From owner-proteins@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!paracel.com!kuo From: kuo@paracel.com ("Benjamin F. Kuo") Newsgroups: bionet.molbio.proteins Subject: Fwd: Smith Waterman website Date: 2 Jul 1997 13:09:55 -0700 Organization: Paracel, Inc. Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <33BAB22D.5B1B@paracel.com> References: <33BA7B7B.2D88@agora.ulaval.ca> Reply-To: kuo@paracel.com NNTP-Posting-Host: net.bio.net ----- Sequence similarity searches using the Smith Waterman algorithm are now available from our website: http://www.paracel.com/demos.htm http://www.paracel.com/SWP_form.html Just paste your query into the form, and get your results within seconds! The SwissProt34 database is currently available, PIR will be added soon. Please contact me if you have any questions. -Jeremy Lawrence Paracel Customer Support jeremy@paracel.com Paracel Inc. 80 South Lake Ave. Pasadena, CA 91101 1-888-PARACEL From owner-proteins@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: "Alexey M. Eroshkin" Newsgroups: bionet.molbio.proteins Subject: ProAnWin update: protein alignment/plots/structure-activity analysis/de sign Date: 2 Jul 1997 09:42:17 +0100 Organization: State Research Center of Virology and Biotechnology VECTOR Lines: 364 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5pd499$nov@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: proteins@dl.ac.uk To: bio-software@dl.ac.uk From: Alexey Eroshkin Cc: mutatiomn@net.bio.net, pop-bio@net.bio.net, peptides@dl.ac.uk, molmodel@dl.ac.uk, mol-evol@dl.ac.uk, microbio@dl.ac.uk, immuno@dl.ac.uk, hiv-biol@dl.ac.uk, fluorpro@dl.ac.uk, biophys@dl.ac.uk, bio-matrix@dl.ac.uk, proteins@dl.ac.uk, virology@dl.ac.uk, xtal-log@dl.ac.uk Subject: ProAnWin update: protein alignment/plots/structure-activity analysis/design Dear all, new version of ProAnWin (Protein Analyst for Win 3.11/95) now publicly available from IUBio as ftp://iubio.bio.indiana.edu/molbio/ibmpc/paw.exe (and paw.readme) If you have access to e-mail only, the program can be obtained via e-mail by sending the following message: To: BITFTP@pucc.Princeton.EDU From: YOUR E-MAIL ADDRESS ftp iubio.bio.indiana.edu uuencode user anonymous cd molbio/ibmpc get paw.exe get paw.readme quit Server will return you UUENCODED program in several files. Running UUDECODE you'll get the archive with the program. ************************************** ProAnWin - Protein Analyst for Windows ************************************** version 3.01 Multiple sequence alignment, analysis of protein sequences and structures, structure-activity relationships, design of protein-engineering experiments Copyright(c)1995-97 I.Pika, A.Frolov, V.Ivanisenko, A.Eroshkin All Trademarks and Registered Names are acknowledged in this document. The files required to run ProAnWin are distributed in the form of a single compressed file (self-extracted). Create a directory "PROANWIN" on your hard disk, for example, C and copy the compressed file to the directory. Unpack the program (type PAW in DOS prompt and answer Yes to all questions). Once you extracted archive files, start Windows and start the program. This program is provided "AS IS" without any warranty, expressed or implied to you or any other person. The authors will not be liable for incidental, consequential or other damages arising through the use of this software. As the program is under further development the documentation may not reflect all current program options. PROGRAM CONTENT: Directory: Main directory - program modules DATA - files with amino acid physico-chemical properties, manual, examples with input and output files ALIGNS - aligned sequences of 50 protein families MAIN PROGRAM FEATURES (* - new feature) - Makes multiple sequence alignment - automatic (Clustal V) and manual, global and local (in selected region); - Threads multiple alignment onto known 3-dimensional structure; - Imports data in all major formats (SWISS-PROT, PIR, FASTA, GCG, Clustal); - Imports protein 3D structure from Protein Data Bank files (PDB format) - Inputs data on protein activities/property or phenotype; - Transforms activity values (log (A), ln (A), A/K, A+k, etc.); * Searches linear and spatial sites, conservative and variable in changes of specified physico-chemical properties (for example, helical hydrophobic moment); * Searches linear and spatial sites, having high and low values of specified physico-chemical properties (for example, Kyte-Doolittle hydrophobicity); * Plots sets of different physico-chemical profiles for individual protein sequence; * Plots specified physico-chemical profiles for the set of sequences; - Searches linear sites in multiple protein alignment and spatial sites in protein 3D structure influencing protein activity/property; * Plots average physico-chemical profile for the family of sequences; * Plots profile of dispersion of physico-chemical profiles for the family of sequences; * Plots physico-chemical profiles for protein 3D structure; - Analyses relationships between site structural characteristics and protein activities by multiple linear regression analysis; - Analyses structural differences between proteins divided by functional, evolutionary or other criteria; - Investigates physico-chemical factors related with activity changes in a set of mutant proteins; * Simulates protein-engineering experiments and predicts protein activity. Has options for automatic mutant generation (to increase or decrease protein activity) and for manual mutant generation; * Predicts activity for newly sequenced proteins; - Makes protein 3D pictures (mono and stereo) with sites highlighted; * Has more then 400 amino acid physico-chemical properties; - Investigates ten types of protein site characteristics, including average values, helical moments, beta-strand moments, etc.; - Saves results to the disk and saves pictures to the clipboard; - Has help and manual. ProAnWin PERMITS TO OBTAIN NEW RESULTS IMPORTANT IN BIOCHEMISTRY, MOLECULAR BIOLOGY ETC., AND TO DESIGN PROTEIN ENGINEERING EXPERIMENTS: 1. The program helps to find information that can not be found by other programs (activity/property-modulating sites, phenotype defining regions); 2. The user has an opportunity to conduct the analysis of structure-activity relationships in sequences and 3D structure. 3. The program permits to generate and to check up a plenty of hypothesis about the role of different sites and their various physico-chemical characteristics in protein activity, that is rather difficult or impossible at the "hand-operated" analysis. 4. Search of structure - activity relations is carried out with the use of multiple regression analysis and the results have statistical evaluations on reliability. 5. The user has an opportunity to work simultaneously with sequences and 3D protein structure (sites marked on the sequence are visualized in 3D structure and vise versa). 6. Alongside with the conventional average physico-chemical characteristics of a sequence site the user analyzes 9 additional characteristics of sequential (linear) sites and 5 characteristics of spatial sites. 7. The program permits considerably to reduce time during creation a mutant proteins with desired property. HOW TO START To investigate protein/peptide family of your interest you should have or prepare sequence data file(s). You can use alternatively sequences data files in FASTA (PEARSON), PIR, SWISS-PROT, CLUSTAL, GCG formats or in INTERNAL 1 format (3 data files with protein names (*.seq), protein activities or grouping (*.act) and aligned sequences (*.ali), see the examples in DATA directory) in the current directory. 3D protein structure you can take from PDB database. To use the program follow the steps: - start the program; - select sequences of the family you are going to investigate; - select a file with required physico-chemical properties of amino acids; - load protein 3D structure (if available); - define an investigated fragment (or up to 8 fragments); - define factors for analysis; and so on. All other information you'll get from MANUAL.TXT or HELP. ProAnWin IS USEFUL IN: - protein structure-function and structure-activity investigations; - designing proteins and peptides with improved activity; - making multiple protein alignments and getting sense from it; - studying phenotype-genotype correlations; - preparation of protein 3D pictures with sites highlighted; - protein features analysis; - comparative protein sequence analysis. PUBLICATIONS: 1. Frolov A.S., Pika I.S., Eroshkin A.M. ProMSED: Protein multiple sequence editor for Windows 3.11/95. CABIOS, 1997, 13, 243-248 2. Morozov B.M., Ivanisenko V.A., Eroshkin A. M., Ugarova N.N. Computer analysis of relations between bioluminescence color and primary structure of beetle luciferases: identification of the sites influencing bioluminescence color. Molec. Biology (Russia), 1996, 30, 1167-1172. 3. Ivanisenko V.A., Pika I.S., Pinin S.I., Fomina T.I., Eroshkin A.M. Studying structure-activity and phenotype-genotype relationships in protein families. Methods, algorithms and applications. Folding and Design, 1996, 1, Suppl., p.84. 4. Eroshkin A.M., Fomin V.I., Zhilkin P.A., Ivanisenko V.A., Kondrakhin Y.V. PROANAL version 2: multifunctional program for analysis of multiple protein sequence alignments and studying structure-activity relationships in protein families. CABIOS, 1995, 11, 39-44. 5. Eroshkin A.M., Zhilkin P.A., Fomin V.I. Algorithm and computer program PROANAL for analysis of relationship between structure and activity in a family of proteins or peptides. CABIOS, 1993, 9, 491-497. 6. Eroshkin A.M., Minenkova O.O., Fomin V.A., Ivanisenko V.A., Ilyichev A.A. Analysis of peptide fragment insertions into major coat protein of bacteriophages M13, f1 and fd. Relation of protein structural characteristics and viability of mutant phages. Molec. Biology (Russia), 1993, 27, 1345-1355. The version installed has limit in the number of analyzed sequences (15). To get unlimited registered version please contact the authors. If you have problems running ProAnWin please consult the manual and HELP carefully to see if they can help. If you still need advice then please contact the authors by e-mail: eroshkin@vector.nsk.su or State Research Center of Virology an Biotechnology "Vector" Koltsovo, Novosibirsk Region, 633159 Russia Tel: (3832) - 647774 Fax: (3832) - 328831 Ask authors for the updated ProAnWin version and ADDITIONAL NEW SOFTWARE TOOLS ProMSED2, ProAnalyst: ProMSED2 ProMSED2, MS Windows application for both automatic and manual DNA and protein sequence alignment, editing, comparison and analysis. ProMSED2 is the enhancement of ProMSED made according to user's remarks and suggestions. The program reads main sequence formats and performs automatic alignments, alignment visualization and editing and it allows sequences to be aligned interactively leaving unchanged previously aligned regions. The program has an user-friendly interface. Manual alignment and sequence analysis are facilitated by coloring schemes reflecting amino acid similarity in mutational, physico-chemical and other properties. Although ProMSED was targeted at protein sequences, it can be used on DNA sequences as well. The program provides flexible tool for sequences alignment, analysis, visualization, edition and presentations. Availability: EMBL library: ftp://ftp.ebi.ac.uk/pub/software/dos/promsed IUBio archive: ftp://iubio.bio.indiana.edu/molbio/ibmpc/promsed2.exe and .readme The program does or has (+ - NEW or enhanced features): + inputs DNA and protein sequences in NBRF/PIR, Pearson (Fasta), MSF (GSG), EMBL/SwissProt, Intelligenetics and CLUSTAL formats; o has interface and functions like in others Windows applications (source file view, font changing, marking/unmarking, block and sequence selection, cut and paste, UNDO, etc.); o loads several sequence families in different windows, adds sequences to existing alignment, combines sequences from various files; + outputs the alignment in several popular formats; + makes presentation quality color and black-and-white prints of complete alignment or any selected block; + saves alignment picture as Windows metafile and bitmap; o permits to apply automatic alignment interactively (with options to change the alignment parameters) to any selected part of sequences of marked block; + calculates sequence similarity of complete sequences, of any selected sequence subset or of marked block in % and in PAM250 units (matrix of amino acid similarity); + calculates total (average for %) sequence similarity value - an estimation of alignment quality; + prints sequence similarity matrix; + sorts sequences by similarity of complete sequences or marked block; + displays conserved and semiconserved positions; + has many amino acid coloring schemes aimed to facilitate manual alignment and understanding protein sequence features. Some schemes are: EVOLUTIONARY CONSERVATIVE (reflects amino acid mutational properties), COMPLEX (similarity of amino acids in physico-chemical properties), HYDROPHOBICITY, CHARGE, BIG RESIDUES, ALPHA-HELIX, HELIX-BREAKERS, etc. The options to input user-defined schemes or change the colors of any amino acid groups are available; + searches subsequences and complex sequence patterns; o has complete HELP. ProAnalyst ProAnayst: DOS version of ProAnWin with additional functionality (single and multiple sequences analysis, profiles analysis, combinatorial libraries; design of protein engineering experiments) Availability: IUBio archive: ftp://iubio.bio.indiana.edu/molbio/ibmpc/panalys1 EMBL library: ftp://ftp.ebi.ac.uk/pub/software/dos/proanalyst Functions: o data conversion from several protein sequence formats (FASTA, SWISS-PROT, PIR, CLUSTAL). o databases with more then 50 amino acid physico-chemical properties; o inputs 3D protein structure in PDB format; o flexible VISUALIZATION OF PROTEIN 3d STRUCTURES with sites highlighted; o inputs user-defined protein activities, properties or related phenotypes; o searching SITES INFLUENCING PROTEIN ACTIVITY and analyzing relationships between protein site structural characteristics and protein activities (properties or related phenotypes); o multiple linear regression analysis of STRUCTURE-ACTIVITY relationships, discriminant analysis and ANOVA; o intra and cross group VARIABILITY analysis; o GENOTYPE -- PHENOTYPE CORRELATION analysis (e.g., for drug resistance in viruses); o alphabetical and physico-chemical analysis of protein features variations (in 1D and 3D structures); o structure-activity determination profile (SAD); o investigation of physico-chemical factors related with activity or property changes in MUTANT PROTEINS; o searching motifs in COMBINATORIAL LIBRARIES (peptide, phage- display libraries, etc.) with MOTIF MAPPING on the target protein; o design PROTEIN-ENGINEERING experiments; o ACTIVITY, PROPERTY AND PHENOTYPE PREDICTION; o sorting sequences by protein activity value, by protein group number and by number of motifs found; o mapping results on 3D structure and sequences. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Alexey Eroshkin Institute of Molecular Biology E.mail: eroshkin@vector.nsk.su State Research Center of Virology and Tel: +7 (3832) - 647774 Biotechnology "Vector" Fax: +7 (3832) - 328831 Koltsovo, Novosibirsk Region 633159 Russia ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-proteins@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!qub.ac.uk!a.wallace From: a.wallace@qub.ac.uk (Andrew Wallace) Newsgroups: bionet.molbio.proteins Subject: Company address sought Date: 2 Jul 1997 04:40:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netusers, I am looking for contact information on a Biotech company called Avidity of Colorado, USA. Can anyone supply me with an address, phone number or email? Thanks for any help you can give, Andrew ------------------------------------------------------------------ Andrew Wallace, Ph.D, Queens University Belfast, N. Ireland (UK) a.wallace@qub.ac.uk http://web.qub.ac.uk/bb/awpage/wallace.html From owner-proteins@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!newsfeed.internetmci.com!usenet.logical.net!news.dal.ca!newsflash.concordia.ca!sunqbc.risq.qc.ca!news.risq.qc.ca!athena.ulaval.ca!not-for-mail From: Anguenot Raphaël Newsgroups: bionet.molbio.proteins Subject: Help!!! difficulties in dephosphorylating a protein Date: Wed, 02 Jul 1997 12:02:05 -0400 Organization: CRH, envirotron, Universite Laval, Quebec, CA Lines: 18 Message-ID: <33BA7B7B.2D88@agora.ulaval.ca> Reply-To: aai395@agora.ulaval.ca NNTP-Posting-Host: gatorg1-110.ulaval.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) CC: bionet.molbio.proteins Hello Friends, > We are working with a plant protein that is totally phosphorylated in > vivo. Assays of dephosphorylation using alkaline phosphatase (CIP) or > acid potato phosphatase were inefficient. We have used different > conditions, but removal of 32-P was not higher than 20% (2 hours > incubation). Does anyone encounter such problem with non-specific > phosphatases? Is there anyone who knows a protocol using general > phosphatases which works properly ? Any lab protocol or references are > welcomed. > > Kindly reply to me or the respective group. > > Thanks in advance > > Raphael > > Email: > aai395@agora.ulaval.ca From owner-proteins@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!geraldo.cc.utexas.edu!not-for-mail From: pat-toes@mail.utexas.edu (Patrick Thibodeau) Newsgroups: bionet.molbio.proteins Subject: LacZ staining in Drosophila midgut Date: 2 Jul 1997 21:30:56 GMT Organization: University of Texas at Austin Lines: 12 Message-ID: <5pehag$91m$1@geraldo.cc.utexas.edu> Reply-To: pat-toes@mail.utexas.edu NNTP-Posting-Host: esb103-pc28.esb.utexas.edu X-Newsreader: WinVN 0.92.6+ Hello. I am intersted in staining the inside of the Drosophila midgut to assay the presence b-gal. I have tried several things and none of them have worked. The larvae (3rd instar) will not eat food carrying the lacZ stain substrates below. Additionally, the stain will not work because the KFeCN solutions are extremly sensitive to acids and will degrade. Does anyone have another protocal for lacZ stains that might be les sensitive to the low pH (around 3) of the anterior midgut? I would appreciate any help. TYIA Patrick Thibodeau Univ. of Texas pat-toes@mail.utexas.edu From owner-proteins@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gsl.net!news.gsl.net!portc01.blue.aol.com!audrey02.news.aol.com!not-for-mail From: huntpharm@aol.com (Huntpharm) Newsgroups: bionet.molbio.proteins Subject: job opportunity in bioinformatics Date: 2 Jul 1997 22:49:10 GMT Lines: 11 Message-ID: <19970702224900.SAA07220@ladder02.news.aol.com> NNTP-Posting-Host: ladder02.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com I am looking for a person to head up bioinformatics. As a visionary you will be responsible for leading a group of five and taking the bioinformatics team to the next level. You will lead this group responsible for the application of computer technology to genomic analysis and research. We are a leading pharmaceutical company with research facilities in Connecticut and can provide excellent benefits (health insurance, dental and vision plans, paid vacations and more. Excellent compensation package. A high impact, high profile position with excellent opportunity for advancement. Please contact Scott Shanes by phone at 609-584-8733 EXT. 218, fax CV to 609-584-9575 or E-Mail to SIS@diedremoire.com or Neurohunt@aol.com. From owner-proteins@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!SCRIPPS.EDU!ozhang From: ozhang@SCRIPPS.EDU (Ouwen Zhang) Newsgroups: bionet.molbio.proteins Subject: myoglobin digested by proteases Date: 3 Jul 1997 11:18:47 -0700 Organization: Scripps Research Insitute Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <33BBED2F.41C6@scripps.edu> NNTP-Posting-Host: net.bio.net Hi everyone: I am wondering whether anyone knows whether detailed limited proteolysis has been done on sperm whale myoglobin, in particular a protease called closttipain. Any help is appreciated. Ouwen From owner-proteins@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!us1.rhbnc.ac.uk!yama.mcc.ac.uk!news.york.ac.uk!not-for-mail From: David Scott Newsgroups: bionet.molbio.proteins,bionet.biophysics Subject: molar absoptivity Date: Thu, 03 Jul 1997 13:08:34 -0700 Organization: University of York. York. Y01 5DD Lines: 19 Sender: djs17@york.ac.uk Message-ID: <33BC06C2.75E9@york.ac.uk> Reply-To: Dept., Biology NNTP-Posting-Host: biolpc227.york.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win16; I) Xref: biosci bionet.molbio.proteins:11124 bionet.biophysics:3294 Hello, Does anyone know how to determine the molar absorptivity of a protein as a function of wavelength, from scratch? Dave. -- ******************************* * Dr. David Scott * * Dept Biology * * University of York * * YORK * * YO1 5DD * * * * United Kingdom * * * * phone +44 1904 432867 * * fax +44 1904 432860 * ******************************* From owner-proteins@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: Jim Hughes Newsgroups: bionet.molbio.proteins Subject: Help on Lipid Binding Proteins Date: Thu, 03 Jul 1997 15:18:06 +0100 Organization: IMM Lines: 8 Message-ID: <33BBB493.7D5@immsvr.jr2.ox.ac.uk> Reply-To: jhughes@immsvr.jr2.ox.ac.uk NNTP-Posting-Host: marlboro.imm.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Macintosh; I; PPC) Hi does anybody have a good system for assaying a protein's ability to bind lipids or phospholipids and how to identify which lipids/phospholipids have been bound? Any suggestion appreciated . many thanks Jim From owner-proteins@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!server1.netnews.ja.net!server5.netnews.ja.net!server3.netnews.ja.net!baron.netcom.net.uk!netcom.net.uk!cpk-news-hub1.bbnplanet.com!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!nih.gov!not-for-mail From: jhmiller@helix.nih.gov (Jay Miller) Newsgroups: bionet.molbio.proteins Subject: Re: Tris/tricine SDS-PAGE Date: 3 Jul 1997 18:02:17 GMT Organization: National Institute of Health Lines: 16 Message-ID: <5pgpf9$6pb$2@light.nih.gov> References: <199706250257.LAA189646@plaza.snu.ac.kr> <5orive$6j0@falcon.le.ac.uk> Reply-To: jhmiller@helix.nih.gov NNTP-Posting-Host: ams06057.niams.nih.gov X-Newsreader: IBM NewsReader/2 2.0 Von Jagow and Schagger wrote a manual in 1995, A Practical Guide to Membrane Purification, Academic Press, in which they suggest shrinking high percentage gels in 50% MeOH, 2% glycerol for 30-60 min and then drying at elevated temp. under vacuum. In <5orive$6j0@falcon.le.ac.uk>, "Dr E. Buxbaum" writes: >skim@PLAZA.SNU.AC.KR wrote: >>Dear everyone, >> >>I am trying to detect the low molecular weight(8KD) protein using >>Tris-Tricine SDS-PAGE. But when I dried the gel, the gel was easily >>crashed. > >I equilibrate my gels in 10% glycerol in aq. bidest. for 30 min before >drying them. Keeps them nice and flexible. > From owner-proteins@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!us1.rhbnc.ac.uk!yama.mcc.ac.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!mac052034.lif.icnet.uk!user From: I.McFarlane@icrf.icnet.uk (Ian McFarlane) Newsgroups: bionet.molbio.proteins Subject: Pharmacia FPLC UV Date: Thu, 03 Jul 1997 18:27:07 +0000 Organization: Imperial Cancer Research Fund Lines: 10 Message-ID: NNTP-Posting-Host: mac052034.lif.icnet.uk X-Newsreader: Value-Added NewsWatcher 2.0b27+ Hi, If I have a peak of protein (say BSA) on a gel exclusion column which gives me 50% of full scale deflection at 1AU=FSD _approximately_ how much protein is that? I know you need to measure area under the curve but can anyone give me a ballpark figure? Thanks in advance, Ian Mc From owner-proteins@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!atl-news-feed1.bbnplanet.com!news.bbnplanet.com!news1.usf.edu!!user From: "Wen-Ming Yang" Newsgroups: bionet.molbio.proteins Subject: Re: E. coli strain BL21 Date: Thu, 03 Jul 1997 15:08:53 +0500 Organization: H Lee Moffitt Cancer Center at USF Lines: 14 Message-ID: <5pgtbd$3gt$1@news.usf.edu> References: NNTP-Posting-Host: pc-mrc-4t-1.moffitt.usf.edu Mime-Version: 1.0 Content-Type: text/plain; charset="" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Internet Mail & News for Macintosh - 3.0 In article , mbzrl@mbn1.biochem.nottingham.ac.uk (Rob) wrote: Help! I am thinking of using E. coli strain BL21 to express a recombinant protein but I have heard that it carries certain health and safety risks. Does anyone have experience in using this strain or know of any special handling procedures or containment levels required to grow this strain. Thanks Rob Why not try to use DH5alpha? From owner-proteins@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!206.172.150.11!news1.bellglobal.com!sunqbc.risq.qc.ca!news.risq.qc.ca!news.mcgill.ca!feed.umontreal.ca!usenet From: "s.a." Newsgroups: bionet.molbio.proteins Subject: Q: Antibody against bacterial ribosomal protein S12 Date: 3 Jul 1997 22:26:49 GMT Organization: Universite de Montreal Lines: 10 Distribution: world Message-ID: <01bc8800$628fcca0$1954cc84@balder.bch> NNTP-Posting-Host: balder.bch.umontreal.ca X-Newsreader: Microsoft Internet News 4.70.1161 Hi, I am working with the S12 protein in E. coli. I can't easily detect it on a Coomassie blue SDS-PAGE. I plan to do an antibody assay. So My question is: Does anybody have a monoclonal antibody against the S12 protein from E. coli. Thanks in advance and have good experiments. -------------------------------------- Guy Tremblay tremblgu@medcn.umontreal.ca From owner-proteins@net.bio.net Thu Jul 03 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!news.theriver.com!news-feed.inet.tele.dk!news.inet.tele.dk!not-for-mail From: Bo Bergmann <120010312330@post5.tele.dk> Newsgroups: bionet.molbio.proteins Subject: HPLC - WIZARD home page update Date: Fri, 04 Jul 1997 14:28:32 +0200 Organization: DTU Lines: 6 Message-ID: <33BCEC70.1C38@post5.tele.dk> NNTP-Posting-Host: ppp304.arh.tele.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02E [da]-TDK20 (Win95; I) CC: Bo, Bergmann The homepage of HPLC - WIZARD has been updated to illustrate the use of the application. Surf by and enlist as beta - tester at: http://home5.inet.tele.dk/daller/index.htm From owner-proteins@net.bio.net Thu Jul 03 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!howland.erols.net!ix.netcom.com!tor-nn1.netcom.ca!news From: williamb@vcn.bc.ca (William Becker) Newsgroups: bionet.molbio.proteins Subject: Help: Enzyme Interactions Date: Sat, 05 Jul 1997 01:05:42 GMT Organization: Netcom Canada Lines: 8 Message-ID: <33bd9cd2.32398444@nntp.netcom.ca> NNTP-Posting-Host: van-bc6-59.netcom.ca X-NETCOM-Date: Fri Jul 04 9:13:37 PM EDT 1997 X-Newsreader: Forte Free Agent 1.1/16.230 I am a non-professional interested in Enzyme Interactions. (for example: between digestive enzymes chymotrypsin and bromelain.) Could someone advise where I might look for more on this. Is this a topic for so-called Computational Biology? Thank you. William From owner-proteins@net.bio.net Fri Jul 04 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!dispatch.news.demon.net!demon!mail2news.demon.co.uk!spherica.demon.co.uk!mrr From: Matt Newsgroups: bionet.molbio.proteins,z-netz.forum.umweltschutz,sci.bio.ecology,sci.environment.waste,sci.materials,sci.polymers,alt.energy.renewable Subject: Re: Biodegradable materials Date: Sun, 06 Jul 97 00:48:33 GMT Organization: Pax Biospherica Message-ID: <868150113snz@spherica.demon.co.uk> References: <5np6tq$c7o$3@news01.btx.dtag.de> Reply-To: mrr@spherica.demon.co.uk X-Mail2News-User: mrr@spherica.demon.co.uk X-Mail2News-Path: punt-1.mail.demon.net!spherica.demon.co.uk X-Newsreader: Demon Internet Simple News v1.30 Lines: 23 > Are you aware of the "packing peanuts" which are made of corn starch? > they are direct replacements for polystyrene "peanuts" but can easily be > dissolved in water and be disposed of down the sink. At last! A good example that's already out there. I remember Jordan's cereal manufacturers in Britain once packaging their 500g muesli in a clear cellulose wrapper, with a note printed on it explaining that the wrapper would rot if allowed to after use. Not sure what they use now, but they don't advertise it. Is there anything else like that around? Why not?? Come on, somebody start a trend... please... Matt -- Clobber Car Culture: Live Life Locally From owner-proteins@net.bio.net Fri Jul 04 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!usc!chi-news.cic.net!newsspool.doit.wisc.edu!news.doit.wisc.edu!blah From: klenchin@facstaff.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: Why 3H-GTP in GTP-binding assay? Date: Wed, 02 Jul 1997 23:28:07 GMT Organization: UW-Madison Lines: 23 Message-ID: <5peo4c$b4e@news.doit.wisc.edu> References: <33B34313.41C67EA6@umich.edu> <5p0i1t$1oim@news.doit.wisc.edu> <5p90l3$lsl@falcon.le.ac.uk> NNTP-Posting-Host: martinlab.biochem.wisc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=KOI8-R Content-Transfer-Encoding: 8bit X-Newsreader: News Xpress 2.01 X-No-Archive: Yes In article <5p90l3$lsl@falcon.le.ac.uk>, "Dr E. Buxbaum" wrote: :klenchin@facstaff.REMOVE_TO_REPLY.wisc.edu (Dima Klenchin) wrote: : :>I am not sure why not 14C-GTP but probably due to even :>lower specific radioactivity and still lower counting efficiency. : :The counting efficiency of 14C is usually around 80-90% (compared to :about 20% with 3H). The biggest problem with 14C is its price tag. The :reason for this is that 14C compounds can only be isolated from organisms :grown on a 14C carbon source. Tritium labeled compounds can be prepared :in many cases by exchanging 1H against 3H essentially by sealing your :compound with 3H water into an ampoule, keeping it warm for a week or so :and then separating it from the water. Note that this process is :reversible, one of the reasons why 3H compounds do not keep as well as :the half life of 3H would suggest. : I stand corrected - counting efficiency of 14C is indeed extremely high. It is VERY low specific radioactivity and high price that makes it unusable for G-protein research. - Dima From owner-proteins@net.bio.net Sat Jul 05 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-xfer.netaxs.com!netnews.upenn.edu!mail.med.upenn.edu!rcowherd From: rcowherd@mail.med.upenn.edu (Robert Cowherd) Newsgroups: bionet.molbio.proteins Subject: Biodegradable materials Date: 7 Jul 1997 05:05:50 GMT Organization: University of Pennsylvania Lines: 13 Message-ID: <5pptfe$hn4@netnews.upenn.edu> NNTP-Posting-Host: mail.med.upenn.edu X-Newsreader: TIN [version 1.2 PL2-upenn1.1] I not sure about this but I vaguely recall that the corn starch merely helps to hold the "bits" of non-degradable plastic together. When the starch is degraded you are left with microscopic particles of plastic. Perhaps someone out there (on the net) knows for sure. It _would_ seem to lower the amount of plastic waste but not eliminate it as popular perception (wishfulness) might have us believe. To be truly environmentally friendly, the polymer should be entirely catabolizable. Perhaps that is why you don't really _see_ ;^} much of it around anymore... JMTCW... Bob Cowherd From owner-proteins@net.bio.net Sat Jul 05 23:00:00 1997 Path: biosci!rutgers!gatech!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-xfer.netaxs.com!netnews.upenn.edu!mail.med.upenn.edu!rcowherd From: rcowherd@mail.med.upenn.edu (Robert Cowherd) Newsgroups: bionet.molbio.proteins Subject: Biodegradable materials Date: 7 Jul 1997 05:11:09 GMT Organization: University of Pennsylvania Lines: 9 Message-ID: <5pptpd$hn4@netnews.upenn.edu> NNTP-Posting-Host: mail.med.upenn.edu X-Newsreader: TIN [version 1.2 PL2-upenn1.1] Just an after thought to my previous posting ... What per se does this thread have to do with bionet.molbio.proteins anyway? Is there a more appropriate newsgroup? Thanks, Bob Cowherd From owner-proteins@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!news.starnet.net!news.starnet.net!news.hn.netlink.co.nz!auckland.ac.nz!ak.netlink.co.nz!usenet From: Ross Prestidge Newsgroups: bionet.molbio.proteins Subject: endotoxin in recombinant proteins? Date: Tue, 08 Jul 1997 10:50:25 +1200 Organization: NetLink Auckland, New Zealand. Lines: 25 Message-ID: <33C172B3.3161@genesis.co.nz> NNTP-Posting-Host: 202.36.157.130 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Macintosh; I; 68K) Can anyone point me to a FAQ on the problem of endotoxin contamination in proteins purified from recombinant E. coli? I am working with a gene which I have expressed from E. coli as a fusion with a His-tag. The tagged protein has been purified on a nickel column, but at this stage has slightly too much endotoxin for my application. My questions are: - Has anyone investigated the best washing conditions for nickel columns to minimise endotoxin carryover? - What is the best source for endotoxin analysis kits? At present I am using the COATEST LAL kit from Chromogenix ( manufactured by Endosafe), and it's working well, but I would be interested in a cheaper alternative. - What is the best way to remove endotoxin from purified recombinant proteins? I have some Pierce Detoxigel, but I haven't tried it yet. I would be interested to hear of your experience with this matrix, optimal buffers for protein work, alternative resins etc. My protein is quite hydrophobic - is there a risk it will bind to the resin? I would be grateful for any help you can give, either by mail or to the newsgroup. Regards, Ross Prestidge From owner-proteins@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!europa.clark.net!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!warwick!news.nott.ac.uk!NewsWatcher!user From: kevin.bailey@nottingham.ac.uk () Newsgroups: bionet.molbio.proteins Subject: Re: myoglobin digested by proteases Followup-To: bionet.molbio.proteins Date: Mon, 07 Jul 1997 15:03:46 +0100 Organization: Cripps Computing Centre, The University of Nottingham Distribution: world Message-ID: References: <33BBED2F.41C6@scripps.edu> NNTP-Posting-Host: wpbjwk1.biochem.nottingham.ac.uk Lines: 17 In article <33BBED2F.41C6@scripps.edu>, ozhang@SCRIPPS.EDU (Ouwen Zhang) wrote: > Hi everyone: > I am wondering whether anyone knows whether detailed limited > proteolysis has been done on sperm whale myoglobin, in particular > a protease called closttipain. > Any help is appreciated. > > Ouwen Don't have anything specific, but as a general piece of advice I'd recommend finding the Swissprot database file for the whale myoglobin and look in the headers; there are usually refs for any sequencing work that has been done, so if you find the refs they will have details of how the sequences were derived and any endoproteases used, including the one you are referring to (clostripain, = arg-C). From owner-proteins@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!surfnet.nl!news.belnet.be!news-zh.switch.ch!rzunews.unizh.ch!newsadm From: Rolf Kocherhans Newsgroups: bionet.molbio.proteins Subject: Free practical programs for molecular biologists !!! Date: Mon, 07 Jul 1997 16:17:35 +0200 Organization: University of Zurich Lines: 49 Message-ID: <33C0FA7E.36E9@vetvir.unizh.ch> Reply-To: rolfk@vetvir.unizh.ch NNTP-Posting-Host: 130.60.22.38 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) I wrote a few practical and simple to use programs which facilitate your daily work in the lab such as predicting the size of DNA fragments after digestion (graphical) with restriction enzymes. I would like to make these programs accessible to a broad user group by the Internet. All programs have been tested on MacOS and Windows95. My programs are accessible over the WWW and made functional using Netscape 2.x or Internet Explorer 2.x or higher in association with a free plugin which you have to download and install first. This is what you do: - Download the Roadster plugin http://www.unizh.ch/vetvir/plugin.html) install it on your computer. - Then connect to: http://www.unizh.ch/vetvir/programs.html That's it !! These are my programs which make your live as a molecular biologist easier ! Find here a few more examples or my programs: a. Digest Preview: Enter the size(s) of your DNA fragment(s) and see their migration pattern in a virtual gel in comparison to a 1 kb ladder. b. Adapter Design: Helps to create in frame adapters in order to link incompatible DNA ends together. c. Dilution Calculator: Does all the calculations when you have to make up solutions There are many other programs such as Oligo Tm, Compatible ends etc. Please have a look, comments are welcome! Have fun Rolf Kocherhans mailto:rolfk@vetvir.unizh.ch From owner-proteins@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!csulb.edu!gatech!howland.erols.net!newsxfer3.itd.umich.edu!news.eecs.umich.edu!srvr1.engin.umich.edu!news.cc.ukans.edu!usenet From: PGegen@kuhub.cc.ukans.edu (Dr. Peter Gegenheimer) Newsgroups: bionet.molbio.proteins Subject: Re: E. coli strain BL21 Date: 8 Jul 1997 04:33:08 GMT Organization: University of Kansas, Dept. of Biochemistry, Cell, and Molecular Biology Lines: 24 Message-ID: <5psfu4$qh2@raven.cc.ukans.edu> References: <5pgtbd$3gt$1@news.usf.edu> Reply-To: !PGegen@UKans.edu (Dr. Peter Gegenheimer) NNTP-Posting-Host: rnaworld.bio.ukans.edu X-Newsreader: IBM NewsReader/2 2.0 In <5pgtbd$3gt$1@news.usf.edu>, "Wen-Ming Yang" writes: >In article , >mbzrl@mbn1.biochem.nottingham.ac.uk (Rob) wrote: > >Help! > > I am thinking of using E. coli strain BL21 to express a recombinant >protein but I have heard that it carries certain health and safety risks. >Does anyone have experience in using this strain or know of any special >handling procedures or containment levels required to grow this strain. No special precautions are required for use of E. coli BL21(DE3) except those associated with the gene being expressed. For containment purposes, remember that BL21 is an E. coli B strain, not a K12 strain. o-----------------------------------------------------------------------o | Dr. Peter Gegenheimer | Vox: 913-864-3939 FAX: 913-864-5321 | | Departments of Biochemistry | PGegen@UKans.edu | | and of Botany | http://rnaworld.bio.ukans.edu/ | | | | | University of Kansas | | | 2045 Haworth Hall | "The sleep of reason produces | | Lawrence KS 66045-2106 | monsters." Goya | o______________________________|________________________________________o From owner-proteins@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!U.WASHINGTON.EDU!egn From: egn@U.WASHINGTON.EDU ("E. Kolker") Newsgroups: bionet.molbio.proteins Subject: CALL FOR PAPERS: Recomb 98 Date: 7 Jul 1997 12:07:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 196 Sender: daemon@net.bio.net Distribution: world Message-ID: 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. Conference Events RECOMB 98 will feature 8 invited lectures (to be announced later) by prominent biologists including the following conference events: THE STANISLAW ULAM MEMORIAL COMPUTATIONAL BIOLOGY ADDRESS. The Stanislaw Ulam Memorial Lecture awarded by RECOMB to a scientist who has made major contributions in the computational aspects of the field. THE DISTINGUISHED CONFERENCE LECTURE. The conference will start with the Distinguished Conference Lecture awarded by RECOMB to a scientist who has made major contributions in the biological aspects of the field. THE DISTINGUISHED NEW TECHNOLOGIES LECTURE. A lecture describing emerging, new technologies. 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 From owner-proteins@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!agate!howland.erols.net!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!oleane!jussieu.fr!univ-lille1.fr!not-for-mail From: nathalie.druart@univ-lille1.fr (Nathalie Druart) Newsgroups: bionet.molbio.proteins Subject: Help ! Problems with immunodetection on western blot Date: 8 Jul 1997 08:00:08 GMT Organization: EPGMV Lines: 20 Message-ID: <5pss29$avk$3@netserv.univ-lille1.fr> NNTP-Posting-Host: phyvpc1.univ-lille1.fr Mime-Version: 1.0 X-Newsreader: WinVN 0.93.10 Dear Netters, I have problems with immunodetection on western blot. I am working on chicory protein extract which contains 10% glycerol, 25 mM K phosphate buffer pH 7.5, 5uM FAD, 0.5 mM MgCl2, 50 uM TPP and 0.25 mM DTT. The extract have been tested positively for acetolactate synthase (ALS) activity. Six month ago, the antibody (rabbit) against ALS has been tested and was specific. And now, I have one big problem: with or without primary antibody, the secondary antibody (BIORAD, goat anti-rabbit alkaline phosphatase coupled one) detects the whole proteins as if it was a naphtol blue black coloration ! What can I do ? Have you already had such a problem ? And did you resolve it ? I would appreciate any kind of advice or idea that could help me. Could you mail it or them at: edewaele@pop.univ-lille1.fr Thank you, Delphine From owner-proteins@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!jump.net!grunt.dejanews.com!not-for-mail Date: Tue, 08 Jul 1997 08:22:50 -0600 From: alexander.schramm@uni-essen.de Subject: Oligo construction help requested Newsgroups: bionet.molbio.proteins Message-ID: <868367711.31019@dejanews.com> Organization: Deja News Usenet Posting Service X-Article-Creation-Date: Tue Jul 08 13:15:12 1997 GMT X-Originating-IP-Addr: 132.252.180.5 (spf105.power.uni-essen.de) X-Http-User-Agent: Mozilla/2.0 (compatible; MSIE 3.02; Update a; Windows 95) via Squid Cache version 1.0.5 X-Authenticated-Sender: alexander.schramm@uni-essen.de Lines: 12 Could you please help a moderately frustated graduate student in constructing an oligonucleotide probe out of a N-terminal protein sequence? I used oligos derived from the protein sequence NFKAY as probes in Southern Blots, which did not work, because I sequenced DNA, which is not related to this protein sequence. In order to construct more specific probes, I had the idea to use PNA instead of DNA probes. Has anyone experience with this kind of probe in Southern Blots? Thank you in advance. Alex e-mail: alexander.schramm@uni-essen.de www: http://www.uni-essen.de/mikrobiologie/alex.html -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-proteins@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!botany.uq.edu.au!J.Marcus From: J.Marcus@botany.uq.edu.au ("Marcus, Dr J.") Newsgroups: bionet.molbio.proteins Subject: Re: Specific activity Date: 8 Jul 1997 16:10:53 -0700 Organization: Dept of Botany, Univ of Queensland Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <5B7F4716083@botany.uq.edu.au> References: <33C2B6B0.3859@cc.umanitoba.ca> Reply-To: Marcus@tpp.uq.edu.au NNTP-Posting-Host: net.bio.net Hi Brian, You may have more or less degradation of your protein during your preps which can never be exactly the same. Depending on how much variation you get, I probably would not lose any sleep over it. 10X variation, yes, you should probably worry; 20% variation, I would not worry about it. All the best, John Marcus > I am overexpressing an enzyme in E. coli for kinetic analysis. Can the > E. coli cell density at the time of IPTG induction affect the specific > activity of the enzyme eventhough I purify the enzyme before I assay it? > I ask this because my preps seem to have differing specific activities > and its not due to pipette or protein assay errors. > > Brian > bmark@cc.umanitoba.ca > > _________________________________________________________ John Marcus Marcus@tpp.uq.edu.au (Dr J.Marcus) Cooperative Research Centre for Tropical Plant Pathology 5th Level John Hines Building University of Queensland St. Lucia, QLD 4072 AUSTRALIA Fax: 61-7-3365-4771 Phone: 61-7-3365-4764 From owner-proteins@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!news.cis.ohio-state.edu!magnus.acs.ohio-state.edu!cm119pc14.acs.ohio-state.edu!poi.2 From: poi.2@postbox.acs.ohio-state.edu (Poi Ming Jye) Newsgroups: bionet.molbio.proteins Subject: Help! Protein refolding problem Date: Tue, 8 Jul 1997 22:42:25 GMT Organization: The Ohio State University Lines: 12 Message-ID: NNTP-Posting-Host: cm119-pubpc12.acs.ohio-state.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] Hi, I have a problem in refolding my protein. Well, the major problem is my protein has 7 disulfide bonds. Therefore, in the process of refolding, I often lose a lot of protein due to many steps of refolding and misfolding too. My protocol was developed about 7 years ago, and I am just a first year graduate student, and really know not much about protein. If anyone comes across a more recent protocol on protein folding, especially with S-S bonds, please let me know. Anyone who knows a protocol on purifying proteins with many S-S linkages, please kindly let me know. I would really, really appreciate it. MP. From owner-proteins@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!news.bc.net!dragon.sk.sympatico.ca!canopus.cc.umanitoba.ca!not-for-mail From: Brian Mark Newsgroups: bionet.molbio.proteins Subject: Specific activity Date: Tue, 08 Jul 1997 16:52:48 -0500 Organization: University of Manitoba Lines: 8 Message-ID: <33C2B6B0.3859@cc.umanitoba.ca> Reply-To: bmark@cc.umanitoba.ca NNTP-Posting-Host: tr-ra2.biochem.umanitoba.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) I am overexpressing an enzyme in E. coli for kinetic analysis. Can the E. coli cell density at the time of IPTG induction affect the specific activity of the enzyme eventhough I purify the enzyme before I assay it? I ask this because my preps seem to have differing specific activities and its not due to pipette or protein assay errors. Brian bmark@cc.umanitoba.ca From owner-proteins@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!agate!kos5mac18.berkeley.edu!user From: nigel@nature.berkeley.edu Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: looking for argU expression vector. Date: 9 Jul 1997 01:35:51 GMT Organization: University of California, Berkeley Lines: 81 Message-ID: NNTP-Posting-Host: kos5mac18.berkeley.edu X-Newsreader: Yet Another NewsWatcher 2.1.5 Xref: biosci bionet.molbio.methds-reagnts:59397 bionet.molbio.proteins:11162 Hi, I've got a protein that's been making my life a nightmare...and I think I've finally hit on the reason. Apparently I need to give e.coli a little more argU tRNA so that it can translate it. (I've got three AGG's in a row, as well as four pairs of AGG AGA/AGG). Is there a commercial source for an argU overexpression vector/host? Does anyone out there have a plasmid they'ed care to share? thanks in advance -nigel -- Nigel Walker [>======<] nigel@mendel.berkeley.edu Dept. of Plant Biology \ Mu / (510) 642-6813 Lab 351 Koshland hall \ / (510) 642-4995 Fax U.C. Berkeley \ / (510) 763 7862 Berkeley, CA 94720 \/ http://plantbio.berkeley.edu/~nigel ===========CAAT=======TATAA============================================ |-X-> PS: here's a couple of ref's in case this interests you. 3. (BIOSIS result) Zahn, K. Overexpression of an mRNA dependent on rare codons inhibits protein synthesis and cell growth. Journal of Bacteriology, v.178, n.10, (1996): 2926-2933. Abstract: lambda's int gene contains an unusually high frequency of the rare arginine codons AGA and AGG, as well as dual rare Arg codons at three positions. Related work has demonstrated that Int protein expression depends on the rare AGA tRNA. Strong transcription of the int mRNA with a highly efficient ribosome-binding site leads to inhibition of Int protein synthesis, alteration (if the overall pattern of cellular protein synthesis, and cell death. Synthesis or stability of int and ampicillin resistance mRNAs is not affected, although a portion of the untranslated int mRNA appears to be modified in a site-specific fashion. These phenotypes are not due to a toxic effect of the int gene product and can be largely reversed by supplementation of the AGA tRNA in cells which bear plasmids expressing the T4 AGA tRNA gene. This indicates that depletion of the rare Arg tRNA due to ribosome stalling at multiple AGA And AGG codons on the overexpressed int mRNA underlies all of these phenomena. It is hypothesized that int mRNA's effects on protein synthesis and cell viability relate to phenomena involved in lambda phage induction and excision. 4. (BIOSIS result) Hu, X; Shi, Q; Yang, T; Jackowski, G. Specific replacement of consecutive AGG codons results in high-level expression of human cardiac troponin T in Escherichia coli. Protein Expression and Purification, v.7, n.3, (1996): 289-293. Abstract: The adult isoform of human cardiac troponin T (TnT) contains 288 amino acids, 14 of which (4.9%) are encoded by the rarely used arginine codons (12 AGG, 2 AGA) in Escherichia coli genes. To generate sufficient quantity of TnT protein for antibody production, we cloned the corresponding cDNA and expressed it in E. coli. A low-level expression of TnT that comprised only about 1% of total cell protein was initially observed with the use of the native cDNA. The existence of two pairs of consecutive AGG codons (AGG-165AGG-166 and AGG-215AGG-216) in the cDNA was suspected to be the main cause for this low-level expression. These two pairs of consecutive AGG codons were successively replaced with the major synonymous codon CGT by site-directed mutagenesis. As suspected, a 10-fold increase in TnT expression was obtained when one pair of the rare arginine codons was replaced and a 40-fold increase was achieved when both pairs of the rare codons were replaced. Our finding demonstrates the importance of consecutive rare codons in the suppression of high-level expression of heterologous proteins in E. coli and suggests that in order to maximize protein expression, a similar approach may be taken with other genes which contain consecutive rare codons. From owner-proteins@net.bio.net Mon Jul 07 23:00:00 1997 From: Damn Yankee Newsgroups: bionet.molbio.proteins Organization: Yankee Inc. Subject: !!!Hello!!! NNTP-Posting-Host: 205.139.183.49 Message-ID: <33c0b446.2@nntp.kalnet.net> Date: 7 Jul 97 09:17:58 GMT Lines: 9 Path: biosci!agate!usenet.INS.CWRU.Edu!HSNX.wco.com!newsfeed.dacom.co.kr!newsfeed.internetmci.com!pull-feed.internetmci.com!nntp.kalnet.net!205.139.183.49 Are you looking for a great place to find interesting things on the WWW??? Than look no more because you have found the right place!!! The place you are looking for is Yankee Inc.!!! A great Web Site full of interesting links to interesting places!!! Everything from Adult to Xzlyaphone it's here!!! There is something for everyone and then some!!! So give it a try what do you have to lose except some sleep??? Yankee Inc. http://www.kalnet.net/yank714 Yankee Inc. Your Alternative Web Solution!!! Yankee Inc. http://www.kalnet.net/yank714 If you would like to be removed from my mailing list - hit reply and type "REMOVE" and I will promptly remove you from my list!!! Thank You!!! From owner-proteins@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!RPI.EDU!balajb From: balajb@RPI.EDU ("B. Balaji") Newsgroups: bionet.molbio.proteins Subject: antibodies for PAL and CHS Date: 8 Jul 1997 16:33:43 -0700 Organization: Rensselaer Polytechnic Institute Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <33C2DCC1.1425@rpi.edu> Reply-To: balajb@rpi.edu NNTP-Posting-Host: net.bio.net Dear Netters, I will be glad if someone can provide me the source from where I could obtain antibodies for the plant defense enzymes, phenylalanine ammonia lyase (PAL) and chalcone synthase (CHS) of tomatoes. Thanks in advance for your cooperation. Sincerely, Balaji Please contact: B. Balaji Biology department (MRC 301) Rensselaer Polytechnic Institute Troy, NY 12180-3590 email: balajb@rpi.edu From owner-proteins@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.molbio.proteins Subject: Review articles on bioinformatics Date: 8 Jul 1997 16:11:35 +0100 Lines: 75 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5ptlb7$nms@mserv1.dl.ac.uk> Original-To: bio-info@dl.ac.uk, biophys@dl.ac.uk, comp-bio@dl.ac.uk, proteins@dl.ac.uk Dear netters: Several days ago, I asked "Could any one provide me some references of recent review articles on bioinformatics?" , then almost immediately, I received many letters. To my surprise, most of these letters are not about the reply, on the contrary, they kindly asked me to re-post the messages to them. So I think this topic may interest many people. Now I summarize the responses as follows: Printed sources about BioInformatics & the InterNet. Resources, Reviews 1993-1996. Trends in Genetics 11(6) : 223-228 (June 1995). World Wide Web resources for the biologist. Rob Harper (EBI). Molecular Medicine 333(10): 645-647 (Sept 1995). Molecular medicine: hunting for genes in computer data bases. Mark Boguski (NCBI). Kemia-Kemi 22(8): 691-696 (1995). Marcomolecular modelling for the 21st Century. Mark Johnson et al. (Turku, Fi) Current Opinions in Genetics and Development 4: 383-388 (1994). Bioinformatics. Mark Boguski (NCBI). Trends in Biotechnology 12: 76-80 (March 1994). High performance searching of biosequence databases. Andrew Coulson (Edin.). Nature Genetics 6: 119-129 (Feb 1994). Issues in searching molecular sequence databases. Stephen Altschul et al (NCBI). Nature 375: 262 (May 1995). The boom in bioinformatics (employment review). Diane Gershon. Science 262: 502-503 (Oct 1993). Managing the genome data deluge. Peter Aldhous. Nature 376: 647-648. Challenging times for bioinformatics. Chris Sander et al. (EMBL). Molecular Medicine Today March 1996: 98-102. The Web: sequence databases and homology searching using the World Wide Web. Science 272: 1730-1732. Hot property: biologists who compute. Elliot Marshall. The Biochemist Oct/Nov 1996: 32-33. Bioinformatics. Clare Sansom, (Birkbeck). "Methods in Enzymology", vol. 266 "Computer Methods for Macromolecular Sequence Analysis" (1996) R.F. Doolittle Ed.; Academic Press. Up-to-date, and very comprehensive. Science 273: 545-708 (21 Aug. 1996) Not the entire issue, of course, but there is a concentration of good articles there. The URL is http://www.techfak.uni-bielefeld.de/bcd/Curric/syllabi.html mirrored at http://merlin.mbcr.bcm.tmc.edu:8001/bcd/Curric/syllabi.html and http://www.biotech.ist.unige.it/bcd/Curric/syllabi.html http://www.techfak.uni-bielefeld.de/bcd/welcome.html) I would like to thank specially the folowing netters: Dr. Andrew Lloyd Dr. Georg Fuellen Dr. Iddo Friedberg Without their kind help, we can not have so much useful information. Ren Zhang From owner-proteins@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!panix!news.columbia.edu!sawasdee.cc.columbia.edu!mdt1 From: M David Tilson Newsgroups: bionet.molbio.proteins Subject: re: need software to run antique Rainin HPLC (rabbit pumps) Date: Tue, 8 Jul 1997 10:28:16 -0400 Organization: Columbia University Lines: 21 Message-ID: NNTP-Posting-Host: sawasdee.cc.columbia.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have a 12 y/o Rainin Rabbit that I am trying to rehabilitate. Got the pumps up and running yesterday, but I've lost the software for the old Apple IIe. Does anybody have an IBM PC DOS or Windows program that will run a gradient?? I don't really need sophisticated data acquisition, as the old chart recorder will be fine for preparative purposes. TIA, _dave_ E-mail: mdt1@columbia.edu URL : http://www.columbia.edu/~mdt1/ 1 = one (not little L), and don't forget the trailing "/") Phone : 212-523-7779 SnailM: M David Tilson, SLRHC, 1000 Tenth Avenue, NY, NY 10019 From owner-proteins@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!newsfeed.direct.ca!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!129.240.148.41!nntp.uio.no!mn6.swip.net!seunet!news2.swip.net!mailgate.astra.com!not-for-mail From: Steve Gardner Newsgroups: bionet.molbio.proteins,bionet.software.x-plor,bionet.xtallography,bionet.structural-nmr Subject: Re: Ca virtual torsion angles Date: Wed, 09 Jul 1997 09:07:25 +0200 Organization: Astra Bioinformatics Centre Lines: 26 Message-ID: <33C338AD.4EBB@draco.se.astra.com> References: <33B852E5.31CD@spork.niddk.nih.gov> NNTP-Posting-Host: dpsgr.draco.se.astra.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (WinNT; I) To: John Kuszewski Xref: biosci bionet.molbio.proteins:11163 bionet.software.x-plor:1381 bionet.xtallography:3620 bionet.structural-nmr:2118 John Kuszewski wrote: > > Hi, > > I've been playing with using the "virtual torsion angle" > defined by the positions of four consecutive residues' > alpha carbons to define pieces of structure. > > I've heard of other people doing this before. > > Does anyone know if there's a standard name for this > angle (ala calling the N..Ca..C..N angle "psi")? > -- > _____________ In the Iditis database, and I believe in Kabsch and Sander's DSSP program this is called ALPHA. ---------------------------------------------------------------------- Dr Steve Gardner Director Tel: +46 46 33 60 00 Astra Bioinformatics Centre Fax: +46 46 33 71 44 PO BOX 34 E-mail: steve.gardner@draco.se.astra.com S-221 00 Lund Sweden From owner-proteins@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!news1.bellglobal.com!sunqbc.risq.qc.ca!athena.ulaval.ca!not-for-mail From: Savita Visal Newsgroups: bionet.molbio.proteins Subject: Looking for a Post-Doctorate position Date: Wed, 09 Jul 1997 10:59:13 +0000 Organization: Dept.Biochem, Natl Chem Lab. Pune, India Lines: 138 Message-ID: <33C36EFF.3751@agora.ulaval.ca> Reply-To: bio@ems.ncl.res.in NNTP-Posting-Host: gatorg1-110.ulaval.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Dear Friends, I am advertising the Resume of my friend Dr. W Ramakrishna. He is looking for a Post-doctorate position. Savita ======--------=========------========--------=======--------========= Resume Name W.RAMA KRISHNA Address Plant Molecular Biology Unit, Division of Biochemistry National Chemical Laboratory, Pune 411 008 INDIA Research Experience: Presently working as a postdoctoral fellow at NCL, Pune, India Projects: 1) Microsatellite markers and homeobox genes and their use in phylogenetic analysis in cereals. 2)Sex determination in papaya. Educational Qualification Ph.D - DNA fingerprinting and molecular characterization of (1995) microsatellites and minisatellites in rice Laboratory Training in Molecular Biology DNA, RNA isolation, Southern and Northern hybridizations, DNA sequencing, genomic library construction, polysome isolation, preparation of wheat germ lysate, in vitro translation, RAPD & locus specific PCR, RT-PCR, DDRT-PCR, Phylogenetic analysis. References Dr. P.K. Ranjekar, Dr. Vidya S. Gupta Deputy Director & Head, Scientist, Plant Molecular Biology Unit, Plant Molecular Biology Unit, Div Biochem Sci., Div Biochem Sci., Natl Chem Lab., Nat Cheml Lab., Pune - 411 008 INDIA Pune - 411 008 INDIA email - bio@ems.ncl.res.in email - bio@ems.ncl.res.in Fax 91-0212-338234 Fax 0212-338234, Tel 91-0212-338234 Tel 0212-342779 Manuscripts 1. DNA fingerprinting in rice with oligonucleotides specific for simple repetitive DNA sequences. W. Ramakrishna, M.D. Lagu, V.S. Gupta & P.K.Ranjekar. Theoretical & Applied Genetics (1994) 88 : 402-406. 2. DNA fingerprinting detects genetic variation in rice using hypervariable DNA sequences. W. Ramakrishna, K.V.Chowdari, M.D. Lagu, V.S. Gupta & P.K.Ranjekar. Theoretical & Applied Genetics (1995) 90 : 1000-1006. 3. (CAC)5 detects DNA fingerprints and sequences homologous to gene transcripts in rice. V.S.Gupta, W.Ramakrishna, S.R.Rawat & P.K.Ranjekar. Biochemical Genetics (1994) 32 : 1/2 : 1-8. 4. DNA fingerprinting detects genetic variability in the pearl millet downy mildew pathogen (Sclerospora graminicola) using simple sequence repeats. J.G.Sastry, W.Ramakrishna, S.Sivaramakrishnan, R.P.Thakur, V.S. Gupta & P.K. Ranjekar. Theoretical & Applied Genetics (1995) 91 : 856-861. 5. DNA fingerprinting of Indian isolates of Xanthomonous oryzae pv oryzae. M.D.Rajebhonsle, K.V.Chowdari, W.Ramakrishna, S.Tamhankar, V.S.Gupta, S.S.Gnanamanickam & P.K.Ranjekar. Theoretical & Applied Genetics (In Press). Manuscripts communicated \ Underpreparation 1. Evolutionary changes associated with domestication at a (GA)n microsatellite locus in rice. W.Ramakrishna, A.M.Wadia, V.S.Gupta & P.K.Ranjekar. 2. Phylogenetic conservation and evolution of human sex determining region (SRY) gene in papaya - a dioecious plant. W.Ramakrishna, A.S.Parasnis, B.B.Dholakia, V.S.Gupta & P.K.Ranjekar (communicated to Nature Genetics) 3. Knotted1 homeobox - evolutionary significance in cereals. A.Deshpande, W.Ramakrishna, G.Mulay, V.S.Gupta & P.K.Ranjekar (to be communicated to Nature) 4. Amplification and sequencing of homeobox and microsatellites from fossils of cereals. W.Ramakrishna, A.Deshpande, A.M.Wadia, V.S.Gupta & P.K.Ranjekar (to be communicated to Nature) 5. Sex specific organization of a microsatellite in papaya. A.S.Parasnis, W.Ramakrishna, V.S.Gupta & P.K.Ranjekar (communicated to Proc.Natl.Acad.Sci.USA) 6. mRNA differential display identifies sex specific transcripts in papaya. W.Ramakrishna, A.S.Parasnis, V.S.Gupta & P.K.Ranjekar. 7. Sequence variations of rice (GATA)n microsatellite during cloning. A.M.Wadia, W.Ramakrishna, V.S.Gupta & P.K.Ranjekar. 8. Polymorphic organisation of knotted1 homeobox in cereals. A.Deshpande, W.Ramakrishna, G.Mulay, V.S.Gupta & P.K.Ranjekar 9. Microsatellite polymorphisms in somaclonal variants in rice. K.V.Choudari, W.Ramakrishna, S.Tamhankar, V.S.Gupta, & P.K.Ranjekar. 10.Molecular cloning and analysis of one member of a polymorphic family of GATA hybridizing DNA repeats in rice. A.M.Wadia, W.Ramakrishna, K.V.Chowdari, V.S.Gupta & P.K.Ranjekar. Patents Filed 1. A process for preparation of duplex polynucleotide useful for sex determination of papaya plant. A.S.Parasnis, W.Ramakrishna,V.S.Gupta & P.K.Ranjekar (Indian patent). 2. A method for early detection of sex of papaya plant using a microsatellite. A.S.Parasnis, W.Ramakrishna, V.S.Gupta & P.K.Ranjekar. (US patent- in preparation) From owner-proteins@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!europa.clark.net!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!is.bbsrc.ac.uk!news From: dunnsm@bbsrc.ac.uk (steve) Newsgroups: bionet.molbio.proteins Subject: Acid native-PAGE buffer(s) Date: 9 Jul 1997 13:40:38 GMT Organization: Institute of Arable Crops Research, Rothamsted Message-ID: <5q04cm$8ou@is.bbsrc.ac.uk> NNTP-Posting-Host: pc867.res.bbsrc.ac.uk X-Newsreader: WinVN 0.92.6+ Lines: 9 Hello All, I'm planning on performing a native-PAGE expt. on a couple of proteins with fairly high predicted pI values (approx. 8.8-9.0) and so I'm looking for an acid buffer system that operates at around pH 5-6 (I'd rather not go more acid than this). Does anybody have tried and tested recipes for a discontinuos system in this pH range? Many thanks for any info/advice. Steve dunnsm@bbsrc.ac.uk From owner-proteins@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!server1.netnews.ja.net!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!131.103.1.114!chi-news.cic.net!newsspool.doit.wisc.edu!news.doit.wisc.edu!blah From: klenchin@facstaff.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: Pharmacia FPLC UV Date: Wed, 09 Jul 1997 21:57:35 GMT Organization: UW-Madison Lines: 14 Message-ID: <5q11da$12fg@news.doit.wisc.edu> References: NNTP-Posting-Host: martinlab.biochem.wisc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=KOI8-R Content-Transfer-Encoding: 8bit X-Newsreader: News Xpress 2.01 X-No-Archive: Yes In article , I.McFarlane@icrf.icnet.uk (Ian McFarlane) wrote: :Hi, : :If I have a peak of protein (say BSA) on a gel exclusion column which :gives me 50% of full scale deflection at 1AU=FSD _approximately_ how much :protein is that? I know you need to measure area under the curve but can :anyone give me a ballpark figure? Yuo can very roughly consider that to be ~ 0.5 mg/ml. As to how much protein, this obviously depends on volume of your peak. - Dima From owner-proteins@net.bio.net Tue Jul 08 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-xfer.netaxs.com!hammer.uoregon.edu!leto.ou.edu!news.ou.edu!news.ecn.uoknor.edu!news.cis.okstate.edu!nntp.ksu.edu!pgman.biol.ksu.edu!user From: "James Funderburgh" Newsgroups: bionet.molbio.proteins Subject: fixation of microfilaments Date: Wed, 09 Jul 1997 12:32:06 -0500 Organization: Kansas State University Lines: 4 Message-ID: NNTP-Posting-Host: pgman.biol.ksu.edu X-Newsreader: Microsoft Internet Mail and News for Macintosh - 1.1 (34) I am interested in methods for optimal fixation that would allow immunofluoresence visualization of microfilaments in marine invertebrate eggs. If anyone would be willing to share any ideas, an e-mail to Gary Conrad at gwconrad@ksu.edu would be much appreciated. From owner-proteins@net.bio.net Tue Jul 08 23:00:00 1997 From: Damn Yankee Newsgroups: bionet.molbio.proteins Organization: Yankee Inc. Subject: I Am Very Sorry!!! NNTP-Posting-Host: 205.139.183.55 Message-ID: <33c2555f.1@nntp.kalnet.net> Date: 8 Jul 97 14:57:35 GMT Lines: 5 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!pull-feed.internetmci.com!nntp.kalnet.net!205.139.183.55 I would like to apologise to this newsgroup and everyone who reads this newsgroup!!! I promise never to post or send spam to this or any other newsgroup that does not pertain to my posting!!! Please accept my humble apology and again I will never post spam here again!!! Thank You!!! Andrew Schero yank714@kalnet.net From owner-proteins@net.bio.net Wed Jul 09 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!ais.net!vixen.cso.uiuc.edu!news.uoregon.edu!news.rediris.es!news.csic.es!news From: cibsm1s@fresno.csic.es (Jesus Sanz) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: looking for argU expression vector. Date: 10 Jul 1997 13:19:15 GMT Organization: CIB/CSIC Lines: 35 Message-ID: <5q2ngj$63e@granado> References: NNTP-Posting-Host: jesus.cib.csic.es X-Newsreader: WinVN 0.92.6+ Xref: biosci bionet.molbio.methds-reagnts:59447 bionet.molbio.proteins:11170 In article , nigel@nature.berkeley.edu says: > >Hi, > >I've got a protein that's been making my life a nightmare...and I think >I've finally hit on the reason. Apparently I need to give e.coli a little >more argU tRNA so that it can translate it. (I've got three AGG's in a >row, as well as four pairs of AGG AGA/AGG). > >Is there a commercial source for an argU overexpression vector/host? Does >anyone out there have a plasmid they'ed care to share? > >thanks in advance > >-nigel > Nigel, I got plasmid pSBET (a,b & c) free from their authors. I have not tried it yet. The description of the plasmid is shown in BioTechniques 19: 196-200 (1995). You can write to this address: Dr. Hans-Henning Steinbiss Max Planck Institute fur Zuchtungsforschung Abteilung Genetische Grundlagen der Pflanzenzuchtung Carl-von-Linne Weg 10, D-50829 Koln, Germany Good luck Jesus Sanz cibsm1s@fresno.csic.es From owner-proteins@net.bio.net Wed Jul 09 23:00:00 1997 From: randy97 Subject: http://www.love.com Newsgroups: bionet.molbio.proteins NNTP-Posting-Host: pgh.nauticom.net Message-ID: <33c528d1.0@pgh.nauticom.net> Date: 10 Jul 97 18:24:17 GMT Lines: 9 Path: biosci!agate!hammer.uoregon.edu!hunter.premier.net!europa.clark.net!newsfeed.internetmci.com!pgh.nauticom.net!pgh.nauticom.net Looking to find people in your area that enjoy the same things as this newsgroup? Check out http://www.love.com It's free, it's new, and it's awesome. Rand From owner-proteins@net.bio.net Wed Jul 09 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!news.uoregon.edu!news.acsu.buffalo.edu!acsu.buffalo.edu!lhall327-2.pharm.buffalo.edu!user From: ericsson@acsu.buffalo.edu Newsgroups: bionet.molbio.proteins Subject: Digitonin solubilization Date: Thu, 10 Jul 1997 20:09:25 -0400 Organization: SUNY at Buffalo Lines: 23 Message-ID: NNTP-Posting-Host: lhall327-2.pharm.buffalo.edu NNTP-Posting-User: ericsson The digitonin that we have (from Fisher) is very hard to dissolve in water solution: It requires dissolving in MeOH and then adding dropwise to the water solution. Boiling brings it into solution, but it comes out of solution, in part, again when the solution cools. I wish to avoid the possible interference from having 4% MeOH in my solution, and so ask if there is a watersoluble form of digitonin? Or how to make it go into solution? Christer -- Christer Ericsson State University of New York at Buffalo Department of Biochemical Pharmacology 327 Hochstetter Hall-North Campus Buffalo, NY 14260-1200 email ericsson@acsu.buffalo.edu phone (716) 645-3926 fax (716) 645-3850 URL: http://tyr.cmb.ki.se Videoconference: CU-SeeMe IP# 128.205.183.71 From owner-proteins@net.bio.net Thu Jul 10 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Luc CAMOIN Newsgroups: bionet.molbio.proteins Subject: Problem GST-Fusion Protein in Ecoli Date: 11 Jul 1997 11:09:06 +0100 Lines: 27 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5q50o2$m93@mserv1.dl.ac.uk> X-Sender: camoin@icgm.cochin.inserm.fr Original-To: proteins@dl.ac.uk Hi, I expressed a GST-fusion protein in Ecoli. The theoretical molecular weight is 43 kDa. Western blot with anti-GST antibodies showed a band at 66 kDa. Purification on Glutathione-sepharose-4B concentrate an unique band at 34 kDa. This 34 kDa band is not recognize with anti-GST antibodies. I need some advice to explain these results. Is it known that a Ecoli protein bind strongly to Glutathione affinity column? This 34 kDa is it a protein or fragment related to my recombinant fusion protein? I'am not familiar with these techniques so all advices will be welcome. Thank you very much 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 Thu Jul 10 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Luc CAMOIN Newsgroups: bionet.molbio.proteins Subject: Protein tags, Western blot, affinity Date: 11 Jul 1997 11:27:18 +0100 Lines: 15 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5q51q6$nso@mserv1.dl.ac.uk> X-Sender: camoin@icgm.cochin.inserm.fr Original-To: proteins@dl.ac.uk Hi, I'am looking advice about protein tag. Is it better to put the tag on C-terminal instead than N-terminal? Which tags are the best for detection in western blot? Which tags are the best for affinity purification of recombinant protein? thanks in advance Luc CAMOIN From owner-proteins@net.bio.net Thu Jul 10 23:00:00 1997 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!news-zh.switch.ch!news.belwue.de!news-stu1.dfn.de!news-kar1.dfn.de!news-was.dfn.de!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!vixen.cso.uiuc.edu!sdd.hp.com!hamblin.math.byu.edu!news.Arizona.EDU!not-for-mail From: Christopher Chapman Newsgroups: bionet.molbio.proteins Subject: Protein creation in the cell Date: Fri, 11 Jul 1997 12:00:54 -0700 Organization: The University of Arizona Lines: 42 Message-ID: <33C682E5.5B5702D3@ag.arizona.edu> NNTP-Posting-Host: satl6.agforbes.arizona.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) X-Priority: 3 (Normal) I am considering working on the protein folding problem from the theoretical side for my dissertation topic, and am looking for some very specific information. First of all, I would like a pointer to some material that outlines how proteins are formed within the cell itself, from DNA transcription to how the ribosomes construct them. Second, I have heard that there are molecules in solution that actually may guide the folding process, is this true? Any studies you could point me to? Thirdly, I was wondering if proteins _always_ refold spontaneously in solution to their native conformations after being unfolded. Are their folded states natural and spontaneous, or is it dependant on the process that creates them? Again, are there any studies that you could point me to? I have seen many studies that show that predicted tertiary structures are of lesser energy (higher entropy) according to the fitness functions being used than the native structure would have. Is this because the fitness functions are not accurate or because native structures do not really lie in the absolute minimum of the potential energy surface (i.e. - the lowest energy point in conformation state). Is it possible that the structures are guided somehow to a local minimum, rather than folding independantly to the global minimum? Has anyone done an extensive simulation to prove that the native structures are indeed at the global minimum potential energy point in conformation space? Finally, If there is anyone with protein folding knowledge who wouldn't mind making themselves available to me to consult from time to time, I would appreciate it. I won't require much of your time, but I am an engineer and my expertise is in the physics, computational, and applied side of things. I am not a molecular biologists, and I feel that many of the attempts to apply computational chemistry to this problem have ignored the complexity of the cellular system and how it affects the process of folding. Thanks for any reply. Christopher Chapman cchapman@ag.arizona.edu The Department of Ag. & Biosystems Engineering The University of Arizona From owner-proteins@net.bio.net Thu Jul 10 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!ais.net!News1.Toronto.iSTAR.net!news.istar.net!news2.interlog.com!news.interlog.com!yblee From: samuel.lee@utoronto.ca (Samuel P. Lee) Newsgroups: bionet.molbio.proteins Subject: Re: Digitonin solubilization Date: Sat, 12 Jul 97 01:29:39 GMT Organization: University of Toronto Lines: 25 Message-ID: <5q6mtn$6l@news.interlog.com> References: NNTP-Posting-Host: ip213-144.cc.interlog.com X-Newsreader: News Xpress Version 1.0 Beta #4 >The digitonin that we have (from Fisher) is very hard to dissolve in water >solution: It requires dissolving in MeOH and then adding dropwise to the >water solution. Boiling brings it into solution, but it comes out of >solution, in part, again when the solution cools. I wish to avoid the >possible interference from having 4% MeOH in my solution, and so ask if >there is a watersoluble form of digitonin? Or how to make it go into >solution? > >Christer We purchase our digitonin from Gallard-Schlesinger (sp?). I have no scientific evidence for this, but, according to my predecessors, digitonin from Gallard stays in aqueous solution much better than digitonin from the more popular companies. It's more expensive, but, I believe it's worth the trouble caused by precipitating particles. Boiling and vigorous stirring is still required to put it in solution, but, all of it usually stays in solution after it cools. After several weeks of storage, you sometimes start to see particle formation, but, you just boil the solution again. Sam Lee Department of Pharmacology University of Toronto samuel.lee@utoronto.ca From owner-proteins@net.bio.net Thu Jul 10 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!server1.netnews.ja.net!server5.netnews.ja.net!server3.netnews.ja.net!baron.netcom.net.uk!netcom.net.uk!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!infeed2.internetmci.com!newsfeed.internetmci.com!news1.bellglobal.com!sunqbc.risq.qc.ca!news.risq.qc.ca!news.mcgill.ca!news From: Eric Campeau, ecampe@po-box.mcgill.ca Newsgroups: bionet.molbio.proteins Subject: pHook vectors from Invitrogen: any good ? Date: 11 Jul 1997 17:53:28 GMT Organization: McGill University Lines: 10 Message-ID: <5q5ruo$6ge@sifon.cc.mcgill.ca> NNTP-Posting-Host: i-02.das.mcgill.ca X-Newsreader: SPRY News 3.03 (SPRY, Inc.) Hi, Our lab is thinking about buying one of the pHook kit from Invitrogen. It allows you to isolate transfected cells from untransfected ones with the help of magnetic beads. We would like to have comments from people that tried it, with AND without success. Also, if you've heard of other systems that could do the same job, let us know ! Thank you very much ! From owner-proteins@net.bio.net Thu Jul 10 23:00:00 1997 Path: biosci!rutgers!newsin.iconnet.net!news.inc.net!uwm.edu!vixen.cso.uiuc.edu!howland.erols.net!newsfeed.nacamar.de!fu-berlin.de!cs.tu-berlin.de!uni-duisburg.de!sun3.hrz.uni-essen.de!news From: "Alexander Schramm" Newsgroups: bionet.molbio.proteins Subject: Re: Help! Protein refolding problem Date: 9 Jul 1997 12:36:23 GMT Organization: Universitaet Essen GH, Germany Lines: 17 Message-ID: <01bc8c64$b241b480$045dfc84@hot2.fb09.uni-essen.de> References: NNTP-Posting-Host: hot.fb09.uni-essen.de X-Newsreader: Microsoft Internet News 4.70.1161 Poi Ming Jye schrieb im Beitrag ... > Hi, > I have a problem in refolding my protein. Well, the major problem is my > protein has 7 disulfide bonds. Therefore, in the process of refolding, I > often lose a lot of protein due to many steps of refolding and misfolding too. If you want to express the protein in E.coli you may add a leader peptide to your protein, so that it is transported to the periplasm. This is the compartment, where S-S-bridges will be correctly formed. Alex alexander.schramm@uni-essen.de From owner-proteins@net.bio.net Fri Jul 11 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!csulb.edu!gatech!howland.erols.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!131.103.1.114!chi-news.cic.net!mr.net!newshub.tc.umn.edu!newsstand.tc.umn.edu!limerick.cbs.umn.edu!hiroki From: hiroki@limerick.cbs.umn.edu (Hiroki) Newsgroups: bionet.molbio.proteins Subject: Re: Acid native-PAGE buffer(s) Date: 12 Jul 1997 07:19:51 GMT Organization: University of Minnesota Lines: 30 Message-ID: <5q7b6n$i44@epx.cis.umn.edu> References: <5q04cm$8ou@is.bbsrc.ac.uk> Reply-To: hiroki@limerick.cbs.umn.edu NNTP-Posting-Host: limerick.cbs.umn.edu X-Newsreader: TIN [version 1.2 PL2] The author you probably want to look up is Jovin, from way back when. Analytical Biochem I think. If it's really 8.8-9, you'll probably get decent resolution even at pH 7 or so. I've used something like 25mM His, 25mM Mops throughout (or was it MES?) at about pH 6.2 or so. Running buffer same as in the gel. Didn't really bother trying to make a real stacking gel, I just cut back on the acrylamide, and got good resolution, so stopped at that point. 75% Glycerol 25% of the buffer, and a smidgen of methylgreen for the loading dye. I know it's not a discontinuous acid system, the only one I vaguely remember is supposed to form "dumbell" shaped bands. Hiroki steve (dunnsm@bbsrc.ac.uk) wrote: : Hello All, : I'm planning on performing a native-PAGE expt. on a couple of proteins : with fairly high predicted pI values (approx. 8.8-9.0) and so I'm looking : for an acid buffer system that operates at around pH 5-6 (I'd rather not : go more acid than this). Does anybody have tried and tested recipes for : a discontinuos system in this pH range? : Many thanks for any info/advice. : Steve : dunnsm@bbsrc.ac.uk From owner-proteins@net.bio.net Fri Jul 11 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!news.univ-aix.fr!newsup.univ-mrs.fr!u372-vif.univ-mrs.fr!user From: spirou@inserm-U372.univ-mrs.fr (Bruno Spire) Newsgroups: bionet.molbio.proteins Subject: universite d'ete sur le sida destine aux jeunes chercheurs Date: 11 Jul 1997 09:39:30 GMT Organization: INSERM Lines: 64 Message-ID: NNTP-Posting-Host: u372-vif.univ-mrs.fr L'association aides, association de lutte contre le sida organise pour la troisieme fois une universite d'ete du 7 au 13 septembre 1997 a la londe des maures, var, france .Le but de cette formation, est de ³ sortir les chercheurs de l¹ hyperspecialisation dans laquelle leur formation universitaire les a enfermes, et de favoriser les interfaces entre les multiples disciplines que mobilise la recherche sur le VIH ². Cette formation, envisagee comme un point de rencontre entre les differentes specialisations universitaires, est proposée a des etudiants de troisieme cycle internes compris qui s'engageant dans un projet de recherche ou un projet clinique lie a la thematique autour du Sida. Le programme scientifique se compose de plusieurs modules (immunologie, virologie, aspects de la maladie) et a ete etabli dans l'optique de presenter une revue la plus exhaustive possible des differents aspects de l'infection à VIH. L'enseignement est destine aux etudiants de 3eme cycle et aux post-doc ou chercheurs voulant reorienter leur thematique L¹enseignement propose au cours de cette formation se compose de modules abordant les themes suivants : la biologie du VIH, les interactions entre le systeme immunitaire et le VIH, les aspects cliniques et ethiques de l¹infection par le VIH, et les aspects sociaux lies à l¹infection. Le virus VIH, Histoire naturelle, Pathogenese: VIH et systeme immunitaire Réplication virale Mécanismes d¹entree et recepteurs Cycle viral : du provirus au bourgeonnement en passant par le virus integre. Les genes accessoires. Importance in vitro et in vivo. Apport de sciences sociales et epidemiologie. Aspects cliniques Les antireroviraux-problemes de resistances Modeles animaux Aspects therapeutiques Aspects ethiques Presentation de l¹approche associative de la lutte contre le sida : Parallelement à l¹enseignement scientifique qui leur est propose, les participants auront au cours de cette semaine la possibilité de participer à des soirees-debats, organisees a leur intention par les volontaires de AIDES Provence. Modalites d'inscription : adresser CV + lettre de motivation + projet de recherche (une page max) a Aides Provence 1 rue gilbert dru 13002 Marseille. Frais : gratuit mais un cheque de caution de 500 FF sera demande pour ne pas bloquer des places qui sera rendu a la fin du cours. Renseignements administratifs au 04 91 14 05 15 Renseignements scientifiques au 04 91 82 75 90 (Bruno Spire) Email spirou@inserm-u372.univ-mrs.fr From owner-proteins@net.bio.net Fri Jul 11 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!news.univ-aix.fr!newsup.univ-mrs.fr!u372-vif.univ-mrs.fr!user From: spirou@inserm-U372.univ-mrs.fr (Bruno Spire) Newsgroups: bionet.molbio.proteins Subject: Re: Digitonin solubilization Date: 11 Jul 1997 10:58:24 GMT Organization: INSERM Lines: 6 Message-ID: References: NNTP-Posting-Host: u372-vif.univ-mrs.fr aIn article , ericsson@acsu.buffalo.edu wrote: >Try the one from Sigma, you add it in boiling water at 2%, cool rapidly by putting the flask under running water, leave 2 days in the dark and filter. From owner-proteins@net.bio.net Fri Jul 11 23:00:00 1997 Path: biosci!rutgers!gatech!cpk-news-hub1.bbnplanet.com!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!tulane.edu!nick.arc.nasa.gov!news.Hawaii.Edu!munnari.OZ.AU!metro!metro!news From: "Michael Bonifacio" Newsgroups: bionet.molbio.proteins Subject: Disulphide Bonds Date: 11 Jul 1997 22:21:03 GMT Organization: Home Lines: 6 Distribution: inet Message-ID: <01bc8e49$21b38060$9d394e81@mbonifac.ucc.su.OZ.AU> NNTP-Posting-Host: mp-9-33.mp.usyd.edu.au X-Newsreader: Microsoft Internet News 4.70.1161 Hi, Does anyone know whether DTT breaks any bonds other than disulfides. Regards Michael Bonifacio From owner-proteins@net.bio.net Fri Jul 11 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!news.maxwell.syr.edu!news.he.net!news.reference.com!not-for-mail From: lvirden@cas.org Newsgroups: bionet.plants,bionet.general,bionet.molbio.proteins Subject: Re: Looking for articles on pectin methylesterases Date: 11 Jul 1997 18:37:26 GMT Organization: Reference.Com Posting Service Lines: 30 Message-ID: <5q5uh6$qup$1@orthanc.reference.com> References: <862588616.22077@dejanews.com> <336FAE51.5777@lx.student.wau.nl> NNTP-Posting-Host: shadowfax.reference.com Originator: panuser@reference.com () Xref: biosci bionet.plants:16016 bionet.general:27509 bionet.molbio.proteins:11184 On Tue, 06 May 1997 15:18:57 -0700, Rolf Marteijn wrote: > Bonjour, > > > Is there a site, other than ENTREZ, which > > lets someone look for articles one a keyword > > search basis ? > > > Unfortunately only Medline is online so far (or am I wrong?). Actually, one could always pop over to and see about the various internet services that CAS has to purchase. Also, see for a collection of chemistry related resources, both commercial and non. -- Posted using Reference.COM http://www.reference.com Browse, Search and Post Usenet and Mailing list Archive and Catalog. InReference, Inc. accepts no responsibility for the content of this posting. From owner-proteins@net.bio.net Sat Jul 12 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!news.apfel.de!newsfeed.nacamar.de!wuff.mayn.de!wuff.franken.de!news.CS.Uni-Magdeburg.De!RRZ.Uni-Koeln.DE!news.rhrz.uni-bonn.de!news.ruhr-uni-bochum.de!not-for-mail From: "Thorsten Schmidt" Newsgroups: bionet.molbio.proteins Subject: DAB as a Peroxidase Substrate Date: 13 Jul 1997 11:46:08 GMT Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 15 Message-ID: <01bc8f82$60ff5d40$35019386@schmidtdw.rz.ruhr-uni-bochum.de> NNTP-Posting-Host: dialppp-1-53.rz.ruhr-uni-bochum.de X-Newsreader: Microsoft Internet News 4.70.1155 Dear Sir or Madam! I use the Vectastain ABC Elite Kit with the DAB Substrate Kit for Peroxidase for Immunhistochemistry. My Question is: What is the exact chemical reaction, which is catalysed by the peroxidase? Or, in other words, what is the exact chemical structure of the reddish brown staining product which the Peroxidase synthesizes out of DAB and hydrogen peroxide? Thank you very much in advance for your answer. Thorsten Schmidt From owner-proteins@net.bio.net Sat Jul 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 Jul 1997 02:00:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199707130900.CAA08175@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. 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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. 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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 Sat Jul 12 23:00:00 1997 Path: biosci!rutgers!gatech!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!europa.clark.net!dispatch.news.demon.net!demon!bullseye.news.demon.net!demon!newsgate.unisource.nl!halley.pi.net!news From: jacob Newsgroups: bionet.molbio.proteins Subject: Asian Ladies Date: 13 Jul 1997 18:53:55 GMT Organization: World Access/Planet Internet Message-ID: <5qb883$rtk@halley.pi.net> NNTP-Posting-Host: 145.220.210.27 Lines: 10 I've found the pefect site with nude Asian ladies. Much more than you can find in any newsgroup. http://home.pi.net/~sappie/playboy.htm From owner-proteins@net.bio.net Sat Jul 12 23:00:00 1997 Path: biosci!rutgers!gatech!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!infeed2.internetmci.com!newsfeed.internetmci.com!news.wolsi.com!news.aros.net!news.cs.utah.edu!news.cc.utah.edu!not-for-mail From: zinc Newsgroups: bionet.molbio.proteins Subject: Re: Protein creation in the cell Date: 13 Jul 1997 16:42:45 -0600 Organization: University of Utah Computer Center Lines: 62 Message-ID: References: <33C682E5.5B5702D3@ag.arizona.edu> NNTP-Posting-Host: zifi.genetics.utah.edu Mime-Version: 1.0 (generated by tm-edit 7.106) Content-Type: text/plain; charset=US-ASCII To: Christopher Chapman X-Newsreader: Gnus v5.4.37/XEmacs 19.15 X-Face: &dh1aHu*v\s24A9~2qU[ln~;(Cz#X]d2r-@X>#j9U@vx!v8%IYU''n-H1D)}U(-0Te~ LD|Cyg6Gh-aFN{B*VSKhs}en{nXo3xkveE#BxR9 writes: > I am considering working on the protein folding problem from the > theoretical side for my dissertation topic, and am looking for some very > specific information. There's a ton of it out there, even books. > First of all, I would like a pointer to some material that outlines how > proteins are formed within the cell itself, from DNA transcription to > how the ribosomes construct them. Find a nice general biochemistry text, Zubay or Stryer will work fine. > Second, I have heard that there are molecules in solution that actually > may guide the folding process, is this true? Any studies you could > point me to? This is true. They are called chaperonins and they've been studied for at least the past 25 years. Have fun reviewing that literature - heh, i almost did one of my qualifying exams on them... > Thirdly, I was wondering if proteins _always_ refold spontaneously in > solution to their native conformations after being unfolded. No. you might as well shoot yourself in the foot if you're going to say 'always' in science. some proteins can do this, some need help, some just won't refold. > Are their > folded states natural and spontaneous, or is it dependant on the process > that creates them? Again, are there any studies that you could point me > to? I have seen many studies that show that predicted tertiary > structures are of lesser energy (higher entropy) according to the > fitness functions being used than the native structure would have. Is > this because the fitness functions are not accurate or because native > structures do not really lie in the absolute minimum of the potential > energy surface (i.e. - the lowest energy point in conformation state). > Is it possible that the structures are guided somehow to a local > minimum, rather than folding independantly to the global minimum? Has > anyone done an extensive simulation to prove that the native structures > are indeed at the global minimum potential energy point in conformation > space? I strongly suggest you first read some biochemistry; either that or take a biochem class. Nothing can substitute for the basics. Additionally, you should point your browser to http://www4.ncbi.nlm.nih.gov/Entrez/medline.html and do some literature searches. a cursor search for 'protein and folding' revealed more than 8000 matches. adding the word 'problem' brings this down to 214 matches. have fun... -pjf -- "Those that give up essential liberty to obtain a little temporary safety deserve neither liberty nor safety." -- Benjamin Franklin (1773) finger zinc-pgp@zifi for PGP key zifi runs LINUX 2.0.30 -=-=-=WEB=-=-=-> http://zifi.genetics.utah.edu From owner-proteins@net.bio.net Sun Jul 13 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: Kim Newsgroups: bionet.molbio.proteins Subject: Relibase at www.ebi Date: 14 Jul 1997 08:44:33 +0100 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5qcld1$m1u@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk Lines: 50 RELIBASE at EBI on URL http://www2.ebi.ac.uk:8081/home.html ( manfred email: hendlich@pharmazie.uni-marburg.de) Relibase by Manfred Hendlich is the first web based non-commercial service that can access the PDB by true 2D search queries, on the 3D database. 3D queries are being developed now. However, results of the searches are delivered in 3D via VRML options that can display the requested interactions. RELIBase is an archive for structural data about receptor/ligand complexes. The main purpose of RELIBase is to provide an selective and efficient access to the receptor/ligand complexes currently deposited in the Brookhaven Protein Databank (PDB) and to make the enormous wealth of information contained in the receptor/ligand structures available for structure based drug design studies. The www public accss relibase data base and search tools can be used to input a sub-structure search object either by text, a smiles string, or by an interactive java based molecule editor, and the system can perform the following functions: Fast identification of all ligands which contain a specific functional group Identification of receptor/ligand complexes with specific spatial interactions Analysis of interaction preferences of functional groups. Mutations. Protein modifications. Cross links to several protein sequence databases and the Beilstein Database of small molecules (not available on the WWW). From owner-proteins@net.bio.net Sun Jul 13 23:00:00 1997 Path: biosci!agate!usenet.INS.CWRU.Edu!HSNX.wco.com!news.theriver.com!news-feed.inet.tele.dk!newsfeed.nacamar.de!wuff.mayn.de!wuff.franken.de!news.CS.Uni-Magdeburg.De!RRZ.Uni-Koeln.DE!news.rhrz.uni-bonn.de!news.ruhr-uni-bochum.de!not-for-mail From: "Thorsten Schmidt" Newsgroups: bionet.molbio.proteins Subject: DAB as a Peroxidase Substrate Date: 14 Jul 1997 16:02:26 GMT Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 16 Message-ID: <01bc8fac$994c69c0$15039386@schmidtdw.rz.ruhr-uni-bochum.de> NNTP-Posting-Host: dialppp-1-215.rz.ruhr-uni-bochum.de X-Newsreader: Microsoft Internet News 4.70.1155 Dear Sir or Madam! I use the Vectastain ABC Elite Kit with the DAB Substrate Kit for Peroxidase for Immunhistochemistry. My Question is: What is the exact chemical reaction, which is catalysed by the peroxidase? Or, in other words, what is the exact chemical structure of the reddish brown staining product which the Peroxidase synthesizes out of DAB and hydrogen peroxide? Thank you very much in advance for your answer. Thorsten Schmidt From owner-proteins@net.bio.net Sun Jul 13 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!news-xfer.netaxs.com!netnews.upenn.edu!news From: JP Newsgroups: bionet.molbio.proteins Subject: Structure and Dimensions of Polymerized Hemoglobin Date: 14 Jul 1997 23:49:34 GMT Organization: University of Pennsylvania Lines: 12 Message-ID: <5qedue$m2t@netnews.upenn.edu> NNTP-Posting-Host: ts12-02.upenn.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) Hello. I am an undergrad working on a couple of problems for a Biochem. class and was hoping that someone in this newsgroup might be able to point me in the right direction. I must determine the structure and dimemsions of polymerized hemoglobin generated from the complete poly. from all the Hb in a single RBC. Also I must determine the Ka for sickle cell Hb and Conc. of Hb in sickle cell cytoplasm. I am a tad confused and any help ( recomended articles, books, or just a shove in the right direction) would be wonderful. If possible please e-mail me directly Thanx JBP From owner-proteins@net.bio.net Mon Jul 14 23:00:00 1997 Path: biosci!botany.uq.edu.au!J.Marcus From: J.Marcus@botany.uq.edu.au ("Marcus, Dr J.") Newsgroups: bionet.molbio.proteins Subject: Re: Protein precipitation in HPLC buffer Date: 15 Jul 1997 15:18:49 -0700 Organization: Dept of Botany, Univ of Queensland Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <65F18853F59@botany.uq.edu.au> References: <33CB25F1.C16E6922@uku.fi> Reply-To: Marcus@tpp.uq.edu.au NNTP-Posting-Host: net.bio.net > Hi! > I am trying to purify a protein using C18 RP-HPLC. Unfortunately it > precipitates when sample mixed with A buffer (0.1% TFA in water). > Is there another good buffer system (pH>6) for the protein separation on > You can try phosphate buffer (say 10-20 mM, pH 2.0, 4.4 and 6.5). Silica is notorious for not liking Alkaline pHs so I would not go above pH 6.5. Regards, John _________________________________________________________ John Marcus Marcus@tpp.uq.edu.au (Dr J.Marcus) Cooperative Research Centre for Tropical Plant Pathology 5th Level John Hines Building University of Queensland St. Lucia, QLD 4072 AUSTRALIA Fax: 61-7-3365-4771 Phone: 61-7-3365-4764 From owner-proteins@net.bio.net Mon Jul 14 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!infeed1.internetmci.com!newsfeed.internetmci.com!europa.clark.net!news-feed.inet.tele.dk!uninett.no!sn.no!usenet From: "Bjoern K. Pedersen" Newsgroups: bionet.molbio.proteins Subject: AlkPhosphatase in Bile Date: Tue, 15 Jul 1997 09:52:52 +0200 Organization: SN Internett Lines: 5 Message-ID: <33CB2C54.16BA@sn.no> Reply-To: eped@sn.no NNTP-Posting-Host: fp8-2.ppp.sn.no Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0C-SNINETT (Win95; I) I need to meassure the level of alkaline phospatase in Bile. The level of billirubin is 10.000 mM/l Does anyone have suggestions? -- - Bjørn K. Pedersen From owner-proteins@net.bio.net Mon Jul 14 23:00:00 1997 From: Gundars Goldsteins Newsgroups: bionet.molbio.proteins Subject: Protein precipitation in HPLC buffer Date: Tue, 15 Jul 1997 10:25:37 +0300 Organization: University of Kuopio Lines: 11 Message-ID: <33CB25F1.C16E6922@uku.fi> NNTP-Posting-Host: keula96.uku.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (WinNT; I) X-Priority: 3 (Normal) 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.sprintlink.net!Sprint!news.stupi.se!news.sto.telegate.se!nntp.inet.fi!news.funet.fi!luotsi.uku.fi!usenet Hi! I am trying to purify a protein using C18 RP-HPLC. Unfortunately it precipitates when sample mixed with A buffer (0.1% TFA in water). Is there another good buffer system (pH>6) for the protein separation on C18 ? TIA, Gundars From owner-proteins@net.bio.net Mon Jul 14 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.direct.ca!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!131.103.1.114!chi-news.cic.net!ftpbox.mot.com!newsfeed.acns.nwu.edu!news.cc.uic.edu!not-for-mail From: Keld Sorensen Newsgroups: bionet.molbio.proteins Subject: Re: Disulphide Bonds Date: Mon, 14 Jul 1997 08:45:43 +0000 Organization: University of Illinois, College of Medicine Lines: 5 Message-ID: <33C9E736.1EFC@uic.edu> References: <01bc8e49$21b38060$9d394e81@mbonifac.ucc.su.OZ.AU> NNTP-Posting-Host: slip-rock-02.dialin.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) To: Michael Bonifacio /snip Question on whether mercapto compounds cleave other bonds than SS bonds/ Mercapto compounds tend to break the "bond of friendship" if you use them too much out in the open in your laboratory !!! From owner-proteins@net.bio.net Tue Jul 15 23:00:00 1997 Newsgroups: bionet.molbio.proteins Path: biosci!rutgers!umdnj!njmsa!sarafian From: sarafian@njmsa.UMDNJ.EDU (Stefan G. Sarafianos) Subject: protein-protein interactions Message-ID: Sender: news@umdnj.edu () Organization: Univ. of Medicine and Dentistry of NJ Date: Wed, 16 Jul 1997 18:03:26 GMT Lines: 12 Hi, Anybody has any references or any info about techniques for detecting protein-protein interactions with colorimetric or fluoresence techniqes? I f the method could be applied for interactions of the protein with itself -polymerization- that would be great. Thank you for your time, Stefan G. Sarafianos post-doc Center for Advanced Biothechnology and Medicine Rutgers university/UMDNJ Oiscataway, USA From owner-proteins@net.bio.net Tue Jul 15 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!howland.erols.net!infeed1.internetmci.com!newsfeed.internetmci.com!newsrelay.netins.net!usenet.cat.pdx.edu!nntp.reed.edu!amon.reed.edu!jnotis From: John Notis Newsgroups: bionet.molbio.proteins Subject: Re: Protein tags, Western blot, affinity Date: Wed, 16 Jul 1997 15:42:13 -0700 Organization: Reed College, Portland, Oregon Lines: 35 Message-ID: References: <5q51q6$nso@mserv1.dl.ac.uk> NNTP-Posting-Host: amon.reed.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <5q51q6$nso@mserv1.dl.ac.uk> On 11 Jul 1997, Luc CAMOIN wrote: > Hi, > > I'am looking advice about protein tag. > > Is it better to put the tag on C-terminal instead than N-terminal? > > Which tags are the best for detection in western blot? > > Which tags are the best for affinity purification of recombinant protein? > > thanks in advance > > Luc CAMOIN > > > > If you put the tag on the c-terminal end of the protein, you will only get signal if the entire protein is there, since transcription is N-->C. However, the c-terminal of some proteins is buried within the structure, so the tag may not be apparent to antibody, or it may disrupt the three-dimensional structure of the protein and ruin it's activity. We commonly use the HA tag in our lab for wetern detection, and we use 6His tags on our recombinant proteins for purification with Ni/NTA agarose. Invitrogen makes vectors for both tags, and we use Qiagen Ni/NTA affinity gel. Incidentally, I prefer batch purification vs. column with the affinity resin. I get lower background and better adsorption of the target protein. Good luck and have fun. -John Notis From owner-proteins@net.bio.net Tue Jul 15 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!131.103.1.114!chi-news.cic.net!newsjunkie.ans.net!newsfeeds.ans.net!news.pprd.abbott.com!tvsfrank!bussierd From: bussierd@tvsfrank (Dirkson E. Bussiere-42T) Newsgroups: bionet.molbio.proteins Subject: switching cations Date: 16 Jul 1997 23:34:28 GMT Organization: Abbott Labs Lines: 23 Message-ID: <5qjlq4$4ct4@fizban.pprd.abbott.com> NNTP-Posting-Host: tvsfrank.pprd.abbott.com X-Newsreader: TIN [version 1.2 PL2] I'm trying to swap the Zn2+ in an enzyme with other divalent cations, but everytime I do it, the protein precipitates. I more or less dialyze the protein in 50mM Tris-HCL, pH 7.4, with 1-10 mM of the cation2+; the protein is stable in the Tris by itself. Does anyone know of a way to stablize the transition? One caveat: the enzyme is quite concentrated (2.1 mg/ml), and I have thought of diluting it a bit. But I will have to reconcentrate it to 12 mg/ml, so this does not seem to solve the problem. Any ideas would be appreciated. -Dirk -- -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Dirk Bussiere bussierd@tvsfrank.pprd.abbott.com Abbott Laboratories Office: (847)935-0916 Department 42T FAX: (847)937-2625 100 Abbott Park Rd. Abbott Park, IL 60064-3500 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From owner-proteins@net.bio.net Tue Jul 15 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!131.103.1.114!chi-news.cic.net!newsjunkie.ans.net!newsfeeds.ans.net!news.pprd.abbott.com!tvsfrank!bussierd From: bussierd@tvsfrank (Dirkson E. Bussiere-42T) Newsgroups: bionet.molbio.proteins Subject: switching cations Date: 16 Jul 1997 23:34:07 GMT Organization: Abbott Labs Lines: 24 Message-ID: <5qjlpf$4ct3@fizban.pprd.abbott.com> NNTP-Posting-Host: tvsfrank.pprd.abbott.com X-Newsreader: TIN [version 1.2 PL2] I'm trying to swap the Zn2+ in an enzyme with other divalent cations, but everytime I do it, the protein precipitates. I more or less dialyze the protein in 50mM Tris-HCL, pH 7.4, with 1-10 mM of the cation2+; the protein is stable in the Tris by itself. Does anyone know of a way to stablize the transition? One caveat: the enzyme is quite concentrated (2.1 mg/ml), and I have thought of diluting it a bit. But I will have to reconcentrate it to 12 mg/ml, so this does not seem to solve the problem. Any ideas would be appreciated. -Dirk -- -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Dirk Bussiere bussierd@tvsfrank.pprd.abbott.com Abbott Laboratories Office: (847)935-0916 Department 42T FAX: (847)937-2625 100 Abbott Park Rd. Abbott Park, IL 60064-3500 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From owner-proteins@net.bio.net Tue Jul 15 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!newsfeed.nacamar.de!blackbush.xlink.net!news-ge.switch.ch!news-zh.switch.ch!rzunews.unizh.ch!NewsWatcher!user From: zjons@vetbio.unizh.ch (Zophonias O. Jonsson) Newsgroups: bionet.molbio.proteins Subject: Re: protein-protein interactions Date: Wed, 16 Jul 1997 21:39:07 +0100 Organization: Universitat Zurich-Irchel Lines: 32 Message-ID: References: NNTP-Posting-Host: 130.60.120.18 In article , sarafian@njmsa.UMDNJ.EDU (Stefan G. Sarafianos) wrote: > Hi, > Anybody has any references or any info about techniques for detecting > protein-protein interactions with colorimetric or fluoresence techniqes? > I f the method could be applied for interactions of the protein > with itself -polymerization- that would be great. > Thank you for your time, > Stefan G. Sarafianos > post-doc > Center for Advanced Biothechnology and Medicine > Rutgers university/UMDNJ > Oiscataway, USA Try looking up some of the work of the groups of Peter H. von Hippel or Stephen J. Benkovic on the phage T4 DNA replication fork. They have studied the interactions of the gp45 clamp (which forms a trimer) with itself and other proteins using fluorescence. Looks like just what you are looking for Zophonias __