From owner-proteins@net.bio.net Sat Nov 01 22:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!193.174.75.126!news-was.dfn.de!news-fra1.dfn.de!news-koe1.dfn.de!news.ruhr-uni-bochum.de!not-for-mail From: Marc Saric Newsgroups: bionet.molbio.proteins Subject: Re: Proteins in Alzheimer's Date: Sun, 02 Nov 1997 14:48:17 +0100 Organization: Ruhr-University of Bochum Lines: 25 Message-ID: <345C84A1.67AC82A9@rz.ruhr-uni-bochum.de> References: <971027004622_-90914345@mrin44.mail.aol.com> Reply-To: Marc.Saric@rz.ruhr-uni-bochum.de NNTP-Posting-Host: dialppp-1-88.rz.ruhr-uni-bochum.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.03 [en] (Win95; I) To: NewNovels@aol.com NewNovels@aol.com wrote: > > A few years ago in my graduate class in Advances in Neurobiology and > Behavior, One of my classmates reported a paper in Alzheimer's disease. I > could not recall the exact problem in that paper but i remembered i made a > conclusion which is this: > "A change in the secondary/tertiary structure of a protein would > attract/require a different reactant/enzyme(s) thus producing > (directly/indirectly) the so called plaques". > I never followed this up but sometimes i am just bothered about this, and i > want it cleared. Was the mutation in the genetic or the protein level? I think this is still unclear. For BSE and CJD the "prion-hypothesis" suggests a change on the protein-level. Despite the fact that Stanley Prusiner got the Nobel-prize for this hypothesis, it hasn´t been proved to full extent until now. -- Bye, Marc Saric Visit http://www.rat.de/marc_saric/ From owner-proteins@net.bio.net Sun Nov 02 22:00:00 1997 Path: biosci!PUBMS.PKU.EDU.CN!liuying From: liuying@PUBMS.PKU.EDU.CN Newsgroups: bionet.molbio.proteins Subject: Re: Biorad Protein Standards migrating Date: 3 Nov 1997 05:00:56 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <63ctkr$d8k@singer.cent.gla.ac.uk> NNTP-Posting-Host: net.bio.net I think the degrade of the marker is the answer.Try a new marker. Ying Liu On 31 Oct 1997, Obaid Yusuf Khan wrote: > I am using the Biorad Kaleidoscope Prestained Standards to size my proteins > on a 12% PAGE gel ("29:1). The markers below 31800 KD are very faint and > fuzzy and I am unable to see the 17800 and 7100 KD markers. > I am using the markers without any heat denaturing (I presume they dont require > it). > Does any one have any tips to offer me on this please. > Thanks > Obaid Khan > > > From owner-proteins@net.bio.net Sun Nov 02 22:00:00 1997 Path: biosci!rutgers!uwm.edu!news.he.net!news-peer.gip.net!news.gsl.net!gip.net!news.maxwell.syr.edu!eerie.fr!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!drm21 From: drm21@mole.bio.cam.ac.uk (David Micklem) Newsgroups: bionet.molbio.proteins Subject: Domains with more than one function Date: Mon, 03 Nov 1997 21:10:59 +0000 Organization: Wellcome/CRC Institute Lines: 30 Message-ID: NNTP-Posting-Host: drm-mac1.welc.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.0 Hi, I was hoping to tap the collected wisdom to find out if there are published examples of different members of a family of domains having different functions. A not-quite-perfect example would be the finding (IIRC) that some homeodomains bind to other proteins through one 'face' of the domain, and to DNA with another 'face'. Ideally, I'm looking for examples of a motif (or domain) which has a well characterised function (eg Zn-fingers and DNA binding) in most proteins, but which has been shown to have another function (eg protein-protein interaction) in other proteins. (I used the Zn-finger example because I vaguely recall hearing that this was true of Zn-fingers - but I haven't been able to track down a reference!) Many thanks for any assistance (and no, I'm not an student trying to cheat on exam/essay questions!) David -- D.R.Micklem, Time flies like an arrow... Wellcome/CRC Institute, Fruit flies like a banana. Cambridge CB2 1QR, UK Email:drm21@mole.bio.cam.ac.uk Unsolicited mail will incur a US$100 processing charge. From owner-proteins@net.bio.net Sun Nov 02 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!news.idt.net!dispose.news.demon.net!demon!diablo.theplanet.net!svr-c-01.core.theplanet.net!not-for-mail From: "Andrew Pridmore" Newsgroups: bionet.molbio.proteins Subject: 2D electrophoresis headache! Date: Mon, 3 Nov 1997 22:10:43 -0000 Organization: [not set] Message-ID: <63li7v$aqs$2@svr-c-02.core.theplanet.net> NNTP-Posting-Host: modem54.c2r4.pol.co.uk X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Lines: 15 I have been attempting obtain whole-cell protein profiles of the oral anaerobe Porphyromonas gingivalis using two-dimensional electrophoresis, basically according to the method of O'Farrell (1975). I get clear bands in the first dimension (isoelectric focussing in tube gels) but these proteins fail to transfer into the second dimension slab gel. I have varied the concentration of SDS, pH and incubation time in the second dimension buffer, and ensured good contact between the two gels. None of these variables produce an improvement. 2D electrophoresis is not known for being straightforward, but does anyone have any experience of these problems and any suggestions for improving my results? From owner-proteins@net.bio.net Sun Nov 02 22:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.ox.ac.uk!ocms0001 From: ocms0001@ermine.ox.ac.uk (Dennis Benjamin) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: Activity restored by mixing recombinant domains? Followup-To: bionet.molbio.methds-reagnts,bionet.molbio.proteins Date: 3 Nov 1997 13:45:18 GMT Organization: Oxford University, England Lines: 12 Message-ID: <63kkhe$3u4$1@news.ox.ac.uk> References: NNTP-Posting-Host: ermine.ox.ac.uk X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.methds-reagnts:62586 bionet.molbio.proteins:11824 Lloyd Graham (lloyd.graham@molsci.csiro.au) wrote: : I'm looking for any precedents where the domains of a monofunctional : enzyme have been expressed separately as inactive proteins, but when mixed : together they associate to form a complex with significant enzymatic : activity. Markby et. al., Science 262 p1895 (1993), separately expressed 2 halves of a heterotrimeric G protein alpha chain; GTPase activity was regained upon mixing the two domains. Dennis From owner-proteins@net.bio.net Sun Nov 02 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.nacamar.de!uni-erlangen.de!winx03!news From: s88891@stud-mail.uni-wuerzburg.de (Mathias Holpert) Newsgroups: bionet.molbio.proteins Subject: Re: Domains with more than one function Date: Mon, 03 Nov 1997 23:55:18 GMT Organization: University of Wuerzburg, Germany Lines: 30 Message-ID: <345f6147.5460621@news.informatik.uni-wuerzburg.de> References: NNTP-Posting-Host: wex127.extern.uni-wuerzburg.de Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Forte Agent 1.5/32.451 On Mon, 03 Nov 1997 21:10:59 +0000, drm21@mole.bio.cam.ac.uk (David Micklem) wrote: snip > >Ideally, I'm looking for examples of a motif (or domain) which has a well >characterised function (eg Zn-fingers and DNA binding) in most proteins, >but which has been shown to have another function (eg protein-protein >interaction) in other proteins. > >(I used the Zn-finger example because I vaguely recall hearing that this >was true of Zn-fingers - but I haven't been able to track down a >reference!) > >Many thanks for any assistance (and no, I'm not an student trying to cheat >on exam/essay questions!) > >David Hi David, one example I can recall is the LAGLI-DADG motif which has been found in several intron-encoded proteins. It is thoght to be involved in dsDNA endonuclease and in RNA maturase function. But this is not a perfect example: this motif hasn´t been shown to be directly involved in catalysis yet. Hope this helps Mathias From owner-proteins@net.bio.net Sun Nov 02 22:00:00 1997 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!193.10.88.100!news00.sunet.se!sunic!mn6.swip.net!seunet!news2.swip.net!mailgate.astra.com!not-for-mail From: "Doug Hubatsch" Newsgroups: bionet.cellbiol,bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Sonication with PMSF/EGTA produces a precipitate.....why? Date: 3 Nov 1997 22:31:10 GMT Organization: ARCM Lines: 10 Message-ID: <01bce8a7$e01cfd70$373412ac@dough> NNTP-Posting-Host: 172.18.52.55 X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.cellbiol:8355 bionet.molbio.methds-reagnts:62608 bionet.molbio.proteins:11827 Anybody else come across this? When I sonicate bacteria in .1 mM PMSF/10 mM EDTA, add 1% SDS and incubate for 30 min. at RT I get a DNA-like precipitate. I don't think its because of the SDS, boiling the mixture doesn't put the precipitate back into solution. The concentrations for PMSF and EDTA are well below other reported concentrations so I don't really have any idea what could be causing it. Any ideas? Doug From owner-proteins@net.bio.net Mon Nov 03 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!192.48.96.125!in3.uu.net!munnari.OZ.AU!metro!metro!news From: "Michael Bonifacio" Newsgroups: bionet.molbio.proteins Subject: Is this Newgroup working Date: Tue, 4 Nov 1997 22:25:06 +1100 Organization: Home Lines: 5 Distribution: inet Message-ID: <63n0f9$bht@metro.usyd.edu.au> NNTP-Posting-Host: mp-7-19.mp.usyd.edu.au X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Hi Everyone, I am having trouble accessing this group , so this is simply a test message. From owner-proteins@net.bio.net Mon Nov 03 22:00:00 1997 Path: biosci!agate!newsgate.duke.edu!kwatra2.mc.duke.edu!user From: edroush@acpub.duke.edu (Eric Roush) Newsgroups: bionet.cellbiol,bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: Sonication with PMSF/EGTA produces a precipitate.....why? Date: Tue, 04 Nov 1997 18:35:31 -0500 Organization: Glow-n-the-Dark Radiochemicals, Inc. Lines: 23 Distribution: world Message-ID: References: <01bce8a7$e01cfd70$373412ac@dough> NNTP-Posting-Host: kwatra2.mc.duke.edu Xref: biosci bionet.cellbiol:8356 bionet.molbio.methds-reagnts:62655 bionet.molbio.proteins:11831 In article <01bce8a7$e01cfd70$373412ac@dough>, "Doug Hubatsch" wrote: > Anybody else come across this? When I sonicate bacteria in .1 mM PMSF/10 > mM EDTA, add 1% SDS and incubate for 30 min. at RT I get a DNA-like > precipitate. I don't think its because of the SDS, boiling the mixture > doesn't put the precipitate back into solution. The concentrations for > PMSF and EDTA are well below other reported concentrations so I don't > really have any idea what could be causing it. > > Any ideas? Is there any reason to think that this precipitate is something other than DNA? It's been a while since I lysed bacteria, but I remember the early steps of the process being quite gelatinous in consistancy, not clearing up until after DNase treatment. -- Eric Roush When an eel edroush@acpub.duke.edu bites your heel, also coache@aol.com makes you squeal, pain you feel, that's a moray. From owner-proteins@net.bio.net Mon Nov 03 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!fu-berlin.de!news.tu-darmstadt.de!grapool30.rz.uni-frankfurt.de!not-for-mail From: "Dr. Ekkehart Berndt" Newsgroups: bionet.molbio.proteins Subject: Re: Biorad Protein Standards migrating Date: Tue, 04 Nov 1997 14:09:26 -0800 Organization: Uni-Frankfurt / AK Sandmann / Biosynthesis Group Lines: 6 Message-ID: <345F9D16.68EA@em.uni-frankfurt.de> References: <63ctkr$d8k@singer.cent.gla.ac.uk> NNTP-Posting-Host: ca23.botanik.uni-frankfurt.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.01 (Win95; I; 16bit) I found it always very difficult calculating the molecular mass out of the migration of BioRad´s Kaleidascope-Prestained Standards. Unstained standards seem to work better. Also good results can be obtained by determining the molecular mass with a size-exclusion liquid chromatography, especially when native proteins are of interest. From owner-proteins@net.bio.net Mon Nov 03 22:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeeds.sol.net!uwm.edu!msunews!news.gmi.edu!zombie.ncsc.mil!cs.umd.edu!news.umbc.edu!umbc7.umbc.edu!zhowar1 From: the kid's alright Newsgroups: bionet.molbio.proteins Subject: TCA precipitation chemistry question Date: Fri, 31 Oct 1997 13:35:57 -0500 Organization: University of Maryland, Baltimore County Lines: 10 Message-ID: NNTP-Posting-Host: umbc7.umbc.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-MD5: 25b6a0be5cf279a47a2b1c0ca7be9a8c Can anybody explain to me the chemical mechanism of TCA precipitation of proteins? Just a brief headstart would be fine, I can't seem to find this in any chemistry book. Thanks, Zach From owner-proteins@net.bio.net Tue Nov 04 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Luc CAMOIN Newsgroups: bionet.molbio.proteins Subject: Ecoli contaminant Histag purification Date: 5 Nov 1997 16:46:52 -0000 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <63q7ts$q0v@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk Dear Netters, We tried to purify our His-tagged recombinant protein expressed in Ecoli using Nickel affinity purification columns. Two proteins were retained and eluted at 100 mM imidazole. These two proteins were sequenced. One was a FKBP-TYPE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE SLYD from Ecoli. This protein was known to bind Ni with high affinity. The second one was a chaperonin protein GROEL from Ecoli. This protein contains one His and one Cys. Has anybody identified already this last proteins in immobilized metal affinity chromatography? Does anyone have any explanation about this binding? Thanks in advance Luc CAMOIN From owner-proteins@net.bio.net Tue Nov 04 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!205.252.116.205!howland.erols.net!news.maxwell.syr.edu!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!enterprise.mpi.com!client124.mpi.com!user From: user@mpi.com Newsgroups: bionet.molbio.proteins Subject: EDTA in lysis buffer? Date: Wed, 05 Nov 1997 11:47:49 -0500 Organization: Milleneum Pharmaceuticals Lines: 10 Message-ID: NNTP-Posting-Host: client124.mpi.com I've been playing around with conditions for lysis of mammalian cells lately (for subsequent IP or western analysis), and I'm wondering about the advantages and disadvantages of including EDTA. Many people do; many others don't. I've heard some stories of protein interactions breaking up as a result of the chelating properties of EDTA, which I suppose could be a potential disadvantage if studying specific interactions. What are the advantages? Inhibition of enzymatic activities (like proteases)? Cleaning up non-specific interactions? Any other thoughts? -HS From owner-proteins@net.bio.net Tue Nov 04 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-xfer.netaxs.com!news.voicenet.com!dsinc!pitt.edu!newsfeed.pitt.edu!pxpst2 From: pxpst2@vms.cis.pitt.delet.edu (Peter) Newsgroups: bionet.molbio.proteins Subject: Re: Determination of very small quantities of protein in phospholipids Date: Wed, 05 Nov 1997 11:27:59 -0500 Organization: University of Pittsburgh Lines: 30 Message-ID: References: <3460732D.680E@biochemtech.uni-halle.de> NNTP-Posting-Host: pelli.pathology.pitt.edu X-Newsreader: MT-NewsWatcher 2.3.5 In article <3460732D.680E@biochemtech.uni-halle.de>, Aurich@biochemtech.uni-halle.de wrote: > Hallo, > > can anyone help? I´m searching for a method or possibility to > determinate a quantity of 10 - 100 µg protein/g phospholipid. Laser flouresence. Peter -- "Don't you eat that yellow snow WAtch out where the Huskies go" --------------------------------------------------------------------- Let us not forget those marketing boys from SPAM CENTRAL bestrealtor@marketingmaster.com info@herbchew.com clickthru@timefreedom.com invite@onlinenow.net zippydj@nevwest.com Offer@shire.com empower@empowerlabs.com dynamarket@vaprnet.com root@mail.icongrp.com cashrewards@hotmail.com From owner-proteins@net.bio.net Tue Nov 04 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!portc02.blue.aol.com!pitt.edu!newsfeed.pitt.edu!pxpst2 From: pxpst2@vms.cis.pitt.delet.edu (Peter) Newsgroups: bionet.molbio.proteins Subject: Re: TCA precipitation chemistry question Date: Wed, 05 Nov 1997 11:27:11 -0500 Organization: University of Pittsburgh Lines: 42 Message-ID: References: NNTP-Posting-Host: pelli.pathology.pitt.edu X-Newsreader: MT-NewsWatcher 2.3.5 In article , the kid's alright wrote: > Can anybody explain to me the chemical mechanism of TCA precipitation of > proteins? Just a brief headstart would be fine, I can't seem to find this > in any chemistry book. TCA is used because it is capable of mantaining a very acid pH in dilute aqueous form(<7%). It is also NOT a strong Acid so it will not hydrolyze pepetide bonds. The exception to this is the making of a TCA stock greater than 30 percent. TCA may breakdown and HCl will form, which will hydrolyze peptide bonds. How does it work? Acid precip. works by altering the hydration spheres. It "squeezes" water out of the protein. One may say it dehydrates the protein similar to the way alchohol works. The problem with this method is that not all proteins precipitate equally and small proteins sometimes not at all. Unless you are working with high protein content(>1mg/ml), TCA is not a good method of protein recovery. Extraction is much better Peter -- "Don't you eat that yellow snow WAtch out where the Huskies go" --------------------------------------------------------------------- Let us not forget those marketing boys from SPAM CENTRAL bestrealtor@marketingmaster.com info@herbchew.com clickthru@timefreedom.com invite@onlinenow.net zippydj@nevwest.com Offer@shire.com empower@empowerlabs.com dynamarket@vaprnet.com root@mail.icongrp.com cashrewards@hotmail.com From owner-proteins@net.bio.net Tue Nov 04 22:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!fu-berlin.de!news-ber1.dfn.de!news-lei1.dfn.de!news.uni-leipzig.de!mlucom4.urz.uni-halle.de!newsmaster From: Ines Aurich Newsgroups: bionet.molbio.proteins Subject: Determination of very small quantities of protein in phospholipids Date: Wed, 05 Nov 1997 14:22:53 +0100 Organization: University Halle, Germany Lines: 5 Message-ID: <3460732D.680E@biochemtech.uni-halle.de> Reply-To: Aurich@biochemtech.uni-halle.de NNTP-Posting-Host: 141.48.11.133 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0Gold (Win95; I) Hallo, can anyone help? I´m searching for a method or possibility to determinate a quantity of 10 - 100 µg protein/g phospholipid. Ines From owner-proteins@net.bio.net Tue Nov 04 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!fu-berlin.de!news.belwue.de!newsserv.zdv.uni-tuebingen.de!not-for-mail From: "Harold V. Taylor" Newsgroups: bionet.molbio.proteins Subject: Re: Biorad Protein Standards migrating Date: Wed, 05 Nov 1997 19:15:10 -0800 Organization: University of Tuebingen Lines: 22 Message-ID: <3461363E.5603@uni-tuebingen.de> References: <63ctkr$d8k@singer.cent.gla.ac.uk> Reply-To: cbiei01@uni-tuebingen.de NNTP-Posting-Host: eis4.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) Obaid Yusuf Khan wrote: > > I am using the Biorad Kaleidoscope Prestained Standards to size my proteins > on a 12% PAGE gel ("29:1). Dear Obaid, your problem is that you're using a 12 % PAGE gel. Proteins smaller than approx. 25 kDa get fuzzy on non-gradient gels. Either try tris-tricine gels and higher acrylamid concentrations or tris-glycine and gradient gels. Have fun, ;-) Harold V. Taylor 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 Nov 04 22:00:00 1997 Path: biosci!agate!newsgate.duke.edu!usenet From: "Michael J. Morales" Newsgroups: bionet.molbio.proteins Subject: Re: EDTA in lysis buffer? Date: Wed, 05 Nov 1997 12:06:22 -0500 Organization: Duke University, Durham, NC, USA Lines: 32 Message-ID: <3460A78D.E76C6783@acpub.duke.edu> References: NNTP-Posting-Host: async249-124.async.duke.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) X-Priority: 3 (Normal) X-Corel-MessageType: EMail user@mpi.com wrote: > I've been playing around with conditions for lysis of > mammalian cells > lately (for subsequent IP or western analysis), and I'm > wondering about > the advantages and disadvantages of including EDTA. Many > people do; many > others don't. I've heard some stories of protein > interactions breaking up > as a result of the chelating properties of EDTA, which I > suppose could be > a potential disadvantage if studying specific > interactions. What are the > advantages? Inhibition of enzymatic activities (like > proteases)? > Cleaning up non-specific interactions? Any other > thoughts? > > -HS Addition of EDTA inhibits metaloproteases, so is usually desirable. However, in some cases, such as downstream use of an immobilized metal column, EDTA must be avoided. Hope this helps Mike Morales From owner-proteins@net.bio.net Tue Nov 04 22:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!204.254.98.218!mint.net!not-for-mail From: "Monica Marie Arroyo" Newsgroups: bionet.molbio.proteins Subject: Creatine phosphokinase Date: 6 Nov 1997 01:31:56 GMT Organization: Maine InternetWorks Lines: 5 Message-ID: <01bceab8$e5c7f460$16748bce@takahiro> NNTP-Posting-Host: dialup-p-2.mint.net X-Trace: garnet.mint.net 878779916 23657 (None) 206.139.116.22 X-Complaints-To: usenet@mint.net X-Newsreader: Microsoft Internet News 4.70.1155 Could anybody tell me how many subunits does creatine phosphokinase have? Thanks, Monica From owner-proteins@net.bio.net Tue Nov 04 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!192.48.96.125!in3.uu.net!munnari.OZ.AU!bunyip.cc.uq.edu.au!inet6.citec.com.au!citecuf.citec.qld.gov.au!news From: Alison Leakey Newsgroups: bionet.molbio.proteins Subject: anti-fMLP WANTED Date: Thu, 06 Nov 1997 13:30:32 +1000 Organization: North Queensland Clinical School Lab Lines: 17 Message-ID: <346139D8.3591@citec.qld.gov.au> Reply-To: clinsch@citec.qld.gov.au NNTP-Posting-Host: pisterp.health.qld.gov.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; 68K) Hi everyone, I was wondering if an antibody to the bacterial peptide fMLP exists (commercially available or not)???? If you know, I would greatly appreciate any information Yours sincerely Alison Alison Leakey PhD Student Department of Medicine North Queensland Clinical School Please reply to clinsch@citec.qld.gov.au From owner-proteins@net.bio.net Tue Nov 04 22:00:00 1997 Path: biosci!IAE.SYB.AC.CN!wfwu From: wfwu@IAE.SYB.AC.CN ("wfwu@iae.syb.ac.cn") Newsgroups: bionet.molbio.proteins Subject: Solid-phase refolding Date: 5 Nov 1997 17:43:23 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <346121E6.70B1@iae.syb.ac.cn> Reply-To: wfwu@iae.syb.ac.cn NNTP-Posting-Host: net.bio.net Does anyone know some reference about solid-phase refolding which is refolding recombinant protein on the surface of resin? Thanks for your help! From owner-proteins@net.bio.net Tue Nov 04 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!torn!ccshst05.cs.uoguelph.ca!ccshst01!dvadnais From: dvadnais@uoguelph.ca (D. Vadnais) Newsgroups: bionet.molbio.proteins Subject: Isoelectric Focusing Date: 6 Nov 1997 00:32:57 GMT Organization: University of Guelph Lines: 8 Message-ID: <63r37p$cgv@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: ccshst01.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] I am going to use IEF slab gels from Bio-Rad to separate invertase isozymes from alfalfa. I have never done this procedure before, and I am not really sure of the protocol. I have only the protocols that are used for 2D gel electrophoresis using the capillary tubes. I need to know what buffers I should be using to run these gels, and what type of loading buffer I require for my samples. Thanks in advance for any information you can give me. Dave From owner-proteins@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.ecrc.net!news-raspail.gip.net!news.gsl.net!gip.net!news-stkh.gip.net!news.gsl.net!gip.net!masternews.telia.net!News.Amsterdam.UnisourceCS!amsterdam.news.unisource.nl!gate.news.unisource.nl!bullseye.news.demon.net!demon!news.demon.co.uk!demon!beccas.demon.co.uk!rebecca From: Rebecca Mills Newsgroups: bionet.cellbiol,bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: Sonication with PMSF/EGTA produces a precipitate.....why? Date: Wed, 5 Nov 1997 18:43:46 +0000 Organization: Becca Distribution: world Message-ID: References: <01bce8a7$e01cfd70$373412ac@dough> NNTP-Posting-Host: beccas.demon.co.uk X-NNTP-Posting-Host: beccas.demon.co.uk [158.152.173.86] MIME-Version: 1.0 X-Newsreader: Turnpike Version 3.01 Lines: 21 Xref: biosci bionet.cellbiol:8375 bionet.molbio.methds-reagnts:62740 bionet.molbio.proteins:11851 >In article <01bce8a7$e01cfd70$373412ac@dough>, "Doug Hubatsch" > wrote: > >> Anybody else come across this? When I sonicate bacteria in .1 mM PMSF/10 >> mM EDTA, add 1% SDS and incubate for 30 min. at RT I get a DNA-like >> precipitate. I don't think its because of the SDS, boiling the mixture >> doesn't put the precipitate back into solution. The concentrations for >> PMSF and EDTA are well below other reported concentrations so I don't >> really have any idea what could be causing it. >> >> Any ideas? > >Is there any reason to think that this precipitate is something >other than DNA? It's been a while since I lysed bacteria, but >I remember the early steps of the process being quite gelatinous >in consistancy, not clearing up until after DNase treatment. > PMSF precipitates in aqueous solutions. -- Rebecca Mills From owner-proteins@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!news.iupui.edu!physics.nmr.iupui.edu!user From: bray@iupui.edu (Bruce D. Ray) Newsgroups: bionet.molbio.proteins Subject: Re: Creatine phosphokinase Date: Thu, 06 Nov 1997 10:31:36 -0600 Organization: IUPUI Physics Dept. Lines: 21 Message-ID: References: <01bceab8$e5c7f460$16748bce@takahiro> NNTP-Posting-Host: physics.nmr.iupui.edu In article <01bceab8$e5c7f460$16748bce@takahiro>, "Monica Marie Arroyo" wrote: > Could anybody tell me how many subunits does creatine phosphokinase have? > > Thanks, > > Monica Creatine phosphokinase {EC 2.7.3.2} has two identical subunits. Molecular weight of the rabbit muscle enzyme is 81 k Daltons, which means that each subunit is 40.5 k Daltons. -- Warning to commercial e-mailers {spammers}: The e-mail address provided above is for information purposes only. Do not send un solicited commercial e-mail to this address. From owner-proteins@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!agate!howland.erols.net!news-peer.gip.net!news.gsl.net!gip.net!news-xfer.netaxs.com!news.misty.com!news.uwa.edu.au!not-for-mail From: Sonja Bauk Newsgroups: bionet.molbio.methds-reagnts,bionet.general,bionet.molbio.proteins Subject: Lyophilised sera Date: Thu, 06 Nov 1997 19:36:20 -0800 Organization: University of Western Australia Lines: 22 Message-ID: <34628CB4.6891@urc.urc.uwa.edu.au> NNTP-Posting-Host: box241.urc.uwa.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (WinNT; I) Xref: biosci bionet.molbio.methds-reagnts:62715 bionet.general:28607 bionet.molbio.proteins:11845 Hello, I am trying to find some information on the reconstitution of lyophilised sera. The sera been stored at -20 C for 16 years, and has become lyophilised _unintentionally_ due to air leakage from the tubes. The aim is to measure the original concentration of a small protease (33kDa) (or basically get the best approximation) amongst different groups of people. The idea is to resuspend the residue with a known amount of deionised water, measure the concentrations of the protease and a "reference protein" (which has a relatively small range of normal values in the population) and determine the correct dilution factor and (hence the approximate original concentration of the protease). I have not been able to find references to any similar procedures, and would greatly appreciate a push in the right direction, in the form of comments, suggestions or references. Regards, Sonja. ps. lyophilise, lyophilize. It's all a matter of taste ;) From owner-proteins@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!news.starnet.net!axb.slu.edu!news From: Darren Tyson Newsgroups: bionet.molbio.proteins Subject: Re: Isoelectric Focusing Date: Thu, 06 Nov 1997 13:55:56 -0600 Organization: Saint Louis University (remove ".nospam" from address) Lines: 25 Message-ID: <346220CC.1F385C77@slu.edu> References: <63r37p$cgv@ccshst05.cs.uoguelph.ca> Reply-To: tysondr.nospam@slu.edu NNTP-Posting-Host: 165.134.82.91 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (Win95; I) To: "D. Vadnais" D. Vadnais wrote: > I am going to use IEF slab gels from Bio-Rad to separate invertase > isozymes from alfalfa. I have never done this procedure before, and I am > not really sure of the protocol. I have only the protocols that are used > for 2D gel electrophoresis using the capillary tubes. I need to know > what buffers I should be using to run these gels, and what type of > loading buffer I require for my samples. > Thanks in advance for any information you can give me. > Dave Dave, I use the BioRad IEF precast gels which have well in my hands. The cathode buffer is 20 mM lysine, 20 mM arginine. The anode buffer is 7 mM phosphoric acid. Running conditions are 100 V for 1 hr, 250 V for 1 hr and 500 V for 30 min. Hope this helps. Darren From owner-proteins@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!tresnet.com!margajulia From: margajulia@tresnet.com ("Margarita Julia-Sape") Newsgroups: bionet.molbio.proteins Subject: High molecular weight proteins Date: 6 Nov 1997 10:40:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <199711061840.KAA13966@net.bio.net> NNTP-Posting-Host: net.bio.net I need to find a commercial source of purified high molecular weight proteins, to use them as mol weight markers in SDS electrophoresis. I've heard something about thyroglobulin, which weighs about 600 KDa. Thanks in advance for any information. From owner-proteins@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!not-for-mail From: Jong Newsgroups: bionet.molbio.proteins Subject: (no subject) Date: Thu, 06 Nov 1997 17:25:14 +0000 Organization: Lab. of Mol. Biol., Chothia group Lines: 8 Message-ID: <3461FD7A.41C6@mrc-lmb.cam.ac.uk> NNTP-Posting-Host: alf2.mrc-lmb.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; OSF1 V4.0 alpha) Dear , Could anybody tell me where I can get the latest TREMBL database? Thanks, Jong From owner-proteins@net.bio.net Wed Nov 05 22:00:00 1997 From: Dean.Sequera@am.pharmacia.com Subject: Re: Isoelectric Focusing Date: Thu, 06 Nov 1997 11:13:39 -0600 Message-ID: <878834838.23976@dejanews.com> Newsgroups: bionet.molbio.proteins Organization: Deja News Posting Service Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!204.238.120.130!jump.net!grunt.dejanews.com!not-for-mail References: <63r37p$cgv@ccshst05.cs.uoguelph.ca> X-Article-Creation-Date: Thu Nov 06 16:47:18 1997 GMT X-Authenticated-Sender: Dean.Sequera@am.pharmacia.com X-Http-User-Agent: Mozilla/4.0 (compatible; MSIE 4.0; Windows 95) X-Originating-IP-Addr: 206.6.175.122 () Lines: 25 In article <63r37p$cgv@ccshst05.cs.uoguelph.ca>, dvadnais@uoguelph.ca (D. Vadnais) wrote: > > I am going to use IEF slab gels from Bio-Rad to separate invertase > isozymes from alfalfa. I have never done this procedure before, and I am > not really sure of the protocol. I have only the protocols that are used > for 2D gel electrophoresis using the capillary tubes. I need to know > what buffers I should be using to run these gels, and what type of > loading buffer I require for my samples. > Thanks in advance for any information you can give me. > Dave I suggest you contact our offices at Pharmacia Biotech to get a free copy of the Hoefer Protein Electrophoresis Applications Guide. It is complete with theory, practice, pictures, illustrations, etc. Isoelectric focusing is covered in extensive detail. Contact: Pharmacia Biotech Inc. 500, Morgan Boulevard Baie d'Urfe Quebec H9X 3V1 514-457-7000 Ask for Marie-France Belanger, the electrophoresis specialist in your area. -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-proteins@net.bio.net Wed Nov 05 22:00:00 1997 Newsgroups: bionet.molbio.proteins Path: biosci!rutgers!rockyd!notes From: Satish Nair Subject: Re: Ecoli contaminant Histag purification X-Nntp-Posting-Host: skbind2.rockefeller.edu Content-Type: text/plain; charset=us-ascii Message-ID: <34628C7F.167E@rockvax.rockefeller.edu> Sender: notes@rockyd.rockefeller.edu (News Administrator) Content-Transfer-Encoding: 7bit Organization: Rockefeller University References: <63q7ts$q0v@mserv1.dl.ac.uk> Mime-Version: 1.0 Date: Fri, 7 Nov 1997 03:35:27 GMT X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) Lines: 24 Luc CAMOIN wrote: > > Dear Netters, > > We tried to purify our His-tagged recombinant protein expressed in > Ecoli using Nickel affinity purification columns. Two proteins were > retained and eluted at 100 mM imidazole. These two proteins were sequenced. > One was a FKBP-TYPE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE SLYD from > Ecoli. This protein was known to bind Ni with high affinity. > The second one was a chaperonin protein GROEL from Ecoli. This > protein contains one His and one Cys. > Has anybody identified already this last proteins in immobilized > metal affinity chromatography? > Does anyone have any explanation about this binding? > > Thanks in advance > > Luc CAMOIN The GroEL is probably not binding to the resin as much as it is probably binding to your protein (as a chaperonin involved in protein folding, it would make sense that it would bind to your protein). You may want to look up (Trends in Genetics, Vol. 12 p. 209) as it mentions one possible way of ridding the GroEl contaminant. From owner-proteins@net.bio.net Thu Nov 06 22:00:00 1997 From: rozynek@bgfa.ruhr-uni-bochum.de (Peter Rozynek) Newsgroups: bionet.molbio.proteins Subject: Protein crystallization Date: Fri, 07 Nov 1997 13:55:52 GMT Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 5 Message-ID: <34631c65.12175784@www.bgfa.ruhr-uni-bochum.de> NNTP-Posting-Host: lufu.bgfa.ruhr-uni-bochum.de X-Newsreader: Forte Free Agent 1.11/32.235 Path: biosci!news.ic.sunysb.edu!news-pen-15.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.131!news-pen-1.sprintlink.net!news-east.sprintlink.net!news-dc-26.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!news-was.dfn.de!news-fra1.dfn.de!news-koe1.dfn.de!news.ruhr-uni-bochum.de!not-for-mail We have isolated a plant protein in efficient purity and amount which has been identified as important allergen and is also thought to play a important role in natural rubber synthesis. We´d like to analyze the 3-D structure of this protein. Any suggestions/hints/propasals for protein crystallization and or cooperation is greatly appreciated. From owner-proteins@net.bio.net Thu Nov 06 22:00:00 1997 Path: biosci!musc.edu!vakseri From: vakseri@musc.edu (Ilya Vakser) Newsgroups: bionet.molbio.proteins Subject: Postdocs/Graduate Students in Protein Docking and Structure Prediction Date: 7 Nov 1997 14:30:58 -0800 Organization: Medical University of South Carolina Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <34639674.714170FE@musc.edu> NNTP-Posting-Host: net.bio.net Applications are invited for postdoctoral and graduate student positions in my laboratory at the Medical University of South Carolina. The main subjects of the research are computational studies of fundamental principles of molecular recognition, docking methodology, structure prediction, including membrane proteins modeling, and applications to signal transduction pathways and other molecular systems. Candidates for a postdoctoral position should have a background in biochemical or physics/mathematics/computer science areas. Computer programming skills will be a plus. The Medical University of South Carolina at Charleston provides a challenging research environment in pharmacology and biochemistry with the emphasis on the development of structural studies. The positions offer a rare opportunity to enjoy fundamental research at the cutting edge of computer modeling in structural biology in a relaxing atmosphere of a charming semi-tropical ocean resort. Charleston is a cosmopolitan community with rich cultural life (theaters, concerts, art galleries), great food, and beautiful beaches. To apply send a letter and CV with names of at least 2 referees. Ilya A. Vakser Assistant Professor of Pharmacology Department of Cell and Molecular Pharmacology Medical University of South Carolina 171 Ashley Avenue Charleston, SC 29425 Email: vakseri@musc.edu, Phone:(803)792-2471, Fax:(803)792-2475 From owner-proteins@net.bio.net Thu Nov 06 22:00:00 1997 Message-ID: <3460B9DF.228B6F32@zzevolution.bmc.uu.se> Date: Wed, 05 Nov 1997 19:24:31 +0100 From: David Freistroffer Organization: Uppsala University, Molecular Biology X-Mailer: Mozilla 4.01 [en] (Win95; I) MIME-Version: 1.0 Newsgroups: bionet.molbio.proteins Subject: buying MRE600 cells X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: terminator.bmc.uu.se Lines: 10 Path: biosci!news.ic.sunysb.edu!news-pen-15.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.131!news-pen-1.sprintlink.net!news-east.sprintlink.net!news-dc-26.sprintlink.net!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!193.10.88.100!news00.sunet.se!sunic!newsfeed.uu.se!terminator.bmc.uu.se Does anyone know where I can buy frozen E coli MRE600 cells? Any idea about the cost and/or quality? Thanks, David Take off the zz infront of 'evolution.bmc..' to send mail. From owner-proteins@net.bio.net Thu Nov 06 22:00:00 1997 Path: biosci!agate!usenet.INS.CWRU.Edu!vncnews!HSNX.wco.com!news.walltech.com!nntp.mainstreet.net!su-news-feed1.bbnplanet.com!su-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!news.idt.net!news-peer-east.sprintlink.net!news.sprintlink.net!Sprint!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins Subject: Re: Protein crystallization Date: Fri, 07 Nov 1997 14:18:32 -0800 Organization: University of Leicester (PCFS User) Lines: 48 Message-ID: <346393B8.4832@le.ac.uk> References: <34631c65.12175784@www.bgfa.ruhr-uni-bochum.de> NNTP-Posting-Host: pc47.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.01 (Win16; I) Peter Rozynek wrote: > > We have isolated a plant protein in efficient purity and amount which > has been identified as important allergen and is also thought to play > a important role in natural rubber synthesis. We´d like to analyze the > 3-D structure of this protein. Any suggestions/hints/propasals for > protein crystallization and or cooperation is greatly appreciated. The first thing to do is to find conditions under which the protein crystallizes. These then are optimized later. For initial screening, place 10 ul protein solution (say 5-10 mg/ml) and 10 ul precipitating agent together in the middle of a silanized cover slip. Fill a well of a 24 well plate with 1 ml of the precipitating reagent and put some vaseline on the rim. Place the cover slip (drop hanging from the underside) onto the well, so that you get a sealed chamber, with the drop of protein solution hanging from the ceiling. Keep for 2 weeks vibration free at constant temperature (usually 4 degrees C). During this time water will evaporate from the drop into the liquid reservoir, until the concentrations in both are identical (isothermic distillation). This gives you a slow increase of precipitating agent, and hopefully crystalls. After these 2 weeks, check for crystalls in the hanging drop under the microscope. As precipitating agents you may try different concentrations in different buffers (borate, tris, hepes, imidazole, acetate, citrate) of ethanol, propanol, acetone, polyethylene glycol (of different MW), ethylene glycol, ammonium sulfate, NaCl, MgSO4,.... Try them in combination too. There are sets of precipitation solution available ready made, which simplifies the setup slightly. As you can see, you are realy playing the numbers game here. If you get crystalls under any of those conditions, try to optimise them. Once you are that far, you may want to look for cooperation with somebody with experience in X-ray crystallography. They will be able to advice you on how to grow larger crystalls suitable for their maschines. Oh, one more thing: Make sure you know how crystalls of your precipitating agents look like. Protein and salt crystalls can be distinguished by two methods: a) A salt crystall, when crushed with a probe, will emit a grinding sound. If you hear nothing, then you have just destroyed a perfectly good protein crystall. b) Protein crystalls readily take up dye, if that is added to the mother liquor, because there is a lot of water space in them. In salt crystalls the ions are tightly packed, the crystall won't take up the dye. From owner-proteins@net.bio.net Thu Nov 06 22:00:00 1997 Path: biosci!rutgers!gatech!4.1.16.34.MISMATCH!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!140.163.96.254!news.ski.mskcc.org!m-tritel From: m-tritel@ski.mskcc.nospam.org (Marc Tritel) Newsgroups: bionet.molbio.proteins Subject: HIV-1 gp41 Western Date: Fri, 07 Nov 1997 10:37:54 -0500 Organization: Memorial Sloan Kettering Lines: 7 Message-ID: NNTP-Posting-Host: 140.163.95.146 X-Newsreader: Yet Another NewsWatcher 2.2.0b7 I've spent a lot of time trying to get a good Western blot of HIV-1 gp41 TM protein (from lysates of cos-7 cells transfected with a non-infectious [pol-,pro-] proviral construct,IP'd with human anti-HIV serum) and am unable to reproducibly get a satisfactory Western. This is because of the sporadic appearance of a non-specific band that co-migrates with gp41. I have tried 2 commercial monoclonal antibodies, ABi and NEN, both of which are supposedly good for Western. Does anybody have any suggestions for me. From owner-proteins@net.bio.net Fri Nov 07 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!uninett.no!news-feed.inet.tele.dk!news.inet.tele.dk!not-for-mail From: "Jens Kondrup" Newsgroups: bionet.molbio.proteins Subject: TCA precipitation of proteins Date: Sat, 8 Nov 1997 23:59:22 +0100 Organization: RIGSHOSPITALET Lines: 4 Message-ID: <642qt4$1nda$1@news.inet.tele.dk> NNTP-Posting-Host: ppp148.kbh.tele.dk X-Newsreader: Microsoft Outlook Express 4.71.0544.0 X-MimeOLE: Produced By Microsoft MimeOLE Engine V4.71.0544.0 Is TCA better than PCA? Jens Kondrup From owner-proteins@net.bio.net Sat Nov 08 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!scanner.worldgate.com!rover.ucs.ualberta.ca!not-for-mail From: wklimke@gpu.srv.ualberta.ca (William Klimke) Newsgroups: bionet.molbio.proteins Subject: Immunoprecipitation of membrane proteins Date: 10 Nov 1997 01:44:38 GMT Organization: Biosciences Lines: 7 Message-ID: <645ou6$fr4$1@pulp.ucs.ualberta.ca> NNTP-Posting-Host: sandi.biology.ualberta.ca Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Trace: pulp.ucs.ualberta.ca 879126278 16228 (None) 129.128.82.48 X-Complaints-To: usenet@pulp.ucs.ualberta.ca X-Newsreader: WinVN 0.99.9 (Released Version) (x86 32bit) I am planning on using immunoprecipitation to determine protein-protein interactions of an outer membrane protein in Escherichia coli. I know that they have used IPP to pull down proteins in mitochondrial membranes. Does anybody have, or know of, any useful protocols that I might be able to use. William Klimke From owner-proteins@net.bio.net Sat Nov 08 22:00:00 1997 Path: biosci!agate!howland.erols.net!rill.news.pipex.net!pipex!taps.news.pipex.net!pipex!warm.news.pipex.net!pipex!duke.telepac.pt!news.telepac.pt!not-for-mail From: "Vera Alexandra Guerra Duarte" Newsgroups: bionet.molbio.proteins Subject: Prion Protein and amyloid Date: 9 Nov 1997 22:20:54 GMT Lines: 9 Message-ID: <01bced5e$447bbd00$38ae41c2@default> NNTP-Posting-Host: 194.65.174.56 X-Newsreader: Microsoft Internet News 4.70.1155 Hello there! I am a Portuguese Biochemist who wants to know more about the structure and function of the prion protein. As it is one of the proteins that can form amyloid, I would also appreciate some information on b-protein of the Alzheimer's disease. Thanks in advance, Tiago Fleming. From owner-proteins@net.bio.net Sun Nov 09 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins Subject: Re: Immunoprecipitation of membrane proteins Date: Mon, 10 Nov 1997 12:51:00 -0800 Organization: University of Leicester (PCFS User) Lines: 24 Message-ID: <346773B4.6F32@le.ac.uk> References: <645ou6$fr4$1@pulp.ucs.ualberta.ca> NNTP-Posting-Host: pc47.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win16; I) William Klimke wrote: > > I am planning on using immunoprecipitation to determine protein-protein > interactions of an outer membrane protein in Escherichia coli. I know that > they have used IPP to pull down proteins in mitochondrial membranes. Does > anybody have, or know of, any useful protocols that I might be able to use. I like to use dead Staph. aureus cells (Pansorbin, Calbiochem) for IPs. You add a small amount of the suspension to your sample, incubate on ice and spin. The pellet can then be resuspended directly in SDS sample buffer. Calbiochem produces a handy (and free) booklet on the use of Pansorbin. Before you can precipitate, however, you'l have to isolate and solubilize the membranes from your E. coli cells, without breaking protein-protein interactions. There is no way to predict which conditions will be optimal for your particular proteins. Mild detergents like dodecylmaltoside, octylglucoside, C12E8, hecameg or similar may work. Sometimes you can also get away with Triton-X100, which is cheaper. Increase the detergent concentration, starting from the cmc, at a const [protein] of 1-2 mg/ml and see at which concentration your protein becomes solubilized, without breaking protein-protein interactions. The whole thing unfortunately is black art, not science. Good luck! From owner-proteins@net.bio.net Sun Nov 09 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!news-feed1.tiac.net!news-master.tiac.net!news@tiac.net From: propdig Newsgroups: bionet.molbio.proteins Subject: National Biotech Register(NatBio) New Service Date: Mon, 10 Nov 1997 15:31:20 -0500 Organization: propdig Lines: 5 Message-ID: <34676F18.6A93@barryinc.com> Reply-To: propdig@barryinc.com NNTP-Posting-Host: p11.ts7.lowel.ma.tiac.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0C-NSCP (Win95; U) NatBio, http://www.barryin.com/bio is pleased to introduce a new service on our web site. A Biotech Industry Company profile search. Are you looking for information on a particular Biotech company? We probably have it. We also invite you to check out your own company. If it is not listed, email us the data and we will add it for free. From owner-proteins@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!webtv.net!not-for-mail From: Serena2@webtv.net Newsgroups: bionet.molbio.proteins Subject: protein folding Date: Wed, 12 Nov 1997 01:51:38 -0500 Organization: WebTV Subscriber Lines: 7 Message-ID: <64bjlq$p61$1@newsd-113.bryant.webtv.net> NNTP-Posting-Host: localhost.webtv.net Mime-Version: 1.0 (WebTV) Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT anyone have any exp w/ glutathione oxidation, cysteine oxidation, folding using detergents, , or other additives thank for your help.... Serena Morales , From owner-proteins@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.algonet.se!4.1.16.34.MISMATCH!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!210.120.128.205!newsfeed.dacom.co.kr!not-for-mail From: "JEON JUNG-WON" Newsgroups: bionet.molbio.proteins Subject: How toxic acetonitrile is? Date: Wed, 12 Nov 1997 00:15:45 +0900 Organization: KGCC Lines: 15 Message-ID: <649sq8$il4$1@news1.dacom.co.kr> NNTP-Posting-Host: 210.120.130.59 X-Newsreader: Microsoft Outlook Express 4.71.1008.3 X-MimeOle: Produced By Microsoft MimeOLE Engine V4.71.1008.3 I'd like to use acetonitrile in RPC process to purify protein. If I use about 10liters acetonitrile in a week, do I need special facility to ventilite? In case of in laminar flow condition like clean booth, do I wearing a special raspiratory equipment? and how about waste treatment.. I need infomation jwjeon@kgcc.co.kr From owner-proteins@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.algonet.se!news.maxwell.syr.edu!sunqbc.risq.qc.ca!newsflash.concordia.ca!pitt.edu!newsfeed.pitt.edu!pxpst2 From: pxpst2@vms.cis.pitt.delet.edu (Peter) Newsgroups: bionet.molbio.proteins Subject: Re: How toxic acetonitrile is? Date: Tue, 11 Nov 1997 10:56:56 -0500 Organization: University of Pittsburgh Lines: 28 Message-ID: References: <649sq8$il4$1@news1.dacom.co.kr> NNTP-Posting-Host: pelli.pathology.pitt.edu X-Newsreader: MT-NewsWatcher 2.3.5 In article <649sq8$il4$1@news1.dacom.co.kr>, "JEON JUNG-WON" wrote: > I'd like to use acetonitrile in RPC process to purify protein. > If I use about 10liters acetonitrile in a week, do I need special facility > to ventilite? Not really, ACN is not terrible flammible and in HPLC methods it is ussually diluted at least two fold with water. > > In case of in laminar flow condition like clean booth, do I wearing a > special raspiratory equipment? NO. You do not need resparitory equipment. ACN is really not toxic as long as you DO NOT DRINK IT. It has a relatively high VP so it does not go into the gas phase easily. > > and how about waste treatment.. Dispose of with other Organic Waste. Consult your local eviornmental/chemistry guys for the specifics. Each institution has there own way of adhereing to OHSA rules > > I need infomation Any specific questions feel free to email me. Peter pxpst2@vms.cis.pitt.edu From owner-proteins@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!utoronto.ca!masood.zangeneh From: masood.zangeneh@utoronto.ca Newsgroups: bionet.molbio.proteins Subject: (none) Date: 11 Nov 1997 15:49:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello I am in a desparate need to know how many uncoupling proteins have been found so far. if you know where I can search for it or if you know someone who knows about it I would appreciate if you could inform me. Regards, masood zangeneh university of Toronto From owner-proteins@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!rutgers!uwm.edu!newsfeeds.sol.net!nntp.uio.no!news.kth.se!gvh-caballo.biokemi.su.se!user From: urbig@biokemi.su.se (Thomas) Newsgroups: bionet.molbio.proteins Subject: Re: Chemical cross-linking Date: Thu, 06 Nov 1997 16:22:15 +0200 Lines: 21 Message-ID: References: <638kd4$hde$1@pulp.ucs.ualberta.ca> NNTP-Posting-Host: gvh-caballo.biokemi.su.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit In article <638kd4$hde$1@pulp.ucs.ualberta.ca>, wklimke@gpu.srv.ualberta.ca (William Klimke) wrote: > Does anybody know of any articles/reviews on chemical cross-linking of > proteins (especially to other proteins)? I would appreciate any which > have a theoretical as well as practical treatment. > > Bill Klimke > Dept. of Bioscie > University of Alberta Look at: S. S. Wong: Chemistry of protein conjugation and cross-linking, CRC Press, Boca Raton 1993. The most comprehensive collection of methods, techniques and reagents with tons of literature links. Thomas -- Thomas Urbig email: urbig@biokemi.su.se From owner-proteins@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!news.indiana.edu!news.iupui.edu!not-for-mail From: Yan Lin Newsgroups: bionet.molbio.proteins Subject: Why AK is not expressed consistantly? Date: Wed, 12 Nov 1997 22:01:05 -0600 Organization: Indiana University - Purdue Univeristy At Indianapols,IN Lines: 20 Message-ID: <346A7B7D.712E@ruby.iupui.edu> Reply-To: iahd500@ruby.iupui.edu NNTP-Posting-Host: 134.68.134.56 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) Hi all, I'm a graduate student doing biophysics with a stronger background in physics than in bio-related areas. Earlier this year we obtained an E. coli strain (SMH 50) which overexpresses adenylate kinase (AK). My very first prep went very well - a yield of >70mg/L was obtained with excellent enzyme activity. But, ever since then I have not been able to get consistant results in quantity and activity. To make sure that the bacteria from a "strong and healthy" origin are picked before large scale amplification I've been measuring the ratio of Volume_Activity (U/ml) and OD at 280nm for crude extract of each 5ml overnight preculture. This ratio varies in a wide range, eg. 5 ~ 100 U/OD. What troubles me is if a saved culture sample (plated on agar dish, or with 15% glycerol in freezer or liquid nitrogen) with high Activity/OD is inoculated again the ratio may turn out to be much lower after overnight shaking. I'd like to know if this Activity/OD is the best measure of the efficiency of protein expression in bacteria cells. What are the possible reasons for low and/or inconsistant expression? Many thanks for your help. From owner-proteins@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!TC3NET.COM!cola From: cola@TC3NET.COM (Nicolas Bayoff) Newsgroups: bionet.molbio.proteins Subject: somatotropin/prolactin Date: 12 Nov 1997 13:27:23 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <346A1F60.52B6@tc3net.com> NNTP-Posting-Host: net.bio.net I am trying to locate a bio-active test kit or method that would assit me in specifically differentiating the activity of alligator somatotropin and prolactin. Is there a concrete method to show the specific activity of each of these hormones? Is there perhaps a similar method that is used in the poultry science field as alligators appear to have fairly similar sequence profiles. Thank you Nicolas Bayoff From owner-proteins@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!CSHL.ORG!leemor From: leemor@CSHL.ORG (Leemor Joshua-Tor) Newsgroups: bionet.molbio.proteins Subject: Re: Chemical cross-linking Date: 12 Nov 1997 12:54:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Check out also: Fancy et al, New chemistry for the study of multiprotein complexes: the six-histidine tag as a receptor for a protein crosslinking reagent, Chemistry & Biology, 3, 551-559 (1996). >In article <638kd4$hde$1@pulp.ucs.ualberta.ca>, >wklimke@gpu.srv.ualberta.ca (William Klimke) wrote: > >> Does anybody know of any articles/reviews on chemical cross-linking of >> proteins (especially to other proteins)? I would appreciate any which >> have a theoretical as well as practical treatment. >> >> Bill Klimke >> Dept. of Bioscie >> University of Alberta > >Look at: S. S. Wong: Chemistry of protein conjugation and cross-linking, >CRC Press, Boca Raton 1993. >The most comprehensive collection of methods, techniques and reagents with >tons of literature links. > >Thomas > >-- >Thomas Urbig >email: urbig@biokemi.su.se ******************************************************************* Leemor Joshua-Tor, Ph.D. Assistant Investigator Keck Structural Biology Cold Spring Harbor Laboratory Tel. (516) 367 8821 1 Bungtown Road Fax (516) 367 8873 Cold Spring Harbor, NY 11724 e-mail: leemor@cshl.org ******************************************************************* From owner-proteins@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!gmorley From: gmorley@hgmp.mrc.ac.uk (Mr. G. Morley) Newsgroups: bionet.molbio.proteins Subject: Phospho-amino acids>????? Date: 12 Nov 1997 17:09:30 GMT Organization: MRC Human Genome Mapping Project Resource Centre Lines: 14 Message-ID: <64cnsa$de0$1@niobium.hgmp.mrc.ac.uk> NNTP-Posting-Host: tin.hgmp.mrc.ac.uk HI.. got a bit of a duff question here.. is it only the phospho-tyrosine residues that can act as docking sites for proteins? If so does this mean that the affects of phospho serine and phospho threonine is entirely structural in nature? I was just wondering as it occured to me the other day that SH2 domains bind Y-p not Tp- or S-p and I could not think of anything which did bind these amino acids.... if anyone does know of an example I would greatly appreciate it... thanks gary morley gmorley@rpms.ac.uk From owner-proteins@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!BOTANY.UQ.EDU.AU!J.Marcus From: J.Marcus@BOTANY.UQ.EDU.AU ("Marcus, Dr J.") Newsgroups: bionet.molbio.proteins Subject: Re: Why AK is not expressed consistantly? Date: 12 Nov 1997 20:42:58 -0800 Organization: Dept of Botany, Univ of Queensland Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: <336372E72D0@botany.uq.edu.au> References: <346A7B7D.712E@ruby.iupui.edu> Reply-To: Marcus@tpp.uq.edu.au NNTP-Posting-Host: net.bio.net If E.coli does not like AK (i.e. it is slightly toxic to the cells or perhaps it doesn't like using up so much energy to express it), then some mutation may be selected for that prevents high expression. I would be tempted to try starting from the very beginning with fresh plasmid containing your gene of interest. Ideally, this plasmid will not have "lived" inside an E.coli cell too long and so won't have been altered itself. Often, in expression systems, it is recommended to re-transform the E.coli that you will be using for your expression every time you get ready to grow up a batch. All the best. John Marcus > Hi all, > > I'm a graduate student doing biophysics with a stronger background in > physics than in bio-related areas. Earlier this year we obtained an E. > coli strain (SMH 50) which overexpresses adenylate kinase (AK). My very > first prep went very well - a yield of >70mg/L was obtained with > excellent enzyme activity. But, ever since then I have not been able to > get consistant results in quantity and activity. To make sure that the > bacteria from a "strong and healthy" origin are picked before large > scale amplification I've been measuring the ratio of Volume_Activity > (U/ml) and OD at 280nm for crude extract of each 5ml overnight > preculture. This ratio varies in a wide range, eg. 5 ~ 100 U/OD. What > troubles me is if a saved culture sample (plated on agar dish, or with > 15% glycerol in freezer or liquid nitrogen) with high Activity/OD is > inoculated again the ratio may turn out to be much lower after overnight > shaking. I'd like to know if this Activity/OD is the best measure of > the efficiency of protein expression in bacteria cells. What are the > possible reasons for low and/or inconsistant expression? > > Many thanks for your help. > > _________________________________________________________ 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 Nov 11 22:00:00 1997 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!news.maxwell.syr.edu!newsfeed.acns.nwu.edu!news.acns.nwu.edu!news From: Chii-Shen Yang Newsgroups: bionet.molbio.proteins Subject: Re: High molecular weight proteins Date: Wed, 12 Nov 1997 16:18:54 -0600 Organization: Northwestern University, Evanston, IL, US Lines: 19 Message-ID: <346A2B4D.BCD1D9EA@nwu.edu> References: <199711061840.KAA13966@net.bio.net> NNTP-Posting-Host: yang.neuro.nwu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=big5 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (Win95; I) It kind of dependent on how high you need. We use Sigma High Molecular Weight Standard Mixture (SDS-6H) which has 205K, 116K, 97K, 66K, 45K and 29K. Hope this helps. Chii-Shen Yang c-yang@nwu.edu Margarita Julia-Sape wrote: > I need to find a commercial source of purified high molecular weight > proteins, to use them as mol weight markers in SDS electrophoresis. I've > heard something about thyroglobulin, which weighs about 600 KDa. Thanks in > advance for any information. From owner-proteins@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!rutgers!gatech!205.252.116.205.MISMATCH!howland.erols.net!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!nntp2.news.xara.net!xara.net!server6.netnews.ja.net!singer.cent.gla.ac.uk!usenet From: 9321531k@clinmed.gla.ac.uk (Obaid Yusuf Khan) Newsgroups: bionet.molbio.proteins Subject: Is a tagged protein more prone to degradation? (Lysis protocols??) Date: 12 Nov 1997 13:39:07 GMT Organization: University of Glasgow Lines: 9 Message-ID: <64cbhr$jdp@singer.cent.gla.ac.uk> NNTP-Posting-Host: pc-165.medtherap.gla.ac.uk Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.8 (16bit) I am trying to do a western blot with a protein which is tagged with a hemagglutinin antigen epitope tag. The western worked with the antibody but a second attempt failed, which I think is due to the tagged protein getting degraded during lysis of the tissue cultured cells. I will appreciate if anyone can tell me about a tested protein extraction protocol which uses protease inhibitors etc, or is specially employed for tagged proteins. Thanks very much Obaid Khan From owner-proteins@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!MAILHOST.TCS.TULANE.EDU!lharris From: lharris@MAILHOST.TCS.TULANE.EDU ("Lisa Harrison-Bernard, PhD.") Newsgroups: bionet.molbio.proteins Subject: housekeeping protein Date: 13 Nov 1997 13:02:39 -0800 Organization: Tulane Medical School, Physiology Dept. Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <346B6AC2.25A7@mailhost.tcs.tulane.edu> NNTP-Posting-Host: net.bio.net Could someone advise on a good antibody to use for housekeeping purposes for Western blot analysis of rat kidney protein? From owner-proteins@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!eerie.fr!jussieu.fr!u-psud.fr!not-for-mail From: "Mark A. Blight" Newsgroups: bionet.molbio.proteins Subject: p-Nitrophenol Protease Substrates? Date: Thu, 13 Nov 1997 12:26:19 +0100 Organization: Institut de Génétique et Microbiologie Lines: 33 Message-ID: <346AE3D9.19EE@igmors.u-psud.fr> NNTP-Posting-Host: bmec1.igmors.u-psud.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.01Gold (Macintosh; I; PPC) Hi, I am trying to characterize a novel protease secreted by a bacterium. Could anyone help me with the following questions please: (i) What kind of tests must I do to characterize the type of protease by its cleavage site? i.e. serine protease etc. (ii) Do you know of any "general" p-nitrophenol protease substrates that I can use to biochemically characterise the protease? (temperature, pH, salt dependence etc). If not, what about any "specific" substrates for other proteases that I could try? Thanks for any help you can give. Please reply by e-mail if poss. Cheers, Mark _________________________________ Dr. Mark A. Blight, CNRS URA2225, Institut de Génétique et Microbiologie, Université de Paris Sud, Bâtiment 409, 91405 Orsay, France. Tel: +33 1 69156699 Fax: +33 1 69157808 e-mail: blight@igmors.u-psud.fr Internet: http://www.igmors.u-psud.fr/holland/holland-home-page-gb.html _________________________________ From owner-proteins@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.proteins Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 13 Nov 1997 02:00:15 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199711131000.CAA19317@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 Wed Nov 12 22:00:00 1997 Path: biosci!rutgers!uwm.edu!news-penn.gip.net!news-peer.gip.net!news.gsl.net!gip.net!EU.net!blackbush.xlink.net!rz.uni-karlsruhe.de!news.urz.uni-heidelberg.de!phoenix.mgen.uni-heidelberg.de!chw From: Christoph Winter Newsgroups: bionet.molbio.proteins Subject: Re: Solid-phase refolding Date: 13 Nov 1997 16:10:17 GMT Organization: MolGen Lines: 19 Distribution: world Message-ID: <64f8p9$2eb@sun0.urz.uni-heidelberg.de> References: <346121E6.70B1@iae.syb.ac.cn> NNTP-Posting-Host: phoenix.mgen.uni-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_68K X-XXMessage-ID: X-XXDate: Thu, 13 Nov 1997 16:10:13 GMT Hi! >Does anyone know some reference about solid-phase refolding which is >refolding recombinant protein on the surface of resin? Try Stempfer, G., Höll, Neugebauer, B., Rudolph, R. (1996), "Improved refolding of an immobilized fusion protein.", Nature Biotechnology, 14:329-334. BTW: Never use a Ni-chelate coloumn and renature with Arg-buffer ;-) Regards Christoph From owner-proteins@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!netnews.com!news.idt.net!dispose.news.demon.net!demon!news.demon.co.uk!demon!busi-solgro.demon.co.uk!not-for-mail From: "mark" Newsgroups: bionet.molbio.proteins Subject: protein structure help req. Date: Thu, 13 Nov 1997 21:43:20 -0000 Message-ID: <879457402.22840.0.nnrp-09.9e98d597@news.demon.co.uk> NNTP-Posting-Host: busi-solgro.demon.co.uk X-NNTP-Posting-Host: busi-solgro.demon.co.uk [158.152.213.151] X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Lines: 11 hi,apologies if this req. is in the wrong ng. as part of my wifes studies in biology she has been requested to give an account of the structure of proteins and using suitable examples explain how their structure enables them to carry out their function,showing relevant diagrams. i am aware that this may be extremely basic to many posters/readers,but if any one can provide us with some information we would be extremely grateful. many thanks in advance.. mark@busi-solgro.demon.co.uk From owner-proteins@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!dispose.news.demon.net!demon!news.demon.co.uk!demon!segapod.demon.co.uk!user From: asam@segapod.demon.co.uk (Asam Bashir) Newsgroups: bionet.molbio.proteins Subject: subscribe Date: Thu, 13 Nov 1997 19:56:39 GMT Organization: Bash Institute of Thought Message-ID: NNTP-Posting-Host: segapod.demon.co.uk X-NNTP-Posting-Host: segapod.demon.co.uk [194.222.211.238] Lines: 1 subscribe From owner-proteins@net.bio.net Thu Nov 13 22:00:00 1997 Path: biosci!rutgers!gatech!205.252.116.205.MISMATCH!howland.erols.net!news.maxwell.syr.edu!uninett.no!news.algonet.se!130.240.42.8.MISMATCH!feed1.news.luth.se!luth.se!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!193.166.5.150.MISMATCH!news.funet.fi!news.helsinki.fi!not-for-mail From: Kaj Stenberg Newsgroups: bionet.molbio.proteins Subject: Re: protein structure help req. Date: 14 Nov 1997 10:09:00 GMT Organization: University of Helsinki Lines: 31 Message-ID: <64h7vs$dms$1@oravannahka.Helsinki.FI> References: <879457402.22840.0.nnrp-09.9e98d597@news.demon.co.uk> NNTP-Posting-Host: vesuri.helsinki.fi X-Trace: oravannahka.Helsinki.FI 879502140 14044 (None) 128.214.205.10 X-Complaints-To: usenet@oravannahka.Helsinki.FI X-Newsreader: TIN [UNIX 1.3 unoff BETA 970613; alpha OSF1 V4.0] mark wrote: > hi,apologies if this req. is in the wrong ng. > as part of my wifes studies in biology she has been requested to give an > account of the structure of proteins and using suitable examples explain how > their structure enables them to carry out their function,showing relevant > diagrams. > i am aware that this may be extremely basic to many posters/readers,but if > any one can provide us with some information we would be extremely grateful. > many thanks in advance.. > mark@busi-solgro.demon.co.uk If you can use a library I recommend Branden's book "introduction to protein structure". That would give a good starting point (a more detailed would be A. Fersht's book, forgot the name right now, maybe "Enzyme structure and function") -- ============================================================================ Kaj Stenberg, Ph. D Department of Biosciences tel. +358-9-708 59032 Division of Biochemistry fax +358-9-708 59068 P. O. Box 56, Viikinkaari 5 e-mail kstenber@kruuna.helsinki.fi FIN-00014 University of Helsinki http://www.helsinki.fi/~kstenber/ Finland This message is enviromentally friendly: every bit was created using 100% recycled electrons. ============================================================================= From owner-proteins@net.bio.net Thu Nov 13 22:00:00 1997 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.erols.net!news.maxwell.syr.edu!uninett.no!news-stkh.gip.net!news.gsl.net!gip.net!news.kolumbus.fi!news.uninet.ee!kadri.ut.ee!tamm!tpungas From: tpungas@tamm.eenet.ee (Tanel Pungas) Newsgroups: bionet.molbio.proteins Subject: adenovirus E1B55K purification! Date: 14 Nov 1997 18:32:24 GMT Organization: Estonian Biocentre Lines: 16 Message-ID: <64i5fo$flp$2@kadri.ut.ee> NNTP-Posting-Host: tamm.ebc.ee Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: kadri.ut.ee 879532344 16057 (None) 193.40.23.2 X-Complaints-To: usenet@kadri.ut.ee X-Newsreader: TIN [version 1.2 PL2] Hello! Has anyone done expression of adenovirus E1B55K in E.coli with His-tag?Is it possible at all? Thanks! -- TANEL PUNGA, B.Sc. 23 Riia Street Fax:372-7-420286 Institute of Molecular Tel:372-7-420218 and Cell Biology E-mail:tpungas@ebc.ee EE2400 Tartu, ESTONIA From owner-proteins@net.bio.net Thu Nov 13 22:00:00 1997 Newsgroups: bionet.molbio.proteins Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.algonet.se!130.240.42.8.MISMATCH!feed1.news.luth.se!luth.se!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!130.237.207.77.MISMATCH!news.ki.se!news From: Andrei.Zhukov@imm.ki.se (Andrei Zhukov) Subject: assay for protein-bound detergent wanted Sender: news@news.ki.se (News admin) Message-ID: Date: Tue, 11 Nov 1997 12:13:46 GMT Nntp-Posting-Host: norma.imm.ki.se Mime-Version: 1.0 Organization: Karolinska Institute X-Newsreader: WinVN 0.99.2 Lines: 7 I am isolating a membrane protein using a non-ionic, UV-absorbing, detergent with detergent removal at the last step. Could anyone give me a reference to or description of a method to assay the amount of residual detergent in my final preparation? Thank you in advance, Andrei Zhukov From owner-proteins@net.bio.net Thu Nov 13 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!newbabylon.rs.itd.umich.edu!not-for-mail From: "Larry \"Harris\" Taylor, Ph.D." Newsgroups: bionet.molbio.proteins Subject: Re: protein structure help req. Date: 14 Nov 1997 18:52:19 GMT Organization: University of Michigan ITD News Server Lines: 40 Message-ID: <01bcf126$b9b6d6b0$babad68d@wakil214> References: <879457402.22840.0.nnrp-09.9e98d597@news.demon.co.uk> NNTP-Posting-Host: host-186.subnet-186.med.umich.edu X-Newsreader: Microsoft Internet News 4.70.1161 Mark, There are a lot of very good useful sites on the web ...go to your favorite search engine and search under MOLECULAR MODELING or PROTEIN STRUCTURE. One very good course in protein structure on the net is: Protein Structure-Internet Course - http://www.cryst.bbk.ac.uk/PPS/index.html To take full advantage of this course, you will need MAGE and and a protein coordinate viewer (like RasMole ... others are also available which will work) Links to Rasmole and Mage are at this site. Larry Taylor MHRI University of Michigan Protein Structure-Internet Course - http://www.cryst.bbk.ac.uk/PPS/index.html mark wrote in article <879457402.22840.0.nnrp-09.9e98d597@news.demon.co.uk>... > hi,apologies if this req. is in the wrong ng. > as part of my wifes studies in biology she has been requested to give an > account of the structure of proteins and using suitable examples explain how > their structure enables them to carry out their function,showing relevant > diagrams. > i am aware that this may be extremely basic to many posters/readers,but if > any one can provide us with some information we would be extremely grateful. > many thanks in advance.. > mark@busi-solgro.demon.co.uk > > > From owner-proteins@net.bio.net Thu Nov 13 22:00:00 1997 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.erols.net!newsfeed.internetmci.com!192.48.96.123!in1.uu.net!news-nb.rutgers.edu!amenti.rutgers.edu!not-for-mail From: meton@rci.rutgers.edu (Daniel Gonzalez) Newsgroups: bionet.molbio.proteins Subject: Green Fluorescent Protein Purificaton Short Course Date: 14 Nov 1997 16:27:15 -0500 Organization: Rutgers University Lines: 58 Message-ID: <64ifnj$t35$1@amenti.rutgers.edu> NNTP-Posting-Host: amenti.rutgers.edu Summary: Hands-On Laboratory Course Using the Green-Fluorescent Protein (GFP) Keywords: Green Fluorescent Protein Purificaton Short Course I have been asked to announce the following, The State University of New Jersey Rutgers Campus at New Brunswick Office of Continuing Professional Education Programs in Biotechnology, Presents: Protein Purification: Isolation, Analysis, and Characterization of GFP, A Five and One-Half Day Hands-On Laboratory Course Using the remarkable Green-Fluorescent Protein (GFP), A Novel Marker For Gene Expression, as the source material January 11-16, 1998, March 15-20, 1998, June 7-12, 1998, July 12-17, 1998,and August 2-7, 1997 More than 500 scientists from around the world have strongly recommended this intensive course as an opportunity to develop protein research and analytical skills in a retreat setting. Participants work hard, identify and solve problems in the lab and enjoy camaraderie and good food and beer with colleagues. This five-day laboratory course covers a wide variety of conventional methods for protein isolation, purification, and characterization. The course format integrates hands-on laboratory exercises with classroom lectures, demonstrations, study breaks, and short take-home assignments. A special feature of the course is that all laboratory work will be performed on the same starting sample (Aequorea GFP*), which will be purified from an exceedingly crude form to near homogeneity as judged by high performance liquid chromatography (HPLC), SDS gel electrophoresis, isoelectric focusing, and capillary zone electrophoresis. This feature provides a continuity of purpose, integrating dozens of preparative and analytical protein techniques in a way that few competing courses can match. A problem-solving approach will be used throughout the course. Under the guidance of experienced lab instructors, participants will work in groups of three to plan their own protocols, analyze data, and interpret results. A student-teacher ratio not greater than 8:1 will be maintained and the faculty coordinators will be present throughout the course. *Note: The use of GFP from a recombinant source (E. coli) is also being used as starting material due to its popularity within the scientific community. For further details you can reach us, by E-mail at: meton@rci.rutgers.edu by phone at: (908) 932-9071 extension 219 by FAX at: (908) 932-8965 for a brochure and further information please visit the GFP purification short course official Web site at: http://www.rci.rutgers.edu/~meton/protein.html From owner-proteins@net.bio.net Sat Nov 15 22:00:00 1997 Path: biosci!agate!ihnp4.ucsd.edu!news.sdsc.edu!newshub.csu.net!csulb.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!eerie.fr!jussieu.fr!curie.fr!not-for-mail From: Alexis Gautreau Newsgroups: bionet.molbio.proteins Subject: Re: TCA precipitation of proteins Date: Sun, 16 Nov 1997 21:38:59 +0100 Organization: Institut Curie Lines: 15 Message-ID: <346F59E3.4697@curie.fr> References: <642qt4$1nda$1@news.inet.tele.dk> Reply-To: gautreau@curie.fr NNTP-Posting-Host: shift53.curie.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: fechner.curie.fr 879712548 2772 (None) 193.49.205.233 X-Complaints-To: usenet@fechner.curie.fr X-Mailer: Mozilla 3.01 [fr] (Win95; I) To: Jens Kondrup Jens Kondrup wrote: > > Is TCA better than PCA? > Jens Kondrup Hi, For precipitating proteins, just in order to reduce the volume, before a blot. I use a very simple protocol: Just complete the lysate up to 85%acetone spin 800g 5min (no fast zizz, as proteins precipitate stick to the tube) Dry the pellet 5 min at RT And resuspend in SDS-Loading buffer. Thats it! Alexis Gautreau -- ÐÏࡱá From owner-proteins@net.bio.net Sat Nov 15 22:00:00 1997 Path: biosci!LEONARDO.LS.HUJI.AC.IL!yoramg2 From: yoramg2@LEONARDO.LS.HUJI.AC.IL (Yoram Gerchman) Newsgroups: bionet.molbio.proteins Subject: BsA and pH Date: 16 Nov 1997 01:33:34 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Greetings to all. Dose anyone know of an effect of pH on BSA structure/function? ......................................................................... Yoram Gerchman Division of Microbial & Molecular Ecology The Institute of Life Sciences Hebrew University of Jerusalem Givat Ram, Jerusalem 91904, Israel Tel: 972-2-6585175 From owner-proteins@net.bio.net Sat Nov 15 22:00:00 1997 Path: biosci!agate!ihnp4.ucsd.edu!munnari.OZ.AU!metro!metro!news From: Phil Robinson Newsgroups: bionet.molbio.proteins Subject: Re: Phospho-amino acids>????? Date: Mon, 17 Nov 1997 10:12:23 +1100 Organization: CMRI, Sydney Lines: 22 Distribution: inet Message-ID: <346F7DD6.37708D47@postbox.usyd.edu.au> References: <64cnsa$de0$1@niobium.hgmp.mrc.ac.uk> Reply-To: phrobins@postbox.usyd.edu.au NNTP-Posting-Host: 129.78.220.141 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (Win95; I) To: "Mr. G. Morley" Mr. G. Morley wrote: > HI.. got a bit of a duff question here.. is it only the > phospho-tyrosine residues that can act as docking sites > for proteins? If so does this mean that the affects of phospho > serine and phospho threonine is entirely structural in nature? > I was just wondering as it occured to me the other day that > SH2 domains bind Y-p not Tp- or S-p and I could not think of anything > which did bind these amino acids.... if anyone does know > of an example I would greatly appreciate it... > thanks > gary morley > gmorley@rpms.ac.uk 14-3-3 proteins bind to phosphoserine. see..A. J. Muslin, J. W. Tanner, P. M. Allen, and A. S. Shaw. Interaction of 14-3-3 with signaling proteins is mediated by the recognition of phosphoserine. Cell 84:889-897, 1996. There are also a few more recent papers. Phil Robinson Sydney, Australia From owner-proteins@net.bio.net Sat Nov 15 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!204.127.161.1!wnfeed!worldnet.att.net!205.252.116.205!howland.erols.net!torn!kone!news.ccs.queensu.ca!not-for-mail From: 4jch3@qlink.queensu.ca (Hesketh J Christian) Newsgroups: bionet.molbio.proteins Subject: Ion Channel FTP site Date: 17 Nov 1997 04:21:02 GMT Organization: Queen's University, Kingston Lines: 20 Message-ID: <64ogne$ouo@knot.queensu.ca> NNTP-Posting-Host: qlink.queensu.ca X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] An ion channel FTP site has just been constructed. It contains image files of ion channel-related material. PDB files of ion channel ligands and models. Biophysical software is also available at this site. Several ion channel animations are also available. This site also accepts uploads of ionchannel-related material. Visit this free FTP site at: ftp://130.15.246.149 The login is anonymous, use your e-mail address as the password. Sincerely, --------------------------------------------------------------------------- J. Christian Hesketh Queen's University - Kingston, Canada Phone (613) 531-8048 e-mail: 4jch3@qlink.queensu.ca Web Page (Research in Ion Channels): http://qlink.queensu.ca/~4jch3 -Current research in ion channels with a biophysical perspective From owner-proteins@net.bio.net Sun Nov 16 22:00:00 1997 Path: biosci!daresbury!uninett.no!newsfeed.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!news-koe1.dfn.de!news.ruhr-uni-bochum.de!not-for-mail From: "Thorsten Schmidt" Newsgroups: bionet.molbio.proteins Subject: Big problems with cell-transfection Date: 17 Nov 1997 21:52:16 GMT Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 40 Message-ID: <01bcf3a2$f5b40b00$82019386@schmidtdw.rz.ruhr-uni-bochum.de> NNTP-Posting-Host: dialppp-1-130.rz.ruhr-uni-bochum.de X-Newsreader: Microsoft Internet News 4.70.1155 Dear reader! I have big problems with cell-transfection of mammalian cells. I want to transfect mammalian cells in cell culture with 1) expression vectors and/or 2) antisense oligos using liposomes. I tried two different liposomes: DOTAP (boehringer) and DAC-30 (Eurogentec). But my transfection efficiency is extremly low. I tested it with transfection of a beta-Gal vector and X-Gal histochemistry and found only 1-5 % stained cells! The problem is that I have to use 1) human and 2) neuronal / brain cell. And so, I tried TC 32 and U87 cells. Perhaps you can tell me a special cell line which can better be transfected and tell me where I can get it? It would be too kind if you´d send me an answer. Thank you so much in advance for yous assistance. Thorsten I have problems finding appropriate cells for transfection, From owner-proteins@net.bio.net Sun Nov 16 22:00:00 1997 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-fra1.dfn.de!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Robin Munro Newsgroups: bionet.molbio.proteins Subject: DRAGON and SAP release (ANNOUNCE) Date: Mon, 17 Nov 1997 17:58:30 +0000 Organization: MRC Lines: 53 Message-ID: <347085C6.3DCDF255@nimr.mrc.ac.uk> Reply-To: Robin.Munro@nimr.mrc.ac.uk NNTP-Posting-Host: proline.nimr.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX 6.3 IP32) ---- ATTENTION ALL PROTEIN MODELLERS ---- NEW DRAGON RELEASE, ** AND ** SAP STRUCTURE COMPARISON PROGRAM NOW AVAILABLE DRAGON Version 4.17.7 is now available in SGI executable format at the following site:- http://www.nimr.mrc.ac.uk/~mathbio/a-aszodi/dragon.html This is a minor update to the previous version (4.17.6) containing the following changes:- - OpenGL graphics is now supported in all three DRAGON executable formats; - an output file directory may be specified which will be created by the program if it does not exist already; - a few default parameter values have been changed; - the distributions now include the CLUMSY program for clustering the structures produced by DRAGON; - the N64 executables are tuned to the R10000 processor instead of the R8000. DRAGON is a protein modelling tool using Distance Geometry. It was developed at the Division of Mathematical Biology of the National Institute for Medical Research in London between 1993 and 1996. DRAGON attempts to predict the tertiary structure of a small soluble protein, given its sequence, the secondary structure and possibly a set of interresidue distance restraints. If the structures of some of the sequences in the multiple alignment is known, then you can attempt comparative modelling. DRAGON communicates with you through a simple command-line interface which is used to specify parameter values and input filenames. Further information and references can be found at:- http://www.nimr.mrc.ac.uk/~mathbio/a-aszodi/dragon.html#moinfo http://www.nimr.mrc.ac.uk/~mathbio/r-munro/dragon.html Enjoy! Andras Aszodi (PS. This message was posted by Robin Munro on behalf of A.A.) ------- SAP can be found at: ftp://glycine.nimr.mrc.ac.uk/pub/sap/ or links from a collection of protein links: http://www.nimr.mrc.ac.uk/~mathbio/r-munro/prot-link.html SAP is an updated program for the comparison of 2 protein structures (first implemented as SSAP) by Taylor and Orengo (1989). SAP returns a superposition of the 2 proteins in PDB format as well as printing the alignment information, score and RMSd's for the protein. A fast protein visualization tool (PROTDRAW) is also included for viewing proteins. Have fun, Robin Munro. From owner-proteins@net.bio.net Sun Nov 16 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!nih.gov!not-for-mail From: jhmiller@helix.nih.gov (Jay Miller) Newsgroups: bionet.molbio.proteins Subject: Re: BsA and pH Date: 17 Nov 1997 14:48:28 GMT Organization: National Institutes of Health Lines: 16 Distribution: world Message-ID: <64plfs$5rh$1@light.nih.gov> References: Reply-To: jhmiller@helix.nih.gov NNTP-Posting-Host: ams06057.niams.nih.gov X-Newsreader: IBM NewsReader/2 2.0 Going from pH 7.4 to 2.5 will slightly unfold BSA. We just looked at S (sub 20,w) and it went from 4.34 to 3.04. In , yoramg2@LEONARDO.LS.HUJI.AC.IL (Yoram Gerchman) writes: >Greetings to all. >Dose anyone know of an effect of pH on BSA structure/function? > >.......................................................................... >Yoram Gerchman >Division of Microbial & Molecular Ecology >The Institute of Life Sciences >Hebrew University of Jerusalem >Givat Ram, Jerusalem 91904, Israel >Tel: 972-2-6585175 > From owner-proteins@net.bio.net Sun Nov 16 22:00:00 1997 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!204.127.161.1!wnfeed!worldnet.att.net!205.252.116.205!howland.erols.net!recycled.news.erols.com!news-out.communique.net!communique!news.pn.com!nntp.pn.com!mozo.cc.purdue.edu!news From: Jelena Zaitseva Newsgroups: bionet.molbio.proteins Subject: Re: assay for protein-bound detergent wanted Date: 17 Nov 1997 18:54:42 GMT Organization: Dept. of Biochemistry, Purdue University Lines: 16 Message-ID: <64q3ti$68s@mozo.cc.purdue.edu> References: NNTP-Posting-Host: bc323a.biochem.purdue.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) Andrei.Zhukov@imm.ki.se (Andrei Zhukov) wrote: >I am isolating a membrane protein using a non-ionic, UV-absorbing, detergent with detergent removal at >the last step. Could anyone give me a reference to or description of a method to assay the amount of >residual detergent in my final preparation? > >Thank you in advance, >Andrei Zhukov Check out: J.Philippot "Biochimica et Biophysica Acta",734 (1983).137-143. Lena. From owner-proteins@net.bio.net Sun Nov 16 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!sunqbc.risq.qc.ca!rcogate.rco.qc.ca!clicnet!news.clic.net!usenet From: "Alain Gagné" Newsgroups: bionet.molbio.proteins Subject: Atherosclerosis in animals other than humans? Date: Mon, 17 Nov 1997 23:21:41 -0500 Organization: ClicNet Telecommunications, Inc. Lines: 52 Message-ID: <347117D3.FE3D1ACE@qbc.clic.net> NNTP-Posting-Host: pm-004.qbc.clic.net Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------D15F5A66AF2E2611B45235BE" X-Mailer: Mozilla 4.01 [en] (Win95; U) X-Priority: 3 (Normal) This is a multi-part message in MIME format. --------------D15F5A66AF2E2611B45235BE Content-Type: text/plain; charset=iso-8859-1 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Content-Transfer-Encoding: 8bit Hello I want to know if someone have information about atherosclerosis in animals. I know that it's frequent in humans, pig and monkey but i want to know if some mammals species was protected from having atherosclerosis in normal living conditions. I have read somewere that carnivores species ( dog, cats, mink ) are protected, is it true? References will be really appreciated. Please reply by e-mail if possible... Thanks for all! Alain Gagné, Biologist, Québec, Canada E-Mail: gagne@qbc.clic.net --------------D15F5A66AF2E2611B45235BE Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Gagné, Alain Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Gagné, Alain n: Gagné;Alain adr: 80 Paul Borduas;;;Loretteville;Québec;G2A 3M6;Canada email;internet: gagne@qbc.clic.net tel;work: 418-842-8203 tel;fax: 418-845-5887 tel;home: 418-842-8203 note: UIN: 2286441 x-mozilla-cpt: ;0 x-mozilla-html: TRUE end: vcard --------------D15F5A66AF2E2611B45235BE-- From owner-proteins@net.bio.net Sun Nov 16 22:00:00 1997 Path: biosci!TC3NET.COM!cola From: cola@TC3NET.COM (Nicolas Bayoff) Newsgroups: bionet.molbio.proteins Subject: (no subject) Date: 17 Nov 1997 16:00:20 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <3470DAC2.38DD@tc3net.com> NNTP-Posting-Host: net.bio.net I am trying to locate a bioactive test that will specifically differentiate between non-mammalian prolactin and somatotropin. Thank you Nicolas Bayoff From owner-proteins@net.bio.net Mon Nov 17 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!newsfeed.eerie.fr!newsfeed.nacamar.de!news.icm.edu.pl!news.task.gda.pl!sunrise.pg.gda.pl!not-for-mail From: "Szymon" Newsgroups: bionet.molbio.proteins Subject: Silicones Date: 18 Nov 1997 22:02:34 GMT Organization: Politechnika Gdanska Lines: 8 Message-ID: <01bcf46d$9dd006c0$0f02000a@ppp> NNTP-Posting-Host: amedec.amg.gda.pl X-Newsreader: Microsoft Internet News 4.70.1155 I have started working with problem of interaction between plasma proteins and silicone (polidimethylosiloxane). I wonder if someone here has some experience with examining conformational changes by turbidimetrical or nephelometrical methods, or with molecular modelling of such silicone structures (appropriate atom parameters, force fields, etc.). I would be gratefull for any information (I'm just a beginner, II year student) Szymon Zietkiewicz From owner-proteins@net.bio.net Mon Nov 17 22:00:00 1997 From: huntpharm@aol.com (Huntpharm) Newsgroups: bionet.molbio.proteins Subject: US-NY-JOB OPPORTUNITY IN EYE RESEARCH Date: 18 Nov 1997 12:49:16 GMT Lines: 16 Message-ID: <19971118124901.HAA03056@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com Path: biosci!news.ic.sunysb.edu!news-pen-15.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.131!news-pen-1.sprintlink.net!news-east.sprintlink.net!news-dc-26.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!152.163.199.19!portc03.blue.aol.com!audrey01.news.aol.com!not-for-mail I am looking for a Scientist to work in a lab evaluating the potential utility of neurotrophic factors in the treatment of retinal degeneration / injury. The candidate should be experienced in retinal biology with studies of the retina in developing and mature rodents. Working knowledge of techniques in the in vivo evaluation of the structural and function integrity of the retina. Relevant methodologies include eye surgery in small animals, retinal histology, measurement of ERG's, etc. Experienced with intraocular delivery of drugs and implantation of devices would be a plus. You should possess a Ph.D. or M.D. in neurobiology, ophthamology or realted field with 2 years postdoctoral experience. We are a leading biotech company with research facilities in Tarrytown, NY and can provide excellent benefits (health insurance, dental, and vision plan, stock options, paid vacation and more). A high impact, high profile position with excellent opportunity for advancement. Please contact Scott Shanes by phone at 609-584-8733 Ext. 218, fax CV and cover letter to 609-584-9575 or E-Mail to sis@diedrmoire.com From owner-proteins@net.bio.net Tue Nov 18 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!news.shef.ac.uk!not-for-mail From: MBP95GG@shef.ac.uk (G Garcia-asua) Newsgroups: bionet.molbio.proteins Subject: protein staining problems Date: 19 Nov 1997 19:37:47 GMT Organization: Your Organization Lines: 5 Message-ID: <64vf6b$g4c$1@bignews.shef.ac.uk> NNTP-Posting-Host: pc065095.shef.ac.uk Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 Why can't I stain my protein with coomasie, silver or anything else I've tried? Any help? Will Garcia-Asua From owner-proteins@net.bio.net Tue Nov 18 22:00:00 1997 Path: biosci!agate!howland.erols.net!surfnet.nl!newshost.vu.nl!not-for-mail From: Marisol Rodriguez Pena Newsgroups: bionet.molbio.proteins Subject: Re: Is a tagged protein more prone to degradation? (Lysis protocols??) Date: Wed, 19 Nov 1997 13:04:00 +0000 Organization: Vrije Universiteit, Amsterdam, The Netherlands Lines: 20 Message-ID: <3472E3C0.1461@chem.vu.nl> References: <64cbhr$jdp@singer.cent.gla.ac.uk> NNTP-Posting-Host: macdyn149.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) Is your protein in the membrane?. I did in the past western blots trying to detect GPCR tagged with Flag, HA or His epitopes in expression systems such as Cos or 293 and I got nothing. By that time I thought either the protein was degraded during membrane isolation, was not completely solubilized or the antibodies were not strong enought to resist the washing steps I was using because the receptor was expressed in binding assays (>1 pmol/mg prot) 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 Nov 18 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!dispose.news.demon.net!demon!newsfeed.nacamar.de!univ-lyon1.fr!pcb-briolay.univ-lyon1.fr!user From: nosjean@univ-lyon1.fr (Olivier Nosjean) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Structure prediction Date: 19 Nov 1997 12:12:22 GMT Organization: Univ. C. Bernard - Lyon 1 . France Message-ID: References: NNTP-Posting-Host: pcb-briolay.univ-lyon1.fr Lines: 26 In article (Dans l'article) , s9348190@scientia.up.ac.za wrote (écrivait) : > Hi > > I am interested in protein secondary structure prediction. Could anyone > suggest a good review, or website regarding this subject. > > I am also interested in software for this task! > > Thanks in advance > > Jonathan Tools and references on : http://www.ibcp.fr Olivier Olivier Nosjean Laboratoire de Physico-Chime Biologique Univ. C. Bernard - Lyon 1 France From owner-proteins@net.bio.net Tue Nov 18 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!uninett.no!newsfeed.nacamar.de!blackbush.xlink.net!rz.uni-karlsruhe.de!news.urz.uni-heidelberg.de!phoenix.mgen.uni-heidelberg.de!chw From: Christoph Winter Newsgroups: bionet.molbio.proteins Subject: Re: Solid-phase refolding Date: 19 Nov 1997 15:33:11 GMT Organization: MolGen Lines: 32 Distribution: world Message-ID: <64v0rn$qut@sun0.urz.uni-heidelberg.de> References: <64f8p9$2eb@sun0.urz.uni-heidelberg.de> NNTP-Posting-Host: phoenix.mgen.uni-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_68K X-XXMessage-ID: X-XXDate: Wed, 19 Nov 1997 15:33:11 GMT I (chw!) got another mail regarding the problem... From: Andrew Bradbury Pharmacia sell a very good anti-M13 HRP labelled polyclonal. Michael Tesar of GBF mte@GBF-Braunschweig.DE has an anti-g3p mAb which is very good, and Paola delmastro Galfre at IRBM (+39 6 910931) has some anti M13 mAbs, but I don't think she gives them out. good luck best wishes Andrew Bradbury Andrew Bradbury SISSA c/o ICGEB Area di Ricerca Padriciano 99 Trieste 34012 Italy Tel +39 40 398995 Fax +39 40 398991 bradbury@icgeb.trieste.it From owner-proteins@net.bio.net Tue Nov 18 22:00:00 1997 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.131!news-pen-1.sprintlink.net!news-east.sprintlink.net!news-dc-26.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!news.idt.net!news.voicenet.com!dsinc!nntp.upenn.edu!taurus.fccc.edu!sauder From: sauder@castor.fccc.edu (John Michael Sauder) Newsgroups: bionet.molbio.proteins Subject: Re: protein structure help req. Date: 19 Nov 1997 16:51:31 GMT Organization: Fox Chase Cancer Center, Philadelphia, PA Lines: 10 Message-ID: <64v5ej$f9f$1@taurus.fccc.edu> References: <879457402.22840.0.nnrp-09.9e98d597@news.demon.co.uk> NNTP-Posting-Host: castor.rm.fccc.edu In article <879457402.22840.0.nnrp-09.9e98d597@news.demon.co.uk> "mark" writes: >as part of my wifes studies in biology she has been requested to give an >account of the structure of proteins and using suitable examples explain how >their structure enables them to carry out their function,showing relevant >diagrams. > mark@busi-solgro.demon.co.uk Any recent Biochemistry textbook should be able to give a sufficient level of information on exactly this. (Or at least have a few references that also might prove helpful.) From owner-proteins@net.bio.net Tue Nov 18 22:00:00 1997 Path: biosci!TC3NET.COM!cola From: cola@TC3NET.COM (Nicolas Bayoff) Newsgroups: bionet.molbio.proteins Subject: hormones Date: 19 Nov 1997 08:31:26 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <34731472.2C9E@tc3net.com> NNTP-Posting-Host: net.bio.net Does anyone know of a source for affinity purified polyconal antibodies against chicken somatotropin and against prolactin. I am working with reptilian samples and need to differentiate my samples. Thank you Nicolas Bayoff From owner-proteins@net.bio.net Tue Nov 18 22:00:00 1997 Path: biosci!agate!howland.erols.net!csir.uni.net.za!news.up.ac.za!b027pc245.up.ac.za!s9348190 From: s9348190@scientia.up.ac.za Newsgroups: bionet.molbio.proteins Subject: Protein Structure prediction Date: Wed, 19 Nov 1997 11:51:17 Organization: University of Pretoria Lines: 10 Message-ID: NNTP-Posting-Host: b027pc245.up.ac.za X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Hi I am interested in protein secondary structure prediction. Could anyone suggest a good review, or website regarding this subject. I am also interested in software for this task! Thanks in advance Jonathan From owner-proteins@net.bio.net Wed Nov 19 22:00:00 1997 Path: biosci!rutgers!uwm.edu!news-penn.gip.net!news-peer.gip.net!news.gsl.net!gip.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!uunetukout!join.news.pipex.net!pipex!uunetukin!server1.netnews.ja.net!hgmp.mrc.ac.uk!mail.dcs.warwick.ac.uk!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins Subject: Re: protein staining problems Date: Thu, 20 Nov 1997 11:12:31 -0800 Organization: University of Leicester (PCFS User) Lines: 11 Message-ID: <34748B9F.1B9D@le.ac.uk> References: <64vf6b$g4c$1@bignews.shef.ac.uk> NNTP-Posting-Host: pc47.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win16; I) G Garcia-asua wrote: > > Why can't I stain my protein with coomasie, silver or anything else > I've tried? Any help? A little bit more information would be needed to answer your question. What is your sample and how was it treated? Presumably you are talking about the staining of proteins in gels after electrophoresis. Which method did you use here: Laemli, Weber-Osborn, Lichtner-Wolf...? Round gels, large flat gels, minigels? Which staining methods did you use? For silver staining alone there must be dozens of recepies. From owner-proteins@net.bio.net Wed Nov 19 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!uninett.no!sn.no!news-stkh.gip.net!news.gsl.net!gip.net!news.kolumbus.fi!news.uninet.ee!kadri.ut.ee!tamm!mspeek From: mspeek@tamm.eenet.ee (Mart Speek) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Structure prediction Date: 20 Nov 1997 09:26:06 GMT Organization: Estonian Biocentre Lines: 36 Message-ID: <650vne$l83$1@kadri.ut.ee> References: NNTP-Posting-Host: tamm.ebc.ee Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: kadri.ut.ee 880017966 21763 (None) 193.40.23.2 X-Complaints-To: usenet@kadri.ut.ee X-Newsreader: TIN [version 1.2 PL2] Dear Jonathan; I think you might want to try PhD method of B. Rost & C. Sander, availabile online at: http://www.public.iastate.edu/~pedro/pprotein_query.html thru ---> Pedro biom. res. tools at: http://www.fmi.ch/biology/rt_1.html Your sequence request will be processed and result returned by email!!! Refs: Profile network prediction of secondary structure (PHDsec): Rost, Burkhard; Sander, Chris: Prediction of protein structure at better than 70% accuracy. J. Mol. Biol., 1993, Vol. 232, pp. 584-599. HOPE this HELPS! Martz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | * | Mart Speek, PhD | | * * | Assistant Professor | | * o o * | 46 Vanemuise St. rm 138 | | * - * | Chair of Biochemistry | | * - * * * | Institute of Molecular and Cell Biology | | * - * *. .* | University of Tartu | | * - * * ^ * | Tartu, EE2400 | | * - * *-* | ESTONIA (Europe) | |* * - * *-* *| tel(fax): 372-7-465823 (838) | |* * * - * * * * *-* * *| email: mspeek@ebc.ee | -------------------------------------------------------------------- From owner-proteins@net.bio.net Wed Nov 19 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.ecrc.net!newsfeed.nacamar.de!newsfeed.eerie.fr!jussieu.fr!univ-lille1.fr!not-for-mail From: Cyril Ruckebusch Newsgroups: bionet.molbio.proteins Subject: infrared spectro study of hemoglobin Date: Thu, 20 Nov 1997 18:11:48 +0100 Organization: Universite des Sciences et Technologies de LILLE, France Lines: 7 Message-ID: <34746F54.6B27EA6D@univ-lille1.fr> NNTP-Posting-Host: pcirtf4.univ-lille1.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.02 [en] (Win95; I) hi, Has anyone already study Hemoglobin using Fourier Transform IR for concentrations as low as 0.2% in water-alcohol solution. The ultimate achievement is to drive a synthesis of peptides using IR spectroscopic suitable captors (which do not exist). Thanks for any kind of suggestion From owner-proteins@net.bio.net Wed Nov 19 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!F.Wouters From: F.Wouters@nospam.icrf.icnet.uk (Dr. Fred S. Wouters) Newsgroups: bionet.molbio.proteins,bionet.molec-model,sci.bio.misc Subject: Re: Help needed finding molecular picture Date: 20 Nov 1997 18:04:02 GMT Organization: ICRF Lines: 24 Message-ID: References: <34563B99.53F3A1E5@neiu.edu> NNTP-Posting-Host: 143.65.52.69 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.proteins:11915 bionet.molec-model:1939 In article <34563B99.53F3A1E5@neiu.edu>, Wayne Genualdi wrote: > Biology newsgroups, > > I am in search of 2 pictures... one molecular picture of > chicken egg protein and another molecular picture of a cooked or > denatured chicken egg protein. I don't know the actual names of the > proteins because I am unfamiliar with the biology terminology. I have > looked at several web book databases, but I really don't know what I am > looking for. If you know what the molecular structures are called or > know where to find molecular pictures of them on the web, please contact > me. Thank you. > > Wayne Genualdi Hi, I'd say you're looking for ovalbumin. Suggest you try searching brookhaven protein database (PDB). good luck! -- remove nospam from e-mail adress to reply From owner-proteins@net.bio.net Wed Nov 19 22:00:00 1997 Path: biosci!rutgers!news-relay.ncren.net!nntp-xfer.ncsu.edu!not-for-mail From: Brett Phinney Newsgroups: bionet.molbio.proteins Subject: Protein, RNA and Lipid Separation Date: Thu, 20 Nov 1997 10:08:35 -0500 Organization: NC State University Lines: 18 Message-ID: <34745273.ACA8141D@mail.urtexas.edu> NNTP-Posting-Host: bch112.bch.ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (Win95; I) I'm working with a membrane containing virus and I was wondering if there was an easy way to separate the membrane proteins from the membrane lipids and the viruses RNA. As a side question, when I load whole virus on a SDS-PAGE gel, I can get a good separation of the proteins I am looking for. My question is, what happens to the RNA and Lipids that get loaded onto the gel? Do they run through the gel, get stuck at the top, or complex with my proteins somehow? Thanks a lot in advance Brett From owner-proteins@net.bio.net Wed Nov 19 22:00:00 1997 Path: biosci!rutgers!uwm.edu!news-penn.gip.net!news-peer.gip.net!news.gsl.net!gip.net!sunqbc.risq.qc.ca!news.uow.edu.au!metro!metro!news From: Phil Robinson Newsgroups: bionet.molbio.proteins Subject: Web site for crystal structure prediction? Date: Fri, 21 Nov 1997 08:16:46 +1100 Organization: CMRI, Sydney Lines: 11 Distribution: inet Message-ID: <3474A8BE.D7CF1052@postbox.usyd.edu.au> Reply-To: phrobins@postbox.usyd.edu.au NNTP-Posting-Host: 129.78.220.136 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (Win95; I) I have heard there is a web site for submitting a protein sequence and having it modelled against the known crystal structure of a related protein. The output is supposed to be a pdb file, which I can then view on my PC with Web Lab Viewer or other viewer. Does anyone have an URL for such a modelling site? I cannot find it. I realiase there are major limitations on such predictions, but there are also some useful aspects. Thanks, Phil Sydney, Australia From owner-proteins@net.bio.net Thu Nov 20 22:00:00 1997 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-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!199.1.13.10!news1.channel1.com!news.pn.com!nntp.pn.com!news-feeder.onramp.net!news.onramp.net!news From: "Cynthia S. Smagula" Newsgroups: bionet.molbio.proteins Subject: BioToolKit: Protein Structural Imaging and Analysis Tools Date: Fri, 21 Nov 1997 20:10:45 -0500 Organization: BIOTA Publications Lines: 15 Message-ID: <3476310E.5ACA@onramp.net> Reply-To: biota@onramp.net NNTP-Posting-Host: isdn14-57.dllstx.onramp.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) The BioToolKit, now hosted by BioSupplyNet at http://www.biosupplynet.com provides links to nearly 200 protein structural imaging and analysis tools . The BioToolKit, a searchable and browsable database of 400 internet research applications, includes up-to-date links to nucleic acid, genome, and protein databases, online applications for data retrieval and data analysis, and tools for molecular visualization. The BioToolKit is designed for speed, with pulldown menus to provide rapid access to each section. The BioSupplyNet web site is the online companion to the Source Book, a comprehensive directory of molecular biology products and suppliers. The Source Book was originally published by the Cold Spring Harbor Laboratory Press to supply essential information on sources of reagents and supplies to users of the well-known Molecular Cloning Manuals published by CSHLP. From owner-proteins@net.bio.net Thu Nov 20 22:00:00 1997 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!logbridge.uoregon.edu!sunqbc.risq.qc.ca!newsfeed.eerie.fr!jussieu.fr!centre.univ-orleans.fr!univ-tours.fr!MOREAUT From: moreaut@univ-tours.fr Newsgroups: bionet.molbio.proteins Subject: Assay for allosteric enzymes Date: 21 Nov 1997 09:04:45 GMT Organization: Universite de TOURS - France Lines: 26 Message-ID: <653ird$lqg@centre.univ-orleans.fr> Reply-To: moreaut@univ-tours.fr NNTP-Posting-Host: balzac.univ-tours.fr dear readers, I would like to setup a one-day practical session related to allosteric enzyme kinetics for bachelor's degree students. The enzyme they were studying up to now was rabbit phosphorylase b but I am not satisfied with the assay. Then I am looking for another allosteric enzyme to study, preferentially commercially available and assayed with a photometric procedure. I was thinking to phosphofructokinase or ATC (Aspartate Trans Carbamylase) but I have no idea if this system is appropriate. Any ideas or a detailed protocol are welcomed. Thank you very much in advance for your assistance. Thierry Moreau *---------------------------------------------------------------------------* | Dr. Thierry MOREAU | | Laboratoire d'Enzymologie et Chimie des Proteines | | CNRS EP 117 Phone: (33) 02 47 36 61 77 | | 2bis, Bd Tonnelle Fax: (33) 02 47 36 60 46 | | 37032 TOURS cedex FRANCE Email: moreaut@univ-tours.fr | | | | Please visit PROLYSIS at: http://delphi.phys.univ-tours.fr/Prolysis | *------------