From owner-proteins@net.bio.net Thu May 01 23:00:00 1997 Path: biosci!UMABNET.AB.UMD.EDU!dberman From: dberman@UMABNET.AB.UMD.EDU (Dora Berman) Newsgroups: bionet.molbio.proteins Subject: getting rid of hemoglobin Date: 2 May 1997 14:10:28 -0700 Organization: UMSOM Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <336A8175.168C@umabnet.ab.umd.edu> NNTP-Posting-Host: net.bio.net Hi, I prepare cytosolic extracts from chunks of fat containing some blood vessels. I need to get rid of the hemoglobin present in the extracts in order to assay for the activity and expression of lipolytic enzymes in the extract. I will appreciate any input on how to selectively remove the hemoglobin from my extracts. From owner-proteins@net.bio.net Thu May 01 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!newsfeeds.sol.net!hammer.uoregon.edu!zephyr.texoma.net!uunet!in3.uu.net!204.238.120.21!jump.net!grunt.dejanews.com!not-for-mail Date: Fri, 02 May 1997 11:02:12 -0600 From: p6msv003@cicrp.jussieu.fr Subject: Looking for articles on pectin methylesterases Newsgroups: bionet.plants,bionet.general,bionet.molbio.proteins Message-ID: <862588616.22077@dejanews.com> Reply-To: p6msv003@cicrp.jussieu.fr Organization: Deja News Usenet Posting Service To: p6msv003@cicrp.jussieu.fr X-Article-Creation-Date: Fri May 02 15:56:57 1997 GMT X-Originating-IP-Addr: 134.157.110.1 (ibm0.cicrp.jussieu.fr) X-Http-User-Agent: Mozilla/2.0 (X11; I; AIX 1) X-Authenticated-Sender: p6msv003@cicrp.jussieu.fr Lines: 18 Xref: biosci bionet.plants:15362 bionet.general:26640 bionet.molbio.proteins:10641 Hi ! I'm a student in Paris, and I'm desperately looking for biology articles about pectin methylesterases ! Is there a site, other than ENTREZ, which lets someone look for articles one a keyword search basis ? Thanks for your help ! (send any answers to my email address: p6msv003@cicrp.jussieu.fr) Chantal -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-proteins@net.bio.net Thu May 01 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!newsfeeds.sol.net!europa.clark.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsjunkie.ans.net!newsfeeds.ans.net!lantana.singnet.com.sg!newsfeed.singnet.com.sg!id4.nus.edu.sg!nuscc.nus.sg!sbsdjl From: sbsdjl@leonis.nus.sg (ding jeak ling) Newsgroups: bionet.molbio.proteins Subject: Protein modelling job vacancies Date: 3 May 1997 01:49:49 GMT Organization: National University of Singapore Lines: 29 Message-ID: <5ke5jt$pf8@nuscc.nus.sg> NNTP-Posting-Host: sbsdjl@leonis.nus.sg X-Newsreader: TIN [version 1.2 PL2] ......................................................................... "Positions available - for a period of 2 years" (1) Research Fellow with PhD. Prerequisites include experience in computer aided molecular modelling of macroproteins, ligand-binding and conformational studies. Creative flair and ability to solve problems, as exemplified by a strong publication track record are helpful. Salary: commensurate with experience, up to a maximum of US$47,000 per annum (inclusive of 13th month payment and variable bonuses). (2) Research Assistant with BSc Hons. in Cell and Molecular Biology. To carry out genetic engineering experiments and research and development in gene expression. Knowledge in computational molecular biology will be an advantage. Salary: commensurate with qualification and experience, up to US25,000 per annum. (Current Exchange rate is US$1 = S$1.41) Interested applicants should write/enquire and send CV to: JL Ding (PhD) Marine Biotechnology Laboratory School of Biological Sciences National University of Singapore Kent Ridge, Singapore 119260 Tel: 65-7722776 Fax: 65-7792486 E.mail:sbsdjl@leonis.nus.sg .............................................................................. From owner-proteins@net.bio.net Thu May 01 23:00:00 1997 Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gsl.net!portc01.blue.aol.com!audrey02.news.aol.com!not-for-mail From: squick2653@aol.com (SQuick2653) Newsgroups: bionet.molbio.proteins Subject: ICDD Diffraction Data Crystallography Scholarship Awards Date: 2 May 1997 16:36:42 GMT Organization: AOL http://www.aol.com Lines: 79 Message-ID: <19970502163500.MAA09538@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com ICDD Diffraction Data Crystallography Scholarship Awards The International Centre for Diffraction Data (ICDD) is a non-profit scientific organization dedicated to collecting, editing, publishing, and distributing powder diffraction data for the identification of crystalline materials. The membership of the ICDD consists of worldwide representation from academe, government, and industry. It is our mission to continue as the world center for quality powder diffraction data to meet the needs of the technical community. The ICDD promotes the applications of materials characterization methods in science and technology by providing a forum for the exchange of ideas and information by means of technical meetings, schools, and conferences. The science of crystallography has played a key role in the development of X-ray diffraction, electron diffraction and neutron diffraction for the elucidation of the atomic structure of matter. Crystallography is an interdisciplinary branch of science taught in departments of physics, chemistry, geology, molecular biology, metallurgy and materials science. To encourage promising graduate students to pursue crystallographically-oriented research, the International Centre for Diffraction Data (ICDD) has established a Crystallography Scholarship Fund. While the Ewald Prize is awarded every three years to an internationally recognized crystallographer, little effort has been made by science departments to cultivate aspiring crystallographers. Convinced of the beneficial, scientific impact of the proposed scholarships for crystallographically-oriented research, the ICDD has solicited funds from private and industrial sectors to support this program. The ICDD has awarded two scholarships in 1992, two in 1993, three in 1994, three in 1995, four in 1996, and four in 1997. Applications for the 1998 awards must be received by ICDD no later than 31 October 1997. Qualifications for the applicants: The applicant should be a graduate student seeking a degree with major interest in crystallography e.g. crystal structure analysis, crystal morphology, modulated structures, correlation of atomic structure with physical properties, systematic classification of crystal structures, phase identification and materials characterization. There are no restrictions on country, race, age or sex. The term of the scholarship is one year. Application for one renewal may be made by the recipient at the end of the first year. Because a limited number of scholarships are awarded, renewal applications will be considered on a competitive basis in conjunction with all applications that have been submitted up to the closing date. Submit: 1.Curriculum Vitae, listing degree(s) held and degree(s) sought. 2.A one-page proposal by the graduate student describing the type of crystallographic research to be partially supported by the scholarship. 3.A supportive letter from the sponsoring professor of an accredited university or an institute of technology on institution letterhead. Restrictions on the scholarship fund: 1.The scholarship stipend of $2,000 is to be used by the graduate student to help defray tuition, laboratory fees and cost of books and/or journals on crystallography. A portion of the stipend may be applied to registration fees to accredited scientific meetings related to crystallography. 2.No more than one scholarship will be awarded to applicants at any one accredited institution per year. 3.The funds of the scholarship are not to be used for travel. The awarding of the scholarships shall be administered by a committee consisting of the ICDD Chairman, the Chairman of the ICDD Technical Committee, the Chairman of the ICDD Education Subcommittee and one or two individuals without a conflict of interest. One or more accredited professors (with no conflicts of interest) may be invited to assist in the selection of successful candidates. Applications must be received by 31 October 1997. Please mail to: Secretary, International Centre for Diffraction Data 12 Campus Boulevard Newtown Square, PA 19073-3273 U.S.A. From owner-proteins@net.bio.net Thu May 01 23:00:00 1997 Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!news.daimi.aau.dk!biobase!usenet From: Marek Treiman Newsgroups: bionet.molbio.proteins Subject: Gel analysis software Date: Fri, 02 May 1997 20:42:16 +0200 Organization: University of Copenhagen Lines: 15 Message-ID: <336A3588.31E@biobase.dk> Reply-To: mat@biobase.dk NNTP-Posting-Host: ppcmt1.mfi.ku.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) Hello netters, Can anyone recommend a public domain/low cost software for analysis of digitalized gel images? The commercial versions seem outrageously expensive (2,000 $ and up)! Tips greatly appreciated! Cheers Marek -- Marek Treiman, MD,DMS Associate Professor Department of Medical Physiology The Panum Institute University of Copenhagen Blegdamsvej 3C Tel. +45-35327510 Fax +45-35327537 2200 Copenhagen N E-mail mat@biobase.dk Denmark From owner-proteins@net.bio.net Thu May 01 23:00:00 1997 Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news.sprintlink.net!Sprint!howland.erols.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!warwick!crocus!lsuta From: Mr B J Thomas Newsgroups: bionet.molbio.proteins Subject: A E Garrod. His place in Genetic History. Date: Fri, 2 May 1997 16:04:32 +0100 Organization: University of Warwick, UK Lines: 15 Message-ID: References: <51jq44$2ko@atlantis.utmb.edu> NNTP-Posting-Host: crocus-fddi.csv.warwick.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: lsuta@crocus In-Reply-To: <51jq44$2ko@atlantis.utmb.edu> Could any of your clever professional types recommend to be any literature recent or otherwise which talks about A E Garrod? eg Auto/biographies, recent papers, books, e-mail addressed or web sites of useful places to visit, personal comments.... anything. It's a matter of life or death. Like most of Biology really. Cheers, -Ben -------------------------------------------------------------------------- Ben Thomas: lsuta@warwick.ac.uk Biological Sciences: Warwick Universty -------------------------------------------------------------------------- From owner-proteins@net.bio.net Thu May 01 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.molbio.proteins Subject: About 1BMFG Date: 2 May 1997 09:57:12 +0100 Lines: 13 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5kca98$1gj@mserv1.dl.ac.uk> Original-To: comp-bio@dl.ac.uk, peptides@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk Dear netters: In the recent version(March 1997)of the PDB_select list database (EMBL, Heidelberg), there is a protein 1BMFG. The file shows that there are 122 residues in which 108 belong to alpha-helix and 97 beta-strand. This is a obvious mistake, since 108+97 > 122. It would be greatly appreciated if someone could help to correct the mistake. Thanks! My e-mail address: ctzhang@tju.edu.cn Ren Zhang From owner-proteins@net.bio.net Thu May 01 23:00:00 1997 Path: biosci!daresbury!uninett.no!sn.no!nntp.uio.no!news.apfel.de!news.maxwell.syr.edu!ott.istar!news.istar.net!news.nstn.ca!coranto.ucs.mun.ca!news.unb.ca!usenet From: elf8365@umoncton.ca (Levon Fendekian) Newsgroups: bionet.molbio.proteins Subject: PGal concentration Date: Tue, 29 Apr 1997 12:20:57 GMT Organization: University of New Brunswick Lines: 13 Message-ID: <3365e796.56679645@news.unb.ca> NNTP-Posting-Host: 139.103.29.50 X-Newsreader: Forte Free Agent 1.1/32.230 Hi, I'm trying to use PGal to select lacI- mutants. Does anybody know what is the proper concentration of PGal to use (in a minimal media without glucose)? Thank you, Andre Gallant Graduate student Departement de Chimie et Biochimie Universite de Moncton From owner-proteins@net.bio.net Sat May 03 23:00:00 1997 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!azure.xara.net!xara.net!Aladdin!aladdin.net!ns2.aladdin.net!RMplc!yama.mcc.ac.uk!liv!news From: antonio@liverpool.ac.uk Subject: Re: peptide alpha amino group protection reagent? Content-Type: text/plain; charset=us-ascii Message-ID: <336C9025.506F@liverpool.ac.uk> Sender: news@liverpool.ac.uk (News System) Nntp-Posting-Host: pc028010.med.liv.ac.uk Content-Transfer-Encoding: 7bit Organization: The University of Liverpool References: Mime-Version: 1.0 Date: Sun, 4 May 1997 13:33:25 GMT X-Mailer: Mozilla 2.02 (Win16; I) Lines: 36 :-Peter wrote: > > Hi, > > Non-chemist here... First time poster, long time lurker... > > I have an extremely hydrophobic peptide, to which I would like to > conjugate NHS-Digoxigenin (after an EDC reaction) to the COOH terminus. > There are no glu or asp groups present, and no epsilon amino groups > present. > > Unfortunately, I neglected to have the alpha amino group on the amino > terminus blocked during or after synthesis. This means the post-EDC > peptide will have two reactive amines, which for my purposes is not a good > thing. > > Can anyone suggest a readily available, hydrophobic "blocker" I can use to > inactivate the alpha amino group? This modifier must be membrane > permeable, and it would be even sweeter if a radiolabelled version were > available too. > > Thanks. > > :-PeterIf you dont actually require the N terminal amine you could just acetylate the peptide with acetic anhydride in say DCM, 15-30 min stirring at room temp at a 1.1 fold XS of acetic anhydride should work ok, though follow the reaction by RP-HPLC to confirm completion. This would block the N-terminus very effectively and by use of acylases not necesarily irreversable. I would of thought that a radiolabelled version of acetic anhydride would be available. I hope this helps. Len Bell. lgbell@liv.ac.uk From owner-proteins@net.bio.net Sun May 04 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!su-news-hub1.bbnplanet.com!cpk-news-feed4.bbnplanet.com!news.bbnplanet.com!maze.dpo.uab.edu!usenet From: "Richard J. Dudley" Newsgroups: bionet.molbio.proteins Subject: Re: Protein precipitation methods Date: Mon, 05 May 1997 13:25:39 -0500 Organization: Dep't of Neurobiology, UAB Lines: 8 Message-ID: <336E2620.58C8@nrc.uab.edu> References: <3324c369.51519941@news.unb.ca> Reply-To: rdudley@nrc.uab.edu NNTP-Posting-Host: 7100-two.nrc.uab.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Macintosh; I; 68K) There's also the Methanol-chloroform proecdure. Analytical biochemistry 138: 141-143 (Wessel and Flugge) --- --- --- Richard J. Dudley (rdudley@nrc.uab.edu) Department of Neurobiology University of Alabama School of Medicine http://www.nrc.uab.edu/ From owner-proteins@net.bio.net Sun May 04 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!europa.clark.net!dciteleport.com!usenet.logical.net!node2.frontiernet.net!usenet From: "Thomas J. Kempkes" Newsgroups: bionet.molbio.proteins Subject: Need good p53 links Date: 6 May 1997 00:39:55 GMT Organization: Frontier Internet Rochester N.Y. (716)-777-SURF Lines: 5 Message-ID: <01bc59d7$9115d8a0$c4187fcf@default> NNTP-Posting-Host: usr3-196.dial.roc.frontiernet.net X-Newsreader: Microsoft Internet News 4.70.1155 I would like to know of any good links (www, usenet) which consistently give good info re: p53 tumor suppressor. I'm looking for info for both novices and veterans to the molbio field. --Kempkes From owner-proteins@net.bio.net Sun May 04 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!news.mel.aone.net.au!harry From: harry@projectx.com.au (Harry Banaharis) Newsgroups: bionet.molbio.proteins Subject: protein folding web site Date: Sun, 04 May 1997 00:38:31 +1100 Organization: Project X Lines: 11 Message-ID: NNTP-Posting-Host: harry.projectx.com.au Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.1 I am interested in the development of a web site devoted to providing information on protein folding prediction strategies, algorithms, software, recent developments, etc. Being involved in a local Internet Service Provider in Melbourne, Australia, I am able to supply a Virtual Web Server on a Webfarm based on Silicon Graphics servers connected to the 'net via a 512 kb Frame Relay link. I am seeking to work with a group who can contribute to the development and maintenance of this site. Please email me if you are interested in participating. Include your area of specialisation (if any), level of HTML/graphic design/JavaScript/Java expertise and how you would like to contribute. From owner-proteins@net.bio.net Mon May 05 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!portc02.blue.aol.com!audrey02.news.aol.com!not-for-mail From: cplefebvre@aol.com (CPLefebvre) Newsgroups: bionet.molbio.proteins Subject: Triton/acid/urea gels Date: 6 May 1997 18:52:21 GMT Organization: AOL, http://www.aol.fr Lines: 2 Message-ID: <19970506185100.OAA19815@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Does anyone has a good and reliable protcol for running Triton/acid/urea gels to analyze histone hyperacetylation rate? Thanks netters! From owner-proteins@net.bio.net Mon May 05 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!news.scripps.edu!not-for-mail From: Rolf Marteijn Newsgroups: bionet.plants,bionet.general,bionet.molbio.proteins Subject: Re: Looking for articles on pectin methylesterases Date: Tue, 06 May 1997 15:18:57 -0700 Organization: The Scripps Research Institute Lines: 24 Message-ID: <336FAE51.5777@lx.student.wau.nl> References: <862588616.22077@dejanews.com> NNTP-Posting-Host: 192.26.254.53 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) To: p6msv003@cicrp.jussieu.fr Xref: biosci bionet.plants:15399 bionet.general:26714 bionet.molbio.proteins:10656 Bonjour, > I'm a student in Paris, > and I'm desperately looking for > biology articles about > pectin methylesterases ! > Is there a site, other than ENTREZ, which > lets someone look for articles one a keyword > search basis ? Entrez features the Medline database with added information. However, if you want non-medical info about pectin methylesterases, you'll probably better start looking in different databases. They can probably been found at a university library (should be available in Paris ;). Look for the BA (biological abstracts) or the CAB (Chemical ABstracts) databases (on CD-ROM or local networks). If you want some more biotech info, look on the Derwents (?) Biotechnology Abstracts database. Unfortunately only Medline is online so far (or am I wrong?). Regards, Rolf From owner-proteins@net.bio.net Mon May 05 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!feed1.news.erols.com!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!netcom.net.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news.ox.ac.uk!bhamcs!bham!usenet From: altabios@bham.ac.uk (John E. Fox) Newsgroups: bionet.molbio.proteins Subject: protein mass spec problem Date: 6 May 1997 15:02:56 GMT Organization: Alta Bioscience Message-ID: <5knh70$qih@usenet.bham.ac.uk> NNTP-Posting-Host: bcs118.bham.ac.uk X-Newsreader: WinVN 0.90.6 Lines: 33 Electrospray Mass Spectrometry on a purified recombinant protein. Why multiple peaks? We have expressed a recombinant subunit of a protein from a photosynthetic bacterium in E.coli. The subunit is soluble and easily purified. It readily binds its substrate, indicating that it is properly folded. It looks good on SDS-PAGE. N-terminal amino acid analysis of the subunit gives a reasonably clear sequence, identical to that predicted from the gene sequence. Analysis of the pure protein by electrospray mass spec. produces four peaks. Peak one corresponds to the mass predicted from the gene sequence (40287). Peak two is the mass of peak one plus 129. Peak three is about 125 mass units larger than peak two. Peak four is about 105 mass units larger still. The heights of peaks one and two are similar, peak three is about half as big, and peak four maybe half as much again. Does anyone know why we might be getting these multiple forms? The protein was purified in Tris buffer, 5mM ammonium sulphate, 1mM dithiothrietol and dialysed against water before mass spec. John Fox ****************************************************************** Alta BioScience Email: altabios@bham.ac.uk School of Biochemistry Phone: 0121-414-5450 The University of Birmingham Fax: 0121-414-3376 Edgbaston, BIRMINGHAM, B15 2TT, UK From owner-proteins@net.bio.net Mon May 05 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!news-peer.gsl.net!news-hk.gsl.net!news.gsl.net!newsgate.cuhk.edu.hk!newsfeeder.ust.hk!news.ust.hk!uststu1!bc_yks From: Yeung Kam Sze Newsgroups: bionet.molbio.proteins Subject: small polypeptides Date: Tue, 6 May 1997 18:39:05 +0800 Organization: Hong Kong University of Science and Technology Lines: 11 Message-ID: NNTP-Posting-Host: uststu1.ust.hk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: bc_yks@uststu1 hi all, can anyone tell me where i can get data and details of small polypeptide, e.g within 10 aa with know structure. thx very much kams a biochem student in hk From owner-proteins@net.bio.net Mon May 05 23:00:00 1997 Path: biosci!botany.uq.edu.au!J.Marcus From: J.Marcus@botany.uq.edu.au ("Marcus, Dr J.") Newsgroups: bionet.molbio.proteins Subject: Re: protein mass spec problem Date: 6 May 1997 15:40:08 -0700 Organization: Dept of Botany, Univ of Queensland Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: <27A708B459D@botany.uq.edu.au> References: <5knh70$qih@usenet.bham.ac.uk> Reply-To: Marcus@tpp.uq.edu.au NNTP-Posting-Host: net.bio.net Hi John, Your added 129 Da could be explained by an added glutamic acid, 125 Da would be explained by an additional glutimine or lysine residue, 105 comes close to the mass expected for an added cys (i.e. 103.2). How you are getting these additional residues from an expressed sequence is another matter which escapes me. Is it possible that stop codon (TAA) could be mistaken for a glu codon (GAA)? This might explain how you are getting the extra 129 Da. This seems a bit far out but maybe it is worth considering. Hope this helps. Regards, John Marcus > Analysis of the pure protein by electrospray mass spec. produces four peaks. > Peak one corresponds to the mass predicted from the gene sequence (40287). > Peak two is the mass of peak one plus 129. > Peak three is about 125 mass units larger than peak two. > Peak four is about 105 mass units larger still. > The heights of peaks one and two are similar, peak three is about half > as big, and peak four maybe half as much again. > > Does anyone know why we might be getting these multiple forms? > > The protein was purified in Tris buffer, > 5mM ammonium sulphate, 1mM dithiothrietol and dialysed > against water before mass spec. > > John Fox _________________________________________________________ John Marcus Marcus@tpp.uq.edu.au (Dr J.Marcus) Cooperative Research Centre for Tropical Plant Pathology 5th Level John Hines Building University of Queensland St. Lucia, QLD 4072 AUSTRALIA Fax: 61-7-3365-4771 Phone: 61-7-3365-4764 From owner-proteins@net.bio.net Tue May 06 23:00:00 1997 From: Chang Shu Wang Newsgroups: bionet.molbio.proteins,bionet.immunology Subject: casein as substrate Date: Wed, 07 May 1997 20:45:16 -0700 Organization: Research center, Hotel-Dieu hospital of Quebec Lines: 4 Message-ID: <33714C4C.4DE5@agora.ulaval.ca> NNTP-Posting-Host: staa007.ulaval.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Path: biosci!rutgers.rutgers.edu!gatech!news1.mid-ga.com!nntp.mid-ga.com!news.oru.edu!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!ott.istar!news.istar.net!news.nstn.ca!news.dal.ca!newsflash.concordia.ca!SUNqbc.risq.net!athena.ulaval.ca!not-for-mail Xref: biosci bionet.molbio.proteins:10665 bionet.immunology:11701 I want to use casein (Sigma product C-5890)as substrate for some enzymatic analysis and zymography of some proteases. However, I don't know how to dissolve casein for solution preparation. If someone has experiences, please give me an info., thanks. From owner-proteins@net.bio.net Tue May 06 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!news-was.dfn.de!news-kar1.dfn.de!newsfeed.nacamar.de!uunet!in1.uu.net!199.79.199.5!news.kersur.net!not-for-mail From: packard@kersur.net Newsgroups: bionet.molbio.proteins Subject: Irregular bands with my protein gels Date: Wed, 07 May 1997 01:18:13 GMT Organization: Kersur Technologies Lines: 15 Message-ID: <336fd837.46083173@news.kersur.net> NNTP-Posting-Host: dialup236.kersur.net X-Newsreader: Forte Free Agent 1.1/16.230 I'm having some problems with irregular bands on my protein gels. I'm running a purified antigen (approx. 60 KD) using a 10% acrylamide gel. The problem is that after staining/destaining my bands appear dumbell shaped. This doesn't happen all the time (about 50 % of the time). I must adhere to GMP documents..so there are few changes I can make in the procedure. I was wondering if this is a technique issue or something real simple that I'm missing. Any help would be greatly appreciated! Please feel free to email me if you would like more info about my dilema. Thanks you for your time. My email address is packard@kersur.net Kevin M Packard From owner-proteins@net.bio.net Tue May 06 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news.maxwell.syr.edu!news-was.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!news-zh.switch.ch!rzunews.unizh.ch!toukie From: toukie@zui.unizh.ch (Dr. S. Shapiro) Newsgroups: bionet.molbio.proteins Subject: Fab or Ig X-ray xtal structure Date: 7 May 1997 14:13:54 GMT Organization: University of Zurich, Switzerland Lines: 16 Message-ID: <5kq2n2$cfo@rzunews.unizh.ch> NNTP-Posting-Host: rzurs10.unizh.ch X-Newsreader: TIN [version 1.2 PL2] Dear Colleagues; I am seeking information on the X-ray (or neutron) diffraction struc- ture of the binding site of antibodies that specifically bind phenolic-type compounds (such as _but not restricted to_ 2,4-dinitrophenol). If you can provide me with any useful references, or possibly even a PDB file, kindly contact me _directly_ at toukie@zui.unizh.ch Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From owner-proteins@net.bio.net Tue May 06 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!qmw!alpha.qmw.ac.uk!zgha210 From: Jim Reid Newsgroups: bionet.molbio.proteins Subject: Q: pH indicator - following H+ release on stopped flow? Date: Wed, 7 May 1997 12:25:49 +0100 Organization: Queen Mary & Westfield College, London, UK Lines: 15 Message-ID: NNTP-Posting-Host: alpha.qmw.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Has anyone out there recently used pH indicators in a stopped flow (or any spec really - I don't see why it would make a difference!) to follow the rate of proton release? If so any tips on how to go about it? I am planning to use the method of Khalifah (JBC 246,2561) and any advice on the necessary tweeks required would be appreciated. I will of course do - try- this anyway (using less valuable samples!) before there is any reply but still it would be fun to hear whats been done. Thanks, Jim Reid. From owner-proteins@net.bio.net Tue May 06 23:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Andy Phillips Newsgroups: bionet.molbio.proteins Subject: Re: Irregular bands with my protein gels Date: Wed, 07 May 1997 11:59:50 +0100 Organization: BBSRC, IACR Long Ashton Research Station Lines: 32 Message-ID: <337060A6.1CF3E8FC@bbsrc.ac.uk> References: <336fd837.46083173@news.kersur.net> Reply-To: andy.phillips@bbsrc.ac.uk NNTP-Posting-Host: pc0628.lars.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0b3 [en] (Win95; I) To: packard@kersur.net CC: andy.phillips@bbsrc.ac.uk X-Priority: 3 (Normal) packard@kersur.net wrote: > > I'm having some problems with irregular bands on my protein gels. I'm > running a purified antigen (approx. 60 KD) using a 10% acrylamide gel. > The problem is that after staining/destaining my bands appear dumbell > shaped. This doesn't happen all the time (about 50 % of the time). I > must adhere to GMP documents..so there are few changes I can make in > the procedure. I was wondering if this is a technique issue or > something real simple that I'm missing. Any help would be greatly > appreciated! Please feel free to email me if you would like more info > about my dilema. Thanks you for your time. My email address is > packard@kersur.net > > Kevin M Packard > > I vaguely remember an article by Ed Southern in an old Methods in Enzymology (about 1981?) concerning vertical agarose gels for DNA separation. He mentioned that the glycerol usually added to loading dye makes the DNA samples run as dumbells, as it makes the sample stick to the walls of the well. His cure to this was to use an alternative to the glycerol - I seem to remember (this was 17 years ago!) that he used 10% Ficoll. Whether this would work in an SDS gel is another matter - is Ficoll heat stable? I tried, but failed, to find this article in my reprint collection, and ISI doesn't go back far enough. Andy Andy From owner-proteins@net.bio.net Tue May 06 23:00:00 1997 Path: biosci!nimr.mrc.ac.uk!d-fesque From: d-fesque@nimr.mrc.ac.uk (didier) Newsgroups: bionet.molbio.proteins Subject: Re: problem with PAGE_SDS Date: 7 May 1997 03:54:28 -0700 Organization: we Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <33706054.2CF7@nimr.mrc.ac.uk> Reply-To: d-fesque@nimr.mrc.ac.uk NNTP-Posting-Host: net.bio.net you wrote >I'm having some problems with irregular bands on my protein gels. I'm running a purified antigen (approx. 60 KD) using a 10% acrylamide gel. The problem is that after staining/destaining my bands appear dumbell shaped. This doesn't happen all the time (about 50 % of the time). I must adhere to GMP documents..so there are few changes I can make in the procedure. I was wondering if this is a technique issue or something real simple that I'm missing. Any help would be greatly appreciated! Please feel free to email me if you would like more info about my dilema. Thanks you for your time. My email address is packard@kersur.net Kevin M Packard hi, have a look to the pH of your stacking buffer, the pH of the Tris solution is instable at 6.8, this induce change in the migration of protein during PAGE. the simple way to avoid this is to freeze aliquot of thius buffer (20ml) and after using this aliquot store it at 4 degre , for a few week! didier From owner-proteins@net.bio.net Tue May 06 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news-peer.sprintlink.net!news.sprintlink.net!Sprint!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!usenet From: Thomas Cameron Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.immunology,bionet.cellbiol Subject: ELISA for Hisx6 proteins Date: Wed, 07 May 1997 20:27:29 -0700 Organization: Massachvsetts Institvte of Technology Lines: 8 Message-ID: <33714821.167E@risotto.mit.edu> NNTP-Posting-Host: risotto.mit.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) Xref: biosci bionet.molbio.methds-reagnts:57446 bionet.molbio.proteins:10666 bionet.immunology:11703 bionet.cellbiol:7267 Has anybody ever set up a ELISA using either Hisx6 tagged proteins or S-peptide to S-protein affinity? I think I remember seeing an ELISA plate sold by SIGMA that specifically binds HIS-tagged proteins, but I can't find the info anymore. -- Thomas Cameron From owner-proteins@net.bio.net Tue May 06 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!gondor!newshub.sdsu.edu!newshub.csu.net!csulb.edu!hammer.uoregon.edu!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!newsxfer.itd.umich.edu!news.mtu.edu!msunews!netnews.upenn.edu!taurus.fccc.edu!sauder From: sauder@castor.fccc.edu (John Michael Sauder) Newsgroups: bionet.molbio.proteins Subject: Re: protein folding web site Date: 7 May 1997 14:49:46 GMT Organization: Fox Chase Cancer Center, Philadelphia, PA Lines: 21 Message-ID: <5kq4qb$hl3$1@taurus.fccc.edu> References: NNTP-Posting-Host: castor.rm.fccc.edu In article harry@projectx.com.au (Harry Banaharis) writes: >I am interested in the development of a web site devoted to providing >information on protein folding prediction strategies, algorithms, software, >recent developments, etc. [snip] > >Please email me if you are interested in participating. Include your area >of specialisation (if any), level of HTML/graphic design/JavaScript/Java >expertise and how you would like to contribute. I'd be interested to a limited degree, as I currently have plenty of other projects I'm working on. Also, my area of expertise is more along the lines of experimental folding, not computational, although I have an interest in this area as well. You might check out our site: http://www.fccc.edu/research/labs/roder Take a look at "Other folding groups" for links to other labs who are interested in the folding problem, from either an experimental or computational point of view. I'd like to continue to expand this list as much as possible... From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news-peer.sprintlink.net!Sprint!news-pull.sprintlink.net!news.sprintlink.net!newsfeed.direct.ca!nntp.portal.ca!news.bc.net!info.ucla.edu!nnrp.info.ucla.edu!Tao's computer!tshi From: tshi@ucla.edu (shi tao) Newsgroups: bionet.molbio.proteins Subject: Re: shortest proteins. Date: Thu, 8 May 1997 10:27:58 Organization: UCLA Lines: 13 Message-ID: References: NNTP-Posting-Host: ts50-8.wla.ts.ucla.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] The smallest protein contains about 40 aa, but forget the name of it. There was a paper, which I also forgot, showing a about 30-aa long engineered peptide. That had some enzyme function. > do anyone of you know the shortest protein which contain only the >standard 20 aa residues? or any polypeptide is also ok. > i need it urgent. >kams :) From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!uunet!in1.uu.net!192.215.247.55!news1.ni.net!news From: Eduardo Leeche Newsgroups: bionet.molbio.proteins Subject: Re: shortest proteins. Date: Thu, 08 May 1997 12:48:09 -0700 Organization: none Lines: 1 Message-ID: <33722DF9.988@ix.netcom.com> References: NNTP-Posting-Host: 206.183.213.134 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; U) No, but good luck on your test/homework From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!howland.erols.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!server6.netnews.ja.net!str-ccsun!strath-cs!dcl-cs!bath.ac.uk!aber!not-for-mail From: prm@aber.ac.uk (Pedro Mendes) Newsgroups: bionet.metabolic-reg,bionet.cellbiol,bionet.molbio.proteins,bionet.biophysics,sci.bio.misc Subject: 1998 GRC on Macromolecular Organization and Cell Function Followup-To: bionet.metabolic-reg Date: 7 May 1997 09:30:10 GMT Organization: Univ Wales Aberystwyth Lines: 24 Distribution: world Message-ID: <5kpi32$1k0$1@infoserv.aber.ac.uk> NNTP-Posting-Host: pcjafc.dbs.aber.ac.uk Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Disclaimer: Warning - Sender not verified X-Newsreader: WinVN 0.99.7 Keywords: conference web page Xref: biosci bionet.metabolic-reg:1214 bionet.cellbiol:7272 bionet.molbio.proteins:10675 bionet.biophysics:3009 sci.bio.misc:8838 Gordon Research Conference on Macromolecular Organization and Cell Function September 13-17, 1998, Queen's College, University of Oxford Chaired by Douglas Kell (Aberystwyth) and John Wilson (Michigan) Full details (including application form) can be found on: http://gepasi.dbs.aber.ac.uk/grc98.html From the conference program: "The focus of the conference is on the functional organization of cellular components, and the critical role of this organization in metabolism and its regulation. [...] Conference participants have been especially sensitive to the fact that much of this organization may be destroyed, or at least grossly perturbed, when studies are performed in vitro. Thus, a persistent feature in the conference has been the cautious extrapolation of in vitro results to the in vivo condition, as well as development and application of techniques that allow one to study cellular structure and function in vivo. [...]" Check it at http://gepasi.dbs.aber.ac.uk/grc98.html From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!ais.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!news.he.net!news.pagesat.net!news.cerf.net!news1.ni.net!news From: Pete Newsgroups: bionet.molbio.proteins Subject: Re: shortest proteins. Date: Thu, 08 May 1997 10:29:49 -0700 Organization: cercla Lines: 1 Message-ID: <33720D8D.28E1@cercla.com> References: NNTP-Posting-Host: 206.183.213.134 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; U) How about glutathione? From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!newsfeeds.sol.net!europa.clark.net!feed1.news.erols.com!howland.erols.net!newshub2.home.com!newshub1.home.com!news.home.com!news1.best.com!wizard.pn.com!news.gte.com!news-in.tiac.net!posterchild!news@tiac.net From: Property Digest Newsgroups: bionet.molbio.gene-orgbionet.molbio.genome-program,bionet.molbio.hiv,bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.molbio.rapd Subject: new pages on NatBio Web Site Date: Thu, 08 May 1997 12:39:20 -0700 Organization: U.S. Real Estate Register Lines: 9 Message-ID: <33722BE8.954@barryinc.com> NNTP-Posting-Host: p7.ts23.metro.ma.tiac.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win16; I) Xref: biosci bionet.molbio.hiv:3587 bionet.molbio.methds-reagnts:57458 bionet.molbio.proteins:10673 bionet.molbio.rapd:1898 National Biotech Register(NatBio), a comprehensive up-to-date reference guide on research and product development activity in the Biotech Industry, is pleased to announce the addition of two new pages on our web site: http://www.barryinc.com/bio ..The first page is a help wanted in the Biotech field, while the second is a bulletin board page. This page will allow people in the Biotech industry to exchange ideas, search for products and or research services, as well as giving you a forum to announce new discoveries. Come check out these new pages and help expand on them. From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!ais.net!news.maxwell.syr.edu!news.apfel.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Structure of His-Tag complex Date: Thu, 8 May 1997 17:28:50 +0200 Organization: University of Wuerzburg, Germany Lines: 28 Message-ID: References: <01bc5baf$547cca00$0100007f@schmidtdw.rz.ruhr-uni-bochum.de> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Thorsten Schmidt (Thorsten.Schmidt@rz.ruhr-uni-bochum.de) wrote: > When one loads the column with a protein mixture only the target protein > forms with its histidines a complex with the nickel and the resin. > After washing steps the protein can be eluted with a buffer containing > Imidazole. > > I want to know the exact structure of this complex and the reason, why > it is possible to elute the protein with Imidazole. Depending on the resin that you use, the Ni2+ is complexed by two (IDA), three (NTA) or four (TALON) valences; that is, there are four (IDA), three (NTA) or two (TALON) left for the histidines to bind. The chemical structure of the complex can be found in the various leaflets given away by the companies who want to sell that stuff. If you mean "structure" in terms of 3 D coordinates, I have been told that "His-Tags" are usually pretty flexible and therefore do not show up in X-ray structures. The reason why it is possible to elute the protein with imidazol is pretty obvious if you have a look at the chemical structure of it. It competes with the histidine for the metal ion. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!news.maxwell.syr.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!howland.erols.net!vixen.cso.uiuc.edu!aries!marsagli From: marsagli@aries.scs.uiuc.edu (Michael Marsaglia) Newsgroups: bionet.molbio.proteins Subject: Re: shortest proteins. Date: 8 May 1997 15:15:21 GMT Organization: University of Illinois at Urbana Lines: 14 Message-ID: <5ksqm9$90k@vixen.cso.uiuc.edu> References: NNTP-Posting-Host: aries.scs.uiuc.edu Yeung Kam Sze writes: >hi all, > do anyone of you know the shortest protein which contain only the >standard 20 aa residues? or any polypeptide is also ok. > i need it urgent. >kams :) Do you want a peptide or a protein? If a peptide is OK look up hormones in any intro biochemistry book. I am an analytical chemist so I may be wrong but the shortest peptide I found was thyrotropin releasing hormone. Mike From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!daresbury!uninett.no!sn.no!nntp.uio.no!news.maxwell.syr.edu!howland.erols.net!torn!resunix.sickkids.on.ca!not-for-mail From: Randy Willis Newsgroups: bionet.molbio.proteins Subject: Re: Structure of His-Tag complex Date: Thu, 08 May 1997 10:14:09 -0400 Organization: The Hospital For Sick Children Lines: 26 Message-ID: <3371DFB1.167E@gandalf.psf.sickkids.on.ca> References: <01bc5baf$547cca00$0100007f@schmidtdw.rz.ruhr-uni-bochum.de> NNTP-Posting-Host: gandalf.sickkids.on.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP17) To: Thorsten Schmidt Thorsten Schmidt wrote: Thorsten wrote: > I want to know the exact structure of this complex and the reason, why > it is possible to elute the protein with Imidazole. Thorsten, I don't know about any structures out there, except for some recent work on the gly-gly-his motif by people working in my department (B.Sarkar, G.Gasmi, A.Singer, J.Forman-Kay), but the reason that one elutes with imidazole is a case of simple competition. If you look up the structure of imidazole and histidine, you will find that imidazole is the side chain of the amino acid histidine. Thus, the free imidazole simply competes (a higher molar ratio) for the nickel ions against the histidine. Randall C Willis, Researcher Biochemistry, Hosp for Sick Children 3522-555 University Ave Toronto, ON CANADA M5G 1X8 416-813-5933 (ph) -5022 (fax) willis@gandalf.psf.sickkids.on.ca From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!howland.erols.net!news.maxwell.syr.edu!news-was.dfn.de!news-fra1.dfn.de!news-koe1.dfn.de!news.ruhr-uni-bochum.de!not-for-mail From: "Thorsten Schmidt" Newsgroups: bionet.molbio.proteins Subject: Structure of His-Tag complex Date: 8 May 1997 12:57:27 GMT Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 23 Message-ID: <01bc5baf$547cca00$0100007f@schmidtdw.rz.ruhr-uni-bochum.de> NNTP-Posting-Host: dialppp-1-182.rz.ruhr-uni-bochum.de X-Newsreader: Microsoft Internet News 4.70.1155 Dear reader! The His-Tag-System is widely used for protein purification. (Novagene, Quiagen ...) Using a special expression vector, a "His-Tag", a repeat of six Histidines, is added to the target protein. A special resin is then loaded with nickel-ions. When one loads the column with a protein mixture only the target protein forms with its histidines a complex with the nickel and the resin. After washing steps the protein can be eluted with a buffer containing Imidazole. I want to know the exact structure of this complex and the reason, why it is possible to elute the protein with Imidazole. Can you help me, perhaps tell me a reference? Thank you very much in advance for your answer Thorsten From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!news-peer.gsl.net!news-hk.gsl.net!news.gsl.net!newsgate.cuhk.edu.hk!newsfeeder.ust.hk!news.ust.hk!uststu5.ust.hk!bc_yks From: Yeung Kam Sze Newsgroups: bionet.molbio.proteins Subject: shortest proteins. Date: Thu, 8 May 1997 19:09:32 +0800 Organization: Hong Kong University of Science and Technology Lines: 8 Message-ID: NNTP-Posting-Host: uststu5.ust.hk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: bc_yks@uststu5.ust.hk hi all, do anyone of you know the shortest protein which contain only the standard 20 aa residues? or any polypeptide is also ok. i need it urgent. kams :) From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!news-out.communique.net!communique!hunter.premier.net!news.maxwell.syr.edu!news.apfel.de!news-fra1.dfn.de!news-ber1.dfn.de!news-lei1.dfn.de!news-nue1.dfn.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.immunology,bionet.cellbiol Subject: Re: ELISA for Hisx6 proteins Followup-To: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.immunology,bionet.cellbiol Date: Thu, 8 May 1997 11:46:06 +0200 Organization: University of Wuerzburg, Germany Lines: 12 Message-ID: References: <33714821.167E@risotto.mit.edu> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Xref: biosci bionet.molbio.methds-reagnts:57447 bionet.molbio.proteins:10667 bionet.immunology:11705 bionet.cellbiol:7268 Thomas Cameron (cameron@risotto.mit.edu) wrote: > I think I remember seeing an ELISA plate sold by SIGMA that specifically > binds HIS-tagged proteins, but I can't find the info anymore. Quiagen sells Ni-NTA-coated plates. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!news.starnet.net!news.starnet.net!axb.slu.edu!news From: Darren Tyson Newsgroups: bionet.molbio.proteins Subject: Re: Structure of His-Tag complex Date: Thu, 08 May 1997 12:04:20 -0500 Organization: Saint Louis University Lines: 44 Message-ID: <5kt10l$feb@axb.slu.edu> References: <01bc5baf$547cca00$0100007f@schmidtdw.rz.ruhr-uni-bochum.de> NNTP-Posting-Host: 165.134.73.104 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win95; I) To: Thorsten Schmidt Thorsten Schmidt wrote: > > Dear reader! > > The His-Tag-System is widely used for protein purification. > (Novagene, Quiagen ...) > > Using a special expression vector, a "His-Tag", a repeat of six Histidines, > > is added to the target protein. > A special resin is then loaded with nickel-ions. > When one loads the column with a protein mixture only > the target protein forms with its histidines a complex with the nickel and > the resin. > After washing steps the protein can be eluted with a buffer containing > Imidazole. > > I want to know the exact structure of this complex and the reason, why > it is possible to elute the protein with Imidazole. > > Can you help me, perhaps tell me a reference? > > Thank you very much in advance for your answer > > Thorsten Thorsten, QIAGEN's web site has plenty of information available regarding purification of His-tagged proteins. In particular, they have an online version of the QIAexpressionist which is a great resource for the theory behind the expression and purification of recombinant His-tagged proteins. The URL is http://www.qiagen.com/qexpress/startqxp.html Hope this helps, Darren ********** Darren Tyson Ph.D. Candidate in Cell & Molecular Biology Saint Louis University tysondr@slu.edu From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.apfel.de!fu-berlin.de!news.belwue.de!news.uni-ulm.de!rz.uni-karlsruhe.de!news.rhein-neckar.de!birdland.rhein-neckar.de!ibis.rhein-neckar.de!steffen.roth From: steffen.roth@rhein-neckar.de (Steffen Roth) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.immunology,bionet.cellbiol Subject: Re: ELISA for Hisx6 proteins Date: Thu, 8 May 1997 18:47:56 Organization: RNI Lines: 11 Message-ID: References: <33714821.167E@risotto.mit.edu> NNTP-Posting-Host: ibis.rhein-neckar.de X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Xref: biosci bionet.molbio.methds-reagnts:57467 bionet.molbio.proteins:10680 bionet.immunology:11713 bionet.cellbiol:7274 >Thomas Cameron (cameron@risotto.mit.edu) wrote: >> I think I remember seeing an ELISA plate sold by SIGMA that specifically >> binds HIS-tagged proteins, but I can't find the info anymore. >Quiagen sells Ni-NTA-coated plates. >--Cornelius. ... Xenopore (xenopore@xenopore.com) also sells Ni-NTA coated plates. Steffen From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!MANI.CBS.UMN.EDU!npv From: npv@MANI.CBS.UMN.EDU (Nora Plesofsky-Vig) Newsgroups: bionet.molbio.proteins Subject: commercial availability of plant RNA viruses Date: 8 May 1997 17:51:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9705090153.AA01692@mani.cbs.umn.edu> Reply-To: nora@biosci.cbs.umn.edu NNTP-Posting-Host: net.bio.net We would like to test UV cross-linking between RNA and binding proteins by using RNA viruses. Does anyone know of a commercial source for one or more of these? Thanks alot. Nora Plesofsky-Vig nora@biosci.cbs.umn.edu From owner-proteins@net.bio.net Wed May 07 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!rill.news.pipex.net!pipex!oleane!in2p3.fr!news-ge.switch.ch!news-zh.switch.ch!rzunews.unizh.ch!NewsWatcher!user From: zjons@vetbio.unizh.ch (Zophonias O. Jonsson) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.immunology,bionet.cellbiol Subject: Re: ELISA for Hisx6 proteins Date: Thu, 08 May 1997 21:15:30 +0100 Organization: Universitat Zurich-Irchel Lines: 27 Message-ID: References: <33714821.167E@risotto.mit.edu> NNTP-Posting-Host: 130.60.120.18 Xref: biosci bionet.molbio.methds-reagnts:57466 bionet.molbio.proteins:10677 bionet.immunology:11712 bionet.cellbiol:7273 In article <33714821.167E@risotto.mit.edu>, Thomas Cameron wrote: > Has anybody ever set up a ELISA using either Hisx6 tagged proteins or > S-peptide to S-protein affinity? > > I think I remember seeing an ELISA plate sold by SIGMA that specifically > binds HIS-tagged proteins, but I can't find the info anymore. > > -- > Thomas Cameron You can get Ni-NTA plates (or 8-well strips) from Quiagen. However, they are quite expensive and in my experience (and according to the two other people in our lab that have tried to use them) not very useful. You might have better luck. Zophonias _____________________________________________________________________ Zophonias O. Jonsson Institut fur Veterinarbiochemie Tel: (41-1)-257-54-75 Universitat Zurich-Irchel Fax: (41-1)-362-05-01 Winterthurerstrasse 190 CH-8057 Zurich Switzerland _____________________________________________________________________ From owner-proteins@net.bio.net Thu May 08 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.maxwell.syr.edu!news.cis.ohio-state.edu!nntp.sei.cmu.edu!bb3.andrew.cmu.edu!newsfeed.pitt.edu!pelli.pathology.pitt.edu!user From: pxpst2+@pitt.edu (peter) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: Buffer for lyophylization Date: 9 May 1997 20:08:33 GMT Organization: Univ.of Pittsburgh Lines: 19 Message-ID: References: NNTP-Posting-Host: pelli.pathology.pitt.edu Xref: biosci bionet.molbio.methds-reagnts:57502 bionet.molbio.proteins:10692 /In article /, /michael.didonato@utoronto.ca (Michael DiDonato) wrote: / /> I am wondering if anyone knows which is the best buffer to lyophylize from? /> Excluding water, what buffer would leave beind the least amount of salt /> upon lyophylization? /> /> Any suggestions are extremely appreciated. /> /> Mike I have had success with ammonium acetate up to 50 mM, but any volitile salts could be used like amonium bicarb. The term lyophilize means that you must freeze your sample and then sublime the salts off. Most peaple allow the sample to thaw in the vacuum which greatly increases the time needed to remove the volitile salts. One can also use extraction by Phenol ether to remove non volitile salts but traces will remain. Peter Pediaditakis pxpst2@vms.cis.pitt.edu From owner-proteins@net.bio.net Thu May 08 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!nntp.uio.no!news2.interlog.com!news.interlog.com!news From: "Klaassen" Newsgroups: bionet.molbio.proteins Subject: tRNA-- i need help Date: 9 May 1997 20:42:54 GMT Organization: KMW Lines: 19 Message-ID: <01bc5cb9$e02d46a0$2683bdcd@klaassen.oix.com> NNTP-Posting-Host: 205.189.131.38 X-Newsreader: Microsoft Internet News 4.70.1157 I was hoping that someone could help me with a question I have :) I was looking in my Biology text book, and I'm a bit confused about tRNA. I realize that the anticodon attaches to the codon of the mRNA (through the ribosome)... but I'm not able to understand is the codon of the tRNA.. is it the same as the codon on the mRNA, which would be the compliment to the anticodon on the tRNA. More than half of the pictures I have seen of the codon have four nucleotides, and none of them match up with the anticodon. Infact, none of the tRNA codons that I have seen match up with the anticodons of the same tRNA. Another question I have is also about the codon on the tRNA. Wich way is it read. Different books are telling me different things. Is it read from the 3` end like DNA, or is it read backwards? Depending on the way that it is read changes the amino acids that they code for It's all just that little bit to far over my head... I would apreciate any help I could get!!!! From owner-proteins@net.bio.net Thu May 08 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!newsfeeds.sol.net!hammer.uoregon.edu!csulb.edu!drivel.ics.uci.edu!news.service.uci.edu!news1.ni.net!news From: Kapri Vega Newsgroups: bionet.molbio.proteins Subject: Re: shortest proteins. Date: Fri, 09 May 1997 12:20:24 -0700 Organization: Network Intensive Lines: 2 Message-ID: <337378F8.571@ins.uk.edu> References: NNTP-Posting-Host: 206.183.213.134 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; U) Actually, the original post asked for peptides as well. Glutathione (gamma-glutamylcysteinylglycine) is quite valid. From owner-proteins@net.bio.net Thu May 08 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.maxwell.syr.edu!nntp.uio.no!news2.interlog.com!news.interlog.com!news From: "Klaassen" Newsgroups: bionet.molbio.proteins Subject: A question about tRNA Date: 9 May 1997 20:06:37 GMT Organization: KMW Lines: 20 Message-ID: <01bc5cb4$cdd9c140$2683bdcd@klaassen.oix.com> NNTP-Posting-Host: 205.189.131.38 X-Newsreader: Microsoft Internet News 4.70.1157 I was hoping that someone could help me with a question I have :) I was looking in my Biology text book, and I'm a bit confused about tRNA. I realize that the anticodon attaches to the codon of the mRNA (through the ribosome)... but I'm not able to understand is the codon of the tRNA.. is it the same as the codon on the mRNA, which would be the compliment to the anticodon on the tRNA. More than half of the pictures I have seen of the codon have four nucleotides, and none of them match up with the anticodon. Infact, none of the tRNA codons that I have seen match up with the anticodons of the same tRNA. Another question I have is also about the codon on the tRNA. Wich way is it read. Different books are telling me different things. Is it read from the 3` end like DNA, or is it read backwards? Depending on the way that it is read changes the amino acids that they code for It's all just that little bit to far over my head... I would apreciate any help I could get!!!! From owner-proteins@net.bio.net Thu May 08 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!newsin.iconnet.net!news.inc.net!uwm.edu!newsfeeds.sol.net!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!uunet!in3.uu.net!136.142.185.26!newsfeed.pitt.edu!pelli.pathology.pitt.edu!user From: pxpst2+@pitt.edu (peter) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Identification Date: 9 May 1997 20:18:58 GMT Organization: Univ.of Pittsburgh Lines: 17 Distribution: world Message-ID: References: <3373A5D6.4C42@rutchem.rutgers.edu> NNTP-Posting-Host: pelli.pathology.pitt.edu /In article <3373A5D6.4C42@rutchem.rutgers.edu>, hall@rutchem.rutgers.edu wrote: /> What is the basic way to absolutely determine an unknown protein? We /> are using SEC to separate human proteins from plasma. How can we /> absolutely determine the molecular weight of these proteins and identify /> them. /> Thanks for your help, /> Gene You must use sedimentation and SEC. Due to tertiary structure either method could give errors. By the way SEC is good for big proteins it stinks for small or heavily folded proteins (ie kringle containing proteins). Also there is the glycosylaton which will introduce errors in the sedintation method( alters bouyency). The only way to nail down the mass is to partially sequence the protein and then go to a cDNA library and get the cDNA and sequence it. but the above two methods will give you a good idea. Peter Pediaditakis pxpst2@vms.cis.pitt.edu From owner-proteins@net.bio.net Thu May 08 23:00:00 1997 Path: biosci!RUTCHEM.RUTGERS.EDU!hall From: hall@RUTCHEM.RUTGERS.EDU ("Gene S. Hall") Newsgroups: bionet.molbio.proteins Subject: Protein Identification Date: 9 May 1997 12:32:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <3373A5D6.4C42@rutchem.rutgers.edu> Reply-To: hall@rutchem.rutgers.edu NNTP-Posting-Host: net.bio.net What is the basic way to absolutely determine an unknown protein? We are using SEC to separate human proteins from plasma. How can we absolutely determine the molecular weight of these proteins and identify them. Thanks for your help, Gene -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Prof. Gene S. Hall, Analytical Chemist Phone: 908-445-2590 ICPMS Laboratory FAX: 908-445-5312 Department of Chemistry Rutgers, The State University of New Jersey New Brunswick, NJ 08903 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From owner-proteins@net.bio.net Thu May 08 23:00:00 1997 Path: biosci!UMBI.UMD.EDU!collins From: collins@UMBI.UMD.EDU (John Collins) Newsgroups: bionet.molbio.proteins Subject: Re: shortest proteins. Date: 9 May 1997 11:26:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Someone has played a mean joke on you. Glutathione is a tripeptide, described in any biochemistry book. On Fri, 9 May 1997, Yeung Kam Sze wrote: > thx! but where can i get the detailed information? e.g how many residue > it contains? does it has a pdb code? > On Thu, 8 May 1997, Pete wrote: > > How about glutathione? From owner-proteins@net.bio.net Thu May 08 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.maxwell.syr.edu!news-peer.gsl.net!news-hk.gsl.net!news.gsl.net!newsgate.cuhk.edu.hk!newsfeeder.ust.hk!news.ust.hk!uststu6.ust.hk!bc_yks From: Yeung Kam Sze Newsgroups: bionet.molbio.proteins Subject: Re: shortest proteins. Date: Fri, 9 May 1997 21:12:20 +0800 Organization: Hong Kong University of Science and Technology Lines: 48 Message-ID: References: <5ksqm9$90k@vixen.cso.uiuc.edu> NNTP-Posting-Host: uststu6.ust.hk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=iso_8859_1 X-Sender: bc_yks@uststu6.ust.hk To: Michael Marsaglia In-Reply-To: <5ksqm9$90k@vixen.cso.uiuc.edu> hi Mike, thx for your information! i am finding some short chain polypeptide or protein w' standard aa residues. where can i get details about thyrotropin releasing hormone? regards, Kams :) On 8 May 1997, Michael Marsaglia wrote: > Yeung Kam Sze writes: > > >hi all, > > > do anyone of you know the shortest protein which contain only the > >standard 20 aa residues? or any polypeptide is also ok. > > i need it urgent. > > >kams :) > Do you want a peptide or a protein? If a peptide is OK look up hormones in > any intro biochemistry book. I am an analytical chemist so I may be wrong > but the shortest peptide I found was thyrotropin releasing hormone. > > Mike > > , ';; ,;' ;; ;; , ,; ;' ';, ,,,,, ;;,,, ,;' ; ;; ;' ';;,, ;;; ,,,;;;'' ;;, ; ';; , ,;' ';;;;,, ;; ;; ;' ,, ,,;'' ; ;;;; ,;;' ,, '';;;, ;; ;; ,;,;;''''' ,,,;';; , ;;';; ,;; ';;'' ;; ,,;;,,,;;'' , '' ;;;;' ,;'' ,' '' ; ,, ;; ';;; '' ,,,,,;;'' ,;;;;' ' ,;,,;;'';, ,;;' ;; ';; ''''' ; ;;;;; ;;';; ;' ,; ''''; ,; ,,' ;; ,, ; '' ;; ,;',;' ,;' , ;,;' ,;;' ;;; ''' ; ;; ' ,;' ;;' ;;;,;; ,,, ';' ;; ,;'',;;' ''''';;'' ,,;;; ----------- Department of Biochemistry, Hong Kong University of Science and Technology URL:mailto:bc_yks@stu.ust.hk /-----\ ,o. 8 8 URL:http://susis.ust.hk/~kams | `o--| d bzzzzzzzza8o8b Don't Worry! Be Happy! \-----/ `o' Golden Time Golden Key From owner-proteins@net.bio.net Thu May 08 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.maxwell.syr.edu!news-peer.gsl.net!news-hk.gsl.net!news.gsl.net!newsgate.cuhk.edu.hk!newsfeeder.ust.hk!news.ust.hk!uststu6.ust.hk!bc_yks From: Yeung Kam Sze Newsgroups: bionet.molbio.proteins Subject: Re: shortest proteins. Date: Fri, 9 May 1997 20:57:19 +0800 Organization: Hong Kong University of Science and Technology Lines: 9 Message-ID: References: <33720D8D.28E1@cercla.com> NNTP-Posting-Host: uststu6.ust.hk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: bc_yks@uststu6.ust.hk To: Pete In-Reply-To: <33720D8D.28E1@cercla.com> thx! but where can i get the detailed information? e.g how many residue it contains? does it has a pdb code? On Thu, 8 May 1997, Pete wrote: > How about glutathione? > > From owner-proteins@net.bio.net Thu May 08 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.apfel.de!news-fra1.dfn.de!news-koe1.dfn.de!news.ruhr-uni-bochum.de!not-for-mail From: "Thorsten Schmidt" Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: Buffer for lyophylization Date: 9 May 1997 17:59:41 GMT Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 16 Message-ID: <01bc5ca2$c4fcf220$39019386@schmidtdw.rz.ruhr-uni-bochum.de> References: NNTP-Posting-Host: dialppp-1-57.rz.ruhr-uni-bochum.de X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.molbio.methds-reagnts:57497 bionet.molbio.proteins:10683 Hi Mike! > I am wondering if anyone knows which is the best buffer to lyophylize from? > Excluding water, what buffer would leave beind the least amount of salt > upon lyophylization? > I´m not sure, but if you lyophylize I think only the water is removed. I don´t know but how do you think salts are removed? I would say that it must be preferable to use a buffer containing a low salt concentration to protect the proteins during lyophylization from degradation. Thorsten From owner-proteins@net.bio.net Thu May 08 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!news.maxwell.syr.edu!howland.erols.net!torn!resunix.sickkids.on.ca!michael.didonato From: michael.didonato@utoronto.ca (Michael DiDonato) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Buffer for lyophylization Date: Fri, 09 May 1997 11:12:44 -0400 Organization: Hospital For Sick Children Lines: 15 Message-ID: NNTP-Posting-Host: 142.20.38.15 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 Xref: biosci bionet.molbio.methds-reagnts:57492 bionet.molbio.proteins:10682 I am wondering if anyone knows which is the best buffer to lyophylize from? Excluding water, what buffer would leave beind the least amount of salt upon lyophylization? Any suggestions are extremely appreciated. Mike -- Michael DiDonato Department of Biochemistry Research Hospital for Sick Children Toronto, Ontario, Canada michael.didonato@utoronto.ca From owner-proteins@net.bio.net Thu May 08 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!theplanet.net!knews.uk0.vbc.net!vbcnet-gb!idiscover.co.uk!orac.idiscover.net!194.216.165.60 From: "SpaceboY" Newsgroups: bionet.molbio.proteins Subject: The effect of ethanol on the activity of pepsin Date: 9 May 97 23:21:18 GMT Organization: Internet Discovery Customer News Service Lines: 9 Message-ID: <01bc5cce$a35c8820$3ca5d8c2@nexus.idiscover.co.uk> NNTP-Posting-Host: orac.idiscover.net X-Newsreader: Microsoft Internet News 4.70.1155 Can someone explain how ethanol may affect the activity of pepsin. I have found that the rate of reaction catalysed by pepsin is greatly reduced even by adding ethanol of just 1% concentration. This seems to suggest that only a small percentage of alcohol reaches the gut when someone drinks an alcoholic drink, otherwise pepsin would be nearly totally inactive. If anyone could give me some ideas, or point me toward relevant literature, I owuld greatly appreciate it. Andre. From owner-proteins@net.bio.net Thu May 08 23:00:00 1997 Path: biosci!daresbury!uninett.no!sn.no!nntp.uio.no!news.apfel.de!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!torn!nott!freenet-news.carleton.ca!FreeNet.Carleton.CA!dg628 From: dg628@FreeNet.Carleton.CA (Angela C. Murphy) Newsgroups: bionet.molbio.proteins Subject: Re: Buffer for lyophylization Date: 9 May 1997 20:33:12 GMT Organization: The National Capital FreeNet Lines: 33 Message-ID: <5l01m8$cm6@freenet-news.carleton.ca> References: Reply-To: dg628@FreeNet.Carleton.CA (Angela C. Murphy) NNTP-Posting-Host: freenet6.carleton.ca X-Given-Sender: dg628@freenet6.carleton.ca (Angela C. Murphy) It depends on what you mean by "salt". Any acid will form a salt with free amino groups, including the C-terminus of a peptide or protein. You will have to go above the pI of a peptide or protein to have most or all of the amino groups as free bases. If you want to accomplish this with something volatile, you might try ammonium bicarbonate or dilute ammonia. If you don't care about whether the amino groups form salts, then dilute acetic acid or TFA or triethylammonium acetate or trifluoracetate or ammonium acetate or trifluoracetate will do. Angela C. Murphy Michael DiDonato (michael.didonato@utoronto.ca) writes: > I am wondering if anyone knows which is the best buffer to lyophylize from? > Excluding water, what buffer would leave beind the least amount of salt > upon lyophylization? > > Any suggestions are extremely appreciated. > > Mike > > -- > Michael DiDonato > Department of Biochemistry Research > Hospital for Sick Children > Toronto, Ontario, Canada > michael.didonato@utoronto.ca -- ************************************************** Angela C. Murphy Bowie, MD USA angelam@capaccess.org dg628@freenet.carleton.ca ************************************************** From owner-proteins@net.bio.net Fri May 09 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!ais.net!news.texas.net!davej From: davej@sedona.net (Dave Jensen) Newsgroups: bionet.molbio.proteins Subject: Bio-career Discussion Forum Date: Sat, 10 May 1997 09:34:41 -0700 Organization: Search Masters International Lines: 44 Message-ID: NNTP-Posting-Host: client44.sedona.net Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.4 A new, non-commercial career discussion forum is available for your browsing and posting interests. No commercial posts or spam are allowed on this news forum, and it is entirely moderated so as to make it 100% worthy of your contribution. There are hundreds of posts on dozens of topics of interest to anyone in the sciences. If you'd like, post your questions and find dozens of other people who may have had similar experiences and who you can network with or get some advice from. Already, networking subgroups have sprouted from the biotechnology section of this career discussion forum. Here are some topics JUST FROM THE LAST WEEK, and we have hundreds of archived posts: Career change to CRA Should you mention your advisor as a reference ? Best MBA for biotech Liberal Arts Positions? Scientist salaries? Temporary Placement Firms, any good? Multiple job offers, maybe? Salary trends Keeping the interview alive... One worried soon to be graduate. Changing jobs/employers Join our career discussion forum at http://cns.bio.com/hr/forum/ regards, Dave Jensen, Moderator From owner-proteins@net.bio.net Fri May 09 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!feeder.chicago.cic.net!newsrelay.netins.net!composer.inav.net!usenet From: Robert J Jensen Newsgroups: bionet.molbio.proteins,bionet.immunology Subject: Re: casein as substrate Date: Sat, 10 May 1997 20:14:26 -0500 Organization: Internet Navigator, Inc. Lines: 3 Message-ID: <33751D72.6C6D@inav.net> References: <33714C4C.4DE5@agora.ulaval.ca> NNTP-Posting-Host: dip59.inav.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; 68K) Xref: biosci bionet.molbio.proteins:10703 bionet.immunology:11736 You need to buy the "sodium salt" of casein. Heat to 37C and dissolve over 30-45 minutes while stiring. I had the same problem. rjj From owner-proteins@net.bio.net Fri May 09 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news From: Lipid Research Laboratory Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: Buffer for lyophylization Date: Sat, 10 May 1997 16:43:37 -0400 Organization: Institute of Clinical Research Lines: 26 Message-ID: <3374DDF9.7A8F@erols.com> References: Reply-To: rlax@erols.com NNTP-Posting-Host: spg-as48s14.erols.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received-On: 10 May 1997 16:37:44 GMT X-Mailer: Mozilla 3.01 (Win95; I) Xref: biosci bionet.molbio.methds-reagnts:57517 bionet.molbio.proteins:10701 Michael DiDonato wrote: > > I am wondering if anyone knows which is the best buffer to lyophylize from? > Excluding water, what buffer would leave beind the least amount of salt > upon lyophylization? > > Any suggestions are extremely appreciated. > > Mike > > -- > Michael DiDonato > Department of Biochemistry Research > Hospital for Sick Children > Toronto, Ontario, Canada > michael.didonato@utoronto.ca I use routinely ammonium bicarbonate. Before the lyophilization step the protein sample is dialyzed against ammonium bicarbonate (25 mM usually). Also, I add 0.1% 2-mercaptoethanol in the buffer. Philippe Marmillot George Washington University Lipid Research - VA medical Center 50 Irving Street NW Washington, DC 20422 From owner-proteins@net.bio.net Fri May 09 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!news-out.communique.net!communique!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!worldnet.att.net!newsadm From: Mark Dalton Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: Buffer for lyophylization Date: Sat, 10 May 1997 07:47:42 -0500 Organization: AT&T Lines: 22 Message-ID: <33746E6E.5689@worldnet.att.net> References: Reply-To: mdalton@worldnet.att.net NNTP-Posting-Host: 207.146.216.171 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02E (Macintosh; U; PPC) Xref: biosci bionet.molbio.methds-reagnts:57513 bionet.molbio.proteins:10697 Michael I would use amonium acetate or am. carbonate at 50mM if you wish to totally get rid of the salt by mult. lyopholyzation steps. Just keep adding water and refreezing and relyopholyze the amonium acetate/carb will disipate after two or three cycles. Mark Michael DiDonato wrote: > > I am wondering if anyone knows which is the best buffer to lyophylize from? > Excluding water, what buffer would leave beind the least amount of salt > upon lyophylization? > > Any suggestions are extremely appreciated. > > Mike > > -- > Michael DiDonato > Department of Biochemistry Research > Hospital for Sick Children > Toronto, Ontario, Canada > michael.didonato@utoronto.ca From owner-proteins@net.bio.net Sat May 10 23:00:00 1997 Path: biosci!daresbury!uninett.no!sn.no!nntp.uio.no!newsfeed.nacamar.de!rill.news.pipex.net!pipex!tank.news.pipex.net!pipex!news00.sunet.se!sunic!news99.sunet.se!mn5.swip.net!news From: "Patrick Van de Velde" Newsgroups: bionet.molbio.proteins Subject: Biotinylated IgM (mouse anti human CD34+) Date: 10 May 1997 20:54:56 GMT Organization: - Lines: 16 Message-ID: <01bc5d83$ca568ce0$7b73f482@s-30798> NNTP-Posting-Host: dialup115-6-3.swipnet.se NNTP-Posting-User: s-30798 X-Newsreader: Microsoft Internet News 4.70.1155 Hi, I am facing some problems with a purification in which biotinylated IgM is used. Normally this arrives under dry ice - but I syspect that there might have been a freeze thaw cycle and refreeze again. Therefor I suspect that there are some broken IgM fragments that are still active against the epitope but aren't biotinylated anymore and therefor block the binding site but are not captured by the avidin column. Does anybody has some information on freeze-thaw stability on biotinylated IgM ? Please forward your ideas to patrick.van.de.velde@mailbox.swipnet.se From owner-proteins@net.bio.net Sat May 10 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!newsfeed.nacamar.de!nntp.uio.no!uninett.no!news.uni-c.dk!news.daimi.aau.dk!not-for-mail From: Per Mygind Newsgroups: bionet.molbio.proteins,bionet.immunology Subject: Re: casein as substrate Date: Sun, 11 May 1997 15:44:25 +0100 Organization: DAIMI, Computer Science Dept. at Aarhus University Lines: 20 Message-ID: <3375DB49.5960@biobase.dk> References: <33714C4C.4DE5@agora.ulaval.ca> <33751D72.6C6D@inav.net> NNTP-Posting-Host: majestetix.medmicro.aau.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; SunOS 5.5.1 sun4m) Xref: biosci bionet.molbio.proteins:10705 bionet.immunology:11739 Robert J Jensen wrote: > > You need to buy the "sodium salt" of casein. Heat to 37C and dissolve > over 30-45 minutes while stiring. I had the same problem. > rjj The following reciepe can be used with succes to dissolve pure casien powder; (5 liter is obtained, with a concentration of 1%) You might therefore want to scale down the reciepe; 1.100 grams of Casein is added to 1 liter of 1M NaOH 2.Dissolving overnight at room temperature using stirring 3.Add 500 mmole of NaCl and 250 mmole of Tris-Base 4.Titrate the sollution with 300 mM HCl (approximately 3 liters !!) 5.To adjust the pH you might even have to add pure HCl (37%) 6.Remember to use magnetic stirring throughout the process Have fun ;-) Cand.scient Per Mygind, University of Aarhus, Denmark From owner-proteins@net.bio.net Sat May 10 23:00:00 1997 Path: biosci!botany.uq.edu.au!J.Marcus From: J.Marcus@botany.uq.edu.au ("Marcus, Dr J.") Newsgroups: bionet.molbio.proteins Subject: Re: The effect of ethanol on the activity of pepsin Date: 11 May 1997 15:38:36 -0700 Organization: Dept of Botany, Univ of Queensland Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <4762676FCF@botany.uq.edu.au> References: <01bc5cce$a35c8820$3ca5d8c2@nexus.idiscover.co.uk> Reply-To: Marcus@tpp.uq.edu.au NNTP-Posting-Host: net.bio.net Have you looked at the effect of ethanol on other enzymes. It really does not take much organic solvent to destroy activity. Your thought about inhibition of pepsin is interesting. John > Can someone explain how ethanol may affect the activity of pepsin. I have > found that the rate of reaction catalysed by pepsin is greatly reduced even > by adding ethanol of just 1% concentration. This seems to suggest that > only a small percentage of alcohol reaches the gut when someone drinks an > alcoholic drink, otherwise pepsin would be nearly totally inactive. If > anyone could give me some ideas, or point me toward relevant literature, I > owuld greatly appreciate it. > > Andre. > > _________________________________________________________ John Marcus Marcus@tpp.uq.edu.au (Dr J.Marcus) Cooperative Research Centre for Tropical Plant Pathology 5th Level John Hines Building University of Queensland St. Lucia, QLD 4072 AUSTRALIA Fax: 61-7-3365-4771 Phone: 61-7-3365-4764 From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news.maxwell.syr.edu!newsfeed.nacamar.de!newsfeed.de.ibm.net!ibm.net!02-newsfeed.univie.ac.at!03-newsfeed.univie.ac.at!news.univie.ac.at!news-admin@univie.ac.at From: a8803349@unet.univie.ac.at (Martin Offterdinger) Newsgroups: bionet.molbio.proteins Subject: Immunofluorescence Date: Mon, 12 May 1997 09:17:08 GMT Organization: AKH Lines: 14 Message-ID: <3376dfef.676016@news.univie.ac.at> NNTP-Posting-Host: grunt.imed1.akh-wien.ac.at X-Newsreader: Forte Free Agent 1.1/16.230 Hi I am just getting involved with immunofluorescence for the first time and have some really basic questions: 1) Is there any good and recent review arcticle describing the whole method. 2) Which fluorochrome should be chosen for parafin embedded sections?(single labelling) I learned that many people use fluorescein, but this fluorochrome seems to be very sensitive to bleaching-so why is it still the most commonly used? I rather would like to use something else like Texas red or PE-is there anyone who has experience with this?? Thank you very much, Martin From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Songlin Li Newsgroups: bionet.molbio.proteins Subject: about pI of EcoRI (fwd) Date: 12 May 1997 09:21:02 +0100 Lines: 22 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5l6jte$4k0@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: proteins@dl.ac.uk This might be a business secret. But I would like to know the pI of EcoRI. I want to purify a EcoRI derivative through an anion exchange column. Any comment would be greatly appreciated. Songlin ---------------------------------------------------- Songlin Li, PhD Lundberg Institute Medicinaregatan 9C S-413 90 Goteborg Sweden E-mail: songlin@bcbp.gu.se URL: http://www.lundberg.gu.se/~songlin/ Telephone: +46 (31) 773 3927 Telefax: +46 (31) 773 3910 ---------------------------------------------------- From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news-peer.gsl.net!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!aars!not-for-mail From: lluis@aars.mit.edu (Lluis Ribas) Newsgroups: bionet.molbio.proteins Subject: Re: A question about tRNA Date: 12 May 1997 07:30:22 GMT Organization: Massachvsetts Institvte of Technology Lines: 35 Message-ID: <5l6gue$odp@senator-bedfellow.MIT.EDU> References: <01bc5cb4$cdd9c140$2683bdcd@klaassen.oix.com> NNTP-Posting-Host: aars.mit.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Klaassen (klaassen@oix.com) wrote: : : I was hoping that someone could help me with a question I have :) : : I was looking in my Biology text book, and I'm a bit confused about tRNA. : I realize that the anticodon attaches to the codon of the mRNA (through the : ribosome)... but I'm not able to understand is the codon of the tRNA.. is : it the same as the codon on the mRNA, which would be the compliment to the : anticodon on the tRNA. More than half of the pictures I have seen of the : codon have four nucleotides, and none of them match up with the anticodon. : Infact, none of the tRNA codons that I have seen match up with the : anticodons of the same tRNA. : : Another question I have is also about the codon on the tRNA. Wich way is : it read. Different books are telling me different things. Is it read from : the 3` end like DNA, or is it read backwards? Depending on the way that it : is read changes the amino acids that they code for : : It's all just that little bit to far over my head... I would apreciate any : help I could get!!!! tRNAs have no codons. They recognize an mRNA codon through their complementary anticodons and carry the amino acid that corresponds to that triplet at the other end of their structure. THey are not read like mRNA's, but recognized through their three-dimensional structure by aminoacyl-tRNA synthetases. Those enzymes are responsible for the specific attachment of the amino acids to their correct tRNA's. The transfer of that amino acid to the polypeptide chain takes place in the ribosome, after the pairing of the mRNA codon with the tRNA anticodon. Lluis : From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!azure.xara.net!xara.net!netcom.net.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!nntp0.brunel.ac.uk!strath-cs!news.qub.ac.uk!not-for-mail From: Andrew Wallace Newsgroups: bionet.molbio.proteins Subject: Re: protein mass spec problem Date: Mon, 12 May 1997 09:52:41 +0100 Organization: Queens University Belfast Lines: 15 Message-ID: <3376DA58.E53@see.signature.qub.ac.uk> References: <5knh70$qih@usenet.bham.ac.uk> Reply-To: a.wallace@see.signature.qub.ac.uk NNTP-Posting-Host: awall.bc.qub.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) To: "John E. Fox" John E. Fox wrote: > > Electrospray Mass Spectrometry on a purified recombinant protein. > Why multiple peaks? Could they be different salts of the protein, e.g. Tris, Na+, etc.? This is often observed with smaller peptides, for example. Andrew -- - note antispam feature in header. My real address is: ================================================================== Andrew Wallace,Ph.D., Queens University Belfast, N. Ireland (UK) a.wallace@qub.ac.uk http://web.qub.ac.uk/bb/awpage/wallace.html ================================================================== From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins Subject: Re: Immunofluorescence Date: 12 May 1997 12:48:01 GMT Organization: University of Leicester (PCFS User) Lines: 14 Message-ID: <5l73i1$bn@falcon.le.ac.uk> References: <3376dfef.676016@news.univie.ac.at> NNTP-Posting-Host: pc47.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) a8803349@unet.univie.ac.at (Martin Offterdinger) wrote: >I learned that many people use fluorescein, but this fluorochrome >seems to be very sensitive to bleaching-so why is it still the most >commonly used? Because the amount of emitted light for a given amount of absorbed light, the fluorescent yield, is very high in fluorescein. Additionally, the wavelength of the yellow-green fluorescence of fluorescein is close to the peek sensitivity of the human eye. Both factors result in brighter pictures. Fluorescein is also relatively cheap. The problem of bleaching can be controlled to some extend by the use of anti-fade mouning media. From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news-peer.sprintlink.net!news.sprintlink.net!Sprint!howland.erols.net!math.ohio-state.edu!newsfeed.acns.nwu.edu!news.cc.uic.edu!not-for-mail From: Keld Sorensen Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.immunology,bionet.cellbiol Subject: Re: ELISA for Hisx6 proteins Date: Mon, 12 May 1997 09:01:59 +0000 Organization: University of Illinois, College of Medicine Lines: 1 Message-ID: <3376DC86.73E9@uic.edu> References: <33714821.167E@risotto.mit.edu> NNTP-Posting-Host: slip-rock-01.dialin.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) Xref: biosci bionet.molbio.methds-reagnts:57538 bionet.molbio.proteins:10714 bionet.immunology:11744 bionet.cellbiol:7288 Pierce carries Metal-Chelate plates as well as metal-chelate-HRP. From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.apfel.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: protein mass spec problem Date: Mon, 12 May 1997 19:27:06 +0200 Organization: University of Wuerzburg, Germany Lines: 25 Message-ID: References: <5knh70$qih@usenet.bham.ac.uk> <3376DA58.E53@see.signature.qub.ac.uk> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Andrew Wallace (a.wallace@see.signature.qub.ac.uk) wrote: > John E. Fox wrote: > > Electrospray Mass Spectrometry on a purified recombinant protein. > > Why multiple peaks? > > Could they be different salts of the protein, e.g. Tris, Na+, etc.? > This is often observed with smaller peptides, for example. Could this also happen with MALDI? We have a recombinant protein that gave *only* a peak which is 59 m/z too large. This would correspond nicely to acetate, and indeed the protein was lyophilized from a 10 mM ammonium acetate solution. DNA sequence of the expression vector looks okay. N-terminal posttranslational modification can be excluded because the protein is cleaved from GST with Thrombin after purification. The protein also reacts with antibodies made against a full-sized version (recombinant, from Sf9 cells). Puzzled, --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.maxwell.syr.edu!news-peer.sprintlink.net!news-pull.sprintlink.net!news.sprintlink.net!Sprint!chi-news.cic.net!ftpbox.mot.com!newsfeed.acns.nwu.edu!news.cc.uic.edu!not-for-mail From: Keld Sorensen Newsgroups: bionet.molbio.proteins Subject: Re: The effect of ethanol on the activity of pepsin Date: Mon, 12 May 1997 12:26:36 +0000 Organization: University of Illinois, College of Medicine Lines: 3 Message-ID: <33770C7B.BE2@uic.edu> References: <01bc5cce$a35c8820$3ca5d8c2@nexus.idiscover.co.uk> NNTP-Posting-Host: slip-rock-02.dialin.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) To: SpaceboY What pepsin assay did you use? What did the inhibition curve look like? Keld Sorensen. From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!gondor!newshub.sdsu.edu!newshub.csu.net!mr.net!newsfeed.direct.ca!newsfeed.nacamar.de!news-kar1.dfn.de!news-stu1.dfn.de!news-mue1.dfn.de!news-nue1.dfn.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Identification Date: Mon, 12 May 1997 10:04:24 +0200 Organization: University of Wuerzburg, Germany Lines: 22 Distribution: world Message-ID: <8ui6l5.jfa.ln@wpxx02.toxi.uni-wuerzburg.de> References: <3373A5D6.4C42@rutchem.rutgers.edu> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Gene S. Hall (hall@RUTCHEM.RUTGERS.EDU) wrote: > What is the basic way to absolutely determine an unknown protein? We > are using SEC to separate human proteins from plasma. How can we ^^^size exclusion chromatography? > absolutely determine the molecular weight of these proteins and identify > them. To determine the molecular weight: - crude estimate: SDS polyacrylamide electrophoresis - precise determination: mass spectroscopy To identify proteins: - antibodies on western blot - N-terminal sequencing (or sequencing of -- e.g. tryptic -- peptides) --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!uunet!in3.uu.net!206.229.87.25!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news-peer.gsl.net!news-paris.gsl.net!news.gsl.net!rain.fr!infonie.fr!not-for-mail From: "zougari sadeq" Newsgroups: bionet.biology.n2-fixation,bionet.jobs.wanted,bionet.molbio.proteins,bionet.molbio.rapd,bionet.plants,uk.jobs.wanted Subject: Seeking postdoc in biol.Mol; genetics; Plant breeding; Proteins Biochemistry Date: 12 May 1997 14:43:25 GMT Organization: infonie.fr Lines: 141 Message-ID: <01bc5ee3$70d7a8a0$031965c3@zougari> NNTP-Posting-Host: 195.101.25.3 X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.biology.n2-fixation:709 bionet.jobs.wanted:13126 bionet.molbio.proteins:10717 bionet.molbio.rapd:1906 bionet.plants:15445 ZOUGARI BEN ELKHAYAT My Abdessadeq Address for correspondance: Laboratoire de Biotechnologie et Amélioration des Plantes Institut National Polytechnique, Ecole Nationale Supérieure Agronomique de Toulouse 145, Avenue de Muret F-31076 Toulouse Cedex France Tel: 33 5 61 34 12 64 Fax: 33 5 62 13 65 65 e-mail:sadeq04@infonie.fr As you can see in my Curriculum Vitae, i have my expertise and interests in working on projects, such as plant breeding, diallels analysis, statistics, plant-microbe interactions, molecular genetics and protein biochemistry. Please find enclosed my Curriculum Vitae and the names of tree Professors with whom i have worked. With my best regards. references: C. PLANCHON, Professor head of the Department of Biotechnology and Plant Breeding at l'Institut National Polytechnique de Toulouse - Ecole Nationale Supérieure AgronomiqueToulouse E-mail: planchon@ensat.fr Phone / Fax: 33 5. 62.13.65.65 M.T. ESQUERRE-TUGAYE, Professor Centre de Physiologie Végétale ( Role of Lipoxygenase in plant-microorganism interactions) Université Paul Sabatier de Toulouse - UMR5546 CNRS E-mail: esquerre@cict.fr Phone / Fax: Tél. 33 5.61.55.67.61 ROUGE, Professor Université Paul Sabatier de Toulouse Laboratoire de Biologie Cellulaire Email: rouge@cicit.fr Tèl: 33 5 61 55 66 11 ----------------------------------- CURRICULUM VITAE ------------------------------------ 1991-1996: PhD work in Plant Biotechnology at the University of Paul Sabatier Toulouse III and l'Institut National Polytechnique de Toulouse - Ecole Nationale Supérieure Agronomique under the guidance of Professor Claude Planchon; head of the Department of Biotechnology and Plant Breeding . ------------------------------------------------------------------------ 1990 - 1991: End of studies Diploma (DEA) of Plant Biotechnology. Option: Interaction Plant Micro-organism at the University of Paul Sabatier Toulouse France ------------------------------------------------------------------------ 1989 - 1990: Master of Cellular Biology. Option: Microbiology at the University of Paul Sabatier Toulouse, France ------------------------------------------------------------------------ 1988 - 1989: Licence Diploma of Biochemistry at the University of Paul Sabatier Toulouse, France ------------------------------------------------------------------------ 1986 - 1988: General University studies: Diploma of Biology at the University of Cadi Ayyad, Faculté des sciences Marrakech, Morocco ------------------------------------------------------------------------ June 1986: Bachelorship of Natural Sciences, Marrakech, Morocco ------------------------------------------------------------------------ SPECIALIZATIONS : · Genetic improvement of soybean seed quality: Genetic determinism study of the expression of soluble proteins and lipoxygenases seed contents with a complete diallel between five genotypes, in natural conditions and in pots. ­ RAPD (PCR) in soybean genotype ® diallel Analyse using Griffing et Hayman methods · Statistics analysis: PCSM, Systat, Statitcf and Sigma Plot. · Plant physiology: relations (carbon) C-N (nitrogen), N-mobilization analysis during seed filling peroid · Biochemistry, Enzymology et Immunology: Þ isolation and purification of seed protein by affinity Chromatography on Sephadex G100 Þ determination of nitrogenase activity of soybean nodule using the Acetylène Reduction Assay by gaz Chromatography (DELSI DI 200) Þ determination of soybean seed lipoxygenase activity polarographically using an Oxygraph Hansatech DWI. Þ spectroscopy Analysis: UV direct Spectroscopy ­ UV Difference Spectroscopy Þ Polyacrylamide gel electophoresis using the Phast-system (Pharmacia) Þ Proteins determinations: a- de Kjeldahl Method b- colorimetric Method BCA (Pierce) Þ hemagglutination Technique: determination of hemagglutination activity on standart micro-titration plates Þ Indirect ELISA (Enzyme Linked Immunosorbent Assay) measurement on standart micro-plates using either rabbit polyclonal antibodies against PsA or monoclonal antibody (6,F8) made against the Lathyrus odoratus lectin. REFERENCES 1) ZOUGARI, A., GUY, S., and PLANCHON, C. 1995. Genotypic lipoxygenase variation in soybean seeds and response to nitrogen nutrition. Plant Breeding 114, 313-316. 2) ZOUGARI, A., P., CHÊNE., H. MAZARGUIL., and P. ROUGÊ. 1993. Unfolding of pea lectin in the presence of guanidium chloride and urea. Lectins: Biology, Biochemistry, Clinical Biochemistry. [Ed] Textop. p143-150. 3) ZOUGARI, A., SUC, S., and PLANCHON, C. 1995. Amélioration de la qualité de la graine (improvement of soybean seed quality): – voies génétiques et agronomiques: Paramètres de la qualité de la graine. Groupe pluridisciplinaire de recherche sur le soja, Auzeville, Fév. 1992, 2-6. 4) ZOUGARI, A. 1995. Amélioration de la qualité de la graine Communication orale. Groupe pluridisciplinaire de recherche sur le soja, Auzeville, Fév. 1992. 5) ZOUGARI, A., PLANCHON, C ., and ECOCHARD, R. 1996. Inheritence of protein content and lipoxygenase activity in soybean seed (Glycine max (L.) merr.) in cours of writing. 6) ZOUGARI, A. 1990. Dénaturation de la lectine de pois: approche structurale et biologique. D.E.A U.P.S.Toulouse , 23 p 7) ZOUGARI, A. 1996. Genetic improvement of soybean seed quality (Glycine max (L. ) merr. ): lipoxygenases, and proteins and response to nitrogen nutrition '. PhD thesis INP,119 p. ------------------------------------- SUMMARY OF PhD THESIS ------------------------------------- TITLE: Genetic improvement of soybean seed quality (Glycine max (L. ) merr. ): lipoxygenases, and proteins and response to nitrogen nutrition. ------------------------------------------------------------------------ SUMMARIZES: The use of soybean seed in human foods can be favored by a reduction of the lipoxygenase content. This investigation aim to analyze the variability and the genetic determinism of lipoxygenase and proteins seed contents. The study of lipoxygenase activity, determined polarographically on seeds taken from plants grown under controlled conditions with a mineral or symbiotique nitrogen feeding, shows a large genotypique variability for lipoxygenases contents, enhanced by high dinitrogen fixation. In these same conditions of culture, during the seed filling period, lipoxygenases accumulation appears massive until the physiological maturity stage (R7) and is followed by a partial degradation. The lipoxygenases may play a role in the temporary storage of nitrogen. Finally a genetic study is realized in natural conditions and in pots, with a complete diallel between five genotypes, representative of a great variability for soluble proteins and lipoxygenases seed contents. Hybrids F1 show a strong effect of heterosis for soluble proteins, lipoxygenase 1 and total lipoxygenases contents. For these last, hybrids show a strong homeostatique behavior with weaker contents than those of the parents. Though, values of contents in soluble proteins indicate a positive overdominance as well as a great sensitivity to environnementales variations. Genetic determinism of the expression of soluble proteins and lipoxygenases contents appears complex and linked to significants additive, non-additive and reciprocal effects. Thus, the reduction of lipoxygenases contents and the improvement of proteins contents can be considered on a genetic context implying the nuclear and cytoplasmique genomes together with more efficent dinitrogen fixation, with respect of dinitrogen fixation From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!europa.clark.net!news-peer.gsl.net!ix.netcom.com!netcom.net.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!mac052034.lif.icnet.uk!user From: I.McFarlane@icrf.icnet.uk (Ian McFarlane) Newsgroups: bionet.molbio.proteins Subject: TCA and HIC protein pufn Date: Mon, 12 May 1997 15:49:26 +0000 Organization: Imperial Cancer Research Fund Lines: 9 Message-ID: NNTP-Posting-Host: mac052034.lif.icnet.uk X-Newsreader: Value-Added NewsWatcher 2.0b27+ Hi, My protein of interest happens to be soluble in 10% TCA. I am going to use TCA as the first step in its pufn. Does anyone know if I can go on to do hydrophobic interaction chromatography without dialysing away the TCA. Obviously anion or cation exchange would require dialysis. Any suggestions? Ian Mc From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!STU.UST.HK!bc_yks From: bc_yks@STU.UST.HK (Yeung Kam Sze) Newsgroups: bionet.molbio.proteins Subject: Re: shortest proteins. Date: 12 May 1997 12:29:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Hi all, I found that Glutathione is make up of gamma-Glu, is it standard a.a. residue? Thx! Regards, Kams :) On Fri, 9 May 1997, John Collins wrote: > Someone has played a mean joke on you. Glutathione is a tripeptide, > described in any biochemistry book. > > On Fri, 9 May 1997, Yeung Kam Sze wrote: > thx! but where can i get the > detailed information? e.g how many residue > it contains? does it has a > pdb code? > On Thu, 8 May 1997, Pete wrote: > > How about glutathione? > , ';; ,;' ;; ;; , ,; ;' ';, ,,,,, ;;,,, ,;' ; ;; ;' ';;,, ;;; ,,,;;;'' ;;, ; ';; , ,;' ';;;;,, ;; ;; ;' ,, ,,;'' ; ;;;; ,;;' ,, '';;;, ;; ;; ,;,;;''''' ,,,;';; , ;;';; ,;; ';;'' ;; ,,;;,,,;;'' , '' ;;;;' ,;'' ,' '' ; ,, ;; ';;; '' ,,,,,;;'' ,;;;;' ' ,;,,;;'';, ,;;' ;; ';; ''''' ; ;;;;; ;;';; ;' ,; ''''; ,; ,,' ;; ,, ; '' ;; ,;',;' ,;' , ;,;' ,;;' ;;; ''' ; ;; ' ,;' ;;' ;;;,;; ,,, ';' ;; ,;'',;;' ''''';;'' ,,;;; ----------- Department of Biochemistry, Hong Kong University of Science and Technology URL:mailto:bc_yks@stu.ust.hk /-----\ ,o. 8 8 URL:http://susis.ust.hk/~kams | `o--| d bzzzzzzzza8o8b Don't Worry! Be Happy! \-----/ `o' Golden Time Golden Key From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!gondor!sol.ctr.columbia.edu!spool.mu.edu!howland.erols.net!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!news-xfer.cybernet.dk!netcom.net.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!gmorley From: gmorley@hgmp.mrc.ac.uk (Mr. G. Morley) Newsgroups: bionet.molbio.proteins Subject: Postdoc position available Date: 12 May 1997 14:49:23 GMT Organization: MRC Human Genome Resource Centre Lines: 9 Message-ID: <5l7alj$4ok@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: tin.hgmp.mrc.ac.uk A molecular biologist postdoc position is available to work in the institute of Obstretrics and Gynaecology at the Hammersmith hospital, London, England. For more details please check out: http://www.caduceus.demon.co.uk/postdoc.html or e-mail Dr.Nick Dibb at: ndibb@rpms.ac.uk From owner-proteins@net.bio.net Sun May 11 23:00:00 1997 Path: biosci!webtv.net!uunet!in3.uu.net!134.222.90.2!EU.net!sun4nl!surfnet.nl!Hermes.nki.nl!not-for-mail From: Jan Koster Newsgroups: bionet.molbio.proteins Subject: The Integrin Page Date: Mon, 12 May 1997 15:22:40 +0100 Organization: The Netherlands Cancer Institute, Amsterdam Lines: 21 Message-ID: <337727B0.5539@nki.nl> NNTP-Posting-Host: pca118.nki.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) I'd like to bring the existence of The integrin Page to your attention. The site is completely devoted to the fascinating cell adhesion receptors called integrins. It features: - Basic information about integrins - Direct links to sequences of integrin subunits in the EMBL database with clickable references. - Antibody data for all the subunits (already 126 Ab are present) - And much more. Recent additions to the homepage are: - factsheets for every integrin subunit. - a questions and answers section. - links from Ab to commercial sources (just started). You are all welcome on The Integrin Page. It can be accessed at: http://www.geocities.com/CapeCanaveral/9629 From owner-proteins@net.bio.net Mon May 12 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!csn!nntp-xfer-1.csn.net!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!newsxfer.itd.umich.edu!sol.ctr.columbia.edu!hamblin.math.byu.edu!news.Arizona.EDU!not-for-mail From: valeryt@ag.arizona.edu (Valery Thompson) Newsgroups: bionet.molbio.proteins Subject: C-terminal sequencing Date: 13 May 1997 16:14:39 GMT Organization: University of Arizona Lines: 20 Message-ID: <5la41f$151m$1@news.ccit.arizona.edu> NNTP-Posting-Host: val.agshantz.arizona.edu X-Newsreader: WinVN 0.92.6+ I am interested in doing c-terminal amino acid sequence analysis of a protein blotted onto PVDF. I know that there is instrumentation to do this, but I am trying to find a place that has such an instrument and that accepts outside business. University of Michigan used to do this, but I found out today that they no longer accept samples from other universities. Does anyone know of a facility that I could contact? Thanks. Valery F. Thompson Senior Research Specialist Muscle Biology Group Universtiy of Arizona Tucson, AZ 85721 (520) 621-9926 valeryt@ag.arizona.edu From owner-proteins@net.bio.net Mon May 12 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins Subject: Re: TCA and HIC protein pufn Date: 13 May 1997 15:21:22 GMT Organization: University of Leicester (PCFS User) Lines: 21 Message-ID: <5la0ti$8v5@falcon.le.ac.uk> References: NNTP-Posting-Host: pc47.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) I.McFarlane@icrf.icnet.uk (Ian McFarlane) wrote: >My protein of interest happens to be soluble in 10% TCA. I am going to use >TCA as the first step in its pufn. Does anyone know if I can go on to do >hydrophobic interaction chromatography without dialysing away the TCA. >Obviously anion or cation exchange would require dialysis. Any >suggestions? I have never tried HIC from TCA solutions. However, if this does not work, there are at least two options other than dialysis. The first would be gel filtration, which at the same time as removing TCA can be used as second purification step (by MW, obviously). The other option would be ultrafiltration in a stirred cell, like the ones produced by Amicon. The solute is pressed through a membrane by nitrogen pressure, proteins above the cut off size of the membrane are retained. Simply concentrate your sample to, say, 1/10 or 1/20 of its original volume, add your starting buffer for the next step and concentrate again. This process is a lot quicker than dialysis (normally 2-3 h total) and gives you a concentrated sample, which is easier to work with (although this is not too relevant with HIC). From owner-proteins@net.bio.net Mon May 12 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!solace!nntp.uio.no!newsfeed.nacamar.de!rill.news.pipex.net!pipex!server1.netnews.ja.net!server6.netnews.ja.net!str-ccsun!strath-cs!news.qub.ac.uk!not-for-mail From: Andrew Wallace Newsgroups: bionet.molbio.proteins Subject: Re: Protein Identification Date: Tue, 13 May 1997 13:11:28 +0100 Organization: Queens University Belfast Lines: 22 Message-ID: <33785A67.57B2@see.signature.qub.ac.uk> References: <3373A5D6.4C42@rutchem.rutgers.edu> Reply-To: a.wallace@see.signature.qub.ac.uk NNTP-Posting-Host: awall.bc.qub.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) To: hall@rutchem.rutgers.edu Gene S. Hall wrote: > > What is the basic way to absolutely determine an unknown protein? We > are using SEC to separate human proteins from plasma. How can we > absolutely determine the molecular weight of these proteins and identify > them. > Thanks for your help, > Gene You might also consider electrospray or time-of-flight mass spectrometry (e.g. MALDI-TOF). It is even possible to determine the amino acid sequence of the protein using MS-MS or the new ion trap instruments if it is not too large (>200 kDa). One person mentioned sequencing the cDNA but this will not take account of post-translational modifications. Andrew -- - note antispam feature in header. My real address is: ================================================================== Andrew Wallace,Ph.D., Queens University Belfast, N. Ireland (UK) a.wallace@qub.ac.uk http://web.qub.ac.uk/bb/awpage/wallace.html ================================================================== From owner-proteins@net.bio.net Mon May 12 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.proteins Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 13 May 1997 02:00:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199705130900.CAA05946@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. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-proteins@net.bio.net Mon May 12 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!gondor!newshub.sdsu.edu!news.sgi.com!enews.sgi.com!newshub1.home.com!news.home.com!nick.arc.nasa.gov!purdue!haven.umd.edu!news.umbc.edu!not-for-mail From: cweiss1@umbc.edu (Christopher Weiss) Newsgroups: bionet.molbio.proteins Subject: Backbone bond angle data Date: 13 May 1997 15:38:59 -0400 Organization: University of Maryland, Baltimore County Lines: 19 Message-ID: <5lag0j$58a@umbc10.umbc.edu> NNTP-Posting-Host: umbc10.umbc.edu NNTP-Posting-User: cweiss1 I need protein backbone bond angle and bond length data. Not tortional angles. Angles and lengths needed: N-terminus H-N-H N-terminus H-N-C N-Calpha-H N-Calpha-C(carboxyl) O=C-Calpha O=C-N H-N-H (in peptide bond) C-N-Calpha C-terminus Calpha-C=O C-terminus Calpha-C-O C-terminus O=C-O Did I miss any? Thanks, Christopher From owner-proteins@net.bio.net Mon May 12 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsserver.jvnc.net!princeton!cnn.Princeton.EDU!usenet From: Nancy Vogelaar Newsgroups: bionet.molbio.proteins Subject: Re: Protein Identification Date: Mon, 12 May 1997 21:06:54 -0400 Organization: Princeton University Lines: 167 Message-ID: <3377BEAE.794B@atp.princeton.edu> References: <3373A5D6.4C42@rutchem.rutgers.edu> <8ui6l5.jfa.ln@wpxx02.toxi.uni-wuerzburg.de> NNTP-Posting-Host: atp.princeton.edu Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------15FB59E21CFB" X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) This is a multi-part message in MIME format. --------------15FB59E21CFB Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > Gene S. Hall (hall@RUTCHEM.RUTGERS.EDU) wrote: > > What is the basic way to absolutely determine an unknown protein? We > > are using SEC to separate human proteins from plasma. How can we > > absolutely determine the molecular weight of these proteins and identify > > them. Missed the beginning of this discussion and my apologies if this is redundant. If one has an idea of the protein's molecular weight and pI (via 2D gel for instance) there is a database which can suggest potential proteins. I think it should contain many human plasma proteins. http://expasy.hcuge.ch/www/guess-prot.html Nancy --------------------------------------------------------------------- Nancy Vogelaar Protein Crystallography Department of Chemistry Phone: (609) 258-2927 Princeton University Fax: (609) 258-6746 Princeton, NJ 08544 email: gc@atp.princeton.edu --------------------------------------------------------------------- --------------15FB59E21CFB Content-Type: text/html; charset=us-ascii; name="guess-prot.html" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="guess-prot.html" Content-Base: "http://expasy.hcuge.ch/www/guess-prot. html" ExPASy - TagIdent tool

TagIdent tool (formerly GuessProt)

TagIdent is a tool which allows
  1. the generation of a list of proteins close to a given pI and Mw,
  2. the identification of proteins by matching a short sequence tag of up to 6