From owner-proteins@net.bio.net Wed Jul 01 23:00:00 1998 From: "Christian Reiser, PhD" Newsgroups: bionet.molbio.proteins Subject: Searching for a company "Rent A scientist" Date: Fri, 03 Jul 1998 07:50:38 +0200 Organization: Regionales Rechenzentrum Erlangen, Germany Message-ID: <359C712E.71C64DFA@rzmail.uni-erlangen> NNTP-Posting-Host: 131.188.231.11 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; I) Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!woodstock.news.demon.net!demon!dispose.news.demon.net!demon!newsfeed.nacamar.de!uni-erlangen.de!uni-wuerzburg.de!news.uni-erlangen.de!not-for-mail Lines: 14 Hi, does anybody know a company renting scientists or facilities for solving problems in life science, biochemistry, microbiology (theme "Rent A Scientist") eg. overexpression and purification of a protein ? Thanks for your help. Chris Christian Reiser, PhD Med. IV, Nephrology Loschgestr. 8 D-91054 Erlangen Germany From owner-proteins@net.bio.net Thu Jul 02 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news-peer.gip.net!news-lond.gip.net!news.gsl.net!gip.net!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!tin!dswan From: dan Newsgroups: bionet.molbio.proteins Subject: Analysis of predicted protein sequences. Date: Fri, 3 Jul 1998 13:17:07 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 33 Message-ID: NNTP-Posting-Host: tin.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: dswan@tin X-No-Archive: Yes Hello all, I have recently been fortunate enough to clone a novel gene, I have 2.7kb of coding sequence and a predicted translation. I am looking for analysis programs that will help me determine possible functions for the protein. However, when I say it is a novel gene, it is a novel gene - and I can't find anything like it in the protein databases. I have used most suites for motif recognition / homology comparison / secondary structure prediction, but all I can find is a potential NLS... If anyone has any suggestions for WWW / email servers that they are particularly impressed with or use regularly and wouldn't mind a little correspondance about the output of such systems I would be very grateful. As an aside the N-terminus is serine/threonine rich, with three stretches of 7+ serines in a row. There is also a single stretch of histidines (again 7+) which as a motif seems to be present in some classes of homeobox genes, but *outside* the box region. If anyone could shed some light on potential roles / interactions of these regions I would also like to know. Thanks in advance, Daniel Swan Graduate student (47 days left and counting) MRC Clinical Sciences Centre, ICSM Hammersmith Hospital, London. +44 (0) 181 383 8298 From owner-proteins@net.bio.net Thu Jul 02 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!vixen.cso.uiuc.edu!thor.cmp.ilstu.edu!news From: Marc Domanus Newsgroups: bionet.molbio.proteins Subject: Cross-Linked Molecular Weight Markers Date: Fri, 03 Jul 1998 13:41:57 -0500 Organization: Illinois State University Lines: 20 Message-ID: <359D25F5.4DFFEC64@rs6000.cmp.ilstu.edu> NNTP-Posting-Host: 138.87.99.75 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; I) Does anyone know of a high molecular weight protein marker for use with SDS-PAGE that has a range around 100,000-500,00 Da? I have tried Sigma's phosphorylase b cross-linked rabbit marker (P8906) and followed the recommended protocol. I am only able to see the 97,400 monomer; however, the dimer which should contain 28% overall intensity, for lot#105H9400, is not visible. Has anyone had luck with Sigma's phosphorylase b marker? If so, which lot number was used and were any changes made to Sigma's recommended protocol? For example, I have been unable to get the majority of the protein into solution. Any suggestions? Thanks for the help. Marc Domanus mhdoman@rs6000.cmp.ilstu.edu From owner-proteins@net.bio.net Thu Jul 02 23:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!164.67.42.145!awabi.library.ucla.edu!164.67.43.25!news.ucla.edu!not-for-mail From: Ng Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Chemical phosphorylation of proteins Date: 4 Jul 1998 00:24:18 GMT Organization: Molecular Biology Institute, UCLA Lines: 8 Message-ID: <6njsni$b33$1@carroll.library.ucla.edu> NNTP-Posting-Host: mendel.mbi.ucla.edu X-Newsreader: TIN [UNIX 1.3 unoff BETA 970731; alpha OSF1 V4.0] Xref: biosci bionet.molbio.methds-reagnts:68736 bionet.molbio.proteins:12965 Could someone point me to some resource that discusses different reagents for phosphorylating proteins with chemicals (such as acetyl phosphate)? Or suggest reagents? Thanks. -- Ho Leung Ng holeung@ucla.edu From owner-proteins@net.bio.net Fri Jul 03 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: bhanga@my-dejanews.com Newsgroups: bionet.molbio.proteins Subject: chaperone german Date: Sat, 04 Jul 1998 14:36:33 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 10 Message-ID: <6nlelh$2pk$1@nnrp1.dejanews.com> NNTP-Posting-Host: 134.155.51.100 X-Article-Creation-Date: Sat Jul 04 14:36:33 1998 GMT X-Http-User-Agent: Mozilla/4.0 (compatible; MSIE 4.01; Windows 95) X-Http-Proxy: 1.0 www-cache.uni-mannheim.de:3128 (Squid/1.1.18) for client 134.155.17.200 Chaperone - heat shock proteine hsp 70 / hsp 60 / hsp 90 / GroEL / DnaKJ Skript zu einem Vortrag in Januar 1998 Übersicht über Wirkungsweise und Biochemie vonm Chaperonen http://members.tripod.com/~anicca/ -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-proteins@net.bio.net Sun Jul 05 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!la-news-feed1.bbnplanet.com!news.bbnplanet.com!newsfeed1.earthlink.net!nntp.earthlink.net!not-for-mail From: John Philo <"jphilo*NO SPAM12*"@earthlink.net> Newsgroups: bionet.molbio.proteins Subject: Re: Searching for a company "Rent A scientist" Date: Mon, 06 Jul 1998 12:54:23 -0700 Organization: Alliance Protein Laboratories Lines: 41 Message-ID: <35A12B6F.1BCA0B17@earthlink.net> References: <359C712E.71C64DFA@rzmail.uni-erlangen> NNTP-Posting-Host: 1cust85.tnt1.thousand-oaks.ca.da.uu.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (Win95; U) To: "Christian Reiser, PhD" Christian Reiser, PhD wrote: > > Hi, > does anybody know a company renting scientists or facilities for solving > problems in life science, biochemistry, microbiology (theme "Rent A > Scientist") eg. overexpression and purification of a protein ? > Thanks for your help. > > Chris > > Christian Reiser, PhD > Med. IV, Nephrology > Loschgestr. 8 > D-91054 Erlangen > Germany That is an awfully broad question! What you are talking about is generally called a contract research or contract manufacturing organization (CRO or CMO), and there are hundreds, if not thousands, of them. For example, my company Alliance Protein Laboratories does protein purification (microgram to gram scale) and biophysical characterization of proteins on a contract basis. It is not clear what you mean by "solving problems". That sounds more like something for a consultant. There are hundreds of biotech/pharmaceutical consultants, and many CRO companies also do consulting (as mine does). If what you are looking for is to give someone a gene and have them express and purify it, there are certainly companies out there that will do that. I don't offhand know any in Germany, but there should be one or more. Try searching for "contract research" AND "protein" on the Internet, and the web pages of organizations such as the Biotechnology Industry Association (www.bio.org) or the Drug Industry Association (www.diahome.org). The latter has a database of hundreds of CROs, although most are providers of clinical trials or work with small molecules rather than proteins. John Philo, Alliance Protein Laboratories *** Remove "*NO SPAM12*" from return address before replying. *** From owner-proteins@net.bio.net Sun Jul 05 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!howland.erols.net!ix.netcom.com!news From: Mark Atlas Newsgroups: bionet.molbio.proteins Subject: Upcoming lab equipment online auctions with Going, Going...Sold! Date: Mon, 06 Jul 1998 15:23:48 GMT Organization: ICGNetcom Lines: 145 Message-ID: <6nqq1q$4mu@sjx-ixn3.ix.netcom.com> NNTP-Posting-Host: sji-ca5-80.ix.netcom.com X-NETCOM-Date: Mon Jul 06 8:21:30 AM PDT 1998 X-Newsreader: NETCOMplete/4.0 Upcoming lab equipment online auctions with Going, Going...Sold! Going, Going Sold is now in it's 9th month of operations. It has rapidly become a standard for buying and selling quality and functional used labware. Come buy and visit http://www.going-going-sold.com Unlike other services, we handle all aspects of the sale and provide you with in lab evaluations of equipment. We also guarantee that if you bid on a product that the seller must sell the equipment. This is the only auction online which makes these guarantees as we are bonded auctioneers who run the auction. If your equipment is not found on the site you can also contact us to provide a value added custom equipment search service. Below are some upcoming auctions ***************************************************** Sale Closing : 7/10/98 Opening Prices ***************************************************** 1. Centra 4B $1,395.00 ------------------------------------------------------------ 2. Beckman DU-62 $4,200.00 ------------------------------------------------------------ 3. Gilson HPLC System $5,450.00 ------------------------------------------------------------ 4. Beckman Gamma Counter $2,750.00 ------------------------------------------------------------ 5. Plasma 40 ICAP $1,500.00 ------------------------------------------------------------ 6. Varian Atomic Absorbtion Spec $1,000.00 ------------------------------------------------------------ 7. UV Spec $500.00 ------------------------------------------------------------ 8. Varian 3400 GC, Tekamr LSC 2016/ALS 2000 Purge and trap $3,000.00 ------------------------------------------------------------ 9. Colorimeter $350.00 ------------------------------------------------------------ 10. Varian 3400 w/(TSD,ECD), integrator $2,500.00 ------------------------------------------------------------ 11. Varian 3300 w/FID and Hall detector Tekmar LSC 2000 $2,500.00 ------------------------------------------------------------ 12. PE FTIR w/ color plotter $1,000.00 ------------------------------------------------------------ 13. CEM Microwave digestion system $400.00 ------------------------------------------------------------ ***************************************************** Sale Closing : 7/15/98 Opening Prices ***************************************************** 1. Sorvall RC 3B and Rotor $7,400.00 ------------------------------------------------------------ 2. Beckman GPR Centrifuge $3,100.00 ------------------------------------------------------------ 3. Beckman L5-50 Centrifuge $3,400.00 ------------------------------------------------------------ 4. Beckman L5-75 Centrifuge $7,400.00 ------------------------------------------------------------ 5. Beckman L7-65 Ultra Centrifuge $4,850.00 ------------------------------------------------------------ 6. Beta Scint. Counter $13,000.00 ------------------------------------------------------------ 7. Amino Acid Analyzer $35,000.00 ------------------------------------------------------------ 8. Beckman DU-70 $4,900.00 ------------------------------------------------------------ 9. Tekmar 2000 sampler $6,900.00 ------------------------------------------------------------ 10. Liquid Chromatograph $27,900.00 ------------------------------------------------------------ 11. Varian 3400 GC $8,500.00 ------------------------------------------------------------ 12. IR Spectrometer $10,000.00 ------------------------------------------------------------ 13. Waters HPLC System (newer)600E/486/717 $15,300.00 ------------------------------------------------------------ ***************************************************** Sale Closing : 7/17/98 Opening Prices ***************************************************** 1. Beckman TJ-6R Centrifuge $2,250.00 ------------------------------------------------------------ 2. Purifier Class II $2,500.00 ------------------------------------------------------------ 3. Model 996 PDA Detector $4,750.00 ------------------------------------------------------------ 4. Optima Ultracentrifuge $20,000.00 ------------------------------------------------------------ 5. Phase Contrast Microscope $2,000.00 ------------------------------------------------------------ 6. ABEC Bioreactor $77,500.00 ------------------------------------------------------------ 7. Gruenburg Depyro Oven $1,700.00 ------------------------------------------------------------ 8. Preparative HPLC pumping system and column $31,000.00 ------------------------------------------------------------ 9. Fraction collector for Prep system item 304 $3,600.00 ------------------------------------------------------------ ***************************************************** Sale Closing : 7/22/98 Opening Prices ***************************************************** 1. automatic abbe refractometer $2,100.00 ------------------------------------------------------------ 2. Beckman DU-7 $3,500.00 ------------------------------------------------------------ 3. Waters 717 autosampler $4,700.00 ------------------------------------------------------------ 4. HP MS Engine/Electrospray System $63,000.00 ------------------------------------------------------------ 5. HP 5890 GC $12,000.00 ------------------------------------------------------------ 6. Environmental Chamber $5,250.00 ------------------------------------------------------------ 7. New Olympus Microscope $1,600.00 ------------------------------------------------------------ 8. ICP plasma 1000 $8,500.00 ------------------------------------------------------------ 9. Kjeldahl ( Macro) Distillation Unit $1,800.00 ------------------------------------------------------------ 10. Laboratory Furniture $6,000.00 ------------------------------------------------------------ ***************************************************** Sale Closing : 7/24/98 Opening Prices ***************************************************** 1. Grass Inst. Recorder/Polygraph $6,500.00 ------------------------------------------------------------ 2. Hitachi Z-9000 $15,750.00 ------------------------------------------------------------ 3. Perkin Elmer Plasma 400 Spec $21,000.00 ------------------------------------------------------------ 4. Zeiss EM 10 Transmitting Electron Microscope $22,750.00 ------------------------------------------------------------ 5. Particle Analysis Instruments $1,500.00 From owner-proteins@net.bio.net Sun Jul 05 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!europa.clark.net!194.182.148.154!news-feed.inet.tele.dk!bofh.vszbr.cz!news.inet.tele.dk!not-for-mail From: "PH" Newsgroups: bionet.molbio.proteins Subject: adrenomedullin receptors Date: Mon, 6 Jul 1998 15:09:04 +0200 Lines: 17 Message-ID: <6nqhus$1d8m$2@news-inn.inet.tele.dk> NNTP-Posting-Host: ppp103.bir.tele.dk X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Dear Sirs! I'm looking for cell-lines expressing the adrenomedullin- and the PAMP (proadrenomedullin N-terminal 20 peptide) receptors. Can anybody help ? Philip Hasbak, MD Dept. of Nuclear medicine Gentofte Hospital Univesity of Copenhagen Denmark E-mail: Philip@post1.tele.dk From owner-proteins@net.bio.net Sun Jul 05 23:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news.sprintlink.net!193.10.88.101!newsfeed.sunet.se!news01.sunet.se!news99.sunet.se!news.kth.se!dhcp-139.biokemi.su.se!user From: urbig@biokemi.su.se (Thomas) Newsgroups: bionet.molbio.proteins Subject: Re: Anti-histag antibodies etc Date: Mon, 06 Jul 1998 14:10:47 +0200 Lines: 28 Message-ID: References: <359A5802.6267749C@nott.ac.uk> NNTP-Posting-Host: dhcp-139.biokemi.su.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit In article <359A5802.6267749C@nott.ac.uk>, Simon.Dawson@nott.ac.uk wrote: > Hi all, > I was wondering if anyone out there knows what anti-histag type antibodies > are available and which give the best results. I have the M2 anti-flag > antibody from Kodak/IBI and the anti-Xpress antibody from Invitrogen. > I seem to remember a while back that someone out there knew of the existence > of an HRP-NTA conjugated antibody that bound directly to the histag and can be > detected with an HRP substrate. Was I imagining that?? If anyone can confirm > this and knows where I can get hold of such an antibody, could they let me > know? It would be much appreciated. Thanks. > > > Simon. Qiagen produces a Ni+-NTA coupled directly to HRP or AP. I tried the AP-conjugate and it worked fine. The 4HIS and 5HIS ab´s are also good (immunprecip!) but for standard westerns the conjugate gives faster results and great signal to noise ratio. Thomas -- Thomas Urbig urbig@biokemi.su.se From owner-proteins@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Luc CAMOIN Newsgroups: bionet.molbio.proteins Subject: GST fusion protein Date: 7 Jul 1998 08:33:55 +0100 Lines: 30 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6nsj13$p6c@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk, atg@cochin.inserm.fr Dear netters, I expressed a fusion protein produced in E Coli. The fusion protein is a GST tagged protein and the predicted molecular weight is around 45 kDa. My protein of interest is a very hydrophobic protein of 19 kDa. Purification on Glutathione sepharose 4B and western blot with anti GST revealed only a band around 25 kDa. This molecular weight and reactivity with anti GST could suggest that this protein is GST alone. Can we conclude that the contact between GST and the protein of interest is a protease sensitive region? Is this a known problem? Did you also find this problem in your experiments? Can you give me references about this problem? Thanks in advance, Luc CAMOIN Institut _/_/_/_/ _/_/_/_/ _/_/_/_/ _/_/ _/ Luc CAMOIN Cochin _/ _/ _/ _/ _/ _/_/ CNRS UPR 415 de _/ _/ _/ _/_/ _/ _/ _/ 22 rue Mechain Genetique _/ _/ _/ _/ _/ _/ 75014 Paris France Moleculaire _/_/_/_/ _/_/_/_/ _/_/_/_/ _/ _/ Tel:+33 1 40 51 64 98 http://www.cochin.inserm.fr/upr415/UPR415E2.htm From owner-proteins@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!agate!newsfeed.wli.net!newshub.northeast.verio.net!newsfeed.ecrc.net!wuff.mayn.de!informatik.tu-muenchen.de!news.ruhr-uni-bochum.de!not-for-mail From: Marc Saric Newsgroups: bionet.molbio.proteins,bionet.software,de.sci.biologie,de.sci.chemie Subject: van der Waals Radius of Certain Atoms Date: Tue, 07 Jul 1998 12:48:40 +0200 Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 40 Message-ID: <35A1FD08.173619D4@bph.ruhr-uni-bochum.de> NNTP-Posting-Host: bessel.bph.ruhr-uni-bochum.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.04 [en] (Win95; I) Xref: biosci bionet.molbio.proteins:12972 bionet.software:21378 Hi all, I have a problem with the definition of van der Waals radii: The problem: I want to extend a the amber94-library for the free molecular modelling programm Molmol (Bruker & ETH Zuerich, R.Koradi), especially Mg, Ca, Fe and other inorganic atoms are missing in the standard library. The problem is, that I can´t find a consistens set of vdW-Radii (i.e. the predefined numbers differ from what I got from several tables (IUPAC- periodic-system published by VCH-Verlagsgesellschaft for example). In general this is no big problem as these radii are only used for display purposes, but I think the "size"-relations between different atom-types should be saved, which means, one has to stick to a single definition of vdW-radii. In the amber94-lib published with Molmol, it is mentioned, that there is apparently no common solution for this problem, and that vdW-Radii are somewhat arbitrary choosen (i.e. defining the radius as 80% vdW or 100% or whatever). Is there any common definition of vdW-Radii or does someone know what to use best for representation of atoms in modelling programs??? Thanks in advance! -- Bye, Marc Saric Lehrstuhl fuer Biophysik Projektgruppe Theoretische Biophysik http://www.bph.ruhr-uni-bochum.de/ Ruhr-Universitaet Bochum Germany From owner-proteins@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news-peer.gip.net!news-lond.gip.net!news.gsl.net!gip.net!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Tim Hubbard Newsgroups: bionet.molbio.proteins Subject: Call for prediction targets for CASP3 Date: 7 Jul 1998 13:58:27 +0100 Lines: 263 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6nt61j$eck@mserv1.dl.ac.uk> X-Sender: th@pop.sanger.ac.uk Original-To: bionews@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk, pdb-l@pdb.pdb.bnl.gov Call for prediction targets for CASP3 ===================================== This is a call to X-ray crystallographers and NMR spectroscopists for targets for CASP3, the third experiment in critical assessment of techniques for protein structure prediction. In 1994 the first protein structure prediction experiment was held to evaluate prediction methods through blind prediction. Details of about 33 protein sequences, which were expected to be solved before the end of 1994, were submitted by experimentalists and this allowed 135 blind predictions to be made by 35 different groups. The results of the experiment are published in the November 1995 issue of Proteins: Structure, Function, and Genetics, volume 23, No 3. A second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (December 1996) was a culmination of the second 9 month long, community wide experiment. Before that meeting, 42 structural targets provided by crystallographers and NMR spectroscopists were made available to the prediction community. Prior to the public release of structures, more than 900 predictions by approximately 70 research groups world wide were collected, and led to the most objective assessment of prediction methods so far. The results are published in a special issue of Proteins: Structure, Function and Genetics, Suppl.1, 1997. The third experiment is now running and will culminate in a meeting in December 1998. As before, the goal is to obtain an in-depth and objective assessment of our current abilities and inabilities in this area. To this end, participants will predict as much as possible about a set of soon to be known structures in advance of the meeting. Sessions will be devoted to presentation of the results and comparison with experiment, and to the description of the methods used. As before, for the experiment to succeed, it is essential that we obtain the help of the experimental community. Therefore, we would like to invite Protein crystallographers and NMR spectroscopists who expect to solve a structure before 1st October 1998 to submit the sequence so that attempts can be made to predict it before it is publically announced. Each prediction will be given a deadline prior to the date on which the first information about the structure is to be made public. Targets of all sizes and types are required. Small structures (less than 100 residues) are needed to test some of the ab initio structure prediction methods. Proteins with folds related to those of known structures are needed to test fold identification methods. Proteins with sequences homologous to that of one or more known structures are needed to test comparative modeling methods. We would like to collect as many targets are possible. All that is requested is: - the sequence or a sequence accession number of the protein - an estimate of the likely date of public release (and updates if the work procedes faster or slower) - a commitment to make the coordinates available to the independent assessors not latter than 1st October should the structure be solved by then. Any coordinates provided will be treated with strict confidentiality as requested and used only to evalute the accuracy of predictions. For further information and on-line forms and documents see: http://predictioncenter.llnl.gov/casp3/ A Target protein submission form is also attached to this message and can be mailed to casp3@predictioncenter.llnl.gov John Moult CARB, University of Maryland, USA Tim Hubbard Sanger Centre, Hinxton, UK Jan Pedersen Acadia Pharmaceuticals, Denmark Krzysztof Fidelis Lawrence Livermore National Laboratory, USA CASP3 organising committee ---- Instructions for completing this form ------------------------------------- (0) Please only use this form if you are unable to complete the WWW version at http://predictioncenter.llnl.gov/casp3/ (1) Save this page as a text file (2) Complete all sections (3) send by email to casp3@predictioncenter.llnl.gov (4) if you have filled out the form correctly, you should receive an email acknowledgement (though not necessarily immediately) cut here ------------------------------------------------------------------------- CASP3: Third Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction Target submission form ====================== This is the text version of the Prediction target submission form for the Third Critical Assessment of Techniques for Protein Structure Prediction Experiment (CASP3). Introduction ============ Protein crystallographers and NMR spectroscopists are asked to provide details of structures they expect to have solved before 1st September 1998 using this form. Targets of all sizes and types are required. Small structures (less than 100 residues) are needed to test some of the ab initio structure prediction methods. Proteins with folds related to those of known structures are needed to test fold recognition methods. Proteins with sequences homologous to that of one or more known structures are needed to test comparative modelling methods. To be useful to the predictors, a period of at least a month is required before any details of the structure will be released. Please notify us immediately when the details are going to be made public, so that we can ask the predictors to stop work in a timely manner. This can be done by sending a mail to casp3@predictioncenter.llnl.gov In order for the predictions to be assessed in time for the meeting in December, we will need a set of co-ordinates by the beginning of September at the latest. If necessary, these can be for limited distribution until the meeting. A. Scientific information ========================= 1. [ ] Protein Name 2. [ ] Organism Name 3. [ ] Number of amino acids (does not need to be exact) Please provide accession number and the name of the database of the protein (4. and 5.) or the actual sequence (6.) (both if possible). 4. [ ] Accession number 5. Sequence Database [ ] Swiss-prot [ ] PIR [ ] Genbank [ ] EMBL [ ] Other [ ] 6. Amino acid sequence One letter code (ACEDFTK) is preferred, but three letter code (ala cys glu asp) can also be processed. 7. Are there homologous sequences of known structure to this protein Yes [ ] No [ ] 8. Current state of the experimental work Please describe briefly where things are at, addressing as many of the following points as you wish to/are relevant/can. The more information, the easier it is for a modeler to decide whether to predict your structure. Protein supply? Crystals? Diffraction quality? Molecular replacement in progress? Molecular replacement solution in hand? Heavy atom derivative search in progress? Heavy atom derivatives in hand? 9. Do you already have an interpretable map? Yes [ ] No [ ] 10. [ ] Estimated date of chain tracing completion. In order to assess the predictions before the meeting, this date should be before 1st September 1998. 11. [ ] Estimated date of public release of structure 12. If you have any other useful information about this sequence family please enter it below B. Administrative information ============================= 13. [ ] Name 14. Mailing address: [ ] Institution [ ] Street/P.O. Box [ ] City [ ] State/Province [ ] ZIP/Postal code [ ] Country 15. [ ] Tel 16. [ ] Fax 17. [ ] Email 18. How did you hear about this prediction experiment? [ ] Nature Add [ ] Poster [ ] Newsgroup [ ] Email [ ] Other [ ] 19. Do you wish to remain anonymous until the structure is publically announced? Yes [ ] No [ ] ------------------------------------------------------------------------- ---------------------------------------------------------------------------- Dr Tim Hubbard email: th@sanger.ac.uk Head, Human Genome Analysis Tel (direct): +44 1223 494983 Sanger Centre Tel (switch): +44 1223 834244 Wellcome Trust Genome Campus, Hinxton Fax: +44 1223 494919 Cambridgeshire. CB10 1SA. UK. URL: http://www.sanger.ac.uk/Users/th ---------------------------------------------------------------------------- From owner-proteins@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Christopher Hatton Newsgroups: bionet.molbio.proteins Subject: 30% sequence identity Date: 07 Jul 1998 15:23:20 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 22 Message-ID: NNTP-Posting-Host: caelum.ebi.ac.uk X-Newsreader: Gnus v5.5/Emacs 20.2 In response to the earlier question about the source of the information that proteins with more than 30% sequence identity have broadly similar structures, the paper C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells & J. M. Thornton, 1997, Structure vol. 5, 1093. states "At 30% sequence identity, proteins will almost certainly have the same overall fold." It also refers to three other papers on the matter: C. Chothia & A. M. Lesk, 1986, EMBO J. vol. 5, 823. T. P. Flores, C. A. Orengo & J. M. Thornton, 1993, Protein Sci. vol 7, 31. C. Sander & R. Schneider, 1991, Proteins vol. 9, 56. Dan Hatton From owner-proteins@net.bio.net Mon Jul 06 23:00:00 1998 From: Cornelius Krasel Subject: Re: GST fusion protein Newsgroups: bionet.molbio.proteins References: <6nsj13$p6c@mserv1.dl.ac.uk> Distribution: bionet User-Agent: tin/pre-1.4-980514 (UNIX) (Linux/2.0.34 (i486)) MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Date: Tue, 7 Jul 1998 12:53:00 +0200 Message-ID: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de Lines: 22 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newspeer.monmouth.com!uni-erlangen.de!uni-wuerzburg.de!not-for-mail Luc CAMOIN wrote: > Purification on Glutathione sepharose 4B and western blot with anti GST > revealed only a band around 25 kDa. This molecular weight and reactivity > with anti GST could suggest that this protein is GST alone. > Can we conclude that the contact between GST and the protein of interest is > a protease sensitive region? I have had similar problems in some of my experiments and have reached this conclusion. The protease sensitivity of the linker region depends, amongst other things, on the length of the linker and on the bacterial strain in which you express your protein of interest. An approach to circumvent this problem which sometimes works is to express your GST fusion protein in a protease- negative E. coli strain (e.g. BL21) at lower temperatures (e.g. 25°C instead of 37°C). Hope that helps, --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP4 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!newsfeed.internetmci.com!128.174.5.49!vixen.cso.uiuc.edu!dhardy From: dhardy@students.uiuc.edu (david joseph hardy) Newsgroups: bionet.molbio.proteins Subject: NAMD (parallel molecular dynamics) 1.5 beta 6 available Date: 7 Jul 1998 22:35:19 GMT Organization: University of Illinois at Urbana-Champaign Lines: 83 Message-ID: <6nu7r7$aco$1@vixen.cso.uiuc.edu> NNTP-Posting-Host: ux9.cso.uiuc.edu Announcing the release of NAMD version 1.5 beta 6 ------------------------------------------------- The Theoretical Biophysics group at the Beckman Institute, the University of Illinois would like to announce the availability of version 1.5 beta 6 of NAMD, a high-performance molecular mechanics program for simulating large biomolecular systems on parallel and distributed computers. This software is being made available to the molecular modeling community free of charge and includes commented source code and extensive documentation. New in this version ------------------- * Enhanced performance by as much as 30%. * Modified to work with the latest version of DPMTA (2.7). * Included DPMTA source to make installation easier. * Simplified build process, fewer options to specify, better documentation. * Several bug fixes. ==================== Basic information about NAMD ====================== Obtaining NAMD -------------- A more complete description of NAMD is available on the NAMD home page: http://www.ks.uiuc.edu/Research/namd/ The software itself is available via anonymous ftp in the directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/namd/ Email questions to namd@ks.uiuc.edu. Features -------- Efficient full electrostatics: NAMD incorporates the Distributed Parallel Multiple Tree Algorithm (DPMTA) developed by the Scientific Computing Group at Duke University to provide full electrostatic interactions in O(N) time. To further reduce the computational cost, DPMTA is integrated using a multiple timestep integration scheme which computes full electrostatic interactions only periodically during the simulation. Scalable parallelism: NAMD has an efficient parallel design that allows large systems to scale well to many processors. The use of a spatial decomposition scheme combined with message-driven execution achieves load balance and the overlap of communication and computation. Modifiable: A major design goal of NAMD is to allow researchers to implement new algorithms and techniques easily. To achieve this, NAMD design and implementation is fully documented in the NAMD Programmer's Guide. NAMD has an object-oriented design implemented in C++ to provide a high degree of modularity and data abstraction. Portable: For communication, NAMD uses PVM (Parallel Virtual Machine) from Oak Ridge National Laboratories, which has itself been ported to most architectures. Porting NAMD is then simply a matter of having PVM and a reasonable C++ compiler. We have successfully ported NAMD to all of our UNIX computers, which include HP, SGI, and Sun, both single processor and shared memory multiprocessor. Compatibility with X-PLOR: The input and output files used by NAMD are identical to those used by the program X-PLOR. Thus, simulations can be easily migrated between the two packages, allowing the output of NAMD to be analyzed using X-PLOR or any other tool built for these file formats. Standard MD features: NAMD implements standard molecular dynamics features such as energy minimization, velocity rescaling, spherical boundary conditions, harmonic constraints, and Langevin dynamics. ========================================================================== Theoretical Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign David Hardy namd@ks.uiuc.edu July 7, 1998 From owner-proteins@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!SLIP.NET!grizzly From: grizzly@SLIP.NET (Michael Sherrell) Newsgroups: bionet.molbio.proteins Subject: Sequencers and synthesizers Date: 7 Jul 1998 14:58:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BDA9B7.C0681D80@sf-pm17-36-100.dialup.slip.net> NNTP-Posting-Host: net.bio.net I have a number of peptide and oligo synthesizers and sequencers for = sale: PerSeptive 9050, ~$10K PerSeptive Expedite 8909, <=3D $14K ABI 394, rebuilt, warranteed, Oligonet-ready, ~$12K ABI 394, rebuilt, warranteed, non-Oligonet, ~$11K ABI 391, rebuilt, warranteed, $7K ABI 430, rebuilt, warranteed, ~$12K ABI 433, rebuilt by ABI, warranteed, < $40K ABI 373 stretch, 5-filter, Genescan, 36-lane, $29K ABI 477, <=3D $10K ABI 120, 130, $2.5K also: LC-MS: Finnigan MAT 900, <$50K Finnigan MAT 90, ~$45K MicroMass Quattro II, ~$200K =09 MALDI-TOF: HP, masses to 500 KDa, lightly used, <=3D$60K Finnigan Laser MAT 2000, <$40K Other expensive hi-tech items: Bio-Dot sub-microliter 8-channel aspirate/dispense system (typically = 96-well microplate source, glass slide, microwell plate or membrane = target), < 1 year old Molecular Devices 445SI-MAC Phosphorimagers, ~ 3 years old, currently = operating and under maintenance contact, pretty low price I also have available a few other synthesizers and sequencers and a = wide selection of HPLCs, mass specs, and other lab instruments. Please contact me to discuss any of these items, or if you have any = items you might like to sell. Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com From owner-proteins@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!agate!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!awabi.library.ucla.edu!164.67.43.25!news.ucla.edu!not-for-mail From: Ng Newsgroups: bionet.molbio.proteins Subject: Re: proteins with 30% homology should have the same general fold: reference for this ? Date: 8 Jul 1998 04:06:43 GMT Organization: Molecular Biology Institute, UCLA Lines: 21 Message-ID: <6nur8j$t8r$1@carroll.library.ucla.edu> References: <6ne6le$ndl@sifon.cc.mcgill.ca> NNTP-Posting-Host: mendel.mbi.ucla.edu X-Newsreader: TIN [UNIX 1.3 unoff BETA 970731; alpha OSF1 V4.0] There's probably an older reference than this, but you may want to look at Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 1991, 9:56-58. For a very recent critical reassessment of using sequence identity as a measure of homology, see Brenner, SE; Chothia, C; Hubbard, TJP. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998 MAY 26, V95 N11:6073-6078. -- Ho Leung Ng holeung@ucla.edu From owner-proteins@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!newsfeed.internetmci.com!209.150.97.11!feeder.qis.net!newsfeed1.earthlink.net!nntp.earthlink.net!not-for-mail From: "God" Newsgroups: alt.business,alt.business.misc,alt.elvis.sighting,alt.fan.howard-stern,alt.fitness.marketplace,alt.forsale.nutrition,alt.health,alt.invest,alt.support.diet.low-carb,bionet.molbio.proteins,fidonet.dieting,misc.fitness.misc,misc.fitness.weights Subject: Hey Lucky People, Why not invest in nutrition food bars? Date: Thu, 9 Jul 1998 00:03:04 -0400 Organization: EarthLink Network, Inc. Lines: 28 Message-ID: <6o1fhk$apv$1@ash.prod.itd.earthlink.net> NNTP-Posting-Host: 2cust85.tnt1.mia1.da.uu.net X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Why not invest in nutrition food bars? “The fastest growing segment, of the natural food industry is nutrition food bars which is now a staple food in mainstream diets.” Spence Information Services of San Fransico Sales of Clif and Balance nutrition bars have doubled during each of the last three years. This presents a wonderful investment opportunity and we have developed the perfect fat burning formula for a nutrition bar that will follow the success of Clif and Balance nutrition bars. The Balance bars currently gross 7 million dollars a month. Three years ago they grossed less then 1 million dollars a year. Our nutrition food bar is ready to roll out into the marketplace, so doesn’t miss this spectacular investment opportunity. Serious Inquiries Only. Please Call: Professor Richard Hughes (949)883-3007 or E-mail Perfectlite@geocities.com Check out our website for additional information: http://www.geocities.com/HotSprings/Villa/5677 From owner-proteins@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!feeder.qis.net!newshub.northeast.verio.net!news.idt.net!newsfeed1.earthlink.net!nntp.earthlink.net!not-for-mail From: "Richard Hughes" Newsgroups: alt.business,alt.business.misc,alt.computer,alt.elvis.sighting,alt.fan.howard-stern,alt.fitness.marketplace,alt.forsale.nutrition,alt.health,alt.invest,alt.support.diet,alt.support.diet.low-carb,bionet.molbio.proteins,fidonet.dieting,sci.med. Subject: Why not invest in nutrition food bars? Date: Wed, 8 Jul 1998 23:34:12 -0400 Organization: EarthLink Network, Inc. Lines: 28 Message-ID: <6o1drj$6tk$1@ash.prod.itd.earthlink.net> NNTP-Posting-Host: 2cust85.tnt1.mia1.da.uu.net X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Why not invest in nutrition food bars? “The fastest growing segment, of the natural food industry is nutrition food bars which is now a staple food in mainstream diets.” Spence Information Services of San Fransico Sales of Clif and Balance nutrition bars have doubled during each of the last three years. This presents a wonderful investment opportunity and we have developed the perfect fat burning formula for a nutrition bar that will follow the success of Clif and Balance nutrition bars. The Balance bars currently gross 7 million dollars a month. Three years ago they grossed less then 1 million dollars a year. Our nutrition food bar is ready to roll out into the marketplace, so doesn’t miss this spectacular investment opportunity. Serious Inquiries Only. Please Call: Professor Richard Hughes (949)883-3007 or E-mail Perfectlite@geocities.com Check out our website for additional information: http://www.geocities.com/HotSprings/Villa/5677 From owner-proteins@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!xfer.kren.ne.kr!xfer.kren.nm.kr!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: rdudley@aherf.edu Newsgroups: bionet.molbio.proteins Subject: Re: GST fusion protein Date: Wed, 08 Jul 1998 12:49:41 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 31 Message-ID: <6nvpt5$muc$1@nnrp1.dejanews.com> References: <6nsj13$p6c@mserv1.dl.ac.uk> NNTP-Posting-Host: 199.234.107.24 X-Article-Creation-Date: Wed Jul 08 12:49:41 1998 GMT X-Http-User-Agent: Mozilla/4.03 [en] (WinNT; I) In article <6nsj13$p6c@mserv1.dl.ac.uk>, Luc CAMOIN wrote: > Dear netters, > > I expressed a fusion protein produced in E Coli. The fusion protein is a > GST tagged protein and the predicted molecular weight is around 45 kDa. My > protein of interest is a very hydrophobic protein of 19 kDa. > Purification on Glutathione sepharose 4B and western blot with anti GST > revealed only a band around 25 kDa. This molecular weight and reactivity > with anti GST could suggest that this protein is GST alone. > Can we conclude that the contact between GST and the protein of interest is > a protease sensitive region? Is this a known problem? Did you also find > this problem in your experiments? Can you give me references about this > problem? Make sure there isn't a frame shift between the GST and your protein. Also, is there the chance that you have a mixed population in your cultures? (i.e., some bacteria contain a GST-only plasmid, and some contain a GST+insert plasmid) I only aske because I was working with a protein that had a very hydrophibic region, and eventually found it would stick to the glutathione sepharose in a non-specific manner. We coul dnever elute it with GST alone. You may want to do a trial experiment where you run out a sample of every step along the way--including crude lysae, unbound fraction, purified sample, and some of the sepharose--and do a western blot. rich rdudley@aherf.edu -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-proteins@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!GRAY.ISIR.MINSK.BY!stk4114 From: stk4114@GRAY.ISIR.MINSK.BY (Sergey Gridushko) Newsgroups: bionet.molbio.proteins Subject: Albumin reseach information Date: 8 Jul 1998 05:58:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <199807081302.QAA09804@gray.isir.minsk.by> NNTP-Posting-Host: net.bio.net Is there anywhere Albumin's site/newsgroup/pages/ any resourses ? thanx. From owner-proteins@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!GRAY.ISIR.MINSK.BY!stk4114 From: stk4114@GRAY.ISIR.MINSK.BY (Sergei Gridushko) Newsgroups: bionet.molbio.proteins Subject: albumin reseach information Date: 8 Jul 1998 05:54:07 -0700 Organization: ISIR Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <35A3F665.5F47@gray.isir.minsk.by> Reply-To: stk4114@gray.isir.minsk.by NNTP-Posting-Host: net.bio.net Is there anywhere Albumin's site/newsgroup/pages/ any resourses ? thanx. From owner-proteins@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!STUDENT2.MAHIDOL.AC.TH!g3937506 From: g3937506@STUDENT2.MAHIDOL.AC.TH (Jongrak Kittiworakarn) Newsgroups: bionet.molbio.proteins Subject: Re: GST fusion protein Date: 8 Jul 1998 18:40:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 74 Sender: daemon@net.bio.net Distribution: world Message-ID: <35A41E2B.9085DBDB@student.mahidol.ac.th> NNTP-Posting-Host: net.bio.net > Hi Luc: Did you check your crude E.coli lysate before loading to the glutathione column?You might found your protien in the crude but not bind to the column as I. I have an experience in expression of hydrophobic peptide ( 8 kDa and 25 kDa) with GST fusion. The expressed protein was in a very high level (30-40% of total crude E.coli lysate), but it was in insoluble form. After refolding of the protein, I got the soluble form. But the refolded protein neither showed GST activity nor bound to s-hexyl glutathione agarose. I think the fusion protein might interfere the GST activity although it have a propered fold in some extend. If this is your case, you may try cleaving your protein out with protease. Then purify the part of your interest by some other method. Jongrak > GST fusion protein > > Luc CAMOIN (camoin@cochin.inserm.fr) > 7 Jul 1998 08:33:55 +0100 > > * Messages sorted by: [ date ][ thread ][ subject ][ author ] > * Next message: Cornelius Krasel: "Re: GST fusion protein" > * Previous message: John Philo: "Re: Searching for a company "Rent A scientist"" > * Next in thread: Cornelius Krasel: "Re: GST fusion protein" > * Reply: Cornelius Krasel: "Re: GST fusion protein" > * Reply: rdudley@aherf.edu: "Re: GST fusion protein" > > ------------------------------------------------------------------------ > > To: protein-analysis@net.bio.net > > From: Luc CAMOIN > > Subject: GST fusion protein > > Date: 7 Jul 1998 08:33:55 +0100 > > Dear netters, > > I expressed a fusion protein produced in E Coli. The fusion protein is a > GST tagged protein and the predicted molecular weight is around 45 kDa. My > protein of interest is a very hydrophobic protein of 19 kDa. > Purification on Glutathione sepharose 4B and western blot with anti GST > revealed only a band around 25 kDa. This molecular weight and reactivity > with anti GST could suggest that this protein is GST alone. > Can we conclude that the contact between GST and the protein of interest is > a protease sensitive region? Is this a known problem? Did you also find > this problem in your experiments? Can you give me references about this > problem? > > Thanks in advance, > > Luc CAMOIN > > Institut _/_/_/_/ _/_/_/_/ _/_/_/_/ _/_/ _/ Luc CAMOIN > Cochin _/ _/ _/ _/ _/ _/_/ CNRS UPR 415 > de _/ _/ _/ _/_/ _/ _/ _/ 22 rue Mechain > Genetique _/ _/ _/ _/ _/ _/ 75014 Paris France > Moleculaire _/_/_/_/ _/_/_/_/ _/_/_/_/ _/ _/ Tel:+33 1 40 51 64 98 > http://www.cochin.inserm.fr/upr415/UPR415E2.htm > ------------------------------------------------------------------------ > > * Next message: Cornelius Krasel: "Re: GST fusion protein" > * Previous message: John Philo: "Re: Searching for a company "Rent A scientist"" > * Next in thread: Cornelius Krasel: "Re: GST fusion protein" > * Reply: Cornelius Krasel: "Re: GST fusion protein" > * Reply: rdudley@aherf.edu: "Re: GST fusion protein" From owner-proteins@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news.maxwell.syr.edu!news.mel.connect.com.au!munnari.OZ.AU!news.usyd.edu.au!seagoon.newcastle.edu.au!not-for-mail From: Rick Thorne Newsgroups: bionet.molbio.proteins Subject: Best Protease Cleavage for Fusion Protein? Date: Thu, 09 Jul 1998 02:27:40 +1000 Organization: rthorne@mail.newcastle.edu.au Lines: 26 Message-ID: <35A39DF7.8825D098@mail.newcastle.edu.au> Reply-To: rthorne@mail.newcastle.edu.au NNTP-Posting-Host: c25mc4-asy5.newcastle.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) Dear All, I am planning to construct a recombinant (fusion) molecule to be produced in CHO cells, with the ultimate aim to produce around 1mg of the purifed protein. Rather than producing a secreted form of the molecule, I want to make it as a transmembrane protein (Type 1). The complication is that "maturely" glycosylated surface expressed molecules are required for analysis, and therefore it should not be purified from whole cell lysates (which would be contaminated with the precursor of the protein). The plan is to cleave it from the cell surface by introduction of a protease site in the extracellular domain of the protein, close to the transmembrane. DOes anyone know of this approach being successfully used before. It is most common to first purify the fusion protein and then cleave off the fusion partner (eg: GST). Therefore the type of cleavage site is not so critical. However does anyone have a suggestion as to which cleavage method might be most applicable to live cells?? Thanks, Rick Thorne Cancer Research Unit, The University of Newcastle, Newcastle, Australia. From owner-proteins@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!howland.erols.net!frankfurt.de.uu.net!news.uni-stuttgart.de!news.ruhr-uni-bochum.de!not-for-mail From: Heiko.Koch@ruhr-uni-bochum.de (Heiko Koch) Newsgroups: bionet.molbio.proteins Subject: Help with activity test Date: Wed, 08 Jul 1998 14:30:43 GMT Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 49 Message-ID: <35a38277.30552113@news.ruhr-uni-bochum.de> NNTP-Posting-Host: r06-596.molgen.ruhr-uni-bochum.de X-Newsreader: Forte Free Agent 1.11/32.235 Hello, perhaps someone is able to help me. I am working on a ADP-ribosyltransferase. This enzyme transfers the ADP moiety of NAD to the target enzyme. The determination of the activity works by using radioactive labeled NAD. The method is described in Rohrer, H.; Zillig,W. and R. Mailhammer (1975), Eur. J. Biochem. 60/ 227-238. The radioactive label is transferred to the target and the amount of labeled target is determine in a scintilator. The reaction is stopped by adding 25 µl 50% TCA to the 100 µl incubation mixture. The mixture should be transfered to an Nitrocellulose filter and the filter must be washed to remove the unbound labeled NAD. And this is the problem. Controls with no ribosyltransferase have as much cpm´s as the tests with ribosyltransferase The problem is how to remove the non bound radioactive NAD. I tried the following methods: · Transferring the mixtures onto the Filters and washing with 10% TCA by vacuum · Transferring the mixtures onto the Filters and washing with Tris buffer by vacuum · Transferring the mixture to the Filter with a pipet an dry them at RT, washing the Filter in a tube with 10 ml binding buffer from blotting method · Centrifuge the participated Proteins, and wash them in 500 ml Aceton. Dissolve the pellet in water and apply them directly to liquid scintilation. · Centrifuge the participated Proteins, dissolve them in water and participate them again by adding TCA and Centrifugation. The pellet is dissolved again in water an transferred directly to liquid scintilation. Perhaps someone has got an idea how to modify the test, to remove the unbound radioactivity. Thanks for help, with best regards Heiko Koch Heiko.Koch@ruhr-uni-bochum.de From owner-proteins@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news.maxwell.syr.edu!uninett.no!online.no!not-for-mail From: Are Kristiansen Newsgroups: bionet.molbio.proteins Subject: Nomenclature of numbering of amino acids Date: Thu, 09 Jul 1998 08:24:48 +0200 Organization: Telenor Online Public Access Lines: 21 Message-ID: <35A46230.E26C5E66@pronova.no> NNTP-Posting-Host: 193.215.34.251 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; I) Hallo, I have received the proof of an article to be published in BBA. As I do not have immediate access to recent editions of the journal and I am already late in returning the proof, I direct the question to this newsgroup: The journal has superscripted all numbers of amino acids. Instead of for example Trp28, it reads Trp, i.e. the amino acid (Trp) is normal font, but the number (28) is superscript. I suppose this is a misunderstanding in the typesetting, or is it common to "superscript" numbers of amino acids? Are Kristiansen R&D Scientist Pronova Biomedical Gaustadalleen 21 N-0371 Oslo, Norway From owner-proteins@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-feed.inet.tele.dk!bofh.vszbr.cz!online.no!not-for-mail From: Are Kristiansen Newsgroups: bionet.molbio.proteins Subject: Nomenclature of numbering of amino acids Date: Thu, 09 Jul 1998 08:23:55 +0200 Organization: Telenor Online Public Access Lines: 21 Message-ID: <35A461FB.46292639@pronova.no> NNTP-Posting-Host: 193.215.34.251 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; I) Hallo, I have received the proof of an article to be published in BBA. As I do not have immediate access to recent editions of the journal and I am already late in returning the proof, I direct the question to this newsgroup: The journal has superscripted all numbers of amino acids. Instead of for example Trp28, it reads Trp, i.e. the amino acid (Trp) is normal font, but the number (28) is superscript. I suppose this is a misunderstanding in the typesetting, or is it common to "superscript" numbers of amino acids? Are Kristiansen R&D Scientist Pronova Biomedical Gaustadalleen 21 N-0371 Oslo, Norway From owner-proteins@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!newspeer.monmouth.com!uninett.no!online.no!not-for-mail From: Are Kristiansen Newsgroups: bionet.molbio.proteins Subject: Nomenclature of numbering of amino acids Date: Thu, 09 Jul 1998 08:27:16 +0200 Organization: Telenor Online Public Access Lines: 21 Message-ID: <35A462C4.3357A8BA@pronova.no> NNTP-Posting-Host: 193.215.34.251 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; I) Hallo, I have received the proof of an article to be published in BBA. As I do not have immediate access to recent editions of the journal and I am already late in returning the proof, I direct the question to this newsgroup: The journal has superscripted all numbers of amino acids. Instead of for example Trp28, it reads Trp, i.e. the amino acid (Trp) is normal font, but the number (28) is superscript. I suppose this is a misunderstanding in the typesetting, or is it common to "superscript" numbers of amino acids? Are Kristiansen R&D Scientist Pronova Biomedical Gaustadalleen 21 N-0371 Oslo, Norway From owner-proteins@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-feed.inet.tele.dk!bofh.vszbr.cz!online.no!not-for-mail From: Are Kristiansen Newsgroups: bionet.molbio.proteins Subject: Nomenclature of numbering of amino acids Date: Thu, 09 Jul 1998 08:27:02 +0200 Organization: Telenor Online Public Access Lines: 21 Message-ID: <35A462B6.DF8E18C6@pronova.no> NNTP-Posting-Host: 193.215.34.251 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; I) Hallo, I have received the proof of an article to be published in BBA. As I do not have immediate access to recent editions of the journal and I am already late in returning the proof, I direct the question to this newsgroup: The journal has superscripted all numbers of amino acids. Instead of for example Trp28, it reads Trp, i.e. the amino acid (Trp) is normal font, but the number (28) is superscript. I suppose this is a misunderstanding in the typesetting, or is it common to "superscript" numbers of amino acids? Are Kristiansen R&D Scientist Pronova Biomedical Gaustadalleen 21 N-0371 Oslo, Norway From owner-proteins@net.bio.net Wed Jul 08 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!feed2.news.erols.com!erols!howland.erols.net!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!usenet From: David Green Newsgroups: bionet.molbio.proteins Subject: Re: Nomenclature of numbering of amino acids Date: Thu, 09 Jul 1998 09:24:31 -0400 Organization: Massachusetts Institute of Technology Lines: 29 Message-ID: <35A4C48F.1C0EFF88@lms.mit.edu> References: <35A461FB.46292639@pronova.no> NNTP-Posting-Host: born.lms.mit.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (X11; U; Linux 2.0.30 i686) Are Kristiansen wrote: > The journal has superscripted all numbers of amino acids. Instead of for > example Trp28, it reads Trp, i.e. the amino acid (Trp) > is normal font, but the number (28) is superscript. > > I suppose this is a misunderstanding in the typesetting, or is it common > to "superscript" numbers of amino acids? > Superscripting the residue number is an accepted representation. Several journals use this method (Science is one), while others (such at JMB) use the alternative, non-superscripted representation. If the instructions say to superscript, I would do so. -- ************************************************ David F. Green Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Ave., Rm. 6-133 Cambridge, MA 02139 E-mail: dfgreen@lms.mit.edu Phone: (617) 258-6229 ************************************************ From owner-proteins@net.bio.net Wed Jul 08 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!howland.erols.net!vixen.cso.uiuc.edu!newsfeed.acns.nwu.edu!news.acns.nwu.edu!med048050.medicine.nwu.edu!user From: sg@nwu.edu (Stephen Gately) Newsgroups: bionet.molbio.proteins Subject: Reduced Protein Gel Behavior Date: Thu, 09 Jul 1998 17:26:42 -0500 Organization: Northwestern university Lines: 10 Message-ID: NNTP-Posting-Host: med048050.medicine.nwu.edu I have a protein that migrates as a doublet at approximately 52 kD on denaturing/non-reducing gels. If I run the sample reduced (BME) the protein still runs as a doublet, but the molecular mass increases to 60-64 kD. Any thoughts on this occurence? Thanks, Steve From owner-proteins@net.bio.net Wed Jul 08 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!logbridge.uoregon.edu!howland.erols.net!newsfeed.internetmci.com!207.217.77.43!newsfeed1.earthlink.net!nntp.earthlink.net!not-for-mail From: John Philo <"jphilo*NO SPAM12*"@earthlink.net> Newsgroups: bionet.molbio.proteins Subject: Re: Nomenclature of numbering of amino acids Date: Thu, 09 Jul 1998 14:21:25 -0700 Organization: Alliance Protein Laboratories Lines: 39 Message-ID: <35A53455.F5A40D17@earthlink.net> References: <35A462C4.3357A8BA@pronova.no> NNTP-Posting-Host: 1cust145.tnt1.thousand-oaks.ca.da.uu.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (Win95; U) To: Are Kristiansen I believe this is a typesetting mistake. I happen to have recently become an Editor for BBA Protein Structure and Enzymology and I have never seen the formatting style you describe. The BBA Instructions to Authors appear not to specify a nomenclature or formatting for this. A quick perusal of two recent issues suggests there is, in fact, some variation from paper to paper. One paper used "Trp 28" (with a space) and another "Trp28". The common style for designating mutants seems to be "W28A" as used by most journals. You can contact the editorial office through bba@elsevier.nl John Philo, Alliance Protein Laboratories ------------ Are Kristiansen wrote: > > Hallo, > > I have received the proof of an article to be published in BBA. As I do > not have immediate access to recent editions of the journal and I am > already late in returning the proof, I direct the question to this > newsgroup: > > The journal has superscripted all numbers of amino acids. Instead of for > example Trp28, it reads Trp, i.e. the amino acid (Trp) > is normal font, but the number (28) is superscript. > > I suppose this is a misunderstanding in the typesetting, or is it common > to "superscript" numbers of amino acids? > > Are Kristiansen > R&D Scientist > Pronova Biomedical > Gaustadalleen 21 > N-0371 Oslo, Norway *** Remove "*NO SPAM12*" from return address before replying. *** From owner-proteins@net.bio.net Wed Jul 08 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!newshub.northeast.verio.net!fu-berlin.de!molbio4.nawi.uni-wh.DE!not-for-mail From: Andreas Savelsbergh Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Cultivation of E. coli at lower temperature Date: Thu, 09 Jul 1998 16:08:39 +0200 Organization: University Witten/Herdecke Lines: 16 Message-ID: <35A4CEE6.A4874A8D@uni-wh.de> NNTP-Posting-Host: molbio4.nawi.uni-wh.de (193.175.78.33) Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Access: 16 1666 1667 X-Trace: fu-berlin.de 899993412 6495 (none) 193.175.78.33 X-Mailer: Mozilla 4.03 [en] (Win95; I) Xref: biosci bionet.molbio.methds-reagnts:68858 bionet.molbio.proteins:12994 Hi all, my own experience and that of lab-fellows says that pre-cultivation of E. coli (BL21(DE3)pLysS) for expression cultures of toxic proteins at lower temperatures gives sometimes better results (= cells grow) than pre-cultivation at 37°C (= cells don't grow). Expression itself sometimes is only possible at 30 °C, while at 37°C nothing grows or is expressed. My question is: Does anybody have a reasonable explanation for that? Are there proteases which are less active at lower temperatures. Does anybody know a reference for that? Thanks, Andreas From owner-proteins@net.bio.net Wed Jul 08 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!logbridge.uoregon.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: rdudley@aherf.edu Newsgroups: bionet.molbio.proteins Subject: Re: Nomenclature of numbering of amino acids Date: Thu, 09 Jul 1998 13:15:27 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 30 Message-ID: <6o2fpf$ois$1@nnrp1.dejanews.com> References: <35A461FB.46292639@pronova.no> NNTP-Posting-Host: 199.234.107.24 X-Article-Creation-Date: Thu Jul 09 13:15:27 1998 GMT X-Http-User-Agent: Mozilla/4.03 [en] (WinNT; I) In article <35A461FB.46292639@pronova.no>, Are Kristiansen wrote: > Hallo, > > I have received the proof of an article to be published in BBA. As I do > not have immediate access to recent editions of the journal and I am > already late in returning the proof, I direct the question to this > newsgroup: > > The journal has superscripted all numbers of amino acids. Instead of for > example Trp28, it reads Trp, i.e. the amino acid (Trp) > is normal font, but the number (28) is superscript. > > I suppose this is a misunderstanding in the typesetting, or is it common > to "superscript" numbers of amino acids? > > Are Kristiansen > R&D Scientist > Pronova Biomedical > Gaustadalleen 21 > N-0371 Oslo, Norway Superscripting is a new one on me also. I've always seen, and always written, Y28 (and for a histidine mutant, Y28H). rich rdudley@aherf.edu -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-proteins@net.bio.net Wed Jul 08 23:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news-lond.gip.net!news.gsl.net!gip.net!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!server1.netnews.ja.net!hgmp.mrc.ac.uk!gmorley From: gmorley@hgmp.mrc.ac.uk (Mr. G. Morley) Newsgroups: bionet.molbio.proteins Subject: Pi-3 kinase in vector? Date: 9 Jul 1998 11:27:57 GMT Organization: MRC Human Genome Mapping Project Resource Centre Lines: 11 Message-ID: <6o29ft$jfj$1@niobium.hgmp.mrc.ac.uk> NNTP-Posting-Host: tin.hgmp.mrc.ac.uk Hello all, I would be very, very gratefull if someone can send me the human PI-3 kinase p110 catalytic subunit in a vector I can clone it out of (such as a simple plasmid). I would of course pay for any shipping costs.... Thanks in advance, Gary Morley Dept. Haematology U.C.L. London. From owner-proteins@net.bio.net Wed Jul 08 23:00:00 1998 Newsgroups: bionet.molbio.proteins Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news2.ais.net!jamie!ais.net!ix.netcom.com!atlantis From: atlantis@netcom.com (JJ Miranda) Subject: Re: Nomenclature of numbering of amino acids Message-ID: Organization: Netcom On-Line Services X-Newsreader: TIN [version 1.2 PL2] References: <35A461FB.46292639@pronova.no> Date: Thu, 9 Jul 1998 07:22:34 GMT Lines: 28 Sender: atlantis@netcom10.netcom.com To the best of my knowledge, or at least my experience, I've never seen a superscript before and don't know what it could mean. Sincere regards, JJ Miranda Are Kristiansen (akristiansen@pronova.no) wrote: : Hallo, : I have received the proof of an article to be published in BBA. As I do : not have immediate access to recent editions of the journal and I am : already late in returning the proof, I direct the question to this : newsgroup: : The journal has superscripted all numbers of amino acids. Instead of for : example Trp28, it reads Trp, i.e. the amino acid (Trp) : is normal font, but the number (28) is superscript. : I suppose this is a misunderstanding in the typesetting, or is it common : to "superscript" numbers of amino acids? : Are Kristiansen : R&D Scientist : Pronova Biomedical : Gaustadalleen 21 : N-0371 Oslo, Norway From owner-proteins@net.bio.net Wed Jul 08 23:00:00 1998 From: Cornelius Krasel Subject: Re: Cultivation of E. coli at lower temperature Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins References: <35A4CEE6.A4874A8D@uni-wh.de> User-Agent: tin/pre-1.4-980514 (UNIX) (Linux/2.0.34 (i486)) MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Date: Thu, 9 Jul 1998 20:29:04 +0200 Message-ID: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de Lines: 25 Path: biosci!news.Stanford.EDU!newsfeed.concentric.net!news-peer-west.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!news-peer.gip.net!news-lond.gip.net!news.gsl.net!gip.net!newsfeed.metronet.de!uni-erlangen.de!uni-wuerzburg.de!not-for-mail Xref: biosci bionet.molbio.methds-reagnts:68879 bionet.molbio.proteins:12996 In bionet.molbio.methds-reagnts Andreas Savelsbergh wrote: > my own experience and that of lab-fellows says that pre-cultivation of > E. coli (BL21(DE3)pLysS) for expression cultures of toxic proteins at > lower temperatures gives sometimes better results (= cells grow) than > pre-cultivation at 37°C (= cells don't grow). Expression itself > sometimes is only possible at 30 °C, while at 37°C nothing grows or is > expressed. > My question is: Does anybody have a reasonable explanation for that? Are > there proteases which are less active at lower temperatures. Does > anybody know a reference for that? My uneducated guess (no reference, sorry): Most enzymes are less active at lower temperatures. Furthermore, proteins may fold more stably at lower temperatures (although this is not always true; there are also cold-sensitive proteins), and the bacteria have more time to accommodate to adverse conditions (at 37°C in a well-shaken culture, E.coli does almost nothing but divide). --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP4 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Wed Jul 08 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!woodstock.news.demon.net!demon!dispose.news.demon.net!demon!newsfeed.nacamar.de!univ-lyon1.fr!cri.ens-lyon.fr!news From: Joel Baguet Newsgroups: bionet.molbio.proteins Subject: concentration of conditioned medium Date: Thu, 09 Jul 1998 18:01:00 +0000 Organization: Ecole Normale Superieure de Lyon Message-ID: <35A5055C.2BF7@ens-lyon.fr> Reply-To: Joel.Baguet@ens-lyon.fr NNTP-Posting-Host: mac-lr5-118a-oncovirus.ens-lyon.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; 68K) Lines: 7 Dear Netter's Does anybody know what are the best methods to concentrate medium conditioned by cells in culture for two-dimensional gel electrophoresis. Thank you From owner-proteins@net.bio.net Wed Jul 08 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news2.ais.net!jamie!ais.net!uunet!in3.uu.net!news1.optus.net.au!vrn.edu.au!towncrier.cc.monash.edu.au!not-for-mail From: Mark Cauchi Newsgroups: bionet.molbio.proteins Subject: Recombinant DNA Techniques Workshop Date: Fri, 10 Jul 1998 14:43:31 +1000 Organization: Monash University Lines: 8 Message-ID: <35A59BF3.4E84@med.monash.edu.au> Reply-To: Mark.Cauchi@med.monash.edu.au NNTP-Posting-Host: microb36.med.monash.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win16; I) The Micromon Unit at the Department of Microbiology, Monash University in Melbourne, Australia will be running its Recombinant DNA Techniques Course between the 15-20 November, 1998. This is an introductory-intermediate level course which offers a skills-based training package. If you would like further information, details can be found on our web page at http://www.med.monash.edu.au/micro/department/dnacorse.htm From owner-proteins@net.bio.net Thu Jul 09 23:00:00 1998 Path: biosci!agate!howland.erols.net!surfnet.nl!news-ge.switch.ch!news-fra1.dfn.de!news-koe1.dfn.de!news.rwth-aachen.de!not-for-mail From: Edith Duerbaum Newsgroups: bionet.molbio.proteins Subject: looking for biotest-electrophoresis chambers Date: Fri, 10 Jul 1998 14:58:53 -0700 Organization: Aachen University of Technology / Rechnerbetrieb Informatik Lines: 10 Message-ID: <35A68E9D.5634@post.rwth-aachen.de> NNTP-Posting-Host: s3m063.dialup.rwth-aachen.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 2.02 [de] (Win16; I) Hi netters, We ´ve been using biotest-electrophoresis chambers for cellogel-foil (electrophoresis of Gc, Bf if this means anything to you..:-)), and some are leaking after several years of dutiful service... Biotest doesn´t sell them anymore, so can anybody provide me with a new source? Thanks a lot! Edith Duerbaum From owner-proteins@net.bio.net Thu Jul 09 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!newscore.univie.ac.at!newsfeed03.univie.ac.at!03-newsfeed.univie.ac.at!news.univie.ac.at!not-for-mail From: a8803349.nospam@unet.univie.ac.at (Martin Offterdinger) Newsgroups: bionet.molbio.proteins Subject: Re: Reduced Protein Gel Behavior Date: Fri, 10 Jul 1998 08:56:04 GMT Organization: AKH Lines: 29 Message-ID: <35a5d625.4941492@news.univie.ac.at> References: NNTP-Posting-Host: grunt.imed1.akh-wien.ac.at X-Newsreader: Forte Free Agent 1.1/16.230 On Thu, 09 Jul 1998 17:26:42 -0500, sg@nwu.edu (Stephen Gately) wrote: >I have a protein that migrates as a doublet at approximately 52 kD on >denaturing/non-reducing gels. If I run the sample reduced (BME) the >protein still runs as a doublet, but the molecular mass increases to 60-64 >kD. > >Any thoughts on this occurence? > >Thanks, > >Steve Steve! 1) I think that you are having a protein with an intenal S-S bond, that leads to intenal loop formation thus "shortening " the unreduced protein. If you reduce the protein the loop is destroyed and you see the full length. 2) The double band should be independent of this phenomenon and may have various reasons. Partial degradation, differential phosphorylation , glycosylation,.... Hope this is of some help! Martin Martin Offterdinger Internal Med.I,Dept. Oncology University of Vienna Austria E-Mail:a8803349.nospam@unet.univie.ac.at (remove nospam before mailing) From owner-proteins@net.bio.net Thu Jul 09 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!wn4feed!worldnet.att.net!140.142.64.3!news.u.washington.edu!protein.chem.washington.edu!tomasz From: John Tomaszewski Newsgroups: bionet.molbio.proteins Subject: Suggestions needed: Adjusting a DL39-based auxotroph to minimal media. Date: Fri, 10 Jul 1998 15:09:00 -0700 Organization: University of Washington Lines: 26 Message-ID: NNTP-Posting-Host: protein.chem.washington.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: nntp4.u.washington.edu 900108171 36416 (None) 140.142.64.7 X-Complaints-To: help@cac.washington.edu Hi all, In the past I've had no trouble getting M15 and BL21 strains of E.coli to grow in minimal media (M9 supplemented with vitamins and minerals, or another MOPS-based media) but I'm having a dickens of a time with this DL39-derived Asp auxotroph to come around. It grows very well in LB but, in M9 containing 100-400mg/L Asp, the highest OD600 I've seen was 0.8 and it's usually 0.4-0.5. I've tried both, taking aliquots of growing cultures and adding to new media, and centrifuging growing cultures (5min, 4000RPM) and resuspending the pellets in fresh media, to no avail. Thus far all has been done either as 100ml cultures in 500ml Erl. flasks or 250ml cultures in 1L Erl. flasks, 37 deg. C, 300RPM. I'm trying to get them up above one before using them to start a 5L culture in the fermenter. Any suggestions or critiques would be greatly appreciated. Sincerely, John T. ******************************************************************** ** ** ** ** * ** DEPARTMENT OF CHEMISTRY ** ** ** ** ** * ** tomasz@protein.chem.washington.edu ** ** ** ** ** * ** (206) 616-2993 ** ** ***** ***** JOHN TOMASZEWSKI ** ******************************************************************** From owner-proteins@net.bio.net Fri Jul 10 23:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!cyclone.mbnet.mb.ca!ptdnetP!newsgate.ptd.net!fastnet!howland.erols.net!newsfeed.internetmci.com!209.150.97.11!feeder.qis.net!newsfeed1.earthlink.net!nntp.earthlink.net!not-for-mail From: "God" Newsgroups: alt.business,alt.business.misc,alt.elvis.sighting,alt.fan.howard-stern,alt.fitness.marketplace,alt.forsale.nutrition,alt.health,alt.invest,alt.society.modern-life,alt.support.diet,alt.support.diet.low-carb,bionet.molbio.proteins,fidonet.dietin Subject: The World's Greatest Nutrition Bar! 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Our nutrition food bar is ready to roll out into the marketplace, so doesn’t miss this spectacular investment opportunity. Serious Inquiries Only. Please Call: Professor Richard Hughes (949)883-3007 or E-mail Perfectlite@geocities.com Check out our website for additional information: http://www.geocities.com/HotSprings/Villa/5677 From owner-proteins@net.bio.net Fri Jul 10 23:00:00 1998 Path: biosci!news.Stanford.EDU!nntp.Stanford.EDU!ram From: Dr. Ram Samudrala Newsgroups: bionet.molbio.proteins Subject: Re: proteins with 30% homology should have the same general fold: reference for this ? Date: 11 Jul 1998 07:55:10 GMT Organization: Department of Structural Biology, Stanford University Lines: 18 Message-ID: <6o75ou$sqp$1@nntp.Stanford.EDU> References: <6ne6le$ndl@sifon.cc.mcgill.ca> Reply-To: expt@alanine.ram.org NNTP-Posting-Host: zen.stanford.edu X-Newsreader: TIN [UNIX 1.3 unoff BETA release 970206] Eric Campeau wrote: > every teacher in protein structure classes say that if a protein has a 30% >homology to a related protein, it should have the same general fold. However, >they do do not cite the reference to this .... is there anybody that could give >me the reference for this "fact" ? Well, you can just do a few sequence comparisons for proteins with known structure and see if the folds are the same. So it's completely testable. Though I'd add that this "rule" applies only to proteins in nature and not to designed proteins (cf. the Parcelus challenge). --Ram email@urls || http://www.ram.org || http://www.twisted-helices.com/th The dollar will never fall as low as what some people will do to get it. ---Alfred E. Neuman From owner-proteins@net.bio.net Sat Jul 11 23:00:00 1998 Message-ID: <35A987F7.CC9@antibodyresource.com> Date: Sun, 12 Jul 1998 22:07:44 -0600 From: The Antibody Resource Page X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC) MIME-Version: 1.0 Newsgroups: bionet.molbio.proteins Subject: Win a free book on antibody purification. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: 207.241.85.73 Lines: 34 Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-dc-2.sprintlink.net!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!news-peer.gip.net!news.gsl.net!gip.net!newsfeed.internetmci.com!207.241.0.194!news.wwa.com!news-mw.idsonline.com!207.241.85.73 Visit The Antibody Resource Page (http://www.antibodyresource.com/) and find out how you can win "Purification Tools for Monoclonal Antibodies" by Peter Gagnon. While you are there see the new section on custom polyclonal suppliers! Here are some other useful sections that can be found on the page: 1. How to Find an Antibody - a variety of ways on and off the web to find the antibody you are looking for. There are links to free search engines that allow you to search a multitude of companies for the specific antibody that you need. 2. Online Companies - links to over 120 companies that sell antibodies or antibody related products. Is your company listed on this page? 3. Antibody Image Gallery - see some of the latest in animated antibody graphics. 4. Educational Resources - links to pages on immunochemistry, antibody production, autoimmunity, vaccines, immunology and much more. This page is divided up into sections on research, educational, and health resources. Check it all out at: http://www.antibodyresource.com/ ps. The ARP was voted among the top 25 biotechnology webpages for 1997 by Genetic Engineering News! From owner-proteins@net.bio.net Sat Jul 11 23:00:00 1998 Path: biosci!agate!newsfeed.wli.net!su-news-hub1.bbnplanet.com!la-news-feed1.bbnplanet.com!news.bbnplanet.com!newsfeed1.earthlink.net!newsfeed.concentric.net!ozemail!ozemail.com.au!ozreader From: Patrick T Kent Newsgroups: bionet.molbio.proteins Subject: Benzoic Acid Date: Mon, 13 Jul 1998 12:53:33 +0930 Organization: The House Of Deighton-Kent Lines: 27 Message-ID: <35A97DAB.9ED1DD24@ozemail.com.au> References: <6ne6le$ndl@sifon.cc.mcgill.ca> <6o75ou$sqp$1@nntp.Stanford.EDU> Reply-To: Patrick T Kent NNTP-Posting-Host: sladl4p09.ozemail.com.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) Hi, I hope someone here can help me. I have been asked by a friend to try and use the internet to find out what foods Benzoic Acid naturally occurs in. I have spent 6 hours searching and can only find out about the chemical manufacturers, or books available, containing the search words. This is an important issue to this person for health reasons, (he has lots of quite serious problems), so I would really like to be able to at least give him a partial answer if not a comprehensive one. (Don't ask me why he needs to know - I have no idea. I think it is to avoid medication with chemicals he is allergic to, but that's really only a guess.) If anyone can either answer, or even offer any advice (via email) on where I might be able to search further, I would really appreciate it. Thanks in advance, warmest regards Patrick T Kent From owner-proteins@net.bio.net Sun Jul 12 23:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.proteins Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 13 Jul 1998 02:00:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199807130900.CAA01247@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-proteins@net.bio.net Sun Jul 12 23:00:00 1998 Path: biosci!CAMBRIDGE.ORG!symposia From: symposia@CAMBRIDGE.ORG (James Larkin) Newsgroups: bionet.molbio.proteins Subject: Upcoming Meetings Date: 13 Jul 1998 07:05:31 -0700 Organization: Cambridge Healthtech Institute Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <35AA1487.33F3@cambridge.org> NNTP-Posting-Host: net.bio.net I thougth these 4 meetings might be of interest to your group. NMR TECHNOLOGY: Developments and Applications October 29-30, 1998 =95 Baltimore, Maryland PROTEIN EXPRESSION November 2-3, 1998 =95 Washington, D.C. PROTEIN PRODUCTION November 4-5, 1998 =95 Washington, D.C. Advances in MASS SPECTROMETRY for Genomic and Biomolecular Research=20 January 7-8, 1999 =95 Orlando, Florida For more information please contact Cambridge Healthtech Institute 1037 Chestnut St. Newton Upper Falls, MA 02464 PH: 617-630-1300 Fax: 617-630-1325 Email: chi@healthtech.com From owner-proteins@net.bio.net Sun Jul 12 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!newsfeed.internetmci.com!207.207.0.26!nntp.giganews.com!news.giganews.com.POSTED!not-for-mail From: rathbun@sedona.net Newsgroups: bionet.molbio.proteins Subject: POSITION: Product Manager/Molecular Biology Products Organization: Sedona Internet Services, Inc. Reply-To: rathbun@sedona.net X-Newsreader: Forte Free Agent 1.0.82 Lines: 90 Message-ID: Date: Mon, 13 Jul 1998 17:27:09 GMT NNTP-Posting-Host: 204.245.58.163 NNTP-Posting-Date: Mon, 13 Jul 1998 12:27:09 CDT COMPANY SUMMARY: The company is mid-sized company specializing in the development and manufacture of innovative products serving the life science research market. The company currently offers more than 2,000 products designed to facilitate gene expression and analysis, gene cloning, PRC analysis and many other molecular biology techniques used in developmental genetics, cellular biology, cancer research, antisense DNA research, genome mapping, neurobiology, oncology and several other areas. The company is very technology oriented and places great emphasis on quality, innovation, fiscal stability and responsiveness and responsibility towards customers and the community. 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This includes excellent proficiency in English (both written and verbal) and in the use of the scientific literature · Computer literacy to include operation of a Personal Computer (IBM clone and/or Mac); proficiency in the use of the Internet. · Knowledge of and experience in GMP/GLP environments. · Able to manage multiple priorities and deadlines in an expedient and decisive manner. · Must have sufficient emotional maturity and fortitude to flourish in an environment with constantly changing workloads and work requirements and must evolve with the position. If you have an interest in this or other opportunities, please send us your resume/CV as an Attached File to an email or send by mail/FAX to RS&A to the attention of Ann Rathbun, Managing Director. All correspondence is held in strict confidence. Rathbun, Sapir & Associates P.O. Box 2337 Sedona, AZ 86339-2337 * USA (520) 203-0074 Office (520) 203-0075 FAX E-mail: rathbun@sedona.net From owner-proteins@net.bio.net Mon Jul 13 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: pkkf2@cam.ac.uk Newsgroups: bionet.molbio.proteins Subject: Gz and JNK/p38/MAPK Date: Tue, 14 Jul 1998 08:27:41 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 13 Message-ID: <6of4ps$dj3$1@nnrp1.dejanews.com> NNTP-Posting-Host: 202.40.139.35 X-Article-Creation-Date: Tue Jul 14 08:27:41 1998 GMT X-Http-User-Agent: Mozilla/4.04 [en] (Win95; I) X-Http-Proxy: 1.0 wwwproxy.ust.hk:8080 (Squid/1.1.9) for client 143.89.69.174 Does anybody know of any paper on coupling between Gz and JNK/p38/MAPK? I couldn't find much on medline. Many thanks in advance. Please reply to my email address as well. Regards, Kenneth ______________________________________ 2nd year medical science undergraduate Downing College, Cambridge. -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-proteins@net.bio.net Mon Jul 13 23:00:00 1998 Path: biosci!organon.oss.akzonobel.nl!anonymous From: anonymous@organon.oss.akzonobel.nl ("Anonymous@Organon.oss.akzonobel.nl") Newsgroups: bionet.molbio.proteins Subject: Difference between homology, identity and similarity Date: 14 Jul 1998 23:48:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <35AC504D.2DC85239@organon.oss.akzonobel.nl> NNTP-Posting-Host: net.bio.net Hello, Could someone explain to me the difference between protein sequence homology, identity, and similarity ? Thanks Joop From owner-proteins@net.bio.net Tue Jul 14 23:00:00 1998 Path: biosci!news.Stanford.EDU!nntp.Stanford.EDU!ram From: Dr. Ram Samudrala Newsgroups: bionet.molbio.proteins Subject: Re: Difference between homology, identity and similarity Date: 15 Jul 1998 08:10:46 GMT Organization: Department of Structural Biology, Stanford University Lines: 32 Distribution: world Message-ID: <6oho66$q97$2@nntp.Stanford.EDU> References: <35AC504D.2DC85239@organon.oss.akzonobel.nl> Reply-To: expt@alanine.ram.org NNTP-Posting-Host: zen.stanford.edu X-Newsreader: TIN [UNIX 1.3 unoff BETA release 970206] "Anonymous@Organon.oss.akzonobel.nl" wrote: >Could someone explain to me the difference between protein sequence >homology, identity, and similarity ? It depends on the context. Some people would say that homology means that the sequences are evolutionarily related, identity is the fraction of amino acids that are the same between a pair of sequences after an alignment of the sequences (which can be done using only sequence information or structural information or some other information, but usually it is based on sequence information alone), and similarity is the score assigned based on an alignment using some similarity matrix. Some people use homology and identity interchangeably (most notably, Branden and Tooze, p249 (caption) in Introduction to Protein Structure). Others may say homology is more akin to similarity and use those interchangeably (this is something I particularly noticed at CASP, see Proteins: Structure Function Genetics Supplemental 1, 1997). I am not one of those people who thinks that the usage has to be one way or another (particularly with regards to what "homology" is). As I say above, I think it depends on the context and as long as it is clear (from the context or from an explicit statement) what people mean, that's all that's necessary. --Ram email@urls || http://www.ram.org || http://www.twisted-helices.com/th God is a conjecture; but I desire that your conjectures should not reach beyond your creative will. Could you /create/ a god? Then do not speak to me of any gods. But you could well create the overman. ---Nietzsche From owner-proteins@net.bio.net Tue Jul 14 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!fu-berlin.de!cpeter.dialup.fu-berlin.DE!not-for-mail From: deleteme_cpeter@zedat.fu-berlin.de (Christoph Peter) Newsgroups: bionet.molbio.proteins Subject: How much Protein needed for sequencing? Date: Tue, 14 Jul 1998 06:23:57 GMT Organization: Freie Universitaet Berlin Lines: 13 Message-ID: <35aaf5f3.1810987@news.fu-berlin.de> Reply-To: deleteme_cpeter@zedat.fu-berlin.de NNTP-Posting-Host: cpeter.dialup.fu-berlin.de (130.133.221.185) Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Access: 16 17 18 X-Trace: fu-berlin.de 900493988 21906 (none) 130.133.221.185 X-Newsreader: Forte Free Agent 1.11/16.235 Hi dear scientific community! What is the minimum amount of protein, in micrograms (50kDa) or picomoles, on a SDS-PAGE (or western-blotted) which could still be reliably sequenced by a state-of-the-art-method? Many thanks in advance............................Christoph -- Christoph Peter PhD Student (Biotechnology) cpeter at zedat dot fu-berlin dot de >Alles wird gut!<(Beate) From owner-proteins@net.bio.net Tue Jul 14 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!europa.clark.net!192.174.65.44!newscore.univie.ac.at!newsfeed03.univie.ac.at!03-newsfeed.univie.ac.at!news.univie.ac.at!not-for-mail From: a8803349.nospam@unet.univie.ac.at (Martin Offterdinger) Newsgroups: bionet.molbio.proteins Subject: Re: Antigenicity profile programs Date: Thu, 16 Jul 1998 06:02:06 GMT Organization: AKH Lines: 23 Message-ID: <35ad9724.1132608@news.univie.ac.at> References: NNTP-Posting-Host: grunt.imed1.akh-wien.ac.at X-Newsreader: Forte Free Agent 1.1/16.230 On Wed, 15 Jul 1998 15:52:52 -0700, Thomas Tan wrote: >Hello, > >Does anyone know of a good program than can give antigenicity profiles for >proteins? I would like to find peptide sequences for use as antigens to >generate polyclonal antibodies. Thank you in advance. > >Sincerely, > >Thomas Tan Most Sequence Analysis programms like Gene Runner can calculate ANtigenicity ! martin Martin Offterdinger Internal Med.I,Dept. Oncology University of Vienna Austria E-Mail:a8803349.nospam@unet.univie.ac.at (remove nospam before mailing) From owner-proteins@net.bio.net Tue Jul 14 23:00:00 1998 Path: biosci!YAHOO.COM!p_hufnagel From: p_hufnagel@YAHOO.COM (Peter Hufnagel) Newsgroups: bionet.molbio.proteins Subject: bacillus megaterium for secretion Date: 15 Jul 1998 00:46:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <19980715074313.5949.rocketmail@send1b.yahoomail.com> NNTP-Posting-Host: net.bio.net I would like to use bacillus megaterium for protein overexpression and secretion. Can anyone recommend a signal sequence that has proven useful in a bacillus system? Since I want to do structural studies, the signal sequence has to be exactly cleaved off by b.m.´s signal peptidase. Thanks a lot in advance. Peter ***** _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From owner-proteins@net.bio.net Tue Jul 14 23:00:00 1998 Newsgroups: bionet.molbio.proteins Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!news.maxwell.syr.edu!howland.erols.net!ix.netcom.com!atlantis From: atlantis@netcom.com (JJ Miranda) Subject: Re: How much Protein needed for sequencing? Message-ID: Organization: Netcom On-Line Services X-Newsreader: TIN [version 1.2 PL2] References: <35aaf5f3.1810987@news.fu-berlin.de> Date: Thu, 16 Jul 1998 00:24:37 GMT Lines: 24 Sender: atlantis@netcom20.netcom.com Dear Cristoph, Silver stained, in SDS-PAGE, with a good mass spec lab can do it with low picomoles. It's very protein dependant. Some groups have even claimed to be able ot do femtomoles. If you want to be sure to get a sequence, make sure that you stay in the picomole range. Sincere regards, JJ Christoph Peter (deleteme_cpeter@zedat.fu-berlin.de) wrote: : Hi dear scientific community! : What is the minimum amount of protein, in micrograms (50kDa) or : picomoles, on a SDS-PAGE (or western-blotted) which could still be : reliably sequenced by a state-of-the-art-method? : Many thanks in advance............................Christoph : -- : Christoph Peter : PhD Student (Biotechnology) : cpeter at zedat dot fu-berlin dot de : >Alles wird gut!<(Beate) From owner-proteins@net.bio.net Tue Jul 14 23:00:00 1998 Path: biosci!news.Stanford.EDU!nntp.Stanford.EDU!cardinal2.Stanford.EDU!tomtan From: Thomas Tan Newsgroups: bionet.molbio.proteins Subject: Antigenicity profile programs Date: Wed, 15 Jul 1998 15:52:52 -0700 Lines: 10 Sender: tomtan@cardinal2.Stanford.EDU Message-ID: NNTP-Posting-Host: cardinal2.stanford.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, Does anyone know of a good program than can give antigenicity profiles for proteins? I would like to find peptide sequences for use as antigens to generate polyclonal antibodies. Thank you in advance. Sincerely, Thomas Tan From owner-proteins@net.bio.net Tue Jul 14 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!news.maxwell.syr.edu!newsfeed.internetmci.com!206.52.4.10!news-stl.cp.verio.net!news.starnet.net!newsreader.wustl.edu!not-for-mail From: " " < chanlab@im.wustl.edu> Newsgroups: bionet.molbio.proteins Subject: endoproteinase glu c Date: Wed, 15 Jul 1998 17:48:34 +0000 Organization: Washington University in St. Louis Lines: 6 Message-ID: <6ojbh8$gvs$1@newsreader.wustl.edu> NNTP-Posting-Host: 128.252.178.165 Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express for Macintosh - 4.01 (295) Hi Has anyone used Boehringer Mannheim's endoproteinase glu c sequencing grade? If so did anyone have success resuspending this enzyme in water or some other volatile buffer like ammonium carbonate and freezing for use at later date? thanks Mark From owner-proteins@net.bio.net Tue Jul 14 23:00:00 1998 Path: biosci!IR2CBM.CNRS-MRS.FR!athel From: athel@IR2CBM.CNRS-MRS.FR (Athel Cornish-Bowden) Newsgroups: bionet.molbio.proteins Subject: Re: Nomenclature of numbering of amino acids Date: 15 Jul 1998 08:05:03 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Are Kristiansen wrote: > > Hallo, > > I have received the proof of an article to be published in BBA. As I do > not have immediate access to recent editions of the journal and I am > already late in returning the proof, I direct the question to this > newsgroup: > > The journal has superscripted all numbers of amino acids. Instead of for > example Trp28, it reads Trp, i.e. the amino acid (Trp) > is normal font, but the number (28) is superscript. > > I suppose this is a misunderstanding in the typesetting, or is it common > to "superscript" numbers of amino acids? > IUBMB have a web site devoted to amino acid recommendations. As the original document is quite long it is broken into numerous pages, the bit most relevant to your query starting at http://www.chem.qmw.ac.uk/iupac/AminoAcid/AA22.html#AA22. It doesn't seem to contain a direct unambiguous answer to your query, but if you examine what it does itself you'll see that it uses Trp-29 (with a hyphen and no superscript) to refer to the 29th residue of a protein if this is a Trp, whereas [Trp]albumin (for example) would be a modified albumin in which the 29th residue was replaced with Trp. If I understand your example correctly the superscripts used by BBA would appear to be a mistake. Athel Cornish-Bowden Email: athel@ibsm.cnrs-mrs.fr Site map: http://ir2lcb.cnrs-mrs.fr/~athel/sitemap.htm New Beer in an Old Bottle: http://ir2lcb.cnrs-mrs.fr/~athel/buchner.htm From owner-proteins@net.bio.net Tue Jul 14 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!newsfeed.wli.net!news2.ais.net!jamie!ais.net!news.indiana.edu!not-for-mail From: Joe Nan Newsgroups: bionet.molbio.proteins Subject: Where to get sequenes Date: Wed, 15 Jul 1998 23:24:28 -0500 Organization: Indiana University, Bloomington Lines: 7 Message-ID: <35AD807B.5B38@indiana.edu> References: NNTP-Posting-Host: starfish.bio.indiana.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) Help! Can anybody tell me where to get the amino acid sequences for subunits 10 and 11 of bovine mitochondrial cytochrome bc1 complex. I don't seem to be able to find them from the GenBank nor PDB. I know they have to be available as the crystal structure of the 11 subunit complex has already been solved. But don't know where the other places to find them with keywords. With many thanks. From owner-proteins@net.bio.net Wed Jul 15 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: sweiss@pomona.edu Newsgroups: bionet.molbio.proteins Subject: Western Blot Suggestions? Date: Thu, 16 Jul 1998 20:59:16 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 13 Message-ID: <6olpj4$kjc$1@nnrp1.dejanews.com> NNTP-Posting-Host: 140.163.99.133 X-Article-Creation-Date: Thu Jul 16 20:59:16 1998 GMT X-Http-User-Agent: Mozilla/3.01 (Macintosh; I; 68K) I'm having trouble getting positive western blot results on an anti-body found in patient serum. The anti-body was evident in immunohistochemistry on rat tissue but did not show up in westerns when screened against cortex and purkinjie proteins. I have tried SDS-Page and am attempting non-denaturing non- reducing gels. Has anyone encountered similar difficulties or has any suggestions. (non-denaturing, non-reducing protocols) or does anyone have any other suggestions. Thanks Shennan Weiss -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-proteins@net.bio.net Wed Jul 15 23:00:00 1998 Newsgroups: bionet.molbio.proteins Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!news.maxwell.syr.edu!ix.netcom.com!atlantis From: atlantis@netcom.com (JJ Miranda) Subject: Alkaline Phosphatase Message-ID: Organization: Netcom On-Line Services X-Newsreader: TIN [version 1.2 PL2] Date: Thu, 16 Jul 1998 18:09:54 GMT Lines: 11 Sender: atlantis@netcom20.netcom.com Hi all, I've done a quick literature search but maybe I missed something... Has anyone solved the reaction mechanism of alkaline phosphatase. I know that it's simple hydrolosis to remove the phosphate group, but... 1. Has the active site been elucidated? 2. Has anyone characterized the enzyme-substrate complex? Sincere regards, JJ Miranda From owner-proteins@net.bio.net Wed Jul 15 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!nntp-out.monmouth.com!newspeer.monmouth.com!btnet-peer!btnet!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!server1.netnews.ja.net!bham!med180.bham.ac.uk!user From: noone@cancer.bham.ac.uk (noone) Newsgroups: bionet.molbio.proteins Subject: Re: How much Protein needed for sequencing? Date: Thu, 16 Jul 1998 15:57:13 +0100 Organization: noone Lines: 32 Message-ID: References: <35aaf5f3.1810987@news.fu-berlin.de> NNTP-Posting-Host: med180.bham.ac.uk In article <35aaf5f3.1810987@news.fu-berlin.de>, deleteme_cpeter@zedat.fu-berlin.de wrote: > Hi dear scientific community! > > What is the minimum amount of protein, in micrograms (50kDa) or > picomoles, on a SDS-PAGE (or western-blotted) which could still be > reliably sequenced by a state-of-the-art-method? > > Many thanks in advance............................Christoph > -- > Christoph Peter > PhD Student (Biotechnology) > cpeter at zedat dot fu-berlin dot de > > >Alles wird gut!<(Beate) Hi Christoph, if you're talking about Edman degradation, you need about 1 picomol or more (e.g. on an ABI Procise) in most labs. Thumb rule is that if you can stain your protein on a PVDF membrane with Coomassie, it's usually enough for sequencing (if it's not > 200 kD or so). If your protein is already known you can do Mass-Spec which needs less than that (I think the EMBL-Labs in Heidelberg offer a commercial service). The "cracks" in Germany are in Muenchen (Ansorge) and Heidelberg, but they should have a good sequencing facility at the MDC in Berlin as well. Hope this helps, Peter From owner-proteins@net.bio.net Wed Jul 15 23:00:00 1998 Path: biosci!medecine.unige.ch!Elisabeth.Gasteiger From: Elisabeth.Gasteiger@medecine.unige.ch (Elisabeth Gasteiger) Newsgroups: bionet.molbio.proteins Subject: RE: Where to get sequenes Date: 16 Jul 1998 05:28:42 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <35ADF15D.FB6A7FC3@medecine.unige.ch> NNTP-Posting-Host: net.bio.net > Subject: Where to get sequenes > > Date: Wed, 15 Jul 1998 23:24:28 -0500 > > > Help! > Can anybody tell me where to get the amino acid sequences for subunits > 10 and 11 of bovine mitochondrial cytochrome bc1 complex. I don't seem > to be able to find them from the GenBank nor PDB. I know they have to be > available as the crystal structure of the 11 subunit complex has already > been solved. But don't know where the other places to find them with > keywords. With many thanks. I think the SWISS-PROT entries UCRX_BOVIN (P00130) and UCRY_BOVIN (P07552) are the sequences you are looking for. You can use the Sequence Retrieval System SRS (http://www.expasy.ch/srs5/) to search SWISS-PROT, TrEMBL and TrEMBL_NEW with keywords like Organism: bovin AND all text: bc1 I hope this helps. Best regards Elisabeth Gasteiger, SWISS-PROT group Geneva -- ----------------------------------------------------------------- Elisabeth Gasteiger Swiss Institute of Bioinformatics c/o Department of Medical Biochemistry 1, rue Michel Servet Tel. (+41 22) 702 54 79 CH - 1211 Geneva 4 Switzerland Fax (+41 22) 702 55 02 Elisabeth.Gasteiger@medecine.unige.ch http://www.expasy.ch/ ----------------------------------------------------------------- From owner-proteins@net.bio.net Wed Jul 15 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!news.maxwell.syr.edu!newsm.ibm.net!ibm.net!news.biu.ac.il!news.huji.ac.il!not-for-mail From: "Jonathan B. Marder" Newsgroups: bionet.molbio.proteins Subject: Re: endoproteinase glu c Date: Thu, 16 Jul 1998 09:42:30 +0300 Organization: Hebrew University Lines: 20 Approved: marder@agri.huji.ac.il Message-ID: <6ok7e6$54u$1@news.huji.ac.il> References: <6ojbh8$gvs$1@newsreader.wustl.edu> NNTP-Posting-Host: marder.agri.huji.ac.il Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.3110.22 X-Mimeole: Produced By Microsoft MimeOLE V4.72.3110.22 >Has anyone used Boehringer Mannheim's endoproteinase glu c sequencing grade? > If so did anyone have success resuspending this enzyme in water or some >other volatile buffer like ammonium carbonate and freezing for use at later >date? This is V8 protease right? If so, I have good experience keeping it as frozen stock (10 mg/ml in water) at -80 celcius. Jonathan B. Marder Department of Agricultural Botany, The Hebrew University of Jerusalem Faculty of Agriculture, P.O.Box 12, Rehovot 76100, ISRAEL Phone: +972 8 9481918 Fax: +972 8 9467763 Web page: http://www.agri.huji.ac.il/~marder From owner-proteins@net.bio.net Wed Jul 15 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news2.ais.net!jamie!ais.net!news.indiana.edu!not-for-mail From: Joe Nan Newsgroups: bionet.molbio.proteins Subject: Re: Where to get sequenes Date: Thu, 16 Jul 1998 17:40:45 -0500 Organization: Indiana University, Bloomington Lines: 15 Message-ID: <35AE816D.7589@indiana.edu> References: <35ADF15D.FB6A7FC3@medecine.unige.ch> NNTP-Posting-Host: starfish.bio.indiana.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) Thanks for pointing to the good source. I have got the sequences I needed and learned a good way of searching too. With best regards. > I think the SWISS-PROT entries UCRX_BOVIN (P00130) > and UCRY_BOVIN (P07552) are the sequences you are looking for. > You can use the Sequence Retrieval System SRS > (http://www.expasy.ch/srs5/) > to search SWISS-PROT, TrEMBL and TrEMBL_NEW with keywords like > Organism: bovin > AND > all text: bc1 > > I hope this helps. > Best regards > Elisabeth Gasteiger, SWISS-PROT group Geneva From owner-proteins@net.bio.net Wed Jul 15 23:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!island.idirect.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!207.217.77.43!newsfeed1.earthlink.net!nntp.earthlink.net!not-for-mail From: "Dr.Hughes" Newsgroups: alt.business,alt.business.misc,alt.elvis.sighting,alt.fitness.marketplace,alt.forsale.nutrition,alt.health,alt.invest,alt.life.universe.everything,alt.support.diet,alt.support.diet.low-carb,bionet.molbio.proteins,fidonet.dieting,misc.fitness.m Subject: A Great Nutrition Bar!! Date: Thu, 16 Jul 1998 22:09:57 -0400 Organization: EarthLink Network, Inc. Lines: 27 Message-ID: <6ombso$gep$1@fir.prod.itd.earthlink.net> NNTP-Posting-Host: 1cust170.tnt1.mia1.da.uu.net X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Why not invest in nutrition food bars? “The fastest growing segment, of the natural food industry is nutrition food bars which is now a staple food in mainstream diets.” Spence Information Services of San Fransico Sales of Clif and Balance nutrition bars have doubled during each of the last three years. This presents a wonderful investment opportunity and we have developed the perfect fat burning formula for a nutrition bar that will follow the success of Clif and Balance nutrition bars. The Balance bars currently gross 7 million dollars a month. Three years ago they grossed less then 1 million dollars a year. Our nutrition food bar is ready to roll out into the marketplace, so doesn’t miss this spectacular investment opportunity. Serious Inquiries Only. Please Call: Professor Richard Hughes (949)883-3007 or E-mail Perfectlite@geocities.com Check out our website for additional information: http://www.geocities.com/HotSprings/Villa/5677 From owner-proteins@net.bio.net Wed Jul 15 23:00:00 1998 Message-ID: <35AE5A05.CA4A70A9@ITSMYSPAMbestlremovelowercaseparttooANDILLFNORD.IFIWANTTOcom> Date: Thu, 16 Jul 1998 12:52:37 -0700 From: Scott Le Grand X-Mailer: Mozilla 4.04 [en] (WinNT; U) MIME-Version: 1.0 Newsgroups: bionet.molbio.proteins Subject: Re: proteins with 30% homology should have the same general fold: reference for this ? References: <6ne6le$ndl@sifon.cc.mcgill.ca> <6o75ou$sqp$1@nntp.Stanford.EDU> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: 209.142.25.132 X-NNTP-Posting-Host: 209.142.25.132 Lines: 37 X-NNTP-Posting-Host: 209.63.114.134 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!newsfeed.internetmci.com!207.0.56.122!news.eli.net!blushng.jps.net!209.142.25.132 My failing memory indicates this observation was first made by Cyrus Chothia in the 1970s or so after a lot of empirical comparison along the lines that Ram suggests. It appears to be one of the rules of thumb that falls out of the process of protein evolution rather than some sort of natural law as the aforementioned Paracelsus challenge illustrated in short order. Of course, the Paracelsus challenge begs the question of just how close naturally evolved proteins out there can get and possess truly divergent conformations. Scott Le Grand VM Labs Dr. Ram Samudrala wrote: > Eric Campeau wrote: > > > every teacher in protein structure classes say that if a protein has a 30% > >homology to a related protein, it should have the same general fold. However, > >they do do not cite the reference to this .... is there anybody that could give > >me the reference for this "fact" ? > > Well, you can just do a few sequence comparisons for proteins with > known structure and see if the folds are the same. So it's completely > testable. Though I'd add that this "rule" applies only to proteins in > nature and not to designed proteins (cf. the Parcelus challenge). > > --Ram > > email@urls || http://www.ram.org || http://www.twisted-helices.com/th > The dollar will never fall as low as what > some peop