From owner-proteins@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!xlink.net!scsing.switch.ch!bernina!news From: Song Tan Newsgroups: bionet.molbio.proteins Subject: Re: Protein Purification Protocols Keywords: protein purification Message-ID: Date: 2 Jul 93 11:30:28 GMT References: Sender: news@bernina.ethz.ch (USENET News System) Reply-To: tan@aeolus.vmsmail.ethz.ch Followup-To: bionet.molbio.proteins Organization: ETH, Zurich, Switzerland Lines: 58 In article knight@grafton.dartmouth.edu (John Boswell) writes: >Hi, > >Could someone in the field please recommend some good texts/references >on protein purification protocols? I have about 15 liters of media from >cell culture, and I need to isolate and purify an expressed protein from >this. I can detect the protein via Western blot, and I also have an >activity assay. What I need are good ways to start to purify the protein, >i.e. protocols for salt-pption., gel-filtration, and other chromatography; >maybe elution via an ethylene glycol gradient. I don't have much experience >with protein purification past a short course I took a bunch of years ago >in graduate school. Any pointers in the right direction would be greatly >appreciated! I'm off to look in the library now... :):) > >Thanks, > >-John Boswell, Ph.D. >Dept. of Chemistry, Biochemistry, and Molecular Biology >Oregon Graduate Institute >Portland, OR 97229 >(knight@grafton.dartmouth.edu) I've found the following book to be an excellent reference source for most modern methods of protein purification. It covers the major techniques and has good discussion of the theoretical basis of the various chromatographic and electrophoretic methods: Protein Purification: Principles, High Resolution Methods, Applications ed. Jan-Christer Janson and Lars Ryden VCH Publishers Inc, NY, NY 10010 ISBN 0-89573-122-3, published 1989 The book is a little sparse on simplified protocols, which conveniently, the next two references (in the IRL Practical Approach series) supply: Protein Purification Methods: A Practical Approach ed. E.L.V. Harris and S. Angal IRL Press ISBN 0-19-963003-8 (softcover), 1989 Protein Purification Applications: A Practical Approach ed. E.L.V. Harris and S. Angal IRL Press ISBN 0-19-963023-2 (softcover), 1989 Hope this helps. Dr. Song Tan Inst fur Molekularbiologie und Biophysik ETH-Honggerberg 8093 Zurich, Switzerland email: tan@aeolus.vmsmail.ethz.ch From owner-proteins@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!CRCVMS.UNL.EDU!CSMITH From: CSMITH@CRCVMS.UNL.EDU Newsgroups: bionet.molbio.proteins Subject: Re: Glycoprotein Stains Message-ID: <01H01HM0I9CG0023M3@crcvms.unl.edu> Date: 2 Jul 93 02:26:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 35 Date: Thu, 1 Jul 1993 07:16 CST From: CSMITH@crcvms.unl.edu Subject: Re: glycoprotein stains To: quinones@ucsc.edu I responded to a query that I think was posted in this net group (I could be wrong), but my response was "returned to sender" ... so I'm re-posting my reply here. Hopefully "quinones@ucsc.edu" will catch it. The original sender was asking for info on how to correlate the PAGE gel glycoprotein stained bands (wet gel) to those of the same gel subsequently stained with CB (dried gel). One potential solution to your problem would be to run PRE-STAINED SDS- PAGE STANDARDS on your gels. We commonly do this as a reference mark, pre- and post gel hydration (drying). By creating a log Mr vs Rf plot for the standards in the wet and dry gel, we can assess the Mr of our unknowns in both gels, respectively. By comparing Mr values we can better objectively say that band A of Z Mr in the wet gel is the same band A of Z' Mr in the dried gel (or immunoblot !!!). WE routinely use the pre-stained standards distributed by Bio-Rad (Hercules, CA), but those of BRL/Life Technologies are just as good. We recommend staying away from SIGMA ... we order alot of stuff from them, but their MW standards ARE NOT one of them. Good Luck Chris Christopher M. Smith Department of Biochemistry University of NEbraska-Lincoln University of Nebraska-Lincoln Lincoln, NE 68583-0718 e-mail: CSMITH@CRCVMS.UNL.EDU From owner-proteins@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!howland.reston.ans.net!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc8.harvard.edu!gisselbr From: gisselbr@husc8.harvard.edu (Stephen Gisselbrecht) Newsgroups: bionet.molbio.proteins Subject: Re: glycoprotein stains Message-ID: <1993Jul2.174950.25444@husc14.harvard.edu> Date: 2 Jul 93 21:49:49 GMT References: <1993Jul2.073109.14425@iscsvax.uni.edu> Organization: Harvard University Science Center Lines: 15 Nntp-Posting-Host: husc8.harvard.edu In article <1993Jul2.073109.14425@iscsvax.uni.edu> klier@iscsvax.uni.edu writes: >I also had trouble reaching the original poster... Yup, me too. Now, maybe I'm missing something here, but it seems to me like you could just photograph the gel next to a ruler after both procedures and convert the distance travelled by each band to "% of gel length". I know that for whole-cell extracts, you probably wouldn't be able to get precise enough to determine which band is which, but this should work for up to 10 or 20 bands. steve gisselbrecht cell & dev. bio. harvard medical school From owner-proteins@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!pbi.nrc.ca!fbekkaoui From: fbekkaoui@pbi.nrc.ca Newsgroups: bionet.molbio.proteins Subject: Protein Purification Protocols Message-ID: <2C3493B3@gate1.pbi.nrc.ca> Date: 2 Jul 93 19:58:00 GMT Sender: kristoff@net.bio.net Reply-To: fbekkaoui@pbi.nrc.ca Distribution: bionet Lines: 51 I would recommend the volume 182 of Methods in Enzymology 1990 "Guide to protein purification" Ed. MP Deutscher Good luck. Fouzi. ------------------------------------------------------------------------------ REPLY FROM: Bekkaoui, Fouzi Return-Path: Received: from net.bio.net by gate1.pbi.nrc.ca id <2C333F8E@gate1.pbi.nrc.ca>; Thu, 01 Jul 93 12:48:30 PDT Received: by net.bio.net (5.65/IG-2.0) id AA01753; Thu, 1 Jul 93 11:45:47 -0700 Received: by net.bio.net (5.65/IG-2.0) id AA01740; Thu, 1 Jul 93 11:45:45 -0700 Message-Id: <9307011845.AA01740@net.bio.net> To: proteins@net.bio.net From: knight@grafton.dartmouth.edu (John Boswell) Subject: Protein Purification Protocols Date: 1 Jul 93 17:53:09 GMT Sender: news@dartvax.dartmouth.edu (The News Manager) Hi, I posted a similar request on another group, then found this one :) Could someone in the field please recommend some good texts/references on protein purification protocols? I have about 15 liters of media from cell culture, and I need to isolate and purify an expressed protein from this. I can detect the protein via Western blot, and I also have an activity assay. What I need are good ways to start to purify the protein, i.e. protocols for salt-pption., gel-filtration, and other chromatography; maybe elution via an ethylene glycol gradient. I don't have much experience with protein purification past a short course I took a bunch of years ago in graduate school. Any pointers in the right direction would be greatly appreciated! I'm off to look in the library now... :):) Thanks, -John Boswell, Ph.D. Dept. of Chemistry, Biochemistry, and Molecular Biology Oregon Graduate Institute Portland, OR 97229 (knight@grafton.dartmouth.edu) -- **************************************************************************** Dr. John Boswell knight@grafton.dartmouth.edu Dept. of Medicine/GI MCN C2104 Vanderbilt University, Nashville, TN 37232 615-322-6367 or 615-343-4747 From owner-proteins@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!ux1.cso.uiuc.edu!newsrelay.iastate.edu!iscsvax.uni.edu!klier From: klier@iscsvax.uni.edu Newsgroups: bionet.molbio.proteins Subject: re:glycoprotein stains Message-ID: <1993Jul2.073109.14425@iscsvax.uni.edu> Date: 2 Jul 93 13:31:09 GMT Organization: University of Northern Iowa Lines: 16 I also had trouble reaching the original poster... Can you put a standard glycoprotein on your gel, then use it to calculate the Rm (relative molbility) for the band of interest? Alternatively, make a photocopy of the shrunken gel (yep, right there on the xerox machine -- I use clear polystyrene boxes and shoot through the box bottom), then fuss around with the enlarging system on the photocopier until you get a copy that matches the size of the rehydrated gel. Then you can do a direct comparison. Or put your photographic negative in an enlarger, and project onto your other photo. Adjust size of image until you can do a direct comparison. Kay Klier Biology Dept UNI From owner-proteins@net.bio.net Fri Jul 02 23:00:00 1993 Path: biosci!CRCVMS.UNL.EDU!CSMITH From: CSMITH@CRCVMS.UNL.EDU Newsgroups: bionet.molbio.proteins Subject: Re: Renaturation/Extraction Recombinant Proteins Message-ID: <01H0434PMAAO002F6J@crcvms.unl.edu> Date: 3 Jul 93 23:04:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 30 Some general info for those who are purifying (or attempting to) recombinant proteins from bacterial hosts. General resources that have been invaluable to us are: One genera;l resource that has been invaluable to us is; Protein Expression and Purification (Academic Press, Inc.), a journal that contains lots of VERY useful info. In many cases the info, tid-bits it contains are not directly applicable to our particular vector or hosts, but provide lots of insight and leads-in to things we might try. e.g., have problems extracting your protein and/or renaturing it (because you used a denaturing extraction protocol) ... why not step back and look at other things you could try to make your host produce the protein in a more "soluble" and extractable form ... see Moore, et al. (1993) Protein Expression and Purification 4:160-163. By growing their bugs in enriched media, they report the high level expression and recovery of their recombinant protein, which normally was sequested in inclusion bodies. Chris Christopher Smith Department of Biochemistry University of Nebraska-Lincoln Lincoln, Nebraska 68583-0718 e-mail: CSMITH@CRCVMS.UNL.EDU phone: (402) 472-6806 From owner-proteins@net.bio.net Fri Jul 02 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!torn!utnut!wave.scar!90taobri From: 90taobri@wave.scar.utoronto.ca (TAO BRIAN T) Newsgroups: bionet.molbio.proteins Subject: Re: Trivia question...why do carrots turn green in cakes? Message-ID: Date: 3 Jul 93 18:31:14 GMT References: Reply-To: 90taobri@wave.scar.utoronto.ca Organization: MuGS Research and Development Facility Lines: 11 To: rhughes@ucsd.edu (Richard J. Hughes) X-Newsreader: MuGS 3.0d27 [Jun 10 93] In article , Richard J. Hughes writes... > > Here is a trivia question. Why do carrot shreds turn green when cooked > in carrot cake? Is this due to oxidation of the beta-carotene? Is > beta-carotene responsible for the orange colour in the first place? Beats me... the carrots in my carrot cake stay nice and orange. What do you put in yours? ;-) Follow-ups to rec.food.cooking... ;-) -- Brian Tao:: taob@io.org (Internex Online, 416-363-3783, 10 lines, v.32bis) ::::::::::: *** Note that my address has changed *** From owner-proteins@net.bio.net Tue Jul 06 23:00:00 1993 Path: biosci!parc!decwrl!ames!haven.umd.edu!uunet!munnari.oz.au!metro!usage!newt.phys.unsw.edu.au!sjt From: sjt@newt.phys.unsw.edu.au (Sarah Tilley) Newsgroups: bionet.molbio.proteins Subject: Re: problems renaturing recombinant protein Keywords: Chaperonins Message-ID: <1993Jul7.074646.22313@usage.csd.unsw.OZ.AU> Date: 7 Jul 93 07:46:46 GMT References: Sender: news@usage.csd.unsw.OZ.AU Reply-To: sjt@newt.phys.unsw.edu.au (Sarah Tilley) Organization: University of NSW Lines: 31 Nntp-Posting-Host: newt.phys.unsw.edu.au -- In article , kcrossgr@mail.sas.upenn.edu (Kirsten Crossgrove) writes: |> |>Hi everyone, |>I'm trying to express a zinc-finger containing protein in E. coli. It |>expresses well but is very insoluble. I can solubilize it in 6M guanidine |>HCl and purify it over a nickel-chelate column (it has a 6 histidine |>N-terminal fusion). However, when I dialyze to get rid of the GuHCl (or 8M |>urea-same result), the protein sometimes precipitates out, and even when it |>doesn't, the activity is extremely low to non-existent. The protein is |>eluted off the column at low pH (usu. 5.9-6.3). The dialysis buffer is: |>10mM HEPES pH 7.9 |>80mM KCl |>1mM DTT |>0.1% Triton X100 |>5-20% glycerol |>10uM ZnCl2 |>I get rid of the GuHCl or urea in a stepwise manner (1M, 0.1M, 0M). |>I've gotten reasonably active preps before, but it is just not consistent |>and lately no matter what I do, I can't get active protein. I think it is a |>problem with the renaturation. |>Any suggestions? |>Thanks. |>Kirsten Crossgrove |> Have you tried the E.coli chaperonin60, GroEL? It has been suggested in some recent articles, that such chaperonins might need to be co-expressed when trying to produce active recombinant proteins. ** Sarah Tilley sjt@newt.phys.unsw.edu.au From owner-proteins@net.bio.net Wed Jul 07 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!math.ohio-state.edu!uwm.edu!rpi!utcsri!utnut!wave.scar!90taobri From: 90taobri@wave.scar.utoronto.ca (TAO BRIAN T) Newsgroups: bionet.general,bionet.molbio.proteins Subject: Increasing pH and temperature stability of enzymes Message-ID: Date: 8 Jul 93 17:23:29 GMT Reply-To: 90taobri@wave.scar.utoronto.ca (Brian Tao) Followup-To: bionet.molbio.proteins Organization: MuGS Research and Development Facility Lines: 12 Xref: biosci bionet.general:5423 bionet.molbio.proteins:719 X-Newsreader: MuGS 3.0d28 [Jul 8 93] Does anyone have experience in inducing point mutations in an enzyme in order to increase its thermal or pH stability? I have two enzymes, each from a different bacterial species. One has a wide pH range of activity (3.5 to 8) and is stable to about 60 C. The other has a narrower pH range, is degraded above 40 C, but it has 3 to 5 times the acitivity of the first. Are there any guidelines or hints for mutating either enzyme so the benefits of both are present in the mutant? References would be greatly appreciated. -- Brian Tao:: taob@io.org (Internex Online, 416-363-3783, 10 lines, v.32bis) ::::::::::: *** Note that my address has changed *** From owner-proteins@net.bio.net Wed Jul 07 23:00:00 1993 Path: biosci!agate!sprite.berkeley.edu!shirriff From: shirriff@sprite.berkeley.edu (Ken Shirriff) Newsgroups: bionet.general,bionet.molbio.proteins Subject: Re: searching_PDB_files Message-ID: <21i3q1$dem@agate.berkeley.edu> Date: 8 Jul 93 21:32:49 GMT References: <1993Jul8.185447.9541@serval.net.wsu.edu> Organization: University of California, Berkeley Lines: 14 Xref: biosci bionet.general:5429 bionet.molbio.proteins:721 NNTP-Posting-Host: hijack.berkeley.edu In article <1993Jul8.185447.9541@serval.net.wsu.edu> qyi@NOSY.chem.wsu.edu (Qian Yi) writes: >I am searching for the coordinates of crystal structure of cytochrome c >peroxidase and cytochrome c complexes. >If someone knows the PDB file names for those coordinates in Protein Data >Bank, or someone has those files, A good source for this is Laura Welsh's annotated PDB file listing, which is in /pub/chemistry/pdbdoc/pdb_file_list.jan.93 at kekule.osc.edu [128.146.36.48]. According to that file, the cycochrome C peroxidase files are 1ccp, 2ccp, 3ccp, 4ccp, and 2cyp. Ken Shirriff shirriff@sprite.Berkeley.EDU From owner-proteins@net.bio.net Wed Jul 07 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!howland.reston.ans.net!darwin.sura.net!news-feed-2.peachnet.edu!umn.edu!gaia.ucs.orst.edu!osshe.edu!news.uoregon.edu!netnews.nwnet.net!serval!NOSY.chem.wsu.edu!qyi From: qyi@NOSY.chem.wsu.edu (Qian Yi) Newsgroups: bionet.general,bionet.molbio.proteins Subject: searching_PDB_files Message-ID: <1993Jul8.185447.9541@serval.net.wsu.edu> Date: 8 Jul 93 18:54:47 GMT Sender: news@serval.net.wsu.edu (USENET News System) Organization: Washington State University Lines: 5 Xref: biosci bionet.general:5428 bionet.molbio.proteins:720 I am searching for the coordinates of crystal structure of cytochrome c peroxidase and cytochrome c complexes. If someone knows the PDB file names for those coordinates in Protein Data Bank, or someone has those files, would you please let me know, or send me a copy of the files if convenient. Thanks. From owner-proteins@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!parc!decwrl!ames!agate!usenet.ins.cwru.edu!cleveland.Freenet.Edu!dd034 From: dd034@cleveland.Freenet.Edu (Seth Daniel Crosby) Newsgroups: bionet.molbio.proteins Subject: Cloning pg amouts of DNA? Message-ID: <21knpn$3tu@usenet.INS.CWRU.Edu> Date: 9 Jul 93 21:26:15 GMT Organization: Case Western Reserve University, Cleveland, Ohio (USA) Lines: 9 NNTP-Posting-Host: hela.ins.cwru.edu I have developed a technique for immunoprecipitation of chromatin using an anti-transcription factor polysera. It works well as indicated by PCR detection of a known target gene. I would like to clone other fragments in order to determine other candidate target genes. The problem is the technique yields picogram quantities of DNA. How do I clone vanishingly small amounts of chromatin!? From owner-proteins@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!darwin.sura.net!haven.umd.edu!uunet!Germany.EU.net!mcsun!news.funet.fi!news.eunet.fi!funic!convex!harper From: harper@convex.csc.FI (Rob Harper) Newsgroups: bionet.general,bionet.molbio.proteins Subject: Re: searching_PDB_files Message-ID: <1993Jul9.072216.21988@nic.funet.fi> Date: 9 Jul 93 07:22:16 GMT References: <1993Jul8.185447.9541@serval.net.wsu.edu> Sender: usenet@nic.funet.fi Organization: Finnish Academic and Research Network Project - FUNET Lines: 33 Xref: biosci bionet.general:5435 bionet.molbio.proteins:722 Nntp-Posting-Host: convex.csc.fi In <1993Jul8.185447.9541@serval.net.wsu.edu> qyi@NOSY.chem.wsu.edu (Qian Yi) writes: >I am searching for the coordinates of crystal structure of cytochrome c >peroxidase and cytochrome c complexes. If someone knows the PDB file names >for those coordinates in Protein Data Bank, or someone has those files, >would you please let me know, or send me a copy of the files if convenient. >Thanks. You can use gopher to search for coordinates I use the gopher at NIH. You will get about three pages of hits on cytochrome c peroxidase Search Protein Data Bank Headers (NIH): cytochrome c peroxidase --> 1. 1CCP YEAST CYTOCHROME |C PEROXIDASE (E.C.1.11 J.WANG,J.M.MAURO,S../ 2. 2CCP YEAST CYTOCHROME |C PEROXIDASE (E.C.1.11 J.WANG,J.M.MAURO,S../ 3. 2CYP CYTOCHROME |C PEROXIDASE (E.C.1.11.1.5) B.C.FINZEL,T.L.POU../ 4. 3CCP YEAST CYTOCHROME |C PEROXIDASE (E.C.1.11 J.WANG,J.M.MAURO,S../ 5. 4CCP YEAST CYTOCHROME |C PEROXIDASE (E.C.1.11 J.WANG,J.M.MAURO,S../ 6. 1BBH CYTOCHROME |C' Z.REN,D.E.MC*REE ../ 7. 1C2R CYTOCHROME |C=2= M.M.BENNING,G.WESE../ 8. 1C53 CYTOCHROME |C-553 A.NAKAGAWA,Y.HIGUC../ 9. 1CC5 CYTOCHROME C=5= (OXIDIZED) C.D.STOUT,D.C.CART../ 10. 1CCR CYTOCHROME |C H.OCHI,Y.HATA,N.TA../ 11. 1CP4 CYTOCHROME P450=CAM= (CAMPHOR MONOOXYGEN R.RAAG,T.L.POULOS ../ 12. 1CY3 CYTOCHROME |C=3= R.HASER,M.FREY,F.P../ 13. 1FCB FLAVOCYTOCHROME |B=2= (E.C.1.1.2.3) F.S.MATHEWS,Z.-* X.../ 14. 1GP1 GLUTATHIONE PEROXIDASE (E.C.1.11.1.9) O.EPP,R.LADENSTEIN../ 15. 1NPX NADH PEROXIDASE (E.C.1.11.1.1) NON-NATIV T.STEHLE,S.A.AHMED../ 16. 1PHA CYTOCHROME P450CAM FROM PSEUDOMONAS PUTI T.L. 27-JUL-92/ 17. 1PHB CYTOCHROME P450CAM FROM PSEUDOMONAS PUTI T.L. 27-JUL-92/ 18. 1PHC CYTOCHROME P450CAM FROM PSEUDOMONAS PUTI T.L. 27-JUL-92/ I suggest you fire up gopher and go get the coordinates you want RGDS -=ROB=- -- Rob Harper E-mail: harper@convex.csc.fi Center for Scientific Computing Molbio/software: harper@nic.funet.fi Tietotie 6, P.O. Box 405 Telephone: +358 0 457 2076 SF-02101 Espoo Finland Fax: +358 0 457 2302 From owner-proteins@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!ux1.cso.uiuc.edu!sdd.hp.com!decwrl!pa.dec.com!hydrox.enet.dec.com!mek From: mek@hydrox.enet.dec.com (Mark Klamerus) Newsgroups: bionet.molbio.proteins Subject: Request for Info on Force Field assisted Particle Recognition Message-ID: <9307091747.AA28395@enet-gw.pa.dec.com> Date: 9 Jul 93 17:47:35 GMT Lines: 33 X-Received: by usenet.pa.dec.com; id AA26845; Fri, 9 Jul 93 10:47:36 -0700 X-Received: by enet-gw.pa.dec.com; id AA28395; Fri, 9 Jul 93 10:47:35 -0700 X-Received: from hydrox.enet; by decwrl.enet; Fri, 9 Jul 93 10:47:35 PDT X-To: bionet.molbio.proteins.usenet X-Apparently-To: bionet.molbio.proteins.usenet Hi, I'm currently in the graduate biocomputing program at Wayne State Univ in Detroit. I'm particuarly focusing in on the computational aspects of proteins (and associated molecules like enzymes, RNA, etc.). I was looking to do my paper/thesis on the information processing aspects of pattern/particle recognition of molecules (real or otherwise) assisted by force fields (the way protein recognize each other and form mosaics). Can anyone point to any works done in this area or provide any suggestions/recommendations. In particular, I've read many articles on Brownian Dynamics, but interested to pointers to articles on molecular liquids, force fields, diffusion, etc. which relate to the above area. I'm not especially interested in the thermodynamics/statistical side of things. At least, not too much on the statistical side. I'm especially interested in abstracting the concepts/theories away from the physical side of things (for now), but will take anything in this area I can get. I'm also open for any opinions on whether this seems to be worthy of study, any direction to focus this research, discouragement (if appropriate), and info on whether this has been done already. thanks very much, Mark Klamerus mek@hydrox.det.dec.com ------- End of Forwarded Message From owner-proteins@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!utcsri!utnut!torn!nott!nrcnet0!biologym54.lan.nrc.ca!campbell From: campbell@biologym54.lan.nrc.ca (Robert L. Campbell) Newsgroups: bionet.general,bionet.molbio.proteins Subject: coordinates for CCP+ cyto C (was Re: searching_PDB_files) Message-ID: Date: 9 Jul 93 17:35:32 GMT References: <1993Jul8.185447.9541@serval.net.wsu.edu> Sender: root@nrcnet0.nrc.ca (Operator) Organization: National Research Council of Canada Lines: 20 Xref: biosci bionet.general:5441 bionet.molbio.proteins:723 Nntp-Posting-Host: 132.246.164.51 In article <1993Jul8.185447.9541@serval.net.wsu.edu> qyi@NOSY.chem.wsu.edu (Qian Yi) writes: >From: qyi@NOSY.chem.wsu.edu (Qian Yi) >Subject: searching_PDB_files >Date: Thu, 8 Jul 93 18:54:47 GMT >I am searching for the coordinates of crystal structure of cytochrome c >peroxidase and cytochrome c complexes. If someone knows the PDB file names >for those coordinates in Protein Data Bank, or someone has those files, >would you please let me know, or send me a copy of the files if convenient. There are structures of complexes between yeast cytochrome C peroxidase and two different cytochrome C's. One structure is a complex with horse heart cytochrome C (code: 1PCB) and the other is a complex with yeast iso-1-cytochrome C (code: 1PCC). Both structures are present in the listing of prerelease coordinates, but the coordinates are not yet available on the Brookhaven computer. Robert Campbell Institute for Biological Sciences campbell@biologym54.lan.nrc.ca National Research Council Canada From owner-proteins@net.bio.net Thu Jul 08 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uknet!doc.ic.ac.uk!agate!spool.mu.edu!olivea!news.bu.edu!pfoster From: pfoster@bu.edu (Patricia Foster) Newsgroups: bionet.molbio.proteins Subject: His-tag Fusions Message-ID: <21l0sp$mbk@news.bu.edu> Date: 10 Jul 93 00:01:29 GMT Organization: Boston University Lines: 25 NNTP-Posting-Host: acs.bu.edu X-Newsreader: TIN [version 1.2 PL0] Hi Netters A number of people have posted about contaminating bands with GSH fusion proteins. I have a contamination band with a his-tag fusion using pET22b from Novagen and purifying on a Ni column. I called them about it, but they said no one else has reported it and it must have something to do with my protein. The band is about 45kD, so is not dnaK. However, I happened to notice in a Novagen advertisment for the pET fusions that *they* show a clear band that looks about 45kK in their example gel! Anyone else have it? Any ideas on how to get rid of it? pat -- Patricia L. Foster Boston University School of Medicine Boston, MA USA pfoster@bu.edu -- Patricia L. Foster Boston University School of Medicine Boston, MA USA pfoster@bu.edu From owner-proteins@net.bio.net Sat Jul 10 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!ux1.cso.uiuc.edu!sdd.hp.com!col.hp.com!csn!news.den.mmc.com!iplmail!markb From: markb@iplmail.orl.mmc.com (Mark Bower) Newsgroups: bionet.molbio.proteins Subject: Re: Request for Info on Force Field assisted Particle Recognition Message-ID: <1993Jul11.150503.8820@iplmail.orl.mmc.com> Date: 11 Jul 93 15:05:03 GMT References: <9307091747.AA28395@enet-gw.pa.dec.com> Sender: markb@iplmail (Mark Bower) Organization: Martin Marietta Lines: 16 In article <9307091747.AA28395@enet-gw.pa.dec.com> Mark Klamerus writes: >I was looking to do my paper/thesis >on the information processing aspects of pattern/particle >recognition of molecules (real or otherwise) assisted by force >fields (the way protein recognize each other and form mosaics). Tom Schneider from NIH is working on the information content required for protein binding/recognition. You might want to check out the bionet.info- theory FAQ at the anonymous ftp archive ncifcrf.gov in pub/delila. They have an extensive bibliography which will surely contain something of interest. This work is not explicity force-field related, but the problem is the same. You might want to subscribe to bionet.info-theory as well. Regards, Mark. From owner-proteins@net.bio.net Sun Jul 11 23:00:00 1993 Path: biosci!SNYSYRV1.bitnet!TAFFETS From: TAFFETS@SNYSYRV1.bitnet Newsgroups: bionet.molbio.proteins Subject: Charge of Tyrosine in a Protein Message-ID: <9307122014.AA14130@net.bio.net> Date: 12 Jul 93 20:09:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 22 We have recently been analyzing some results with site-directed mutations which can be most easily explained if a tyrosine in a protein we have been analyzing was negatively charged while the cells were at pH 7.0. Is this possible (other than if the tyrosine was phosphorylated) and if it is possible can anyone suggest a reference on this? Thanks Steve ******************************************************************************* Steven Taffet, Ph.D. Associate Professor Department of Microbiology and Immunology S.U.N.Y. Health Science Center 750 E. Adams Avenue Syracuse, New York 13210 Phone (315) 464-5419 FAX (315) 464-4417 Bitnet TAFFETS@snysyrv1 Internet TAFFETS@vax.cs.hscsyr.edu ******************************************************************************* From owner-proteins@net.bio.net Sun Jul 11 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!sdd.hp.com!news.cs.indiana.edu!nstn.ns.ca!ac.dal.ca!jopa From: jopa@ac.dal.ca Newsgroups: bionet.general,bionet.molbio.proteins Subject: Re: coordinates for CCP+ cyto C (was Re: searching_PDB_files) Message-ID: <1993Jul12.164708.14933@ac.dal.ca> Date: 12 Jul 93 19:47:08 GMT References: <1993Jul8.185447.9541@serval.net.wsu.edu> Organization: Dalhousie University, Halifax, Nova Scotia, Canada Lines: 27 Xref: biosci bionet.general:5466 bionet.molbio.proteins:729 In article , campbell@biologym54.lan.nrc.ca (Robert L. Campbell) writes: > In article <1993Jul8.185447.9541@serval.net.wsu.edu> qyi@NOSY.chem.wsu.edu (Qian Yi) writes: > >>I am searching for the coordinates of crystal structure of cytochrome c >>peroxidase and cytochrome c complexes. If someone knows the PDB file names >>for those coordinates in Protein Data Bank, or someone has those files, >>would you please let me know, or send me a copy of the files if convenient. > > There are structures of complexes between yeast cytochrome C peroxidase > and two different cytochrome C's. One structure is a complex with horse > heart cytochrome C (code: 1PCB) and the other is a complex with yeast > iso-1-cytochrome C (code: 1PCC). Both structures are present in the listing > of prerelease coordinates, but the coordinates are not yet available on the > Brookhaven computer. The actual identities for these structures are 2pcb,2pcc and they can be obtained by ftp from the brookhaven bank (pdb.pdb.bnl.gov) and they can be found in fullrelease/uncompressed_files/tape3 with the names pdb2pcc.ent and pdb2pcb.ent Hope this helps! Jonathan Parrish Department of Biochemistry Dalhousie University Halifax, N.S. From owner-proteins@net.bio.net Mon Jul 12 23:00:00 1993 Path: biosci!agate!darkstar.UCSC.EDU!orchid.UCSC.EDU!quinones From: quinones@biology.ucsc.edu (Cathy Quinones) Newsgroups: bionet.molbio.proteins Subject: those pesky glycoprotein stains... Message-ID: <21vf4tINNpmm@darkstar.UCSC.EDU> Date: 13 Jul 93 23:06:05 GMT Distribution: usa Organization: Santa Cruz Lines: 20 NNTP-Posting-Host: orchid.ucsc.edu Originator: quinones@orchid.UCSC.EDU Here's another question regarding this thymol-sulfuric acid protocol I am bent on using. The following is a direct quote from the source of the said protocol (Methods in Enzymology. 1990. vol. 182, page 537): 3. Immerse the gel in the above solution containing 0.2% (v/v) thymol (Sigma) for 90 minutes with gentle rocking...... By the way, the "above solution" is a 2-propanol/acetic acid fix. I dutifully placed my order with Sigma, and what I got (all they sell) is thymol in crystal form. My question is: is the "v/v" a typo? In any case, could anybody out there tell me how to make it through step 3 ???! Maybe, someday, I will actually dare to run these gels.... [and, in case the machine does its usual trick, my address is quinones@biology.ucsc.edu ] Thanks! From owner-proteins@net.bio.net Tue Jul 13 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!sun4nl!star.cs.vu.nl!balaena!mac137.bio.vu.nl!user From: vdwal@bio.vu.nl (FJ van der Wal) Newsgroups: bionet.molbio.proteins Subject: in vivo cross-linking Message-ID: Date: 14 Jul 93 11:32:44 GMT Sender: news@bio.vu.nl Followup-To: bionet.molbio.proteins Organization: Vrije Uni., Mol.Micro., Amsterdam, NL Lines: 10 I'm posting this for a frien who is asking: " Has anyone heard about in vivo cross-linking experiments on bacterial membrane proteins using something else than formaldehyde.? I'm looking for references. My e-mail address is: jmghigo@pasteur.fr " If you're able to help us out we would be very grateful to you.Thanks in advance. FJ From owner-proteins@net.bio.net Wed Jul 14 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!swrinde!elroy.jpl.nasa.gov!usc!howland.reston.ans.net!noc.near.net!uunet!utcsri!utnut!wave.scar!90taobri From: 90taobri@wave.scar.utoronto.ca (TAO BRIAN T) Newsgroups: bionet.molbio.proteins Subject: Re: Charge of Tyrosine in a Protein (bounced) Message-ID: Date: 15 Jul 93 06:16:12 GMT Reply-To: 90taobri@wave.scar.utoronto.ca (Brian Tao) Organization: MuGS Research and Development Facility Lines: 35 X-Newsreader: MuGS 3.0d28 [Jul 8 93] My e-mail reply bounced, so I'm reposting it here... ----- Transcript of session follows ----- 550 ... Host unknown ----- Unsent message follows ----- From: 90taobri@wave.scar.utoronto.ca (TAO BRIAN T) Message-Id: <9307132126.AA27139@wave.scar.utoronto.ca.wave.scar.utoronto.ca> To: TAFFETS@SNYSYRV1.bitnet Subject: Re: Charge of Tyrosine in a Protein Date: Tue Jul 13 17:08:19 1993 EST Organization: MuGS Research and Development Facility X-Mailer: MuGS 3.0d28 [Jul 8 93] You previously wrote... > > We have recently been analyzing some results with site-directed > mutations which can be most easily explained if a tyrosine in a protein > we have been analyzing was negatively charged while the cells were at pH > 7.0. Is this possible (other than if the tyrosine was phosphorylated) > and if it is possible can anyone suggest a reference on this? I'm at home right now, so I don't have any references handy, but I don't see why tyrosine can't be deprotonated at pH 7. Its standard pKa is around 10, but check for a strong acceptor in the region of the OH group which could pull off a proton. For example, the chymotrypsin protease mechanism involves a serine protonating an adjacent histidine at physiological pH. The negative serine is then stabilized by the terminal carboxyl group of the substrate. If it can happen to serine (normal pKa of around 14), it's conceivable that the pKa of tyrosine can be lowered below 7. -- Brian Tao:: taob@io.org (Internex Online, 416-363-3783, 10 lines, v.32bis) ::::::::::: *** Note that my address has changed *** From owner-proteins@net.bio.net Wed Jul 14 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!olivea!charnel!rat!decwrl!tribune.usask.ca!kakwa.ucs.ualberta.ca!ee.ualberta.ca!khan From: khan@ee.ualberta.ca (Waleed Khan) Newsgroups: bionet.molbio.proteins Subject: Request info. on Gel Bandshift (Retardation ) Assay Message-ID: Date: 15 Jul 93 05:22:18 GMT Sender: news@kakwa.ucs.ualberta.ca Organization: University Of Alberta, Edmonton Canada Lines: 21 Nntp-Posting-Host: eigen.ee.ualberta.ca I am borrowing this person's ID to post my problem. I am a summer student doing research in the department of nephrology/ immunology. I am currently having difficulties running a bandshift assay. Instead of seeing sharp and distinct bands of protein and DNA complex, I am getting a smear. We are running an 80:1 acrylamide to bisacrylamide, 5% gel. The protein we are using is from a nuclear extraction of Jurkat and peripheral blood lymphocytes. The method of nuclear extraction is followed according to Dignam's protocol. Our probe was originally synthesized on a DNA synthesis machine and purified via a trityl column. We are attempting to purify our probe via cloning and/or an agarose gel. I would like suggestions on improving this experiemental method. If anyone can help me (or direct me to a more appropriate user group), please post a follow up article or email me directly via this ID. Sophia khan@eigen.ee.ualberta.ca U.Alberta, Edmonton From owner-proteins@net.bio.net Wed Jul 14 23:00:00 1993 Path: biosci!BIOBASE.AAU.DK!emrasmus From: emrasmus@BIOBASE.AAU.DK (Erik Michael Rasmussen) Newsgroups: bionet.molbio.proteins Subject: Help_protein Message-ID: <9307150852.AA25272@biobase.aau.dk> Date: 15 Jul 93 08:52:29 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 1 help From owner-proteins@net.bio.net Wed Jul 14 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!math.ohio-state.edu!cs.utexas.edu!uunet!pipex!uknet!mcsun!news.funet.fi!ousrvr.oulu.fi!phoenix.oulu.fi!rehn From: rehn@phoenix.oulu.fi (Marko Rehn) Newsgroups: bionet.molbio.proteins Subject: Re:Help Message-ID: <1993Jul15.112719.28096@ousrvr.oulu.fi> Date: 15 Jul 93 11:27:19 GMT Sender: news@ousrvr.oulu.fi Organization: University of Oulu, Finland Lines: 5 X-Newsreader: TIN [version 1.2 PL0] Do not panic ! Help has been sent to you. rehn@phoenix.oulu.fi From owner-proteins@net.bio.net Thu Jul 15 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!wupost!spool.mu.edu!torn!nott!emr1!weathere From: weathere@emr1.emr.ca (Carl Weatherell) Newsgroups: bionet.molbio.proteins Subject: Effect of Methanol on Stokes Radii Message-ID: <1993Jul16.143640.24418@emr1.emr.ca> Date: 16 Jul 93 14:36:40 GMT Organization: Dept. of Energy, Mines, and Resources, Ottawa Lines: 9 X-Newsreader: TIN [version 1.1 PL8] I am currently examining secondary retention effects on SEC stationary phases under denaturing conditions (3.5mM SDS, variable I and variable [CH3OH], pH=4-7). I understand that the Stokes radius of the SDS-protein complex will increase in the presence of CH3OH. Can anyone suggest why or point me to a general reference so I can determine why. If this question sounds a little silly, it may be because I am an inorganic chemist by trade! Thanks in advance. Carl Weatherell EMAIL weathere@emr1.emr.ca From owner-proteins@net.bio.net Fri Jul 16 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!math.ohio-state.edu!uwm.edu!rutgers!andromeda.rutgers.edu!hu From: hu@andromeda.rutgers.edu (Zhixiang Hu) Newsgroups: bionet.molbio.proteins Subject: Need Bacilus Subtilis expression vectors Keywords: Plasmid, expression, Bacilus subtilis, promoter Message-ID: Date: 17 Jul 93 14:45:45 GMT Organization: Rutgers Univ., New Brunswick, N.J. Lines: 16 Hi! Does anybody know where I can get expression vectors to be used in Bacilus subtilis? I checked ATCC catalog. There are several subtilis expression vectors available, but without any information. They were marked as patented with no patent number. Even ATCC itself has no idea. The other popularly used subtilis plasmids like pUB110, pBS42, are all cloning vectors, i.e. there is no promoter on plasmid could be used. If you happen to know a commercial source or a research group could provide such plasmid, please let me know. My e-mail addr. is hu@andromeda.rutgers.edu Thanks in advance! Have a nice weekend From owner-proteins@net.bio.net Sat Jul 17 23:00:00 1993 Path: biosci!parc!decwrl!ames!agate!howland.reston.ans.net!darwin.sura.net!sgiblab!adagio.panasonic.com!nntp-server.caltech.edu!robin From: robin@cco.caltech.edu (Robert C. Colgrove) Newsgroups: bionet.general,bionet.molbio.proteins Subject: question on optimizing baculovirus expression Summary: Any data on best signals and aug's? Keywords: baculovirus, expression Message-ID: <22d3t2INN7c2@gap.caltech.edu> Date: 19 Jul 93 03:20:02 GMT Organization: California Institute of Technology, Pasadena Lines: 8 Xref: biosci bionet.general:5528 bionet.molbio.proteins:739 NNTP-Posting-Host: alumni.caltech.edu Hi. Sorry if this is a repeat. My first attempt has not even made it to my site in three days so I am reposting. Anyway, I'm gearing up for a run at baculovirus expression of some viral envelope proteins. Any data/opinions on the minimum necessary signal sequence and best "kozak" consensus (I'm using the Invitrogen BluBacIII construct which contains the polyhedrin leader, a mutated AUG and a poly cloning site). thanks robin From owner-proteins@net.bio.net Sat Jul 17 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!wupost!uunet!psinntp!barilvm!vms.huji.ac.il!ramon.bgu.ac.il!viener From: viener@bgumail.bgu.ac.il (dov wiener) Newsgroups: bionet.molbio.proteins Subject: Biosensor projects referees needed - Call for Proposals Message-ID: <1993Jul18.081607.16780@ramon.bgu.ac.il> Date: 18 Jul 93 08:16:07 GMT Sender: usenet@ramon.bgu.ac.il (The Ever-So-Great Usenet) Organization: Ben Gurion University, Beer Sheva, Israel Lines: 89 X-Newsreader: TIN [version 1.2 PL0] CALL FOR PROPOSALS ==================== A group of Israeli companies are in a process of assessing potential generic technologies in the field of BIOSENSORS to be used in the future in different commercial applications. MATIMOP (the Israeli Industry Center for Research & Development), as a public non profit organization acts on behalf of the above mentioned group as a main contractor, to acomplish this study. MATIMOP's speciallization is in providing industry with feasibility studies covering scientific and technical information as well as commercial and marketing analysis. We in MATIMOP are looking for experts in the field of BIOSENSOR technologies with a wide overview and experience who are able to act as our consultants and reviewers on this issue. Most of the work should take place outside Israel, including some interviews with leading research teams active in the BIOSENSORS field. Candidates should be able to examine and assess both: raw data provided by us (mostly via the INTERNET network), as well as results and achievments of researchers to be reviewed. OUTLINE FOR A SURVEY ON BIOSENSORS ================================== PART A: Technology Survey 1. State of the art in biosensor technology, including (but not limited to) biocatalytic (e.g. enzyme electrodes) and bio-affinity (e.g. antibody based) sensors. Survey will discuss the biological, transducer and interface elements of biosensors, for both in vivo and ex vivo applications. All possible application should be included with special stress on infectious diseases, tissue and cell typing, environment. Research should include both published and unpublished data and should expand on "Sensor Technology Sourcebook" and "Advances in Environmental Sensors and Monitoring" published by Technical Insights, Inc. (1992) and "Clinica's Biosensor Report" published by PJB Publications Ltd (1992). Part of the survey will list all companies, research groups and individuals active in the field. 2. State of the art in biosensor and biosensor related worldwide patents. Identification of technological trends, blocking patents and licensing opportunities. 3. Developmental status of the items listed in Part 1 and 2 above, i.e. estimation of time to prototype, time to market, potential for success. 4. Hybrid manufacturing technology in biosensor development and commercialization, including: a. Thin film deposition techniques b. Ceramic materials c. Silk screen printing d. FETs The final feasibilty study should be acomplished by us not later than the end of November 1993. We will appreciate getting your proposal within next week including: 1. Resume 2. List of publications 3. Former experience with industry 4. Estimated time and cost for the assessment of an avarage scientific project: 4.1. when information is provided by us for your assessment only 4.2. when information is to be reached by interviewing a reaeach team. Jacob Bar Manager Data Gathering & Analysis Dep. MATIMOP - Israeli Industry Center for Research & Development Internet: jbari@ccsg.tau.ac.il MCI: 427-1547 From owner-proteins@net.bio.net Sun Jul 18 23:00:00 1993 Path: biosci!vigyan.ernet.in!mbu!mohan From: mbu!mohan@vigyan.ernet.in Newsgroups: bionet.molbio.proteins Subject: (none) Message-ID: <9307200027.AA03061@iisc.ernet.in> Date: 20 Jul 93 00:27:35 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 22 Dear Bio-netters, Does anybody have the program for generation of contact map (phi/psi map) ? In principle the dipepdide can be defined using phi and psi as phi = C'-N-CA-C and psi = N-CA-C'-N our interest is to obtain the map for the ester linked peptide unit, in which phi/psi definition will be phi = C'-N-CA-C and psi = N-CA-C'-O Kindly mail the suggestions, comments or program. Thank you !! e-mail : shobana@mbu.iisc.ernet.in From owner-proteins@net.bio.net Sun Jul 18 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!sdd.hp.com!math.ohio-state.edu!darwin.sura.net!news-feed-2.peachnet.edu!umn.edu!molbio.cbs.umn.edu!paul-b From: paul-b@molbio.cbs.umn.edu (Paul Bucciaglia) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Pre-stained protein markers Message-ID: Date: 19 Jul 93 21:08:59 GMT Sender: news@news2.cis.umn.edu (Usenet News Administration) Organization: College of Biological Sciences, U of MN Lines: 15 Xref: biosci bionet.molbio.proteins:741 bionet.molbio.methds-reagnts:6533 Nntp-Posting-Host: molbio.cbs.umn.edu i Hi We need a procedure for "pre-staining" proteins to run on SDS-PAGE so that the markers are visible on the gel while its running. BioRad sells such markers but they're very pricy. Thanks in advance! Paul bucciaglia U of MN Hort Dept. From owner-proteins@net.bio.net Mon Jul 19 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc8.harvard.edu!gisselbr From: gisselbr@husc8.harvard.edu (Stephen Gisselbrecht) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: Pre-stained protein markers Message-ID: <1993Jul20.114344.26081@husc14.harvard.edu> Date: 20 Jul 93 15:43:44 GMT References: Organization: Harvard University Science Center Lines: 18 Xref: biosci bionet.molbio.proteins:743 bionet.molbio.methds-reagnts:6553 Nntp-Posting-Host: husc8.harvard.edu In article paul-b@molbio.cbs.umn.edu (Paul Bucciaglia) writes: >We need a procedure for "pre-staining" proteins to run on SDS-PAGE so that the markers are visible on the gel while its running. BioRad sells such markers >but they're very pricy. > >Paul bucciaglia >U of MN Hort Dept. Uh, Coomassie Blue will stay on proteins through electrophoresis. (I was going to say that it stains irreversibly, but it's pointed out to me that hot acetic acid will take it off. So if you do your electrophoresis in hot acetic acid, ignore this.) Just add some to whatever markers you normally use and, voila, you have pre-stains. Like all pre-stained markers, though, these will have a different molecular weight than the unstained proteins. steve gisselbrecht cell & dev. bio. harvard medical school From owner-proteins@net.bio.net Mon Jul 19 23:00:00 1993 Path: biosci!UVMVAX.UVM.EDU!W_SHAO From: W_SHAO@UVMVAX.UVM.EDU ("Wei Shao", ADDRESS: IN%"w_shao@uvmvax.uvm.edu") Newsgroups: bionet.molbio.proteins Subject: references about gelshift Message-ID: <01H0S2RJDISW001SHR@uvmvax.uvm.edu> Date: 21 Jul 93 02:12:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 6 Hi, Sophia: I am sorry to forward the information that you are interested. I lost your e-mail address. 1) Berger, S.l. & Kimmel, A. R. (ed). 1987. Guide to Molecular Cloning Techni- ques. Academic Press, Inc., San Diego. Chapter 73. 2) Ausubel, F. M. et al (ed). 1987. Current Protocols in Molecular Biology. John Wiley & Sons. New York. Chapter 12. Hope tey ar From owner-proteins@net.bio.net Mon Jul 19 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!darwin.sura.net!haven.umd.edu!uunet!pipex!uknet!comlab.ox.ac.uk!oxuniv!oxpath!rpgrant From: rpgrant@molbiol.ox.ac.uk Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: Pre-stained protein markers Message-ID: <1993Jul20.095018.1@molbiol.ox.ac.uk> Date: 20 Jul 93 08:50:18 GMT References: Organization: Oxford University Molecular Biology Data Centre Lines: 19 Xref: biosci bionet.molbio.proteins:742 bionet.molbio.methds-reagnts:6544 Nntp-Posting-Host: kasia Nntp-Posting-User: rpgrant In article , Paul Bucciaglia writes: > > Hi > > We need a procedure for "pre-staining" proteins to run on SDS-PAGE so that > the markers are visible on the gel while its running. BioRad sells such markers > but they're very pricy. BRL also sell them - I don't know about the BioRad ones but I dilute the BRL set 1 in 10 (in loading dyes) and they are still visible!! That brings the price down quite nicely ;) -- Richard P. Grant <>< rpgrant@molbiol.ox.ac.uk Sir William Dunn School of Pathology Fax. +44 865 275556 University of Oxford, UK. Tel. +44 865 275565 "It's easy when you know how" From owner-proteins@net.bio.net Mon Jul 19 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!math.ohio-state.edu!howland.reston.ans.net!agate!dog.ee.lbl.gov!network.ucsd.edu!clinical-mac-88.ucsd.edu!user From: UCSD (Dan Kolk) Newsgroups: bionet.molbio.proteins Subject: information on bandshifts Message-ID: Date: 20 Jul 93 19:15:09 GMT Followup-To: bionet.molbio.proteins Organization: UCSD SOM Lines: 8 NNTP-Posting-Host: clinical-mac-88.ucsd.edu Many things can cause smearing in band shifts. I suggest; 1) going with 29:1 acrylamide:bis, there really is no reason to go with 80:1. 2) Try as simple a reaction buffer as possible i.e. 25mM Hepes pH 7.9, 100mM KCl, 5 mM MgCl, 12% glycerol, 1mM EDTA, 1mM DTT. 3) Dialysing your nuclear extracts and adding protease inhibitors. 4) Run your labelled probe on a sequencing gel to make sure it is not degraded. 5) Make up new running buffer and filter it. From owner-proteins@net.bio.net Tue Jul 20 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: pmr1716@ggr.co.uk ("Peter Murray-Rust") Newsgroups: bionet.molbio.proteins Subject: Effect of pressure on enzyme reactions Message-ID: <1993Jul21.164626.20273@gserv1.dl.ac.uk> Date: 21 Jul 93 17:46:30 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 17 Original-To: proteins@uk.ac.daresbury I'd be grateful for any information about whether high-pressure can affect (a) the speed and/or (b) the equilibrium of an enzyme-catalysed reaction, and if so, what pressures are required in practice to make a useful contribution. If this is a well-researched field, I'd be very grateful for pointers to reviews. Thanks, Peter ------------------------------------------------------------------------------ Peter Murray-Rust | "Nothing exists except atoms and empty pmr1716@ggr.co.uk | space; all else is opinion" (Democritos). Protein Structure Group, Glaxo Group Research, Greenford, MIDDX, UB6 0HE, UK ------------------------------------------------------------------------------ From owner-proteins@net.bio.net Wed Jul 21 23:00:00 1993 Path: biosci!daresbury!mrccrc!news.dcs.warwick.ac.uk!warwick!uknet!bnr.co.uk!demon!genesys.demon.co.uk!Duncan From: Duncan@genesys.demon.co.uk ("Dr. Duncan Clark") Newsgroups: bionet.molbio.proteins Subject: Re: Pre-stained protein markers Message-ID: <743196965snz@genesys.demon.co.uk> Date: 20 Jul 93 19:36:05 GMT References: Sender: usenet@demon.co.uk Reply-To: Duncan@genesys.demon.co.uk Organization: GeneSys Ltd. Lines: 31 X-Newsreader: Simple NEWS 1.90 (ka9q DIS 1.21) In article paul-b@molbio.cbs.umn.edu writes: >> >We need a procedure for "pre-staining" proteins to run on SDS-PAGE so that the > markers are visible on the gel while its running. BioRad sells such markers >but they're very pricy. > >Thanks in advance! > >Paul bucciaglia >U of MN Hort Dept. > > I too have been wanting to make my own pre-stained markers. I saw that Stratagene use Uni-Blue A (Sigma and relatively cheap). I also just saw a protocol in June Biotechniques pp 925-930 for blotting stained proteins to transparencies. The authors pre-stained proteins with various dyes (including UniBlue) by conjugating BSA, 100mg, in 0.1M sodium borate buffer 9ml, pH9.0, stirring at room temp. for 2 hours. Dialyse the conjugate against water 2 x 4 litres fro 48 hours. This should work for any protein, however one must calibrate against known standards. Good luck. Duncan -- ----------------------------------------------------------------------------- Duncan Clark | Internet: duncan@genesys@demon.co.uk GeneSys Ltd. | Compuserve: 100015.1406@compuserve.com ----------------------------------------------------------------------------- From owner-proteins@net.bio.net Wed Jul 21 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!noc.near.net!howland.reston.ans.net!ux1.cso.uiuc.edu!vixen.cso.uiuc.edu!newsrelay.iastate.edu!iscsvax.uni.edu!wiens From: wiens@iscsvax.uni.edu Newsgroups: bionet.molbio.proteins Subject: how do we access protein database? Message-ID: <1993Jul22.085449.15024@iscsvax.uni.edu> Date: 22 Jul 93 14:54:49 GMT Organization: University of Northern Iowa Lines: 9 Anyone please, We would like to compare 6 decapeptide sequences to which we have antibodies, to known protein amino acid sequences from a data base, but we haven't done it before and don't know how to access a database such as Protein Data Base or Gopher. Could someone help? We are on a pc hooked up to a university VAX and are used to using internet. Thanks, Darrell and Jacqui From owner-proteins@net.bio.net Wed Jul 21 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!pipex!sunic!corax.udac.uu.se!buzz.bmc.uu.se!daresbury!daresbury!news From: emrasmus@biobase.aau.dk (Erik Michael Rasmussen) Newsgroups: bionet.molbio.proteins Subject: protein_protein_interaction? Message-ID: <1993Jul22.133231.19549@gserv1.dl.ac.uk> Date: 22 Jul 93 14:34:09 GMT Sender: emrasmus@dk.aau.biobase Distribution: bionet Lines: 10 Original-To: proteins@uk.ac.daresbury X-Mailer: ELM [version 2.3 PL11] I would like to examine a protein-protein interaction by PAGE. I believe I can't use SDS. Since I'm not familiar with this I need some advice. Therefore a reference or a protokol to start with would be nice. The two proteins I have are 167 kD and 50 kD. Erik Michael Rasmussen phone (+45) 35322100 Department of Genetics E-mail emrasmus@biobase.aau.dk Institute of Molecular Biology University of Copenhagen From owner-proteins@net.bio.net Wed Jul 21 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!pipex!sunic!corax.udac.uu.se!buzz.bmc.uu.se!daresbury!daresbury!news From: WALLACE@IRBM.IT (Andrew, Tel. +39-6-91093434) Newsgroups: bionet.molbio.proteins Subject: RE: Effect of pressure on enzyme reactions Message-ID: <1993Jul22.122622.16709@gserv1.dl.ac.uk> Date: 22 Jul 93 12:29:36 GMT Sender: WALLACE@IT.IRBM Distribution: bionet Lines: 32 X-Vmsmail-To: SMTP%"pmr1716@ggr.co.uk" Original-To: pmr1716@uk.co.ggr, proteins@uk.ac.daresbury Dear Peter, You write: >I'd be grateful for any information about whether high-pressure can affect (a) >the speed and/or (b) the equilibrium of an enzyme-catalysed reaction, and if I don't know if pressure can affect the speed of an enzyme-catalysed reaction but it should alter the equilibrium position since the enthalpy change involved in the reaction depends on pressure delta H = delta E + P deltaV where H is the enthalpy, E is the energy of the system, P is the pressure and V is the volume of a system (not considering changes in the surroundings). >so, what pressures are required in practice to make a useful contribution. If >this is a well-researched field, I'd be very grateful for pointers to reviews. This (is/used to be) a fairly well-researched field in the context of fast reaction kinetics. Sudden, large pressure changes were used to perturb a system at equilibrium and fast reaction monitoring took place while the system adjusted to the new equilibrium position. Nowadays this kind of thing is more usually done by temperature-jump methods as far as I know. You might try looking in some of the enzyme kinetics books/articles by Alan Fersht for pointers to suitable literature, since I can't recall anything offhand that would be relevant to your particular question. Andrew Wallace Department of Biochemistry IRBM, Pomezia, Italy From owner-proteins@net.bio.net Wed Jul 21 23:00:00 1993 Path: biosci!parc!decwrl!decwrl!elroy.jpl.nasa.gov!usc!sol.ctr.columbia.edu!caen!usenet.cis.ufl.edu!usenet.ufl.edu!darwin.sura.net!newt.welch.jhu.edu!welchdev.welch.jhu.edu!danj From: danj@welchdev.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.proteins Subject: Re: how do we access protein database? Message-ID: <1993Jul22.152547.18139@newt.welch.jhu.edu> Date: 22 Jul 93 15:25:47 GMT References: <1993Jul22.085449.15024@iscsvax.uni.edu> Sender: news@newt.welch.jhu.edu Organization: Johns Hopkins University Genome Data Base (GDB) Lines: 462 Nntp-Posting-Host: welchdev.welch.jhu.edu In article <1993Jul22.085449.15024@iscsvax.uni.edu> wiens@iscsvax.uni.edu writes: >Anyone please, > >We would like to compare 6 decapeptide sequences to which we have antibodies, >to known protein amino acid sequences from a data base, but we haven't done it >before and don't know how to access a database such as Protein Data Base or >Gopher. Could someone help? We are on a pc hooked up to a university VAX and >are used to using internet. > >Thanks, Darrell and Jacqui For a similarity search of your decapeptides against the databases you'll want to use one of the mail servers. The instructions for these servers are a bit long so I'll e-mail them to you seperately from this post. Gopher is also a must for biology now - I'll include some information below to help get you started. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu ------------------------------------------------------------------------ Gopher Info This is a heavily edited version of the Gopher FAQ intended to give people just starting with gopher enough information to get a client and jump into Gopher-space - a complete version can be obtained as described below. Once you have a gopher client point it at merlot.welch.jhu.edu and welcome to gopher-space! Dan Jacobson danj@welchgate.welch.jhu.edu ----- Common Questions and Answers about the Internet Gopher, a client/server protocol for making a world wide information service, with many implementations. Posted to comp.infosystems.gopher, comp.answers, and news.answers every two weeks. The most recent version of this FAQ can be gotten through gopher, or via anonymous ftp: rtfm.mit.edu:/pub/usenet/news.answers/gopher-faq Those without FTP access should send e-mail to mail-server@rtfm.mit.edu with "send usenet/news.answers/finding-sources" in the body to find out how to do FTP by e-mail. ------------------------------------------------------------------- List of questions in the Gopher FAQ: Q0: What is Gopher? Q1: Where can I get Gopher software? Q2: What do I need to access Gopher? Q3: Where are there publicly available logins for Gopher? Q4: Who Develops Gopher Software? Q5: What is the relationship between Gopher and (WAIS, WWW, ftp)? Q6: Are papers or articles describing Gopher available? Q7: What is veronica? Q8: How do I connect to a specific gopher server? Q9: What is Available for Biology? ------------------------------------------------------------------- Q0: What is Gopher? A0: The Internet Gopher client/server provides a distributed information delivery system around which a world/campus-wide information system (CWIS) can readily be constructed. While providing a delivery vehicle for local information, Gopher facilitates access to other Gopher and information servers throughout the world. ------------------------------------------------------------------- Q1: Where can I get Gopher software? A1: via anonymous ftp to boombox.micro.umn.edu. Look in the directory /pub/gopher -------------------------------------------------------------------- Q2: What do I need to access Gopher? A2: You will need a gopher "client" program that runs on your local PC or workstation There are clients for the following systems. The directory following the name is the location of the client on the anonymous ftp site boombox.micro.umn.edu (134.84.132.2) in the directory /pub/gopher. Unix Curses & Emacs : /pub/gopher/Unix/gopher1.12.tar.Z Xwindows (athena) : /pub/gopher/Unix/xgopher1.2.tar.Z Xwindows (Motif) : /pub/gopher/Unix/moog Xwindows (Xview) : /pub/gopher/Unix/xvgopher Macintosh Hypercard : /pub/gopher/Macintosh-TurboGopher/old-versions * Macintosh Application : /pub/gopher/Macintosh-TurboGopher * DOS w/Clarkson Driver : /pub/gopher/PC_client/ NeXTstep : /pub/gopher/NeXT/ VM/CMS : /pub/gopher/Rice_CMS/ or /pub/gopher/VieGOPHER/ VMS : /pub/gopher/VMS/ OS/2 2.0 : /pub/gopher/os2/ MVS/XA : /pub/gopher/mvs/ Many other clients and servers have been developed by others, the following is an attempt at a comprehensive list. A Microsoft Windows Winsock client "The Gopher Book" sunsite.unc.edu:/pub/micro/pc-stuff/ms-windows/winsock/goph_tbk.zip A Macintosh Application, "MacGopher". ftp.cc.utah.edu:/pub/gopher/Macintosh * Another Macintosh application, "GopherApp". ftp.bio.indiana.edu:/util/gopher/gopherapp * A port of the UNIX curses client for DOS with PC/TCP oac.hsc.uth.tmc.edu:/public/dos/misc/dosgopher.exe A port of the UNIX curses client for PC-NFS bcm.tmc.edu:/nfs/gopher.exe A beta version of the PC Gopher client for Novell's LAN Workplace for DOS lennon.itn.med.umich.edu:/dos/gopher A VMS DECwindows client for use with Wollongong or UCX job.acs.ohio-state.edu:XGOPHER_CLIENT.SHARE * Note: these Macintosh clients require MacTCP. Most of the above clients can also be fetched via a gopher client itself. Put the following on a gopher server: Type=1 Host=boombox.micro.umn.edu Port=70 Path= Name=Gopher Software Distribution. Or point your gopher client at boombox.micro.umn.edu, port 70 and look in the gopher directory. There are also a number of public telnet login sites available. The University of Minnesota operates one on the machine "consultant.micro.umn.edu" (134.84.132.4) See Q3 for more information about this. It is recommended that you run the client software instead of logging into the public telnet login sites. A client uses the custom features of the local machine (mouse, scroll bars, etc.) A local client is also faster. --------------------------------------------------------------------- Q3: Where are there publicly available logins (ie places to telnet to in order to get a taste of gopher) for Gopher? A3: Here is a short list, use the site closest to you to minimize network lag. Telnet Public Logins: Hostname IP# Login Area ------------------------- --------------- ------ ------------- consultant.micro.umn.edu 134.84.132.4 gopher North America gopher.uiuc.edu 128.174.33.160 gopher North America panda.uiowa.edu 128.255.40.201 panda North America gopher.sunet.se 192.36.125.2 gopher Europe gopher.chalmers.se 129.16.221.40 gopher Sweden flode.nvg.unit.no 129.241.163.231 gopher Norway info.anu.edu.au 150.203.84.20 info Australia tolten.puc.cl 146.155.1.16 gopher South America ecnet.ec 157.100.45.2 gopher Ecuador gan.ncc.go.jp 160.190.10.1 gopher Japan It is recommended that you run the client software instead of logging into the public login sites. A client uses the custom features of the local machine (mouse, scroll bars, etc.) and gives faster response. Furthermore many of the basic features of clients - saving a file to your hard drive, printing a file to a local printer, viewing images, retrieving files from ftp sites etc.... are not available by the telnet logins. --------------------------------------------------------------------- Q4: Who Develops Gopher Software? A4: Gopher was originally developed in April 1991 by the University of Minnesota Microcomputer, Workstation, Networks Center to help our campus find answers to their computer questions. It has since grown into a full-fledged World Wide Information System used by a large number of sites in the world. Many people have contributed to the project, too numerous to count. The people behind the much of the gopher software can be reached via e-mail at gopher@boombox.micro.umn.edu, or via paper mail: Internet Gopher Developers 100 Union St. SE #190 Minneapolis, MN 55455 USA Or via FAX at: +1 (612) 625-6817 --------------------------------------------------------------------- Q5: What is the relationship between Gopher and (WAIS, WWW, ftp)? A5: Gopher is intimately intertwined with these two other systems. As shipped the Unix gopher server has the capability to: - Search local WAIS indices. - Query remote WAIS servers and funnel the results to gopher clients. - Query remote ftp sites and funnel the results to gopher clients. - Be queried by WWW (World Wide Web) clients (either using built in gopher querying or using native http querying. ------------------------------------------------------------------- Q6: Are papers or articles describing Gopher available? A6: Gopher has a whole chapter devoted to it in : _The_Whole_Internet_, Ed Kroll, O'Reilly, 1992 (Editors note: ..Great book, go out and buy a bunch!) _The_Internet_Passport: NorthWestNet's Guide to Our World Online" By Jonathan Kochmer and NorthWestNet. Published by NorthWestNet, Bellevue, WA. 1993. 516 pp. ISBN 0-9635281-0-6. Contact info: passport@nwnet.net, or (206) 562-3000 _A_Students_Guide_to_UNIX by Harley Hahn. (publisher McGraw Hill, Inc.; 1993 ISBN 0-07-025511-3) Other references include: _The_Internet_Gopher_, "ConneXions", July 1992, Interop. _Exploring_Internet_GopherSpace_ "The Internet Society News", v1n2 1992, (You can subscribe to the Internet Society News by sending e-mail to isoc@nri.reston.va.us) _The_Internet_Gopher_Protocol_, Proceedings of the Twenty-Third IETF, CNRI, Section 5.3 _Internet_Gopher_, Proceedings of Canadian Networking '92 _The_Internet_Gopher_, INTERNET: Getting Started, SRI International, Section 10.5.5 _Tools_help_Internet_users_discover_on-line_treasures, Computerworld, July 20, 1992 _TCP/IP_Network_Administration_, O'Reilly. Balakrishan, B. (Oct 1992) "SPIGopher: Making SPIRES databases accessible through the Gopher protocol". SPIRES Fall '92 Workshop, Chapel Hill, North Carolina. Tomer, C. Information Technology Standards for Libraries, _Journal of the American Society for Information Science_, 43(8):566-570, Sept 1992. ------------------------------------------------------------------- Q7: What is veronica? A7: veronica: Very Easy Rodent-Oriented Net-wide Index to Computerized Archives. veronica offers a keyword search of most gopher-server menu titles in the entire gopher web. As archie is to ftp archives, veronica is to gopherspace. A veronica search produces a menu of gopher items, each of which is a direct pointer to a gopher data source. Because veronica is accessed through a gopher client, it is easy to use, and gives access to all types of data supported by the gopher protocol. To try veronica, select it from the "Other Gophers" menu on Minnesota's gopher server, or point your gopher at: Name=veronica (search menu items in most of GopherSpace) Type=1 Port=70 Path=1/veronica Host=futique.scs.unr.edu ------------------------------------------------------------------------------ Q8: How do I connect to a specific gopher server? A8: Almost all clients have the ability to connect directly to a specific gopher hole. I'll use my server as an example here. If your using a Unix gopher client you would just type: gopher merlot.welch.jhu.edu If your using a VMS gopher client you would just type: gopher merlot.welch.jhu.edu 70 If you're using the X-windows client you would type: xgopher merlot.welch.jhu.edu If you're using Turbogopher - go into the FILE pulldown menu and select "Another Gopher" - a box will pop up asking for the server name - type : merlot.welch.jhu.edu. If you're using the DOS Client (PCgopher III) - Select the Configure pull down menu and choose "Application" and then fill in the box for ... Home Gopher Server: merlot.welch.jhu.edu then go to the FILE pull down menu and select New Gopher. If you still need to go through the geographical hierarchy the path is as follows: --> 8. North America/ --> 3. USA/ --> 21. maryland/ --> 1. Computational Biology (Johns Hopkins University)/ ----------------------------------------------------------------------------- Q9: What is Available for Biology? A9: There is an incredible amount of software, data and information availble to biologists now by gopher. Here is a brief list of the Biological Databases that you can search via gopher: 1. Search BOING (Bio Oriented INternet Gophers) - Lets you search through all the titles of items in Bio-Gophers around the world and access the items returned directly. 2. BDT Tropical Data Base Searches/ 3. Biotechnet Buyers Guide - Online Catalogues for Biology 4. Search Protein Data Bank Headers 5. Chlamydomonas Genetics Center / 6. Crystallization database/ 7. HGMP Databases - Probes and Primers / 8. Museum of Paleontology TYPE Specimen Index 9. MycDB - Mycobacterium DataBase 10. Search (Drosophila) Flybase (Indiana)/ 11. Search (GenBank + SWISS-PROT + PIR + PDB) 12. Search AAtDB - An Arabidopsis thaliana Database 13. Search ACEDB - A Caenorhabditis elegans Database 14. Search CompoundKB - A Metabolic Compound Database 15. Search Databases at Welchlab (Vectors, Promoters, NRL-3D, EST, OMI../ 16. Search EMBL 17. Search GenBank 18. Search Genbank - 2 19. Search Genbank Updates 20. Search LiMB 21. Search PIR 22. Search PIR (keyword,species...) 23. Search PROSITE 24. Search Rebase - Restriction Enzyme Database 25. Search SWISS-PROT 26. Search TFD 27. Search the C. elegans Strain List 28. Search the DNA Database of Japan 29. Search the EC Enzyme Database 30. Search the GrainGenes database 31. Search the Maize Database / 32. Cloning Vectors: plasmids, phage, etc. 33. EPD - Eukaryotic Promoter Database 34. EST - Expressed Sequence Tag Database - Human 35. wEST - Expressed Sequence Tag Database - C. elegans 36. Kabat Database of Proteins of Immunological Interest 37. NRL_3D Protein Sequence-Structure Database 38. OMIM - Online Mendelian Inheritance in Man 39. Seqanalref - Sequence Analysis Bibliographic Reference Data Ban.. 40. Search Rebase - Restriction Enzyme Database 41. Search the EC Enzyme Database 42. Search The Rodent Section of Genbank 43. Database Taxonomy (Genbank, Swiss-Prot ...)/ 44. Retrieve Full PDB Entries by Accession Number 45. Search for All Researchers funded by NIH 46. Search for Genome Researchers funded by DOE 47. Search for Researchers funded by NSF 48. Search for Researchers funded by the USDA 49. E-mail Addresses of Crystallographers/ 50. E-mail Addresses of Yeast Reasearchers/ 51. Phonebooks Around the World/ 52. Search and Retrieve Software for All Computers/ 53. Search and Retrieve Macintosh Software/ 54. Search and Retrieve DOS Software/ 55. Search and Retrieve GNU Software/ 56. Search and Retrieve Software for Biology/ 57. Search for Agricultural Software/ 58. Search and Retrieve Graphics Software and Data/ 59. Search and Retrieve all Online Perl Scripts/ 60. FTP Sites For Biology (57 archives for software and data)/ 61. Search the Genome Data Base (GDB)/ And the list goes on - this is just the beginning ---------------------------------------------------------------------------- Bonus info: Commands for the Unix and telnet clients: or View current item. 0-9 Move to a line #. k or Up-arrow Move pointer up. j or Down-arrow Move pointer down. u Go up a level. m Go to the first screen. q Exit Internet Gopher. > Next Page < Previous Page = Display Technical information about current item. o change options ? This help screen. A and a Save a bookmark s Copy an item to a file v View Bookmarks /word Search for a word in a menu or document Each object can be identified by its "extension" / Item is a directory. . Item is a text file. Item is a search index. Item is a CSO phone book. Item is a telnet session. <) Item is a sound (looks like a speaker) -------------------------------------------------------------------------- From owner-proteins@net.bio.net Wed Jul 21 23:00:00 1993 Path: biosci!steele!news From: shapirop@ohsu.edu Newsgroups: bionet.molbio.proteins Subject: Re: protein_protein_interaction? Message-ID: <1993Jul22.163729.10406@ohsu.edu> Date: 22 Jul 93 16:37:29 GMT References: <1993Jul22.133231.19549@gserv1.dl.ac.uk> Sender: news@ohsu.edu Organization: vollum institute/ohsu Lines: 24 Nntp-Posting-Host: 137.53.73.141 In article <1993Jul22.133231.19549@gserv1.dl.ac.uk> emrasmus@biobase.aau.dk (Erik Michael Rasmussen) writes: >I would like to examine a protein-protein interaction by PAGE. I believe I >can't use SDS. Since I'm not familiar with this I need some advice. >Therefore a reference or a protokol to start with would be nice. >The two proteins I have are 167 kD and 50 kD. > >Erik Michael Rasmussen phone (+45) 35322100 >Department of Genetics E-mail emrasmus@biobase.aau.dk >Institute of Molecular Biology >University of Copenhagen > > Hi Some colleagues at my institution are using two PAGE techniques for studying protein protein interactions, one being band shifting in native PAGE and the other being overlay blotting after SDS-PAGE. They (Daniel W. Carr and John D. Scott) have a review article in TIBS entitled BLOTTING AND BAND SHIFTING: TECHNIQUES FOR STUDYING PROTEIN-PROTEIN INTERACTIONS in Trends in Biochemical Scinces Vol. 17 July 1992 pps. 246-249. PAUL SHAPIRO shapirop@ohsu.edu Vollum Institute PORTLAND, OR From owner-proteins@net.bio.net Wed Jul 21 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!pipex!uknet!pavo.csi.cam.ac.uk!mbfs.bio.cam.ac.uk!seb1005 From: seb1005@mbfs.bio.cam.ac.uk (Steven Brenner) Newsgroups: bionet.molbio.proteins Subject: Re: Message-ID: <1993Jul22.192018.23251@infodev.cam.ac.uk> Date: 22 Jul 93 19:20:18 GMT References: <9307221252.AA12224@emoryu1.cc.emory.edu> Sender: news@infodev.cam.ac.uk (USENET news) Distribution: bionet Organization: U of Cambridge, England Lines: 32 Nntp-Posting-Host: mbfs.bio.cam.ac.uk genekdw@EMORYU1.CC.EMORY.EDU ("Keith D. Wilkinson") writes: >In message >> From: pmr1716@ggr.co.uk ("Peter Murray-Rust") >> Subject: Effect of pressure on enzyme reactions >> I'd be grateful for any information about whether high-pressure can affect >> (a) >> the speed and/or (b) the equilibrium of an enzyme-catalysed reaction, and if >> so, what pressures are required in practice to make a useful contribution. >> If >> this is a well-researched field, I'd be very grateful for pointers to >> reviews. >Try papers by Gregorio Weber at the University of Illinois. His work centered >on the effectcs of pressure on subunit dissociation, but he may reference >effects on catalysis directly. The equilibrium effect should be small but >calculable from first principles. This message hints at the problem I think that you're going to run into doing any "general" work with pressure effects on catalysis. I would expect that at the same pressures that would be likely to affect reaction rates there will also be an effect on protein structure. This effect would, in turn, probably affect catalysis more than the "first principles" equilibrium shift. These are my assumptions, however, and I don't know whether this has been demonstrated to be the case. -- Steven E. Brenner | Department of Biochemistry seb1005@mbfs.bio.cam.ac.uk | University of Cambridge Lab +44 223 333671 | Tennis Court Road Fax +44 223 333345 | Cambridge CB2 1QW, UK From owner-proteins@net.bio.net Wed Jul 21 23:00:00 1993 Path: biosci!EMORYU1.CC.EMORY.EDU!genekdw From: genekdw@EMORYU1.CC.EMORY.EDU ("Keith D. Wilkinson") Newsgroups: bionet.molbio.proteins Subject: Re: Message-ID: <9307221252.AA12224@emoryu1.cc.emory.edu> Date: 22 Jul 93 12:52:21 GMT Sender: daemon@net.bio.net Reply-To: "Keith D. Wilkinson" Distribution: bionet Lines: 25 In message > From: pmr1716@ggr.co.uk ("Peter Murray-Rust") > Subject: Effect of pressure on enzyme reactions > Date: 21 Jul 93 17:46:30 GMT > Sender: list-admin@daresbury.ac.uk > Original-To: proteins@uk.ac.daresbury > > I'd be grateful for any information about whether high-pressure can affect > (a) > the speed and/or (b) the equilibrium of an enzyme-catalysed reaction, and if > so, what pressures are required in practice to make a useful contribution. > If > this is a well-researched field, I'd be very grateful for pointers to > reviews. > > Thanks, > > Peter > Try papers by Gregorio Weber at the University of Illinois. His work centered on the effectcs of pressure on subunit dissociation, but he may reference effects on catalysis directly. The equilibrium effect should be small but calculable from first principles. From owner-proteins@net.bio.net Thu Jul 22 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: WALLACE@IRBM.IT (Andrew, Tel. +39-6-91093434) Newsgroups: bionet.molbio.proteins Subject: RE: how do we access protein database? Message-ID: <1993Jul23.172930.28818@gserv1.dl.ac.uk> Date: 23 Jul 93 17:31:54 GMT Sender: WALLACE@IT.IRBM Distribution: bionet Lines: 26 X-Vmsmail-To: SMTP%"wiens@iscsvax.uni.edu" Original-To: wiens@edu.uni.iscsvax, proteins@uk.ac.daresbury You wrote: >We would like to compare 6 decapeptide sequences to which we have antibodies, >to known protein amino acid sequences from a data base, but we haven't done it >before and don't know how to access a database such as Protein Data Base or >Gopher. Could someone help? We are on a pc hooked up to a university VAX and >are used to using internet. >Thanks, Darrell and Jacqui Sounds like you want to send your sequences to an appropriate fileserver for similarity searching if do not have suitable software (such as the GCG package) on your VAX or something similar on your PC. Judging by your address, the nearest server to you is fileserv@nbrf.georgetown.edu to which you should send a one-line message containing the word 'help' in the body of the message, to receive further details by e-mail. If you need more information, see the excellent article by Steven Heinkoff in the Computer Corner section of the July 1993 issue of Trends in Biochemical Sciences. All the best, Andrew Wallace From owner-proteins@net.bio.net Thu Jul 22 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!newsserver.jvnc.net!jvnc.net!mrl775.jvnc.net!user From: mrl775@tigger.jvnc.net (Keith O. Elliston) Newsgroups: bionet.molbio.proteins Subject: UDP Glucose Binding Motif Message-ID: Date: 23 Jul 93 02:30:46 GMT Sender: news@tigger.jvnc.net (Zee News Genie) Followup-To: bionet.molbio.proteins Organization: JvNCnet Lines: 12 Nntp-Posting-Host: mrl775.jvnc.net Hello I am looking for any documentation on UDP-Glucose binding motifs, particularly in yeast. Does anyone have any information??? Thanks Keith +++++++++++++++++++++++++ Keith Elliston mrl775@tigger.jvnc.net From owner-proteins@net.bio.net Sat Jul 24 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!sangam!vikram!imtech!girish From: girish@imtech.ernet.in (GIRISH SAHNI, SCIENTIST, IMTECH SECTOR 39-A, CHANDIGARH 160014, INDIA) Newsgroups: bionet.molbio.proteins Subject: linker peptide in two-domain fusion protein Message-ID: <5782@imtech.ernet.in> Date: 23 Jul 93 05:58:17 GMT Organization: Inst. of Microbial Technology, Chandigarh, India Lines: 12 Dear Freind, Hi there: I need some suggestions for designing a linker sequence between two independently folded protein domains in a fusion (gene) construct. Perhaps we would have to try a few candidate sequences (3-10 AA long) with varying degrees of flexibility/rigidity, since we cannot predict a priori what the effect may be on unwanted aggregation or steric hindrance associated with the final hybrid protein. Sources where I might ponder these aspects will be welcome, as would actual AA sequences of possible linker peptides. Thank you Girish Sahni IMTECH, India Email: "girish@imtech.ernet.in" From owner-proteins@net.bio.net Sun Jul 25 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!mcsun!sun4nl!star.cs.vu.nl!balaena!mac133.bio.vu.nl!user From: vdwal@bio.vu.nl (FJvanderWal) Newsgroups: bionet.molbio.proteins Subject: needed: random mutation+doped oligo's Message-ID: Date: 26 Jul 93 09:52:41 GMT Sender: news@bio.vu.nl Followup-To: bionet.molbio.proteins Organization: Vrije Uni., Mol.Micro., Amsterdam, NL Lines: 20 I want to change a sequence randomly by using doped oligo's (N-N-C/G) in which N stands for the wild-type nucleotides at the 1st or 2nd position of a triplet, polluted with a certain amount of the other three nucleotides. C/G stands for a mix of C and G at the 3rd position of a triplet; this is to avoid the generation of the two stopcodons ending with a C or a G. The part of the oligo in which I want a 'mutation' is 81 nt's (the oligo itself will be a little longer to include some sites which can be digested after annealing the 3'-ends and subsequent fill-in by a polymerase). Selection of mutants is easy since we have a method in which upon transformation wild-types won't grow on plates containing IPTG. My question is this: How do I determine the frequency of polluted nucleotides, if I want to synthesize a mixed batch of oligo's with only one mutation each? Maybe you could provide me some references or formulas, any information would be very helpfull!. Thanks in advance for your co-operation. Fimme J. van der Wal vdwal@bio.vu.nl From owner-proteins@net.bio.net Sun Jul 25 23:00:00 1993 Path: biosci!uwm.edu!wupost!uunet!pipex!uknet!pavo.csi.cam.ac.uk!mbfs.bio.cam.ac.uk!smb18 From: smb18@mbfs.bio.cam.ac.uk (Simon Brocklehurst) Newsgroups: bionet.molbio.proteins Subject: Re: linker peptide in two-domain fusion protein Message-ID: <1993Jul26.103236.12267@infodev.cam.ac.uk> Date: 26 Jul 93 10:32:36 GMT References: <5782@imtech.ernet.in> Sender: news@infodev.cam.ac.uk (USENET news) Organization: U of Cambridge, England Lines: 40 Nntp-Posting-Host: mbfs.bio.cam.ac.uk girish@imtech.ernet.in (GIRISH SAHNI, SCIENTIST, IMTECH SECTOR 39-A, CHANDIGARH 160014, INDIA) writes: >Dear Freind, Hi there: >I need some suggestions for designing a linker sequence between two >independently folded protein domains in a fusion (gene) construct. >Perhaps we would have to try a few candidate sequences (3-10 AA long) >with varying degrees of flexibility/rigidity, since we cannot predict >a priori what the effect may be on unwanted aggregation or steric >hindrance associated with the final hybrid protein. Sources where I >might ponder these aspects will be welcome, as would actual AA sequences >of possible linker peptides. Thank you > Girish Sahni IMTECH, India > Email: "girish@imtech.ernet.in" There are probably two kinds of sequence that you might want to explore. 1) Sequences made up of Ala and Pro. By varying the number of Ala-Pro pairs you can modulate the flexibility of the linker. 2) Sequences made up of charged amino acid residues e.g. mixing Glu and Lys. It is more difficult to rationilise how flexibility can be modulated by sequence variation in this case. Both these types of sequence are common in long (30-40 aa) linkers joining independently folded domains in multifunctional polypeptides. A good reference to start with is the review by Richard Perham "Domains, motifs and linkers in 2-oxo acid dehydrogenase multienzyme complexes: a paradigm in the design of a multifunctional protein" Biochemistry 30, 8501-8512 Simon M. Brocklehurst Cambridge Centre for Molecular Recognition Dept. of Biochemistry University of Cambridge Tennis Court Road Cambridge UK From owner-proteins@net.bio.net Sun Jul 25 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!pipex!uknet!bcc.ac.uk!bsm.bioc.ucl.ac.uk!mcdonald From: mcdonald@bsm.bioc.ucl.ac.uk (Ian McDonald) Newsgroups: bionet.molbio.proteins Subject: Hydrogen Bond Calculator Message-ID: <1993Jul26.130044.58973@ucl.ac.uk> Date: 26 Jul 93 13:00:44 GMT Sender: news@ucl.ac.uk (Usenet News System) Followup-To: bionet.xtallography bionet.biology.computational bionet.software Organization: Biological Structure and Modellin Unit, UCL Lines: 146 HBPLUS - Free Hydrogen Bond Calculator -------------------------------------- HBPLUS is a hydrogen bond calculation program that has been developed in-house over the course of nearly four years. It calculates positions for polar hydrogens. It also calculates the angles at the hydrogen and the acceptor as well as the donor-acceptor and hydrogen-acceptor distances. The hydrogen bond criteria are customisable. The program inputs a Brookhaven protein database format file, and outputs a list of hydrogen bonds, including geometries, and optionally a Brookhaven protein database file that includes the polar hydrogen positions. It is written in ANSI C and has been checked on several UNIX systems. If you would like a copy of HBPLUS, simply send me a signed copy of the confidentiality agreement at the bottom of this post and I shall email you the source code and documentation. It is free to academic users. HBPLUS is (c) IK McDonald, D Naylor, D Jones and JM Thornton 1993 ----------------------------------------------->8-CUT HERE--- Correspondence to: Ian McDonald (PG) Biological Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London Gower Street LONDON WC1E 6BT UK / EC Email mcdonald@uk.ac.ucl.bsm HBPLUS - Hydrogen Bond Calculation ---------------------------------- CONFIDENTIALITY AGREEMENT ------------------------- In regard to the HBPLUS program, specified in Appendix 1 herewith (the Software) supplied to us, the copyright and other intellectual property rights to which belong to the authors, we __________________________________________________________________ undertake to the authors that we shall be bound by the following terms and conditions:- 1. We will receive the Software and any related documentation in confidence and will not use the same except for the purpose of the department's own research. The Software will be used only by such of our officers or employees to whom it must reasonably be communicated to enable us to undertake our research and who agree to be bound by the same confidence. The department shall procure and enforce such agreement from its staff for the benefit of the authors. 2. The publication of research using the Software must reference "McDonald IK, Naylor DN, Jones DT & Thornton J M (1993), 'HBPLUS', Computer Program, Department of Biochemistry and Molecular Biology, University College London." or successor references as defined by the authors. 3. Research shall take place solely at the department's premises at __________________________________________________________________ 4. All forms of the Software will be kept in a reasonably secure place to prevent unauthorised access. 5. Each copy of the Software or, if not practicable then, any package associated therewith shall be suitably marked (and such marking maintained) with the following copyright notice: "Copyright 1991-3 Ian McDonald, Dorica Naylor, David Jones and Janet M Thornton All Rights Reserved". 6. The Software may be modified but any changes made shall be made available to the authors. 7. The Software shall be used exclusively for academic teaching and research. The Software will not be used for any commercial research or research associated with an industrial company. 8. The confidentiality obligation in paragraph one shall not apply: (i) to information and data known to the department at the time of receipt hereunder (as evidenced by its written records); (ii) to information and data which was at the time of receipt in the public domain or thereafter becomes so through no wrongful act of the department; (iii) to information and data which the department receives from a third party not in breach of any obligation of confidentiality owed to the authors. Please sign this Undertaking and return a copy of it to indicate that you have read, understood and accepted the above terms. For and on behalf of _____________________________ _________________________________________________ .................................................. Dated ............................................ APPENDIX 1 - DETAILS OF THE HBLPUS PROGRAM PROVIDED --------------------------------------------------- Files to be included -------------------- 1. hbplus.c } Source program file 2. hbplus.man } Documentation From owner-proteins@net.bio.net Sun Jul 25 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!sangam!vikram!imtech!girish From: girish@imtech.ernet.in (GIRISH SAHNI, SCIENTIST, IMTECH SECTOR 39-A, CHANDIGARH 160014, INDIA) Newsgroups: bionet.molbio.proteins,bionet.general Subject: stability of streptokinase Message-ID: <5814@imtech.ernet.in> Date: 26 Jul 93 09:08:58 GMT Organization: Inst. of Microbial Technology, Chandigarh, India Lines: 6 Xref: biosci bionet.molbio.proteins:761 bionet.general:5574 I have a problem in stabilizing pure Strptokinase obtained by affinity chromatography of culture fitrates of streptopcocci. The protein is known to be stabilizable w/ 50% Glycerol or BSA, but I dont want any additives. Lyophilization also causes significant loss of activity. Any suggestions will be welcome. G. Sahni IMTECH Chandigarh India Email: "girish@imtech.ernet.in" From owner-proteins@net.bio.net Sun Jul 25 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!news.ans.net!nynexst.com!vermont!smehta From: smehta@kwela.nynexst.com (Sandeep Mehta) Newsgroups: bionet.general,bionet.molbio.proteins,sci.bio.technology,sci.bio Subject: references needed Message-ID: Date: 27 Jul 93 03:18:01 GMT Sender: news@nynexst.com (For News purposes) Reply-To: smehta@nynexst.com Organization: Advanced Speech Systems, IS Lab, NYNEX S&T Inc, White Plains, NY Lines: 16 Xref: biosci bionet.general:5575 bionet.molbio.proteins:762 sci.bio.technology:510 sci.bio:4294 Hello, I'm not sure if this is the correct newsgroup as I am posting this request for a friend who does not have net/email access. I would like to get hold of references to work done on directing antibodies against the multi-drug resistance receptor. I'm sorry I don't have any other details but any help is appreciated. Please reply by email to smehta@nynexst.com. Thanks much. -- Sandeep Mehta smehta@nynexst.com From owner-proteins@net.bio.net Tue Jul 27 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!utcsri!newsflash.concordia.ca!mizar.cc.umanitoba.ca!murphy.biochem.umanitoba.ca!user From: dotzlaw@ccu.umanitoba.ca (Helmut Dotzlaw) Newsgroups: bionet.molbio.proteins Subject: Protein Methods, was:Re: Methods??? Message-ID: Date: 28 Jul 93 16:50:53 GMT References: Sender: news@ccu.umanitoba.ca Followup-To: bionet.molbio.proteins Distribution: bionet Organization: University of Manitoba Lines: 24 Nntp-Posting-Host: murphy.biochem.umanitoba.ca In article , pnh@fcs260c2.ncifcrf.gov (Paul N Hengen) wrote: > How many protein biologists who follow this group also read > bionet.molbio.methds-reagnts? I've noticed that when I read > this newsgroup, I am re-reading articles that are cross-posted > to the methods group. There are also methods discussed here that > are not posted in methods. Why don't people simply post them in > methods? > Because, not everyone who reads this group reads bionet.molbio.methds-reagnts. Let's say, for example, that I am a protein chemist and am simply not interested in PCR, DNA, RNA etc. - I could save considerable time reading .proteins. BTW, I do read both, because I am not strictly a protein chemist. But I have cross-posted and have received replys regarding protein questions from people reading the .proteins group. I really think that there is nothing wrong in cross-posting to the two groups, I'm sure that the subscription list is somewhat different on each. Regards, Helmut From owner-proteins@net.bio.net Tue Jul 27 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!europa.eng.gtefsd.com!darwin.sura.net!fconvx.ncifcrf.gov!fcs260c2!pnh From: pnh@fcs260c2.ncifcrf.gov (Paul N Hengen) Newsgroups: bionet.molbio.proteins Subject: Methods??? Message-ID: Date: 27 Jul 93 16:32:11 GMT Sender: Paul N. Hengen Distribution: bionet Organization: Frederick Cancer Research and Development Center Lines: 11 Nntp-Posting-Host: fcs260c2.ncifcrf.gov How many protein biologists who follow this group also read bionet.molbio.methds-reagnts? I've noticed that when I read this newsgroup, I am re-reading articles that are cross-posted to the methods group. There are also methods discussed here that are not posted in methods. Why don't people simply post them in methods? Paul N. Hengen National Cancer Institute Frederick Cancer Research and Development Center Frederick, Maryland 21702-1201 USA From owner-proteins@net.bio.net Tue Jul 27 23:00:00 1993 Path: biosci!parc!decwrl!decwrl!elroy.jpl.nasa.gov!usc!howland.reston.ans.net!europa.eng.gtefsd.com!emory!emoryu1!rttimme From: rttimme@emory.edu (Dr. Richard Timmer) Newsgroups: bionet.molbio.proteins Subject: Ab. wanted for globin Message-ID: <4057@emoryu1.cc.emory.edu> Date: 28 Jul 93 16:48:24 GMT Organization: Emory University, Atlanta, GA Lines: 13 X-Newsreader: Tin 1.1 PL3 Bionetters: Does anyone out there know of or have polyclonal (or monoclonal) antibodies specific for the following: 1) rabbit alpha globin; and 2) rabbit beta globin. Thanks in advance. **************************************************************************** | Richard Timmer | | Dept. of Physiology | | Emory Univ. School of Medicine voice: 404-727-7411 | | 1648 Pierce Drive fax: 404-727-2648 | | Atlanta, GA 30322 e-mail: rttimme@emoryu1.cc.emory.edu | **************************************************************************** From owner-proteins@net.bio.net Wed Jul 28 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!uunet!spool.mu.edu!umn.edu!gaia.ucs.orst.edu!connected.com!connected.com!not-for-mail From: seth@hebron.connected.com Newsgroups: bionet.molbio.proteins Subject: K00L Internation Numbers Message-ID: <237p9f$n98@hebron.connected.com> Date: 29 Jul 93 06:04:31 GMT Organization: Connected INC -- Internet Services Lines: 8 NNTP-Posting-Host: hebron.connected.com Cc: I found these COOL internation phone sex lines, and they are FREE. So if you want to unload your STUFF all over the PHONE give them a call. 011-239-129-2620 & 011-592-247-846 From owner-proteins@net.bio.net Wed Jul 28 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!uunet!munnari.oz.au!metro!usage!newt.phys.unsw.edu.au!sjt From: sjt@newt.phys.unsw.edu.au (Sarah Tilley) Newsgroups: bionet.molbio.proteins Subject: Quick SDS PAGE question Message-ID: <1993Jul29.034729.25328@usage.csd.unsw.OZ.AU> Date: 29 Jul 93 03:47:29 GMT Sender: news@usage.csd.unsw.OZ.AU Reply-To: sjt@newt.phys.unsw.edu.au (Sarah Tilley) Organization: University of NSW Lines: 10 Nntp-Posting-Host: newt.phys.unsw.edu.au -- Hi, I have a recipe for a 10% SDS gel (supplied by a company) which seems to take to long to polymerise according to my previous experiences with SDS PAGE. When I looked at the recipe, the amount of TEMED seems quite low- 20ul of TEMED and 300ul of 10% AMPS per 60 ml of separating gel. Would I mess up the gel if I increased the TEMED to 50 or 60ul? I have a separate recipe for a 15% gel that uses 170ul TEMED and 450ul of 10% AMPS for 50 mls. Will playing around with these chemicals affect anything else other t han rate of polymerisation? Thanks in advance ** Sarah Tilley sjt@newt.phys.unsw.edu.au From owner-proteins@net.bio.net Wed Jul 28 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!usc!cs.utexas.edu!uunet!munnari.oz.au!uniwa!uniwa!not-for-mail From: andrewh@uniwa.uwa.edu.au (Andrew Hobbs) Newsgroups: bionet.molbio.proteins Subject: Re: Quick SDS PAGE question Message-ID: <23a1ja$b2a@uniwa.uwa.edu.au> Date: 30 Jul 93 02:38:34 GMT References: <1993Jul29.034729.25328@usage.csd.unsw.OZ.AU> Organization: The University of Western Australia Lines: 35 NNTP-Posting-Host: uniwa.uwa.edu.au X-Newsreader: TIN [version 1.2 PL1] Sarah Tilley (sjt@newt.phys.unsw.edu.au) wrote: : -- : Hi, : I have a recipe for a 10% SDS gel (supplied by a company) which seems to take to long to polymerise according to my previous experiences with SDS PAGE. When I looked at the recipe, the amount of TEMED seems quite low- 20ul of TEMED and 300ul of 10% AMPS per 60 ml of separating gel. Would I mess up the gel if I increased the TEMED to 50 or 60ul? I have a separate recipe for a 15% gel that uses 170ul TEMED and 450ul of 10% AMPS for 50 mls. Will playing around with these chemicals affect anything else other t : han rate of polymerisation? : Thanks in advance : ** : Sarah Tilley : sjt@newt.phys.unsw.edu.au In my experience 20 ul TEMED is plenty for a 60 ml gel. I tend to use 5 - 10 ul. The degradation products of TEMED (ie from old TEMED) can in fact inhibit the reaction. If the gel is taking too long to set generally I immediately suspect the degassing was not sufficient or alternatively the ammonium persulphate has gone off (We did have one bottle of Ammonium persulphate which resolutely refused to cause polymerization of acrylamide though the bottle was several years old so I didn't complain) Andrew Hobbs Biochemistry University of Western Australia andrewh@uniwa.uwa.edu.au From owner-proteins@net.bio.net Wed Jul 28 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!math.ohio-state.edu!magnus.acs.ohio-state.edu!csn!ub!acsu.buffalo.edu!ubvms.cc.buffalo.edu!camcb From: camcb@ubvms.cc.buffalo.edu (Chris Baumann) Newsgroups: bionet.molbio.proteins Subject: Re: K00L Internation Numbers Message-ID: Date: 30 Jul 93 01:22:00 GMT References: <237p9f$n98@hebron.connected.com> Sender: nntp@acsu.buffalo.edu Organization: University at Buffalo Lines: 14 News-Software: VAX/VMS VNEWS 1.41 Nntp-Posting-Host: ubvmsb.cc.buffalo.edu In article <237p9f$n98@hebron.connected.com>, seth@hebron.connected.com writes... >I found these COOL internation phone sex lines, and they are FREE. So >if you want to unload your STUFF all over the PHONE give them a call. > > 011-239-129-2620 > > & > > 011-592-247-846 This is not the place for garbage like this. It is disgusting and completly uncalled for. Isn't there any way to screen out comments like these from individuals such as this??? Chris From owner-proteins@net.bio.net Thu Jul 29 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!agate!library.ucla.edu!news.mic.ucla.edu!wlheye.jsei.ucla.edu!zf From: zf@wlheye.jsei.ucla.edu (Zoreh Farahbakhsh) Newsgroups: bionet.molbio.proteins Subject: proteins with one sh group Message-ID: <23bnku$8dl@news.mic.ucla.edu> Date: 30 Jul 93 18:01:02 GMT Organization: UCLA Microcomputer Support Office Lines: 6 NNTP-Posting-Host: wlheye.jsei.ucla.edu Dear friends I like to have some suggestions about how to search for the proteins containing only one sulfhydryl group. Z.T. Farahbakhsh From owner-proteins@net.bio.net Thu Jul 29 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!noc.near.net!saturn.caps.maine.edu!dartvax!grafton.dartmouth.edu!knight From: knight@grafton.dartmouth.edu (John Boswell) Newsgroups: bionet.molbio.proteins Subject: Staining Westerns with Ponceau S Message-ID: Date: 30 Jul 93 20:12:18 GMT Sender: news@dartvax.dartmouth.edu (The News Manager) Organization: Dartmouth College, Hanover, NH Lines: 18 Hi, I'd like to switch to Ponceau S for staining Western Blots (on PVDF membranes), but I don't know the proper concentration/solvent. I currently use Coommassie Blue, but it takes to long to destain. I've used Ponceau before, but I can't remember the concentration. I tried 0.1 and 0.5% w/v in 5% acetic acid, but this was just not sensitive at all (only a few bands showed up, and faintly). When I destained the membrane and restained with coommassie, all my bands showed up nice and dark. Is ponceau inherently less sensitive than coommassie, or do I need to up the ponceau concentration/ staining times considerable? Thanks a bunch to anyone that can help me :) John Boswell -- **************************************************************************** Dr. John Boswell knight@grafton.dartmouth.edu Dept. of Chemistry, Biochemistry and Molecular Biology Oregon Graduate Institute, Portland, OR 503-690-1086 From owner-proteins@net.bio.net Sat Jul 31 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!cs.utexas.edu!swrinde!emory!emoryu1!rttimme From: rttimme@emory.edu (Dr. Richard Timmer) Newsgroups: bionet.molbio.proteins Subject: Ab. wanted for globin Message-ID: <4122@emoryu1.cc.emory.edu> Date: 1 Aug 93 15:59:11 GMT Organization: Emory University, Atlanta, GA Lines: 23 X-Newsreader: Tin 1.1 PL3 Subject: Ab. wanted for globin Newsgroups: bionet.molbio.methds-reagnts Distribution: Summary: Keywords: Bionetters: Does anyone have or know of a source for an antibody (monoclonal or polyclonal) to each of the following: a. rabbit alpha globin b. rabbit beta globin Thanks for any help on the above. **************************************************************************** | Richard Timmer | | Dept. of Physiology | | Emory Univ. School of Medicine voice: 404-727-7411 | | 1648 Pierce Drive fax: 404-727-2648 | | Atlanta, GA 30322 e-mail: rttimme@emoryu1.cc.emory.edu | **************************************************************************** From owner-proteins@net.bio.net Sat Jul 31 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!news!demon!visigoth.demon.co.uk!user From: pettsj@visigoth.demon.co.uk (James Petts) Newsgroups: bionet.molbio.proteins Subject: Re: K00L Internation Numbers Message-ID: Date: 30 Jul 93 16:18:38 GMT References: <237p9f$n98@hebron.connected.com> Sender: news@demon.co.uk (Usenet Administration) Followup-To: bionet.molbio.proteins Organization: No Affiliation Lines: 21 Nntp-Posting-Host: visigoth.demon.co.uk In article , camcb@ubvms.cc.buffalo.edu (Chris Baumann) wrote: > This is not the place for garbage like this. It is disgusting and completly > uncalled for. Isn't there any way to screen out comments like these from > individuals such as this??? Nor are the several hundred other groups he has posted similar messages to, using differenr accounts. Apparently he has lost most of these accounts recently due to the *LARGE* number of complaints being sent to postmaster at his hosts. If this stuff reappears, I urge you to make the same complaints to "postmaster@his.node" ===> James Petts <=== ========================================================================= pettsj@visigoth.demon.co.uk ..oo000oo.. PGP 2.X key on the servers ========================================================================= I feel that if a person can't communicate, the very least he can do is shut up. -- Tom Lehrer ========================================================================= From owner-proteins@net.bio.net Sat Jul 31 23:00:00 1993 Path: biosci!uwm.edu!wupost!math.ohio-state.edu!magnus.acs.ohio-state.edu!wtschant From: wtschant@magnus.acs.ohio-state.edu (William R Tschantz) Newsgroups: bionet.molbio.proteins Subject: Native gel recipe Message-ID: <23hlbm$2ii@charm.magnus.acs.ohio-state.edu> Date: 1 Aug 93 23:58:46 GMT Distribution: na Organization: The Ohio State University Lines: 13 NNTP-Posting-Host: bottom.magnus.acs.ohio-state.edu Hi, I am looking for PAGE native gel recipe which can separate low molecular weight complexes (less than 100KD). References would help also. Any help appreciated. Thanks, Bill -- |Bill Tschantz | How about a Homebrew? |Chemistry Department | |Ohio State University | |wtschant@magnus.acs.ohio-state.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~