From owner-proteins@net.bio.net Sat Jun 01 23:00:00 1996 Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!sgigate.sgi.com!nntp.coast.net!fu-berlin.de!news.belwue.de!news.uni-hohenheim.de!wpxx02.toxi.uni-wuerzburg.de!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: How to purify 16kD protein Date: 2 Jun 1996 17:32:22 GMT Organization: CC University of Hohenheim (not responsible for contents) Lines: 19 Message-ID: <4osj76$1goc@power5.rz.uni-hohenheim.de> References: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Mary P. Remington (mremingt@umabnet.ab.umd.edu) wrote: > A friend needs to purify this protein from a 4 liter culture of > bacteria that is producing. She intents to do a cesium gradient. Is > there another protocol available similar to the Qiagen columns for this > type of protocol? Thanks, Mary I've never heard of the use of cesium chloride gradients for protein purification. Protein would most likely float at the top. To give you more information, it would be necessary for you to share with us what kind of protein it is (not just the size; there are plenty of proteins with approximately that size). --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Sat Jun 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!chi-news.cic.net!news.compuserve.com!news.production.compuserve.com!news From: Survey Administration <74750.1341@CompuServe.COM> Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.molbio.recombination,bionet.molbio.yeast Subject: WE NEED YOUR INPUT Date: 3 Jun 1996 03:20:05 GMT Organization: Kitty Knight Corporation Lines: 25 Message-ID: <4otll5$3ni$6@mhade.production.compuserve.com> Xref: biosci bionet.molbio.methds-reagnts:45225 bionet.molbio.proteins:8022 bionet.molbio.recombination:193 bionet.molbio.yeast:5356 Please excuse this brief intrusion, but we are trying to locate any and all holders of academic degrees conferred within the last ten (10) years. The Kitty Knight Corporation, Boston, MA, is currently searching for qualified individuals to participate in a ***PAID*** study focusing on post-secondary, graduate, and professional education in the United States. Holders of ALL types of degrees in ALL fields of study are needed. We would like to hear from you as long as your degree was earned at an accredited institution in the United States. After an initial screening, qualified participant will be asked to complete a questionaire of approx 150 questions. Everyone who completes the survey will receive a $100 stipend. Naturally, *ALL* information will be held in the strictest confidence. To express interest, please send your name, mailing address, and photocopies of **ALL** degrees you have earned to: The Kitty Knight Corporation, Attn: Study 96-3H, Back Bay Annex, P O Box 546, Boston, MA 02117. (If not obvious from the degree, please indicate the field of study.) Thank You Very Much! From owner-proteins@net.bio.net Sat Jun 01 23:00:00 1996 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!news.uwa.edu.au!newsman.murdoch.edu.au!usenet From: oxberry@numbat.murdoch.edu.au (Megan) Newsgroups: bionet.molbio.proteins Subject: Autoradiography of PAGE gels - please help Date: 3 Jun 1996 01:49:11 GMT Lines: 17 Sender: -Not-Authenticated-[3595] Message-ID: <4otgan$bfv@newsman.murdoch.edu.au> NNTP-Posting-Host: vetmac26.murdoch.edu.au X-Posted-From: InterNews 1.0.1@vetmac26.murdoch.edu.au Xdisclaimer: No attempt was made to authenticate the sender's name. I am trying to identify the protein to which a drug is binding in a unicellular organism using autoradiography and native PAGE gels. I have been adding tritium labelled drug to sonicated cells (with protease inhibitor), incubating the lysate at 4¡C for 24h then running it on a gel. I then fix the gel in 2-propanol/water/acetic acid (25:65:10) for 30min and soak it in Amlify (Amersham) for 30min in the dark. I then dry the gel at 80¡C for 2h on to filter paper and place it against Hyperfilm MP (preflashed) in a cassette for 1-2 weeks at -80¡C. I have had no success at all with this technique even with the positive control I have been using. I would be most grateful for any suggestions regarding this. Thankyou, Megan From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!MANI.CBS.UMN.EDU!npv From: npv@MANI.CBS.UMN.EDU (Nora Plesofsky-Vig) Newsgroups: bionet.molbio.proteins Subject: re: autoradiography of PAGE gels Date: 3 Jun 1996 09:05:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <9606031700.AA00484@mani.cbs.umn.edu> Reply-To: nora@biosci.cbs.umn.edu NNTP-Posting-Host: net.bio.net Megan: It seems likely to me that you may be losing the tritiated drug during the gel fixation step in isopropanol/acetic acid. Is it possible for you to label the drug with carbon-14 and dispense with both the fixation and the Amplify steps for the gel? An alternative would be to cross-link the drug to the protein. Good luck Nora Plesofsky-Vig From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!rutgers!csn!nntp-xfer-1.csn.net!imci3!newsfeed.internetmci.com!in1.uu.net!wizard.pn.com!brighton.openmarket.com!decwrl!tribune.usask.ca!skyfox.usask.ca!yangj From: yangj@skyfox.usask.ca Newsgroups: bionet.molbio.proteins Subject: Energies of hydrogen bonds in proteins Date: 3 JUN 96 11:37:24 GMT Organization: University of Saskatchewan Lines: 9 Message-ID: <3JUN96.11372422@skyfox.usask.ca> NNTP-Posting-Host: sask.usask.ca Hello, everyone, could anybody tell me the energies for hydrogen bonds O-H...O and N-H...O in proteins? Thx in advance for your help. Jian Yang Department of Chemistry University of Saskatchewan Saskatoon, Saskatchewan Canada S7N 5C9 Tel: (306) 966 4366 Email: yangj@sask.usask.ca From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!ott.istar!istar.net!van.istar!van-bc!unixg.ubc.ca!news.bc.net!rover.ucs.ualberta.ca!valiene.biology.ualberta.ca!wgallin From: wgallin@gpu.srv.ualberta.ca (Warren Gallin) Newsgroups: bionet.molbio.proteins Subject: Re: Autoradiography of PAGE gels - please help Date: Mon, 3 Jun 96 15:58:07 GMT Organization: University of Alberta Lines: 28 Message-ID: References: <4otgan$bfv@newsman.murdoch.edu.au> NNTP-Posting-Host: valiene.biology.ualberta.ca X-Newsreader: VersaTerm Link v1.1.4 Although your gel conditions may be non-denaturing, your fixation and enhancement conditions certainly are not. I would guess that even if the drug maintains binding during your electrophoresis step, your are dissoicating the complex and washing away the drug in the post-electrophoresis processing. What you may want to do is to try transferring the proteins from the gel to a membrane and blot with the drug under renaturing conditions. In Article <4otgan$bfv@newsman.murdoch.edu.au>, oxberry@numbat.murdoch.edu.au (Megan) wrote: >I am trying to identify the protein to which a drug is binding in a >unicellular organism using autoradiography and native PAGE gels. I >have been adding tritium labelled drug to sonicated cells (with >protease inhibitor), incubating the lysate at 4oC for 24h then running >it on a gel. I then fix the gel in 2-propanol/water/acetic acid >(25:65:10) for 30min and soak it in Amlify (Amersham) for 30min in the >dark. I then dry the gel at 80oC for 2h on to filter paper and place >it against Hyperfilm MP (preflashed) in a cassette for 1-2 weeks at >-80oC. > >I have had no success at all with this technique even with the positive >control I have been using. Warren Gallin Department of Biological Sciences University of Alberta Edmonton, Alberta T6G 2E9 Canada wgallin@gpu.srv.ualberta.ca From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!sdd.hp.com!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!msvax.mssm.edu!MING From: ming@msvax.mssm.edu Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.molbio.recombination,bionet.molbio.yeast Subject: Re: WE NEED YOUR INPUT Date: 3 Jun 1996 20:37:11 GMT Organization: Mount Sinai Medical Center, New York City Lines: 26 Message-ID: <4ovidn$pmh@news.cuny.edu> References: <4otll5$3ni$6@mhade.production.compuserve.com> Reply-To: ming@msvax.mssm.edu NNTP-Posting-Host: msvax.mssm.edu Xref: biosci bionet.molbio.methds-reagnts:45262 bionet.molbio.proteins:8027 bionet.molbio.recombination:194 bionet.molbio.yeast:5359 In article <4otll5$3ni$6@mhade.production.compuserve.com>, Survey Administration <74750.1341@CompuServe.COM> writes: >Please excuse this brief intrusion, but we are trying to locate >any and all holders of academic degrees conferred within the last >ten (10) years. > >The Kitty Knight Corporation, Boston, MA, is currently searching >for qualified individuals to participate in a ***PAID*** study >focusing on post-secondary, graduate, and professional education >in the United States. > >Holders of ALL types of degrees in ALL fields of study are needed. > We would like to hear from you as long as your degree was earned >at an accredited institution in the United States. > >After an initial screening, qualified participant will be asked to >complete a questionaire of approx 150 questions. Everyone who >completes the survey will receive a $100 stipend. Naturally, >*ALL* information will be held in the strictest confidence. > >To express interest, please send your name, mailing address, and >photocopies of **ALL** degrees you have earned to: The Kitty >Knight Corporation, Attn: Study 96-3H, Back Bay Annex, P O Box >546, Boston, MA 02117. (If not obvious from the degree, please >indicate the field of study.) > >Thank You Very Much! From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!newsserver.jvnc.net!crick.bms.com!usenet From: krystek@alcor.bms.com (Stanley Krystek) Newsgroups: bionet.molbio.proteins Subject: David Parry address Date: 03 Jun 1996 17:16:36 -0400 Organization: Bristol-Myers Squibb, Macromolecular Structure Lines: 13 Sender: krystek@alcor.bms.com Message-ID: NNTP-Posting-Host: alcor.bms.com X-Newsreader: Gnus v5.1 I am looking for the e-mail of David Parry dept of physics and biophysics, massey university thanks in advance -- Stan Krystek Bristol-Myers Squibb krystek@alcor.bms.com From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!waikato!comp.vuw.ac.nz!pc155 From: StentV@agresearch.cri.nz (Vicki Stent) Newsgroups: bionet.molbio.proteins Subject: Solubilising proteins Date: Tue, 04 Jun 96 03:23:05 GMT Organization: AgResearch, Wallaceville Lines: 11 Message-ID: <4p0djf$ca@st-james.comp.vuw.ac.nz> NNTP-Posting-Host: pc155.warc.cri.nz X-Newsreader: News Xpress Version 1.0 Beta #4 I have a 6-His tag protein that is expressed using Novagen's pET vector system. With induction huge amounts of the protein are expressed in an insoluble form (prob. located in inclusion bodies). I would like to know of any ideas/techniques on how to solubilise my protein so I can then attempt to purify the protein by affinity chromatography - I already have some ideas but would be interested in what others have to say. Please email me if you can help. Vicki Stent email: Stentv@agresearch.cri.nz From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!chi-news.cic.net!newsxfer2.itd.umich.edu!news.eecs.umich.edu!newshub.tc.umn.edu!newsstand.tc.umn.edu!maroon.tc.umn.edu!rosto001 From: rosto001@maroon.tc.umn.edu (Alexander P Rostovtsev) Newsgroups: bionet.molbio.proteins Subject: NLS peptide/Multiple Peptide Systems Date: 3 Jun 1996 15:34:25 -0500 Organization: University of Minnesota Lines: 9 Message-ID: NNTP-Posting-Host: maroony.tc.umn.edu Keywords: NLS, SV40 I'm looking for a phone number or e-mail address of Multiple Peptide Synthesis company located in San Diego. These guys make so-called Nuclear Localization Signal (NLS) CGGPKKKRKVG-NH2. If somebody could provide me their address or indicate an alternative supplier it would be greatly appreciated. Dr. Alexander Rostovtsev Biotherapy Program U of Minnesota From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!newsjunkie.ans.net!newsfeeds.ans.net!rcogate.rco.qc.ca!altitude!usenet From: Achim Recktenwald Newsgroups: bionet.molbio.proteins Subject: Re: PAGE of Glycoproteins Date: Mon, 03 Jun 1996 09:27:43 -0500 Organization: IBEX Technologies, Inc. Lines: 45 Message-ID: <31B2F65F.1AD0@ibex.ca> References: <1996May31.180636.1@vmsuser.acsu.unsw.edu.au> NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; PPC) p9001808@vmsuser.acsu.unsw.edu.au wrote: > > We have been trying to identify a membrane bound glycoprotein from a protozoan > for some months now. We run the crude membrane extract on SDS PAGE 12% (4% > stacking gel) and electroblot to PVDF membrane. > By carbohydrate staining we have discovered that the glycoprotein won't > even go into the stacking gel and further, will not transfer to the membrane. > We have tried several brands of PVDF to no avail. > We have investigated the possibility that we have not properly solubilized > the membrane (all samples incubated at 95 degrees C for 6 min 1% SDS 800mM > 2-b-mercaptoethanol and 100mM 2-b-mercaptoethanol included in the PAGE running > buffer) but this has not helped. Does anyone have any ideas or suggestions? > > > David Cross > University of NSW Australia > p9001808@vmsuser.acsu.UNSW.edu.au Glycosylated proteins cannot bind SDS very well ('normal' proteins bind 1.4g/g protein). While most of them bind enough to run in the gel, though at a higher molecular weight, you seem to be working on one which does not like SDS at all. At least this is in my view the easiest explanation to your problem. What is thew molecular weight of the protein ? You could also run into problems, if it is one of the giant ones. Can you run your gel in native electrophoresis? If, yes it would exclude problems due to size. Try to remove the glycosylation by endoH or some other appropriate glycosylase. If the glycosylation is the problem, you should see a difference during SDS-electrophoresis and blotting. Achim ______________________________ Achim Recktenwald, PhD IBEX Technologies, Inc. 5485 rue Pare Montreal, PQ, H4A 2Z9 achim@ibex.ca From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!uwm.edu!news.cse.psu.edu!news.eecs.nwu.edu!newsfeed.acns.nwu.edu!news.cc.uic.edu!usenet From: Keld Sorensen Newsgroups: bionet.molbio.proteins Subject: Re: David Parry address Date: Mon, 03 Jun 1996 17:00:11 -0600 Organization: University of Illinois, College of Medicine Lines: 4 Message-ID: <31B36E7B.1ACB@uic.edu> References: NNTP-Posting-Host: sliprock-02.dialin.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) To: Stanley Krystek Take a look at http://www.four11.com or http://altavista.digital.com From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!metro!news From: jtaylor@medicine.su.oz.au Newsgroups: bionet.molbio.proteins Subject: gel filtration using organic solvents Date: Mon, 03 Jun 1996 03:12:43 GMT Organization: Information Services, The University of Sydney, NSW, Australia Lines: 10 Distribution: inet Message-ID: <4otp17$jab@metro.usyd.edu.au> NNTP-Posting-Host: neuro1.medicine.su.oz.au X-Newsreader: Forte Free Agent 1.0.82 Does anyone know of gel filtration media compatible with organic solvents such as methanol/chloroform that would be suitable for the fractionation of proteins of 10kD-40kD in size? If so could you please E-mail me - jtaylor@medicine.su.oz.au Thanks in advance. From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!sgigate.sgi.com!esiee.fr!jussieu.fr!univ-angers.fr!ciril.fr!usenet From: ferrari@ctrmed.u-nancy.fr (Luc Ferrari) Newsgroups: bionet.molbio.proteins Subject: Re: assay for cytochrome p450 Date: Tue, 04 Jun 1996 07:37:30 GMT Organization: CIRIL, Nancy, France Lines: 34 Message-ID: <4p0lha$9qa@arcturus.ciril.fr> References: NNTP-Posting-Host: microferrari.ctrmed.u-nancy.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Forte Free Agent 1.0.82 "Q. Shang" a écrit: >Hi there, >Does anybody know an assay for cytochrome p450 that would work in a crude >protein extract? I can not use absorbance spectrum because it's not >sensitive enough and there will probably be lots of interference from >other things in the extract. Can I use a peroxidase assay, like they do >with hemoglobin? >Any comments will be greatly appreciated. Hi Tanya, I am surprised that you find spectrum assay not enough sensible. We have the habit to test P450 by this technique and detect small amount to 10 ng/mg of proteins. You should test the technique described by JF Ghersi-Egea in J. Neurosc. Methods 20: 261-269. It also depend of the nature of your protein extract.... Is it full cell or full tissu, or microsomes or mitocondria ?? Sincerely yours Luc Toute opinion exprimée est personelle, et non celle de mon employeur. Luc Ferrari Tél: 83.17.88.02 Centre du Médicament Fax: 83.32.13.22 Faculté de Pharmacie E-mail: ferrari@ctrmed.u-nancy.fr 54000 Nancy From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!news.ac.net!news.cais.net!nntp.uio.no!Norway.EU.net!oslonett.no!sn.no!usenet From: Martin Wardenær Newsgroups: bionet.molbio.proteins Subject: Help: Bioluminescence! Date: Tue, 04 Jun 1996 03:21:23 +0200 Organization: SN Internett Lines: 35 Message-ID: <31B38F93.5C0@sn.no> NNTP-Posting-Host: nm9-1.ppp.sn.no Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win95; I) I have an idea. It has the potential of commercial application, but there are some technical stuff that I need to dig up before I know how it can be done... Bioluminescence is really *not* my field, so I was hoping that someone out there with the appropriate knowledge could fill in some of the blanks. It all boils down to this: Is there a substance (or a set of substances) that 1) has (significant) fluorescent properties and 2) has no "side-effects" to humans (one should be able to drink it without suffering any harm)? (The substance(s) would have to be contained in some fluid form). My uneducated guess has been that bioluminescence is the most probable field within one would find substances that fit such criteria (due to its occurrence in other living organisms). During my sessions at the library, I have come across the reaction between luciferin and luciferase. If I have got it right (from those ancient books...), these will, in the presence of oxygen, react and produce light of some yellow-greenish hue. Also, there are supposed to be many variations of these reactions, with varying builds of luciferin and luciferase. I am not sure whether this is correct, or if so, if there exists any better suited substances/reactions. I would be deeply grateful if anyone could provide me with some information on this (or possibly, point me towards some other source of information). Of course, I can and will be more specific on the criteria and use of the substance(s) when/if necessary. Thanks. -- Martin Wardenaer Art Director NoNonsense From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!taligent!ames!news.tulane.edu!news.starnet.net!newsreader.wustl.edu!biodec.wustl.edu!graham From: graham@biodec.wustl.edu (James Graham) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.molbio.recombination,bionet.molbio.yeast Subject: Re: WE NEED YOUR INPUT Date: 3 Jun 1996 16:51:09 -0500 Organization: Washington University Biology, St. Louis, MO Lines: 12 Message-ID: References: <4otll5$3ni$6@mhade.production.compuserve.com> NNTP-Posting-Host: @biodec.wustl.edu X-Newsreader: NN version 6.5.0 #1 (NOV) Xref: biosci bionet.molbio.methds-reagnts:45267 bionet.molbio.proteins:8029 bionet.molbio.recombination:195 bionet.molbio.yeast:5360 > To express interest, please send your name, mailing address, and > photocopies of **ALL** degrees you have earned to: Careful folks. Why would it be necessary to send actual copies of anything in order to merely "express interest" in a survey? (They're probalby building a directed marketing database from the information you send "expressing interest".) Jim J. Graham PhD Biology Department From owner-proteins@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in2.uu.net!news.u.washington.edu!homer22.u.washington.edu!qshang From: "Q. Shang" Newsgroups: bionet.molbio.proteins Subject: assay for cytochrome p450 Date: Mon, 3 Jun 1996 16:24:02 -0700 Organization: University of Washington Lines: 23 Message-ID: NNTP-Posting-Host: homer22.u.washington.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII NNTP-Posting-User: qshang Hi there, Does anybody know an assay for cytochrome p450 that would work in a crude protein extract? I can not use absorbance spectrum because it's not sensitive enough and there will probably be lots of interference from other things in the extract. Can I use a peroxidase assay, like they do with hemoglobin? Any comments will be greatly appreciated. Tanya ----------------------------- Tanya Shang Department of Biochemistry Box 357350 University of Washington Seattle, WA 98195 qshang@u.washington.edu ----------------------------- From owner-proteins@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!netnews.nwnet.net!news.u.washington.edu!homer10.u.washington.edu!qshang From: "Q. Shang" Newsgroups: bionet.molbio.proteins Subject: Re: assay for cytochrome p450 Date: Tue, 4 Jun 1996 09:57:39 -0700 Organization: University of Washington Lines: 15 Message-ID: References: <4p0lha$9qa@arcturus.ciril.fr> NNTP-Posting-Host: homer10.u.washington.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII NNTP-Posting-User: qshang In-Reply-To: <4p0lha$9qa@arcturus.ciril.fr> To clarify my question: the samples I will be using is total cell extract from plant cell culture; sometimes salt fractionated cell extract. Luc, thanks for your suggestions. Tanya ----------------------------- Tanya Shang Department of Biochemistry Box 357350 University of Washington Seattle, WA 98195 qshang@u.washington.edu ----------------------------- From owner-proteins@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!IRIS.LSC.PKU.EDU.CN!lisl From: lisl@IRIS.LSC.PKU.EDU.CN (Li Songlin) Newsgroups: bionet.molbio.proteins Subject: (none) Date: 4 Jun 1996 03:33:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9606050115.AA15351@IRIS.lsc.pku.edu.cn> NNTP-Posting-Host: net.bio.net From owner-proteins@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!sgigate.sgi.com!nntp.coast.net!fu-berlin.de!news.belwue.de!news.uni-hohenheim.de!wpxx02.toxi.uni-wuerzburg.de!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Autoradiography of PAGE gels - please help Date: 4 Jun 1996 11:01:43 GMT Organization: CC University of Hohenheim (not responsible for contents) Lines: 29 Message-ID: <4p152n$h0q@power5.rz.uni-hohenheim.de> References: <4otgan$bfv@newsman.murdoch.edu.au> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Megan (oxberry@numbat.murdoch.edu.au) wrote: > I am trying to identify the protein to which a drug is binding in a > unicellular organism using autoradiography and native PAGE gels. I > have been adding tritium labelled drug to sonicated cells (with > protease inhibitor), incubating the lysate at 4¡C for 24h then running > it on a gel. I then fix the gel in 2-propanol/water/acetic acid > (25:65:10) for 30min and soak it in Amlify (Amersham) for 30min in the > dark. I then dry the gel at 80¡C for 2h on to filter paper and place > it against Hyperfilm MP (preflashed) in a cassette for 1-2 weeks at > -80¡C. > > I have had no success at all with this technique even with the positive > control I have been using. Would it be possible to photocrosslink the drug to the binding protein? The failure of the control to work is an indication that either the affinity of the drug to the protein might be too low or that the protein is denatured during the process (fixation is likely to denature your protein; after all, most proteins do not survive 10% acetic acid...). I have no experience myself with this kind of stuff, so the above are only suggestions. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!news.service.uci.edu!rablab.biochem.uci.edu!user From: dmthomas@orion.oac.uci.edu (Didier Thomas) Newsgroups: bionet.molbio.proteins Subject: Swiss 3T3 transfection Date: Tue, 04 Jun 1996 11:31:13 +1000 Organization: UC Irvine Lines: 12 Message-ID: NNTP-Posting-Host: rablab.biochem.uci.edu Can someone tell me what is the best method to transfect Swiss 3T3. I have tried the calcium phosphate method, but it does not work. Thanks. -- Didier Thomas University of California, Irvine College of Medicine Dept. of Biological Chemistry Med. Sci. I, Room D214 Irvine, CA 92717 USA From owner-proteins@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: dunnsm@bbsrc.ac.uk (Steve) Newsgroups: bionet.molbio.proteins Subject: Re: staining a chargeless protein Date: 4 Jun 1996 13:07:37 GMT Organization: Institute of Arable Crops Research, Rothamsted Lines: 18 Message-ID: <4p1cep$sn5@is.bbsrc.ac.uk> References: <4nb7ud$s4v@overload.lbl.gov> <4nmmak$5pj@seagoon.newcastle.edu.au> <31A51F85.5DCE@ion.bpmf.ac.uk> NNTP-Posting-Host: pc773.res.bbsrc.ac.uk X-Newsreader: WinVN 0.92.6+ In article <31A51F85.5DCE@ion.bpmf.ac.uk>, Dr Clinton A L Monfries says: > >Phillip J Robinson wrote: >> >> Olin Anderson wrote: >> The only >> >amino group is the N-terminal and it seems unreactive/blocked. The >> >only amino acids in the polypeptide are P, G, Q, Y, T, and S. Any >> >suggestions how to stain/detect this polypeptide in a gel? >> Post-electrophoresis, try oxidising the Y T S hydroxyls to aldehydes using periodate (as for schiffs reagent staining of glycoproteins) prior to silver staining under ACIDIC conditions (not ammoniacal-based methods). If you're desperate, I have a long-winded protocol somewhere... Good luck, Steve. From owner-proteins@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!panix!news.columbia.edu!news From: Hirsh Lab Newsgroups: bionet.molbio.proteins Subject: a galactose-specific lectin column resin? Date: 4 Jun 1996 19:40:17 GMT Organization: Columbia University, Biochemistry Department Lines: 18 Message-ID: <4p23f1$nej@apakabar.cc.columbia.edu> NNTP-Posting-Host: ps5501f.cpmc.columbia.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.molbio.proteins Does anybody know of a company which makes an affinity matrix with a lectin attached that specifically binds to galactose residues. I would like to use a column with such a resin in order to purify a glycoprotein which I know contains terminal galactose residues on its attached carbohydrate chain(s). Alternatively, I would be happy to know about any galactose-specific lectins that are linked to say biotin or digoxygenin. Thanks in advance. Sincerely, Christopher G. Winter cgw1@columbia.edu From owner-proteins@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!CS.SANDIA.GOV!scistra From: scistra@CS.SANDIA.GOV (Sorin C. Istrail) Newsgroups: bionet.molbio.proteins Subject: RECOMB 97: Submission Deadline Extension!!! Date: 5 Jun 1996 15:56:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 199 Sender: daemon@net.bio.net Distribution: world Message-ID: <9606052252.AA25067@frodo.cs.sandia.gov.noname> NNTP-Posting-Host: net.bio.net **** New Submission Deadline: August 10, 1996 **** CALL FOR PAPERS FIRST ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB 97) January 20-22, 1997 Eldorado Hotel Santa Fe, New Mexico Sponsored by Association for Computing Machinery with support from SLOAN Foundation US Department of Energy http://www.cs.sandia.gov/recomb97 The First Annual Conference on Research in Computational Molecular Biology (RECOMB 97), co-sponsored by the SLOAN Foundation, the Association for Computing Machinery (ACM) and US Department of Energy will be held in Santa Fe, New Mexico, January 20--22, 1997. Papers reporting on original research (both theoretical and experimental) in all areas of computational molecular biology are sought, including surveys of important recent results/directions. Typical but not exclusive topics of interest include: - Genomics - Molecular sequence analysis - Recognition of genes and regulatory elements - Molecular evolution - Protein structure - Combinatorial libraries and drug design - DNA computing ABSTRACT SUBMISSION: Authors are requested to send 10 copies (preferably two sided copies) of a detailed extended abstract (5-10 pages) to: Professor Michael Waterman RECOMB 97 Program Chair University of Southern California Department of Mathematics, DRB 155 Los Angeles, CA 90089-1113 An abstract must be received by August 10, 1996. This is a firm deadline. Simultaneous submission to another conference or journal is allowed. CONFERENCE PROCEEDINGS: The extended abstracts for the Conference will be published by ACM Press and will be available at the Conference. A selection of the accepted extended abstracts in their final journal versions will be invited to appear in a special issue of the Journal of Computational Biology devoted to RECOMB 97. NOTIFICATION: The conference submissions will be refereed by the program committee. Authors will be notified of acceptance or rejection by a letter mailed on or before October 10, 1996. A final copy of each accepted paper is required by November 10, 1996. An author of each accepted paper is expected to attend the Symposium and present the paper; otherwise alternative arrangements should be made to have the paper presented. Limited financial support for the authors of the accepted papers will be available. ABSTRACT PREPARATION: An abstract should start with a succinct statement of the problem, the results achieved, their significance and a comparison with previous work. This material should be understandable to nonspecialists. A technical exposition directed to the specialist should follow. The length, excluding cover page and bibliography, should not exceed 10 pages. The manuscript should be easy to read, preferably using 11 point font size on U.S. standard 8 1/2 by 11 inch paper. If authors believe that more details are necessary to substantiate the claims of the paper, they may include a clearly marked appendix. An E-mail address for the contact author should be included. Conference Events THE STANISLAW ULAM MEMORIAL COMPUTATIONAL BIOLOGY ADDRESS. The Banquet of the Conference will host the Stanislaw Ulam Memorial Lecture awarded by RECOMB to a scientist who has made major contributions in the computational aspects of the field. Dr. Eric Lander (MIT) will be delivering the first Stanislaw Ulam Address. THE DISTINGUISHED CONFERENCE LECTURE. The conference will start with the Distinguished Conference Lecture awarded by RECOMB to a scientist who has made major contributions in the biological aspects of the field. Dr. Rich Roberts (New England Biolabs), the 1994 Nobel Laureate will be delivering the Distinguished Conference Lecture. THE DISTINGUISHED NEW TECHNOLOGIES LECTURE. A lecture describing emerging, new technologies will be delivered by Dr. Robert Lipshutz (Affymetrix). BEST PAPER BY A YOUNG SCIENTIST AWARD. This award will be given to the best paper written solely by one or more recent graduates or students. An abstract is eligible if all authors are recent graduates (within 2 years from Ph.D.) or full-time students at the time of submission. This should be indicated in the submission letter. The program committee may decline to make the award or may split it among several papers. STEERING COMMITTEE: Sorin Istrail (Sandia National Laboratories) Richard Karp (University of Washington) Thomas Lengauer (GMD-SCAI, Germany) Pavel Pevzner, RECOMB General Chair (University of Southern California) Ron Shamir (Tel-Aviv University, Israel) Michael Waterman, RECOMB General Chair (University of Southern California) PROGRAM COMMITTEE MEMBERS: Steven Altschul (National Center for Biotechnology Information) Bonnie Berger, Publication Chair (MIT) Ken Dill (University of California San Francisco) Martin Farach (Rutgers University) Phil Green (University of Washington) Sorin Istrail, Conference Chair (Sandia National Laboratories) Richard Karp (University of Washington) Martin Karplus (Harvard University) Thomas Lengauer (GMD-SCAI, Germany) Webb Miller (Pennsylvania State University) Gene Myers (University of Arizona) Maynard Olson (University of Washington) Pavel Pevzner, (University of Southern California) Rich Roberts (New England Biolabs) David Sankoff (University of Montreal) Ron Shamir (Tel-Aviv University, Israel) Temple Smith (Boston University) Terry Speed (University of California Berkeley) Gary Stormo (University of Colorado) Martin Vingron (German Cancer Center) Tandy Warnow (University of Pennsylvania) Michael Waterman, Chair of the Program Committee (University of Southern California) Bruce Weir (North Carolina State University) The PMMB Meeting exploring the applications of statistics in molecular biology will be held in Santa Fe on January 14-19, 1997, just preceding RECOMB 97. Contact Sylvia Spengler sylviaj@violet.berkeley.edu (510)643-7799 for further information. LOCAL ARRANGEMENTS COMMITTEE: William Hart (Sandia National Laboratories), Chris Fields (National Center for Genome Resources), Sylvia Spengler (Coordinator with the PMMB Conference). Information about local arrangements can be obtained by consulting the conference web page http://www.cs.sandia.gov/recomb97 or from the Conference Chair: Sorin Istrail Sandia National Labs Department 9423, MS 1110 Albuquerque, NM 87185-1110, USA phone: (505) 845-7612 fax: (505) 845-7442 scistra@cs.sandia.gov http://www.cs.sandia.gov/~scistra From owner-proteins@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!news2.cais.net!news.cais.net!nntp.uio.no!Norway.EU.net!oslonett.no!sn.no!usenet From: Martin Wardenær Newsgroups: bionet.molbio.proteins Subject: Re: Help: Bioluminescence! Date: Wed, 05 Jun 1996 13:05:33 +0200 Organization: SN Internett Lines: 4 Message-ID: <31B569FD.3B6B@sn.no> References: <31B38F93.5C0@sn.no> NNTP-Posting-Host: nm11-11.ppp.sn.no Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win95; I) I have changed my Email address. The correct address is now "martinw@sn.no". Martin From owner-proteins@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!uwm.edu!news.cse.psu.edu!gvls1!udel!cnn.Princeton.EDU!berthaw.princeton.edu!micky From: micky@berthaw.princeton.edu (Michael West) Newsgroups: bionet.molbio.proteins Subject: CNBr Cleavage of soluble proteins Date: 5 Jun 1996 23:05:37 GMT Organization: Princeton University Lines: 17 Message-ID: <4p53s1$abi@cnn.Princeton.EDU> NNTP-Posting-Host: berthaw.princeton.edu I am gearing up to do CNBr cleavage of candidates from a library of fusion proteins. I am cleaving a leader sequence from the C-terminal end and a antibody and His-tag from the N-terminal end. The resulting protein is ~8kd and should be soluble. I would like to hear from anyone who has successfully performed this type of cleavage and/or I would like to find a good references on the subject. Thanks, Michael -- "...none of the tears that we cry in sorrow or rage Can make any difference, or turn back the page..." -DG ************************************************************************ Michael West micky@berthaw.princeton.edu From owner-proteins@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!MBCRR.HARVARD.EDU!bsturner From: bsturner@MBCRR.HARVARD.EDU (Bradley Turner) Newsgroups: bionet.molbio.proteins Subject: Re: a galactose-specific lectin column resin-Source Date: 5 Jun 1996 08:52:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 90 Sender: daemon@net.bio.net Distribution: world Message-ID: <199606051548.LAA24494@mbcrr.harvard.edu> NNTP-Posting-Host: net.bio.net Christopher, You might try contacting: EY Laboratories 107 North Amphlett Blvd. San Mateo, CA 94401 USA 415-342-3296 phone 415-342-2648 fax 800-821-0044 They have a very large selection of immobilized and conjugated lectins. Some of those that have some sort of B-Galactose specificity include: Viscum album (VAA) Allomyrina dichomata (Allo A) Agaricus bisporus (ABA) Abrus precatorius (APA) Arachis hypogaea (PNA) Cytisus scoparius (CSA) Tricosanthes kirilowii (TKA) Ricinus communis I (RCA I) Ricinus communis II (RCA II) Some of the above also react with other residues, and there are others in their catalogue that react with a-galactose (plus other residues). Disclaimer: I am only a satisfied customer , and have no commercial interests EY Labs. The above represent only my opinions and not those of my employer. I hope this helps, Brad ************************************************************** Bradley Turner Beth Israel Hospital Harvard Medical School 617-667-1215 phone Division of Gastroenterology 617-667-2767 fax Room Dana 536 turner@sprcore.bih.harvard.edu 330 Brookline Avenue bsturner@mbcrr.harvard.edu Boston, MA 02215 bturner@bih.harvard.edu ************************************************************** BEGIN INCLUDED MESSAGE------------------------------------------------------ From BIOSCI-REQUEST@net.bio.net Tue Jun 4 20:28:59 1996 Return-Path: BIOSCI-REQUEST@net.bio.net Received: from net.bio.net (daemon@net.bio.net [204.31.212.2]) by mbcrr2.dfci.harvard.edu (8.7.5/8.6.9) with SMTP id QAA12853 for ; Tue, 4 Jun 1996 16:28:54 -0400 (EDT) Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id NAA08410; Tue, 4 Jun 1996 13:05:58 -0700 Received: (from news@localhost) by net.bio.net (8.6.12/8.6.6) id NAA08406; Tue, 4 Jun 1996 13:05:57 -0700 To: protein-analysis@net.bio.net From: Hirsh Lab Subject: a galactose-specific lectin column resin? Date: 4 Jun 1996 19:40:17 GMT Message-ID: <4p23f1$nej@apakabar.cc.columbia.edu> NNTP-Posting-Host: ps5501f.cpmc.columbia.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.molbio.proteins Status: R Does anybody know of a company which makes an affinity matrix with a lectin attached that specifically binds to galactose residues. I would like to use a column with such a resin in order to purify a glycoprotein which I know contains terminal galactose residues on its attached carbohydrate chain(s). Alternatively, I would be happy to know about any galactose-specific lectins that are linked to say biotin or digoxygenin. Thanks in advance. Sincerely, Christopher G. Winter cgw1@columbia.edu END OF INCLUDED MESSAGE----------------------------------------------------- From owner-proteins@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!MBCRR.HARVARD.EDU!bsturner From: bsturner@MBCRR.HARVARD.EDU (Bradley Turner) Newsgroups: bionet.molbio.proteins Subject: Re: a galactose-specific lectin column resin? Date: 5 Jun 1996 09:31:03 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 70 Sender: daemon@net.bio.net Distribution: world Message-ID: <199606051621.MAA25508@mbcrr.harvard.edu> NNTP-Posting-Host: net.bio.net Christopher, You might also try to connect to: http://www.biosupplynet.com A web site that lists suppliers of various biochemical supplies and reagents. It also gives email addresses and Web (URL) links, and is searchable! Again, Hope this helps, Brad ************************************************************** Bradley Turner Beth Israel Hospital Harvard Medical School 617-667-1215 phone Division of Gastroenterology 617-667-2767 fax Room Dana 536 turner@sprcore.bih.harvard.edu 330 Brookline Avenue bsturner@mbcrr.harvard.edu Boston, MA 02215 bturner@bih.harvard.edu ************************************************************** BEGIN INCLUDED MESSAGE----------------------------------------------------- From BIOSCI-REQUEST@net.bio.net Tue Jun 4 20:28:59 1996 Return-Path: BIOSCI-REQUEST@net.bio.net Received: from net.bio.net (daemon@net.bio.net [204.31.212.2]) by mbcrr2.dfci.harvard.edu (8.7.5/8.6.9) with SMTP id QAA12853 for ; Tue, 4 Jun 1996 16:28:54 -0400 (EDT) Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id NAA08410; Tue, 4 Jun 1996 13:05:58 -0700 Received: (from news@localhost) by net.bio.net (8.6.12/8.6.6) id NAA08406; Tue, 4 Jun 1996 13:05:57 -0700 To: protein-analysis@net.bio.net From: Hirsh Lab Subject: a galactose-specific lectin column resin? Date: 4 Jun 1996 19:40:17 GMT Message-ID: <4p23f1$nej@apakabar.cc.columbia.edu> NNTP-Posting-Host: ps5501f.cpmc.columbia.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.molbio.proteins Status: R Does anybody know of a company which makes an affinity matrix with a lectin attached that specifically binds to galactose residues. I would like to use a column with such a resin in order to purify a glycoprotein which I know contains terminal galactose residues on its attached carbohydrate chain(s). Alternatively, I would be happy to know about any galactose-specific lectins that are linked to say biotin or digoxygenin. Thanks in advance. Sincerely, Christopher G. Winter cgw1@columbia.edu END OF INCLUDED MESSAGE---------------------------------------------------- From owner-proteins@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!metro!metro!wabbit.its.uow.edu.au!socs.uts.edu.au!ib_lc630.bio.uts.edu.au!peter From: Peter Hains Newsgroups: bionet.molbio.proteins Subject: Codon preference usage Date: 5 Jun 1996 23:37:30 GMT Organization: University of Technology, Sydney Australia. Lines: 7 Distribution: world Message-ID: <4p55nq$1vt@woodstock.socs.uts.EDU.AU> NNTP-Posting-Host: 138.25.241.85 X-Newsreader: Nuntius Version 1.2 X-XXMessage-ID: X-XXDate: Thu, 6 Jun 1996 17:45:00 GMT I have recently constructed a snake cDNA library. As such, I am now designing primers to screen the library. The primers are being designed from amino acid sequence and are therfore degenerate. I was hoping that out there somewhere is a database of codon usage preferences for reptiles, preferably snakes. Thanks in advance. Peter. From owner-proteins@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!tank.news.pipex.net!pipex!usenet.eel.ufl.edu!bofh.dot!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins Subject: Re: How to purify 16kD protein Date: 5 Jun 1996 08:30:42 GMT Organization: University of Leicester, UK (PCFS User) Lines: 16 Message-ID: <4p3gji$h3o@falcon.le.ac.uk> References: <4osj76$1goc@power5.rz.uni-hohenheim.de> NNTP-Posting-Host: pc47.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) It may not float, depending on salt concentration, but it would most likely be denatured, it may be even precipitated. If affinity chromatography is not an option, ion exchange may be the best first step. This would concentrate the protein into a small volume and remove many contaminants. Supernatants of bacterial cultures contain little protein, so after ion exchange and may be gel filtration (Sephadex 25?) I would expect an almost pure protein. HIC may also be an option. If there is little contamination with other proteins in the first place, it might even be sufficient to remove low molecular weight materials (salts ect.) by concentrating in an Amicon ultrafiltration device, taking up in buffer and repeating. From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!chi-news.cic.net!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!oleane!jussieu.fr!univ-lille1.fr!usenet From: Philippe Lefebvre Newsgroups: bionet.molbio.proteins Subject: Re: CNBr Cleavage of soluble proteins Date: 6 Jun 1996 09:55:08 GMT Organization: INSERM Lines: 5 Message-ID: <4p69ts$l80@netserver.univ-lille1.fr> References: <4p53s1$abi@cnn.Princeton.EDU> NNTP-Posting-Host: biostruct.univ-lille2.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) Well, CNBr is a very potent and selective cleavage agent, BUT in 70% formic acid. I don't know whether this is compatible with your goals (ie native or denaturated proteins) Dr Phil Good From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!newsxfer2.itd.umich.edu!tank.news.pipex.net!pipex!oleane!jussieu.fr!citi2.fr!news From: federici Newsgroups: bionet.molbio.proteins Subject: Re: gel filtration using organic solvents Date: 6 Jun 1996 07:52:35 GMT Organization: CITI2 - Universite Rene Descartes, Paris Lines: 6 Message-ID: <4p62o3$l11@bisance.citi2.fr> References: <4otp17$jab@metro.usyd.edu.au> NNTP-Posting-Host: federici.cochin.inserm.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: jtaylor@medicine.su.oz.au X-URL: news:4otp17$jab@metro.usyd.edu.au Pharmacia sell 3 filtration gels designed for organic solvents: -sephadex LH-20 -sephadex LH-60 -sephasorb HP Ultrafine From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!news.belnet.be!infoserv.rug.ac.be!news From: bdevrees@allserv.rug.ac.be (Bart Devreese) Newsgroups: bionet.molbio.proteins Subject: protein submission in database Date: 6 Jun 1996 07:45:47 GMT Organization: University of Gent Lines: 10 Message-ID: <4p62bb$a5h@infoserv.rug.ac.be> NNTP-Posting-Host: bdvpc1.rug.ac.be X-Newsreader: WinVN 0.92.6+ Hi there, I am looking for a method to submit PROTEIN sequences to swissprot or PIR using WWW. I found several methods to submit sequences, but they were restricted to nucleic acid sequences. Best Regards, Bart Devreese Univ. of Gent Lab for protein biochemistry and protein engineering Bart.Devreese@rug.ac.be From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!Germany.EU.net!howland.reston.ans.net!surfnet.nl!highway.leidenuniv.nl!ruly46!mirihyel From: Peter Hohenstein Newsgroups: bionet.molbio.proteins Subject: Re: Help: Bioluminescence! Date: Thu, 6 Jun 1996 13:46:08 +0200 Organization: Leiden University, The Netherlands Lines: 44 Message-ID: References: <31B38F93.5C0@sn.no> NNTP-Posting-Host: ruly46.medfac.leidenuniv.nl Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8BIT X-Sender: mirihyel@ruly46 In-Reply-To: <31B38F93.5C0@sn.no> On Tue, 4 Jun 1996, Martin Wardenær wrote: > My uneducated guess has been that bioluminescence is the most probable > field within one would find substances that fit such criteria (due > to its occurrence in other living organisms). During my sessions at the > library, I have come across the reaction between luciferin and > luciferase. If I have got it right (from those ancient books...), these > will, in the presence of oxygen, react and produce light of some > yellow-greenish hue. Also, there are supposed to be many variations of > these reactions, with varying builds of luciferin and luciferase. I > am not sure whether this is correct, or if so, if there exists any > better suited substances/reactions. Hi Martin, Couple of years ago I used luciferas as a reporter system for promoter research. The normal luciferase reaction uses free oxygen, Mg2+ and ATP as energy source. Promega improved it to the use of acetyl CoA as an energy source. For more info check out theis www site (a start good might be http://www.promega.com/pnotes/54/5105e/5105e.html) or technical bullitin #TB101. Another possibility good be the use of Green Fluorescent Protein (GFP). This protein is isolated from a certain kind of jellyfish, Aquoria victoria, and several companies have tools with it. It emmits green without the need for a special substrate. For info, check out TIG (1995), 11, 320-329. There are also some articles about improving the fluorescence and changing the emmission wavelength, I think they were in PNAS, don't know which, I lost them. GoodLuck Peter Hohenstein Dept. Human Genetics University of Leiden The Netherlands From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in2.uu.net!news.tuwien.ac.at!atp6000.tuwien.ac.at!rams From: rams@atp6000.tuwien.ac.at (Ernesto Rams) Newsgroups: bionet.molbio.proteins Subject: Cuban genetic and biotecnology publications Date: 6 Jun 1996 15:34:37 GMT Organization: Vienna University of Technology, Austria Lines: 133 Message-ID: <4p6tqd$18j@news.tuwien.ac.at> NNTP-Posting-Host: atp6000.tuwien.ac.at X-Newsreader: TIN [version 1.2 PL2] Elfos Scientiae publishes scientific books and journals on the following topics: - Human therapy with interferons, lymphokines, cytokines, growth factors, and other biomolecules; - molecular genetics, and recombinant DNA technology; - monoclonal antibodies, hybridomas, molecular immunology; - recombinant vaccines and new methods for diagnosis; - production and purification of recombinant molecules and biotechnological products; - scaling-up, downstream, process control and automatization; - application of recombinant DNA techniques and products in agriculture, animal science, and industry; - transgenesis. Our publications are: BIOTECNOLOGIA APLICADA This is a quarterly serial publication. It appeared in 1984 under the name of Interferon y Biotecnologia until 1989 (Vol. 6 No. 3) and since 1990 (Vol. 7 No. 1) it is published as BIOTECNOLOGIA APLICADA, sponsored by the Ibero-Latin-American Society of Biotechnology Applied to Health. It publishes original papers in the following sections: review articles, research articles, techniques, short reports, and focus. The Journal includes as well advertisements of products, services, courses, meetings and seminars. The articles are published in Spanish or English, indistinctly. The No. 1 of each volume contains the cumulative index of the preceding volume. ISSN 0864-4551 90-100 pages, 20 x 27 cm, chrome. English and/or Spanish. Prices (USD) Institutional Personal Subscriptions 1996: $75.00 $60.00 Separated issues: $24.00 $20.00 Back subscriptions: $48.00 $30.00 Back issues: $20.00 $16.00 ADVANCES IN MODERN BIOTECHNOLOGY This is a book series containing the structured short reports of the papers presented as oral or poster presentations in the Biotechnology Congresses of Havana. Their contents are divided in topics: therapy and disease prevention, monoclonal antibodies, immunotechnology and diagnosis, cellular and molecular biology, plant biotechnology, animal science, biotechnology industry, among others. Three volumes have been published: - volume 1, corresponds to the event organized in 1992. It contains 526 articles covering all the fields of modern biotechnology; - volume 2 (1994), with 450 papers, is related to biotechnology applied to human health; - volume 3 (1995), with 380 articles, is dedicated to a wide spectrum of biotechnology and its applications to agriculture, industry and animal science. 210-300 pages, 20 x 27 cm, bond, soft cover. In Spanish and/or English. Prices (USD) Vol. 1 (ISBN 959-235-001-9), 1992 $10.00 Vol. 2 (ISBN 959-235-002-7), 1994 $12.00 Vol. 3 (ISBN 959-235-003-5), 1995 $15.00 RECOMBINANT VACCINES FOR THE CONTROL OF CATTLE TICK This book addresses the important question of the control of ectoparasite employing new immunological approaches. The development of protective vaccines against Boophillus microplus, the first vaccine against ectoparasites and the first recombinant antiparasitic vaccine on the market is discussed in this book. Tick biology, antigen characterization, process design, analytical methods, computer simulation of both infestation and vaccination strategies and vaccine preclinical and clinical data collected in Australia, Canada, Colombia, Cuba and Mexico are presented in the book in an understandable way. The book, which is the first in the series Monograph published by Elfos Scientiae, is of interest for parasitologists, immunologists, veterinarians, molecular biologists, and engineers and biochemists involved in the design and characterization of new vaccines. The author, Dr. Jose de la Fuente, is the Director for Research and Development at the Center for Genetic Engineering and Biotechnology in Havana and is a member of the Cuban and New York Academies of Sciences. ISBN 959-235-005-1 242 p., 55 fig., 58 tab., 15 x 21 cm, soft cover. In English. Price: $30.00 USD ANTICUERPOS MONOCLONALES This book covers the basic theoretical elements and a detailed description of reproducible procedures of the technology for the generation of monoclonal antibodies secretory cells. This technique has revolutionized the possibilities of use of the immunoglobulins for research, diagnosis, therapy and industry. This book, first of the series Theory and Practice by Elfos Scientiae, is aimed for technicians and professional personnel interested in this technology. Its author, Jorge V. Gavilondo Cowley, works since 1982 on the obtainment of monoclonal antibodies from hybridomes. Dr. Gavilondo has published, in international scientific journals, over 80 articles related with Hodgkin's disease, tumoral transformation and dissemination, monoclonal antibodies and recombinant antibodies. He has been invited to collaborate and deliver conferences in scientific institutions and universities of more than twenty countries. He is a member of the Editorial Board of the journal BioTechniques and the Directive Boards of the Ibero-Latin-American Society of Biotechnology and the Cuban Society of Immunology. ISBN 959-235-004-3 180 p., 24 fig., 15 x 21 cm, soft cover. In Spanish. Price: $20.00 USD ---------------------------------------------------------------- Payments should be made by telegraph transfer by the equivalent of the amount to pay, according to the day's exchange rate, in any of the currencies and through one of following banks: Canadian Dollars National Bank of Canada, Montreal German Mark Deutsche Sudamerikanische Bank, Hamburg Pound Sterling National Westminster Bank, London Swiss Francs Union Bank of Switzerland, Zurich The transfers should be made to the Banco Financiero Internacional, S.A., Linea y O, Plaza, Havana, Cuba, to the account No. 402.01.8064 of the Centro de Ingenieria Genetica y Biotecnologia. 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New E-mail address ******************************** From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in2.uu.net!newsfeed.pitt.edu!newsflash.concordia.ca!canopus.cc.umanitoba.ca!cc-hsc-k-box12.cc.umanitoba.ca!user From: egreif@cc.umanitoba.ca (Elke) Newsgroups: bionet.molbio.proteins Subject: 2D PAGE pH gradients Date: Thu, 06 Jun 1996 11:03:45 -0600 Organization: University of Manitoba Lines: 13 Message-ID: NNTP-Posting-Host: cc-hsc-k-box12.cc.umanitoba.ca Has anyone tried measuring the gradient of IEF tube gels by first cutting the first dimension gel into 0.5cm pieces , leaving each piece in about 300-400 uL of water and leaving the whole rack in the coldroom overnight, then measuring the pH the next day to make sure the ampholytes are working properly? I've done it sort of and it sure takes a long time for the pH to stabilize to read each sample. Elke egreif@ccu.umanitoba.ca -- Hey, hey, hey, hey! It was the DNA. Hey, hey, hey, hey! That made me this way. From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!herts.ac.uk!P.Ofarrell From: P.Ofarrell@herts.ac.uk (Paul O'Farrell) Newsgroups: bionet.molbio.proteins Subject: protein expression Date: 6 Jun 1996 02:25:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <8338.9606060921@altair.herts.ac.uk> NNTP-Posting-Host: net.bio.net Hi there, is anyone able to offer either (or both) of the following : i) A bacterial strain expressing a protein as an inclusion body (any bug (well, non-pathogenic hopefully!), any protein) ii) An E. coli strain expressing a protein using the Invitrogen Thiofusion vector system. These are both required for undergraduate practicals we want to run here at the University of Hertfordshire. All the best, Paul Dr. Paul A. O'Farrell, Div of Biosciences, University of Hertfordshire, Hatfield, Herts., AL10 9AB, England. Ph: +44 (0)1707 284527. Fax: +44 (0)1707 285046 Email P.Ofarrell@herts.ac.uk From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!rutgers!csn!nntp-xfer-1.csn.net!ncar!imci4!newsfeed.internetmci.com!in2.uu.net!rcogate.rco.qc.ca!altitude!usenet From: Achim Recktenwald Newsgroups: bionet.molbio.proteins,de.sci.biologie,sci.bio.misc,bionet.metabolic-reg,bionet.molbio.methds-reagnts,sci.bio.microbiology,bionet.microbiology,bionet.molbio.yeast,sci.bio.botany,bionet.general,bionet.plants,bionet.cellbiol Subject: Conc. metabolites in cells ? Date: Thu, 06 Jun 1996 14:51:15 -0500 Organization: IBEX Technologies, Inc. Lines: 38 Message-ID: <31B736B3.4B7A@ibex.ca> NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; PPC) Xref: biosci bionet.molbio.proteins:8061 sci.bio.misc:3404 bionet.metabolic-reg:758 bionet.molbio.methds-reagnts:45432 sci.bio.microbiology:3592 bionet.microbiology:6284 bionet.molbio.yeast:5381 sci.bio.botany:2266 bionet.general:22046 bionet.plants:11608 bionet.cellbiol:4860 I am looking for a table listing the normal concentrations of typical cell metabolites, e.g., amino acids, NAD, ATP, ions, sugars, major proteins, etc. A few years back I once stumbled over such a table. Unfortunately, I did not make a copy. The only entries I can remember: typical cell protein concentration 100-300mg/mL acetate ion 0.2 - 0.25 M Does anybody know where to find such a table ? I am also looking for a database, printed, CD-ROM, or on the Net, with physiological data; e.g., average yield for fermentative bacterial growth on glucose 10.5g cells / mol ATP; list of average generation times of different bacteria; metabolic specialties; and so on. When I posted this message a few weeks ago, I received the following references: Neidhardt, F. C., et al: Physiology of the Bacterial Cell, Sinauer Associates, 1990 Neidhardt, F. C. (editor): Escherichia coli and Salmonella, ASM Press, 2nd edition, ASM Press, 1996 I would like to find more references, if posasible with even more detailed information. I am also interested in concentrations of metabolites in eucaryotic cells, esp. mammals and/or humans, but also plants. If you know of any good reference, please email it to me, or post it on the Net. Any help would be appreciated. Achim From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!rutgers!csn!nntp-xfer-1.csn.net!ncar!imci4!newsfeed.internetmci.com!in2.uu.net!rcogate.rco.qc.ca!altitude!usenet From: Achim Recktenwald Newsgroups: bionet.molbio.proteins,de.sci.biologie,de.sci.chemie,sci.bio.misc,sci.chem,bionet.metabolic-reg,bionet.molbio.methds-reagnts,bionet.biophysics Subject: Why is solubility phe > tyr ? Date: Thu, 06 Jun 1996 14:46:43 -0500 Organization: IBEX Technologies, Inc. Lines: 44 Message-ID: <31B735A3.30D8@ibex.ca> NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 2.02 (Macintosh; I; PPC) Xref: biosci bionet.molbio.proteins:8060 sci.bio.misc:3403 sci.chem:57878 bionet.metabolic-reg:757 bionet.molbio.methds-reagnts:45431 bionet.biophysics:2086 I have a question concerning the solubilities of the amino acids phenylalan= ine and = tyrosine. I had posted this message already a few weeks ago, but received no answer, = therefore, I am = trying again, and to more Newsgroups. I am working with an enzyme that accepts phenylalanine (phe) and tyrosine (= tyr) as = substrate. When I prepared the first time stock solutions I was surprised to notice th= at phe is = soluble in water at pH 7 +/- 1 pH to approx. 180 mM, while with tyr I can p= repare at the = same conditions only a 10 mM solution. Tyr differs from phe only in an additional hydroxyl-group. I had always assumed an increase in polarity would also make a substance mo= re water = soluble. Can anybody explain to me, why the p-OH group in tyrosine has such a strong= effect on the = solubility of the amino acid, nin effect decreasing it almost to 1/20 of ph= e. Is this only valid for the free enzyme, or would this also be the case for = the amino acid = side-chains in proteins? Does this mean, phe-side-chains have a more hydro= philic = character than tyr=B9s in proteins? Achim From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!arclight.uoregon.edu!news.bc.net!news.mindlink.net!van-bc!unixg.ubc.ca!lpss From: lpss@unixg.ubc.ca (Alex Chang) Newsgroups: bionet.molbio.proteins Subject: Nef protein structure Date: 7 Jun 1996 03:42:20 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 10 Message-ID: <4p88es$o97@nntp.ucs.ubc.ca> NNTP-Posting-Host: netinfo.ubc.ca X-Newsreader: TIN [version 1.2 PL2] I read Grzesiek's paper in Nature Structure Biology 3(4):340, about the solution structure of HIV Nef. I couldn't find the coordinates from PDB, anyone knows how to get them? (they mentioned that the coordinates have been deposited in PDB). -- Alex Chang Pathology University of British Columbia achang@hivnet.ubc.ca From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!IX.NETCOM.COM!schmidel From: schmidel@IX.NETCOM.COM ("Dyann K. Schmidel") Newsgroups: bionet.molbio.proteins Subject: The Biotech Biblionet Date: 6 Jun 1996 20:13:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <31B7C743.2DB0@ix.netcom.com> NNTP-Posting-Host: net.bio.net The Biotech BiblioNet (a monthly bibliography of recently published biotech articles) has been relocated to the following address. http://schmidel.com/biotech.htm This web site now features a search utility and direct links to online abstracts. Dyann K. Schmidel, Ph.D. Dyann@Schmidel.com From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Richard Lathrop Newsgroups: bionet.molbio.proteins,bionet.molec-model,bionet.xtallography Subject: Protein Structure Prediction -- PSB'97 Date: 6 Jun 1996 15:30:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 95 Sender: daemon@net.bio.net Distribution: world Message-ID: <9606061418.aa24239@paris.ics.uci.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molbio.proteins:8063 bionet.molec-model:967 bionet.xtallography:2638 (please excuse cross-posts) PLEASE POST PLEASE POST PLEASE POST **** FIELD DAY for PROTEIN STRUCTURE PREDICTION **** SECOND Call for Papers and Referees Second Pacific Symposium on Biocomputing Maui, Hawaii --- January 6--9, 1997 http://cgl.ucsf.edu/psb/psb.html co-chairs: Daniel Fischer, Adam Godzik, Su Chung, S. Subbiah, Richard Lathrop Protein structure prediction directly confronts experimental evidence by its very nature. As we all know, the pressure to publish positive results biases what we see in the literature, making it difficult to separate true insights from exaggerated claims. Consequently workers in the field need to discuss informally and frankly: What works? What doesn't? Why not? And what can we all learn from it? This year, two special sessions will focus on: * PROTEIN THREADING, or ``The post-Asilomar blues,'' by Daniel Fischer and Adam Godzik. * SIDE-CHAIN PACKING, or ``The importance of being well-packed,'' by Su Chung and S. Subbiah. The special sessions will facilitate a series of panels, discussion groups, posters, and workshops: * informal talks (10-15 minutes) for groups to showcase recent efforts. * panel discussions on several hot topics (speakers, topics, solicited). * non-competitive prediction workshops for your sequences and software. The goal is to draw together active researchers in a non-competitive, open, and participatory examination of what actually works, and why. For information about specific session activities please contact the special session organizers directly, as listed below. PSB'97 will publish accepted peer-reviewed full papers in an archival Proceedings. All full papers will be peer-reviewed by at least three referees. Each accepted full paper will be allocated 12 pages in the Proceedings. The best peer-reviewed papers will be selected for oral presentation (30 minutes) to the full assembled Conference. Papers are solicited on any aspect of protein structure prediction, especially those directed at the two special sessions. Preferred papers will confront prediction with experimental data, quantify the effectiveness of the techniques employed, and elucidate the reasons behind the successes and limitations encountered. Predictions should be tested on data not used to derive predictive parameters (e.g., cross-validation, or train/test set, methodologies), and should so state. To be eligible for review and publication in the Proceedings, each full paper must be accompanied by a cover letter stating that it contains original unpublished results not currently under consideration elsewhere and that all co-authors concur with its contents. The cover letter should provide an email contact address and state whether the paper is directed to Protein Threading, Side-chain Packing, or general protein structure prediction. Participants who do not wish to submit a full paper are welcome to submit a two page abstract, which will be distributed at the meeting separately from the archival Proceedings. All participants are welcome to display posters and give live computer demonstrations. DEADLINES: Paper submission deadline: July 1, 1996 Notification of paper acceptances: August 22, 1996 Camera ready copy due: September 15, 1996 Conference: January 6-9, 1997 at the Ritz-Carlton Kapalua, Maui SUBMIT SIX (6) COPIES OF ALL FULL PAPERS TO: PSB-97, c/o Section on Medical Informatics Stanford University Medical School, MSOB X215 Stanford, CA 94305-5479 USA CONTACT FOR MORE INFORMATION: * Protein Threading, or ``The post-Asilomar blues'' --- Daniel Fischer: fischer@mbi.ucla.edu; (310) 206-3642 --- Adam Godzik: adam@scripps.edu; (619) 554-4823 * Side-chain Packing, or ``The importance of being well-packed'' --- Su Chung: schung@usuhsb.usuhs.mil; (301) 295-3562 --- S. Subbiah: subbiah@cellbio.stanford.edu; (415) 725-0754 * Other topics and general information --- Richard Lathrop: rickl@uci.edu; (714) 824-4021 The Protein Structure Prediction field day is a portion of the 1997 Pacific Symposium on Biocomputing. Please see http://cgl.ucsf.edu/psb/psb.html for information about the general conference. PLEASE POST PLEASE POST PLEASE POST From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!rutgers!csn!nntp-xfer-1.csn.net!ncar!imci4!newsfeed.internetmci.com!in2.uu.net!rcogate.rco.qc.ca!altitude!usenet From: Achim Recktenwald Newsgroups: bionet.molbio.proteins,de.sci.biologie,de.sci.chemie,sci.bio.misc,sci.chem,bionet.metabolic-reg,bionet.molbio.methds-reagnts,bionet.biophysics Subject: Why is solubility phe > tyr ? Date: Thu, 06 Jun 1996 14:54:52 -0500 Organization: IBEX Technologies, Inc. Lines: 44 Message-ID: <31B7378C.17A@ibex.ca> NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 2.02 (Macintosh; I; PPC) Xref: biosci bionet.molbio.proteins:8062 sci.bio.misc:3405 sci.chem:57879 bionet.metabolic-reg:759 bionet.molbio.methds-reagnts:45433 bionet.biophysics:2087 I have a question concerning the solubilities of the amino acids phenylalan= ine and = tyrosine. I had posted this message already a few weeks ago, but received no answer, = therefore, I am = trying again, and to more Newsgroups. I am working with an enzyme that accepts phenylalanine (phe) and tyrosine (= tyr) as = substrate. When I prepared the first time stock solutions I was surprised to notice th= at phe is = soluble in water at pH 7 +/- 1 pH to approx. 180 mM, while with tyr I can p= repare at the = same conditions only a 10 mM solution. Tyr differs from phe only in an additional hydroxyl-group. I had always assumed an increase in polarity would also make a substance mo= re water = soluble. Can anybody explain to me, why the p-OH group in tyrosine has such a strong= effect on the = solubility of the amino acid, nin effect decreasing it almost to 1/20 of ph= e. Is this only valid for the free enzyme, or would this also be the case for = the amino acid = side-chains in proteins? Does this mean, phe-side-chains have a more hydro= philic = character than tyr=B9s in proteins? Achim From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!GUARANY.CPD.UNB.BR!wagnerf From: wagnerf@GUARANY.CPD.UNB.BR (wagner fontes) Newsgroups: bionet.molbio.proteins Subject: re:protein submission in database Date: 6 Jun 1996 11:16:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net >I am looking for a method to submit PROTEIN sequences to swissprot or >PIR using WWW. I found several methods to submit sequences, but they >were restricted to nucleic acid sequences. Dear Bart, I did submit a protein sequence to PIR a few days ago, and also realized that WWW submission is available only for nucleic acid. The options are disk or e-mail submission. They have a program called Authorin to electronically submit your data. Another way is filling a form and e-mailing it. try to get more info at http://csi.gmu.edu/NBRF/index.html Hope it helps, Wagner. ****************************************************************************** Wagner Fontes wagnerf@guarany.cpd.unb.br http://www.angelfire.com/pages0/wagnerf/index.html Brazilian Protein Sequencing Center Biochemistry / Protein Chemistry lab University of Brasilia Phone (55 61) 348 2142 Brazil FAX (55 61) 272 4548 ****************************************************************************** From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!agate!nature.berkeley.edu!lhom From: lhom@nature.berkeley.edu (Louis Hom) Newsgroups: bionet.molbio.proteins,sci.chem Subject: DMF or DMSO? Date: 6 Jun 1996 17:12:18 GMT Organization: University of California, Berkeley Lines: 9 Message-ID: <4p73hi$amm@agate.berkeley.edu> NNTP-Posting-Host: nature.berkeley.edu Xref: biosci bionet.molbio.proteins:8057 sci.chem:57872 So I bought this peptide substrate in the acetate salt form (the only form available) and I'd like to make a stock solution of it in an organic solvent -- but I can't figure out whether it's more likely to dissolve in DMSO or DMF. Any ideas? (BTW, the molecule is Z-Arg-Arg-MeONapAmide) -- _______________________________________________________________________________ Lou Hom >K '93 "If brevity be the soul of wit, lhom@nature.berkeley.edu play on!" http://www.ocf.berkeley.edu/~lhom From owner-proteins@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.uth.tmc.edu!bmb155.med.uth.tmc.edu!user From: tliang@utmmg.med.uth.tmc.edu (T. Chyau Liang) Newsgroups: bionet.molbio.proteins,sci.chem Subject: Re: DMF or DMSO? Date: Thu, 06 Jun 1996 13:24:10 +0100 Organization: U. Texas-Houston Lines: 21 Message-ID: References: <4p73hi$amm@agate.berkeley.edu> NNTP-Posting-Host: bmb155.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit Xref: biosci bionet.molbio.proteins:8059 sci.chem:57874 In article <4p73hi$amm@agate.berkeley.edu>, lhom@nature.berkeley.edu (Louis Hom) wrote: > So I bought this peptide substrate in the acetate salt form (the only form > available) and I'd like to make a stock solution of it in an organic > solvent -- but I can't figure out whether it's more likely to dissolve in > DMSO or DMF. Any ideas? (BTW, the molecule is Z-Arg-Arg-MeONapAmide) > -- You should be able to dissolved it in either solvent. I personally prefer DMSO, because DMF tends to decompose and generate some dimethylamine (the fishy smell when you open the bottle), which can hydrolyze your substrate over time. This peptide looks like the cathepsin substrate. Take a look at Methods Enzymology, vol. 80. Regards, T. Chyau Liang U. Texas-Houston From owner-proteins@net.bio.net Thu Jun 06 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!comp.vuw.ac.nz!waikato!news.massey.ac.nz!sysadmin From: Jane.Wyatt.1@massey.ac.nz Newsgroups: bionet.molbio.proteins Subject: Re: David Parry address Date: 7 Jun 1996 10:16:15 GMT Organization: Massey University Lines: 29 Message-ID: <4p8vhf$kgj@cc-server9.massey.ac.nz> References: NNTP-Posting-Host: cc-ra4000-1-15.massey.ac.nz Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) To: krystek@alcor.bms.com krystek@alcor.bms.com (Stanley Krystek) wrote: > >I am looking for the e-mail of David Parry >dept of physics and biophysics, massey university > >thanks in advance > > >-- > Stan Krystek > Bristol-Myers Squibb > krystek@alcor.bms.com > > Hi Stan, David's email is: d.parry@massey.ac.nz To check this go to the Massey University home-page on: http://www.massey.ac.nz/ Hope this helps, From owner-proteins@net.bio.net Thu Jun 06 23:00:00 1996 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!moose.bioc.cam.ac.uk!user From: nef1002@cus.cam.ac.uk (Nick Fisher) Newsgroups: bionet.molbio.proteins,sci.chem Subject: Re: DMF or DMSO? Date: Fri, 07 Jun 1996 11:12:27 +0100 Organization: Dept. of Biochemistry, University of Cambridge Lines: 31 Message-ID: References: <4p73hi$amm@agate.berkeley.edu> NNTP-Posting-Host: moose.bioc.cam.ac.uk Xref: biosci bionet.molbio.proteins:8066 sci.chem:57930 In article , tliang@utmmg.med.uth.tmc.edu (T. Chyau Liang) wrote: > In article <4p73hi$amm@agate.berkeley.edu>, lhom@nature.berkeley.edu > (Louis Hom) wrote: > > > So I bought this peptide substrate in the acetate salt form (the only form > > available) and I'd like to make a stock solution of it in an organic > > solvent -- but I can't figure out whether it's more likely to dissolve in > > DMSO or DMF. Any ideas? (BTW, the molecule is Z-Arg-Arg-MeONapAmide) > > -- > > You should be able to dissolved it in either solvent. I personally prefer > DMSO, because DMF tends to decompose and generate some dimethylamine (the > fishy smell when you open the bottle), which can hydrolyze your substrate > over time. > > This peptide looks like the cathepsin substrate. Take a look at Methods > Enzymology, vol. 80. > > Regards, > > T. Chyau Liang > U. Texas-Houston I prefer to use DMSO over DMF, if only because DMF is a suspected carcinogen. Nick Fisher Cambridge University -- From owner-proteins@net.bio.net Thu Jun 06 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!news.ysu.edu!usenet.ins.cwru.edu!po.CWRU.Edu!rdh5 From: rdh5@po.CWRU.Edu (Robert D. Hoffman) Newsgroups: bionet.molbio.proteins Subject: Re: How to purify 16kD protein Date: 7 Jun 1996 16:17:40 GMT Organization: Case Western Reserve University, Cleveland, OH (USA) Lines: 24 Message-ID: <4p9kn4$7s2@madeline.INS.CWRU.Edu> References: Reply-To: rdh5@po.CWRU.Edu (Robert D. Hoffman) NNTP-Posting-Host: christopher.ins.cwru.edu In a previous article, mremingt@umabnet.ab.umd.edu (Mary P. Remington) says: > A friend needs to purify this protein from a 4 liter culture of >bacteria that is producing. She intents to do a cesium gradient. Is >there another protocol available similar to the Qiagen columns for this >type of protocol? Thanks, Mary > > It will take a little fiddling to establish the exact conditions, but I would recommend that she explore doing ammonium sulfate cuts to concentrate and purify the protein before thinking about columns. First determine how much ammonium sulfate is required to precipitate the protein of interest. Next, add less than the amount of ammonium sulfate required for precipitation, and centrifuge. To the supernatant, add ammonium sulfate to just precipitate the protein of interest, and centrifuge again. This time keep the pellet. Dissolve in buffer (as little as possible), dialyze, and you're off. This is a very gentle procedure that does not usually denature enzymes. Good luck! -- Robert D. Hoffman, M.D., Ph.D.//Assistant Professor, Pathology Institute of Pathology//Case Western Reserve University 2085 Adelbert Road//Cleveland, Ohio 44106, USA rdh5@po.cwru.edu//HOFFMAN@ncifcrf.gov From owner-proteins@net.bio.net Thu Jun 06 23:00:00 1996 Path: biosci!rutgers!uwm.edu!chi-news.cic.net!nntp.coast.net!oleane!jussieu.fr!citi2.fr!news From: federici Newsgroups: bionet.molbio.proteins Subject: Re: Solubilising proteins Date: 7 Jun 1996 10:50:25 GMT Organization: CITI2 - Universite Rene Descartes, Paris Lines: 4 Message-ID: <4p91hh$2bq@bisance.citi2.fr> References: <4p0djf$ca@st-james.comp.vuw.ac.nz> NNTP-Posting-Host: federici.cochin.inserm.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: StentV@agresearch.cri.nz X-URL: news:4p0djf$ca@st-james.comp.vuw.ac.nz You can try 8M urea and carry out affinity chromatography (Ni-column) in the presence of it. From owner-proteins@net.bio.net Thu Jun 06 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!globe.indirect.com!s71.phxslip4.indirect.com!user From: mthompson@asu.edu (M Thompson) Newsgroups: bionet.molbio.proteins Subject: Attachment methods for chromophore onto a protein Date: 8 Jun 1996 00:15:50 GMT Organization: Arizona State University Lines: 8 Message-ID: NNTP-Posting-Host: s71.phxslip4.indirect.com I am looking for methods to attach a chromophore, such as thiazole orange and yellow, to a cysteine at residue 1 via a disulfide bridge. One idea is the disufyl-dipyridyl activation of either the chromophore or the protein, with subsequent covalent bond formation of the other. I was wondering if there is an individual who may have experimented with this reaction or has thoughts on this approach or possibly another method. Thanks in advance. From owner-proteins@net.bio.net Thu Jun 06 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!newsfeed.internetmci.com!newsfeed.randomc.com!news.sprintlink.net!news-dc-9.sprintlink.net!moonbeam.aecom.yu.edu!usenet From: ?@aecom.yu.edu (?) Newsgroups: bionet.molbio.proteins Subject: Re: Solubilising proteins Date: 7 Jun 1996 18:21:40 GMT Organization: Albert Einstein College of Medicine Lines: 10 Message-ID: <4p9rvk$35s@moonbeam.aecom.yu.edu> References: <4p0djf$ca@st-james.comp.vuw.ac.nz> NNTP-Posting-Host: jmblab.aecom.yu.edu X-Newsreader: WinVN 0.92.6+ Viki, Try expressing your protein in a bacterial system that manufactures chaperone proteins, such as GroEL and GroES. These have been found to increase the soluability of 'difficult' proteins. I refer you to an article by Caspers et al., in Cellular and Molecular Biology,1994 40(5)pp635-644 Dr Jim McIlroy Dept of Molecular Pharmacology AECOM Bronx, NYC 10461 From owner-proteins@net.bio.net Thu Jun 06 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.uth.tmc.edu!bmb155.med.uth.tmc.edu!user From: tliang@utmmg.med.uth.tmc.edu (T. Chyau Liang) Newsgroups: bionet.molbio.proteins,de.sci.biologie,de.sci.chemie,sci.bio.misc,sci.chem,bionet.metabolic-reg,bionet.molbio.methds-reagnts,bionet.biophysics Subject: Re: Why is solubility phe > tyr ? Date: Fri, 07 Jun 1996 13:31:15 +0100 Organization: U. Texas-Houston Lines: 32 Message-ID: References: <31B735A3.30D8@ibex.ca> NNTP-Posting-Host: bmb155.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit Xref: biosci bionet.molbio.proteins:8072 sci.bio.misc:3418 sci.chem:57970 bionet.metabolic-reg:761 bionet.molbio.methds-reagnts:45482 bionet.biophysics:2093 Solubility is determined by the equilibrium between the solid form and the solvated form of the molecule. The phenol group of Tyr apparently "aggregates" better, i.e., the solid form of Tyr is more favored than the solvated form when compared to Phe. In short, it is not because Phe is more hydrophilic than Tyr. Another little known fact is that pure d- or l- amino acids have better solubilities (also by significant factors) than the racemic d,l mixture. Presumably,this is due to the same mechanism and not because the the d- or l- form is more hydrophilic than the d,l mixture. Hope this helps. T. Chyau Liang U.Texas-Houston [snip] > Can anybody explain to me, why the p-OH group in tyrosine has such a strong= > effect on the = > > solubility of the amino acid, nin effect decreasing it almost to 1/20 of ph= > e. > > Is this only valid for the free enzyme, or would this also be the case for = > the amino acid = > > side-chains in proteins? Does this mean, phe-side-chains have a more hydro= > philic = > > character than tyr=B9s in proteins? From owner-proteins@net.bio.net Thu Jun 06 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!tank.news.pipex.net!pipex!oleane!nntp.coast.net!torn!ccshst05.uoguelph.ca!news From: rmartins@uoguelph.ca (Rui Pires Martins) Newsgroups: bionet.molbio.proteins,bionet.general Subject: uncoupling protein in brown adipose tissue Date: Fri, 07 Jun 1996 08:19:43 GMT Organization: University of Guelph Lines: 7 Message-ID: <4pb2oj$3uk@ccshst05.uoguelph.ca> NNTP-Posting-Host: ppp01-01.net.uoguelph.ca X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.molbio.proteins:8077 bionet.general:22118 I am posting this because I am looking for a protocol to assay for uncoupling protien found in brown adipose mitochondria. There seems to be much in the literature about the protein, but nothing I have found has given me any insight as to how to assay for its activity. Can anyone give any insight? please post here of email me directly at rmatins@uoguelph.ca. Thanks. From owner-proteins@net.bio.net Thu Jun 06 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!howland.reston.ans.net!news-e2a.gnn.com!pop.gnn.com!Lacluster From: Lacluster@gnn.com () Newsgroups: bionet.molbio.proteins Subject: Re: CNBr Cleavage of soluble proteins Date: Fri, 07 Jun 1996 22:28:11 Organization: GNN Lines: 8 Message-ID: <4pb005$n97@news-e2d.gnn.com> References: <4p53s1$abi@cnn.Princeton.EDU> <4p69ts$l80@netserver.univ-lille1.fr> NNTP-Posting-Host: 32-112.client.gnn.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-GNN-NewsServer-Posting-Date: 8 Jun 1996 04:36:21 GMT X-Mailer: GNNmessenger 1.3 CNBr is an old workhorse, and works well as long as the methionine is not oxidized to any great extent. The high formic acid content can be problematic -- I remember doing those cleavages and removing excess reagent and acid by lyophilization. Needless to say, the lyophilizer suffered terribly from this treatment. 70% HCOOH will solubilize just about anything, however, which helps if one of your cleavage products is particularly greasy... From owner-proteins@net.bio.net Thu Jun 06 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!howland.reston.ans.net!news-e2a.gnn.com!pop.gnn.com!Lacluster From: Lacluster@gnn.com () Newsgroups: bionet.molbio.proteins Subject: Re: Solubilising proteins Date: Fri, 07 Jun 1996 22:25:40 Organization: GNN Lines: 11 Message-ID: <4pavrf$n6s@news-e2d.gnn.com> References: <4p0djf$ca@st-james.comp.vuw.ac.nz> <4p9rvk$35s@moonbeam.aecom.yu.edu> NNTP-Posting-Host: 32-112.client.gnn.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-GNN-NewsServer-Posting-Date: 8 Jun 1996 04:33:51 GMT X-Mailer: GNNmessenger 1.3 I would advise caution if you intend using urea to solubilize. Unless you deionize your urea solutions first, or use ultrapure grade urea, you run the risk of modifying lysyl residues through cyanylation. Urea spontaneously disproportionates to ammonium cyanate, and an 8 M solution can have as much as 50 mM cyanate in it. I have had good luck solubilizing inclusions in ~1% SDS, then removing the SDS by passage over a resin such as Bio-Rad's AG11A8 at alkaline pH. It helps the refolding if the protein has a high alpha helical content in the native state, since SDS tends to favor helix formation. From owner-proteins@net.bio.net Thu Jun 06 23:00:00 1996 Newsgroups: bionet.molbio.proteins,sci.chem Path: biosci!rutgers!uwm.edu!math.ohio-state.edu!usc!elroy.jpl.nasa.gov!swrinde!newsfeed.internetmci.com!portal.gmu.edu!hearst.acc.Virginia.EDU!murdoch!faraday.clas.Virginia.EDU!jmt2a From: jmt2a@faraday.clas.Virginia.EDU (Jeremy M. Travins) Subject: Re: DMF or DMSO? X-Nntp-Posting-Host: faraday.clas.virginia.edu Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: uva References: <4p73hi$amm@agate.berkeley.edu> Date: Fri, 7 Jun 1996 15:52:54 GMT Lines: 7 Xref: biosci bionet.molbio.proteins:8071 sci.chem:57952 More than likely, it will dissolve in either solvent. DMF (b.p. ~150) is much easier to get rid of than DMSO (b.p. > 200) should you wish to recover your peptide. Be sure to protect this stock solution from the open air as DMF and DMSO are both very hygroscopic. Jeremy From owner-proteins@net.bio.net Thu Jun 06 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!news.ycc.yale.edu!news From: Gerard Kleywegt Newsgroups: bionet.molbio.proteins Subject: Re: Nef protein structure Date: Fri, 07 Jun 1996 12:29:54 -0400 Organization: Disorganised at present Lines: 36 Message-ID: <31B85902.794B@laplace.csb.yale.edu> References: <4p88es$o97@nntp.ucs.ubc.ca> NNTP-Posting-Host: kepler.csb.yale.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b3 (X11; I; IRIX 5.2 IP19) To: Alex Chang Alex Chang wrote: > > I read Grzesiek's paper in Nature Structure Biology 3(4):340, about the > solution structure of HIV Nef. I couldn't find the coordinates from PDB, > anyone knows how to get them? (they mentioned that the coordinates have > been deposited in PDB). > > -- > Alex Chang > Pathology > University of British Columbia > achang@hivnet.ubc.ca you can always search the pending and waiting list: gopher://pdb.pdb.bnl.gov/77/xstatusindex/status searching for Nef gives: Idcode: 1NEF Tracking Number: T8199 Entry Description: HEV-1 NEF Authors: G.M.CLORE,S.GRZESIEK,A.BAX,A.M.GRONENBORN Status for 1NEF: --incomplete-->--processing-->--depositor-->**REVIEW**>--rel All materials arrived as of: Feb 23 1996 Accession Date: Feb 23 1996 so: should be coming soon to a pdb mirror near you ! --gerard -------------------------------------------------------- Gerard CD Kleywegt Presently at Yale (mailto:gkleyweg@laplace.csb.yale.edu) Normally in Uppsala (mailto:gerard@xray.bmc.uu.se) From owner-proteins@net.bio.net Fri Jun 07 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!axe.netdoor.com!not-for-mail From: rth@netdoor.com (Rosemary T. Hoffman) Newsgroups: bionet.molbio.proteins Subject: PAGE of Glycoproteins Date: 8 Jun 1996 17:49:56 GMT Organization: Internet Doorway, Inc. 800-952-1570 Lines: 23 Message-ID: <4pceg4$70p@axe.netdoor.com> NNTP-Posting-Host: lance.netdoor.com X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] The original post described efforts to study a membrane protein that wouldn't enter a 12% polyacrylamide gel and wouldn't transfer to PVDF. (A 4% stacking gel was used.) I'd suggest trying a 3% stacking gel and 7% separating gel. If the protein enters the stacking gel but not the separating gel, then try a gradient gel. BioRad sells pre-cast 4-20% minigels or you can pour your own. Precipitating the protein in advance with acetone and then dissolving it in buffer before adding SDS-beta mercaptoethanol sample buffer and boiling for 5 minutes may help too. Perhaps there are lipids attached to the protein which would probably be removed by this step. For blotting, I've had good luck transferring a 160 kDa protein which may be as much as 50% sugar by using an overnight wet electroblotting procedure basically as described in the original Towbin article. I blotted to either PVDF or plain nitrocellulose. References to the gradient gel procedure, blotting, and lectin reactions with Western blots are given in a recent JBC article (#19 1996. Hoffman RT, Schmidt, ER, and Case ST) which tells what I did for the past 6 years. Hope this helps. Rosemary Hoffman From owner-proteins@net.bio.net Fri Jun 07 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news.cse.psu.edu!news.math.psu.edu!chi-news.cic.net!arclight.uoregon.edu!news.bc.net!torn!ccshst05.uoguelph.ca!ccshst01!rmartins From: rmartins@uoguelph.ca (Rui Martins) Newsgroups: bionet.molbio.proteins,bionet.general Subject: Re: uncoupling protein in brown adipose tissue Followup-To: bionet.molbio.proteins,bionet.general Date: 8 Jun 1996 21:18:01 GMT Organization: University of Guelph Lines: 9 Message-ID: <4pcqm9$50n@ccshst05.uoguelph.ca> References: <4pb2oj$3uk@ccshst05.uoguelph.ca> NNTP-Posting-Host: ccshst01.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.proteins:8080 bionet.general:22129 Rui Pires Martins (rmartins@uoguelph.ca) wrote: : I am posting this because I am looking for a protocol to assay for : uncoupling protien found in brown adipose mitochondria. There seems : to be much in the literature about the protein, but nothing I have : found has given me any insight as to how to assay for its activity. : Can anyone give any insight? please post here of email me directly at : rmatins@uoguelph.ca. Thanks. i just realised, and this shouldn't make a difference, really, but i had a typo in my email address...that's rmartins@uoguelph.ca From owner-proteins@net.bio.net Fri Jun 07 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!swrinde!sgigate.sgi.com!nntp.coast.net!news.kei.com!newsfeed.internetmci.com!in2.uu.net!earth.superlink.net!news From: Eric Lucas Newsgroups: bionet.molbio.proteins,sci.chem Subject: Re: DMF or DMSO? Date: Sat, 08 Jun 1996 15:33:11 -0500 Organization: SuperNet Inc. (908) 828-8988 Lines: 40 Message-ID: <31B9E387.46F4@peabody.sct.ucarb.com> References: <4p73hi$amm@agate.berkeley.edu> Reply-To: "" NNTP-Posting-Host: p3.superlink.net Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 3.0b2 (Macintosh; I; 68K) Xref: biosci bionet.molbio.proteins:8079 sci.chem:58056 Jeremy M. Travins wrote: > = > More than likely, it will dissolve in either solvent. > DMF (b.p. ~150) is much easier to get rid of than DMSO > (b.p. > 200) should you wish to recover your peptide. > Be sure to protect this stock solution from the open air as DMF > and DMSO are both very hygroscopic. > = > Jeremy Close. DMF boils at 153 =B0C, DMSO at 189 =B0C, but boiling points are a= = fairly poor indication of vapor pressure under vacuum (i.e., lyophilizing= = or rotovaping). I don't have a pvap information. I do remember as an = undergrad simply rotovaping DMSO to dry it (i.e., you don't need more = than 1 theoretical plate to separate DMSO and water pretty efficiently. = And rotovaping was much easier than doing a standard distillation.) = Worked very nicely, but did take an hour or so to do 500 mL with a 60 =B0= C = bath. Because of carcinogenicity and Me2NH formation, DMSO seems the clear = choice, as long as they are both good solvents (and, as everyone else has= = said, I would expect them to be.) Eric From owner-proteins@net.bio.net Sat Jun 08 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!newsfeed.internetmci.com!uwm.edu!vixen.cso.uiuc.edu!uchinews!scb1 From: scb1@midway.uchicago.edu (Samuel C. Blackman) Subject: Any experience using Bio-Rad Prep Cells? X-Nntp-Posting-Host: kimbark-nfs.uchicago.edu Message-ID: Sender: news@midway.uchicago.edu (News Administrator) Organization: The University of Chicago Date: Mon, 10 Jun 1996 05:06:02 GMT Lines: 13 I'm interested in using the Bio-Rad preparative electrophoresis equipment and IEF apparatus for purification of a receptor protein from platelets. Does anyone in bionet-land have any experience using this system? Thanks! -- Sam -- Samuel C. Blackman ! InterNet : blackman@tigger.uic.edu MD/PhD Student (3/7) ! Disclaimer : Who cares what I say, I'm a student! Univ. of Ill. at Chicago ! Quote : "Quandro potro io finir di stupire?" Dept. of Pharmacology ! Phone : 312/996-4983 (lab) Fax: 312/996-1225 From owner-proteins@net.bio.net Sun Jun 09 23:00:00 1996 Path: biosci!rutgers!uwm.edu!chi-news.cic.net!newsfeed.internetmci.com!in1.uu.net!rcogate.rco.qc.ca!altitude!usenet From: Achim Recktenwald Newsgroups: bionet.molbio.proteins Subject: Re: 2D PAGE pH gradients Date: Mon, 10 Jun 1996 07:57:00 -0500 Organization: IBEX Technologies, Inc. Lines: 22 Message-ID: <31BC1B9C.1B94@ibex.ca> References: NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; PPC) To: Elke Elke wrote: > > Has anyone tried measuring the gradient of IEF tube gels by first cutting > the first dimension gel into 0.5cm pieces , leaving each piece in about > 300-400 uL of water and leaving the whole rack in the coldroom overnight, > then measuring the pH the next day to make sure the ampholytes are working > properly? > I've done it sort of and it sure takes a long time for the pH to stabilize > to read each sample. > Elke > egreif@ccu.umanitoba.ca > It takes a long time, since there only a few molecules left, the ampholytes, that determine the pH. During the IEF-run all the other ions were removed. I usually used a pH-electrode with a flat tip to measure the pH of IEF-gels. Never tried it with tubes. Achim From owner-proteins@net.bio.net Sun Jun 09 23:00:00 1996 Newsgroups: bionet.molbio.proteins,bionet.celegans Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!newsfeed.internetmci.com!hunter.premier.net!netnews.worldnet.att.net!uunet!in2.uu.net!nih-csl!postman From: John Kuszewski Subject: Re: help with a biochemistry lab Content-Type: text/plain; charset=us-ascii Message-ID: <31BC7C14.2912@spork.niddk.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: spicy.niddk.nih.gov Content-Transfer-Encoding: 7bit Organization: Nat'l Insts of Health References: Mime-Version: 1.0 Date: Mon, 10 Jun 1996 19:48:36 GMT X-Mailer: Mozilla 2.01 (X11; I; SunOS 5.4 sun4m) Lines: 52 Xref: biosci bionet.molbio.proteins:8090 bionet.celegans:933 Johns Hopkins uses hen egg white lysozyme for its intro biochem lab. Easy to make a whole bunch of it, obvious where it comes from, and easy to assay in a biologically meaningful (as well as very cool) way--by looking at the turbidity of a solution of bacteria that have been fed to the lysozyme, you can watch them get eaten over time. All in all a great choice for an intro lab. Hope this helps. --JK Bruce Wightman wrote: > > I was wondering if anyone could provide suggestions for good proteins to > partially purify/purify for an introductory biochemistry lab for > undergraduates. I'd like to be able to give students an experience with > purification by gel filtration, ion exchange, and/or affinity > chromatography. Preferably, the protein should have an activity that can > be assayed easily and cheaply. The starting material should be something > that's clearly recognizable as "life". Unfortunately, the number of steps > has to be very limited, as time does not allow anything particularly > complicated. Also, it has to be doable at room temperature. > > Any ideas, good references, or protocols? > > Thanks- > Bruce Wightman > Department of Molecular and Cell Biology > 401 Barker Hall- Garriga Lab > University of California > Berkeley, CA 94720-3204 -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| My parents went to Zaire and all I got was this lousy retrovirus. From owner-proteins@net.bio.net Sun Jun 09 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!quagga.ru.ac.za!inet.up.ac.za!nobby.up.ac.za!bmans From: bmans@scientia.up.ac.za Newsgroups: bionet.molbio.proteins Subject: 2-dimensional electrophoresis Date: Mon, 10 Jun 1996 14:21:22 Organization: University of Pretoria Lines: 23 Message-ID: NNTP-Posting-Host: nobby.up.ac.za X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Hi there, We are doing 2-dimensional electrophoresis using the Biorad method. The IEF gels contain acrylamide/bisacrylamide, triton X-100, glycerol and ampholines. After staining the first dimension sample as well as standards are focussed in sharp bands after 1000 V for 3 hours. After second-dimensional SDS-electrophoresis the bands shows a horizontal ladder pattern of the same molecular weight. Is there any way to prevent this or explain this phenomenon. The proteins are pure and were identified by immunoblots and Coomassie staining. Concentrations are low so there is no overloading effect on the IEF gel. We found this effect with different proteins. What sort of sample buffer do any of you use in preparing your sample for the first dimension. Why do many of the 2-dimensional electrophoretrograms that are published contain similar horizontal streaks ?????? :-( Ben From owner-proteins@net.bio.net Sun Jun 09 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!news.ac.net!news.cais.net!news.structured.net!usenet From: m3995@jorsm.com (Eric W Blissmer) Newsgroups: bionet.molbio.proteins Subject: RECYCLE your used TYVEK coveralls- we offer to buy them! Date: 10 Jun 1996 19:30:24 GMT Organization: JORSM Internet Lines: 26 Message-ID: <4pht4g$cfq@news.structured.net> NNTP-Posting-Host: pm2s9.jorsm.com X-Newsreader: WinVN 0.92.6+ HELP PRESERVE THE ENVIRONMENT-- WHILE INCREASING YOUR PROFIT$... ========================================================== Reproce$$ Your TYVEK Coverall Garments. Miller's Precision Enterprises was founded in 1987 to recover disposable *Tyvek garments from the cleanroom industry. Recently, MPE was named DuPonts EXCLUSIVE Tyvek reprocessor for North America, and currently recovers Tyvek from many of the largest (and smallest) Pharmaceutical companies in the U.S. MPE's clean area system is designed to be easy to set up and administer. It requires NO more LABOR than throwing the garments out, yet it BENEFITS the ENVIRONMENT and YOUR COMPANY. Landfill space and the FEE to the disposal firm are SAVED by your company, and you receive a salvage value for the products you are currently PAYING to dispose of! If you have ANY questions, or would like to ENLIST YOUR COMPANY IN THIS PROFITABLE, ENVIRONMENTALLY BENEFICIAL PROGRAM, please call: Eric Blissmer- R&D Mgr. ph: (219) 865-3322 fx: (219) 865 0132 MPE, Inc. 445 Junction Av. Email: m3995@jorsm.com Schererville, IN 46375 CHECK OUT OUR WEB PAGE FOR MORE INFO: http://crown.icongrp.com/~mpe/ From owner-proteins@net.bio.net Sun Jun 09 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!news.cis.okstate.edu!usenet From: Ron Tate Newsgroups: bionet.molbio.proteins Subject: Re: Any experience using Bio-Rad Prep Cells? Date: Mon, 10 Jun 1996 16:35:51 -0500 Organization: Oklahoma State University, Biochemistry and Molecular Biology Lines: 25 Message-ID: <31BC9537.6AF6@bmb-fs1.biochem.okstate.edu> References: NNTP-Posting-Host: firefly3.biochem.okstate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win95; I) Samuel C. Blackman wrote: > > I'm interested in using the Bio-Rad preparative electrophoresis equipment > and IEF apparatus for purification of a receptor protein from platelets. > Does anyone in bionet-land have any experience using this system? > > Thanks! > > -- Sam I have used the prep cell once now in an initial experiment, its really pretty easy to use but it eats up quite a bit of buffer per run. My results weren't what I wanted but then I ignored their recommendation and poured a much higher concentration gel than what they recommend and after 24 hours my proteins were nicely separated but still in the gel and migrating, so follow instructions. -- >>>>>>---------------------------> >Ron Tate >Lab of Franklin Leach >Dept. of Biochem. & Molecular Biology >Oklahoma State University rtate@bmb-fs1.biochem.okstate.edu (405) 744-9326 --------------------------------------------- From owner-proteins@net.bio.net Sun Jun 09 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!news.cis.okstate.edu!usenet From: Ron Tate Newsgroups: bionet.molbio.proteins,bionet.celegans Subject: Re: help with a biochemistry lab Date: Mon, 10 Jun 1996 16:19:07 -0500 Organization: Oklahoma State University, Biochemistry and Molecular Biology Lines: 27 Message-ID: <31BC914B.6A3@bmb-fs1.biochem.okstate.edu> References: NNTP-Posting-Host: firefly3.biochem.okstate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win95; I) Xref: biosci bionet.molbio.proteins:8092 bionet.celegans:935 Bruce Wightman wrote: > > I was wondering if anyone could provide suggestions for good proteins to > partially purify/purify for an introductory biochemistry lab for > undergraduates. I'd like to be able to give students an experience with > purification by gel filtration, ion exchange, and/or affinity > chromatography. Preferably, the protein should have an activity that can > be assayed easily and cheaply. The starting material should be something > that's clearly recognizable as "life". Unfortunately, the number of steps > has to be very limited, as time does not allow anything particularly > complicated. Also, it has to be doable at room temperature. > > Any ideas, good references, or protocols? How about lysozyme from egg white, its pretty easily purified by ion exchange and the assay is pretty easy too. Just another suggestion, its done here in an undergraduate lab course. -- >>>>>>---------------------------> >Ron Tate >Lab of Franklin Leach >Dept. of Biochem. & Molecular Biology >Oklahoma State University rtate@bmb-fs1.biochem.okstate.edu (405) 744-9326 --------------------------------------------- From owner-proteins@net.bio.net Sun Jun 09 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!news.cis.okstate.edu!usenet From: Ron Tate Newsgroups: bionet.molbio.proteins,bionet.celegans Subject: Re: help with a biochemistry lab Date: Mon, 10 Jun 1996 16:15:48 -0500 Organization: Oklahoma State University, Biochemistry and Molecular Biology Lines: 24 Message-ID: <31BC9084.C60@bmb-fs1.biochem.okstate.edu> References: NNTP-Posting-Host: firefly3.biochem.okstate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win95; I) Xref: biosci bionet.molbio.proteins:8091 bionet.celegans:934 Bruce Wightman wrote: > > I was wondering if anyone could provide suggestions for good proteins to > partially purify/purify for an introductory biochemistry lab for > undergraduates. I'd like to be able to give students an experience with > purification by gel filtration, ion exchange, and/or affinity > chromatography. Preferably, the protein should have an activity that can > be assayed easily and cheaply. The starting material should be something > that's clearly recognizable as "life". Unfortunately, the number of steps > has to be very limited, as time does not allow anything particularly > complicated. Also, it has to be doable at room temperature. > > Any ideas, good references, or protocols? -- >>>>>>---------------------------> >Ron Tate >Lab of Franklin Leach >Dept. of Biochem. & Molecular Biology >Oklahoma State University rtate@bmb-fs1.biochem.okstate.edu (405) 744-9326 --------------------------------------------- From owner-proteins@net.bio.net Sun Jun 09 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!newsfeed.internetmci.com!chi-news.cic.net!nntp.coast.net!fu-berlin.de!news.belwue.de!news.uni-hohenheim.de!wpxx02.toxi.uni-wuerzburg.de!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins,bionet.celegans Subject: Re: help with a biochemistry lab Followup-To: bionet.molbio.proteins,bionet.celegans Date: 10 Jun 1996 18:09:31 GMT Organization: CC University of Hohenheim (not responsible for contents) Lines: 19 Message-ID: <4phocr$k88@power5.rz.uni-hohenheim.de> References: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Xref: biosci bionet.molbio.proteins:8087 bionet.celegans:932 Bruce Wightman (wightman@mendel.berkeley.edu) wrote: > I was wondering if anyone could provide suggestions for good proteins to > partially purify/purify for an introductory biochemistry lab for > undergraduates. Maybe GST would work. It's a single-step purification from bacteria which can be done easily in two days, yielding milligrams of pure protein from one liter of bacterial culture. If you prepare it at room temperature, yields will probably drop slightly, but who cares. Affinity is assayed photo- metrically with Dichloronitrobenzol plus Glutathione. Just a suggestion, --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Sun Jun 09 23:00:00 1996 Path: biosci!agate!spool.mu.edu!usenet.eel.ufl.edu!newsfeed.internetmci.com!chi-news.cic.net!cougar.olivet.edu!reed-006.olivet.edu!dginn From: dginn@olivet.edu Newsgroups: bionet.molbio.proteins Subject: Rat Type I collagen cDNA probe needed Date: Mon, 10 Jun 1996 14:40:42 +1000 Organization: Olivet Nazarene University Lines: 10 Message-ID: NNTP-Posting-Host: reed-006.olivet.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] Greetings, I am looking for a plasmid probe with a cDNA sequence for Rat Type I collagen gene [alpha1(I) and/or alpha2(I)]. Does anyone know where I could get ahold of this probe - either a company or a laboratory? Thanks a lot! Dwight Ginn Olivet Nazarene University From owner-proteins@net.bio.net Sun Jun 09 23:00:00 1996 Path: biosci!KRISHNA.DCRT.NIH.GOV!geetha From: geetha@KRISHNA.DCRT.NIH.GOV ("geetha vasudevan") Newsgroups: bionet.molbio.proteins Subject: Graphics and modeling programs for DEC-ALPHA.. Date: 10 Jun 1996 08:59:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9606101156.ZM10481@krishna.dcrt.nih.gov> NNTP-Posting-Host: net.bio.net Hello : I am trying to find out if there are graphics visualization and modeling programs (like WHATIF) available for DEC-ALPHA machines.. I find that most of them (if not all) are available for SGI.. Thanks for any info.. -GV -- [mails to geetha@helix will be forwarded to geetha@krishna.dcrt] | GEETHA VASUDEVAN Ph.#: (301)-402-0506 (w) | | Post Doctoral Visiting Fellow Fax#: (301)-496-2172 (w) | | Anal.Bio.Sec., Lab.of Str.Biol. E-mail: geetha@helix.nih.gov | | Bldg.12A/Room 2041,DCRT, NIH, Bethesda, MD 20892-5626 | From owner-proteins@net.bio.net Sun Jun 09 23:00:00 1996 Path: biosci!agate!garriga4.berkeley.edu!user From: wightman@mendel.berkeley.edu (Bruce Wightman) Newsgroups: bionet.molbio.proteins,bionet.celegans Subject: help with a biochemistry lab Date: Mon, 10 Jun 1996 10:26:47 -0800 Organization: UCBerkeley Lines: 18 Message-ID: Reply-To: wightman@mendel.berkeley.edu NNTP-Posting-Host: garriga4.berkeley.edu Xref: biosci bionet.molbio.proteins:8086 bionet.celegans:931 I was wondering if anyone could provide suggestions for good proteins to partially purify/purify for an introductory biochemistry lab for undergraduates. I'd like to be able to give students an experience with purification by gel filtration, ion exchange, and/or affinity chromatography. Preferably, the protein should have an activity that can be assayed easily and cheaply. The starting material should be something that's clearly recognizable as "life". Unfortunately, the number of steps has to be very limited, as time does not allow anything particularly complicated. Also, it has to be doable at room temperature. Any ideas, good references, or protocols? Thanks- Bruce Wightman Department of Molecular and Cell Biology 401 Barker Hall- Garriga Lab University of California Berkeley, CA 94720-3204 From owner-proteins@net.bio.net Mon Jun 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!newsfeed.internetmci.com!in2.uu.net!rcogate.rco.qc.ca!altitude!usenet From: Achim Recktenwald Newsgroups: bionet.molbio.proteins Subject: Re: CNBr Cleavage of soluble proteins Date: Tue, 11 Jun 1996 08:53:53 -0500 Organization: IBEX Technologies, Inc. Lines: 30 Message-ID: <31BD7A71.4772@ibex.ca> References: <4p53s1$abi@cnn.Princeton.EDU> <4p69ts$l80@netserver.univ-lille1.fr> <4pb005$n97@news-e2d.gnn.com> NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; PPC) Lacluster@gnn.com wrote: > > CNBr is an old workhorse, and works well as long as the methionine is not > oxidized to any great extent. The high formic acid content can be > problematic -- I remember doing those cleavages and removing excess reagent > and acid by lyophilization. Needless to say, the lyophilizer suffered > terribly from this treatment. 70% HCOOH will solubilize just about > anything, however, which helps if one of your cleavage products is > particularly greasy... I would recommend to carboxymethylate the cysteines first. Also, never dry your samples to completeness, always leave the CNBr-fragments in a little bit of liquid. Since the peptides are usually quite large, hydrophobic ones often do not get into solution again, once they have been dried completely. If you have a protein with large hydrophobic patches, you can use formic acid as high as 88%. You have to dilute the solution with about 15x the reaction volume with water before lyophilization. Usually, after a first round of lyophilization I diluted again with water and repeated the lyophilization to remove digestion side-reaction products and an excess of formic acid. If you use 88% acid, you might have to do it a third time. The CNBr-digestion is usally very simple, problems may occur afterwards, when you want to purify the petides by chromatography. Good luck, Achim From owner-proteins@net.bio.net Mon Jun 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in2.uu.net!01-newsfeed.univie.ac.at!03-newsfeed.univie.ac.at!sbg.ac.at!news From: Markus Jaritz Newsgroups: bionet.molbio.proteins Subject: Re: Graphics and modeling programs for DEC-ALPHA.. Date: Tue, 11 Jun 1996 11:12:05 +0200 Organization: Computing Services, University of Salzburg Lines: 40 Message-ID: <31BD3865.41C6@Elsa.came.sbg.ac.at> References: <9606101156.ZM10481@krishna.dcrt.nih.gov> NNTP-Posting-Host: elsa.came.sbg.ac.at Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; IRIX 5.3 IP22) To: geetha vasudevan geetha vasudevan wrote: > > Hello : > > I am trying to find out if there are graphics visualization and modeling > programs (like WHATIF) available for DEC-ALPHA machines.. I find that > most of them (if not all) are available for SGI.. > Thanks for any info.. > > -GV > > -- > [mails to geetha@helix will be forwarded to geetha@krishna.dcrt] > > | GEETHA VASUDEVAN Ph.#: (301)-402-0506 (w) | > | Post Doctoral Visiting Fellow Fax#: (301)-496-2172 (w) | > | Anal.Bio.Sec., Lab.of Str.Biol. E-mail: geetha@helix.nih.gov | > | Bldg.12A/Room 2041,DCRT, NIH, Bethesda, MD 20892-5626 | Hi Geetha, Rasmol is ok for DEC ALPHA, e.g. at http://www.umass.edu/microbio/rasmol/getras.htm Markus ============================================================== Markus Jaritz Center for Applied Molecular Engineering University of Salzburg Institute for Chemistry and Biochemistry Jakob Haringer Str. 1 Salzburger Techno-Z 5020 Salzburg Austria From owner-proteins@net.bio.net Mon Jun 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!EU.net!Norway.EU.net!nntp.uio.no!news.cais.net!mr.net!newshub.tc.umn.edu!newsstand.tc.umn.edu!maroon.tc.umn.edu!rosto001 From: rosto001@maroon.tc.umn.edu (Alexander P Rostovtsev) Newsgroups: bionet.molbio.proteins,bionet.celegans Subject: Re: help with a biochemistry lab Date: 11 Jun 1996 09:04:17 -0500 Organization: University of Minnesota Lines: 6 Message-ID: References: NNTP-Posting-Host: maroon.tc.umn.edu Xref: biosci bionet.molbio.proteins:8098 bionet.celegans:936 Any glycolisys enzyme from yeasts. Lots of fun for students. Dept. of Biochemistry of Moscow State University has published student cookbook on this subject. If you're interested - e-mail me for further info. Alexander Rostovtsev U of Minnesota Biotherapy Program From owner-proteins@net.bio.net Mon Jun 10 23:00:00 1996 Path: biosci!JWCI.ORG!dale From: dale@JWCI.ORG (Dale Yuzuki) Newsgroups: bionet.molbio.proteins Subject: Shaker flask to Fermentor scale-up Q Date: 11 Jun 1996 16:29:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <9606111623.aa11066@jwi-adm.jwci.org> NNTP-Posting-Host: net.bio.net Hi all, We are currently expressing a GST fusion protein in BL21 using shaker flasks. As we want to get much more recombinant protein we found a group that is willing to run their fermentor for us. Can anyone point me to references that use BL21 in fermentation? Is minimal media the way to go? Are there differences in the induction time used, etc.? Pharmacia hasn't been able to help with this. Any help would be appreciated. Please email directly to dale@jwci.org. Thanks in advance. Dale Yuzuki John Wayne Cancer Inst. dale@jwci.org From owner-proteins@net.bio.net Mon Jun 10 23:00:00 1996 Message-ID: <31BD41C4.41C6@sgiclu.chemie.uni-konstanz.de> Date: Tue, 11 Jun 1996 11:52:05 +0200 From: Marcus Macht Organization: University of Konstanz X-Mailer: Mozilla 3.0b4 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 Newsgroups: bionet.molbio.proteins Subject: Re: CNBr Cleavage of soluble proteins References: <4p53s1$abi@cnn.Princeton.EDU> <4p69ts$l80@netserver.univ-lille1.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 23 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-konstanz.de! Philippe Lefebvre wrote: > > Well, CNBr is a very potent and selective cleavage agent, BUT in 70% formic acid. > I don't know whether this is compatible with your goals (ie native or denaturated > proteins) > Dr Phil Good You do not necessarily have to use 70% formic acid. The BrCN cleavage works also very well in 60% H2O/ 40% acetonitrile with 0.1% TFA. I have applied this variant several times and it has the advantage, that no formylation during the cleavage occurs. Literature for this modified method is: M.O. Glocker, B. Arbogast, J. Scheurs, M.L. Deinzer, Biochemistry 32(1993), p.482 Yours sincerely Marcus Macht ********************************************************************* * Papernet: * * * Marcus Macht * InterNet: * * AG Przybylski * macht@chclu.chemie.uni-konstanz.de * * Faculty Chemistry * * * University of Konstanz * VoiceNet: * * PO Box 5560 M 732 * ++49-07531-883436 * * 78464 Konstanz, Germany * * ********************************************************************* From owner-proteins@net.bio.net Mon Jun 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news.cse.psu.edu!news.eecs.nwu.edu!newsfeed.acns.nwu.edu!news.cc.uic.edu!usenet From: Keld Sorensen Newsgroups: bionet.molbio.proteins Subject: Re: help with a biochemistry lab Date: Tue, 11 Jun 1996 10:06:06 -0600 Organization: University of Illinois, College of Medicine Lines: 5 Message-ID: <31BD996E.F10@uic.edu> References: NNTP-Posting-Host: sliprock-03.dialin.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) I recall purifying HRP (from horseradish obviously) - it was easy and the enzyme is easy to detect with TMB or other commercial substrate. Keld. From owner-proteins@net.bio.net Mon Jun 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!EU.net!Norway.EU.net!nntp.uio.no!news.kth.se!news From: Arne Elofsson Newsgroups: bionet.molbio.proteins Subject: Re: Graphics and modeling programs for DEC-ALPHA.. Date: 11 Jun 1996 18:44:49 +0200 Lines: 37 Message-ID: References: <9606101156.ZM10481@krishna.dcrt.nih.gov> <31BD3865.41C6@Elsa.came.sbg.ac.at> NNTP-Posting-Host: assar.biokemi.su.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Gnus v5.2.15/XEmacs 19.13 Markus Jaritz writes: > > geetha vasudevan wrote: > > > > Hello : > > > > I am trying to find out if there are graphics visualization and modeling > > programs (like WHATIF) available for DEC-ALPHA machines.. I find that > > most of them (if not all) are available for SGI.. > > Thanks for any info.. > > > > Hi Geetha, > > Rasmol is ok for DEC ALPHA, e.g. at > > http://www.umass.edu/microbio/rasmol/getras.htm > From the top of my head rasmol, whatif, molmod (from Wutrich and co-workers), xtalview (from ucsd ?) Commercially I think ICM, Quanta and maybee insight runs. (These might need some graphics board) Probably some other. arne -- ----------------------------------------------------------------- From: Arne Elofsson Email: arne@rune.biokemi.su.se Tel:+46(0)8-161553 WWW: http://www.biokemi.su.se/~arne/ From owner-proteins@net.bio.net Tue Jun 11 23:00:00 1996 From: howard.olson@awaiter.com (Howard Olson) Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!netcom.net.uk!netcom.com!netcomsv!uu3news.netcom.com!netcomsv!uu4news.netcom.com!awaiter!howard.olson Newsgroups: bionet.molbio.proteins Subject: Selenocysteine codon? Message-ID: <834586701@awaiter.com> Date: Wed, 12 Jun 1996 13:38:21 GMT Distribution: world Organization: Awaiter BBS 510-939-9992 Lines: 7 I read years ago in Nature that the selenium analog of cysteine, selenocysteine had its own codon. Can anyone give me a recent reference? Thanks in Advance, Howard From owner-proteins@net.bio.net Tue Jun 11 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!newsfeed.internetmci.com!cyberspace.com!news.sprintlink.net!news-stk-3.sprintlink.net!news.sprintlink.net!news-fw-12.sprintlink.net!news2.usa1.com!not-for-mail From: wang@covalent.usa1.com (Wang, Yi-Ming) Subject: Actin, aborption max 260nm?? Message-ID: <6c7cc$e1da.8d@news2.usa1.com> Date: Wed, 12 Jun 1996 19:29:10 GMT X-Newsreader: WinVN 0.93.11 MIME-Version: 1.0 Lines: 21 Hi! All, I just noticed the absorption spectrum of my actin sample (bovine musle from Sigma) in pH 7.0 phosphate buffer shows a UV absorption max at 260nm. I would think the max for a big protein molecule like actin should be at 280nm. Does anyone know where the max should be? My sample of actin is almost 4 years old and was kept in a freezer. I am not sure that may be a problem. Thanks for your input. Yi-Ming =================================================================== Yi-Ming Wang, Ph.D. Phone: 617-938-1140 Covalent Associates, Inc. Fax: 617-938-1364 10 State Street Email: wang@covalent.usa1.com Woburn, MA 01801