From owner-proteins@net.bio.net Wed Jan 01 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!mindspring!newspump.sol.net!newsfeeds.sol.net!uwm.edu!news.cse.psu.edu!news.ece.nwu.edu!newsfeed.acns.nwu.edu!news.cc.uic.edu!usenet From: Ed Arias Newsgroups: bionet.molbio.proteins Subject: Chain Letter Scam! Date: Thu, 02 Jan 1997 09:03:35 -0500 Organization: University of Illinois at Chicago Lines: 17 Message-ID: <32CBC037.43FE@uic.edu> References: <32CB3B30.10B4@earthlink.net> NNTP-Posting-Host: slip5a-13.dialin.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01Gold (Win95; I) Mike McKinney wrote: > > Subject: MONEY, IS IT REAL > Date: Wed, 01 Jan 1997 17:26:07 -0600 > From: jmmckinney@earthlink.net > Organization: None > Newsgroups: adsp.german > > MAKE MONEY ON THE NET, IS IT TRUE??? check this out before you get caught up in this... http://www.usps.gov/websites/depart/inspect/chainlet.htm -- Ed Arias University of Illinois at Chicago Dept of Physiology & Biophysics Chicago, IL 60612 From owner-proteins@net.bio.net Wed Jan 01 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.erols.net!newspump.sol.net!newsfeeds.sol.net!uniserve!van-bc!unixg.ubc.ca!news.bc.net!torn!resunix.sickkids.on.ca!NewsWatcher!user From: Newswatcher@sickkids.on.ca (Newswatcher) Newsgroups: bionet.molbio.proteins Subject: Room Sharing at Biopyhsical Society Meeting Date: Thu, 02 Jan 1997 15:55:41 -0600 Organization: The Hospital for Sick Children Lines: 19 Message-ID: NNTP-Posting-Host: 142.20.24.101 Hi, Friends: I am looking for a female nonsmoker to share a twin room (Holiday Inn Superdome) during the Biophysical Society Meeting, March 1-6, 1997 in New Orleans, Louisiana. If you're interested, would you please contact me at the following address? I am a quite female, nonsmoker. My arrival date is March 1st, departure on March 6. I would be happy to hear from you. My phone number is 416-813-5855, fax number is 416-813-5022, Atten: Li-Ping. E-Mail: lliu@sickkids.on.ca Best Regards Li-Ping Liu Biochem. Res., Room 3523 Hospital for Sick Children Toronto, Canada M5G 1X8 -- Do not send email to Newswatcher@sickkids.on.ca. It will be bounced. From owner-proteins@net.bio.net Thu Jan 02 22:00:00 1997 Newsgroups: bionet.molbio.proteins Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!bunyip.cc.uq.oz.au!marlin.jcu.edu.au!news From: lachlan harris Subject: protein problems on gels Content-Type: text/plain; charset=us-ascii Message-ID: <32CED947.24E1@jcu.edu.au> Sender: news@marlin.jcu.edu.au (USENET News System) Content-Transfer-Encoding: 7bit Cc: lachlan.harris@jcu.edu.au Organization: James Cook University Mime-Version: 1.0 Date: Sat, 04 Jan 1997 14:27:19 -0800 X-Mailer: Mozilla 2.01 (Win16; I) Lines: 9 Can anyone help me with this problem? I have a pure microbial protein which when run on an SDS non-reduced (ie no mercaptoethanol) PAGE gel runs at approximately 50 KDa. When the same protein is run under SDS-reduced conditions two subunits appear- one running at approx 40 KDa and the other at approx 60 KDa. It was my understanding that the two subunits should add up to be the same size as the protein run under SDS-non reduced conditons. But this isn't happening. Does anyone know why? From owner-proteins@net.bio.net Thu Jan 02 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.nacamar.de!news.icm.edu.pl!uw.edu.pl!news.nask.pl!lublin.pl!biopc07.umcs.lublin.pl!tchorz From: tchorz@biotop.umcs.lublin.pl (Marek Tchorzewski) Newsgroups: bionet.molbio.proteins Subject: DNA Software Date: Fri, 3 Jan 1997 12:29:29 GMT Organization: Marie Curie-Sklodowska University Lines: 20 Message-ID: NNTP-Posting-Host: biopc07.umcs.lublin.pl Dear Netters, First of all, Happy New Year 1997 to all of you !!! On the other hand, I need advice concerning programs for DNA and protein analysis. I am going to buy such program however I am not fully determined which program I should purchase. So far, I have seen DNAsis and DNAstar, however I am not sufficiently confident that these programs are reliable, and can provide me with the best options. So, could you advice me, which programs is actually the best on the market. Marek Tchorzewski PhD Univ. of Maria Curie-Sklodowska Dept. of Molecular Biology Lublin, Poland From owner-proteins@net.bio.net Thu Jan 02 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.erols.net!news.nacamar.de!news.icm.edu.pl!uw.edu.pl!cyfronet!usenet From: kata@rabbit.if-pan.krakow.pl (Miroslaw Kata) Newsgroups: bionet.molbio.proteins Subject: Help: measurig low level of Nitric Oxide Date: 3 Jan 1997 11:01:30 GMT Organization: Institute of Pharmacology Lines: 18 Distribution: world Message-ID: <5aioua$f9m@info.cyf-kr.edu.pl> Reply-To: kata@rabbit.if-pan.krakow.pl NNTP-Posting-Host: farm220.if-pan.krakow.pl X-Newsreader: News for Windows NT X1.0-90 Hallo, I work in Pharmacology Institute. Recently I’m working with neuronal Nitric Oxide synthase (nNOS). I measure nNOS activity (in rat brain tissue) using a method based on conversion radioactive Arg to Cyt. It’s work quite good but I have problems with repeated results. I think about new devices for NO measuring (using NO sensor), Nitric Oxide Meter available from a few sources. I would like to contact with someone who use this technic and would like to share opinion about this devices. Thank you in advance. Miroslaw Kata Institute of Pharmacology 12 Smetna Street 31-343 Krakow Poland kata@rabbit.if-pan.krakow.pl From owner-proteins@net.bio.net Thu Jan 02 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.erols.net!vixen.cso.uiuc.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!martinlab From: klenchin@facstaff.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: Immunoprecipitation-quantitative?? Date: Fri, 03 Jan 97 17:20:38 GMT Organization: UW-Madison Lines: 19 Message-ID: <5ajis0$2pbk@news.doit.wisc.edu> References: <32ccbd2b.481197@news.univie.ac.at> NNTP-Posting-Host: martinlab.biochem.wisc.edu X-Newsreader: News Xpress Version 1.0 Beta #4 X-No-Archive: Yes In article <32ccbd2b.481197@news.univie.ac.at>, a8803349@unet.univie.ac.at (Martin Offterdinger) wrote: ->Hi ->I am wondering if it is possibble to set up a quantitative ->immunoprecipitaion to analyse the regulation of expression of a ->particular cell surface receptor: What I would like to do is to ->immunoprecipitate the receptor and do a western afterwards with ->hormone treated and untreated cells and compare the relative ->expression. Do you think that this would be an appribiate approach?? I'd be very sceptical of such approach and certainly would not trust results quantitatively. One poorly reproducible and highly non-linear technique (IP) on top of another highly non-linear (western). Most people have enough troubles introducing all sort of errors in "quantitative" westerns. However, if nothing else is feasible, I'd go for western alone, omitting IP as essentially redundant step. - Dima From owner-proteins@net.bio.net Thu Jan 02 22:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!news3.cac.psu.edu!news.cse.psu.edu!news.ece.nwu.edu!newsfeed.acns.nwu.edu!news.cc.uic.edu!usenet From: Keld Sorensen Newsgroups: bionet.molbio.proteins Subject: Re: separation of phosphorylated and non-phosphorylated peptide Date: Fri, 03 Jan 1997 10:03:44 +0000 Organization: University of Illinois, College of Medicine Lines: 38 Message-ID: <32CCD980.7F8B@uic.edu> References: <199612231757.MAA09819@clas.ufl.edu> NNTP-Posting-Host: slip-rock-09.dialin.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) To: jshao@BOTANY.UFL.EDU For kinase assays, most researchers use phosphocellulose filter paper to trap the peptide. Phosphocellulose is available in either sheets or as small filter units that fit inside an Eppendorf tube (Pierce Prod 29520). This works well for all basic peptides (carrying a positive charge at low pH) since the interaction is ionic. Note that the interaction is NOT specific for phosphorylated stuff. Phosphocellulose is also available in the format of a column (Whatman) - you may check with Dima on that (do a search on DejaNews for phosphocellulose). If you are looking for something that specifically interacts with phosphorylated stuff, you are looking at iron-IDA columns or filter papers. IDA matrices are available from a several manufacturers - Pierce sells a complete kit call "Phospho-gel" (Prod 44932) as well as just the IDA support. Other companies also sell just the IDA support. Pierce is also the only company that sells iron-IDA paper in the filter buckets for the Eppendorf tubes - this system can be used as really small columns. The tradename of the filters in the buckets is "SpinZyme" - if you do a search on JBC you will find about 12 or so references using them. There is also a new product out called INDIA- phosphoprobe-HRP. It is basically iron-IDA coupled onto HRP - should work for your westerns etc., but is not for purification. It is important to note that all phospho-compounds will stick to iron-IDA columns, and all basic molecules will stick to phosphocellulose...... so it is often hard to separate all the things you want separated in one session. Keld Sorensen. From owner-proteins@net.bio.net Thu Jan 02 22:00:00 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!cam-news-hub1.bbnplanet.com!howland.erols.net!vixen.cso.uiuc.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!martinlab From: klenchin@facstaff.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: DNA Software Date: Fri, 03 Jan 97 17:27:05 GMT Organization: UW-Madison Lines: 22 Message-ID: <5ajj83$2pbk@news.doit.wisc.edu> References: NNTP-Posting-Host: martinlab.biochem.wisc.edu X-Newsreader: News Xpress Version 1.0 Beta #4 X-No-Archive: Yes In article , tchorz@biotop.umcs.lublin.pl (Marek Tchorzewski) wrote: ->Dear Netters, -> ->First of all, Happy New Year 1997 to all of you !!! -> ->On the other hand, I need advice concerning programs ->for DNA and protein analysis. ->I am going to buy such program however I am not ->fully determined which program I should purchase. -> ->So far, I have seen DNAsis and DNAstar, however ->I am not sufficiently confident that these programs ->are reliable, and can provide me with the best options. Then, if you can run UNIX, buy GCG, which is supposed to be an "industry standard" among such suites. However, IMO, DNAstar is reliable and generally OK (meaning they all are bad, non-ideal, and anyway useless if user does not understand what he/she is doing, but... nothing's perfect). - Dima From owner-proteins@net.bio.net Thu Jan 02 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!visi.com!uunet!in2.uu.net!165.87.194.248!news-m01.ny.us.ibm.net!newsfeed.de.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: Immunoprecipitation-quantitative?? Date: Fri, 03 Jan 1997 08:07:27 GMT Organization: AKH Lines: 9 Message-ID: <32ccbd2b.481197@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 wondering if it is possibble to set up a quantitative immunoprecipitaion to analyse the regulation of expression of a particular cell surface receptor: What I would like to do is to immunoprecipitate the receptor and do a western afterwards with hormone treated and untreated cells and compare the relative expression. Do you think that this would be an appribiate approach?? Any contributions to this are appreciated!! Thank you -Martin From owner-proteins@net.bio.net Fri Jan 03 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.uoregon.edu!tezcat!feed1.news.erols.com!howland.erols.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!uunet!in3.uu.net!198.6.9.51!news.thepoint.net!news.iquest.net!ind-0007-25 From: vanfrank@iquest.net (Richard Van Frank) Newsgroups: bionet.molbio.proteins Subject: Re: protein problems on gels Date: 4 Jan 1997 17:55:38 GMT Organization: IQuest Network Services Lines: 15 Message-ID: <5am34l$8l0_001@ind-0007-25.iquest.net> References: <32CED947.24E1@jcu.edu.au> NNTP-Posting-Host: ind-0007-25.iquest.net X-Newsreader: News Xpress Version 1.0 Beta #4 In article <32CED947.24E1@jcu.edu.au>, lachlan harris wrote: >Can anyone help me with this problem? I have a pure microbial protein >which when run on an SDS non-reduced (ie no mercaptoethanol) PAGE gel >runs at approximately 50 KDa. When the same protein is run under >SDS-reduced conditions two subunits appear- one running at approx 40 KDa >and the other at approx 60 KDa. > >It was my understanding that the two subunits should add up to be the >same size as the protein run under SDS-non reduced conditons. But this >isn't happening. Does anyone know why? I don't believe this is a subunit problem. The subunit can't be larger than the original protein. I believe you are not geting a complete reduction but not knowing the conditons you are using I can't say for sure. Try more sever reduction conditions. From owner-proteins@net.bio.net Fri Jan 03 22:00:00 1997 Path: biosci!health.uem.mz!hmuking From: hmuking@health.uem.mz (hmuking) Newsgroups: bionet.molbio.proteins Subject: (none) Date: 4 Jan 1997 05:14:57 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701041313.FAA01845@net.bio.net> NNTP-Posting-Host: net.bio.net subscribe protein-analysis Humberto Muquingue end -------- JHumberto N.Muquingue MFACULDADE DE MEDICINA LCAIXLA POSTALJ 257 OMAPUTO KMOZAMBIQUE From owner-proteins@net.bio.net Sat Jan 04 22:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!cpk-news-feed1.bbnplanet.com!nih.gov!usenet From: Rod Levine Newsgroups: bionet.molbio.proteins Subject: Re: protein problems on gels Date: Sun, 05 Jan 1997 18:56:45 -0500 Organization: NIH Lines: 40 Message-ID: <32D03FBD.5B24@nih.gov> References: <32CED947.24E1@jcu.edu.au> Reply-To: rlevine@nih.gov NNTP-Posting-Host: slashppp99.nih.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) To: lachlan harris lachlan harris wrote: > > Can anyone help me with this problem? I have a pure microbial protein > which when run on an SDS non-reduced (ie no mercaptoethanol) PAGE gel > runs at approximately 50 KDa. When the same protein is run under > SDS-reduced conditions two subunits appear- one running at approx 40 KDa > and the other at approx 60 KDa. > > It was my understanding that the two subunits should add up to be the > same size as the protein run under SDS-non reduced conditons. But this > isn't happening. You could spend a fair bit of time sorting this one out. If you have access to a MALDI mass spec (perhaps in a core facility), the fastest solution would be to run the protein in the MALDI, with and without reduction. You'll likely get accurate molecular weights quickly, and with very little material used. If you can't get to a MALDI, then there are several possibilities which come to mind, none all that attractive, but the one I would consider first is this: 1) You do have a monomer whose true molecular weight is close to 60 kD. 2) Treatment with beta-mercaptoethanol reduces one or more disulfide bridges, allowing the protein to "open up" and run at 60 kD instead of 50 kD. 3) The 40 kD is an artifact -- a clipped form produced during beta-mercaptoethanol treatment. There is ample documentation of such artifacts in the literature. To reduce the chance of this happening, try adding 1 mM EDTA or DPTA in addition to the mercaptan (the reactions are generally catalyzed by trace concentration of transition metals). Also try to minimize or even eliminate the boiling step. Go for the MALDI if at all possible. Rod Levine NIH rlevine@nih.gov From owner-proteins@net.bio.net Sat Jan 04 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!news-stkh.gsl.net!news.gsl.net!news-paris.gsl.net!news.gsl.net!news-peer.gsl.net!news.gsl.net!howland.erols.net!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in2.uu.net!128.250.1.21!munnari.OZ.AU!news.unimelb.EDU.AU!wehi.edu.au!woozle.mel.dbe.csiro.au!whiskers From: Keith.Gough@mel.dbe.csiro.au (Keith Gough) Newsgroups: bionet.molbio.proteins Subject: Immobilised thrombin Date: Mon, 06 Jan 97 05:52:24 GMT Organization: CSIRO Lines: 5 Message-ID: <5aq3uo$mrc_002@mel.dbe.csiro.au> NNTP-Posting-Host: whiskers.mel.dbe.csiro.au X-Newsreader: News Xpress Version 1.0 Beta #3 Does anyone know of a commercial source of thrombim immobilised on agarose/acrylamide beads for easy removal of thrombin? Thanks Keith From owner-proteins@net.bio.net Sat Jan 04 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!masternews.telia.net!newssrv.ita.tip.net!down.spin.it!usenet From: Adriano Savoini Newsgroups: bionet.molbio.proteins Subject: Re: protein problems on gels Date: Sun, 05 Jan 1997 19:59:04 -0800 Organization: Spin - Trieste - Italy Lines: 21 Message-ID: <32D07888.1E00@up.spin.it> References: <32CED947.24E1@jcu.edu.au> NNTP-Posting-Host: ppp06.ts.spin.it Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win16; I) lachlan harris wrote: > > Can anyone help me with this problem? I have a pure microbial protein > which when run on an SDS non-reduced (ie no mercaptoethanol) PAGE gel > runs at approximately 50 KDa. When the same protein is run under > SDS-reduced conditions two subunits appear- one running at approx 40 KDa > and the other at approx 60 KDa. > > It was my understanding that the two subunits should add up to be the > same size as the protein run under SDS-non reduced conditons. But this > isn't happening. Does anyone know why? Hi lachlan, first check your "pure" preparation on an isofocussing gel to see if it is really pure.Second, purify the 50KDa band from the non reducing gel and rerun it on a reducing one, to be 100% sure you are dealing with the right molecule. A couple of times, this procedure let me know I had others things in the preparation. Ciao Adriano Savoini asavoini@up.spin.it From owner-proteins@net.bio.net Sun Jan 05 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeeds.sol.net!hammer.uoregon.edu!newsfeed.kreonet.re.kr!news.interpia.net!snunews.snu.ac.kr!not-for-mail From: "Lee, Ji Hyun" Newsgroups: bionet.molbio.proteins,bionet.cellbiol,bionet.microbiology Subject: Are small proteins underestimated on SDS-PAGE? Date: Tue, 07 Jan 1997 16:23:32 +0900 Organization: College of Pharmacy, Seoul National University Lines: 9 Message-ID: <32D1F9F4.6800@plaza.snu.ac.kr> Reply-To: newera@plaza.snu.ac.kr NNTP-Posting-Host: 147.46.8.60 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Xref: biosci bionet.molbio.proteins:9665 bionet.cellbiol:6362 bionet.microbiology:8399 When much proteins of large molecular weight co-exist, do proteins of small molecular weights tend to be underestimated on SDS-PAGE? In other words, compared to their absolute contents their bands look light in mixture of very much of other proteins but when only they are SDS-PAGEd their bands look dark despite of the same contents. Is it possible? What reference is helpful to me? Any comments will be appreciated. Thank you. From owner-proteins@net.bio.net Sun Jan 05 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeeds.sol.net!newspump.sol.net!howland.erols.net!newsfeed.internetmci.com!uunet!in3.uu.net!128.164.9.1!gwu.edu!mnrao From: mnrao@gwis2.circ.gwu.edu (Manjunath N.Rao) Newsgroups: bionet.molbio.proteins Subject: Protein sequencing Date: 6 Jan 1997 21:43:47 GMT Organization: The George Washington University, Washington DC Lines: 14 Message-ID: <5arrmj$6v5$1@cronkite.seas.gwu.edu> NNTP-Posting-Host: gwis2.circ.gwu.edu X-Newsreader: TIN [version 1.2 PL2] Hello everyone, I am in search of either University facilities or private companies that perform protein sequencing from the carboxyl end unlike the usual NH2 end. If anyone in this group is aware of such a facility and have used one such I would appreciate it very much if you can let me know. Thanks in advance. -- ******************************* Manjunath N.Rao ************************* From owner-proteins@net.bio.net Sun Jan 05 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!uunet!in1.uu.net!205.152.0.23!news.atl.bellsouth.net!news.mco.bellsouth.net!news.cha.bellsouth.net!news.mia.bellsouth.net!news.msy.bellsouth.net!newsrelay.iastate.edu!news.iastate.edu!news From: Charles Brockhouse Newsgroups: bionet.molbio.proteins Subject: APT paper Date: Mon, 06 Jan 1997 11:04:43 -0600 Organization: Entomology, Iowa State University Lines: 11 Message-ID: <32D130AB.1A7C@iastate.edu> Reply-To: chbrock@iastate.edu NNTP-Posting-Host: pc12050.ent.iastate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win16; I) Does anyone know a commercial source of aminophenylthioether cellulose paper? Thanks for the help. -- Charles L. Brockhouse Insect Genetics, Entomology Iowa State University Ames, IA., 50011-3222 Tel: (515) 294-4570 Fax: (515) 294-5957 From owner-proteins@net.bio.net Sun Jan 05 22:00:00 1997 Path: biosci!RYBURN.SWMED.EDU!Johnston#m#_Stephen From: Johnston#m#_Stephen@RYBURN.SWMED.EDU ("Johnston, Stephen") Newsgroups: bionet.molbio.proteins Subject: Research Associate Position Date: 6 Jan 1997 11:02:39 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Research Associate Position Open: I am looking for a PhD with a strong background in biochemistry/molecular biology to join my lab. The position involves developing protocols and technologies related to protein purification and analysis. The position is dynamic and involves interacting with several research areas in my and collaborating labs. The position can be permanent and evolve to a faculty slot. Full Univ. of Texas- Southwestern benefits are provided and the salary is quite competitive. The laboratory is in new, beautiful space and is equiped with the most up-to-date technologies. Southwestern is the most dynamic medical center in the country and a great place for research. For more information contact me by email (johnston@ryburn.swmed.edu) or call 214-648-1415. Professor Stephen Albert Johnston, Medicine and Biochemistry, UT-Southwestern Medical Center. From owner-proteins@net.bio.net Sun Jan 05 22:00:00 1997 Path: biosci!agate!howland.erols.net!feed1.news.erols.com!cwix!uunet!in2.uu.net!192.174.65.41!01-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: Re: Immunoprecipitation-quantitative?? Date: Tue, 07 Jan 1997 07:25:24 GMT Organization: AKH Lines: 25 Message-ID: <32d1f9bc.188722@news.univie.ac.at> References: <32ccbd2b.481197@news.univie.ac.at> <5ajis0$2pbk@news.doit.wisc.edu> NNTP-Posting-Host: grunt.imed1.akh-wien.ac.at X-Newsreader: Forte Free Agent 1.1/16.230 On Fri, 03 Jan 97 17:20:38 GMT, (Dima Klenchin) wrote: >In article <32ccbd2b.481197@news.univie.ac.at>, > a8803349@unet.univie.ac.at (Martin Offterdinger) wrote: >->Hi >->I am wondering if it is possibble to set up a quantitative >->immunoprecipitaion to analyse the regulation of expression of a >->particular cell surface receptor: What I would like to do is to >->immunoprecipitate the receptor and do a western afterwards with >->hormone treated and untreated cells and compare the relative >->expression. Do you think that this would be an appribiate approach?? > >I'd be very sceptical of such approach and certainly would not trust results >quantitatively. One poorly reproducible and highly non-linear technique >(IP) on top of another highly non-linear (western). Most people have enough >troubles introducing all sort of errors in "quantitative" westerns. >However, if nothing else is feasible, I'd go for western alone, omitting IP >as essentially redundant step. > >- Dima > The problem is that Western alone would not be sufficient sensitive to detect the receptor-therefore I do not think that IP is a redundant step-I would like to use it essenitally to increase sensitivity. Martin From owner-proteins@net.bio.net Sun Jan 05 22:00:00 1997 Path: biosci!agate!howland.erols.net!news3.cac.psu.edu!usenet From: "Steven F. Goldberg" Newsgroups: bionet.molbio.proteins Subject: GST-SH3 fusions Date: Mon, 06 Jan 1997 19:42:50 -0500 Organization: Penn State University, Center for Academic Computing Lines: 20 Message-ID: <32D19C0A.520E@psu.edu> Reply-To: sgoldberg@psu.edu NNTP-Posting-Host: br2-xyp-ts1-p12.nb.hmc.psu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) I am a graduate student working in a lab that has recently discovered a novel human melanoma metastasis suppressor gene ("KiSS-1" - JNCI (1996) 88: 1731-1737), the predicted protein of which contains a consensus sequence indicative of an SH3 ligand. As part of my thesis research, I intend to identify proteins that interact with KiSS-1. Therefore, I am trying to assemble a panel of GST fusions of proteins containing SH3 domains (e.g. src, abl, lyn) with which to determine 1) whether KiSS-1 binds an SH3 domain, and 2) the binding specificity of such interaction. I would be very interested in hearing from anybody who might be willing to make such a GST-SH3 fusion available to me for these experiments. Thank you very much for your time and consideration. Steven F. Goldberg sgoldberg@psu.edu Penn State College of Medicine Hershey, Pennsylvania From owner-proteins@net.bio.net Sun Jan 05 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!uunet!in1.uu.net!128.196.139.12!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!news From: "Chong K. Jue" Newsgroups: bionet.molbio.proteins Subject: Re: DNA Software Date: Mon, 06 Jan 1997 12:19:36 -0800 Organization: Hunter College Lines: 56 Message-ID: <32D15E58.3F7@genectr.hunter.cuny.edu> References: NNTP-Posting-Host: 146.95.14.153 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) Marek Tchorzewski wrote: > > Dear Netters, > > First of all, Happy New Year 1997 to all of you !!! > > On the other hand, I need advice concerning programs > for DNA and protein analysis. > I am going to buy such program however I am not > fully determined which program I should purchase. > > So far, I have seen DNAsis and DNAstar, however > I am not sufficiently confident that these programs > are reliable, and can provide me with the best options. > > So, could you advice me, which programs is actually > the best on the market. > > Marek Tchorzewski PhD > Univ. of Maria Curie-Sklodowska > Dept. of Molecular Biology > Lublin, Poland It sounds to me that you are working with a personal computer with access to some kind of network that connects you to the Internet. I've been working with GCG for a number of years and I think it is generally good. I used to run GCG in a VAX minicomputer through the institute network and it wasn't too bad. It is certainly not like Mac or Windows, and commands are not too obviously(no pull down menu). These days I am running GCG in a UNIX environment, and UNIX is a pain for people like me(The author of "UNIX for Dummy" did say that she used to hate it and love it now after she learnt it). Some of the programs for multiple sequence alignments and comparisons, such as GAP, PILEUP and PRETTY, in GCG are really powerful. I am not aware of other programs that would match it. If your school has GCG in the network, that would be great. If your school does not, you need to talk to other schools that provide such programs. Hopefully, they'll give you an account so that you can use their computer. In addition, you have to install a software in your computer to connect to computers in other schools. TELNET is commonly used for Windows and Versaterm is common for Mac. On the other hand, if you spend most of your time constructing plasmid, looking of cut sites, and generate plasmid graphic on computer, Generunner is pretty good for Windows platform. If you have a Mac, try Gene Construction Kit or MacVector. All of those programs are relatively user friendly. I rarely have to use the the manual to figure out how to get things done in these programs, unlike GCG. Of course, you can buy as many programs as you like. Hope it helps. Chong ---- Chong K. Jue Dept of Biological Sciences Hunter College New York, NY 10021 Email: jue@genectr.hunter.cuny.edu From owner-proteins@net.bio.net Mon Jan 06 22:00:00 1997 Path: biosci!agate!spool.mu.edu!newspump.sol.net!howland.erols.net!worldnet.att.net!cbgw2.lucent.com!news.bu.edu!usenet From: Hector Lucero Newsgroups: bionet.molbio.proteins Subject: Searching for a Dot Plot for protein Date: Tue, 07 Jan 1997 22:44:45 -0800 Organization: Boston University Lines: 9 Message-ID: <32D3425D.5637@acs.bu.edu> Reply-To: hlucero@acs.bu.edu NNTP-Posting-Host: ppp-77-32.bu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I; 16bit) Hi there, I need to search for internal sequence homology in my protein sequence. Does anybody knows about a server that has a Dot Plot program for protein sequence analysis?. Thanks in advance Hector From owner-proteins@net.bio.net Mon Jan 06 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsxfer3.itd.umich.edu!news.itd.umich.edu!usenet From: Rachel Ogorzalek Loo Newsgroups: bionet.molbio.proteins Subject: Re: Protein sequencing Date: 7 Jan 1997 13:50:54 GMT Organization: University of Michigan Lines: 9 Message-ID: <5atkbu$7p0@lastactionhero.rs.itd.umich.edu> References: <5arrmj$6v5$1@cronkite.seas.gwu.edu> NNTP-Posting-Host: host-50.subnet-33.med.umich.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1 (Windows; U; 16bit) The University of Michigan Protein and Carbohydrate Structure Facility http://www.brcf.med.umich.edu offers C-terminal sequencing as a service. Contact Charles Mitchell at (313) 763-6710 (313) 936-2638 FAX From owner-proteins@net.bio.net Mon Jan 06 22:00:00 1997 Path: biosci!agate!howland.erols.net!usenet.kornet.nm.kr!snunews.snu.ac.kr!not-for-mail From: "Lee, Ji Hyun" Newsgroups: bionet.molbio.proteins,bionet.cellbiol,bionet.microbiology Subject: Small proteins are underestimated on SDS-PAGE? Date: Tue, 07 Jan 1997 21:40:04 +0900 Organization: College of Pharmacy, Seoul National University Lines: 19 Message-ID: <32D24424.A19@plaza.snu.ac.kr> Reply-To: newera@plaza.snu.ac.kr NNTP-Posting-Host: 147.46.8.60 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Xref: biosci bionet.molbio.proteins:9667 bionet.cellbiol:6364 bionet.microbiology:8400 When much proteins of large molecular weight co-exist, do proteins of small molecular weights(6500 dalton) tend to be underestimated on SDS-PAGE? In other words, compared to their absolute contents their bands look light in mixture of very much of other proteins but when only they are SDS-PAGEd their bands look dark despite of the same contents. Is it possible? Any comments and any reference will be appreciated. Thank you. From owner-proteins@net.bio.net Mon Jan 06 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!hunter.premier.net!news.sprintlink.net!news-peer.sprintlink.net!EU.net!sun4nl!Inter.NL.net!sci.kun.nl!not-for-mail From: ronsmul@sci.kun.nl (Ronald Smulders) Newsgroups: bionet.molbio.proteins Subject: CD analysis of beta-sheet Date: 7 Jan 1997 16:36:11 +0100 Organization: University of Nijmegen, The Netherlands Lines: 13 Message-ID: <5atqhb$fj1@wn2.sci.kun.nl> NNTP-Posting-Host: wn2.sci.kun.nl X-Newsreader: NN version 6.5.0 #7 (NOV) Hi CD experts I'm working on a typical beta-sheet protein. So the CD spectrum displays a minimum at about 218 nm and the curve crosses the x-axis at about 200 nm. Now, when we analyze the protein after a period of heat exposure we see an increase of the amplitude: so the spectrum does not shift but only the ellipticity increases. Does anyone know how to interprete this result? Does this result indicate that the amount of random coil increases upon heating? Thanks in advance for your comments Ronald Smulders, The University of Nijmegen From owner-proteins@net.bio.net Mon Jan 06 22:00:00 1997 Newsgroups: bionet.molbio.proteins Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!vixen.cso.uiuc.edu!uwm.edu!news.he.net!nr1.scn.co.jp!news01.so-net.or.jp!sinfony-news01!wnoc-tyo-news!news.imnet.ad.jp!gan!ksasaki From: ksasaki@ncc.go.jp Subject: Re: Immunoprecipitation-quantitative?? X-Sender: ksasaki@gan2.ncc.go.jp Content-Type: text/plain; charset=iso-2022-jp To: bionet-molbio-proteins@gan1.ncc.go.jp Message-ID: <9701080417.AA26319@gan1.ncc.go.jp> Sender: ksasaki@gan.ncc.go.jp (Kazuki Sasaki) Organization: National Cancer Center JAPAN Mime-Version: 1.0 Date: Wed, 8 Jan 1997 04:17:04 GMT Return-Path: X-Mailer: Eudora-J(1.3.3J7) Return-Receipt-To: ksasaki@ncc.go.jp Lines: 31 >>->I am wondering if it is possibble to set up a quantitative >>->immunoprecipitaion to analyse the regulation of expression of a >>->particular cell surface receptor: What I would like to do is to >>->immunoprecipitate the receptor and do a western afterwards with >>->hormone treated and untreated cells and compare the relative >>->expression. Do you think that this would be an appribiate approach?? >>I'd be very sceptical of such approach and certainly would not trust results >>quantitatively. One poorly reproducible and highly non-linear technique >>(IP) on top of another highly non-linear (western). I wish to know why you are so skeptical about western. I don't think western is HIGHLY non-linear so far as you determine the linearlity range of the amount relative to the density of a band in advance. >The problem is that Western alone would not be sufficient sensitive to >detect the receptor-therefore I do not think that IP is a redundant >step-I would like to use it essenitally to increase sensitivity. If your protein of interest cannnot be detected without IP (that is, using more lysate than in western), IP followed by western for normalization seems feasible. I've been there with a kind of receptor tyrosine kinase. There are a number of papers taking your approach for relative quantitation. Kazuki From owner-proteins@net.bio.net Mon Jan 06 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!news-xfer.netaxs.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in3.uu.net!129.63.1.1!ulowell.uml.edu!news.cs.umb.edu!oitnews.harvard.edu!das-news2.harvard.edu!fas-news.harvard.edu!fas!vsolomon From: vsolomon@fas.harvard.edu (Vincent Solomon) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Baculovirus questions Date: 8 Jan 1997 01:36:45 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 37 Message-ID: <5autnd$kba@decaxp.harvard.edu> NNTP-Posting-Host: fas.harvard.edu X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.methds-reagnts:53208 bionet.molbio.proteins:9670 I'm looking to start expressing & purifying some proteins via the baculovirus system. I've never done this before and so I thought someone experienced with this system might be able to answer a few questions. 1) Which system works the best and is the most cost-efficient? A friend of mine uses the Pharmingen system and is happy with it. From what I understand, the limiting and most costly reagent is the linear baculovirus DNA, which costs about $300 for 5 transfections (we already have access to the rest of the reagents, including insect cells). I've also been looking at this system from Gibco called Bac-to-Bac. It does all the necessary recombination in bacteria rather than insect cells and so doesn't require the linear baculo DNA. However, their kit costs almost $500 and also limits you to 5 transfections. From what I understand, the limiting reagent in their kit are the competent bacteria that contain the baculo DNA, but it seems to me that one should be able to grow more of these bugs and thus make as many different proteins as you want from this single kit. Anyone know anything about this? 2) The proteins I'm most interested in producing are transmembrane glycoproteins that are highly modified by glycosylation and disulfide bonds. Which of the various baculovirus promoters should I use? I've read that while the very late promoters like polyhedron give you more yield, the late promoters like the basic protein promoter and the 39k protein promoter give you better post-translational modifications and may be a better choice for proteins that are highly modified. Also, would there be any benefit to using baculovirus signal peptides rather that WT signal peptides for this type of protein? Thanks in advance for any feedback at all on these questions. I hope I can return the favor in the future. Vince Solomon Microbiology & Molecular Genetics Harvard Med School -- From owner-proteins@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!biosci!not-for-mail From: Chana Gabay Newsgroups: bionet.immunology,bionet.molbio.proteins,bionet.molecules.peptides,bionet.software Subject: help: Replacement to Silent ratio calculation Date: 8 Jan 1997 23:07:38 -0800 Organization: The hebrew University of Jerusalem Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <5b25fq$c5@net.bio.net> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.immunology:10607 bionet.molbio.proteins:9678 bionet.molecules.peptides:589 bionet.software:17562 Dear Netters, We are interested in finding the R/S (R=replacement, S= silent) ratio of somatic point mutations in the immunoglobulin variable region genes. This is done by aligning the DNA sequence of the mutated gene to its germline counterpart defining its mutations, and determining their type (replacement or silent mutation). This is done by translating the sequence into a protein and comparing it to the translation of the germline sequence. (A silent mutation in the DNA will produce the same amino acid as is in the germline, while a replacement mutation will give rise to a different amino acid.) Since the random mutation frequency differs for each of the 4 DNA nucleotide bases, one has to introduce these frequencies into the calculation to obtain the expected R/S value for the studied gene. These calculations which lead to determination of the R/S values due to random mutations, could then be compared with the actual R/S ratio and large divergence from the expected random R/S value would suggest that a positive or negative selection process is taking place. I would like to know whether there is an available computer program to calculate the random R/S ratio, and from whom it can be obtained. I would appreciate if anyone could point me in the right direction and please, Cc: to me by e-mail chana_g@gene.md.huji.ac.il -------------------------- as well as to newsgroups. Thanks in advance, Chana Gabay From owner-proteins@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!arclight.uoregon.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in3.uu.net!138.133.17.7!amgen!usenet From: John Philo Newsgroups: bionet.molbio.proteins Subject: Re: CD analysis of beta-sheet Date: Wed, 08 Jan 1997 15:25:23 -0800 Organization: Amgen Inc. Lines: 46 Message-ID: <32D42CE3.3958@amgen.com> References: <5atqhb$fj1@wn2.sci.kun.nl> Reply-To: jphilo@amgen.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) To: Ronald Smulders Ronald Smulders wrote: > > Hi CD experts > > I'm working on a typical beta-sheet protein. So the CD spectrum displays a > minimum at about 218 nm and the curve crosses the x-axis at about 200 nm. > Now, when we analyze the protein after a period of heat exposure we see > an increase of the amplitude: so the spectrum does not shift but only the > ellipticity increases. Does anyone know how to interprete this result? Does > this result indicate that the amount of random coil increases upon heating? > > Thanks in advance for your comments > > Ronald Smulders, The University of Nijmegen No claim here to be a CD 'expert', but I can think of two explanations: 1) one possible trivial explanation is that the protein concentration increased when you heated the sample due to evaporation of water. Obviously whether this is the true explanation depends on exactly how you did the experiment, but this can happen more easily than you might think. 2) The more likely explanation is that you are forming denatured forms of the protein that contain more beta sheet. It is quite common for heat-denatured proteins to form very stable intermolecular beta sheets, so beta sheet content can rise even though you are denaturing the protein. Usually when this happens the light scattering goes up as aggregates are formed, and this may lead to higher photomultiplier voltages to compensate for the loss of light due to scattering. Many CD instruments save a record of the PM voltage during the scan, so you might look at that. If indeed you are forming denatured states, you should see significant changes in the tertiary structure peaks in the near-uv CD spectrum. If you could possibly get someone to do FTIR spectra on this protein that would help a lot. FTIR is generally much better at picking up beta structure, and can often distinguish parallel from anti-parallel. FTIR is complementary to CD, which is very good at alpha helix but not so good at beta sheet. ' Hope this helps. Good luck. John Philo, Protein Chemistry Amgen Inc., Thousand Oaks, CA jphilo@amgen.com *** Disclaimer: These are the opinions of the poster not Amgen Inc.*** From owner-proteins@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsserver.jvnc.net!netnews.sbphrd.com!news From: William P Prichett Newsgroups: bionet.software,bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: ?? Kinetics Software - Post Date: Wed, 08 Jan 1997 15:29:26 -0800 Organization: SmithKline Beecham Lines: 9 Message-ID: <32D42DD6.70A3@sbphrd.com> References: <32AEF4BF.5C7A@apl.washington.edu> <32BF3C94.4319@cam.org> NNTP-Posting-Host: ued656.um.us.sbphrd.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) Xref: biosci bionet.software:17559 bionet.molbio.proteins:9675 bionet.molbio.methds-reagnts:53251 I would like to add to the list of Kaliedagraph users. I really like the easy of use, especially the non linear curve fit. Very simple. Synergy is at http://www.synergy.com/ Good Luck, Bill From owner-proteins@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!ROCKVAX.ROCKEFELLER.EDU!terkuil From: terkuil@ROCKVAX.ROCKEFELLER.EDU (Benno ter Kuile) Newsgroups: bionet.molbio.proteins Subject: Malate synthase Date: 8 Jan 1997 06:46:23 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701081446.JAA23917@rockvax.rockefeller.edu> NNTP-Posting-Host: net.bio.net I am looking for a protocol for measuring the activity of malate synthase and would obviously be very grateful if someone could provide one. I am not a subscriber to this group, so please send any replies directly to me. Thanks in advance, Benno ter Kuile From owner-proteins@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!agate!howland.erols.net!feed1.news.erols.com!news.bconnex.net!clicnet!news.clic.net!rcogate.rco.qc.ca!altitude!usenet From: "Achim Recktenwald, PhD" Newsgroups: bionet.molbio.proteins,bionet.cellbiol,bionet.microbiology Subject: Re: Are small proteins underestimated on SDS-PAGE? Date: Wed, 08 Jan 1997 07:57:40 -0500 Organization: IBEX Technologies, Inc., Biochemistry, 5485 Pare, Montreal, PQ, H4P 1P7, Canada Lines: 19 Message-ID: <32D399C3.ACD@ibex.ca> References: <32D1F9F4.6800@plaza.snu.ac.kr> NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) To: newera@plaza.snu.ac.kr Xref: biosci bionet.molbio.proteins:9673 bionet.cellbiol:6371 bionet.microbiology:8428 Lee, Ji Hyun wrote: > > When much proteins of large molecular weight co-exist, do proteins of > small molecular weights tend to be underestimated on SDS-PAGE? In other > words, compared to their absolute contents their bands look light in > mixture of very much of other proteins but when only they are SDS-PAGEd > their bands look dark despite of the same contents. > Is it possible? What reference is helpful to me? > Any comments will be appreciated. > > Thank you. Though I cannot give you a literature reference, from my own experience I think this to be true. Achim From owner-proteins@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!sn.no!news-stkh.gsl.net!news.gsl.net!news-paris.gsl.net!news.gsl.net!news-peer.gsl.net!news.gsl.net!news.sprintlink.net!news-peer.sprintlink.net!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!mindspring!newspump.sol.net!newsfeeds.sol.net!ix.netcom.com!news From: derek12@ix.netcom.com(Russell Lamar Howard) Newsgroups: bionet.molbio.proteins Subject: RE:TCA precipitation Date: 9 Jan 1997 02:14:38 GMT Organization: Netcom Lines: 3 Message-ID: <5b1kae$kqd@sjx-ixn4.ix.netcom.com> NNTP-Posting-Host: atl-ga24-23.ix.netcom.com X-NETCOM-Date: Wed Jan 08 6:14:38 PM PST 1997 I need some info on TCA precip. I'm fairly new at it and would like a "generic" method to using it. Also, what is a SDS_page From owner-proteins@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!hermod.uio.no!nntp.uio.no!news-feed.inet.tele.dk!arclight.uoregon.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!howland.erols.net!cs.utexas.edu!geraldo.cc.utexas.edu!netnews.uthscsa.edu!usenet From: Jeff Seale Newsgroups: bionet.molbio.proteins,bionet.microbiology,bionet.immunology,sci.bio.microbiology,bionet.general Subject: Chaperonin Web Page Date: Thu, 09 Jan 1997 10:07:42 -0800 Organization: University of Texas Health Science Center at San Antonio Lines: 10 Message-ID: <32D533EE.432E@bioc02.uthscsa.edu> NNTP-Posting-Host: horowitz-lab1.uthscsa.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win16; I) Xref: biosci bionet.molbio.proteins:9681 bionet.microbiology:8440 bionet.immunology:10610 sci.bio.microbiology:5050 bionet.general:25066 There have been a few recent additions to the Chaperonin Web Page. The latest addition is a page that contains links to the Web pages of chaperonin/heat shock protein researchers. If you are working in the field of heat shock proteins and your lab has a web page that details your work, please email me the URL and I'll add it to the page. You can see the Chaperonin Web Page at: http://bioc09.uthscsa.edu/~seale/Chap/chap.html -Jeff From owner-proteins@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!agate!howland.erols.net!surfnet.nl!highway.leidenuniv.nl!ruly46!mirihyel From: Peter Hohenstein Newsgroups: bionet.molbio.proteins Subject: 35S metabolic labeling of ES cells Date: Thu, 9 Jan 1997 17:07:28 +0100 Organization: Leiden University, The Netherlands Lines: 17 Message-ID: NNTP-Posting-Host: ruly46.medfac.leidenuniv.nl Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: mirihyel@ruly46 Hi, I'm planning to use 35S metabolic labeled ES (embryonal stemcells - murine) cells for an immunprecipitation. Is there anybody having experience with labeling of ES cells? Thanks for any info Peter Hohenstein Dept. Human Genetics University of Leiden The Netherlands tel. (+)31 71 5276086 From owner-proteins@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!su-news-feed4.bbnplanet.com!jeeves.usfca.edu!news From: Michelle Chihara Newsgroups: bionet.molbio.proteins Subject: micro N-term procedure? Date: Thu, 09 Jan 1997 13:54:08 -0700 Organization: Tripod Lines: 6 Message-ID: <32D55AEF.2251@tripod.com> Reply-To: michelle@tripod.com NNTP-Posting-Host: chihara.hip.berkeley.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) I am looking for a simple procedure to do N-terminal determination on proteins after non-denaturing PAGE. Can anyone point me at a good protocol? Thanks. Please reply to: Chihara@usfca.edu From owner-proteins@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!news.uoregon.edu!news.rediris.es!news.cica.es!news From: "Biol. Cel." Newsgroups: bionet.molbio.proteins Subject: searching postdoctoral position Date: Thu, 09 Jan 1997 08:39:51 -0800 Organization: Centro Informatico Cientifico de Andalucia Lines: 25 Message-ID: <32D51F57.7AD6@lucano.uco.es> Reply-To: bc2biced@lucano.uco.es NNTP-Posting-Host: ciebce04.uco.es Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0 (Win16; I) I am looking for a post-doc position at a research group of biochemistry, molecular or cell biology that are working with cell differentiation or apoptosis preferably. At this time I am working in Dr. P. Navas’ lab (Dept Cell Biology, Univ. Cordoba Spain) in cell differentiation induced by vitamin D3 and the possible potentiative role of antioxidants as helpers in this process, also I colaborate in other subjects suc apoptosis. This work includes analysis of factors like: proteins, gene regulation, secons messengers, immunology, etc. I have a background in flow cytometry, enzymology, HPLC, electrophoresis, western and northern and other standard methods in cell biology. I could obtain a post-doctoral fellowship of ECC or Spanish Ministry of Education and Science. I could start in the next September or at the beginning of the next year, after obtain my PhD degree. Yours sincerely, Guillermo López Lluch My CV and a detailed application is available on request under my e-mail address (bc2lollg@lucano.uco.es). From owner-proteins@net.bio.net Wed Jan 08 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!news-peer.gsl.net!news.gsl.net!news-penn.gsl.net!news.gsl.net!news.NetVision.net.il!news From: Mark Klein Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.molbio.rapd Subject: FREE pH measurement booklet Date: 9 Jan 1997 10:49:48 GMT Organization: NetVision LTD. Lines: 9 Message-ID: <5b2igc$2bp@news.NetVision.net.il> NNTP-Posting-Host: ts006p13.pop2a.netvision.net.il Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.2N (Windows; I; 16bit) Xref: biosci bionet.molbio.methds-reagnts:53275 bionet.molbio.proteins:9679 bionet.molbio.rapd:1770 A free pH booklet is available which contains valuable information on basic pH measurement theory, pH measurement techniques, selecting the proper pH electode for a particular application, and a pH troubleshooting guide. The booklet is available from Lazar Research Labs. Inc. by emailing service@lazarlab.com or faxing 1-213-931-1434. The booklet can also be obtained from the Lazar web site at http://www.lazarlab.com From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!rutgers!gatech!news.sprintlink.net!news-peer.sprintlink.net!worldnet.att.net!arclight.uoregon.edu!newsfeed.direct.ca!torn!ccshst05.cs.uoguelph.ca!ccshst01!wyu From: wyu@uoguelph.ca (Wenjin Yu) Newsgroups: bionet.molbio.proteins Subject: Help Date: 10 Jan 1997 12:38:11 GMT Organization: University of Guelph Lines: 25 Message-ID: <5b5d7j$4ek@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: ccshst01.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] Dear colleagues, We've isolated and cDNA encoding a protein which should have a weight of 25 kD dased on computer program calculation. However, after we did Western blot using antibodies specific to this protein we got a 33kD band on SDS-PAGE (under reduced conditions). Although this protein is a glycoprotein, it shouldn't change so much since only one glyco-site was found. Does any one can explain this for me? Any suggestions are highly appreciated. Please respond by e-mail. Wenjin Yu ================================================================== || Wen-Jin Yu * E-Mail: wyu@uoguelph.ca || || Dept. of Botany * Tel.(home): (519)836-2868 || || University of Guelph * Tel.(work): (519)824-4120, x4779 || || Guelph, Ont. Canada * Fax: (519)767-1991 || || N1G 2W1 * URL: http://www.uoguelph.ca/~wyu || ================================================================== From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!sol.ctr.columbia.edu!spool.mu.edu!newspump.sol.net!howland.erols.net!worldnet.att.net!news.alt.net!usenet From: Rick Bright Newsgroups: bionet.molbio.proteins Subject: low salt deproteinating Date: Fri, 10 Jan 1997 09:56:30 -0600 Organization: Auburn University at Montgomery Lines: 8 Message-ID: <32D666AE.EAB@mnw.net> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win95; I) I am trying to find a technique to deproteinate extracted DNA using a low salt solution in the place of proteinase. Does anyone have a reference for a protocol? Thank you. Rick Bright rbright@mnw.net From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!hermod.uio.no!nntp.uio.no!news-feed.inet.tele.dk!arclight.uoregon.edu!news.sprintlink.net!news-peer.sprintlink.net!howland.erols.net!spool.mu.edu!usenet.eel.ufl.edu!usenet.nerdc.ufl.edu!usenet.ufl.edu!usenet From: Daniel Lackner Newsgroups: bionet.molbio.proteins Subject: Re: DNA Software Date: Fri, 10 Jan 1997 10:45:14 -0500 Organization: University of Florida Lines: 36 Message-ID: <32D66409.5D7E@nersp.nerdc.ufl.edu> References: NNTP-Posting-Host: muzyczk2.molegen.ufl.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Marek Tchorzewski wrote: > > Dear Netters, > > First of all, Happy New Year 1997 to all of you !!! > > On the other hand, I need advice concerning programs > for DNA and protein analysis. > I am going to buy such program however I am not > fully determined which program I should purchase. > > So far, I have seen DNAsis and DNAstar, however > I am not sufficiently confident that these programs > are reliable, and can provide me with the best options. > > So, could you advice me, which programs is actually > the best on the market. > > Marek Tchorzewski PhD > Univ. of Maria Curie-Sklodowska > Dept. of Molecular Biology > Lublin, Poland Dear Dr. Tchorzewski: In our lab, we have found the DNAsis program to be OK in protein analysis but the worst in its analysis in DNA and primer design. The main problem is the company expects the buyer to also purchase another $800 CD for the protein database. If i could do it all over again, i would buy a program that allows direct internet connections with NCBI to import protein database info. For DNA analysis, i feel that Vector NTI is the best program on the market. Daniel Lackner University of Florida From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!rutgers!gatech!arclight.uoregon.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!howland.erols.net!swrinde!sdd.hp.com!night.primate.wisc.edu!ames!purdue!mozo.cc.purdue.edu!news From: alan friedman Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: NEB IMPACT 1 intein expression system Date: Fri, 10 Jan 1997 10:54:43 -0600 Organization: Purdue University Lines: 6 Message-ID: <32D66CEC.650F@bilbo.bio.purdue.edu> Reply-To: afried@bilbo.bio.purdue.edu NNTP-Posting-Host: friedman.bio.purdue.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Macintosh; I; PPC) Xref: biosci bionet.molbio.methds-reagnts:53339 bionet.molbio.proteins:9686 I'm looking for any experience that people have had with the NEB intein expression/cleavage system. It looks like a great idea. I'm very curious to hear how it works in practice. Thanks. alan friedman From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!SEDONA.NET!rathbun From: rathbun@SEDONA.NET (RS&A) Newsgroups: bionet.molbio.proteins Subject: Position: HPLC/GC Scientist Date: 10 Jan 1997 23:22:23 -0800 Organization: Sedona Internet Services, Inc. Lines: 66 Sender: daemon@net.bio.net Distribution: world Message-ID: <32D74031.3B84@sedona.net> Reply-To: rathbun@sedona.net NNTP-Posting-Host: net.bio.net Analytical Assay Development = Associate Scientist We are seeking a scientist experienced in the development, optimization and validation of analytical chromatography assays to support our biopharmaceutical client company=92s recombinant products. General Job Responsibilities/Requirements = =B7 Develop HPLC, GC, & electrophoretic assays such as SDS-PAGE, western blot, IEF, CE, amino acid analysis, and monosaccharide analysis. = =B7 Analytical methods development, optimization, & validation to support= Phase I, II, and III clinical products (monoclonal antibodies and subunit vaccines). Assays pertain to both product characterization and measurement of trace levels of process contaminants. =B7 Supervise 6 bench scientists (levels B.S., M.S., and Ph.D.). = = =B7 Provide significant intellectual input to methods development; critically review all analytical results. = =B7 Have solid experience in working in a GMP/GCP laboratory. = = =B7 Write SOPs, validation protocols and reports, and analytical sections= of IND and BLA submissions. REQUIRED: =B7 Ph.D. in a biological or chemical science; preferably analytical chemistry, biochemistry, chemistry, chemical engineering or MS-level candidate with a strong track record. =B7 4 or more years of pharmaceutical/biotechnology work experience company. = = =B7 Supervisory experience (2 or more employees). If you have an interest in this or other opportunities, please email your resume as an attached file or mail/FAX your CV/resume to RS&A to the attention of Ann G. Rathbun, Managing Director. All correspondence is held in strict confidence. Rathbun, Sapir & Associates = P.O. Box 2337 Sedona, AZ 86339-2337 * USA = (520) 284-3360 Office (520)284-3361 FAX E-mail: rathbun@ sedona.net From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!SEDONA.NET!rathbun From: rathbun@SEDONA.NET (RS&A) Newsgroups: bionet.molbio.proteins Subject: Position: Immuno- & Cell-based Assay Scientist Date: 10 Jan 1997 23:21:48 -0800 Organization: Sedona Internet Services, Inc. Lines: 59 Sender: daemon@net.bio.net Distribution: world Message-ID: <32D7400C.65D6@sedona.net> Reply-To: rathbun@sedona.net NNTP-Posting-Host: net.bio.net Immunoassay Development Scientist We are seeking a scientist experienced in the development, optimization and validation of Immunoassays and cell-based Bioassays for the characterization/quantification of our biopharmaceutical client company=92s recombinant products. General Job Responsibilities/Requirements = =B7 Develop biological and immunological based assays such as cell/receptor binding, cytotoxicity, & MLR. Current assay formats include ELISA, RIA, Hemagglutination, western blots, Threshold Systems, etc. =B7 Supervise 7 bench scientists including 1 PhD and 1 MS = = =B7 Provide significant intellectual input to methods development; critically review all analytical results. = =B7 Have solid experience in working in a GMP/GCP laboratory. = = =B7 Write SOPs, validation protocols and reports, and analytical sections= of IND and BLA submissions. REQUIRED: =B7 Ph.D. in a biological or chemical science; preferably analytical chemistry, biochemistry, chemistry, chemical engineering or MS-level candidate with a strong track record. =B7 4 or more years of pharmaceutical/biotechnology work experience company. = = =B7 Supervisory experience (2 or more employees). If you have an interest in this or other opportunities, please email your resume as an attached file or mail/FAX your CV/resume to RS&A to the attention of Ann G. Rathbun, Managing Director. All correspondence is held in strict confidence. Rathbun, Sapir & Associates = P.O. Box 2337 Sedona, AZ 86339-2337 * USA = (520) 284-3360 Office (520)284-3361 FAX E-mail: rathbun@ sedona.net From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!nntp.uio.no!news.radio.cz!CESspool!news-feed.inet.tele.dk!news.algonet.se!hammer.uoregon.edu!news-xfer.netaxs.com!feed1.news.erols.com!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!sol.ctr.columbia.edu!spool.mu.edu!usenet.eel.ufl.edu!usenet.nerdc.ufl.edu!usenet.ufl.edu!mitzi.rsmas.miami.edu!miasun.med.miami.edu!newssun!tguettou From: Toumy Guettouche Newsgroups: bionet.molbio.proteins Subject: Re: Affi-Chromat. with antibodys???? Date: Fri, 10 Jan 1997 19:51:57 -0500 Organization: University of Miami, School of Medicine Lines: 37 Message-ID: NNTP-Posting-Host: newssun.med.miami.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <1997Jan10.173801@crick.rz-berlin.mpg.de> On 10 Jan 1997 jaensch@mpimg-berlin-dahlem.mpg.de wrote: > I would like to purify a protein complex with the help of affinity > chromatography. Therefore, I coupled an antibody, which recognizes one subunit > to CNBR-Sepharose (Pharmacia). > I have the following questions in this regard: > > 1. Is it resonable to couple antibodys to CNBR-Sepharose? This is pretty common. You could also use a crosslinker (NHS-Ester) to link your antibody to beads. This has the advantage that you have a spacer between your bead and the antibody which decreases steric hindrance. > > 2. Which buffers are recommended for the affinity binding and for the elution That depends on your protein. Typically people use 10-50mM Tris pH7-8, or TBS or Hepes with about 150mM NaCl or KCl to decrease nonspecific binding. you can also add glycerol to stabilize your protein. Detergents like Tween and Triton-X help reducing non-specific binding. Elution is usually done with 10mM Glycine pH 2.8-3 and immediate neutralisation after elution. If you have a peptide you can also elute by competing off your protein, which is more gentle , but leaves you with the problem of peptide removal. There is also a buffer from Pierce that is supposed to be pretty gentle for elution, hence the name Gentle buffer. you might want to check out some literature, like "Antibodies, A Laboratory Manual" by Ed Harlow and David Lane. Some companies (e.g Pharmacia, Biorad, Pierce) also have pretty good handbooks. Hope that helps Toumy From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!insync!news-feed.inet.tele.dk!news.algonet.se!eua.ericsson.se!erinews.ericsson.se!newsfeed.sunet.se!news99.sunet.se!news.funet.fi!news.kbfi.ee!kadri.ut.ee!tamm!tpungas From: tpungas@tamm.eenet.ee (Tanel Pungas) Newsgroups: bionet.molbio.proteins Subject: CDNB Assay for GST Date: 10 Jan 1997 16:00:07 GMT Organization: Estonian Biocentre Lines: 13 Message-ID: <5b5p27$oh0@kadri.ut.ee> NNTP-Posting-Host: tamm.ebc.ee X-Newsreader: TIN [version 1.2 PL2] Hello! Does anybody have been busy with CDNB (1-chloro-2,4-dinitrobenzene) assay for GST? Is it suitable assay for GST concentration measurement? Are there any articles about this assay? Thanks! -- TANEL PUNGA, B.Sc. 23 Riia Street Fax:372-7-420286 Institute of Molecular Tel:372-7-420218 and Cell Biology E-mail:tpungas@ebc.ee EE2400 Tartu, ESTONIA ******************************************************** From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!news-pull.sprintlink.net!news.sprintlink.net!news-ana-7.sprintlink.net!news2.i-2000.com!jenkintown7.access1.dh.i-2000.net!user From: ebrown@i-2000.com (Ellie Brown) Newsgroups: bionet.molbio.proteins Subject: Re: CD analysis of beta-sheet Date: Fri, 10 Jan 1997 20:44:38 -0500 Organization: home Lines: 14 Message-ID: References: <5atqhb$fj1@wn2.sci.kun.nl> <32D42CE3.3958@amgen.com> NNTP-Posting-Host: jenkintown7.access1.dh.i-2000.net X-Newsreader: Yet Another NewsWatcher 2.0.1 In article <32D42CE3.3958@amgen.com>, jphilo@amgen.com wrote: > Ronald Smulders wrote: I missed the original post, but have just been discussing this kind of situation with my student. Is the absolute value of the ellipticity increasing or decreasing? If it is decreasing, I would suggest aggregation leading to light scattering. If the absolute value is increasing, perhaps more beta structure is being formed. Have you calculated the % beta etc. under the two circumstances? There was a paper by Greenfield within the last couple of years in Anal. Biochem. that compares several algorithms, some work better than others with predominately beta proteins. Ellie Brown ERRC-USDA Wyndmoor, PA 19038 From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.uoregon.edu!tezcat!feed1.news.erols.com!news.dra.com!news.good.net!news.good.net!news.goodnet.com!phx-ts2-16.goodnet.com!user From: mthompson@asu.edu (MThompson) Newsgroups: bionet.biophysics,bionet.molbio.proteins,bionet.info-theory,bionet.molbio.evolution,bionet.molbio.methds-reagnts Subject: What is the SMALLEST DNA BINDING DOMAIN? Date: Fri, 10 Jan 1997 13:11:27 -0700 Organization: Arizona State University Lines: 5 Message-ID: NNTP-Posting-Host: phx-ts2-16.goodnet.com Xref: biosci bionet.biophysics:2531 bionet.molbio.proteins:9694 bionet.info-theory:4517 bionet.molbio.evolution:5503 bionet.molbio.methds-reagnts:53365 I am searching for a small independently folding (or in presence of a metal ion), DNA binding domain. Would like it to be sequence specific, but would greatly appreciate all suggestions. Be as detailed as possible or please cite a reference, or name that I can locate it in the literature. Thanks very much. From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.nacamar.de!fu-berlin.de!news-ber1.dfn.de!news-fra1.dfn.de!news-koe1.dfn.de!main.Germany.EU.net!Germany.EU.net!EU.net!news.sprintlink.net!news-peer.sprintlink.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-feed1.bbnplanet.com!nih.gov!usenet From: John Kuszewski Newsgroups: bionet.molbio.proteins Subject: predicting radius of gyration Date: Fri, 10 Jan 1997 17:20:13 -0500 Organization: Nat'l Insts of Health Lines: 26 Message-ID: <32D6C09D.401F@spork.niddk.nih.gov> NNTP-Posting-Host: spork.niddk.nih.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; SunOS 5.5 sun4u) Hi, Does anyone have an equation to predict the radius of gyration of a globular protein from the number of residues in it? Could you post it or email it to me? Thanks. -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spork.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| My parents went to Zaire and all I got was this lousy retrovirus. From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!hermod.uio.no!nntp.uio.no!news.nacamar.de!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!portc02.blue.aol.com!audrey01.news.aol.com!not-for-mail From: eheilweil@aol.com (EHeilweil) Newsgroups: bionet.molbio.proteins Subject: Re: separation of phosphorylated and non-phosphorylated peptide Date: 10 Jan 1997 22:28:38 GMT Organization: AOL http://www.aol.com Lines: 2 Message-ID: <19970110222500.RAA25411@ladder01.news.aol.com> References: <32CCD980.7F8B@uic.edu> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Phosphocellulose paper in sheets or small circles for use in Kinase assays is also available from Whatman Inc., Clifton NJ (1-800-922-0361) From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.sgi.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-feed1.bbnplanet.com!nih.gov!usenet From: fkfried@helix.nih.gov (Dr. Fred K. Friedman) Newsgroups: bionet.molbio.proteins Subject: postdoctoral position Date: Fri, 10 Jan 1997 19:29:43 GMT Organization: National Cancer Institute, NIH Lines: 12 Message-ID: <5b653n$odq@light.nih.gov> NNTP-Posting-Host: zack.nci.nih.gov X-Newsreader: Forte Free Agent 1.0.82 A postdoctoral research position is available to study structure-function relationships of cytochrome P450, employing biochemical/biophysical approaches. Research includes kinetic and thermodynamic characterization of P450 interactions with substrates, ligands and other proteins. For a summary of our recent work in this area, point your WWW browser to http://www.nci.nih.gov/intra/LMC/fkf.HTM. This position is for a recent Ph.D. graduate and will be available as early as March. To apply, send CV and names and phone numbers of three references to Dr. Fred K. Friedman, National Cancer Institute, Bldg. 37, Room 3E-24, Bethesda, MD 20892. Or send email to fkfried@helix.nih.gov From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.sgi.com!news.corp.sgi.com!enews.sgi.com!EU.net!Germany.EU.net!main.Germany.EU.net!news-koe1.dfn.de!news-han1.dfn.de!news-ham1.dfn.de!news-ber1.dfn.de!fu-berlin.de!crick.rz-berlin.mpg.DE!not-for-mail From: jaensch@mpimg-berlin-dahlem.mpg.de Newsgroups: bionet.molbio.proteins Subject: Affi-Chromat. with antibodys???? Date: 10 Jan 97 17:38:01 +0100 Organization: MPI f. Molekulare Genetik, Berlin Lines: 14 Distribution: world Message-ID: <1997Jan10.173801@crick.rz-berlin.mpg.de> NNTP-Posting-Host: crick.rz-berlin.mpg.de (141.14.129.205) X-Access: 16 25 816 I would like to purify a protein complex with the help of affinity chromatography. Therefore, I coupled an antibody, which recognizes one subunit to CNBR-Sepharose (Pharmacia). I have the following questions in this regard: 1. Is it resonable to couple antibodys to CNBR-Sepharose? 2. Which buffers are recommended for the affinity binding and for the elution Thank you for helping me!!!!! Lothar Jaensch, Universitaet Hannover of the protein complex? (The antibodys should not be damaged) From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!arclight.uoregon.edu!news.bc.net!rover.ucs.ualberta.ca!gallin2.biology.ualberta.ca!wgallin From: wgallin@gpu.srv.ualberta.ca (Warren Gallin) Newsgroups: bionet.molbio.proteins Subject: Re: Help Date: Fri, 10 Jan 97 16:32:16 GMT Organization: University of Alberta Lines: 26 Message-ID: References: <5b5d7j$4ek@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: gallin2.biology.ualberta.ca X-Newsreader: VersaTerm Link v1.1.4 In Article <5b5d7j$4ek@ccshst05.cs.uoguelph.ca>, wyu@uoguelph.ca (Wenjin Yu) wrote: >Dear colleagues, > > We've isolated and cDNA encoding a protein which should have a >weight of 25 kD dased on computer program calculation. However, after we >did Western blot using antibodies specific to this protein we got a 33kD >band on SDS-PAGE (under reduced conditions). Although this protein is a >glycoprotein, it shouldn't change so much since only one glyco-site was >found. Does any one can explain this for me? Any suggestions are highly >appreciated. This is not an uncommon phenomenon. It has been discussed here before, with suggestions ranging from extreme pI to regions of high proline content as possible explanations. The whole cadherin class of cell adhesion molecules show this kind of anomalous migration (predicted molecular weight about 80 kD, Laemmli gels show about 110-120 kD, deglycosylated). One thing you can try is running a Weber Osborn gel, with phosphate buffer and no stacking; this system doesn't seem to give such anomalous mobilities. Warren Gallin Department of Biological Sciences University of Alberta Edmonton, Alberta T6G 2E9 Canada wgallin@gpu.srv.ualberta.ca From owner-proteins@net.bio.net Thu Jan 09 22:00:00 1997 Path: biosci!SEDONA.NET!rathbun From: rathbun@SEDONA.NET (RS&A) Newsgroups: bionet.molbio.proteins Subject: Position: Cell-based Bioassay Scientist Date: 10 Jan 1997 23:23:00 -0800 Organization: Sedona Internet Services, Inc. Lines: 42 Sender: daemon@net.bio.net Distribution: world Message-ID: <32D74055.6BFE@sedona.net> Reply-To: rathbun@sedona.net NNTP-Posting-Host: net.bio.net Bioassay Development Scientist We are seeking a scientist experienced in the development of immunoassays and cell-based bioassays for the characterization/quantification of proteins for our biopharmaceutical client company. This Scientist would work on the development and application of cell based bioassays for the measurement of specific activity. The incumbent will join a research team responsible for the characterization and production of molecules for IND studies. An ideal candidate will have a Ph.D. in Cell Biology or related discipline with 1-4 years experience working with Bioassays, Cell Culture and ELISA. We are seeking candidates whose research focus has been developing and applying cell based assays for the purpose of quantifying biotechnology products/proteins. Working knowledge of drug development issues and a knowledge of GLP assay validation would be beneficial but is not required. Experience in cell surface receptors, cytokines, cell signaling pathways and/or control of cell cyle events is preferred. This scientist should have experience in assays such as cell kill assays and cytokine production assays. REQUIRED: =B7 Ph.D. in Cell Biology, Biochemistry, Chemistry or related discipline with emphasis on protein characterizations. =B7 1+ years experience in industry or Postdoc [academic or industrial] developing cell-based assays. = If you have an interest in this or other opportunities, please email your resume as an attached file or mail/FAX your CV/resume to RS&A to the attention of Ann G. Rathbun, Managing Director. All correspondence is held in strict confidence. Rathbun, Sapir & Associates = P.O. Box 2337 Sedona, AZ 86339-2337 * USA = (520) 284-3360 Office (520)284-3361 FAX E-mail: rathbun@ sedona.net From owner-proteins@net.bio.net Fri Jan 10 22:00:00 1997 Path: biosci!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins Subject: Re: predicting radius of gyration Date: 11 Jan 1997 15:17:07 GMT Organization: University of Leicester, UK (PCFS User) Lines: 10 Message-ID: <5b8atj$m3f@falcon.le.ac.uk> References: <32D6C09D.401F@spork.niddk.nih.gov> 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) John Kuszewski wrote: >Does anyone have an equation to predict the radius of >gyration of a globular protein from the number of >residues in it? Perkins gave algorithms to calculate several parameters for proteins from their sequence data in Eur.J.Biochem. 157 (1986) 169-180. I am not quite shure whether radius of gyration was amongst them. From owner-proteins@net.bio.net Fri Jan 10 22:00:00 1997 Path: biosci!agate!spool.mu.edu!newspump.sol.net!newsfeeds.sol.net!hammer.uoregon.edu!leto!news.ou.edu!news.ecn.uoknor.edu!news.cis.okstate.edu!nntp.ksu.edu!usenet.umr.edu!raghav From: raghav@saucer.cc.umr.edu (Raghavender Pillutla) Newsgroups: bionet.molbio.proteins Subject: Are there .brk files in PDB???? Date: 11 Jan 1997 20:43:18 GMT Organization: UMR Missouri's Technological University Lines: 9 Message-ID: <5b8u16$k9t$1@news.cc.umr.edu> NNTP-Posting-Host: saucer.cc.umr.edu X-Newsreader: TIN [version 1.2 PL2] Hello Everyone, Are there any files available in Protein Data Bank of Brookhaven National Laboratory with the extension .brk. If there are, I would like to know what these files contain and how are they different from .pdb files. I need the information for a program I am using, So I'd appreciate if someone could help me. Thank You very much. Raghu. From owner-proteins@net.bio.net Fri Jan 10 22:00:00 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!su-news-hub1.bbnplanet.com!newsxfer3.itd.umich.edu!howland.erols.net!math.ohio-state.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.biophysics,bionet.molbio.proteins,bionet.info-theory,bionet.molbio.evolution,bionet.molbio.methds-reagnts Subject: Re: What is the SMALLEST DNA BINDING DOMAIN? Date: 11 Jan 1997 21:24:21 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 25 Message-ID: References: Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: ebv.oncology.wisc.edu X-Newsreader: slrn (0.9.2.1 BETA UNIX) Xref: biosci bionet.biophysics:2536 bionet.molbio.proteins:9705 bionet.info-theory:4523 bionet.molbio.evolution:5508 bionet.molbio.methds-reagnts:53387 On Sat, 11 Jan 1997 11:52:26 EST, jstrassw@OPAL.TUFTS.EDU wrote: >Well, the Bovine Papillomavirus DNA binding domain (minimal) iosonlt 85 AA >although tit forms a dimer. It has the aadvantage of many characterized >mutations, and an excellent crystal structure (1.2A) and binds >sequence-specific to a palindropme at 10 -12 M. > >I also study it! The Kd value that you have listed for the minimal portion of "BPV-E2 DNA binding domain" binding it's cognate site is very different from that which has been published. For instance, from J. Virol. 71:828-831 (1997) (a publication from the Androphy lab), the Kd of the 87 a.a minimal DNA binding domain for it's cognate site is listed as approximately 7.0 nM (i.e. 7 x 10e-9 M), while a larger fragment, containing 127 a.a has a Kd of about 0.9 nM, and even this is quite far from the picomolar affinity you have listed .... Later, Ashok -- Ashok Aiyar, Ph.D. McArdle Laboratory for Cancer Research University of Wisconsin-Madison From owner-proteins@net.bio.net Fri Jan 10 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!hermod.uio.no!nntp.uio.no!news.nacamar.de!news.icm.edu.pl!hammer.uoregon.edu!news-xfer.netaxs.com!feed1.news.erols.com!howland.erols.net!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.tufts.edu!opal.tufts.edu!jstrassw From: Newsgroups: bionet.biophysics,bionet.molbio.proteins,bionet.info-theory,bionet.molbio.evolution,bionet.molbio.methds-reagnts Subject: Re: What is the SMALLEST DNA BINDING DOMAIN? Date: Sat, 11 Jan 1997 11:52:26 EST Organization: Tufts University Lines: 31 Message-ID: References: NNTP-Posting-Host: opal.tufts.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII To: MThompson In-Reply-To: Xref: biosci bionet.biophysics:2535 bionet.molbio.proteins:9704 bionet.info-theory:4522 bionet.molbio.evolution:5507 bionet.molbio.methds-reagnts:53381 Hello! Well, the Bovine Papillomavirus DNA binding domain (minimal) iosonlt 85 AA although tit forms a dimer. It has the aadvantage of many characterized mutations, and an excellent crystal structure (1.2A) and binds sequence-specific to a palindropme at 10 -12 M. I also study it! John ------------------------------------------------------------------------ John Strasswimmer, MD,PhD Candidate | Phone (617) 636 8396 Tufts - New England Medical Center | Fax (617) 636 6190 Box 166 | Email: jstrassw@opal.tufts.edu Boston, MA 02111 USA | HTTP://WWW.healthsci.tufts.edu/microbiology/strass/JSpage.HTML *** Co-Author of "HyperBug" Microbiology Teaching Software *** | Remember, Your employer is eavesdropping... ------------------------------------------------------------------------ On Fri, 10 Jan 1997, MThompson wrote: > I am searching for a small independently folding (or in presence of a > metal ion), DNA binding domain. Would like it to be sequence specific, but > would greatly appreciate all suggestions. Be as detailed as possible or > please cite a reference, or name that I can locate it in the literature. > Thanks very much. > > From owner-proteins@net.bio.net Fri Jan 10 22:00:00 1997 Path: biosci!agate!howland.erols.net!feed1.news.erols.com!hunter.premier.net!news.uoregon.edu!news.unisys.com.br!news From: quatroa5@unisys.com.br Newsgroups: bionet.molbio.proteins Subject: omega 3, EPA e DHA Date: Sat, 11 Jan 1997 16:39:42 GMT Organization: Unisys Brasil Ltda. (Sao Paulo - Brazil) Lines: 12 Message-ID: <329ef9d4.11831157@news.unisys.com.br> NNTP-Posting-Host: rionb01p46.unisys.com.br X-Newsreader: Forte Free Agent 1.1/16.230 I´m a brazilian doctor and I realy need some relevant information about OMEGA3, EPA and DHA, because I developing a work here with this proteins. I´ve search in the www and didn´t find anythin interesting. please, I´ll wait for the results at the pax@geocities.com thanks for all. From owner-proteins@net.bio.net Fri Jan 10 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!vixen.cso.uiuc.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!daemon From: klenchin@facstaff.wisc.edu (Dima Klenchin) Newsgroups: bionet.biophysics,bionet.molbio.proteins,bionet.info-theory,bionet.molbio.evolution,bionet.molbio.methds-reagnts Subject: Re: What is the SMALLEST DNA BINDING DOMAIN? Date: Sun, 12 Jan 97 07:45:45 GMT Organization: UW-Madison Lines: 29 Message-ID: <5ba4tt$22b0@news.doit.wisc.edu> References: NNTP-Posting-Host: f181-185.net.wisc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=KOI8-R Content-Transfer-Encoding: 8bit X-No-Archive: Yes Xref: biosci bionet.biophysics:2539 bionet.molbio.proteins:9708 bionet.info-theory:4529 bionet.molbio.evolution:5511 bionet.molbio.methds-reagnts:53393 In article , aiyar@ebv.oncology.wisc.edu wrote: #On Sat, 11 Jan 1997 11:52:26 EST, jstrassw@OPAL.TUFTS.EDU # wrote: # #>Well, the Bovine Papillomavirus DNA binding domain (minimal) iosonlt 85 AA #>although tit forms a dimer. It has the aadvantage of many characterized #>mutations, and an excellent crystal structure (1.2A) and binds #>sequence-specific to a palindropme at 10 -12 M. #> #>I also study it! # #The Kd value that you have listed for the minimal portion of "BPV-E2 #DNA binding domain" binding it's cognate site is very different from #that which has been published. # #For instance, from J. Virol. 71:828-831 (1997) (a publication from #the Androphy lab), the Kd of the 87 a.a minimal DNA binding domain #for it's cognate site is listed as approximately 7.0 nM (i.e. 7 x 10e-9 M), #while a larger fragment, containing 127 a.a has a Kd of about 0.9 nM, #and even this is quite far from the picomolar affinity you have listed .... Umm, I know nothing about DNA binding, but biology is not a quantitative science, so 3 orders of magnitude makes no difference (since nobody knows how to apply those numbers anyway). Couldn't resist, - Dima From owner-proteins@net.bio.net Fri Jan 10 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!not-for-mail From: toms@ncifcrf.gov (Tom Schneider) Newsgroups: bionet.biophysics,bionet.molbio.proteins,bionet.info-theory,bionet.molbio.evolution,bionet.molbio.methds-reagnts Subject: Re: What is the SMALLEST DNA BINDING DOMAIN? Followup-To: bionet.info-theory Date: 12 Jan 1997 00:25:49 GMT Organization: NCI-FCRDC Frederick Biomedical Supercomputing Center Lines: 17 Message-ID: <5b9b2d$2gg6@ncisun1-nf0.ncifcrf.gov> References: NNTP-Posting-Host: kaylor.ncifcrf.gov X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Xref: biosci bionet.biophysics:2537 bionet.molbio.proteins:9707 bionet.info-theory:4525 bionet.molbio.evolution:5509 bionet.molbio.methds-reagnts:53389 jstrassw@OPAL.TUFTS.EDU wrote: : Well, the Bovine Papillomavirus DNA binding domain (minimal) iosonlt 85 AA : although tit forms a dimer. It has the aadvantage of many characterized : mutations, and an excellent crystal structure (1.2A) and binds : sequence-specific to a palindropme at 10 -12 M. : : I also study it! Cool! What's the sequence logo look like? Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov http://www-lmmb.ncifcrf.gov/~toms/ From owner-proteins@net.bio.net Fri Jan 10 22:00:00 1997 Path: biosci!agate!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!newsout1.alt.net!news1.alt.net!usenet.eel.ufl.edu!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins Subject: Re: RE:TCA precipitation Date: 11 Jan 1997 15:12:21 GMT Organization: University of Leicester, UK (PCFS User) Lines: 15 Message-ID: <5b8akl$m3f@falcon.le.ac.uk> References: <5b1kae$kqd@sjx-ixn4.ix.netcom.com> 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) derek12@ix.netcom.com(Russell Lamar Howard) wrote: >I need some info on TCA precip. I'm fairly new at it and would like a >"generic" method to using it. Also, what is a SDS_page SDS-PAGE stands for Sodium Dodecyl Sulfate PolyAcrylamide Gel Electrophoresis, an analytical method introduced by Laemli some 20 years ago to separate proteins based on differences in molecular weight. Get a book on protein chemistry or practical biochemistry to learn all the details. If you are developing a new method, I would advice against TCA precipitation and recommend chloroform/methanol precipitation instead. The method was published by Wessel & Fluegge in Anal. Biochem., somewhere in the mid 80s. Protein recovery is much better. From owner-proteins@net.bio.net Sat Jan 11 22:00:00 1997 Path: biosci!botany.uq.edu.au!J.Marcus From: J.Marcus@botany.uq.edu.au ("Marcus, Dr J.") Newsgroups: bionet.molbio.proteins Subject: patent issues with novel protein Date: 12 Jan 1997 15:29:46 -0800 Organization: Dept of Botany, Univ of Qld Lines: 41 Sender: daemon@net.bio.net Distribution: world Message-ID: <494C96F2BA6@botany.uq.edu.au> Reply-To: Marcus@tpp.uq.edu.au NNTP-Posting-Host: net.bio.net Dear netters, We have discovered a novel bioactive protein (i.e. no significant sequence similarities) from a plant source. As we are going through patenting issues we are faced with several questions that we have not found easy answers to. We want to claim homologues of the protein but would like to have a specific %identity or %similarity number to claim. Seeing as we have a completely novel protein, what %identity might we be able to claim? We would like to claim all isolated proteins with as little at 1% similarity but that is obviously not realistic. 30%identity seems more realistic and 70% might be what the examiners allow. Do we need to exemplify the % identity number by showing another protein that has the same bioactivity and that %identity? What issues do we need to take into account as we try to claim homolgues of the protein? Any help you can provide in this matter would be most appreciated. Sincerely Yours, John Marcus _________________________________________________________ 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 Sat Jan 11 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news-xfer.netaxs.com!newsfeeds.sol.net!nntp.uio.no!news.apfel.de!news-fra1.dfn.de!news-koe1.dfn.de!news.ruhr-uni-bochum.de!usenet From: "Thorsten Schmidt" Newsgroups: bionet.molbio.proteins Subject: Can I prepare SDS-PAGE gel mixes in advance? Date: 12 Jan 1997 13:40:33 GMT Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 24 Message-ID: <01bc008e$1c29f8c0$0c019386@schmidtdw.rz.ruhr-uni-bochum.de> NNTP-Posting-Host: dialppp-12.rz.ruhr-uni-bochum.de X-Newsreader: Microsoft Internet News 4.70.1155 Dear reader! I make many Western blots and SDS-PAGE-gels. For each gel, I have to mix - Acrylamid-Mix (29 % acrylamid / 0,8 % bis-aa) - Tris-Buffer - Water - 10 % SDS - TEMED - 10 % APS to pour a 3% and a 10% gel. Is there anything to be said against preparing a 3 % and a 10 % gel-mix by mixing the componets (except for APS & TEMED) in advance? It would minimize time by just adding TEMED & APS to a aliquot! Or isn´t it good to store such a mix for a longer time? Thank you for your answer Thorsten Schmidt From owner-proteins@net.bio.net Sat Jan 11 22:00:00 1997 Path: biosci!rutgers!news.sgi.com!mr.net!newsfeeds.sol.net!hammer.uoregon.edu!news.icm.edu.pl!uw.edu.pl!news.nask.pl!01-newsfeed.univie.ac.at!swidir.switch.ch!news.grnet.gr!news.auth.gr!usenet From: "Stavros P. Zanos" Newsgroups: bionet.biophysics,bionet.cellbiol,bionet.immunology,bionet.molbio.proteins,bionet.molecules.peptides,bionet.neuroscience,sci.med.pharmacy Subject: Phosphorylation of G-proteins Date: 12 Jan 1997 10:15:11 GMT Organization: Medical School, Thessaloniki Lines: 15 Message-ID: <01bc000c$e56f1080$0f02000a@slirp.hol.gr> NNTP-Posting-Host: antigoni.med.auth.gr X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.biophysics:2540 bionet.cellbiol:6398 bionet.immunology:10642 bionet.molbio.proteins:9709 bionet.molecules.peptides:598 bionet.neuroscience:17653 sci.med.pharmacy:39351 It has come to my knowledge that G proteins undergo phosphorylation by cAMP- and calcium-dependent protein kinases and by tyrosine kinases. Having undertaken the writing of a part of a seminar on autonomic NS pharmacology, I was wandering if anyone out there knew something about the physiological role of G protein phosphorylation, especially in relation to neurotransmission and synaptic plasticity processes. Any details on the phosphorylation sites and regulation are also welcome. References to book chapters or journal articles are welcome. Thank you in advance. S.P. Zanos Aristotle U. Med. School Thessaloniki, Greece From owner-proteins@net.bio.net Sat Jan 11 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!math.ohio-state.edu!jussieu.fr!fdn.fr!r2d2.fdn.org!med.univ-tours.fr!univ-angers.fr!ciril.fr!cnusc.fr!univ-lyon1.fr!pasteur.fr!oleane!calvacom!dd11 From: dd11@calvanet.calvacom.fr (Dominique Delefortrie) Newsgroups: bionet.software,bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: ?? Kinetics Software - Post Date: Sun, 12 Jan 1997 20:09:52 +0100 Organization: CalvaCom Data Networks International Communications Lines: 14 Message-ID: <19970112200952561895@mar17.calvacom.fr> References: <32AEF4BF.5C7A@apl.washington.edu> <32BF3C94.4319@cam.org> <32D42DD6.70A3@sbphrd.com> NNTP-Posting-Host: mar22.calvacom.fr X-Newsreader: MacSOUP F2.2b5 Xref: biosci bionet.software:17586 bionet.molbio.proteins:9711 bionet.molbio.methds-reagnts:53398 William P Prichett wrote: > I would like to add to the list of Kaliedagraph users. I really like the > easy of use, especially the non linear curve fit. Very simple. Synergy I do agree ! It is very simple to enter the equation of the studied phenomenon, e.g. the Michaelis-Menten equation, and plot against it ! There exists also a not-so-bad shareware : EnzymeKinetics 1.3 Demo along with numerous models -- <> (-8 DD From owner-proteins@net.bio.net Sat Jan 11 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!not-for-mail From: toms@ncifcrf.gov (Tom Schneider) Newsgroups: bionet.biophysics,bionet.molbio.proteins,bionet.info-theory,bionet.molbio.evolution,bionet.molbio.methds-reagnts Subject: Re: What is the SMALLEST DNA BINDING DOMAIN? Followup-To: bionet.biophysics,bionet.molbio.proteins,bionet.info-theory,bionet.molbio.evolution,bionet.molbio.methds-reagnts Date: 13 Jan 1997 04:18:35 GMT Organization: NCI-FCRDC Frederick Biomedical Supercomputing Center Lines: 40 Message-ID: <5bcd2r$2gg8@ncisun1-nf0.ncifcrf.gov> References: <5ba4tt$22b0@news.doit.wisc.edu> NNTP-Posting-Host: kaylor.ncifcrf.gov X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Xref: biosci bionet.biophysics:2543 bionet.molbio.proteins:9715 bionet.info-theory:4535 bionet.molbio.evolution:5516 bionet.molbio.methds-reagnts:53402 Dima Klenchin (klenchin@facstaff.wisc.edu) wrote: : In article , aiyar@ebv.oncology.wisc.edu wrote: : #On Sat, 11 Jan 1997 11:52:26 EST, jstrassw@OPAL.TUFTS.EDU : # wrote: : # : #>Well, the Bovine Papillomavirus DNA binding domain (minimal) iosonlt 85 AA : #>although tit forms a dimer. It has the aadvantage of many characterized : #>mutations, and an excellent crystal structure (1.2A) and binds : #>sequence-specific to a palindropme at 10 -12 M. : #> : #>I also study it! : # : #The Kd value that you have listed for the minimal portion of "BPV-E2 : #DNA binding domain" binding it's cognate site is very different from : #that which has been published. : # : #For instance, from J. Virol. 71:828-831 (1997) (a publication from : #the Androphy lab), the Kd of the 87 a.a minimal DNA binding domain : #for it's cognate site is listed as approximately 7.0 nM (i.e. 7 x 10e-9 M), : #while a larger fragment, containing 127 a.a has a Kd of about 0.9 nM, : #and even this is quite far from the picomolar affinity you have listed .... : : Umm, I know nothing about DNA binding, but biology is not a quantitative : science, so 3 orders of magnitude makes no difference (since nobody knows : how to apply those numbers anyway). It makes a big difference, and those numbers can be applied, using advanced molecular machine theory. I'll present the results later in several new papers that are almost finished. If you would like to prepare yourself for reading the new papers, read the ccmm, edmm and nano2 papers. If THOSE don't make sense yet, read the earlier papers on binding site information theory and sequence logos. All papers are available through my web site. Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov http://www-lmmb.ncifcrf.gov/~toms/ From owner-proteins@net.bio.net Sat Jan 11 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!not-for-mail From: toms@ncifcrf.gov (Tom Schneider) Newsgroups: bionet.biophysics,bionet.molbio.proteins,bionet.info-theory,bionet.molbio.evolution,bionet.molbio.methds-reagnts Subject: Re: What is the SMALLEST DNA BINDING DOMAIN? Followup-To: bionet.biophysics,bionet.molbio.proteins,bionet.info-theory,bionet.molbio.evolution,bionet.molbio.methds-reagnts Date: 13 Jan 1997 04:32:07 GMT Organization: NCI-FCRDC Frederick Biomedical Supercomputing Center Lines: 17 Message-ID: <5bcds7$2gg10@ncisun1-nf0.ncifcrf.gov> References: <5bcck5$ho9@nntp3.u.washington.edu> NNTP-Posting-Host: kaylor.ncifcrf.gov X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Xref: biosci bionet.biophysics:2544 bionet.molbio.proteins:9716 bionet.info-theory:4537 bionet.molbio.evolution:5517 bionet.molbio.methds-reagnts:53403 Angeline Kantola (kantola@u.washington.edu) wrote: : C2H2 zinc fingers are everywhere (there are other kinds of zinc fingers as : well), so finding information about them should be easy. Mia Schmiedeskamp : and Rachel Klevit wrote a review of zinc fingers a few years back, which : is probably a good place to start. Thanks for the tip. I could not locate this in medline entrez. Schmiedeskamp does appear but is the wrong topic. R. Klevit wrote a number of papers on the subject. Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov http://www-lmmb.ncifcrf.gov/~toms/ From owner-proteins@net.bio.net Sat Jan 11 22:00:00 1997 Path: biosci!news.artemis.com!uunet!in2.uu.net!140.142.64.3!news.u.washington.edu!kantola From: kantola@u.washington.edu (Angeline Kantola) Newsgroups: bionet.biophysics,bionet.molbio.proteins,bionet.info-theory,bionet.molbio.evolution,bionet.molbio.methds-reagnts Subject: Re: What is the SMALLEST DNA BINDING DOMAIN? Date: 13 Jan 1997 04:10:45 GMT Organization: University of Washington, Seattle Lines: 24 Message-ID: <5bcck5$ho9@nntp3.u.washington.edu> References: NNTP-Posting-Host: carson.u.washington.edu Xref: biosci bionet.biophysics:2542 bionet.molbio.proteins:9714 bionet.info-theory:4534 bionet.molbio.evolution:5515 bionet.molbio.methds-reagnts:53401 In article , MThompson wrote: >I am searching for a small independently folding (or in presence of a >metal ion), DNA binding domain. Would like it to be sequence specific, but >would greatly appreciate all suggestions. Be as detailed as possible or >please cite a reference, or name that I can locate it in the literature. >Thanks very much. Cys2-His2 zinc fingers are on the order of 30 amino acids long. As the name suggests, a zinc atom is critical for structural integrity of the functional domain. Proteins which bind DNA via C2H2 zinc fingers do so sequence specifically. There's no evidence that single zinc fingers bind nucleic acids, though. A minimum of three of these fingers are required to bind or, as in the case of yeast ADR1, two fingers and a non-finger N termial region. C2H2 zinc fingers are everywhere (there are other kinds of zinc fingers as well), so finding information about them should be easy. Mia Schmiedeskamp and Rachel Klevit wrote a review of zinc fingers a few years back, which is probably a good place to start. Best of luck, Angie Kantola From owner-proteins@net.bio.net Sun Jan 12 22:00:00 1997 Path: biosci!daresbury!yama.mcc.ac.uk!usenet From: Simon Hubbard Newsgroups: bionet.molbio.proteins Subject: Re: Are there .brk files in PDB???? Date: Mon, 13 Jan 1997 16:41:59 +0000 Organization: UMIST Lines: 23 Message-ID: <32DA65D7.446B@sjh.bi.umist.ac.uk> References: <5b8u16$k9t$1@news.cc.umr.edu> NNTP-Posting-Host: sjh.bi.umist.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; IRIX64 6.2 IP26) Raghavender Pillutla wrote: > > Hello Everyone, > > Are there any files available in Protein Data Bank of Brookhaven National > Laboratory with the extension .brk. If there are, I would like to know > what these files contain and how are they different from .pdb files. I > need the information for a program I am using, So I'd appreciate if > someone could help me. Thank You very much. > > Raghu. There is no difference in the contents, just the extension name. The PDB distribution is sometimes found in other forms too, such as pdb****.ent or pdb****.pdb (ent presumably stands for entry). -Simon- _____________________________________________________________________ Dr. Simon Hubbard TEL: +44 (0)161 200 8930 Wellcome Trust Research Associate FAX: +44 (0)161 236 0409 Biochemistry & Applied Molec. Biology mailto:sjh@sjh.bi.umist.ac.uk UMIST, PO Box 88, Manchester M60 1QD http://sjh.bi.umist.ac.uk/~sjh From owner-proteins@net.bio.net Sun Jan 12 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!info-server.surrey.ac.uk!usenet From: bss3pk@surrey.ac.uk (Pete) Newsgroups: bionet.molbio.proteins Subject: Re: Affi-Chromat. with antibodys???? Date: Mon, 13 Jan 1997 12:53:47 GMT Organization: University of Surrey, UK Lines: 22 Message-ID: <5bd6db$6fn@info-server.surrey.ac.uk> References: <1997Jan10.173801@crick.rz-berlin.mpg.de> NNTP-Posting-Host: sbspcpk2.sbs.surrey.ac.uk X-Newsreader: Forte Free Agent 1.0.82 jaensch@mpimg-berlin-dahlem.mpg.de wrote: >I would like to purify a protein complex with the help of affinity >chromatography. Therefore, I coupled an antibody, which recognizes one subunit >to CNBR-Sepharose (Pharmacia). >I have the following questions in this regard: >1. Is it resonable to couple antibodys to CNBR-Sepharose? Yes, but you must bear in mind that the pores in CnBr-Seph. are not exactly cavernous; therefore you may encounter diffusion/capacity and tailing problems with larger antigens getting in and out of the pores which are lined with large IgG molecules. >2. Which buffers are recommended for the affinity binding and for the elution How long is a piece of string? Adsorbtion in PBS/TBS with elution at pH 2 does the trick 90% of the time, but you will only find out by trial and error. Pete From owner-proteins@net.bio.net Sun Jan 12 22:00:00 1997 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!hunter.premier.net!feed1.news.erols.com!insync!news-feed.inet.tele.dk!sn.no!news-stkh.gsl.net!news.gsl.net!eru.mt.luth.se!solace!mn6.swip.net!plug.news.pipex.net!pipex!oleane!pasteur.fr!jussieu.fr!univ-angers.fr!ciril.fr!u-strasbg.fr!news From: Florian NACHON Newsgroups: bionet.molbio.proteins Subject: coating Date: Mon, 13 Jan 1997 13:00:31 +0100 Organization: Chimie Bioorganique Lines: 4 Message-ID: <32DA23DF.C54@pharma.u-strasbg.fr> Reply-To: nachon@pharma.u-strasbg.fr NNTP-Posting-Host: mgpwmac2.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) i would like to coat tubes before fraction HPLC to be collected. do you know some protocols (using PPG 4000 or silicon). thanx for any suggestion. From owner-proteins@net.bio.net Sun Jan 12 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.erols.net!vixen.cso.uiuc.edu!uwm.edu!newsfeeds.sol.net!mr.net!newshub.tc.umn.edu!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.gwdg.de!news From: "C. Morys-Wortmann" Newsgroups: bionet.molbio.proteins Subject: Re: bsa lysine Date: Mon, 13 Jan 1997 12:25:03 +0100 Organization: max-planck-institute for experimental medicine Lines: 19 Message-ID: <32DA1B8F.7AD9@exmdi1.mpiem.gwdg.de> References: NNTP-Posting-Host: exmim3.mpiem.gwdg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) To: POSTEL Caroline POSTEL Caroline wrote: > > hello > I would like to know how many mysine where is in BSA(bovine serum albumin) > Than you There are 59 lysine in BSA, but only 30-35 are accessible for coupling reactions. (van Regenmortel, M.H.V. et al., Synthetic polypeptides as antigens, Elsevier 1988, page 98) Hope this helps Corinna -- Dr. Corinna Morys-Wortmann Max-Planck-Institut fuer experimentelle Medizin Hermann-Rein-Str. 3 37075 Goettingen Tel.: 0551/3899-506 Germany Fax: 0551/3899-500 From owner-proteins@net.bio.net Sun Jan 12 22:00:00 1997 Newsgroups: bionet.biophysics,bionet.molbio.proteins,bionet.molbio.evolution Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!hermod.uio.no!nntp.uio.no!news.maxwell.syr.edu!arclight.uoregon.edu!news.bc.net!nntp.mbnet.mb.ca!utcsri!utgpu!utinfo!bloch!gardner From: gardner@bloch (Kevin Gardner) Subject: Re: What is the SMALLEST DNA BINDING DOMAIN? X-Nntp-Posting-Host: bloch.med.utoronto.ca Message-ID: Followup-To: bionet.biophysics,bionet.molbio.proteins,bionet.molbio.evolution Sender: nntp@utcc.utoronto.ca (News) Organization: UTCC Campus Access X-Newsreader: TIN [version 1.2 PL2] References: <5bcck5$ho9@nntp3.u.washington.edu> Date: Mon, 13 Jan 1997 16:59:38 GMT Lines: 53 Xref: biosci bionet.biophysics:2548 bionet.molbio.proteins:9725 bionet.molbio.evolution:5528 (Followups trimmed) Angeline Kantola (kantola@u.washington.edu) wrote: : Cys2-His2 zinc fingers are on the order of 30 amino acids long. As the : name suggests, a zinc atom is critical for structural integrity of the : functional domain. Proteins which bind DNA via C2H2 zinc fingers do so : sequence specifically. There's no evidence that single zinc fingers bind : nucleic acids, though. A minimum of three of these fingers are required to : bind or, as in the case of yeast ADR1, two fingers and a non-finger N : termial region. : C2H2 zinc fingers are everywhere (there are other kinds of zinc fingers as : well), And I'd like to bring up one of those other kinds of zinc fingers: the Zn(2)Cys(6) binuclear cluster class, whose best known member is the S. cerevisiae GAL4 transcriptional activator. Somewhat similarly to the Cys2-His2 group above, the part of the domain that binds DNA and 2*Zn(II) is about 30aa in length and recognizes a 5'-CGG-3' triplet. This is somewhat of an oversimplification, though. Similarly to the Cys2-His2 case, specificity is derived from using multiple domains; in contrast, though, these domains are non-covalently dimerized, making the spacing between two inverted CGG elements as the prime source of specificity. When you add the additional linker & dimerization helix onto the DNA-binding domain, the total length kicks up to ca. 50-60aa. References: aside from my own work (NMR studies of GAL4 and LAC9, a K. lactis GAL4 homologue :), I'd check into: *specificity: several recent papers by Aseem Ansari in Mark Ptashne's group and references therein. *sequence homology in group: alignment paper in NAR last month (NAR 24(1996): 4599-4607) *structural biology: two crystal structures of protein DNA/complexes by Ronan Marmorstein when he was in Steve Harrison's group (GAL4 and PPR1); additional NMR studies by several groups including Gerhard Wagner, Ernest Laue, Joe Coleman and others. Cheers, Kevin -- ************************************************************************* Kevin Gardner gardner@bloch.med.utoronto.ca University of Toronto http://abragam.med.utoronto.ca/~gardner Dept. of Medical Genetics & Microbiology phone: 416-978-0642/FAX: -6885 From owner-proteins@net.bio.net Sun Jan 12 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!sn.no!nntp.uio.no!news.apfel.de!news-fra1.dfn.de!news-koe1.dfn.de!main.Germany.EU.net!Dortmund.Germany.EU.net!Germany.EU.net!EU.net!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!feed1.news.erols.com!howland.erols.net!math.ohio-state.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!daemon From: klenchin@facstaff.wisc.edu (Dima Klenchin) Newsgroups: bionet.biophysics,bionet.molbio.proteins,bionet.info-theory,bionet.molbio.evolution,bionet.molbio.methds-reagnts Subject: Re: What is the SMALLEST DNA BINDING DOMAIN? Date: Mon, 13 Jan 97 15:30:00 GMT Organization: UW-Madison Lines: 47 Message-ID: <5bdkgf$228m@news.doit.wisc.edu> References: <5ba4tt$22b0@news.doit.wisc.edu> <5bcd2r$2gg8@ncisun1-nf0.ncifcrf.gov> NNTP-Posting-Host: f182-050.net.wisc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=KOI8-R Content-Transfer-Encoding: 8bit X-No-Archive: Yes Xref: biosci bionet.biophysics:2547 bionet.molbio.proteins:9723 bionet.info-theory:4539 bionet.molbio.evolution:5525 bionet.molbio.methds-reagnts:53412 In article <5bcd2r$2gg8@ncisun1-nf0.ncifcrf.gov>, toms@ncifcrf.gov (Tom Schneider) wrote: #Dima Klenchin (klenchin@facstaff.wisc.edu) wrote: #: In article , # aiyar@ebv.oncology.wisc.edu wrote: #: #On Sat, 11 Jan 1997 11:52:26 EST, jstrassw@OPAL.TUFTS.EDU #: # wrote: #: # #: #>Well, the Bovine Papillomavirus DNA binding domain (minimal) iosonlt 85 AA #: #>although tit forms a dimer. It has the aadvantage of many characterized #: #>mutations, and an excellent crystal structure (1.2A) and binds #: #>sequence-specific to a palindropme at 10 -12 M. #: #the Kd of the 87 a.a minimal DNA binding domain #: #for it's cognate site is listed as approximately 7.0 nM (i.e. 7 x 10e-9 M), #: #while a larger fragment, containing 127 a.a has a Kd of about 0.9 nM, #: #and even this is quite far from the picomolar affinity you have listed .... #: #: Umm, I know nothing about DNA binding, but biology is not a quantitative #: science, so 3 orders of magnitude makes no difference (since nobody knows #: how to apply those numbers anyway). # #It makes a big difference, and those numbers can be applied, using advanced #molecular machine theory. I'll present the results later in several new #papers that are almost finished. If you would like to prepare yourself for #reading the new papers, read the ccmm, edmm and nano2 papers. If THOSE don't #make sense yet, read the earlier papers on binding site information theory #and sequence logos. All papers are available through my web site. Of course they do. There are all sorts of different things one can do comparing numbers. However, going back to the obscured to me Bovine Papillomavirus DNA binding domain, I'd like to ask one Q. Will our understanding of the biology of this virus change to _any_ extent should someone prove that affinity is 1 pM instead of 1 nM (or vice versa)? I bet - no. Sure, it'll make a lot of difference to people studying what combination of aa in what milieu works best when binding to a given structure, but for biology of the virus... Nowhere in the viral lifecycle we can apply those numbers to derive new and meaningful information about this organism. Thanks for reply, Tom. Intersting WEB site. I'll try to read the papers. I sure liked the idea of "No Consensus Sequences!" cause they make less and less sense as we go along the unknowns. . - Dima From owner-proteins@net.bio.net Sun Jan 12 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.proteins Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 13 Jan 1997 02:00:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701131000.CAA07220@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/. 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Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-proteins@net.bio.net Mon Jan 13 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!gondor!newshub.sdsu.edu!news.sgi.com!enews.sgi.com!ix.netcom.com!newsfeeds.sol.net!news.maxwell.syr.edu!usenet.kornet.nm.kr!news.postech.ac.kr!newsfeed.kreonet.re.kr!news.kaist.ac.kr!news From: "Jang Young Lee" Newsgroups: bionet.molbio.proteins Subject: blue dye column Date: 15 Jan 1997 07:27:22 GMT Organization: »ýÈ­ÇаøÇÐ½Ç Lines: 13 Message-ID: <01bc02b5$0d4fc900$0815f88f@hskim.kaist.ac.kr> NNTP-Posting-Host: hskim.kaist.ac.kr X-Newsreader: Microsoft Internet News 4.70.1155 Currently, I am working with a cibacron blue dye columne to purify a dehydrogenase of my interest. The enzyme does not show activity without NAD. As far as I know, cibacron blue has a relatively strong affinity towards NAD requiring enzyme. To the contrary, the activity was found in non-bound fractoin in my case. Can anyone give me a reasonable explanation on this. I'd also like to know the optimized elution strategy for this dye column (although I know that it depends on the protein.). Thanks. Jang Lee, jylee@boineer.kaist.ac.kr From owner-proteins@net.bio.net Mon Jan 13 22:00:00 1997 Path: biosci!agate!howland.erols.net!EU.net!Norway.EU.net!sn.no!hermod.uio.no!nntp.uio.no!news.apfel.de!fu-berlin.de!arnold.chemie.fu-berlin.DE!not-for-mail From: strecker@chemie.fu-berlin.de (Andreas Strecker) Newsgroups: bionet.molbio.proteins Subject: Re: Can I prepare SDS-PAGE gel mixes in advance? Date: Tue, 14 Jan 1997 17:45:40 GMT Organization: Freie Universitaet Berlin Lines: 32 Message-ID: <32dbc50b.7125475@news.fu-berlin.de> References: <01bc008e$1c29f8c0$0c019386@schmidtdw.rz.ruhr-uni-bochum.de> Reply-To: strecker@chemie.fu-berlin.de NNTP-Posting-Host: arnold.chemie.fu-berlin.de (160.45.28.9) X-Access: 16 17 19 X-Newsreader: Forte Free Agent 1.1/16.230 On 12 Jan 1997 13:40:33 GMT, "Thorsten Schmidt" wrote: >Dear reader! > >I make many Western blots and SDS-PAGE-gels. > >For each gel, I have to mix >- Acrylamid-Mix (29 % acrylamid / 0,8 % bis-aa) >- Tris-Buffer >- Water >- 10 % SDS >- TEMED >- 10 % APS > >to pour a 3% and a 10% gel. > >Is there anything to be said against preparing a 3 % and a 10 % gel-mix >by mixing the componets (except for APS & TEMED) in advance? > >It would minimize time by just adding TEMED & APS to a aliquot! >Or isn´t it good to store such a mix for a longer time? > Hi Thorsten! There simply is NOTHING to say against storing premixed gel solutions as long as you keep them in a freezer (-20 degr.). You should be able to keep them at least for a couple of months. And it improves the reproducibility of your gels (if that is important for you). We have made good experience with it. Andreas From owner-proteins@net.bio.net Mon Jan 13 22:00:00 1997 Newsgroups: bionet.biophysics,bionet.molbio.proteins,bionet.info-theory,bionet.molbio.evolution,bionet.molbio.methds-reagnts Path: biosci!bcm.tmc.edu!cs.utexas.edu!news-xfer.netaxs.com!hammer.uoregon.edu!arclight.uoregon.edu!news.bc.net!nntp.mbnet.mb.ca!utcsri!utgpu!lamoran From: lamoran@gpu.utcc.utoronto.ca (L.A. Moran) Subject: Re: What is the SMALLEST DNA BINDING DOMAIN? Message-ID: Organization: UTCNS Public Access References: <5bcck5$ho9@nntp3.u.washington.edu> Date: Tue, 14