From owner-proteins@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!europa.eng.gtefsd.com!howland.reston.ans.net!math.ohio-state.edu!usc!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!wccf.mit.edu!huh From: huh@wccf.mit.edu (GENE SIMON HUH) Newsgroups: bionet.molbio.proteins Subject: proteins of desired molecular weight range Keywords: molecular weight Message-ID: <2NOV199314140109@wccf.mit.edu> Date: 2 Nov 93 19:14:00 GMT Organization: MIT - Whitaker College Lines: 7 NNTP-Posting-Host: wccf.mit.edu News-Software: VAX/VMS VNEWS 1.41 Hello, Can anybody tell me if there is an easy way to get the names of all proteins within a specified molecular weight range? I assume that database search programs must be fitted for this kind of query, but I haven't seen anything of the type. Thanks in advance, Gene Huh HUH@wccf.mit.edu From owner-proteins@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!nntp.club.cc.cmu.edu!pitt.edu!ache.pharm.pitt.edu!user From: drg@prophet.pharm.pitt.edu (Duke Groebe) Newsgroups: bionet.molbio.proteins Subject: Re: protein sequence data base Message-ID: Date: 2 Nov 93 19:27:57 GMT References: <93294.143248AXC19@psuvm.psu.edu> Sender: news+@pitt.edu Followup-To: bionet.molbio.proteins Organization: University of Pittsburgh Lines: 26 In article , drg@prophet.pharm.pitt.edu (Duke Groebe) wrote: *> *> In article <93294.143248AXC19@psuvm.psu.edu>, AXC19@psuvm.psu.edu wrote: *> > *> > I need some guidance on what and where or who to go to ...I finally got the *ami *> > no acid sequence of a protein of interest...Now, how can I do an aminoacid *comp *> > arison to other proteins and figure out if it has already been isolated. *Any h *> > elp will be appreciated. *> > Thanks, *> > Aida Cancel *> > axc19@psuvm.psu.edu If you don't have a gopher service and you want software, ftp to ftp.bio.indiana.edu, login as "anonymous" and give your e-mail address as the password. Once you've learned how to get around the directories and files using the ftp, you can find lotsa software there that will do exactly what you want and more. Duke From owner-proteins@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: sgex400@uk.ac.lon.sghms (MJ Duggan) Newsgroups: bionet.molbio.proteins Subject: Re: protein sequence data base (fwd) Message-ID: <1993Nov2.124026.2213@gserv1.dl.ac.uk> Date: 2 Nov 93 12:38:59 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 39 Precedence: first-class Original-To: proteins@uk.ac.daresbury X-Mailer: ELM [version 2.3 PL8] The question (see below) was about how to do database searches if you haven't doenthem before. I was in this situation a few months ago, and rather than fuss around finding someone with the program and database locally I used the email servers available by Internet. Either Blitz at EMBL or Blast at NCBI are very good and very easy to use. There was a good article in the Computer Corner bit of TIBS about 6 Months ago, that has all the addresses. > > In article <93294.143248AXC19@psuvm.psu.edu>, AXC19@psuvm.psu.edu wrote: > > > > I need some guidance on what and where or who to go to ...I finally got the ami > > no acid sequence of a protein of interest...Now, how can I do an aminoacid comp > > arison to other proteins and figure out if it has already been isolated. Any h > > elp will be appreciated. > > Thanks, > > Aida Cancel > > axc19@psuvm.psu.edu > > > Well, first of all you need access to the various protein databases that > are out there. Second, you need a program that can access the files in > those databases and search them for the sequence(s) you want to look for. > Since you're at PSU, you may already have such a capacity in your > department, if not next door (isn't there a big biotech center there?). > Ask around there for freebie help. > > You may be able to find all the free software you need via the multitude of > gopher servers on the Net. Try them also. > > You can buy both databases and sequence analysis programs from Gentics > Computer Group, Inc. (GCG) Telephone: 608-231-5200; E-mail: Help@GCG.com. > Intelligenetics also sells the stuff (I forget the phone #, but they > advertise alot). > > Good luck, > > Duke > From owner-proteins@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!gatech!howland.reston.ans.net!spool.mu.edu!bloom-beacon.mit.edu!mcrcim.mcgill.edu!sifon!athena.ulaval.ca!maxwell!apham From: apham@maxwell.phy.ulaval.ca (Alain Pham) Newsgroups: bionet.molbio.proteins Subject: TSPP: A chemical product wanted Message-ID: Date: 2 Nov 93 20:15:45 GMT Sender: news@athena.ulaval.ca Reply-To: apham@maxwell.phy.ulaval.ca Organization: Sun Microsystems, Inc. Lines: 19 Nntp-Posting-Host: maxwell.lx.phy.ulaval.ca Hi, For my research I'm presently looking for this chemicals: Tetrasodium 5, 10,15, 20-tetra(4-sulfonatophenyl)-porphin Does anyone knows about it ? Does anyone knows about any chemical companies in USA or Europe selling this product ? If you have any information please feel free to mail me directly at apham@phy.ulaval.ca Thanks for any help. Regards. Alph ^---^ apham@phy.ulaval.ca |0 0| (^ ^) v-v From owner-proteins@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!warwick!nott-cs!macfd.biochem.nott.ac.uk!user From: mbxfd@unicorn.nott.ac.uk (Fergus Doherty) Newsgroups: bionet.molbio.proteins Subject: Antibodies to cytochrome c? Message-ID: Date: 3 Nov 93 14:20:34 GMT Sender: news@cs.nott.ac.uk Followup-To: bionet.molbio.proteins Organization: Nottingham University, UK. Lines: 14 Nntp-Posting-Host: macfd Bionetters Anyone know where I can get antibodies to mammalian cytochrome c (horse heart preferably, but other commercially available cytochrome c would do), to the whole protein or to peptides derived from it? Thanks Fergus Doherty, dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH Tel: 602 709366 FAX 602 422225 Internet: mbxfd@unicorn.nott.ac.uk From owner-proteins@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!sangam!vikram!imtech!nitika From: nitika@imtech.ernet.in Newsgroups: bionet.molbio.proteins Subject: PERIPLASMIC PROTEIN ISOLATION. Message-ID: <8084@imtech.ernet.in> Date: 4 Nov 93 08:49:19 GMT Organization: Inst. of Microbial Technology, Chandigarh, India Lines: 7 Dear SCIENTISTS, I am isolating the periplasmic fraction of E.coli for release of an enzyme. Am presently usind osmotic shock treatment( sucrose shock) as well as combinee treatment with lysozyme. Both the methods are leading to the lysis of the cells without miantenance of intact spheroplasts.What could be the reason? Kindly suggest another method. Thank you. NITIKA THAPAR. From owner-proteins@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!math.ohio-state.edu!uwm.edu!fnnews.fnal.gov!nntp-server.caltech.edu!nntp-server.caltech.edu!rpm From: rpm@bach.wag.caltech.edu (Richard P. Muller) Newsgroups: bionet.molbio.proteins Subject: Crystallization of Membrane Proteins Message-ID: Date: 5 Nov 93 23:45:41 GMT Organization: Materials Simulations Center Lines: 27 NNTP-Posting-Host: bach.wag.caltech.edu I would be interested in hearing comments on a technique published recently in Science (262, p.734) to solubilize membrane proteins. This technique complexes the proteins with an alpha helix with a flat hydrophobic surface which interacts with the flat hydrophobic surfaces of the membrane proteins. Results were cited where 85% of bacteriorhodopsin and 60% of rhodopsin remained in solution in their native forms after 2 days. I'm interested in studying the chemistry of membrane proteins. One constant frustration is that few reliable crystal structures exist for membrane proteins. Because my background is quantum chemistry rather than protein crystallography, I'm unfamiliar with the subtleties involved in crystallizing proteins. How widely applicable is the technique used in this paper? Can I expect to see hundreds of crystal structures for membrane proteins flowing into the protein data base, or am I overestimating the importance of this work? To my eyes the technique seems to be of monumental impact. Thanks in advance for any help you can provide. -- ---------+---------+---------+---------+---------+---------+---------+ Richard P. Muller rpm@wag.caltech.edu Beckman Institute 139-74 (818) 395-2722 Office California Institute of Technology (818) 568-9484 Home Pasadena, California 91124 (818) 568-0918 FAX From owner-proteins@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!xlink.net!math.fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: PERIPLASMIC PROTEIN ISOLATION. Message-ID: <2bdh6hINNgpj@sat.ipp-garching.mpg.de> Date: 5 Nov 93 12:33:21 GMT References: <8084@imtech.ernet.in> Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 24 NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.1 PL8] nitika@imtech.ernet.in wrote: : I am isolating the periplasmic fraction of E.coli for release : of an enzyme. Am presently usind osmotic shock treatment( sucrose shock) : as well as combinee treatment with lysozyme. Both the methods are leading : to the lysis of the cells without miantenance of intact spheroplasts.What : could be the reason? Kindly suggest another method. Thank you. Two years ago I used the following method for the release of antibody Vl fragment expressed in E. coli periplasm: - Add 2 ml 1 mM EDTA in BBS (which is 160 mM NaCl, 200 mM boric acid, pH 8 with NaOH) per gram wet cell weight. - Stir the solution at least 30 minutes at 4 degrees Celcius. - Get rid of the spheroblasts by centrifugation (SS34, 20 min, 20000 rpm, 4C). - Get rid of membrane fragments etc. by sterilfiltration of the supernatant. Hope it helps, Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de, krasel@vms.biochem.mpg.de */ /* "People are DNA's way of making more DNA." (R. Dawkins/anonymous) */ From owner-proteins@net.bio.net Fri Nov 05 22:00:00 1993 Path: biosci!CS.Arizona.EDU!biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!vixen.cso.uiuc.edu!tsikar1.life.uiuc.edu!user From: David_Nunn@qms1.life.uiuc.edu (David Nunn) Newsgroups: bionet.molbio.proteins Subject: mutator strain or plasmid Message-ID: Date: 6 Nov 93 18:25:22 GMT Followup-To: bionet.molbio.proteins Organization: University of Illinois (Microbiology) Lines: 21 NNTP-Posting-Host: tsikar1.life.uiuc.edu Does anyone have a favorite mutator strain of E. coli or mutator plasmid that they have used successfully for random mutagenesis? I'd prefer a strain or compatible plasmid in which I could mutagenize sequences cloned in a broad host range plasmid (IncP1) and then be able to mobilize directly out of the strain into Pseudomonas (EC strain must be Tc-sensitive and auxotrophic) I've got either a bum strain of EC LE30 (mutD) or it just isn't doing the trick (mutagenesis-wise). I've been good and kept it on minimal media-only one transfer since receiving it-but it still is not working. Maybe just need a new strain? Any suggestions? David Nunn Department of Microbiology University of Illinois Urbana, IL 61801 (217) 333-6131 From owner-proteins@net.bio.net Fri Nov 05 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!vixen.cso.uiuc.edu!tsikar1.life.uiuc.edu!user From: David_Nunn@qms1.life.uiuc.edu (David Nunn) Newsgroups: bionet.molbio.proteins Subject: mutator strain or plasmid Message-ID: Date: 6 Nov 93 18:25:22 GMT Followup-To: bionet.molbio.proteins Organization: University of Illinois (Microbiology) Lines: 21 NNTP-Posting-Host: tsikar1.life.uiuc.edu Does anyone have a favorite mutator strain of E. coli or mutator plasmid that they have used successfully for random mutagenesis? I'd prefer a strain or compatible plasmid in which I could mutagenize sequences cloned in a broad host range plasmid (IncP1) and then be able to mobilize directly out of the strain into Pseudomonas (EC strain must be Tc-sensitive and auxotrophic) I've got either a bum strain of EC LE30 (mutD) or it just isn't doing the trick (mutagenesis-wise). I've been good and kept it on minimal media-only one transfer since receiving it-but it still is not working. Maybe just need a new strain? Any suggestions? David Nunn Department of Microbiology University of Illinois Urbana, IL 61801 (217) 333-6131 From owner-proteins@net.bio.net Sat Nov 06 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!math.ohio-state.edu!magnus.acs.ohio-state.edu!csn!ub!galileo.cc.rochester.edu!news From: mjhf@troi.cc.rochester.edu (M.J. Horsfall) Newsgroups: bionet.molbio.proteins Subject: Re: mutator strain or plasmid Message-ID: <1993Nov7.165234.20315@galileo.cc.rochester.edu> Date: 7 Nov 93 16:52:34 GMT References: Sender: news@galileo.cc.rochester.edu Organization: University of Rochester Computing Center Lines: 20 Nntp-Posting-Host: troi.cc.rochester.edu In David_Nunn@qms1.life.uiuc.edu (David Nunn) writes: > I've got either a bum strain of EC LE30 (mutD) or it just isn't doing the >trick (mutagenesis-wise). I've been good and kept it on minimal media-only >one transfer since receiving it-but it still is not working. Maybe just >need a new strain? In minimal media, mutD can increase the background mutation frequency some 500-fold, but in rich media (i.e., LB) this increase is something like 50,000-fold. Are you doing your mutagenesis in rich media? see Schaaper, 1988 (PNAS 85:8126); Schaaper and Radman (1989) EMBO J. 8:3511 Does this help? Hope so. Mike -- Michael Horsfall Ph.D. (( mjhf@troi.cc.rochester.edu Department of Biophysics )) Phone:(716)-275-8703 (Lab) University of Rochester 5'-GCAAGTCGGAG-3' Fax:(716)-275-6007(Dept) From owner-proteins@net.bio.net Sat Nov 06 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!agate!library.ucla.edu!csulb.edu!nic.csu.net!eis.CalState.EDU!jng From: jng@eis.calstate.edu (Joseph S. Ng) Newsgroups: bionet.molbio.proteins Subject: Elastin Search continues... Message-ID: Date: 8 Nov 93 05:54:26 GMT Organization: Calif State Univ/Electronic Information Services Lines: 12 Hi yall! Anyone out there have anything current on elastin? Yes? Mail me, we'll chat...No? Mail me anyway, and we'll chat... -- JoE Hougang is an address Ng, that is... Aukang is home __________________ *** Forever In HIS hands *** ### Through Him that constraineth me ### From owner-proteins@net.bio.net Sun Nov 07 22:00:00 1993 Path: biosci!bcm!TAMUTS.TAMU.EDU!cs.utexas.edu!uunet!yeshua.marcam.com!zip.eecs.umich.edu!umn.edu!mayonews.mayo.edu!RICKE@rcf.mayo.edu From: ricke@rcf.mayo.edu Newsgroups: bionet.molbio.proteins Subject: Forwarded post Message-ID: <2bmibp$pri@fermat.mayo.edu> Date: 8 Nov 93 22:48:25 GMT Reply-To: ricke@rcf.mayo.edu Organization: Research Computing Facility, Mayo Foundation, Rochester MN, USA Lines: 43 NNTP-Posting-Host: newton.mayo.edu Posting on behalf of M. G. Smyth & P. Gunning - D. Ricke From: SMTP%"gunnip@essex.ac.uk" 5-NOV-1993 08:02:52.46 Subj: Assistance required From: P Gunning Subject: Electroelution & Silver-Staining Q1. Can anyone tell me how to electroelute a protein ( MW 146 kDa,) from a urea gel ( 8M?) I've tried the usual electroelution methods with no success. Q2. The quickest silver staining method I know is the one by Heukeshoven and Dernick, 1985, electrophoresis 6:103.) I did try a rapid stain from Biorad but this method was not as good as the one by H&D. Can anyone recommend alternatives? Please reply to : smyth@afrc.ac.uk, because I don't have access to USENET/BIONET Thanks, Martin G. Smyth ________________________________________________________________________________ Martin G. Smyth AFRC Institute for Animal Health Compton Laboratory Berkshire RG16 0NN UK Ph: +44 635 578411 ext 541 ( Laboratory, Mon-Fri 0900 to 1700 GMT ) +44 635 578888 ( Laboratory, outside above hours ) +44 635 578137 ( Home ) e-mail: smyth@afrc.ac.uk ******************************************************************************** Many thanks, Paul Gunning Physics Department University of Essex Colchester CO4 3SQ From owner-proteins@net.bio.net Sun Nov 07 22:00:00 1993 Path: biosci!bcm!TAMUTS.TAMU.EDU!cs.utexas.edu!uunet!munnari.oz.au!metro!129!tony From: tony@atp.biochem.su.oz.au (Anthony Weiss) Newsgroups: bionet.molbio.proteins Subject: Re: Elastin Search continues... Message-ID: Date: 9 Nov 93 00:00:52 GMT References: Sender: news@ucc.su.OZ.AU Organization: Dept Biochem,Uni Sydney,NSW,Australia Lines: 46 Nntp-Posting-Host: eukaryote.biochem.su.oz.au X-Newsreader: VersaTerm Link v1.1.1 In Article , jng@eis.calstate.edu (Joseph S. Ng) wrote: >Hi yall! > >Anyone out there have anything current on elastin? Yes? Mail me, we'll >chat...No? Mail me anyway, and we'll chat... > >-- >JoE Hougang is an address >Ng, that is... Aukang is home > __________________ > > *** Forever In HIS hands *** > ### Through Him that constraineth me ### Joe OK, I'll take a bite at this. A search of Medline shows: 1 * elastin/ * 569 * * * * * * * * * * * * * * * * * * * * * * ******************* Ovid - Medline <1989 to November 1993> ********************* In other words, 569 references since 1989, just in the journals covered by Medline. Perhaps your librarian can help you out. ------------------------------------------------------------------ Anthony S Weiss, PhD email:asw@atp.biochem.su.oz.au Department of Biochemistry weiss@angis.su.oz.au University of Sydney NSW 2006 Telephone: +61 2 692 3464 Australia FAX: +61 2 692 4726 ------------------------------------------------------------------ From owner-proteins@net.bio.net Tue Nov 09 22:00:00 1993 Path: biosci!relay.the.net!SHAUN%JASON.DECNET From: SHAUN%JASON.DECNET@relay.the.net ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: Odd results with Proline in peptide synethsis Message-ID: <01H55NCUZ76Q0023ZW@nic.the.net> Date: 10 Nov 93 23:59:16 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 11 Dear All, We've recently gotten some seemingly bizarre results from synthesis of a peptide containing a number of prolyl residues. Specifically, we've found that the chain spontaneously cleaves during synthesis, but the cleavage is not at a proline :-? . Would some of you who might have seen effects somewhat like this e-mail us. We'd appreciate some discussion. Thanks a bunch. Cheers, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Wed Nov 10 22:00:00 1993 Path: biosci!daresbury!not-for-mail From: dmartin@crc.ac.uk (David Martin x3175) Newsgroups: bionet.molbio.proteins Subject: Architectural protein drawings Message-ID: <2bthh9$mnj@mserv1.dl.ac.uk> Date: 11 Nov 93 14:17:13 GMT Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Lines: 10 Original-To: proteins@dl.ac.uk I am trying to track down a package that will draw protein ribbons with arrows for beta sheet and cylinders for alpha helices. someone in my lab mentioned "MOLSCRIPT" but apart from that I can't find anything to give me the sort of pictures I want. Any help would be greatly appreciated. ....David Martin dmartin@crc.ac.uk From owner-proteins@net.bio.net Thu Nov 11 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!europa.eng.gtefsd.com!avdms8.msfc.nasa.gov!sol.ctr.columbia.edu!news.kei.com!newsstand.cit.cornell.edu!NewsWatcher!user From: fox@penelope.bio.cornell.edu (Kristin M. Fox) Newsgroups: bionet.molbio.proteins Subject: Re: Architectural protein drawings Message-ID: Date: 12 Nov 93 20:06:59 GMT References: <2bthh9$mnj@mserv1.dl.ac.uk> Sender: kf13@cornell.edu (Verified) Followup-To: bionet.molbio.proteins Distribution: bionet Organization: Cornell University Lines: 67 NNTP-Posting-Host: 132.236.171.92 In article , fox@penelope.bio.cornell.edu (Kristin M. Fox) wrote: > In article <2bthh9$mnj@mserv1.dl.ac.uk>, dmartin@crc.ac.uk (David Martin > x3175) wrote: > > > > > I am trying to track down a package that will draw protein ribbons with > > arrows for beta sheet and cylinders for alpha helices. someone in my > > lab mentioned "MOLSCRIPT" but apart from that I can't find anything to > > give me the sort of pictures I want. > > > > Any help would be greatly appreciated. > > > > ....David Martin > > dmartin@crc.ac.uk > > Are you looking for programs which produce printed outputs of > ribbon drawings or programs which display such diagrams on > computer graphics? > MOLSCRIPT is a gook program to produce black and white > outputs (color is available). > Some other programs which make ribbon drawings > MIDAS ribbons and space filling diagrams and much more > for computer graphics > INSIGHT a commercial package for graphics, pretty expensive > > If you are interested in any of these I can post the Email > addresses where you can obtain them. > > Kristin I have received several requests to post the ways of obtaining ribbon drawing programs, so here is the info I have: MOLSCRIPT Ref: J. Appl. Cryst. (1991) 24, 946-950. Can be obtained from the author Dr. Per J. Kraulis at Dept. of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1 QW England MIDASPLUS(TM) Ref: J. Mol. Graphics 6, 13-27 (1988). This was developed by the Computer Graphics Laboratory at UCSF, and is available from them at: Computer Graphics Laboratory School of Pharmacy University of California, San Francisco INSIGHT a commercial package available from BIOSYM Technologies, Inc. Eastern Regional Office 4 Century Drive Parsippany, NJ 07054 RIBBONS written by Mike Carson Email: carson@gtx.cmc.uab.edu carson@uabcmc.bitnet Good luck. Kristin From owner-proteins@net.bio.net Thu Nov 11 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!uwm.edu!rpi!sarah!psinntp!psinntp!newstand.syr.edu!lynx.cat.syr.edu!unaltuna From: unaltuna@lynx.cat.syr.edu (Mehmet Kemal Unaltuna) Newsgroups: bionet.molbio.proteins Subject: Protein Comparison Keywords: aminoacid composition Message-ID: <1993Nov12.005349.19959@newstand.syr.edu> Date: 12 Nov 93 05:53:48 GMT Organization: Syracuse University Lines: 9 Hello! I would like to know whether there is a computer program which can make a comparison of an AMINOACID COMPOSITION (not sequence) of an unknown protein with other known proteins to see whether it matches to another protein. I would appreciate any kind of information regarding this. Please send your response to: unaltunn@vax.cs.hscsyr.edu Thanks, Nihan Unaltuna. From owner-proteins@net.bio.net Thu Nov 11 22:00:00 1993 Path: biosci!summers From: summers@net.bio.net (Murray Summers) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Comparison Keywords: aminoacid composition Message-ID: Date: 12 Nov 93 14:48:13 GMT References: <1993Nov12.005349.19959@newstand.syr.edu> Organization: BIOSCI International Newsgroups for Biology Lines: 24 In article <1993Nov12.005349.19959@newstand.syr.edu> unaltuna@lynx.cat.syr.edu (Mehmet Kemal Unaltuna) writes: >Hello! I would like to know whether there is a computer program which can >make a comparison of an AMINOACID COMPOSITION (not sequence) of an unknown >protein with other known proteins to see whether it matches to another >protein. I would appreciate any kind of information regarding this. >Please send your response to: > > unaltunn@vax.cs.hscsyr.edu > > Thanks, Nihan Unaltuna. IntelliGenetics' program, PC/GENE(R), will do exactly this analysis. It is a DOS application that will run on any MS-DOS capable machine. Please contact us for more information. Murray R. Summers Senior Sales Representative IntelliGenetics, Inc. 700 E. El Camino Real, Suite 300 Mountain View, CA 94040 415-962-7300 800-876-9994 415-962-7302 (FAX) From owner-proteins@net.bio.net Thu Nov 11 22:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!howland.reston.ans.net!sol.ctr.columbia.edu!news.kei.com!newsstand.cit.cornell.edu!NewsWatcher!user From: fox@penelope.bio.cornell.edu (Kristin M. Fox) Newsgroups: bionet.molbio.proteins Subject: Re: Architectural protein drawings Message-ID: Date: 12 Nov 93 12:53:34 GMT References: <2bthh9$mnj@mserv1.dl.ac.uk> Sender: kf13@cornell.edu (Verified) Followup-To: bionet.molbio.proteins Distribution: bionet Organization: Cornell University Lines: 28 NNTP-Posting-Host: 132.236.171.92 In article <2bthh9$mnj@mserv1.dl.ac.uk>, dmartin@crc.ac.uk (David Martin x3175) wrote: > > I am trying to track down a package that will draw protein ribbons with > arrows for beta sheet and cylinders for alpha helices. someone in my > lab mentioned "MOLSCRIPT" but apart from that I can't find anything to > give me the sort of pictures I want. > > Any help would be greatly appreciated. > > ....David Martin > dmartin@crc.ac.uk Are you looking for programs which produce printed outputs of ribbon drawings or programs which display such diagrams on computer graphics? MOLSCRIPT is a gook program to produce black and white outputs (color is available). Some other programs which make ribbon drawings MIDAS ribbons and space filling diagrams and much more for computer graphics INSIGHT a commercial package for graphics, pretty expensive If you are interested in any of these I can post the Email addresses where you can obtain them. Kristin From owner-proteins@net.bio.net Fri Nov 12 22:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Comparison Keywords: aminoacid composition Message-ID: Date: 13 Nov 93 10:15:06 GMT References: <1993Nov12.005349.19959@newstand.syr.edu> Organization: BIOSCI International Newsgroups for Biology Lines: 11 I have issued a stern warning to all IntelliGenetics employees that a repeat of an incident like this will cost the offender their access to the news network. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-proteins@net.bio.net Fri Nov 12 22:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Comparison Keywords: aminoacid composition Message-ID: Date: 13 Nov 93 09:02:20 GMT References: <1993Nov12.005349.19959@newstand.syr.edu> Organization: BIOSCI International Newsgroups for Biology Lines: 16 Murray, Unfortunately I just had another incident from another commercial user earlier today along similar lines. PLEASE, commercial people should NOT respond to general questions on the newsgroups about software. If a question is raised specifically about a commercial product then it is O.K. to respond; otherwise, this forum is for discussion among users, not sellers. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-proteins@net.bio.net Fri Nov 12 22:00:00 1993 Path: biosci!parc!decwrl!ames!haven.umd.edu!news.umbc.edu!europa.eng.gtefsd.com!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!news From: wnowatzk@ucs.indiana.edu (Bill Nowatzke) Newsgroups: bionet.molbio.proteins Subject: Temp. staining of SDS PAGE gels prior to renaturation?? Message-ID: Date: 13 Nov 93 14:24:42 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: IU Chemistry Lines: 15 X-Xxdate: Sat, 13 Nov 93 09:26:40 GMT Nntp-Posting-Host: nowatzke-willia.tuliptree.indiana.edu X-Useragent: Nuntius v1.1.1d7 I have been trying to follow a R. Burgess paper in which enzymatic activity was regained in a protein purification after crushing the suspected protein band from the gel. The problem that I have been having is the transient staing of the gel to identify the approx Mr prior to cutting out the band. The original paper recommends ppt the SDS in the gel with 0.2M KCl for 5 min and then destaining with water for up to one hr. When I tried this the portion of the gel below the dye front became very white, implying ppt, but the portion of the gel above the dye front only became slight opaque and I could only see very faint bands of heavly overloaded lanes. I was made aware of another transient staining tech using a 0.3M copper soln which I tried on the same gel with poor results (although this gel would not fully destaing from the KCl treatment and that probably interfered). I would appreciate any advice/procedures that you may have successfully used or heard about. Thanks in advance! From owner-proteins@net.bio.net Fri Nov 12 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!paladin.american.edu!europa.eng.gtefsd.com!library.ucla.edu!agate!doc.ic.ac.uk!pipex!sunic!corax.udac.uu.se!rigel.bmc.uu.se!gerard From: gerard@rigel.bmc.uu.se (Gerard Kleijwegt) Newsgroups: bionet.molbio.proteins Subject: Re: Architectural protein drawings Message-ID: <2c1cin$8ht@corax.udac.uu.se> Date: 13 Nov 93 01:17:11 GMT References: <2bthh9$mnj@mserv1.dl.ac.uk> Distribution: bionet Organization: Uppsala University Lines: 33 NNTP-Posting-Host: rigel.bmc.uu.se In article , fox@penelope.bio.cornell.edu (Kristin M. Fox) writes: |> MOLSCRIPT |> Ref: J. Appl. Cryst. (1991) 24, 946-950. |> Can be obtained from the author Dr. Per J. Kraulis at |> Dept. of Biochemistry |> University of Cambridge (1) Per Kraulis left England some time ago and is back in Sweden (I ate a pizza with him last night so I should know ;-) His current e-mail address is: pjk@oyster.csb.ki.se (2) Addendum to the list of graphics programs: O (successor of FRODO; both written by Alwyn Jones); e-mail: alwyn@xray.bmc.uu.se --Gerard ****************************************************************** Gerard J. Kleywegt _____ Department of Molecular Biology | | / \ Biomedical Centre / \ --- | | University of Uppsala | | | | | | Uppsala | | | | | | SWEDEN | | \ / --- --- |____| E-mail: gerard@xray.bmc.uu.se ****************************************************************** "He's probably pining for the fiords ..." ****************************************************************** The opinions in this mail/post are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ****************************************************************** From owner-proteins@net.bio.net Sat Nov 13 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!spool.mu.edu!darwin.sura.net!fconvx.ncifcrf.gov!fcs260c!mack From: mack@fcs260c.ncifcrf.gov (Joe Mack) Newsgroups: bionet.molbio.proteins Subject: Re: Temp. staining of SDS PAGE gels prior to renaturation?? Message-ID: Date: 14 Nov 93 04:01:10 GMT References: Sender: usenet@ncifcrf.gov (C News) Organization: Frederick Cancer Research and Development Center Lines: 19 Nntp-Posting-Host: fcs260c.ncifcrf.gov In article Bill Nowatzke writes: >I have been trying to follow a R. Burgess paper in which enzymatic >activity was regained in a protein purification after crushing the >suspected protein band from the gel. The problem that I have been having >is the transient staing of the gel to identify the approx Mr prior to >cutting out the band. The original paper recommends ppt the SDS in the >gel with 0.2M KCl for 5 min and then destaining with water for up to one >hr. When I tried this the portion of the gel below the dye front became >very white, implying ppt, but the portion of the gel above the dye front >only became slight opaque and I could only see very faint bands of heavly >overloaded lanes. I was made aware of another transient staining tech >using a 0.3M copper soln which I tried on the same gel with poor results >(although this gel would not fully destaing from the KCl treatment and >that probably interfered). >I would appreciate any advice/procedures that you may have successfully >used or heard about. Thanks in advance! I've heard of people soaking the gel in KOAc, where the protein becomes opaque. Joe Mack mack@ncifcrf.gov From owner-proteins@net.bio.net Sat Nov 13 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!news.uiowa.edu!news.weeg.uiowa.edu!bbaker From: bbaker@news.weeg.uiowa.edu (Buck Dharma) Newsgroups: bionet.molbio.proteins Subject: How to get PDB entries via email? Message-ID: <1993Nov13.235323.25849@news.weeg.uiowa.edu> Date: 13 Nov 93 23:53:23 GMT Organization: University of Iowa, Iowa City, IA, USA Lines: 10 Hello.... Can someone tell me how to get 3D coords from the BNL protein data bank via email? I know the address is pdb@chm.chm.bnl.gov, but thats about it. Thanks... -brian From owner-proteins@net.bio.net Sun Nov 14 22:00:00 1993 Path: biosci!hubcap!darwin.sura.net!spool.mu.edu!sol.ctr.columbia.edu!caen!batcomputer!munnari.oz.au!metro!129!tony From: tony@atp.biochem.su.oz.au (Anthony Weiss) Newsgroups: bionet.molbio.proteins Subject: Automatic pipettors: which filters? Message-ID: Date: 15 Nov 93 07:54:40 GMT Sender: news@ucc.su.OZ.AU Followup-To: bionet.molbio.proteins Organization: Dept Biochem,Uni Sydney,NSW,Australia Lines: 17 Nntp-Posting-Host: eukaryote.biochem.su.oz.au X-Newsreader: VersaTerm Link v1.1.1 We want to get the right replacement filters for our handheld rechargeable automatic pipettors. You know the ones: stick in a glass or disposable plastic pipette for tissue culture work. We have been told we need some fancy double membrane system to protect the pump. What kind of filters do you use? ------------------------------------------------------------------ Anthony S Weiss, PhD email:asw@atp.biochem.su.oz.au Department of Biochemistry weiss@angis.su.oz.au University of Sydney NSW 2006 Telephone: +61 2 692 3464 Australia FAX: +61 2 692 4726 ------------------------------------------------------------------ From owner-proteins@net.bio.net Sun Nov 14 22:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!mnemosyne.cs.du.edu!nyx10!pfinerty From: pfinerty@nyx10.cs.du.edu (fork) Newsgroups: bionet.molbio.proteins Subject: Re: Temp. staining of SDS PAGE gels prior to renaturation?? Message-ID: <1993Nov16.031148.28573@mnemosyne.cs.du.edu> Date: 16 Nov 93 03:11:48 GMT References: Sender: usenet@mnemosyne.cs.du.edu (netnews admin account) Organization: Nyx, Public Access Unix at U. of Denver Math/CS dept. Lines: 16 X-Disclaimer: Nyx is a public access Unix system run by the University of Denver for the Denver community. The University has neither control over nor responsibility for the opinions of users. In article , Hiroki Morizono wrote: >My memory is pretty shaggy, but I've used >a dye for westerns which stained protein pink on nitrocellulose, >then wash off. Sorry I can't remember the name, but it may be found >in Maniatis or the Red Book. >Hiroki that pink dye is ponceau s. you can also use fast green FCF on nitro. that's what i usu use (the fast green). ciao, -patrick -- pjf -- biochem grad student teach me to fish and i'll steal your pole From owner-proteins@net.bio.net Sun Nov 14 22:00:00 1993 Path: biosci!bcm!avdms8.msfc.nasa.gov!europa.eng.gtefsd.com!uunet!news.claremont.edu!nntp-server.caltech.edu!nntp-server.caltech.edu!rpm From: rpm@bach.wag.caltech.edu (Richard P. Muller) Newsgroups: bionet.molbio.proteins Subject: "Bead" force fields for protein simulations Message-ID: Date: 15 Nov 93 21:55:14 GMT Distribution: bionet Organization: Materials Simulations Center Lines: 20 NNTP-Posting-Host: bach.wag.caltech.edu I am looking for references or a good review article on "bead" models for protein simulations. By a bead model I mean one in which an entire amino acid residue is represented in the force field as a single particle. Thanks in advance for any help you can provide. Rick P.S. For those of you who requested a summary of my recent posting on the membrane protein crystallization method in Science, I am putting together the summary now and will post shortly. -- ---------+---------+---------+---------+---------+---------+---------+ Richard P. Muller rpm@wag.caltech.edu Beckman Institute 139-74 (818) 395-2722 Office California Institute of Technology (818) 568-9484 Home Pasadena, California 91125 (818) 585-0918 FAX From owner-proteins@net.bio.net Sun Nov 14 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!torn!nott!nrcnet0!nrcbsa!phi From: phi@nrcbsa.bio.nrc.ca (Dr. Barry Phipps) Newsgroups: bionet.molbio.proteins Subject: Re: Architectural protein drawings Message-ID: <1993Nov15.123829.24294@nrcnet0.nrc.ca> Date: 15 Nov 93 12:38:29 GMT References: <2bthh9$mnj@mserv1.dl.ac.uk> Sender: root@nrcnet0.nrc.ca (Operator) Distribution: bionet Organization: National Research Council, Ottawa, Canada Lines: 29 Nntp-Posting-Host: 132.246.240.13 X-Newsreader: TIN [version 1.1 PL8] David Martin x3175 (dmartin@crc.ac.uk) wrote: : I am trying to track down a package that will draw protein ribbons with : arrows for beta sheet and cylinders for alpha helices. someone in my : lab mentioned "MOLSCRIPT" but apart from that I can't find anything to : give me the sort of pictures I want. : Any help would be greatly appreciated. : ....David Martin : dmartin@crc.ac.uk Hi David, Another excellent program is SETOR written by Steve Evans at the Institute for Biological Sciences, NRC, Canada. I think it runs only on SGI/IRIX at the moment (I could be wrong). It is available to academic/government organizations for free or a nominal fee. Contact: Dr. Steve Evans Institute for Biological Sciences National Research Council M54, Montreal Road Ottawa, Ontario CANADA K1A 0R6 Phone 613-990-0858 E-mail elmo@nrcbsa.bio.nrc.ca Barry Phipps From owner-proteins@net.bio.net Sun Nov 14 22:00:00 1993 Path: biosci!BRAGG1.BCHS.UH.EDU!EVA From: EVA@BRAGG1.BCHS.UH.EDU (Eva Istvan) Newsgroups: bionet.molbio.proteins Subject: (none) Message-ID: <931115002106.20a002df@BRAGG1.BCHS.UH.EDU> Date: 15 Nov 93 06:21:06 GMT Sender: news@net.bio.net Distribution: bionet Lines: 1 help From owner-proteins@net.bio.net Sun Nov 14 22:00:00 1993 Path: biosci!hubcap!darwin.sura.net!howland.reston.ans.net!xlink.net!fauern!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Temp. staining of SDS PAGE gels prior to renaturation?? Message-ID: <2c7gltINNqi1@sat.ipp-garching.mpg.de> Date: 15 Nov 93 09:03:57 GMT References: Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 16 NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.1 PL8] Hiroki Morizono (hiroki@limerick.cbs.umn.edu) wrote: : My memory is pretty shaggy, but I've used : a dye for westerns which stained protein pink on nitrocellulose, : then wash off. Sorry I can't remember the name, but it may be found : in Maniatis or the Red Book. This is probably Ponceau Red. For other advice how to stain blots, see for example "Gel electrophoresis of proteins: A practical approach". This does not cover the topic of the subject line, however. --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3975 */ /* "People are DNA's way of making more DNA." (R. Dawkins/anonymous) */ From owner-proteins@net.bio.net Sun Nov 14 22:00:00 1993 Path: biosci!hubcap!darwin.sura.net!spool.mu.edu!umn.edu!limerick.cbs.umn.edu!hiroki From: hiroki@limerick.cbs.umn.edu (Hiroki Morizono) Newsgroups: bionet.molbio.proteins Subject: Re: Temp. staining of SDS PAGE gels prior to renaturation?? Message-ID: Date: 15 Nov 93 08:01:40 GMT References: Sender: news@news2.cis.umn.edu (Usenet News Administration) Reply-To: hiroki@limerick.cbs.umn.edu Organization: University of Minnesota, Twin Cities Lines: 5 Nntp-Posting-Host: limerick.cbs.umn.edu X-Newsreader: Tin 1.1 PL5 My memory is pretty shaggy, but I've used a dye for westerns which stained protein pink on nitrocellulose, then wash off. Sorry I can't remember the name, but it may be found in Maniatis or the Red Book. Hiroki From owner-proteins@net.bio.net Mon Nov 15 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!decwrl!decwrl!waikato!canterbury.ac.nz!chmeds.ac.nz!mkennedy From: mkennedy@chmeds.ac.nz (Martin Kennedy) Newsgroups: bionet.molbio.proteins Subject: Re: LB or not LB? Message-ID: <1993Nov17.150534.357@chmeds.ac.nz> Date: 17 Nov 93 03:05:34 GMT References: <2cb1oq$oho@mserv1.dl.ac.uk> Distribution: bionet Lines: 30 In article <2cb1oq$oho@mserv1.dl.ac.uk>, JAB5@VAX.YORK.AC.UK writes: > There seems to be 2 recipies for "LB" in the literature. > My recollection is that it stood for Luria-Bertani Broth and > contained 5g NaCl per litre. > Modern recipies have 10g NaCl per litre. Although in some > applications, I'm sure it has little effect, I have found > that for high expression levels of some proteins the high > NaCl medium leads to insolubility problems. It has been > Jim Brannigan Just to add to the confusion, and to confirm that the problem has been around a while, an old but classic text lists two recipes on p433: one is for LB Medium with 10g NaCl/L, the other is for Luria Broth at 0.5g/L. The text is: Miller, J.H. (1972) Experiments in molecular genetics I also remember reading in a similarly ancient text that there were "several" recipes for LB; some of the confusion may have arisen from confusion of the above recipes. -- Cheers, Martin NNNN NN Martin A Kennedy (E-mail = mkennedy@chmeds.ac.nz) ZZZZZZZ NN NN NN Cytogenetic and Molecular Oncology Unit ZZZ NN NN NN Christchurch School of Medicine ZZZ NN NNNN Christchurch, New Zealand ZZZZZZZ Phone (64-3)364-0880 Fax (64-3)364-0750 From owner-proteins@net.bio.net Mon Nov 15 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!news.claremont.edu!nntp-server.caltech.edu!nntp-server.caltech.edu!rpm From: rpm@bach.wag.caltech.edu (Richard P. Muller) Newsgroups: bionet.molbio.proteins Subject: Summary -- Membrane protein crystallization technique Message-ID: Date: 16 Nov 93 23:20:42 GMT Distribution: bionet Organization: Materials Simulations Center Lines: 162 NNTP-Posting-Host: bach.wag.caltech.edu Schafmeister et al. (Science 262:734 (1993)) recently published a method for solubilizing membrane proteins by complexing them with alpha helices with one flat hydrophobic side to interact with the transmembrane protein. Two weeks ago I posted a message to bionet.molbio.proteins asking for comments on the procedure, and whether such a method was general enough so that crystal structures of a large number of membrane proteins would soon be available. What follows is a summary of the responses I received. Thanks to everyone who took the time. ------------------------------ [This is from one of the authors of the paper...] From schaf@cgl.ucsf.edu Wed Nov 10 07:20:49 1993 Date: Mon, 8 Nov 1993 19:25:30 -0800 From: schaf@cgl.ucsf.edu To: rpm@wag.caltech.edu Subject: Re: Crystallization of Membrane Proteins Newsgroups: bionet.molbio.proteins References: I think it's a "wait and see" kind of thing. We are still developing the technique, we haven't been able to set up any crystallization trials yet. Currently we are trying to develop peptides that form stable peptide/protein aggregates in order to set up crystal trials. We have a peptide that is considerably better than the one described in the paper but it still isn't good enough, meaning that at a peptide/BR ratio of 400:1 aggregation stops and I get an essentially monomeric species with a molecular weight of ~85kD (one BR ~20 peptides) but that is too much peptide to concentrate down for crystallization trials. .Chris. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Christian E.A.F. Schafmeister Biophysics graduate student University of California, San Francisco UUCP: ucbvax!ucsfcgl!schaf "Biophysics . . . THE future." INTERNET: schaf@cgl.ucsf.edu ------------------------------------ From krasel@alf.biochem.mpg.de Wed Nov 10 07:20:38 1993 Date: Sat, 6 Nov 1993 12:24:06 +0100 From: krasel@alf.biochem.mpg.de (Cornelius Krasel) To: rpm@wag.caltech.edu (Richard P. Muller) Subject: Re: Crystallization of Membrane Proteins Newsgroups: bionet.molbio.proteins X-Newsreader: TIN [version 1.1 PL8] [stuff deleted] What is IMHO funny with this technique is that the authors were not able to maintain PhoE in solution. PhoE has a distinctivly different fold from most transmembrane proteins because it forms a beta barrel in the membrane. Thanks for your help, Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de, krasel@vms.biochem.mpg.de */ /* "People are DNA's way of making more DNA." (R. Dawkins/anonymous) */ ------------------- When I responded to Dr. Krassel that perhaps the alpha helices could not complex with the beta barrel, and that perhaps the Schafmeister method would only work for alpha helical bundles, he responded... ------------------- From krasel@alf.biochem.mpg.de Wed Nov 10 07:20:42 1993 Date: Sun, 7 Nov 1993 13:48:02 +0100 From: krasel@alf.biochem.mpg.de (Cornelius Krasel) To: krasel@wag.caltech.edu, rpm@wag.caltech.edu Subject: Re: Crystallization of Membrane Proteins I am not very familiar with the theoretical foundations of protein interaction, but it seems possible to me that PD1 can interact better with alpha helices by forming part of an alpha-helical bundle (as it forms a bundle with itself in the crystal structure). Since PD1 was designed to form a flat hydrophobic surface this surprises me a bit: interhelical interactions are usually accounted for by interactions between the bulges and grooves of helices. As long as the structure of PD1 is not deposited one can probably only speculate if there is also a bulge-groove interaction in the four helix bundle. A transmembrane beta barrel might possibly form another pattern of grooves on its surface. One could control this by looking at the published structure for OmpF which is said to resemble PhoE most. There is also the structure for the porin from Rhodobacter capsulatus which forms a beta- barrel as well. Just speculating, Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de, krasel@vms.biochem.mpg.de */ /* "People are DNA's way of making more DNA." (R. Dawkins/anonymous) */ ---------------------- From mack@ncifcrf.gov Mon Nov 15 07:58:47 1993 Date: Thu, 11 Nov 93 10:07:42 EST From: mack@ncifcrf.gov To: rpm@wag.caltech.edu Subject: Re: Crystallization of Membrane Proteins Newsgroups: bionet.molbio.proteins In-Reply-To: Organization: Frederick Cancer Research and Development Center Cc: Dear Pat, There's someone doing lipid layer 2-D crystallisation in Pat Brown's lab at Stanford. They might be able to give you more info. DOn't have ph# or name sorry. Just call Pat. Joe Mack mack@ncifcrf.gov --------------- From SHAUN%JASON.DECNET@relay.the.net Mon Nov 15 07:59:16 1993 Date: 11 Nov 1993 19:04:41 -0600 (CST) From: "Shaun D. Black" Subject: Re: Crystallization of Membrane Proteins To: rpm@wag.caltech.edu X-Envelope-To: rpm@bach.wag.caltech.edu X-Vms-To: THENIC::IN%"rpm@bach.wag.caltech.edu" Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT I just got my Science and read the article that you referred to. It is a very interesting paper and has promise on a number of fronts, in my estimate. Whether or not it pays off in the area of crystallization of membrane proteins is another question, but it is a real possibility. As far as I know, this is the only investigation of its kind. We ought to keep our eyes open for other studies that follow their ideas. Cheers, =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | Bitnet: shaun%jason.decnet@thenic.bitnet = = UT Health Center, Tyler | Phone: (903)877-2806 FAX: (903)877-7558 = = Tyler, TX 75710-2003 | B-) (Start every day with a smile...) = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -------- I didn't include people who requested that I post a summary. Thanks to everyone who took the time to respond. -- ---------+---------+---------+---------+---------+---------+---------+ Richard P. Muller rpm@wag.caltech.edu Beckman Institute 139-74 (818) 395-2722 Office California Institute of Technology (818) 568-9484 Home Pasadena, California 91125 (818) 585-0918 FAX From owner-proteins@net.bio.net Mon Nov 15 22:00:00 1993 Path: biosci!RCF.MAYO.EDU!MORBECK From: MORBECK@RCF.MAYO.EDU Newsgroups: bionet.molbio.proteins Subject: hydropathically complementary sequence program? Message-ID: <931116163058.2020a749@rcf.mayo.edu> Date: 16 Nov 93 22:30:58 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 14 I just found a reference that gives information about a program called AMINOMAT. The program was designed to select an ideal complementary sequence for a peptide based on hydropathy. The paper was out of G. Fassina's lab in Milan, Italy and appeared in Arch. Bioch. Biophys. in July, '92. The paper states that the program would be available upon request soon. Can someone give me more info about this and how to obtain it? Also, are there any other programs available that do a similar thing? Thanks in advance. Dean E. Morbeck Department of Biochemistry Mayo Clinic Morbeck@Mayo.edu From owner-proteins@net.bio.net Mon Nov 15 22:00:00 1993 Path: biosci!daresbury!not-for-mail From: JAB5@VAX.YORK.AC.UK Newsgroups: bionet.molbio.proteins Subject: LB or not LB? Message-ID: <2cb1oq$oho@mserv1.dl.ac.uk> Date: 16 Nov 93 17:14:02 GMT Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Lines: 20 Original-To: PROTEINS@dl.AC.UK Dear colleagues, There seems to be 2 recipies for "LB" in the literature. My recollection is that it stood for Luria-Bertani Broth and contained 5g NaCl per litre. Modern recipies have 10g NaCl per litre. Although in some applications, I'm sure it has little effect, I have found that for high expression levels of some proteins the high NaCl medium leads to insolubility problems. It has been such a problem to me that our lab now affectionately calls my formulation OGB ("Old Git Broth") as it seems that only us "elder" molbiologists remember it!! Does anyone have a clue if I'm right and where the higher NaCl recipie first came to being?? Thanks and Beware, Jim Brannigan Chemistry Dept University of York York YO1 5DD UK From owner-proteins@net.bio.net Mon Nov 15 22:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uknet!gdt!bsspak From: bsspak@midge.bath.ac.uk (P A Keller) Newsgroups: bionet.molbio.proteins Subject: Re: How to get PDB entries via email? Message-ID: Date: 16 Nov 93 10:31:06 GMT References: <1993Nov13.235323.25849@news.weeg.uiowa.edu> Reply-To: P.A.Keller@bath.ac.uk Organization: Department of Biology and Biochemistry, University of Bath, UK Lines: 54 In the referenced article, bbaker@news.weeg.uiowa.edu (Buck Dharma) writes: > >Hello.... > >Can someone tell me how to get 3D coords from the BNL protein data bank >via email? I know the address is pdb@chm.chm.bnl.gov, but thats about it. > >Thanks... > > -brian > Funny you should ask this: I have been trying to find out the same for a colleague, without much success. In principle, if you send the message send info bbaker@news.weeg.uiowa.edu to fileserv@pb1.pdb.bnl.gov, you should get back all the information you need, but in practice this service does not seem to be well maintained. It may have improved since I last tried it, but I never succeeded in getting any information on the fileserver's command set in this way, so it seemed fairly useless to me. The simple answer is: use anonymous ftp or Gopher to pdb.pdb.bnl.gov in preference to e-mail, if you can. If you must use e-mail, the best way is to use an e-mail ftp server (i.e. you send an e-mail message to the server, which does the anonymous ftp for you, and e-mails the results back). For information on one such service, send the message: help quit with a blank subject line to ftpmail@decwrl.del.com . In this way, you can 'dir' the top-level directory at BNL, and find out what files contain information about the contents of the data bank. I can only assume that Brookhaven are having severe long-term problems with their e-mail server - enquiries which I made over a month ago about this have not been answered yet, and the response from the e-mail server is very slow, with enquiries often disappearing completely. So far, I have not succeeded in retrieving a single coordinate file by using Brookhaven's own fileserver. Good luck, Peter. ======================================================================== Peter Keller. Tel.: (+44/0)225 826826 x 4302 Dept. of Biochemistry, Fax.: (+44/0)225 826449 University of Bath, Email: P.A.Keller@bath.ac.uk (Internet) Bath, BA2 7AY, UK. P.A.Keller%bath.ac.uk@UKACRL (Bitnet) ======================================================================== I can no longer phone out ... E-mail is my lifeline ... Please use it! ======================================================================== From owner-proteins@net.bio.net Mon Nov 15 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!pipex!zaphod.crihan.fr!univ-lyon1.fr!ghost.dsi.unimi.it!genes!pedraza From: pedraza@genes.icgeb.trieste.it (Alicia Pedraza) Newsgroups: bionet.molbio.proteins Subject: plasmid expressing chaperones Keywords: chaperones Message-ID: <1993Nov16.091205.14880@genes.icgeb.trieste.it> Date: 16 Nov 93 09:12:05 GMT Organization: ICGEB Lines: 13 Hi! Does anyone know from where I can get a plasmid expressing HSC 70 and / or HSP 70 chaperones (for eucaryotes) ? Thanks. Alicia -- Alicia Pedraza | Fax: +39-40-226555 Molecular Immunology Group ICGEB | Padriciano 99, 34012 Trieste, ITALY | E-mail: pedraza@icgeb.trieste.it From owner-proteins@net.bio.net Mon Nov 15 22:00:00 1993 Path: biosci!relay.the.net!SHAUN%JASON.DECNET From: SHAUN%JASON.DECNET@relay.the.net ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: Summary: HPLC gel-filtration of proteins Message-ID: <01H5EG8Q0LQA0007UX@nic.the.net> Date: 17 Nov 93 06:09:19 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 78 Dear Colleagues, My original post was: >I have occasion to do a series of molecular weight determinations of >proteins in the presence and absence of detergents. Years ago I used >ToyoSoda PW and SW silica-based columns; the PW bound all of my proteins, >and the SW worked fairly well. My question is: what is your experience >with HPLC gel filtration columns for proteins presently? What/which are >best? Protein binding? Silica vs plastic polymers? Effects of detergent? Replies received: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Carl Weatherell (weathere@emr1.emr.ca) I am presently examining secondary retention effects on ToyaSodaPW and SW columns using factorial experimental design... What I have found thus far W.R.T. the 2 stationary phases are, briefly: -efficiency of the PW phase is much larger than that of the SW phase -ion exclusion effects on the SW phase are larger than that of the PW -the PW phase is extremely hydrophobic... complete retention of all denatured proteins is observed at 0.4M NaCl in 3.5mM SDS, pH=4 or 7 -both phases adsorb SDS -a good eluent to achieve optimum resolution with no protein binding to the stationary phase consists of 3.5mM SDS, pH=4 (50mM PO4 buffer with 0.1M NaCl) =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Pier Carlo Montecucchi (100143.765@compuserve.com) I have used TSK 3000 SW Spherogel column (600 x 7.5 mm I.D.) from Beckman. Eluent: 0.01% acetic acid Flow Rate: 1 ml/min Detection: 220nm Sometimes the data obtained by GP-HPLC should be treated with caution as a consequence (i) of aspecific interactions between the solutes and the stationary phase and (ii) of the effect of the mobile phase (pH value and salt concentration) on the tertiary structure of the molecules. Using this system, I was able to determine the MW of a small molecule (MW 1000) and to separate this low molecular weight immunoregulin from salts. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Ann C. Rice (acrice@gems.vcu.edu) I am using the Phenomenex SEC 2000 HPLC gel filtration column presently and think it works well. You can go down to pH 2.5 and it will take 6M guanidine and 0.05% SDS. They make 3 sizes depending on the mwt range of the proteins you want to characterize. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Further investigation of various columns available netted: --------------------------------------------------------------------------- Manufacturer Column Dimensions Phase Dia Pores Avg N/m Range $ ------------- ------------ ----------- --------- ------ -------- ----- --- ToyoHaas TSK3000SWXL 7.8x300 mm 5u 250A 25,800 -500K 750 " TSK3000SW 7.5x300 mm 10u 250A 8,500 -500K 700 Beckman Ultrasphero- 7.5x300 mm 5u 245A 24,400 -700K 620 gel 3000 Phenomenex BioSep-SEC- 7.8x300 mm 5u 290A 21,200 -700K 595 S3000 Rainin Hydropore- 4.6x250 mm 5u 300A 11,100 -1M 700 5-SEC --------------------------------------------------------------------------- All the columns were prepared from silica; the Phenomenex and Rainin are "hydrophilic bonded silica", and the Beckman claims a "proprietary" silica type. The TSK3000SWXL had the highest plate count and also resolved large proteins the best of all the columns surveyed. Plates/meter were obtained by averaging the plates measured for 3-4 proteins in test chromatograms; proteins were typically thyroglobulin, ovalbumin, cytochrome c in each case. Recoveries were compared between the TSK3000SWXL and BioSep-SEC-S3000 columns; the TSK showed somewhat better recoveries, especially for large molecular weight proteins. Hope this is helpful. Best regards, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Tue Nov 16 22:00:00 1993 Path: biosci!SFSUVAX1.SFSU.EDU!rbernste From: rbernste@SFSUVAX1.SFSU.EDU (RLB) Newsgroups: bionet.molbio.proteins Subject: How to say Voet? Message-ID: Date: 17 Nov 93 10:44:11 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 Dear ProtNetters: Can anyone say for certain exactly how the authors of the biochemistry text, Voet and Voet, pronounce their last name? Regards, Rick Bernstein From owner-proteins@net.bio.net Tue Nov 16 22:00:00 1993 Path: biosci!MVAX.WISTAR.UPENN.EDU!WILLARD From: WILLARD@MVAX.WISTAR.UPENN.EDU Newsgroups: bionet.molbio.proteins Subject: How to say Voet. Message-ID: <01H5F5N05GAOBB1HC5@WISTB.WISTAR.UPENN.EDU> Date: 17 Nov 93 16:37:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 7 Yes. I had Don Voet for a biological macromolecules/enzymology course. You pronounce it with 2 syllables: VO (rhymes with GO) and IT (Rhymes with sh...), well you get the picture. So VO-IT (spelled Voet). Rob University of Pennsylvania Dept. of Chemistry/Wistar Institute From owner-proteins@net.bio.net Tue Nov 16 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!pipex!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: pronounciation of Voet Message-ID: <1993Nov17.163026.4679@infodev.cam.ac.uk> Date: 17 Nov 93 16:30:26 GMT References: <9311171433.AA27392@emoryu1.cc.emory.edu> Sender: news@infodev.cam.ac.uk (USENET news) Distribution: bionet Organization: U of Cambridge, England Lines: 18 Nntp-Posting-Host: mbfs.bio.cam.ac.uk genekdw@EMORYU1.CC.EMORY.EDU ("Keith D. Wilkinson") writes: >> Can anyone say for certain exactly how the authors of the biochemistry >> text, Voet and Voet, pronounce their last name? >> Regards, Rick Bernstein >"Vote", as in everyone should. One of my professors (who knows the Voets) always pronounced it with two syllables: "VOH-eht". -- Steven E. Brenner | Department of Biochemistry S.E.Brenner@bioc.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 Tue Nov 16 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!noc.near.net!delphi.bc.edu!bcvms.bc.edu!markmano From: markmano@bcvms.bc.edu Newsgroups: bionet.molbio.proteins Subject: Combinatorial regulation: an island? Message-ID: <1993Nov17.214652.1@bcvms.bc.edu> Date: 18 Nov 93 01:46:52 GMT Organization: Boston College Lines: 32 NNTP-Posting-Host: bcvax2.bc.edu Can any one take me out of the following island: I have got interested in the following "combinatorial- regulation" : Protein A as a homodimer has a certain function. it can form a heterodimer with a homologous, but not identical protein B, but A-B heterodimer has a different function. I have started looking throu the "protein world map" using homology as my compass, everytime I'll find a protein that have the same mechanism I'll go to proteins homologous to it, but I'll also look at homology to other domains of that protein. I have so far to my surprise (and dissapointment??) found my-self in an island. I have found many proteins that do that, but only from four structural motifs (Leu-Zipper ; Adhesion molecule motifs (Ig and FN3, and probably the end domains of Intermediate filaments) All These are easy to connect in terms of finding "evolutionary bridges" (proteins that have both domains are for my search an evolutionary bridge). can any one take me to an "island" further away - I would especialy be interested in an *enzyme* that have this type of regulation. I personally believe that I am looking for the diamond where the light is, but there might be (should be) more of them where its dark. Thanks Ofer. Ofer Markman Boston College, Merkert Chemistry Center Chestnut Hill MA 02167 E-mail:markman@bcchem.bc.edu markmano@bcvms.bc.edu From owner-proteins@net.bio.net Tue Nov 16 22:00:00 1993 Path: biosci!EMORYU1.CC.EMORY.EDU!genekdw From: genekdw@EMORYU1.CC.EMORY.EDU ("Keith D. Wilkinson") Newsgroups: bionet.molbio.proteins Subject: Re:pronounciation of Voet Message-ID: <9311171433.AA27392@emoryu1.cc.emory.edu> Date: 17 Nov 93 14:33:36 GMT Sender: daemon@net.bio.net Reply-To: "Keith D. Wilkinson" Distribution: bionet Lines: 41 In message <9311171331.AA16146@emoryu1.cc.emory.edu> writes: > @CMSA.BERKELEY.EDU:BIOSCI-REQUEST@NET.BIO.NET> > Received: from cmsa.Berkeley.EDU (NJE origin MAILER@UCBCMSA) by > EMUVM1.CC.EMORY.EDU (LMail V1.1d/1.7f) with BSMTP id 0091; Wed, > 17 Nov 1993 08:26:07 -0500 > Received: from CMSA.BERKELEY.EDU by cmsa.Berkeley.EDU (Mailer R2.08 R208004) > with BSMTP id 6013; Wed, 17 Nov 93 05:26:21 PST > Received: from UCBCMSA (NJE origin SMTPSERV@UCBCMSA) by CMSA.BERKELEY.EDU > (LMail V1.1d/1.7f) with BSMTP id 8195; Wed, 17 Nov 1993 05:26:22 -0800 > Received: from net.bio.net by cmsa.Berkeley.EDU (IBM VM SMTP V2R2) with TCP; > Wed, 17 Nov 93 05:26:21 PST > Received: by net.bio.net (5.65/IG-2.0) > id AA18109; Wed, 17 Nov 93 02:46:20 -0800 > Received: from sfsuvax1.sfsu.edu by net.bio.net (5.65/IG-2.0) with SMTP > id AA18094; Wed, 17 Nov 93 02:46:08 -0800 > Received: by sfsuvax1.sfsu.edu (5.57/Ultrix2.4-C) > id AA07192; Wed, 17 Nov 93 02:46:08 -0800 > Date: Wed, 17 Nov 1993 02:44:11 -0800 (PST) > From: RLB > Subject: How to say Voet? > To: proteins@net.bio.net > Message-Id: > Mime-Version: 1.0 > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Dear ProtNetters: > > Can anyone say for certain exactly how the authors of the biochemistry > text, Voet and Voet, pronounce their last name? > > Regards, Rick Bernstein > > > > :: How to say Voet? "Vote", as in everyone should. From owner-proteins@net.bio.net Wed Nov 17 22:00:00 1993 Path: biosci!news.cs.umb.edu!hsdndev!howland.reston.ans.net!pipex!sunic!corax.udac.uu.se!zeta.bmc.uu.se!daresbury!bioftp.unibas.ch!rc1!vub!pjdebles From: pjdebles@vub.vub.ac.be (Pieter De Bleser) Newsgroups: bionet.molbio.proteins Subject: pI of TGF-beta Message-ID: <3559@rc1.vub.ac.be> Date: 18 Nov 93 08:43:06 GMT Sender: news@rc1.vub.ac.be Organization: Vrije Universiteit Brussel Faculteit Geneeskunde en Farmacie Lines: 17 X-Newsreader: TIN [version 1.1 PL9] Dear bionetters, Does anyone know the pI of TGF-beta, or has a pointer to where I can find this data? Thanks, -- ____________________________________________________________________________ Pieter De Bleser Laboratory for Cell Biology and Histology, Free University of Brussels, Laarbeeklaan 103, B -1090 Brussels, Belgium Phone:+32-2-4774407; Fax:+32-2-4774000; Email: pjdebles@cyto.vub.ac.be ____________________________________________________________________________ From owner-proteins@net.bio.net Wed Nov 17 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!usc!yeshua.marcam.com!charnel!OAVAX.CSUCHICO.EDU!BMCNULTY From: bmcnulty@OAVAX.CSUCHICO.EDU (bob) Newsgroups: bionet.neuroscience,bionet.molbio.proteins,bionet.molbio.methds-reagnts,bionet.molbio.hiv,bionet.drosophila,bionet.general Subject: I NEED HELP Message-ID: <2cf4dqINNkn4@charnel.ecst.csuchico.edu> Date: 18 Nov 93 06:23:54 GMT Reply-To: bmcnulty@OAVAX.CSUCHICO.EDU Organization: California State University, Chico Lines: 64 Xref: biosci bionet.neuroscience:2047 bionet.molbio.proteins:1054 bionet.molbio.methds-reagnts:9173 bionet.molbio.hiv:259 bionet.drosophila:160 bionet.general:6580 NNTP-Posting-Host: oavax.csuchico.edu I am the manager of a stockroom/lab facility which is responsible for servicing the needs (chemical, reagents, and equipment) of a Biology department in a small university (14 - 16000 students). The facility I manage supplies these items for over 80 laboratory class sections per week with only 3 personnel while at the same time managing a service/checkout window which is open for 6 hours each day (9:00am 'til 3:00pm). The department has 20 PHD faculty and several part time MS instructors or TAs. I seem to have found myself in the middle of a rather large debate with one faculty member who insists that he/she have unlimited access (a key and pass code) to the area I manage (which is currently under alarm and houses well over $1,000,000 worth of inventory) because she/he needs supplies to do unfunded research at hours other than those when the facility I manage is open. The other faculty are either supported by grants or are not actively involved in research. IN AN EFFORT TO SOLVE THIS DILEMMA I NEED YOUR HELP!!! I SEEK ONLY DATA. If you would be so kind.... please answer the following questions and e- mail them to me directly so I may scientifically support my position. I WILL USE NO NAMES OR ADDRESS IN MY REPORT, JUST THE DATA I COLLECT FROM THE QUESTIONS BELOW!!! ********************* CUT HERE ***************************************** With what academic institution are you affiliated? _______________________________ Do faculty at your institution have a key or unlimited access to the main stockroom/supply/support facility? __________________________________ *************************************************************************** Thank you for your time and the effort! BMCNULTY@OAVAX.CSUCHICO.EDU //////// "Adapt, Migrate, or Die" ( ) \ @ @ / BMCNULTY@OAVAX.CSUCHICO.EDU -------w---U---w---- Bob McNulty, CA. STATE UNIV., CHICO From owner-proteins@net.bio.net Wed Nov 17 22:00:00 1993 Path: biosci!CMU.UNIGE.CH!BAIROCH From: BAIROCH@CMU.UNIGE.CH (Amos Bairoch) Newsgroups: bionet.molbio.proteins Subject: Release notes of SWISS-PROT 27 / PROSITE 11 Message-ID: <01H5H5EGJCAQ000SL4@cmu.unige.ch> Date: 18 Nov 93 21:52:53 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 915 SWISS-PROT RELEASE 27.0 RELEASE NOTES 1. INTRODUCTION 1.1 Evolution Release 27.0 of SWISS-PROT contains 33329 sequence entries, comprising 11'484'420 amino acids abstracted from 32314 references. This represents an increase of 5.6% over release 26. The recent growth of the data bank is summarized below. Release Date Number of entries Nb of amino acids 3.0 11/86 4160 969 641 4.0 04/87 4387 1 036 010 5.0 09/87 5205 1 327 683 6.0 01/88 6102 1 653 982 7.0 04/88 6821 1 885 771 8.0 08/88 7724 2 224 465 9.0 11/88 8702 2 498 140 10.0 03/89 10008 2 952 613 11.0 07/89 10856 3 265 966 12.0 10/89 12305 3 797 482 13.0 01/90 13837 4 347 336 14.0 04/90 15409 4 914 264 15.0 08/90 16941 5 486 399 16.0 11/90 18364 5 986 949 17.0 02/91 20024 6 524 504 18.0 05/91 20772 6 792 034 19.0 08/91 21795 7 173 785 20.0 11/91 22654 7 500 130 21.0 03/92 23742 7 866 596 22.0 05/92 25044 8 375 696 23.0 08/92 26706 9 011 391 24.0 12/92 28154 9 545 427 25.0 04/93 29955 10 214 020 26.0 07/93 31808 10 875 091 27.0 10/93 33329 11 484 420 1.2 Source of data Release 27.0 has been updated using protein sequence data from release 37.0 of the PIR (Protein Identification Resource) protein data bank, as well as translation of nucleotide sequence data from release 36.0 of the EMBL Nucleotide Sequence Database. As an indication to the source of the sequence data in the SWISS-PROT data bank we list here the statistics concerning the DR (Database cross- references) pointer lines: Entries with pointer(s) to only PIR entri(es): 4553 Entries with pointer(s) to only EMBL entri(es): 4557 Entries with pointer(s) to both EMBL and PIR entri(es): 23557 Entries with no pointers lines: 662 2. DESCRIPTION OF THE CHANGES MADE TO SWISS-PROT SINCE RELEASE 26 2.1 Sequences and annotations About 1532 sequences have been added since release 26, the sequence data of 213 existing entries has been updated and the annotations of 3000 entries have been revised. In particular we have used reviews articles to update the annotations of the following groups or families of proteins: - Aspartate and glutamate racemases - Bacteriophage T4 proteins - Band 3 anion proteins - Beta amylases - Cysteine synthases - Deoxyribonuclease I - Epenymins - Epimorphin family - GTP1/Obg family - Fork head domain proteins - G-linked receptors family 2 - Glutamate 5-kinase - HIT family - Lysyl oxidases - mutT domain proteins - Nitrilases / cyanide hydratase - Peripherin / rom-1 - Phosphatidylinositol 3-kinases - Pollen proteins Ole e I family - Prokaryotic transglycosylases - Protein prenyltransferases alpha subunit repeat - Renal dipeptidases - Trehalases 2.2 A special emphasis on four "model" organisms We have selected four organisms that are the target of genome sequencing and/or mapping projects and for which we intend to: - Be as complete as possible. All sequences available at a given time should be immediatly included in SWISS-PROT. This also includes sequence corrections and updates. - Provide a high level of annotations. - Cross-references to specialized database(s) that contain, among other data, some genetic information about the genes that code for these proteins. - Provide specific indices or documents. The four organisms selected are: o Caenorhabditis elegans (worm) o Drosophila melanogaster (fly) o Escherichia coli o Saccharomyces cerevisiae (yeast) Such a special effort has been going on for more than a year for Escherichia coli (thanks to a very fruitful collaboration with Ken Rudd), it has started in this release for yeast: about 300 new yeast sequences were entered; about 1500 entries were reannotated and a new document (YEAST.TXT) is provided that list yeast entries in SWISS-PROT classified by gene name and synonym(s). The next release will target C.elegans thanks to a collaboration with the group at the Sanger Genome Center in Hinxton (UK). The Drosophila "project" should start a bit later. Organism Database Index file X-referenced provided -------------- ---------------------- -------------- C.elegans WormPep Next release D.melanogaster Flybase In preparation E.coli EcoGene ECOLI.TXT S.cerevisiae LISTA (in preparation) YEAST.TXT 2.3 The Expasy World-Wide Web server The recent months have seen a tremendous increase in the availability of software tools and applications that allow to efficiently make use of the varied resources which are part of the Internet network. Three of these `Network Information Tools' (NIR) are widely used by the biological community: WAIS (Wide Area Information Server), Gopher and, more recently, the World-Wide Web (WWW). As many organizations provide WAIS or Gopher servers that offer access to SWISS-PROT and PROSITE, we felt that there was no need to set up ourselves such a service. But no such server was yet available for WWW. The World-Wide Web (WWW), which originated at CERN, is a powerful global information system merging networked information retrieval and hypertext. It gives access, using hypertext links, to the documents and information contained in all the existing WWW servers around the world, as well as to the data obtainable through other information retrieval systems like WAIS, Gopher, X500, etc. To access a WWW server, one has to run on a local computer a client program (a WWW browser), which displays hypertext documents. The user can then either request a keyword search or jump to another document by following a hypertext link. WWW has the outstanding advantage of extending the hypertext model to the whole world (by allowing hypertext jumps to documents anywhere on the internet network) and by being device and user-interface independent (browsers exist for a variety of computers and user-interfaces, including Unix workstations running XWindows, MacIntoshes and PCs with Microsoft Windows). A WWW server has been set up by Ron Appel from the group of Denis Hochstrasser at the Faculty of Medicine of the University of Geneva on the ExPASy molecular biology server. It allows access, using the user- friendly hypertext model, to the SWISS-PROT and SWISS-2DPAGE databases and, through any SWISS-PROT protein sequence entry, to other databases such as EMBL, PROSITE, REBASE, Flybase, PDB and OMIM. Using a browser which is able to display images one can also remotely access 2D gels image data from SWISS-2DPAGE. A WWW server can be accessed on the internet through its Uniform Resource Locator (URL), the addressing system defined by the WWW model. The URL for the ExPASy molecular biology WWW server is: http://expasy.hcuge.ch/ or http://129.195.254.61/ To access a WWW server, you need to run a browser (or client) program on your local computer. Browsers exist for a variety of machines and may be obtained by anonymous ftp. Here is a selected list (taken from the CERN WWW server) of currently available browsers and the ftp address from which they can be retrieved: NCSA Mosaic a very flexible and powerful browser with a graphical user interface. Available for Unix boxes using X11/Motif; for Mc Intoshes and for Microsoft Windows. FTP site: ftp.ncsa.uiuc.edu (in /Web/xmosaic). lynx a full screen browser for vt100s using full screen, arrow keys, highlighting, etc. FTP site: ftp2.cc.ukans.edu (in /pub/lynx). www a basic line mode browser giving access to WWW from any dumb terminal. FTP site: info.cern.ch (in /pub/www). To access all the data available from SWISS-2DPAGE, the user's local computer needs to run an image viewing program. For most browsers on Unix workstations the default program is xv, a shareware application developed by John Bradley at University of Pennsylvania. The program can be found by ftp at export.lcs.mit.edu (in /contrib). For more information on the ExPASy WWW server, please contact Dr. Ron Appel: Email: appel@cih.hcuge.ch Tel: +41-22-372 62 64 Fax: +41-22-372 61 98 2.4 Changes in the DR line We have added cross-references to the WormPep collection of candidate protein translations from the Caenorhabditis elegans genome sequencing project (see section 2.2 of these notes). These cross-references are present in the DR lines: Data bank identifier: WORMPEP Primary identifier : Cosmid-derived name given to that protein by the C.elegans genome sequencing project. In general this name will not change. Secondary identifier: Number attributed by the C.elegans genome sequencing project to that protein. This number will change when the sequence is updated. Example : DR WORMPEP; ZK637.7; CE00437. 2.5 Weekly updates of SWISS-PROT Since release 24, we provide weekly updates of SWISS-PROT. These updates are available by anonymous FTP. Three files are updated every week: new_seq.dat Contains all the new entries since the last full release. upd_seq.dat Contains the entries for which the sequence data has been updated since the last release. upd_ann.dat Contains the entries for which one or more annotation fields have been updated since the last release. Currently these files are available on the following anonymous ftp servers: Organism EMBL ftp server Address ftp.embl-heidelberg.de (or 192.54.41.33) Directory /pub/databases/swissprot/new Organism ExPASy (Geneva University Expert Protein Analysis System) Address expasy.hcuge.ch (or 129.195.254.61) Directory /databases/swiss-prot/updates Organism National Center for Biotechnology Information (NCBI) Address ncbi.nlm.nih.gov (or 130.14.20.1) Directory /repository/swiss-prot/updates !! Important notes !!! Although we try to follow a regular schedule, we do not promise to update these files every week. In some cases two weeks will elapse in- between two updates. Due to the current mechanism used to build a release the entries that are provided in these updates are not guaranteed to be error free. Also, for the same reason, new entries do not contain an OC (Organism Classification) line. 3. ENZYME AND PROSITE 3.1 The ENZYME data bank Release 14.0 of the ENZYME data bank is distributed with release 27 of SWISS-PROT. ENZYME release 14.0 contains information relative to 3489 enzymes. 3.2 The PROSITE data bank 3.2.1 What's new in release 11.0 Release 11.0 of the PROSITE data bank is distributed with release 27 of SWISS-PROT. Release 11.0 contains 715 documentation chapters that describes 926 different patterns. Since the last major release of PROSITE (release 10.00 of December 1992), 80 new chapters have been added and 306 chapters have been updated. The new chapters are listed below: - Protein splicing signature - CAP-Gly domain signature - MAM domain signature - Prokaryotic transcription elongation factors signatures - MCM2/3/5 family signature - XPGC protein signatures - Bacterial regulatory proteins, arsR family signature - Bacterial regulatory proteins, deoR family signature - Dps protein family signatures - Ribosomal protein L27 signature - Ribosomal protein L36 signature - mutT domain signature - 3-hydroxyisobutyrate dehydrogenase signature - Dihydroorotate dehydrogenase signatures - Alanine dehydrogenase and pyridine nucleotide transhydrogenase - Lysyl oxidase putative copper-binding region signature - 6-hydroxy-D-nicotine oxidase and reticuline oxidase FAD-binding - Cytochrome c oxidase subunit VB, zinc binding region signature - Indoleamine 2,3-dioxygenase signatures - Glycine radical signature - Uroporphyrin-III C-methyltransferase signatures - Protein prenyltransferases alpha subunit repeat signature - Phosphatidylinositol 3-kinase signatures - Glutamate 5-kinase signature - Guanylate kinase signature - ADP-glucose pyrophosphorylase signatures - 2'-5'-oligoadenylate synthetases signatures - Deoxyribonuclease I signatures - Glucoamylase active site region signature - Trehalase signatures - Glycosyl hydrolases family 8 signature - Prokaryotic transglycosylases signature - Renal dipeptidase active site - Serine proteases, ompT family signatures - Proteasome B-type subunits signature - Signal peptidases II signature - Cytidine & deoxycytidylate deaminases zinc-binding region signature - GTP cyclohydrolase I signatures - Nitrilases / cyanide hydratase signatures - Orn/DAP/Arg decarboxylases family 2 signatures - Uroporphyrinogen decarboxylase signatures - Alpha-isopropylmalate and homocitrate synthases signatures - Beta-eliminating lyases pyridoxal-phosphate attachment site - Dihydroxy-acid and 6-phosphogluconate dehydratases signatures - Prephenate dehydratase signatures - Cysteine synthase pyridoxal-phosphate attachment site - Cys/Met metabolism enzymes pyridoxal-phosphate attachment site - Cytochrome c and c1 heme lyases signatures - Aspartate and glutamate racemases signatures - Mandelate racemase / muconate lactonizing enzyme family signatures - Phosphoglucomutase and phosphomannomutase phosphoserine signature - D-alanine--D-alanine ligase signatures - Carbamoyl-phosphate synthase subdomain signatures - Nickel-dependent hydrogenases b-type cytochrome subunit signatures - Adrenodoxin family, iron-sulfur binding region signature - ABC-2 type transport system integral membrane proteins signature - Acyl-CoA-binding protein signature - LacY family proton/sugar symporters signatures - Sodium:alanine symporter family signature - Sodium:galactoside symporter family signature - Osteopontin signature - Peripherin / rom-1 signature - Interleukins -4 and -13 signature - Erythropoietin signature - Galanin signature - Chaperonins clpA/B signatures - Bacterial type II secretion system protein D signature - Bacterial type II secretion system protein F signature - MARCKS family signatures - Elongation factor 1 beta/beta'/delta chain signatures - Eukaryotic initiation factor 4E signature - Calsequestrin signatures - GTP1/OBG family signature - HIT family signature - Ependymins signatures - Epimorphin family signature - Yeast PIR proteins repeats signature - Oleosins signature - Pollen proteins Ole e I family signature - Hypothetical YCR59c/yigZ family signature 3.2.2 Future developments Starting with the next major releases (12.0 of May 1994), PROSITE will be extended to include weight matrices (also known as profiles). There are a number of protein families as well as functional or structural domains that cannot be detected using patterns due to their extreme sequence divergence. Typical examples of important functional domains which are weakly conserved are the immunoglobulin domains, the SH2 and SH3 domains, or the fibronectin type III domain. In such domains there are only a few sequence positions which are well conserved. Any attempt of building a consensus pattern for such regions will either fail to pick up a significant proportion of the protein sequences that contain such region (false negative) or will pick up too many proteins that do not contain the region (false positive). The use of technique based on weight matrices or profiles allows the detection of such proteins or domains. Dr. Philipp Bucher at ISREC in Lausanne and myself are collaborating to include such methods into PROSITE. This collaboration also includes other participants such as Roland Luethy (AMGEN), Michael Gribskov (SDSC) and Steve Altschul (NCBI). If you are interested in participating in this project please contact Philipp Bucher at: pbucher@isrec-sun1.unil.ch We will include in the next release note of SWISS-PROT (Release 28 of February 1994) a brief description of the PROSITE syntax extension for profiles. The full description will be available in the User's Manual of release 11.1 of PROSITE (February 1994). Important notice for software developers: the integration of profiles into PROSITE will not "break" the current format. The profiles entries in the PROFILE.DAT file will be tagged with the token "MATRIX" on the "ID" line (currently, only "PATTERN" and "RULE" are used as tokens); a new line-type "MA" will be used in these entries to store all the weight matrices specific parameters. The format of the PROFILE.DOC file will not be changed. 4. WE NEED YOUR HELP ! We welcome feedback from our users. We would especially appreciate that you notify us if you find that sequences belonging to your field of expertise are missing from the data bank. We also would like to be notified about annotations to be updated, if, for example, the function of a protein has been clarified or if new post-translational information has become available. APPENDIX A: SOME STATISTICS A.1 Amino acid composition A.1.1 Composition in percent for the complete data bank Ala (A) 7.66 Gln (Q) 4.02 Leu (L) 9.20 Ser (S) 7.09 Arg (R) 5.23 Glu (E) 6.26 Lys (K) 5.81 Thr (T) 5.83 Asn (N) 4.45 Gly (G) 7.04 Met (M) 2.35 Trp (W) 1.30 Asp (D) 5.27 His (H) 2.25 Phe (F) 3.99 Tyr (Y) 3.22 Cys (C) 1.78 Ile (I) 5.55 Pro (P) 5.03 Val (V) 6.52 Asx (B) 0.005 Glx (Z) 0.005 Xaa (X) 0.02 A.1.2 Classification of the amino acids by their frequency Leu, Ala, Ser, Gly, Val, Glu, Thr, Lys, Ile, Asp, Arg, Pro, Asn, Gln, Phe, Tyr, Met, His, Cys, Trp A.2 Repartition of the sequences by their organism of origin Total number of species represented in this release of SWISS-PROT: 4143 A.2.1 Table of the frequency of occurrence of species Species represented 1x: 1879 2x: 685 3x: 387 4x: 247 5x: 186 6x: 143 7x: 88 8x: 78 9x: 76 10x: 48 11- 20x: 151 21- 50x: 103 51-100x: 33 >100x: 39 A.2.2 Table of the most represented species Number Frequency Species 1 2530 Human 2 2376 Escherichia coli 5 1563 Baker's yeast (Saccharomyces cerevisiae) 4 1496 Mouse 5 1385 Rat 6 654 Bovine 7 579 Fruit fly (Drosophila melanogaster) 8 495 Bacillus subtilis 9 489 Chicken 10 369 African clawed frog (Xenopus laevis) 11 341 Salmonella typhimurium 341 Rabbit 13 311 Pig 14 251 Vaccinia virus (strain Copenhagen) 15 224 Maize 16 200 Bacteriophage T4 17 193 Human cytomegalovirus (strain AD169) 18 190 Arabidopsis thaliana (Mouse-ear cress) 19 183 Vaccinia virus (strain WR) 20 180 Rice 21 166 Pseudomonas aeruginosa 166 Tobacco 23 164 Pea 24 162 Wheat 25 155 Caenorhabditis elegans 155 Fission yeast (Schizosaccharomyces pombe) 27 138 Barley 28 133 Soybean 29 131 Slime mold (Dictyostelium discoideum) 30 130 Spinach 31 129 Staphylococcus aureus 32 127 Sheep 33 119 Marchantia polymorpha (Liverwort) 34 118 Rhodobacter capsulatus 35 117 Dog 36 114 Pseudomonas putida 37 111 Neurospora crassa 38 110 Klebsiella pneumoniae 39 104 Bacillus stearothermophilus A.3 Repartition of the sequences by size From To Number From To Number 1- 50 1966 1001-1100 321 51- 100 3345 1101-1200 199 101- 150 4723 1201-1300 156 151- 200 3191 1301-1400 97 201- 250 2804 1401-1500 86 251- 300 2469 1501-1600 44 301- 350 2289 1601-1700 46 351- 400 2377 1701-1800 37 401- 450 1780 1801-1900 43 451- 500 1933 1901-2000 31 501- 550 1325 2001-2100 13 551- 600 922 2101-2200 40 601- 650 645 2201-2300 48 651- 700 488 2301-2400 16 701- 750 475 2401-2500 18 751- 800 368 >2500 100 801- 850 270 851- 900 293 901- 950 182 951-1000 189 Currently the ten largest sequences are: RYNR_RABIT 5037 a.a. RYNR_HUMAN 5032 a.a. APB_HUMAN 4563 a.a. APOA_HUMAN 4548 a.a. RRPA_CVMJH 4488 a.a. DYHC_TRIGR 4466 a.a. GRSB_BACBR 4451 a.a. PLEC_RAT 4140 a.a. POLG_BVDV 3988 a.a. VGF1_IBVB 3951 a.a. APPENDIX B: ON-LINE EXPERTS B.1 List of on-line experts for PROSITE and SWISS-PROT Field of expertise Name Email address --------------------------- ------------------ ---------------------------- Alcohol dehydrogenases Joernvall H. hans.jornvall@k1m.ki.se Persson B. bengt.persson@embl- heidelberg.de Aldehyde dehydrogenases Joernvall H. hans.jornvall@k1m.ki.se Persson B. bengt.persson@embl- heidelberg.de Alpha-crystallins/HSP-20 Leunissen J.A.M. jackl@caos.caos.kun.nl de Jong W. u629000@hnykun11.bitnet Alpha-2-macroglobulins Van Leuven F. fred@blekul13.bitnet AA-tRNA synthetases class II Leberman R. leberman@frembl51.bitnet Apolipoproteins Boguski M.S. boguski@ncbi.nlm.nih.gov AraC family HTH proteins Ramos J.L. jlramos@cnbvx3.cnb.uam.es Arrestins Kolakowski L.F.Jr. kolakowski@helix.mgh. harvard.edu Asparaginase / glutaminase Gribskov M. gribskov@sdsc.edu ATP synthase c subunit Recipon H. recipon@ncbi.nlm.nih.gov Band 4.1 family proteins Rees J. jrees@vax.oxford.ac.uk Beta-lactamases Brannigan J. jab5@vaxa.york.ac.uk Beta-transducin family Boguski M.S. boguski@ncbi.nlm.nih.gov C-type lectin domain Drickamer K. drick@cuhhca.hhmi.columbia. edu Chalcone/stilbene synthases Schroeder J. raf@sun1.ruf.uni-freiburg.de Chaperonins cpn10/cpn60 Georgopoulos C. georgopo@cmu.unige.ch Chaperonins TCP1 family Willison K.R. willison@icr.ac.uk Chitinases Henrissat B. bernie@cermav.grenet.fr Clusterin Peitsch M.C. peitsch@ulbio1.unil.ch Cold shock domain Landsman D. landsman@ncbi.nlm.nih.gov CTF/NF-I Mermod N. nmermod@ulys.unil.ch Gronostajski R. gronosr@ccsmtp.ccf.org Cytochromes P450 Holsztynska E.J. ela@netcom.uucp netcom!ela@apple.com DEAD-box helicases Linder P. linder@urz.unibas.ch Deoxyribonuclease I Peitsch M.C. peitsch@ulbio1.unil.ch dnaJ family Kelley W. kelley@cmu.unige.ch EF-hand calcium-binding Cox J.A. cox@sc2a.unige.ch Kretsinger R.H. rhk5i@virginia.bitnet Elongation factor 1 Amons R. wmbamons@rulgl.leidenuniv.nl Enoyl-CoA hydratase Hofmann K.O. khofmann@biomed.biolan.uni- koeln.de Fatty acid desaturases Piffanelli P. piffanelli@jii.afrc.ac.uk fruR/lacI family HTH proteins Reizer J. jreizer@ucsd.edu GATA-type zinc-fingers Boguski M.S. boguski@ncbi.nlm.nih.gov GDT/GTP dissociation stimul. Boguski M.S. boguski@ncbi.nlm.nih.gov GltP family of transporters Hofmann K.O. khofmann@biomed.biolan.uni- koeln.de Glucanases Henrissat B. bernie@cermav.grenet.fr Beguin P. phycel@pasteur.bitnet Glutamine synthetase Tateno Y. ytateno@genes.nig.ac.jp G-protein coupled receptors Chollet A. arc3029@ggr.co.uk Attwood T.K. bph6tka@biovax.leeds.ac.uk Kolakowski L.F.Jr. kolakowski@helix.mgh. harvard.edu GTPase-activating proteins Boguski M.S. boguski@ncbi.nlm.nih.gov HIT family Seraphin B. seraphin@embl-heidelberg.de HMG1/2 and HMG-14/17 Landsman D. landsman@ncbi.nlm.nih.gov Inorganic pyrophosphatases Kolakowski L.F.Jr. kolakowski@helix.mgh. harvard.edu Integrases Roy P.H. 2020000@saphir.ulaval.ca Kringle domain Ikeo K. kikeo@genes.nig.ac.jp Lipocalins Boguski M.S. boguski@ncbi.nlm.nih.gov Peitsch M.C. peitsch@ulbio1.unil.ch lysR family HTH proteins Henikoff S. henikoff@sparky.fhcrc.org MAC components / perforin Peitsch M.C. peitsch@ulbio1.unil.ch Malic enzymes Glynias M. mglynias@ncsa.uiuc.edu MAM domain Bork P. bork@embl-heidelberg.de MIP family proteins Reizer J. jreizer@ucsd.edu Myelin proteolipid protein Hofmann K.O. khofmann@biomed.biolan.uni- koeln.de Pancreatic trypsin inhibitor Ikeo K. kikeo@genes.nig.ac.jp PEP requiring enzymes Reizer J. jreizer@ucsd.edu pfkB carbohydrate kinases Reizer J. jreizer@ucsd.edu Phytochromes Partis M.D. partis@gcri.afrc.ac.uk Plant viruses icosahedral Koonin E.V. koonin@ncbi.nlm.nih.gov capsid proteins Protein kinases Hanks S. hanks@vuctrvax.bitnet Hunter T. hunter@salk-sc2.sdsc.edu PTS proteins Reizer J. jreizer@ucsd.edu Restriction-modification Bickle T. bickle@urz.unibas.ch enzymes Roberts R.J. roberts@neb.com Ribosomal protein S15 Ellis S.R. srelli01@ulkyvm.bitnet Ring-cleavage dioxygenases Harayama S. sharayam@ddbj.nig.ac.jp Signal sequence peptidases von Heijne G. gvh@csb.ki.se Dalbey R.E. rdalbey@magnus.acs.ohio- state.edu Sodium symporters Reizer J. jreizer@ucsd.edu Subtilases Brannigan J. jab5@vaxa.york.ac.uk Siezen R.J. nizo@caos.caos.kun.nl Thiol proteases Turk B. turk@ijs.ac.mail.yu Thiol proteases inhibitors Turk B. turk@ijs.ac.mail.yu TNF family Jongeneel C.V. vjongene@isrecmail.unil.ch TPR repeats Boguski M.S. boguski@ncbi.nlm.nih.gov Transit peptides von Heijne G. gvh@csb.ki.se Type-II membrane antigens Levy S. levy@cellbio.stanford.edu Uracil-DNA glycosylase Aasland R. aasland@embl-heidelberg.de Vitamin K-depend. Gla domain Price P.A. pprice@ucsd.edu XPGC protein Clarkson S.G. clarkson@cmu.unige.ch Xylose isomerase Jenkins J. jenkins@frira.afrc.ac.uk WAP-type domain Claverie J.-M. jmc@ncbi.nlm.nih.gov ZP domain Bork P. bork@embl-heidelberg.de African swine fever virus Yanez R.J. ryanez@cbm2.uam.es Bacteriophage P4 Halling C. chh9@midway.uchicago.edu Caenorhabditis elegans Sonnhammer E. esr@mrc-molecular.biology. cam.ac.uk Chloroplast encoded proteins Hallick R.B. hallick@arizona.edu Drosophila Ashburner M. ma11@phx.cam.ac.uk Escherichia coli Rudd K. rudd@ncbi.nlm.nih.gov Salmonella typhimurium Rudd K. rudd@ncbi.nlm.nih.gov Snakes Stocklin R. stocklin@cmu.unige.ch B.2 Requirements to fulfill to become an on-line expert An expert should be a scientist working with specific famili(es) of proteins (or specific domains) and who would: a) Review the protein sequences in SWISS-PROT and the patterns/matrices in PROSITE relevant to their field of research. b) Agree to be contacted by people that have obtained new sequence(s) which seem to belong to "their" familie(s) of proteins. c) Have access to electronic mail and be willing to use it to send and receive data. If you are willing to be part of this scheme please contact Amos Bairoch at the following electronic mail address: bairoch@cmu.unige.ch APPENDIX C: RELATIONSHIPS BETWEEN BIOMOLECULAR DATABASES The current status of the relationships (cross-references) between some biomolecular databases is shown in the following schematic: ********************** *********************** * EPD [Euk. Promot.] * * EMBL Nucleotide * <----> ********************** * Sequence Data * ****************** * Library * ********************** * FLYBASE * <--> *********************** <----- * ECD [E. coli map] * * [Drosophila * ^ ^ ********************** * genomic d.b.] * <------+ | | ****************** | | +--------- ********************** | | * TFD [Trans. fact.] * | | +--------> ********************** | | | ****************** v v v ********************** * REBASE * *********************** * ENZYME [Nomencl.] * * [Restriction * <--- * SWISS-PROT * <----- ********************** * enzymes] * * Protein Sequence * | ****************** * Data Bank * v *********************** ********************** ****************** ^ ^ | | ^ ^ | * OMIM [Diseases] * * EcoGene/EcoSeq * | | | | | | +--------> ********************** * [E. coli] * <-----+ | | | | | ****************** | | | | +-----------> ********************** | | | | * ECO2DBASE [2D] * | | | | ********************** ****************** | | | | * PROSITE * <--------+ | | +---------------> ********************** * [Patterns] * | | * SWISS-2DPAGE [2D] * ****************** | +---------------+ ********************** | v | | *********************** | ********************** +--------> * PDB [3D structures] * +--> * Aarhus/Ghent [2D] * *********************** ********************** From owner-proteins@net.bio.net Wed Nov 17 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!news.univie.ac.at!edvz.sbg.ac.at!wst!ortnerm From: ortnerm@wst.edvz.sbg.ac.at (Maria Ortner) Newsgroups: bionet.molbio.proteins Subject: Release 1.0 of PROSA available Message-ID: Date: 18 Nov 93 17:12:12 GMT Sender: ortnerm@wst (Maria Ortner) Reply-To: ortnerm@wst.edvz.sbg.ac.at (Maria Ortner) Organization: University of Salzburg / Austria Lines: 47 PROSA - PROtein Structure Analysis ================================== Version 1.0 for SGI Iris/Indigo Copyright (C) by CAME - Center of Applied Molecular Engineering PROSA analyses the energy distribution in proteins. If you are a protein X-ray crystallographer, an NMR-spectroscopist or (beware) a protein structure predictor this program may be of interest to you. Suppose that you are confronted with a NATIVE protein structure (i.e. a protein in its natural functioning state). The structure may have been determined by X-ray, NMR, molecular modelling or it may be a structure which was designed to fool specialists in protein structure theory. How could you tell whether the structure is correct or incorrect? Note that even experimentalists are human beings and prone to errors. All of them are honest and trustworthy people. But if you base your experiments on published structures you are better off if you check the structures as far as possible before you start wasting your time. If you are going to use the results of protein modelling or prediction then you are in a bad shape anyway. PROSA is a programm which analyses the energy distribution in protein structures as a function of sequence position. Native structures have balanced energy distributions - faulty structures have high energy peaks or are strained all over the place. So much for the theory. In case you are really interested please consult the references at the end of the manual. Just look at a few native graphs and you get the point. In interpreting the results produced by PROSA keep in mind the following: BE SUSPICIOUS OF EXPERIMENTAL DATA BUT NEVER TRUST THEORETICAL METHODS DISTRIBUTION ============ PROSA runs on Silicon Graphics Workstations with IRIX 4.0.1 or higher. You can get the latest version of the program by anonymous ftp from Gundi.came.sbg.ac.at (141.201.27.11) , PROSA/ Please get and read the README file. From owner-proteins@net.bio.net Thu Nov 18 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!darwin.sura.net!fconvx.ncifcrf.gov!fcs260c!mack From: mack@fcs260c.ncifcrf.gov (Joe Mack) Newsgroups: bionet.molbio.proteins Subject: Re: pI of TGF-beta Message-ID: Date: 19 Nov 93 23:16:49 GMT References: <3559@rc1.vub.ac.be> Sender: usenet@ncifcrf.gov (C News) Organization: Frederick Cancer Research and Development Center Lines: 23 Nntp-Posting-Host: fcs260c.ncifcrf.gov In article <3559@rc1.vub.ac.be> pjdebles@vub.vub.ac.be (Pieter De Bleser) writes: >Dear bionetters, > > >Does anyone know the pI of TGF-beta, or has a pointer to where I can >find this data? > > >Thanks, > >-- >____________________________________________________________________________ >Pieter De Bleser >Laboratory for Cell Biology and Histology, >Free University of Brussels, >Laarbeeklaan 103, B -1090 Brussels, Belgium >Phone:+32-2-4774407; Fax:+32-2-4774000; Email: pjdebles@cyto.vub.ac.be >____________________________________________________________________________ Find a place that has the GCG set of programs and databases. Get an account. Findout about all the neat programs thay have for protein peopple and molecular biologists. Use the program "ISOELECTRIC". Joseph Mack mack@ncifcrf.gov From owner-proteins@net.bio.net Thu Nov 18 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!europa.eng.gtefsd.com!emory!emory!usenet From: medtjm@bimcore.emory.edu (T. J. Murphy) Newsgroups: bionet.molbio.proteins Subject: WANTED: Used UV Detector for HPLC Message-ID: <2cjld3INNmsm@emory.mathcs.emory.edu> Date: 19 Nov 93 23:38:11 GMT Reply-To: medtjm@bimcore.emory.edu Organization: Biomolecular Computing Resource, Emory University Lines: 11 NNTP-Posting-Host: bimcore.cc.emory.edu I would like to buy an experienced optical detector for an Isco HPLC system. The device should have 200-220 nm (peptide bond) capability. Would prefer not to pay $2000 for a new one. Please respond by e-mail. Thanks in advance. --- TJ Murphy Asst. Professor Dept of Pharmacology Emory University School of Medicine From owner-proteins@net.bio.net Fri Nov 19 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!hearst.acc.Virginia.EDU!murdoch!galen.med.Virginia.EDU!jv4s From: jv4s@galen.med.Virginia.EDU (Beavis) Newsgroups: bionet.molbio.proteins Subject: Re: pI of TGF-beta Message-ID: Date: 20 Nov 93 19:51:39 GMT References: <3559@rc1.vub.ac.be> Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia Lines: 9 I was told it was 9.5 ( I do not know if it differs from beta1 to beta2) TGF alpha is around 6.5. Plenty of info in the Medline database. Jay -- eh eheeh eh he heh eh eh heh heh ehe heh From owner-proteins@net.bio.net Fri Nov 19 22:00:00 1993 Path: biosci!news.cs.umb.edu!hsdndev!husc-news.harvard.edu!husc.harvard.edu!husc10!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.molbio.proteins Subject: Re: pI of TGF-beta Message-ID: Date: 20 Nov 93 15:35:23 GMT References: <3559@rc1.vub.ac.be> Organization: Harvard University, Cambridge, Massachusetts Lines: 33 NNTP-Posting-Host: husc10.harvard.edu mack@fcs260c.ncifcrf.gov (Joe Mack) writes: >In article <3559@rc1.vub.ac.be> pjdebles@vub.vub.ac.be (Pieter De Bleser) writes: >>Dear bionetters, >> >> >>Does anyone know the pI of TGF-beta, or has a pointer to where I can >>find this data? >> >>____________________________________________________________________________ >Find a place that has the GCG set of programs and databases. Get an account. >Findout about all the neat programs thay have for protein peopple and molecular >biologists. Use the program "ISOELECTRIC". Ahh, but did the original poster want the PREDICTED pI or the ACTUAL pI? Particularly with the multitude of post-translational modifications in mammalian cells (and especially since many of these involve derivatizing charged amino acid side chains or adding charged moieties), it is an important distinction. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@biosun.harvard.edu P.S. Taking into account both the N-terminal peptide processing and the observed blockage of the mature protein's N-terminus to Edman degredation (and assuming the blocking group is non-charged), the pI of the major isoform of TGF-beta (Human) is predicted to be 4.75 using the 'iso' program from my MOLBIO++ library. From owner-proteins@net.bio.net Sun Nov 21 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!gatech!mailer.acns.fsu.edu!garnet.acns.fsu.edu!rose From: rose@garnet.acns.fsu.edu (Kermit Rose) Newsgroups: bionet.neuroscience,bionet.molbio.proteins,bionet.molbio.methds-reagnts,bionet.molbio.hiv,bionet.drosophila,bionet.general Subject: Re: I NEED HELP Message-ID: <2cpc1r$go8@mailer.fsu.edu> Date: 22 Nov 93 03:35:23 GMT References: <2cf4dqINNkn4@charnel.ecst.csuchico.edu> Organization: Florida State University Lines: 81 Xref: biosci bionet.neuroscience:2067 bionet.molbio.proteins:1062 bionet.molbio.methds-reagnts:9262 bionet.molbio.hiv:260 bionet.drosophila:164 bionet.general:6608 NNTP-Posting-Host: garnet.acns.fsu.edu bmcnulty@OAVAX.CSUCHICO.EDU (bob) writes: > > > I am the manager of a stockroom/lab facility which is responsible for > servicing the needs (chemical, reagents, and equipment) of a Biology > department in a small university (14 - 16000 students). The facility I > manage supplies these items for over 80 laboratory class sections per week > with only 3 personnel while at the same time managing a service/checkout > window which is open for 6 hours each day (9:00am 'til 3:00pm). The > department has 20 PHD faculty and several part time MS instructors or TAs. > > I seem to have found myself in the middle of a rather large debate with one > faculty member who insists that he/she have unlimited access (a key and > pass code) to the area I manage (which is currently under alarm and houses > well over $1,000,000 worth of inventory) because she/he needs supplies to > do unfunded research at hours other than those when the facility I manage > is open. The other faculty are either supported by grants or are not > actively involved in research. > > > > IN AN EFFORT TO SOLVE THIS DILEMMA I NEED YOUR HELP!!! > > I SEEK ONLY DATA. I would predict that this would not solve the dilemma. Did you propose to the researcher that you pull the items needed with one day's notice. If the need is really for research, it would be only a minor handicap to have to plan the materials to be used and call with a list. On the other hand, if the researcher is addicted to some medicine and does not wish to admit it, you have somewhat of a problem here. I suggest that you talk to the researcher again and try to come to a procedure that will solve both the needs of the researcher and the security needs. > > If you would be so kind.... please answer the following questions and e- > mail them to me directly so I may scientifically support my position. > > I WILL USE NO NAMES OR ADDRESS IN MY REPORT, JUST THE DATA I COLLECT FROM > > THE QUESTIONS BELOW!!! > > ********************* CUT HERE ***************************************** > > > With what academic institution are you affiliated? > > _______________________________ > > > > Do faculty at your institution have a key or unlimited access to the main > > > stockroom/supply/support facility? __________________________________ > > > > > > *************************************************************************** > > > Thank you for your time and the effort! > > BMCNULTY@OAVAX.CSUCHICO.EDU > > > > > //////// "Adapt, Migrate, or Die" > ( ) > \ @ @ / BMCNULTY@OAVAX.CSUCHICO.EDU > -------w---U---w---- > Bob McNulty, CA. STATE UNIV., CHICO -- rose@garnet.acns.fsu.edu To be sure I see your response, use e-mail. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - You may post, repost, or publish ANY communication received from me. From owner-proteins@net.bio.net Sun Nov 21 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!elroy.jpl.nasa.gov!swrinde!dptspd!TAMUTS.TAMU.EDU!mac2wild2.tamu.edu!user From: pjh3142@rigel.tamu.edu (Pascal Hua) Newsgroups: bionet.molbio.proteins Subject: How does the cell deal with over-expression ? Message-ID: Date: 22 Nov 93 20:12:07 GMT Followup-To: bionet.molbio.proteins Organization: Texas A&M Lines: 26 NNTP-Posting-Host: mac2wild2.tamu.edu Hello, I have a second question that I wanted to keep separate form the other one for clarity purpose :-)). How do you think a metabolic pathway handles the over-expression of one of the enzyme along the way to keep the flux through the pathway constant ? Many enzymes have been over-expressed. The purpose might have been just enzyme purification, or trying to increase the flux through the pathway. Quite often, the flux did not increase, and the conclusion was that a step RbeforeS is the rate limiting step (see other post about that). But what happens to the substrate(s)/product(s) of this enzyme that has been over-expressed ? Are they any experimental evidences of how it is done inside the cell ? Pascal Hua pjh3142@rigel.tamu.edu Biochemistry & Biophysics Texas A&M University. Cross-posted to: bionet.biology.computational bionet.cellbiol bionet.general bionet.info-theory bionet.metabolic-reg bionet.molbio.proteins From owner-proteins@net.bio.net Sun Nov 21 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!elroy.jpl.nasa.gov!swrinde!dptspd!TAMUTS.TAMU.EDU!mac2wild2.tamu.edu!user From: pjh3142@rigel.tamu.edu (Pascal Hua) Newsgroups: bionet.molbio.proteins Subject: What is a rate limiting step ? Message-ID: Date: 22 Nov 93 20:08:02 GMT Followup-To: bionet.molbio.proteins Organization: Texas A&M Lines: 38 NNTP-Posting-Host: mac2wild2.tamu.edu Hello, This question might seem easy, but I found it not so obvious as I thought about it more: What does rate limiting mean to you ? It is used quite often, and not only in biology. The example I am dealing with is a common one, a metabolic pathway. The simplest way to see it, is that there is not RenoughS of the first enzyme on the pathway and RplentyS of the following enzymes. When more of the first enzyme is made, the flux through the pathway increases in a direct (not necessarily linear) function of this first enzyme. Does it mean that this first enzyme is used at saturation of its substrate(s) ? If not, the element that keeps those substrate(s) constant would be the real rate limiting step by providing the right flux of substrate so as to keep it constant ! If that flux does not change, an increase in the quantity and consequently in flux of the first enzyme would have the effect of lowering the concentration of its substrate until the activity was restored to its original value ! I feel that I am chasing the chicken and the egg story. But I think it is important, because what we consider as RregulatoryS enzymes (cooperative binding, aloesteric effector) exhibit those effects mostly at sub-saturating concentrations of substrates. How can they be rate limiting and take advantage of those characteristics ? Pascal Hua pjh3142@rigel.tamu.edu Biochemistry & Biophysics Texas A&M University. Cross-posted to: bionet.biology.computational bionet.cellbiol bionet.general bionet.info-theory bionet.metabolic-reg bionet.molbio.proteins From owner-proteins@net.bio.net Sun Nov 21 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!emory!nigel.msen.com!yale.edu!cs.yale.edu!Angela.Baldo From: amb93002@uconnvm.uconn.edu (Angela M. Baldo) Newsgroups: bionet.neuroscience,bionet.molbio.proteins,bionet.molbio.methds-reagnts,bionet.molbio.hiv,bionet.drosophila,bionet.general Subject: I need isolates of D. mauritiana Message-ID: <1993Nov22.151143.15483@cs.yale.edu> Date: 22 Nov 93 15:11:43 GMT Sender: -Not-Authenticated-[4807] Organization: University of Connecticut Lines: 12 Xref: biosci bionet.neuroscience:2071 bionet.molbio.proteins:1066 bionet.molbio.methds-reagnts:9280 bionet.molbio.hiv:262 bionet.drosophila:167 bionet.general:6613 X-Posted-From: InterNews 1.0@babyblue.cs.yale.edu. Nntp-Posting-Host: histone.mcb.uconn.edu Xdisclaimer: No attempt was made to authenticate the sender's name. Does anyone out there have access to D. mauritiana flies not related to the one available from Bowling Green? I have been told by one source that only one isolate was ever captured, by Jean David. Can anyone corroborate? M. Solignac published a paper in JME 1986 which described using the mitochondrial DNA from several strains of D. mauritiana. It is not exactly clear whether these are separate isolates. Thank you in advance for any information you can offer. anja From owner-proteins@net.bio.net Sun Nov 21 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!paladin.american.edu!news.univie.ac.at!edvz.sbg.ac.at!wst!ortnerm From: ortnerm@wst.edvz.sbg.ac.at (Maria Ortner) Newsgroups: bionet.molbio.proteins Subject: REMARK on PROSA: 1 Name <-> 2 Programs Message-ID: Date: 22 Nov 93 16:47:12 GMT Sender: ortnerm@wst (Maria Ortner) Reply-To: ortnerm@wst.edvz.sbg.ac.at (Maria Ortner) Organization: University of Salzburg / Austria Lines: 10 The name PROSA (PROtein Structure Analysis) from the CAME - Center of Applied Molecular Engineering conflicts with the name PROSA (PROfile Search Analysis) from the SQUIRREL package from C. Gartmann & U. Grob. We will change the name of our PROtein Structure Analysis program in the next version. Maria Ortner CAME - Center of Applied Molecular Engineering From owner-proteins@net.bio.net Sun Nov 21 22:00:00 1993 Path: biosci!nii.ernet.in!jawahar From: jawahar@nii.ernet.in (G. Jawahar Swaminathan) Newsgroups: bionet.molbio.proteins Subject: Need Doc. File For PIR ! Message-ID: <9311220613.AA22573@ern.doe.ernet.in> Date: 21 Nov 93 18:52:06 GMT Sender: news@net.bio.net Distribution: bionet Lines: 23 Hi, We have the PIR version v3/2.4 (december 1992) which runs on the vax/vms system. Unfortunately we have al the document files relating to the use of PSQ NAQ, and NRL_3D database, but are lacking in the document file needed for scoring matrices or running the ALIGN program !! If anyone has the necessary document files for the same, can you send it to my address given below, or can you direct me to the right place from where they may be available ? Thanx in advance. jawahar p.s ONLY ALIGN AND MATRIX DOCUMENTS FILES ARE NEEDED. Please email it to the address given below. -X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X- G.Jawahar Swaminathan Phone: 91-11-686 3004 to 6863009 Protein Chemistry Lab \ / Extn: 234, 309 National Institute of Immunology, | Gram: IMMUNOLOGY, New Delhi Aruna Asaf Ali Marg, \ / \ / Email: Jawahar@NII.ernet.in New Delhi - 110 067. | | Fax: 91-11-686 2125 INDIA UUCP: ...uunet!sangam!vikram!nii!jawahar! =============================================================================== From owner-proteins@net.bio.net Sun Nov 21 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!uni-heidelberg!rz.uni-karlsruhe.de!xlink.net!sol.ctr.columbia.edu! howland.reston.ans.net!usc!elroy.jpl.nasa.gov!swrinde!dptspd!TAMUTS.TAMU.EDU!mac2wild2.tamu.edu!user From: pjh3142@rigel.tamu.edu (Pascal Hua) Newsgroups: bionet.molbio.proteins Subject: How does the cell deal with over-expression ? Message-ID: Date: 22 Nov 93 20:12:07 GMT Followup-To: bionet.molbio.proteins Organization: Texas A&M Lines: 26 NNTP-Posting-Host: mac2wild2.tamu.edu Hello, I have a second question that I wanted to keep separate form the other one for clarity purpose :-)). How do you think a metabolic pathway handles the over-expression of one of the enzyme along the way to keep the flux through the pathway constant ? Many enzymes have been over-expressed. The purpose might have been just enzyme purification, or trying to increase the flux through the pathway. Quite often, the flux did not increase, and the conclusion was that a step RbeforeS is the rate limiting step (see other post about that). But what happens to the substrate(s)/product(s) of this enzyme that has been over-expressed ? Are they any experimental evidences of how it is done inside the cell ? Pascal Hua pjh3142@rigel.tamu.edu Biochemistry & Biophysics Texas A&M University. Cross-posted to: bionet.biology.computational bionet.cellbiol bionet.general bionet.info-theory bionet.metabolic-reg bionet.molbio.proteins From owner-proteins@net.bio.net Sun Nov 21 22:00:00 1993 Path: biosci!hubcap!darwin.sura.net!howland.reston.ans.net!gatech!mailer.acns.fsu.edu!garnet.acns.fsu.edu!rose From: rose@garnet.acns.fsu.edu (Kermit Rose) Newsgroups: bionet.neuroscience,bionet.molbio.proteins,bionet.molbio.methds-reagnts,bionet.molbio.hiv,bionet.drosophila,bionet.general Subject: Re: I NEED HELP Message-ID: <2cpc1r$go8@mailer.fsu.edu> Date: 22 Nov 93 03:35:23 GMT References: <2cf4dqINNkn4@charnel.ecst.csuchico.edu> Organization: Florida State University Lines: 81 Xref: biosci bionet.neuroscience:2070 bionet.molbio.proteins:1063 bionet.molbio.methds-reagnts:9264 bionet.molbio.hiv:261 bionet.drosophila:165 bionet.general:6610 NNTP-Posting-Host: garnet.acns.fsu.edu bmcnulty@OAVAX.CSUCHICO.EDU (bob) writes: > > > I am the manager of a stockroom/lab facility which is responsible for > servicing the needs (chemical, reagents, and equipment) of a Biology > department in a small university (14 - 16000 students). The facility I > manage supplies these items for over 80 laboratory class sections per week > with only 3 personnel while at the same time managing a service/checkout > window which is open for 6 hours each day (9:00am 'til 3:00pm). The > department has 20 PHD faculty and several part time MS instructors or TAs. > > I seem to have found myself in the middle