From owner-proteins@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!usenet From: Robert Russell Newsgroups: bionet.molbio.proteins,bionet.software,bionet.structural-nmr,bionet.xtallography Subject: ANNOUNCE- *** PROTEIN 3D STRUCTURE ALIGNMENT SOFTWARE - STAMP v4.0 *** Date: 2 Nov 1995 18:18:48 GMT Organization: Imperial Cancer Research Fund Lines: 41 Message-ID: <47b228$b0d@charlie.lif.icnet.uk> NNTP-Posting-Host: bonsai.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.2 IP22) To: gjb@bioch.ox.ac.uk X-URL: news:bionet.molbio.proteins Xref: biosci bionet.molbio.proteins:6167 bionet.software:13809 bionet.structural-nmr:868 bionet.xtallography:2137 NEW RELEASE OF STAMP (Structural Alignment of Multiple Proteins) Version 4.0 STAMP is a package comprising 15 programs for alignment and analysis of protein three-dimensional structures. The major features are: 1) Fast alignment and superimposition of two or more protein structures 2) Generation and display superimposed protein 3D structures and sequence alignments 3) Comparison of a protein 3D structure to a database of other 3D structures 4) Direct interface to MOLSCRIPT and ALSCRIPT drawing programs 5) A clear method for assigning which regions within a family of proteins are structurally equivalent, without the need for graphical intervention. STAMP is available free of charge to non-profit organisations, and to others for a fee. A license must be completed by all prospective users. Users of previous versions of STAMP can obtain the new version with the same license. The new version (4.0) has corrected several bugs, ontains a much improved manual and includes several new programs, including those for the generation of MOLSCRIPT input, and for the generation of averaged structures. For further details as to the program and licenses, see: WWW http://geoff.biop.ox.ac.uk/ FTP ftp://geoff.biop.ox.ac.uk/README ftp://geoff.biop.ox.ac.uk/STAMP.LIC or contact Geoff Barton via mailto:gjb@bioch.ox.ac.uk Robert B. Russell Biomolecular Modelling, Imperial Cancer Research Fund 44 Lincoln's Inn Fields, P.O. Box 123, London, WC2A 3PX, U.K. Tel: 44 171 269 3583 FAX: 44 171 269 3479 mailto:russell@icrf.icnet.uk WWW http://bonsai.lif.icnet.uk/people/rob/rob.html From owner-proteins@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!hodes.com!netcomsv!uu4news.netcom.com!netcomsv!uu3news.netcom.com!ix.netcom.com!netnews From: mbmorton@ix.netcom.com (michelle morton ) Newsgroups: bionet.biophysics,bionet.cellbiol,bionet.general,bionet.microbiology,bionet.molbio.proteins Subject: biophysics vs. biochem speculatin'.... Date: 2 Nov 1995 11:00:40 GMT Organization: Netcom Lines: 26 Message-ID: <47a8co$3s5@ixnews2.ix.netcom.com> NNTP-Posting-Host: ix-lb5-12.ix.netcom.com X-NETCOM-Date: Thu Nov 02 3:00:40 AM PST 1995 Xref: biosci bionet.biophysics:1379 bionet.cellbiol:3318 bionet.general:18250 bionet.microbiology:3810 bionet.molbio.proteins:6165 Got a question that's been puzzling me. My cat's fur is so soft that petting him is like touching a cashmere or angora sweater. My question is this - is *softness* due to: a) the **physical** arrangement of the peptide bonds - do the bonds and the amino acids they're attached to form a smooth, rather than jagged or discrete, surface? b) the tertiary or quarternary folding of the protein(s) in his fur - ie, are the proteins physically arranged in some special way so that they are experienced by us as being *soft*? c) the sequencing of the amino acids themselves, or d) some other phenomenom that I haven't thought of and probably can't even imagine right now? Obviously, as a student I have wwwaaaaaayyyy too much time on my time on my hands :>!!! This is one of several "philosophy" of chemistry questions I have that keep me from ever getting around to figuring out how to solve world hunger or bring about total global peace on earth and other really important stuff like that! Soooooooo, if you can help me out, I'd really appreciate it. Thanx in advance for your info. michelle (my mind's awanderin', awanderin', just awanderin' away) m From owner-proteins@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!in2p3.fr!univ-lyon1.fr!jussieu.fr!centre.univ-orleans.fr!univ-tours.fr!MOREAUT From: moreaut@univ-tours.fr Newsgroups: bionet.molbio.proteins Subject: extinction coef of lysozyme?? Date: 2 Nov 1995 16:46:55 GMT Organization: Universite de TOURS - France Lines: 23 Message-ID: <47aslv$fom@centre.univ-orleans.fr> Reply-To: moreaut@univ-tours.fr NNTP-Posting-Host: balzac.univ-tours.fr Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit dear netters, I am looking for the molar extinction coefficient value of chicken lysozyme at 280nm, pH7.0? Does anybody know this value? Thanks in advance. Best regards. *------------------------------------------------------------------* | Dr. Thierry MOREAU | | | | Laboratoire d'Enzymologie et Chimie des Proteines | | | | URA CNRS 1334 Phone: (33) 47 36 62 06 | | 2bis, Bd Tonnelle Fax: (33) 47 36 60 46 | | 37032 TOURS cedex Email: moreaut@univ-tours.fr | | FRANCE | | | *------------------------------------------------------------------* From owner-proteins@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!news00.sunet.se!sunic!news99.sunet.se!columba.udac.uu.se!mun5.mun.uu.se!user From: stefanba@bio.embnet.se (Stefan Bäckström) Newsgroups: bionet.molbio.proteins Subject: Detection of protein in acrylamide Date: Thu, 02 Nov 1995 18:14:51 +0100 Organization: Department of Developmental Neuroscience Lines: 7 Message-ID: NNTP-Posting-Host: mun5.mun.uu.se Is it possible (somehow) to detect a specific protein with ab in an acrylamide gel without having to blot it to a membrane first ? Maby by drying the gel, making it porous or something (I don't know, that's why I'm asking..) Stefan From owner-proteins@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-stuttgart.de!uni-regensburg.de!lrz-muenchen.de!news From: Wolfgang Schechinger Newsgroups: bionet.molbio.proteins Subject: Re: MWG-BIOTECH FAX NO/E-MAIL Date: 2 Nov 1995 14:35:07 GMT Organization: Institute for Diabetes Research Lines: 25 Distribution: world Message-ID: <47akur$cat@sparcserver.lrz-muenchen.de> References: <477m17$r1@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: u7k0201.ppp.lrz-muenchen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) To: pdezoysa@hgmp.mrc.ac.uk Phone: +49 8092 8289-0 Fax -21084 email: oligo@mwgdna.com The numbers are from their'r catalogue on my bench. Have a nice day! PS: No affiliation with MWG. -- +++++++++++++++++++++++++++++++++++++++++++ Wolfgang Schechinger Institute for Diabetes Reserch Koelner Platz 1 80804 Munich Germany Phone +49 (89) 30 79 31 24 Fax +49 (89) 30 81 733 email u7k0201@sunmail.lrz-muenchen.de (Standard disclaimer applies) +++++++++++++++++++++++++++++++++++++++++++ From owner-proteins@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!newsgate.watson.ibm.com!swiss.ans.net!kelso.pprd.abbott.com!usenet From: Seth Crosby Newsgroups: bionet.molbio.proteins Subject: stripping Westerns Date: 2 Nov 1995 22:41:07 GMT Organization: Abbott Laboratories Lines: 6 Message-ID: <47bhe3$3vs@kelso.pprd.abbott.com> NNTP-Posting-Host: crosby.pprd.abbott.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.molbio.proteins Is there a protocol for stripping antibodies off Western blots (nitrocellulose)? Couldn't find any in the Antibody Bible. Seth Crosby Abbott Labs From owner-proteins@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!zombie.ncsc.mil!cs.umd.edu!haven.umd.edu!purdue!mozo.cc.purdue.edu!bac2.addl.purdue.edu!user From: akin@sage.cc.purdue.edu (Aydemir Akin) Newsgroups: bionet.molbio.proteins Subject: Re: Protease consensus sites, reference? Date: Thu, 02 Nov 1995 19:29:58 +0800 Organization: School of Veterinary Medicine, Purdue University Lines: 26 Message-ID: References: NNTP-Posting-Host: bac2.addl.purdue.edu In article , pawlowski@bms.com (John Pawlowski) wrote: > Hi, > Can anyone point me to a comprehensive reference (print or electronic) > which lists consensus sequences recognized by various proteases? Thanks > much in advance. > > -- > John Pawlowski > Bristol-Myers Squibb > pawlowski@bms.com Have you tried PROSITE and BLOCKS databases (ftp:ncbi.nlm.nih.gov @/respository). Ithink they have data files with the information you are looking for. Good luck, -- Aydemir Akin, D.V.M. 1175 Animal Disease Diagnostic Lab Purdue University West Lafayette, IN 47907-1175 akin@sage.cc.purdue.edu From owner-proteins@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!utcsri!utnut!torn!ccshst05.cs.uoguelph.ca!ccshst01.cs.uoguelph.ca!vmulpuri From: vmulpuri@uoguelph.ca (Venkateswara rao Mulpuri) Newsgroups: bionet.molbio.proteins Subject: proteins Date: 2 Nov 1995 20:27:40 GMT Organization: University of Guelph Lines: 11 Message-ID: <47b9js$lid@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: ccshst01.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] Hi : Can any one inform us about the NAD kinase. We are interested to know the amino acid sequence of NAD kinase in order to synthesize nucleotide probes for our future studies. Your assistance shall be highly appreciated. Thanx Mulpuri V. Rao From owner-proteins@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!dundee.ac.uk!mal.bioch.dundee.ac.uk!user From: mfwhite@bad.dundee.ac.uk (Malcolm White) Newsgroups: bionet.molbio.proteins Subject: Continuous elution preparative electrophoresis Date: 2 Nov 1995 17:35:54 GMT Organization: University of Dundee Lines: 10 Message-ID: NNTP-Posting-Host: mal.bioch.dundee.ac.uk X-Newsreader: Yet Another NewsWatcher 2.0b30 Just wondering if anyone out there has tried out the Biorad Prep Cell or Mini Prep Cell for protein purification. I am thinking about buying the mini prep cell for use as a purification step, and I would be interested in any comments, tips or reccomendations about this technique. Thanks, Malcolm From owner-proteins@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!news.math.psu.edu!psuvax1!news.eecs.nwu.edu!newsfeed.acns.nwu.edu!news.acns.nwu.edu!lucky139.acns.nwu.edu!user From: george-munson@nwu.edu (George Munson) Newsgroups: bionet.biophysics,bionet.cellbiol,bionet.general,bionet.microbiology,bionet.molbio.proteins Subject: Re: biophysics vs. biochem speculatin'.... Date: Thu, 02 Nov 1995 21:30:34 -0600 Organization: Northwestern University Lines: 29 Message-ID: References: <47a8co$3s5@ixnews2.ix.netcom.com> NNTP-Posting-Host: lucky139.acns.nwu.edu Xref: biosci bionet.biophysics:1380 bionet.cellbiol:3323 bionet.general:18254 bionet.microbiology:3820 bionet.molbio.proteins:6173 > Got a question that's been puzzling me. My cat's fur is so soft that > petting him is like touching a cashmere or angora sweater. My question > is this - is *softness* due to: > > a) the **physical** arrangement of the peptide bonds - do the bonds and > the amino acids they're attached to form a smooth, rather than jagged > or discrete, surface? > > b) the tertiary or quarternary folding of the protein(s) in his fur - > ie, are the proteins physically arranged in some special way so that > they are experienced by us as being *soft*? > > c) the sequencing of the amino acids themselves, or > > d) some other phenomenom that I haven't thought of and probably can't > even imagine right now? Hmm. Okay this is my best guess and I chose "b." I doubt tactile perception is sensitive enough to distinguish peptide bonds or aa sequence per se. What you perceive is the much larger scale of the hair which is of course ultimately a result of c, a, and b. My guess is softness is related to rigidity or the lack thereof. Rigidity of the overall hair would likely arise from intermolecular disulfide cross linkages which would be tertiary/quartenary in nature. -- George Munson BMBCB, Northwestern University Evanston, IL USA george-munson@nwu.edu From owner-proteins@net.bio.net Wed Nov 01 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!utcsri!utnut!torn!ccshst05.cs.uoguelph.ca!ccshst01.cs.uoguelph.ca!vmulpuri From: vmulpuri@uoguelph.ca (Venkateswara rao Mulpuri) Newsgroups: bionet.molbio.proteins Subject: Re: PAGE: Run times and voltages Date: 2 Nov 1995 20:36:42 GMT Organization: University of Guelph Lines: 22 Message-ID: <47ba4q$lid@ccshst05.cs.uoguelph.ca> References: <1995Oct31.025700.29994@marlin.jcu.edu.au> NNTP-Posting-Host: ccshst01.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] Nick Moody (nicholas.moody@jcu.edu.au) wrote: : It is standard practise in our Department to run SDS-PAGE gels at 200V : until the dye front reaches the end of the gel (usually 45 miuntes). In : other papers I have read they use lower voltages for longer times (eg 40V : for 3 to 4 hours). Can anyone tell me if there are any advantages in : using lower voltages and longer times. I use 10% discontinuous SDS=PAGE : gels and need to silver stain them. : Thanks : -- : Nicholas Moody : Department of Biomedical and Tropical Veterinary Sciences : James Cook University : Townsville, Qld., 4811 : Australia : Tel: +61 077 814 631 : Fax: +61 077 796 371 From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!noc.near.net!das-news2.harvard.edu!fas-news.harvard.edu!fas.harvard.edu!berriz From: Zorro Newsgroups: bionet.biophysics,bionet.molbio.proteins Subject: HELP: simple graphics/animation job Date: 3 Nov 1995 13:40:45 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 22 Message-ID: <47d64t$8q2@decaxp.harvard.edu> Reply-To: berriz@husc.harvard.edu NNTP-Posting-Host: fas.harvard.edu Keywords: animation engines, players(?) X-Newsreader: NN version 6.5.0 #3 (NOV) Originator: berriz@fas.harvard.edu Xref: biosci bionet.biophysics:1387 bionet.molbio.proteins:6180 Hello. I'm a researcher in molecular dynamics (and all but illiterate when it comes to computer graphics). I do computer simulations of biopolymer dynamics on an IBM RISC System 6000 machine running AIX. It would be to me very useful to crudely visualize these simulations. I can easily produce tons of "frames" consisting of the 3D coordinates of each monomer of the simulated polymer chain, as the simulation unfolds. (Of course, from these coordinates, a crude picture of the chain can be obtained by "connecting the dots" with line segments.) What I need is a program that will sequentially display a time-series of such frames. I'm hoping to find freely available source code to do this. I would greatly appreciate information on FTP sites and WWW pages where I may be able to find such tools. Thank you. Z. From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Cormac Shaw Newsgroups: bionet.molbio.proteins Subject: Re: Continuous elution preparative electrophoresis Date: 3 Nov 1995 14:26:09 -0000 Organization: University College Dublin Lines: 28 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <47d8q1$6sm@mserv1.dl.ac.uk> X-mailer: Pegasus Mail/Windows (v1.11a) Original-To: proteins@dl.ac.uk On 2 Nov 1995 mfwhite@bad.dundee.ac.uk (Malcolm White) wrote: > Just wondering if anyone out there has tried out the Biorad Prep Cell or > Mini Prep Cell for protein purification. > I am thinking about buying the mini prep cell for use as a purification > step, and I would be interested in any comments, tips or reccomendations > about this technique. Dear Malcolm, The Microbial enzyme research group in this dept. recently acquired a Biorad Prep Cell and it has been found to be useful especially in purifying and seperating isoenzymes. Be warned though that the simple step protocols which initally came with the apperatus were concentrated heavily on SDS treated protiens whereas we needed to work on native gels. The method for working out the correct concentration of gel to use also relies on you being readily able to visualise the enzyme/protein on the test gels - not so easy in our case since they hadn't been purified yet (chiken and egg situation). However, maybe the proteins of yuor interest can be stained and identified more easily. So while it took a little more trial and error than Biorad would lead you to believe the system did deliver results that could not easily be attained otherwise. Hope this helps. ________________________________________________________ Cormac Shaw, BSc. / cshaw@ollamh.ucd.ie / Dept. of Industrial Microbiology, University College, Dublin 4, Ireland. From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!sdd.hp.com!col.hp.com!news.cis.okstate.edu!usenet From: Ron Tate Newsgroups: bionet.molbio.proteins Subject: Re: Help with in situ Enzymatic Digestion for Protein Sequencing Date: 2 Nov 1995 22:01:56 GMT Organization: Dept. of Biochemistry and Molecular Bio. Oklahoma State University Lines: 31 Message-ID: <47bf4k$l3c@news.cis.okstate.edu> References: <478jd1$7fa@vixen.cso.uiuc.edu> NNTP-Posting-Host: btl5.biochem.okstate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:478jd1$7fa@vixen.cso.uiuc.edu "X. Ni" wrote: >Hi, > >I am working on a protein purification. Right now, the final protein >I got is that there are three bands on the SDS-PAGE, one major band and >two minor bands. I pretty sure, if not absolutely, the major band is the >protein I want. I sent the sample to a protein sequencing facility, and >they run the sample on the SDS-PAGE first. Then they transfer the >proteins to a membrane. Then they cut the major band to do the >sequencing. Unfortunately, I was told the N-terminus was blocked. Because >the major band is really difficult to separated from on of the minor >band, neither by size, charge nor hydrophobicity. I want to use in situ >enzymatic digestion on the membrane. Does anyone know how to do it in >detail ( I knew someone did it before)? Or any sequcencing facility can >do it for me in the United States, especially, in the midwest area of the >U.S.? Any suggestions or comments are welcome. > >Thank you very much. > My first concern would be rather the N-terminal blockage you are seeing is an artifact caused by the SDS-PAGE. Since this was perfor= med by the sequencing facility staff they may have taken precautions (i.e. polymerize gel overnight and then prerun and run with Na-= thioglycolate in the run buffer) to prevent this but I would find out. If in fact those kind of precautions were taken and your prot= ein is blocked then you might want to check out a book called- "A Practical Guide to Protein and Peptide Purification for Microsequencing" published by Academic Press Inc.- It has protocols for cleavage and internal sequencing. Also, we have a sequencing facility in our Core Facility here at Oklahoma State University. If you would like to talk to the man in = charge send e-mail to Dr. Steve White at swhite@bmb-fs1.biochem.okstate.edu Happy Hunting From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!newsfeed.ACO.net!sbg.ac.at!news From: Thomas HEISTRACHER Newsgroups: bionet.molec-model,bionet.molbio.proteins,bionet.xtallography,bionet.structural-nmr,bionet.biophysics,sci.chem,sci.comp-aided Subject: Re: Internet Drug Design Course Date: 3 Nov 1995 09:42:45 GMT Organization: uni.sbg Lines: 30 Message-ID: <47co6l$dt3@dwst13.edvz.sbg.ac.at> References: <47241o$1r3@holly.sandwich.pfizer.com> NNTP-Posting-Host: dbio26.bio.sbg.ac.at Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 32bit) To: hartla@edvz.sbg.ac.at Xref: biosci bionet.molec-model:650 bionet.molbio.proteins:6177 bionet.xtallography:2138 bionet.structural-nmr:874 bionet.biophysics:1384 sci.chem:42399 sci.comp-aided:929 jpo@siris7 (John Overington) wrote: > We (Peter Murray-Rust of Glaxo Wellcome, and John Overington of Pfizer) >would like to announce an initiative in industrial training for medicinal >chemists interested in applying protein structure-based drug design (SBDD) >techniques as part of their jobs. Additionally, skills in effectively using >the internet as a scientific resource will also be developed. The course will >use self-paced, internet-based training, coupled to close contact with >course 'tutors', working in the pharmaceutical industry. > > We are currently looking for further partners to offer financial support, >and course material. Partners need to have a presence in the UK to qualify for >potential funding under a Technology Foresight grant; although the basic >course material will be generally accessible over the internet to the wider >community. > > Further details, and a draft prospectus can be found at >http://www.cryst.bbk.ac.uk/SBDD/course.html > > If you have any further questions, we would be pleased to answer them. > > John Overington jpo@guitar.rockefeller.edu > Peter Murray-Rust ubcg09q@cryst.bbk.ac.uk > >-- >Dr. John Overington email: overingtonj@pfizer.com >Pfizer Central Research phone: +44-(0)1304-618467 >Sandwich, Kent, CT13 9NJ fax: +44-(0)1304-618422 >United Kingdom cc-mail: overington_j@sandwich.pfizer.com From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!newsjunkie.ans.net!inet.d48.lilly.com!40!sk Newsgroups: bionet.molbio.proteins Subject: Re: S. japonicum GST Antibody/serum Message-ID: From: sk@lilly.com (Stuart Kuhstoss) Date: Fri, 3 Nov 95 20:03:30 GMT References: <477mkg$r1@mercury.hgmp.mrc.ac.uk> Distribution: world Organization: Lilly Research Laboratories Nntp-Posting-Host: sak.d50.lilly.com X-Newsreader: VersaTerm Link v1.1 Lines: 18 In Article <477mkg$r1@mercury.hgmp.mrc.ac.uk>, pdezoysa@hgmp.mrc.ac.uk (Dr. P.A. de Zoysa) wrote: >I would like to obtain some S. japonicum GST antibody/serum for detecting some fusion proteins that I am planning on making. I know that Pharmacia already sell this as a part of a kit (most of which is of no use to me). So if anybody out there has spare antibody I would greatly appreciate some. Alternatively if anyone of you netters knows of a commercial outlet that sells the antibody separately please let me know. > >Thanks, > >Priyal de Zoysa. Santa Cruz Biotech sells anti GST antibodies. We've been using them on and off for some time, and they seem fine. Stu Kuhstoss From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!news.mid.net!news.ksu.ksu.edu!news.cis.okstate.edu!usenet From: Ron Tate Newsgroups: bionet.molbio.proteins Subject: Re: Gel Isolation for Bioactivity? Date: 3 Nov 1995 17:05:15 GMT Organization: Dept. of Biochemistry and Mol. Bio., Okla. St. U. Lines: 32 Message-ID: <47di4b$add@news.cis.okstate.edu> References: NNTP-Posting-Host: btl1.biochem.okstate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:m9h-0111951458330001@med048050.medicine.nwu.edu m9h@nwu.edu (Mustafo Hrundi Jr. III) wrote: >I would appreciate any protocols for cutting out a protein band from a >12%, 1.5 mm polyacrylamide gel in order to elute the protein and test it >for bioactivity. > >Any information will be appreciated > >Thanks > >-- >Mustafo the Man >"the solitude of the ocean is compromised by the waves wave" Hello, I have done something similar to what you're asking about, 12% 1.5mm PAGE. I Loaded multiple lanes side by side with sample and one lane with MW markers. After the run I pulled one of the glass plates off a= nd cut the gel parallel with the lanes so I had one piece of gel with the MW stds. lane and a sample lane and another piece with the= rest of the sample lanes. Then leaving both pieces laying together I sliced the piece with samples into 2-3mm slices perpendicular = to the lanes being sure to nick the slice locations in the gel piece that had the one sample and the MW markers. I then stained the = piece with sample and MW markers and took the slices chopped them into smaller pieces and put them into microfuge tubes with enough = buffer to cover them and then used a microfuge pestle to grind them up, set them on ice over night and then put them into the microf= uge to pellet the slurry and poured off the super. The super is then ready to assay. Another technique that I haven't tried yet but seems good, is to use Amicons Micropure apparatus. They now have what they call a ge= l nebulizer. As I understand it you put your gel piece and buffer into this nebulizer put it into the micropure device and spin it.= The gel is forced through a small pore to make a slurry then the super is driven through a filter and into a Microcon concentrator= So you're suppossed to get extraction, filtration and concentration of your protein all in one step. I think it was designed for= DNA and agarose gels so I'm not sure how well it will work with 12% PAG. Happy Hunting Ron Tate OSU BMB From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!news-server.ncren.net!news.duke.edu!usenet From: "Dr. David Rosen" Newsgroups: bionet.biophysics,bionet.cellbiol,bionet.general,bionet.microbiology,bionet.molbio.proteins Subject: Re: biophysics vs. biochem speculatin'.... Date: 3 Nov 1995 14:47:01 GMT Organization: Duke University, Durham, NC, USA Lines: 11 Message-ID: <47da15$2is@news.duke.edu> References: <47a8co$3s5@ixnews2.ix.netcom.com> <47cjfq$t3q@vixen.cso.uiuc.edu> NNTP-Posting-Host: inxs.chem.duke.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 4.1.2 sun4c) X-URL: news:47cjfq$t3q@vixen.cso.uiuc.edu Xref: biosci bionet.biophysics:1391 bionet.cellbiol:3334 bionet.general:18269 bionet.microbiology:3835 bionet.molbio.proteins:6187 I think the "moisture" that keeps hair "soft and manageable" is a lipid (oil) rather than water. Lanolin is one oil that keeps hair slippery. I think the physical structure of the hair may explain other things in the "feel" of the fur. Thick hair strands feel different from fine fur strands. Incidently, I don't think anyone should apologize for asking questions like this. Questions asked for "idle" curiousity end up being more important than "relevant" questions. Basic research is in the long run more useful than applied research. I suggest that our student NOT take any answers for granted, make a project out of testing some hypothesis, and perhaps make a bundle off of Lady Clairol. From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Germany.EU.net!news.dfn.de!news.belwue.de!News.Uni-Marburg.DE!news.th-darmstadt.de!faui0n.informatik.uni-erlangen.de!uni-erlangen.de!lrz-muenchen.de!news From: diabetes@lrz.uni-muenchen.de (Wolfgang Schechinger) Newsgroups: bionet.molbio.proteins Subject: Re: Detection of protein in acrylamide Date: Fri, 03 Nov 1995 11:27:26 GMT Organization: Institute for Diabetes Research Lines: 32 Distribution: world Message-ID: <47cqvi$rrr@sparcserver.lrz-muenchen.de> References: NNTP-Posting-Host: u7k0201.ppp.lrz-muenchen.de X-Newsreader: Forte Free Agent 1.0.82 stefanba@bio.embnet.se (Stefan Bäckström) wrote: >Is it possible (somehow) to detect a specific protein with ab in an >acrylamide gel without having to blot it to a membrane first ? >Maby by drying the gel, making it porous or something (I don't know, >that's why I'm asking..) >Stefan Hi Stefan! If you mark your protein before electrophoresis with a radiactive label (e.g. photoaffinity or hot NTP + periodate-oxidation + cyanoborohydride reduction (for NTP binding proteis) - there are a couple of references in Methods in Enzymology 182 or so) you could visualize your protein with an X-ray film or fluorescence. Hav a nice day! Wolfgang +++++++++++++++++++++++++++++++++++++++++++ Wolfgang Schechinger Institute for Diabetes Reserch Koelner Platz 1 80804 Munich Germany Phone +49 (89) 30 79 31 24 Fax +49 (89) 30 81 733 email u7k0201@sunmail.lrz-muenchen.de (Standard disclaimer applies) +++++++++++++++++++++++++++++++++++++++++++ From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!news From: pdezoysa@hgmp.mrc.ac.uk (Dr. P.A. de Zoysa) Newsgroups: bionet.molbio.proteins Subject: +ve Control For Glycosylation/Processing Date: 3 Nov 1995 11:01:51 GMT Organization: UK HGMP Resource Centre Lines: 19 Distribution: world Message-ID: <47csqv$o9p@mercury.hgmp.mrc.ac.uk> Reply-To: pdezoysa@hgmp.mrc.ac.uk NNTP-Posting-Host: iron.hgmp.mrc.ac.uk Hi Netters, My Ph.D student would like to obtain a eukaryotic reporter gene (e.g. S. cerevisiae alpha-factor) cloned into a T3/T7 vector which can be used to monitor glycosylation/processing by canine microsomal membranes during transcription/translation in a coupled system. If anyone out there can help Lara would be very grateful. Thanks, Priyal de Zoysa. -------------------------------------------------------------------------------------- Dr. Priyal A. de Zoysa E-MAIL: pdz@rfhsm.ac.uk Academic Dept. of Medicine, Tel: +44-171-794-0500x5059 10th Floor, RFHSM, Pond St., Fax: +44-171-794-3472 Hampstead, London, UK, NW3 2PF. -------------------------------------------------------------------------------------- From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!CBDCOM.APGEA.ARMY.MIL!anstroup From: anstroup@CBDCOM.APGEA.ARMY.MIL ("CPT Adam N. Stroup") Newsgroups: bionet.molbio.proteins Subject: Di- & Tripeptides, X-Pro/X-X-Pro Date: 3 Nov 1995 08:34:36 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511031127.aa03940@cbda8.cbdcom.apgea.army.mil> NNTP-Posting-Host: net.bio.net Greetings all, I'm characterizing an X-Pro dipeptidase and would like to try different substrates--anyone willing to part with X-Pro di- or X-X-Pro tripeptides? Protecting groups OK too! Thanks Ad anstroup@cbda.apgea.army.mil From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!hodes.com!netcomsv!uu4news.netcom.com!netcomsv!uu3news.netcom.com!ix.netcom.com!netcom.com!tday.slip.netcom.com!user From: tday@netcom.com (Tony Day) Subject: Help with Hill Equn. needed Message-ID: Sender: netnews@mork.netcom.com Nntp-Posting-Host: tday.slip.netcom.com Organization: NETCOM On-line Communication Services (408 261-4700 guest) Date: Fri, 3 Nov 1995 03:37:42 GMT Lines: 17 We have a protein which is destabilised by a small molecule. The effect saturates at low mM concentrations. The argument in the lab is whether it is non-specific or specific. I measured a series of inactivation rates at different inactivator concentrations. The data were fitted to a non-linear form of the Hill Eqn.. This gave a good fit with a Hill coefficient of 1.02. at a Kd of ~.8mM. Also the residuals looked random. However, I am a novice at using the Hill Equn. My question is as follows: Is there any other reasonable interpretation of the good fit and Hill coefficient of 1, than a specific single binding site (or identical sites)? In particular, could it plausibly be non-specific binding? Many thanks in advance. Tony Day From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!news.math.psu.edu!psuvax1!news.eecs.nwu.edu!newsfeed.acns.nwu.edu!movietone.ils.nwu.edu!news.ecn.bgu.edu!vixen.cso.uiuc.edu!newsrelay.iastate.edu!hobbes.physics.uiowa.edu!news.uiowa.edu!red.weeg.uiowa.edu!cgreiner From: "C. Greiner" Newsgroups: bionet.biophysics,bionet.cellbiol,bionet.general,bionet.microbiology,bionet.molbio.proteins Subject: Re: biophysics vs. biochem speculatin'.... Date: Fri, 3 Nov 1995 01:39:37 -0600 Organization: University of Iowa, Iowa City, IA, USA Lines: 36 Distribution: world Message-ID: References: <47a8co$3s5@ixnews2.ix.netcom.com> NNTP-Posting-Host: red.weeg.uiowa.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: cgreiner@red.weeg.uiowa.edu In-Reply-To: Xref: biosci bionet.biophysics:1383 bionet.cellbiol:3328 bionet.general:18260 bionet.microbiology:3826 bionet.molbio.proteins:6176 On Thu, 2 Nov 1995, George Munson wrote: > > a) the **physical** arrangement of the peptide bonds - do the bonds and > > the amino acids they're attached to form a smooth, rather than jagged > > or discrete, surface? > > > > b) the tertiary or quarternary folding of the protein(s) in his fur - > > ie, are the proteins physically arranged in some special way so that > > they are experienced by us as being *soft*? > > > > c) the sequencing of the amino acids themselves, or > > > > d) some other phenomenom that I haven't thought of and probably can't > > even imagine right now? > > Hmm. Okay this is my best guess and I chose "b." I doubt tactile > perception is sensitive enough to distinguish peptide bonds or aa sequence > per se. What you perceive is the much larger scale of the hair which is > of course ultimately a result of c, a, and b. My guess is softness is > related to rigidity or the lack thereof. Rigidity of the overall hair > would likely arise from intermolecular disulfide cross linkages which > would be tertiary/quartenary in nature. > -- > George Munson > BMBCB, Northwestern University > Evanston, IL USA > george-munson@nwu.edu > Although I agree (mostly) with George I wonder if the answer is not "d" with the "softness" relating to the degree of secretion of oils onto the hair rather than the actual molecular structure of the hair itself. Thus the reason high price furs are often from water associated mammals (oil serves as a water barrier) e.g. beaver, mink, fur seal, otter, etc... From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!news1.digital.com!decwrl!lll-winken.llnl.gov!uwm.edu!vixen.cso.uiuc.edu!ux4.cso.uiuc.edu!f-omana From: f-omana@ux4.cso.uiuc.edu (Francis Oliver Omana) Newsgroups: bionet.biophysics,bionet.cellbiol,bionet.general,bionet.microbiology,bionet.molbio.proteins Subject: Re: biophysics vs. biochem speculatin'.... Date: 3 Nov 1995 08:22:18 GMT Organization: University of Illinois at Urbana Lines: 64 Message-ID: <47cjfq$t3q@vixen.cso.uiuc.edu> References: <47a8co$3s5@ixnews2.ix.netcom.com> NNTP-Posting-Host: ux4.cso.uiuc.edu Xref: biosci bionet.biophysics:1382 bionet.cellbiol:3327 bionet.general:18258 bionet.microbiology:3825 bionet.molbio.proteins:6175 mbmorton@ix.netcom.com (michelle morton ) writes: >Got a question that's been puzzling me. My cat's fur is so soft that >petting him is like touching a cashmere or angora sweater. My question >is this - is *softness* due to: >a) the **physical** arrangement of the peptide bonds - do the bonds and >the amino acids they're attached to form a smooth, rather than jagged >or discrete, surface? >b) the tertiary or quarternary folding of the protein(s) in his fur - >ie, are the proteins physically arranged in some special way so that >they are experienced by us as being *soft*? >c) the sequencing of the amino acids themselves, or >d) some other phenomenom that I haven't thought of and probably can't >even imagine right now? >Obviously, as a student I have wwwaaaaaayyyy too much time on my time >on my hands :>!!! This is one of several "philosophy" of chemistry >questions I have that keep me from ever getting around to figuring out >how to solve world hunger or bring about total global peace on earth >and other really important stuff like that! Soooooooo, if you can help >me out, I'd really appreciate it. Thanx in advance for your info. Cats. I'm allergic to cats. But I think they're cute, so I play with them anyway. My friends all have short-hair cats, which means their hairs are kinda fragile and break off. These fragments are also light and have a tendency to get caught in my nasal passages and cause a huge response by my body's immune system. That is the reason I like long-hair cats better. Their hair is much more sturdy and remains in long strands when they break; the hair stays on the floor, know what I mean? Now about cat hair...I haven't read any articles about cat hair, but I do know something about human hair..its supercoiled alpha-helical structure, for instance. Human hair breaks and has split ends sometimes too if the supercoils start separating. Hmmm...guess I should start using conditioner to avoid having *gasp* Damaged hair! "hair, you're damaged goods." I'd say. Hair conditioner....what a concept. Back in the old days, did anyone have shiny, bouncy, silky hair like what you get with a vial of VO5? Maybe that's why they wore bonnets and hats in those 19th century photos? Read the ingredients on a bottle of conditioner. They're mostly emulsions of some type or other, and what I think they do (i don't make the product, i can only hypothesize) is bind to hair and keep the hair strands from linking to each other. Penetrating through and coating the hair, the molecules may provide a more uniform surface than the supercoils alone. then, as you stroke the hair with your fingers, you don't detect roughness on the strands. Furthermore, these molecules may protect the supercoils from being damaged physically, chemically or by the sun's radiation. Water content also plays a role in softness. Ask someone who uses fabric softener! Better yet, which is softer -- a dry towel or a damp one? have you ever left clothes in a dryer for too long? Well? HAVE YOU? So, to summarize. your cat's fur is soft probably bacause its hairs are coated with a natural substance that protects the supercoiled alpha helices from damage, and/or your cat's hairs retain moisture well. F.O. Biophysicist by day, lab vampire at night f-omana@students.uiuc.edu From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!rutgers!gatech!stallion.jsums.edu!news.uoregon.edu!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!news.sprintlink.net!wizard.pn.com!Germany.EU.net!EU.net!newsfeed.internetmci.com!chi-news.cic.net!simtel!lll-winken.llnl.gov!usenet From: Chris Barry Newsgroups: bionet.biophysics,bionet.cellbiol,bionet.general,bionet.microbiology,bionet.molbio.proteins Subject: Re: biophysics vs. biochem speculatin'.... Date: 3 Nov 1995 05:08:41 GMT Organization: Lawrence Livermore National Laboratory Lines: 2 Message-ID: <47c84p$s85@lll-winken.llnl.gov> References: <47a8co$3s5@ixnews2.ix.netcom.com> NNTP-Posting-Host: mackiller.llnl.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; Linux 1.1.72 i486) X-URL: news:47a8co$3s5@ixnews2.ix.netcom.com Xref: biosci bionet.biophysics:1381 bionet.cellbiol:3326 bionet.general:18257 bionet.microbiology:3824 bionet.molbio.proteins:6174 Have you wased your cat lately? From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!lll-winken.llnl.gov!uwm.edu!vixen.cso.uiuc.edu!news.ecn.bgu.edu!usenet.ins.cwru.edu!peds22060.GENE.CWRU.Edu!rxw13 From: rxw13@po.cwru.edu (Dr. Ron) Newsgroups: bionet.biophysics,bionet.cellbiol,bionet.general,bionet.microbiology,bionet.molbio.proteins Subject: Re: biophysics vs. biochem speculatin'.... Date: Fri, 3 Nov 1995 11:41:32 E.S.T. Organization: Case Western Reserve University, Cleveland OH (USA) Lines: 27 Message-ID: References: <47a8co$3s5@ixnews2.ix.netcom.com> NNTP-Posting-Host: peds22060.gene.cwru.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] Xref: biosci bionet.biophysics:1390 bionet.cellbiol:3333 bionet.general:18268 bionet.microbiology:3834 bionet.molbio.proteins:6186 > mbmorton@ix.netcom.com (michelle morton ) writes: >Got a question that's been puzzling me. My cat's fur is so soft that >petting him is like touching a cashmere or angora sweater. My question >is this - is *softness* due to: ... >Obviously, as a student I have wwwaaaaaayyyy too much time on my time >on my hands :>!!! This is one of several "philosophy" of chemistry >questions I have that keep me from ever getting around to figuring out >how to solve world hunger or bring about total global peace on earth >and other really important stuff like that! Soooooooo, if you can help >me out, I'd really appreciate it. Thanx in advance for your info. Never apologize for thinking, Mich. Lotsa good ideas have their origins in idle thoughts. I don't have an answer, but a speculation -- 'softness' in fur is a lack of resistance to pressure, yet a resilience once that pressure is removed. Probalby all of your options are involved -- protein tertiery and quaternary structure that permits easy alignment of individual hairs, possibly a thin monomolecular film lanolin coating that prevents electrostatic interactions between strands - but isn't thick enough to feel greasy or allow stickiness. It might be interesting for a industrial polymer company to find out what ARE the differences between angora-y soft cats and plain ordinary cats at the molecular and physical levels, if they already haven't -- presumably, preety much the same structural proteins -- maybe differences in proline content? From owner-proteins@net.bio.net Thu Nov 02 22:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!uwm.edu!chi-news.cic.net!news.uiowa.edu!usenet From: kpmurphy@blue.weeg.uiowa.edu (murphy kenneth p) Newsgroups: bionet.molbio.proteins Subject: Re: Help with Hill Equn. needed Date: 3 Nov 1995 16:41:13 GMT Organization: University of Iowa, Iowa City, IA, USA Lines: 34 Distribution: world Message-ID: <47dgn9$d0s@flood.weeg.uiowa.edu> References: NNTP-Posting-Host: red.weeg.uiowa.edu In article , Tony Day wrote: >We have a protein which is destabilised by a small molecule. The effect >saturates at low mM concentrations. The argument in the lab is whether it >is non-specific or specific. I measured a series of inactivation rates at >different inactivator concentrations. The data were fitted to a >non-linear form of the Hill Eqn.. This gave a good fit with a Hill >coefficient of 1.02. at a Kd of ~.8mM. Also the residuals looked random. > >However, I am a novice at using the Hill Equn. > >My question is as follows: Is there any other reasonable interpretation >of the good fit and Hill coefficient of 1, than a specific single binding >site (or identical sites)? In particular, could it plausibly be >non-specific binding? > >Many thanks in advance. > >Tony Day Tony, When you say the protein is "destabilized", do you mean it loses activity, or that it' melting temperature is lowered or what? In light of your discussion of inactivation rates, it's difficult to tell. Regards, Kip -- Dr. Kenneth P. Murphy e-mail: k-murphy@uiowa.edu Department of Biochemistry office: (319)335-8910 University of Iowa lab: (319)335-7936 Iowa City, IA 52242 FAX: (319)335-9570 From owner-proteins@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!gatech!usenet.eel.ufl.edu!news.uoregon.edu!chi-news.cic.net!news.compuserve.com!news.production.compuserve.com!news From: Dmitri Davvydov <73522.3465@CompuServe.COM> Newsgroups: bionet.molbio.proteins,bionet.software Subject: CARY VARIAN OS/2 SOFTWARE Date: 4 Nov 1995 07:38:52 GMT Organization: Institute of Biomedical Chemistry, Moscow Lines: 75 Message-ID: <47f5ac$sno$1@mhade.production.compuserve.com> Xref: biosci bionet.molbio.proteins:6192 bionet.software:13832 In his message Manoj Ramjee wrote: > Our lab has a Cary 1E and we are looking to update. At the > moment the offers are whether we stay with the DOS version of > the software or whether we 'upgrade' to OS/2 ? We are getting > a Pentium machine to run the Cary but the software issue has > not been solved. Apart from the Varian WWW site info > (http://www.varian.com), I would welcome additional comments > on the following please. > 1. Does anyone use this system and do you like it ? > 2. What are the prolems encountered ? > 3. What is OS/2 like ? (It takes up around 80 MB on the HD and > 12 MB RAM to run!) > 4. Is there a Win95 version on the horizon ? > 5. Anything else you think we should know before going on. 1. I've some experience using Cary 3E with both DOS and OS/2 software. OS/2 version is much more user friendly, flexible and convenient. In fact, it isn't a version, it is entirely new software package. It looks very close to my idea of normal instrument control program which I've in mind. If the principles of DOS version are somewhat archaic, OS/2 mouse-and-window-oriented, multitasking program is one of the best instrument-controlling programs I've ever seen (however, when I start to work with it, knowing clumsy and unconvenient DOS version, I had a very sceptic mood). The program appears just like usual Windows-oriented programs and takes few tenths of minuts to be familiar with it. The program gives you nice abilities of spectra overlapping, mathematical operations on spectra, export and import your data in ASCII using user-specified delimiters; you can save and retreive your methods, etc. 2. Hovewer, the program is a little bit underdone. As usually, it has some bugs. However, these bugs are never fatal. They appears usually after few hours of work, when the program is saturated with your data. These bugs leads to some messages like "Can't retrive method", "Can't open window", etc. It's a bit annoying, but still tolerable (you can simply reboot the system). But what is important - you never loose your data. On my opinion an amount of bugs here is well reasonable for so large program. 3. OS/2 is true multitasking operating system. Only Windows-95 approaches this lewel. User interface of OS/2 is Windows- or Macintosh-alike. However, OS/2 is totally compatible with DOS- and Windows. Almost all DOS- and Windows-oriented programs work well under OS/2. OS/2 is multitasking operating system. Many programs can work simultaneously and share data at the same time in your system. You can easily jump between windows of OS/2, Windows- and DOS-based applications. Actually you don't need Windows (even W95) if you have OS/2 on your computer. However, to have the best results you should be carefull choosing instalation options. The best way is to replace DOS by OS/2, instead of creating a multisystem computer. Since OS/2 well emulates DOS, you will still have ability to run all DOS-oriented programs in DOS environment. Windows you don't need here - OS/2 totally replaces it for Windows-oriented programs. Just try OS/2 - you can see that it's a nice alternative to W95. Since of multitasking nature of OS/2 you can combine Varian software with your favorite data-fitting programs at the same time. For example, we have adapted our DOS-oriented data fitting and handling software SpectraLab (see Miniprint suppl. to our paper in Arch.Biochem.Biophys., v. 320(2) 330-344 (1995)) to work with Varian software, so we can make fitting of kinetic curves, spectra decomposition, SVD-analysis (principal component anlysis) by runing both programs together and sharing the data area. Testing the Varian OS/2 software for the first time I did not believed that it's realy suitable for work. I've never seen something really good for an instrument control before. Actually, I do prefer to adapt my own program (SpectraLab) to work with any instrument I use. But working with OS/2 version of Varian software I've found that it's well tolerable, so I can save my time and work using this program instead of adapting my own software. Feel free to ask more questions, if necessary. Dr. Dmitri Davydov, Institute of Biomedical Chemistry, Russian Acad. of Medical Science, Moscow. -- From owner-proteins@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!usc!newshub.cts.com!carndog From: gambler@cts.com (Phil Terman) Newsgroups: bionet.molbio.proteins Subject: Western Blot with PVDF membrane Date: Sat, 04 Nov 95 21:32:37 GMT Organization: CTSNET Lines: 1 Distribution: world Message-ID: <47gtib$qeh@news2.cts.com> NNTP-Posting-Host: carndog.cts.com What is a good pvdf membrane for western blots? From owner-proteins@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!netnews.nwnet.net!netnews.cc.wwu.edu!news From: Andrea Powers Newsgroups: bionet.molbio.proteins Subject: folin assay Date: 4 Nov 1995 22:41:15 GMT Organization: Western Washington University Lines: 11 Message-ID: <47gq6b$mkp@ra.cc.wwu.edu> NNTP-Posting-Host: indigo1.chem.wwu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.molbio.proteins Can anyone help me find the recipie for the folin developing agent used in the folin assay? The stuff we have in the lab has been giving me a prcipitate, so I assume thta it's too strong, but I dont know what to dilute it to, or if I need to add anything else. The label says 1:1, and the only protocol I can find was written for a lab class where the solutions were all made up by a TA. I would be extremly grtefull for any help - - anya powers n9210808@henson.cc.wwu.edu From owner-proteins@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!simtel!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!News.Uni-Marburg.DE!news.th-darmstadt.de!faui0n.informatik.uni-erlangen.de!uni-erlangen.de!winx03!wpxx02.toxi.uni-wuerzburg.de!krasel From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: stripping Westerns Date: 4 Nov 1995 19:10:24 GMT Organization: Dept. of Pharmacology, U Wuerzburg Lines: 16 Message-ID: <47gdr0$4io@winx03.informatik.uni-wuerzburg.de> References: <47bhe3$3vs@kelso.pprd.abbott.com> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [version 1.2 PL2] Seth Crosby (crosby@milbrandt.wustl.edu) wrote: > Is there a protocol for stripping antibodies off Western blots > (nitrocellulose)? Couldn't find any in the Antibody Bible. There is one in the leaflet that comes with the ECL kit. I think it involves heating in 2-ME. Another possibility is to strip with 100 mM Glycine pH 2.5. Disclaimer: I'm not much of a Western blotting expert. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!scsing.switch.ch!news.belwue.de!News.Uni-Marburg.DE!news.th-darmstadt.de!faui0n.informatik.uni-erlangen.de!uni-erlangen.de!winx03!wpxx02.toxi.uni-wuerzburg.de!krasel From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Help with in situ Enzymatic Digestion for Protein Sequencing Date: 4 Nov 1995 19:08:35 GMT Organization: Dept. of Pharmacology, U Wuerzburg Lines: 14 Message-ID: <47gdnj$4io@winx03.informatik.uni-wuerzburg.de> References: <478jd1$7fa@vixen.cso.uiuc.edu> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [version 1.2 PL2] X. Ni (ni@aries.scs.uiuc.edu) wrote: [digestion of protein on a membrane?] It is possible (see also the other thread in this group), however, I think it is more common to do the digestion not on the membrane but in the SDS gel (at least that was how my unknown protein was digested). Good luck! --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Fri Nov 03 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!uwm.edu!lll-winken.llnl.gov!osi-east2.es.net!doevm!paladin.american.edu!news.jhu.edu!welchlink.welch.jhu.edu!ntheo From: ntheo@welchlink.welch.jhu.edu (NICHOLAS THEODORAKIS ) Newsgroups: bionet.molbio.proteins Subject: Re: Detection of protein in acrylamide Date: 4 Nov 1995 18:58:15 GMT Organization: Johns Hopkins University, Welch Medical Library Lines: 23 Message-ID: <47gd47$b4s@news.jhu.edu> References: NNTP-Posting-Host: 128.220.59.78 In article , Stefan Bdckstrvm wrote: >Is it possible (somehow) to detect a specific protein with ab in an >acrylamide gel without having to blot it to a membrane first ? > >Maby by drying the gel, making it porous or something (I don't know, >that's why I'm asking..) > >Stefan Actually, I believe this technique pre-dates Western blotting. In an old laboratory manual, I found a reference for doing so: K. Burridge (1978) Methods in Enzymology 50:54-64. Be forewarned: the washes in this procedure take two days! -- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Nick Theodorakis ntheo@welchlink.welch.jhu.edu Johns Hopkins Medical School, Baltimore, MD From owner-proteins@net.bio.net Sat Nov 04 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!simtel!zombie.ncsc.mil!cs.umd.edu!haven.umd.edu!purdue!lerc.nasa.gov!magnus.acs.ohio-state.edu!panderso From: panderso@magnus.acs.ohio-state.edu (Patricia J Anderson) Newsgroups: bionet.molbio.proteins Subject: RE: Western Blot with PVDF membrane Date: 5 Nov 1995 21:30:02 GMT Organization: The Ohio State University Lines: 6 Message-ID: <47jacq$m6i@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: beauty.magnus.acs.ohio-state.edu Try immobilon by millipore...it comes in sheets as well as a roll.. works for me! trish anderson eternal grad student... From owner-proteins@net.bio.net Sat Nov 04 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!ix.netcom.com!netcom.com!tday.slip.netcom.com!user From: tday@netcom.com (Tony Day) Subject: Re: Help with Hill Equn. needed Message-ID: Sender: netnews@mork.netcom.com Nntp-Posting-Host: tday.slip.netcom.com Organization: NETCOM On-line Communication Services (408 261-4700 guest) References: <47dgn9$d0s@flood.weeg.uiowa.edu> Date: Sun, 5 Nov 1995 01:22:13 GMT Lines: 24 In article <47dgn9$d0s@flood.weeg.uiowa.edu>, kpmurphy@blue.weeg.uiowa.edu (murphy kenneth p) wrote: > > Tony, > When you say the protein is "destabilized", do you mean it loses activity, or > that it' melting temperature is lowered or what? In light of your discussion > of inactivation rates, it's difficult to tell. > I mean that its melting temperature is decreased. This can be seen in DSC. However, the inactivation is measured by incubating the enzyme at a fixed temperature with increasing concentrations of inactivant. Samples are taken at different times and the rate of loss of activity measured. This rate is taken as a measure of 'binding' (yes I know that I'm making several assumptions doing this:)). The data also fits Scatchard type eqn. which assumes one site, but not one which assumes 2 sites or many. The question I still have in my mind is whether this apparent 1site (or 1 type of non-interacting sites) could really be a non-specific binding leading to inactivation. Tony From owner-proteins@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!news.uiowa.edu!usenet From: kpmurphy@blue.weeg.uiowa.edu (murphy kenneth p) Newsgroups: bionet.molbio.proteins Subject: Re: Help with Hill Equn. needed Date: 6 Nov 1995 14:17:17 GMT Organization: University of Iowa, Iowa City, IA, USA Lines: 41 Distribution: world Message-ID: <47l5dd$jc6@flood.weeg.uiowa.edu> References: <47dgn9$d0s@flood.weeg.uiowa.edu> NNTP-Posting-Host: red.weeg.uiowa.edu In article , Tony Day wrote: >In article <47dgn9$d0s@flood.weeg.uiowa.edu>, kpmurphy@blue.weeg.uiowa.edu >(murphy kenneth p) wrote: > > >> >> Tony, >> When you say the protein is "destabilized", do you mean it loses >activity, or >> that it' melting temperature is lowered or what? In light of your discussion >> of inactivation rates, it's difficult to tell. >> > >I mean that its melting temperature is decreased. This can be seen in >DSC. However, the inactivation is measured by incubating the enzyme at a >fixed temperature with increasing concentrations of inactivant. Samples >are taken at different times and the rate of loss of activity measured. >This rate is taken as a measure of 'binding' (yes I know that I'm making >several assumptions doing this:)). > >The data also fits Scatchard type eqn. which assumes one site, but not one >which assumes 2 sites or many. The question I still have in my mind is >whether this apparent 1site (or 1 type of non-interacting sites) could >really be a non-specific binding leading to inactivation. >Tony If the addition of a "ligand" destabilizes the protein, i.e. lowers the deltaG, then that ligand must bind to the unfolded form. It seems reasonable that this would be a non-specific binding. Of course, one can always describe binding in either site-specific or non-specific formalisms. Look at the work on urea and GuHCl denaturation. Regards, Kip -- Dr. Kenneth P. Murphy e-mail: k-murphy@uiowa.edu Department of Biochemistry office: (319)335-8910 University of Iowa lab: (319)335-7936 Iowa City, IA 52242 FAX: (319)335-9570 From owner-proteins@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!gatech!howland.reston.ans.net!newsfeed.internetmci.com!in1.uu.net!mercury.near.net!noc.near.net!usenet.uchc.edu!Tim From: tkuwada@neuron.uchc.edu (Tim) Newsgroups: bionet.molbio.proteins Subject: Wanted-Aggrecan G1 Ab Date: 6 Nov 1995 22:05:03 GMT Organization: Univ of CT Health Center Lines: 8 Sender: -Not-Authenticated-[4752] Message-ID: <47m0qf$44b@threed.uchc.edu> NNTP-Posting-Host: tanzlab.uchc.edu X-Posted-From: InterNews 1.0@threed.uchc.edu. Xdisclaimer: No attempt was made to authenticate the sender's name. Does anyone have an antibody to the G1 globular domain of aggrecan? Our lab has managed to lose our supply and needs a little Ab for a few preliminary experiments. Thank in advance. Tim Kuwada University of Connecticut Medical School tkuwada@neuron.uchc.edu 203-679-2906 From owner-proteins@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!sdd.hp.com!usc!chi-news.cic.net!simtel!harbinger.cc.monash.edu.au!news.rmit.EDU.AU!news.unimelb.EDU.AU!ucsvc.ucs.unimelb.edu.au!u2528082 From: u2528082@ucsvc.ucs.unimelb.edu.au Newsgroups: bionet.biophysics,bionet.cellbiol,bionet.general,bionet.microbiology,bionet.molbio.proteins Subject: Re: biophysics vs. biochem speculatin'.... Date: 7 Nov 95 12:29:54 +1100 Organization: The University of Melbourne Lines: 48 Distribution: world Message-ID: <1995Nov7.122954@ucsvc.ucs.unimelb.edu.au> References: <47a8co$3s5@ixnews2.ix.netcom.com> NNTP-Posting-Host: hermes.ucs.unimelb.edu.au Xref: biosci bionet.biophysics:1403 bionet.cellbiol:3361 bionet.general:18322 bionet.microbiology:3868 bionet.molbio.proteins:6211 In article , "C. Greiner" writes: > > > On Thu, 2 Nov 1995, George Munson wrote: > >> > a) the **physical** arrangement of the peptide bonds - do the bonds and >> > the amino acids they're attached to form a smooth, rather than jagged >> > or discrete, surface? >> > >> > b) the tertiary or quarternary folding of the protein(s) in his fur - >> > ie, are the proteins physically arranged in some special way so that >> > they are experienced by us as being *soft*? >> > >> > c) the sequencing of the amino acids themselves, or >> > >> > d) some other phenomenom that I haven't thought of and probably can't >> > even imagine right now? >> >> Hmm. Okay this is my best guess and I chose "b." I doubt tactile >> perception is sensitive enough to distinguish peptide bonds or aa sequence >> per se. What you perceive is the much larger scale of the hair which is >> of course ultimately a result of c, a, and b. My guess is softness is >> related to rigidity or the lack thereof. Rigidity of the overall hair >> would likely arise from intermolecular disulfide cross linkages which >> would be tertiary/quartenary in nature. >> -- >> George Munson >> BMBCB, Northwestern University >> Evanston, IL USA >> george-munson@nwu.edu >> > > Although I agree (mostly) with George I wonder if the answer is not "d" > with the "softness" relating to the degree of secretion of oils onto the > hair rather than the actual molecular structure of the hair itself. Thus > the reason high price furs are often from water associated mammals (oil > serves as a water barrier) e.g. beaver, mink, fur seal, otter, etc... As all Australians know, the softness of wool is directly associated with fibre diameter. Wool with diameters over 20 microns is considered relativelycoarse and is itchy or scratchy on the skin. Diameters in the 12-14 micron range is considered superfine and is soft to the touch eg. cashmere. EM of these fibres show a relatively scaley appearance. To think that you can determine aa bonding by touch-wow. John Walker From owner-proteins@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!sdd.hp.com!usc!chi-news.cic.net!uwm.edu!uwvax!newssinet!hakata!inn!hisham.agri.kagoshima-u.ac.jp!user From: hisham@adm.agri.kagoshima-u.ac.jp (Hisham Ibrahim) Newsgroups: bionet.molbio.proteins Subject: Re: extinction coef of lysozyme?? Date: Tue, 07 Nov 1995 12:57:43 +0900 Organization: Kagoshima Univ. Lines: 14 Message-ID: References: <47aslv$fom@centre.univ-orleans.fr> NNTP-Posting-Host: 163.209.150.27 In article <47aslv$fom@centre.univ-orleans.fr>, moreaut@univ-tours.fr wrote: > dear netters, > > I am looking for the molar extinction coefficient value of chicken > lysozyme at 280nm, pH7.0? For Hen Egg-white Lysozyme Molar Extinction Coefficient (1 %, 280 nm) = 26.9 Did you mean this? If not let me know. Best luck! Hisham --------------------------End----------------------------------- From owner-proteins@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!cs.utexas.edu!usc!chi-news.cic.net!uwm.edu!uwvax!newssinet!hakata!inn!hisham.agri.kagoshima-u.ac.jp!user From: hisham@adm.agri.kagoshima-u.ac.jp (Hisham Ibrahim) Newsgroups: bionet.molbio.proteins Subject: Re: folin assay Date: Tue, 07 Nov 1995 13:17:08 +0900 Organization: Kagoshima Univ. Lines: 17 Message-ID: References: <47gq6b$mkp@ra.cc.wwu.edu> NNTP-Posting-Host: 163.209.150.27 In article <47gq6b$mkp@ra.cc.wwu.edu>, Andrea Powers wrote: > Can anyone help me find the recipie for the folin developing agent used in the > folin assay? The stuff we have in the lab has been giving me a prcipitate, so > I assume thta it's too strong, but I dont know what to dilute it to, or if I > need to add anything else. The label says 1:1, and the only protocol I can find > was written for a lab class where the solutions were all made up by a TA. I > would be extremly grtefull for any help - - Usually we do not prepare Folin reagent because it is commercially available from "nacalai tesque" code No. 372-05. This concentrated reagent need to be diluted 12 times before use (1:11) in Lowry method modified by Miller. Best luck. Hisham =========================== End ======================================== From owner-proteins@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!van-bc!unixg.ubc.ca!hayci.generes.ca!user From: kalch@ulam.generes.ca (Michael kalchman) Newsgroups: bionet.molbio.proteins Subject: Re: S. japonicum GST Antibody/serum Date: Mon, 06 Nov 1995 18:48:21 -0800 Organization: ubc Lines: 19 Distribution: world Message-ID: References: <477mkg$r1@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: hayci.generes.ca In article , sk@lilly.com (Stuart Kuhstoss) wrote: > In Article <477mkg$r1@mercury.hgmp.mrc.ac.uk>, pdezoysa@hgmp.mrc.ac.uk (Dr. > P.A. de Zoysa) wrote: > >I would like to obtain some S. japonicum GST antibody/serum for detecting some > fusion proteins that I am planning on making. I know that Pharmacia already > sell this as a part of a kit (most of which is of no use to me). So if > anybody out there has spare antibody I would greatly appreciate some. > Alternatively if anyone of you netters knows of a commercial outlet that > sells the antibody separately please let me know. Hi, The molecular probes antibody is great. You can use it at a high dilution (1:8000) with ECL detection. I think 0.5 mL should last you about a very long time. Michael From owner-proteins@net.bio.net Sun Nov 05 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!ix.netcom.com!netcom.com!tday.slip.netcom.com!user From: tday@netcom.com (Tony Day) Subject: Re: Help with Hill Equn. needed Message-ID: Sender: netnews@mork.netcom.com Nntp-Posting-Host: tday.slip.netcom.com Organization: NETCOM On-line Communication Services (408 261-4700 guest) References: <47dgn9$d0s@flood.weeg.uiowa.edu> <47l5dd$jc6@flood.weeg.uiowa.edu> Date: Mon, 6 Nov 1995 16:01:49 GMT Lines: 26 > >The data also fits Scatchard type eqn. which assumes one site, but not one > >which assumes 2 sites or many. The question I still have in my mind is > >whether this apparent 1site (or 1 type of non-interacting sites) could > >really be a non-specific binding leading to inactivation. > >Tony > > If the addition of a "ligand" destabilizes the protein, i.e. lowers the deltaG, > then that ligand must bind to the unfolded form. It seems reasonable that this > would be a non-specific binding. Of course, one can always describe binding in > either site-specific or non-specific formalisms. Look at the work on urea and > GuHCl denaturation. > Unfortunately, this protein unfolds irreversibly, and has several unfolding transitions visible in DSC. So it is also possible that it binds to a folded intermediate (or the fully folded form) and destabilises that, rather than stabilising the unfolded form. This still begs the question, if the binding were non-specific, wouldn't the data be a poor fit to a n=1 binding equn.? Tony From owner-proteins@net.bio.net Sun Nov 05 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!torn!utnut!oci!news From: Flip Hoedemaeker Subject: Re: Western Blot with PVDF membrane Content-Type: text/plain; charset=us-ascii Message-ID: Sender: news@oci.utoronto.ca Content-Transfer-Encoding: 7bit Organization: Ontario Cancer Institute References: <47gtib$qeh@news2.cts.com> Mime-Version: 1.0 Date: Mon, 6 Nov 1995 19:39:16 GMT X-Mailer: Mozilla 1.1N (Windows; I; 16bit) Lines: 9 gambler@cts.com (Phil Terman) wrote: >What is a good pvdf membrane for western blots? My guess is that most PVDF membranes will work equally well. I've used Millipore immobilon-P succesfully, low background staining! Flip From owner-proteins@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!news.ios.com!ppp-17.ts-5.nyc.idt.net!user From: Efrain@soho.ios.com (Efrain Gonzalez) Newsgroups: bionet.molbio.proteins Subject: IBI MacVector? Where can I get it? Date: 6 Nov 1995 17:32:01 GMT Organization: Internet Online Services Lines: 10 Message-ID: NNTP-Posting-Host: ppp-17.ts-5.nyc.idt.net Does anyone know where I can get a copy of International Biotechnologies Inc.'s Macvector? Does anyone know if another good program for protein sequence analysis exists for Mac or Power Mac? Please E-mail me any responses. Thank you for you help. -- ---- Efrain@soho.ios.com From owner-proteins@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!fdn.fr!jussieu.fr!pasteur.fr!infobiogen.fr!bioftp.unibas.ch!daresbury!hgmp.mrc.ac.uk!news From: pdezoysa@hgmp.mrc.ac.uk (Dr. P.A. de Zoysa) Newsgroups: bionet.molbio.proteins Subject: +ve Control for Glycosylation/Processing Date: 6 Nov 1995 10:39:29 GMT Organization: UK HGMP Resource Centre Lines: 19 Distribution: world Message-ID: <47kol1$6jb@mercury.hgmp.mrc.ac.uk> Reply-To: pdezoysa@hgmp.mrc.ac.uk NNTP-Posting-Host: iron.hgmp.mrc.ac.uk Hi Netters, My Ph.D student would like to obtain a eukaryotic reporter gene (e.g. S. cerevisiae alpha-factor) cloned into a T3/T7 vector which can be used to monitor glycosylation/processing by canine microsomal membranes during transcription/translation in a coupled system. If anyone out there can help, Lara would be very grateful. Thanks, Priyal de Zoysa. -------------------------------------------------------------------------------------- Dr. Priyal A. de Zoysa E-MAIL: pdz@rfhsm.ac.uk Academic Dept. of Medicine, Tel: +44-171-794-0500x5059 10th Floor, RFHSM, Pond St., Fax: +44-171-794-3472 Hampstead, London, UK, NW3 2PF. -------------------------------------------------------------------------------------- From owner-proteins@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!newsspool.doit.wisc.edu!news.doit.wisc.edu!kermit From: klenchin@macc.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: Western Blot with PVDF membrane Date: 6 Nov 1995 14:44:31 GMT Organization: University of Wisconsin at Madison Lines: 20 Message-ID: <47l70f$1ksm@news.doit.wisc.edu> References: <47gtib$qeh@news2.cts.com> NNTP-Posting-Host: kermit.bocklabs.wisc.edu X-Newsreader: News Xpress Version 1.0 Beta #4 In article <47gtib$qeh@news2.cts.com>, gambler@cts.com (Phil Terman) wrote: >What is a good pvdf membrane for western blots? Much stronger binding (proteins almost never go through the membrane) and higher capacity. __ / /\ Dima Klenchin / / \ / / /\ \ klenchin@macc.wisc.edu / / /\ \ \ tel. (608)262-4380 / /_/__\ \ \ FAX (608)262-4570 /________\ \ \ \___________\/ From owner-proteins@net.bio.net Sun Nov 05 22:00:00 1995 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!news.sesqui.net!oitnews.harvard.edu!das-news2.harvard.edu!fas-news.harvard.edu!fas.harvard.edu!rickles From: rickles@fas.harvard.edu (Richard Rickles) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: FENTOMOLE PROTEIN SEQUENCING Date: 7 Nov 1995 03:29:01 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 7 Message-ID: <47mjpt$fef@decaxp.harvard.edu> NNTP-Posting-Host: fas.harvard.edu X-Newsreader: NN version 6.5.0 #3 (NOV) Xref: biosci bionet.molbio.methds-reagnts:35997 bionet.molbio.proteins:6212 FEMTOMOLE PROTEIN SEQUENCING-Means you CAN identify those proteins on PVDF from 2D gels and minigels... brauer@ariad.com From owner-proteins@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!simtel!swidir.switch.ch!scsing.switch.ch!rzunews.unizh.ch!NewsWatcher!user From: maga@vetbio.unizh.ch (Giovanni Maga) Newsgroups: bionet.molbio.proteins Subject: Re: PAGE: Run times and voltages Date: Tue, 07 Nov 1995 11:11:58 +0000 Organization: University of Zurich Irchel- Biochemistry Lines: 21 Message-ID: References: <1995Oct31.025700.29994@marlin.jcu.edu.au> NNTP-Posting-Host: 130.60.120.10 In article <1995Oct31.025700.29994@marlin.jcu.edu.au>, Nick Moody wrote: > It is standard practise in our Department to run SDS-PAGE gels at 200V > until the dye front reaches the end of the gel (usually 45 miuntes). In > other papers I have read they use lower voltages for longer times (eg 40V > for 3 to 4 hours). Can anyone tell me if there are any advantages in > using lower voltages and longer times. I use 10% discontinuous SDS=PAGE > gels and need to silver stain them. > Sometimes, high voltage can give troubles in the resolution of bands (smiling effects, smears), but the limit depends on the buffer system you are using, the AA/bisAA ratio, the gel% and also on the amount of proteins you add. I am not aware of any general rule, but the empirical one (try and see). In my case, I usually run SDS-PAGEs of 6, 7.5, 10 or 12% either for blotting or for staining (silver, comassie) at 80-90 V until the proteins enter completely the lower gel, then I shift up to 130-140 V until the dye reaches the bottom. It takes about 1 h with a small gel apparatus (given that the upper gel is about 0.5 cm high). Giovanni. From owner-proteins@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!scsing.switch.ch!rzunews.unizh.ch!NewsWatcher!user From: maga@vetbio.unizh.ch (Giovanni Maga) Newsgroups: bionet.molbio.proteins Subject: Re: Help with Hill Equn. needed Date: Tue, 07 Nov 1995 11:59:27 +0000 Organization: University of Zurich Irchel- Biochemistry Lines: 76 Message-ID: References: <47dgn9$d0s@flood.weeg.uiowa.edu> <47l5dd$jc6@flood.weeg.uiowa.edu> NNTP-Posting-Host: 130.60.120.10 In article , tday@netcom.com (Tony Day) wrote: > > Unfortunately, this protein unfolds irreversibly, and has several > unfolding transitions visible in DSC. So it is also possible that it > binds to a folded intermediate (or the fully folded form) and destabilises > that, rather than stabilising the unfolded form. This still begs the > question, if the binding were non-specific, wouldn't the data be a poor > fit to a n=1 binding equn.? > > Tony No, if even multiple (i.e non-specific) binding events are independent and equivalent to each other. The Hill's equation apply to the case when, in the presence of multiple binding sites, the affinity of an empty site for the incoming ligand is modified (either increased or reduced) when another site is already occupied. If you fit the equation to a nH=1 it means that either you have a single site or all the binding events are equivalent (no cooperativity). Indeed, with nH=1 the Hill equation reduces to a simple Michelis-Menten equation. Anyway, even if you do not have cooperativity, but simply nonequivalent binding sites, the Hill equation should give you a negative cooperativity (nH<1). Usually, the classical approach is to test before if you have apparent cooperativity and then use the Hill equation to determine the nH. One way to do that is to determine your inactivation rates at different ligand concentration, then plot it as Eadie-Hofstee plot. If you have linear fitting, cooperativity is unlikely. If you have non-linear fitting, you can test cooperativity. However, non-linearity can arise from different reasons, but linearity means that your ligand binds a single site or that there are multiple sites, but they are equivalent and independent (inependent but non-equivalent binding sites should give negative cooperativity). If I am correct, you incubate the protein at fixed T, fixed time with increasing amount of ligand, then use an activity assay as a measure of inactivation. Thus (excluding interferences of your ligand in the activity assay), if you have linear rate change dependence from the ligand concentration, that does not allow you to conclude that there is a single binding event for each protein molecule, but simply that there is no cooperativity in binding. There is anyway a further complication. Since you are usign an indirect assay, the inactivation (decrease in rate of the reaction) that you observe is due to the decrease of the active fraction of the enzyme that partecipates in the reaction. Thus, the linearity of your inactivation rate would refer to the rate of decrease of your active enzyme concentration, but can you relate it directly to the rate of binding of your ligand? What I mean is that, if your enzyme is inactive just as a first unfolded intermediate, it can still bind other ligand molecules that will affect the further unfolding (accelerating it probably), without anyway affecting the enzymatic activity (that is already impaired). Thus, all you can say from these experiments is that the rate of ligand binding that leads to the enzyme inactivation is linear, but this does not mean that your inactive protein does not bind still other ligand molecules. Since you are interested in measuring the rate of unfolded intermediates formation in the presence of your ligand, you should be able to compare the relative activities of the different unfolded intermediates (maybe performing reactions at different temperatures) and look if all the intermediates forms at the same rate in the presence or in the absence of your ligand molecule. Since you can detect the different unfolded intermediates directly by DSC, you can try to see if at any given temperature the kinetic of accumulation of these intermediates is the same with or without the ligand. In order to verify that you have a 1:1 ratio of ligand-protein, you have to determine the actual concentration of both in your assay and then to correct it for the fraction of both that truly partecipate in the reaction. You can try to isolate the protein and the protein/ligand complex by gel filtration to see if it forms aggregates and from the MW estimate the ratio ligand/protein. Indeed, it can be that your ligand acts as an anti-chaperon, binding unfolded intermediates and stabilizing them. Did you check the effect of temperature on the binding affinity? (i.e. partially unfolding the protein and then adding the ligand to see if any of the intermediates you see has higher affinity?). I apologize for this very long and maybe not clear letter. Good Luck. G.Maga, PhD Institute of Veterinary Biochemistry University of Zuerich (CH) From owner-proteins@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!van-bc!news.mindlink.net!agate!lhom From: lhom@nature.Berkeley.EDU (Louis Hom) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Selective Solubilization Date: 7 Nov 1995 22:18:49 GMT Organization: Agricultural and Resource Economics Lines: 7 Message-ID: <47om09$e87@agate.berkeley.edu> NNTP-Posting-Host: nature.berkeley.edu Xref: biosci bionet.molbio.proteins:6220 bionet.molbio.methds-reagnts:36053 Does anyone know of a study where samples were selectively solubilized using different concentrations of the same detergent (as oppposed to selective solubilization using a set of different detergents)? -- _______________________________________________________________________________ Lou Hom >K '93 God bless America -- home to some of lhom@nature.berkeley.edu the best laws that money can buy. From owner-proteins@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!zombie.ncsc.mil!cs.umd.edu!haven.umd.edu!purdue!oitnews.harvard.edu!NewsWatcher!user From: marty@ionchannel.med.harvard.edu (Martin J. Gallagher) Newsgroups: bionet.molbio.proteins Subject: Re: Help with Hill Equn. needed Date: 7 Nov 1995 18:07:55 GMT Organization: Dept. of Neurobiology, Harvard Medical School Lines: 36 Message-ID: References: NNTP-Posting-Host: 134.174.159.173 In article , tday@netcom.com (Tony Day) wrote: > We have a protein which is destabilised by a small molecule. The effect > saturates at low mM concentrations. The argument in the lab is whether it > is non-specific or specific. I measured a series of inactivation rates at > different inactivator concentrations. The data were fitted to a > non-linear form of the Hill Eqn.. This gave a good fit with a Hill > coefficient of 1.02. at a Kd of ~.8mM. Also the residuals looked random. > > However, I am a novice at using the Hill Equn. > > My question is as follows: Is there any other reasonable interpretation > of the good fit and Hill coefficient of 1, than a specific single binding > site (or identical sites)? In particular, could it plausibly be > non-specific binding? > > Many thanks in advance. > > Tony Day Can you get/synthesize a radioactive analog of your ligand? -- Marty -- Martin J. Gallagher phone: (617) 432-1729 Dept. of Neurobiology fax: (617) 734-7557 Harvard Medical School E-mail:marty@ionchannel.med.harvard.edu 220 Longwood Ave http://ionchannel.med.harvard.edu/~marty Boston, MA 02115 ===================================================================== Finger, or WWW for PGP Public Key ===================================================================== -- 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 Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!zombie.ncsc.mil!cs.umd.edu!haven.umd.edu!purdue!lerc.nasa.gov!magnus.acs.ohio-state.edu!rneiswander!milkman From: milkman@postbox.acs.ohio-state.edu Newsgroups: bionet.molbio.proteins Subject: Extinction coefficient of hGH Date: Tue, 7 Nov 1995 14:50:11 GMT Organization: The Ohio State University Lines: 4 Message-ID: NNTP-Posting-Host: 128.146.211.222 X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] Can anyone tell me the extinction coefficient of hGH (human growth hormone). We have determined one value and the literature lists one that is twice as high thanks From owner-proteins@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!idefix.CS.kuleuven.ac.be!news.fundp.ac.be!chokotoff.biocell.fundp.ac.be!user From: michet@biocell.fundp.ac.be (Michael HERMAN) Newsgroups: bionet.molbio.proteins Subject: LIPOGLYCOPROTEIN : PURIFICATION Date: Tue, 07 Nov 1995 15:01:37 -0600 Organization: F.U.N.D.P - Cellular Biochemistry Lines: 14 Message-ID: NNTP-Posting-Host: chokotoff.biocell.fundp.ac.be Could you help us for the purification of a lipoglycoproteic exotoxin (250 Kd) from a medium cultur. Thank's by advance -- Michael HERMAN Laboratory of Cellular Biochemistry, Facultes Universitaires ND de la Paix, 61, rue de Bruxelles, B-5000 Namur (Belgium). Fax: ++/32/81/72.41.35. Email: michet@biocell.fundp.ac.be From owner-proteins@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!IRIS.LSC.PKU.EDU.CN!lisl From: lisl@IRIS.LSC.PKU.EDU.CN (Li Songlin) Newsgroups: bionet.molbio.proteins Subject: (none) Date: 7 Nov 1995 23:44:35 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511082239.AA15709@IRIS.lsc.pku.edu.cn> NNTP-Posting-Host: net.bio.net Does anyone know where I can book IPP (inositol pentaphosphate) or IHP (inositol hexaphosphate)? I am from China. Or maybe you are just using it and could kindly share me some. 1 gram is enough. Songlin Li. lisl@iris.lsc.pku.edu.cn From owner-proteins@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!usc!sdd.hp.com!col.hp.com!news.cis.okstate.edu!usenet From: ron tate Newsgroups: bionet.molbio.proteins Subject: Source for Dye Affinity Chro. kits Date: 7 Nov 1995 21:52:32 GMT Organization: OSU Lines: 11 Message-ID: <47okf0$n3o@news.cis.okstate.edu> NNTP-Posting-Host: amort2.biochem.okstate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: News:bionet.molbio.proteins I hope someone can point me in the right direction, a few months back I thought I was seeing an ad in some journals for a Dye Affinity chromatography kit. It had small columns with different dyes to use for pilot runs in determining which dye column would be useful for purifiing your favorite protein. Now I am interested in it and cannot find it anywhere. Was I just dreaming? Thanks in advance ron tate From owner-proteins@net.bio.net Mon Nov 06 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!uknet!daresbury!not-for-mail From: psansom@hgmp.mrc.ac.uk (Mr. P.A. Sansom) Newsgroups: bionet.molbio.proteins Subject: Potentiation of bioactive peptides by peptidase inhibition? Date: 7 Nov 1995 11:37:23 -0000 Lines: 28 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <47ngdj$d2a@mserv1.dl.ac.uk> content-length: 1214 Original-To: proteins@dl.ac.uk RE : Potentiation of peptide bioactivity by inhibition of proteolysis. I've been examining the effects of exogenous peptides on protein biosynthesis. From the results so far, it seems likely that these peptides (5-15 amino acids) are acting indirectly by preventing proteolysis of endogenous peptides, possibly growth factors, by aminopeptidases. This effect is specific to certain exogenous peptides, suggesting that particular cleavage sites are involved, and thus particular peptidases. Does anybody know of documented examples where addition of peptides to a culture system has resulted in the potentiation of the effects of endogenous peptide factors? I don't mean addition of analogues or derivatives of neuropeptides and hormones, but of short novel peptides which are wholly unrelated to the endogenous bioactive peptide. The mechanism does not necessarily need to be by peptidase inhibition, although this would be a bonus. I know it's a drag, but if possible please email a reply to me as well as to the newsgroup, as my access is VERY limited at the moment, and I don't want to miss any potential threads. Thanks very much in advance Paul psansom@hgmp.mrc.ac.uk Currently representing myself! From owner-proteins@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!newsfeed.internetmci.com!news.compuserve.com!news.production.compuserve.com!news From: Patrick R. Jones <102570.2734@CompuServe.COM> Newsgroups: bionet.cellbiol,bionet.general,bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.software Subject: Help with research - Free!!! Date: 7 Nov 1995 19:12:22 GMT Organization: Personal Lines: 23 Message-ID: <47ob2m$j3n$1@mhafc.production.compuserve.com> Xref: biosci bionet.cellbiol:3389 bionet.general:18365 bionet.molbio.methds-reagnts:36084 bionet.molbio.proteins:6226 bionet.software:13865 I am a biology undergraduate biology student and I am looking for a project to work on. I am not going to school winter quarter ( out of money, you know ) and I need something to keep my brain tuned into biology. I can’t take an internship or something like a internship because I have a family and a job; the job has nothing to do with biology. I would like to help someone or group do something. I am interested in biochemistry, DNA sequencing, biocomputing, etc. I would do work on a project for no charge. In return the work has to be the kind on which a paper could be written and I would like to be a co-author. In other words I help you with some research and you help me with my career. Unless you are in the Salt Lake City, Utah area this work should be something that can be done over the Internet or phone. Going to another location, unless your willing to pay, is not an option ( remember I am poor ). Please respond by e-mail; my address is 102570.2734@CompuServe.COM. I would have posted my resume, but the software I am using won't let me. Thank you for your time Patrick R. Jones -- <> From owner-proteins@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!URANO.MIA.UV.MX!fmontes From: fmontes@URANO.MIA.UV.MX (Fernando M. Montes Gonzalez) Newsgroups: bionet.molbio.proteins Subject: Positions on protein analysis available Date: 8 Nov 1995 09:51:57 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511081756.AA04314@urano.mia.uv.mx> NNTP-Posting-Host: net.bio.net Two positions are available for research in protein sequences and structure analysis applied to the Study of the Immune Molecular Recognition Process. Our group in Molecular Bioinformatics and Immune Recognition are opening a new laboratory in protein modeling and sequence analysis. We are seeking for two Ph.D. with experience in sequence and/or structure analysis of proteins or in the the study of the molecular mechanism of immune recognition. Our area of research is the study of the molecular basis of immune recognition. This problem is studied from a wide spectrum that goes from the analysis of the structural diversity of the germline repertoire, the comparison of the immune molecular recognition strategies in vertebrates, the construction of a 3-d specialized database of Igs, Mhc and Tcr and it analysis, molecular dynamics studies of the Fv, etc. We try to integrate these studies in the context of theoretical models and the general theory of the immune response. We are planing to extend in the future our studies to other recognition models like those of the endocrine or nervous systems. The two positions available are for a period of three years of renewal. After this period, if the work is evaluated as satisfactory the position will come permanent. The new laboratory is the result from an agreement between the National University of Mexico and the Veracruzana University. The seat of the laboratory will be the City of Xalapa at the state of Veracruz. Xalapa (1500 m. over the sea level) is a medium size city (300,000) and is the capital of the state of Veracruz. For information about the Veracruzana University please see at: http://www.coacade.uv.mx/ For information about our Molecular Biology Laboratory here in Xalapa please see at: http://uv4.ivest.uv.mx/ The candidates must send their curriculum vitae with all its publications to the e-address indicated at the end of this message. You can find information about our research in: J. Mol. Evol. (1994) 38:100 J. Mol. Evol. (1995) 41:41 Biosystems (1995) 32:25 J. Mol. Biol. (1995) 246:74 Int. J. Pept. Prot. Res. (1995) 45:180 Prot. Sci. (1995) oct. issue. Immunogenenics (1995) in press. J. Mol. Biol. (1995) in press. Please contact with Dr. Enrique Vargas-madrazo at: evargas@uv4.invest.uv.mx or evargas@speedy.coacade.uv.mx From owner-proteins@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Cormac Shaw Newsgroups: bionet.molbio.proteins Subject: Help:Protease/amylase seperation Date: 8 Nov 1995 12:09:54 -0000 Organization: University College Dublin Lines: 29 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <47q6mi$k74@mserv1.dl.ac.uk> X-mailer: Pegasus Mail/Windows (v1.11a) Original-To: proteins@dl.ac.uk Hi there, I wonder if any of you could help me with a small protein seperation problem. As part of my study of the domain structure of an amylase, I have been attempting to partially hydrolyse the enzyme and establish the size and biological activity (if any) of the hydrolysis products using subtilisin (Boehinger-Mannheim). The problem is seperating theprotease from the amylase components after digestion. Gel filtration (on Superose 12) gives me a protein elution profile which just shows a complex mixture of subtilisin components and some other tiny trace peaks which are presumably from the amylase but they're all mixed up together. The literature contains similar seperations but they all to seem to have nice clear enzyme peaks with no sign of the subtilisin at all - what's their secret (could it be that they just have hugh excesses of their enzyme? My levels are unfortunately pretty low). I am considering trying to remove the subtilisin by affinity chromatography (using Bacitracin-Superose 4B) but this looks messy and I'm doubtful if it will remove all the subtilisin components - the protease seems to breakdown itself during incubation. Any suggestions as to simpler / quicker methods would be greatly appreciated. Thanks for reading, C. ________________________________________________________ Cormac Shaw, BSc. / cshaw@acadamh.ucd.ie / Dept. of Industrial Microbiology, University College, Dublin 4, Ireland. [Insert humourous latin/phrase of your choice here] From owner-proteins@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!in2p3.fr!univ-lyon1.fr!rockendo.univ-lyon1.fr!pcomm From: pcomm@cismibm.univ-lyon1.fr (Pierre Commercon) Newsgroups: bionet.molbio.proteins Subject: PAPPA Antibody Date: Wed, 8 Nov 1995 15:23:30 Organization: Universite Lyon1 Pharmacie Lines: 13 Message-ID: NNTP-Posting-Host: rockendo.univ-lyon1.fr X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Hello I need a monoclonal or polyclonal antibody to Pregnancy Associated Plasma Protein A. I know the Dako one, and I need an other one Thanks in advance Congratulations Pcomm@cismibm.univ-lyon1.fr From owner-proteins@net.bio.net Tue Nov 07 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!sdd.hp.com!col.hp.com!news.cis.okstate.edu!news.ecn.uoknor.edu!munnari.OZ.AU!news.hawaii.edu!news From: an394259@anon.penet.fi (Sarah Chase) Subject: *** EARN $150,000 IN 30 DAYS LEGALLY!!! *** X-Nntp-Posting-Host: nts106.dialup.hawaii.edu Message-ID: Sender: news@news.hawaii.edu Organization: University of Hawaii X-Newsreader: Forte Agent .99.82 Date: Fri, 3 Nov 1995 04:02:30 GMT Lines: 136 Earn $150,000.00 in 30 days $$$ FOR YOUR RECIPES $$$ Please do NOT change anything contained in this letter EXCEPT as directed! EARN AS MUCH AS $150,000.00 OR MORE IN 30 DAYS, LEGALLY! EARN MORE THAN EXTRA MONEY!! YOU WILL BECOME FINANCIALLY INDEPENDENT!! Here ‘s how to do it. IT WORKS EVERY TIME! Again, don’t change anything. 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Ogea -- It changed my life! ***************************************************************************** P. S. Why not try it yourself? Mathematically it is possible, but ONLY IF EVERYONE PARTICIPATES! This system works for the BENEFIT OF ALL, so remember to begin with your name in the #4 position, for MAXIMUM SALES AND PROFITS! THIS IS EASY AND YOU GET LOTS OF MONEY!! GOOD LUCK !!!!! END From owner-proteins@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!Germany.EU.net!ieunet!news.tcd.ie!bioftp.unibas.ch!daresbury!yama.mcc.ac.uk!news.lancs.ac.uk!news From: R.Lauder@lancaster.ac.uk (B Lauder) Newsgroups: bionet.molbio.proteins Subject: Aminopeptidase M - Are GAGs a problem Date: 8 Nov 1995 17:29:56 GMT Organization: Lancaster University Lines: 21 Message-ID: <47qpek$44h@info1.lancs.ac.uk> NNTP-Posting-Host: bsa046000002.lancs.ac.uk Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.6 I'm wanting to isolate some GAGs by digestion of the protein to which they are attached (perhaps by papain) and then use a further enzyme to cleave the final few amino acids which remain attached to the GAG (I want the linkage region intact, with the amino acid to which the GAG is linked present). I guessed that aminopeptidase would be the thing to go for. However, I have no experience of this procedure and wonder if the enzyme will stop cleaving the N-terminal amino acid when it reaches the GAG chain ? If it does will a carboxypeptidase do the job okay from the other end? I'd be grateful for any comments on enzyme choice or on the potential problems. Thanks -- ======================================================== Bob Lauder Biological Sciences, University of Lancaster, UK Home page - http://bssv01.lancs.ac.uk/gig/ppl/bob/home.htm From owner-proteins@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!psgrain!nntp.ski.mskcc.org!news From: Your Name Newsgroups: bionet.molbio.proteins Subject: Radiolabelled NADPH? Date: 8 Nov 1995 19:45:18 GMT Organization: Sloan-Kettering Institute Lines: 11 Message-ID: <47r1ce$nou@research-01.ski.mskcc.org> NNTP-Posting-Host: mac-100.rrl-g2.ski.mskcc.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.molbio.proteins Hi, I need to get hold of some radiolabelled NADPH. Does anybody know of a company that sells this compound? If so please let me know at m-mayhew@ski.mskcc.org. Many thanks Mark. From owner-proteins@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!btnet!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: jallsop@hgmp.mrc.ac.uk (Jenny Allsop) Newsgroups: bionet.molbio.proteins Subject: none Date: 8 Nov 1995 14:41:30 -0000 Lines: 8 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <47qfiq$rf@mserv1.dl.ac.uk> content-length: 180 Original-To: proteins@dl.ac.uk I would like to find the postal address of a company called MYOGENICS from Cambridge, Mass. Please can someone supply this information for us. Regards, Jenny j.allsop@ucl.ac.uk From owner-proteins@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!scsing.switch.ch!news.dfn.de!fu-berlin.de!zrz.TU-Berlin.DE!cs.tu-berlin.de!faui0n.informatik.uni-erlangen.de!uni-erlangen.de!winx03!wpxx02.toxi.uni-wuerzburg.de!krasel From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Source for Dye Affinity Chro. kits Date: 8 Nov 1995 19:48:09 GMT Organization: Dept. of Pharmacology, U Wuerzburg Lines: 17 Message-ID: <47r1hp$jn6@winx03.informatik.uni-wuerzburg.de> References: <47okf0$n3o@news.cis.okstate.edu> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [version 1.2 PL2] ron tate (rtate@bmb-fs1.biochem.okstate.edu) wrote: > I hope someone can point me in the right direction, a few months back I > thought I was seeing an ad in some journals for a Dye Affinity > chromatography kit. It had small columns with different dyes to use for > pilot runs in determining which dye column would be useful for purifiing > your favorite protein. Now I am interested in it and cannot find it > anywhere. Was I just dreaming? Sigma sells dye resin kits (I don't think they sell the test kits in prepacked columns). It might be that Amicon offers similar things. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.tamu.edu!news.utdallas.edu!news.swmed.edu!news From: "R. Bryan Sutton" Newsgroups: bionet.molbio.proteins Subject: Re: Source for Dye Affinity Chro. kits Date: 9 Nov 1995 03:09:54 GMT Organization: University of Texas Southwestern Medical Center Lines: 3 Message-ID: <47rre2$1p4@swsu65.swmed.edu> References: <47okf0$n3o@news.cis.okstate.edu> <47rr6m$1p4@swsu65.swmed.edu> NNTP-Posting-Host: dan.swmed.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) X-URL: news:47rr6m$1p4@swsu65.swmed.edu By the way, the kit was called "Dyematrix kit". From owner-proteins@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.tamu.edu!news.utdallas.edu!news.swmed.edu!news From: "R. Bryan Sutton" Newsgroups: bionet.molbio.proteins Subject: Re: Source for Dye Affinity Chro. kits Date: 9 Nov 1995 03:05:58 GMT Organization: University of Texas Southwestern Medical Center Lines: 9 Message-ID: <47rr6m$1p4@swsu65.swmed.edu> References: <47okf0$n3o@news.cis.okstate.edu> NNTP-Posting-Host: dan.swmed.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) X-URL: news:47okf0$n3o@news.cis.okstate.edu Amicon used to sell such a kit. They published a really good book on the subject " Dye-ligand Chromatography ". This book is older than God, so be forewarned. Bryan Sutton University of Texas Southwestern Medical Center Dallas,TX From owner-proteins@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!OSF1.GMU.EDU!psubedi1 From: psubedi1@OSF1.GMU.EDU ("Prakash Subedi") Newsgroups: bionet.molbio.proteins Subject: (none) Date: 8 Nov 1995 19:20:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net UNSUBSCRIBE Prakash Subedi From owner-proteins@net.bio.net Tue Nov 07 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!library.ucla.edu!agate!darkstar.UCSC.EDU!usenet From: Kimmen Voronov Sjolander Newsgroups: bionet.molbio.proteins Subject: Dirichlet mixture paper available via ftp and on the web Date: 9 Nov 1995 01:37:54 GMT Organization: University of California, Santa Cruz Lines: 44 Message-ID: <47rm1i$5k6@darkstar.UCSC.EDU> NNTP-Posting-Host: pomo.cse.ucsc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; SunOS 4.1.4 sun4c) X-URL: news://darkstar/bionet.molbio.proteins The Computational Biology group at University of California, Santa Cruz, is pleased to announce the following paper available via ftp and on the web. ------------------------------------ ``Dirichlet Mixtures: A Method for Improving Detection of Weak but Significant Protein Sequence Homology", Sjolander, K., Karplus, K., Brown, M., Hughey, R., Krogh, A., Mian, I.S., and Haussler, D. ------------------------------------ URL: http://www.cse.ucsc.edu/research/compbio/dirichlet.html ftp: ftp.cse.ucsc.edu pub/protein/dirichlet/dirichlet.jnl.ps.Z (A nine-component Dirichlet mixture estimated on the Blocks database is also available at this site.) ------------------------------------ Abstract: This paper presents the mathematical foundations of Dirichlet mixtures, which have been used to improve database search results for homologous sequences, when a variable number of sequences from a protein family or domain are known. We present a method for condensing the information in a protein database into a mixture of Dirichlet densities. These mixtures are designed to be combined with observed amino acid frequencies, to form estimates of expected amino acid probabilities at each position in a profile, hidden Markov model, or other statistical model. These estimates give a statistical model greater generalization capacity, such that remotely related family members can be more reliably recognized by the model. Dirichlet mixtures have been shown to outperform substitution matrices and other methods for computing these expected amino acid distributions in database search, resulting in fewer false positives and false negatives for the families tested. This paper corrects a previously published formula for estimating these expected probabilities, and contains complete derivations of the Dirichlet mixture formulas, methods for optimizing the mixtures to match particular databases, and suggestions for efficient implementation. From owner-proteins@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!torn!ccshst05.cs.uoguelph.ca!ccshst01.cs.uoguelph.ca!chouse From: chouse@uoguelph.ca (Chris J House) Newsgroups: bionet.molbio.proteins Subject: B-galactosidase Date: 10 Nov 1995 00:54:10 GMT Organization: University of Guelph Lines: 9 Message-ID: <47u7ri$naa@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: ccshst01.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] Does anyone know of an ftp site with images I can have a look at of B-galactosidase and perhaps other products of the lac-operon (E.coli). Specifically E.coli DH5a (pLAC). Thanks in advance for any info. Please email response to: Chouse@uoguelph.ca From owner-proteins@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!MANI.CBS.UMN.EDU!npv From: npv@MANI.CBS.UMN.EDU (Nora Plesofsky-Vig) Newsgroups: bionet.molbio.proteins Subject: re: dye affinity resins Date: 9 Nov 1995 08:16:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <9511091614.AA01339@mani.cbs.umn.edu> Reply-To: nora@biosci.cbs.umn.edu NNTP-Posting-Host: net.bio.net Sigma does sell a variety of the dye affinity resins in prepacked columns, and they seem to work fine. Nora Plesofsky-Vig From owner-proteins@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!news.cuny.edu!msvax.mssm.edu!FERRO From: ferro@msvax.mssm.edu Newsgroups: bionet.molbio.proteins Subject: Re: Help:Protease/amylase seperation Date: 9 Nov 1995 11:49:45 GMT Organization: Mount Sinai Medical Center, New York City Lines: 43 Distribution: bionet Message-ID: <47spsp$uck@news.cuny.edu> References: <47q6mi$k74@mserv1.dl.ac.uk> Reply-To: ferro@msvax.mssm.edu NNTP-Posting-Host: msvax.mssm.edu I would start to try a longer incubation time of your prep with subtilisin. This way the contaminants will be much lower, and the overlap during Superose 12 will be reduced giving you a good chance to get pure amylase peaks. If it doesn't work, you should try a FPLC ion-exchange column. hope it helps emer In article <47q6mi$k74@mserv1.dl.ac.uk>, Cormac Shaw writes: >Hi there, > I wonder if any of you could help me with a small >protein seperation problem. >As part of my study of the domain structure of an amylase, I have >been attempting to partially hydrolyse the enzyme and establish the >size and biological activity (if any) of the hydrolysis products >using subtilisin (Boehinger-Mannheim). > The problem is seperating theprotease from the >amylase components after digestion. Gel filtration (on Superose 12) >gives me a protein elution profile which just shows a complex mixture >of subtilisin components and some other tiny trace peaks which are >presumably from the amylase but they're all mixed up together. The >literature contains similar seperations but they all to seem to have >nice clear enzyme peaks with no sign of the subtilisin at all - >what's their secret (could it be that they just have hugh excesses of >their enzyme? My levels are unfortunately pretty low). > I am considering trying to remove the subtilisin by affinity >chromatography (using Bacitracin-Superose 4B) but this looks messy >and I'm doubtful if it will remove all the subtilisin components - >the protease seems to breakdown itself during incubation. Any >suggestions as to simpler / quicker methods would be greatly >appreciated. > >Thanks for reading, C. >________________________________________________________ >Cormac Shaw, BSc. / cshaw@acadamh.ucd.ie / Dept. of >Industrial Microbiology, University College, Dublin 4, >Ireland. >[Insert humourous latin/phrase of your choice here] From owner-proteins@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!news.belnet.be!infoserv.rug.ac.be!gonzy.rug.ac.be!user From: gonzalez.vandriessche@rug.ac.be (gonzalez van driessche) Newsgroups: bionet.molbio.proteins Subject: search to journal Date: 9 Nov 1995 10:14:13 GMT Organization: university gent Lines: 12 Message-ID: NNTP-Posting-Host: gonzy.rug.ac.be Dear collegues, Who can help me to obtain a copy from the following journal: Muranova, T.A. & Muranov, A.V. (1979) Sov. J. Bioorg. Chem. 5, 747-750 It describe the use of methylamine for converting of pyroglutamic acid into non-blocked glutamic acid derivative. We do not have such journal in either library from Belgium. Thanks in advance, gonzalez (gonzalez.vandriessche@rug.ac.be) From owner-proteins@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!sgigate.sgi.com!sdd.hp.com!vixen.cso.uiuc.edu!uwm.edu!lll-winken.llnl.gov!simtel!swidir.switch.ch!scsing.switch.ch!news.dfn.de!RRZ.Uni-Koeln.DE!news.rhrz.uni-bonn.de!news.uni-stuttgart.de!uni-regensburg.de!lrz-muenchen.de!news From: diabetes@lrz.uni-muenchen.de (Wolfgang Schechinger) Newsgroups: bionet.molbio.proteins Subject: Re: IP5/IP6 to lisl@IRIS.LSC.PKU.EDU.CN (Didn't reach you by email) Date: Wed, 08 Nov 1995 21:49:47 GMT Organization: Institute for Diabetes Research Lines: 60 Distribution: world Message-ID: <47r5b0$4n6@sparcserver.lrz-muenchen.de> NNTP-Posting-Host: u7k0201.ppp.lrz-muenchen.de X-Newsreader: Forte Free Agent 1.0.82 Hi. I tried to mail my reply directly, but i got it back: user unknown. Please check your email address! On 7 Nov 1995 23:44:35 -0800, you wrote: >Does anyone know where I can book IPP (inositol pentaphosphate) or IHP (inositol >hexaphosphate)? I am from China. Or maybe you are just using it and could kindly >share me some. 1 gram is enough. >Songlin Li. Hi Songlin! IP6 (phytic acid, if you mean meso-inositol-hexakisphosphate) should be avialble from a lot of common suppliers: Fluka (fax +49 731 973-3160 in Germany) is selling 50ml of 40% in water soln. for approx 18 US$ I found a number in Japan from them, too: Phone is +81-3-5640-8860 (SAF Japan, Chuo-ku, Tokyo 103) Sigma is selling the stuff as a 90% solid. 5gms are about 50US$. They have various metal salts: Ca, Ba -100x more expensive, Mg2K4, Mg/K, K2, K, Na10 Sigma/Aldrich have a URL: http://www.sigma.sial.com If you want, I will forward your inquiry to Sigma or Fluka in Germany. Mail me if you like. IP is probably sold by calbiochem, but I'm not sure at all - somebody has 'thefted' their catalogue from my desk. If you can't get any source, please mail and I`ll have a look again. You also might try to post your request to: alt.drugs.chemistry, bionet.molbio.methds-reagnts, de.sci.chemie, fido.ger.chemie, fj.sci.bio, fr.bio.biomol, sci.chem, sci.bio, sci.engr.chem, sci.bio.technology, zer.z-netz.wissenschaft.chemie have a niced day! Wolfgang >lisl@iris.lsc.pku.edu.cn +++++++++++++++++++++++++++++++++++++++++++ Wolfgang Schechinger Chemist, PhD Student Institute for Diabetes Reserch Koelner Platz 1 80804 Munich Germany Phone +49 (89) 30 79 31 24 Fax +49 (89) 30 81 733 email u7k0201@sunmail.lrz-muenchen.de (Standard disclaimer applies) +++++++++++++++++++++++++++++++++++++++++++ From owner-proteins@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!cs.utk.edu!cssun.mathcs.emory.edu!swrinde!sdd.hp.com!vixen.cso.uiuc.edu!uwm.edu!lll-winken.llnl.gov!simtel!swidir.switch.ch!scsing.switch.ch!news.dfn.de!fu-berlin.de!zrz.TU-Berlin.DE!cs.tu-berlin.de!faui0n.informatik.uni-erlangen.de!uni-erlangen.de!lrz-muenchen.de!news From: diabetes@lrz.uni-muenchen.de (Wolfgang Schechinger) Newsgroups: bionet.molbio.proteins Subject: Re: Source for Dye Affinity Chro. kits Date: Wed, 08 Nov 1995 21:29:30 GMT Organization: Institute for Diabetes Research Lines: 38 Distribution: world Message-ID: <47r44o$3g7@sparcserver.lrz-muenchen.de> References: <47okf0$n3o@news.cis.okstate.edu> NNTP-Posting-Host: u7k0201.ppp.lrz-muenchen.de X-Newsreader: Forte Free Agent 1.0.82 ron tate wrote: Hi Ron! Suppose you are thinking of the BioRad stuff. There were some blue dye affinity columns maybe useful for ATP binding proteins. I think that any supplier of media (see: Sigma, Pharmacia, TosoHaas, list is not complete) might have some affinity resins for sale. If you should need an address, fee free to mail. Wolfgang >I hope someone can point me in the right direction, a few months back I >thought I was seeing an ad in some journals for a Dye Affinity >chromatography kit. It had small columns with different dyes to use for >pilot runs in determining which dye column would be useful for purifiing >your favorite protein. Now I am interested in it and cannot find it >anywhere. Was I just dreaming? >Thanks in advance >ron tate +++++++++++++++++++++++++++++++++++++++++++ Wolfgang Schechinger Chemist, PhD Student Institute for Diabetes Reserch Koelner Platz 1 80804 Munich Germany Phone +49 (89) 30 79 31 24 Fax +49 (89) 30 81 733 email u7k0201@sunmail.lrz-muenchen.de (Standard disclaimer applies) +++++++++++++++++++++++++++++++++++++++++++ From owner-proteins@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!news.nic.surfnet.nl!ruu.nl!news From: n.dekker@chem.ruu.nl Newsgroups: bionet.molbio.proteins Subject: Re: Source for Dye Affinity Chro. kits Date: Thu, 09 Nov 1995 18:35:49 +0100 Organization: Academic Compter Centre Utrecht Lines: 1 Message-ID: <30A23BF5.6243@chem.ruu.nl> References: <47okf0$n3o@news.cis.okstate.edu> NNTP-Posting-Host: cble60.chem.ruu.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b1 (Macintosh; I; 68K) It's a BIORAD product so check their products guide. From owner-proteins@net.bio.net Wed Nov 08 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!ieunet!HEAnet!news.ul.ie!ul.ie!vaughanb From: vaughanb@ul.ie (Bren) Subject: Thermophiles and the Internet Message-ID: Sender: usenet@ul.ie Nntp-Posting-Host: itdsrv1.ul.ie Organization: University of Limerick X-Newsreader: TIN [version 1.2 PL2] Date: Thu, 9 Nov 1995 16:10:18 GMT Lines: 12 Hi... I was just wondering if there are any www/ftp sites or indeed newsgroups which deal with thermophiles.... thanks bren ---- Bren Vaughan brendan.vaughan@ul.ie http://skynet.ul.ie/~bren To sleep, perchance to have a cool gory nightmare.... :[ From owner-proteins@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!news1.digital.com!ames!waikato!auckland.ac.nz!ccu1.auckland.ac.nz!surus From: surus@ccu1.auckland.ac.nz (Surus) Newsgroups: bionet.molbio.proteins Subject: ultrafiltration to v. small volume Date: 10 Nov 1995 03:07:06 GMT Organization: University of Auckland Lines: 10 Message-ID: <47ufkq$5ao@net.auckland.ac.nz> NNTP-Posting-Host: ccu1.auckland.ac.nz Summary: I am looking for means of concentrating a small volume of membrane prot Keywords: protein concentration ultrafiltraton detergent small volume X-Newsreader: NN version 6.5.0 #6 (NOV) I am trying to find the most efficient way of concentrating a small volume of membrane protein solution containing detergent to a volume of c. 100-200 ul. As the protein of interest exists in small concentration, the device used must have v. low protein absorption characteristics. I cannot increase the conc. of detergent ( this excludes speedvac or lyophilisation?). Does anyone know whether there are available ultrafiltration devices (10,000- 30,000 MW cutoff) for such small volumes? Or perhaps there is some other way of solving this problem. Many thanks, Andre. From owner-proteins@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news From: Tim Hubbard Newsgroups: bionet.molbio.proteins Subject: postdoc available: structural biology/programming/SCOP database Date: 10 Nov 1995 00:31:46 GMT Organization: Centre for Protein Engineering Lines: 41 Message-ID: <47u6hi$37u@lyra.csx.cam.ac.uk> NNTP-Posting-Host: ccpeshiva1-mac2.mrc-lmb.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.molbio.proteins Medical Research Council ======================== Laboratory of Molecular Biology and Centre for Protein Engineering Postdoctoral Position / Computer Programmer ------------------------------------------- Applications are invited for a three year BBSRC-funded position to work with Drs C. Chothia and T. Hubbard on the development and use of the Structural Classification of Proteins (scop) database. This database is one of the most popular sources of information on protein structures and is used widely for research. On the internet at , it is accessed world-wide. The work will include the development of software tools for the maintenance, extension and exploitation of the database. It will also offer the chance to carry out novel research on protein structure and evolution. Candidates with suitable backgrounds for this position would include those with a PhD in structural biology and strong programming skills and computer programmers with an interest in structural biology. The starting salary will be between 16,628 and 18,985 pounds depending on qualifications and experience. Informal enquires can be made to Dr Hubbard by phone (+44 1223 402131) or by email (th@mrc-lmb.cam.ac.uk). Applications, including a curriculum vitae and the names and addresses of two referees should be sent, quoting reference CPE/TH, to Sheila Jenkins, Personnel Officer, MRC Centre, Hills Road, Cambridge CB2 2QH by 10th December 1995. Applications from overseas are welcome. The Medical Research Council is an Equal Opportunities Employer. (this advertisment also appeared in Nature, 2nd November 1995, Classified-12) From owner-proteins@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!agate!lhom From: lhom@nature.Berkeley.EDU (Louis Hom) Newsgroups: bionet.molbio.proteins Subject: COOH Sequencing Date: 9 Nov 1995 21:32:28 GMT Organization: Agricultural and Resource Economics Lines: 6 Message-ID: <47ts1c$2on@agate.berkeley.edu> NNTP-Posting-Host: nature.berkeley.edu Does there exist a convenient method for carboxy-terminal sequencing? -- _______________________________________________________________________________ Lou Hom >K '93 "Pe--li--gro . . . Pe-li-gro. . . lhom@nature.berkeley.edu Peligro. Ah, peligro!" http://www.ocf.berkeley.edu/~lhom **SPLAT!** From owner-proteins@net.bio.net Wed Nov 08 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!sdd.hp.com!vixen.cso.uiuc.edu!uwm.edu!chi-news.cic.net!simtel!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-ulm.de!rz.uni-karlsruhe.de!news.uni-stuttgart.de!uni-regensburg.de!lrz-muenchen.de!faui0n.informatik.uni-erlangen.de!uni-erlangen.de!winx03!wpxx02.toxi.uni-wuerzburg.de!krasel From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: *** EARN $150,000 IN 30 DAYS LEGALLY!!! *** Date: 9 Nov 1995 16:17:41 GMT Organization: Dept. of Pharmacology, U Wuerzburg Lines: 13 Message-ID: <47t9j5$h8a@winx03.informatik.uni-wuerzburg.de> References: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [version 1.2 PL2] This chain letter was posted by somebody who tries to smear the anon.penet.fi server in Finland. The message has originated from nts106.dialup.hawaii.edu. Please send complaints to root@news.hawaii.edu postmaster@news.hawaii.edu Thanks, --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@