From owner-proteins@net.bio.net Sun Jan 02 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!news.cs.umb.edu!hsdndev!howland.reston.ans.net!paladin.american.edu!darwin.sura.net!sgiblab!munnari.oz.au!hp9000.csc.cuhk.hk!slip060.csc.cuhk.hk!b137795 From: b137795@mailserv.cuhk.hk Subject: collagen antibodies Summary: looking for antibodies against human collagen Sender: usenet@hp9000.csc.cuhk.hk (News Administration) Message-ID: Date: Sat, 1 Jan 1994 02:12:13 GMT Nntp-Posting-Host: slip060.csc.cuhk.hk Organization: The Chinese University of Hong Kong Keywords: collagen antibody Lines: 14 Dear netters, Does anyone konw where we can purchase some antibodies or monoclonal antibodies against different types of human collagens? Thank you very much. ming-chiu Fung Biology Dept. CUHK e-mail: mingchiufung@cuhk.hk From owner-proteins@net.bio.net Sun Jan 02 22:00:00 1994 Path: biosci!hubcap!darwin.sura.net!gatech!concert!bigblue.oit.unc.edu!samba.oit.unc.edu!not-for-mail From: Ken.Winslow@launchpad.unc.edu (ken Wwinslow) Newsgroups: bionet.metabolic-reg,bionet.molbio.proteins,bionen.neuroscience Subject: Cause of Migraine Date: 2 Jan 1994 18:41:29 GMT Organization: University of North Carolina Extended Bulletin Board Service Lines: 11 Message-ID: <2g74gp$55r@samba.oit.unc.edu> NNTP-Posting-Host: lambada.oit.unc.edu Xref: biosci bionet.metabolic-reg:134 bionet.molbio.proteins:1169 Pursuing a triggering enzymatic event preceeding a disturbance of catecholamine and indoleamine reactions that influences both pathways as an explanation of symptom disparities in a currently unrecognized regulatory mechanism. Please e-mail any thoughts on areas of possible research. -- The opinions expressed are not necessarily those of the University of North Carolina at Chapel Hill, the Campus Office for Information Technology, or the Experimental Bulletin Board Service. internet: laUNChpad.unc.edu or 152.2.22.80 From owner-proteins@net.bio.net Sun Jan 02 22:00:00 1994 Newsgroups: bionet.metabolic-reg,bionet.molbio.proteins,bionen.neuroscience Path: biosci!daresbury!doc.ic.ac.uk!warwick!pipex!uunet!yeshua.marcam.com!zip.eecs.umich.edu!umn.edu!limerick.cbs.umn.edu!hiroki From: hiroki@limerick.cbs.umn.edu (Hiroki Morizono) Subject: Re: Cause of Migraine Message-ID: Followup-To: bionet.metabolic-reg,bionet.molbio.proteins,bionen.neuroscience Sender: news@news2.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: limerick.cbs.umn.edu Reply-To: hiroki@limerick.cbs.umn.edu Organization: University of Minnesota, Twin Cities X-Newsreader: TIN [version 1.2 PL2] References: <2g74gp$55r@samba.oit.unc.edu> Date: Mon, 3 Jan 1994 21:05:10 GMT Lines: 11 Xref: biosci bionet.metabolic-reg:135 bionet.molbio.proteins:1170 ken W winslow (Ken.Winslow@launchpad.unc.edu) wrote: : Pursuing a triggering enzymatic event preceeding a disturbance of : catecholamine and indoleamine reactions that influences both pathways as : an explanation of symptom disparities in a currently unrecognized : regulatory mechanism. : Please e-mail any thoughts on areas of possible research. I get really bad headaches after reading (non)sentences like that.... Can you rephrase it in standard English? :-) Hiroki From owner-proteins@net.bio.net Mon Jan 03 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!EU.net!sun4nl!star.cs.vu.nl!balaena!mac134.bio.vu.nl!user From: cweijden@bio.vu.nl (C v/d Weijden) Subject: transposon Tn916 Message-ID: Followup-To: bionet.molbio.proteins Sender: news@bio.vu.nl Organization: Mol.Micro, Vrije Uni., Amsterdam, NL Date: Tue, 4 Jan 1994 09:59:50 GMT Lines: 11 Could somebody tell me how to get my hands on a strain or plasmid which contains transposon Tn916? I like to use this E. faecalis transposon for insertional mutagenesis in a compatible strain. My E-mail address is: PTJ.Willemsen.omb.acta@med.vu.nl -- P.T.J. Willemsen Dept. Oral Microbiology Free University Amsterdam The Netherlands From owner-proteins@net.bio.net Mon Jan 03 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!ee.und.ac.za!ucthpx!uctvax.uct.ac.za!schren13 From: schren13@uctvax.uct.ac.za Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Signal Seq. Trap Message-ID: <1994Jan4.170854.205783@uctvax.uct.ac.za> Date: 4 Jan 94 17:08:54 +0200 Organization: University of Cape Town Lines: 15 Xref: biosci bionet.molbio.methds-reagnts:10051 bionet.molbio.proteins:1172 I am looking for a SIGNAL SEQUENCE TRAP CAN ANYONE HELP ? The plasmid-trap I have in mind should have the following features: 1) ori for replication in E.coli 2) medium copy number in E.coli 3) antibiotic resistance marker 4) upstream E.coli -10/-35 promoter 5) multiple cloning site downstream from promoter 6) signal-minus indicator gene downstream from cloning site (eg phoA) Should anyone know of such a construct please let me know. My e-mail address is rscholle@physio.uct.ac.za From owner-proteins@net.bio.net Mon Jan 03 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!warwick!pipex!howland.reston.ans.net!darwin.sura.net!news-feed-1.peachnet.edu!news-feed-2.peachnet.edu!news From: tbailey@sun.cc.westga.edu Newsgroups: bionet.molbio.proteins Subject: amino acids Date: Wed, 05 Jan 94 00:09:42 PST Organization: University System of Georgia (PeachNet) Lines: 20 Message-ID: <2gdi7j$4it@news-feed-2.PeachNet.EDU> NNTP-Posting-Host: telebit-245.oit.peachnet.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am a mathematician and I have just joined this group. Please note that I am a tyro in this area. Recently I begin to take amino acid supplements,especially L-lysine. As a consequence, my mood has changed in a very positive way. There has also been another positive benefit. The vitreous in my eyes has partially changed to liquid and hence I have flashes. I seem to have more of them when I am hungry. I have always consumed lots of protein. Could it be that my body does not efficiently change protein into amino acids? I would appreciate any feedback. With best regards, Terry Bailey tbailey@sun.cc.westga.edu From owner-proteins@net.bio.net Tue Jan 04 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!noc.near.net!news.cs.brandeis.edu!brenner From: brenner@rose.brandeis.edu (Charles Brenner) Subject: Re: FPLC systems Message-ID: <1994Jan5.180409.2051@news.cs.brandeis.edu> Sender: news@news.cs.brandeis.edu (USENET News System) Organization: Brandeis University References: Date: Wed, 5 Jan 1994 18:04:09 GMT Lines: 17 stiles@uhunix.uhcc.Hawaii.Edu (John Stiles) writes: > We are looking at purchasing a FLPC system for protein isolation and purification. We have been using a Pharmacia system which seems OK. We have information on Pharmacia and Waters 650 Advanced Protein Purification System. Any one have any experience with these or others? Any advice welcomed. Thanks. Pharmacia columns are extremely expensive. The FPLC gained popularity with biologists because it was designed for protein purification rather than typical reversed phase applications. The Waters seems to be as easy to use as the Pharmacia and ought to cost a lot less to run over the years. CB -- Charles Brenner, Ph.D. Fellow of the Leukemia Society of America Rosenstiel Center, rm 610 phone (617) 736-4944 Brandeis University fax (617) 736-2405 Waltham, MA 02254-9110 brenner@auriga.rose.brandeis.edu From owner-proteins@net.bio.net Tue Jan 04 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!munnari.oz.au!news.Hawaii.Edu!uhunix.uhcc.Hawaii.Edu!stiles From: stiles@uhunix.uhcc.Hawaii.Edu (John Stiles) Subject: FPLC systems Message-ID: Sender: news@news.Hawaii.Edu Organization: University of Hawaii Date: Tue, 4 Jan 1994 21:47:50 GMT Lines: 9 Dear Fellow Netpersons: We are looking at purchasing a FLPC system for protein isolation and purification. We have been using a Pharmacia system which seems OK. We have information on Pharmacia and Waters 650 Advanced Protein Purification System. Any one have any experience with these or others? Any advice welcomed. Thanks. John Stiles Dept. Plant Molecular Physiology Univ. Hawaii stiles@uhunix.uhcc.hawaii.edu From owner-proteins@net.bio.net Tue Jan 04 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!news.claremont.edu!nntp-server.caltech.edu!rickert From: rickert@cco.caltech.edu (Keith Warren Rickert) Newsgroups: bionet.molbio.proteins Subject: Re: amino acids Date: 5 Jan 1994 06:54:00 GMT Organization: California Institute of Technology, Pasadena Lines: 45 Message-ID: <2gdo68$34e@gap.caltech.edu> References: <2gdi7j$4it@news-feed-2.PeachNet.EDU> NNTP-Posting-Host: sandman.caltech.edu In <2gdi7j$4it@news-feed-2.PeachNet.EDU> tbailey@sun.cc.westga.edu writes: >Recently I begin to take amino acid supplements,especially >L-lysine. As a consequence, my mood has changed in a very >positive way. >There has also been another positive benefit. The vitreous >in my eyes has partially changed to liquid and hence I have >flashes. I seem to have more of them when I am hungry. >I have always consumed lots of protein. Could it be that >my body does not efficiently change protein into amino >acids? I would appreciate any feedback. First of all, this isnt really an appropriate group for this kind of a discussion. This is really meant for the molecular biology of proteins, and protein purification, etc. I would think somewhere in sci.med was more useful, or perhaps in altnet somewhere. Very few people have problems digesting proteins to amino acids, or making use of amino acids once they have been broken down. I suspect that you would have noticed much larger medical problems if you had. Lysine, however, is one of the essential amino acids in human metabolism, and as such cant be made from other amino acids. If your protein intake is of low quality, i.e. in this case lacking in lysine, you will be deficient, even if your total quantity of protein intake is ok. Mood alterations, I have no idea on. Liquefaction of the vitreous humor in your eye sounds.. improbable at best. You might be seing increases in floaters and flashes for other reasons, but I dont know. I'd recommend taking the question elsewhere. Now, if you wanted to get advice on conditions for breaking down proteins for purposes of amino acid analysis...that would be rather more within the ken of the people here... Keith -- Keith Rickert | "That was only one of the many occasions on which rickert@cco.caltech.edu | I met my death - an experience I don't hesitate keith@imppig.caltech.edu | strongly to recommend" - Baron von Munchchausen From owner-proteins@net.bio.net Tue Jan 04 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: JAWAHAR Newsgroups: bionet.molbio.proteins Subject: Substance P monoclonals anyone ?? Date: 5 Jan 1994 16:54:49 -0000 Lines: 19 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gercp$2mk@mserv1.dl.ac.uk> X-Vms-Mail-To: UUCP%"proteins@net.bio.net" Original-To: proteins@net.bio.net Hello, Does anyone out there know if there are commercially available or otherwise produced MoABs against the neuropeptide Substance P.. If anyone has any idea whatsoever about this monoclonal, please get in touch with me at the address given below by email.. Any help renedered will be greatly appreciated.. Thank you in advance. jawahar -X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X- G.Jawahar Swaminathan Phone: 91-11-686 3004 to 6863009 Protein Chemistry Lab \ / Extn: 234, 309 National Institute of Immunology, | Gram: IMMUNOLOGY, New Delhi Aruna Asaf Ali Marg, \ / \ / Email: Jawahar@NII.ernet.in New Delhi - 110 067. | | Fax: 91-11-686 2125 INDIA UUCP: ...uunet!sangam!vikram!nii!jawahar! =============================================================================== From owner-proteins@net.bio.net Wed Jan 05 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!newsserver.jvnc.net!cyanamid!ptag2.pt.cyanamid.com!bascombn From: bascombn@ptag2.pt.cyanamid.com Subject: Re: FPLC systems Message-ID: <1994Jan6.100216.1@ptag2.pt.cyanamid.com> Lines: 16 Sender: news@cyanamid.uucp Organization: AMERICAN CYANAMID AGRICULTURAL RESEACH CENTER References: Date: Thu, 6 Jan 1994 15:02:16 GMT In article , stiles@uhunix.uhcc.Hawaii.Edu (John Stiles) writes: > Dear Fellow Netpersons: > > We are looking at purchasing a FLPC system for protein isolation and purification. We have been using a Pharmacia system which seems OK. We have information on Pharmacia and Waters 650 Advanced Protein Purification System. Any one have any experience with these or others? Any advice welcomed. Thanks. > > John Stiles > Dept. Plant Molecular Physiology > Univ. Hawaii > > stiles@uhunix.uhcc.hawaii.edu We have purchased the BioCad and have been very pleased. We also have the FPLC but the softward for the BioCAD is fantastic and the resolution and speed from the POROS columns is excellent. From owner-proteins@net.bio.net Wed Jan 05 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!saimiri.primate.wisc.edu!caen!malgudi.oar.net!news.ysu.edu!psuvm!axc19 Organization: Penn State University Date: Thu, 6 Jan 1994 10:04:48 EST From: Message-ID: <94006.100448AXC19@psuvm.psu.edu> Newsgroups: bionet.molbio.proteins Subject: EEKQLN Lines: 5 I have found a protein sequence : EEKQLN and it appears to be homologous to sev eral other proteins...However, I have not been able to identify any special purpose for it...Does anyone out ther knows what the importance of this sequenc e is. By the way it does appear to be a calcium-binding protein. axc19@psuvm.psu.edu From owner-proteins@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "" Newsgroups: bionet.molbio.proteins Subject: CPK molecular models purchasing onfo needed Date: 7 Jan 1994 22:43:59 -0000 Lines: 19 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gkojf$qef@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk From: GROVE::UDBR006 "Rebecca Liesl Beavil" 7-JAN-1994 10:23:04.90 To: UDAA420 CC: Subj: Does anybody know where I can purchase the CPK molecular models? I use them for undergraduate practicals, and need some more connectors, but I can't find anyone who knows where, or if I can still buy them. Thanks, Rebecca Beavil Kings College London (Email:UDBR006@uk.ac.kcl.cc.bay) From owner-proteins@net.bio.net Fri Jan 07 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!gatech!news-feed-2.peachnet.edu!athena.cs.uga.edu!pollux!ramanath From: ramanath@pollux.cs.uga.edu (CHANDRA RAMANATHAN) Newsgroups: bionet.molbio.proteins Subject: RNA SECONDARY STRUCTURE Date: 9 Jan 1994 00:02:18 GMT Organization: University of Georgia, Athens Lines: 12 Distribution: world Message-ID: <2gnhia$krv@athena.cs.uga.edu> NNTP-Posting-Host: pollux.cs.uga.edu Dear Netters: I am looking for a RNA secondary structure prediction program, other than the FOLD program in GCG. I would highly appreciate if you can help me in this regard. Thanks in advance, Chandra S. Ramanathan College of Pharmacy University of Georgia E-Mail Add: ramanath@pollux.cs.uga.edu From owner-proteins@net.bio.net Sat Jan 08 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Edwin Wright" Newsgroups: bionet.molbio.proteins Subject: Protein Sequence - Combinatoric Table Date: 9 Jan 1994 15:31:15 -0000 Lines: 12 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gp803$pbj@mserv1.dl.ac.uk> X-Nupop-Charset: English Does anyone know of any research underway to produce some kind of table or universal combinatoric sequence structure for all proteins, in an effort to delimit the possible combinations of protein sequences? Edwin Wright 85 Spinnaker Drive, A-602 Halifax, Nova Scotia CANADA B3N 3E3 Telephone: (902) 477-5037 Email: ewright@fox.nstn.ns.ca =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Sat Jan 08 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!agate!library.ucla.edu!news.mic.ucla.edu!unixg.ubc.ca!zinc.ecc.ubc.ca!sarven From: sarven Newsgroups: bionet.molbio.proteins Subject: Protein isolation Date: 10 Jan 1994 02:14:55 GMT Organization: ubc Lines: 9 Distribution: world Message-ID: <2gqdmv$ed7@nntp.ucs.ubc.ca> NNTP-Posting-Host: zinc.ecc.ubc.ca X-UserAgent: Nuntius v1.1.1d24 X-XXMessage-ID: X-XXDate: Sun, 9 Jan 94 03:32:21 GMT Hi! Could someone out there be kind enough to send me (or give me the reference for) a reliable, quick protocol for isolating total protein from tissues for Western blots. Thanks Sarven From owner-proteins@net.bio.net Sat Jan 08 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!usc!yeshua.marcam.com!zip.eecs.umich.edu!umn.edu!limerick.cbs.umn.edu!hiroki From: hiroki@limerick.cbs.umn.edu (Hiroki Morizono) Subject: Knauer SuperLoop Message-ID: Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: limerick.cbs.umn.edu Reply-To: hiroki@limerick.cbs.umn.edu Organization: University of Minnesota, Twin Cities X-Newsreader: TIN [version 1.2 PL2] Date: Mon, 10 Jan 1994 06:12:12 GMT Lines: 10 Anyone out there had any experience with Knauer's SuperLoop-- It's a way of injecting large volumes of sample onto a PrepHPLC column, similar to Pharmacia's, only it is able to withstand higher pressure. (supposed to anyway) Anyway, we got one, and it is giving me all sorts of problems with leaks around its central piston. Help much appreciated, Hiroki hiroki@limerick.cbs.umn.edu From owner-proteins@net.bio.net Sun Jan 09 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!EU.net!ub4b!reks.uia.ac.be!news From: przemko@reks.uia.ac.be (Przemko) Subject: Re: RNA SECONDARY STRUCTURE Message-ID: <1994Jan10.084325.16783@reks.uia.ac.be> Sender: news@reks.uia.ac.be (USENET News System) Organization: University of Antwerp X-Newsreader: Date: Mon, 10 Jan 1994 08:43:25 GMT Lines: 21 In article <2gnhia$krv@athena.cs.uga.edu> ramanath@pollux.cs.uga.edu (CHANDRA RAMANATHAN) writes: >Dear Netters: > > I am looking for a RNA secondary structure prediction program, other than > the FOLD program in GCG. I would highly appreciate if you can help me in > this regard. > > Thanks in advance, > Chandra S. Ramanathan > College of Pharmacy > University of Georgia > > E-Mail Add: ramanath@pollux.cs.uga.edu Hi! I would also like to know. I realize it is a wrong group but since the original was posted here... Przemko From owner-proteins@net.bio.net Sun Jan 09 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!geraldo.cc.utexas.edu!folate.cm.utexas.edu!appling From: Dean R. Appling Newsgroups: bionet.molbio.proteins Subject: Re: RNA SECONDARY STRUCTURE Date: 10 Jan 1994 16:01:29 GMT Organization: University of Texas at Austin Lines: 65 Distribution: world Message-ID: <2gru4p$opa@geraldo.cc.utexas.edu> References: <2gnhia$krv@athena.cs.uga.edu> NNTP-Posting-Host: folate.cm.utexas.edu X-UserAgent: Version 1.1.3 X-XXMessage-ID: X-XXDate: Mon, 10 Jan 94 16:00:47 GMT Subject: RNA SECONDARY STRUCTURE From: CHANDRA RAMANATHAN, ramanath@pollux.cs.uga.edu Date: 9 Jan 1994 00:02:18 GMT In article <2gnhia$krv@athena.cs.uga.edu> CHANDRA RAMANATHAN, ramanath@pollux.cs.uga.edu writes: >Dear Netters: > > I am looking for a RNA secondary structure prediction program, other than > the FOLD program in GCG. I would highly appreciate if you can help me in > this regard. > > Thanks in advance, > Chandra S. Ramanathan > College of Pharmacy > University of Georgia > > E-Mail Add: ramanath@pollux.cs.uga.edu Try MulFold (the following is from its documentation): MulFold is a Macintosh version of MFOLD, software for prediction of RNA secondary structure by free energy minimization, version 2.0 including suboptimal folding with temperature dependence, by Michael Zuker and John Jaeger. Paper publications about this software include: M. Zuker On Finding All Suboptimal Foldings of an RNA Molecule. Science, 244, 48-52, (1989) J. A. Jaeger, D. H. Turner and M. Zuker Improved Predictions of Secondary Structures for RNA. Proc. Natl. Acad. Sci. USA, BIOCHEMISTRY, 86, 7706-7710, (1989) This version is limited to 300 bases per folding, and requires 1 megabyte of free memory to run. It should operate on a Mac Plus, but a Mac II or better is suggested due its time-consuming calculations. MulFold will operate in the background under MultiFinder so that your Mac is useful for other things during the several hours MulFold may be running. This program is a hybrid of the original VMS-Vax program and Macintosh user interface. Where possible I revised the Vax user interface to use menu selections. However, a portion of the Vax interface remains. It is available for anonymous ftp: ftp iubio.bio.indiana.edu user: anonymous cd [archive.molbio.mac] get mulfold.hqx The .CT output files may be viewed directly with LoopViewer (available in the same ftp directory as loopviewer.hqx). Don Gilbert Biocomputing Office, Biology Department Indiana University, Bloomington, IN 47405 Email: Don.Gilbert@IUBio.Bio.Indiana.Edu We have used MulFold along with Loopviewer on our Macs and find them quite satisfactory. From owner-proteins@net.bio.net Sun Jan 09 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!darwin.sura.net!news-feed-2.peachnet.edu!athena.cs.uga.edu!pollux!ramanath From: ramanath@pollux (CHANDRA RAMANATHAN) Newsgroups: bionet.molbio.proteins Subject: Re: RNA SECONDARY STRUCTURE Date: 11 Jan 1994 02:04:02 GMT Organization: University of Georgia, Athens Lines: 17 Distribution: world Message-ID: <2gt1ei$94e@athena.cs.uga.edu> References: <2gnhia$krv@athena.cs.uga.edu> NNTP-Posting-Host: pollux.cs.uga.edu X-Newsreader: Tin 1.1 PL4 Dear Netters : Thanks for your kind response. As one friend mentioned, I agree that this is not the right group to enquire about RNA structures. But I am highly satisfied with the response and I would like to ask for another help. Most of the programs handle only small RNA sequences. Is there any program which can handle big sequences(10,000 bp). I have some access to supercomputing facilities, which these big sequences require. I would highly appreciate if you can help me in this regard. Thanking you in advance, CHANDRA S. RAMANATHAN E-MAIL ADD : ramanath@pollux.cs.uga.edu From owner-proteins@net.bio.net Sun Jan 09 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!trane.uninett.no!nac.no!nntp-oslo.uninett.no!usenet From: ragnar.flengsrud@ibf.nlh.no Newsgroups: bionet.molbio.proteins Subject: Re: Protein isolation Date: 10 Jan 1994 19:59:46 GMT Organization: agricultural univ. of norway Lines: 21 Distribution: world Message-ID: <2gsc3i$832@ratatosk.uninett.no> References: <2gqdmv$ed7@nntp.ucs.ubc.ca> NNTP-Posting-Host: biorf.nlh.no In article <2gqdmv$ed7@nntp.ucs.ubc.ca> sarven writes: >Hi! > >Could someone out there be kind enough to send me (or give me the >reference for) a reliable, quick protocol for isolating total protein >from tissues for Western blots. > >Thanks > >Sarven > Hi, My suggestion is that you start with Methods in Enzymology, volume 182: Guide to Protein Purification. Special attention should be payed to pp. 425-495 (Purification Procedures: Electrophoretic Methods. Hope this helps. Regards, Ragnar Flengsrud, Dept of Biotechn. Sci., Agricultural University of Norway. From owner-proteins@net.bio.net Mon Jan 10 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Rafael N Szeinfeld Newsgroups: bionet.molbio.proteins Subject: Free Radicals & Proteins Date: 11 Jan 1994 21:19:39 -0000 Lines: 10 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gv55b$qk1@mserv1.dl.ac.uk> Original-To: protein analysis Hi Netters, Could someone out there direct me to some references on the interaction of free radicals and proteins (specifically enzymes). I'm beggining to work on the subject so if someone wants to discuss would be great. Thanks for your attention & Help. Rafael Najmanovich szeinfel@fox.cce.usp.br From owner-proteins@net.bio.net Mon Jan 10 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!torn!nott!emr1!weathere From: weathere@emr1.emr.ca (Carl Weatherell) Subject: Monomers and Dimers of Collagen Message-ID: <1994Jan11.235412.26389@emr1.emr.ca> Organization: Natural Resources Canada, Ottawa X-Newsreader: TIN [version 1.1 PL8] Date: Tue, 11 Jan 1994 23:54:12 GMT Lines: 8 Does anyone know where I might be able to acquire the alpha and beta strands of a Type I collagen? (I'm trying to avoid CM-cellulose type chromatographic preparations) Also, can these strands be stabilized over long periods to prevent recombination into the gamma sheet conformation? Will SDS do the trick?? Carl Weatherell weathere@emr1.emr.ca From owner-proteins@net.bio.net Tue Jan 11 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!hubcap!darwin.sura.net!howland.reston.ans.net!pipex!demon!visigoth.demon.co.uk!user From: pettsj@visigoth.demon.co.uk (James Petts) Subject: Sulphatases Message-ID: Followup-To: bionet.molbio.proteins Sender: news@demon.co.uk (Usenet Administration) Nntp-Posting-Host: visigoth.demon.co.uk Organization: Black Hand of the 7th Day Panthers of Anachronism Date: Wed, 12 Jan 1994 13:32:44 GMT Lines: 8 Does anybody have a rough idea of the number of steroidal sulphatases in man, and if there are not many, their names/distribution? -- James Petts ----------- P.S. Please excuse my rottn' english you see moomins go to school only as long as it amuses them. From owner-proteins@net.bio.net Tue Jan 11 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!uunet!pipex!demon!visigoth.demon.co.uk!user From: pettsj@visigoth.demon.co.uk (James Petts) Subject: Small Disulphide Bridges Peptides Message-ID: Followup-To: bionet.molbio.proteins Sender: news@demon.co.uk (Usenet Administration) Nntp-Posting-Host: visigoth.demon.co.uk Organization: Black Hand of the 7th Day Panthers of Anachronism Date: Thu, 13 Jan 1994 07:38:06 GMT Lines: 10 Time to ask help from the mighty collective wisodom of the net again :-) Can anybody point me to experimental and/or theoretical studies on conformations of small (n=3-7 residues) disulphide-bridged peptides? -- James Petts ----------- P.S. Please excuse my rottn' english you see moomins go to school only as long as it amuses them. From owner-proteins@net.bio.net Tue Jan 11 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: Langevin Eric Newsgroups: bionet.molbio.proteins Subject: innocent question Date: 12 Jan 1994 13:28:56 -0000 Lines: 23 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2h0tuo$pn3@mserv1.dl.ac.uk> Original-To: "/S=proteins/O=daresbury/PRMD=UK.AC/C=GB/" Hello there. I'm looking for various public domain software for protein sequence analysis (domain identification, pattern searching, sequence alignment) to start my thesis job. I should build an integrated system, with many "expert system" features, for protein function identification... Is it the right mailing list to contact? Thanks for any response, Eric Langevin. -----___________________________----- "I can mislead, I couldn't lie". Th. d'Avila. Eric Langevin langevin@cih.hcuge.ch tel. (+4122) 37 26 280 fax (+4122) 37 26 198 Numerical Imagery and Artificial Intelligence Unit (UIN) Hospital Informatics Center (CIH) Geneva University Hospital (HCUG) 24, rue Micheli-du-Crest, 1211 Geneve 14 , Switzerland From owner-proteins@net.bio.net Wed Jan 12 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!agate!msuinfo!netnews.upenn.edu!dsinc!ub!acsu.buffalo.edu!ubvms.cc.buffalo.edu!v098p82f From: v098p82f@ubvms.cc.buffalo.edu (Joseph M Falcone) Subject: amino acid sequence Message-ID: News-Software: VAX/VMS VNEWS 1.41 Keywords: protein sequence Sender: nntp@acsu.buffalo.edu Nntp-Posting-Host: ubvmsb.cc.buffalo.edu Organization: University at Buffalo Date: Thu, 13 Jan 1994 19:44:00 GMT Lines: 13 hello, I was wonderiing if anyone out there can help me find the amino acid sequence of calf spleen phosphodiesterase, if it has been studied? I've checked medline and a little in chem abstracts, but have found nothing. Any information would be appreciated. thanks joe falcone v098p82f@ubvms.cc.buffalo.edu From owner-proteins@net.bio.net Wed Jan 12 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!hubcap!darwin.sura.net!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!mentor.cc.purdue.edu!news From: westerm@aclcb.purdue.edu Subject: Re: RNA SECONDARY STRUCTURE Message-ID: Sender: news@mentor.cc.purdue.edu (USENET News) Organization: Purdue University X-Newsreader: Date: Thu, 13 Jan 1994 18:36:45 GMT Lines: 20 In article <2gt1ei$94e@athena.cs.uga.edu> ramanath@pollux (CHANDRA RAMANATHAN) writes: > Most of the programs handle only small RNA sequences. Is there any program > which can handle big sequences(10,000 bp). I have some access to > supercomputing facilities, which these big sequences require. I would > highly appreciate if you can help me in this regard. The existing programs don't predict correct structures for small sequences and thus there is no reason to suspect they will predict larger sequences with any accuracy. All you will get is garbage. Never-the-less, if you wish to modify the source code for MFold and you have a large enough computer, you should be able to run MFold on 10,000 bases. I've done a "pseudo-fold" (that is, just looking at the closest 200 bp when considering a fold instead of doing a true global folding) on HIV (~10,000 bp) using both MFold and a yet-to-be-released custom RNA folding program. It works. It took days of computer time. And the results were unreliable. But it can be done. If you limit MFold to just examining the From owner-proteins@net.bio.net Thu Jan 13 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!munnari.oz.au!newshost.anu.edu.au!rscmacl10.anu.edu.au!user From: crowther@rsc3.anu.edu.au (Jeff) Newsgroups: bionet.molbio.proteins Subject: Re: FPLC systems Followup-To: bionet.molbio.proteins Date: Sat, 15 Jan 1994 14:47:37 +1000 Organization: Worst at Best Lines: 24 Message-ID: References: <1994Jan5.180409.2051@news.cs.brandeis.edu> NNTP-Posting-Host: 150.203.36.10 In article <1994Jan5.180409.2051@news.cs.brandeis.edu>, brenner@rose.brandeis.edu (Charles Brenner) wrote: > stiles@uhunix.uhcc.Hawaii.Edu (John Stiles) writes: > > > We are looking at purchasing a FLPC system for protein isolation and purification. We have been using a Pharmacia system which seems OK. We have information on Pharmacia and Waters 650 Advanced Protein Purification System. Any one have any experience with these or others? Any advice welcomed. Thanks. > > Pharmacia columns are extremely expensive. The FPLC gained popularity...... We use the Pharmacia FPLC and whatever columns we can pickup on the cheap including mixing an matching flow adaptors etc and have found the system to run very well. Don't know about the Waters 650 system or the computer program FPLC Manager to go with the Pharmacia FPLC (Don't have the program) but have used HPLC Manager on Pharmacia HPLC and it was not TOO bad but could have used a little work for my personal liking. -- My Best Regards Jeff Centre for Molecular Structure and Function Australian National University Research School of Chemistry From owner-proteins@net.bio.net Fri Jan 14 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!pipex!pavo.csi.cam.ac.uk!nntp-serv!esr From: esr@al.* (Sonnhammer E./Durbin) Subject: Re: Protein Sequence - Combinatoric Table In-Reply-To: "Edwin Wright"'s message of 9 Jan 1994 15:31:15 -0000 Message-ID: Sender: news@infodev.cam.ac.uk (USENET news) Nntp-Posting-Host: al.mrc-lmb.cam.ac.uk Organization: /hgmp0/esr/.organization References: <2gp803$pbj@mserv1.dl.ac.uk> Distribution: bionet Date: Sat, 15 Jan 1994 17:29:03 GMT Lines: 29 "Edwin Wright" writes: Does anyone know of any research underway to produce some kind of table or universal combinatoric sequence structure for all proteins, in an effort to delimit the possible combinations of protein sequences? Edwin, I think you would get more answers if you more explicitly say what you mean by your question. Are you referring to the combinatorial nature of protein domains in mosaic proteins, or something else? What would the table you're asking for look like and what do you mean by "universal combinatoric sequence structure for all proteins"? Also, what kind of questions would you like to answer - something like "given protein domain A, which other domains has it been observed to be fused to?", or what? I have been involved in a project where the goal was to cluster a protein sequence database into families of domains, taking the combinatorial nature of proteins into account. If this is any help to you, you can pick up the resulting clustered database (as multiple sequence alignments) and a preprint of the paper by anon. FTP at cele.mrc-lmb.cam.ac.uk in /pub/prodom. Erik Sonnhammer Sanger Centre Cambridge UK From owner-proteins@net.bio.net Sun Jan 16 22:00:00 1994 Path: biosci!s.u-tokyo!kuis-news!wnoc-kyo-news!aist-nara!wnoc-tyo-news!news.u-tokyo.ac.jp!sinetnews!daffy!uwvax!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!lrellick From: lrellick@magnus.acs.ohio-state.edu (Lorraine M Rellick) Newsgroups: bionet.molbio.proteins Subject: need help with solvation energies... Date: 17 Jan 1994 17:38:51 GMT Organization: The Ohio State University Lines: 3 Message-ID: <2heifb$p9v@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: top.magnus.acs.ohio-state.edu Could someone point me in the direction of the latest work being done on incorporation of solvation energies in peptide folding algorithms? Thanks - Lori From owner-proteins@net.bio.net Sun Jan 16 22:00:00 1994 Path: biosci!s.u-tokyo!kuis-news!wnoc-kyo-news!sh.wide!wnoc-tyo-news!news.u-tokyo.ac.jp!sinetnews!daffy!uwvax!uchinews!vixen.cso.uiuc.edu!howland.reston.ans.net!usenet.ins.cwru.edu!lerc.nasa.gov!purdue!mentor.cc.purdue.edu!inet.d48.lilly.com!inet!sk Newsgroups: bionet.molbio.proteins Subject: Re: electroanalitical methods Message-ID: From: sk@lilly.com (stuart kuhstoss) Date: Mon, 17 Jan 94 19:32:49 GMT References: <2hdt5v$gk0@mserv1.dl.ac.uk> Distribution: bionet,world Organization: Lilly Research Laboratories Nntp-Posting-Host: sak.d50.lilly.com X-Newsreader: VersaTerm Link v1.1 Lines: 27 In Article <2hdt5v$gk0@mserv1.dl.ac.uk>, Mauricio Cesar Palmieri wrote: >Dear Netters, >I am looking for some references about pKa determination in polypeptides >and proteins using electroanalitical methods. >If someone could help me please contact me in the adress above. >All help will welcome. >Thank you, > >Mauricio. >:wq >------------------------------------------------------------------------ >Mauricio Cesar Palmieri >Mestrando em Biotecnologia > >UNIVERSIDADE DE SAO PAULO >BRAZIL > >E - mail: mcpalmie@fox.cce.usp.br > >Letters to: >Universidade Estadual Paulista >Depto. Bioquimica >R. Prof Francisco Degni s/n >Araraquara - SP - Brazil >CEP 14800-900 > From owner-proteins@net.bio.net Sun Jan 16 22:00:00 1994 Path: biosci!ysics.physics.sunysb.edu!psinntp!psinntp!uunet!pipex!uknet!daresbury!not-for-mail From: Mauricio Cesar Palmieri Newsgroups: bionet.molbio.proteins Subject: electroanalitical methods Date: 17 Jan 1994 11:35:27 -0000 Lines: 25 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2hdt5v$gk0@mserv1.dl.ac.uk> Original-To: proteins@net.bio.net Dear Netters, I am looking for some references about pKa determination in polypeptides and proteins using electroanalitical methods. If someone could help me please contact me in the adress above. All help will welcome. Thank you, Mauricio. :wq ------------------------------------------------------------------------ Mauricio Cesar Palmieri Mestrando em Biotecnologia UNIVERSIDADE DE SAO PAULO BRAZIL E - mail: mcpalmie@fox.cce.usp.br Letters to: Universidade Estadual Paulista Depto. Bioquimica R. Prof Francisco Degni s/n Araraquara - SP - Brazil CEP 14800-900 From owner-proteins@net.bio.net Sun Jan 16 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!s.u-tokyo!kuis-news!wnoc-kyo-news!sh.wide!wnoc-tyo-news!news.u-tokyo.ac.jp!sinetnews!daffy!uwvax!uchinews!vixen.cso.uiuc.edu!howland.reston.ans.net!usenet.ins.cwru.edu!nigel.msen.com!yale.edu!cs.yale.edu!loglady.ninds.nih.gov!johnk From: johnk@loglady.ninds.nih.gov (John Kuszewski) Subject: Re: need help with solvation energies... Message-ID: <1994Jan17.191308.17800@cs.yale.edu> Sender: news@cs.yale.edu (Usenet News) Nntp-Posting-Host: spasm.niddk.nih.gov Reply-To: johnk@spasm.niddk.nih.gov Organization: NIDDK-n-JHU References: <2heifb$p9v@charm.magnus.acs.ohio-state.edu> Date: Mon, 17 Jan 1994 19:13:08 GMT Lines: 34 Lorraine M Rellick writes: |> Could someone point me in the direction of the latest |> work being done on incorporation of solvation energies |> in peptide folding algorithms? |> Thanks - Lori I just gave a talk on this. See "Surface area included in energy refinement of proteins: A comparative study on atomic solvation parameters" W. Braun et al. JMB 233, 275 (1993) for an overview. Scheraga's ECEPP also includes surface area calculations--the algorithm is very fast but not always right. See "MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives", H. Scheraga et al., J. Computational Chem. 13, 1-11 (1992). Scheraga seems to think he has the folding problem solved with ECEPP, but I disagree. Finally, a plug for some code written by Yours Truly: an extension to X-PLOR (a molecular dynamics / distance geometratio popular with people who solve structures) that handles solvation energy as well. It's not that fast right now, but it'll get better. It's very flexible though. Right now, I have solvation numbers from K.P. Murphy and E. Freire working (can't find the ref for their paper), and I just about have G.I. Makhatadze and P. Privalov's numbers (JMB 232, 639 (1993)) going too. Write me if you're interested in this code--I have no idea how I'll distribute it yet. -- John Kuszewski johnk@spasm.niddk.nih.gov I'm not an idiot, but I play one on USENET. From owner-proteins@net.bio.net Sun Jan 16 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!paladin.american.edu!darwin.sura.net!guvax.acc.georgetown.edu!fleming From: fleming@guvax.acc.georgetown.edu Newsgroups: bionet.molbio.proteins Subject: Re: FPLC systems Message-ID: <1994Jan17.085153.6768@guvax> Date: 17 Jan 94 08:51:53 -0500 References: <1994Jan5.180409.2051@news.cs.brandeis.edu> Followup-To: bionet.molbio.proteins Distribution: world Organization: Georgetown University Lines: 16 The lab I came from had the Waters 650 system for the last 2-3y. I found the programming to be much easier than the FPLC I now have to work with. If I was buying I would opt for the Waters 650, but with a more 'FPLC like' injection port -the waters has a leur lock fitting which is very poor if using/loading less than 200uL. Having said that we did run almost entirely with pharmacia columns -just made some little plastic/teflon adaptors (all the parts needed came with the waters machine). The tunable detectors (std with the waters) is far superior to the single wavelength pharm -sensitivity, offset etc. Also our dept service tech was full of praise for the mechanics of the waters pumping system, but only luke warm on the FPLC. Good luck. Whatever you get the FPLC columns are really the std. Rob Powell rpowel02@gumedlib.dml.georgetown.edu Dept of Bioc & Mol Biol Georgetown, Uni From owner-proteins@net.bio.net Mon Jan 17 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!darwin.sura.net!news-feed-1.peachnet.edu!umn.edu!maroon.tc.umn.edu!herro001 From: herro001@maroon.tc.umn.edu (Michael J Herron-1) Subject: Re: FPLC systems Message-ID: Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: maroon.tc.umn.edu Organization: University of Minnesota References: <1994Jan5.180409.2051@news.cs.brandeis.edu> <1994Jan17.085153.6768@guvax> Date: Tue, 18 Jan 1994 18:41:01 GMT Lines: 9 The FPLC _columns_ are really nice, but I found the controller a bit awkard. Since most protiens don't mind the low metal ion concentrations from metallic pumps, it might be cheaper to use the FPLC columns on a standard HPLC (that you might already have) Just be sure that your high pressure control will work for the relativley soft FPLC gels. Mike Herron herro001.staff.tc.umn.edu From owner-proteins@net.bio.net Mon Jan 17 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!newcastle.ac.uk!eata!nmjc3 From: M.Collins@newcastle.ac.uk (M.J. Collins) Subject: Purple proteins Nntp-Posting-Host: eata Message-ID: Organization: University of Newcastle upon Tyne, UK, NE1 7RU Keywords: albumin hydrolysis purple Date: Tue, 18 Jan 1994 09:36:56 GMT Lines: 14 Cold acid hydrolysis (HCl 33% wt vol] of a 5% solution of ovalbumin produces a deep purple colour. Does anyone know why? The ovalbumin is from a reputable supplier but has been hanging around in the lab as a dry powder for some time (5+ years?) in a dark brown bottle. benjamin.stern@newcastle.ac.uk Newcastle Research Group in Fossil Fuels and Environmental Geochemistry University of Newcastle upon Tyne From owner-proteins@net.bio.net Tue Jan 18 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!sol.ctr.columbia.edu!news.kei.com!yeshua.marcam.com!zip.eecs.umich.edu!umn.edu!lynx.unm.edu!dns1.NMSU.Edu!smori From: smori@nmsu.edu (Shahram Mori) Newsgroups: bionet.molbio.proteins Subject: problem with ptn squcing Date: 20 Jan 1994 00:42:48 GMT Organization: New Mexico State University, Las Cruces, NM Lines: 10 Message-ID: <2hkk28INNllo@dns1.NMSU.Edu> NNTP-Posting-Host: dante.nmsu.edu X-Newsreader: TIN [version 1.2 PL1] Dear Netters We have been trying to do protein sequences of the N-terminal of a protein by edman's degradation method. However the N-terminal seems to be blocked. Is there any quick enzymatic procedure to find out the nature of the first amino acid? This protein seems to have a high amount of Lysine in it. Thanks Shahram e-mail smori@nmsu.edu From owner-proteins@net.bio.net Tue Jan 18 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!agate!library.ucla.edu!news.ucdavis.edu!othello.ucdavis.edu!ez002976 From: ez002976@othello.ucdavis.edu () Subject: personal to isabel weiersbye Message-ID: Sender: usenet@ucdavis.edu (News Guru) Organization: University of California, Davis X-Newsreader: TIN [version 1.2 PL2] Date: Wed, 19 Jan 1994 15:03:12 GMT Lines: 1 From owner-proteins@net.bio.net Wed Jan 19 22:00:00 1994 Path: biosci!daresbury!keele!uknet!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!robertson4.life.uiuc.edu!user From: chiou-miin_wang@qms1.life.uiuc.edu (Chiou-Miin Wang) Newsgroups: bionet.molbio.proteins Subject: neurosecretory protein isolation Followup-To: bionet.molbio.proteins Date: 20 Jan 1994 20:41:49 GMT Organization: Univ. Illinois Lines: 21 Distribution: world Message-ID: NNTP-Posting-Host: robertson4.life.uiuc.edu Hi, My name is Chiou-Miin Wang and I am writing to request any protocols that would help me isolate a very rare protein from the nervous system of the tobacco hornworm, Manduca sexta. I have a monoclonal antibody (P1F10) which recognizes a single pair of cells in each ganglion from late embryo throughout the adult stage. From the dendrite pattern and cell type, they look like neurosecretory cells. The P1F10 antigen could be their secretory product. I have tried to brute-force purify the protein by dissecting 1000 nervous systems and attempted affinity chromatography with the monoclonal antibody and have gotten ambiguous results to say the least. Are there any expression cDNA library procedures that anyone could recommend to me? Are there any other methods I should look into? Thanks! Chiou-Miin Wang Dept. Entomology University of Illinois chiou-miin_wang@qms1.life.uiuc.edu From owner-proteins@net.bio.net Wed Jan 19 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!lhc!darwin.sura.net!gatech!usenet.ins.cwru.edu!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!decwrl!decwrl!netcomsv!chiron.com!chiremv!hof From: hof@chiremv.chiron.com (Frank Ho) Subject: SDS determination Message-ID: Summary: How to determine SDS concentration in solution? Keywords: SDS Sender: news@chiron.com Nntp-Posting-Host: chiremv Organization: Chiron Corporation Distribution: usa Date: Thu, 20 Jan 1994 22:55:28 GMT Lines: 4 Hi everyone! I need to know if there are protocols or references available for me to determine the sodium dodecyl sulfate concentration in a solution containing proteins. Thank you for your help! From owner-proteins@net.bio.net Thu Jan 20 22:00:00 1994 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!cs.utexas.edu!uunet!sangam!vikram!imtech!mrigank From: mrigank@imtech.ernet.in (Dr. Mrigank) Newsgroups: bionet.molbio.proteins,sci.chem Subject: proc. of american and European peptide sym. ? Message-ID: <9041@imtech.ernet.in> Date: 21 Jan 94 15:08:01 +0530 Distribution: world Organization: Inst. of Microbial Technology, Chandigarh, India Lines: 17 Xref: biosci bionet.molbio.proteins:1213 sci.chem:8112 Hi netters I am looking for the information about the editor, publisher and price of each volume of : 1. Proceedings of American Peptide Symposium From vol I to latest. 2. Proceedings of European Peptide Symposium From vol I to latest. Please reply by e-mail and not post here. Thanks -- Dr. Mrigank \/Phone +91 172 45004 x216 Institute of Microbial Technology /\Email: mrigank@imtech.ernet.in P O Box 1304, Sector 39A \/UUCP:...!uunet!sangam!vikram!imtech!mrigank Chandigarh 160 014 India. /\Fax +91 172 40985 ==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+ -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From owner-proteins@net.bio.net Thu Jan 20 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!pipex!warwick!nott-cs!macfd.biochem.nott.ac.uk!user From: mbxfd@unicorn.nott.ac.uk (Fergus Doherty) Subject: Pancreatic zymogen granule proteins? Message-ID: Followup-To: bionet.molbio.proteins Sender: news@cs.nott.ac.uk Nntp-Posting-Host: macfd Organization: Nottingham University, UK. Date: Fri, 21 Jan 94 17:29:43 GMT Lines: 14 Try as I might I can't find a paper showing SDS-PAGE of pancrearic zymogen granule (content, not membrane ) proteins. We have a protein which is detected by an antibody, it appears quite abundant in the granule so I thought, someone must know what it is! So what I would like is an SDSPAGE pattern and indications of the identities of known proteins. Any pointers? Also any methods, especially ion exchange, for resolving (at least partially) granule proteins? Any help appreciated. Fergus Doherty, dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH Tel: 602 709366 FAX 602 422225 Internet: mbxfd@unicorn.nott.ac.uk From owner-proteins@net.bio.net Thu Jan 20 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!doc.ic.ac.uk!warwick!pavo.csi.cam.ac.uk!mbfs.bio.cam.ac.uk!mjgh From: mjgh@mbfs.bio.cam.ac.uk (Martin Hughes (Bioc)) Subject: Biotin containing proteins Message-ID: <1994Jan21.094706.7695@infodev.cam.ac.uk> Sender: news@infodev.cam.ac.uk (USENET news) Nntp-Posting-Host: mbfs.bio.cam.ac.uk Organization: U. of Cambridge, England Date: Fri, 21 Jan 1994 09:47:06 GMT Lines: 18 Hello! This may be a shot in the dark, but what the hell! Does anyone out there know much about biotin-containing proteins? Specifically, the intra-cellular location and the Mr of the subunits. The enzymes I am aware of which contain biotin are Pyruvate Carboxylase, Acyl CoA Carboxylase and Acetyl CoA Carboxylase. Anyone know of any others? Whilst this is for work on plant cells, any info at all would be welcome. Thanks for reading! Cheers Martin -- Martin J. G. Hughes Department of Biochemistry, University of Cambridge, Cambridge, UK. Email: mjgh@mbfs.bio.cam.ac.uk From owner-proteins@net.bio.net Thu Jan 20 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!destroyer!nntp.cs.ubc.ca!unixg.ubc.ca!bpgm From: bpgm@unixg.ubc.ca (Brent Pollock) Newsgroups: bionet.molbio.proteins Subject: Re: SDS determination Date: 21 Jan 1994 18:32:28 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 16 Distribution: usa Message-ID: <2hp73s$pp9@nnrp.ucs.ubc.ca> References: NNTP-Posting-Host: unixg.ubc.ca Keywords: SDS Try: Reynolds & Tanford (1970). Proc. Nat. Acad. Sci. U.S.A. Vol. 66, No. 3, pp.1002-1007. The references cited therein are: Ray et al. (1966). Biochemistry. 5: 2606. and Reynolds et al. (1967). Biochemistry. 6:937. Share & Enjoy! Brent Pollock [stuff deleted] >Hi everyone! I need to know if there are protocols or references available >for me to determine the sodium dodecyl sulfate concentration in a solution >containing proteins. Thank you for your help! From owner-proteins@net.bio.net Thu Jan 20 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!lrellick From: lrellick@magnus.acs.ohio-state.edu (Lorraine M Rellick) Newsgroups: bionet.molbio.proteins Subject: modeling cytoplasmic tail of transmem prots Date: 21 Jan 1994 19:46:52 GMT Organization: The Ohio State University Lines: 2 Message-ID: <2hpbfc$4pj@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: top.magnus.acs.ohio-state.edu Dear net-mates, anyone doing work on conformational modeling of cytoplasmic tails of transmem proteins? - Lori From owner-proteins@net.bio.net Fri Jan 21 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Edwin Wright" Newsgroups: bionet.molbio.proteins Subject: Re: Protein Sequence - Combinatoric Table Date: 23 Jan 1994 03:28:17 -0000 Lines: 128 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2hsqsh$lqc@mserv1.dl.ac.uk> X-Nupop-Charset: English Original-To: proteins@net.bio.net In Message Sat, 15 Jan 1994 17:29:03 GMT, esr@al.* (Sonnhammer E./Durbin) writes: > >"Edwin Wright" writes: > > Does anyone know of any research underway to produce some kind of table or > universal combinatoric sequence structure for all proteins, in an effort to > delimit the possible combinations of protein sequences? > > >Edwin, > >I think you would get more answers if you more explicitly say what you >mean by your question. Are you referring to the combinatorial nature >of protein domains in mosaic proteins, or something else? What would >the table you're asking for look like and what do you mean by >"universal combinatoric sequence structure for all proteins"? > Also, what kind of questions would you like to answer - something >like "given protein domain A, which other domains has it been observed >to be fused to?", or what? > >I have been involved in a project where the goal was to cluster a >protein sequence database into families of domains, taking the >combinatorial nature of proteins into account. If this is any help to >you, you can pick up the resulting clustered database (as multiple >sequence alignments) and a preprint of the paper by anon. FTP at >cele.mrc-lmb.cam.ac.uk in /pub/prodom. > >Erik Sonnhammer >Sanger Centre >Cambridge UK Erik, Thank you for replying to the subject query. I shall endeavour to articulate this query more explicitly: First of all, as you well know, from a purely mathematical perspective, the number of combinations of protein sequences (given 20 amino acids) is enormous; e.g., for a protein sequence of say, 100 residues, the total number of hypothetical sequences is 20^100 (or approximately 10^130). Clearly, the total number of different protein sequences in the biosphere (millions or possibly tens of millions, i.e. 10^6 - 10^7) is just a fraction of this 10^130). Presumably, the total number of possible biologically viable protein sequences is much closer to 10^7 than to 10^130; hence, it should be theoretically possible to delimit this smaller (i.e. 10^7) number. Given the average protein sequence length (10^2 - 10^3 residues), it should be possible to contruct a hierarchical table or hierarchical "universal combinatoric sequence structure", i.e. a singular generic (but hierarchically and combinatorially structured) protein sequence which could account for the approximately 10^7 different protein sequences in the biosphere. Such a generic sequence would presumably include all known motifs (cf. PROSITE Dictionary); a hierarchical numbering system, e.g. 1 1.1 1.1.1 2 2.1 etc. would be imposed on both motif and non-motif seqments of the sequence - in essence, this generic sequence would be one "supermotif", if you will. As an example, the following hypothetical sequence segment: 5 31 F M P F W might be hierarchically written (albeit roughly) as: 1 6 50 125 409 743 END .......... F ...... - ....... - ....... - ........ W ....... 50.1 125.1 409.1 M 125.1.1 409.1.1 125.1.2.1 409.1.2 125.2 F 125.2.1 P A very crude analogy would be the tRNA nucleotide sequence (76 - 95 nucleotides) in which each nucleotide is (absolutely) numbered 1 to 76; the inclusion of any of the remaining 19 nucleotides (depending upon the specific tRNA sequence) is numbered at a lower (hierarchical) level than the primary 76 nucleotides, i.e. in the case of the D-loop, the numbering is ...17 and/or 17A, 18, 19, 20 and/or 20A and/or 20B, 21,...etc.; in the case of the variable loop, the numbering is ...47 and/or 47A and/or...and/or 47P, 48,...etc.; as the tRNA sequence "motif" includes the allowed nucleotides for each of the 95 possible positions in addition to the hierarchical structure, the generic protein sequence "supermotif" would similarly include the allowed amino acids for each of its 1,...1.1,...1.1.2, ...2,...etc. (i.e. hierarchical) positions. NOTE: The hierarchical protein sequence structure may or may not relate to any phylogenetic hierarchies, but would essentially reflect a "generically inherent hierarchy" in the biosynthesis of proteins. Given the 10^4 - 10^5 different protein sequences currrently available in data bases, there may be sufficient data to establish the basic structure of a generic protein sequence, with new data either corroborating the generic combinatorial and hierarchical structure or necessitating revisions. I suspect that delimitation of the combinatorial and hierarchical structure of biologically viable protein sequences would provide fundamental insight into the essential nature of proteins. I would greatly appreciate hearing about any research even remotely related to this concept. Your own research "to cluster a protein sequence data base into a family of domains, taking the combinatorial nature of proteins into account" sounds interesting; I'll try to get your preprint throught Anonymous FTP. Regards, Edwin Wright 85 Spinnaker Drive, A-602 Halifax, Nova Scotia CANADA B3N 3E3 Telephone: (902) 477-5037 Email: ewright@fox.nstn.ns.ca =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Sat Jan 22 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Mr Georges L Friedli Newsgroups: bionet.molbio.proteins Subject: subscription Date: 23 Jan 1994 19:24:56 -0000 Lines: 2 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2huiu8$plo@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk Subscription for bsp1gf@surrey.ac.uk From owner-proteins@net.bio.net Sun Jan 23 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!EU.net!sun4nl!star.cs.vu.nl!balaena!mac131.bio.vu.nl!user From: vdwal@bio.vu.nl (FJ van der Wal) Subject: P.C.K.Lau address Message-ID: Followup-To: bionet.molbio.proteins Sender: news@bio.vu.nl Organization: Mol.Micro, Vrije Uni., Amsterdam, NL Date: Mon, 24 Jan 1994 12:27:46 GMT Lines: 14 Hi, I'm looking for the e-mail address of R.L.Somorjai. He's co-writer of "Distinctive properties of signal sequences from bacterial lipoproteins" (1988) in Prot.Eng 2 pp15-20. I'd like to correspond with him about some of the signal peptides compared with each other in that article, especially about the Lysis Protein Signal Peptides. Coulds somebody give me his e-mail address? -- Fimme Jan van der Wal dep. Molecular Microbiology Vrije Universiteit Amsterdam de Boelelaan 1087 1081 HV Amsterdam, NL vdwal@bio.vu.nl From owner-proteins@net.bio.net Sun Jan 23 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!cs.utexas.edu!swrinde!emory!nigel.msen.com!yale.edu!news.yale.edu!news From: CRAFT@biomed.med.yale.edu () Subject: postdoc wanted Message-ID: <1994Jan24.211300.6807@news.yale.edu> Sender: news@news.yale.edu (USENET News System) Nntp-Posting-Host: biomed.med.yale.edu Organization: Yale University Date: Mon, 24 Jan 1994 21:13:00 GMT X-News-Reader: VMS NEWS 1.20 Lines: 19 A POSTDOCTORAL FELLOW is sought to study the effects of potential anti-inflammatory dr4 tory drugs upon neutrophil signal transduction and cellular function. According to the interests of the fellow, research may later extend to other aspects of leukocyte function, particularly the study of mechanisms and regulation of inflammatory reactions. A recent Ph.D. is preferred, but the candidate must be a US citizen or permanet resident. Some familiarity with techniques of RIA, enzyme assay, microscopy, and protein purificationm, electrophoresis, and immunoblotting is desired. Position available immediately. Send curriculum vitae and 3 letters of reference to Stephen E. Malawista, M.D. Section of Rheumatology 608 LCI Yale School of Medicine 333 Cedar Street New Haven, CT 06520-8031 From owner-proteins@net.bio.net Sun Jan 23 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Shaun D. Black" Newsgroups: bionet.molbio.proteins Subject: Colorimetric assay for UDPGT needed Date: 25 Jan 1994 01:18:36 -0000 Lines: 8 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i1s1c$c12@mserv1.dl.ac.uk> X-Envelope-To: proteins@net.bio.net X-Vms-To: THENIC::IN%"proteins@net.bio.net" Original-To: proteins@net.bio.net Greetings, Does anyone know of a straightforward colorimetric assay for UDP- glucuronosyl transferase (the lumenal microsomal enzyme)? Thanks in advance, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Mon Jan 24 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!usc!howland.reston.ans.net!pipex!warwick!news.dcs.warwick.ac.uk!mrccrc!daresbury!bioftp.unibas.ch!rc1.vub.ac.be!rc4!fopperdo From: fopperdo@rc1.vub.ac.be (F.R. OPPERDOES) Newsgroups: bionet.molbio.proteins Subject: MOWSE, molec. mass search Date: 25 Jan 1994 13:00:00 GMT Organization: Brussels Free Universities (VUB/ULB), Belgium Lines: 6 Message-ID: <2i354g$3h6@rc1.vub.ac.be> NNTP-Posting-Host: rc4.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] I would like to know whether the molecular weight search peptide mass database ( MOWSE) is available or can be accessed via the internet? Fred Opperdoes ICP-TROP Brussels From owner-proteins@net.bio.net Mon Jan 24 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!pipex!uknet!daresbury!s-crim1!lhb From: lhb@s-crim1.ac.uk (L.H. Bell) Newsgroups: bionet.molbio.proteins Subject: Re: MOWSE, molec. mass search Date: 25 Jan 1994 14:47:13 GMT Organization: SEQNET Lines: 20 Sender: lhb@s-crim1 (L.H. Bell) Distribution: world Message-ID: <2i3bdh$e6k@mserv1.dl.ac.uk> References: <2i354g$3h6@rc1.vub.ac.be> NNTP-Posting-Host: s-crim1.dl.ac.uk In article <2i354g$3h6@rc1.vub.ac.be>, fopperdo@rc1.vub.ac.be (F.R. OPPERDOES) writes: |> I would like to know whether the molecular weight search peptide mass database ( |> MOWSE) is available or can be accessed via the internet? |> |> Fred Opperdoes |> ICP-TROP Brussels |> ******************************************************************** Search queries should be mailed to mowse@daresbury.ac.uk (short form mowse@dl.ac.uk). Search results will be returned directly to your e_mail address. Comments, please, to mbdpn@s-crim1.dl.ac.uk. ******************************************************************** D.J.C. Pappin, P. Hojrup and A.J. Bleasby 'Rapid Identification of Proteins by Peptide-Mass Fingerprinting'. Current Biology (1993), vol 3, 327-332. From owner-proteins@net.bio.net Mon Jan 24 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!keele!uknet!pipex!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!end.chem.indiana.edu!user From: wnowatzk@ucs.indiana.edu (Bill) Subject: PVDF direct blot/sequencing Message-ID: Followup-To: bionet.molbio.proteins Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: end.chem.indiana.edu Organization: Indiana University Date: Tue, 25 Jan 1994 19:01:27 GMT Lines: 12 I have had a bit of trouble transferring my 95 kD protein from a 10%SDS PAGE to a BioRad PVDF membrane. I am considering trying a direct blot method mentioned in the BioRad PVDF mb info booklet and further referenced to David Speicher. I am wondering if anyone has experience with this technique and what kind of success you have achieved upon sequencing? I could also use some experimental condition recommendations- should I dilute my protein (currently in a Tris buffer at about 2.4 mg/mL) into 200 µL and rotate this in a small eppendorf tube containing a small strip of PVDF overnight at 4 C? I am also curious to know if certain buffers interefere with N terminal sequencing? Thanks in advance. wnowatzk@ucs.indiana.edu From owner-proteins@net.bio.net Mon Jan 24 22:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!rc1.vub.ac.be!ub4b!EU.net!uunet!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!husc10!robison1 Newsgroups: bionet.molbio.proteins Subject: Re: Protein Sequence - Combinatoric Table Message-ID: From: robison1@husc10.harvard.edu (Keith Robison) Date: 24 Jan 94 02:21:49 GMT References: <2hsqsh$lqc@mserv1.dl.ac.uk> Distribution: bionet Organization: Harvard University, Cambridge, Massachusetts NNTP-Posting-Host: husc10.harvard.edu Lines: 19 See the work of Gonnet, Benner, and co-workers. (Do a search in SeqAnalRef or the bionet archives -- I don't have the citations handy). The data structure they create is a sort of a transform of what you describe -- a tree of all known (well, from SwissProt) protein-subsequences. That is, for any specified exact subsequence you can look up every protein with that sequence. Significant documentation for their system (Darwin) is available via E-mail &/| FTP. Again, Gonnet has posted to the bionet groups, and so the bionet archives are a good place to look for further leads. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI krobison@nucleus.harvard.edu From owner-proteins@net.bio.net Mon Jan 24 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.molbio.proteins Subject: BAC acrylamide Date: 26 Jan 1994 00:09:43 -0000 Lines: 21 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i4cc7$9nr@mserv1.dl.ac.uk> X-Vms-To: PROTEIN Original-To: proteins@net.bio.net >I am cleaving a radioactive protein of 67 kD into two large fragments. I >then separate the fragments from the parent protein by SDS-PAGE. I would like >to get an accurate count of the radioactive fragments from slices that are >excised from the gel. Is there a way to dissolve the gel and make the >counts fully available to a liquid scintillation cocktail? >Or is there some other trick that can be used to get the same result? Look into "BAC Acrylamide" (I think BioRad has it); this type of acrylamide has a disulphide bond in it and once you've cut out the band you can dissolve away the acrylamide with BME or DTT... -------------------------------------------------------------------------------- Chris Rampitsch | RAMPITSCH@BCRSSU.AGR.CA Dept. Plant Science, Univ. of BC | Phone (604) 494-7711 Vancouver, British Columbia | Fax (604) 494-0755 Canada V6T 2A2 _/\_ ---------------------------------- __\ /__ ------------------------------------ "Most people don't act stupid;... \__ __/ ..it's the real thing." A.E.Neuman ______________________________________||________________________________________ From owner-proteins@net.bio.net Mon Jan 24 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!keele!uknet!pipex!uunet!nih-csl!djpf@helix.nih.gov From: djpf@helix.nih.gov (d fitzgerald) Subject: Countng prot bands after SDS-PAGE Message-ID: <1994Jan25.212125.3206@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: nci Date: Tue, 25 Jan 1994 21:21:25 GMT Lines: 8 I am cleaving a radioactive protein of 67 kD into two large fragments. I then separate the fragments from the parent protein by SDS-PAGE. I would like to get an accurate count of the radioactive fragments from slices that are excised from the gel. Is there a way to dissolve the gel and make the counts fully available to a liquid scintillation cocktail? Or is there some other trick that can be used to get the same result? Thanks in advance for any help that is offered. From owner-proteins@net.bio.net Mon Jan 24 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Bob Lauder" Newsgroups: bionet.molbio.proteins Subject: Re: protein modification (fwd) Date: 25 Jan 1994 20:49:11 -0000 Lines: 20 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i40k7$19d@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk > > Is there any information somehere on known sequences in > > proteins suceptible to be post-translationelly modified, that would concern a Serine in the sequence KSSK. And would lead to a shift in mobility > > of several Kda. > > > What is the residue N-terminal of this? If it is Asparagine then the > Ser could be contributing to the N-linked glycosylation site. > What about O-linked glycosylation? O-linked KS would need a xxSGxx, however as you mention N-linked needs NxS/T. For a post-translational modification to add several Kda I guess glycosylation would be the only (?) answer. ============================================================================== Bob Lauder, bsa016@cent1.lancs.ac.uk Post Doctoral Research Associate, Division of Biological Sciences, VOICE - (+44) (0)524 65201 Ex 3461 Lancaster University, FAX - (+44) (0)524 843854 U.K. From owner-proteins@net.bio.net Mon Jan 24 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: MJ Duggan Newsgroups: bionet.molbio.proteins Subject: protein modification (fwd) Date: 25 Jan 1994 18:29:06 -0000 Lines: 21 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i3odi$o6f@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk (proteins news-group) > > Hello dear friends > > I try again a difficult question: > Is there any information somehere on known sequences in > proteins suceptible to be post-translationelly modified, that would concern a Serine in the sequence KSSK. And would lead to a shift in mobility > of several Kda. > > > Thanks networkers > What is the residue N-terminal of this? If it is Asparagine then the Ser could be contributing to the N-linked glycosylation site. What about O-linked glycosylation? Am I right in assuming that the post-translational modification is leading to an increase in the MW? More information would make it easier to help. Mike Duggan From owner-proteins@net.bio.net Mon Jan 24 22:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!rc1.vub.ac.be!ub4b!EU.net!Germany.EU.net!netmbx.de!zib-berlin.de!news.belwue.de!news.uni-freiburg.de!sun1.ruf.uni-freiburg.de!eschiltz From: eschiltz@sun1.ruf.uni-freiburg.de (Emile Schiltz) Newsgroups: bionet.molbio.proteins Subject: Re: Electroanalitical methods Date: 25 Jan 1994 17:32:59 GMT Organization: Rechenzentrum der Universitaet Freiburg, Germany Lines: 40 Distribution: bionet Message-ID: <2i3l4b$9gv@sun8.ruf.uni-freiburg.de> References: <2i340v$97p@mserv1.dl.ac.uk> NNTP-Posting-Host: sun1.ruf.uni-freiburg.de X-Newsreader: TIN [version 1.2 PL1] Mauricio Cesar Palmieri (mcpalmie@fox.cce.usp.br) wrote: : Dear Frriends, : I am looking for help to find some reference about pKa determination : of proteins an polypeptides by Electroanalitical methods. : Any informations will be appreciated. : Thanks in advance. : ------------------------------------------------------------------------ : Mauricio Cesar Palmieri : Mestrando em Biotecnologia : : UNIVERSIDADE DE SAO PAULO : BRAZIL : E - mail: mcpalmie@fox.cce.usp.br : Letters to: : Universidade Estadual Paulista : Depto. Bioquimica : R. Prof Francisco Degni s/n : Araraquara - SP - Brazil : CEP 14800-900 hello Mauricio, the ways one thinks of for pKa-determination for proteins are - isoelectric focussing - capillary electrophoresis - chromatofocussing hope this helps Mil -- Emile Schiltz or Institute of Organic Chemistry and Biochemistry Albertstrasse 21, D-79104 Freiburg, Germany phone: +49 761 203 6090 From owner-proteins@net.bio.net Mon Jan 24 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Mauricio Cesar Palmieri Newsgroups: bionet.molbio.proteins Subject: Electroanalitical methods Date: 25 Jan 1994 12:41:03 -0000 Lines: 22 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i340v$97p@mserv1.dl.ac.uk> Original-To: methods@net.bio.net, proteins@net.bio.net Dear Frriends, I am looking for help to find some reference about pKa determination of proteins an polypeptides by Electroanalitical methods. Any informations will be appreciated. Thanks in advance. ------------------------------------------------------------------------ Mauricio Cesar Palmieri Mestrando em Biotecnologia UNIVERSIDADE DE SAO PAULO BRAZIL E - mail: mcpalmie@fox.cce.usp.br Letters to: Universidade Estadual Paulista Depto. Bioquimica R. Prof Francisco Degni s/n Araraquara - SP - Brazil CEP 14800-900 From owner-proteins@net.bio.net Mon Jan 24 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!pipex!zaphod.crihan.fr!jussieu.fr!citi2.fr!not-for-mail From: belle@bisance.citi2.fr (belle-bisance) Newsgroups: bionet.molbio.proteins Subject: protein modification Date: 25 Jan 1994 17:47:02 +0100 Organization: CITI2 - Universite Rene Descartes, Paris Lines: 20 Message-ID: <2i3ie6$7ur@bisance.citi2.fr> NNTP-Posting-Host: bisance.citi2.fr X-Newsreader: TIN [version 1.2 PL2] Hello dear friends I try again a difficult question: Is there any information somehere on known sequences in proteins suceptible to be post-translationelly modified, that would concern a Serine in the sequence KSSK. And would lead to a shift in mobility of several Kda. Thanks networkers .   From owner-proteins@net.bio.net Tue Jan 25 22:00:00 1994 Path: biosci!daresbury!daresbury!not-for-mail From: mbrgw@s-crim1.dl.ac.uk (R.G. Walters) Newsgroups: bionet.molbio.proteins Subject: Re: Countng prot bands after SDS-PAGE Date: 26 Jan 1994 11:39:43 -0000 Organization: Daresbury Lab., Warrington, U.K. Lines: 27 Distribution: bionet Message-ID: <2i5kpvINNh0n@s-crim1.dl.ac.uk> References: <1994Jan25.212125.3206@alw.nih.gov> NNTP-Posting-Host: s-crim1.dl.ac.uk In article <1994Jan25.212125.3206@alw.nih.gov> djpf@helix.nih.gov (d fitzgerald) writes: >I am cleaving a radioactive protein of 67 kD into two large fragments. I >then separate the fragments from the parent protein by SDS-PAGE. I would like >to get an accurate count of the radioactive fragments from slices that are >excised from the gel. Is there a way to dissolve the gel and make the >counts fully available to a liquid scintillation cocktail? >Or is there some other trick that can be used to get the same result? I asked about this a couple of weeks ago (THANKS to all those that replied - I hadn't got round to reporting SUCCESS yet). Having played with it a little bit, the best method (if you don't want to spend money on special gel solubilisers) is that of Goodman (Anal. Biochem 42, 481 (1973)). It works even if you have dried the gel down onto paper! Cut the band(s) of interest out, and put them in a vial, and add approx 0.25ml (the less, the better) of a 99:1 mix of 30% H2O2:conc ammonium hydroxide (i.e. ammonia in water) and incubate at 37C overnight (don't put the lids on too tight, and watch out for nasty smelling stuff). Then add scintillant (depending on the type, you may have to add somw water first). Robin Walters. Robert Hill Institute, Sheffield UK. A fact is an opinion that everyone agrees with. From owner-proteins@net.bio.net Tue Jan 25 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!xlink.net!zib-berlin.de!news.belwue.de!news.uni-freiburg.de!sun1.ruf.uni-freiburg.de!eschiltz From: eschiltz@sun1.ruf.uni-freiburg.de (Emile Schiltz) Newsgroups: bionet.molbio.proteins Subject: Re: protein modification Date: 26 Jan 1994 08:01:35 GMT Organization: Rechenzentrum der Universitaet Freiburg, Germany Lines: 31 Message-ID: <2i580v$glk@sun8.ruf.uni-freiburg.de> References: <2i3ie6$7ur@bisance.citi2.fr> NNTP-Posting-Host: sun1.ruf.uni-freiburg.de X-Newsreader: TIN [version 1.2 PL1] belle-bisance (belle@bisance.citi2.fr) wrote: : Hello dear friends : I try again a difficult question: : Is there any information somehere on known sequences in : proteins suceptible to be post-translationelly modified, that would concern a Serine in the sequence KSSK. And would lead to a shift in mobility : of several Kda. : Thanks networkers Did you try PROSITE ? It contains also the sequences specifically modified. Regards, Mil : . :  : :  -- Emile Schiltz or Institute of Organic Chemistry and Biochemistry Albertstrasse 21, D-79104 Freiburg, Germany phone: +49 761 203 6090 From owner-proteins@net.bio.net Tue Jan 25 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!gatech!mailer.acns.fsu.edu!iris3.chem.fsu.edu!rrk From: rrk@iris3.chem.fsu.edu (Randal R. Ketchem) Newsgroups: bionet.molbio.proteins Subject: Re: anyone know if there is a insightII listserv or newsgp? Date: 26 Jan 1994 18:15:52 GMT Organization: National High Magnetic Field Laboratory Lines: 11 Message-ID: <2i6c0o$lhb@mailer.fsu.edu> References: <2i6353$q9d@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: iris3.chem.fsu.edu In article <2i6353$q9d@charm.magnus.acs.ohio-state.edu> lrellick@magnus.acs.ohio-state.edu (Lorraine M Rellick) writes: >Anyone know where I can find an insightII listserv. or newsgp? >- Lori The following is from the mail signature of the Biosym mailing list: This list is called DIBUG@COMP.BIOZ.UNIBAS.CH and covers the Discover, Insight and Biosym products User group. Mail (un)subscribe messages to DIBUG-REQUEST@COMP.BIOZ.UNIBAS.CH, other to DIBUG-ADMIN@COMP.BIOZ.UNIBAS.CH The archive is available on bioftp.unibas.ch as FTP and GOPHER service. From owner-proteins@net.bio.net Tue Jan 25 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Edwin Wright" Newsgroups: bionet.molbio.proteins Subject: Institute for Scientific Computation Date: 27 Jan 1994 00:45:39 -0000 Lines: 20 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i72rj$c4r@mserv1.dl.ac.uk> X-Nupop-Charset: English Original-To: proteins@net.bio.net Does anyone have an email address for the following person: Gaston H. Gonnet Institute for Scientific Computation Swiss Federal Institute of Technology CH-8092 Zurich Switzerland Regards, --------------------------------------------------------------------------- Edwin Wright 85 Spinnaker Drive, A-602 Halifax, Nova Scotia CANADA B3N 3E3 Telephone: (902) 477-5037 Email: ewright@fox.nstn.ns.ca =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Tue Jan 25 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!lrellick From: lrellick@magnus.acs.ohio-state.edu (Lorraine M Rellick) Newsgroups: bionet.molbio.proteins Subject: anyone know if there is a insightII listserv or newsgp? Date: 26 Jan 1994 15:44:35 GMT Organization: The Ohio State University Lines: 2 Message-ID: <2i6353$q9d@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: top.magnus.acs.ohio-state.edu Anyone know where I can find an insightII listserv. or newsgp? - Lori From owner-proteins@net.bio.net Wed Jan 26 22:00:00 1994 Path: biosci!daresbury!keele!uknet!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!koniskyj3.life.uiuc.edu!user From: paul_haney@qms1.life.uiuc.edu (paul haney) Newsgroups: bionet.molbio.proteins Subject: E-Mail Address Request Followup-To: bionet.molbio.proteins Date: Wed, 26 Jan 1994 21:51:07 -0600 Organization: UIUC Lines: 22 Message-ID: NNTP-Posting-Host: koniskyj3.life.uiuc.edu Hello. I'm trying to contact the following person by E-mail. If anyone happens to know his address, or that of someone else in the same institute, it would be greatly appreciated. He is: Jan Maarten van Dijl Department of Genetics Center of Biological Sciences NL-9571 NN Haren (Gn) The Netherlands Thank you. ----------------------------- Ed Beaty Department of Microbiology University of Illinois Ed_Beaty@qms1.life.uiuc.edu From owner-proteins@net.bio.net Wed Jan 26 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!cs.utexas.edu!uunet!mnemosyne.cs.du.edu!nyx10!pfinerty From: pfinerty@nyx10.cs.du.edu (fork) Subject: database question Message-ID: <1994Jan27.225745.12757@mnemosyne.cs.du.edu> X-Disclaimer: Nyx is a public access Unix system run by the University of Denver for the Denver community. The University has neither control over nor responsibility for the opinions of users. Sender: usenet@mnemosyne.cs.du.edu (netnews admin account) Organization: Nyx, Public Access Unix at U. of Denver Math/CS dept. Date: Thu, 27 Jan 94 22:57:45 GMT Lines: 14 hey folks, i'm looking for a protein database that could be queried using only the amino acid composition of a protein. anyone know if such a thing exists? thanks for the tips, -patrick finerty u of utah biochemistry grad student -- pjf -- biochem grad student finger me for a good time From owner-proteins@net.bio.net Wed Jan 26 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!europa.eng.gtefsd.com!darwin.sura.net!ua1ix!news From: Subject: Re: SDS determination Message-ID: <1994Jan27.141227.153165@ua1ix.ua.edu> Sender: news@ua1ix.ua.edu Nntp-Posting-Host: trouble.biology.as.ua.edu Organization: The University of Alabama X-Newsreader: WinVN version 0.80 References: <2hp73s$pp9@nnrp.ucs.ubc.ca> Date: Thu, 27 Jan 1994 14:12:27 GMT Lines: 21 In article <2hp73s$pp9@nnrp.ucs.ubc.ca>, bpgm@unixg.ubc.ca (Brent Pollock) says: > >Try: > Reynolds & Tanford (1970). Proc. Nat. Acad. Sci. U.S.A. Vol. 66, > No. 3, pp.1002-1007. >The references cited therein are: > Ray et al. (1966). Biochemistry. 5: 2606. >and Reynolds et al. (1967). Biochemistry. 6:937. > >Share & Enjoy! >Brent Pollock > >[stuff deleted] >>Hi everyone! I need to know if there are protocols or references available >>for me to determine the sodium dodecyl sulfate concentration in a solution >>containing proteins. Thank you for your help! > >Also: See Calbiochem's handbook: "A Guide to the Properties and Uses of Detergents in Biology and Biochemistry". Available free: (800) 854-3417 or call their Technical Service: (800) 628-8470 with questions. Good source. Helpful people. Excellent reference list. From owner-proteins@net.bio.net Wed Jan 26 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!xlink.net!zib-berlin.de!netmbx.de!Germany.EU.net!EU.net!uknet!pipex!sunic!news.funet.fi!news.eunet.fi!funic!convex!harper From: harper@convex.csc.FI (Rob Harper) Subject: Re: Institute for Scientific Computation Message-ID: <1994Jan27.111536.20483@nic.funet.fi> Sender: usenet@nic.funet.fi Nntp-Posting-Host: convex.csc.fi Organization: Finnish Academic and Research Network Project - FUNET References: <2i72rj$c4r@mserv1.dl.ac.uk> Distribution: bionet Date: Thu, 27 Jan 94 11:15:36 GMT Lines: 22 In <2i72rj$c4r@mserv1.dl.ac.uk> "Edwin Wright" writes: >Does anyone have an email address for the following person: > Gaston H. Gonnet > Institute for Scientific Computation > Swiss Federal Institute of Technology > CH-8092 Zurich > Switzerland Try the following address. gonnet@inf.ethz.ch (Gaston Gonnet) RGDS -=ROB=- -- R. Andrew Harper E-mail: harper@convex.csc.fi Center for Scientific Computing Molbio/software: harper@nic.funet.fi Tietotie 6, P.O. Box 405 Telephone: +358 0 457 2076 SF-02101 Espoo Finland Fax: +358 0 457 2302 From owner-proteins@net.bio.net Wed Jan 26 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!paladin.american.edu!darwin.sura.net!news.gdb.org!dev.gdb.org!danj From: danj@dev.gdb.org (Dan Jacobson) Subject: Re: MOWSE, molec. mass search Message-ID: <1994Jan25.191852.6785@news.gdb.org> Sender: news@news.gdb.org Nntp-Posting-Host: dev.gdb.org Organization: The Johns Hopkins University - Genome Data Base (GDB) References: <2i354g$3h6@rc1.vub.ac.be> Date: Tue, 25 Jan 1994 19:18:52 GMT Lines: 23 In article <2i354g$3h6@rc1.vub.ac.be> fopperdo@rc1.vub.ac.be (F.R. OPPERDOES) writes: >I would like to know whether the molecular weight search peptide mass database ( >MOWSE) is available or can be accessed via the internet? > Yes - there's an e-mail server. To get instructions on how to use it send a message with the word - Help in the body of the message to mowse@dl.ac.uk Best of luck, Dan Jacobson danj@gdb.org Johns Hopkins University From owner-proteins@net.bio.net Wed Jan 26 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!usenet.ins.cwru.edu!lerc.nasa.gov!magnus.acs.ohio-state.edu!mwadhwa From: mwadhwa@magnus.acs.ohio-state.edu (Manpreet S Wadhwa) Newsgroups: bionet.molbio.proteins Subject: sensitive assay for amines Date: 28 Jan 1994 07:19:19 GMT Organization: The Ohio State University Lines: 32 Message-ID: <2iae9n$5jo@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: bottom.magnus.acs.ohio-state.edu Hello netters, lately i've been working with polylysine of different chain lengths. i need to start using a sensitive assay for routine and reliable quantitation of amines (polylysine) in my samples. the assay needs to be very sensitive in order to quantitate sub-nanomole levels of amines. a preliminary literature search and a look at pierce catalog revealed many potential methods: ninhydrin method coomasie dye method o-pthalaldehyde method trinitrobenzene sulfonic acid method dansyl chloride method both a spectrophotometer and a fluorimeter are available to me so i can use any of these methods. which assay would you recommend for a)reliability b)sensitivity c)robustness with different sample conditions d)convenience and rapidity maybe this is faq. if so, please direct me to an archive. please post your responses to this group or email me direct at wadhwa@ohstphrm.bitnet . If there is sufficient interest in this topic i will post a summary. thanks, manpreet s. wadhwa grad student division of pharmaceutics ohio state university From owner-proteins@net.bio.net Wed Jan 26 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!news.byu.edu!news.kei.com!sol.ctr.columbia.edu!howland.reston.ans.net!agate!library.ucla.edu!news.ucdavis.edu!hamlet.ucdavis.edu!szsclark From: szsclark@hamlet.ucdavis.edu (Sonya Clark) Subject: Recycling Cyanogen bromide activated sepharose affinity columns? Message-ID: Sender: usenet@ucdavis.edu (News Guru) Organization: University of California, Davis X-Newsreader: TIN [version 1.2 PL2] Date: Fri, 28 Jan 1994 02:22:43 GMT Lines: 14 Dear Netters - I am purifying antibodies from a polyclonal prep by running them over a CNBr-activated Sepharose affinity column of my antigen. As CNBr-activated Sepharose is expensive &/or horrible to make, I'd like to strip the column of the antigen currently bound, and re-use the sepharose to make another affinity column. Does anyone have a protocol to do this? Would eluting the column with harsh eluents (eg. Guanidine/urea/SDS) work? and would I then be able to re-use the sepharose to couple another antigen? Any advice appreciated. Cheers. Sonya Clark. Botany Dept., UCDavis szsclark@ucd.edu From owner-proteins@net.bio.net Wed Jan 26 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!keele!uknet!pipex!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!cs.umd.edu!lhc!NewsWatcher!user From: baxevani@ncbi.nlm.nih.gov (Andy Baxevanis) Subject: Re: MOWSE, molec. mass search Message-ID: Followup-To: bionet.molbio.proteins Sender: news@nlm.nih.gov Organization: NIH References: <2i354g$3h6@rc1.vub.ac.be> Date: Wed, 26 Jan 94 18:13:52 GMT Lines: 18 In article <2i354g$3h6@rc1.vub.ac.be>, fopperdo@rc1.vub.ac.be (F.R. OPPERDOES) wrote: > > I would like to know whether the molecular weight search peptide mass database ( > MOWSE) is available or can be accessed via the internet? > > Fred Opperdoes > ICP-TROP Brussels The MOWSE server address is mowse@dl.ac.uk. To obtain the help documentation, send a message to mbdpn@s-crim1.dk.ac.uk; in the body of the message, type only the word HELP. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Andy Baxevanis National Center for Biotechnology Information National Institutes of Health baxevani@ncbi.nlm.nih.gov From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!s-crim1!lhb From: lhb@s-crim1.ac.uk (L.H. Bell) Newsgroups: bionet.molbio.proteins Subject: Re: MOWSE, molec. mass search Date: 25 Jan 1994 14:47:13 GMT Organization: SEQNET Lines: 20 Sender: lhb@s-crim1 (L.H. Bell) Distribution: world Message-ID: <2i3bdh$e6k@mserv1.dl.ac.uk> References: <2i354g$3h6@rc1.vub.ac.be> NNTP-Posting-Host: s-crim1.dl.ac.uk In article <2i354g$3h6@rc1.vub.ac.be>, fopperdo@rc1.vub.ac.be (F.R. OPPERDOES) writes: |> I would like to know whether the molecular weight search peptide mass database ( |> MOWSE) is available or can be accessed via the internet? |> |> Fred Opperdoes |> ICP-TROP Brussels |> ******************************************************************** Search queries should be mailed to mowse@daresbury.ac.uk (short form mowse@dl.ac.uk). Search results will be returned directly to your e_mail address. Comments, please, to mbdpn@s-crim1.dl.ac.uk. ******************************************************************** D.J.C. Pappin, P. Hojrup and A.J. Bleasby 'Rapid Identification of Proteins by Peptide-Mass Fingerprinting'. Current Biology (1993), vol 3, 327-332. From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: Mauricio Cesar Palmieri Newsgroups: bionet.molbio.proteins Subject: Electroanalitical methods Date: 25 Jan 1994 12:41:03 -0000 Lines: 22 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i340v$97p@mserv1.dl.ac.uk> Original-To: methods@net.bio.net, proteins@net.bio.net Dear Frriends, I am looking for help to find some reference about pKa determination of proteins an polypeptides by Electroanalitical methods. Any informations will be appreciated. Thanks in advance. ------------------------------------------------------------------------ Mauricio Cesar Palmieri Mestrando em Biotecnologia UNIVERSIDADE DE SAO PAULO BRAZIL E - mail: mcpalmie@fox.cce.usp.br Letters to: Universidade Estadual Paulista Depto. Bioquimica R. Prof Francisco Degni s/n Araraquara - SP - Brazil CEP 14800-900 From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!lhc!biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!darwin.sura.net!fconvx.ncifcrf.gov!mack From: mack@ncifcrf.gov (Joe Mack) Subject: Re: Recycling Cyanogen bromide activated sepharose affinity columns? Message-ID: Organization: Frederick Cancer Research and Development Center References: Date: Fri, 28 Jan 1994 18:20:36 GMT Lines: 31 In article szsclark@hamlet.ucdavis.edu (Sonya Clark) writes: >Dear Netters - I am purifying antibodies from a polyclonal prep by >running them over a CNBr-activated Sepharose affinity column of my >antigen. As CNBr-activated Sepharose is expensive &/or horrible to make, Well it isn't that expensive compared to the time saved by buying it (unless you're a graduate student whose time isn't valued much) and it isn't all that bad to make (N-methyl-pyrrolidone/Na2CO3 method ) if you have a fume hood but anyhow >I'd like to strip the column of the antigen currently bound, and re-use >the sepharose to make another affinity column. the real point is that the activated bond from the CNBr is used up by the coupling procedure. Even if you could get the protein off, you're back to unactivated sepharose. Joe Mack mack@ncifcrf.gov Does anyone have a protocol >to do this? Would eluting the column with harsh eluents (eg. >Guanidine/urea/SDS) work? and would I then be able to re-use the sepharose >to couple another antigen? Any advice appreciated. Cheers. > >Sonya Clark. >Botany Dept., >UCDavis >szsclark@ucd.edu > From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!warwick!news.dcs.warwick.ac.uk!mrccrc!daresbury!bioftp.unibas.ch!rc1.vub.ac.be!rc4!fopperdo From: fopperdo@rc1.vub.ac.be (F.R. OPPERDOES) Newsgroups: bionet.molbio.proteins Subject: MOWSE, molec. mass search Date: 25 Jan 1994 13:00:00 GMT Organization: Brussels Free Universities (VUB/ULB), Belgium Lines: 6 Message-ID: <2i354g$3h6@rc1.vub.ac.be> NNTP-Posting-Host: rc4.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] I would like to know whether the molecular weight search peptide mass database ( MOWSE) is available or can be accessed via the internet? Fred Opperdoes ICP-TROP Brussels From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!husc10!robison1 Newsgroups: bionet.molbio.proteins Subject: Re: Protein Sequence - Combinatoric Table Message-ID: From: robison1@husc10.harvard.edu (Keith Robison) Date: 24 Jan 94 02:21:49 GMT References: <2hsqsh$lqc@mserv1.dl.ac.uk> Distribution: bionet Organization: Harvard University, Cambridge, Massachusetts NNTP-Posting-Host: husc10.harvard.edu Lines: 19 See the work of Gonnet, Benner, and co-workers. (Do a search in SeqAnalRef or the bionet archives -- I don't have the citations handy). The data structure they create is a sort of a transform of what you describe -- a tree of all known (well, from SwissProt) protein-subsequences. That is, for any specified exact subsequence you can look up every protein with that sequence. Significant documentation for their system (Darwin) is available via E-mail &/| FTP. Again, Gonnet has posted to the bionet groups, and so the bionet archives are a good place to look for further leads. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI krobison@nucleus.harvard.edu From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!darwin.sura.net!fconvx.ncifcrf.gov!mack From: mack@ncifcrf.gov (Joe Mack) Subject: Re: Recycling Cyanogen bromide activated sepharose affinity columns? Message-ID: Organization: Frederick Cancer Research and Development Center References: Date: Fri, 28 Jan 1994 18:20:36 GMT Lines: 31 In article szsclark@hamlet.ucdavis.edu (Sonya Clark) writes: >Dear Netters - I am purifying antibodies from a polyclonal prep by >running them over a CNBr-activated Sepharose affinity column of my >antigen. As CNBr-activated Sepharose is expensive &/or horrible to make, Well it isn't that expensive compared to the time saved by buying it (unless you're a graduate student whose time isn't valued much) and it isn't all that bad to make (N-methyl-pyrrolidone/Na2CO3 method ) if you have a fume hood but anyhow >I'd like to strip the column of the antigen currently bound, and re-use >the sepharose to make another affinity column. the real point is that the activated bond from the CNBr is used up by the coupling procedure. Even if you could get the protein off, you're back to unactivated sepharose. Joe Mack mack@ncifcrf.gov Does anyone have a protocol >to do this? Would eluting the column with harsh eluents (eg. >Guanidine/urea/SDS) work? and would I then be able to re-use the sepharose >to couple another antigen? Any advice appreciated. Cheers. > >Sonya Clark. >Botany Dept., >UCDavis >szsclark@ucd.edu > From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!europa.eng.gtefsd.com!news.ans.net!malgudi.oar.net!news.ysu.edu!psuvm!pxh Organization: Penn State University Date: Fri, 28 Jan 1994 12:32:29 EST From: Deepti Pradhan Message-ID: <94028.123229PXH@psuvm.psu.edu> Newsgroups: bionet.molbio.proteins Subject: BSA and liposomes Lines: 10 Hi netters/nettors! Does anyone know if the great scavenger BSA binds liposomes? I know it binds lipids, but what if they are presented in the form of a liposome? Please post here or e-mail me directly. Thanks, Deepti Deepti Pradhan PXH@PSUVM.PSU.EDU (814)863-1767 (Work) Dept. of Biochemistry and Molecular Biology Penn State University University Park, PA-16802 From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!europa.eng.gtefsd.com!fs7.ece.cmu.edu!cantaloupe.srv.cs.cmu.edu!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!husc10!robison1 Newsgroups: bionet.molbio.proteins Subject: Re: Amino acid composition searching (Was: database question) Message-ID: From: robison1@husc10.harvard.edu (Keith Robison) Date: 28 Jan 94 14:06:24 GMT References: <1994Jan27.225745.12757@mnemosyne.cs.du.edu> Organization: Harvard University, Cambridge, Massachusetts NNTP-Posting-Host: husc10.harvard.edu Lines: 28 See: Analytical Biochemistry 198, 330-333 Biochem Soc Trans 6:787 Biotechniques 12:886 The Sibbald et al program from the Anal.Bioch. ref is available by FTP, but I forget both the address & the name of the program. There was also a PNAS paper in the last year or so, I think by Shaw. I can't find the reference right now. Good places to look for this sort of query is Amos Bairoch's SeqAnalRef and Sarah Barron's GenTools Bibliography, both available from the GDB gopher (gopher.gdb.org). I found the three refs above with NetEntrez. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI krobison@nucleus.harvard.edu From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!newsserver.jvnc.net!jvnc.net!Tigger!kodak From: kodak@tigger.jvnc.net (Joe Kaufman) Subject: Re: database question Message-ID: Sender: news@tigger.jvnc.net (Zee News Genie) Nntp-Posting-Host: kodak.jvnc.net Organization: Scientific Imaging Systems, Eastman Kodak Co. X-Newsreader: VersaTerm Link v1.1.1 References: <1994Jan27.225745.12757@mnemosyne.cs.du.edu> Date: Fri, 28 Jan 1994 08:55:16 GMT Lines: 34 In Article <1994Jan27.225745.12757@mnemosyne.cs.du.edu>, pfinerty@nyx10.cs.du.edu (fork) wrote: > >hey folks, i'm looking for a protein database that could be queried using >only the amino acid composition of a protein. anyone know if such a thing >exists? > > >thanks for the tips, > >-patrick finerty > >u of utah biochemistry grad student >-- >pjf -- biochem grad student >finger me for a good time MacVector, a comprehensive sequence analysis package for the Macintosh, can use the IUPAC protein alpha-bet to search NCBI's Entrez:Sequences database. This database contains entries from 9 different sources including SWISS-PROT and PIR. If you are interested, you can obtain a copy of the demo version by calling our technical service group (800) 243-2555. They can answer additional questions you may have. ----------------------------- Joe Kaufman Voice (800) 243-2555 x5618 Software Development Eastman Kodak Company Scientific Imaging Systems 25 Science Park New Haven, CT. 06511 kodak@tigger.jvnc.net From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!newsserver.jvnc.net!jvnc.net!Tigger!kodak From: kodak@tigger.jvnc.net (Joe Kaufman) Subject: Re: database question Message-ID: Sender: news@tigger.jvnc.net (Zee News Genie) Nntp-Posting-Host: kodak.jvnc.net Organization: Scientific Imaging Systems, Eastman Kodak Co. X-Newsreader: VersaTerm Link v1.1.1 References: <1994Jan27.225745.12757@mnemosyne.cs.du.edu> Date: Fri, 28 Jan 1994 08:52:40 GMT Lines: 34 In Article <1994Jan27.225745.12757@mnemosyne.cs.du.edu>, pfinerty@nyx10.cs.du.edu (fork) wrote: > >hey folks, i'm looking for a protein database that could be queried using >only the amino acid composition of a protein. anyone know if such a thing >exists? > > >thanks for the tips, > >-patrick finerty > >u of utah biochemistry grad student >-- >pjf -- biochem grad student >finger me for a good time MacVector, a comprehensive sequence analysis package for the Macintosh, can use the IUPAC protein alpha-bet to search NCBI's Entrez:Sequences database. This database contains entries from 9 different sources including SWISS-PROT and PIR. If you are interested, you can obtain a copy of the demo version by calling our technical service group (800) 243-2555. They can answer additional questions you may have. ----------------------------- Joe Kaufman Voice (800) 243-2555 x5618 Software Development Eastman Kodak Company Scientific Imaging Systems 25 Science Park New Haven, CT. 06511 kodak@tigger.jvnc.net From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!lhc!biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!europa.eng.gtefsd.com!news.ans.net!malgudi.oar.net!news.ysu.edu!psuvm!pxh Organization: Penn State University Date: Fri, 28 Jan 1994 12:32:29 EST From: Deepti Pradhan Message-ID: <94028.123229PXH@psuvm.psu.edu> Newsgroups: bionet.molbio.proteins Subject: BSA and liposomes Lines: 10 Hi netters/nettors! Does anyone know if the great scavenger BSA binds liposomes? I know it binds lipids, but what if they are presented in the form of a liposome? Please post here or e-mail me directly. Thanks, Deepti Deepti Pradhan PXH@PSUVM.PSU.EDU (814)863-1767 (Work) Dept. of Biochemistry and Molecular Biology Penn State University University Park, PA-16802 From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!daresbury!keele!uknet!pipex!howland.reston.ans.net!sol.ctr.columbia.edu!news.columbia.edu!bonjour.cc.columbia.edu!ps44 From: ps44@bonjour.cc.columbia.edu (Pavel Sova) Newsgroups: bionet.molbio.proteins Subject: Re: database question Date: 29 Jan 1994 04:32:21 GMT Organization: Columbia University Lines: 29 Message-ID: <2icosl$j1f@apakabar.cc.columbia.edu> References: <1994Jan27.225745.12757@mnemosyne.cs.du.edu> NNTP-Posting-Host: bonjour.cc.columbia.edu In article , Joe Kaufman wrote: >In Article <1994Jan27.225745.12757@mnemosyne.cs.du.edu>, >pfinerty@nyx10.cs.du.edu (fork) wrote: >> >>hey folks, i'm looking for a protein database that could be queried using >>only the amino acid composition of a protein. anyone know if such a thing >>exists? >> >> >>thanks for the tips, >> >>-patrick finerty ...stuff deleted... Patrick, you can search by e-mail all possible databases available through ncbi server by program called blast. Blast searches nucleotide or protein sequence databases according to program called (blastn or blastp) in your e-mail message. I don't have address of server at home (where I am now), but send me an e-mail and I will reply with more information. Pavel Sova Mol.Virol.Laboratory Columbia University New York ps44@columbia.edu From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: "Shaun D. Black" Newsgroups: bionet.molbio.proteins Subject: Colorimetric assay for UDPGT needed Date: 25 Jan 1994 01:18:36 -0000 Lines: 8 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i1s1c$c12@mserv1.dl.ac.uk> X-Envelope-To: proteins@net.bio.net X-Vms-To: THENIC::IN%"proteins@net.bio.net" Original-To: proteins@net.bio.net Greetings, Does anyone know of a straightforward colorimetric assay for UDP- glucuronosyl transferase (the lumenal microsomal enzyme)? Thanks in advance, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!news.columbia.edu!bonjour.cc.columbia.edu!ps44 From: ps44@bonjour.cc.columbia.edu (Pavel Sova) Newsgroups: bionet.molbio.proteins Subject: Re: database question Date: 29 Jan 1994 04:32:21 GMT Organization: Columbia University Lines: 29 Message-ID: <2icosl$j1f@apakabar.cc.columbia.edu> References: <1994Jan27.225745.12757@mnemosyne.cs.du.edu> NNTP-Posting-Host: bonjour.cc.columbia.edu In article , Joe Kaufman wrote: >In Article <1994Jan27.225745.12757@mnemosyne.cs.du.edu>, >pfinerty@nyx10.cs.du.edu (fork) wrote: >> >>hey folks, i'm looking for a protein database that could be queried using >>only the amino acid composition of a protein. anyone know if such a thing >>exists? >> >> >>thanks for the tips, >> >>-patrick finerty ...stuff deleted... Patrick, you can search by e-mail all possible databases available through ncbi server by program called blast. Blast searches nucleotide or protein sequence databases according to program called (blastn or blastp) in your e-mail message. I don't have address of server at home (where I am now), but send me an e-mail and I will reply with more information. Pavel Sova Mol.Virol.Laboratory Columbia University New York ps44@columbia.edu From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!swrinde!emory!nigel.msen.com!yale.edu!news.yale.edu!news From: CRAFT@biomed.med.yale.edu () Subject: postdoc wanted Message-ID: <1994Jan24.211300.6807@news.yale.edu> Sender: news@news.yale.edu (USENET News System) Nntp-Posting-Host: biomed.med.yale.edu Organization: Yale University Date: Mon, 24 Jan 1994 21:13:00 GMT X-News-Reader: VMS NEWS 1.20 Lines: 19 A POSTDOCTORAL FELLOW is sought to study the effects of potential anti-inflammatory dr4 tory drugs upon neutrophil signal transduction and cellular function. According to the interests of the fellow, research may later extend to other aspects of leukocyte function, particularly the study of mechanisms and regulation of inflammatory reactions. A recent Ph.D. is preferred, but the candidate must be a US citizen or permanet resident. Some familiarity with techniques of RIA, enzyme assay, microscopy, and protein purificationm, electrophoresis, and immunoblotting is desired. Position available immediately. Send curriculum vitae and 3 letters of reference to Stephen E. Malawista, M.D. Section of Rheumatology 608 LCI Yale School of Medicine 333 Cedar Street New Haven, CT 06520-8031 From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!news.unomaha.edu!crcnis1.unl.edu!unlinfo.unl.edu!markwell From: markwell@unlinfo.unl.edu (john markwell) Newsgroups: bionet.molbio.proteins Subject: Re: Recycling Cyanogen bromide activated sepharose affinity columns? Date: 28 Jan 1994 13:26:33 GMT Organization: University of Nebraska--Lincoln Lines: 31 Distribution: world Message-ID: <2ib3q9$ceu@crcnis1.unl.edu> References: NNTP-Posting-Host: unlinfo.unl.edu szsclark@hamlet.ucdavis.edu (Sonya Clark) writes: >Dear Netters - I am purifying antibodies from a polyclonal prep by >running them over a CNBr-activated Sepharose affinity column of my >antigen. As CNBr-activated Sepharose is expensive &/or horrible to make, >I'd like to strip the column of the antigen currently bound, and re-use >the sepharose to make another affinity column. Does anyone have a protocol >to do this? Would eluting the column with harsh eluents (eg. >Guanidine/urea/SDS) work? and would I then be able to re-use the sepharose >to couple another antigen? Any advice appreciated. Cheers. >Sonya Clark. >Botany Dept., >UCDavis >szsclark@ucd.edu I don't think that CNBr-Sepharose can be reactivated. As I recall, the coupling of proteins and other molecules is by forming a covalent bond, usually to primary amines (e.g. Lys epsilon-amino). After the antigen, protein, molecule, etc. is coupled, the matrix is treated with an excess of amino groups to block the remaining active groups. Thus use of CNBr-Sephadex is a one-shot process. The commercially available product is expensive, but it is relatively easy to manufacture in the lab. I hope this helps. John -- John Markwell Phone: 402-472-2924 Dept. Biochemistry FAX: 402-472-7842 University of Nebraska Internet: markwell@unl.edu Lincoln, NE 68583-0718 From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!daresbury!keele!uknet!pipex!howland.reston.ans.net!sol.ctr.columbia.edu!news.unomaha.edu!crcnis1.unl.edu!unlinfo.unl.edu!markwell From: markwell@unlinfo.unl.edu (john markwell) Newsgroups: bionet.molbio.proteins Subject: Re: Recycling Cyanogen bromide activated sepharose affinity columns? Date: 28 Jan 1994 13:26:33 GMT Organization: University of Nebraska--Lincoln Lines: 31 Distribution: world Message-ID: <2ib3q9$ceu@crcnis1.unl.edu> References: NNTP-Posting-Host: unlinfo.unl.edu szsclark@hamlet.ucdavis.edu (Sonya Clark) writes: >Dear Netters - I am purifying antibodies from a polyclonal prep by >running them over a CNBr-activated Sepharose affinity column of my >antigen. As CNBr-activated Sepharose is expensive &/or horrible to make, >I'd like to strip the column of the antigen currently bound, and re-use >the sepharose to make another affinity column. Does anyone have a protocol >to do this? Would eluting the column with harsh eluents (eg. >Guanidine/urea/SDS) work? and would I then be able to re-use the sepharose >to couple another antigen? Any advice appreciated. Cheers. >Sonya Clark. >Botany Dept., >UCDavis >szsclark@ucd.edu I don't think that CNBr-Sepharose can be reactivated. As I recall, the coupling of proteins and other molecules is by forming a covalent bond, usually to primary amines (e.g. Lys epsilon-amino). After the antigen, protein, molecule, etc. is coupled, the matrix is treated with an excess of amino groups to block the remaining active groups. Thus use of CNBr-Sephadex is a one-shot process. The commercially available product is expensive, but it is relatively easy to manufacture in the lab. I hope this helps. John -- John Markwell Phone: 402-472-2924 Dept. Biochemistry FAX: 402-472-7842 University of Nebraska Internet: markwell@unl.edu Lincoln, NE 68583-0718 From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.molbio.proteins Subject: Re: Amino acid composition searching (Was: database question) Date: 28 Jan 1994 21:01:05 -0000 Lines: 17 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2ibueh$p62@mserv1.dl.ac.uk> X-Vms-To: IN%"proteins@net.bio.net" X-Vms-Cc: IN%"pfinerty@nyx10.cs.du.edu" Original-To: proteins@net.bio.net Patrick Finerty (pfinerty@nyx10.cs.du.edu) asks > hey folks, i'm looking for a protein database that could be queried using > only the amino acid composition of a protein. anyone know if such a thing > exists? The PSQ program, provided with the tape distribution of the PIR-International Protein Sequence databases has that capability. Unfortunately, the PSQ program is not provided with the CD-ROM distribution, and that capability is not yet provided in the ATLAS program that does come with the CD-ROM. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!Germany.EU.net!netmbx.de!zib-berlin.de!news.belwue.de!news.uni-freiburg.de!sun1.ruf.uni-freiburg.de!eschiltz From: eschiltz@sun1.ruf.uni-freiburg.de (Emile Schiltz) Newsgroups: bionet.molbio.proteins Subject: Re: Electroanalitical methods Date: 25 Jan 1994 17:32:59 GMT Organization: Rechenzentrum der Universitaet Freiburg, Germany Lines: 40 Distribution: bionet Message-ID: <2i3l4b$9gv@sun8.ruf.uni-freiburg.de> References: <2i340v$97p@mserv1.dl.ac.uk> NNTP-Posting-Host: sun1.ruf.uni-freiburg.de X-Newsreader: TIN [version 1.2 PL1] Mauricio Cesar Palmieri (mcpalmie@fox.cce.usp.br) wrote: : Dear Frriends, : I am looking for help to find some reference about pKa determination : of proteins an polypeptides by Electroanalitical methods. : Any informations will be appreciated. : Thanks in advance. : ------------------------------------------------------------------------ : Mauricio Cesar Palmieri : Mestrando em Biotecnologia : : UNIVERSIDADE DE SAO PAULO : BRAZIL : E - mail: mcpalmie@fox.cce.usp.br : Letters to: : Universidade Estadual Paulista : Depto. Bioquimica : R. Prof Francisco Degni s/n : Araraquara - SP - Brazil : CEP 14800-900 hello Mauricio, the ways one thinks of for pKa-determination for proteins are - isoelectric focussing - capillary electrophoresis - chromatofocussing hope this helps Mil -- Emile Schiltz or Institute of Organic Chemistry and Biochemistry Albertstrasse 21, D-79104 Freiburg, Germany phone: +49 761 203 6090 From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!parc!barrnet.net!sgiblab!sgigate.sgi.com!olivea!charnel!psgrain!library.ucla.edu!europa.eng.gtefsd.com!emory!nigel.msen.com!yale.edu!news.yale.edu!news From: CRAFT@biomed.med.yale.edu () Subject: postdoc wanted Message-ID: <1994Jan24.211300.6807@news.yale.edu> Sender: news@news.yale.edu (USENET News System) Nntp-Posting-Host: biomed.med.yale.edu Organization: Yale University Date: Mon, 24 Jan 1994 21:13:00 GMT X-News-Reader: VMS NEWS 1.20 Lines: 19 A POSTDOCTORAL FELLOW is sought to study the effects of potential anti-inflammatory dr4 tory drugs upon neutrophil signal transduction and cellular function. According to the interests of the fellow, research may later extend to other aspects of leukocyte function, particularly the study of mechanisms and regulation of inflammatory reactions. A recent Ph.D. is preferred, but the candidate must be a US citizen or permanet resident. Some familiarity with techniques of RIA, enzyme assay, microscopy, and protein purificationm, electrophoresis, and immunoblotting is desired. Position available immediately. Send curriculum vitae and 3 letters of reference to Stephen E. Malawista, M.D. Section of Rheumatology 608 LCI Yale School of Medicine 333 Cedar Street New Haven, CT 06520-8031 From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!zaphod.crihan.fr!jussieu.fr!citi2.fr!not-for-mail From: belle@bisance.citi2.fr (belle-bisance) Newsgroups: bionet.molbio.proteins Subject: protein modification Date: 25 Jan 1994 17:47:02 +0100 Organization: CITI2 - Universite Rene Descartes, Paris Lines: 20 Message-ID: <2i3ie6$7ur@bisance.citi2.fr> NNTP-Posting-Host: bisance.citi2.fr X-Newsreader: TIN [version 1.2 PL2] Hello dear friends I try again a difficult question: Is there any information somehere on known sequences in proteins suceptible to be post-translationelly modified, that would concern a Serine in the sequence KSSK. And would lead to a shift in mobility of several Kda. Thanks networkers .   From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: "Bob Lauder" Newsgroups: bionet.molbio.proteins Subject: Re: protein modification (fwd) Date: 25 Jan 1994 20:49:11 -0000 Lines: 20 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i40k7$19d@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk > > Is there any information somehere on known sequences in > > proteins suceptible to be post-translationelly modified, that would concern a Serine in the sequence KSSK. And would lead to a shift in mobility > > of several Kda. > > > What is the residue N-terminal of this? If it is Asparagine then the > Ser could be contributing to the N-linked glycosylation site. > What about O-linked glycosylation? O-linked KS would need a xxSGxx, however as you mention N-linked needs NxS/T. For a post-translational modification to add several Kda I guess glycosylation would be the only (?) answer. ============================================================================== Bob Lauder, bsa016@cent1.lancs.ac.uk Post Doctoral Research Associate, Division of Biological Sciences, VOICE - (+44) (0)524 65201 Ex 3461 Lancaster University, FAX - (+44) (0)524 843854 U.K. From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!end.chem.indiana.edu!user From: wnowatzk@ucs.indiana.edu (Bill) Subject: PVDF direct blot/sequencing Message-ID: Followup-To: bionet.molbio.proteins Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: end.chem.indiana.edu Organization: Indiana University Date: Tue, 25 Jan 1994 19:01:27 GMT Lines: 12 I have had a bit of trouble transferring my 95 kD protein from a 10%SDS PAGE to a BioRad PVDF membrane. I am considering trying a direct blot method mentioned in the BioRad PVDF mb info booklet and further referenced to David Speicher. I am wondering if anyone has experience with this technique and what kind of success you have achieved upon sequencing? I could also use some experimental condition recommendations- should I dilute my protein (currently in a Tris buffer at about 2.4 mg/mL) into 200 µL and rotate this in a small eppendorf tube containing a small strip of PVDF overnight at 4 C? I am also curious to know if certain buffers interefere with N terminal sequencing? Thanks in advance. wnowatzk@ucs.indiana.edu From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: MJ Duggan Newsgroups: bionet.molbio.proteins Subject: protein modification (fwd) Date: 25 Jan 1994 18:29:06 -0000 Lines: 21 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2i3odi$o6f@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk (proteins news-group) > > Hello dear friends > > I try again a difficult question: > Is there any information somehere on known sequences in > proteins suceptible to be post-translationelly modified, that would concern a Serine in the sequence KSSK. And would lead to a shift in mobility > of several Kda. > > > Thanks networkers > What is the residue N-terminal of this? If it is Asparagine then the Ser could be contributing to the N-linked glycosylation site. What about O-linked glycosylation? Am I right in assuming that the post-translational modification is leading to an increase in the MW? More information would make it easier to help. Mike Duggan From owner-proteins@net.bio.net Thu Jan 27 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!nih-csl!djpf@helix.nih.gov From: djpf@helix.nih.gov (d fitzgerald) Subject: Countng prot bands after SDS-PAGE Message-ID: <1994Jan25.212125.3206@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: nci Date: Tue, 25 Jan 1994 21:21:25 GMT Lines: 8 I am cleaving a radioactive protein of 67 kD into two large fragments. I then separate the fragments from the parent protein by SDS-PAGE. I would like to get an accurate count of the radioactive fragments from slices that are excised from the gel. Is there a way to dissolve the gel and make the counts fully available to a liquid scintillation cocktail? Or is there some other trick that can be used to get the same result? Thanks in advance for any help that is offered. From owner-proteins@net.bio.net Fri Jan 28 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!newsserver.jvnc.net!jvnc.net!Tigger!kodak From: kodak@tigger.jvnc.net (Joe Kaufman) Subject: Re: database question Message-ID: Sender: news@tigger.jvnc.net (Zee News Genie) Nntp-Posting-Host: kodak.jvnc.net Organization: Scientific Imaging Systems, Eastman Kodak Co. X-Newsreader: VersaTerm Link v1.1.1 References: <1994Jan27.225745.12757@mnemosyne.cs.du.edu> Date: Fri, 28 Jan 1994 08:52:40 GMT Lines: 34 In Article <1994Jan27.225745.12757@mnemosyne.cs.du.edu>, pfinerty@nyx10.cs.du.edu (fork) wrote: > >hey folks, i'm looking for a protein database that could be queried using >only the amino acid composition of a protein. anyone know if such a thing >exists? > > >thanks for the tips, > >-patrick finerty > >u of utah biochemistry grad student >-- >pjf -- biochem grad student >finger me for a good time MacVector, a comprehensive sequence analysis package for the Macintosh, can use the IUPAC protein alpha-bet to search NCBI's Entrez:Sequences database. This database contains entries from 9 different sources including SWISS-PROT and PIR. If you are interested, you can obtain a copy of the demo version by calling our technical service group (800) 243-2555. They can answer additional questions you may have. ----------------------------- Joe Kaufman Voice (800) 243-2555 x5618 Software Development Eastman Kodak Company Scientific Imaging Systems 25 Science Park New Haven, CT. 06511 kodak@tigger.jvnc.net From owner-proteins@net.bio.net Fri Jan 28 22:00:00 1994 Path: biosci!rutgers!ukma!gatech!mailer.acns.fsu.edu!iris3.chem.fsu.edu!rrk From: rrk@iris3.chem.fsu.edu (Randal R. Ketchem) Newsgroups: bionet.molbio.proteins Subject: Re: anyone know if there is a insightII listserv or newsgp? Message-ID: <2i6c0o$lhb@mailer.fsu.edu> Date: 26 Jan 94 18:15:52 GMT References: <2i6353$q9d@charm.magnus.acs.ohio-state.edu> Organization: National High Magnetic Field Laboratory Lines: 10 NNTP-Posting-Host: iris3.chem.fsu.edu In article <2i6353$q9d@charm.magnus.acs.ohio-state.edu> lrellick@magnus.acs.ohio-state.edu (Lorraine M Rellick) writes: >Anyone know where I can find an insightII listserv. or newsgp? >- Lori The following is from the mail signature of the Biosym mailing list: This list is called DIBUG@COMP.BIOZ.UNIBAS.CH and covers the Discover, Insight and Biosym products User group. Mail (un)subscribe messages to DIBUG-REQUEST@COMP.BIOZ.UNIBAS.CH, other to DIBUG-ADMIN@COMP.BIOZ.UNIBAS.CH The archive is available on bioftp.unibas.ch as FTP and GOPHER service. From owner-proteins@net.bio.net Fri Jan 28 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!library.ucla.edu!news.ucdavis.edu!hamlet.ucdavis.edu!szsclark From: szsclark@hamlet.ucdavis.edu (Sonya Clark) Subject: Recycling Cyanogen bromide activated sepharose affinity columns? Message-ID: Sender: usenet@ucdavis.edu (News Guru) Organization: University of California, Davis X-Newsreader: TIN [version 1.2 PL2] Date: Fri, 28 Jan 1994 02:22:43 GMT Lines: 14 Dear Netters - I am purifying antibodies from a polyclonal prep by running them over a CNBr-activated Sepharose affinity column of my antigen. As CNBr-activated Sepharose is expensive &/or horrible to make, I'd like to strip the column of the antigen currently bound, and re-use the sepharose to make another affinity column. Does anyone have a protocol to do this? Would eluting the column with harsh eluents (eg. Guanidine/urea/SDS) work? and would I then be able to re-use the sepharose to couple another antigen? Any advice appreciated. Cheers. Sonya Clark. Botany Dept., UCDavis szsclark@ucd.edu From owner-proteins@net.bio.net Fri Jan 28 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!uunet!mnemosyne.cs.du.edu!nyx10!pfinerty From: pfinerty@nyx10.cs.du.edu (fork) Subject: database question Message-ID: <1994Jan27.225745.12757@mnemosyne.cs.du.edu> X-Disclaimer: Nyx is a public access Unix system run by the University of Denver for the Denver community. The University has neither control over nor responsibility for the opinions of users. Sender: usenet@mnemosyne.cs.du.edu (netnews admin account) Organization: Nyx, Public Access Unix at U. of Denver Math/CS dept. Date: Thu, 27 Jan 94 22:57:45 GMT Lines: 14 hey folks, i'm looking for a protein database that could be queried using only the amino acid composition of a protein. anyone know if such a thing exists? thanks for the tips, -patrick finerty u of utah biochemistry grad student -- pjf -- biochem grad student finger me for a good time From owner-proteins@net.bio.net Fri Jan 28 22:00:00 1994 Path: biosci!rutgers!princeton!att-in!fnnews.fnal.gov!overload.lbl.gov!agate!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!lrellick From: lrellick@magnus.acs.ohio-state.edu (Lorraine M Rellick) Newsgroups: bionet.molbio.proteins Subject: anyone know if