From owner-proteins@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!UTSW.SWMED.EDU!IYER From: IYER@UTSW.SWMED.EDU Newsgroups: bionet.molbio.proteins Subject: protein footprinting Date: 2 Nov 1994 09:16:38 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HJ02QGFWQA8YBZ6E@UTSW.SWMED.EDU> NNTP-Posting-Host: net.bio.net Dear protein experts, has anyone ever heard of protein -protein footprinting?? pl send me your replies at iyer@swmed.utsw.edu thanks a lot N.iyer From owner-proteins@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uunet!newstf01.cr1.aol.com!newsbf01.news.aol.com!not-for-mail From: akravetz@aol.com (AKravetz) Newsgroups: bionet.molbio.proteins Subject: Re: YY1 expression and purification. Date: 2 Nov 1994 03:20:03 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 8 Sender: news@newsbf01.news.aol.com Message-ID: <397i3j$keq@newsbf01.news.aol.com> References: <38ks3c$r5e@nuscc.nus.sg> NNTP-Posting-Host: newsbf01.news.aol.com In article <38ks3c$r5e@nuscc.nus.sg>, mcbtansh@leonis.nus.sg (Tan Shyh Han) writes: yes, I do, what do you want to know, To get YY1 expressed well, use the Qiagen pQ vectors. they express well, A slight change, use only 6M guandine-hcl, if any questions, email me at kravetz@sluvca.slu.edu andy From owner-proteins@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!swrinde!pipex!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!mrc-lmb.cam.ac.uk!sanz From: sanz@mrc-lmb.cam.ac.uk (Sanz J./Fersht) Newsgroups: bionet.molbio.proteins Subject: Re: Serine phosphorylation Date: 2 Nov 1994 10:12:41 GMT Organization: MRC Laboratory of Molecular Biology, Cambridge UK Lines: 10 Distribution: bionet Message-ID: <397omp$37h@lyra.csx.cam.ac.uk> References: <3937l7$afm@mserv1.dl.ac.uk> NNTP-Posting-Host: al.mrc-lmb.cam.ac.uk Thank you very much for all the help. Jesus -- Dr. Jesus M. Sanz Phone (34)(1)5611800 Centro de Investigaciones Biologicas Fax (34)(1)5644570 Velazquez, 144 28006-Madrid email: cibsm1s@cc.csic.es Spain From owner-proteins@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!news.sprintlink.net!qns1.qns.com!constellation!news.uoknor.edu!ppp200.modems.uoknor.edu!user From: gddavis@essex.ecn.uoknor.edu (Greg Davis) Newsgroups: bionet.molbio.proteins Subject: AatII Restriction Enzyme Followup-To: bionet.molbio.proteins Date: 1 Nov 1994 17:38:54 GMT Organization: University of Oklahoma - Biochemical Engineering Lines: 9 Distribution: world Message-ID: NNTP-Posting-Host: 129.15.92.200 Can anyone tell me how the activity (cutting efficiency) of AatII compares to very active enzymes such as EcoRI? Thanks. * Greg Davis * * gddavis@essex.ecn.uoknor.edu * * University of Oklahoma * * Biotechnology Research * From owner-proteins@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!univ-lyon1.fr!ws41.cnusc.fr!ciril.fr!thot.u-strasbg.fr!usenet From: nussbaum@neurochem.u-strasbg.fr Newsgroups: bionet.molbio.proteins Subject: galactosyltransferase Date: 2 Nov 1994 09:14:57 GMT Organization: cnrs Lines: 6 Message-ID: <397lah$1b9@thot.u-strasbg.fr> NNTP-Posting-Host: noiset.u-strasbg.fr X-Newsreader: We would like to test antibodies raised against UDP-galactose: N-acetylglucosamine galactosyltransferase (EC 2.4.1.38) with a galactosyltransferase preparation obtained from rat brain. If somebody could provide a sample, please inform me Many thanks Nuss From owner-proteins@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uunet!heifetz.msen.com!zib-berlin.de!fauern!uni-regensburg.de!pc3600.klinik.uni-regensburg.de!Robert.Hofmeister From: Robert.Hofmeister@klinik.uni-regensburg.de (Robert Hofmeister) Newsgroups: bionet.molbio.proteins Subject: APOLIPOPROTEIN E IN KERATINOCYTES Date: Wed, 2 Nov 1994 09:53:00 Organization: Institut für Klinische Chemie & Laboratoriumsmedizin Lines: 5 Distribution: world Message-ID: NNTP-Posting-Host: pc3600.klinik.uni-regensburg.de Keywords: apo E, keratinocytes X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Hi, does anyone know in how to increase apoE production in cultured human keratinocytes ? Any idea of what stimulating conditions, drugs or other means could be applied ? Do you know anyone who is involved in a similar problem ? Thank you so much for your help. (Robert.Hofmeister@klinik.uni-regensburg.de) From owner-proteins@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!fotgar.uba.ar!pedro From: pedro@fotgar.uba.ar ("Pedro Fernandez Murray ") Newsgroups: bionet.molbio.proteins Subject: LAP specificity Date: 2 Nov 1994 09:18:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <2eb7c305.fotgar@fotgar.uba.ar> NNTP-Posting-Host: net.bio.net I am studying the effect of substrate phosphorylation on aminopeptidase activity. Preliminary experiments carried out with Leucine aminopeptidase= (LAP) purified from swine kidney using a synthetic heptapeptide=20 (L-R-R-A-S-L-G) as substrate have shown that the peptide was hydrolyzed t= o=20 its constituent aminoacids. These results are not in accordance with the = 20 previously reported LAP substrate specificity, since, in my hands the enz= yme could hydrolyze basic residues of this synthetic peptide. Please, I would= appreciated bibliographic references dealing with the substrate specifici= ty=20 studies on the LAP of swine kidney (or bovine lens). Any additional comme= nts will be welcome. --- Pedro Fernandez Murray=20 From owner-proteins@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!scsing.switch.ch!elna.ethz.ch!smac.ethz.ch!user From: tan@aeolus.vmsmail.ethz.ch (Song Tan) Newsgroups: bionet.molbio.proteins Subject: Re: AatII Restriction Enzyme Date: Wed, 02 Nov 1994 18:01:28 +0100 Organization: ETH Zurich, Switzerland Lines: 22 Distribution: world Message-ID: References: NNTP-Posting-Host: smac.ethz.ch In article , gddavis@essex.ecn.uoknor.edu (Greg Davis) wrote: > Can anyone tell me how the activity (cutting efficiency) of AatII compares > to very active enzymes such as EcoRI? > This is just one data point, and it's not even my own work. Thomas Rechsteiner, a postdoc in our lab, had to use AatII a while ago and he had lots of problems getting proper cutting with AatII (from Biolabs). He tried cutting pUC and pBR based plasmids and found that he could nick the DNA on one strand, but he couldn't get complete double stranded cuts unless he digested for a LONG time. Since then, I've mentally pegged AatII as one of those enzymes to stay away from where possible, but I'd love to hear others' experiences. -- Song Tan Institute for Molecular Biology and Biophysics ETH-Honggerberg (Swiss Federal Institute of Technology) 8093 Zurich, Switzerland email: tan@aeolus.vmsmail.ethz.ch From owner-proteins@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!EU.net!uunet!noc.near.net!chaos.dac.neu.edu!lynx.dac.neu.edu!pthomas From: pthomas@lynx.dac.neu.edu (Paul Thomas) Newsgroups: bionet.molbio.proteins Subject: Re: help--AA sequence analysis Date: 2 Nov 1994 17:20:20 GMT Organization: Northeastern University, Boston, MA. 02115, USA Lines: 14 Distribution: world Message-ID: <398hok$lcp@chaos.dac.neu.edu> References: <396k5p$hrs@senator-bedfellow.MIT.EDU> NNTP-Posting-Host: lynx.dac.neu.edu X-Newsreader: TIN [version 1.2 PL1] John O Konz (johnkonz@athena.mit.edu) wrote: : I've noticed a large number of programs available on the net to compare : sequences to each other, etc, but is there a program available that simply : takes the sequence and gives the number of each amino acid, or percent by : weight? Thanks. : John John, Are you familiar with the GCG package? Within the group of Protein Analysis programs in that pakcage there is one, 'PeptideSort', that is intended for peptide analysis but as part of its output provides the composition of the whole protein in terms of numbers of residues. Paul Thomas From owner-proteins@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!sol.ctr.columbia.edu!hamblin.math.byu.edu!news.Arizona.EDU!helium.gas.uug.arizona.edu!bear From: bear@helium.gas.uug.arizona.edu (Soaring Bear) Newsgroups: bionet.molbio.proteins Subject: Re: active site tyrosines? Date: 2 Nov 1994 16:07:36 GMT Organization: University of Arizona, Unix Users Group Lines: 20 Message-ID: <398dg8$aro@news.CCIT.Arizona.EDU> References: <38jhjc$4ud@sun2.ruf.uni-freiburg.de> NNTP-Posting-Host: helium.gas.uug.arizona.edu In article <38jhjc$4ud@sun2.ruf.uni-freiburg.de>, Matthias Dreyer wrote: > does anyone of you know an enzyme with a catalytically active >tyrosine residue that is deprotonated during catalysis? The only one >I am aware of is fructose-1,6-bisphosphate aldolase, and to >my knowledge the tyrosine is probably not fully deprotonated,but rather >serves as a proton donor and acceptor at the same time. Tyr is the active aa in topoisomerase, in the trans-esterification with DNA phosphates. It's proton definitly moves though I don't know of any studies which have demonstrated exact path. bear -- * UU UU SOARING BEAR * * UU UU A Pharmaceutical Molecular Modeling * * UUUU AAA U.A. New Pharmacy 404, Tucson, AZ 85721 * * AA AA e-mail:bear@ellington.pharm.arizona.edu * From owner-proteins@net.bio.net Tue Nov 01 22:00:00 1994 Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!news.UVic.CA!spruce.pfc.forestry.ca!PFC.Forestry.CA!AEKRAMODDOUL From: aekramoddoul@PFC.Forestry.CA (Ekramoddoullah, Abul Kalam M.) Subject: Re: Quantitative protein determinations in plant extracts Message-ID: <1994Nov1.232711.25054@spruce.pfc.forestry.ca> Sender: news@spruce.pfc.forestry.ca Nntp-Posting-Host: pfc.pfc.forestry.ca Reply-To: aekramoddoul@PFC.Forestry.CA Organization: Forestry Canada (Pacific Forestry Centre) References: Date: Tue, 1 Nov 1994 23:27:11 GMT Lines: 25 Xref: biosci bionet.molbio.methds-reagnts:20405 bionet.molbio.proteins:3027 In article , bipin dalmia writes: > >what is an absolute method of protein determination in plant extracts >besides gravimetric analysis? in particular, does anyone have data on how >nitrogen combustion, Kjeldahl or any other method compare when >determining total protein content in any kind of crude preparations? we >are getting pretty large differences between lowry (folin), BCA and >bradford assays. these were done with BSA as a standard, and all buffer >inteferences were eliminated. > >bip Not knowing how you had prepared the crude extract and type of plant and tissue used for extraction, I have a feeling that your extracts contained phenolic copmpunds free or bound which give rise this difference. I had a similar problem a few years ago with conifer tissues. I had overcome these obstacles by developing a suitable method for protein extraction and subsequent method for the determination protein in plant extracts. The latter method will be published in Phytochemical Analysis shortly. If you would like to discuss this further, please feel free to give me a call me at following number. Thanks Abul EKRAMODDOULLAH, ABUL KALAM M. Title: Research Scientist Forestry Canada Phone: (604) 363-0600 Victoria, B.C. Internet: AEKRAMODDOUL@A1.PFC.Forestry.CA From owner-proteins@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!EU.net!uunet!psinntp!alsys1!alsys1.aecom.yu.edu From: gindi@alsys1.aecom.yu.edu (gindi) Newsgroups: bionet.molbio.proteins Subject: udp-n-acetyl-glucosamine Message-ID: <3298@alsys1.aecom.yu.edu> Date: 2 Nov 94 17:51:14 GMT Sender: news@alsys1.aecom.yu.edu Lines: 5 Nntp-Posting-Host: cushing.aecom.yu.edu X-Posted-From: InterNews 1.0.1@cushing.aecom.yu.edu X-Authenticated: gindi on POP host alsys1.aecom.yu.edu UDP-n-acetyl-glucosamine can be found in glycoproteins. What happens to this sugar molecule when it detaches from the glycoprotein. Is it reutilized in glycoprotein synthesis, is it oxidized to CO2, is it excreted. I am unable to find this information after searching the literAture. From owner-proteins@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!MANI.CBS.UMN.EDU!npv From: npv@MANI.CBS.UMN.EDU (Nora Plesofsky-Vig) Newsgroups: bionet.molbio.proteins Subject: AatII cutting Date: 2 Nov 1994 12:26:07 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411022026.AA01148@mani.cbs.umn.edu> Reply-To: nora@molbio.cbs.umn.edu NNTP-Posting-Host: net.bio.net In response to the question of whether AatII is a problem as a restriction enzyme, I have had very good luck in using it for cloning, except when the enzyme was old. With relatively fresh AatII from Promega, the enzyme cut the pGEM plasmid and the inserted DNA fine. Nora Plesofsky-Vig University of Minnesota nora@molbio.cbs.umn.edu From owner-proteins@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!agate!library.ucla.edu!psgrain!nntp.ski.mskcc.org!mac-171.rrl-g4.ski.mskcc.org!user From: sjeffrey@mskcc.org (Sue Jeffrey) Newsgroups: bionet.molbio.proteins Subject: Chimeric receptor choice Followup-To: bionet.molbio.proteins Date: 2 Nov 1994 20:07:12 GMT Organization: Memorial Sloan-Kettering Cancer Center Lines: 12 Message-ID: NNTP-Posting-Host: mac-171.rrl-g4.ski.mskcc.org I'm trying to construct a chimeric receptor and I would like input on a suitable extracellular portion. I would like it to be as small as possible, since the vector I am using has a size constraint (it should be about 1-1.5 kb max for the extracellular portion). Other criteria: it should only be present on specialized cells, and have commercially available ligand and antibody. Originally I was using the cFMS receptor (CSF-1 receptor) but it is too large. Any advice would be appreciated. Sue Jeffrey Memorial Sloan-Kettering Cancer Center New York City email: sjeffrey@ski.mskcc.org From owner-proteins@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: vachon@bio.grenet.fr (Gilles VACHON) Newsgroups: bionet.molbio.proteins Subject: Pr. Bouriotis fax/e-mail ?? Date: 3 Nov 1994 09:41:20 -0000 Lines: 17 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <39ab80$pim@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk Posted-Date: Thu, 3 Nov 1994 10:40:33 +0000 Dear networkers Does anyone on the net know the e-mail/fax/tel/address of Pr. Bouriotis (Crete) who works on prokaryotic enzymes? Thanks for your help Dr. Gilles Vachon c/o Pr. MACHE Laboratoire de Biologie Moleculaire Vegetale CERMO, 3eme etage Universite J. Fourier, BP 53X 38041 GRENOBLE CEDEX FRANCE Tel: (33) 76 51 45 48 fax: (33) 76 51 43 36 e-mail: vachon@bio.grenet.fr From owner-proteins@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!cea.fr!usenet From: cisitm@albert.cad.cea.fr (Pierre Didierjean) Newsgroups: bionet.molbio.proteins Subject: *** Q: WHAT KIND OF PEOPLE ON THE NET ? Date: 3 Nov 1994 16:17:14 GMT Organization: SSII Lines: 28 Sender: cisitm@albert.cad.cea.fr Message-ID: <39b2ea$9pn@anemone.saclay.cea.fr> NNTP-Posting-Host: nyassa.cad.cea.fr I'd like to know what kind of people i find on the net. Students, Commercials, Adminitrations, Scientifics or what ?? Is anybody knows that or have statistical results ? What are YOU doing in life ? I am a system administrator. Thanks for the answers and sorry for my english ..... Bye +-----------------------------------------------------------------------------+ | Pierre DIDIERJEAN | | | | Administrateur Systeme UNIX | | Cisi, Aix-en-Provence | | France | +-----------------------------------------------------------------------------+ | email : cisitm@albert.cad.cea.fr | +-----------------------------------------------------------------------------+ From owner-proteins@net.bio.net Wed Nov 02 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!rutgers!gatech!howland.reston.ans.net!newsserver.jvnc.net!cyanamid!igate.cyanamid.com!sandy From: sandy@icr.pt.cyanamid.COM (Sandy Silverman) Subject: Re: Chitinase assay In-Reply-To: GReguera@microbio.umass.edu's message of Fri, 21 Oct 1994 14:54:42 Message-ID: Sender: news@cyanamid.uucp Organization: American Cyanamid Company References: Date: Thu, 3 Nov 1994 22:01:46 GMT Lines: 7 See Kuranda and Robbins, PNAS 84:2585-2589 (1987) for assay with methylumbelliferyl-chititriose fluorescence assay. ------Sandy -- Sanford Silverman >Opinions expressed here are my own< American Cyanamid silvermans@pt.cyanamid.com "Yeast is Best" From owner-proteins@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!mule.fhcrc.org!news From: Tim Buss Newsgroups: bionet.molbio.proteins Subject: Protein disulphide isomerase Date: 3 Nov 1994 20:35:18 GMT Organization: Fred Hutchinson Cancer Research Center Lines: 7 Distribution: world Message-ID: <39bhi6$p7n@mule.fhcrc.org> NNTP-Posting-Host: 140.107.14.25 X-UserAgent: Nuntius v1.1.1d24 X-XXDate: Thu, 3 Nov 94 20:38:28 GMT Does anybody use protein disulphide isomerase??? If so, please can you tell me where you get it. Any advice on its use would also be appreciated! Thanks in advance, Tim Buss From owner-proteins@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!scripps.edu!misrael From: misrael@scripps.edu (Mark Israel) Newsgroups: bionet.molbio.proteins Subject: Re: Newest version of Raster3d ? Date: 3 Nov 1994 23:35:22 GMT Organization: The Scripps Research Institute, La Jolla, California, USA Lines: 24 Message-ID: <39bs3r$1fu@riscsm.scripps.edu> References: NNTP-Posting-Host: struct.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In article , amuelle3@gwdu03.gwdg.de (Arne Mueller ) writes: > I'm a student of biology in Germany and want to install Raster3d. Perhaps > somebody of you can tell me which is the newest version of the program > (and where to get)and which other tools are useful for the work with > Raster3d. There's no new version. :-( The old version is available by anonymous ftp from stanzi.bchem.washington.edu (128.95.12.38). This outstanding rendering program badly needs a new user interface. Raster3D is public domain, so anyone can do it. I have now been giving the job of developing Duncan McRee's XtalView program suite. I hope to implement Raster3D as a submenu in XtalView/xfit, so that you can use xfit to select your atoms and view, and then go to the Raster3D submenu to choose rendering options. Supportive e-mail would help me persuade my bosses that this needs doing, since the users here at Scripps favour a different rendering program (AVS, which costs money). Look for results next year some time! -- misrael@scripps.edu Mark Israel From owner-proteins@net.bio.net Thu Nov 03 22:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!news.service.uci.edu!newt.mmg.uci.edu!user From: mlwaterm@uci.edu (Marian Waterman) Newsgroups: bionet.molbio.proteins Subject: Re: protein footprinting Date: 4 Nov 1994 20:49:35 GMT Organization: MicroBiology, UC Irvine Lines: 24 Distribution: world Message-ID: References: <01HJ02QGFWQA8YBZ6E@UTSW.SWMED.EDU> NNTP-Posting-Host: newt.mmg.uci.edu In article <01HJ02QGFWQA8YBZ6E@UTSW.SWMED.EDU>, IYER@UTSW.SWMED.EDU wrote: > Dear protein experts, > has anyone ever heard of protein -protein footprinting?? > pl send me your replies at iyer@swmed.utsw.edu > thanks a lot > N.iyer Yes, Michael Carey at UCLA has been working to optimize this technology. The theory is similar to DNAase I footprinting. Protein is radiolabelled with a kinase, and subjected to limited proteolysis while complexed with a second, interacting protein. Regions of the protein involved in direct protein-protein contact will be protected from proteolytic clipping. The reaction is run on SDS-PAGE next to a control digest of the radiolabelled protein alone, and the two patterns compared. Michael was able to correctly identify the domain of TFIIB that is directly contacted by the transcription activation of herpes VP16 protein. Marian Waterman Microbiology and Molecular Genetics UC Irvine mlwaterm@uci.edu From owner-proteins@net.bio.net Thu Nov 03 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: yduroche@cri.ens-lyon.fr (Yves Durocher) Newsgroups: bionet.molbio.proteins Subject: Anti-lamin antibodies Date: 4 Nov 1994 09:50:10 -0000 Lines: 7 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <39d04i$73m@mserv1.dl.ac.uk> content-length: 157 Original-To: proteins@dl.ac.uk Is someone know where to get anti-lamin antibodies ? I looked in every available catalogue in the lab...niet. Thanks in advance Yves Durocher Lyon, France From owner-proteins@net.bio.net Thu Nov 03 22:00:00 1994 Path: biosci!UCSD.EDU!lgoldstein From: lgoldstein@UCSD.EDU (larry goldstein) Newsgroups: bionet.molbio.proteins Subject: Re: protein footprinting Date: 4 Nov 1994 14:06:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <199411042206.OAA10435@ucsd.edu> NNTP-Posting-Host: net.bio.net their are also methods based on chemical protection, i.e., one assays modification of cysteines or methionines by NCS (reportedly oxidizes solvent exposed residues faster than buried residues) in the presence of some binding protein. modification is assessed by cleavage with NTCB or CnBr. the catch for all of these methods is whether one is looking at residues buried in a binding interface or residues in a region of protein that changes conformation upon binding. anybody manage to distinguish these two possibilities without a crystal structure? larry goldstein ucsd >In article <01HJ02QGFWQA8YBZ6E@UTSW.SWMED.EDU>, IYER@UTSW.SWMED.EDU wrote: > >> Dear protein experts, >> has anyone ever heard of protein -protein footprinting?? >> pl send me your replies at iyer@swmed.utsw.edu >> thanks a lot >> N.iyer > > >Yes, Michael Carey at UCLA has been working to optimize this technology. >The theory is similar to DNAase I footprinting. Protein is radiolabelled >with a kinase, and subjected to limited proteolysis while complexed with a >second, interacting protein. Regions of the protein involved in direct >protein-protein contact will be protected from proteolytic clipping. The >reaction is run on SDS-PAGE next to a control digest of the radiolabelled >protein alone, and the two patterns compared. Michael was able to >correctly identify the domain of TFIIB that is directly contacted by the >transcription activation of herpes VP16 protein. > >Marian Waterman >Microbiology and Molecular Genetics >UC Irvine > >mlwaterm@uci.edu From owner-proteins@net.bio.net Thu Nov 03 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!think.com!mbcrr!schmidt From: schmidt@mbcrr.dfci.harvard.edu (Bill Schmidt) Newsgroups: bionet.molbio.proteins Subject: Gopher/WWW Servers Announcement Date: 4 Nov 1994 20:57:45 GMT Organization: Dana-Farber Cancer Institute Lines: 121 Distribution: world Message-ID: <39e789INNnnc@early-bird.think.com> NNTP-Posting-Host: mbcrr.harvard.edu Originator: schmidt@mbcrr The BioMolecular Engineering Research Center & Molecular Biology Computer Research Resource at Boston University (collectively referred to here as BMERC) announces the availability of its Gopher and World Wide Web (WWW) servers. * The URL for the BMERC WWW server Home Page is: http://bmerc-www.bu.edu/ * The gopher server can be accessed at the address given immediately below. NOTE that the gopher can be accessed BOTH through gopher and through a link provided on the BMERC WWW server Home Page. bmerc-gopher.bu.edu ---------------------------------------------------------------- The BMERC research objectives are summarized immediately below, and the tools and interfaces described below which are available through the BMERC gopher/WWW servers either support, or result from, the Center's work. * To develop statistical and other computational approaches which will detect syntactic and semantic patterns in DNA, RNA, and protein sequences. * To use statistical/computational approaches to identify the structure, function, and regulation associated with such patterns. The component tools and interfaces, described below, are in an early stage of development. We will continue to expand and develop these tools/interfaces based on our own experiences with them, and by actively soliciting and incorporating feedback from our collaborators, user community, and beta test sites. E-MAIL SERVER ------------- An e-mail server, called the Protein Sequence Analysis (PSA) System, is available for researchers who have amino acid sequences for proteins of unknown structure and for which no homologous sequences are known. The server takes a single amino acid sequence as input, and analyzes it to determine the probable tertiary structural class of the protein and the probable secondary structure for each of the residues. The output consists of four files which are emailed to the requestor; three postscript files which graphically summarize the analysis, and a text file. Instructions for accessing the server, a short description of the calculations being performed and associated journal references are available through the gopher/WWW servers. PROTEIN STRUCTURE/HOMOLOG DATABASE ---------------------------------- The gopher/WWW servers provide access to ProLink, a locally-developed integrated database of protein structure, sequence homolog, and functional pattern information installed in a relational format under Sybase. The current data is derived from the Brookhaven Protein Data Bank (proteins of known structure), Protein Family Pattern Database (also known as the Plsearch Database), Enzyme Nomenclature Database, Protein Core Structures Database (currently under development here at BMERC), and includes homolog links to the BLOCKS database, GenPept, SWISS-PROT and Medline. It also has indirect links to Prosite, OMIM and GDB databases. Currently, ProLink can be searched using the gopher/WWW SQL query library, a set of prepackaged SQL queries. In the near future, access to ProLink will be greatly expanded by increasing the size of the SQL query library, and by implementing the WWW server's mosaic-based forms interface. In the latter approach, a user is able to specify a wide range of search parameters, thereby permitting the user to tailor a search to his/her specific interests. SOFTWARE DISTRIBUTION --------------------- Through its FTP site, accessible through its gopher/WWW servers, BMERC distributes, free of charge as part of its dissemination program, software that it develops in meeting the objectives listed above, as well as non-commerical software developed by others, datafiles, and support information. In particular, the PLSearch database of homologous protein family patterns, and the associated search-and-discovery software, is available. Bill Schmidt Interface Specialist BioMolecular Engineering Research Center (BMERC) Boston University 36 Cummington Street Boston, MA 02215 USA (617) 353-7123 gophradm@darwin.bu.edu wwwadmin@darwin.bu.edu From owner-proteins@net.bio.net Thu Nov 03 22:00:00 1994 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!gatech!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!pobox.upenn.edu!yluo From: yluo@pobox.upenn.edu (yuling luo) Newsgroups: bionet.molbio.proteins Subject: Re: PROTEIN PURIFICATION - WOE IS ME!!! Date: 5 Nov 1994 06:55:42 GMT Organization: University of Pennsylvania Lines: 54 Message-ID: <39fa9e$has@netnews.upenn.edu> References: <391abg$3fq@mark.ucdavis.edu> NNTP-Posting-Host: pobox.upenn.edu X-Newsreader: TIN [version 1.2 PL2-upenn1.1] Since it is a membrane bound and high pI protein, I will not be surprise if it sticks to other negatively charged or hydrophic proteins. I have a few suggestions. 1) run through a Q-sepharose column to get rid of a lot of the acidic protein first, then use the the wash through to load the S-sepharose column. 2) try high salt and high pH loading conditions. 3) try different brand of resins. Good luck. Marc Goldstein (ez001427@dale.ucdavis.edu) wrote: : Andy- : I have tried on several occaisions to purify basic proteins on S : media. I rarely get it to work well. I have learned instead to use Q : media, with sodium phosphate buffer at low (10-15 mM) concentration. I : know that it probably sounds odd, but I find that this often works well. : If the pH of the buffer is 7.5 to 8, most proteins will stick to the : resin, but highly basic ones should (and often do) flow through. : Is your protein really basic or is it supposed to be basic, based : on a calculated pI? Often there is a big difference between calculated : and actual isoelectric points. : Good luck. Be sure to post a result so we can all see what : finally worked for you! : Marc Goldstein : University of California, Davis : Section of Plant Biology : magoldstein@ucdavis.edu : Andy Hill (afh30@dka.sm.ic.ac.uk) wrote: : : Hi There! : : I am trying to purify a protein which i am overexpressing in a mammalian : : cell culture system. It is soluble in anionic detergents (membrane bound) : : and is very basic. Hence I am trying to use a strong cation exchanger to : : purify the protein away from other cellular proteins. : : I am using S-Sepharose and lysing the cells in B-D-Octyl-Glucoside or : : Sulfobetaine SB3-12. I have tried altering the pH and the composition of : : my buffers (used Triethanolamine at ph 7.5, MES at pH 6.5). I generally : : run a gradient of 0-1M salt in buffer over a 10ml column using Bio-Rad : : Econo-System setup. The problem is that EVERYTHING comes out in the void : : volume - i.e. nothing will stick to the column. I equilibrate the column : : in the running buffer beforehand - after taking it out of the 20% ethanol : : soultion. : : Could anyone out there suggest anything I could try to get at least : : something to stick so I know the resin works! As I am very new to this : : kind of work I may have missed something simple - any comments would be : : greatly appreciated! : : Thanks : : Andy From owner-proteins@net.bio.net Fri Nov 04 22:00:00 1994 Path: biosci!ITSA.UCSF.EDU!nmatsui From: nmatsui@ITSA.UCSF.EDU (Neil M Matsui) Newsgroups: bionet.molbio.proteins Subject: Number of sequences Date: 5 Nov 1994 08:01:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Could anyone please tell me how many proteins were sequenced in the past year? If possible, break this down into sequencing by Edman degradation and mass spectrometry. Also, how many partial sequences were found? These data would be very useful to me. Thank you. Neil Matsui (nmatsui@itsa.ucsf.edu) University of California, San Francisco From owner-proteins@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!ns1.faseb.org!darwin.sura.net!nntp.st.usm.edu!whale.st.usm.edu!mjlogan From: mjlogan@whale.st.usm.edu (Mark Jason Logan) Newsgroups: bionet.molbio.proteins Subject: CONTIN Date: 7 Nov 1994 19:40:46 GMT Organization: University of Southern Mississippi Lines: 9 Message-ID: <39lvru$i71@server.st.usm.edu> NNTP-Posting-Host: whale.st.usm.edu X-Newsreader: TIN [version 1.2 PL1] Does anyone know where I can get a copy of the circular dichroism analysis package CONTIN by S. Provencher? I tried looking at embl heidelberg but had no luck locating it. If at all possible I need a copy that will run on a IBM compatible PC. Thanks alot Mark From owner-proteins@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!spool.mu.edu!caen!usenet.coe.montana.edu!Msu.oscs.montana.edu!fintan_v From: fintan_v@Msu.oscs.montana.edu Newsgroups: bionet.molbio.proteins Subject: Old HP HPLC software wanted Date: Mon, 07 Nov 1994 12:13:52 Organization: Montana State University Lines: 18 Message-ID: <009871C1.7E3EEE60@Msu.oscs.montana.edu> Reply-To: fintan_v@Msu.oscs.montana.edu NNTP-Posting-Host: ercvx1.erc.montana.edu We are in a bind and would appreciate any help offered with the following problem. We are using an old HP 79994A workstation to run a HPLC. We would like to be able to take the files generated by this machine, and use some of the nice high tech curve fitting programs that are available. The problem is that this workstation uses a propriatary system that makes the disks (720k 3 1/2") unreadable on a PC. We have contacted HP and they told us that they used to have software that could be put onto a PC and would allow reading of the disks. However they no longer sell the program (discontinued). Does anyone have a copy of this software that we could have? It is called "I2080A LIF Files Utility" Alternatively does anyone know of any other software capable of carrying out this reading/conversion task. Thanks From owner-proteins@net.bio.net Sun Nov 06 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!sunsite.doc.ic.ac.uk!cc.ic.ac.uk!bc-26.sm.ic.ac.uk!user From: afh30@dka.sm.ic.ac.uk (Andy Hill) Subject: PROTEIN PURIFICATION WOES - AN UPDATE!!! Message-ID: Nntp-Posting-Host: bc-26.sm Organization: Prion Disease Group, SMHMS. Date: Mon, 07 Nov 1994 16:22:02 +0000 Lines: 37 Hi Again Firstly, thanks to all those who e-mailed me and posted messages. There were several suggestions which I am following up, namely: 1) Reducing pH to <4 to ppt DNA (or using PEI, protamine sulfate, etc...) 2) Trying Exclusion on Q-media first then running through S-media 3) Dilution of detergent to levels below CMC 4) Alternative buffer systems 5) Checking pI of the protein (sorry if I excluded any others, but I took them all into consideration!) OK, I tried diluting out the detergent to below CMC and running on S-Sepharose, but still got flat line after the void on the chart. I also tried reducing the pH to below 4 but this didn't seem to work either. I couldn't try the precipitations because we didnt have any PEI or protamine sulfate at the time! However, I did manage to get a good separation of proteins by running my cell extract on a Q-column (I used a Bio-Rad Econo-Q-Column). So I now have separated my protein away from a lot of other acidic proteins. I am still analysing the fractions but I guess the next step would be to put the excluded fractions on the S-Sepharose. Not bad for a Friday afternoon!!! I have just looked at the predicted net charge of the protein at pH 7 and it is +7 - is this enough for good separation? It goes up to +28 at pH 4 but I would like to avoid acid treatment on the protein. Anyway, thanks again for your ideas! Andy From owner-proteins@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!THEORY.BCHS.UH.EDU!dbd From: dbd@THEORY.BCHS.UH.EDU (Dan Davison) Newsgroups: bionet.molbio.proteins Subject: NNSSP and SSP SERVER FORMAT CHANGE- SSP Details Date: 7 Nov 1994 06:59:20 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 161 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411071459.AA00934@theory.BCHS.UH.EDU> NNTP-Posting-Host: net.bio.net The recently announced secondary structure prediction programs NNSSP and SSP have had a minor but important change to their *required* input. Please note the following: The Baylor College Of Medicine Computational Biology Group Houston, TX announces a new service SSP Prediction of a-helix and b-strand segments of globular proteins *************************************************************************** *********** NOTE FORMAT HAS CHANGED AGAIN!! ********************* *************************************************************************** Analysis of uncharacterized human sequences is available by sending a file containing a sequence name on the first line and sequence on subsequent lines (no more than 80 char/line) to (a sequence name in the first string) service@bchs.uh.edu with the Subject line "SSP". Example: mail -s SSP service@bchs.uh.edu < test.seq where test.seq a file with the sequence. NOTE: This service is temporarily being provided through the University of Houston Gene-Server. Only two jobs will be run at a time. Method description: ********************** Our segment-oriented method is designed to locate secondary structure elements and uses linear discriminant analysis to assign segments of a given amino acid sequence to a particular type of secondary structure, by taking into account the amino acid composition of internal parts of segments as well as their terminal and adjacent regions. Four linear discriminant functions were constructed for recognition of short and long a-helix and b-strand segments, respectively. These functions combine 3 characteristics: hydrophobic moment, segment singlet and pair preferences to an a-helix or b-strand. Accuracy: ************************ Overall 3-states (a, b, c) prediction gives ~65.1% (68.2% with using homologous sequences) correctly predicted residues on 126 non-homologous proteins using the jack-knife test procedure (The accuracy is good if you have no homologous sequences to apply Sander et al. method (Rost,Sander, Mol.Biol,1993,232,584-599) that has about 71% accuracy with using these sequences and about 61% without them). Analysis of the prediction results shows a high prediction accuracy of long secondary structure segments (~89% of a- helices of length greater than 8 and ~71% of b-strands of length greater than 6 are correctly located with probability of correct prediction 0.82 and 0.78 respectively). Using the mean values of discriminant functions over the aligned sequences of homologous proteins, we achieved a prediction accuracy of 68.2%. It must be mentioned that our variant of nearest-neighbor algorithm with using multiply sequence alignments of homologous proteins has 72% accuracy and 67.6% accuracy without homologous proteins (see "nnssp" program of this server). Submitting sequences via email: *********************************** For email submission the sequences must have the following format: a) if you send one sequence: 1 line - sequence name 2 line - number 1 in format I5 3 and subsequent lines - amino acid sequence for example : ADENYLATE KINASE 1 RLLRAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLA KTFIDQGKLIPDDVMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAY QIDTVINLNVPFEVIKQRLTARWIHPGSGRVYNIEFNPPKTMGIDDLTGE PLVQREDDRPETVVK............ (Restrict the line length to 75 characters). b) if you send multiple aligned sequences 1 line - sequence name 2 line - number of aligned sequences and length of protein 3 and subsequent lines - aligned sequences in format 60a1 (where 3-d line is empty or with numbers as well as other lines which separate parts of aligned sequences) for example: ACTINOXANTHIN 5 107 10 20 30 40 50 60 (numbers not APAFSVSPASGASDGQSVSVSVAAAGETYYIAQaAPVGGQDAaNPATATSFTTDASGAAS necessary) APAFSVSPASGLSDGQSVSVSGAAAGETYYIAQCAPVGGQDACNPATATSFTTDASGAAS APTATVTPSSGLSDGTVVKVAGAgaGTAYDVGQCAWVdgVLACNPADFSSVTADANGSAS APGVTVTPATGLSNGQTVTVSATgpGTVYHVGQCAVvpGVIGCDATTSTDVTADAAGKIT ATPKSSSGGAGASTGSGTSSAAVTSgaASSAQQSGLQGATGAGGGSSSTPGTQPGSGAGG 70 80 90 100 FSFTVRKSYAGQTPSGTPVGSVDbATDAbNLGAGNSGLNLGHVALTF FSFV-RKSYAGZTPSGTPVGSVDCATDACNLGAGNSGLNLGHVALTF TSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGpgVAISF AQLKVHSSFQAVvaNGTPWGTVNCKVVSCSAGLGSDSGEGAAQAITF AIAARPVSAMGGtpPHTVPGSTNTTTTAMAGGVGGPgaNPNAAALM- (you can use small letters for Cys amino acids, if you want) Alignment MUST be without deletions in the 1-st (query) sequence!!! You could send the file containing the sequence to: service@bchs.uh.edu The subject line must be: Subject: SSP Example: mail -s SSP service@bchs.uh.edu < test.seq Example of SSP output: ***************************** ADENYLATE KINASE 10 20 30 40 50 pred A: aaaaaaaaa aaaaaaaaa aaaaaaaaa aaa AA N 4.1 C N 2.2 C N 4.4 C N pred B: bbbb BB N2 C Predic aaaaaaaaa bbbb aaaaaaaaa aaaaaaaaa aaa a/acid RLLRAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLA 60 70 80 90 100 pred A: aaaaaa aaaaaaaaaaaaaaaaaaaaaaa aaaaaaaaa AA 2.2 C N 4.2 CN 2.4 C N 5.4 C pred B: bbbbbbb BB N 2.6 C Predic aaaaaa aaaaaaaaaaaaaaaaaaaaaaa aaaaaaaaa a/acid KTFIDQGKLIPDDVMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAY The output of the prediction program presents not only final optimal variant of the secondary structure assign ment, but also a set of potential a-helix and b-strand segments that were computed without consideration of their competition. Because the protein secondary structure is finally stabilized during the formation of the tertiary structure, the alternative variants of the a-helix and b-strand segments may be important for methods of tertiary structure prediction. Reference: 1.Solovyev V.V.,Salamov A.A. Method of calculation of discrete secondary structures in globular proteins. Molek. Biol. 25:810-824,1991 (in Russ.) 2.Solovyev V.V.,Salamov A.A. 1994, Secondary structure prediction based on discriminant analysis. In Computer analysis of Genetic macromolecules. (eds. Kolchanov N.A., Lim H.A.), World Scientific, p.352-364. 3. Solovyev V.V., Salamov A.A. Predicting a-helix and b-strand segments of globular proteins. CABIOS (1994) (accepted). Problems, comments, and suggestion: Can be mailed to solovyev@cmb.bcm.tmc.edu. From owner-proteins@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!THEORY.BCHS.UH.EDU!dbd From: dbd@THEORY.BCHS.UH.EDU (Dan Davison) Newsgroups: bionet.molbio.proteins Subject: NNSSP and SSP SERVER FORMAT CHANGE Date: 7 Nov 1994 06:37:46 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 161 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411071437.AA00919@theory.BCHS.UH.EDU> NNTP-Posting-Host: net.bio.net The recently announced secondary structure prediction programs NNSSP and SSP have had a minor but important change to their *required* input. Please note the following: The Baylor College Of Medicine Computational Biology Group Houston, TX announces a new service SSP Prediction of a-helix and b-strand segments of globular proteins *************************************************************************** *********** NOTE FORMAT HAS CHANGED AGAIN!! ********************* *************************************************************************** Analysis of uncharacterized human sequences is available by sending a file containing a sequence name on the first line and sequence on subsequent lines (no more than 80 char/line) to (a sequence name in the first string) service@bchs.uh.edu with the Subject line "SSP". Example: mail -s SSP service@bchs.uh.edu < test.seq where test.seq a file with the sequence. NOTE: This service is temporarily being provided through the University of Houston Gene-Server. Only two jobs will be run at a time. Method description: ********************** Our segment-oriented method is designed to locate secondary structure elements and uses linear discriminant analysis to assign segments of a given amino acid sequence to a particular type of secondary structure, by taking into account the amino acid composition of internal parts of segments as well as their terminal and adjacent regions. Four linear discriminant functions were constructed for recognition of short and long a-helix and b-strand segments, respectively. These functions combine 3 characteristics: hydrophobic moment, segment singlet and pair preferences to an a-helix or b-strand. Accuracy: ************************ Overall 3-states (a, b, c) prediction gives ~65.1% (68.2% with using homologous sequences) correctly predicted residues on 126 non-homologous proteins using the jack-knife test procedure (The accuracy is good if you have no homologous sequences to apply Sander et al. method (Rost,Sander, Mol.Biol,1993,232,584-599) that has about 71% accuracy with using these sequences and about 61% without them). Analysis of the prediction results shows a high prediction accuracy of long secondary structure segments (~89% of a- helices of length greater than 8 and ~71% of b-strands of length greater than 6 are correctly located with probability of correct prediction 0.82 and 0.78 respectively). Using the mean values of discriminant functions over the aligned sequences of homologous proteins, we achieved a prediction accuracy of 68.2%. It must be mentioned that our variant of nearest-neighbor algorithm with using multiply sequence alignments of homologous proteins has 72% accuracy and 67.6% accuracy without homologous proteins (see "nnssp" program of this server). Submitting sequences via email: *********************************** For email submission the sequences must have the following format: a) if you send one sequence: 1 line - sequence name 2 line - number 1 in format I5 3 and subsequent lines - amino acid sequence for example : ADENYLATE KINASE 1 RLLRAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLA KTFIDQGKLIPDDVMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAY QIDTVINLNVPFEVIKQRLTARWIHPGSGRVYNIEFNPPKTMGIDDLTGE PLVQREDDRPETVVK............ (Restrict the line length to 75 characters). b) if you send multiple aligned sequences 1 line - sequence name 2 line - number of aligned sequences and length of protein 3 and subsequent lines - aligned sequences in format 60a1 (where 3-d line is empty or with numbers as well as other lines which separate parts of aligned sequences) for example: ACTINOXANTHIN 5 107 10 20 30 40 50 60 (numbers not APAFSVSPASGASDGQSVSVSVAAAGETYYIAQaAPVGGQDAaNPATATSFTTDASGAAS necessary) APAFSVSPASGLSDGQSVSVSGAAAGETYYIAQCAPVGGQDACNPATATSFTTDASGAAS APTATVTPSSGLSDGTVVKVAGAgaGTAYDVGQCAWVdgVLACNPADFSSVTADANGSAS APGVTVTPATGLSNGQTVTVSATgpGTVYHVGQCAVvpGVIGCDATTSTDVTADAAGKIT ATPKSSSGGAGASTGSGTSSAAVTSgaASSAQQSGLQGATGAGGGSSSTPGTQPGSGAGG 70 80 90 100 FSFTVRKSYAGQTPSGTPVGSVDbATDAbNLGAGNSGLNLGHVALTF FSFV-RKSYAGZTPSGTPVGSVDCATDACNLGAGNSGLNLGHVALTF TSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGpgVAISF AQLKVHSSFQAVvaNGTPWGTVNCKVVSCSAGLGSDSGEGAAQAITF AIAARPVSAMGGtpPHTVPGSTNTTTTAMAGGVGGPgaNPNAAALM- (you can use small letters for Cys amino acids, if you want) Alignment MUST be without deletions in the 1-st (query) sequence!!! You could send the file containing the sequence to: service@bchs.uh.edu The subject line must be: Subject: SSP Example: mail -s SSP service@bchs.uh.edu < test.seq Example of SSP output: ***************************** ADENYLATE KINASE 10 20 30 40 50 pred A: aaaaaaaaa aaaaaaaaa aaaaaaaaa aaa AA N 4.1 C N 2.2 C N 4.4 C N pred B: bbbb BB N2 C Predic aaaaaaaaa bbbb aaaaaaaaa aaaaaaaaa aaa a/acid RLLRAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLA 60 70 80 90 100 pred A: aaaaaa aaaaaaaaaaaaaaaaaaaaaaa aaaaaaaaa AA 2.2 C N 4.2 CN 2.4 C N 5.4 C pred B: bbbbbbb BB N 2.6 C Predic aaaaaa aaaaaaaaaaaaaaaaaaaaaaa aaaaaaaaa a/acid KTFIDQGKLIPDDVMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAY The output of the prediction program presents not only final optimal variant of the secondary structure assign ment, but also a set of potential a-helix and b-strand segments that were computed without consideration of their competition. Because the protein secondary structure is finally stabilized during the formation of the tertiary structure, the alternative variants of the a-helix and b-strand segments may be important for methods of tertiary structure prediction. Reference: 1.Solovyev V.V.,Salamov A.A. Method of calculation of discrete secondary structures in globular proteins. Molek. Biol. 25:810-824,1991 (in Russ.) 2.Solovyev V.V.,Salamov A.A. 1994, Secondary structure prediction based on discriminant analysis. In Computer analysis of Genetic macromolecules. (eds. Kolchanov N.A., Lim H.A.), World Scientific, p.352-364. 3. Solovyev V.V., Salamov A.A. Predicting a-helix and b-strand segments of globular proteins. CABIOS (1994) (accepted). Problems, comments, and suggestion: Can be mailed to solovyev@cmb.bcm.tmc.edu. From owner-proteins@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!THEORY.BCHS.UH.EDU!dbd From: dbd@THEORY.BCHS.UH.EDU (Dan Davison) Newsgroups: bionet.molbio.proteins Subject: NNSSP and SSP SERVER FORMAT CHANGE Date: 7 Nov 1994 06:36:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 145 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411071436.AA00918@theory.BCHS.UH.EDU> NNTP-Posting-Host: net.bio.net The recently announced secondary structure prediction programs NNSSP and SSP have had a minor but important change to their *required* input. Please note the following: The Baylor College Of Medicine Computational Biology Group Houston, TX announces a new service NNSSP Prediction of protein secondary sturcture by combining nearest-neighbor algorithms and multiple sequence alignments (version 1. 10.5.94) *************************************************************************** *********** NOTE FORMAT HAS CHANGED AGAIN !! ********************* *************************************************************************** Analysis of protein primary sequences is available through the University of Houston Gene-Server by sending the file containing a sequence (a sequence name in the first string) to service@bchs.uh.edu with the subject line "nnssp". Example: mail -s nnssp service@bchs.uh.edu < test.seq where test.seq a file with the sequence. Method description: ********************** Yi and Lander (*) developed a neural-network and nearest-neighbor method with a scoring system that combined a sequence similarity matrix with the local structural environment scoring scheme of Bowie et al.(**) for predicting protein secondary structure. We have improved their scoring system by taking into consideration N- and C-terminal positions of a-helices and b-strands and also b-turns as distinctive types of secondary structure. Another improvement, which also significantly decrease the time of computation, is performed by restricting a data base with a smaller subset of proteins which are similar with a query sequence. Using multiple sequence alignments rather than single sequences and a simple jury decision method we achieved an over all three-state accuracy of 72.2%, which is better than that observed for the most accurate multilayered neural network approach, tested on the same data set of 126 non-homologous protein chains. (*) Yi T-M., Lander E.S. (1993) Protein secondary structure prediction using nearest-neighbor methods. J.Mol.Biol.,232:1117-1129. (**) Bowie J.U., Luthy R., Eisenberg D. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.) Accuracy: ************************ Overall 3-states (a, b, c) prediction gives ~67.6% correctly predic- ted residues on 126 non-homologous proteins using the jack-knife test procedure. Using multiple sequence alignments instead of single sequences increases prediction accuracy up to 72.2%. Submitting sequences via email: *********************************** For email submission the sequences must have the following format: a) if you send one sequence: 1 line - sequence name 2 line - number 1 in format I5 3 and subsequent lines - amino acid sequence for example : ADENYLATE KINASE 1 RLLRAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLA KTFIDQGKLIPDDVMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAY QIDTVINLNVPFEVIKQRLTARWIHPGSGRVYNIEFNPPKTMGIDDLTGE PLVQREDDRPETVVK............ (Restrict the line length to 75 characters). b) if you send multiple aligned sequences 1 line - sequence name 2 line - number of aligned sequences and length of protein 3 and subsequent lines - aligned sequences in format 60a1 (where 3-d line is empty or with numbers as well as other lines which separate parts of aligned sequences) ACTINOXANTHIN 5 107 10 20 30 40 50 60 (numbers not necessary) APAFSVSPASGASDGQSVSVSVAAAGETYYIAQaAPVGGQDAaNPATATSFTTDASGAAS APAFSVSPASGLSDGQSVSVSGAAAGETYYIAQCAPVGGQDACNPATATSFTTDASGAAS APTATVTPSSGLSDGTVVKVAGAgaGTAYDVGQCAWVdgVLACNPADFSSVTADANGSAS APGVTVTPATGLSNGQTVTVSATgpGTVYHVGQCAVvpGVIGCDATTSTDVTADAAGKIT ATPKSSSGGAGASTGSGTSSAAVTSgaASSAQQSGLQGATGAGGGSSSTPGTQPGSGAGG 70 80 90 100 FSFTVRKSYAGQTPSGTPVGSVDbATDAbNLGAGNSGLNLGHVALTF FSFV-RKSYAGZTPSGTPVGSVDCATDACNLGAGNSGLNLGHVALTF TSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGpgVAISF AQLKVHSSFQAVvaNGTPWGTVNCKVVSCSAGLGSDSGEGAAQAITF AIAARPVSAMGGtpPHTVPGSTNTTTTAMAGGVGGPgaNPNAAALM- (you can use small letters for Cys aminoacids, if you want) Alignment MUST be without deletions in the 1-st (query) sequence!!! You could send the file containing the sequence to: service@bchs.uh.edu Subject line must be: nnssp Example: mail -s nnssp service@bchs.uh.edu < test.seq Example of NNSSP output: ***************************** ADENYLATE KINASE 10 20 30 40 50 Predic aaaaaaa bbb aaaaaaaa aa a/acid RLLRAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLA 60 70 80 90 100 Predic aaaaaa aaaaaaaaaaaaaa aaaaaaaaaa a/acid KTFIDQGKLIPDDVMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAY 110 120 130 140 150 Predic bbbb aaaaaaaa bb bbbbbb a/acid QIDTVINLNVPFEVIKQRLTARWIHPGSGRVYNIEFNPPKTMGIDDLTGE 160 170 180 190 200 Predic aaaaaaaaaaa aaaaaaaaaa bb aaa a/acid PLVQREDDRPETVVKRLKAYEAQTEPVLEYYRKKGVLETFSGTETNKIWP 210 Predic aaaaaaaa a/acid HVYAFLQTKLPQRS Reference: Salamov A.A., Solovyev V.V. (1994) Prediction of protein secondary sturcture by combining nearest-neighbor algorithms and multiply sequence alignments. Submitted to J.Mol.Biol. Problems, comments, and suggestion: Can be mailed to solovyev@cmb.bcm.tmc.edu. From owner-proteins@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: yduroche@cri.ens-lyon.fr (Yves Durocher) Newsgroups: bionet.molbio.proteins Subject: pET restriction map Date: 7 Nov 1994 14:04:02 -0000 Lines: 4 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <39lc4i$4b1@mserv1.dl.ac.uk> content-length: 137 Original-To: proteins@dl.ac.uk Is somebody can tell me where I can obtain the complete restriction map of the bacterial vector pET ? (More precisely pET-3c) Thanks... From owner-proteins@net.bio.net Sun Nov 06 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!fconvx.ncifcrf.gov!mack From: mack@ncifcrf.gov (Joe Mack) Subject: Re: pET restriction map Message-ID: Organization: Frederick Cancer Research and Development Center References: <39lc4i$4b1@mserv1.dl.ac.uk> Distribution: bionet Date: Mon, 7 Nov 1994 16:52:46 GMT Lines: 8 In article <39lc4i$4b1@mserv1.dl.ac.uk> yduroche@cri.ens-lyon.fr (Yves Durocher) writes: >Is somebody can tell me where I can obtain the complete restriction map of >the bacterial vector pET ? (More precisely pET-3c) >Thanks... > Call up Novagen - they have it all on disk - for US$10. Joe Mack mack@ncifcrf.gov From owner-proteins@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!THEORY.BCHS.UH.EDU!dbd From: dbd@THEORY.BCHS.UH.EDU (Dan Davison) Newsgroups: bionet.molbio.proteins Subject: PIR Release 42 Available Date: 7 Nov 1994 07:09:41 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411071509.AA00951@theory.BCHS.UH.EDU> NNTP-Posting-Host: net.bio.net PIR Release 42 is available from the UH Gene-Server Gopher, FTP, and e-mail service. As usual, the VMS format files have been transferred to Unix compress format; the original VMS files are in vms_lzw. That compression format preserves the RMS attributes of the files. ASCII files are in ftp://ftp.bchs.uh.edu/pub/gene-server/pir/pir_rel42/ascii VMS files for use in Unix GCG 7.X and 8.X are in ftp://ftp.bchs.uh.edu/pub/gene-server/pir/pir_rel42/vms VMS files preserving the VMS RMS attributes (for use with the PIR sequence analysis system) are in ftp://ftp.bchs.uh.edu/pub/gene-server/pir/pir_rel42/vms_lzw Gopher access to PIR is on gopher://gopher.bchs.uh.edu E-mail access is via gene-server@bchs.uh.edu send the word "HELP" in the subject or body of the message to get info on using the Gene-Server email system. If you have any questions on Gene-Server services, please contact davison@uh.edu. dan davison From owner-proteins@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!scripps.edu!bsd From: bsd@scripps.edu (Bruce Duncan) Newsgroups: bionet.info-theory,bionet.molbio.proteins Subject: Identification of Protein Domains Date: 8 Nov 1994 06:12:10 GMT Organization: The Scripps Research Institute, La Jolla, California, USA Lines: 26 Distribution: world Message-ID: <39n4rr$po2@riscsm.scripps.edu> NNTP-Posting-Host: convex-gw.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Xref: biosci bionet.info-theory:2792 bionet.molbio.proteins:3050 (Sorry for the repost, our mailer is sick...) Greetings, Does anyone know of a computer program that can automatically identify the domains in a protein given the x-ray structure?? A rough definition of domain is a stretch of sequence that is "locally-compact" in 3-D space. I have not seen a formal definition. Domain boundary residues are usually (always??) in random coils. Note that a single chain (subunit) can have several domains. Also, real Brookhaven pdb files don't include complete chain id information and sometimes have gaps in regions of low density. I'd like code that would work from C-alpha coordinates. Any suggestions??? Thanks, -bsd- --- Bruce Duncan The Scripps Research Institute bsd@scripps.edu -- Bruce Duncan The Scripps Research Institute bsd@scripps.edu From owner-proteins@net.bio.net Mon Nov 07 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!paladin.american.edu!constellation!news.uoknor.edu!ppp200.modems.uoknor.edu!user From: gddavis@essex.ecn.uoknor.edu (Greg Davis) Newsgroups: bionet.molbio.proteins Subject: Site Directed Mutagenesis - Current Limitations Followup-To: bionet.molbio.proteins Date: 8 Nov 1994 16:23:20 GMT Organization: University of Oklahoma - Biochemical Engineering Lines: 21 Distribution: world Message-ID: NNTP-Posting-Host: 129.15.92.200 I am interested in finding information on the current limitations in site directed mutagenesis. Specifically: 1. What are largest synthetic oligonucleotides that can be synthesized for use as primers without significant sequence errors occurring during their synthesis? (~60 bases is what I've previously heard.) 2. What is the largest sequence that has been inserted into plasmid dsDNA in site directed mutagensis using synthetic oligonucleotide primers? (the latest info I have says 18 bases) Does anyone know of any published/non-published results in excess of these? * Greg Davis * "You would be intersted to note that by * Graduate student * enforcing musical rule #753, you have just * University of Oklahoma * gotten rid of infinity of musical horse * Biotechnology Research * trot, and have thus moved to a musical * gddavis@essex.ecn.uoknor.edu * state of lower entropy" - Gary Jacobs From owner-proteins@net.bio.net Mon Nov 07 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!newsflash.concordia.ca!news.mcgill.ca!news From: popa0077@PO-Box.McGill.CA Newsgroups: bionet.molbio.proteins Subject: Source of myc epitope monoclonal Ab? Date: 8 Nov 1994 19:02:22 GMT Organization: McGill University Computing Centre Lines: 6 Message-ID: <39ohvu$o90@sifon.cc.mcgill.ca> NNTP-Posting-Host: a-09.das.mcgill.ca X-Newsreader: AIR News 3.X (SPRY, Inc.) Can anyone tell me who sells the monoclonal Ab 9E10, directed against the myc epitope? Any help would be greatly appreciated! Thanx, Troy From owner-proteins@net.bio.net Mon Nov 07 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!jcort From: jcort@u.washington.edu (J Cort) Newsgroups: bionet.molbio.proteins Subject: Re: Circular Dichroism Help!! Date: 8 Nov 1994 21:29:44 GMT Organization: University of Washington Lines: 55 Message-ID: <39oqk8$a1o@nntp1.u.washington.edu> References: <3971gp$cp1@server.st.usm.edu> NNTP-Posting-Host: homer10.u.washington.edu In article <3971gp$cp1@server.st.usm.edu>, Mark Jason Logan wrote: > >I have a few questions about CD. > >1) When is an increase in molar ellipticity significant? Is a change of >3-5% significant? This change in ellipticity could be significant, but you should rule out simple explanations for it. Maybe the protein or peptide is thermally frayable and the temperature changed. Maybe the spectra were recorded on different days and the concentration changed due to adhesion to the container, or from evaporation of water, or from drift in the sensitivity of the instrument. A change of 3-5% certainly doesn't indicate a massive structural reorganization, but it could be telling you something. >2) Also what would happen to the molar ellipticity if a helical bundle >composed of four monomeric helices was transformed to bundles containing >two monomeric helices? As long as the helicity of each helix remains constant, the molar ellipticity shouldn't change, unless the contacts between helicies in the bundle themselves (assuming they have no effect on helicity) are influencing the rotatory characteristics of the individual residues and the helicies. I would expect to see a decrease in the molar ellipticity upon dissociation of the four helix bundle if the bundle is actually stabilizing the helicies. >3) Can any one give me their opinion of the several different methods >available to calculate the total secondary structural content via >CD(Greenfield & Fasman, Chen, Russe, etc). I am using several of these >methods and routinely get extremely high values for the total secondary >structure content (as well as some negative values for certain >structures). I realize that these methods are designed to tackle proteins >containing a wide range of secondary structures, but how well do they work >on proteins that are say 80% helical? Results from these programs are often reported in the literature, occasionally (references available on request) without any of the original spectra from which the amounts of different secondary structures were calculated. This disturbs me quite a bit, not only because one cannot reconstruct a CD spectrum from the output of these programs, but also because the output is sometimes quite clearly wrong. I know of one example in which a peptide which quite clearly consisted of mostly random coil was reported to be 50% beta sheet simply because that's what the program said. (I can provide the citation for this if anyone wants to look it up). CD spectral deconvolution is an important goal, and I have no doubt that the deconvolution methods listed above can be useful, but one must be very careful when interpreting and believing the results. Most importantly, raw data or spectra should always accompany the output of a deconvolution procedure which is reported in the literature. John Cort john@peptide.chem.washington.edu From owner-proteins@net.bio.net Mon Nov 07 22:00:00 1994 Newsgroups: bionet.jobs,bionet.molbio.proteins,bionet.xtallography Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!olivea!decwrl!ames!waikato!comp.vuw.ac.nz!canterbury.ac.nz!otago.ac.nz!sanger.otago.ac.nz!craigm From: craigm@sanger.otago.ac.nz (Craig Marshall) Subject: PhD Scholarship in New Zealand Message-ID: Sender: usenet@news.otago.ac.nz (News stuff) Nntp-Posting-Host: sanger.otago.ac.nz Organization: University of Otago X-Newsreader: TIN [version 1.1 PL8] Date: Wed, 9 Nov 1994 01:55:58 GMT Lines: 26 Xref: biosci bionet.jobs:6254 bionet.molbio.proteins:3054 bionet.xtallography:1318 University of Otago Postgraduate Award -------------------------------------- A Postgraduate Award for study leading to a PhD from the University of Otago is available for three years from 1995 at a rate of $NZ12,000pa plus scholarship fees. The project offered involves the study of proteins from antarctic fish. These fish live at a temperature of -1.86 celsius at which temperature they are supercooled. The upper lethal temperature is about 5 celsius. The project would look at characterizing proteins from fish collected from McMurdo Sound and the Ross Sea to determine their kinetic properties at different temperatures. This work would lead to the determination of the structure of cold-adapted proteins by X-ray crystallography. We are particularly interested in the way that proteins have been modified to allow catalysis at low temperatures and the information this may provide about general properties of protein structures. Field trips to Antarctica would be an integral part of this work. For further information, contact Craig Marshall at the address below. -- Craig Marshall craigm@sanger.otago.ac.nz Biochemistry Department Phone +64 3 479 7570 University of Otago Fax +64 3 479 7866 From owner-proteins@net.bio.net Tue Nov 08 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: yduroche@cri.ens-lyon.fr (Yves Durocher) Newsgroups: bionet.molbio.proteins Subject: Recombinant LAMIN C Date: 9 Nov 1994 17:37:07 -0000 Lines: 7 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <39r1c3$shf@mserv1.dl.ac.uk> content-length: 182 Original-To: proteins@dl.ac.uk I would be interested to get a plasmid/bacteria expressing lamin C (nuclear envelope protein). Is someone knows where to get such a construct ? Thanks Yves Durocher, Lyon, France From owner-proteins@net.bio.net Tue Nov 08 22:00:00 1994 Path: biosci!BIOAX1.BIO.ORNL.GOV!GEWIESSA From: GEWIESSA@BIOAX1.BIO.ORNL.GOV (Andreas Gewiess) Newsgroups: bionet.molbio.proteins Subject: Re: pdb on cd-rom...HELP!!!! Date: 9 Nov 1994 13:06:23 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 78 Sender: daemon@net.bio.net Distribution: world Message-ID: <199411092106.NAA02612@net.bio.net> NNTP-Posting-Host: net.bio.net >here's hoping that someone will know what I'm asking here... > >I've got the distribution files from the protein data bank >in brookhaven on cd-rom and I'm trying to get it set up >on a powermac. My problem is getting the kinemage application >to run correctly...I can get MAGE to run but I need PREKIN >to "massage" the PDB datafiles into kinemage format (? from >what I understand). I used StuffIt to translate the one >.hqx file I found and it seems only to correspond to mage. >How do I get the PREKIN application??? I hope and pray that >someone knows the answer to this because it's driving me >insane and the documentation I have doesn't say anything >about the nuts and bolts of setting up the applications, >so I feel like a total moron!! If you have any advice, >email me at >owens@predcent.berkeley.edu >and I'll be forever grateful. > >christine owens > Dear Christine, all files you need (including PREKIN_2.5) can be found at: orion.oac.uci.edu://protein/Kinemage/macMAGE excerpt from the readme file: Protein Science Kinemage Directory 250- 250-Kinemages are "kinetic protein images" that accompany 250-many of the articles published in Protein Science. The 250-files with extension *.kin are ascii files that are 250-read by the program MAGE to produce kinemages. Kinemages 250-are produced from Brookhaven PDB formatted files using 250-the program PREKIN. 250- 250-Macintosh Users should retrieve Kinemage software and 250-related files from the macMAGE subdirectory. Executable 250-files such as Mage_3.2, PKin_2.5, or *.sea files should 250-be transferred as MacBinary II files. All executable files 250-are also available as binhex (*.Hqx) files which should be 250-transferred as ascii files and decoded using BinHex 4.0 250-or Stuff-It. "Combo" packages of complete software for each system are 250-available as compressed self-expanding archives in the 250-macMAGE and pcMAGE directories. Please note that the 250-PREKIN software for creating kinemages is located in 250-the appropriate MAGE subdirectory. 250- The "combo" pack's filename is ftp://orion.oac.uci.edu//protein/Kinemage/macMAGE/MAGE_all.sea or ftp://orion.oac.uci.edu//protein/Kinemage/macMAGE/MAGE_all.sea.Hqx Good luck! If you have trouble getting the files, drop me a note. Andreas ----------------------------------------------------------------- Andreas Gewiess Biology Division, Oak Ridge National Lab., Oak Ridge, Tennessee (615) 574-1210, gewiessa@bioax1.bio.ornl.gov "Was waere die Wahrheit, wenn sie nicht erschiene?" (Hegel) ----------------------------------------------------------------- From owner-proteins@net.bio.net Tue Nov 08 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!uhog.mit.edu!sgiblab!spool.mu.edu!caen!newsxfer.itd.umich.edu!news.itd.umich.edu!usenet From: Rick Neubig Newsgroups: bionet.molbio.proteins Subject: Postdoc position available - G protein kinetics Date: 9 Nov 1994 16:39:32 GMT Organization: University of Michigan Lines: 20 Message-ID: <39qu04$pac@lastactionhero.rs.itd.umich.edu> NNTP-Posting-Host: warbler.med.umich.edu Postdoctoral position at the University of Michigan available immediately to study G protein conformational changes and subunit-subunit interactions by real-time spectroscopic methods (see Biochem. 32:2409-2414, 1993; JBC 269:13771-13778, 1994). Candidate should have experience in membrane protein biochemistry, fluorescence spectroscopy, and/or rapid kinetics methods. Send curriculum vitae and names of references to: Dr. Richard Neubig, Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109-0632. E-mail rneubig@umich.edu. The University of Michigan is an Affirmative Action/Equal Opportunity Employer. Applications from qualified, women, minorities and/or disabled individuals are encouraged. _________________________________________________________ Rick Neubig RNeubig@umich.edu Professor of Pharmacology University of Michigan Phone (313) 763-3650 FAX (313) 763-4450 From owner-proteins@net.bio.net Tue Nov 08 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!olivea!spool.mu.edu!howland.reston.ans.net!pipex!uunet!news.claremont.edu!nntp-server.caltech.edu!kmng From: kmng@cco.caltech.edu (Kingman Ng) Newsgroups: bionet.molbio.proteins Subject: dhfr protein quantitation Date: 9 Nov 1994 08:15:10 GMT Organization: California Institute of Technology, Pasadena Lines: 6 Message-ID: <39q0ee$ck1@gap.cco.caltech.edu> NNTP-Posting-Host: piccolo.cco.caltech.edu Hi, just wondering if anybody is aware of any quick assays or extinction coefficient at 280 nm to determine the enzyme concentration of dihydrofolate reductase (dhfr). Thanks! Kingman From owner-proteins@net.bio.net Tue Nov 08 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Huesken Dieter MSM FO23 CH Newsgroups: bionet.molbio.proteins Subject: Phosphordiesterase I Date: 9 Nov 1994 17:25:27 -0000 Lines: 16 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <39r0m7$s1a@mserv1.dl.ac.uk> Autoforwarded: FALSE Original-Encoded-Info-Types: Undefined Importance: normal Original-To: News EURO Methoden+Reagentien , News USA Methoden+Reagentien , News EURO Protein , News USA Protein Dear folks, To complete my experiments I'm seeking a specific enzyme which is an 5' exonuclease (cleaves from 3' to 5') that is blocked when a 3' phosphate terminus is on the substrate. After searching the EC database I found the phosphordiesterase I (EC. 3.1.4.1 ) with these features. I'm looking for a source to obtain this enzyme under regular basis. I would appreciate any info on the subject. Thanks, Dieter Dieter Huesken CIBA-GEIGY Limited Central Research Laboratories R-1060.1.42 CH-4002 Basle, Switzerland Phone ++41 61 697 53 13 From owner-proteins@net.bio.net Tue Nov 08 22:00:00 1994 Path: biosci!agate!garnet.berkeley.edu!owens From: owens@garnet.berkeley.edu () Newsgroups: bionet.molbio.proteins Subject: pdb on cd-rom...HELP!!!! Date: 9 Nov 1994 19:54:16 GMT Organization: University of California, Berkeley Lines: 22 Message-ID: <39r9d8$70c@agate.berkeley.edu> NNTP-Posting-Host: garnet.berkeley.edu here's hoping that someone will know what I'm asking here... I've got the distribution files from the protein data bank in brookhaven on cd-rom and I'm trying to get it set up on a powermac. My problem is getting the kinemage application to run correctly...I can get MAGE to run but I need PREKIN to "massage" the PDB datafiles into kinemage format (? from what I understand). I used StuffIt to translate the one .hqx file I found and it seems only to correspond to mage. How do I get the PREKIN application??? I hope and pray that someone knows the answer to this because it's driving me insane and the documentation I have doesn't say anything about the nuts and bolts of setting up the applications, so I feel like a total moron!! If you have any advice, email me at owens@predcent.berkeley.edu and I'll be forever grateful. christine owens From owner-proteins@net.bio.net Tue Nov 08 22:00:00 1994 Path: biosci!news.alaska.edu!netnews.nwnet.net!mule.fhcrc.org!news From: Tim Buss Newsgroups: bionet.molbio.proteins Subject: Re: Site Directed Mutagenesis - Current Limitations Date: 9 Nov 1994 17:40:48 GMT Organization: Fred Hutchinson Cancer Research Center Lines: 14 Distribution: world Message-ID: <39r1j0$kfa@mule.fhcrc.org> References: NNTP-Posting-Host: 140.107.14.25 X-UserAgent: Nuntius v1.1.1d24 X-XXDate: Wed, 9 Nov 94 17:44:03 GMT Site Directed Mutagenesis - Current Limitations In article Greg Davis, gddavis@essex.ecn.uoknor.edu writes: >1. What are largest synthetic oligonucleotides that can be synthesized > for use as primers without significant sequence errors occurring > during their synthesis? (~60 bases is what I've previously heard.) I've synthesised oligos up to 130 bases on ABI 394's and 380B's without problems. I do recommend, though, gel purifying these as the amount of full length product is relatively low. Tim. From owner-proteins@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!usenet.ins.cwru.edu!lerc.nasa.gov!magnus.acs.ohio-state.edu!lcsmith From: lcsmith@magnus.acs.ohio-state.edu (Laurie C Smith) Newsgroups: bionet.molbio.proteins,bionet.cellbio,bionet.general Subject: Post-Doctoral position available Date: 10 Nov 1994 15:46:06 GMT Organization: The Ohio State University Lines: 21 Message-ID: <39tf7u$l4k@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: bottom.magnus.acs.ohio-state.edu Xref: biosci bionet.molbio.proteins:3064 bionet.general:11921 There is one position available immediately at The Ohio State University for a post-doctoral researcher. This position will be in the laboratory of Dr. Pappachan E. Kolattukudy, Professor and Director of the Neurobiotechnology Center. This position will study the enzymology of hydrocarbon biosynthesis. PhD and appropriate experience required. Salary: $22,000 or higher depending on experience Please send e-mail with qualifications to lcsmith@magnus.acs.ohio-state.edu C.V. and other materials can be sent to Laurie Smith, Biotechnology Center, 206 Rightmire Hall, 1060 Carmack Road, Columbus, Ohio 43210. Do not reply on newsgroup - it will not be read. The Ohio State University is an Equal Opportunity/Affirmative Action Employer. Women, Vietnam-era veterans, disabled veterans and individuals with disabilities are encouraged to apply. From owner-proteins@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!sgiblab!swrinde!ihnp4.ucsd.edu!sdcc12!sdcc3!rblewitt From: rblewitt@sdcc3.ucsd.edu (Richard Nelson) Newsgroups: bionet.molbio.proteins Subject: IgA protease Message-ID: <75636@sdcc12.ucsd.edu> Date: 10 Nov 94 08:44:50 GMT Sender: news@sdcc12.ucsd.edu Organization: University of California, San Diego Lines: 10 Nntp-Posting-Host: sdcc3.ucsd.edu I am in need of IgA protease. does anybody know of a source for it? thanks Rick -- _____________________________________________________________________ _____________________________.sig____________________________________ _____________________________________________________________________ The generic .sig Richard Nelson rblewitt@ucsd.edu From owner-proteins@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.cac.psu.edu!usenet From: fsl@psu.edu Newsgroups: bionet.molbio.proteins Subject: Re: Chitinase assay Date: Thu, 10 Nov 94 15:33:09 PDT Organization: Penn State University, Center for Academic Computing Lines: 19 Message-ID: <39tue3$8mg@hearst.cac.psu.edu> References: NNTP-Posting-Host: cosdan.bio.psu.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Newsreader: NEWTNews & Chameleon -- TCP/IP for MS Windows from NetManage In article , writes: > I am trying to find a good and fast chitinase assay for culture supernatants. > All the references I have, get an extended digestion of the type of chitin > used as substrate in hours or two days at most, but with my samples it takes > even more than a week. I think that the chitinases I'm working with have > an extremely lowest activity than the ones used in the assays from the > references. > I tried using chitin azure (chitin dyed with Remazol Brilliant Violet 5R), > but after four days of incubation there is no change in OD, even in those > samples taken for cultures that were degrading colloidal chitin (so I > know that the enzymes were active when I started the assay). > I would strongly appreciate any suggestion you can give me. > Thanks in advance, > > Gemma Maybe your "chitinase" is not a chitinase? dc From owner-proteins@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!agate!news.ucdavis.edu!rocky!ez041797 From: ez041797@rocky.ucdavis.edu (Jean-Manuel Henry) Newsgroups: bionet.molbio.proteins Subject: Heat inactivation, Technique? Date: 10 Nov 1994 11:26:13 GMT Organization: University of California, Davis Lines: 13 Message-ID: <39t00l$g76@mark.ucdavis.edu> NNTP-Posting-Host: rocky.ucdavis.edu X-Newsreader: TIN [version 1.2 PL2] Hi, I am an undergraduate doing an internship in a lab. My project is to study the heat stabilities of ATP sulfurylase from a mesophile and a thermophile. At this point all that I am trying to do is to obtain nice looking semilog plots of remaining activity vs. time. I am incubating thew enzymes at 60 C and stopping the inactivation at different times by diluting an aliquot from the incubation mixture into ice cold buffer. My problem is that I am having difficulty getting "nice" lines which are reproducible). I am wondering if anyone has done this type of thing before and has any suggestions on how to reduce error. Any tips would be very helpful, thanks. From owner-proteins@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!lll-winken.llnl.gov!decwrl!nntp.crl.com!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: IgA protease Date: 10 Nov 1994 20:05:15 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 13 Message-ID: <39tudr$1ftl@sat.ipp-garching.mpg.de> References: <75636@sdcc12.ucsd.edu> NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] Richard Nelson (rblewitt@sdcc3.ucsd.edu) wrote: > I am in need of IgA protease. does anybody know of a source for it? Commercial e.g. from Boehringer Mannheim. Otherwise you could try the group of Thomas Meyer at the Max Planck-Institut fuer Biologie in Tuebingen, Germany (zip is D-72074, address is Corrensstrasse). --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "People are DNA's way of making more DNA." (Edward O. Wilson, 1975) */ From owner-proteins@net.bio.net Wed Nov 09 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!torn!news.unb.ca!UNBVM1.CSD.UNB.CA From: CORRIGAN S Newsgroups: bionet.molbio.proteins Subject: DNA fingerprinting in the forensic sciences Date: 10 NOV 94 19:05:19 AST Organization: The University of New Brunswick Lines: 13 Sender: usenet@UNB.CA Message-ID: <10NOV94.20615901.0063@UNBVM1.CSD.UNB.CA> NNTP-Posting-Host: unbvm1.csd.unb.ca Hi all, I am a student at the University of New Brunswick in Saint John, Canada who is looking for information on DNA fingerprinting in the forensic sciences. This is not a report to see if O.J. is quilty or innocent but I am researching the pros and cons of the methods involved both by the police and scientists (ie. creating data banks, what are the legalities of taking samples from people, what kind of standards do different labs follow and what is being done to come up with a general standard for all, molecular biologists to follow etc). Anyway any help you could provide would be greatly appreciated. Thank you for your time and I hope to hear from you soon. Please send replies to T6Ko@UNBSJ.ca From owner-proteins@net.bio.net Thu Nov 10 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!olivea!koriel!lll-winken.llnl.gov!uwm.edu!news.moneng.mei.com!howland.reston.ans.net!news.sprintlink.net!pipex!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!genmac18.biochem.mpg.de!user From: spang@vms.biochem.mpg.de (Anne Spang) Newsgroups: bionet.molbio.proteins Subject: Citrate Synthase Date: 11 Nov 1994 19:15:28 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 9 Message-ID: NNTP-Posting-Host: genmac18.biochem.mpg.de Hi everybody! I am looking for somebody working with human citrate synthase or interested in human citrate synthase! Please send a mail to Spang@vms.biochem.mpg.de Thanx Anne From owner-proteins@net.bio.net Thu Nov 10 22:00:00 1994 Path: biosci!BROWNVM.BROWN.EDU!KMILLER From: KMILLER@BROWNVM.BROWN.EDU (Ken Miller) Newsgroups: bionet.molbio.proteins Subject: Re: DNA fingerprinting in the forensic sciences Date: 11 Nov 1994 05:32:23 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <199411111332.FAA13639@net.bio.net> NNTP-Posting-Host: net.bio.net >Posted on 10 Nov 1994 at 19:15:25 by CORRIGAN S > > I am researching the pros and cons of the methods >involved both by the police and scientists (ie. creating data banks, >what are the legalities of taking samples from people, what kind of >standards do different labs follow and what is being done to come up >with a general standard for all, molecular biologists to follow >etc). Best advice is to look at the October 27 1994 issue of NATURE (see Nature 371: 735-738) for an article by Lander & Budowle. As you will see, the general standards have been set, the boundary conditions have been agreed to, and the technique is on very firm scientific ground. In short, the things that you might hope are being done HAVE been done! Good luck with your report! From owner-proteins@net.bio.net Thu Nov 10 22:00:00 1994 Path: biosci!agate!library.ucla.edu!news.mic.ucla.edu!wlheye.jsei.ucla.edu!lukasz From: lukasz@wlheye.jsei.ucla.edu (Lukasz Salwinski) Newsgroups: bionet.molbio.proteins Subject: Re: Site Directed Mutagenesis - Current Limitations Date: 11 Nov 1994 16:11:49 GMT Organization: Jules Stein Eye Institute Lines: 14 Distribution: world Message-ID: <3a0546$58g@news.mic.ucla.edu> References: NNTP-Posting-Host: wlheye.jsei.ucla.edu I've made ~75mer once on Milligene's Cyclone synthetizer and used for site directed (through PCR) without any purification. Worked fine :) lukasz -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ....life's complex. It has real and imaginary parts .... --------------------------------------------------------------- Lukasz Salwinski Jules Stein Eye Institute,UCLA phone: (310) 206-8831 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From owner-proteins@net.bio.net Thu Nov 10 22:00:00 1994 Path: biosci!agate!library.ucla.edu!csulb.edu!nic-nac.CSU.net!loghost.sdsc.edu!news.tc.cornell.edu!news.cac.psu.edu!howland.reston.ans.net!pipex!uunet!utcsri!utnut!nott!nrcnet0.nrc.ca!BRI.NRC.CA!Feng.Ni From: Feng.Ni@BRI.NRC.CA (Feng Ni) Newsgroups: bionet.molbio.proteins Subject: Research Assistant in Portein Chemistry Date: 11 Nov 1994 16:50:49 GMT Organization: Institut de recherche en biotechnologie, Montréal Lines: 25 Distribution: world Message-ID: <3a07d9$akh@nrcnet0.nrc.ca> NNTP-Posting-Host: bobino.bri.nrc.ca Research Assistant Position in Portein Chemistry The NMR laboratory of the Biotechnology Research Institute (BRI) is looking for a research assistant in protein chemistry/molecular biology. The candidate MUST have a BS or MS degree in biochemistry or a related field. Relavant experience includes cloning, protein expression and protein purifica- tion. The applicant must also have worked with various chromatography methods including HPLC, FPLC and affinity collumns. This position will be supported by the Natural Science and Engineering Research Council (NSERC) and the Medical Research Council of Canada (MRC). For more information, please contact: Dr. Feng Ni Biotechnology Research Institute 6100 Royalmount Ave. Montreal, Quebec, H4P 2R2 Canada phone: (514)-496-6729 fax: (514)-496-5143 e_mail: fengni@bobino.bri.nrc.ca From owner-proteins@net.bio.net Thu Nov 10 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!uunet!newsflash.concordia.ca!news.mcgill.ca!clouso.crim.ca!athena.ulaval.ca!rhizobium.rsvs.ulaval.ca!user From: mounir@biota.rsvs.ulaval.ca (Mounir) Subject: Sarcosyl fractionnation . Content-Type: text/plain; charset=ISO-8859-1 Message-ID: Followup-To: bionet.molbio.proteins Sender: news@athena.ulaval.ca Nntp-Posting-Host: rhizobium.rsvs.ulaval.ca Content-Transfer-Encoding: 8bit Organization: Rhizobium.rsvs.ulaval.ca Mime-Version: 1.0 Date: Fri, 11 Nov 1994 19:49:07 GMT Lines: 17 I'm working on the isolation of siderophore receptors on the outer membrane of Rhizobium. I used the sarcosyl fractionnation to isolate the outer membrane proteins but i have a very poor yield of bands when i run the SDS-page electrophoresis. If there's anyone who have suggestions about the isolation technique using sarcosyl or outer membrane protein electrophoresis i would really appreciate it. Mounir. -- ------------------------------- " Use your illusion " G'N'R. 8-3) From owner-proteins@net.bio.net Thu Nov 10 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!newsxfer.itd.umich.edu!zip.eecs.umich.edu!caen!usenet.coe.montana.edu!netnews.nwnet.net!news.u.washington.edu!laudonw From: laudonw@u.washington.edu (Laudon Williams) Newsgroups: bionet.jobs,bionet.jobs.wanted,bionet.molbio.proteins Subject: Free seminar, Detroit, November 17th Date: 12 Nov 1994 02:33:00 GMT Organization: University of Washington Lines: 18 Message-ID: <3a19gs$1rv@nntp1.u.washington.edu> NNTP-Posting-Host: homer07.u.washington.edu Xref: biosci bionet.jobs:6302 bionet.jobs.wanted:394 bionet.molbio.proteins:3073 Dr. DicQie Fuller, Research Scientist in the fields of nutrition and health science and author of the soon to be released Prentice-Hall book "The Healing Power of Enzymes" will be conducting a series of free lectures covering her latest theories and research in the area of enzyme therapy and supplementation. Her presentation in the Detroit area will be on Thursday, November 17th at 7:30p.m. Location: Sheraton Oaks Hotel 2700 Sheraton Drive Novi, MI A limited number of seats are available to health professionals on a complementary basis. For reservations call Michelle at 1 (800) 263-9897. From owner-proteins@net.bio.net Fri Nov 11 22:00:00 1994 Path: biosci!THEORY.BCHS.UH.EDU!dbd From: dbd@THEORY.BCHS.UH.EDU (Dan Davison) Newsgroups: bionet.molbio.proteins Subject: Summary of UH Gene-Server Services Date: 12 Nov 1994 11:20:42 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 159 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411121920.AA01273@theory.BCHS.UH.EDU> NNTP-Posting-Host: net.bio.net The University of Houston Gene-Server Services and Changes November, 1994 1. Recently Added Services 2. Services to be removed 3. Service Interruptions 4. Addresses a. Gopher b. WWW c. WAIS d. FTP e. E-mail f. PIR Releases and Technical Notes 5. Some technical notes about servers 6. Acknowledgements ______________________________________________________________________________ 1. Recently added services In collaboration with Dr. Victor Solovyev of the Computational Biology Group, Baylor College of Medicine, we recently added a series of servers for human gene identification and protein secondary structure analysis. hexon - find coding regions hspl - splice site prediction for human genes fexh - find exons in human genes fgeneh - human gene modeling ssp - protein secondary structure protein nnssp - neural net-based protein secondary structure prediction Full details of each of these have been posted separately. You can obtain help files by sending the subject line man such as Subject: man hexon to service@bchs.uh.edu ______________________________________________________________________________ 2. Services to be removed Due to better services being available elsewhere, the UH Gene-Server will discontinue providing GenBank entries on November 30, 1994. Users requesting GenBank entries after that date will receive a note referring them to the RETRIEVE server at ncbi.nlm.nih.gov. PIR and software retrieval by e-mail will NOT be affected by this change. ______________________________________________________________________________ 3. Service Interruptions Due to circumstances beyond our control, there have been a number of network and power outages recently. We apologize for the inconvenience and will continue to work to minimize the effects of power and network problems. ______________________________________________________________________________ 4. Addresses a. Gopher The UH Gene-Server Gopher service is available at gopher.bchs.uh.edu; it contains PIR sequence retrieval pointers to other Bio-Gophers, and some local information. The URL is gopher://gopher.bchs.uh.edu b. WWW The Web pages offering access to the FTP site, descriptions of software, a yellow pages of molecular biology software, and more. Point your WWW browser at www.bchs.uh.edu. The URL is http://www.bchs.uh.edu c. WAIS WAIS indexed software descriptions are most easily accessed by using a Web or Gopher client to www.bchs.uh.edu or gopher.bchs.uh.edu, respectively. d. FTP The Gene-Server anonymous FTP area offers PIR releases, Mac, DOS, Unix, and VMS molecular biology software, and more. It can be accessed by anonymous FTP'ing to ftp.bchs.uh.edu e. E-mail services 1. Users with access to electronic mail may retrieve molecular biology software and data from the Gene-Server. To start, send the word "HELP" in the subject line or in the body of the message to gene-server@bchs.uh.edu 2. Human DNA sequence characterization and Protein secondary structure prediction are available from server@bchs.uh.edu Send the word "info" or "help" to that address to get started. f. PIR releases and Technical Notes PIR releases are found on ftp.bchs.uh.edu in pub/gene-server/pir/pir_relXX, where XX is the release number (Current release is 42). There are three directories: ascii - the ascii version of PIR as released by NBRF. Compressed with Unix compress. vms - the "converted' VMS version of PIR, for use with the GCG 6.X and 7.X program suite (I'm not sure about 8.0 - we can't run Solaris and can't check). Compressed with Unix compress. vms_lzw - the VMS version of PIR that retains VMS RMS (file) attributes, for NBRF's sequence analysis and handling system. Compressed with LZCOMP. VMS executables of LZCOMP and LZDCOMP are in pub/gene-server/pir. Version-specific files and release notes are available in ...pir/pir_relXX, as described above. PIR Technical Notes, which are important to check if you write software to parse PIR format, are in pub/gene-server/pir/pir_tech. The most recent note is PIRTECH06.LIS. ______________________________________________________________________________ 5. Some technical notes about servers Important note: nnssp, the neural net secondary structure prediction program, takes a lot of CPU time on my workstation, so it runs at a very low priority. No more than two analysis routines may run at one time due to CPU constraints. The Gene-Server uses the archive-server scripts from Brian Reid at DECWRL, with extensive modifications. The service@bchs.uh.edu address uses the Enterprise Integration Technologies ServiceMail Toolkit, written in Ousterhout's Tool Command Language (Tcl). ______________________________________________________________________________ 6. Acknowledgements The Gene-Server project was started by Jack Chappelear and Dan Davison, with assistance from Edward Chen, Bob Rimkus, and Manish Doshi. The various incarnations of the Gene-Server have been supported by the University of Houston VP for Information Technology, the UH Institute for Molecular Biology, and the National Science Foundation (BIR-91-91165 and BIR 94-03562). Questions about the Gene-Server can be directed to Dan Davison, davison@uh.edu. Questions about specific analysis services should be directed to the address given in the help file for that service. From owner-proteins@net.bio.net Fri Nov 11 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uunet!haven.umd.edu!purdue!lerc.nasa.gov!kira.cc.uakron.edu!neoucom.edu!news.ysu.edu!psuvm!rjc8 Organization: Penn State University Date: Sat, 12 Nov 1994 15:03:35 EST From: Richard Cyr Message-ID: <94316.150335RJC8@psuvm.psu.edu> Newsgroups: bionet.molbio.proteins Subject: address for R. Bernstein Lines: 3 I am looking Rick Bernstein's e-mail address. Richard Cyr RJC8@PSU.EDU From owner-proteins@net.bio.net Sun Nov 13 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!sunsite.doc.ic.ac.uk!dundee.ac.uk!NewsWatcher From: (k.c.breen@dundee.ac.uk) Newsgroups: bionet.molbio.proteins Subject: Lectureship Followup-To: bionet.molbio.proteins Date: 12 Nov 1994 12:14:12 GMT Organization: The University, Dundee, DD1 4HN, Scotland, UK. Lines: 27 Distribution: world Message-ID: <3a2bik$fnp@dux.dundee.ac.uk> NNTP-Posting-Host: 134.36.198.60 Fixed-Term Lectureship in Pharmacology Applications are invited for a Lectureship in Pharmacology at the University of Dundee, Scotland, tenable from 1st January 1995. The appointment will be made on a fixed-term basis for a period of three years. The candidate will join a Department with a strong interest in Neuroscience and will be expected to undertake an vigorous independent programme of research. Applicants with an interest in the molecular basis of neurodegeneration or glycobiology are particularly invited to apply. The successful candidate will be encouraged to interact with a dynamic research group with interests in these fields. The appointee will also be expected to undertake general teaching duties for students of science and pre-clinical medical students. Salary will be commensurate with experience and will be on the lecturer A scale (£14,756-£19326). Informal enquiries should be addressed to Dr. Kieran Breen at +44-1382-633900 ext. 2522 (E-mail: k.c.breen@dundee.ac.uk). CV (3 copies) together with the names and addresses of 3 referees should be sent to Personnel Services, The University, Dundee DD1 4HN, Scotland, U.K. quoting ref: est/16/45. The university is an Equal Opportunities Employer. From owner-proteins@net.bio.net Sun Nov 13 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!uunet!psinntp!hk.super.net!news.ust.hk!usthk.ust.hk!boningli From: boningli@usthk.ust.hk Subject: postDr Message-ID: <1994Nov14.134353.1@usthk.ust.hk> Lines: 28 Sender: usenet@uxmail.ust.hk (usenet account) Nntp-Posting-Host: ustcc3.ust.hk Organization: The Hong Kong University of Science & Technology (HKUST) Date: Mon, 14 Nov 1994 05:43:53 GMT The Hong Kong University of Science and Technology Postdoctoral Position A postdoctoral position is available immediately to study: 1) the temporal and spatial regulation of ACC synthase and ACC oxidase gene expression during plant development and differentiation; 2) the structure and function relationship of these two enzymes. Successful candidates should have experience in plant molecular biology and/or protein biochemistry. Appointment will be for one year with possible renewal for up to two additional years. The monthly salary is at least HK$16000 (equivalent to about US$2100) plus fringe benefit and housing. The Hong Kong University of Science and Technology campus locates right on the beach of clear water bay of Hong Kong and offers an exciting environment, the state of art equipment and modern libraries for doing cutting-edge researches. Interested individuals should send CV to : Drs Ning Li / Shang Fa Yang Department of Biology The Hong Kong University of Science and Technology Clear Water Bay Hong Kong E-mail: BONINGLI@usthk.ust.hk FAX: 852-358-1559 TEL: 852-358-7335; 852-358-7311 From owner-proteins@net.bio.net Sun Nov 13 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!ns1.faseb.org!darwin.sura.net!fconvx.ncifcrf.gov!reming From: reming@ncifcrf.gov (Mary Remington) Subject: Non-isotopic Western Blots-Best Message-ID: Organization: Frederick Cancer Research and Development Center Date: Mon, 14 Nov 1994 15:07:30 GMT Lines: 5 Our laboratory will be doing Western blots in a BSL 3 and it would simplify our lives greatly to use a non-isotopic method. I would appreciate any thoughts on the kits on the market for this purpose. Many thanks, Mary From owner-proteins@net.bio.net Sun Nov 13 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!uni-muenster.de!ifimac04.uni-muenster.de!user From: infekt@uni-muenster.de (M.A.Schmidt) Newsgroups: bionet.molbio.proteins Subject: help with commercial transducin source Date: Mon, 14 Nov 1994 16:42:50 +0100 Organization: ZMBE - Institut fuer Infektiologie Lines: 6 Message-ID: NNTP-Posting-Host: ifimac04.uni-muenster.de Hi out there, Does anyone know where one can get transducin from bovine retina commercially? (Working with all these eyes looking at you is a real drag) Your help would be greatly appreciated! With many thanks M.Alexander Schmidt From owner-proteins@net.bio.net Sun Nov 13 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!dundee.ac.uk!NewsWatcher From: k.c.breen@dundee.ac.uk Newsgroups: bionet.molbio.proteins Subject: Subcellular fractionation Followup-To: bionet.molbio.proteins Date: 8 Nov 1994 09:45:26 GMT Organization: University of Dundee Lines: 19 Distribution: world Message-ID: <39nhbm$si4@dux.dundee.ac.uk> NNTP-Posting-Host: 134.36.198.60 We are studying the cellular expression of an enzyme which can exist both in the Golgi and at the level of the cell membrane. In vivo, subcellular fractionation is relatively straightforward using a differential gradient system. However, I have not come accross a parallel method for separating the plasma membranes and Golgi fractions from a cultured cell monolayer. This is a particular problem when the small amount of starting material is taken into consideration. Has anybody elso come accross this problem, or how it may be addressed? Kieran Breen Dept. of Pharmacology, University of Dundee, Ninewells Hospital & Medical School, Dundee DD1 9SY, Scotland, U.K. k.c.breen@dundee.ac.uk From owner-proteins@net.bio.net Sun Nov 13 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!news.graphics.cornell.edu!ghost.dsi.unimi.it!news.unige.it!moana!biodev From: biodev@moana (Gruppo Biodevices) Newsgroups: bionet.molbio.proteins Subject: cytochrome C modification Date: 14 Nov 1994 16:15:34 GMT Organization: Univ. of Genoa, Italy Lines: 25 Message-ID: <3a82f6$jj3@alpha.cisi.unige.it> NNTP-Posting-Host: moana.ibf.unige.it X-Newsreader: TIN [version 1.2 PL2] Keywords: Hi world! I'm a PH.D. student in protein chemistry at the Institute of Biophysiscs of Genova (Italy) I'm searching for people that work in this field and especially (but not only...) on cytochrome C modification. The aim of our research is the realization of LangmuirBlodgett films of cytochromes for bioelectronics. If you are involved in this field or you are interested to protein chemistry, please write to me : Marco Lanzi Inst. of Biophysics University of Genova Italy E-mail: biodev.ibf.unige.it fax: ++39-10-6513106 tel: ++39-10-6516052 From owner-proteins@net.bio.net Sun Nov 13 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!newsserver.jvnc.net!raffles.technet.sg!nuscc.nus.sg!sci30828 From: sci30828@leonis.nus.sg (C G PADMASHREE) Newsgroups: bionet.molbio.proteins Subject: Gel Mobility shift assay Date: 10 Nov 1994 13:15:19 GMT Organization: National University of Singapore Lines: 5 Message-ID: <39t6d7$ja2@nuscc.nus.sg> NNTP-Posting-Host: sci30828@leonis.nus.sg X-Newsreader: TIN [version 1.2 PL2] I am an inexperienced undergraduate who has been assigned a project on gel mobility shift assays involving binding of steroid hormones to their receptors.I request for help to find suitable references on this subject.Early help would be greatly appreciated.Thank you. XYZ From owner-proteins@net.bio.net Sun Nov 13 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!spool.mu.edu!uwm.edu!msuinfo!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!extro!mauland From: mauland@extro.ucc.su.OZ.AU (Merran Auland) Subject: Na+/K-ATPase Message-ID: Sender: news@ucc.su.OZ.AU Nntp-Posting-Host: extro.ucc.su.oz.au Organization: Information Services, Sydney University, Sydney, NSW, Australia Date: Mon, 14 Nov 1994 21:34:25 GMT Lines: 13 Does anyone here know where I might get some antibodies to the Na/K-ATPase. Specifically those directed towards the ouabain binding site ? If anyone works with Na/K-ATPase...... to what size product can you cleave the enzyme with proteases before it looses the capacity to bind Ouabain ? Please write to me direct if you can help me with any of this Thanx Merran merrana@pharmacy.pharm.su.oz.au From owner-proteins@net.bio.net Mon Nov 14 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!imbb1.imbb.forth.gr!nefeli.imbb.forth.gr!SKOUFOS From: skoufos@nefeli.imbb.forth.gr Newsgroups: bionet.molbio.proteins Subject: Re: Gel Mobility shift assay Date: Tue, 15 Nov 1994 15:53:25 GMT Organization: Imbb-forth,CREtE, creece Lines: 14 Message-ID: <009877FF.94C3961A@nefeli.imbb.forth.gr> References: <39t6d7$ja2@nuscc.nus.sg> Reply-To: skoufos@nefeli.imbb.forth.gr NNTP-Posting-Host: nefeli.imbb.forth.gr In article <39t6d7$ja2@nuscc.nus.sg>, sci30828@leonis.nus.sg (C G PADMASHREE) writes: >I am an inexperienced undergraduate who has been assigned a project on >gel mobility shift assays involving binding of steroid hormones to their >receptors.I request for help to find suitable references on this >subject.Early help would be greatly appreciated.Thank you. > Try a reference availablr in most molecular biology labs: Ausubel et.al. (eds) Current protocols in Molecular Biology (Red Book) Volume 2, Chapter 12 "DNA-Protein interactions" Emmanuel From owner-proteins@net.bio.net Tue Nov 15 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!uunet!haven.umd.edu!purdue!mozo.cc.purdue.edu!fspc62.foodsci.purdue.edu!MURIANAP From: MURIANAP@FOODSCI.PURDUE.EDU (Pete Muriana) Newsgroups: bionet.molbio.proteins Subject: ?Premade SDS-PAGE gels to fit Hoeffer SE-600 unit? Date: Wed, 16 Nov 1994 16:48:59 Organization: FOOD SCIENCE DEPT./PURDUE UNIVERSITY Lines: 12 Message-ID: NNTP-Posting-Host: fspc62.foodsci.purdue.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Can anyone recommend a manufacturer of pre-made SDS-PAGE gels that may fit the Hoeffer SE600 series gel unit? Thanks, -Peter ********************************************************************** * Peter M. Muriana, Ph.D. 317-494-8284 TEL * * Dept. of Food Science 317-494-7953 FAX * * Purdue University murianap@foodsci.purdue.edu * * Smith Hall * * W. Lafayette, IN 47907-1160 * ********************************************************************** From owner-proteins@net.bio.net Tue Nov 15 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!pipex!uunet!nih-csl!Phoebe.Rice From: phoebe@vger.niddk.nih.gov (Phoebe Rice) Subject: Re: 3D building Message-ID: <1994Nov16.161550.7386@alw.nih.gov> X-Posted-From: InterNews 1.0@nih-csl.dcrt.nih.gov. Lines: 7 Sender: -Not-Authenticated-[3796] Organization: National Institutes of Health References: <3aako7$96c@news.univ-rennes1.fr> Date: Wed, 16 Nov 1994 16:15:50 GMT Xdisclaimer: No attempt was made to authenticate the sender's name. If there are no x-ray or NMR structures for proteins which are clearly homologous to yours, IMHO, your chances of successfull 3D modelling are close to zero no matter how you go about it. (Or maybe I don't understand your question properly?) Phoebe Rice Phoebe@vger.niddk.nih.gov From owner-proteins@net.bio.net Tue Nov 15 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!univ-lyon1.fr!zaphod.crihan.fr!news.univ-rennes1.fr!zeus.univ-poitiers.fr!CRISO From: criso@zeus.univ-poitiers.fr Newsgroups: bionet.molbio.proteins Subject: 3D building Date: 15 Nov 1994 15:39:51 GMT Organization: Univ. Poitiers, CICUP, France Lines: 3 Message-ID: <3aako7$96c@news.univ-rennes1.fr> Reply-To: criso@zeus.univ-poitiers.fr NNTP-Posting-Host: zeus.univ-poitiers.fr I am trying to modelize a protein with por homology with PDB sequences. A secondary structure model was obtained from sequences alignments and then predict secondary structure alignments. This model is built from 6 segments select in PDB protein sequences. Thus at this stage, how such elements can be fit together to built a 3D model. Do you know some protocol or software usable on such a work. Thanks for your help and sorry for my english. Christian LACOMBE. Institut de Biologie Moleculaire et Ingenierie Genetique. Universite de POITIERS (France). Email criso@zeus.univ-poitiers.fr From owner-proteins@net.bio.net Tue Nov 15 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!uhog.mit.edu!sgiblab!spool.mu.edu!howland.reston.ans.net!news.sprintlink.net!malgudi.oar.net!kira.cc.uakron.edu!neoucom.edu!news.ysu.edu!psuvm!pxh Organization: Penn State University Date: Wed, 16 Nov 1994 12:59:47 EST From: Deepti Pradhan Message-ID: <94320.125947PXH@psuvm.psu.edu> Newsgroups: bionet.molbio.proteins Subject: BLOCKS Lines: 41 Would anyone please mail me information on interpretation of BLOCK searches, beyond what is provided in the help file? To be more specific, I am provid- ing an example, with questions: This was obtained after sending a query sequence "combined" ->260 nt: ----------------------------------------------- 1395=99.63th percentile of anchor block scores for shuffled queries P not calculated for single block BL00154A |--- 290 amino acids---| BL00154 AA:::::::::::.......BBB::::::::...............CCCC:.....DDDD combined AA BL00154A <->A (120,836):15 ATN3_HUMAN 170 VNAEEVVVGDLVEIKGGDRVPADLRIIS | | | ||| | ||| ||| | combined 16 VHwEkVNVGDIVIIKGkEyIPADtVLLS Questions: 1. What does the "290 amino acids" refer to? 2. What does lower case indicate? And upper case? 3. Is there a "good" min., max (the numbers after <->A, in parantheses, i.e., 120, 836). -------------------------------------------------------- This was obtained using GET BLOCK00154A ======================================================================== ID ATPASE_E1_E2; BLOCK AC BL00154A; distance from previous block=(120,836) DE E1-E2 ATPases phosphorylation site proteins. BL DAD motif; width=28; seqs=73; 99.5%=614; strength=2008 ATC1_YEAST ( 164) VLASTLVPGDLVHFRIGDRIPADIRIIE 51 ATC3_SCHPO ( 134) IDSHLLVPGDVVVLKTGDVVPADLRLVE 40 Questions: What do the #s in () mean [164 and 134 in this example], and those at the end of each of those lines? ------------------- Pardon the very likely stupidity displayed by these questions - please point me to a book, if possible. Thanks, Deepti From owner-proteins@net.bio.net Tue Nov 15 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!pipex!uknet!comlab.ox.ac.uk!barlow From: barlow@bioch.ox.ac.uk (Paul Barlow) Subject: Post Doc Message-ID: <1994Nov16.212528.21806@nmrm.bioch.ox.ac.uk> Originator: barlow@nmrm.ocms Keywords: Jobs NMR viruses receptors Organization: Department of Biochemistry, University of Oxford Date: Wed, 16 Nov 1994 21:25:28 GMT Lines: 35 Two POSTDOCTORAL positions are available immediately at the University of EDINBURGH within a new Unit that is shared by the Division of Biology and the Department of Chemistry. 1 - We are looking for somebody with experience in the application of mulidimensional heteronuclear NMR techniques to any system but preferably biological macromolecules. This post is funded by the BBSRC for 3 years and is to elucidate the structures of cell-surface receptors for 2 major human viruses. We currently have 20% access on a 600MHz spectrometer that is about to be upgraded to include a third rf channel and pulsed field gradients. We expect to be funded soon for the purchase of a second instrument that will be devoted entirely to the work of our group and our collaborators. Computing equipment and protein production facilities are excellent. Oh yes, and Edinburgh is a great city to live in. Please let me know if you are interested (barlow@bioch.ox.ac.uk) 2 - We are also looking for someone with experience in the recombinant expression of proteins from bacterial, yeast, insect or mammalian vectors. This is an MRC-funded post for about 30 months. We will ask the successful candidate to produce 10's of mg quantities of protein for our structural studies, and to conduct mutagenesis/functional studies on cell-surface receptor:virus interactions. We are looking for a highly motivated scientist, capable of setting up molecular biology techniques in a new lab. By the way Edinburgh is a great place to live, and one of the most beautiful cities in Europe. Please let me know if you are interested (barlow@bioch.ox.ac.uk) or phone (44)(0)316504727/(44)(0)316504704 Paul Barlow. From owner-proteins@net.bio.net Tue Nov 15 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!darwin.sura.net!nntp.st.usm.edu!whale.st.usm.edu!mjlogan From: mjlogan@whale.st.usm.edu (Mark Jason Logan) Newsgroups: bionet.molbio.proteins Subject: ANS Fluorescence Date: 16 Nov 1994 18:13:38 GMT Organization: University of Southern Mississippi Lines: 30 Message-ID: <3adi4i$lqd@server.st.usm.edu> NNTP-Posting-Host: whale.st.usm.edu X-Newsreader: TIN [version 1.2 PL1] Hello again, I am currently working with a de novo designed helical bundle protein. I have examined the fluorescence behavior of 1-anilino-8-naphthalene sulfonate in the presence of my protein as a function of pH. At pH 2.3 the fluorescence spectrum is characterized by a sizeable increase in intensity and a blue shift in the wavelength of maximal emission. As the pH is lowered to 1.8 the fluorescence intensity is increased but red shifted by approximately 30 nm (relative to sample at pH 2.3). Now I realize that quantum yield and emission maxima are related to a variety of factors such as fluorophore rigidity, solvent relaxation, and the existance of two excited state species what I would like to know is how do this factors contribute to the fluorescence of ANS. I have read in the literture that for 2-p-toluidinylnaphthalene-6-sulfonate the shift of emission maxima is related to solvent relaxation and hence micorpolarity whereas the quantum yield is effected by the conformational freedom or microviscosity experienced by the probe. Incidentally, with regards to the effects of microviscosity on quantum yield I have seen several conflicting reports where no effect on the quantum yield due to microviscosity was observed. Go figure? Any comments would be appreciated since I am in the process of writing my thesis and would like to get a better handle on this ASAP. Regards, Mark P.S. please e-mail replies to mjlogan@whale.st.usm.edu From owner-proteins@net.bio.net Tue Nov 15 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!columba.udac.uu.se!rigel.bmc.uu.se!gerard From: gerard@rigel.bmc.uu.se (Gerard Kleijwegt) Newsgroups: bionet.molbio.proteins Subject: Re: 3D building Date: 16 Nov 1994 16:34:27 GMT Organization: Uppsala University Lines: 14 Distribution: world Message-ID: <3adcaj$pe9@columba.udac.uu.se> References: <3aako7$96c@news.univ-rennes1.fr> NNTP-Posting-Host: rigel.bmc.uu.se In article <3aako7$96c@news.univ-rennes1.fr>, criso@zeus.univ-poitiers.fr writes: |> I am trying to modelize a protein with por homology with PDB sequences. A secondary structure model was obtained from sequences alignments and then predict secondary structure alignments. This model is built from 6 segments select in PDB protein sequences |> . Thus at this stage, how such elements can be fit together to built a 3D model. Do you know some protocol or software usable on such a work. |> Thanks for your help and sorry for my english. |> Christian LACOMBE. Institut de Biologie Moleculaire et Ingenierie Genetique. Universite de POITIERS (France). Email criso@zeus.univ-poitiers.fr don't waste your time; crystallise it or put it into an NMR tube with low homology, only experimental structure determination can give you an answer; all the rest is make-believe and wishful thinking --gerard From owner-proteins@net.bio.net Tue Nov 15 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!jawerthe From: jawerthe@ATHENA.MIT.EDU (Jason A Wertheim) Newsgroups: bionet.molbio.proteins Subject: Interferon-gamma Date: 17 Nov 1994 06:38:52 GMT Organization: Massachusetts Institute of Technology Lines: 12 Message-ID: <3aetps$m0e@senator-bedfellow.MIT.EDU> NNTP-Posting-Host: cacciatore.mit.edu I have just begun a research project aimed at creating a polymeric controlled release system for rabbit gamma-interferon. I am looking for an assay to determine the amount of interferon released by our system. The procedure would have to be able yield a good resolution at concentrations in the neighborhood o 30-80 picograms/ml. I have tried the Eliza assay; however, I have found it too cumbersome to test 200-300 samples by this method. I was wondering if anyone knows of any alternatives. If anyone has any suggestions, or if anyone has worked with interferons, I would appreciate an email sent to my account. Thank you. Jason Wertheim From owner-proteins@net.bio.net Tue Nov 15 22:00:00 1994 Path: biosci!agate!news.ucdavis.edu!dale!ez001427 From: ez001427@dale.ucdavis.edu (Marc Goldstein) Newsgroups: bionet.molbio.proteins Subject: Activated gel supports. Comments? Date: 17 Nov 1994 01:19:34 GMT Organization: University of California, Davis Lines: 17 Message-ID: <3aeb36$3pm@mark.ucdavis.edu> NNTP-Posting-Host: dale.ucdavis.edu X-Newsreader: TIN [version 1.2 PL2] Netters- I'm thinking of using affinity chromatography to purify an antibody out of a crude rabbit serum, and I am wondering which affinity supports work well for medium sized (~70 kDa) protein antigens. I'd like to link the antigen to the support, and run the serum through, then elute the specific IgG off. I've looked up the Pharmacia activated supports, and also those from Pierce. Any comments on the utility of these or other activated resins, in terms of good or bad experiences, etc. would be appreciated. Thanks! Marc A. Goldstein Section of Plant Biology UC Davis magoldstein@ucdavis.edu From owner-proteins@net.bio.net Wed Nov 16 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!ns1.faseb.org!darwin.sura.net!howland.reston.ans.net!swiss.ans.net!newsgate.watson.ibm.com!hawnews.watson.ibm.com!puffin!dflash From: dflash@watson.ibm.com (The dFLASH Project) Subject: dFLASH server for latest GenBank/PIR/SwissProt (Release 1.1.0) Sender: news@hawnews.watson.ibm.com (NNTP News Poster) Message-ID: Date: Thu, 17 Nov 1994 17:24:22 GMT Disclaimer: This posting represents the poster's views, not necessarily those of IBM. Nntp-Posting-Host: puffin.watson.ibm.com Organization: IBM T.J. Watson Research Lines: 476 The dFLASH Group wishes to announce release 1.1.0 of the dFLASH electronic mail server. Beginning with this release of the server, we will be supporting the latest release of the GENBANK, PIR and SWISSPROT databases. In particular, users can now carry out searches in GENBANK Release 85 (September 30, 1994) PIR Release 42 (September 30, 1994) --> DEFAULT Database <-- SWISSPROT Release 30 (October 30, 1994) Full bibliographic references can optionally be included with the computed alignments, for all three databases. Notice that a number of necessary changes and additions have been incorporated in the "query language". For example, since we now support a larget set of databases, "target protein" is not a valid directive anymore! The appended help file describes the changes and available functions in detail. NEW FEATURES: o the reported results can now be sorted using a sorting key specified by the user via the "query language" o a smart-email filter has been implemented: various specification errors are now caught and corrected automatically; notifications are sent to the user for all taken actions. It is our intention to update the server with the latest release of each of the above dbases within the first two weeks after it becomes available. The server is accessible through the Internet and is now operating 24 hours a day, 7 days a week and can be accessed both directly and through "Grail" of the Oak Ridge National Lab. Sincerely, The dFLASH Group ------------------------------> CUT HERE <----------------------------------- !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !! The dFLASH server now supports the GenBank, PIR and SWISSPROT databases. !! !! The supported releases are: !! !! GENBANK Release 85 (September 30, 1994) !! !! PIR Release 42 (September 30, 1994) --> DEFAULT Database <-- !! !! SWISSPROT Release 30 (October 30, 1994) !! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !! N O T A B E N E !! !! The dFLASH server is still under development. If some of the answers do !! !! not make sense it is very likely that this is due to a bug in our code. !! !! Please, email bug reports and comments to dflash@watson.ibm.com with !! !! subject line "bug" or "comments". !! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Dear User, welcome to Release 1.1.0 of the the dFLASH server! The dFLASH server is a "homologous sequence retrieval" program for PROTEIN and DNA sequences. dFLASH is a parallel system running on an IBM SP/x architecture. Intra-node communication, evidence integration and alignment are performed in parallel. The system has been implemented using IBM's Concert/C language for distributed programming. The server is available 24 hours a day, 7 days a week and can be accessed both directly and through "Grail" of the Oak Ridge National Lab. Incremental changes and improvements made to the server will be reflected in the "Message of the day" at the beginning of this help file: we recommend that users periodically issue a `send help' request for up to date information on the server. For the moment, we can process requests originating from email addresses of the form user@[machine.][subdomain.]institution.type or user%machine@[machine.][subdomain.]institution.type or "string::user"@[machine.][subdomain.]institution.type We plan to further expand the accepted formats, depending on demand. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ HOW TO USE THE SERVER: You can use the dFLASH facilities by sending an email ---------------------- message with the appropriate syntax to the address "dflash@watson.ibm.com" (without the quotes). SUBJECT LINE: It is important that the "Subject" line of your message contain ------------- one of: { dflash, dFlash, dFLASH, DFLASH }. Messages whose subject line does NOT conform to this rule, **WILL BE LEFT UNPROCESSED**. The reason for that restriction is that we want to be able to automatically distinguish between messages that are addressed to the server and those that are meant for one of the group members. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ MESSAGE FORMAT: The typical message-body of an email request looks as follows --------------- BLOSUM 62 (optional | DIRECTIVE) VERBOSE 10 20 (optional | DIRECTIVE) SEQUENCES 100 (optional | DIRECTIVE) ALIGNMENTS 50 (optional | DIRECTIVE) THRESHOLD 30 (optional | DIRECTIVE) KEY XMATCH (optional | DIRECTIVE) SOURCE PROTEIN (optional | DIRECTIVE) TARGET SP (optional | DIRECTIVE) BEGIN (mandatory | DIRECTIVE) >A_ONE_LINE_TEST_SEQ_LABEL (mandatory -- notice the '>' ) a_sequence_of_{amino_acids,nucleic_acids,spaces,tabs} 1 (mandatory terminator) The PAM/BLOSUM, VERBOSE, SEQUENCES, ALIGNMENTS, THRESHOLD, KEY, SOURCE and TARGET directives can appear in any order but they *must* precede the BEGIN directive. The BEGIN line must be followed by the LABEL line which in turn should be followed by the test sequence. The test sequence should contain at least 18(=proteins)/54(=dna) and not more than 1500 amino acid or nucleotide characters. But it may contain ANY NUMBER of CARRIAGE RETURN TAB and SPACE characters; the latter are not of course counted while computing the length of the test sequence. There is NO case sensitivity in the label and the test sequence itself. If the test sequence is longer than 1500 characters, the e-mail filter will truncate it to the first 1500 characters and will send a note to that effect to the originator of the query; the filter will then submit the truncated sequence to the search engine. NOTA BENE: The words appearing on the lines marked DIRECTIVE above can be in ---------- lower case or upper case; in other words, you can have pam or PAM, threshold or THRESHOLD, alignments or ALIGNM