From owner-proteins@net.bio.net Mon Sep 01 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!204.238.120.130!jump.net!grunt.dejanews.com!not-for-mail Date: Tue, 02 Sep 1997 12:02:30 -0600 From: scottnorton@mailcity.com Subject: Recycling pipette tips Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Message-ID: <873210068.21944@dejanews.com> Reply-To: scottnorton@mailcity.com Organization: Deja News Posting Service To: scottnorton@mailcity.com Recycling: pipette tips X-Article-Creation-Date: Tue Sep 02 14:21:08 1997 GMT X-Originating-IP-Addr: 205.139.231.124 (pm3x28.dialip.mo.net) X-Http-User-Agent: Mozilla/3.01 (Win95; I) X-Authenticated-Sender: scottnorton@mailcity.com Lines: 9 Xref: biosci bionet.molbio.methds-reagnts:60844 bionet.molbio.proteins:11437 Does anyone know of a company or companies that recycle pipette tips. We go through an immense amount in my lab and it seems like such a great waste. I sure would appreciate any suggestions. Thanks, Scott Norton -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-proteins@net.bio.net Mon Sep 01 23:00:00 1997 Path: biosci!GUARANY.CPD.UNB.BR!zanotta From: zanotta@GUARANY.CPD.UNB.BR (pedro jose portugal zanotta) Newsgroups: bionet.molbio.proteins Subject: Re: Concentrating Membrane Proteins Date: 2 Sep 1997 08:03:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <19970901030801.XAA01638@ladder02.news.aol.com> NNTP-Posting-Host: net.bio.net On 1 Sep 1997, RSjolund wrote: > I've got a 32 kDa protein from a plant cell plasma membrane. It is > extracted well in a medium containing CHAPS, but if I precipitate it with > ammonium sulphate (40% saturation) if does NOT go back into solution. > What are some good techniques for concentrating the protein (prior to 2D > gels). The goal is to sequence the protein. > > Dick Sjolund > Biological Sciences > Univ. of Iowa > > r-sjolund@uiowa.edu > > you can try TCA precipitation plus washing the pellet with cold (-20) aceton. In order to ressuspend it put some non-ionic detergent in the buffer. Hope this helps! From owner-proteins@net.bio.net Mon Sep 01 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: lefranc@ligm.crbm.cnrs-mop.fr (Marie-Paule Lefranc) Newsgroups: bionet.molbio.proteins Subject: IMGT NEWS Date: 3 Sep 1997 07:41:50 +0100 Lines: 34 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5uj0re$i8e@mserv1.dl.ac.uk> X-Sender: chantal@ligm.crbm.cnrs-mop.fr Original-To: bionews@dl.ac.uk, bio-www@dl.ac.uk, gdb@dl.ac.uk, genbank@dl.ac.uk, immuno@dl.ac.uk, mol-evol@dl.ac.uk, molmodel@dl.ac.uk, molreps@dl.ac.uk, pop-bio@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, tibs@dl.ac.uk Dear Colleague, I am pleased to send you the latest IMGT news for information and diffusion. With many thanks. Best regards. Professor Marie-Paule LEFRANC _____________________ IMGT NEWS-August 1997 "Alleles and mutations" IMGT, the international ImMunoGeneTics database, announces a STANDARDIZED description of allele polymorphisms and mutations for all immunoglobulin and T cell receptor V-REGIONs of all species, based on the IMGT unique numbering (IMGT NEWS - March 1997). Allele alignments and tables for the human IGH, IGK and IGL V-REGIONs are freely available at IMGT http://imgt.cnusc.fr:8104 IMGT initiator and coordinator : Prof. Marie-Paule Lefranc Laboratoire d'ImmunoGenetique Moleculaire, LIGM UMR 5535 (CNRS - Universite Montpellier II) 1919 route de Mende 34293 Montpellier Cedex 5 - France Tel: +33 (0)4 67 61 36 34 - Fax: +33 (0)4 67 04 02 31 lefranc@ligm.crbm.cnrs-mop.fr IMGT reference : Giudicelli et al., Nucleic Acids Research, 25, 206-211(1997) From owner-proteins@net.bio.net Mon Sep 01 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed1-hme1!newsfeed.internetmci.com!199.117.161.1!csn!nntp-xfer-1.csn.net!magnus.acs.ohio-state.edu!smtp.service.ohio-state.edu!rdisilvexx From: rdisilvexx@smtp.service.ohio-state.edu (Robert DiSilvestro) Newsgroups: bionet.molbio.proteins Subject: isozyme definition Date: Tue, 2 Sep 1997 20:39:39 GMT Organization: The Ohio State University Lines: 7 Message-ID: NNTP-Posting-Host: 140.254.42.101 X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #4] I am reviewing a paper where the term "isozymes" is being used in a way I do not typically use it. I'm not sure if my limited use is correct. I tend to use the term for enzymes with similar catalytic activity, but fairly subtle structural differences. Would one apply the term to 3 enzymes which have totally different structures, but the same catalytic action? To E-mail me, remove the xxx from my name. From owner-proteins@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!agate!usenet.INS.CWRU.Edu!vncnews!HSNX.wco.com!feta.direct.ca!newsfeed.direct.ca!howland.erols.net!news.apfel.de!newscore.univie.ac.at!01-newsfeed.univie.ac.at!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins Subject: Re: isozyme definition Date: 3 Sep 1997 09:09:42 GMT Organization: University of Leicester (PCFS User) Lines: 14 Message-ID: <5uj9gm$qot@falcon.le.ac.uk> References: NNTP-Posting-Host: pc47.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) rdisilvexx@smtp.service.ohio-state.edu (Robert DiSilvestro) wrote: >I am reviewing a paper where the term "isozymes" is being used in a way I >do not typically use it. I'm not sure if my limited use is correct. I tend >to use the term for enzymes with similar catalytic activity, but fairly subtle >structural differences. Would one apply the term to 3 enzymes which >have totally different structures, but the same catalytic action? I would tend to use it for enzymes of the same function which occur in the same organism, but possibly in different organs and/or different developmental stages. Limiting the use to "subtle structural differences" would require definition of "subtle". Any such definition would be arbitrary. From owner-proteins@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!daresbury!uninett.no!Norway.EU.net!EU.net!cpk-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!xfer.kren.nm.kr!newsfeed.kornet.nm.kr!news-stock.gsl.net!news-dc.gsl.net!news-raspail.gip.net!news.gsl.net!gip.net!newscore.univie.ac.at!03-newsfeed.univie.ac.at!news.univie.ac.at!loop.mdy.univie.ac.at!hs From: hs@mdy.univie.ac.at (Hellfried Schreiber) Newsgroups: bionet.molbio.proteins Subject: ICMSB97 - Final Programme Date: 3 Sep 1997 19:04:39 GMT Organization: Vienna University, Austria Lines: 262 Sender: hs@loop.mdy.univie.ac.at (Hellfried Schreiber) Message-ID: <5ukcc7$1c0q@www.univie.ac.at> NNTP-Posting-Host: loop.mdy.univie.ac.at ------------------- Final Programme ------------------- S E C O N D I N T E R N A T I O N A L C O N F E R E N C E O N M O L E C U L A R S T R U C T U R A L B I O L O Y >> I C M S B 97 << SEPTEMBER 10 - 14, 1997 VIENNA, AUSTRIA Organized by the Austrian Chemical Society Working Group Biophysical Chemistry ---------------------------------------------------------------------- Scientific Schedule and Social Programme ======================================== * Wednesday 10.9.97 From 14:00 Registration 19:00 Dr. Max Perutz (Honorary) Glutamine Repeats and Inherited Neurodegenerative Diseases 20:00 Welcome Get-Together * Thursday 11.9.97 STRUCTURE AND PREDICTION +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9:00 Announcements 9:10 H. Michel (Plenary) Structure and Possible Mechanism of Action of the Cytochrome c Oxidase from Paracoccus denitrificans 9:55 R. Crowther (Plenary) The Fold of the Core Protein of Hepatitis B Virus Determined by Electron Cryo-Microscopy 10:40 Coffee Break 11:10 T. Richmond (Plenary) X-Ray Structure of the Nucleosome Core Particle at 2.8A Resolution 11:55 R. Dutzler (Short Commun.) Sugar Transport through Maltoporin: From Structure to Mechanism of a Facilitated Diffusion Channel 12:15 J.-P. Renaud (Short Commun.) Ligand Binding to Retinoid Receptors 12:35 Lunch 14:00 G. Rose (Plenary) Simulation of Protein Folding Using LINUS 14:45 B. Rost (Plenary) Learning from Evolution to Predict Protein Structure 15:30 L. LoConte (Short Commun.) Visible Volume: A New Way of Exploring Protein Structures 15:50 Coffee Break 16:20 S. Benner (Plenary) Natural History and the Physical Sciences: Predicting the Structure of Proteins 17:05 M. Sippl (Plenary) Molecular Forces in Protein Folding and Prediction 17:50 M. Rodionov (Short Commun.) Amino Acid Interaction Patterns and Sequence Conservation in Protein Superfamilies 18:10 Close 20:00 Cocktail Reception for all participants and accompanying people at the City Hall of Vienna "Wiener Rathauskeller" * Friday 12.9.97 MACROMOLECULAR INTERACTIONS +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9:00 Announcements 9:10 W. van Gunsteren (Plenary) Calculation of Free Energy and Binding Constants for Biomolecular Complexes 9:55 A. Frankel (Plenary) Design and Evolution of RNA-Binding Proteins 10:40 Coffee Break 11:10 T. Steitz (Plenary) DNA and RNA Polymerases: Structural Diversity and Common Mechanisms 11:55 P. Walsh (Short Commun.) RNA Binding by the N-Terminus of the Wilms, Tumor 1 Tumor Suppressor Protein 12:15 J. Forbes (Short Commun.) Probing the Hydrophobic Interactions of Surfaces, Peptides, and Macromolecules with the Atomic Force Microscope 12:35 Lunch 14:00 Poster Session I 15:30 Coffee Break 16:00 R. Rigler (Plenary) Fluorescence Correlation Spectroscopy, Detection and Selection of Single Molecules 16:45 A. Watts (Plenary) Atomic Resolution of Bound Ligands in Functionally Active, Membrane Receptors using Non-Crystallographic Methods 17:30 G. Miller (Short Commun.) Molecular Dynamics Simulations on G Protein-Coupled Receptors: Implementation and Validation of a Membrane Mimetic 17:50 Close This evening has been left free for participants to enjoy Vienna * Saturday 13.9.97 CATALYSIS AND DESIGN +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9:00 Announcements 9:10 O. Jardetzky (Plenary) Protein Dynamics and Conformational Transitions in Allosteric Proteins 9:55 A. Wlodawer (Plenary) Retroviral Integrases - the Last Frontier in Designing Drugs against AIDS 10:40 Coffee Break 11:10 R. Goody (Plenary) Problems and Perspectives in Designing Drugs against AIDS 11:55 H. Bjrkbacka (Short Commun.) Conformational Changes Induced Upon Oxidation of Chloroplastic Carbonic Anhydrase Studied by Intrinsic Tryptophan Fluorescence 12:15 K. Sakakibara (Short Commun.) Molecular Design of the Amide Transition-state Analog by Molecular Mechanics 12:35 Lunch 14:00 Poster Session II 15:30 Coffee Break 16:00 M. Weir (Plenary) Role of Structural Biology in Drug Discovery 16:45 K. Mueller (Plenary) Combined Rational and Random Design Concepts in Drug Discovery 17:30 J. Priestle (Plenary) A Target Based Strategy for Drug Discovery 18:15 Close On this evening, participants are encouraged to attend the dinner at a wine cellar in the city centre. The "Heurigen" atmosphere, with wine and Viennese food is very characteristic of Vienna * Sunday 14.9.97 FOLDING +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9:00 Announcements 9:10 R. Baldwin (Plenary) Nature of the Apomyoglobin Folding Pathway 9:55 K. Dill (Plenary) Sightseeing along the Landscapes of Protein Folding 10:40 Coffee Break 11:10 C. Dobson (Plenary) Exploring the Structural Basis of Protein Folding 11:55 A. N=94ppert (Short Commun.) Initial Hydrophobic Collapse is not Necessary for Protein Folding: A Study by Stopped-Flow Dynamic Light Scattering and Stopped-Flow Circular Dichroism 12:15 I. Bahar (Short Commun.) Simulation of Protein Folds Using a Low Resolution Model 12:35 Lunch 14:00 P. Schuster (Plenary) RNA Structures Beyond the One Sequence-One Structure Paradigm 14:45 F. Hartl (Plenary) Chaperone-Assisted Protein Folding 15:30 End of Conference -------------------------------------------------------------------------- For further information contact: Dr. Andreas Kungl Gesellschaft Oesterreichischer Chemiker AG Biophysikalische Chemie Nibelungengasse 11 A-1010 Wien, Austria Tel.: ++ 43 1 5874249 or ++ 43 1 5873980 FAX.: ++ 43 1 5878966 e-mail: biophys@goech.co.at ============================================================================ Distribution: Followup-To: Organization: Univ. of Vienna, Inst. for Theoretical Chemistry Keywords: -- +-----------------------------------------------------------------------------+ | | | Hellfried Schreiber, Ph.D. | | | +---------------------------------------+-------------------------------------+ | | | | Institute for Theoretical Chemistry | | | Theoretical Biochemistry Group | Mail: hs@mdy.univie.ac.at | | Waehrigerstrasse 17 | Voice: +43 1 40480 - 618 | | A-1090 Wien, Austria, Europe | FAX: +43 1 4028525 | | | | +-----------------------------------------------------------------------------+ From owner-proteins@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!CC.USU.EDU!arsphys From: arsphys@CC.USU.EDU (Phil Harrison) Newsgroups: bionet.molbio.proteins Subject: Re: isozyme definition Date: 3 Sep 1997 09:23:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <3.0.1.32.19970903104211.006bc98c@cc.usu.edu> NNTP-Posting-Host: net.bio.net Robert DiSilvestro wrote: >I am reviewing a paper where the term "isozymes" is being used in a way I >do not typically use it. I'm not sure if my limited use is correct. I tend >to use the term for enzymes with similar catalytic activity, but fairly subtle >structural differences. Would one apply the term to 3 enzymes which >have totally different structures, but the same catalytic action? My tendency is the same as yours, but may I throw another term into the ring? Namely: --isoforms-- . I have understood this term to apply to very closely related forms of the same enzyme, differing perhaps in a single amino acid, or just a few, resulting in a slight shift in isoelectric point. So in an IEF gel you could get a group of closely separated bands with the same activity. How does this fit in with isozymes? Phil Harrison arsphys@cc.usu.edu From owner-proteins@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Luc CAMOIN Newsgroups: bionet.molbio.proteins Subject: RIA antibodies Date: 3 Sep 1997 13:53:41 +0100 Lines: 23 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5ujmkl$egs@mserv1.dl.ac.uk> X-Sender: camoin@icgm.cochin.inserm.fr Original-To: proteins@dl.ac.uk Dear everyone, I am trying to use an affinity purify polyclonal antibody in radioimmunoassay. I would like to have an idea of the microgram amount of antibody to use in this kind of experiment. Does any one have any experience in this matter? Thanks you for your time. Luc CAMOIN Institut _/_/_/_/ _/_/_/_/ _/_/_/_/ _/_/ _/ Luc CAMOIN Cochin _/ _/ _/ _/ _/ _/_/ CNRS UPR 415 de _/ _/ _/ _/_/ _/ _/ _/ 22 rue Mechain Genetique _/ _/ _/ _/ _/ _/ 75014 Paris France Moleculaire _/_/_/_/ _/_/_/_/ _/_/_/_/ _/ _/ Tel:+33 1 40 51 64 98 From owner-proteins@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!agate!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!feta.direct.ca!newsfeed.direct.ca!news-feed.inet.tele.dk!news.algonet.se!news-fra.maz.net!news-hh.maz.net!news-zh.switch.ch!elna.ethz.ch!not-for-mail From: werner@agrl.ethz.ch (Patricia Werner) Newsgroups: bionet.molbio.proteins Subject: rTEV-protease Date: 3 Sep 1997 12:25:04 GMT Organization: ETH Zuerich Lines: 14 Message-ID: <5ujkv0$apn$2@elna.ethz.ch> Reply-To: werner@inw.agrl.ethz.ch NNTP-Posting-Host: zb-153.ethz.ch X-Newsreader: WinVN 0.92.1 I hope somebody can help me! I am isolating a protein with His-Tag. In order to get rid of the poly-histidine I am doing a rTEV-protease digestion. The problem is, that in the end of the isolation the protein is in 4M Urea, 500 mM Imidazol, but the protein doesn't work with such high Urea concentrations. So I am trying to change the buffer by centrifugation with centricon concentrators from amicon. But yield is only about 10%. The protein seems to dissapear during the concentration procedure. I can find it neither in the flow-through, nor in the retentate. Thanks in advance Please send e-mail to: werner@inw.agrl.ethz.ch From owner-proteins@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!newsfeed.nacamar.de!news-hh.maz.net!news-zh.switch.ch!news.belnet.be!news.vub.ac.be!usenet From: Alain Jacquet Newsgroups: bionet.molbio.proteins Subject: outer membrane isolation Date: Wed, 03 Sep 1997 11:49:33 +0200 Organization: ULB Lines: 7 Message-ID: <340D32AD.17C2@sga.ulb.ac.be> NNTP-Posting-Host: sga-pc5.ulb.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win16; I) Dear readers Does anyone know a protocol for E.coli outer membrane isolation? Thanks in advance. Alain Jacquet From owner-proteins@net.bio.net Tue Sep 02 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!news.cis.ohio-state.edu!magnus.acs.ohio-state.edu!smtp.service.ohio-state.edu!rdisilvexx From: rdisilvexx@smtp.service.ohio-state.edu (Robert DiSilvestro) Newsgroups: bionet.molbio.proteins Subject: More info on the isoenzyme question Date: Wed, 3 Sep 1997 17:59:10 GMT Organization: The Ohio State University Lines: 11 Message-ID: NNTP-Posting-Host: 140.254.42.101 X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #4] I had posted about use of the term isozyme. Since I have gotten a few questions about how "subtle" the structural differences are between forms, let me just give some specifics. I had hesitated on this to avoid possibly "blowing my cover" as a reviewer. The enzymes are the superoxide dismutases (SODs). Two of them have active sites which contain copper and zinc, the other has an active site with manganese. The MWs are quite different for all 3, and antibodies to one generally don't react with the other two. Cells contain one of the Cu-Zn enzymes (mostly in the cytosol), and the one Mn enzyme (in the mitochondria). The other SOD is secreted to the outside of cells and is called extracellular SOD. Thus, these are three structurally distinct enzymes which have a similar enzyme activity. From owner-proteins@net.bio.net Wed Sep 03 23:00:00 1997 Path: biosci!agate!newsgate.duke.edu!nntprelay.mathworks.com!howland.erols.net!newsfeed1-hme1!newsfeed.internetmci.com!204.238.120.130!jump.net!grunt.dejanews.com!not-for-mail Date: Thu, 04 Sep 1997 15:05:03 -0600 From: mgross@midway.uchicago.edu Subject: ala dehydrotase assay Newsgroups: bionet.molbio.proteins,sci.bio.misc Message-ID: <873393184.22190@dejanews.com> Reply-To: mgross@midway.uchicago.edu Organization: Deja News Posting Service X-Article-Creation-Date: Thu Sep 04 17:13:07 1997 GMT X-Originating-IP-Addr: 128.135.90.30 (mgross1.bsd.uchicago.edu) X-Http-User-Agent: Mozilla/3.0 (Win16; I) X-Authenticated-Sender: mgross@midway.uchicago.edu Lines: 8 Does any one know of an method to detect aminolevulinic acid dehydrotase in a cell-free system? We are using rabbit reticulocyte extracts. Thanks -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-proteins@net.bio.net Wed Sep 03 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!dundee.ac.uk!mal.bioch.dundee.ac.uk!user From: mfwhite@bad.dundee.ac.uk (Malcolm White) Newsgroups: bionet.molbio.proteins Subject: Postdoc on archaeal recombination enzymes in Dundee, Scotland Date: 4 Sep 1997 08:09:08 GMT Organization: Dundee University Lines: 27 Message-ID: NNTP-Posting-Host: mal.bioch.dundee.ac.uk X-Newsreader: MT-NewsWatcher 2.3.1 THE UNIVERSITY OF DUNDEE DEPARTMENT OF BIOCHEMISTRY POSTDOCTORAL POSITION Purification of Holliday junction resolving enzymes from Archaea A three year position, funded by the BBSRC, is available from 1 November 1997 to purify and characterise Holliday junction endonucleases from archaeal sources. Experience in one or more of the following areas would be an advantage: protein purification, enzymology, DNA:protein interactions, molecular biology. Informal enquiries to Dr Malcolm White are encouraged (Tel. 01382-345111; FAX 01382-201063; E-mail mfwhite@bad.dundee.ac.uk; http://www.dundee.ac.uk/biochemistry/mfw.htm) Salary will be on the RA1A scale and start at up to £16,927 depending on age and experience. -- __________________________________________ Dr Malcolm F. White Honorary Lecturer University of Dundee Scotland From owner-proteins@net.bio.net Wed Sep 03 23:00:00 1997 Path: biosci!MAIL.CRYST.BBK.AC.UK!software From: software@MAIL.CRYST.BBK.AC.UK (software) Newsgroups: bionet.molbio.proteins Subject: Course Announcement - Principles of Protein Structure Date: 4 Sep 1997 02:46:42 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <340E83B4.FB58BD45@mail.cryst.bbk.ac.uk> NNTP-Posting-Host: net.bio.net An Advanced Certificate in Principles of Protein Structure Using the Internet '97/'98 --------------------------------------------------------------- Web site: http://www.cryst.bbk.ac.uk/PPS2/index.html We are pleased to announce that we are now accepting registrations for this course. This award winning course is taught purely over the internet and involves a number of innovative technologies including use of BioMOO for on-line tutorials, email discussion lists, and the WWW for course material. For more information please browse the URL given above. Please send any queries / requests for application forms to Claire Burton (c.burton@mail.cryst.bbk.ac.uk). The fee for students within the European Union is #260, for non-EEA students the cost is #575. Fee payments for overseas students are made by cheque in pounds sterling drawn on a British bank. From owner-proteins@net.bio.net Thu Sep 04 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!eerie.fr!jussieu.fr!u-psud.fr!not-for-mail From: bruno Collinet Newsgroups: bionet.molbio.proteins Subject: Dihydrofolate reductase and b-lactamase activities Date: Fri, 05 Sep 1997 11:50:23 +0200 Organization: Laboratoire de Modelisation et d'Ingénierie des Proteines (universite Paris-sud) Lines: 6 Message-ID: <340FD5DF.11F4@epcm.u-psud.fr> NNTP-Posting-Host: wagner.epcm.u-psud.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 [fr] (Win95; I) Hi, I am looking for a simple protocol to determine the activity of DHFR and beta-lactamase TEM1 of E-coli. I believe there are diferent protocols (among all the articles I have read) and i would know the most commonly used and admitted... Thank you for any help/reference you could give. From owner-proteins@net.bio.net Thu Sep 04 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsxfer3.itd.umich.edu!oleane!jussieu.fr!u-psud.fr!not-for-mail From: grima@iaf.cnrs-gif.fr (B. Grima) Newsgroups: bionet.molbio.proteins Subject: B galactosidase Date: 5 Sep 1997 15:40:17 GMT Organization: CNRS, Institut Alfred Fessard Lines: 5 Sender: -Not-Authenticated-[4959] Message-ID: <5up951$nl0$1@upsn21.u-psud.fr> NNTP-Posting-Host: mac38.iaf.cnrs-gif.fr X-Newsreader: InterNews 2.0@mac38.iaf.cnrs-gif.fr[U] XDisclaimer: User not authenticated hi I would like to measure in vitro B Gal activity in transformant flies. Who knows differences between CPRG assay and ONPG assay? Thanks in advance From owner-proteins@net.bio.net Sat Sep 06 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!howland.erols.net!newsxfer3.itd.umich.edu!gumby!newspump.wustl.edu!fas-news.harvard.edu!remeans From: remeans@fas.harvard.edu (Robert Means) Newsgroups: bionet.molbio.proteins Subject: High MW protein resolution Date: 7 Sep 1997 13:09:48 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 6 Message-ID: <5uu92s$5sc$1@news.fas.harvard.edu> NNTP-Posting-Host: login2.fas.harvard.edu X-Newsreader: TIN [version 1.2 PL2] Can anybody give me a pointer to a method for looking at very small shifts, say 2Kd in mobility in >100Kd proteins? I have tried running long, low percentage gels, but this doesn't seem to be enough. Thanks, Bob Means REMeans@fas.harvard.edu From owner-proteins@net.bio.net Sun Sep 07 23:00:00 1997 Path: biosci!CCVAX.MMC.EDU!willia48 From: willia48@CCVAX.MMC.EDU Newsgroups: bionet.molbio.proteins Subject: Workshop Announcement Date: 8 Sep 1997 10:45:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 75 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Workshop Announcement on Computer Applications in Neuroscience and Molecular Biology A workshop organized by Meharry Medical College will be held in Nashville, TN at Opryland Hotel, November 14-15, 1997 entitled, "Computers and the biological sciences" The workshop is intended to serve a broad audience of individuals, from advanced undergraduates to senior researchers wishing to incorporate new technologies into their research programs. Topics will range from approaches to database searching of protein sequences, and primary structure-function analyses to computational neuroscience, including modeling hippocampal function and studies of neural correlates of visual awareness. All individuals interested in potential uses of computer analyses in neuroscience and molecular biology are welcome. Applications for attendance are currently being solicited and early response is encouraged as the number of individuals who can participate will be limited in order to keep the workshop proceedings informal. In addition, there are a limited number of scholarships available to cover hotel and registration fees. A registration fee of $75 will be charged those not covered by scholarship. Speakers are listed below: Dr. George Wilcox, University of Minnesota Dr. Christian Halloy, University of Tennessee Dr. Neil Burgess, University College, London Dr. Apostostolos Georgopoulus, Minnesota Dr. Fabrizio Gabbiani, Cal Tech Dr. Stephen Altschul, NIH Dr. Barry Honig, Columbia University Dr. Temple Smith, Boston University In order to formally apply or for more information contact the Minority Biomedical Research Support (MBRS) Program at Meharry office at the following numbers: 615-327-6847 615-327-6179 (FAX) or address: MBRS Program Meharry Medical College 1005 DB Todd Blvd. Nashville, TN 37208 Alternatively, you may contact via e-mail either: Dr. Sanika Chirwa at chirwa83@ccvax.mmc.ed or Dr. Scott Williams at willia48@cccvax.mmc.edu Note applications should include a CV, a letter indicating your interest in this symposium and how it would benefit your career/educational program. Minorities are encouraged to apply. From owner-proteins@net.bio.net Sun Sep 07 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!newsfeed.dacom.co.kr!feta.direct.ca!newsfeed.direct.ca!news.he.net!supernews.com!Supernews69!not-for-mail From: dalmiabk@phibred.com (bipin k. dalmia) Newsgroups: bionet.molbio.proteins Subject: Re: High MW protein resolution Date: Mon, 08 Sep 1997 17:36:53 GMT Organization: All USENET -- http://www.Supernews.com Lines: 26 Message-ID: <34143728.334286787@207.126.101.81> References: <5uu92s$5sc$1@news.fas.harvard.edu> NNTP-Posting-Host: 2428@204.233.143.2 X-Newsreader: Forte Free Agent 1.1/32.230 On 7 Sep 1997 13:09:48 GMT, remeans@fas.harvard.edu (Robert Means) wrote: > > Can anybody give me a pointer to a method for looking at very >small shifts, say 2Kd in mobility in >100Kd proteins? I have tried running >long, low percentage gels, but this doesn't seem to be enough. Thanks, >Bob Means >REMeans@fas.harvard.edu > i assume you are trying SDS-PAGE. how about IEF gels? the 2 kDa change may change the pI enough to allow resolution. or if you have purified protein, try SDS-PAGE of some kind of a partial digest of the protein and look for difference in banding patterns. then there always is mass-spec. bip Bipin K. Dalmia, Ph.D. Protein Expression and Purification Pioneer Hi-Bred International, Inc. Johnston, Iowa 50131 dalmiabk@phibred.com From owner-proteins@net.bio.net Mon Sep 08 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!news-ge.switch.ch!news-zh.switch.ch!elna.ethz.ch!not-for-mail From: werner@inw.agrl.ethz.ch (Patricia Werner) Newsgroups: bionet.molbio.proteins Subject: subscribe Date: 9 Sep 1997 11:26:06 GMT Organization: ETH Zuerich Lines: 1 Message-ID: <5v3boe$npe$1@elna.ethz.ch> NNTP-Posting-Host: zb-153.ethz.ch X-Newsreader: WinVN 0.92.1 subscribe bionet.molbio.proteins From owner-proteins@net.bio.net Mon Sep 08 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!warwick!bham!not-for-mail From: Annonymous Newsgroups: bionet.molbio.proteins Subject: Old MBR Fermenters Date: Tue, 09 Sep 1997 10:23:08 +0100 Organization: The University of Birmingham, UK. Lines: 8 Message-ID: <3415157B.B7DED39E@bham.ac.uk> NNTP-Posting-Host: bcs177.bham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0 [en] (Win95; I) X-Priority: 3 (Normal) I have an old MBR mini bioreactor 1 litre continuous fermenter which it is now difficult and expensive to get parts for. I'm looking for anyone who has one of these lying around unused and unwanted. Please contact Sarah Lissenden at Birmingham University on s.lissenden@bham.ac.uk for further information. Thanks From owner-proteins@net.bio.net Mon Sep 08 23:00:00 1997 Path: biosci!ALPHA.INCQS.FIOCRUZ.BR!ivano From: ivano@ALPHA.INCQS.FIOCRUZ.BR (Ivano de Filippis) Newsgroups: bionet.molbio.proteins Subject: Re: More info on the isoenzyme question Date: 9 Sep 1997 10:45:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <9709101755.AA02272@alpha.incqs.fiocruz.br> NNTP-Posting-Host: net.bio.net At 17:59 03/09/97 GMT, you wrote: >I had posted about use of the term isozyme. Since I have gotten a few >questions about how "subtle" the structural differences are between forms, let >me just give some specifics. I had hesitated on this to avoid possibly >"blowing my cover" as a reviewer. The enzymes are the superoxide >dismutases (SODs). Two of them have active sites which contain copper and >zinc, the other has an active site with manganese. The MWs are quite >different for all 3, and antibodies to one generally don't react with the >other two. Cells contain one of the Cu-Zn enzymes (mostly in the cytosol), >and the one Mn enzyme (in the mitochondria). The other SOD is secreted to the >outside of cells and is called extracellular SOD. Thus, these are three >structurally distinct enzymes which have a similar enzyme activity. > > As I mentioned before (to your personal e-mail), if the three enzymes have the same catalystic activities, they are isoenzymes [iso(functional)enzymes]. Regards, Ivano de Filippis Fundacao Oswaldo Cruz - FIOCRUZ Instituto Nacional de Controle de Qualidade em Saude - INCQS Depto. de Microbiologia Lab. de Materiais de Referencia Av. Brasil, 4365 - Manguinhos Rio de Janeiro - 21045-900 - BRASIL Tel.: 55-21-598-4290/4291/4292/4293 FAX: 55-21-290-0915 E-mail: ivano@alpha.incqs.fiocruz.br From owner-proteins@net.bio.net Mon Sep 08 23:00:00 1997 Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!nntp.news.xara.net!xara.net!news.maxwell.syr.edu!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!128.228.4.60!news.cuny.edu!nntp.upenn.edu!taurus.fccc.edu!not-for-mail From: Gordon Chan Newsgroups: bionet.molbio.proteins Subject: Re: High MW protein resolution Date: Tue, 09 Sep 1997 17:53:47 +0000 Organization: Fox Chase Cancer Center Lines: 4 Message-ID: <34158D2A.43D@fccc.edu> References: <5uu92s$5sc$1@news.fas.harvard.edu> NNTP-Posting-Host: injector.fccc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.02Gold (Macintosh; U; 68K) Try lower cross-linker ratio, we have good success with 8.5% gel (acrylamide:bis, 100:1). We work with proteins that are larger than 300kd. Good luck. From owner-proteins@net.bio.net Tue Sep 09 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!univ-lyon1.fr!jussieu.fr!citi2.fr!federici.cochin.inserm.fr!user From: federici@icgm.cochin.inserm.fr (Federici) Newsgroups: bionet.molbio.proteins Subject: Re: Concentrating Membrane Proteins Date: 10 Sep 1997 07:10:43 GMT Organization: ICGM CNRS UPR415 Lines: 18 Message-ID: References: <19970901030801.XAA01638@ladder02.news.aol.com> NNTP-Posting-Host: federici.cochin.inserm.fr X-Newsreader: Yet Another NewsWatcher F2.0 In article (Dans l'article) <19970901030801.XAA01638@ladder02.news.aol.com>, rsjolund@aol.com (RSjolund) wrote (écrivait) : > I've got a 32 kDa protein from a plant cell plasma membrane. It is > extracted well in a medium containing CHAPS, but if I precipitate it with > ammonium sulphate (40% saturation) if does NOT go back into solution. > What are some good techniques for concentrating the protein (prior to 2D > gels). The goal is to sequence the protein. > > Dick Sjolund > Biological Sciences > Univ. of Iowa > > r-sjolund@uiowa.edu Hi! Have you tried filtration upon membrane, using concentrators of Amicon? From owner-proteins@net.bio.net Tue Sep 09 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!europa.clark.net!164.124.107.4!newsfeed.dacom.co.kr!newsfeed.kornet.nm.kr!news-stock.gsl.net!gsl-penn-ns.gsl.net!news.gsl.net!gip.net!news.belnet.be!news.vub.ac.be!usenet From: erik jongert Newsgroups: bionet.molbio.proteins Subject: Salmonella aro clones Date: Wed, 10 Sep 1997 18:20:26 +0200 Organization: Vrije Universirteit Brussel Lines: 9 Message-ID: <3416C8CA.50D@vub.ac.be> NNTP-Posting-Host: imolpc35.vub.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Hello, I'm looking for plasmids encoding Salmonella typhimurium aroC or aroD. I'd like to use the aro genes for gene replacement into Salmonella typhimurium. If you have a plasmid encoding one of these genes please contact me: ejongert@vub.ac.be thanx From owner-proteins@net.bio.net Tue Sep 09 23:00:00 1997 Path: biosci!U.WASHINGTON.EDU!egn From: egn@U.WASHINGTON.EDU ("E. Kolker") Newsgroups: bionet.molbio.proteins Subject: (none) Date: 10 Sep 1997 20:33:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 202 Sender: daemon@net.bio.net Distribution: world Message-ID: <199709110333.UAA11576@saul7.u.washington.edu> NNTP-Posting-Host: net.bio.net CALL FOR PAPERS SECOND ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB 98) March 22 - 25, 1998 New York City Sponsored by Association for Computing Machinery SIGACT with support from SLOAN Foundation US Department of Energy http://www.mssm.edu/biomath/recomb98.html The Second Annual Conference on Research in Computational Molecular Biology (RECOMB 98), sponsored by the Association for Computing Machinery Special Interest Group on Algorithms and Computation Theory (ACM-SIGACT) with support from the SLOAN Foundation, and US Department of Energy will be held in New York City, March 22 - 25, 1998. Papers reporting on original research (both theoretical and experimental) in all areas of computational molecular biology are sought, including surveys of important recent results/directions. Typical but not exclusive topics of interest include: - Genomics - Molecular sequence analysis - Recognition of genes and regulatory elements - Molecular evolution - Protein structure - Combinatorial libraries and drug design ABSTRACT SUBMISSION: Authors are requested to send 10 copies (preferably two sided copies) of a detailed extended abstract (5-10 pages) to: Professor Pavel Pevzner RECOMB 98 Program Chair University of Southern California Department of Mathematics, DRB 155 Los Angeles, CA 90089-1113 An abstract must be received by October 20, 1997. This is a firm deadline. Simultaneous submission to another conference or journal is allowed. CONFERENCE PROCEEDINGS: The extended abstracts for the Conference will be published by ACM Press and will be available at the Conference. A selection of the accepted extended abstracts in their final journal versions will be invited to appear in a special issue of the Journal of Computational Biology devoted to RECOMB 98. NOTIFICATION: The conference submissions will be refereed by the program committee. Authors will be notified of acceptance or rejection by a letter mailed on or before December 15, 1997. A final copy of each accepted paper is required by January 10, 1997. An author of each accepted paper is expected to attend the Symposium and present the paper; otherwise alternative arrangements should be made to have the paper presented. ABSTRACT PREPARATION: An abstract should start with a succinct statement of the problem, the results achieved, their significance and a comparison with previous work. This material should be understandable to nonspecialists. A technical exposition directed to the specialist should follow. The length, excluding cover page and bibliography, should not exceed 10 pages. The manuscript should be easy to read, preferably using 11 point font size on U.S. standard 8 1/2 by 11 inch paper. If authors believe that more details are necessary to substantiate the claims of the paper, they may include a clearly marked appendix. An E-mail address for the contact author should be included. INVITED SPEAKERS: Charles Cantor (Boston University) Thomas Caskey (Merck) David Cox (Stanford University) Ron Davis (Stanford University) Klaus Gubernator (CombiChem) Joshua Lederberg (Rockfeller University) Michael Levitt (Stanford University) David Schwartz (New York University) John Yates (University of Washington) CONFERENCE EVENTS RECOMB 98 will feature 9 invited lectures including the following conference events: THE STANISLAW ULAM MEMORIAL COMPUTATIONAL BIOLOGY ADDRESS awarded by RECOMB to a scientist who has made major contributions in the computational aspects of the field. Professor Joshua Lederberg of Rockfeller University will deliver the Statislav Ulam Memorial Computational Biology Address. THE DISTINGUISHED BIOLOGY LECTURE awarded by RECOMB to a scientist who has made major contributions in the biological aspects of the field. Professor Ron Davis of Stanford University will deliver the Distinguished Biology Lecture. THE DISTINGUISHED NEW TECHNOLOGIES LECTURE describing emerging, new technologies. Professor David Cox of Stanford University will deliver the Distinguished New Technologies Lecture. BEST PAPER BY A YOUNG SCIENTIST AWARD. This award will be given to the best paper written solely by one or more recent graduates or students. An abstract is eligible if all authors are recent graduates (within 2 years from Ph.D.) or full-time students at the time of submission. This should be indicated in the submission letter. The program committee may decline to make the award or may split it among several papers. STEERING COMMITTEE: Sorin Istrail, RECOMB General Vice-Chair (Sandia National Laboratories) Richard Karp (University of Washington) Thomas Lengauer (GMD-SCAI, Germany) Pavel Pevzner, RECOMB General Chair (University of Southern California) Ron Shamir (Tel-Aviv University, Israel) Michael Waterman, RECOMB General Chair (University of Southern California) PROGRAM COMMITTEE: Craig Benham (Mount Sinai School of Medicine) Gary Benson (Mount Sinai School of Medicine) Bonnie Berger (MIT) Martin Farach (Rutgers University) Phil Green (University of Washington) Dan Gusfield (University of California Davis) David Haussler (University of California Santa Cruz) Sorin Istrail (Sandia National Laboratories) Richard Karp (University of Washington) Minoru Kanehisa (Kyoto University, Japan) Eugene Koonin (National Center for Biotechnology Information) Thomas Lengauer (GMD-SCAI, Germany) Webb Miller (Pennsylvania State University) Gene Myers (University of Arizona) Pavel Pevzner, Program Committee Chair (University of Southern California) David Searls (SmithKline Beecham) Ron Shamir (Tel-Aviv University, Israel) Terry Speed (University of California Berkeley) Martin Vingron (German Cancer Center) Michael Waterman (University of Southern California) ORGANIZING COMMITTEE: Craig Benham (Mount Sinai School of Medicine) Gary Benson, Conference Chair (Mount Sinai School of Medicine) Martin Farach (Rutgers University) Eugene Kolker, Publicity Chair (University of Washington) Information about local arrangements can be obtained by consulting the conference web page http://www.mssm.edu/biomath/recomb98.html or from the Conference Chair: Professor Gary Benson Department of Biomathematical Sciences Box 1023 The Mount Sinai Medical Center One Gustave L. Levy Place New York, NY 10029-6574 (212) 241-5777 phone (212) 860-4630 fax benson@ecology.biomath.mssm.edu -------------------------------------------------------------------- Eugene Kolker Dept of Molecular Biotechnology, Box 357730 Tel: +1-206-685-6941 University of Washington School of Medicine Fax: +1-206-685-7301 Seattle, WA 98195-7730, USA egn@u.washington.edu NEW (!) WEB: http://bozeman.genome.washington.edu/~eugene From owner-proteins@net.bio.net Tue Sep 09 23:00:00 1997 Path: biosci!IR2CBM.CNRS-MRS.FR!athel From: athel@IR2CBM.CNRS-MRS.FR (Athel) Newsgroups: bionet.molbio.proteins Subject: Re: More info on the isoenzyme question Date: 10 Sep 1997 01:55:14 -0700 Organization: CNRS Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <341660EB.53A@ibsm.cnrs-mrs.fr> Reply-To: athel@ir2cbm.cnrs-mrs.fr NNTP-Posting-Host: net.bio.net Robert DiSilvestro wrote: >I had posted about use of the term isozyme. >Since I have gotten a few questions about how >"subtle" the structural differences are between >forms, let me just give some specifics. I had >hesitated on this to avoid possibly "blowing >my cover" as a reviewer. The enzymes are the >superoxide dismutases (SODs). Two of them have >active sites which contain copper and zinc, the >other has an active site with manganese... After reading your original question, but before seeing the above, I was going to comment that until the growth of molecular genetics superoxide dismutase was the only well known example of the sort of thing you are talking about. Maybe that is still true, as I can't immediately think of another example. In general I wouldn't talk about isoenzymes when the enzymes occur in different organisms, but only when two proteins catalysing the same reaction occur in the same organism. So far as superoxide dismutase is concerned this largely deals with your problem, because nearly all organisms either have Cu/Zn enzymes or they have Mn enzymes; they don't usually have both. However, the light-emitting bacterium Photobacter leiognathi has a Cu/Zn enzyme, more usually found in higher organisms, and it probably has a Mn enzyme as well (I don't remember). If so, I think it has isoenzymes regardless of how different in structure they are. The Cu/Zn enzyme of Photobacter leiognathi was reported by Martin and Fridovich in J. Biol. Chem. 256, 6080-6089 (1981), incidentally. Athel Cornish-Bowden From owner-proteins@net.bio.net Tue Sep 09 23:00:00 1997 Message-ID: <34152352.59E2@came.sbg.ac.at> Date: Tue, 09 Sep 1997 12:22:10 +0200 From: Walter Koppensteiner Organization: Center for Applied Molecular Engineering X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 Newsgroups: bionet.molbio.proteins Subject: Non-redundant list of protein complexes Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: agnes.came.sbg.ac.at Lines: 20 Path: biosci!bloom-beacon.mit.edu!thetimes.pixel.kodak.com!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!206.229.87.50!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!194.59.190.100!newsfeed.ecrc.net!newscore.univie.ac.at!03-newsfeed.univie.ac.at!news.sbg.ac.at!agnes.came.sbg.ac.at Hi, does anybody have extracted a list of non-redundant protein complexes from the PDB. I want to analyse intermolecular interactions and need a representative dataset of 3D structures. The pdb_select list from embl only lists monomeric chains. Also a list of protein/dna(rna) complexes would be appreciated. Thanks in advance, Walter -- =============================================================== Walter Koppensteiner University of Salzburg Center of Applied Molecular Engineering Jakob Haringer Strasse 3 Phone: +43-662-8044-5794 A-5020 Salzburg, Austria Email: walter@came.sbg.ac.at =============================================================== From owner-proteins@net.bio.net Wed Sep 10 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.nacamar.de!fu-berlin.de!informatik.tu-muenchen.de!news.ruhr-uni-bochum.de!not-for-mail From: "Thorsten Schmidt" Newsgroups: bionet.molbio.proteins Subject: How to deglycosylate a protein? Date: 11 Sep 1997 20:59:26 GMT Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 23 Message-ID: <01bcbef5$9e16f1a0$30019386@schmidtdw.rz.ruhr-uni-bochum.de> NNTP-Posting-Host: dialppp-1-48.rz.ruhr-uni-bochum.de X-Newsreader: Microsoft Internet News 4.70.1155 Dear reader! I examine a protein which I can detect by Western Blots. It is detected at a higher molecular wight than expected according to the aminoacid sequence. I now want to test whether it is glycosylated or not! How can I do this? What do I need? Are there enzymes/kits availible for deglycosylation? Are there different types of protein glycolysation and can I examine them all just with one test? Can I conclude protein glycosylation just from special aminoacid sequences? It would be too kind if you´ll send me an answer Thank you so much in advance Thorsten Schmidt From owner-proteins@net.bio.net Wed Sep 10 23:00:00 1997 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.molbio.proteins Subject: RECOMB98 Invited Speakers Date: 11 Sep 1997 14:35:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 204 Sender: daemon@net.bio.net Distribution: world Message-ID: <199709112135.OAA30679@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net CALL FOR PAPERS SECOND ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB 98) March 22 - 25, 1998 New York City Sponsored by Association for Computing Machinery SIGACT with support from SLOAN Foundation US Department of Energy http://www.mssm.edu/biomath/recomb98.html The Second Annual Conference on Research in Computational Molecular Biology (RECOMB 98), sponsored by the Association for Computing Machinery Special Interest Group on Algorithms and Computation Theory (ACM-SIGACT) with support from the SLOAN Foundation, and US Department of Energy will be held in New York City, March 22 - 25, 1998. Papers reporting on original research (both theoretical and experimental) in all areas of computational molecular biology are sought, including surveys of important recent results/directions. Typical but not exclusive topics of interest include: - Genomics - Molecular sequence analysis - Recognition of genes and regulatory elements - Molecular evolution - Protein structure - Combinatorial libraries and drug design ABSTRACT SUBMISSION: Authors are requested to send 10 copies (preferably two sided copies) of a detailed extended abstract (5-10 pages) to: Professor Pavel Pevzner RECOMB 98 Program Chair University of Southern California Department of Mathematics, DRB 155 Los Angeles, CA 90089-1113 An abstract must be received by October 20, 1997. This is a firm deadline. Simultaneous submission to another conference or journal is allowed. CONFERENCE PROCEEDINGS: The extended abstracts for the Conference will be published by ACM Press and will be available at the Conference. A selection of the accepted extended abstracts in their final journal versions will be invited to appear in a special issue of the Journal of Computational Biology devoted to RECOMB 98. NOTIFICATION: The conference submissions will be refereed by the program committee. Authors will be notified of acceptance or rejection by a letter mailed on or before December 15, 1997. A final copy of each accepted paper is required by January 10, 1997. An author of each accepted paper is expected to attend the Symposium and present the paper; otherwise alternative arrangements should be made to have the paper presented. ABSTRACT PREPARATION: An abstract should start with a succinct statement of the problem, the results achieved, their significance and a comparison with previous work. This material should be understandable to nonspecialists. A technical exposition directed to the specialist should follow. The length, excluding cover page and bibliography, should not exceed 10 pages. The manuscript should be easy to read, preferably using 11 point font size on U.S. standard 8 1/2 by 11 inch paper. If authors believe that more details are necessary to substantiate the claims of the paper, they may include a clearly marked appendix. An E-mail address for the contact author should be included. INVITED SPEAKERS: Charles Cantor (Boston University) Thomas Caskey (Merck) David Cox (Stanford University) Ron Davis (Stanford University) Klaus Gubernator (CombiChem) Joshua Lederberg (Rockfeller University) Michael Levitt (Stanford University) David Schwartz (New York University) John Yates (University of Washington) CONFERENCE EVENTS RECOMB 98 will feature 9 invited lectures including the following conference events: THE STANISLAW ULAM MEMORIAL COMPUTATIONAL BIOLOGY ADDRESS awarded by RECOMB to a scientist who has made major contributions in the computational aspects of the field. Professor Joshua Lederberg of Rockfeller University will deliver the Statislav Ulam Memorial Computational Biology Address. THE DISTINGUISHED BIOLOGY LECTURE awarded by RECOMB to a scientist who has made major contributions in the biological aspects of the field. Professor Ron Davis of Stanford University will deliver the Distinguished Biology Lecture. THE DISTINGUISHED NEW TECHNOLOGIES LECTURE describing emerging, new technologies. Professor David Cox of Stanford University will deliver the Distinguished New Technologies Lecture. BEST PAPER BY A YOUNG SCIENTIST AWARD. This award will be given to the best paper written solely by one or more recent graduates or students. An abstract is eligible if all authors are recent graduates (within 2 years from Ph.D.) or full-time students at the time of submission. This should be indicated in the submission letter. The program committee may decline to make the award or may split it among several papers. STEERING COMMITTEE: Sorin Istrail, RECOMB General Vice-Chair (Sandia National Laboratories) Richard Karp (University of Washington) Thomas Lengauer (GMD-SCAI, Germany) Pavel Pevzner, RECOMB General Chair (University of Southern California) Ron Shamir (Tel-Aviv University, Israel) Michael Waterman, RECOMB General Chair (University of Southern California) PROGRAM COMMITTEE: Craig Benham (Mount Sinai School of Medicine) Gary Benson (Mount Sinai School of Medicine) Bonnie Berger (MIT) Martin Farach (Rutgers University) Phil Green (University of Washington) Dan Gusfield (University of California Davis) David Haussler (University of California Santa Cruz) Sorin Istrail (Sandia National Laboratories) Richard Karp (University of Washington) Minoru Kanehisa (Kyoto University, Japan) Eugene Koonin (National Center for Biotechnology Information) Thomas Lengauer (GMD-SCAI, Germany) Webb Miller (Pennsylvania State University) Gene Myers (University of Arizona) Pavel Pevzner, Program Committee Chair (University of Southern California) David Searls (SmithKline Beecham) Ron Shamir (Tel-Aviv University, Israel) Terry Speed (University of California Berkeley) Martin Vingron (German Cancer Center) Michael Waterman (University of Southern California) ORGANIZING COMMITTEE: Craig Benham (Mount Sinai School of Medicine) Gary Benson, Conference Chair (Mount Sinai School of Medicine) Martin Farach (Rutgers University) Eugene Kolker, Publicity Chair (University of Washington) Information about local arrangements can be obtained by consulting the conference web page http://www.mssm.edu/biomath/recomb98.html or from the Conference Chair: Professor Gary Benson Department of Biomathematical Sciences Box 1023 The Mount Sinai Medical Center One Gustave L. Levy Place New York, NY 10029-6574 (212) 241-5777 phone (212) 860-4630 fax benson@ecology.biomath.mssm.edu Sorry, if you get this mail twice. -------------------------------------------------------------------- Eugene Kolker Dept of Molecular Biotechnology, Box 357730 Tel: +1-206-685-6941 University of Washington School of Medicine Fax: +1-206-685-7301 Seattle, WA 98195-7730, USA egn@u.washington.edu NEW (!) WEB: http://bozeman.genome.washington.edu/~eugene From owner-proteins@net.bio.net Wed Sep 10 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!panix!news.panix.com!not-for-mail From: iayork@panix.com (Ian A. York) Newsgroups: bionet.molbio.proteins Subject: Re: How to deglycosylate a protein? Date: 11 Sep 1997 17:45:31 -0400 Organization: Panix Lines: 46 Message-ID: <5v9opr$avp@panix.com> References: <01bcbef5$9e16f1a0$30019386@schmidtdw.rz.ruhr-uni-bochum.de> NNTP-Posting-Host: panix.com X-Newsposter: trn 4.0-test55 (26 Feb 97) In article <01bcbef5$9e16f1a0$30019386@schmidtdw.rz.ruhr-uni-bochum.de>, Thorsten Schmidt wrote: > >I now want to test whether it is glycosylated or not! >How can I do this? What do I need? If it's N-glycosylated, treatment with endoglycosidase F will cleave the glycoproteins and you'll see the MW of the protein drop. If it's O-glycosylated ... someone else will hae to tell you what to use because I can't remember. EndoF is available from various places; I most recently got it from New England Biolabs, which calls it "peptide: N-glycosidase F (PNGase F)". >Are there enzymes/kits availible for deglycosylation? NEB sells it as a kit with instructions. It's very simple. >Are there different types of protein glycolysation and can I examine >them all just with one test? There are many kinds of N-glycosylation, but as far as I know EndoF will strip off all of them. You can refine the analysis with other enzymes, if you want. As for O-glycosylation, that's less likely to be causing the MW shift you see (in my humble and no doubt ill-informed opinion), so you'll want to start with Endo F. >Can I conclude protein glycosylation just from special aminoacid sequences? You can make guesses. You need to see a signal sequence (because the protein has to be transferred into the endoplasmic reticulum for the glycosylation machinery to reach it) plus either NXT or NXS. The presence of these does not guarantee that they'll be used, but if you see these in the presence of a MW shift the odds are pretty good that they are used, I think. Hope this helps. Ian -- Ian York (iayork@panix.com) "-but as he was a York, I am rather inclined to suppose him a very respectable Man." -Jane Austen, The History of England From owner-proteins@net.bio.net Wed Sep 10 23:00:00 1997 Newsgroups: bionet.molbio.proteins Path: biosci!rutgers!rockyd!notes From: Satish Nair Subject: Re: GST fusions and antibodies X-Nntp-Posting-Host: skbind2.rockefeller.edu Content-Type: text/plain; charset=us-ascii Message-ID: <34187F1F.41C6@rockvax.rockefeller.edu> Sender: notes@rockyd.rockefeller.edu (News Administrator) Content-Transfer-Encoding: 7bit Organization: Rockefeller University References: Mime-Version: 1.0 Date: Thu, 11 Sep 1997 23:30:39 GMT X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) Lines: 26 Mara Michelle Casar wrote: > > I am trying to get some information about producting antibodies to GST > fusion proteins. I have two proteins I want to send off for > immunizations, but I need advice first: > > 1. To cleave or not to cleave? My fused piece is about 9 kD, and seems > pretty stable, but is it better to send the whole protein, which should > be more immunogenic? > > 2. Any recommendations on companies? My lab has used Cocalico before, but > I'm open to suggestions. > > If you have done this, please send me your thoughts on the matter... I > have heard lots of conflicting things from many people! > > Thanks in advance, > Mara Casar Hi, I don't know how relevant this may be to you but there are anti-GST antibodies available which may serve your purpose (I think Pharmacia sells them but please don't consider this a plug). If you want an antibody that uses part of your fusion peptide as an epitope, then you'd certaintly want to cleave. From owner-proteins@net.bio.net Wed Sep 10 23:00:00 1997 Path: biosci!agate!newsgate.duke.edu!godzilla4.acpub.duke.edu!mmc9 From: Mara Michelle Casar Newsgroups: bionet.molbio.proteins Subject: GST fusions and antibodies Date: Thu, 11 Sep 1997 13:45:26 -0400 Organization: Duke University, Durham, NC, USA Lines: 18 Message-ID: NNTP-Posting-Host: godzilla4.acpub.duke.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am trying to get some information about producting antibodies to GST fusion proteins. I have two proteins I want to send off for immunizations, but I need advice first: 1. To cleave or not to cleave? My fused piece is about 9 kD, and seems pretty stable, but is it better to send the whole protein, which should be more immunogenic? 2. Any recommendations on companies? My lab has used Cocalico before, but I'm open to suggestions. If you have done this, please send me your thoughts on the matter... I have heard lots of conflicting things from many people! Thanks in advance, Mara Casar (reply to casar@niehs.nih.gov or to the above address) From owner-proteins@net.bio.net Thu Sep 11 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!hunter.premier.net!uunet!in1.uu.net!128.230.129.112!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!dundee.ac.uk!not-for-mail From: James Abbott Newsgroups: bionet.molbio.proteins Subject: Re: Need a tip about colony lift Date: Fri, 12 Sep 1997 19:45:10 -0700 Organization: University of Dundee Lines: 18 Message-ID: <3419FE36.2EDF@dundee.ac.uk> References: <3419655E.F8AAB8DE@med.kuleuven.ac.be> NNTP-Posting-Host: ch1.biolsci.dundee.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Stephane Jenne wrote: > The trouble is that I do not lift all colonies on one hand and > that I lift the whole colony on the other hand. I would rather prefer > to have a part of all the colonies. When you do a colony lift, you do not remove all the bacteria from your plate. Consequently, to enable you to go back to your colonies when you've selected your required recombinants via the colony blot, simply reincubate the plate, and your colonies will grow again. The only word of warning doing this is to watch your aseptic techniques, since any antibiotics in your media will probably be quite depleted, so if you are not careful, you may find all kinds of lovely things growing :-) I know this isn't quite what your question asked for, but it's a different way round the problem. James From owner-proteins@net.bio.net Thu Sep 11 23:00:00 1997 Path: biosci!agate!howland.erols.net!EU.net!news0.Belgium.EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!usenet From: Stephane Jenne Newsgroups: bionet.molbio.proteins Subject: Need a tip about colony lift Date: Fri, 12 Sep 1997 17:53:12 +0200 Organization: K.U.Leuven Lines: 11 Message-ID: <3419655E.F8AAB8DE@med.kuleuven.ac.be> Reply-To: stephane.jenne@med.kuleuven.ac.be NNTP-Posting-Host: proxy.med.kuleuven.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 (Macintosh; I; 68K) X-Priority: 2 (High) Hi guys, I have a slight problem with a screening experiment, it involvres the lifting of colonies from a LB agar plate using a nitrocellulose filter> The trouble is that I do not lift all colonies on one hand and that I lift the whole colony on the other hand. I would rather prefer to have a part of all the colonies. Does someone have experience about that, all ideas are welcome. Thanks =;-) From owner-proteins@net.bio.net Thu Sep 11 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!news-ge.switch.ch!newscore.univie.ac.at!newsfeed.ecrc.net!news-feed1.eu.concert.net!news.worldonline.nl!not-for-mail From: "Kenneth Jie" Newsgroups: bionet.molbio.proteins Subject: enzyms Date: 12 Sep 1997 14:59:52 GMT Organization: Jie Lines: 7 Message-ID: <01bcbf8c$88ff7160$1b97f1c3@kenneth> NNTP-Posting-Host: gd1-p27.worldonline.nl X-Newsreader: Microsoft Internet News 4.70.1157 Hello, If you have some questions, with answers about enzyms, please e-mail them to me, I need them for my school. My e-mail addres is: kjie@knmg.nl From owner-proteins@net.bio.net Thu Sep 11 23:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!pitt.edu!portc02.blue.aol.com!prodigy.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.nacamar.de!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.gwdg.de!not-for-mail From: Christian Ebeling Newsgroups: bionet.molbio.proteins Subject: need pET-vector Date: Thu, 11 Sep 1997 17:06:09 +0200 Organization: GWDG, Goettingen Lines: 12 Message-ID: <341808E1.7F02@gwdg.de> Reply-To: cebelin@gwdg.de NNTP-Posting-Host: ubmgpf.uni-molgen.gwdg.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0Gold (WinNT; I) Christian Ebeling Institute of Molecular Genetics Griesebachstr. 8 37077 Götingen Tel.:399654 e-mail: cebelin@gwdg.de I need a pET-vector with a Kan-resistance or/and the restrictions sites NdeI/NcoI. Could anyone help me and send me DNA? I have the pET-vector pET21d. Perhaps i can help you. From owner-proteins@net.bio.net Thu Sep 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!208.134.241.18!newsfeed1-hme1!newsfeed.internetmci.com!204.238.120.130!jump.net!grunt.dejanews.com!not-for-mail Date: Fri, 12 Sep 1997 22:52:00 -0600 From: ttadifa@penlabs.com Subject: Re: peptide synthesis for antibody Newsgroups: bionet.molbio.proteins Message-ID: <874116728.17944@dejanews.com> Organization: Deja News Posting Service References: X-Article-Creation-Date: Sat Sep 13 02:12:10 1997 GMT X-Originating-IP-Addr: 206.245.233.86 (scar1-fw1-glbl1-pat.actioninc.com) X-Http-User-Agent: Mozilla/2.0 (compatible; MSIE 3.01; AK; Windows 95) X-Authenticated-Sender: ttadifa@penlabs.com Lines: 16 In article , Sandra Pena De Ortiz wrote: > > Hi: > > What is the smallest number of amino acid residues in a peptide to > produce a polyclonal antibody? Thanks in advance > > Sandra Pena de Ortiz, Ph.D. Minimum 16 residues. Amrit -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-proteins@net.bio.net Thu Sep 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!news-peer.bt.net!btnet-feed1!btnet!zetnet.co.uk!user From: nigel.osborn@zetnet.co.uk (Nigel J.Osborn) Newsgroups: bionet.molbio.proteins Subject: Protein sequence databases Date: Fri, 12 Sep 1997 20:50:02 -0100 Organization: Amersham, Bucks Lines: 9 Message-ID: NNTP-Posting-Host: man-056.dialup.zetnet.co.uk I'm trying to find any protein sequence databases available for non-academic people on the Internet. I'm especially interested in ones that might have sequences for Hepetitis antigens. Anyone know of any? Nigel. From owner-proteins@net.bio.net Thu Sep 11 23:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!newsfeed.internetmci.com!193.174.75.126!news-was.dfn.de!news-kar1.dfn.de!news-stu1.dfn.de!news-mue1.dfn.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: GST fusions and antibodies Date: Fri, 12 Sep 1997 11:14:30 +0200 Organization: University of Wuerzburg, Germany Lines: 18 Message-ID: References: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Mara Michelle Casar (mmc9@acpub.duke.edu) wrote: > I am trying to get some information about producting antibodies to GST > fusion proteins. I have two proteins I want to send off for > immunizations, but I need advice first: > > 1. To cleave or not to cleave? My fused piece is about 9 kD, and seems > pretty stable, but is it better to send the whole protein, which should > be more immunogenic? However, you would then have to purify your serum over a GST-GSH column since you will get a lot of anti-GST. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Fri Sep 12 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.proteins Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 13 Sep 1997 02:00:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199709130900.CAA11376@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-proteins@net.bio.net Fri Sep 12 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!news.icm.edu.pl!newsfeed.nacamar.de!news-kar1.dfn.de!news-stu1.dfn.de!news-mue1.dfn.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Protein sequence databases Date: Sat, 13 Sep 1997 15:25:44 +0200 Organization: University of Wuerzburg, Germany Lines: 19 Message-ID: References: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Nigel J.Osborn (nigel.osborn@zetnet.co.uk) wrote: > I'm trying to find any protein sequence databases available for > non-academic people on the Internet. I'm especially interested in ones that > might have sequences for Hepetitis antigens. Here are some places to start: http://molbio.info.nih.gov/molbio/ http://www.mips.biochem.mpg.de/ http://www.embl-heidelberg.de/srs/srsc http://expasy.hcuge.ch/sprot/sprot-top.html http://www.gdb.org/Dan/proteins/owl.html --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Fri Sep 12 23:00:00 1997 Path: biosci!rutgers!uwm.edu!gsl-penn-ns.gsl.net!news.gsl.net!gip.net!news.voicenet.com!news-xfer.netaxs.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!192.48.96.123!in1.uu.net!151.99.250.2!server-b.cs.interbusiness.it!news.tin.it!news From: "Claudio Luparello" Newsgroups: bionet.molbio.proteins Subject: protein to DNA Date: 10 Sep 1997 14:53:44 GMT Organization: Telecom Italia Net Lines: 6 Message-ID: <01bcbdfa$15ca89c0$799f1fc3@cluparel> NNTP-Posting-Host: palermo7-58.tin.it X-Newsreader: Microsoft Internet News 4.70.1155 Is there anybody who knows if a site exists in the net where aminoacid to DNA sequence translation can be made? (in practice the reverse of the canonic "translate" program). Send information to cluparel@tin.it. Thank you. Claudio Luparello, Dipartimento di Biologia Cellulare e dello Sviluppo, Viale delle scienze, 90128 Palermo (Italy). fax +39 91 420897. From owner-proteins@net.bio.net Sat Sep 13 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!prodigy.com!nntp.earthlink.net!raw From: raw@healthcareforums.com (Ruth Ann) Newsgroups: bionet.molbio.proteins Subject: * BioNET COMMUNICATIONS Freeware * Date: Sun, 14 Sep 1997 00:53:46 -0800 Organization: Worldwide Healthcare Forums Lines: 48 Message-ID: NNTP-Posting-Host: 38.28.35.248 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.2.0b13 *NEW* PeopleLink: Instant Online Communication with your Family + BioNET Colleagues & Friends. Free: PeopleLink is a new communications service that lets people stay in touch no matter where they are on the Internet. The PeopleLink application notifies users whenever selected friends, colleagues or family members appear online, and enables them to instantly communicate in real-time. Combining the interactivity of chat with the selectivity and privacy of email. PeopleLink provides the simplest, safest, and most dependable way for online Healthcare Professionals to connect and communicate. PeopleLink is free to users, takes less than 5 minutes to download at 28.8, sets up easily, and is available for Windows 95, Windows 3.x, Macintosh PowerPC and 68K platforms. Download at http://www.healthcareforums.com/plink.html ---------------------------------- Visit 200 Healthcare Forums in English - http://www.healthcareforums.com Biomedical FORUM can be found under the main topic - Field of Specialty. Worldwide Healthcare Forums SITE TRANSLATIONS: Deutsch Healthcare FORUMS - http://www.healthcareforums.com/wwwboard/index4.html Español Healthcare FORUMS - http://www.healthcareforums.com/wwwboard/index5.html Français Healthcare FORUMS - http://www.healthcareforums.com/wwwboard/index6.html *COMING SOON* Japanese Healthcare FORUMS Chinese Healthcare FORUMS ---------------------------------- NEW SUPER SEARCH ENGINE PAGE with 28 ENGINES http://www.healthcareforums.com/Sengines.html ---------------------------------- POST A MESSAGE & START THREAD AT ||||||||||||||||||||||||||||||||||||||||||||||||||| www.healthcareforums.com ||||||||||||||||||||||||||||||||||||||||||||||||||| From owner-proteins@net.bio.net Sat Sep 13 23:00:00 1997 Path: biosci!agate!ihnp4.ucsd.edu!munnari.OZ.AU!metro!metro!news From: Phillip Robinson Newsgroups: bionet.molbio.proteins Subject: Re: phosphoryalation patterns MAPK Date: Fri, 12 Sep 1997 16:03:29 +1000 Organization: Information Technology Services, The University of Sydney, NSW, Australia Lines: 20 Distribution: inet Message-ID: <3418DB31.7ABF@mail.usyd.edu.au> References: <34058E6E.7516@lmb1.rug.ac.be> NNTP-Posting-Host: mp-9-38.mp.usyd.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) > Does anybody know where I can find information on the consensus > sequences used as phosphorylation sites for kinases in general, > especially MAP kinases? Does there exist software to screen > for consensus phosphorylation patterns in protein sequences? Try Methods in Enzymology vol 200/201, especially chapters by Rick Pearson/Bruce Kemp for excellent summaries. Another good source is "The protein kinase Facts Book" by G Hardie/S Hanks and Academic Press. A computer search of Prosite will reveal many phosphorylation sites. However, just remember that these are *predictions* only and are sometimes a mile off reality. I don't know of any other programs. Phil ________________________________________________ Children's Medical Research Institute , Sydney, NSW AUSTRALIA ;--_|\ / \ ( *<- phrobins@mail.usyd.edu.au \_;--._/ ____________________________________________v___ From owner-proteins@net.bio.net Sat Sep 13 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!logbridge.uoregon.edu!newsfeed.direct.ca!news.he.net!calwebnntp!news-feed.inet.tele.dk!news.daimi.aau.dk!not-for-mail From: Per Mygind Newsgroups: bionet.molbio.proteins,bionet.microbiology,bionet.molbio.methds-reagnts Subject: S-layer protein Date: Sun, 14 Sep 1997 17:48:30 +0100 Organization: DAIMI, Computer Science Dept. at Aarhus University Lines: 33 Message-ID: <341C155E.74DA@biobase.dk> NNTP-Posting-Host: majestetix.medmicro.aau.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; SunOS 5.5.1 sun4m) Xref: biosci bionet.molbio.proteins:11484 bionet.microbiology:10990 bionet.molbio.methds-reagnts:61191 Dear Netters I'm working with s-layer proteins and expression. Therefore I'm wondering whether anyone is working in this field ??? I would like to express my protein in a different host by genetic engeneering. Is it possible in any system to express s-layer proteins 'natively', meaning corretly folded on the outer membrane ?? Is all s-layer proteins also lipoproteins ??? and so on......... Any good references on this subject ??? If you have any expertise in this field, please contact me With regards Per Mygind -- ************************************************************************ If you are are not part of the solution, you are part of the precipitate ************************************************************************ Per Mygind, Cand.scient Department of Medical Microbiology and Immunology The Bartholin Building University of Aarhus Denmark phone : 89 42 17 47 fax : From owner-proteins@net.bio.net Sat Sep 13 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!164.67.42.145!nntp.info.ucla.edu!132.239.254.208!ihnp4.ucsd.edu!munnari.OZ.AU!metro!metro!news From: Phillip Robinson Newsgroups: bionet.molbio.proteins Subject: Designing peptides for raising antibodies Date: Fri, 12 Sep 1997 17:37:46 +1000 Organization: Information Technology Services, The University of Sydney, NSW, Australia Lines: 20 Distribution: inet Message-ID: <3418F14A.48BA@mail.usyd.edu.au> NNTP-Posting-Host: mp-9-38.mp.usyd.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Any ideas on how to make a best 'educated' choice about designing a synthetic peptide from a protein sequence for raising antibodies? What parameters/amino acids are good, what's bad? I have tried 'Hydrophilicity' according to Hopp & Woods (1981) PNAS, but I don't know if this is the best criteria, or even a good one. The program I use, AnTheProt, also has an 'Antigenicity' plot according to Wellings (no reference?), but the output seems to have no relationship to the above hydrophilicity plot. What is this actually calculating? Anyway, I think it will be valuable to collate feedback on people's experiences or feelings on this topic. Phil ________________________________________________ Children's Medical Research Institute , Sydney, NSW AUSTRALIA ;--_|\ / \ ( *<- phrobins@mail.usyd.edu.au \_;--._/ ____________________________________________v___ From owner-proteins@net.bio.net Sun Sep 14 23:00:00 1997 Newsgroups: bionet.molbio.proteins Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!192.48.96.123!in1.uu.net!uucp2.uu.net!world!oravaxcm From: oravaxcm@world.std.com (Charles A Miller) Subject: What is the correlation of an F-tailed protein? Message-ID: Organization: The World Public Access UNIX, Brookline, MA X-Newsreader: TIN [version 1.2 PL2] Date: Tue, 16 Sep 1997 05:48:17 GMT Lines: 16 I'm not quite sure how to ask this question, but what is the significance of a phenylalanine as the c-terminal aa in a given protein, specifically a lipoprotein? I have heard that this is a common "signature", and it does seem to show up in a many of the sequences that I have seen which contain a putative lipoprotein leader sequence. Does anyone know the reason for this? What is the function (if any)? Thanks! Chuck Miller oravaxcm@world.std.com From owner-proteins@net.bio.net Sun Sep 14 23:00:00 1997 Path: biosci!agate!overload.lbl.gov!news From: Olin Anderson Newsgroups: bionet.molbio.proteins Subject: BLAST suggestions Date: Mon, 15 Sep 1997 08:11:46 -0700 Organization: U.S. Department of Agriculture Lines: 5 Message-ID: <341D5032.7FFC@pw.usda.gov> NNTP-Posting-Host: wheat.pw.usda.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; SunOS 5.5.1 sun4c) Does anyone know of a clear reference on how to interpret BLAST scores. I have the online manuals describing the program, but I am really looking suggestions on exactly what the scores mean; i.e., what is a normal threshold for a match, etc. From owner-proteins@net.bio.net Sun Sep 14 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!cloudbreak.rs.itd.umich.edu!newsxfer.itd.umich.edu!newbabylon.rs.itd.umich.edu!not-for-mail From: philip andrews Newsgroups: bionet.molbio.proteins Subject: postdoctoral opening Date: Mon, 15 Sep 1997 09:46:28 -0400 Organization: University of Michigan ITD News Server Lines: 33 Message-ID: <341D3C34.5CE9@umich.edu> NNTP-Posting-Host: host-218.subnet-33.med.umich.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win95; I) POST-DOCTORAL POSITIONS IN PROTEOMICS/FUNCTIONAL GENOMICS Post-doctoral positions available immediately to develop new technologies for ultra-high throughput analysis of complex systems at the molecular level. Highly motivated individuals with solid expertise in 2-D gel electrophoresis, mass spectrometry, or bioinformatics are encouraged to apply. Fellows will participate in an intensive team effort to develop new technologies for mass mapping of proteins for identification and characterization of post-translational modifications. Electrophoresis: Solid knowledge of the principles of electrophoresis and extensive practical experience in 2-D gel electrophoresis are required. Experience with thin-layer gel electrophoresis and capillary electrophoresis desired but not essential. Experience with yeast or mammalian systems also desired. Mass spectrometry: Research experience with MALDI or ESMS required as is expertise in protein chemistry. Applicants should have strong publication records addressing application of mass spectrometry to protein chemistry or molecular biology issues. Bioinformatics: Research experience involving bioinformatics required with publications in this field and a solid biochemistry background. Solid programming skills required as well as familiarity with customized database searches and handling very large files. Experience with Oracle and/or AVS Express a plus. UNIX and network experience also useful. Send resumes to P. C. Andrews, Dept. of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109-0674. FAX: 313.936.2638 email: andrewsp@umich.edu. Equal Opportunity/Affirmative Action Employer From owner-proteins@net.bio.net Sun Sep 14 23:00:00 1997 Newsgroups: bionet.molbio.proteins Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!yama.mcc.ac.uk!liv!news From: len bell Subject: Re: Protein sequence databases Content-Type: text/plain; charset=us-ascii Message-ID: <341D57C7.6F96@liv.ac.uxk> Sender: news@liverpool.ac.uk (News System) Nntp-Posting-Host: pc028010.med.liv.ac.uk Reply-To: lgbell@liv.ac.uxk Content-Transfer-Encoding: 7bit Organization: The University of Liverpool References: Mime-Version: 1.0 Date: Mon, 15 Sep 1997 15:44:08 GMT X-Mailer: Mozilla 3.02C-PGMNS (Win16; I) Lines: 18 Nigel J.Osborn wrote: > > I'm trying to find any protein sequence databases available for > non-academic people on the Internet. I'm especially interested in ones that > might have sequences for Hepetitis antigens. > > Anyone know of any? > > Nigel. Both SWISS-PROT and the Brookhaven PDB are 'open access' protein sequence databases. I havent got a note of the ULR but I suspect a quick check on a search engine will turn them up quite easily. -- Dr Len Bell, University of Liverpool. email: lgbell@liv.ac.uk (del 'x' in reply to address) From owner-proteins@net.bio.net Mon Sep 15 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!csulb.edu!logbridge.uoregon.edu!newsfeed.internetmci.com!152.163.199.19!portc03.blue.aol.com!audrey02.news.aol.com!not-for-mail From: huntpharm@aol.com (Huntpharm) Newsgroups: bionet.molbio.proteins Subject: US/NJ-COMPUTER AND SCIENCE JOB OPPORTUNITY Date: 16 Sep 1997 14:48:11 GMT Lines: 14 Message-ID: <19970916144800.KAA09153@ladder02.news.aol.com> NNTP-Posting-Host: ladder02.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com SnewsLanguage: English I am looking for a person to be the Database Administrator for Semi-Automated Drug Discovery. You will be responsible for computer-assisted data analysis, database entries/searches, database management, and writing experimental protocols. You should have knowledge of PC's and databases, excellent verbal and interpersonal skills and the ability to interact in a large group of people. The candidate will have 1+ years experience and possess a B.S. or M.S.degree in Biology, Chemistry, Computer Science or related field. We are a leading pharmaceutical company with research facilities in New Jersey and can provide excellent benefits (health insurance, dental, and vision plan, paid vactation and more). A high impact, high profile position with excellent opportunity for advancement. Please contact Scott Shanes by phone at 609-584-8733 Ext. 218, fax resume and cover letter to 609-584-9575 or E-Mail to sis@dmc10.com. From owner-proteins@net.bio.net Mon Sep 15 23:00:00 1997 Message-ID: <341CFB19.446B@came.sbg.ac.at> Date: Mon, 15 Sep 1997 11:08:41 +0200 From: Walter Koppensteiner Organization: Center for Applied Molecular Engineering X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 Newsgroups: bionet.molbio.proteins Subject: Non-redundant list of protein complexes Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: agnes.came.sbg.ac.at Lines: 20 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsfeed.ecrc.net!newscore.univie.ac.at!03-newsfeed.univie.ac.at!news.sbg.ac.at!agnes.came.sbg.ac.at Hi, does anybody have extracted a list of non-redundant protein complexes from the PDB. I want to analyse intermolecular interactions and need a representative dataset of 3D structures. The pdb_select list from embl only lists monomeric chains. Also a list of protein/dna(rna) complexes would be appreciated. Thanks in advance, Walter -- =============================================================== Walter Koppensteiner University of Salzburg Center of Applied Molecular Engineering Jakob Haringer Strasse 3 Phone: +43-662-8044-5794 A-5020 Salzburg, Austria Email: walter@came.sbg.ac.at =============================================================== From owner-proteins@net.bio.net Mon Sep 15 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.ecrc.net!news-feed1.eu.concert.net!news.worldonline.nl!not-for-mail From: "Kenneth Jie" Newsgroups: bionet.molbio.proteins Subject: enzyms Date: 16 Sep 1997 17:57:06 GMT Organization: Jie Lines: 9 Message-ID: <01bcc2c9$f1bde3e0$2597f1c3@kenneth> NNTP-Posting-Host: gd1-p37.worldonline.nl X-Newsreader: Microsoft Internet News 4.70.1157 Hi, I need some questions about enzyms and I need the answers with them too. please give them to me... It's for school. Michael e-mail: kjie@knmg.nl From owner-proteins@net.bio.net Tue Sep 16 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!thetimes.pixel.kodak.com!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!206.229.87.50!news-pull.sprintlink.net!news-in-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!newsfeed.ecrc.net!newscore.univie.ac.at!news-ge.switch.ch!news.rccn.net!news.ist.utl.pt!Student.iseg.utl.pt!not-for-mail From: pmartins@isa.utl.pt (Pedro Martins) Newsgroups: bionet.molbio.proteins Subject: Glycoproteins Date: Tue, 16 Sep 1997 16:34:12 GMT Organization: ISEG Lines: 14 Message-ID: <341e5304.9277689@news.iseg.utl.pt> NNTP-Posting-Host: dbbiopub1.isa.utl.pt X-Newsreader: Forte Free Agent 1.11/32.235 Hello. I need help. I am working with leguminosae glycoprotein (Lupinus albus, Phaseolus vulgaris, Vicia faba, ...). I want to deglycosylate glycoproteins mantaining intact the peptidic chain so that I can produce specific antybodies. I've been reading some articles about this subject but so far I only could found methods that preserve the sugar, breaking the peptide chain. I am not interested in enzymatic release of O- and N-linked oligosaccharide chains or release of N-linked chains by hydrazinolysis. Could someone help me. TIA. Astride e-mail:aa13082@isa.utl.pt From owner-proteins@net.bio.net Tue Sep 16 23:00:00 1997 Path: biosci!daresbury!uninett.no!Norway.EU.net!EU.net!newsfeed.internetmci.com!194.162.162.196!newsfeed.nacamar.de!wuff.mayn.de!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!server5.netnews.ja.net!server6.netnews.ja.net!server4.netnews.ja.net!server2.netnews.ja.net!bham!med803.bham.ac.uk!user From: noone@bham.ac.uk (CRC Institute for Cancer Studies) Newsgroups: bionet.molbio.proteins Subject: cleavage of protein in SDS-gel Date: Wed, 17 Sep 1997 15:33:42 +0100 Organization: CRC Lines: 13 Message-ID: NNTP-Posting-Host: med803.bham.ac.uk Hi, I am looking for a method to cleave a protein (ca. 400 kDa) in a gel. Due to the size, I thought of BrCN. However, all methods I could get hold of involved electroelution (which I think won't work with such a protein). Maybe AspN or ArgC would be alternatives? Thanks in advance, Peter p.weber@bham.ac.uk From owner-proteins@net.bio.net Tue Sep 16 23:00:00 1997 Newsgroups: bionet.molbio.proteins Path: biosci!agate!hammer.uoregon.edu!csulb.edu!logbridge.uoregon.edu!newsfeed.internetmci.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!yama.mcc.ac.uk!liv!news From: gcr@liv.ac.uk (gcr) Subject: Protamine expression in E. coli or Baculovirus? Content-Type: Text/Plain; charset=US-ASCII Message-ID: Sender: news@liverpool.ac.uk (News System) Nntp-Posting-Host: pc027049.ctb.liv.ac.uk Organization: University of Liverpool X-Newsreader: WinVN 0.99.7 Mime-Version: 1.0 Date: Wed, 17 Sep 1997 12:52:55 GMT X-Authenticated-User: gcr Lines: 30 Dear all, Has anyone any (even the slightest) experience in expression of a cloned protamine gene (mine derived from salmon) into an E. coli or Baculovirus system? At the moment we are unsuccesful in its expression and think it is a 'toxic' peptide in the E. coli strains used. (pET 21a vector, BL21(DE3) and BL21(DE3)pLysS E. coli strains). Also when using the Bac-to-Bac baculovirus kit from Gibco-BRL, the recombinant bacmid does not appear to remain stable at the E. coli stage and wild type revertants are very hard to avoid, which subsequently, after transfection into Sf9 cells, are overproduced in the viral stock. Any tips please ??? Thanks, GcR ___________________________________ Gert Roosen PhD. Student Royal Liverpool University Hospital Duncan Building Prescot Street L69 3BX Liverpool, UK. + 44 (0)151 706 4326 (tel) + 44 (0)151 706 4311 (fax) gcr@liv.ac.uk (email) From owner-proteins@net.bio.net Tue Sep 16 23:00:00 1997 Path: biosci!rutgers!gatech!newsxfer3.itd.umich.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!europa.clark.net!203.216.4.6!newsfeed.gol.com!nspixp!news.imnet.ad.jp!newsgw.affrc.go.jp!news From: Kajiwara Hideyuki Newsgroups: bionet.molbio.proteins Subject: Re: peptide synthesis for antibody Date: Thu, 18 Sep 1997 14:01:58 -0800 Organization: National Institute of Agrobiological Resources Lines: 21 Message-ID: <3421A4D7.18AC@abr.affrc.go.jp> References: <874116728.17944@dejanews.com> Reply-To: kajiwara@abr.affrc.go.jp NNTP-Posting-Host: 150.26.150.140 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 [ja] (Macintosh; I; 68K) > In article , > Sandra Pena De Ortiz wrote: > > > > Hi: > > > > What is the smallest number of amino acid residues in a peptide to > > produce a polyclonal antibody? Thanks in advance > > > > Sandra Pena de Ortiz, Ph.D. If you use multiple antigenic peptides, less than 10 amino acids were possible to prepare anti-MAP polyclonal antibodies. _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ Hideyuki Kajiwara National Institute of Agrobiological Resources Dept. of Biotechnology, Lab. of Gene Engineering E-mail: kajiwara@abr.affrc.go.jp Fax: 81-298-38-7073 _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-proteins@net.bio.net Tue Sep 16 23:00:00 1997 Path: biosci!rutgers!news-relay.ncren.net!unc-cs!fddinewz.oit.unc.edu!amber!mman From: Michael Man Newsgroups: bionet.molbio.proteins Subject: calculate distance between 2 aa Date: Wed, 17 Sep 1997 22:35:00 -0400 Organization: The University of North Carolina at Chapel Hill Lines: 11 Message-ID: References: <341D3C34.5CE9@umich.edu> NNTP-Posting-Host: amber.bios.unc.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: mman@amber In-Reply-To: <341D3C34.5CE9@umich.edu> Is there a program that I can use to calculate the distance between 2 amino acids in a protein having known structure? More specifically, I want to get the identity of the 10 closest amino acids in the neighborhood of a given a.a.. Please reply to my email address. -michael mman@bios.unc.edu From owner-proteins@net.bio.net Wed Sep 17 23:00:00 1997 Path: biosci!daresbury!uninett.no!Norway.EU.net!EU.net!newsfeed.Austria.EU.net!newscore.univie.ac.at!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!gmorley From: gmorley@hgmp.mrc.ac.uk (Mr. G. Morley) Newsgroups: bionet.molbio.proteins Subject: dimeric receptor degradation Date: 18 Sep 1997 15:38:40 GMT Organization: MRC Human Genome Mapping Project Resource Centre Lines: 15 Message-ID: <5vrhu0$nck$1@niobium.hgmp.mrc.ac.uk> NNTP-Posting-Host: tin.hgmp.mrc.ac.uk Hi... bit of a strange question...but does anyone know if there has been any evidence (ie: papers, etc) that dimeric tyrosine kinase cell surface receptors can be slowed in their degredation in response to ligand by lysosoaml or ubiquitin inhibitors. I believe quite a lot of evidence has accumulated suggesting that these receptors are ubiquitinated prior to degradation. However I have not come across any reference to halting this process. I would be very, very, very gratefull if anyone could enlighten me, if so please e-mail me at: gmorley@rpms.ac.uk Thanks in advance, Gary Morley. From owner-proteins@net.bio.net Wed Sep 17 23:00:00 1997 Path: biosci!agate!ihnp4.ucsd.edu!munnari.OZ.AU!bunyip.cc.uq.edu.au!inet6.citec.com.au!citecuf.citec.qld.gov.au!news From: Alison Leakey Newsgroups: bionet.molbio.proteins Subject: concentration of low molecular weight protein Date: Fri, 19 Sep 1997 16:44:11 +1000 Organization: North Queensland Clinical School Lab Lines: 17 Message-ID: <34221F3A.6F29@citec.qld.gov.au> Reply-To: leakeya@citec.qld.gov.au NNTP-Posting-Host: pisterp.health.qld.gov.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; 68K) How do I concentrate a low molecular weight protein (less than 5kDa) from gel filtration fractions ie. dilute???, keeping in mind that filtration devices and dialysis tubing concentrate above this size. I have tried ammonium sulphate precipitation (up to 80%) with poor results. It just doesn't want to precipitate!!! -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* Alison Leakey PhD Student North Queensland Clinical School Laboratory Ground Floor, Pathology Building, Townsville General Hospital Phone me at (077) 81 9662 FAX me at (077) 81 9649 *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* From owner-proteins@net.bio.net Thu Sep 18 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!news.sprintisp.com!sprintisp!cdc2.cdc.net!news.maxwell.syr.edu!newsfeed.internetmci.com!139.130.235.93!news.telstra.net!loomi.telstra.net!not-for-mail From: John Maddern Newsgroups: bionet.molbio.proteins Subject: Proteolytic Enzyme enhancers Date: Sat, 20 Sep 1997 14:51:40 +0930 Organization: Telstra Internet Browse Server Lines: 6 Message-ID: <34235D63.7D60CD4@olis.net.au> Reply-To: jm@olis.net.au NNTP-Posting-Host: ppp0e.olis.net.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) X-Priority: 3 (Normal) I can find heaps of info on proteolytic enzyme inhibitors on the net, but next to nothing on biological or at least organic enhancement of the reactions. I'm informed that they exist, even for low temp (say 15C...59F). Anyone out there shed some light on this please. From owner-proteins@net.bio.net Thu Sep 18 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!www.nntp.primenet.com!globalcenter1!news.primenet.com!nntp.primenet.com!newsfeed.internetmci.com!164.67.42.145!nntp.info.ucla.edu!128.120.8.185!mark.ucdavis.edu!dilbert.ucdavis.edu!not-for-mail From: szrathje@dilbert.ucdavis.edu (John Rathjen) Newsgroups: bionet.molbio.proteins Subject: Postdoc in Plant Signal Transduction Date: 19 Sep 1997 22:15:20 GMT Organization: University of California, Davis Lines: 22 Message-ID: <5vutho$m82$3@mark.ucdavis.edu> NNTP-Posting-Host: dilbert.ucdavis.edu X-Trace: mark.ucdavis.edu 874707320 22786 (None) 128.120.8.189 X-Complaints-To: usenet@ucdavis.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] POSTDOCTORAL RESEARCHER IN STRUCTURE-FUNCTION STUDIES OF PLANT DISEASE RESISTANCE GENES Ð NSF CENTER FOR ENGINEERING PLANTS FOR RESISTANCE AGAINST PATHOGENS (CEPRAP), UNIVERSITY OF CALIFORNIA, DAVIS. We are seeking a postdoctoral researcher with experience in protein biochemistry and preferably plant molecular genetics. The primary focus of the position is to characterize the early molecular events occurring in disease resistance in plants, with the long-term goal of engineering novel resistance in plants. This will initially involve studying proteins interacting with the Pto and Prf gene products of tomato using a variety of approaches including the yeast two-hybrid system (Science 274:2063-2065, 1996). The researcher will be expected to use other approaches and explore other systems when appropriate as the field develops and other resistance genes are cloned. The position is open until filled. Letters of application should include curriculum vitae, bibliography, statement of research interests, and the names of three references. Applications should be sent to Richard Michelmore, CEPRAP, University of California, Davis, CA 95616, FAX: 916-752-9659, or rwmichelmore@ucdavis.edu. The University of California is an equal opportunity/affirmative action employer. From owner-proteins@net.bio.net Thu Sep 18 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsfeed.internetmci.com!198.82.160.249!solaris.cc.vt.edu!newsgate.duke.edu!galactose.mc.duke.edu.uucp!tschantz From: tschantz@galactose.mc.duke.edu (William P. Tschantz) Newsgroups: bionet.molbio.proteins,bionet.cellbiol Subject: How to deplete Oxygen from enzyme assay? Date: 19 Sep 1997 17:52:51 GMT Organization: Duke University; Durham, N.C. Lines: 18 Distribution: world Message-ID: <5vue5j$rcm$1@news.duke.edu> NNTP-Posting-Host: galactose.mc.duke.edu Xref: biosci bionet.molbio.proteins:11510 bionet.cellbiol:8090 Hi I am looking for an easy way to deplete a system of oxygen. I suspect that the enzyme i am working on uses molecular oxygen in its mechanism and would like to test it. I have tried degassing my samples and reaction vial with nitrogen, but have gotten messy results. Enzyme linked assays would be the easiest i think. Any ideas appreciated. Thanks in advance. Bill -- | William R. Tschantz, Ph.D. * Drink Real Beer | | Dept of Pharm and Cancer Biology* Have a Homebrew! | | Duke University, Durham, NC * It's Good for you! | | tschantz@galactose.mc.duke.edu * | From owner-proteins@net.bio.net Thu Sep 18 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!news-was.dfn.de!news-fra1.dfn.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.gwdg.de!not-for-mail From: Christian Ebeling Newsgroups: bionet.molbio.proteins Subject: membrane protein heterodimer Date: Sat, 20 Sep 1997 05:23:20 +0200 Organization: Institut fuer Molekulare Genetik Lines: 10 Message-ID: <342341A8.64D4@gwdg.de> Reply-To: cebelin@gwdg.de NNTP-Posting-Host: ubmgpf.uni-molgen.gwdg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (WinNT; I) Hello, i need for my project membran proteins from any organism which forms a specific heterodimer with a strong affinity. This heterodimer should also have the property of easy overproduction and purification in E.coli. Has anyone an idea? Christian e-mail: cebelin@gwdg.de From owner-proteins@net.bio.net Thu Sep 18 23:00:00 1997 Path: biosci!rutgers!gatech!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!193.174.75.126!news-was.dfn.de!news-fra1.dfn.de!news-ber1.dfn.de!news-lei1.dfn.de!news-nue1.dfn.de!chico.franken.de!uni-erlangen.de!winx03!news From: s88891@stud-mail.uni-wuerzburg.de (Mathias Holpert) Newsgroups: bionet.molbio.proteins Subject: Re: BLAST suggestions Date: Fri, 19 Sep 1997 13:10:57 GMT Organization: University of Wuerzburg, Germany Lines: 15 Message-ID: <34227002.4363744@news.informatik.uni-wuerzburg.de> References: <341D5032.7FFC@pw.usda.gov> NNTP-Posting-Host: wex124.extern.uni-wuerzburg.de Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Forte Agent 1.5/32.451 On Mon, 15 Sep 1997 08:11:46 -0700, Olin Anderson wrote: >Does anyone know of a clear reference on how to interpret >BLAST scores. I have the online manuals describing the >program, but I am really looking suggestions on exactly >what the scores mean; i.e., what is a normal threshold >for a match, etc. There is a book out there which I could recommend on that topic. It´s about the use of the internet in biology, giving information about lots of search engines and databases- with lots of examples. I don´t know the date it was published, but the rest is: ´Internet Tools for the New Biology´, Leonard F. Peruski Jr., ASM Press, 199? (should be ´96 or ´97- most probably ´97). From owner-proteins@net.bio.net Thu Sep 18 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!csulb.edu!logbridge.uoregon.edu!newsfeed.internetmci.com!169.132.11.200!news.idt.net!wuff.mayn.de!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!warwick!not-for-mail From: David Jones Newsgroups: bionet.molec-model,bionet.molbio.proteins Subject: Re: Membrane Proteins: Database, Topology, Prediction methods Date: 19 Sep 1997 12:31:04 GMT Organization: University of Warwick, UK Lines: 49 Message-ID: <5vtra8$l5$1@violet.csv.warwick.ac.uk> References: <874659586.26023@dejanews.com> NNTP-Posting-Host: globin.csv.warwick.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: TIN [UNIX 1.3 unoff BETA 970406; IP26 IRIX64 6.2] Xref: biosci bionet.molec-model:1825 bionet.molbio.proteins:11506 In bionet.molec-model Christian.Lacombe@cri.univ-poitiers.fr wrote: > I am looking for a recent "Membrane Proteins Database" similar to the > TMbase built by Kay Hofman at Lausanne (Switzerland). As, in this database > entries are from the SwissProt25 (1994?), I easily imagine that the > membrane spanning domains (when predicted) are not predicted with > up-to-date prediction methods. I need also topology information. The transmembrane records in SWISSPROT are very unreliable. Quite a few recent papers on topology prediction have made use of the 68 or so proteins I collected when developing MEMSAT [Biochemistry 33:3038-3049(1994)]. Back then I had to get most of the information for those proteins from the literature along with some careful by-eye studies of the sequences and their hydrophobicity plots. We are now developing an updated version of MEMSAT, and are in the process of expanding the original dataset. Unfortunately 4-years on it still looks like the only reliable option is to plough through the literature - though at least there are a now couple of new 3-D structures available! If anyone has a more up-to-date collection then I'd certainly like to hear about it too. > It seems that surface amphipatic small helices (the so-called "fusion > helices"?) are not included in TMbase: how such membrane segments are > detected since algorithms predicted only transmembrane segments? And > finally, how distinguish membrane sheets and membrane helices with > prediction method? Best advice at the moment is to model porin-homologue proteins by careful comparative modelling - using a sequence profile of some description. until we have more than one example of beta-sheet containing TM proteins there little else that's sensible to do. Unlike helical bundles, you can't just predict strands individually and hope to make sense of the results - unless you know your protein looks like porin, you have no way of knowing how the strands should be arranged in 3-D space. However, both transmembrane strands (in porin) and amphipathic helices are amenable to standard globular protein prediction methods. For helical proteins, the best strategy would be to carefully predict the TM helices, then apply any half-decent secondary structure prediction method (even a helical wheel plot will do) to any long connecting loops you end up with. If the connecting loops are very long, then you can expect that this is probably an inserted globular domain (so all bets are off for those regions). Oh and watch out for the signal peptides... >---------------------------------------------------------------------------< This message was written, produced and executively directed by Dr David Jones Address: Dept. of Biological | Email: jones@globin.bio.warwick.ac.uk Sciences, University of Warwick, | Tel: +44 1203 523729 Coventry CV4 7AL, U.K. | Fax: +44 1203 523568 From owner-proteins@net.bio.net Thu Sep 18 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!204.238.120.130!jump.net!grunt.dejanews.com!not-for-mail Date: Fri, 19 Sep 1997 04:35:08 -0600 From: Christian.Lacombe@cri.univ-poitiers.fr Subject: Membrane Proteins: Database, Topology, Prediction methods Newsgroups: bionet.molec-model,bionet.molbio.proteins Message-ID: <874659586.26023@dejanews.com> Organization: Deja News Posting Service X-Article-Creation-Date: Fri Sep 19 08:59:46 1997 GMT X-Originating-IP-Addr: 193.51.68.231 (bmo19.campus.univ-poitiers.fr) X-Http-User-Agent: Mozilla/4.01 [en] (Win95; I) X-Authenticated-Sender: Christian.Lacombe@cri.univ-poitiers.fr Lines: 14 Xref: biosci bionet.molec-model:1824 bionet.molbio.proteins:11505 I am looking for a recent "Membrane Proteins Database" similar to the TMbase built by Kay Hofman at Lausanne (Switzerland). As, in this database entries are from the SwissProt25 (1994?), I easily imagine that the membrane spanning domains (when predicted) are not predicted with up-to-date prediction methods. I need also topology information. It seems that surface amphipatic small helices (the so-called "fusion helices"?) are not included in TMbase: how such membrane segments are detected since algorithms predicted only transmembrane segments? And finally, how distinguish membrane sheets and membrane helices with prediction method? Many thanks for your help -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-proteins@net.bio.net Thu Sep 18 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!csulb.edu!logbridge.uoregon.edu!newsfeed.direct.ca!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!server1.netnews.ja.net!server5.netnews.ja.net!server3.netnews.ja.net!news.icnet!mac052034.lif.icnet.uk!user From: I.McFarlane@icrf.icnet.uk (Ian McFarlane) Newsgroups: bionet.molbio.proteins Subject: Re: concentration of low molecular weight protein Date: Fri, 19 Sep 1997 10:21:28 +0000 Organization: Imperial Cancer Research Fund Lines: 17 Message-ID: References: <34221F3A.6F29@citec.qld.gov.au> <3422A068.852@le.ac.uk> NNTP-Posting-Host: mac052034.lif.icnet.uk X-Newsreader: Value-Added NewsWatcher 2.0b27+ In article <3422A068.852@le.ac.uk>, "Dr E. Buxbaum" wrote: > Alison Leakey wrote: > > > > How do I concentrate a low molecular weight protein (less than 5kDa) > > from gel filtration fractions ie. dilute???, keeping in mind that > > filtration devices and dialysis tubing concentrate above this size. > > Have you tried concentrating chromatographic techniques (reverse phase > chromatography, ion exchange)? You could run your gel filtration column in a volatile buffer such as ammonium acetate and then freeze-dry (lyophilise). Usually with small proteins/peptides RP-HPLC is the final step as this gives the protein in a small volume of volatile buffer. Ian Mc From owner-proteins@net.bio.net Thu Sep 18 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!158.43.192.17!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins Subject: Re: concentration of low molecular weight protein Date: Fri, 19 Sep 1997 08:55:20 -0700 Organization: University of Leicester (PCFS User) Lines: 8 Message-ID: <3422A068.852@le.ac.uk> References: <34221F3A.6F29@citec.qld.gov.au> NNTP-Posting-Host: pc47.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.03 (Win16; I) Alison Leakey wrote: > > How do I concentrate a low molecular weight protein (less than 5kDa) > from gel filtration fractions ie. dilute???, keeping in mind that > filtration devices and dialysis tubing concentrate above this size. Have you tried concentrating chromatographic techniques (reverse phase chromatography, ion exchange)? From owner-proteins@net.bio.net Thu Sep 18 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!ai-lab!netnews.com!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!207.103.147.20!news.voicenet.com!dsinc!pitt.edu!newsfeed.pitt.edu!pelli.pathology.pitt.edu!user From: pxpst2@vms.cis.pitt.edu (Peter) Newsgroups: bionet.molbio.proteins Subject: Re: concentration of low molecular weight protein Date: Fri, 19 Sep 1997 10:09:10 -0400 Organization: U. of Pitt. Patholgy Lines: 35 Message-ID: References: <34221F3A.6F29@citec.qld.gov.au> NNTP-Posting-Host: pelli.pathology.pitt.edu X-newsreader: MT-NewsWatcher 2.2.2 In article <34221F3A.6F29@citec.qld.gov.au>, leakeya@citec.qld.gov.au wrote: .> How do I concentrate a low molecular weight protein (less than 5kDa) .> from gel filtration fractions ie. dilute???, keeping in mind that .> filtration devices and dialysis tubing concentrate above this size. .> .> I have tried ammonium sulphate precipitation (up to 80%) with poor .> results. It just doesn't want to precipitate!!! Why precipitate your protein. Precipitation of protein has three big problems and you have run into two of them. the thre problems are 1) does not work well with dilute proteins 2) does not work well with small proteins 3) proteins often hard to resolvate the solution to your problem is to do a phase extraction with Phenol. A good paper for reference is "Concentration of Dilute Protein for Electrophoresis", Anal. Biochem., 226, 382-383 (1995). Hope this helps, BTW I had the same problem and it really slowed my work. Peter -- "Don't you eat that yellow snow watch out where the huskys go" From owner-proteins@net.bio.net Thu Sep 18 23:00:00 1997 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.erols.net!newsxfer3.itd.umich.edu!uunet!in4.uu.net!138.133.17.7!amgen!news From: John Philo Newsgroups: bionet.molbio.proteins,bionet.cellbiol Subject: Re: How to deplete Oxygen from enzyme assay? Date: Fri, 19 Sep 1997 13:42:24 -0700 Organization: Amgen Lines: 46 Message-ID: <3422E3B0.4F91@amgen.com> References: <5vue5j$rcm$1@news.duke.edu> Reply-To: jphilo@amgen.com NNTP-Posting-Host: worf.amgen.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01GoldC-CIS0597c (Win95; U) To: "William P. Tschantz" Xref: biosci bionet.molbio.proteins:11511 bionet.cellbiol:8094 William P. Tschantz wrote: > > Hi > > I am looking for an easy way to deplete a system of oxygen. I suspect > that the enzyme i am working on uses molecular oxygen in its mechanism and > would like to test it. I have tried degassing my samples and reaction > vial with nitrogen, but have gotten messy results. Enzyme linked assays > would be the easiest i think. > > Any ideas appreciated. > > Thanks in advance. > > Bill Based on my 'former life' as a hemoglobin researcher, you might consider the following things: 1) the strongest oxygen destroyer is sodium dithionite, but this is also a powerful reductant and may reduce metals in the active site of your enzyme (if it really uses oxygen I am assuming you are dealing with a metalloenzyme). Dithionite can also have some nasty contaminants and byproducts of its activity. In the hemoglobin field there is much lore regarding brands of dithionite, and the common lab chemical suppliers don't have high grade dithionite, so you may want to secure some from a hemoglobin lab. 2) I had a lot of success with an mixed enzyme system: glucose oxidase, catalase, and glucose. The drawback of this system is that the glucose oxidase converts dioxygen to peroxide, and that may destroy your enzyme before the catalase gets to it. I believe this system is still commonly used for hemoglobin work by Gary Ackers lab (Washington U. Med School). 3) A second possible enzyme system is protocatechuate dioxygenase + protocatechuic acid. This one has the advantage that it destroys dioxygen in one step. With any of these systems, the key is to use them to remove traces of oxygen remaining AFTER you have already done a good job of degassing with nitro