From owner-proteins@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!news.he.net!newsfeed.usit.net!news.usit.net!not-for-mail From: defarr@use.usit.net (Dennis Farr) Newsgroups: bionet.molbio.proteins Subject: corelation between codon and protein secondary structures Date: 2 Jan 1998 20:07:34 GMT Organization: United States Internet, Inc. Lines: 30 Message-ID: <68jhe6$m0t$1@news.usit.net> NNTP-Posting-Host: 199.1.48.3 Summary: Codons and protein structure -- corelated? Keywords: Protein structure prediction X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] In 1989, I gathered up information on the secondary structure of a few proteins and the corresponding DNA code for those proteins, where I could find both sets of data for a protein. I found around twenty proteins for which I had both data sets. I then checked the correlation between codon and secondary structure type for each amino acid that can be represented by multiple codons. (There are 21 amino acids and 64 codons.) I found significant correlation coefficients for several cases. This was an admittedly very small sample. I believe it would be quite easy to repeat my study using currently available datasets and come up with a much larger sample size with very little effort. I am seeking information on whether or not someone has done similar work, or has the resources to do so. I am no longer able to spend the kind of spare time I put into the first study, but would be glad to help out or provide additional details to anyone interested. Caveats: I know the correlation I found is supposed to be impossible. I do not propose a direction for the arrow from cause to effect for the correlation I found, if it holds up under additional scrutiny. I am a computer programmer by trade, and a mathematician by training, not a molecular biologist. I believe the phenomenon I seem to have discovered, or at least conjectured, should be investigated. The cost to do so is cheap. The impact of even a small correlation between structure and codon would be an improvement in protein structure prediction. Using codon rather than amino acid sequence as input to a protein structure prediction algorithm adds almost 2 bits of information per amino acid to the input. If the additional information is at all relevant, the resulting predicted structure should be 'better'. From owner-proteins@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!UNIXG.UBC.CA!allenm From: allenm@UNIXG.UBC.CA (Allen J Milligan) Newsgroups: bionet.molbio.proteins Subject: Re: correlation between codon and protein secondary structure Date: 2 Jan 1998 13:12:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net There is no reason to believe that the correlation you found is impossible. Take a look at Taylor FJR and Coates D. 1989 The code within codons Biosystems 22:177-187. The authors found a strong correlation with the messenger RNA codon and amino acid function. Breifly: The first base is correlated with the amino acid sythetic pathway. The second base is correlated with hydrophobicity, hydrophilicity. The third base is correlated with molecular weight. Allen J Milligan Department of Botany University of British Columbia From owner-proteins@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!MAIL.UFV.BR!mafra From: mafra@MAIL.UFV.BR (Claudio Mafra) Newsgroups: bionet.molbio.proteins Subject: Periodic titles Date: 2 Jan 1998 08:29:39 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <3.0.1.32.19980102143208.007b32b0@mail.ufv.br> NNTP-Posting-Host: net.bio.net Dear I am looking for the editor and the complete and correct title of the following journals: 1-Infect. Agents Dis. 2-Computers Chem. Thanks, Regards Claudio Mafra *********************************************************************** Laboratotio de Biologia e Controle de Hematozoarios Nucleo de Biotecnologia Aplicada a Agropecuaria Departamento de Veterinaria Universidade Federal de Vicosa 36.570-000 - Vicosa - MG Brasil *********************************************************************** http://www.ufv.br/ http://www.bioagro.ufv.br/ *********************************************************************** From owner-proteins@net.bio.net Sun Jan 04 22:00:00 1998 Path: biosci!UNIXG.UBC.CA!allenm From: allenm@UNIXG.UBC.CA (Allen Milligan) Newsgroups: bionet.molbio.proteins Subject: Re: corelation between codon and protein secondary structures Date: 5 Jan 1998 11:57:38 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <2.2.32.19980105195352.006b2ebc@pop.unixg.ubc.ca> NNTP-Posting-Host: net.bio.net There is no reason to believe that the correlation you found is impossible. Take a look at Taylor FJR and Coates D. 1989 The code within codons Biosystems 22:177-187. The authors found a strong correlation with the messenger RNA codon and amino acid function. Breifly: The first base is correlated with the amino acid sythetic pathway. The second base is correlated with hydrophobicity, hydrophilicity. The third base is correlated with molecular weight. Allen J Milligan Department of Botany University of British Columbia From owner-proteins@net.bio.net Sun Jan 04 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!sunqbc.risq.qc.ca!newsflash.concordia.ca!pitt.edu!dsinc!nntp.upenn.edu!news.tju.edu!pnorton From: pnorton@lac.jci.tju.edu (Pamela Norton) Newsgroups: bionet.molbio.proteins Subject: Re: corelation between codon and protein secondary structures Date: Mon, 05 Jan 1998 12:30:34 -0500 Organization: Thomas Jefferson University Lines: 48 Message-ID: References: <68jhe6$m0t$1@news.usit.net> NNTP-Posting-Host: norton1.jmc.tju.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.0 In article <68jhe6$m0t$1@news.usit.net>, defarr@use.usit.net (Dennis Farr) wrote: > In 1989, I gathered up information on the secondary structure of a few proteins > and the corresponding DNA code for those proteins, where I could find both sets of > data for a protein. I found around twenty proteins for which I had both data sets. > > I then checked the correlation between codon and secondary structure type for > each amino acid that can be represented by multiple codons. (There are 21 amino > acids and 64 codons.) I found significant correlation coefficients for several > cases. In most organisms, the 64 codons specify 20 amino acids; additional ones are generated by post-translational modifications. It is well known that codon usage is biased, and this bias is not the same for different taxonomic groups. Did you analysis assume equal codon use? Would you be willing to share a few details about the results that you obtained? The proteins chosen for the analysis might also influence the outcome. snip > > Caveats: I know the correlation I found is supposed to be impossible. I do not > propose a direction for the arrow from cause to effect for the correlation I > found, if it holds up under additional scrutiny. I am a computer programmer by > trade, and a mathematician by training, not a molecular biologist. Nothing is impossible. snip > Pam Norton -- Pamela A. Norton, Ph.D. Associate Professor of Medicine Thomas Jefferson University Philadelphia, PA 19107 p_norton@lac.jci.tju.edu From owner-proteins@net.bio.net Sun Jan 04 22:00:00 1998 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.molbio.proteins Subject: Recomb98: Registration Date: 5 Jan 1998 16:22:51 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <199801060022.QAA23213@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net CALL FOR RECOMB 98 Registration Registration is now starting for RECOMB 98. Please visit our website for registration instructions: http://www.mssm.edu/biomath/recomb98.html If you do NOT want to be in our mailing list, please reply with Subject line "Recomb98: remove". From owner-proteins@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!193.174.75.126!news-was.dfn.de!news-kar1.dfn.de!hades.rz.uni-sb.de!ukmhg03.med-hg.uni-sb.de!user From: hgtsei@med-rz.uni-sb.de (Thomas Seib) Newsgroups: bionet.molbio.proteins Subject: Re: Protein identity Date: 6 Jan 1998 16:03:13 GMT Organization: University of Saarland, Computing Center, Germany. Lines: 25 Message-ID: References: <68binj$poo$1@news.fas.harvard.edu> NNTP-Posting-Host: ukmhg03.med-hg.uni-sb.de In article <68binj$poo$1@news.fas.harvard.edu>, remeans@fas.harvard.edu (Robert Means) wrote: > Hello All, > Here is a slightly stupid question. Our lab has recently gotten > into doing a lot of protein alignments. Is there a public domain program > out there for taking two (or more) proteins either > and comparing them to give a % amino acid similarity, identity, and/or > homology? We have been doing alignments with clustalW if this is useful > info. Any help would be greatly appreciated. > > Bob Means Hello Bob, AnTheProt will do the job ("Analyze The Proteins"). It is a public domain program running under Windows95. Sorry for not having the www- adress available! If you don´t find it using searching engines, please contact me and I will look for the adress. Matthias -- Thomas Seib Kantstr. 12 66292 Riegelsberg From owner-proteins@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.internetmci.com!206.229.87.25!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!rill.news.pipex.net!pipex!server1.netnews.ja.net!news.nott.ac.uk!Fergus.Doherty From: Fergus.Doherty@nottingham.ac.uk (Fergus Doherty) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: SDSPAGE Problems Date: Tue, 06 Jan 1998 15:55:37 +0000 Organization: Nottingham University Lines: 27 Message-ID: NNTP-Posting-Host: wmbpm8.nottingham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 Xref: biosci bionet.molbio.methds-reagnts:63949 bionet.molbio.proteins:12070 A friend is having problems with his Laemmli system SDSPAGE (BioRad minigel app) as follows: "Here in the lab I have an annoying problem with my gels. I'm using the protocols you gave me and they were OK always. I used those with success in Bath as well. But now, despite I use fresh precisely made solutions, there isn't a proper front line of my gel neither during the run (here I have only little hazy blue clouds in each lane) nor after staining (the upper half has a good resolution while the lower one is too light and there's no strong blue front line). Have you got any idea what might cause this phenomenon?" Any clues? It was working now it's not. You can e-mail any suggestions to Peter Low directly at: peterlow@ludens.elte.hu Thanks -- Fergus Doherty, Dept Biochemistry, Nottingham University, Fergus.Doherty@nottingham.ac.uk 0115 970 9366 (74-41366 internal) From owner-proteins@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!server5.netnews.ja.net!loki.cf.ac.uk!not-for-mail From: "Dr. Alexandra Bermudez Fajardo" Newsgroups: bionet.molbio.proteins Subject: Protein methods? Date: Tue, 06 Jan 1998 17:34:27 -0800 Organization: UWCM, Dept. Medical Biochemistry Lines: 9 Message-ID: <34B2DBA3.13B8@cardiff.ac.uk> NNTP-Posting-Host: d018.mb.uwcm.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win16; I) Does anybody know a method to separate and isolate the prosthetic group FAD (or any flavin group) from proteins. I would like to know also, if someone know a mailing discussion list on biochemistry or biochemical related topics. Thank you in advance, Dr. Bermudez Fajardo e-mail: wmbabf@cardiff.ac.uk From owner-proteins@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!biosci!not-for-mail From: John Tomaszewski Newsgroups: bionet.molbio.proteins Subject: NMR: T1 and T2 analysis techniques Date: 6 Jan 1998 21:27:22 -0800 Organization: University of Washington Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi all, Sorry that this doesn't fit exactly into either of these newsgroups but they seemed to be my best bet. I have a couple non-theoretical questions regarding techniques for working up T1 and T2 15N relaxation data. First, for anyone using Felix to pick and name peaks for this purpose, do you use the manual peak or autopick functions? I'm going to do a comparison of the two this afternoon (see which method yields a better exponential fit) but I'm curious to hear what other people think of these Felix options. The autopick seems to box too small an area to calculate accurate volumes, in my opinion. Second, how do you work up the data? I should be receiving an nawk script that will extract the relaxation times from a volumes table but in the meantime I've been trying to use Excel. (from a post to the Excel newsgroups): This works fine, I can chart them with out any problem and if I choose, plot the line equation (y=ce^-xb) on the chart. My problem is, for these series of 40-60 values I want to extract the relaxation time into a cell to use for further calculations, and so far the only way I can see to do it is to read it off the graph and manually type it into a cell, but with many data values and overlap on the chart, this isn't very efficient. Does anyone know how to generate the line equation or the variables into cells, independant from the chart? Any assistance would be greatly appreciated. Sincerely, John T. ******************************************************************** ** ** ** ** * ** DEPARTMENT OF CHEMISTRY ** ** ** ** ** * ** tomasz@protein.chem.washington.edu ** ** ** ** ** * ** (206) 616-2993 ** ** ***** ***** JOHN TOMASZEWSKI ** ******************************************************************** From owner-proteins@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!mail.dcs.warwick.ac.uk!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: SDSPAGE Problems Date: Tue, 06 Jan 1998 18:08:12 -0800 Organization: University of Leicester (PCFS User) Lines: 29 Message-ID: <34B2E38C.573D@le.ac.uk> References: NNTP-Posting-Host: pc10.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win16; I) Xref: biosci bionet.molbio.methds-reagnts:63967 bionet.molbio.proteins:12074 Fergus Doherty wrote: > "Here in the lab I have an annoying problem with my gels. I'm using > the protocols you gave me and they were OK always. I used those with > success in Bath as well. But now, despite I use fresh precisely made > solutions, there isn't a proper front line of my gel The following possible explanations come to mind: 1) High salt content of sample. Desalt, for example by chloroform/methanol precipitation. 2) pH of gel buffers changed over time. Prepare fresh buffers. 3) Gels to old. A batch of gels can be stored in the fridge for about 2 weeks with few problems. After that, diffusion will eliminate the pH jump between stacking and separating gel. Prepare fresh gels. 4) Comb slightly thicker than spacers or spacers of different thickness. This results in a gap between gel and glas plate and this leads to the observed effect. Use proper comb/spacer combinations. Some manufacturers use different colours for different thickness, this prevents mixing. 5) Stacking gel buffer used for separating gel and vice versa. 6) Decomposition of acrylamide to acrylic acid results in increased conductivity. Acrylic acid can be removed by adding some ion exchanger to the acrylamide stock solution. Prepare (or buy) acrylamide stock in small batches and store in the fridge. Discard if too old. From owner-proteins@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!newsfeed.eerie.fr!jussieu.fr!univ-lyon1.fr!cri.ens-lyon.fr!news From: Joel Baguet Newsgroups: bionet.molbio.proteins Subject: radio labelling phosphorylation of protein Date: Wed, 07 Jan 1998 11:21:40 +0000 Organization: Ecole Normale Superieure de Lyon Lines: 8 Message-ID: <34B36544.74BD@ens-lyon.fr> Reply-To: Joel.Baguet@ens-lyon.fr NNTP-Posting-Host: mac-lr5-118a-oncovirus.ens-lyon.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; 68K) Dear Netter's I want to surexpress a NH2-Met-HMK-Protein in cells by using a virus vector. Does anybody have experience about the radio-labelling phosphorylation of this protein in the cellular extract? Is it the same method that for in vitro translated protein? Thank you for your help From owner-proteins@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.direct.ca!fu-berlin.de!zeru.dialup.fu-berlin.DE!not-for-mail From: Karin Zerulla Newsgroups: bionet.molbio.proteins Subject: Help needed: glycerol gradient centrifugation Date: Wed, 07 Jan 1998 16:13:33 +0100 Organization: Freie Universitaet Berlin Lines: 22 Message-ID: <34B39B9D.61B3@zedat.fu-berlin.de> Reply-To: zeru@zedat.fu-berlin.de NNTP-Posting-Host: zeru.dialup.fu-berlin.de (160.45.245.247) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Access: 16 17 19 X-Mailer: Mozilla 3.0 (Win95; I) Dear netters, I'm trying to purify an unknown DNA-binding protein complex using biochemical methods. The DNA-binding activity is detectable after DEAE-Sephacel-column and Heparin-Agarose-column purification steps, but it's lost while glycerol gradient centrifugation. In the meantime I've learned that my purified protein extract was probably too diluted and I should better use a vertical rotor instead of a swinging out bucket to shorten the centrifugation time. But still there are some questions open: 1. How steep should be a glycerol gradient, if the molecular seize of the protein is unknown? 2. Would it be wise to add BSA to stabilize the protein? 3. Has a saccharose gradient any advantages compared with glycerol gradients? Any suggestions or comments will be greatly appreciated. Thanks in advance Karin Zerulla E-mail: zeru@zedat.fu-berlin.de From owner-proteins@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!rw From: rw@mole.bio.cam.ac.uk (Robert Woodward) Newsgroups: bionet.molbio.proteins Subject: anomalous running of proteins on SDS-PAGE Date: 7 Jan 1998 13:54:28 GMT Organization: University of Cambridge, England Lines: 23 Message-ID: <6901ek$cc5$1@lyra.csx.cam.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk Keywords: SDS-PAGE, anomolous migration X-Newsreader: NN version 6.5.0 #3 (NOV) Dear All, I have a problem with a protein that I am purifying from insect cells The protein that I am expressing has a calculated Mw of around 80KDa. In very small scale cultures the product migrates to a position of around 80KDa when resolved by SDS-PAGE and western blotted. This is the core peptide size and it shows no signs of post translational modification that I can tell. Howeve, upon storage and in some cases before storage with larger scale cultures the apparent Mw of the band shifts to around 50KDa. This shift is not attributable to proteolysis since I get the same size band when I probe westerns with antisera to either end of the polypeptide. Has anyone seen anything like this before or has any ideas what is happening? The protein does have some disulphide bonds so could I be getting odd secondary structure forming which is not denatured even through SDS-PAGE conditions? Any ideas would be great. Email rw200@cus.cam.ac.uk Robert From owner-proteins@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!ais.net!uunet!in3.uu.net!amgen!news From: John Philo Newsgroups: bionet.molbio.proteins Subject: Re: anomalous running of proteins on SDS-PAGE Date: Wed, 07 Jan 1998 08:19:32 -0800 Organization: Amgen Lines: 41 Message-ID: <34B3AB14.50C@amgen.com> References: <6901ek$cc5$1@lyra.csx.cam.ac.uk> Reply-To: jphilo*nospam*@amgen.com NNTP-Posting-Host: worf.amgen.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01GoldC-CIS0597c (Win95; U) To: Robert Woodward Robert Woodward wrote: > > Dear All, > > I have a problem with a protein that I am purifying from insect cells > The protein that I am expressing has a calculated Mw of around 80KDa. > In very small scale cultures the product migrates to a position of > around 80KDa when resolved by SDS-PAGE and western blotted. This is > the core peptide size and it shows no signs of post translational modification > that I can tell. Howeve, upon storage and in some cases before storage > with larger scale cultures the apparent Mw of the band shifts to around 50KDa. > This shift is not attributable to proteolysis since I get the same size > band when I probe westerns with antisera to either end of the polypeptide. > > Has anyone seen anything like this before or has any ideas what is happening? > The protein does have some disulphide bonds so could I be getting odd > secondary structure forming which is not denatured even through SDS-PAGE > conditions? > > Any ideas would be great. > > Email rw200@cus.cam.ac.uk > > Robert > Robert, Since you say that your protein has disulfides, your conclusion that this band shift is not due to proteolysis is not necessarily correct. Your protein could be getting clipped in an interior region, and the clipped pieces held together by the disulfide(s), such that the clipped protein would still be recognized by antibodies directed against both N- and C-terminal regions. You definitely need to run REDUCING SDS gels. John Philo, Protein Chemistry, Amgen -- *** remove "*nospam*" from return address before replying *** From owner-proteins@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!194.162.162.196!newsfeed.nacamar.de!univ-lyon1.fr!cri.ens-lyon.fr!news From: Joel Baguet Newsgroups: bionet.molbio.proteins Subject: in vivo chemical cross-linkers Date: Wed, 07 Jan 1998 18:02:47 +0000 Organization: Ecole Normale Superieure de Lyon Lines: 3 Message-ID: <34B3C347.31C0@ens-lyon.fr> Reply-To: Joel.Baguet@ens-lyon.fr NNTP-Posting-Host: mac-lr5-118a-oncovirus.ens-lyon.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; 68K) Who knows the available chemical cross-linkers (cleavable under reducing conditions if possible) to cross-link nuclear proteins in vivo (cell culture). From owner-proteins@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!howland.erols.net!news2.chicago.iagnet.net!iagnet.net!144.92.88.12!newsspool.doit.wisc.edu!news.doit.wisc.edu!pietz From: pietz@oncology.wisc.edu (Brad Pietz) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: T7 RNA polymerase phage? Date: Wed, 07 Jan 1998 14:58:18 -0600 Organization: McArdle Lab for Cancer Research, UW-Madison Lines: 20 Message-ID: NNTP-Posting-Host: alpha.oncology.wisc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 Xref: biosci bionet.molbio.methds-reagnts:63990 bionet.molbio.proteins:12082 I am attempting to express a phage protein in E. coli that appears to be quite toxic. I am able to transform JM109 just fine with my pET vector construct but am unable to transform any strain containing T7 RNA polymerase (BL21 DE3). I have heard of people infecting JM109 with recombinant phage containing T7 polymerase. Does anyone know of a source for these phage (lambda or M13)? I have also read about a group (Appl Microbiol Biotechnol 47:241-245.) using another plasmid containing a T7 promoter to sop up leaky T7 polymerase in the cell. Does anyone know of a source for this plasmid? Please reply by e-mail to pietz@oncology.wisc.edu -- Vladimir Svetlov McArdle Lab for Cancer Research Dept. Oncology UW-Madison 1400 University Ave. Madison, WI 53706 From owner-proteins@net.bio.net Tue Jan 06 22:00:00 1998 Newsgroups: bionet.molbio.proteins From: CCoburn@pofvax.pnb.sunysb.edu (CCoburn) Subject: Re: corelation between codon and protein secondary structures Organization: SUNY at Stony Brook - Dept. of Physiology & Biophysics References: <68jhe6$m0t$1@news.usit.net> Keywords: Protein structure prediction X-Newsreader: News Xpress 2.01 Date: Wed, 07 Jan 1998 23:58:10 GMT NNTP-Posting-Host: adipose.pnb.sunysb.edu X-NNTP-Posting-Host: adipose.pnb.sunysb.edu Message-ID: <34b416ea.0@news.ic.sunysb.edu> Lines: 32 Path: biosci!news.ic.sunysb.edu!adipose Some work on this problem has been done. A fairly recent reference (with abstract) is given below. Authors Thanaraj TA. Argos P. Title Protein secondary structural types are differentially coded on messenger RNA. Source Protein Science. Vol 5(10) (pp 1973-1983), 1996. Abstract Tricodon regions on messenger RNAs corresponding to a set of proteins from Escherichia coli were scrutinized for their translation speed. The fractional frequency values of the individual codons as they occur in mRNAs of highly expressed genes from Escherichia coli were taken as an indicative measure of the translation speed. The tricodons were classified by the sum of the frequency values of the constituent codons. Examination of the conformation of the encoded amino acid residues in the corresponding protein tertiary structures revealed a correlation between codon usage in mRNA and topological features of the encoded proteins. Alpha helices on proteins tend to be preferentially coded by translationally fast mRNA regions while the slow segments often code for beta strands and coil regions. Fast regions correspondingly avoid coding for beta strands and coil regions while the slow regions similarly move away from encoding alpha helices. Structural and mechanistic aspects of the ribosome peptide channel support the relevance of sequence fragment translation and subsequent conformation. A discussion is presented relating the observation to the reported kinetic data on the formation and stabilization of protein secondary structural types during protein folding. The observed absence of such strong positive selection for codons in non highly expressed genes is compatible with existing theories that mutation pressure may well dominate codon selection in non highly expressed genes. From owner-proteins@net.bio.net Tue Jan 06 22:00:00 1998 Newsgroups: bionet.molbio.proteins Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!rain.fr!scratch2atlantel.fr!not-for-mail From: ESSA BORDEAUX ELEVES Subject: (pas d'objet) Message-ID: <34B3FDD5.670618DC@enfrance.com> Date: Wed, 07 Jan 1998 23:12:37 +0100 X-Mailer: Mozilla 4.03 [fr] (Win95; I) MIME-Version: 1.0 To: Gregory Besserve Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 2 Toujours aucun nouveau message recu !!! From owner-proteins@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news1.chicago.iagnet.net!iagnet.net!btnet-peer!btnet!uknet!ukc!news From: psb2 Newsgroups: bionet.molbio.proteins Subject: Nucleoside transport Date: Wed, 07 Jan 1998 18:05:49 +0000 Organization: University of Kent at Canterbury Lines: 16 Message-ID: <34B3C3FD.6734@ukc.ac.uk> NNTP-Posting-Host: pcl3w4.ukc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (WinNT; I) I am not sure if this is the right group to mail this to, but here goes. If you could suggest a better group then that would be appreciated. I am a student currently studying in my final year for a Bachelor's degree in Biochemistry with Medical Biosciences in the United Kingdom. For my final year I have undertaken a laboratory project. The title of this project is Nucleoside transport in chicken erythrocytes. I am having some trouble finding some background information on this topic, particularly how mammalian red cells compare with nucleated red cells (duck/chicken/avian) in their respective nucleoside transport systems. I would be very grateful if you could point me in the right direction. I know you must be very busy but it would be very helpful indeed if you could assist me. Thanks in advance. P.S Bhangu Email address : psb2@ukc.ac.uk From owner-proteins@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!xfer.kren.nm.kr!su-news-hub1.bbnplanet.com!news.bbnplanet.com!news.alt.net!news.u.washington.edu!not-for-mail From: Uncle S Newsgroups: bionet.molbio.proteins Subject: Re: protein-protein interaction Date: Thu, 08 Jan 1998 19:25:03 -0800 Organization: Interzon.com Lines: 41 Message-ID: <34B5988F.41C6@interzon.com> References: <01bd1c34$a103cd60$8d535fa8@jun> NNTP-Posting-Host: mozart.bmsc.washington.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: nntp3.u.washington.edu 884316305 24127 (None) 140.142.64.4 X-Complaints-To: help@cac.washington.edu X-Mailer: Mozilla 3.0Gold (X11; U; IRIX 5.3 IP12) Lion wrote in this pop quiz: > > How many methods are available for assaying protein-protein interaction? Just two, I'm afraid. > What are these methods? Well, there's the yeast two hybrid (Tm) and the other one doesn't matter. Speaking of Stan Fields, here's a damn good review on the topic: Accession No.: 95223267. Author: Phizicky-E-M. Fields-S. Title: Protein-protein interactions: methods for detection and analysis.Accession No.: 97094553. References: REVIEW ARTICLE: 250 REFS. Source: Microbiol-Rev. 1995 Mar. 59(1). P 94-123. Journal Title: MICROBIOLOGICAL REVIEWS. I can also recommend this one Accession No.: 97094553. Author: McNabb-D-S. Guarente-L. Title: Genetic and biochemical probes for protein-protein interactions. References: REVIEW ARTICLE: 51 REFS. Source: Curr-Opin-Biotechnol. 1996 Oct. 7(5). P 554-9. Journal Title: CURRENT OPINION IN BIOTECHNOLOGY. Medline is so cool that I didn't even have to root through my desk to find those titles. Shamus Young Dept. of Biochemistry University of Washington "The difference between love and hate is: hate lasts." -Bukowski From owner-proteins@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.gip.net!news.gsl.net!gip.net!spring.edu.tw!serv.hinet.net!netnews.hinet.net!news From: "Lion" Newsgroups: bionet.molbio.proteins Subject: protein-protein interaction Date: 8 Jan 1998 13:07:19 GMT Organization: JUN Lines: 2 Message-ID: <01bd1c34$a103cd60$8d535fa8@jun> NNTP-Posting-Host: h141.s83.ts.hinet.net X-Newsreader: Microsoft Internet News 4.70.1155 How many methods are available for assaying protein-protein interaction? What are these methods? From owner-proteins@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!agate!howland.erols.net!recycled.news.erols.com!nntp.news.xara.net!xara.net!server6.netnews.ja.net!server4.netnews.ja.net!server2.netnews.ja.net!news.nott.ac.uk!pdxkgs From: pdxkgs@pdn1.gene.nottingham.ac.uk (K.G.Spink) Newsgroups: bionet.molbio.proteins Subject: protein purification Date: 8 Jan 1998 11:11:37 GMT Organization: University of Nottingham Lines: 3 Message-ID: NNTP-Posting-Host: ppdirg.nottingham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 I am intending to isolate a DNA binding protein by attaching the specific binding site to paramagnetic particles. Does anybody know of a good protocol for binding and/or eluting proteins bound in such a system ? From owner-proteins@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!MANI.CBS.UMN.EDU!npv From: npv@MANI.CBS.UMN.EDU (Nora Plesofsky-Vig) Newsgroups: bionet.molbio.proteins Subject: glutathione S-transferase Date: 8 Jan 1998 14:01:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9801082156.AA01282@mani.cbs.umn.edu> Reply-To: nora@biosci.cbs.umn.edu NNTP-Posting-Host: net.bio.net Can someone tell me if glutathione S-transferase is known to bind ATP, or if someone has found experimentally that it does so? I would appreciate any information or references you have. Thanks. Nora Plesofsky-Vig nora@biosci.cbs.umn.edu From owner-proteins@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!agate!newsgate.duke.edu!solaris.cc.vt.edu!newsrelay.netins.net!nntp.kreonet.re.kr!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!not-for-mail From: Peter Wang Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: T7 RNA polymerase phage? Date: Thu, 08 Jan 1998 17:23:45 +0000 Organization: University of Cambridge, England Lines: 24 Message-ID: <34B50BA1.7E90@mrc-lmb.cam.ac.uk> References: NNTP-Posting-Host: macx45.mrc-lmb.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; 68K) To: Brad Pietz Xref: biosci bionet.molbio.methds-reagnts:64014 bionet.molbio.proteins:12089 Brad Pietz wrote: > I am attempting to express a phage protein in E. coli that appears to be > quite toxic. I am able to transform JM109 just fine with my pET vector > construct but am unable to transform any strain containing T7 RNA > polymerase (BL21 DE3). I have heard of people infecting JM109 with > recombinant phage containing T7 polymerase. Does anyone know of a source > for these phage (lambda or M13)? Invitrogen sells M13/T7 phage as part of their pRSET expression kit; I'm not sure if it's available separately - you could check with them. This question was asked before a while back, and I gave this same answer, so sorry for the a repetition. Cheers, - Peter --------------------------------------------------------- Peter Wang, M.D., Ph.D. MRC Centre for Protein Engineering, Hills Road, Cambridge, CB2 2QH, England Tel (01223) 402104 (international calls +44-1223-402104) Fax (01223) 402140 ( " " +44-1223-402140) --------------------------------------------------------- From owner-proteins@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!fu-berlin.de!news.coli.uni-sb.de!hades.rz.uni-sb.de!ukmhg03.med-hg.uni-sb.de!user From: hgtsei@med-rz.uni-sb.de (Thomas Seib) Newsgroups: bionet.molbio.proteins Subject: Re: Protein identity Date: 8 Jan 1998 15:49:26 GMT Organization: University of Saarland, Computing Center, Germany. Lines: 34 Message-ID: References: <68binj$poo$1@news.fas.harvard.edu> NNTP-Posting-Host: ukmhg03.med-hg.uni-sb.de In article , hgtsei@med-rz.uni-sb.de (Thomas Seib) wrote: > In article <68binj$poo$1@news.fas.harvard.edu>, remeans@fas.harvard.edu > (Robert Means) wrote: > > > Hello All, > > Here is a slightly stupid question. Our lab has recently gotten > > into doing a lot of protein alignments. Is there a public domain program > > out there for taking two (or more) proteins either > > and comparing them to give a % amino acid similarity, identity, and/or > > homology? We have been doing alignments with clustalW if this is useful > > info. Any help would be greatly appreciated. > > > > Bob Means > > Hello Bob, > AnTheProt will do the job ("Analyze The Proteins"). It is a public > domain program running under Windows95. Sorry for not having the www- > adress available! If you don´t find it using searching engines, please > contact me and I will look for the adress. > > Matthias > > -- I have the address now for those who are interested: ftp://ftp.pasteur.fr/pub/GenSoft/MS-Windows/protein/AntheProt.zip Matthias -- Thomas Seib Kantstr. 12 66292 Riegelsberg From owner-proteins@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!usenet From: jamie bickley Newsgroups: bionet.molbio.proteins Subject: ScFv - help! Date: Thu, 08 Jan 1998 14:49:54 +0000 Organization: clrc Lines: 15 Distribution: bionet Message-ID: <34B4E792.3A6F@dl.ac.uk> NNTP-Posting-Host: jhavig.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win16; I) Hi! I'm having afew problems whilst attempting to purify a ScFv sample. The main problem is, it appears to be binding to the column! I have tried and Ion exchange column and a simple exchange chromatography column. I have also tried varying the pH of the buffers. Any idea's? I would appreciate any help. Thanks in advance Joanne Burns J.C.Burns@dl.ac.uk From owner-proteins@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!199.60.229.5!newsfeed.direct.ca!Supernews60!supernews.com!nntp.flash.net!news.mira.net.au!harbinger.cc.monash.edu.au!newshost.carno.net.au!torda From: Andrew.Torda@anu.edu.au Newsgroups: bionet.molbio.proteins,bionet.biophysics,bionet.xtallography Subject: Post-doc in computational chemistry, Canberra, Australia with Andrew Torda Date: 9 Jan 1998 06:00:32 GMT Organization: Research School of Chemistry, Australian National University Lines: 69 Sender: Andrew.Torda@anu.edu.au Message-ID: <694ee0$df5$1@clarion.carno.net.au> Reply-To: Andrew.Torda@anu.edu.au NNTP-Posting-Host: 150.203.35.129 Originator: torda@rsc.anu.edu.au Xref: biosci bionet.molbio.proteins:12093 bionet.biophysics:3888 bionet.xtallography:3972 POST DOCTORAL POSITION Computational Chemistry in The Research School of Chemistry, Canberra, Australia with Andrew Torda Available immediately. The research group of Andrew Torda is oriented towards biomolecular calculation and simulation. We are working in areas such as low-resolution (protein fold recognition) force fields, refinement of experimental structures using MD simulation, mixing knowledge-based force fields with experimental data and combinatorial algorithms for protein sequence optimisation. All the projects in the group involve coding and development - not just applications. It would be an advantage to have a reasonable knowledge of data structures and algorithms and programming experience in a civilized language (not fortran). Possible projects would be centred around some new algorithms for aligning amino acid sequences to structures, based on the force fields we have developed. These might include some entertaining ideas such as quasi-Newtonian dynamics in amusing spaces. Projects are negotiable. Salary: more than $40,963 - $43,834 per annum (the rates just increased a week ago). Grants are provided towards travel and removal. Positions are initially for two years with a possible extension to a third year. There is a housing office to help find accommodation. The Research School of Chemistry is part of the Institute of Advanced Studies which runs special research schools in parallel to the normal teaching schools. There are no undergraduate teaching duties. The university is in the centre of Canberra (the nation's capital). Given the research orientation of the school, there is a lively academic environment. We have close contacts with the school's other theoretical groups in statistical mechanics, polymer theory, quantum chemistry and chemical physics. From the point of view of experimental groups, we maintain close ties to the school's NMR, X-ray crystallography and molecular biology groups. Anyone interested in the Torda group should look at http://www.rsc.anu.edu.au/~torda That also contains a pointer to a page of recent publications. Anyone interested should contact me directly (Andrew.Torda@anu.edu.au). The closing date for applications will be March 3 1998. The administrative procedure is that, if you are interested, you are sent an official application (by slow mail). Applicants then have to fill this out and mail it back (again by slow mail). The official forms will include a request for comments from three referees. There is an old advertisement from a previous school-wide job offer at http://www.rsc.anu.edu.au/RSC/AcademicPositions/RSC_Academic_Positions.html and read under "Postdoctoral Fellowships". Andrew Torda From owner-proteins@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!131.103.1.114!news1.chicago.iagnet.net!iagnet.net!newsspool.doit.wisc.edu!news.doit.wisc.edu!usenet From: klenchin@facstaff.REMOVE_TO_REPLY.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: Help needed: glycerol gradient centrifugation Date: Fri, 09 Jan 1998 04:08:33 GMT Organization: UW-Madison Lines: 37 Message-ID: <6947s1$3t4_002@doit.wisc.edu> References: <34B39B9D.61B3@zedat.fu-berlin.de> NNTP-Posting-Host: f183-150.net.wisc.edu X-Newsreader: News Xpress 2.01 X-No-Archive: Yes In article <34B39B9D.61B3@zedat.fu-berlin.de>, zeru@zedat.fu-berlin.de wrote: >Dear netters, > >I'm trying to purify an unknown DNA-binding protein complex using >biochemical methods. The DNA-binding activity is detectable after >DEAE-Sephacel-column and Heparin-Agarose-column purification steps, but >it's lost while glycerol gradient centrifugation. >In the meantime I've learned that my purified protein extract was >probably too diluted and I should better use a vertical rotor instead of >a swinging out bucket to shorten the centrifugation time. Well, IMO gradients don't serve as efficient purifications steps and in this respect are waste of time. Having said that... >But still there are some questions open: >1. How steep should be a glycerol gradient, if the molecular seize of >the protein is unknown? Should not be steep. Go by iterations here. No other way. >2. Would it be wise to add BSA to stabilize the protein? No (unless you protein is abandont or identitity is known). Will introduce lots of additional contaminants. >3. Has a saccharose gradient any advantages compared with glycerol >gradients? No. >Any suggestions or comments will be greatly appreciated. DEAE-Sephacel -> Heparin -> Mono-S sounds reasonable to try -> Mono-Q would be my further choice/next step. Dima From owner-proteins@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!207.69.200.121!news.mindspring.com!user-37kbbdo.dialup.mindspring.com!user From: prevelig@uab.edu (Peter Prevelige) Newsgroups: bionet.molbio.proteins Subject: Re: protein-protein interaction Date: Fri, 09 Jan 1998 05:08:23 -0600 Organization: Dept. of Microbiology Univ. of Alabama at Birmingham Lines: 39 Message-ID: References: <01bd1c34$a103cd60$8d535fa8@jun> <34B5988F.41C6@interzon.com> NNTP-Posting-Host: user-37kbbdo.dialup.mindspring.com X-Server-Date: 9 Jan 1998 11:05:30 GMT In article <34B5988F.41C6@interzon.com>, Uncle S wrote: >Lion wrote in this pop quiz: >> >> How many methods are available for assaying protein-protein interaction? > >Just two, I'm afraid. > >> What are these methods? > >Well, there's the yeast two hybrid (Tm) and the other one doesn't >matter. Well, there are a whole host of quantitative methods as well. I don't off hand know of a good reference but there may be one out there. I will just list a few for you here. analytical ultracentrifugation - perhaps the best, both velocity and equilibrium BIACore and other plama resonsance techniques - quantitative? well you be the judge :) calorimetry hydrodynamic techniques - column chromatography, large zone and traditional light scattering spectroscopic techniques - CD,fluorescene etc....changes in signal with protein concentration affintity chromatography equilibrium dialysis - if one protein/ligand is small enough mass spectroscopy this is a quick list, i can probably think of half a dozen other techniques. If you are interested in a particular system, feel free to drop me some mail. Peter Prevelige Associate Professor, Dept. of Microbiology Univ. of Alabama @ Birmingham From owner-proteins@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!mail.dcs.warwick.ac.uk!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins Subject: Re: Help needed: glycerol gradient centrifugation Date: Fri, 09 Jan 1998 16:21:28 -0800 Organization: University of Leicester (PCFS User) Lines: 48 Message-ID: <34B6BF08.5E8D@le.ac.uk> References: <34B39B9D.61B3@zedat.fu-berlin.de> NNTP-Posting-Host: pc10.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win16; I) Karin Zerulla wrote: > > Dear netters, > > I'm trying to purify an unknown DNA-binding protein complex using > biochemical methods. The DNA-binding activity is detectable after > DEAE-Sephacel-column and Heparin-Agarose-column purification steps, but > it's lost while glycerol gradient centrifugation. > In the meantime I've learned that my purified protein extract was > probably too diluted and I should better use a vertical rotor instead of > a swinging out bucket to shorten the centrifugation time. If you are doing rate zonal centrifugation (separation by size) you should stick with swinging bucket or vertical tube rotors. Fixed angle rotors can be used for isopycnic centrifugation (separation by density), because this is an equilibrium technique and wall effects are not important. Note that there are quite small swinging bucket rotors available, if necessary on a desktop ultracentrifuge. Remember that for rate zonal experiments, the loading zone should be no more than 1-2% of the gradient, therefore use fairly concentrated samples. Also make sure that the density of your sample is less than the start of your gradient! > But still there are some questions open: > 1. How steep should be a glycerol gradient, if the molecular seize of > the protein is unknown? Usually something like 5-30% is used, but that depends the rotor geometry. The idea is to create a isokinetic gradient, where the increased centrifugal force experienced by the protein molecules as it moves outward is just offset by the increase in density of the medium, so that all particles move with constant (but size dependent) speed through the gradient. See the paper by Martin and Ames (JBC, some 30 years ago) for details. You then adjust for the molecular weight of your protein by changing the run time. > 2. Would it be wise to add BSA to stabilize the protein? No. You create more problems than you solve (contamination, gradient inversion). > 3. Has a saccharose gradient any advantages compared with glycerol > gradients? It is cheaper. Other than that, it depends on the idiosyncrasies of your protein. Another alternative are iodinated gradient media like metrizamide. With those you can create isoosmotic gradients, which may be important if your protein does not like the high osmotic pressure in glycerol or sucrose gradients. They are very expensive, however. From owner-proteins@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: "is.bbsrc.ac.uk" Newsgroups: bionet.molbio.proteins Subject: Re: protein-protein interaction Date: 9 Jan 1998 16:12:23 GMT Organization: institute for animal health Lines: 60 Message-ID: <01bd1d19$8a7bd0c0$572a9b95@pc0287.irad.bbsrc.ac.uk> References: <01bd1c34$a103cd60$8d535fa8@jun> <34B5988F.41C6@interzon.com> NNTP-Posting-Host: pc0287.irad.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_01BD1D19.8B66CD00" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Internet News 4.70.1155 This is a multi-part message in MIME format. ------=_NextPart_000_01BD1D19.8B66CD00 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Peter Prevelige wrote in article ... > In article <34B5988F.41C6@interzon.com>, Uncle S wrote: > > >Lion wrote in this pop quiz: > >> > >> How many methods are available for assaying protein-protein interaction? You can try the following review: Protein-Protein interactions: Methods of detection and Analysis. Phizicky and Fields (1995) Microbiological reviews p94 -123 I hope this helps. Mike I.A.H. Compton U.K. ****** ------=_NextPart_000_01BD1D19.8B66CD00 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable





Peter Prevelige = <prevelig@uab.edu> wrote in article <prevelig-0901980508230001@user-37kbbdo.dialup.mindsp= ring.com>...
> In article <34B5988F.41C6@interzon.com>, Uncle S <UncleS@interzon.com> = wrote:
>
> >Lion wrote in this pop quiz:
> = >>
> >> How many methods are available for assaying = protein-protein interaction?

You can try the following = review:

Protein-Protein interactions: Methods of detection and = Analysis.
Phizicky and Fields (1995) Microbiological reviews p94 = -123

I hope this = helps.


Mike

I.A.H.
Compton
U.K.

******

= ------=_NextPart_000_01BD1D19.8B66CD00-- From owner-proteins@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!198.82.160.249!solaris.cc.vt.edu!newsgate.duke.edu!news-relay.ncren.net!fddinewz.oit.unc.edu!login1.isis.unc.edu!wresch From: Wolfgang Resch Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: T7 RNA polymerase phage? Date: Fri, 9 Jan 1998 10:03:06 -0500 Organization: The University of North Carolina at Chapel Hill Lines: 12 Message-ID: References: NNTP-Posting-Host: login1.isis.unc.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: wresch@login1.isis.unc.edu In-Reply-To: Xref: biosci bionet.molbio.methds-reagnts:64047 bionet.molbio.proteins:12097 novagen sells recombinant lambda phage (CE6) used with their pET expression system. an aliquot of high titer phage enough to start growin your own stock and some more costs about 50 $. buying enough for infections is too expensive. also did you try BL21 DE3 pLysS or pLysP ? more stringent control of the polymerase by expressing small amount of lysozyme from a plasmid. also has the advantage that these cells lyse when you freeze-thaw them because of the lysozyme. wolfgang From owner-proteins@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.algonet.se!newsfeed1.telenordia.se!uni-erlangen.de!winx03!wpxx02.toxi.uni-wuerzburg.de!krasel From: Cornelius Krasel Newsgroups: bionet.molbio.proteins Subject: Re: protein-protein interaction Date: Fri, 9 Jan 1998 15:54:30 +0100 Organization: University of Wuerzburg, Germany Lines: 25 Message-ID: <6nd596.5j9.ln@wpxx02.toxi.uni-wuerzburg.de> References: <01bd1c34$a103cd60$8d535fa8@jun> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 unoff BETA 970930; i486 Linux 2.0.32] Lion wrote: > How many methods are available for assaying protein-protein interaction? > What are these methods? Off the top of my head: * Two-hybrid system and its recent modifications * Coimmunoprecipitation * Far western blotting * BIAcore technology * ELISA * Analytical gel filtration Many of these technologies are variations on a theme: one protein is immobilized, and the interaction of the second protein with the solid phase is detected. Analytical gel filtration detects protein-protein interaction in liquid phase, but the affinity must be quite high to find the complex. Two-hybrid system is a genetic in vivo approach. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP4 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!agate!ihnp4.ucsd.edu!sdd.hp.com!vixen.cso.uiuc.edu!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!is.bbsrc.ac.uk!news From: "is.bbsrc.ac.uk" Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: T7 RNA polymerase phage? Date: 9 Jan 1998 12:01:42 GMT Organization: institute for animal health Lines: 104 Message-ID: <01bd1cf6$90cc90e0$572a9b95@pc0287.irad.bbsrc.ac.uk> References: NNTP-Posting-Host: pc0287.irad.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_01BD1CF6.90CC90E0" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.molbio.methds-reagnts:64041 bionet.molbio.proteins:12095 This is a multi-part message in MIME format. ------=_NextPart_000_01BD1CF6.90CC90E0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Brad Pietz wrote in article ... I hope you find the following iformation helpful, coli that appears to be > quite toxic. I am able to transform JM109 just fine with my pET vector > construct but am unable to transform any strain containing T7 RNA > polymerase (BL21 DE3). I have heard of people infecting JM109 with > recombinant phage containing T7 polymerase. Does anyone know of a source > for these phage (lambda or M13)? There is a bacteriophage CE6 (cat. no. 69390)which can be used to introduce the T7 polymerase. This is a lammda phage recombinant. Studier and Moffat 1986 J. Mol. Biol. 189,113 This can be used with host HMS174, where T7 polymerase production is so high it interferes with mnormal phage development. > I have also read about a group (Appl Microbiol Biotechnol 47:241-245.) > using another plasmid containing a T7 promoter to sop up leaky T7 > polymerase in the cell. Does anyone know of a source for this plasmid? You may want to ,look up studier et al. 1990, Meth. enzymology 185:60-89; dubenodorff and studier 1991 J. Mol. Biol 219, 45-59. which deals with a vectors, with T7lac promotors ( the lac operator downstream of of the T7 promotor ). I have not tried these systems at all, but have got this information from the novagen ( Novagen US:800 526-7319, distributed by someone else in the UK.) manual on pET vectors, so you may want to get hold of that from them as it has more information and references. I hope this helps Mike Jones I.A.H. Compton UK ************************ discalimer, nothing in this post is an endorsment of any comapany or method mentioned. These are personal view points anddo not represent any institute policy or comment. I.A.H. discaliaims any responsibility for this post. All the usual discalaimer stuff. ************************** Nothing can be assumed to be safe Always Use your own brain before doing anythiny and common sense helps. don't you just love discalimers! *************************** Stop Censorship, free information. ------=_NextPart_000_01BD1CF6.90CC90E0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Brad Pietz <pietz@oncology.wisc.edu> wrote in article <pietz-ya02408000R0701981458180001@news.doit.wisc.edu= >...
I hope you find the following = iformation helpful,

coli that appears to be
> quite toxic. =  I am able to transform JM109 just fine with my pET vector
> = construct but am unable to transform any strain containing T7 = RNA
> polymerase (BL21 DE3).  I have heard of people = infecting JM109 with
> recombinant phage containing T7 polymerase. =  Does anyone know of a source
> for these phage (lambda or = M13)?

There is a bacteriophage CE6 (cat. no. 69390)which can =  be used to introduce the T7 polymerase.
This is a lammda phage = recombinant.
Studier and Moffat 1986 J. Mol. Biol. 189,113
This = can be used with host HMS174, where T7 polymerase production is so high =
it interferes with mnormal phage development.

> I have = also read about a group (Appl Microbiol Biotechnol 47:241-245.)
> = using another plasmid containing a T7 promoter to sop up leaky = T7
> polymerase in the cell.  Does anyone know of a source = for this plasmid?

You may want to ,look up studier et al. 1990, = Meth. enzymology 185:60-89; dubenodorff and studier 1991  J. Mol. = Biol 219, 45-59. which deals with a vectors, with T7lac promotors ( the = lac operator downstream
of of the T7 promotor ).  
I have = not tried these systems at all, but have got this information from the = novagen ( Novagen US:800 526-7319, distributed by someone else in the = UK.) manual on  pET vectors, so you may want to get hold of that = from them as it has more information and references.

I hope this = helps

Mike Jones
I.A.H. =
Compton
UK

************************
discalimer, nothing = in this post is an endorsment of any comapany or method mentioned. =
These are personal view points anddo not represent any institute = policy or comment.
I.A.H. discaliaims any responsibility for this = post. All the usual discalaimer = stuff.
**************************
Nothing can be assumed to be = safe Always
Use your own brain before doing anythiny
and common = sense helps. don't you just love = discalimers!
***************************
Stop Censorship, free = information.

------=_NextPart_000_01BD1CF6.90CC90E0-- From owner-proteins@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.direct.ca!fu-berlin.de!bignews.mediaways.net!news-han1.dfn.de!news.gwdg.de!not-for-mail From: Christian Ebeling Newsgroups: bionet.molbio.proteins Subject: pET-vector Date: Fri, 09 Jan 1998 17:19:06 +0100 Organization: Institut fuer Molekulare Genetik Lines: 6 Message-ID: <34B64DFA.6BE3@gwdg.de> Reply-To: cebelin@gwdg.de NNTP-Posting-Host: ubmgpg.uni-molgen.gwdg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (WinNT; I) Hallo, i need for the expression in E.coli a vector (without a amp-resistence) with a N-terminal signal sequence for periplasmic location. I know the pET26b(+) and pET27(b). Could anyone help me with this plasmmids. Perhaps i can help you: I have pET21,20,24 and 30Lic. Christian From owner-proteins@net.bio.net Fri Jan 09 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!ais.net!newsfeed.concentric.net!global-news-master From: hockeyst@concentric.net (sean) Newsgroups: bionet.molbio.proteins Subject: Help a student with science fair Date: Sat, 10 Jan 1998 09:46:46 -0500 Organization: home Lines: 21 Message-ID: NNTP-Posting-Host: ts015d05.sag-mi.concentric.net I am a 15 year old science student that is starting a science fair project concerning experimenting with an inexpensive and safe alternative to polyacrymlide slab gels for protein gel electrophoresis. I will be trying to alter the composition of the agarose-synergel mixture and running standards. Does anyone have any thoughts of things I could do; physically to the gel to help in the separation and resolution of the protein spread. I am trying to derive a process that would make the resolution of the agarose mixture as good or close to a polyacrylmide gel. Anything else that would seem relevant in the chemistry of the electrophoresis process that could be changed to give better resolution would be very appreciated. Could you please email directly Thank you in advance Sean A. Tabacsko Center for the Arts and Sciences Saginaw, MI USA hockeyst@concentric.net From owner-proteins@net.bio.net Fri Jan 09 22:00:00 1998 From: p.bayliss@utoronto.ca Subject: 2D PAGE problem Date: Sat, 10 Jan 1998 23:21:38 -0600 Reply-To: p.bayliss@utoronto.ca Message-ID: <884495442.419168260@dejanews.com> Newsgroups: bionet.molbio.proteins Organization: Deja News Posting Service Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!207.207.0.25!nntp.texas.net!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Sun Jan 11 05:10:42 1998 GMT X-Authenticated-Sender: p.bayliss@utoronto.ca X-Http-User-Agent: Mozilla/3.01 (Win95; I) X-Originating-IP-Addr: 142.150.129.225 (victor.dialin.utoronto.ca) Lines: 20 When I run the first dimension of a 2D gel on this particular sample, something stacks inside the tube (visible by bromophenol blue not getting through it). If left long enough (eg. 4hr) and with less sample, it eventually runs out of the bottom of the tube. It's a nuisance, and may be taking some of my protein with it (especially LMW), and it seems to temporarily shift the pI gradient (bromophenol blue which DOES get past turns yellow, even if it's not near the bottom of the tube). With silver stain, it doesn't stain like normal protein, but stains a very light blue. I haven't stained with coomassie. In the second dimension, it again all runs to more or less the same spot. I'm thinking it's lipid, but I'm not sure. I've tried acetone and also chloroform extraction with minimal success. I'd like to rid myself of it altogether. Has anyone had similar problems, or have any suggestions? Anyone know of a really good way to solubilize proteins and then get rid of lipids? Thanks in advance for your help!! -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-proteins@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-peer-east.sprintlink.net!news.sprintlink.net!Sprint!uunet!in1.uu.net!nntp.earthlink.net!usenet From: "Kevin Shreder, Ph.D." Newsgroups: bionet.molbio.proteins Subject: Win a free book on antibody purification Date: Sun, 11 Jan 1998 08:33:27 -0800 Organization: The Antibody Resource Page Lines: 33 Message-ID: <34B8F457.4349@antibodyresource.com> Reply-To: antibody@antibodyresource.com NNTP-Posting-Host: 153.35.116.118 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0Gold (Win16; U) Come take a look at the Antibody Resource Page and find out how you can win Purification Tools for Monoclonal Antibodies by Peter Gagnon. The Antibody Resource Page will be invaluable to those looking for sources of antibodies, ways to find antibodies, and educational resources about antibodies. Here is just some of what can be found on the page: 1. How to Find an Antibody - a variety of ways on and off the web to find the antibody you are looking for. 2. Online Companies - links to over 110 companies that sell antibodies or antibody related products. Is your company listed on this page? 3. Antibody Image Gallery - some animated gifs have recently been added 4. Bulletin Board - Have a question or have an answer? Then stop by and post a message. 5. Educational Resources - a variety of new links have been added. There are links to pages on immunochemistry, antibody production, autoimmunity, vaccines, immunology and much more. This page is divided up into sections on research, educational, and health resources. ...and there is much more. Check it out at: http://www.antibodyresource.com/ Ps. Don’t forget to visit our sponsors, Research Diagnostics, Inc. (http://www.researchd.com/absort1.htm) and Lab Vision (http://www.labvision.com/)! From owner-proteins@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!uni-erlangen.de!news-nue1.dfn.de!news-lei1.dfn.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.gwdg.de!not-for-mail From: "Christian Ebeling" Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: T7 RNA polymerase phage? Date: Sun, 11 Jan 1998 05:41:55 +0100 Organization: GWDG, Goettingen Lines: 20 Message-ID: <69bff3$amt$1@gwdu19.gwdg.de> References: NNTP-Posting-Host: gwdppp26.gwdg.de X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Xref: biosci bionet.molbio.methds-reagnts:64074 bionet.molbio.proteins:12105 Wolfgang Resch wrote: > >also did you try BL21 DE3 pLysS or pLysP ? more stringent control of the >polymerase by expressing small amount of lysozyme from a plasmid. also has >the advantage that these cells lyse when you freeze-thaw them because of >the lysozyme. This ( pLysS) works great for expresssion of toxic proteins and you will have less transformation problems. Christian ------------ Christian Ebeling Institut fuer Moleculare Genetik Universitaet Goettingen Germany http://www.gwdg.de/~cebelin From owner-proteins@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!newshub1.home.com!news.home.com!xfer.kren.nm.kr!nntp.kreonet.re.kr!news.kigam.re.kr!usenet.seri.re.kr!bioneer.kaist.ac.kr!dykim From: dykim@bioneer.kaist.ac.kr (Dooyeon Kim) Newsgroups: bionet.molbio.proteins Subject: Expressing the cpp32 in yeast nucleus Date: 12 Jan 1998 03:20:31 GMT Organization: Dept. of Biological Sciences, KAIST Lines: 44 Message-ID: <69c25v$15o$3@green.kreonet.re.kr> NNTP-Posting-Host: bioneer.kaist.ac.kr X-Newsreader: TIN [version 1.2 PL2] Hi, Netters. I am trying to express the cpp32(caspase-3) in yeast nucleus. The protease(caspase-3) expressed was designed to contain SV40 nuclear localize signal in its N terminal. The problem is 1. The protease is activated in the yeast by proteolysis of the middle of the protein. Although the cleaved fragment is not dissociated(actually interacts with other fragments to become a complex), I wonder if the SV40 nuclear localize signal(fused in the N-terminal) is working. 2. Caspase-3 is known to exist in cytosol and nucleus. Is it possible to make this protease exist only in nucleus? Any information or advice regarding above problems will be greatly appreciated. Thanks in advance. Bye. -- ___________________________________________________________________________ KAIST, Daejon Korea. Dooyeon Kim ...................... dykim@bioneer.kaist.ac.kr ___________________________________________________________________________ -- ___________________________________________________________________________ KAIST, Daejon Korea. Dooyeon Kim ...................... dykim@bioneer.kaist.ac.kr ___________________________________________________________________________ From owner-proteins@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!rw From: rw@mole.bio.cam.ac.uk (Robert Woodward) Newsgroups: bionet.molbio.proteins Subject: IEF Date: 12 Jan 1998 12:35:38 GMT Organization: University of Cambridge, England Lines: 20 Message-ID: <69d2mq$d69$1@lyra.csx.cam.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk Keywords: IEF X-Newsreader: NN version 6.5.0 #3 (NOV) Dear All, Does anyone in the Cambridge (UK) area have any experience with IEF? I would like to know the IEP of a pertially purified protein that I have antibodies to. I only have standard 1D miniprotean II equipment and I first of all need to know if this could be used in some way, and secondly can you western blot IEF gels and then probe with antibodies so as to identify my protein of interest? If you need specialist equipment is anyone prepared to run a couple of samples out for me (or loan me some equipment)? obviously I would be prepared to pay for materials used etc.. Thanks very much Robert Woodward Email rw200@cus.cam.ac.uk Cambridge University Dept Obs+Gynae Rosie Maternity Hospital Cambridge From owner-proteins@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!193.174.75.126!news-was.dfn.de!news-fra1.dfn.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.ruhr-uni-bochum.de!not-for-mail From: posch@bgfa.ruhr-uni-bochum.de (Anton Posch) Newsgroups: bionet.molbio.proteins Subject: Vertical electrophoresis unit Date: Tue, 13 Jan 1998 08:49:57 GMT Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 6 Message-ID: <34bb2a96.5919940@www.bgfa.ruhr-uni-bochum.de> NNTP-Posting-Host: lufu.bgfa.ruhr-uni-bochum.de X-Newsreader: Forte Free Agent 1.11/32.235 I¦m desperately looking for a supplier of a cooled vertical elelctrophoresis unit running four or five 20x20 cm gel in parallel for second dimension 2D electrophoresis. Any help is greatly appreciated. Toni From owner-proteins@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!DNA-DIAGNOSTICS.COM!mmunzer From: mmunzer@DNA-DIAGNOSTICS.COM (dna-diagnostics.com) Newsgroups: bionet.molbio.proteins Subject: Re: New DNA Technologies Date: 13 Jan 1998 08:35:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BD2016.DD4296E0@cygene-2.biotech.ufl.org> NNTP-Posting-Host: net.bio.net Thank you all for your overwhelmingly positive response to our = announcement of new DNA Diagnostic technologies. Due to the volume of = inquiries, we have compiled a series of FAQ's, to respond to the = majority of your questions. We have posted them on our CyGene web site = along with several letters of opinion from professionals who have = reviewed the TPA and RFTA patent documents. RFTA opinion letters will be = posted on our AGENDA site shortly. We will respond to all other inquiries as soon as possible. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Martin Munzer=20 AGENDA, Inc. http://www.dna-diagnostics.com a.k.a. Advanced Genetic Diagnostic Associates=20 Confirming "Heirlines" Through State of the Art DNA Analysis ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-proteins@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!152.163.199.19!portc03.blue.aol.com!newstf02.news.aol.com!audrey01.news.aol.com!not-for-mail From: squick2653@aol.com (SQuick2653) Newsgroups: bionet.molbio.proteins Subject: 1998 ICDD Crystallography Scholarship Recipients Date: 13 Jan 1998 13:45:24 GMT Lines: 26 Message-ID: <19980113134500.IAA02704@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com International Centre for Diffraction Data 1998 ICDD Crystallography Scholarship Recipients The ICDD Crystallography Scholarship Committee has selected five winners for the 1998 Crystallography Scholarship Awards. They are: Ekaterina Anokhina from Wake Forest University, Winston-Salem, North Carolina; Nathalie Audebrand (also a 1997 recipient) from the Université de Rennes I, Rennes, France; Susanne C. Feil from St. Vincent's Institute of Medical Research,Victoria, Australia; Christopher D. Theis from The Pennsylvania State University, University Park, Pennsylvania; and K. Scott Weil from Carnegie Mellon University, in Pittsburgh, Pennsylvania. Ekaterina Anokhina's studies focus on "Niobium Oxochloride Cluster Compounds: a Quest for Correlations between Configuration of the Clusters, Framework Topology and Properties." Nathalie Audebrand will continue her research of "Structure, Microstructure and Temperature- dependent Diffraction Studies of New Cerium-based Precursors and Related Oxides." The exploration of "Structural and Functional Aspects of Pore-forming Proteins by X-ray Crystallography and Molecular Biology" will be conducted by Susanne Feil. Christopher Theis will study "Ferroelectric Superlattices and Higher n Aurivillius Phases Grown By MBE". "Investigation of the Formation, Structure, and Magnetic Behavior of Compounds in the Nickel- Molybdenum-Nitrogen System" will be researched by K. Scott Weil. ICDD will present each student with a $2000 check to continue their studies in their selected field of crystallographic research. From owner-proteins@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!193.174.75.126!news-was.dfn.de!news-fra1.dfn.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.ruhr-uni-bochum.de!not-for-mail From: posch@bgfa.ruhr-uni-bochum.de (Anton Posch) Newsgroups: bionet.molbio.proteins Subject: Re: vertical electrophoresis unit Date: Tue, 13 Jan 1998 12:47:06 GMT Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 13 Message-ID: <34bb6218.20132272@www.bgfa.ruhr-uni-bochum.de> References: <34BB2DD9.6545@univ-lille1.fr> NNTP-Posting-Host: lufu.bgfa.ruhr-uni-bochum.de X-Newsreader: Forte Free Agent 1.11/32.235 On Tue, 13 Jan 1998 10:03:23 +0100, "eqpcmv@univ-lille1.fr" wrote: >Millipore has such an unit in his catalog : >investigator 2-D electrophoresis system >http://millipore.com > >eric Thank you for this message, but Millipore stopped with this system. Anton Posch From owner-proteins@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!agate!ihnp4.ucsd.edu!sdd.hp.com!usc!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!fu-berlin.de!informatik.tu-muenchen.de!news.ruhr-uni-bochum.de!not-for-mail From: posch@bgfa.ruhr-uni-bochum.de (Anton Posch) Newsgroups: bionet.molbio.proteins Subject: Re: 2D PAGE problem Date: Tue, 13 Jan 1998 20:00:14 GMT Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 29 Message-ID: <34bb8693.29472231@www.bgfa.ruhr-uni-bochum.de> References: <884495442.419168260@dejanews.com> NNTP-Posting-Host: lufu.bgfa.ruhr-uni-bochum.de X-Newsreader: Forte Free Agent 1.11/32.235 On Sat, 10 Jan 1998 23:21:38 -0600, p.bayliss@utoronto.ca wrote: > When I run the first dimension of a 2D gel on this particular sample, >something stacks inside the tube (visible by bromophenol blue not getting >through it). If left long enough (eg. 4hr) and with less sample, it >eventually runs out of the bottom of the tube. It's a nuisance, and may >be taking some of my protein with it (especially LMW), and it seems to >temporarily shift the pI gradient (bromophenol blue which DOES get past >turns yellow, even if it's not near the bottom of the tube). With silver >stain, it doesn't stain like normal protein, but stains a very light >blue. I haven't stained with coomassie. In the second dimension, it >again all runs to more or less the same spot. I'm thinking it's lipid, >but I'm not sure. I've tried acetone and also chloroform extraction with >minimal success. I'd like to rid myself of it altogether. > > Has anyone had similar problems, or have any suggestions? Anyone know >of a really good way to solubilize proteins and then get rid of lipids? > > Thanks in advance for your help!! > >-------------------==== Posted via Deja News ====----------------------- > http://www.dejanews.com/ Search, Read, Post to Usenet Hi 2D-user, I´m working very long with 2D technology, but to give you any advice you have to tell me what sample you work with and how is your sample prepared for IEF AP From owner-proteins@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsfeed.internetmci.com!166.93.8.12!natasha.rmii.com!news.qadas.com!not-for-mail From: johnp@qadas.com (John Pawlowski) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: SDS-PAGE gel-shift to look at protein phosphorylation Date: Tue, 13 Jan 1998 10:02:48 -0700 Organization: QADAS Online Lines: 15 Message-ID: NNTP-Posting-Host: net92.qadas.com X-Newsreader: MicroPlanet Gravity v1.01 Xref: biosci bionet.molbio.methds-reagnts:64115 bionet.molbio.proteins:12115 Hi all, I'm currently looking at the phosphorylation state of a protein by SDS_PAGE gel shift analysis. The protein is about 46 kDa and a noticible shift is seen using 8% polyacrylamide, 1.5 mm gel, approx 15 cm long. Unfortunately the sample is very near the bottom of the gel. I would like to increase the resolution of the gel-shift. Using 6 or 7% gels does not allow good separation of the protein from the dye front. Someone has suggested to me that I try running the sample longer using an 8% gel in a DNA sequencing gel apparatus (0.2 or 0.4 mm thick). Any thoughts on whether or not this approach would work or have any other ideas? ie. playing with the pH of the resolving gel, concentrations of cross- linkers? Any advice will be greatly appreciated. Thanks in advance. John Pawlowski johnp@qadas.com From owner-proteins@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsfeed.internetmci.com!152.163.199.19!portc03.blue.aol.com!audrey01.news.aol.com!not-for-mail From: squick2653@aol.com (SQuick2653) Newsgroups: bionet.molbio.proteins Subject: J.D. Hanawalt Powder Diffraction Award Nominations Date: 13 Jan 1998 14:09:31 GMT Lines: 20 Message-ID: <19980113140900.JAA04595@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com International Centre for Diffraction Data - www.icdd.com J.D. Hanawalt Powder Diffraction Award Nominations The International Centre for Diffraction Data is seeking nominees for the 1998 J.D. Hanawalt Powder Diffraction Award. The award is presented every three years for an important, recent contribution to the field of powder diffraction. The award consists of a citation and a cash gift of $1,000. The award recipient is expected to submit an abstract and present a paper on the work being recognized at an appropriate Powder Diffraction / Crystallographic Meeting. Recipient's travel expenses to the meeting will be provided. Work eligible for consideration must have been published after 1 January 1990. The selection committee welcomes suggestions, nominations, and documentation of accomplishments for possible recipients through 15 February 1998. Contact: Camden R. Hubbard - hubbardcr@ornl.gov Chairman Hanawalt Award Selection Committee c/o International Centre for Diffraction Data 12 Campus Boulevard Newtown Square, PA 19073-3273, U.S.A. From owner-proteins@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!newsfeed.eerie.fr!jussieu.fr!univ-lille1.fr!not-for-mail From: "eqpcmv@univ-lille1.fr" Newsgroups: bionet.molbio.proteins Subject: vertical electrophoresis unit Date: Tue, 13 Jan 1998 10:03:23 +0100 Organization: université des sciences et techniques de lille Lines: 5 Message-ID: <34BB2DD9.6545@univ-lille1.fr> NNTP-Posting-Host: phyvmac2.univ-lille1.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Millipore has such an unit in his catalog : investigator 2-D electrophoresis system http://millipore.com eric From owner-proteins@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.proteins Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 13 Jan 1998 02:00:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199801131000.CAA17257@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-proteins@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.internetmci.com!209.95.128.196!news-nyc.telia.net!masternews.telia.net!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!130.239.8.18.MISMATCH!umdac!umu.se!not-for-mail From: Adrian Clarke Newsgroups: bionet.molbio.proteins Subject: post-doctoral position Date: Wed, 14 Jan 1998 14:30:08 +0100 Organization: UMDAC Lines: 39 Message-ID: <34BCBDE0.52A5AB2E@plantphys.umu.se> NNTP-Posting-Host: adrian.fysbot.umu.se Mime-Version: 1.0 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (Win95; I) POST-DOCTORAL POSITION IN BIOCHEMISTRY / MOLECULAR BIOLOGY

Applications are invited for a two-year post-doctoral position available

immediately at the Department of Plant Physiology, University of Umeå,
Sweden.

The successful applicant will join an active research group
studying a new family of molecular chaperones and proteases in plants
and cyanobacteria. Of particular interest to the group is the role of
these proteins in regulating chloroplast protein structure and function,

and their importance for tolerance to different environmental stress
conditions (for more information, see groups homepage referred to at:
www.plantphys.umu.se/research.shtml). Applicants must have a PhD in
biochemistry, molecular biology or related field. Experience with
protein purification and enzymology would be an advantage.

Applications with Curriculum vitae should be sent before March 13 to:
Adrian Clarke, Department of Plant Physiology, University of Umeå, S-901

87 Umeå, Sweden. Fax: +46 90 786 6676. e-mail:
Adrian.Clarke@plantphys.umu.se

--

Dr. Adrian K. Clarke
Associate Professor
Department of Plant Physiology
University of Umeå
Umeå S-901 87
Sweden
Tel: +46 90 7865209
Fax: +46 90 7866676
  From owner-proteins@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!agate!nntp.flash.net!news.algonet.se!newsfeed1.telenordia.se!newsfeed1.funet.fi!news.funet.fi!ousrvr3.oulu.fi!sun1.oulu.fi!pkursula From: Pete Newsgroups: bionet.molbio.proteins Subject: Zn precipitation of proteins Date: Wed, 14 Jan 1998 12:54:16 +0200 Organization: University of Oulu Lines: 20 Message-ID: NNTP-Posting-Host: sun1.oulu.fi Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: pkursula@sun1.oulu.fi Does anyone know any specific protein complexes that are precipitated from tissue homogenates by the addition of 1 mM Zn chloride. I get a huge precipitate when I add more than 0.1 mM Zn chloride that seems to contain specific proteins. If I only had a clue what these proteins could be... |) |/ |etri |\ursula ------------------------------------------------- "I am somehow less interested in the weight and convolutions of Einstein's brain than in the near certainty that people of equal talent have lived and died in cotton fields and sweatshops." -- Stephen Jay Gould ------------------------------------------------- From owner-proteins@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.internetmci.com!192.87.106.104!surfnet.nl!newshost.vu.nl!not-for-mail From: Marisol Rodriguez Pena Newsgroups: bionet.molbio.proteins Subject: Phosphorilation Date: Wed, 14 Jan 1998 13:36:25 +0000 Organization: Vrije Universiteit, Amsterdam, The Netherlands Lines: 18 Message-ID: <34BCBF59.4B0E@chem.vu.nl> NNTP-Posting-Host: macdyn160.chem.vu.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; 68K) Hellow everybody! I am looking for help regarding phosphorylation of proteins (I am very interested in GPCR) using P33 insteat P32. Any clue about it? Greatings Marisol -- MS Rodriguez Pena, MD, phD Department of Pharmacochemistry, Faculteit der Scheikunde Vrije Universiteit. De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands Tel: 31-20-4447572 Fax: 31-20-4447610 From owner-proteins@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!newsfeed.internetmci.com!158.111.3.26!cdc4.cdc.gov!jmc4@cdc.gov From: bkd1@cdc.gov(Barun De) Newsgroups: bionet.molbio.proteins Subject: globomycin Date: 14 Jan 1998 13:49:04 GMT Organization: CDC, Atlanta, GA, USA Lines: 6 Message-ID: <69ifog$28m2@cdc4.cdc.gov> NNTP-Posting-Host: 158.111.204.71 Dear Friends: I am looking for globomycin(a product of Sanko Corp., Japan).This antibiotic is generally used to study the effects of lipid incorporation into bacterial cells. Please let me know if it is available in the market. I would like to have some for my study. I would greatly appreciate your help in this matter. Thanks, Barun X-Newsreader: WinVN 0.90.5 From owner-proteins@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Jaap Heringa Newsgroups: bionet.molbio.proteins Subject: PhD Studentship Available at NIMR, London Date: Wed, 14 Jan 1998 15:47:46 +0000 Organization: MRC Lines: 42 Message-ID: <34BCDE22.61FD43DF@nimr.mrc.ac.uk> NNTP-Posting-Host: serine.nimr.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 6.2 IP22) A three-year Predoctoral MRC-funded Fellowship is available to UK-Citizens in the Division of Mathematical Biology, National Institute for Medical Research (NIMR), Mill Hill, London. Head of the Division is Dr Willie Taylor. The following is a short outline of the project: PROTEIN STRUCTURAL DOMAINS AND REPEATS; ANALYSIS AND PREDICTION FROM SEQUENCE INFORMATION ALONE The recognition of domains in protein structures is an important prerequisite for areas in protein science such as NMR-based structural elucidation and fold recognition. A number of empirical observations render domain prediction from only sequence information feasible, e.g., (i) domain interfaces show a.a. compositions intermediate to those of core and surface regions, (ii) domain linker regions display distinct compositions and (iii) domains in many proteins are (distant) repeats of a same basic sequence stretch. The project will embark on analysing existing databanks of protein domains and use the information to devise sequence profiles against which query sequences can be matched: A newly developed sensitive protein segment detection method SEGS by Willie Taylor will be of great use at this stage. Of help also will be the sensitive repeat detection method REPRO (see Heringa & Taylor, Curr. Opin. Struct. Biol. 7:416-421, 1997). All above information will be implemented in a computer method aimed at delineating domain boundaries in protein sequences. For more information, contact Dr Jaap Heringa Division of Mathematical Biology National Institute for Medical Research (NIMR) The Ridgeway, Mill Hill, London NW7 1AA, U.K. Tel.: +44 181 959 3666 ext. 2293 Fax : +44 181 913 8545 Email: jaap.heringa@nimr.mrc.ac.uk WWW : http://mathbio.nimr.mrc.ac.uk From owner-proteins@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!agate!arclight.uoregon.edu!leto.ou.edu!news.ou.edu!not-for-mail From: Bob Steinberg Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: SDS-PAGE gel-shift to look at protein phosphorylation Date: Wed, 14 Jan 1998 12:14:40 -0800 Organization: University of Oklahoma Health Sciences Center Lines: 23 Message-ID: <34BD1CB0.384A@etowah.ouhsc.edu> References: Reply-To: rsteinbe@etowah.ouhsc.edu NNTP-Posting-Host: 157.142.56.147 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win16; I) To: John Pawlowski Xref: biosci bionet.molbio.methds-reagnts:64155 bionet.molbio.proteins:12123 John Pawlowski wrote: > > Hi all, > I'm currently looking at the phosphorylation state of a protein by > SDS_PAGE gel shift analysis. The protein is about 46 kDa and a noticible > shift is seen using 8% polyacrylamide, 1.5 mm gel, approx 15 cm long. > Unfortunately the sample is very near the bottom of the gel. I would like > to increase the resolution of the gel-shift. Using 6 or 7% gels does not > allow good separation of the protein from the dye front. Someone has > suggested to me that I try running the sample longer using an 8% gel in a > DNA sequencing gel apparatus (0.2 or 0.4 mm thick). Any thoughts on > whether or not this approach would work or have any other ideas? ie. > playing with the pH of the resolving gel, concentrations of cross- > linkers? Any advice will be greatly appreciated. Thanks in advance. > > John Pawlowski > johnp@qadas.com In my experience, the most important variable is pH of the lower gel-- we generally make a series of gels with lower gel buffer pH varying by about 0.05 pH units between 8.6 and 8.9. Good luck. Bob From owner-proteins@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!news-zh.switch.ch!news.belwue.de!newsserv.zdv.uni-tuebingen.de!not-for-mail From: Nicole Rapior Newsgroups: bionet.molbio.proteins Subject: Re: Zn precipitation of proteins Date: Wed, 14 Jan 1998 15:36:53 -0800 Organization: University of Tuebingen Lines: 29 Message-ID: <34BD4C15.6C96@uni-tuebingen.de> References: Reply-To: cbiei01@uni-tuebingen.de NNTP-Posting-Host: eis2.pci.chemie.uni-tuebingen.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.01Gold (Win16; I) Pete wrote: > > Does anyone know any specific protein complexes that are precipitated > from tissue homogenates by the addition of 1 mM Zn chloride. > > I get a huge precipitate when I add more than 0.1 mM Zn chloride that > seems to contain specific proteins. If I only had a clue what these > proteins could be... > Hi Pete, as you didn't mentioned any other conditions, is it possible that you use a phosphate-buffer? I don't want to insult, you but a lot of people forget that zinc phosphate isn't very soluable! It might be the reason for your precipitate. Bye Nicole -- Nicole Rapior Physiol. Chem. Institut Hoppe-Seyler-Str. 4 D-72076 Tübingen phone: 07071-297-3353 fax: 07071-29-3361 email: cbiei01@uni-tuebingen.de From owner-proteins@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!BOTANY.UQ.EDU.AU!J.Marcus From: J.Marcus@BOTANY.UQ.EDU.AU ("Marcus, Dr J.") Newsgroups: bionet.molbio.proteins Subject: Re: problems during protein expression Date: 14 Jan 1998 22:52:54 -0800 Organization: Dept of Botany, Univ of Queensland Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <2B986E1D73@botany.uq.edu.au> References: <34BD447E.24D0@upei.ca> Reply-To: Marcus@tpp.uq.edu.au NNTP-Posting-Host: net.bio.net Hi Jennifer, You may not have the same bacteria that you started with. Do they smell normal? It is quite easy to tansform other contaminating bacteria; I've done it my self in grad. student days. That would explain the funny color and the less than optimal expression. Try some fresh bacterial stocks. All the best > Hi! My name is Jennifer Morrison. I am a MSc student here at UPEI, and > I was wondering if any of you could help me with a problem I've been > experiencing. In our lab, we have been expressing a de novo protein in > bacterial cells and have had no problems in the past. Lately, our cells > have been gray-black in color when harvested and the protein hasn't > shown up very well, if at all, on gel. If you have any suggestions as > to what our problem may be, or what we could do to fix this problem, > please e-mail me at jmorrison@upei.ca > > Thank you very much! > > _________________________________________________________ John Marcus Marcus@tpp.uq.edu.au (Dr J.Marcus) Cooperative Research Centre for Tropical Plant Pathology 5th Level John Hines Building University of Queensland St. Lucia, QLD 4072 AUSTRALIA Fax: 61-7-3365-4771 Phone: 61-7-3365-4764 From owner-proteins@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!europa.clark.net!192.174.65.44!newscore.univie.ac.at!03-newsfeed.univie.ac.at!news.univie.ac.at!not-for-mail From: a8803349@unet.univie.ac.at (Martin Offterdinger) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: SDS-PAGE gel-shift to look at protein phosphorylation Date: Thu, 15 Jan 1998 08:20:52 GMT Organization: AKH Lines: 31 Message-ID: <34bdc647.542878@news.univie.ac.at> References: <34BD1CB0.384A@etowah.ouhsc.edu> NNTP-Posting-Host: grunt.imed1.akh-wien.ac.at X-Newsreader: Forte Free Agent 1.1/16.230 Xref: biosci bionet.molbio.methds-reagnts:64183 bionet.molbio.proteins:12127 On Wed, 14 Jan 1998 12:14:40 -0800, Bob Steinberg wrote: >John Pawlowski wrote: >> >> Hi all, >> I'm currently looking at the phosphorylation state of a protein by >> SDS_PAGE gel shift analysis. The protein is about 46 kDa and a noticible >> shift is seen using 8% polyacrylamide, 1.5 mm gel, approx 15 cm long. >> Unfortunately the sample is very near the bottom of the gel. I would like >> to increase the resolution of the gel-shift. Using 6 or 7% gels does not >> allow good separation of the protein from the dye front. Someone has >> suggested to me that I try running the sample longer using an 8% gel in a >> DNA sequencing gel apparatus (0.2 or 0.4 mm thick). Any thoughts on >> whether or not this approach would work or have any other ideas? ie. >> playing with the pH of the resolving gel, concentrations of cross- >> linkers? Any advice will be greatly appreciated. Thanks in advance. >> >> John Pawlowski >> johnp@qadas.com > >In my experience, the most important variable is pH of the lower gel-- >we generally make a series of gels with lower gel buffer pH varying by >about 0.05 pH units between 8.6 and 8.9. Good luck. > >Bob I woulg suggest to use higher AA percentages to increase resolution(10-12%). A prestained protein marker would also be of help to avoid running out of your sample of interest. With 6-7 % or even 8% gels, the resolution in your MW range is quite limited! martin From owner-proteins@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!194.162.162.196!newsfeed.nacamar.de!uni-erlangen.de!newsfeed1.telenordia.se!newsfeed1.funet.fi!news.funet.fi!ousrvr3.oulu.fi!sun1.oulu.fi!pkursula From: Pete Newsgroups: bionet.molbio.proteins Subject: Re: Zn precipitation of proteins Date: Thu, 15 Jan 1998 08:49:47 +0200 Organization: University of Oulu Lines: 27 Message-ID: References: <34BD4C15.6C96@uni-tuebingen.de> NNTP-Posting-Host: sun1.oulu.fi Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: pkursula@sun1.oulu.fi In-Reply-To: <34BD4C15.6C96@uni-tuebingen.de> On Wed, 14 Jan 1998, Nicole Rapior wrote: > Pete wrote: > > > > Does anyone know any specific protein complexes that are precipitated > > from tissue homogenates by the addition of 1 mM Zn chloride. > > > > I get a huge precipitate when I add more than 0.1 mM Zn chloride that > > seems to contain specific proteins. If I only had a clue what these > > proteins could be... > > > > Hi Pete, > > as you didn't mentioned any other conditions, is it possible that > you use a phosphate-buffer? I don't want to insult, you but a lot of > people forget that zinc phosphate isn't very soluable! It might be the > reason for your precipitate. > > Bye Nicole > They are proteins, very specific ones. This HAS been checked by SDS PAGE. They precipitate when Zn is increased. No phosphate is present, but other conditions I won't reveal :) No there's nothing special there, and it happens in different buffer systems, too. From owner-proteins@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!128.223.220.30!logbridge.uoregon.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!csn!nntp-xfer-1.csn.net!news.acsu.buffalo.edu!srv1.drenet.dnd.ca!crc-news.doc.ca!nott!torn!garnet.nbnet.nb.ca!news.unb.ca!upei.ca!usenet From: Jennifer Newsgroups: bionet.molbio.proteins Subject: problems during protein expression Date: Wed, 14 Jan 1998 18:04:30 -0500 Organization: University of Prince Edward Island, Charlottetown, PEI Canada Lines: 10 Message-ID: <34BD447E.24D0@upei.ca> Reply-To: jmorrison@upei.ca NNTP-Posting-Host: pc007.irving.upei.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Hi! My name is Jennifer Morrison. I am a MSc student here at UPEI, and I was wondering if any of you could help me with a problem I've been experiencing. In our lab, we have been expressing a de novo protein in bacterial cells and have had no problems in the past. Lately, our cells have been gray-black in color when harvested and the protein hasn't shown up very well, if at all, on gel. If you have any suggestions as to what our problem may be, or what we could do to fix this problem, please e-mail me at jmorrison@upei.ca Thank you very much! From owner-proteins@net.bio.net Wed Jan 14 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!feed1.news.luth.se!luth.se!Cabal.CESspool!bofh.vszbr.cz!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!news.nott.ac.uk!Fergus.Doherty From: Fergus.Doherty@nottingham.ac.uk (Fergus Doherty) Newsgroups: bionet.molbio.proteins Subject: PI-linked proteins soluble in acetone? Date: Thu, 15 Jan 1998 12:41:29 +0000 Organization: Nottingham University Lines: 9 Message-ID: NNTP-Posting-Host: wmbpm8.nottingham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 Does anyone know if PI-linked proteins may be soluble in acetone or other organic solvents? -- Fergus Doherty, Nottingham University, Fergus.Doherty@nottingham.ac.uk 0115 970 9366 (74-41366 internal) From owner-proteins@net.bio.net Wed Jan 14 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!204.186.0.134!ptdnetP!newsgate.ptd.net!fastnet!uunet!in1.uu.net!hearst.acc.Virginia.EDU!murdoch.acc.Virginia.EDU!avery.med.Virginia.EDU!jw4n From: jw4n@avery.med.Virginia.EDU (JW) Newsgroups: bionet.molbio.proteins Subject: postdoc for phosphatase research Date: 15 Jan 1998 15:53:50 GMT Organization: uva Lines: 12 Message-ID: <69lbee$p9b$1@murdoch.acc.Virginia.EDU> NNTP-Posting-Host: avery.med.virginia.edu A postdoc needed for protein phosphatase research in Dr. David L. Brautigan's lab (Center for Cell Signaling, University of Virginia Medical Center). Will start as soon as possible for NIH granted project (see JBC 272:32308, 1997). If interested, please send e-mail to Dr. Brautigan at db8g@virginia.edu. Please don't respond to this message. -- Jun Wu Markey Center for Cell Signaling University of Virginia Medical Center Box 577 HSC From owner-proteins@net.bio.net Wed Jan 14 22:00:00 1998 Path: biosci!agate!ihnp4.ucsd.edu!sdd.hp.com!usc!howland.erols.net!newsfeed.direct.ca!Supernews60!supernews.com!uunet!in4.uu.net!news.anet-chi.com!not-for-mail From: toddc-NoSpAm@NoSpAm-anet-dfw.com (Todd C.) Newsgroups: bionet.molbio.proteins Subject: PEDANT ? Date: Thu, 15 Jan 1998 22:21:55 GMT Organization: ANET Internet Services Lines: 6 Message-ID: <34be8b8e.106603793@news.anet-dfw.com> Reply-To: toddc-NoSpAm@NoSpAm-anet-dfw.com NNTP-Posting-Host: 206.103.93.55 X-Newsreader: Forte Free Agent 1.1/32.230 Does anyome know what happened to PEDANT. Is it no longer publicly accessable? http://pedant.mips.biochem.mpg.de/frishman/pedant.html From owner-proteins@net.bio.net Wed Jan 14 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news1.chicago.iagnet.net!iagnet.net!news-xfer.netaxs.com!fastnet!uunet!in4.uu.net!munnari.OZ.AU!bunyip.cc.uq.edu.au!inet6.citec.com.au!news From: Alison Leakey Newsgroups: bionet.molbio.proteins Subject: peptide binding to plates&/or membranes Date: Fri, 16 Jan 1998 12:41:19 +1000 Organization: North Queensland Clinical School Lab Lines: 14 Message-ID: <34BEC8CE.783C@citec.qld.gov.au> Reply-To: clinsch@citec.qld.gov.au NNTP-Posting-Host: 203.5.10.10 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; 68K) Hi. Does anyone know how to bind peptides to plates and or nitrocellulose membranes for use in ELISA or westerns???? I have used my peptide coupled to a carrier to check by ELISA that my antiserum has worked, however, for my purpose I require that the peptide bind in the uncoupled form. Any suggestions?????? Alison Leakey North Queensland Clinical School Laboratory From owner-proteins@net.bio.net Wed Jan 14 22:00:00 1998 From: "Grizou" Subject: assimilation of proteins Newsgroups: bionet.molbio.proteins Message-ID: <01bd2209$7bd5c860$cf64eccd@daniel> X-Newsreader: Microsoft Internet News 4.70.1155 NNTP-Posting-Host: 205.236.100.207 Date: 15 Jan 98 23:01:01 GMT Organization: TotalNet Inc. Lines: 3 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!204.59.152.222!news-peer.gip.net!news.gsl.net!gip.net!sunqbc.risq.qc.ca!news.total.net!205.236.100.207 how many grams of protiens can the human body assimilate? thank you in advance for your time From owner-proteins@net.bio.net Wed Jan 14 22:00:00 1998 Newsgroups: bionet.molbio.proteins Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!128.230.129.106!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!news.lattis.xara.net!uknet!yama.mcc.ac.uk!liv!news From: gerald Subject: Re: Zn precipitation of proteins Content-Type: text/plain; charset=us-ascii Message-ID: <34BE4ACD.611E@orac.sund.ac.uk> Sender: news@liverpool.ac.uk (News System) NNTP-Posting-Host: pc028010.med.liv.ac.uk Reply-To: hs0lbe@orac.sund.ac.uk Content-Transfer-Encoding: 7bit Organization: The University of Liverpool References: Mime-Version: 1.0 Date: Thu, 15 Jan 1998 17:43:42 GMT X-Mailer: Mozilla 3.02C-PGMNS (Win16; I) Lines: 43 Pete wrote: > > Does anyone know any specific protein complexes that are precipitated > from tissue homogenates by the addition of 1 mM Zn chloride. > > I get a huge precipitate when I add more than 0.1 mM Zn chloride that > seems to contain specific proteins. If I only had a clue what these > proteins could be... > > |) |/ > |etri |\ursula > Well I guess the exact identity could depend upon the tissue that sample was derived from. However, since one of the most common, and strongest, Zn2+ coordinating amino acid residues is His, followed by Glu, what ever they are, they are likely to contain significant amounts of these amino acids with an appropriate geometry for Zn2+ coordination. There are a number of Zn2+ proteins in tissue, Zn2+ being a common metal centre in metalloenzymes. It is also, obviously from their name, directly connected with the DNA associated proteins - zinc-finger proteins, which would clearly occur in almost what ever tissue you were using. A large No of proteins, say albumins, can also exhibit non-specific binding of metal ions such as Cu2+ and probably Zn2+ as well. pH can enhance this effect, ie. higher pH leads to more metal coordination. However your metal concentration [0.1mM] unless your working at pH>8 would not be expected to produce the dramatic effect you describe through these nonspecific associations. So the best idea on how to identify them would be isolate the ppt protein, resuspended them in an EDTA buffer, dialyse out the Zn2+, seperate them out on the SDS-PAGE and get sequencing. Regards, Len -- Dr Len Bell, University of Liverpool. email: lgbell@liv.ac.uk From owner-proteins@net.bio.net Thu Jan 15 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!peerfeed.ncal.verio.net!nntp2.cerf.net!moon.pepperdine.edu!usenet From: zhuqi Newsgroups: bionet.molbio.proteins Subject: help needed Date: Fri, 16 Jan 1998 16:37:25 +0800 Organization: Pepperdine University Lines: 15 Message-ID: <34BF1C45.82A12D65@hunnu.edu.cn> NNTP-Posting-Host: 202.197.120.112 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (Win95; I) Dear sir: I am Grad-student in protein chemistry in mainland of China.I find your address in Bionet.I have a Question :how to get nAch Receptor with cell membrane from muscle & brain of mouse?I want to get it for binding with 125I- labeled neuropeptides. I have already try some methods,but I can not get it .Do you have some better methods?Would you mind tell me about this? Certainlly,this will take you much time,so If you cann't afford ,It will be also OK. Thanks in advance. Sincerely yours: Zhu,Qi From owner-proteins@net.bio.net Thu Jan 15 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!131.103.1.116!news2.chicago.iagnet.net!iagnet.net!144.92.88.12!newsspool.doit.wisc.edu!news.doit.wisc.edu!not-for-mail From: mmentzer@students.wisc.edu (Markus Mentzer) Newsgroups: bionet.molbio.proteins Subject: Protein Ligation Date: 16 Jan 1998 20:32:01 GMT Organization: UW-Madison Lines: 12 Message-ID: <69og41$nqi$1@news.doit.wisc.edu> NNTP-Posting-Host: gjr.anatomy.wisc.edu X-Newsreader: WinVN 0.99.5 I've been trying to find methods of ligating strands of proteins to one another. Specifically, I have been trying to find ways to ligate a small piece of synthetic protein into a natural strand. So far I have found very little on this subject considering the fact that the implications of this technique are tremendous. I was wondering if anyone out there had any ideas for help on this subject. I would greatly appreciate ANY suggestions. Please email me at mmentzer@facstaff.wisc.edu. Thanks for all of your help! Sincerely, Markus From owner-proteins@net.bio.net Thu Jan 15 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news-backup-west.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!128.218.1.200!itssrv1.ucsf.edu!itsa!thorn From: thorn@itsa.ucsf.edu (Kurt Thorn) Newsgroups: bionet.molbio.proteins Subject: Re: Zn precipitation of proteins Date: 16 Jan 1998 00:33:41 GMT Organization: ITS, University of California, San Francisco Lines: 27 Message-ID: <69m9t5$q9i@itssrv1.ucsf.edu> References: <34BE4ACD.611E@orac.sund.ac.uk> NNTP-Posting-Host: itsa.ucsf.edu In article <34BE4ACD.611E@orac.sund.ac.uk>, gerald wrote: >Pete wrote: >> >> Does anyone know any specific protein complexes that are precipitated >> from tissue homogenates by the addition of 1 mM Zn chloride. >> >> I get a huge precipitate when I add more than 0.1 mM Zn chloride that >> seems to contain specific proteins. If I only had a clue what these >> proteins could be... >> Just a wild guess, but could it be tubulin? I know tubulin forms zinc sheets at around that zinc concentration, and that they will precipitate rather nicely. Kurt ------------------------------------------------------------------------------- Kurt Thorn - thorn@itsa.ucsf.edu - http://motorhead.ucsf.edu/~thorn ------------------------------------------------------------------------------- "The universe we observe has precisely the properties we should expect if there is at bottom not design, no purpose, no evil and no good, nothing but pointless indifference." -- Richard Dawkins From owner-proteins@net.bio.net Thu Jan 15 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!uunet!in3.uu.net!xmission!news.cc.utah.edu!news.cs.utah.edu!cc.usu.edu!nntp Newsgroups: bionet.molbio.proteins Subject: Protein Purification Workshop Message-ID: <34BFE86B.10BF@cscfs1.usu.edu> From: Pamela Ginn Date: Fri, 16 Jan 1998 15:08:27 -0800 Organization: Utah State University NNTP-Posting-Host: pam.biotec.usu.edu X-Mailer: Mozilla 2.0 (Win95; I) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Lines: 20 UtahState UNIVERSITY BIOTECHNOLOGY CENTER Biotechnology Workshops that integrate theory with hands-on laboratory projects PROTEIN PURIFICATION Isolation and Characterization FEBRUARY 25 - 27, 1998 Participants will learn to create purification plans and use them to isolate and characterize proteins. For more information please accesss our web site: http://www.usu.edu/~biotech/main.html or contact: Birgit Hertel-Wulff, Workshop Coordinator Telephone: 435-797-0671 · Fax: 435-797-2766 E-mail: bhw@cscfs1.usu.edu From owner-proteins@net.bio.net Thu Jan 15 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-backup-west.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!209.90.0.8!alpha.sky.net!news From: Brian Hollander Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: SDS-PAGE gel-shift to look at protein phosphorylation Date: Fri, 16 Jan 1998 18:09:41 -0600 Organization: SkyNET Corporation Lines: 38 Message-ID: <34BFF6C5.281F99C1@sky.net> References: <34BD1CB0.384A@etowah.ouhsc.edu> <34bdc647.542878@news.univie.ac.at> NNTP-Posting-Host: ts-2-ip30.kc.sky.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (Win95; I) Xref: biosci bionet.molbio.methds-reagnts:64251 bionet.molbio.proteins:12137 My suggestion would be to vary the crosslinker concentration. With "long" gels, as opposed to mini-gels, I have achieved very good resolution of proteins just slightly larger than those you mentioned using 10%T/0.8%C gels. Martin Offterdinger wrote: > > On Wed, 14 Jan 1998 12:14:40 -0800, Bob Steinberg > wrote: > > >John Pawlowski wrote: > >> > >> Hi all, > >> I'm currently looking at the phosphorylation state of a protein by > >> SDS_PAGE gel shift analysis. The protein is about 46 kDa and a noticible > >> shift is seen using 8% polyacrylamide, 1.5 mm gel, approx 15 cm long. > >> Unfortunately the sample is very near the bottom of the gel. I would like > >> to increase the resolution of the gel-shift. Using 6 or 7% gels does not > >> allow good separation of the protein from the dye front. Someone has > >> suggested to me that I try running the sample longer using an 8% gel in a > >> DNA sequencing gel apparatus (0.2 or 0.4 mm thick). Any thoughts on > >> whether or not this approach would work or have any other ideas? ie. > >> playing with the pH of the resolving gel, concentrations of cross- > >> linkers? Any advice will be greatly appreciated. Thanks in advance. > >> > >> John Pawlowski > >> johnp@qadas.com > > > >In my experience, the most important variable is pH of the lower gel-- > >we generally make a series of gels with lower gel buffer pH varying by > >about 0.05 pH units between 8.6 and 8.9. Good luck. > > > >Bob > I woulg suggest to use higher AA percentages to increase > resolution(10-12%). A prestained protein marker would also be of help > to avoid running out of your sample of interest. With 6-7 % or even 8% > gels, the resolution in your MW range is quite limited! > martin From owner-proteins@net.bio.net Fri Jan 16 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.gip.net!news-penn.gip.net!news.gsl.net!gip.net!uwm.edu!news.cse.psu.edu!news.ems.psu.edu!news3.cac.psu.edu!usenet From: msh4@psu.edu (Peggy Halleck) Newsgroups: bionet.molbio.proteins Subject: CA 27.29 antigen Date: Thu, 15 Jan 1998 23:00:57 GMT Organization: BMB Dept. PSU Lines: 5 Message-ID: <34be94a4.31405990@news.psu.edu> Reply-To: msh4@psu.edu NNTP-Posting-Host: stjovite.bmb.psu.edu X-Authinfo-User: msh4@psu.edu X-Newsreader: Forte Free Agent 1.11/32.235 Does anyone have any idea what the half-life of the CA 27.29 antigen is in the bloodstream? Peggy Halleck msh4@psu.edu BMB Penn State University From owner-proteins@net.bio.net Sun Jan 18 22:00:00 1998 Path: biosci!LISTSERV.STARWAVE.COM!espn-sportszone From: espn-sportszone@LISTSERV.STARWAVE.COM (ESPN SportsZone) Newsgroups: bionet.molbio.proteins Subject: ESPN SportsZone Covers Super Bowl XXXII! Date: 19 Jan 1998 21:49:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 53 Sender: daemon@net.bio.net Distribution: world Message-ID: <3.0.32.19980119204818.00917d40@listserv-bc.starwave.com> Reply-To: espn-sportszone@LISTSERV.STARWAVE.COM NNTP-Posting-Host: net.bio.net Dear SportsZone User - You know ESPN SportsZone is all over Super Bowl XXXII! We’re already providing you the best coverage you'll find anywhere! Come with us and we’ll show you what’s going on inside the hype in San Diego.... 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