins.I noticed in the literature that groups who are working on ubiquitin-protein complexes lyse the cells with buffer that does not contain SDS and then precipitate the solution with W.G.A sepharose (not with an antibody against the receptor they are studying). Is this because the contitions required to seperate the protein-ubiquitin complex from the Protein A/G beads (used in a normal antibody ppt) also releases the ubiquitin from the protein?... When I performed a antiubiquitin western after ppt my receptor with antibody I noticed dark bands much lower down the gel than I expected... If anyone could let me know this would be appreciated! Thanks in advance.. Gary Morley (gmorley@rpms.ac.uk) From owner-proteins@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!CSHL.ORG!leemor From: leemor@CSHL.ORG (Leemor) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Software Date: 4 Jul 1996 08:40:42 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net > Dear friends on the net, > I'm wondering if there is a software which can determine and make > graphics of 3D structure of a protein based on its amino acid sequence. > Thank you in advance for your reply. > > Wenjin Yu > > > A 3D structure of a protein can only be _determined_ using crystallography or NMR. You could attempt to model a protein based on homology to other proteins for which 3D structures have been _determined_ by crystallography or NMR. Ab initio _modelling_ can be done with some degree of success but by no means is this a structure you can have full confidence in. Leemor From owner-proteins@net.bio.net Wed Jul 03 23:00:00 1996 Path: biosci!qmw.ac.uk!j.t.s.critchley From: j.t.s.critchley@qmw.ac.uk (John Critchley) Newsgroups: bionet.molbio.proteins Subject: Amino Acid and Peptide Nomenclature Date: 4 Jul 1996 22:53:40 -0700 Organization: QMW (University of London) Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net A WWW version of the IUPAC-IUBMB recommendations on Amino Acid and Peptide Nomenclature published in Eur. J. Biochem. 138, 9-37 (1984) has now been prepared for the Internet. It can be found from the home page of IUPAC Nomenclature: http://www.qmw.ac.uk/~ugca000/iupac.html This version incorporates all published corrections, and others detected during the preparation of the Web version. These corrections are all clearly marked so that readers can correct their hard copy versions. In addition to the original document there are four addenda published in the Newsletter of the Joint Biochemical Nomenclature Committees. Appropriate links to the addenda are added in the main text. Gerry Moss ______________________________________________________________________ Dr G P Moss e-mail g.p.moss@qmw.ac.uk Department of Chemistry Queen Mary & Westfield College Mile End Road London E1 4NS From owner-proteins@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!daresbury!yama.mcc.ac.uk!news.salford.ac.uk!aber!bath.ac.uk!dcl-cs!strath-cs!st-and!bute!jfgm From: Jose F Gutierrez Marcos Newsgroups: bionet.molbio.proteins Subject: GFP users in UK Date: Fri, 5 Jul 1996 13:39:08 +0100 Organization: St. Andrews University Lines: 9 Message-ID: NNTP-Posting-Host: bute.st-and.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII NNTP-Posting-User: jfgm X-Sender: jfgm@bute I would like to contact people with experience in GFP as reporter, please contact my by e-mail: jfgm@st-and.ac.uk Thanks Jose From owner-proteins@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!sdd.hp.com!night.primate.wisc.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!alpha.oncology.wisc.edu!user From: mcmahan@oncology.wisc.edu (Scott McMahan) Newsgroups: bionet.molbio.proteins Subject: Re: E.coli proteins retained on Ni-column Date: Fri, 05 Jul 1996 10:53:21 -0600 Organization: University of Wisconsin-Madison Lines: 18 Message-ID: References: NNTP-Posting-Host: alpha.oncology.wisc.edu X-Newsreader: Yet Another NewsWatcher 2.1.8 In article , federici@icgm.cochin.inserm.fr (Federici) wrote: > But, due to their amino acid content, some E.coli proteins are also bound > to the Ni-column, and disturb the purification of the recombinant protein. > Has anybody identified E.coli proteins which are retained during > purification using a Ni-column? > I would also be very interested in references describing this subset of > E.coli proteins. Check out Wulfing et al Journal Biol Chem 269(4) 2895-2901. They discuss a protein (WHP) which does bind to a Ni-column. -- Scott McMahan mcmahan@oncology.wisc.edu From owner-proteins@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-hohenheim.de!wpxx02.toxi.uni-wuerzburg.de!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: E.coli proteins retained on Ni-column Date: 5 Jul 1996 11:58:39 GMT Organization: CC University of Hohenheim (not responsible for contents) Lines: 16 Message-ID: <4rj01f$jrm@power5.rz.uni-hohenheim.de> References: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Federici (federici@icgm.cochin.inserm.fr) wrote: > Has anybody identified E.coli proteins which are retained during > purification using a Ni-column? I think Andreas Plueckthun published something in this line a few years ago. The protein was cloned and contained an appreciable mount of histidines. Hope that helps, --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-res.gsl.net!news.gsl.net!usenet.eel.ufl.edu!newsfeed.internetmci.com!in2.uu.net!psinntp!psinntp!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!yama.mcc.ac.uk!bignews.shef.ac.uk!usenet From: C.Pical@shef.ac.uk (C E Pical) Newsgroups: bionet.molbio.proteins Subject: Re: E.coli proteins retained on Ni-column Date: 5 Jul 1996 06:59:20 GMT Organization: Molecular Biology & Biotechnology, University of Sheffield , UK Lines: 3 Message-ID: <4rieg8$qb9@bignews.shef.ac.uk> References: NNTP-Posting-Host: pc065058.shef.ac.uk Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 There was an article in TIBS not long ago about this problem, don't remember which issue but it was not long ago. From owner-proteins@net.bio.net Thu Jul 04 23:00:00 1996 Newsgroups: bionet.general,bionet.cellbiol,bionet.cellbiol.cytonet,bionet.diagnostics,bionet.immunology,bionet.molbio.methds.reagnts,bionet.molbio.proteins,bionet.neuroscience Path: biosci!bcm.tmc.edu!cs.utexas.edu!chi-news.cic.net!newsfeeder.sdsu.edu!newspump.sol.net!homer.alpha.net!uwm.edu!news.cse.psu.edu!rutgers!utcsri!utnut!wave.scar!usenet From: Any User <00useran@wave.scar.utoronto.ca> Subject: Re: FDA TO REGULATE RESEARCH ANTIBODIES X-Nntp-Posting-Host: pc208.scar3.utoronto.ca Content-Type: text/plain; charset=us-ascii Message-ID: Sender: usenet@wave.scar.utoronto.ca (news owner) Content-Transfer-Encoding: 7bit Organization: Scarborough College, U of T References: <31D7FA26.377@bioreagents.com> <4ra9jd$ivu@optional.cts.com> <31DA93F5.464B@bioreagents.com> Mime-Version: 1.0 Date: Fri, 5 Jul 1996 16:37:46 GMT X-Mailer: Mozilla 1.2N (Windows; I; 16bit) Lines: 83 Xref: biosci bionet.general:22648 bionet.cellbiol:5052 bionet.cellbiol.cytonet:596 bionet.diagnostics:953 bionet.immunology:9274 bionet.molbio.proteins:8268 bionet.neuroscience:14785 skejrjewlrlerlkjelrmlkel;resr serser eresrserserserserserserJames Stiehr wrote: >Bryan Kiehl wrote: >> >> It is my understanding that the FDA does now require that reagents >> that may be used for diagnostic uses (e.g., cancer markers, infectious >> disease detection, etc.) are to be regulated. >> >> However, it also appears the amount of regulation is minimal. They >> require that the manufacturer follow good manufacturing practices. >> These include proper labeling and documentation during the >> manufacturing processes, as well as being able to field customer >> complaints and document how you deal with these. The regs also require >> that the company submit a notifcation with proposed labeling before >> marketing the product. This is then reviewed by the FDA for truth and >> accuracy. >> >> For example, is the reagent is an antibody, then one must identify >> what the antibody recognizes and be sure that all claims are accurate. >> If this is only a reagent and not a kit, there can be no performance >> claims. These reagents are intended for the user to establish the >> assay method. The user (e.g., pathologist, laboratory) must "validate" >> that the assay using this reagent performs well enough for diagnostic >> uses. The end user must also assure continued performance. >> >> If the manufacturer puts the reagent into kits or claims diagnostic >> performance, then he needs to provide data to the FDA. Otherwise, he >> mostly needs to just assure that the reagents are made well and >> packaged without error. >> >> For most smaller companies this may seem a burden at first, but >> similar regs are being established in Europe under ISO regs. > >Since many of the companies which provide reagetns are small companies, >it becomes a major issue. Look in linscott's directory, you don't see >many large companies with the deep pockets necessary to manage these >regulations. GMP sounds nice and easy, but if you look at the actual >requirements, they are not trivial. If people would like to see it, I >would be happy to add it to the web site that has been created for this >purpose: http://www.earthnet.net/~affinity/fda. > >> I also doubt that true research reagents that are never or rarely >> used in the clniical realm will ever be regulated. Remember, the FDA >> can only come down on a company that sells these reagents to groups >> that really do use them for human diagnostics. > >It is unfortunate that a company cannot decide for itself that it does >not want to be a diagnostic company and offer "dual use" products which >can be identified as not appropriate for diagnostic use. There are >federal consumer laws making it illegal to use a proguct contrary to its >labeled use, however, pathologists (and other physicians) have managed to >exempt themselves from these laws. Unfortunately, this leaves the >supplier responsible for the use of its product. When you consider that >most research reagents are sold to universities and ordered through the >purchasing dept. to be delivered to "receiving" how can a company know >who and how its product is used? > >What about the situation where today we sell a product that is not >clinically relevant, but a paper comes out tomorrow saying it is? In >that case, we have developed a market for a "true research reagent' that >is discovered to have a new application. We still don't want to be a >diagnostic company, yet at that point, according the the regs. we're >selling an IVD and must therefore either conform to the regs and incur >all of the marginal expenses for that single antibody (most of which only >sell $5000-$10,000/year) or remove them from the market. > >Why can't we all be responsible suppliers and consumers (shades of Rodney >King). If FDA, CLIA, suppliers and consumers could all agree to >recognize that a product labeled "For In Vitro Experimental Use Only, Not >for Diagnostic Use" really should not be used in any kind of clinical >setting, then these would not need to be regulated by FDA. If CLIA found >pathologists using them in their lab, sanctions could be applied. If FDA >found suppliers promoting them for clinical use, appropriate disciplinary >action could be taken. Honest companies who supply the research market >with important research tools could go about their business either making >quality products which their customers are happy with or going out of >business if they are not - no harm done to anyone. > >James Stiehr >Affinity Bioreagents, Inc. From owner-proteins@net.bio.net Sat Jul 06 23:00:00 1996 Path: biosci!rutgers!sgigate.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!nnrp.info.ucla.edu!csulb.edu!not-for-mail From: cohlberg@csulb.edu (Jeff Cohlberg) Newsgroups: bionet.molbio.proteins Subject: Re: What is 'Tu' in EF-Tu?? Date: 6 Jul 1996 17:50:58 GMT Organization: Cal State Long Beach Lines: 12 Message-ID: <4rm922$a05@hatathli.csulb.edu> References: <31CEFAEB.6611@techfak.uni-bielefeld.de> <4qodp9$buh@news.ox.ac.uk> <4r45ar$bd@mark.ucdavis.edu> NNTP-Posting-Host: gull.csulb.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] : : Alexander Sczyrba (asczyrba@techfak.uni-bielefeld.de) wrote: : : : Can anybody tell me what the 'Tu' in EF-Tu (elongation factor Tu) : : : stands for?? And what is 'Ts' in EF-Ts?? When EF-T was originally isolated, there were two fractions, the stable fraction, designated Ts, and the unstable fraction, designated Tu. It was later found that Tu could be stabilized by guanine nucleotides. -- Jeffrey A. Cohlberg, Professor Department of Chemistry and Biochemistry California State University, Long Beach 1250 Bellflower Boulevard, Long Beach, CA 90840 Phone: (310) 985-4944 FAX: (310) 985-2315 E-mail: cohlberg@csulb.edu From owner-proteins@net.bio.net Sat Jul 06 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!harbinger.cc.monash.edu.au!betty.eng.monash.edu.au!alexyap From: alexyap@betty.eng.monash.edu.au (Alex Yap) Newsgroups: bionet.molbio.proteins Subject: RMSD algorithm needed Date: 8 Jul 1996 06:13:13 GMT Organization: Monash University Lines: 29 Message-ID: <4rq8tp$6r6@harbinger.cc.monash.edu.au> Reply-To: alexyap@bedrock.eng.monash.edu.au NNTP-Posting-Host: betty.eng.monash.edu.au X-NNTP-Posting-User: alexyap X-Newsreader: TIN [version 1.2 PL1] Hi, Does anyone know where I can get the algorithm for performing minimum RMS deviation alignment between two protein chains? I have a large set of protein backbone conformations expressed as Phi & Psi angles. I have also a target (presumably native) conformation also as a set of Phi & Psi angles. I need to write a C-program to compare each of the conformations in the test set against the target conformation, and calculate the minimum RMS deviation between the alpha carbon atoms. Since there are several thousand conformations in the test set, I cannot use software such as Insight to perform RMSD calculations one by one. So, if anyone has any idea how to get such an algorithm, please tell me where to find it. Thanks in advance. -- Alexander Yap Email: alexyap@acslink.net.au alexyap@bedrock.eng.monash.edu.au Home Page: http://www.peg.apc.org/~alexyap From owner-proteins@net.bio.net Sun Jul 07 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!esiee.fr!sgigate.sgi.com!nntp.coast.net!harbinger.cc.monash.edu.au!munnari.OZ.AU!cs.mu.OZ.AU!news.unimelb.EDU.AU!murphy From: rm@clyde.its.unimelb.edu.au (Roger ) Newsgroups: bionet.molbio.proteins Subject: Re: enzyme kinetics programs?? Date: Tue, 09 Jul 96 04:16:25 GMT Organization: University of Melbourne Lines: 27 Message-ID: <4rspr9$9vp@news.unimelb.EDU.AU> References: <4qr7tv$2ir@mserv1.dl.ac.uk> <31D28A74.4648@ibex.ca> NNTP-Posting-Host: murphy.pharmacology.unimelb.edu.au X-Newsreader: News Xpress 2.0 Beta #0 In article <31D28A74.4648@ibex.ca>, Achim Recktenwald wrote: >Cormac Shaw wrote: > >[snip] > >> Other Windows graphing applications we've looked at are >> "SigmaPlot" (http://www.jandel.com/) which is pretty good for >> presentation but may or may not include the kinetic equations you/we >> want (we're currently checking that out) ... > >You can do the kinetics with Sigmaplot, but it is not very efficient. >Grafit and Enzfitter compile the equations you are fitting to, they are > therefore much faster. >In Sigmaplot you also have to be careful with setting the right constraints, > otherwise it may take >forever or you get not very useful results. I like the program and use it a lot > for plotting, but for >enzyme kinetics Grafit is much better. > >Achim GraphPad's program, PRISM, is another I'd recommend for this sort of application. Cheers, Roger Murphy From owner-proteins@net.bio.net Sun Jul 07 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!comp.vuw.ac.nz!canterbury.ac.nz!news.lincoln.ac.nz!pc097085.lincoln.ac.nz!gourleyt From: gourleyt@lincoln.ac.nz (Gourley, Tania Suzanne) Subject: Not binding in Western Message-ID: Date: Tue, 9 Jul 1996 10:26:39 Organization: Lincoln University, New Zealand X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 6 Does anyone know of any references refering to antibodies which cannot recognise a protein when it is bound to membrane such as in Western blots but can bind free protein. Thanks, Tania From owner-proteins@net.bio.net Sun Jul 07 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-res.gsl.net!news.gsl.net!hunter.premier.net!news2.cais.net!news.cais.net!van-bc!n1van.istar!van.istar!ott.istar!istar.net!torn!ccshst05.uoguelph.ca!ccshst01!dflett From: dflett@uoguelph.ca (Debra E Flett) Newsgroups: bionet.molbio.proteins Subject: random coiling (>50%) Date: 8 Jul 1996 19:51:47 GMT Organization: University of Guelph Lines: 12 Message-ID: <4rrosj$2du@ccshst05.uoguelph.ca> NNTP-Posting-Host: ccshst01.uoguelph.ca Keywords: Secondary Structures of Proteins X-Newsreader: TIN [version 1.2 PL2] Hello! I just joined the newsgroup and am writing in order to obtain information regarding the secondary structures of proteins. I need information on : (1) Proteins that have a large proportion of random coil (>50%). (2) A possible way to search the Brookhaven Protein Data Bank for proteins with a large proportion of random coil. Ant information would be greatly appreciated. Thank you. From owner-proteins@net.bio.net Sun Jul 07 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!nntp.coast.net!fu-berlin.de!news.dfn.de!zeus.rbi.informatik.uni-frankfurt.de!grapool30.rz.uni-frankfurt.de!pcbr2 From: wattenberg@chemie.uni-frankfurt.de (Andreas Wattenberg) Newsgroups: bionet.molbio.proteins Subject: Re: What is 'Tu' in EF-Tu?? Date: 8 Jul 1996 13:08:34 GMT Organization: Universität Frankfurt Lines: 21 Message-ID: <4rr18i$m64@grapool30.rz.uni-frankfurt.de> References: <31CEFAEB.6611@techfak.uni-bielefeld.de> <4qodp9$buh@news.ox.ac.uk> NNTP-Posting-Host: pcbr4.phys.chemie.uni-frankfurt.de X-Newsreader: News Xpress Version 1.0 Beta #4 In article , Maarten de Bruijn wrote: >In article <4qodp9$buh@news.ox.ac.uk>, Dennis Benjamin > writes >>Alexander Sczyrba (asczyrba@techfak.uni-bielefeld.de) wrote: >>: Can anybody tell me what the 'Tu' in EF-Tu (elongation factor Tu) >>: stands for?? And what is 'Ts' in EF-Ts?? >> >>I forget what the capital "T" represents, but the "u" and "s" stand >>for "unstable" and "stable". I'm pretty sure that EF-Tu is unstable >>in the absence of guanine nucleotide. Unfortunately, I can't remember >>where I learned this, but I'll bet that tracking down the original >>papers describing the proteins will give a complete description of >>the significance of "Tu" and "Ts" >T=Transfer? nope, T=Thermal EF-Ts is thermally more stable than EF-Tu. bye, andreas From owner-proteins@net.bio.net Sun Jul 07 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.reston.ans.net!nntp.coast.net!fu-berlin.de!news.dfn.de!zeus.rbi.informatik.uni-frankfurt.de!grapool30.rz.uni-frankfurt.de!pcbr2 From: wattenberg@chemie.uni-frankfurt.de (Andreas Wattenberg) Newsgroups: bionet.molbio.proteins Subject: Re: What is 'Tu' in EF-Tu?? Date: 8 Jul 1996 13:08:27 GMT Organization: Universität Frankfurt Lines: 21 Message-ID: <4rr18b$m64@grapool30.rz.uni-frankfurt.de> References: <31CEFAEB.6611@techfak.uni-bielefeld.de> <4qodp9$buh@news.ox.ac.uk> NNTP-Posting-Host: pcbr4.phys.chemie.uni-frankfurt.de X-Newsreader: News Xpress Version 1.0 Beta #4 In article , Maarten de Bruijn wrote: >In article <4qodp9$buh@news.ox.ac.uk>, Dennis Benjamin > writes >>Alexander Sczyrba (asczyrba@techfak.uni-bielefeld.de) wrote: >>: Can anybody tell me what the 'Tu' in EF-Tu (elongation factor Tu) >>: stands for?? And what is 'Ts' in EF-Ts?? >> >>I forget what the capital "T" represents, but the "u" and "s" stand >>for "unstable" and "stable". I'm pretty sure that EF-Tu is unstable >>in the absence of guanine nucleotide. Unfortunately, I can't remember >>where I learned this, but I'll bet that tracking down the original >>papers describing the proteins will give a complete description of >>the significance of "Tu" and "Ts" >T=Transfer? nope, T=Thermal EF-Ts is thermally more stable than EF-Tu. bye, andreas From owner-proteins@net.bio.net Sun Jul 07 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-res.gsl.net!news.gsl.net!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!nntp.neu.edu!bnorum From: bnorum@lynx.dac.neu.edu (Becky Norum) Newsgroups: bionet.molbio.proteins Subject: Alkaline Phosphatase Assay Date: 9 Jul 1996 02:25:08 GMT Organization: Northeastern University, Boston, MA. 02115, USA Lines: 18 Message-ID: <4rsfu4$gp6@chaos.dac.neu.edu> NNTP-Posting-Host: lynx.dac.neu.edu X-Newsreader: TIN [version 1.2 PL2] I am working on Alkaline Phosphatase and am searching for the kinetic assay that will give the highest specific activity. We generally use the Sigma Alkaline Phosphatase Assay but are trying to get a kinetic assay using DEA as the buffer and PNPP as the substrate to work. Unfortunately, everytime I perform this assay the specific activities obtained are about three-quarters of what we obtain with the Sigma assay when theoretically the DEA assay should yield higher results. If anyone has performed the DEA assay and is willing to talk about their procedure with ,e I would appreciate it. Responses can be emailed to the below address. Thanks, -- Becky Lynn bnorum@lynx.dac.neu.edu 'essie' ------ All the darkness of the world cannot suppress the light from one lit candle. From owner-proteins@net.bio.net Mon Jul 08 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-res.gsl.net!news.gsl.net!nntp.coast.net!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-hohenheim.de!wpxx02.toxi.uni-wuerzburg.de!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Not binding in Western Date: 9 Jul 1996 16:45:27 GMT Organization: CC University of Hohenheim (not responsible for contents) Lines: 15 Message-ID: <4ru2b7$bq8@power5.rz.uni-hohenheim.de> References: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Gourley, Tania Suzanne (gourleyt@lincoln.ac.nz) wrote: > Does anyone know of any references refering to antibodies which cannot > recognise a protein when it is bound to membrane such as in Western blots but > can bind free protein. I think that happens quite often. Check out the catalogue of Transduction Research; they list for every antibody whether it is suitable for Western Blotting, IP or immunofluorescence. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Mon Jul 08 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-res.gsl.net!news.gsl.net!usenet.eel.ufl.edu!tank.news.pipex.net!pipex!oleane!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!news.belnet.be!news.fundp.ac.be!mickeymouse.biocell.fundp.ac.be!user From: madi@biocell.fundp.ac.be (Marc DIEU) Newsgroups: bionet.molbio.proteins Subject: LDL Receptor plasmid Date: 9 Jul 1996 13:53:04 GMT Organization: F.U.N.D.P - Cellular Biochemistry Lines: 25 Message-ID: NNTP-Posting-Host: mickeymouse.biocell.fundp.ac.be I'm looking for two plasmids. One containing the gene coding for the LDL receptor and one containing the gene coding for the scavenger receptor SRAI/SRAII. Does anyone know somebody who has these plamids? Does anyone know how to get these plasmids? Thank you for answering Isabelle Geron Laboratoire de Biochimie Cellulaire FUNDP Rue de Bruxelles, 61 B-5000 Namur Belgium E-mail: isageron@biocell.fundp.ac.be -- Marc DIEU Laboratory of Cellular Biochemistry, Facultés Universitaires ND de la Paix, 61, rue de Bruxelles, B-5000 Namur (Belgium). Fax: ++/32/81/72.41.35. Email: madi@biocell.fundp.ac.be From owner-proteins@net.bio.net Mon Jul 08 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!agate!spool.mu.edu!uwm.edu!news-res.gsl.net!news.gsl.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!bcc.ac.uk!martin From: martin@bsm.bioc.ucl.ac.uk (Andrew Martin) Subject: Re: RMSD algorithm needed Message-ID: <1996Jul9.135857.42254@ucl.ac.uk> Date: Tue, 9 Jul 1996 13:58:57 GMT References: <4rq8tp$6r6@harbinger.cc.monash.edu.au> Organization: University College London X-Newsreader: TIN [version 1.2 PL2] Lines: 27 : Hi, : Does anyone know where I can get the algorithm for : performing minimum RMS deviation alignment between two : protein chains? Hi Alexander, I have a program called ProFit which will do the fitting for you; it will run from a script file so you can easily use it to run through several thousand structures. It's available via my Web page. I also have a program called genloop which will create a backbone (N,CA,C) or CA trace from a set of torsion angles. Contact me by EMail if you want a copy of this. Best wishes, Andrew -- **************************************************************************** Dr. Andrew C.R. Martin, University College London & SciTech Software EMAIL: martin@biochem.ucl.ac.uk Tel:(Work) +44(0)171 419 3890 URL: http://www.biochem.ucl.ac.uk/~martin (Home) +44(0)1372 275775 **************************************************************************** From owner-proteins@net.bio.net Mon Jul 08 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!oleane!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!fht-mannheim!news From: 84075 <84075@novell1.rz.fh-mannheim.de> Subject: Aldose reductase = xylose reductase ? X-Mailer: Mozilla 2.01 (Win16; I) Content-Type: text/plain; charset=iso-8859-1 Sender: news@roxi.rz.fht-mannheim.de (NEWS - system account) Mime-Version: 1.0 Organization: Fachhochschule Mannheim Date: Tue, 9 Jul 1996 22:24:42 GMT Message-ID: <31E2DC2A.7563@novell1.rz.fh-mannheim.de> Content-Transfer-Encoding: 8bit Lines: 10 I“m seeking for informations about xylose reductase, the EC-number I was told was EC 1.1.1.21. But under this number I only find aldose reductase, now my questions are these enzymes the same? If yes i have two more questions, were can I purchase this enzyme and how can I measure his activity? Any information would be greatly apreciated, please send them to 84075@novell1.rz.fh-mannheim.de Thank you Markus From owner-proteins@net.bio.net Mon Jul 08 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeed.internetmci.com!info.ucla.edu!nnrp.info.ucla.edu!csulb.edu!csus.edu!sacsa3.mp.usbr.gov!fwssun1.irm.r6.fws.gov!ash.lab.r1.fws.gov!bob!Bob_Hoesch From: Bob_Hoesch@fws.gov (Bob Hoesch) Newsgroups: bionet.molbio.proteins Subject: Affinity Chromatography Date: Mon, 8 Jul 1996 15:10:26 Organization: U.S. Fish & Wildlife Service Forensics Laboratory Lines: 14 Message-ID: NNTP-Posting-Host: bob.lab.r1.fws.gov X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Can someone suggest a reference for affinity chromatography of whole antiserum to adsorb unwanted specificities? For example, I have rabbit antiserum against whole deer serum. I want to adsorb out the components which cross react with bovine proteins. I was thinking of using epoxy-activated Sepharose to bind with whole bovine serum, reacting with the anti-deer on a column, washing with PBS and eluting with high pH buffer. Any references or comments would be very welcome. Thanks. Bob Hoesch U.S. Fish & Wildlife Forensic Laboratory Ashland, OR From owner-proteins@net.bio.net Mon Jul 08 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!newsxfer2.itd.umich.edu!news.itd.umich.edu!usenet From: Rick Neubig Newsgroups: bionet.molbio.proteins Subject: Re: enzyme kinetics programs?? Date: Tue, 09 Jul 1996 13:00:55 -0400 Organization: University of Michigan Lines: 18 Message-ID: <31E29047.4238@umich.edu> References: <4qr7tv$2ir@mserv1.dl.ac.uk> <31D28A74.4648@ibex.ca> <4rspr9$9vp@news.unimelb.EDU.AU> Reply-To: RNeubig@umich.edu NNTP-Posting-Host: warbler.med.umich.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b4Gold (Win95; I) Roger wrote: > > > > >Achim > > GraphPad's program, PRISM, is another I'd recommend for this sort of > application. > > Cheers, > > Roger Murphy You can get a working demo of Prism at http://www.graphpad.com Rick From owner-proteins@net.bio.net Mon Jul 08 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!wizard.pn.com!brighton.openmarket.com!decwrl!tribune.usask.ca!duke.usask.ca!luray From: Ray Lu Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: beta gal assay Date: Tue, 9 Jul 1996 12:30:11 -0600 Organization: University of Saskatchewan Lines: 20 Message-ID: NNTP-Posting-Host: duke.usask.ca Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Xref: biosci bionet.molbio.proteins:8288 bionet.molbio.methds-reagnts:46684 Recently, I have trouble reproducing my beta gal results in my yeast two hybrid system (from Clontech). I use ONPG as substrate. I have tried a few times now. All samples turned out to be negative, even for the ones that have previously shown positive. I have remade all solutions fresh and retransformed yeast, but it didn't help. Where can go wrong? Anyone has similar experience? ------ Ray LU University of Saskatchewan Dept of Vet Micro, WCVM Sasktoon, SK S7N 5B4 Canada Tel (306)966-7228 Fax (306)966-7244 luray@duke.usask.ca From owner-proteins@net.bio.net Mon Jul 08 23:00:00 1996 Path: biosci!rutgers!uwm.edu!spool.mu.edu!usenet.eel.ufl.edu!news-feed-1.peachnet.edu!news.service.emory.edu!news From: Brett Burkholder Newsgroups: bionet.molbio.proteins,bionet.molbio.proteins.7tms_r,bionet.molbio.yeast Subject: Re: Yeast antibodies!! Date: Tue, 09 Jul 1996 16:06:02 +0000 Organization: Emory University Lines: 36 Message-ID: <31E2836A.645@gmm.gen.emory.edu> References: <4qpl38$kt3$1@mhadf.production.compuserve.com> <4qv8v7$ef9@mark.ucdavis.edu> NNTP-Posting-Host: djdgw486.gen.emory.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) Xref: biosci bionet.molbio.proteins:8289 bionet.molbio.proteins.7tms_r:770 bionet.molbio.yeast:5510 Jonathan Mazer wrote: > > DSF (76042.532@CompuServe.COM) wrote: > : I'm desperately looking for commercially available antibodies to > : ubiquitously expressed yeast proteins, for instance, anti-TATA > : Binding Protein. HELP!! > : Lynette > > I'm afraid you're out of luck. There are no known commercially > available antibodies to yeast proteins that I know about. Your best bet > is to check the literature for a lab that will have made it's own > antibody(ies) against something similar to what you are working on or > what you need. Write or email them and ask for it. Explain, of course, > that you are not trying to copy their work with their antibody. Most labs > will be willing to help. (It will take a little more time, but it should > work.) Good Luck. > > -jsmazer@ucdavis.edu > This is a good suggestion that may work well for you. There may also be a commercial alternative: StressGen (1-800-661-4978, Victoria, BC) carries antibodies for chaperone proteins. For two of these antibodies, one for HSP60 and one for HSP90, StressGen claims cross reactivity with yeast extracts. Since these proteins are ubiquitous and highly conserved, one or both of these may serve you well. These protiens are ubiquitously expressed, but expression is increased under stressful conditions (i.e. extreme temperatures and certain media). That may be the biggest drawback to using them. Brett Burkholder Emory University Genetics and Molecular Medicine From owner-proteins@net.bio.net Mon Jul 08 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news.cse.psu.edu!news.cc.swarthmore.edu!netnews.upenn.edu!news.tju.edu!usenet From: Charles Brenner Newsgroups: bionet.molbio.proteins Subject: Re: Not binding in Western Date: Tue, 09 Jul 1996 11:17:46 -0500 Organization: Kimmel Cancer Institute Lines: 22 Message-ID: <31E28619.5D3E@dada.jci.tju.edu> References: Reply-To: brenner@dada.jci.tju.edu NNTP-Posting-Host: cubist.jci.tju.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b4Gold (Macintosh; I; PPC) Gourley, Tania Suzanne wrote: > > Does anyone know of any references refering to antibodies which cannot > recognise a protein when it is bound to membrane such as in Western blots but > can bind free protein. > > Thanks, > Tania If an antibody is raised to native protein it wouldn't be at all surprising if epitopes are native. Conversely, antibodies raised against SDS-PAGE-run samples may work fine on Western and fail in IP. Charlie -- *********************************************************************** Charles Brenner Laboratory of Protein Structure Assistant Professor and Cellular Function Kimmel Cancer Institute phone (215) 503-4573 Thomas Jefferson University fax (215) 923-2117 233 S 10th St., rm. 833a mailto:brenner@dada.jci.tju.edu Philadelphia, PA 19107 http://asterix.jci.tju.edu/brenner.html *********************************************************************** From owner-proteins@net.bio.net Tue Jul 09 23:00:00 1996 Path: biosci!pbi.nrc.ca!tdemeke From: tdemeke@pbi.nrc.ca ("Demeke, Tigst") Newsgroups: bionet.molbio.proteins Subject: Contamination of PCR/RAPD Date: 10 Jul 1996 07:29:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <31E3CB9C@gate1.pbi.nrc.ca> NNTP-Posting-Host: net.bio.net Clay: A similar problem has been mentioned before for PCR/RAPD. As you have stated you have exhausted the necessary changes that you have to make. But, I think you have not tried another Taq source. There could be some bacterial DNA contamination in some Taq batches. So it may be worthwhile try another source. Good luck! Tigst From owner-proteins@net.bio.net Tue Jul 09 23:00:00 1996 Path: biosci!agate!nature.berkeley.edu!lhom From: lhom@nature.berkeley.edu (Louis Hom) Newsgroups: bionet.molbio.proteins Subject: Cathepsin processing Date: 11 Jul 1996 01:22:39 GMT Organization: University of California, Berkeley Lines: 9 Message-ID: <4s1l0v$elc@agate.berkeley.edu> NNTP-Posting-Host: nature.berkeley.edu Does anyone know (and/or know of a reference that describes) whether cathepsins B and L are self-processing and what rate order it proceeds under? I suspect it's a second order process, but I haven't actually seen that written anywhere. -- _______________________________________________________________________________ Lou Hom >K '93 "Putney is confusing obscenity lhom@nature.berkeley.edu with originality." http://www.ocf.berkeley.edu/~lhom -- Myron X in "Putney Swope" From owner-proteins@net.bio.net Tue Jul 09 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!news-res.gsl.net!news.gsl.net!usenet.eel.ufl.edu!news.ultranet.com!homer.alpha.net!uwm.edu!news.cse.psu.edu!rutgers!csn!nntp-xfer-1.csn.net!magnus.acs.ohio-state.edu!lerc.nasa.gov!purdue!mozo.cc.purdue.edu!not-for-mail From: wilkinst@deft.cc.purdue.edu (Thomas Wilkinson) Newsgroups: bionet.molbio.proteins Subject: gel electrophoresis of peptides... Date: 10 Jul 1996 17:11:23 -0500 Organization: Purdue University Computing Center Lines: 30 Distribution: world Message-ID: <4s19qb$guv@deft.cc.purdue.edu> NNTP-Posting-Host: deft.cc.purdue.edu Newsgroups: bionet.molecules.peptides Subject: gel electrophoresis of peptides... Summary: Followup-To: Distribution: world Organization: Purdue University Computing Center Keywords: Hello, I was wondering if somebody had some experience with SDS gel electrophoresis of peptides. I have a sample that I would like to analyze to see if it contains a short (12-residue) peptide, molecular weight = 1462. The sample is not some mixture of many species...the sample to be analyzed either has the 12-mer, or else the sample contains no peptide whatsoever. Thus, this gel should be really easy to interpret. I also have a similar sample that I would like to analyze for peptide content, except in this case I am looking for the presence or absence of a 33-residue peptide (MW = 3487). I would like to run these samples out on an SDS gel, and then coomassie-stain. My question is that I don't know what the optimal percentage of polyacrylamide would be for this task. What percent gel is best? Is gel electrophoresis of peptides commonly done? Your suggestions are much appreciated. thanks, tom From owner-proteins@net.bio.net Tue Jul 09 23:00:00 1996 Message-ID: <31E3A0AA.767F@hnashe.com> Date: Wed, 10 Jul 1996 13:23:06 +0100 From: Charlie Cox X-Mailer: Mozilla 3.0b3Gold (Win95; I) MIME-Version: 1.0 Newsgroups: de.sci.biologie,bionet.molbio.proteins,de.sci.chemie, Subject: Contributors Wanted Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: l8_ts1.cyberspy.dialin.net Lines: 7 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!new-news.sprintlink.net!newsreader.sprintlink.net!news.sprintlink.net!news-stk-3.sprintlink.net!newsfeed.internetmci.com!btnet!news.uk0.vbc.net!calvin.aspen-internet.net! Contributors Wanted In the summer of 1996, The International Guide for Environmental Solutions will be completed. We require all information/input in the way of editorial, reference material etc mailing lists WWW sites usenet groups etc... for this free service Please visit our test site at www.hnashe.com and e-mail us with your suggestions and what you think should be included. From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!martinlab From: klenchin@macc.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: Is your computer being bugged???? Date: 11 Jul 1996 16:12:32 GMT Organization: UW-Madison Lines: 20 Message-ID: <4s395g$qm2@news.doit.wisc.edu> References: <4s34s8$1l1@hollywood.cinenet.net> NNTP-Posting-Host: martinlab.biochem.wisc.edu X-Newsreader: News Xpress Version 1.0 Beta #4 In article <4s34s8$1l1@hollywood.cinenet.net>, hldco@cine.net (HLD PUBLISHING) wrote: ->Is your computer being monitored by someone else? -> Is someone using your computer without your knowledge? [bunch of commercial crap] And then even better indication that spammers are usually indecent assholes: ->Notice To: Newsgroup Moderators, Managers or Vested Interest Subscribers. ->Due to HLD PUBLISHING limited list of Newsgroups, it is not our policy to ->remove a newsgroup from our list free of charge. To be removed from our ->list of future commericial postings by HLD PUBLISHING COMPANY an Annual ->Charge of Ninety Five dollars is required. Just send $95.00 with your ^^^^^^^^^^^^^^^^^^^^ ->Name, Address and Name of the Newsgroup to be removed from our list. From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!news-res.gsl.net!news.gsl.net!hunter.premier.net!newsfeed.internetmci.com!news.campus.mci.net!news.uky.edu!usenet From: "Michael W. Thompson" Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: How can I inhibit degradation of a dipeptide? Date: 12 Jul 1996 00:21:29 GMT Organization: University of Kentucky Lines: 13 Message-ID: <4s45q9$pk0@service3.uky.edu> References: NNTP-Posting-Host: node-01-11.dialin.uky.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) To: goldberg@bms.com Xref: biosci bionet.molbio.methds-reagnts:46803 bionet.molbio.proteins:8310 I do know of a couple of protease deficient E. Coli strains, but I'm afraid I can't remember their exact phenotypes offhand. They are VT5600, SA2818 and SU12036 as far as I can remember. You could probably find these via the E. Coli strain database, at URL http://cgsc.biology.yale.edu If I can locate the information on these strains I will post them here. Michael Thompson Department of Biochemistry University of Kentucky Lexington, KY 40517-3552 From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!agate!spool.mu.edu!usenet.eel.ufl.edu!news.ultranet.com!homer.alpha.net!uwm.edu!cs.utexas.edu!howland.reston.ans.net!newsfeed.internetmci.com!in1.uu.net!ott.istar!istar.net!news.nstn.ca!coranto.ucs.mun.ca!news.unb.ca!unb.ca!l14y From: l14y@unb.ca Newsgroups: bionet.molbio.proteins Subject: BioRad's InstaGene Matrix -- how does it work? Date: Thu, 11 Jul 1996 23:10:43 GMT Organization: University of New Brunswick Lines: 7 Message-ID: NNTP-Posting-Host: 131.202.97.30 X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] Does anyone know the reagent in BioRads instagene matrix which causes lyses of bacterial cells? Troy Barton University of New Brunswick L14Y@UNB.CA From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-res.gsl.net!news.gsl.net!nntp.coast.net!oleane!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!news.belnet.be!news.fundp.ac.be!mac-biochimie2.biocell.fundp.ac.be!utilisateur From: iernest@biocell.fundp.ac.be (Isabelle Ernest) Newsgroups: bionet.molbio.proteins Subject: Human breakpoint translocation Bcl2 Date: 11 Jul 1996 14:38:22 GMT Organization: F.U.N.D.P - Cellular Biochemistry Lines: 19 Message-ID: NNTP-Posting-Host: mac-biochimie2.biocell.fundp.ac.be X-Newsreader: Yet Another NewsWatcher F2.1.7 I'am looking for different cell lines containing the minor and major breakpoint region of the Bcl2 translocations. Do you know if somebody has this type of cell lines, please reply. Thanks in advance. Isabelle ERNEST e-mail: iernest@biocell.fundp.ac.be -- Isabelle Ernest Cellular Biochemistry, FUNDP 61, rue de Bruxelles B-5000 Namur Belgium Tel : 32-81-724321 Fax : 32-81-724135 e-mail: iernest@biocell.fundp.ac.be From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!nntp.coast.net!news-res.gsl.net!news.gsl.net!usenet.eel.ufl.edu!warwick!yama.mcc.ac.uk!liv!woodie From: woodie@liverpool.ac.uk (Dr I.P. Woodrow) Subject: Re: gel electrophoresis of peptides... Message-ID: Sender: news@liverpool.ac.uk (News System) Nntp-Posting-Host: ash-23.liv.ac.uk Organization: The University of Liverpool References: <4s19qb$guv@deft.cc.purdue.edu> Date: Thu, 11 Jul 1996 13:49:19 GMT Lines: 46 In article <4s19qb$guv@deft.cc.purdue.edu>, wilkinst@deft.cc.purdue.edu (Thomas Wilkinson) writes: > Newsgroups: bionet.molecules.peptides > Subject: gel electrophoresis of peptides... > Summary: > Followup-To: > Distribution: world > Organization: Purdue University Computing Center > Keywords: > > > Hello, > > I was wondering if somebody had some experience with SDS gel electrophoresis of > peptides. I have a sample that I would like to analyze to see if it contains > a short (12-residue) peptide, molecular weight = 1462. > > The sample is not some mixture of many species...the sample to be analyzed > either has the 12-mer, or else the sample contains no peptide whatsoever. Thus, > this gel should be really easy to interpret. I also have a similar sample that > I would like to analyze for peptide content, except in this case I am looking > for the presence or absence of a 33-residue peptide (MW = 3487). > > I would like to run these samples out on an SDS gel, and then coomassie-stain. > My question is that I don't know what the optimal percentage of polyacrylamide > would be for this task. What percent gel is best? Is gel electrophoresis of > peptides commonly done? Your suggestions are much appreciated. > > thanks, > > tom > Is there any particular reason why you need to separate out the peptide anyway? If this is the only component which you will find, then all you need to is to do a protein assay. I believe I am right in thinking that the Bradford assay works by binding to the peptide bond, so you shouldn't have any trouble seeing small peptides. Alternatively you could try using amido black which I know stains small peptides as I have just used it for 7-15 residue small peptides myself. I did dig out an old reference for some protein assay using amido black from years ago, although their technique did seem very long winded. Let me know if you need this, or any other help. GOOD LUCK! Iain From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!news-res.gsl.net!news.gsl.net!hunter.premier.net!newsfeed.internetmci.com!news.campus.mci.net!news.uky.edu!usenet From: "Michael W. Thompson" Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: How can I inhibit degradation of a dipeptide? Date: 12 Jul 1996 00:21:41 GMT Organization: University of Kentucky Lines: 13 Message-ID: <4s45ql$pk0@service3.uky.edu> References: NNTP-Posting-Host: node-01-11.dialin.uky.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) To: goldberg@bms.com Xref: biosci bionet.molbio.methds-reagnts:46805 bionet.molbio.proteins:8312 I do know of a couple of protease deficient E. Coli strains, but I'm afraid I can't remember their exact phenotypes offhand. They are VT5600, SA2818 and SU12036 as far as I can remember. You could probably find these via the E. Coli strain database, at URL http://cgsc.biology.yale.edu If I can locate the information on these strains I will post them here. Michael Thompson Department of Biochemistry University of Kentucky Lexington, KY 40517-3552 From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!news-res.gsl.net!news.gsl.net!hunter.premier.net!newsfeed.internetmci.com!news.campus.mci.net!news.uky.edu!usenet From: "Michael W. Thompson" Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: How can I inhibit degradation of a dipeptide? Date: 12 Jul 1996 00:21:34 GMT Organization: University of Kentucky Lines: 13 Message-ID: <4s45qe$pk0@service3.uky.edu> References: NNTP-Posting-Host: node-01-11.dialin.uky.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) To: goldberg@bms.com Xref: biosci bionet.molbio.methds-reagnts:46804 bionet.molbio.proteins:8311 I do know of a couple of protease deficient E. Coli strains, but I'm afraid I can't remember their exact phenotypes offhand. They are VT5600, SA2818 and SU12036 as far as I can remember. You could probably find these via the E. Coli strain database, at URL http://cgsc.biology.yale.edu If I can locate the information on these strains I will post them here. Michael Thompson Department of Biochemistry University of Kentucky Lexington, KY 40517-3552 From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!news.mira.net.au!harbinger.cc.monash.edu.au!nntp.coast.net!oleane!plug.news.pipex.net!pipex!tube.news.pipex.net!pipex!hole.news.pipex.net!pipex!tank.news.pipex.net!pipex!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!news.ox.ac.uk!biomac7.jr2.ox.ac.uk!vurquidi From: vurquidi@molbiol.ox.ac.uk (Virginia Urquidi) Newsgroups: bionet.molbio.proteins Subject: Binding assays in PVDF membranes Date: Thu, 11 Jul 96 17:01:01 GMT Organization: NDCB Lines: 9 Message-ID: NNTP-Posting-Host: biomac7.jr2.ox.ac.uk X-Newsreader: VersaTerm Link v1.1.6 Does anyone know of a paper where antibodies bound to proteins in immunoblotting membranes have been demonstrated to inhibit protein-protein interactions in overlay assays? I will be very grateful for relevant references. Thank you. V Urquidi From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!agate!usenet From: Steve Feldman Newsgroups: bionet.molbio.proteins Subject: Cleavage of glycosidic linkeages Date: Thu, 11 Jul 1996 10:57:18 -0700 Organization: UC Berkeley, School of Public Health Lines: 3 Message-ID: <31E5407E.6A7A@violet.berkeley.edu> NNTP-Posting-Host: steve.hip.berkeley.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Does anyone know if Heparitinase or other glycosaminoglycan lyases will cleave N-linked or O-linked oligosaccharides from a proteoglycan in a fashion similar to N-glycanase or O-glycanase? From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!newsfeed.internetmci.com!news.ac.net!news.cais.net!nntp.uio.no!biotek19 From: damartin@bioslave.uio.no (David Martin) Newsgroups: bionet.molbio.proteins Subject: Re: gel electrophoresis of peptides... Date: Thu, 11 Jul 96 09:07:52 GMT Organization: Biotechnology Centre of Oslo Lines: 55 Message-ID: <4s2g9o$a1s@ratatosk.uio.no> References: <4s19qb$guv@deft.cc.purdue.edu> NNTP-Posting-Host: biotek19.uio.no X-Newsreader: News Xpress Version 1.0 Beta #3 In article <4s19qb$guv@deft.cc.purdue.edu>, wilkinst@deft.cc.purdue.edu (Thomas Wilkinson) wrote: -->Newsgroups: bionet.molecules.peptides -->Subject: gel electrophoresis of peptides... -->Summary: -->Followup-To: -->Distribution: world -->Organization: Purdue University Computing Center -->Keywords: --> --> -->Hello, --> -->I was wondering if somebody had some experience with SDS gel electrophoresis of -->peptides. I have a sample that I would like to analyze to see if it contains -->a short (12-residue) peptide, molecular weight = 1462. --> -->The sample is not some mixture of many species...the sample to be analyzed -->either has the 12-mer, or else the sample contains no peptide whatsoever. Thus, -->this gel should be really easy to interpret. I also have a similar sample that -->I would like to analyze for peptide content, except in this case I am looking -->for the presence or absence of a 33-residue peptide (MW = 3487). --> -->I would like to run these samples out on an SDS gel, and then coomassie-stain. -->My question is that I don't know what the optimal percentage of polyacrylamide -->would be for this task. What percent gel is best? Is gel electrophoresis of -->peptides commonly done? Your suggestions are much appreciated. --> You are at the lower limit for SDS-PAGE and would need to use a Tris-Tricine buffer system (schagger & von Jagow, Anal. biochem. 1987, 166, 368-379) and a fairly high percentage gel (15%-20%) Even then the 12mer may be too small. Alternatively, if you just wish for a yes or no answer for the presence of peptide, you could dot your sample onto PVDF and stain with amido black. best of luck. .d * David Martin, PhD - Post-Doctoral Research Fellow * * Atherosclerosis and Thrombosis research group * * Biotechnologisenteret i Oslo * * Postboks 1125 Blindern, N-0316 Oslo, Norway * * Tel: +47 22 95 84 54 Fax: +47 22 69 41 30 * * http://www.uio.no/~damartin/ david.martin@biotek.uio.no * From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news.cse.psu.edu!news.cc.swarthmore.edu!netnews.upenn.edu!dsinc!news.acsu.buffalo.edu!news.drenet.dnd.ca!crc-news.doc.ca!nott!nrcnet0.nrc.ca!ratilal From: "Wm L. Crosby" Newsgroups: bionet.molbio.proteins Subject: Postdoctoral Position Date: Thu, 11 Jul 1996 16:05:24 -0600 Organization: National Research Council of Canada Lines: 40 Message-ID: <31E57AA4.465A@pbi.nrc.ca> NNTP-Posting-Host: 204.83.146.17 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b4 (Win95; I) Postdoctoral Position Available Plant Biotechnology Institute - NRC Canada Saskatoon, Canada A postdoctoral (Research Associate) position is available to study the role of protein-protein interactions in floral morphogenesis in Arabidopsis. The successful candidate will be employ existing 2-hybrid, 3-hybrid and related approaches for the analysis of protein complex formation involving homeotic gene products in this model species. The project will focus on the mechanistic role of such interactions in the regulation of floral ontogeny. A candidate with strong molecular biology skills is required for this position. Experience with transgenic plant studies, recombinant yeast systems and/or recombinant antibody phage display technology would be a particular advantage. The position is for an initial period of 2 years with possibilities of extension to a third year subject to satisfactory performance and availability of resources. The position is available on or after September 1, 1996 and offers a competitive salary commensurate with experience. Saskatoon is a pleasant city of 200,000 and is ranked among the most affordable and liveable communities in the country. Situated in the central province of Saskatchewan, the area offers an abundance of urban and outdoor amenities. The PBI is responsible for executing the National Research Council of Canada's plant biotechnology mandate on behalf of the Government of Canada. The Institute is situated on the campus of the University of Saskatchewan (17,000 students) where strong academic and corporate interactions are available, as well as access to excellent physical facilities. Interested individuals are urged to forward their CV along with letters of reference to: Dr. W.L. (Bill) Crosby Gene Technology Group NRC Plant Biotechnology Institute 110 Gymnasium Road Saskatoon, SK S7N 0W9 Canada Tel: (306)975-4187 FAX: -4839 Email: bcrosby@pbi.nrc.ca From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!drm21 From: drm21@mole.bio.cam.ac.uk (David Micklem) Newsgroups: bionet.molbio.proteins Subject: Re: Is your computer being bugged???? Date: Thu, 11 Jul 1996 21:50:23 +0000 Organization: Wellcome/CRC Institute Lines: 40 Message-ID: References: <4s34s8$1l1@hollywood.cinenet.net> <4s395g$qm2@news.doit.wisc.edu> NNTP-Posting-Host: drm-mac1.welc.cam.ac.uk X-Newsreader: Yet Another NewsWatcher 2.2.0b6 In article <4s395g$qm2@news.doit.wisc.edu>, klenchin@macc.wisc.edu (Dima Klenchin) wrote: >In article <4s34s8$1l1@hollywood.cinenet.net>, > hldco@cine.net (HLD PUBLISHING) wrote: >->Is your computer being monitored by someone else? >-> Is someone using your computer without your knowledge? > >[bunch of commercial crap] > >And then even better indication that spammers are usually indecent >assholes: > >->Notice To: Newsgroup Moderators, Managers or Vested Interest >Subscribers. >->Due to HLD PUBLISHING limited list of Newsgroups, it is not our policy >to >->remove a newsgroup from our list free of charge. To be removed from our >->list of future commericial postings by HLD PUBLISHING COMPANY an Annual >->Charge of Ninety Five dollars is required. Just send $95.00 with your > ^^^^^^^^^^^^^^^^^^^^ > >->Name, Address and Name of the Newsgroup to be removed from our list. What? Didn't anybody tell them that the charge for advertising on bionet.* is $300,000 per newsgroup? Too bad! That should sort out our funding problems ;-) What a bunch of ass-holes. _____________________________________________________________ D.R.Micklem, Wellcome/CRC Institute, Time flies like an arrow... Tennis Court Road, Cambridge CB2 1QR Fruit flies like a banana. UK Tel: [+44] (0)1223 334129 Email:drm21@mole.bio.cam.ac.uk Fax: [+44] (0)1223 334089 _____________________________________________________________ From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!usenet From: Krieger Lab Newsgroups: bionet.molbio.proteins Subject: Re: gel electrophoresis of peptides... Date: Thu, 11 Jul 1996 10:11:56 +0000 Organization: Massachvsetts Institvte of Technology Lines: 40 Message-ID: <31E4D36C.135F@mit.edu> NNTP-Posting-Host: montylab.mit.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; 68K) CC: wilkinst@deft.cc.purdue.edu > In article <4s19qb$guv@deft.cc.purdue.edu>, > wilkinst@deft.cc.purdue.edu (Thomas Wilkinson) wrote: > -->Hello, > --> > -->I was wondering if somebody had some experience with SDS gel electrophoresis of > -->peptides. I have a sample that I would like to analyze to see if it contains > -->a short (12-residue) peptide, molecular weight = 1462. > --> > -->The sample is not some mixture of many species...the sample to be analyzed > -->either has the 12-mer, or else the sample contains no peptide whatsoever. Thus, > -->this gel should be really easy to interpret. I also have a similar sample that > -->I would like to analyze for peptide content, except in this case I am looking > -->for the presence or absence of a 33-residue peptide (MW = 3487). > --> > -->I would like to run these samples out on an SDS gel, and then coomassie-stain. > -->My question is that I don't know what the optimal percentage of polyacrylamide > -->would be for this task. What percent gel is best? Is gel electrophoresis of > -->peptides commonly done? Your suggestions are much appreciated. > --> > Sounds like your peptides are too short to do SDS-PAGE with. I'd recommend either: 1) Reverse phase HPLC (assuming you know where they run), or 2) Mass Spectroscopy I'd think that either of these would be preferable to PAGE.... -David . . From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!newsfeed.internetmci.com!in2.uu.net!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: kempbio@aol.com (Kempbio) Newsgroups: bionet.molbio.proteins Subject: Re: Not binding in Western Date: 11 Jul 1996 07:12:41 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 6 Sender: root@newsbf02.news.aol.com Message-ID: <4s2nj9$mer@newsbf02.news.aol.com> References: Reply-To: kempbio@aol.com (Kempbio) NNTP-Posting-Host: newsbf02.mail.aol.com Are you running your PAGE gel under reducing conditions? If so, this may be the cause of the problem. We have seen this with a number of proteins and antibody binding was restored when we used non-reduced conditions on the PAGE gel. Chris From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!howland.reston.ans.net!surfnet.nl!swsbe6.switch.ch!news.belnet.be!news.sri.ucl.ac.be!usenet From: verhelpe Newsgroups: bionet.molbio.proteins Subject: Re: Protein elution from SDS-PAGE gel ?? Date: 11 Jul 1996 09:14:28 GMT Organization: UCL Lines: 12 Distribution: world Message-ID: <4s2glk$bo5@sci3.sri.ucl.ac.be> References: <4r61f8$9mr@worak.kaist.ac.kr> NNTP-Posting-Host: 130.104.5.73 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) Hello there is an apparatus of Biorad : the Prepcell; It s a big SDS-page and you can elute the protein. Bio-rad normally lend easily prepCell. Anne Jungbluth Laboratoire d'orthopedie de l'UCL Avenue Mounier, 53 Tour Pasteur, 5388 1200 Bruxelles jungbluth@orto.ucl.ac.be From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!news-stk-200.sprintlink.net!coopnews.coop.net!boulder.earthnet.net!usenet From: "Phillip E. Schwartz" Newsgroups: bionet.molbio.proteins Subject: New FDA Regs/Antibodies Date: Thu, 11 Jul 1996 12:46:04 -0700 Organization: Affinity BioReagents, Inc. Lines: 42 Message-ID: <31E559FC.1CBC@bioreagents.com> NNTP-Posting-Host: slip12.earthnet.net Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 2.0 (Win16; I) Please help! Will the individual at your organization who is in charge of regulatory affairs or who is concerned about the negative effects new FDA regulations may have on basic scientific and medical research in addition to health care in general please contact me regarding this matter. I am trying to get as many people to comment on and become involved in a grass-roots effort to keep the FDA from including all antibody research reagents as ‘in vitro diagnostic devices’. Granted, some are but most are not. Please review the information at: http:/www.earthnet.net/~affinity/fda/ It would be optimal if this website could be hotlinked to yours to gain the maximum amount of exposure prior to August 30, 1996 public comment deadline. I would appreciate any comments, questions, referred contacts, etc. that may be useful in changing the language of this pending FDA regulation. FDA Regulation: The Immunohistochemistry Reagents and Kits Regulation: 21/CFR 864 Docket Number: 94P-0342 Sincerely, Phillip E. Schwartz Antibody Partnership Project Manager Affinity BioReagents, Inc. 14818 W. 6th Ave., Suite 13A Golden, CO 80401 TEL: 800-527-4535 FAX: 303-278-2424 email: schwartz@bioreagents.com website: http://www.bioreagents.com/affinity From owner-proteins@net.bio.net Wed Jul 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!newsserver.jvnc.net!crick.bms.com!NewsWatcher!user From: goldberg@bms.com (Steven Goldberg) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: How can I inhibit degradation of a dipeptide? Date: Thu, 11 Jul 1996 14:43:50 -0500 Organization: Bristol-Myers Squibb Co. Lines: 26 Message-ID: NNTP-Posting-Host: 140.176.74.203 Xref: biosci bionet.molbio.methds-reagnts:46792 bionet.molbio.proteins:8305 I am working on a project where I have cloned and overexpressed an aminotransferase in E. coli. We are trying to use crude extracts of the recombinant strain in a bioconversion with a dipeptide as substrate. It appears that the reaction is taking place but the product is then being cleaved into its constituent amino acids. The longer after induction the culture is taken, the worse this problem is. (The system uses a minimal medium and L-tryptophan as inducer.) My guess is that the burden of overproducing the aminotransferase is causing a stress response (which might include a protease). I have both ampicillin- and kanamycin-resistant versions of the expressing plasmid and the degradation is decidedly more pronounced in the latter. My questions: 1. Are there any known E. coli strains that lack a protease which would attack a dipeptide? 2. We are currently running our fermentations at 30oC. Would going to a lower temperature help alleviate our problem? How about using a richer medium? 3. Any other hosts (bacterial or yeast) which have low protease activities? Any input would be welcome. Thanks. Steve From owner-proteins@net.bio.net Thu Jul 11 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!news00.sunet.se!sunic!news99.sunet.se!news.chalmers.se!news.gu.se!news From: Vidal Newsgroups: bionet.molbio.proteins Subject: basal tf:s Date: Fri, 12 Jul 1996 12:27:50 -0700 Organization: RCEM Lines: 7 Message-ID: <31E6A736.20B9@ss.gu.se> NNTP-Posting-Host: kkem31.clab.gu.se Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) I have a question concerning the regulation of basal transcription factors such as TFIIA, B, C etc. Does anyone know if these factors are subject to regulation in cultured cell lines? Are the levels of these proteins the same in proliferating cells as in cells which do not proliferate. O Vidal From owner-proteins@net.bio.net Thu Jul 11 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!nntp.coast.net!news00.sunet.se!sunic!news99.sunet.se!news.uni-c.dk!eagle.novo.dk!usenet From: Lauge Schaffer Newsgroups: bionet.molbio.proteins Subject: Re: gel electrophoresis of peptides... Date: Fri, 12 Jul 1996 13:09:55 +0200 Organization: Novo Nordisk A/S Lines: 38 Message-ID: <31E63283.3AF3@novo.dk> References: <4s19qb$guv@deft.cc.purdue.edu> NNTP-Posting-Host: lsc.novo.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b5aGold (Win95; I) Thomas Wilkinson wrote: > > Newsgroups: bionet.molecules.peptides > Subject: gel electrophoresis of peptides... > Summary: > Followup-To: > Distribution: world > Organization: Purdue University Computing Center > Keywords: > > Hello, > > I was wondering if somebody had some experience with SDS gel electrophoresis of > peptides. I have a sample that I would like to analyze to see if it contains > a short (12-residue) peptide, molecular weight = 1462. > > The sample is not some mixture of many species...the sample to be analyzed > either has the 12-mer, or else the sample contains no peptide whatsoever. Thus, > this gel should be really easy to interpret. I also have a similar sample that > I would like to analyze for peptide content, except in this case I am looking > for the presence or absence of a 33-residue peptide (MW = 3487). > > I would like to run these samples out on an SDS gel, and then coomassie-stain. > My question is that I don't know what the optimal percentage of polyacrylamide > would be for this task. What percent gel is best? Is gel electrophoresis of > peptides commonly done? Your suggestions are much appreciated. > > thanks, > > tom This sounds like sending your lunch-box off for elemental analysis to figure out whether you have eaten your sandwiches or not. In your case it sounds like an amino acid analysis, a few steps of peptide sequencing, a mass-spec or a protein determination (e.g. Bradford or Lowry) would give you better information. Lauge From owner-proteins@net.bio.net Thu Jul 11 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!news-res.gsl.net!news.gsl.net!nntp.coast.net!dispatch.news.demon.net!demon!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!news.ox.ac.uk!biomac7.jr2.ox.ac.uk!vurquidi From: vurquidi@molbiol.ox.ac.uk (Virginia Urquidi) Newsgroups: bionet.molbio.proteins Subject: Binding assays in PVDF membranes Date: Fri, 12 Jul 96 12:52:53 GMT Organization: NDCB Lines: 9 Message-ID: NNTP-Posting-Host: biomac7.jr2.ox.ac.uk X-Newsreader: VersaTerm Link v1.1.6 Does anyone know of a paper where antibodies bound to proteins in immunoblotting membranes have been demonstrated to inhibit protein-protein interactions in overlay assays? I will be very grateful for relevant references. Thank you. V Urquidi From owner-proteins@net.bio.net Thu Jul 11 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!uwm.edu!news.cse.psu.edu!news.cc.swarthmore.edu!netnews.upenn.edu!cronkite.ocis.temple.edu!astro.ocis.temple.edu!driska From: driska@astro.ocis.temple.edu (Stephen P. Driska PhD) Newsgroups: bionet.molbio.proteins Subject: Re: gel electrophoresis of peptides... Date: 12 Jul 1996 18:54:42 GMT Organization: Temple University, Academic Computer Services Lines: 43 Distribution: world Message-ID: <4s671i$jtv@cronkite.ocis.temple.edu> References: <4s19qb$guv@deft.cc.purdue.edu> NNTP-Posting-Host: astro.ocis.temple.edu X-Newsreader: TIN [version 1.2 PL2] Thomas Wilkinson (wilkinst@deft.cc.purdue.edu) wrote: : Newsgroups: bionet.molecules.peptides : Subject: gel electrophoresis of peptides... : Summary: : Followup-To: : Distribution: world : Organization: Purdue University Computing Center : Keywords: : Hello, : I was wondering if somebody had some experience with SDS gel electrophoresis of : peptides. I have a sample that I would like to analyze to see if it contains : a short (12-residue) peptide, molecular weight = 1462. : The sample is not some mixture of many species...the sample to be analyzed : either has the 12-mer, or else the sample contains no peptide whatsoever. Thus, : this gel should be really easy to interpret. I also have a similar sample that : I would like to analyze for peptide content, except in this case I am looking : for the presence or absence of a 33-residue peptide (MW = 3487). : I would like to run these samples out on an SDS gel, and then coomassie-stain. : My question is that I don't know what the optimal percentage of polyacrylamide : would be for this task. What percent gel is best? Is gel electrophoresis of : peptides commonly done? Your suggestions are much appreciated. : thanks, : tom No experience with anything like that, but I would recommend Novex (800)456-6839, a company that sells equipment and supplies including precast gels using the tris-tricine gel system that claims to be able to resolve peptides about as small as those you mention. Good luck -- Steve Driska, Physiology Department, Temple University Medical School Philadelphia, PA 19140 USA (215) 707-3283 driska@astro.ocis.temple.edu If I could think of something witty and clever to say, it would go right here ----->> ......................... From owner-proteins@net.bio.net Thu Jul 11 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-res.gsl.net!news.gsl.net!hunter.premier.net!newsfeed.internetmci.com!newsserver.jvnc.net!crick.bms.com!watson.bms.com!curtis From: curtis@watson.bms.com (Michael S Curtis) Newsgroups: bionet.molbio.proteins Subject: Dimerization of Glutathione-S-Transferase Date: 12 Jul 1996 17:47 EST Organization: Bristol Myers Squibb Pharmaceutical Research Institute Lines: 9 Distribution: world Message-ID: <12JUL199617473807@watson.bms.com> NNTP-Posting-Host: watson.bms.com News-Software: VAX/VMS VNEWS 1.41 Does anyone know if glutathione-s-tranferase dimerizes giving a molwt of approx 59,000? If anyone has any info please post. Thanks, Mike C. curtis@bms.com From owner-proteins@net.bio.net Thu Jul 11 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news.cse.psu.edu!news.eecs.nwu.edu!newsfeed.acns.nwu.edu!news.acns.nwu.edu!news From: r-berry@nwu.edu (Robert W. Berry) Newsgroups: bionet.molbio.proteins Subject: Re: gel electrophoresis of peptides... Date: 12 Jul 1996 15:25:14 GMT Organization: Northwestern University, Evanston, IL. USA Lines: 51 Distribution: world Message-ID: <4s5qoq$grk@news.acns.nwu.edu> References: <4s19qb$guv@deft.cc.purdue.edu> Reply-To: r-berry@nwu.edu NNTP-Posting-Host: 165.124.242.54 Mime-Version: 1.0 X-Newsreader: WinVN 0.93.11 In article <4s19qb$guv@deft.cc.purdue.edu>, wilkinst@deft.cc.purdue.edu says... > >Newsgroups: bionet.molecules.peptides >Subject: gel electrophoresis of peptides... >Summary: >Followup-To: >Distribution: world >Organization: Purdue University Computing Center >Keywords: > > >Hello, > >I was wondering if somebody had some experience with SDS gel electrophoresis of >peptides. I have a sample that I would like to analyze to see if it contains >a short (12-residue) peptide, molecular weight = 1462. > >The sample is not some mixture of many species...the sample to be analyzed >either has the 12-mer, or else the sample contains no peptide whatsoever. Thus, >this gel should be really easy to interpret. I also have a similar sample that >I would like to analyze for peptide content, except in this case I am looking >for the presence or absence of a 33-residue peptide (MW = 3487). > >I would like to run these samples out on an SDS gel, and then coomassie-stain. >My question is that I don't know what the optimal percentage of polyacrylamide >would be for this task. What percent gel is best? Is gel electrophoresis of >peptides commonly done? Your suggestions are much appreciated. > >thanks, > >tom > While I agree with the Krieger lab that other methods may be less painful, some years ago we did develop an SDS gel system that was linear down to about 2.5 kD (Anderson, et al., Anal.Biochem. 132:365-375, 1983). With some tinkering, it might work for your applications. -- Robert W. Berry Northwestern University, Evanston, IL. USA r-berry@nwu.edu From owner-proteins@net.bio.net Thu Jul 11 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-res.gsl.net!news.gsl.net!nntp.coast.net!netnews.worldnet.att.net!news.u.washington.edu!homer28.u.washington.edu!sltan From: Seng-Lai Tan Newsgroups: bionet.molbio.proteins Subject: Re: Dimerization of Glutathione-S-Transferase Date: Fri, 12 Jul 1996 17:18:55 -0700 Organization: University of Washington Lines: 27 Message-ID: References: <12JUL199617473807@watson.bms.com> NNTP-Posting-Host: homer28.u.washington.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII NNTP-Posting-User: sltan In-Reply-To: <12JUL199617473807@watson.bms.com> I know for a fact that GST forms dimers. i'm not sure about the mol wt of the dimer. On 12 Jul 1996, Michael S Curtis wrote: > Does anyone know if glutathione-s-tranferase dimerizes giving a molwt of > approx 59,000? If anyone has any info please post. > > Thanks, > > Mike C. > curtis@bms.com > > > > Thomas Seng-Lai Tan ................................... Dept. of Microbiology : Definition of politics : Box 357242 : poly = many or excessive : University of Washington : ticks = bloodsucking creatures : Seattle, WA 98195 : Any questions? :) : :.................................: Phone: 206-543-6700 FAX: 206-543-8296 From owner-proteins@net.bio.net Thu Jul 11 23:00:00 1996 Path: biosci!rutgers!sgigate.sgi.com!news1.best.com!nntp.primenet.com!news.cais.net!hunter.premier.net!newsfeed.internetmci.com!swrinde!sdd.hp.com!night.primate.wisc.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!klenchin From: klenchin@facstaff.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: Dimerization of Glutathione-S-Transferase Date: Sat, 13 Jul 96 05:22:31 GMT Organization: UW-Madison Lines: 8 Distribution: world Message-ID: <4s78an$25u8@news.doit.wisc.edu> References: <12JUL199617473807@watson.bms.com> NNTP-Posting-Host: f182-216.net.wisc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=KOI8-R Content-Transfer-Encoding: 8bit X-Newsreader: News Xpress 2.0 Beta #2 In article <12JUL199617473807@watson.bms.com>, curtis@watson.bms.com (Michael S Curtis) wrote: #Does anyone know if glutathione-s-tranferase dimerizes giving a molwt of #approx 59,000? If anyone has any info please post. Yes, it does. But if you mean on gels, don't be confused: on SDS gel it always runs as a single band. - Dima From owner-proteins@net.bio.net Fri Jul 12 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.proteins Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 13 Jul 1996 02:00:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199607130900.CAA02334@net.bio.net> NNTP-Posting-Host: net.bio.net BIOSCI is about halfway to its funding goal!! I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We are only about halfway to our funding goal and need to raise further funds to avoid having to curtail services at net.bio.net. Fundraising is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we will be getting newer and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. 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. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these spon