From owner-proteins@net.bio.net Sun Sep 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!mcsun!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: Concentrating proteins already in SDS sample buffer? Date: 2 Sep 1996 12:59:58 GMT Organization: University of Leicester, UK (PCFS User) Lines: 9 Message-ID: <50eloe$4lt@falcon.le.ac.uk> References: <507fn2$290@nntp3.u.washington.edu> NNTP-Posting-Host: pc47.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) Xref: biosci bionet.molbio.methds-reagnts:48678 bionet.molbio.proteins:8637 You may try ultrafiltration. Small volumes are handled in centrifugation devices (Millipore, Centricon, Whatman too, I think), but larger volumes (several ml) are better handled in stirred cells (Amicon). I would not use any precipitation techniques, because it is usually difficult to get proteins into solution again afterwards. I had this problem with both TCA precipitation and Chloroform/Methanol, even Phenol/Ether resulted in most of the protein staying in the wells during electrophoresis (but then I am handling a 160 kDa membrane protein, yours may be less fastidious). From owner-proteins@net.bio.net Sun Sep 01 23:00:00 1996 Path: biosci!IBC.WUSTL.EDU!stas From: stas@IBC.WUSTL.EDU (Stanslav Galaktionov) Newsgroups: bionet.molbio.proteins Subject: (none) Date: 2 Sep 1996 14:30:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <199609022131.QAA04206@ibc.wustl.edu> NNTP-Posting-Host: net.bio.net In article , Dmitry Yuryev wrote: # Note my paper describing several widespread errors in #performing Scatchard plot analysis. # http://www.glasnet.ru/~yur77 Dima Klenchin replied: >.....Apart from the above Qs: isn't it the case that the above "revolutionary" >conclusions are actually well-known? And: with non-linear regression >algorithms being included with almost every program (i.e., Excel), >who actually USES Scatchards? And, finally, isn't it clear that any math. >analysis of exp. data requires some assumptions to be made? The point is, that the very use of Scatchard plot for numerical evaluation of the parameters of Michaelis-like eqation is an error. The fundamental principle of statistical data processing reads: one should use for such evaluation directly measured experimental curves, never their transforms. The transforms like 1/y or ln y are especally perfidues if y<1 - which is the case in most Scatchard analyses. On the other hand, bench chemists still use it quite commonly, so that a couple extra warnings would not hurt... Stan =============================================================================== Stan Galaktionov, Ph.D., D.Sc. Washington University Institute e-mail: stas@ibc.wustl.edu for Biomedical Computing Tel.: 314-362-2942 Center for Molecular Design Fax: 314-362-0234 700 Euclid, Box 8036 St. Louis, MO 63110-1012 =============================================================================== From owner-proteins@net.bio.net Sun Sep 01 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.uwa.edu.au!usenet From: Luke Cronin Newsgroups: bionet.molbio.proteins Subject: Need Help: Stucture of alpha-Protein Kinase C (PKC alpha) Date: Mon, 02 Sep 1996 23:15:54 +1100 Organization: The University of Western Australia Lines: 6 Message-ID: <322ACFFA.287B@student.uq.edu.au> Reply-To: s342542@student.uq.edu.au NNTP-Posting-Host: gulag.gu.uwa.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b7 (Win95; I) I anyone can help me with aspect of the structure of Protein Kinase C it would be appreciated. Details such as No. of aminao acid residues, sub unit structures and any other useful information or links. Luke Cronin Email: s342542@student.uq.edu.au From owner-proteins@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Alexy Eroshkin Newsgroups: bionet.molbio.proteins Subject: Protein Multiple Sequences Editor on IuBio FTP-server Date: 3 Sep 1996 11:28:12 +0100 Organization: State Research Center of Virology & Biotechnology VECTOR Lines: 49 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <50h17s$8mv@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk To: proteins@dl.ac.uk From: eroshkin@vector.nsk.su Subject: Protein Multiple Sequences Editor on IuBio FTP-server Dear All, ProMSED, Protein Multiple Sequences EDitor for MS Win 3.x/95 is available now from IuBIO software library: ftp://iubio.bio.indiana.edu/molbio/ibmpc/promsed1.exe (as self-extracted archive). ProMSED is an easy-to-use application for automatic and manual multiple protein sequences alignment, alignment editing, analysis and printing. Interface and the main functions are similar to Microsoft Word. ProMSED can align complete set of sequences, its subset and any selected block, providing thus flexible tool for sequences analysis, visualization, edition and illustrations preparation. Some features: o reads five sequence formats (NBRF/PIR, Pearson (Fasta), EMBL/SwissProt, Intelligenetics and CLUSTAL) and combines sequences from different files; o automatic multiple sequence alignment with ClustalV algorithm; o single and multiple sequence input and edit; o manual alignment includes sequences grouping, blocks deleting, pasting, etc.; o visual analysis is facilitated by amino amino acid coloring reflecting aa similarity in physico-chemical, mutational and other properties; o option for interactive alignment in selected block, leaving unchanged previously aligned regions; o outputs alignment in two formats, produces publication quality alignments; o loads several protein families into different windows; o a HELP is included. Special thanks to Dr. Desmond Higgins for source code of ClustalV. Demo version has limits on length and number of sequences. Comments, bug reports and suggestions for new features are welcome and should be sent by email to eroshkin@vector.nsk.su. Inquiries can be addressed to: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 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 Mon Sep 02 23:00:00 1996 Path: biosci!agate!ames!enews.sgi.com!news.uoregon.edu!news.rediris.es!news.csic.es!news From: cibsm1s@fresno.csic.es (Jesus sanz) Newsgroups: bionet.molbio.proteins Subject: Re: Info on Improper folding and diseases ! Date: 3 Sep 1996 15:55:29 GMT Organization: CIB/CSIC Lines: 32 Message-ID: <50hkdh$nlk@granado> References: <199608310647.XAA03719@CATI.CSUFresno.EDU> NNTP-Posting-Host: jesus.cib.csic.es X-Newsreader: WinVN 0.92.6+ In article <199608310647.XAA03719@CATI.CSUFresno.EDU>, jswamin@CATI.CSUFRESNO.EDU (Jawahar Swaminathan) says: > >Hi ! >I am interested in knowing more about improper >protein folding leading to diseases in animal systems ! >With special reference to humans.. >Can anyone suggest where this kind of information may be >obtainable : on the net, books references etc. ? >Any leads in this matter will be greately apprecaited.. >cheers >Jawahar You can start with these: Bychkova, V.E. & Ptitsyn, O.B. "Folding intermediates are involved in genetic diseases?" FEBS lett. 359, 6-8 (1995) Thomas, P.J., Qu, B-H. & Pedersen, P.L. "Defective protein folding as a basis of human disease" TIBS 20, 456-459 (1995) There are many references therein. Cheers Jesus -------- Jesus Sanz cibsm1s@pinar1.csic.es -------- From owner-proteins@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!agate!newsxfer2.itd.umich.edu!uunet!in3.uu.net!mcsun!EU.net!main.Germany.EU.net!fu-berlin.de!news.belwue.de!news.uni-freiburg.de!sun2.ruf.uni-freiburg.de!eschiltz From: eschiltz@sun2.ruf.uni-freiburg.de (Emile Schiltz) Newsgroups: bionet.molbio.proteins Subject: Re: blotting from Isoelectric gel to pvdf Date: 3 Sep 1996 14:20:05 GMT Organization: Rechenzentrum der Universitaet Freiburg, Germany Lines: 21 Message-ID: <50heql$fgl@n.ruf.uni-freiburg.de> References: NNTP-Posting-Host: sun2.ruf.uni-freiburg.de X-Newsreader: TIN [version 1.2 PL2] Thomas Miller (millertj@esvax.dnet.dupont.com) wrote: : Hello. Any suggestions in trying to blot over from isoelectric gel to : pvdf membrane? : Thank you for any replies. Regards, Tom. : -- : Protein Sequencing lab, Dupont. : Opinions are my own and not of my employer. Hi Tom, Boehringer Ingelheim Bioproducts (was called Serva before) has a precast IEF-PAG under the name of PRENETS, through which you can blot to PVDF without removing the carier. It worked in our hands. Hope this is of some help. Emile -- Emile Schiltz or Institute of Organic Chemistry and Biochemistry Albertstrasse 21, D-79104 Freiburg, Germany phone: +49 761 203 6090 From owner-proteins@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!NMSU.EDU!hroychow From: hroychow@NMSU.EDU ("H. ROYCHOWDHURY") Newsgroups: bionet.molbio.proteins Subject: Re: EDTA shinks DEAE-Sephadex resin? Date: 3 Sep 1996 07:48:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On Sun, 1 Sep 1996, Ming-Ching Hsieh wrote: > Dear Netters: > I used a phosphate buffer, pH6.0 containing 3mM DTT and 10mM EDTA to > equilibrate a DEAE-Sephadex column, but the resin was shunk to at least half > of its original volume. I know the swelling properties of this resin are > dependent on ionic strength and pH. Indeed, the pH of the eluent was only 4.1, > suggesting a pH effect. More suprisingly, this effect seems irreversible > since 0.05M sodium chlorid in distilled water can not regenerate the resin. > The question is why EDTA changes the pH of this particular resin, and what's > the mechanism of it. Any idea is appreiciated. Thanks in advance. > > My question is: Why are you using phosphate buffer for an anion-exchanger and how are you dissolving EDTA at that low pH? >>>>>>>>>>>>>>>>>>>>>>>>>>> Dr. Hiranya S. Roychowdhury Plant Genetic Engineering Lab. Box 3GL, NM State Univ. Las Cruces, NM 88003 Phone: (505) 646-5785 hroychow@nmsu.edu <<<<<<<<<<<<<<<<<<<<<<<<<<< From owner-proteins@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!news.intercall.com!news.sprintlink.net!news-pen-4.sprintlink.net!moonbeam.aecom.yu.edu!usenet From: gottfrie@post.aecom.yu.edu (David S. Gottfried) Newsgroups: bionet.molbio.proteins Subject: Re: Primary structure of proteins Date: 3 Sep 1996 13:28:19 GMT Organization: Albert Einstein College of Medicine Lines: 19 Message-ID: <50hbpj$aa3@moonbeam.aecom.yu.edu> References: <32281FA9.484D@chem.ut.ee> NNTP-Posting-Host: marcus.aecom.yu.edu X-Posted-From: InterNews 1.1@marcus.aecom.yu.edu X-Authenticated: gottfrie on POP host post.aecom.yu.edu In article <32281FA9.484D@chem.ut.ee> Andres Kreegipuu writes: > I am looking for information about the average occurence frecuency of > the 20 natural amino acids in proteins. Are these data available > anywhere? There is a table in the book "Proteins" (2nd Ed.) by Creighton (Freeman Publ., 1993) that is taken from an article by McCaldon and Argos (Proteins, 4:99-122, 1988) who measured frequency in 1021 unrelated proteins. Just to whet your appetite for the numbers: The most common amino acid is Leucine (9.0%) and the least common is Tryptophan (1.3%). ---------------------- David S. Gottfried AECOM - Biophysics gottfrie@aecom.yu.edu From owner-proteins@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsxfer2.itd.umich.edu!uunet!in3.uu.net!mcsun!EU.net!Austria.EU.net!01-newsfeed.univie.ac.at!swidir.switch.ch!in2p3.fr!univ-lyon1.fr!jussieu.fr!infobiogen.fr!lovelace.infobiogen.fr!ahelme From: Alix Helme-Guizon Newsgroups: bionet.molbio.proteins Subject: looking for anti-cytosqueleton antibodies Date: Tue, 3 Sep 1996 15:32:40 +0200 Organization: "GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France" Lines: 10 Message-ID: References: <509bfm$2ho@Trex.IenD.wau.nl> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <509bfm$2ho@Trex.IenD.wau.nl> In order to have proper controls in my Western Blot, i need some efficient antibody against some protein of the neuronal cytosqueleton. I have already buy some commercial antibodies, but they didn't work efficiently on Western blot. If somebody knows a good commercial source of antibody for Western blot, or if you're ready to give me some of your personal stock, please let me know (e mail: ahelme@infobiogen.fr). Thanks. From owner-proteins@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!info.uah.edu!maze.dpo.uab.edu!usenet From: "Richard J. Dudley" Newsgroups: bionet.molbio.proteins Subject: Re: EDTA shinks DEAE-Sephadex resin? Date: Tue, 03 Sep 1996 14:38:57 -0500 Organization: University of Alabama at Birmingham Lines: 24 Message-ID: <322C8950.20F7@nrc.uab.edu> References: NNTP-Posting-Host: 138.26.50.134 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b5 (Macintosh; I; PPC) What is your measurement of "shrinking"? If you're pouring a column, and you notice that as you run buffer through it the volume decreases, what you're seeing is column packing (i.e., the space between the particles is being reduced), rather than a reduction of individual particle size. This phenomenon is exactly what you'd expect, and is a major reason why pouring columns is part art form--you don't want to just add more matrix, as there will be two strata of matrix in the column. This could alter how the column runs, and lead to inconsistent results with each column pour. You need to take the same "concentration" of matrix and pour twice as much into the column. You can attach a funnel to the top of the column and keep topping it off as it settles. It may also help to slowly run the column as it settles to start the packing (but not too fast or you'll channelize the column). Good luck! rich --- --- --- Richard J. Dudley Neurobiology Research Center Dep't of Physiology and Biophysics University of Alabama School of Medicine http://www.nrc.uab.edu From owner-proteins@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!MAGICNET.NET!mbausher From: mbausher@MAGICNET.NET (michael bausher) Newsgroups: bionet.molbio.proteins Subject: Re: Primary structure of proteins Date: 3 Sep 1996 12:46:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <199609031944.PAA09778@magicnet.magicnet.net> NNTP-Posting-Host: net.bio.net Andres: You may want to look as a ref which covers this very question --- entitled "Similar Amino Acid Sequences:Chance or common ancestry.? Science 214,9 (1981). This would give you a start in the right direction. michael bausher mbausher@magicnet.net From: andres@chem.ut.ee Date: 8/31/96 2:19:06PM To: protein-analysis Subject: Primary structure of proteins Hi, I am looking for information about the average occurence frecuency of the 20 natural amino acids in proteins. Are these data available anywhere? Andres Kreegipuu From owner-proteins@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!EPRENDOR.UCHICAGO.EDU!shanchen From: shanchen@EPRENDOR.UCHICAGO.EDU (Shan Chen) Newsgroups: bionet.molbio.proteins Subject: test,ignore Date: 3 Sep 1996 15:04:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <322CAB32.41C6@eprendor.uchicago.edu> NNTP-Posting-Host: net.bio.net This is a test. Ignore. Shan Chen From owner-proteins@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!news.cis.okstate.edu!usenet From: Ron Tate Newsgroups: bionet.microbiology,,bionet.molbio.methds-reagents,,bionet.molbio.proteins Subject: Breaking E. faecalis Date: Tue, 03 Sep 1996 14:35:57 -0500 Organization: Oklahoma State University, Biochemistry and Molecular Biology Lines: 13 Message-ID: <322C889D.468E@bmb-fs1.biochem.okstate.edu> NNTP-Posting-Host: firefly3.biochem.okstate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b5a (Win95; I) Xref: biosci bionet.microbiology:7056 bionet.molbio.proteins:8651 Does anybody have a consistant method for breaking E. faecalis? I typically use sonication but for me it is horribly inconsistant and takes quite a while, I would appreciate hearing your experiences. -- >>>>>>---------------------------> Ron Tate Lab of Franklin Leach Dept. of Biochem. & Molecular Biology Oklahoma State University rtate@bmb-fs1.biochem.okstate.edu (405) 744-9326 --------------------------------------------- From owner-proteins@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in3.uu.net!mcsun!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!news.belnet.be!news.fundp.ac.be!newsmaster From: baudou@lysine.biq.fundp.ac.be (Guy Baudoux) Newsgroups: bionet.molbio.proteins Subject: new multiple sequences alignment server Date: 3 Sep 1996 16:07:08 GMT Organization: FUNDP, Namur, Belgium Lines: 205 Sender: -Not-Authenticated-[7278] Message-ID: <50hl3c$9v6@hermes.fundp.ac.be> NNTP-Posting-Host: biq-mac1.biq.fundp.ac.be X-Posted-From: InterNews 1.0.7@biq-mac1.biq.fundp.ac.be Xdisclaimer: No attempt was made to authenticate the sender's name. MM MM BBBBBBB MMM MMM BB B MM M M MM AA TTTTTT CCCC HH HH BB B OOOOO XX X MM M M MM AAAA TT CC HH HH == BBBBBBB OO OO XX X MM M M MM AA AA TT CC HHHHHHH == BB B OO OO XX MM M M MM AAAAAAAA TT CC HH HH BB B OO OO X XX MM M MM AA AA TT CCCC HH HH BBBBBBB OOOOO X XX Match-Box Server 1.1 multiple sequence alignment server. Guy Baudoux, Isabelle Reginster, Pascal Briffeuil, Eric Depiereux and Ernest Feytmans. Laboratory of Structural Molecular Biology, University of Namur, Belgium Rue de Bruxelles, 61 : Tel: +32-81-72-44-15 5000 Namur, Belgium : Fax: +32-81-72-44-15 E-mail: matchbox-help@biq.fundp.ac.be Project supported by the Walloon Government, Federal State of Belgium. PRESENTATION: We are pleased to announce the availability of a new sequence alignment server, based on the Match-Box software developped by Drs. Eric Depiereux and Ernest Feytmans (1,2). The Match-Box software proposes protein sequence alignment tools based on strict statistical criteria. The method circumvents the gap penalty requirement: in the Match-Box method the gaps are the result of the alignment and not a governing parameter of the matching procedure. The method produces reliable results, as assessed by the tests performed on protein families of known structures and of low sequence similarity. A reliability score is computed in relation with a threshold of similarity progressively raised to extend the aligned regions to their maximal length. The score obtained at each position of the final alignment is printed below the sequences and allows a discriminant reading of each aligned region. Several additional outputs present pairwise similarity analyses in order to allow delineation of relevant subsets of related sequences and to avoid alignment of unrelated sequences. EXAMPLE: The lysozyme and alpha-lactalbumin is a well-known family of enzymes discussed in depth by H.A.McKenzie and F.H.White (3). The sequences of the lysozymes structures 1ALC, 1LZ1, 2LZ2 and 2LZT were aligned with the Match-Box server that gives the following result: Sequences number, length and name _________________________________ 1 122 1ALC 2 130 1LZ1 3 129 2LZ2 4 129 2LZT 10 20 30 40 50 60 70 + + + + + + + 1 kqftkcelsqnlyd--idgygrialpelictMFhtsgydtqai--vendesteyglfqisnalwckssqs 2 kvfercelartlkrLGmdgyrgislanwmclAKwesgyntratNYnagdrstdygifqinsrywcndgkt 3 kvygrcelaaamkrLGldnyrgyslgnwvcaAKfesnfnthatN-rntdgstdygilqinsrwwcndgrt 4 kvfgrcelaaamkrHGldnyrgyslgnwvcaAKfesnfntqatN-rntdgstdygilqinsrwwcndgrt 11111111111113 333333333444444 2222222222 1111111111111111111111111 80 90 100 110 120 130 140 + + + + + + + 1 pqsrnicditcdkflddditddimcakkild-ikgidywiahkalctEKLEQWLCEK--- 2 pgavnachlscsallqdniadavacakrvvrDpqgirawvawrnrcqNRDVRQYVQGCGV 3 pgsknlcnipcsallssditasvncakkiasGgngmnawvawrnrckGTDVHAWIRGCRL 4 pgsrnlcnipcsallssditasvncakkivsDgngmnawvawrnrckGTDVQAWIRGCRL 1111111111111111111111111111111 111111111111111 The Match-Box program tries to find "boxes" (segments that are similar in all sequences submitted by the user): residues included in the boxes are printed in lowercase. Residues in upper case are not aligned, and gaps are placed arbitrarily before the next box. A reliability score is written below each position in the boxes. It is related to the statistical significance of the alignment at this position: the lowest scores corresponds to the highest reliability of the alignment. ACCESSIBILITY: The Match-Box server is available at the Web site: http://www.fundp.ac.be/sciences/biologie/bms/matchbox_submit.html Using this web page, you can submit up to 50 protein sequences of no more than 2000 amino-acids each and receive by e-mail 2 output listings, resulting from two different analysis: * explore : analyses the global similarities between the sequences. * align : produces boxes (blocks) detected in the sequences and arranged in the form of a multiple alignment. This server can also be reached by electronic mail at the address: matchbox@biq.fundp.ac.be where you can send the key word "help" in the body of the message to receive informations about the methods of e-mail submission of data. In a preliminary test period, the server is accessible to any person from academic or commercial institutions. A version of the software, as a standalone program with a graphic interface is under developement. INPUT: The sequences can be submitted in FASTA-like, HSSP, or MSF formats, and the scoring matrices used by the programs can be selected directly from the web page. OUTPUT: The Match-Box server returns by default two listings "explore" and "align". Moreover the user can also ask to receive an alignment in MSF or HSSP format, and a picture of the alignment in PostScript format. DOCUMENTATION: The web page gives access to a series of documents: general presentation, details about the method, examples with explanation of the results. REFERENCES: 1. Depiereux, E. & Feytmans, E. (1991). Simultaneous amd multivariate alignment of protein sequences: correspondance between physicochemical profiles and structurally conserved regions (SCR). Prot. Engng. 4(6), 603-613. 2. Depiereux, E. & Feytmans, E. (1992). MATCH-BOX - A fundamentally new algorithm for the simultaneous alignment of several protein sequences. Comput. Appl. Biosci. 8(5), 501-509. 3. McKenzie, H.A. & White, F.H. (Jr) (1991). Lysozyme and alpha-lactalbumin, function and interrelationships. Adv. Prot. Chem. 41, 173-258. From owner-proteins@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!cam-news-hub1.bbnplanet.com!das-news2.harvard.edu!oitnews.harvard.edu!news From: Matthias Nolte Newsgroups: bionet.molbio.proteins,bionet.xtallography,bionet.neuroscience,sci.med.immunology,bionet.structural-nmr Subject: Re: Pro-dicon protein concentrator Date: Tue, 03 Sep 1996 16:48:04 -0400 Organization: Harvard University Lines: 8 Message-ID: <322C9984.41C6@hubeta.harvard.edu> References: <3226F9A6.794B@pharm.med.yale.edu> NNTP-Posting-Host: bill.harvard.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b6Gold (X11; I; OSF1 V3.2 alpha) Xref: biosci bionet.molbio.proteins:8648 bionet.xtallography:2845 bionet.neuroscience:15564 sci.med.immunology:7343 bionet.structural-nmr:1478 Dear Elias, the Pro-dicon is (now) marketed by Spectrum and is called Micro-ProDiCon. I have the Dialysis/Ultracentrifugation Catalog here, which shows a nice variety of models of this superb concentrator. Spectrum can be reached @ 1-800 634-3300 Matthias From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!cs.utexas.edu!howland.erols.net!vixen.cso.uiuc.edu!sdd.hp.com!night.primate.wisc.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!martinlab From: klenchin@facstaff.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: low pH elution of protease from pepstatin-Sepharose Date: 4 Sep 1996 18:20:37 GMT Organization: UW-Madison Lines: 18 Message-ID: <50kh9l$2ldq@news.doit.wisc.edu> References: <9609041645.AA26792@sun1.bham.ac.uk> NNTP-Posting-Host: martinlab.biochem.wisc.edu X-Newsreader: News Xpress Version 1.0 Beta #4 X-No-Archive: Yes In article <9609041645.AA26792@sun1.bham.ac.uk>, osullida@SUN1.BHAM.AC.UK ("Deirdre O'Sullivan") wrote: ->Hi, -> ->I am trying to figure out how to elute pepsin and other acid proteases ->from pepstatin-sepharose in active form. Methods using high pH (> about 7) irreversibly ->inactivate the enzymes. Other methods use chaotropes. -> ->I can elute about 50% of bound matter using a step change of NaCl from 0 to 1 M. ->That still leaves a lot of protein on the resin ! First, 50% yield is a pretty good result. Second, if you know that chaotropes work, try 1.0-1.5 M LiCl (combining ionic strenght effect that you achieve with Na and mild chaotripic effects of Li+). - Dima From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: jody McGill Newsgroups: bionet.molbio.proteins Subject: Principles of Protein Structure Using the Internet (fwd) Date: 4 Sep 1996 15:18:30 +0100 Lines: 24 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <50k33m$le5@mserv1.dl.ac.uk> X-Sender: jody@iona.cryst.bbk.ac.uk Original-To: To:To:@mail.cryst.bbk.ac.uk, bio-info@dl.ac.uk, bionews@dl.ac.uk, bio-www@dl.ac.uk, str-nmr@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, molmodel@dl.ac.uk, ;;@mail.cryst.bbk.ac.uk, ;;@mail.cryst.bbk.ac.uk Dear All The Crystallography Department of Birkbeck College is running a part-time, London University course on the PRINCIPLES OF PROTEIN STRUCTURE on the Internet. 1. Introduction to Internet Resources 2. Protein Structure 3. Dissertation: structure, function and dynamics The course covers one academic year of three terms, from September 30, 1996 to 4 July 1997. Costs are: 250 pounds sterling for EU students and 550 pounds sterling for other students. For details of course contents, administration and registration URL http://www.cryst.bbk.ac.uk/PPS2/index.html Contact: Jody McGill, Crystallography Department, Birkbeck College London, WC1E 7HX. UK Tel. +44 (0)171 631 6800 Fax. +44 (0)171 631 6803 e.mail: j.mcgill@mail.cryst.bbk.ac.uk From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!news.sgi.com!enews.sgi.com!mcsun!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!strath-cs!queens-belfast.ac.uk!queens-belfast.ac.uk!nntp Newsgroups: bionet.molbio.proteins Subject: Re: Kinetics software Message-ID: <322D8D18.2A25@queens-belfast.ac.uk> From: Andrew Wallace Date: Wed, 04 Sep 1996 15:07:20 +0100 References: <4vnjtn$p0p@bee.uspnet.usp.br> Nntp-Posting-Host: awall.bc.qub.ac.uk X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) MIME-Version: 1.0 CC: a.wallace Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 23 Cristiana M.G. Teixeira wrote: > > Hello!! > > I'm looking for a kinetics software that could give me good > results with Ki calculations. Any sugestions? > > Thanks very much. > > Cristiana Teixeira. It depends a bit on what computer platform you have. The folks around here run GrafIt on their Macs and are pretty happy with that (I heard the new version even does progress curve calculations). If you have a PC-compatible, you can get a program called EnzFitter which I hear is good, at least for PCs. Andrew -- ====================================================================== Andrew Wallace,Ph.D., Queen's University Belfast, N. Ireland (UK) a.wallace@qub.ac.uk http://www.qub.ac.uk/b&bchem/awpage/wallace.htm ====================================================================== From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!agate!spool.mu.edu!usenet.eel.ufl.edu!warwick!leicester!usenet From: Alberto Piccin Newsgroups: bionet.molbio.proteins Subject: protein complex on denaturing gel Date: 4 Sep 1996 17:11:05 GMT Organization: University of Leicester, UK (PCFS User) Lines: 16 Message-ID: <50kd79$48d@falcon.le.ac.uk> NNTP-Posting-Host: pc10.gene.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) Hi dear netters, I am running Musca domestica proteins on a 6% PAGE, blotting and detecting my protein with a policlonal antibody. The protein weights 120 kD (I sequenced the gene) but on the western the antibody picks up a band which is roughly 250 kD. The gel contains 0.1% SDS and I boil the samples 10 min in 2% SDS, 5% mercaptoethanol before loading. Can anyone tell me whether some complex could still resist these conditions, and possibly cite some references? I would discard the possibility that the antibody recognises the wrong protein because the same heavy band is detected in melanogaster transformed with the musca gene. Thanks in advance Alberto From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!agate!spool.mu.edu!usenet.eel.ufl.edu!warwick!leicester!usenet From: Alberto Piccin Newsgroups: bionet.molbio.proteins Subject: protein complex on denaturing gel Date: 4 Sep 1996 16:56:23 GMT Organization: University of Leicester, UK (PCFS User) Lines: 4 Message-ID: <50kcbn$48d@falcon.le.ac.uk> NNTP-Posting-Host: pc10.gene.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) Hi dear netters, From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!SUN1.BHAM.AC.UK!osullida From: osullida@SUN1.BHAM.AC.UK ("Deirdre O'Sullivan") Newsgroups: bionet.molbio.proteins Subject: low pH elution of protease from pepstatin-Sepharose Date: 4 Sep 1996 09:45:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9609041645.AA26792@sun1.bham.ac.uk> NNTP-Posting-Host: net.bio.net Hi, I am trying to figure out how to elute pepsin and other acid proteases from pepstatin-sepharose in active form. Methods using high pH (> about 7) irreversibly inactivate the enzymes. Other methods use chaotropes. I can elute about 50% of bound matter using a step change of NaCl from 0 to 1 M. That still leaves a lot of protein on the resin ! Any assistance appreciated ! From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!in3.uu.net!mcsun!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!strath-cs!queens-belfast.ac.uk!queens-belfast.ac.uk!nntp Newsgroups: bionet.molbio.proteins Subject: Re: Info on Improper folding and diseases ! Message-ID: <322D9633.10A3@queens-belfast.ac.uk> From: Andrew Wallace Date: Wed, 04 Sep 1996 15:46:11 +0100 References: <199608310647.XAA03719@CATI.CSUFresno.EDU> Nntp-Posting-Host: awall.bc.qub.ac.uk X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 29 Jawahar Swaminathan wrote: > > Hi ! > I am interested in knowing more about improper > protein folding leading to diseases in animal systems ! > With special reference to humans.. > Can anyone suggest where this kind of information may be > obtainable : on the net, books references etc. ? > Any leads in this matter will be greately apprecaited.. > cheers > Jawahar A recent article appeared about this in the 15th March issue of Science in a research news piece entitled "Misfolding the way to disease" which gives some useful background on the topic. Some people now think that this is the basis behind diseases like Alzheimer's and the prion diseases (if the prion hypothesis is correct) where misfolding of an existing host protein causes deposition of fibrils of beta-sheet protein and (somehow) cell death with consequent neurological damage. There may be other tissues which are susceptible to this, such as the pancreas, where it is thought that deposition of protein fibrils is associated with diabetes. These are just a few examples but there may be others. Andrew -- ====================================================================== Andrew Wallace,Ph.D., Queen's University Belfast, N. Ireland (UK) a.wallace@qub.ac.uk http://www.qub.ac.uk/b&bchem/awpage/wallace.htm ====================================================================== From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!gondor!newsfeeder.sdsu.edu!news.sgi.com!enews.sgi.com!news.mathworks.com!newsfeed.internetmci.com!news.bctel.net!noc.van.hookup.net!eloi.vir.com!rcogate.rco.qc.ca!altitude!usenet From: Achim Recktenwald Newsgroups: bionet.molbio.proteins,de.sci.chemie,sci.bio.misc,sci.chem,bionet.metabolic-reg,bionet.molbio.methds-reagnts,bionet.biophysics,de.sci.misc Subject: Bis-tris-propane: temp. coeff. (dpKa/dT) ?? Date: Wed, 04 Sep 1996 16:48:25 -0500 Organization: IBEX Technologies, Inc., Biochemistry, 5485 Pare, Montreal, PQ, H4P 1P7, Canada Lines: 17 Message-ID: <322DF927.7352@ibex.ca> NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Xref: biosci bionet.molbio.proteins:8660 sci.bio.misc:4689 sci.chem:63267 bionet.metabolic-reg:831 bionet.molbio.methds-reagnts:48800 bionet.biophysics:2269 Hi all, I am looking for the temperature coefficient(s) [dpKa/dT] of the buffer-substance 'bis-tris-propane' = 1,3-bis[tris(hydroxymethyl)methylamino]propane for some enzyme kinetic experiments. According to the supplier (Sigma) it has the pKa-values: pKa1=6.8 and pKa2=9.0 at T=25C. Sigma doesn't know the dpKa/dT-value(s) either. Can anybody help ? Thanks, Achim From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!cam-news-hub1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!news.msfc.nasa.gov!info.uah.edu!maze.dpo.uab.edu!bmg147.cmc.uab.edu!user From: siyer@bmg.bhs.uab.edu (Arioch, Lord of Chaos) Newsgroups: bionet.molbio.proteins Subject: Re: protein complex on denaturing gel Date: Wed, 04 Sep 1996 17:27:21 +0100 Organization: Lords of Chaos Lines: 14 Message-ID: References: <50kd79$48d@falcon.le.ac.uk> NNTP-Posting-Host: bmg147.cmc.uab.edu if your protein is a 120kda and you're picking up a band that's roughly 250 kda, i'd say that it is most likely a hi.molec.wt aggregate of your protein. how soluble/insoluble is your protein?? if your protein is pretty cranky and not that soluble, then that's what i would venture the other band to be. this idea would be more credible if you found bands that are in the multiples of 120 i.e a 360 kda band etc...i would figure that's easy enough to find out by running a lower percentage gel, although i dont know how low you could go...hope this helps...cheers... -- Arioch, Lord of Chaos siyer@bmg.bhs.uab.edu graduate student, Dept of Biochemistry and Molecular Genetics University of Alabama at Birmingham... From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!in3.uu.net!news.interlog.com!news From: tkrieger@interlog.com (Tim Krieger) Newsgroups: bionet.molbio.proteins Subject: Re: low pH elution of protease from pepstatin-Sepharose Date: Thu, 05 Sep 1996 03:30:12 GMT Organization: InterLog Internet Services Lines: 22 Message-ID: <50l6se$lrf@news.interlog.com> References: <9609041645.AA26792@sun1.bham.ac.uk> Reply-To: tkrieger@interlog.com NNTP-Posting-Host: tkrieger.interlog.com X-Newsreader: Forte Free Agent 1.0.82 osullida@SUN1.BHAM.AC.UK ("Deirdre O'Sullivan") wrote: >Hi, >I am trying to figure out how to elute pepsin and other acid proteases >from pepstatin-sepharose in active form. Methods using high pH (> about 7) irreversibly >inactivate the enzymes. Other methods use chaotropes. >I can elute about 50% of bound matter using a step change of NaCl from 0 to 1 M. >That still leaves a lot of protein on the resin ! >Any assistance appreciated ! Have you tried collecting a 50mM Tris-HCl, pH 7.5, 1M NaCl eluent into test tubes containing an equal volume of 100mM Acetate buffer, pH 4.5? The rapid acidification upon elution sometimes improves yields dramatically. Tim Krieger, Ph.D. Connnaught Laboratories/PMC From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!gondor!newsfeeder.sdsu.edu!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!news.bctel.net!noc.van.hookup.net!eloi.vir.com!rcogate.rco.qc.ca!altitude!usenet From: Achim Recktenwald Newsgroups: bionet.molbio.proteins,de.sci.biologie,sci.chem,bionet.metabolic-reg,bionet.molbio.methds-reagnts,bionet.biophysics, Subject: constant ionic-strength buffers for enzyme kinetics Date: Wed, 04 Sep 1996 16:57:46 -0500 Organization: IBEX Technologies, Inc., Biochemistry, 5485 Pare, Montreal, PQ, H4P 1P7, Canada Lines: 12 Message-ID: <322DFB57.49DB@ibex.ca> NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Xref: biosci bionet.molbio.proteins:8659 sci.chem:63266 bionet.metabolic-reg:830 bionet.molbio.methds-reagnts:48799 bionet.biophysics:2268 In 1982 in Methods in Enzymology, vol. 87, chapter 23, pp.405 K.J. Ellis and J.F. Morrison published a paper titled: Buffers of constant ionic strength for studying pH-depedent processes. It describes how to calculate and prepare buffers and mixtures of buffers of constant ionic strength over a wide pH-range. My question: Does anybody know of other similar publications ? Thanks in advance, Achim From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!harbinger.cc.monash.edu.au!newsroom.utas.edu.au!mpg7-79.appbio.utas.edu.au!user From: Leigh.Schmidtke@appbio.utas.edu.au (Leigh Schmidtke) Newsgroups: bionet.microbiology,,bionet.molbio.methds-reagents,,bionet.molbio.proteins Subject: Re: Breaking E. faecalis Date: 5 Sep 1996 03:10:19 GMT Organization: Department of Biomedical Science, University of Tasmania Lines: 31 Message-ID: References: <322C889D.468E@bmb-fs1.biochem.okstate.edu> NNTP-Posting-Host: mpg7-79.appbio.utas.edu.au Xref: biosci bionet.microbiology:7073 bionet.molbio.proteins:8665 In article <322C889D.468E@bmb-fs1.biochem.okstate.edu>, Ron Tate wrote: > Does anybody have a consistant method for breaking E. faecalis? I > typically use sonication but for me it is horribly inconsistant and > takes quite a while, I would appreciate hearing your experiences. > -- > >>>>>>---------------------------> > Ron > Tate > Lab of Franklin Leach > Dept. of Biochem. & Molecular Biology > Oklahoma State University > rtate@bmb-fs1.biochem.okstate.edu > (405) 744-9326 > --------------------------------------------- You could try an incubation step with lysosyme (450 000 U/mL, 60 minutes at 37šC) before sonication. I found this worked well for a range of Enterococci/Streptococci and Lactococci. If you sonicate, make sure you place your sample on ice. I only used short bursts of say 15 seconds to prevent boiling the sample (sample volumes were <0.5 mL). Depending on what you want to get from the bugs, you could also solubilise with SDS after lysosyme treatment. For a complete run down of the method see; Schmidtke and Carson. Journal of Applied Bacteriology. 1994. 77:229-236. Hope this helps. Leigh Schmidtke Department of Biomedical Science University of Tasmania Leigh.Schmidtke@appbio.utas.edu.au From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!mcsun!EU.net!howland.erols.net!vixen.cso.uiuc.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!martinlab From: klenchin@facstaff.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: Info on Improper folding and diseases ! Date: 5 Sep 1996 00:00:11 GMT Organization: UW-Madison Lines: 15 Message-ID: <50l56b$3b3i@news.doit.wisc.edu> References: <199608310647.XAA03719@CATI.CSUFresno.EDU> NNTP-Posting-Host: martinlab.biochem.wisc.edu X-Newsreader: News Xpress Version 1.0 Beta #4 X-No-Archive: Yes In article <199608310647.XAA03719@CATI.CSUFresno.EDU>, jswamin@CATI.CSUFRESNO.EDU (Jawahar Swaminathan) wrote: ->Hi ! ->I am interested in knowing more about improper ->protein folding leading to diseases in animal systems ! ->With special reference to humans.. ->Can anyone suggest where this kind of information may be ->obtainable : on the net, books references etc. ? ->Any leads in this matter will be greately apprecaited.. I would really need to dig deep in my DB to find the refs but I'm pretty sure that some cases of retinal degeneration are caused by mutations that cause rhodopsin misfolding. - Dima From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.erols.net!vixen.cso.uiuc.edu!sdd.hp.com!night.primate.wisc.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!martinlab From: klenchin@facstaff.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins,de.sci.chemie,sci.bio.misc,sci.chem,bionet.metabolic-reg,bionet.molbio.methds-reagnts,bionet.biophysics,de.sci.misc Subject: Re: Bis-tris-propane: temp. coeff. (dpKa/dT) ?? Date: 4 Sep 1996 23:29:37 GMT Organization: UW-Madison Lines: 19 Message-ID: <50l3d1$3b3i@news.doit.wisc.edu> References: <322DF927.7352@ibex.ca> NNTP-Posting-Host: martinlab.biochem.wisc.edu X-Newsreader: News Xpress Version 1.0 Beta #4 X-No-Archive: Yes Xref: biosci bionet.molbio.proteins:8662 sci.bio.misc:4691 sci.chem:63272 bionet.metabolic-reg:832 bionet.molbio.methds-reagnts:48805 bionet.biophysics:2270 In article <322DF927.7352@ibex.ca>, Achim Recktenwald wrote: ->Hi all, -> ->I am looking for the temperature coefficient(s) [dpKa/dT] of the ->buffer-substance ->'bis-tris-propane' = 1,3-bis[tris(hydroxymethyl)methylamino]propane ->for some enzyme kinetic experiments. -> ->According to the supplier (Sigma) it has the pKa-values: ->pKa1=6.8 and pKa2=9.0 at T=25C. For pKa1, standard conditions: -0.016. Sorry, no info on pKa2. - Dima From owner-proteins@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!agate!ames!enews.sgi.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!news.ucalgary.ca!ts1-port-24.acs.ucalgary.ca!user From: sjszarka@acs.ucalgary.ca (Steven Szarka) Newsgroups: bionet.molbio.proteins Subject: Q: Effect of adjacent amino acids on Cys pKa? Date: Wed, 04 Sep 1996 23:04:37 -0600 Organization: University of Calgary Lines: 6 Message-ID: NNTP-Posting-Host: sjszarka@ts1-port-24.acs.ucalgary.ca X-Newsreader: Value-Added NewsWatcher 2.0b16.0+ Can anyone provide and information or point me in the direction of reference material that deals with changes to the pKa value of Cys sulfur atom due to the charge or lack of in adjacent residues? Thanks Steve From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!rutgers!gatech!usenet.eel.ufl.edu!usenet.nerdc.ufl.edu!usenet.ufl.edu!mitzi.rsmas.miami.edu!miasun.med.miami.edu!newssun!tguettou From: Toumy Guettouche Newsgroups: bionet.molbio.proteins Subject: Re: Help! Immunoprecipitation beads that mouse IgM can bind Date: Thu, 5 Sep 1996 14:18:36 -0400 Organization: University of Miami, School of Medicine Lines: 42 Message-ID: References: NNTP-Posting-Host: newssun.med.miami.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: On Tue, 3 Sep 1996, Naohiro Kohmura wrote: > Hi! > I want to try immunoprecipitation by a mouse monoclonal antibody. > But it is IgM, not IgG. Does anybody know anti-mouse IgM-binding beads, > or beads that mouse IgM can bind? From where can I get? Protein A beads > can > bind to human IgM, but can't to mouse IgM. Any comment? > > Thanks in advance. > > ---- > Naihiro Kohmura > kohmura@nips.ac.jp > > HI there is different things you can try. 1. Make your own beads by linking your antibody to CnBr-activated beads (e.g from Biorad or Pierce). This has been done before and I am sure the companies can provide you with references or a protocoll. 2. You can use an antibody against IgM that binds to Protein A or G (e.g. from Sigma, Boehringer Mannheim ) link it and then depending on your application either bind your antigen first to your IgM antibody and then to your anti IgM-beads, or first bind your IgM antibody to your anti IgM beads and then to your antigen. The former possibility gives you usually a better efficiency in capturing you antigen, but it is not always possible to do it that way. Generally you might get some background problems because of the anti IgM antibody that sometimes reacts with other proteins in preparations. The different anti IgM antibodies you need should also be available by some of the above companies. Hope that helps Toumy From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!agate!news.ucdavis.edu!info.ucla.edu!nnrp.info.ucla.edu!csulb.edu!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsxfer2.itd.umich.edu!portc01.blue.aol.com!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: kle1058@aol.com (Kle1058) Newsgroups: bionet.molbio.proteins Subject: Re: small insert ligation Date: 6 Sep 1996 00:46:09 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 5 Sender: root@newsbf02.news.aol.com Message-ID: <50oaah$c64@newsbf02.news.aol.com> References: <322ED2A8.187D@bms.com> Reply-To: kle1058@aol.com (Kle1058) NNTP-Posting-Host: newsbf02.mail.aol.com When using sticky ends in ligation, I find it useful to heat the DNA to 65 degrees C for 5 minutes, then cooling rapidly at -20 degrees for 1 minute before adding buffer and ligase. Krista Evans From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!cam-news-hub1.bbnplanet.com!www.nntp.primenet.com!nntp.primenet.com!mcsun!EU.net!Norway.EU.net!nntp.uio.no!nntp.uib.no!nntp-bergen.UNINETT.no!nntp-trd.UNINETT.no!daresbury!not-for-mail From: ctzhang@tju.edu.cn Newsgroups: bionet.molbio.proteins Subject: How many proteins in nature Date: 5 Sep 1996 16:52:48 +0100 Lines: 10 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <50mt0g$rfl@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk Hi, Dear netter: There is a key question in my study. I wonder how many proteins exist in nature. Of course, a precise estimate of this figure seems to be impossible at the present stage. What I need is only a rough estimate. Any assistance regarding this matter will be greatly appreciated. My e-mail address: ctzhang@tju.edu.cn From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!news-peer.gsl.net!news.gsl.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!in3.uu.net!mcsun!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!gmorley From: gmorley@hgmp.mrc.ac.uk (Mr. G. Morley) Newsgroups: bionet.molbio.proteins Subject: Help! Dimerisation. Date: 5 Sep 1996 15:04:37 GMT Organization: MRC Human Genome Resource Centre Lines: 15 Message-ID: <50mq65$kpj@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: tin.hgmp.mrc.ac.uk I am trying to design an experiment to measure the extent of dimerisation between two homodimers. I was wondering if anyone could recommend a crosslinker that can be used In Vitro. Ideally the cross-linker would be membrane permiable and can be used on Rat-2 fibroblasts (so not too toxic).If anyone uses or knows of a good one..or has a methodology or practical tips I would be most obligued. Currently I am thinking of DMP or DMS from Pierce..if anyone knows about any drawbacks about these two I would, also, be most obligued. Thank you in advance... Gary Morley gmorley@rpms.ac.uk From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!agate!newsgate.duke.edu!news.duq.edu!usenet From: "Frank R. Gorga" Newsgroups: bionet.molbio.proteins,de.sci.chemie,sci.bio.misc,sci.chem,bionet.metabolic-reg,bionet.molbio.methds-reagnts,bionet.biophysics,de.sci.misc Subject: Re: Bis-tris-propane: temp. coeff. (dpKa/dT) ?? Date: Thu, 05 Sep 1996 09:49:57 -0700 Organization: Duquesne University Lines: 33 Message-ID: <322F04B5.7E8@next.duq.edu> References: <322DF927.7352@ibex.ca> NNTP-Posting-Host: phosphorus.chemistry.duq.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b8Gold (Win16; I) Xref: biosci bionet.molbio.proteins:8669 sci.bio.misc:4709 sci.chem:63315 bionet.metabolic-reg:833 bionet.molbio.methds-reagnts:48833 bionet.biophysics:2272 Achim Recktenwald wrote: > > Hi all, > > I am looking for the temperature coefficient(s) [dpKa/dT] of the > buffer-substance > 'bis-tris-propane' = 1,3-bis[tris(hydroxymethyl)methylamino]propane > for some enzyme kinetic experiments. According to the booklet titled "Buffers" which is free for the asking from Calbiochem (p16)... the delta pKa / deg. C for BIS-TRIS-PROPANE is -0.016. The Calbiochem buffer booklet is ESSENTIAL reading for anyone using buffers and (IMHO) should be reread often! > > According to the supplier (Sigma) it has the pKa-values: > pKa1=6.8 and pKa2=9.0 at T=25C. > > Sigma doesn't know the dpKa/dT-value(s) either. Shame on them! --- Frank *********************************** Frank R. Gorga, Ph.D. Dept. of Chemistry & Biochemistry Duquesne University Pittsburgh, PA 15282 412-396-5858 / 412-396-5683 (fax) gorga@next.duq.edu From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!agate!newsgate.duke.edu!news.duq.edu!newsfeed.pitt.edu!gatech!nntp0.mindspring.com!news.mindspring.com!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!uunet!in2.uu.net!jaring.my!usenet From: yeoong@pc.jaring.my (Ng) Newsgroups: bionet.molbio.proteins Subject: Help Help Date: Fri, 06 Sep 1996 19:06:07 GMT Organization: Unconfigured Lines: 9 Message-ID: <50o813$9v2@jaring.my> NNTP-Posting-Host: j1.jhb4.jaring.my X-Newsreader: Forte Free Agent 1.0.82 I want to get some bussiness information from Japan, but I can’t get the right News Group Agent. Can anybody tell me the best News Group to go. Thank You. Ng K Y From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!agate!newsgate.duke.edu!news.duq.edu!newsfeed.pitt.edu!newsflash.concordia.ca!sunqbc.risq.net!calvin.risq.qc.ca!news.mcgill.ca!news From: SAM Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: a good protocol for far westerns/overlays?? Date: Thu, 05 Sep 1996 14:25:37 +0600 Organization: McGill University Lines: 13 Message-ID: <322E8E81.5904@musicb.mcgill.ca> References: NNTP-Posting-Host: embryo.pharma.mcgill.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win16; I) Xref: biosci bionet.molbio.proteins:8674 bionet.molbio.methds-reagnts:48844 Gerald W. Hart wrote: > > hey all, > does anybody have or know where i can get a good (tried and > tested) protocol for doing far westerns (protein overlays)?? so far, i've > attempted doing it using a standard western blot protocol and i end up > with very dirty looking exposures of the blots (i've already eliminated > adjusting exposure time by ecl, washing a gazillion times and decreasing > the concentration of the secondary antobody...). any help would be > appreciated...thx much...please email to siyer@bmg.bhs.uab.edu . What is your bis:acrylamide ratio? If you make it 1:100 it should do the job. From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.kddnet.ad.jp!sinfony-news!wnoc-tyo-news!aist-nara!wnoc-kyo-news!kuis-news!kudpc!cancer.nca5.ad.jp!nfeed.gw.nagoya-u.ac.jp!news.orion.ac.jp!news.nips.ac.jp!nips087006!kohmura From: kohmura@nips.ac.jp (Naohiro Kohmura) Subject: Help! Immunoprecipitation beads that mouse IgM can bind Sender: news@nips.ac.jp Message-ID: Date: Tue, 3 Sep 1996 03:36:27 GMT Content-Type: text/plain; charset=iso-2022-jp Nntp-Posting-Host: nips087006.nips.ac.jp Mime-Version: 1.0 Organization: National Institute for Physiological Sciences, OKAZAKI X-Newsreader: NewsWatcher-J 2.0J16 Lines: 12 Hi! I want to try immunoprecipitation by a mouse monoclonal antibody. But it is IgM, not IgG. Does anybody know anti-mouse IgM-binding beads, or beads that mouse IgM can bind? From where can I get? Protein A beads can bind to human IgM, but can't to mouse IgM. Any comment? Thanks in advance. ---- Naihiro Kohmura kohmura@nips.ac.jp From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!gondor!newsfeeder.sdsu.edu!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!cs.utexas.edu!howland.erols.net!agate!newsgate.duke.edu!news.duq.edu!newsfeed.pitt.edu!bb3.andrew.cmu.edu!andrew.cmu.edu!mustafa+ From: Mustafa Unlu Newsgroups: bionet.molbio.proteins Subject: Re: protein complex on denaturing gel Date: Thu, 5 Sep 1996 14:33:28 -0400 Organization: Doctoral student, Chemistry, Carnegie Mellon, Pittsburgh, PA Lines: 18 Message-ID: References: <50kd79$48d@falcon.le.ac.uk> NNTP-Posting-Host: po6.andrew.cmu.edu In-Reply-To: <50kd79$48d@falcon.le.ac.uk> Alberto Piccin writes: [snip] > with a policlonal antibody. The protein weights 120 kD (I sequenced > the gene)but on the western the antibody picks up a band which is > roughly 250 kD. The gel contains 0.1% SDS and I boil the samples 10 > min in 2% SDS, 5% mercapto ethanol before Assuming that your antibody is good, a possible reason for the *apparent* MW of 250 kD is pottranslation modification. Your 120 kD number may be the computed MW of the protein from the gene sequence but there are a number of modifications (glycosylation, phosphorylation, etc.) which may change the apparent MW considerably. Regards, M. From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!agate!newsgate.duke.edu!solaris.cc.vt.edu!homer.alpha.net!uwm.edu!spool.mu.edu!newspump.sol.net!news.inc.net!news.sprintlink.net!news-chi-8.sprintlink.net!news.sprintlink.net!news-chi-13.sprintlink.net!news2.noc.netcom.net!noc.netcom.net!nntp!nandu From: nandu@curagen.com (Krishnan Nandabalan) Newsgroups: bionet.molbio.proteins Subject: Post-doctoral Fellow: Functional Genomics-Signal Transduction Date: Thu, 5 Sep 96 20:13:15 GMT Organization: CuraGen Corporation Lines: 56 Message-ID: NNTP-Posting-Host: 199.183.38.43 X-NETCOM-Date: Thu Sep 05 6:05:47 PM PDT 1996 X-Newsreader: VersaTerm Link v1.1.1 CuraGen Corporation 322 East Main St. Branford, CT 06405 (203) 481 1104 (203) 481 1102 - Fax CuraGen Corporation is a dynamic and rapidly expanding biotechnology company on a mission to systematically extract from the human genome those disease related genes for which therapeutics can be successfully designed. CuraGen is pioneering a novel systematic approach to developing pharmaceuticals for treating cancer. In pursuit of its interdisciplinary approach, CuraGen has assembled a research team with expertise in molecular biology, biochemistry, statistical mechanics, computational methods, mathematics, nanofabrication, and spectroscopy. Close ties with several major academic laboratories complement our own resources and facilities. We seek creative and motivated individuals with the dedication and ambition to succeed in an entrepreneurial setting. Compensation package includes opportunity for equity participation. Extensive collaborations with Yale University (12 minutes away), Yale Comprehensive Cancer Center and Cornell University provide excellent opportunities for academic collaborations and publication. CuraGen is a recent winner of two coveted Advanced Technology Program awards from the National Institute for Standards and Technology, and also receives funding from the National Cancer Institute and the National Center for Human Genome Research. CuraGen is an EEO/AA employer. TITLE: Post-doctoral Fellow, Functional Genomics-Signal Transduction CuraGen is seeking Post-doctoral Fellows in Functional Genomics-Signal Transduction. Initially, the successful candidates will work closely with senior scientists. There is room for internal advancement. The successful candidates will have an intimate knowledge of the Signal Transduction phenomena and its relevance to disease processes as evidenced by publications and /or patents. In addition the candidates will have experience in more than one of the following: cell-based assays to monitor gene-expression, in vitro assays to monitor protein-protein interactions, RNA isolation, cDNA synthesis, construction of cDNA and genomic libraries, normalization of cDNA libraries, yeast genetics and molecular biology etc. Applications with resume, a list of three references should be addressed to Dept. of Functional Genomics, CuraGen Corporation, 322 East Main St., Branford, CT 06405. Fax: (203) 481 1102. Krishnan Nandabalan Senior Research Scientist CuraGen Corporation 322 E. Main St. Branford, CT 06405. Fax: (203) 481 1102 From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Iosif Vaisman Newsgroups: bionet.general,bionet.biophysics,bionet.molbio.proteins,bionet.molec-model,bionet.molbio.methds-reagnts,bionet.software,bionet.structural-nmr,bionet.xtallography,bionet.cellbiol,bionet.jobs,bionet.software.gcg,bionet.molbio.bio-matrix Subject: Computational Molecular Biology Workshop, October 15-19, 1996 Date: 5 Sep 1996 15:03:54 -0700 Organization: The University of North Carolina at Chapel Hill Lines: 47 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.general:23165 bionet.biophysics:2276 bionet.molbio.proteins:8677 bionet.molec-model:1132 bionet.molbio.methds-reagnts:48854 bionet.software:16470 bionet.structural-nmr:1480 bionet.xtallography:2850 bionet.cellbiol:5405 bionet.software.gcg:1978 bionet.molbio.bio-matrix:755 CAROLINA WORKSHOPS University of North Carolina at Chapel Hill Computational Molecular Biology October 15 - 19, 1996 This course is designed for scientists with limited prior experience in computational molecular biology. The topics to be covered include: biomolecular informatics and databases, protein and nucleic acid sequence analysis and alignment, 3D protein structure analysis and prediction, molecular modeling and dynamic simulations of proteins and nucleic acids, and structure-based drug design. The workshop will consist of the in-depth theoretical lectures and intensive hands-on laboratory sessions. CAROLINA WORKSHOPS are intensive hands-on courses designed to teach cutting edge methods in molecular biology and biotechnology. Four or five courses on different topics in molecular biology and/or biotechnology are offered each year. The courses are designed for novice students as well as for individuals with prior experience. All students benefit from in-depth interaction with instructors. To apply, send a curriculum vitae and a brief letter describing your research interests and their relevance to the Workshop. Applicants should contact the program office as soon as possible. Please indicate your complete mailing address and telephone/fax number. Application Deadline-September 7, 1996. Tuition - $ 1,200.00. Participation is limited to 15 people. COURSE DIRECTOR: Alexander Tropsha, Ph.D., University of North Carolina at Chapel Hill INSTRUCTORS: Frank K. Brown (Oxford Molecular) David C. Richardson (Duke University) Wayne Litaker (UNC-Chapel Hill) Alexander Tropsha (UNC-Chapel Hill) Michael Mitchell (UNC-Chapel Hill) Iosif I. Vaisman (UNC-Chapel Hill) For further information or to apply, contact: Dr. Wayne Litaker, Facility Director University of North Carolina at Chapel Hill Program in Molecular Biology & Biotechnology 442 Taylor Hall CB 7100 Chapel Hill, North Carolina 27599-7100 TELEPHONE (919) 966-1730, FAX (919) 966-6821 E-MAIL litaker@med.unc.edu From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!news.fibr.net!news.sprintlink.net!news-fw-6.sprintlink.net!news-dc.gsl.net!news.gsl.net!duke.telepac.pt!news.telepac.pt!usenet From: Luis Lopes da Fonseca Newsgroups: bionet.molbio.proteins Subject: help, buffer solution Date: Thu, 05 Sep 1996 23:06:59 -0700 Lines: 17 Message-ID: <322FBF83.59B8@mail.telepac.pt> Reply-To: llfonseca@mail.telepac.pt NNTP-Posting-Host: oei2_p3.telepac.pt Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I; 16bit) I have been asked the following questions, that i am not able to answer. How would you select a buffer solution, if you wanted to: a) purify an enzime b) characterize kineticly an enzime associated with the glicolitic pathway c) determine the enzimatic activity of a NAD dependent dehydrogenase and why (justify)? I thank all the help. Luis llfonseca@mail.telepac.pt Lisbon, Portugal From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!newsserver.jvnc.net!crick.bms.com!usenet From: John Watson Newsgroups: bionet.molbio.proteins Subject: Re: small insert ligation Date: Thu, 05 Sep 1996 09:16:24 -0400 Organization: Bristol-Myers Squibb Company Lines: 31 Message-ID: <322ED2A8.187D@bms.com> References: <4vd8p5$ciu@epervier.CC.UMontreal.CA> Reply-To: watson_j@bms.com NNTP-Posting-Host: s107_static_223.wf.bms.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) Morello Jean-Pierre wrote: > > I'm trying to insert a 200 bp fragment into a 3.4 kb vector using two sticky > site enzymes (Bam HI and HinDIII). The 200 bp insert comes from a PCR product > which has sufficient nucleotides on each end to allow for enzyme digestion. > > So far, I've tried to either purify both pieces of DNA prior to ligation (using the > Geneclean kit from Bio 101) or I've taken DNA straight after digestion and > phenol/chloroform extraction. In both cases I only get recircularized vector > although I have verified that both enzymes have digested the DNA. In addition, > I have treated the vector with alkaline phosphatase and phenol/chloroform > extraction prior to digestion. > > If anyone has experience with small insert (approx. 200-300 bp) ligation > I would greatly appreciate the help. I have done this often for fragments in the size range you describe, though not with those particular sticky ends. Please check our Meth. Enzymol. chapter for detailed protocols: Wilkie et al. (1994). Meth. Enzymol. 237:327-344. Good Luck. ---------------------------------------------------------------------> John Watson | Bristol-Myers Squibb Co. | watson_j@bms.com | ---------------------------------------------------------------------| "If you're not part of the solution, you're part of the precipitate."| ---------------------------------------------------------------------> From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!news.sgi.com!esiee.fr!jussieu.fr!oleane!in2p3.fr!swidir.switch.ch!01-newsfeed.univie.ac.at!02-newsfeed.univie.ac.at!newsfeed.sunet.se!news00.sunet.se!sunic!news99.sunet.se!news.uni-c.dk!news.daimi.aau.dk!biobase!wind From: wind@biobase.dk (Troels Wind) Newsgroups: bionet.molbio.proteins Subject: Re: Preparation small amount protein for Blotting Date: 1 Sep 1996 13:32:07 GMT Organization: The Danish BioBase Lines: 14 Message-ID: <50c38n$6iq@bioalp.biobase.dk> References: <509bfm$2ho@Trex.IenD.wau.nl> NNTP-Posting-Host: biobase.dk X-Newsreader: TIN [version 1.2 PL2] Tatsuya Nagata (tatsuya.nagata@medew.viro.wau.nl) wrote: : I tried to detect viral polymerase from plant sap using specific : antibody and ECL kit. But I could not detect it because plant total : protein was so clude that amount of specific protein was low compreing : amount of other proteins. When I used purifed virus, I could detect it. : But I want to detect from total protein or semi purified protein from : infected plant sap. Can someone help me? Try fractionating your sample, either by ion-exchange or gel-filtration, seperate the resulting fractions by SDS-PAGE and do a Western blot with your specific Ab. This will increase your Polymerase:Junk ratio. Troels From owner-proteins@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!news3.cac.psu.edu!news.cse.psu.edu!news.eecs.nwu.edu!newsfeed.acns.nwu.edu!news.cc.uic.edu!usenet From: Keld Sorensen Newsgroups: bionet.molbio.proteins Subject: Re: Help! Immunoprecipitation beads that mouse IgM can bind Date: Thu, 05 Sep 1996 08:29:25 +0000 Organization: University of Illinois, College of Medicine Lines: 8 Message-ID: <322E8F65.20F9@uic.edu> References: NNTP-Posting-Host: sliprock-01.dialin.uic.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) To: Naohiro Kohmura A protein such as mannose binding protein from rabbit serum will bind IgM - it is available in an immobilized for (bound to crosslinked agarose, i.e. a Sepharose-type support) intended for purification of IgM (column) - I don't have info on its use in IP, but theoretically it should work. The capacity is around 1 mg/ml of support. Keld. From owner-proteins@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!Norway.EU.net!mcsun!EU.net!main.Germany.EU.net!fu-berlin.de!informatik.tu-muenchen.de!Germany.EU.net!news.dfn.de!news.ruhr-uni-bochum.de!news.rhrz.uni-bonn.de!news.rwth-aachen.de!newsserver.rrzn.uni-hannover.de!tubsibr!rzlimes.gbf-braunschweig.de!news From: uka@gbf-braunschweig.de (Uwe Kaerst) Newsgroups: bionet.molbio.proteins,de.sci.chemie,sci.bio.misc,sci.chem,bionet.metabolic-reg,bionet.molbio.methds-reagnts,bionet.biophysics,de.sci.misc Subject: Re: Bis-tris-propane: temp. coeff. (dpKa/dT) ?? Date: 6 Sep 1996 13:30:15 GMT Organization: GBF Lines: 41 Message-ID: <50p917$k5b@rzlimes.gbf-braunschweig.de> References: <322DF927.7352@ibex.ca> NNTP-Posting-Host: etnuka.gbf-braunschweig.de Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.8 (beta 2) Xref: biosci bionet.molbio.proteins:8686 sci.bio.misc:4739 sci.chem:63419 bionet.metabolic-reg:836 bionet.molbio.methds-reagnts:48878 bionet.biophysics:2277 In article <322DF927.7352@ibex.ca>, achim@ibex.ca says... > >Hi all, > >I am looking for the temperature coefficient(s) [dpKa/dT] of the >buffer-substance >'bis-tris-propane' = 1,3-bis[tris(hydroxymethyl)methylamino]propane >for some enzyme kinetic experiments. > >According to the supplier (Sigma) it has the pKa-values: >pKa1=6.8 and pKa2=9.0 at T=25C. > >Sigma doesn't know the dpKa/dT-value(s) either. >Can anybody help ? > > >Thanks, > >Achim Hi Achim, I found the following information in a booklet from Calbiochem: pKa 1 = 6.8 at 20 C, dpKa/C = -0.016 Uwe -- Uwe Kaerst Dept. Enzymology GBF - Gesellschaft fuer Biotechnologische Forschung Mascheroder Weg 1 D-38124 Braunscheig, Germany Tel: +(49) 531 6181 318 Fax: +(49) 531 2612313 EMAIL: kaerst@gbf-braunschweig.de -- Disclaimer -- Standard > Keyword : Opinions, my own, nobody else's, no affiliation, whatsoever ... From owner-proteins@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!uwm.edu!news-peer.gsl.net!news.gsl.net!news.sgi.com!esiee.fr!jussieu.fr!unilim.fr!news From: Maftah Newsgroups: bionet.molbio.proteins Subject: Protein deacetylation Date: 6 Sep 1996 11:15:17 GMT Organization: Laboratoire de Biotechnologie Lines: 18 Message-ID: <50p145$s78@limdns.unilim.fr> NNTP-Posting-Host: macbio8.unilim.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.molbio.proteins Dear netters, Does anybody know how to deacetylate a protein? I am working on a recombinant peptide which has been found to be acetylated on lysin residues (N-acetylation). I need the peptide under its deacetylated form. Thanks a lot to answer to: Abdou Maftah Institut de Biotechnologie 123, avenus A. Thomas 87060, Limges cedex, France Phone: (33) 55 45 76 84 Fax: (33) 55 45 76 53 e-mail: Maftah@unilim.fr From owner-proteins@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!agate!howland.erols.net!surfnet.nl!swsbe6.switch.ch!swidir.switch.ch!in2p3.fr!univ-lyon1.fr!jussieu.fr!unilim.fr!news From: Maftah Newsgroups: bionet.molbio.proteins Subject: (no subject) Date: 6 Sep 1996 10:58:45 GMT Organization: Laboratoire de Biotechnologie Lines: 16 Message-ID: <50p055$s5j@limdns.unilim.fr> NNTP-Posting-Host: macbio8.unilim.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.molbio.proteins Dear netters, Does anybody know how to deactylate a protein? I am working on a recombinant peptide which has been found to be acetylated , probably on lysin residues (N-acetylation). In need the peptide under its deacetylated form. Thanks a lot to answer to: Abdou Maftah Institut de Biotechnologie123, avenue A. Thomas 87060, Limoges cedex, France Phone (33) 55 45 76 84 Fax (33) 55 45 76 53 e-mail maftah@unilim.fr From owner-proteins@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!agate!howland.erols.net!surfnet.nl!highway.leidenuniv.nl!ruly46!mirihyel From: Peter Hohenstein Newsgroups: bionet.molbio.proteins Subject: Re: small insert ligation Date: Fri, 6 Sep 1996 13:00:59 +0200 Organization: Leiden University, The Netherlands Lines: 23 Message-ID: References: <4vd8p5$ciu@epervier.CC.UMontreal.CA> <507dnm$2pn@service3.uky.edu> NNTP-Posting-Host: ruly46.medfac.leidenuniv.nl Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: mirihyel@ruly46 To: "Michael W. Thompson" In-Reply-To: <507dnm$2pn@service3.uky.edu> On 30 Aug 1996, Michael W. Thompson wrote: > However, it's been my experience that PCR products with restriction sites near the > ends (even with 7 to 8 bases stuck on the end to help the restriction digest) are not cut > very well with restriction enzymes. I don't know why. (If anyone out there can find a > reason I'd be grateful to hear it ;) Strange, lately I've been using PCR primers encoding HindIII, BamHI, XhoI or EcoRI sites with 4 nucleotides extra (normally I use GATC) and each time it ligated easy. How do you (if at all) clean up your PCR fragments before digestion? I use standard phenol/chloroform extraction and EtOH precipitation and it works fine with me. Peter Hohenstein Dept. Human Genetics University of Leiden The Netherlands From owner-proteins@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!gondor!sol.ctr.columbia.edu!spool.mu.edu!newspump.sol.net!homer.alpha.net!news.ultranet.com!usenet.eel.ufl.edu!warwick!lyra.csx.cam.ac.uk!moose.bioc.cam.ac.uk!user From: nef1002@cus.cam.ac.uk (Nick Fisher) Newsgroups: bionet.molbio.proteins Subject: Re: Isoelectric point of proteins Date: Fri, 06 Sep 1996 17:20:43 +0100 Organization: Dept. of Biochemistry, University of Cambridge Lines: 30 Message-ID: References: <32309593.5929@mailer.uni-marburg.de> NNTP-Posting-Host: moose.bioc.cam.ac.uk In article <32309593.5929@mailer.uni-marburg.de>, Ole Diettrich wrote: > Dear netters, > I wonder to what extend the isoelectric point of a polypeptide changes > between the native (folded) conformation and denatured (8 M Urea) > conditions. Are the, probably few, charged amino acids within the > molecule affected from the external pH ? > Many thanks in advance, > Ole The difference in pI between a native structure and a denatured one (let's assume it's adopted a completely random coil with no significiant secondary structure) is probably larger than you think. It's not so much that buried "charged" residues are suddenly exposed to the solvent but rather that charged sidechains with abnormal pK's due to the local microenvironment are going to going to shift back to the pK you would predict for them if you had no knowledge of the proteins structure. For example, the sidechains of Asp residues in a tightly clustered "acidic patch" are likely to have a pK somewhat higher than that of a single, sovent exposed Asp on a different part of the protein. I don't have any figures to hand, I'm afraid, but I think you will find a difference in pK between native and denatured states for the reason discussed above. Nick Fisher Biochemistry Dept. Cambridge Univ. -- From owner-proteins@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!gondor!newsfeeder.sdsu.edu!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!news.wwa.com!news From: Technical Assistance Newsgroups: bionet.molbio.proteins Subject: Re: Help! Dimerisation. Date: Fri, 06 Sep 1996 13:18:04 -0500 Organization: Pierce Lines: 34 Message-ID: <32306ADC.D2A@pierce.geis.com> References: <50mq65$kpj@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: 204.248.177.50 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; PPC) To: "Mr. G. Morley" Mr. G. Morley wrote: > > I am trying to design an experiment to measure > > the extent of dimerisation between two homodimers. > > I was wondering if anyone could recommend a > > crosslinker that can be used In Vitro. > > Ideally the cross-linker would be membrane > > permiable and can be used on Rat-2 fibroblasts > > (so not too toxic).If anyone uses or knows of a good > > one..or has a methodology or practical tips I would be > > most obligued. Currently I am thinking of DMP or DMS from > > Pierce..if anyone knows about any drawbacks about these > > two I would, also, be most obligued. > > Thank you in advance... > > > > Both the DMS and DMP would work in this application, however the imidoesters, in general, have a tendency to "leak". I suggest using NHS esters in their place. The NHS esters will not "leak" and they are available in both membrane permeable and membrane non-permeable forms. Tom Brotcke/Pierce Tech. From owner-proteins@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!CCR.DSI.UANL.MX!pearl From: pearl@CCR.DSI.UANL.MX ("Dr. Paul R.Earl") Newsgroups: bionet.molbio.proteins Subject: Biomx, electronic journal Date: 6 Sep 1996 13:28:46 -0700 Organization: UANL Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <3230A62F.7ADE@ccr.dsi.uanl.mx> NNTP-Posting-Host: net.bio.net Please enter Biomx under Yahoo search to get this home page, which is also http://www.uanl.mx/biomx to get the information such as authors' instructions. Thank you. Best Regards, Dr Paul R Earl From owner-proteins@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!agate!howland.erols.net!Frankfurt.Germany.EU.net!main.Germany.EU.net!fu-berlin.de!news.th-darmstadt.de!News.Uni-Marburg.DE!usenet From: Ole Diettrich Newsgroups: bionet.molbio.proteins Subject: Isoelectric point of proteins Date: Fri, 06 Sep 1996 14:20:19 -0700 Organization: Inst. f. Phys. Chem. University of Marburg/Germany Lines: 7 Message-ID: <32309593.5929@mailer.uni-marburg.de> NNTP-Posting-Host: pcmf22.med-forschung.uni-marburg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) Dear netters, I wonder to what extend the isoelectric point of a polypeptide changes between the native (folded) conformation and denatured (8 M Urea) conditions. Are the, probably few, charged amino acids within the molecule affected from the external pH ? Many thanks in advance, Ole From owner-proteins@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!MAROON.TC.UMN.EDU!huang020 From: huang020@MAROON.TC.UMN.EDU (Po-Fu Huang) Newsgroups: bionet.molbio.proteins Subject: subscribe Date: 6 Sep 1996 14:37:33 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net subscribe tine0001@gold.tc.umn.edu Could anyone tell me how to subscribe to this discussion group? Thanks. Po-Fu Huang From owner-proteins@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!BOTANY.UFL.EDU!jshao From: jshao@BOTANY.UFL.EDU Newsgroups: bionet.molbio.proteins Subject: anti-phospho-ser/thr antibody Date: 6 Sep 1996 14:21:25 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <199609062121.RAA16014@clas.ufl.edu> NNTP-Posting-Host: net.bio.net Hi, netters: Are there any venders for the anti-phospho-ser/thr antibody? Has someone tried? What about the specificity? I saw one paper about the generation and use of phosphothreonine ( Heffetz, M. et al, Eur. J. Biochem. 182, 343, 1989), is there a commercial source now? Your answers are highly appreciated. Jiahong Shao Graduate student Dept. of Botany Univ. of Florida From owner-proteins@net.bio.net Fri Sep 06 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsxfer2.itd.umich.edu!portc01.blue.aol.com!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: researchd@aol.com (ResearchD) Newsgroups: bionet.molbio.proteins Subject: Re: anti-phospho-ser/thr antibody Date: 7 Sep 1996 19:25:02 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 7 Sender: root@newsbf02.news.aol.com Message-ID: <50t08e$2lo@newsbf02.news.aol.com> References: <199609062121.RAA16014@clas.ufl.edu> NNTP-Posting-Host: newsbf02.mail.aol.com X-Newsreader: AOL Offline Reader Zymed Corp has new antibodies to both of these . You cna contact them at phone 1-800-874-4494, fax #415-871-4499 (sorry, I do not know thier email or web address). Sincerely, Research Diagnostics Inc web: http://members.aol.com/researchd/index.htm From owner-proteins@net.bio.net Fri Sep 06 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!nctuccca.edu.tw!spring.edu.tw!netnews.ntu.edu.tw!news From: czlee Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: a good protocol for far westerns/overlays?? Date: Sun, 08 Sep 1996 10:29:57 +0000 Organization: National Taiwan University Lines: 4 Message-ID: <3232A025.77FB@ntumc1.mc.ntu.edu.tw> References: NNTP-Posting-Host: @140.112.133.19 Mime-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; 68K) Xref: biosci bionet.molbio.proteins:8695 bionet.molbio.methds-reagnts:48923 Hi! you may used 0.2% tween 20 of TBST sol'n wash the menbrane 10 mins twice or 15 mins twice after antibody treatment. From owner-proteins@net.bio.net Fri Sep 06 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!news.sgi.com!newsfeeder.sdsu.edu!newshub.sdsu.edu!usenet From: Kevin Shreder Newsgroups: bionet.molbio.proteins Subject: Re: anti-phospho-ser/thr antibody Date: Sat, 07 Sep 1996 16:30:58 -1000 Organization: University of California at San Diego Lines: 13 Message-ID: <32322FE2.4D98@ucsd.edu> References: <199609062121.RAA16014@clas.ufl.edu> NNTP-Posting-Host: annex2p14.sdsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; 68K) Try my webpage, The Antibody Resource Page, when looking for antibodies. I have a list of more than 60 online companies that sell antibodies, many with searchable product catalogues. The URL for the page is: http://www-chem.ucsd.edu/Faculty/goodman/antibody.html/abpage.html the list of companies can be found at: http://www-chem.ucsd.edu/Faculty/goodman/antibody.html/onlinecomp.html Kevin Shreder, Ph.D. UCSD From owner-proteins@net.bio.net Sat Sep 07 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!bunyip.cc.uq.oz.au!marlin.jcu.edu.au!news From: robert barlow <"robert barlow"@jcu.edu.au> Subject: HELP! Twitchin kinase Content-Type: text/plain; charset=us-ascii Message-ID: <3234A93C.5147@jcu.edu.au> Sender: news@marlin.jcu.edu.au (USENET News System) Reply-To: robert, barlow@jcu.edu.au Content-Transfer-Encoding: 7bit Organization: James Cook University Mime-Version: 1.0 Date: Mon, 09 Sep 1996 16:33:17 -0700 X-Mailer: Mozilla 3.0 (Win95; I; 16bit) Lines: 3 If any one has information on the protein twitchin kinase could you e-mail it to me at the following address. Robert barlow@jcu.edu.au Any help would be appreciated. From owner-proteins@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!gondor!newsfeeder.sdsu.edu!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!uwm.edu!news.cse.psu.edu!news.cc.swarthmore.edu!netnews.upenn.edu!news From: Freier@mail.med.upenn.edu Newsgroups: bionet.molbio.proteins Subject: E.coli strains for phosphorylation Date: 9 Sep 1996 17:11:17 GMT Organization: University of Pennsylvania Lines: 9 Message-ID: <511j3l$283@netnews.upenn.edu> NNTP-Posting-Host: clevenger.med.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 all, I wanted to know if anyone out there has heard of an E.coli strain or strains which express a protein kinase which I could use for the recombinant expression of proteins that I wish to produce in a phosphorylated form. I think there may be one that expresses Elk, or another called TKB1. Has anybody heard of these and/or where I could find them? TIA brad From owner-proteins@net.bio.net Sun Sep 08 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!saturn!apweiler From: apweiler@saturn.your.domain.here (Rolf Apweiler) Subject: Re: Primary structure of proteins Message-ID: Sender: apweiler@saturn (Rolf Apweiler) Date: Fri, 6 Sep 1996 08:13:32 GMT Lines: 44 Reply-To: apweiler@saturn.your.domain.here (Rolf Apweiler) References: <32281FA9.484D@chem.ut.ee> Organization: European Bioinformatics Institute (EMBL) - UK X-Newsreader: mxrn 6.18-31 In article <32281FA9.484D@chem.ut.ee>, Andres Kreegipuu writes: >Hi, > >I am looking for information about the average occurence frecuency of >the 20 natural amino acids in proteins. Are these data available >anywhere? > >Andres Kreegipuu > Here some statistics from the release notes of SWISS-PROT release 33 (52205 protein sequence entries): APPENDIX A: SOME STATISTICS A.1 Amino acid composition A.1.1 Composition in percent for the complete data bank Ala (A) 7.54 Gln (Q) 4.02 Leu (L) 9.31 Ser (S) 7.19 Arg (R) 5.15 Glu (E) 6.31 Lys (K) 5.94 Thr (T) 5.76 Asn (N) 4.54 Gly (G) 6.86 Met (M) 2.36 Trp (W) 1.26 Asp (D) 5.29 His (H) 2.23 Phe (F) 4.06 Tyr (Y) 3.21 Cys (C) 1.70 Ile (I) 5.72 Pro (P) 4.91 Val (V) 6.52 Asx (B) 0.001 Glx (Z) 0.001 Xaa (X) 0.02 A.1.2 Classification of the amino acids by their frequency Leu, Ala, Ser, Gly, Val, Glu, Lys, Thr, Ile, Asp, Arg, Pro, Asn, Phe, Gln, Tyr, Met, His, Cys, Trp I hope that will help. Cheers Rolf Apweiler (SWISS-PROT Coordinator) From owner-proteins@net.bio.net Sun Sep 08 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!rutgers!uwm.edu!news.sol.net!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!in1.uu.net!nih-csl!NewsWatcher!user From: cor@codon.nih.gov (Cor Witteveen) Subject: HP 8450A Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: 128.231.99.180 Organization: LNC/NIMH Date: Mon, 9 Sep 1996 15:14:42 GMT Lines: 13 Hi, I'm using a Hewlett Packard 8450A, an old diode array spectrophotometer which is controlled by an internal Hewlett packard computer. The machine is still working fine, but analyzing my data is a drag since I am not able to get the data from the HP computer to a dos or macintosh computer. I was wondering whether anybody has a simple data aquisition program that hooks up a dos computer to the HP 8450A through the RS323 port. Controlling the machine this way is not necessary. Just data aquisition or export of stored data from the HP computer to a dos computer would be fine. please e-mail me directly: cor@codon.nih.gov thanks, Cor From owner-proteins@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Alexy Eroshkin Newsgroups: bionet.molbio.proteins Subject: ANNOUNCE ProAnalyst -- new software for protein/peptide analysis Date: 9 Sep 1996 11:57:52 +0100 Organization: State Research Center of Virology & Biotechnology VECTOR Lines: 112 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <510t7g$j5t@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk To: proteins@dl.ac.uk From: eroshkin@vector.nsk.su Subject: ANNOUNCE ProAnalyst - new software for protein/peptide analysis --------------------------------------- ProAnalyst - PROTEIN ANALYST (ver 1.02) --------------------------------------- State Research Center of Virology and Biotechnology Koltsovo, Novosibirsk Region, 633159 Russia and Vladimir Ivanisenko with Alexey Eroshkin are pleased to announce the availability of an easy-to-use, state-of-the-art MS-DOS application designed to solve traditional and new tasks of protein science. ProAnalyst FEATURES: - includes intuitive user interface to facilitate data analysis; - inputs single and multiple protein sequences, activity/property/ genotype data, protein 3D structures; - relates experimental data to protein primary and tertiary structure; - finds sites influencing protein activity/property; - finds relationships between protein sites' characteristics (hydrophobicity, amphipathicity, etc.) and protein activities; - investigates differences between proteins divided by functional, evolutionary or other criteria (for example, relates genotype to phenotype); - investigates physico-chemical factors related with activity changes in a set of mutant proteins (including multiple physico-chemical factors); - simulates protein-engineering experiments and predicts activity of mutant protein; - searches motifs and patterns in combinatorial libraries (peptide and phage-displayed libraries); - provides linear correlation and multiple linear regression analysis, discriminant, ANOVA and alphabetical analysis; - classic profile/plot analysis for a single sequence (hydrophobicity, helical amphipathicity, etc.) suplemented with average, min, max and dispresion plots for a set of sequences; - searches regions with high and low variability of physico-chemical characteristics; - calculates structure-activity correlation profile; - performs cross and inter-group variability analysis based on several matrices of amino acid similarity; - main part of methods works with sequential and spatial sites; - maps obtained results onto 3D structure; - sorts sequences by activity, group number, motifs found; - visualizes multiple alignments and protein 3D structures (stereo) with sites highlighted; - has data converter from several protein sequence formats (FASTA, SWISS-PROT, CLUSTAL, PIR, IG); - has data bases with 50 aligned protein families, more than 60 amino acid properties, HELP, Manual and examples with program applications. ProAnalyst MAY BE USEFUL: - for chemists and biochemists making investigations of protein structure-function and structure-activity analysis; - for protein engineers trying to improve some protein properties; - for molecular biologists that need to get sense from multiple protein alignments and to analyze complicated combinatorial libraries; - for geneticists studying phenotype-genotype correlations; - for those who need color protein 3D pictures with sites highlighted; - for students in any field of PROTEIN SCIENCE; - for those who interested in comparative protein sequence analysis. PUBLICATIONS: 1. 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. 2. 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. 3. 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. 4. Kuzmicheva G.A., Kuvshinov V.N., Razumov I.A., Ivanisenko V.A., Eroshkin A.M., et al. Mapping of group specific hemagglutinating antigenic epitope of alphavirus envelope protein E2 using phage display. Doklady Academii Nauk RAN, in press. 5. Morozov B.M., Ivanisenko V.A., Eroshkin A.M., Ugarova N.N. Analysis of relations between bioluminescence color and the structure of beetle luciferases: identification of the sites influencing bioluminescence color. Molec. Biology (Russia), in press. AVAILABILITY: ProAnalyst is available from EBI software library: ftp://ftp.ebi.ac.uk/pub/software/dos/proanalyst/ (as self-extracted archive). Current version works with up to 15 sequences. The length of sequences must be less than or equal to 5000. Comments, bug reports, suggestions for new features are welcome and should be sent by e-mail to: salex@vector.nsk.su (Vladimir Ivanisenko) or eroshkin@vector.nsk.su (Alexey Eroshkin) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 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 Sun Sep 08 23:00:00 1996 Path: biosci!agate!ihnp4.ucsd.edu!munnari.OZ.AU!harbinger.cc.monash.edu.au!newshost.carno.net.au!newshost.anu.edu.au!torda From: torda@rsc.anu.edu.au (Andrew Torda) Newsgroups: bionet.molbio.proteins Subject: Re: Primary structure of proteins Date: 9 Sep 1996 08:19:06 GMT Organization: Research School of Chemistry, Australian National University Lines: 16 Message-ID: <510jtq$f27@manuel.anu.edu.au> References: <32281FA9.484D@chem.ut.ee> Reply-To: Andrew.Torda@anu.edu.au NNTP-Posting-Host: 150.203.35.129 andres@chem.ut.ee wrote >I am looking for information about the average occurence frecuency of >the 20 natural amino acids in proteins. Are these data available >anywhere? Have a look at White, S.H. J Mol Biol, 227, 991-995 (1992) Amino acid preferences of small proteins. Implications for protein stability and evolution. -Andrew -- This posting is not merely my opinion. It is the official position of my employer, the Australian National University. Andrew Torda, Research School of Chemistry, ANU, Canberra, Australia andrew.torda@anu.edu.au http://rsc.anu.edu.au/~torda From owner-proteins@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!gondor!newsfeeder.sdsu.edu!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!martinlab From: klenchin@facstaff.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins,bionet.cellbiol Subject: Re: Enzymatic Product release question Date: 9 Sep 1996 18:51:10 GMT Organization: UW-Madison Lines: 15 Message-ID: <511ouu$vbq@news.doit.wisc.edu> References: <511mpi$ika@newsgate.duke.edu> NNTP-Posting-Host: martinlab.biochem.wisc.edu X-Newsreader: News Xpress Version 1.0 Beta #4 X-No-Archive: Yes Xref: biosci bionet.molbio.proteins:8703 bionet.cellbiol:5425 In article <511mpi$ika@newsgate.duke.edu>, tschantz@galactose.mc.duke.edu (William P. Tschantz) wrote: ->Hi -> ->I am looking for examples of any proteins that the product does not ->dissociate from the enzyme till either new substrate binds or someother ->protein accepts the product from the enzyme. G-proteins? (Especially trimeric). - Hydrolyse GTP and stay with GDP until activated again to bind new GTP (GDP dissociation is rate limiting and is a subject for activation). - Dima From owner-proteins@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!newshost.convex.com!newsgate.duke.edu!galactose.mc.duke.edu.uucp!tschantz From: tschantz@galactose.mc.duke.edu (William P. Tschantz) Newsgroups: bionet.molbio.proteins,bionet.cellbiol Subject: Enzymatic Product release question Date: 9 Sep 1996 18:14:10 GMT Organization: Duke University; Durham, N.C. Lines: 14 Distribution: world Message-ID: <511mpi$ika@newsgate.duke.edu> NNTP-Posting-Host: galactose.mc.duke.edu Xref: biosci bionet.molbio.proteins:8702 bionet.cellbiol:5422 Hi I am looking for examples of any proteins that the product does not dissociate from the enzyme till either new substrate binds or someother protein accepts the product from the enzyme. I am not aware of anything out in the literature, but then i do not know what type of search words to use in a literature search of the above topic. Any help greatly apprecieated. Thanks in advance Bill From owner-proteins@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!HERMES.CAM.AC.UK!jl216 From: jl216@HERMES.CAM.AC.UK (Ji Luo) Newsgroups: bionet.molbio.proteins Subject: Help! Alkaline phosphatase and ATPase Date: 10 Sep 1996 09:27:21 -0700 Organization: IBLS Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <3235ED02.2D0@hermes.cam.ac.uk> Reply-To: jl216@hermes.cam.ac.uk NNTP-Posting-Host: net.bio.net Hi, I am more of a geneticist and so I don't know if I have posted at the right group. But can anyone tell me the difference between two groups of proteins: the alkaline phosphatase and the ATPase? thanks! Ji From owner-proteins@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!agate!spool.mu.edu!uwm.edu!news-peer.gsl.net!news.gsl.net!swrinde!cs.utexas.edu!atlantis.utmb.edu!news From: "horace d. kelso" Newsgroups: bionet.molbio.proteins Subject: Amino acid analysis Date: 10 Sep 1996 15:53:23 GMT Organization: utmb Lines: 5 Message-ID: <5142tk$qdv@atlantis.utmb.edu> NNTP-Posting-Host: 129.109.54.45 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 32bit) We are a core facility that has the ability to analyze both physiological and hydrolyzed samples for amino acids. If you are interested in having your samples analyzed ,please contact H. Kelso at hkelso@marlin.utmb.edu From owner-proteins@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!agate!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!news.sprintlink.net!news-stk-3.sprintlink.net!news.sprintlink.net!news-ana-24.sprintlink.net!news.hscsyr.edu!newsadm From: Tom Duncan Newsgroups: bionet.molbio.proteins,bionet.cellbiol Subject: Re: Enzymatic Product release question Date: Tue, 10 Sep 1996 08:36:49 -0700 Organization: SUNY Health Science Ctr, Dept Biochemistry Lines: 66 Message-ID: <32358B11.41C6@cross.bmb.hscsyr.edu> References: <511mpi$ika@newsgate.duke.edu> <511ouu$vbq@news.doit.wisc.edu> NNTP-Posting-Host: cross.bmb.hscsyr.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) CC: tschantz@galactose.mc.duke.edu Xref: biosci bionet.molbio.proteins:8706 bionet.cellbiol:5429 In article <511mpi$ika@newsgate.duke.edu>, tschantz@galactose.mc.duke.edu (William P. Tschantz) wrote: >Hi > >I am looking for examples of any proteins that the product does not >dissociate from the enzyme till either new substrate binds or someother >protein accepts the product from the enzyme. and Dima Klenchin wrote: > G-proteins? (Especially trimeric). > - Hydrolyse GTP and stay with GDP until activated again to bind > new GTP (GDP dissociation is rate limiting and is a subject for > activation). > > - Dima > G-protein turnover is limited by slow hydrolysis and slow release of product (GDP), which can be stimulated by other proteins, but this does not involve stimulation of product release by binding of substrate to another site. The behavior of FOF1-type ATP synthases provide a good example of what Mr. Tschantz is looking for. The enzyme has three interacting catalytic sites. The first substrate binds very tightly and the chemical step of ATP synthesis/hydrolysis is readily reversible, but product is also tightly bound and dissociates very slowly. However, binding of substrate to a second and even third site causes rapid dissociation of product from the first site, and the next site containing substrate then becomes the "tight" catalytic site. Of course, in the direction of ATP synthesis, this catalytic cooperativity also depends on energy input from a transmembrane, electrochemical gradient of protons. The first high-resolution crystal structure for the F1-sector was published in 1994 (1st ref below). I've also included two reviews below, along with recent articles from our lab that provide the first clear indication that this cooperative mechanism involves the relative rotation of catalytic sites in the complex. Abrahams, J.P., Leslie, A.G., Lutter, R. & Walker, J.E. (1994). "Structure at 2.8 Angstrom resolution of F1-ATPase from bovine heart mitochondria". Nature 370, 621-628. Boyer, P.D. (1993). "The binding change mechanism for ATP synthase - Some probabilities and possibilities". Biochim. Biophys. Acta 1140, 215-250. Nakamoto, R.K. (1996). "Mechanisms of Active Transport in the FOF1 ATP Synthase". J. Membrane Biol. 151, 101-111. Duncan, T.M., Bulygin, V.B., Zhou, Y., Hutcheon, M.L., & Cross, R.L. (1995). "Rotation of subunits during catalysis by Escherichia coli F1-ATPase". Proc. Natl. Acad. Sci. USA 92, 10964-10968. Zhou, Y., Duncan, T.M., Bulygin, V.B., Hutcheon, M.L., & Cross, R.L. (1996). "ATP hydrolysis by membrane-bound Escherichia coli FOF1 causes rotation of the gamma subunit relative to the Beta subunits". Biochim. Biophys. Acta 1275, 96-100. -- Thomas M. Duncan Dept. Biochemistry & Molecular Biology SUNY Health Science Center 750 E Adams St, Syracuse, NY 13210 Email: duncant@vax.cs.hscsyr.edu or duncant@cross.bmb.hscsyr.edu From owner-proteins@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!news.sgi.com!news-out.microserve.net!news-in.microserve.net!news.sprintlink.net!news-dc-2.sprintlink.net!news.cuny.edu!msvax.mssm.edu!MING From: ming@msvax.mssm.edu Newsgroups: bionet.molbio.proteins Subject: PIR submission? Date: 10 Sep 1996 10:14:28 GMT Organization: Mount Sinai Medical Center, New York City Lines: 4 Message-ID: <513f24$jeb@news.cuny.edu> Reply-To: ming@msvax.mssm.edu NNTP-Posting-Host: msvax.mssm.edu Does anyone know how to correct a protein sequence mistake in PIR-Protein database? Any phone number or email address for PIR? Thanks in advance. ming@msvax.mssm.edu . From owner-proteins@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Re: PIR submission? Date: 10 Sep 1996 14:28:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 77 Sender: daemon@net.bio.net Distribution: world Message-ID: <01I9BKMMFGBA94DO6M@NBRF.Georgetown.Edu> NNTP-Posting-Host: net.bio.net ming@msvax.mssm.edu writes > Does anyone know how to correct a protein sequence mistake in PIR-Pro= > tein database? Any phone number or email address for PIR? Thanks in a= > dvance. Submitting of Sequence Data to NCBI GenBank, EMBL, DDBJ or PIR The National Biomedical Research Foundation Protein Information Resource accepts electronic submission of sequence data. As sequence data submission policies have been designed in agreement with both the nucleotide and protein sequence databanks, we wish to take this opportunity to restate for BIONEWS subscribers a few general guidelines on submission of their sequence data. Researchers should submit nucleotide sequence data directly to GenBank or EMBL for assignment of an accession number prior to publication. Derived amino acid sequence data may also be included at the same time. Amino acid sequence data submitted in this way to GenBank, EMBL or DDBJ will eventually be passed on to PIR if the author permits their public release prior to publication, and need not be submitted separately to PIR. This is done so correct cross-references can be made between nucleotide and protein sequence accession numbers. All other amino acid sequences may be submitted directly to PIR when the authors permit their public release prior to publication. Japanese authors who use the NEC 9801 PC should communicate directly with DDBJ, as these machines use a version of DOS that is significantly different enough to render the discs unreadable on MS-DOS computers here. The staff at DDBJ will forward the data to the appropriate databank via electronic mail. DDBJ may be contacted at: ddbjsubs@flat.nig.ac.jp The address for NCBI GenBank submissions is: GenBank Submissions National Center for Biotechnology Information Bldg. 38A, Room 8N-803 8600 Rockville Pike Bethesda, MD 20894 (for submissions on diskette, indicate whether Mac or PC): E-mail submission of new sequences: gb-sub@ncbi.nlm.nih.gov E-mail submission of updates: update@ncbi.nlm.nih.gov The address for EMBL submissions is: EMBL Data Submissions Postfach 10.2209 D-6900, Heidelburg Federal Republic of Germany Telephone (+49) 6221-387-258 The address for DDBJ submissions is: DNA Database of Japan Center for Genetic Information Research National Institute of Genetics 111 Yata Mishima, Shizuoka 411 JAPAN Telephone (+81) 559-75-3651 Electronic mail: ddbjsubs@flat.nig.ac.jp The address for PIR submissions is: PIR Submissions National Biomedical Research Foundation 3900 Reservoir Road, NW Washington, DC 20007 U.S.A. Telephone: (202) 687-2121 Electronic mail: PIRMAIL@NBRF.Georgetown.EDU The GenBank/EMBL/PIR Electronic Data Submission Form can be obtained by sending a request to one of these addresses. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMASTER@NBRF.GEORGETOWN.EDU (202) 687-2121 From owner-proteins@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!cpk-news-hub1.bbnplanet.com!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!in1.uu.net!news1.ni.net!usenet From: Jeff Brown Newsgroups: bionet.molbio.proteins Subject: Source for P4501A? Date: Tue, 10 Sep 1996 12:15:44 -0700 Organization: SCCWRP Lines: 6 Message-ID: <3235BE60.642D@sccwrp.com> NNTP-Posting-Host: 206.183.213.134 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; U) Is there a source for CYP1A (cytochrome P4501A) antibodies raised against fish? Has anyone tried Chemicon anti-CYP1A1 raised against rat for fish assays? Any information will be appreciated Jeff From owner-proteins@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: jody McGill Newsgroups: bionet.molbio.proteins Subject: Internet Resources/Protein Structure Course using the Internet Date: 10 Sep 1996 10:40:36 +0100 Lines: 32 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <513d2k$itu@mserv1.dl.ac.uk> X-Sender: jody@iona.cryst.bbk.ac.uk Original-To: bio-info@dl.ac.uk, bionews@dl.ac.uk, bio-www@dl.ac.uk, str-nmr@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, molmodel@dl.ac.uk Dear All Registrations are now being accepted for The Crystallography Department of Birkbeck College's Advanced Certificate course on: THE PRINCIPLES OF PROTEIN STRUCTURE using the Internet. This course is of nine months duration using Internet resources such as the BioMoo and the e.mail. The cost for students within the EU is 250 pounds sterling, for overseas students the cost is 550 pounds sterling. The course is divided into three sections: 1. Introduction to Internet Resources 2. Protein Structure 3. Dissertation: structure, function and dynamics For details of course contents, administration and registration URL http://www.cryst.bbk.ac.uk/PPS2/index.html REGISTRATION CLOSES SOMETIME AT THE END OF SEPTEMBER, IF YOU ARE INTERESTED IN APPLYING APPLY NOW!! Contact: Jody McGill, Crystallography Department, Birkbeck College London, WC1E 7HX. UK Tel. +44 (0)171 631 6800 Fax. +44 (0)171 631 6803 e.mail: j.mcgill@mail.cryst.bbk.ac.uk From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Newsgroups: bionet.molbio.proteins Path: biosci!agate!spool.mu.edu!uwm.edu!news-peer.gsl.net!news.gsl.net!usenet.eel.ufl.edu!warwick!yama.mcc.ac.uk!liv!incubus From: incubus@liverpool.ac.uk (Mr. D.M. Shaw) Subject: Re: anti-phospho-ser/thr antibody Message-ID: Sender: news@liverpool.ac.uk (News System) Nntp-Posting-Host: uxa.liv.ac.uk Organization: The University of Liverpool X-Newsreader: TIN [version 1.2 PL2] References: <199609062121.RAA16014@clas.ufl.edu> Date: Wed, 11 Sep 1996 11:27:45 GMT Lines: 14 jshao@BOTANY.UFL.EDU wrote: : Hi, netters: : Are there any venders for the anti-phospho-ser/thr antibody? Has someone : tried? What about the specificity? : I saw one paper about the generation and use of phosphothreonine ( Heffetz, : M. et al, Eur. J. Biochem. 182, 343, 1989), is there a commercial source : now? : Your answers are highly appreciated. : Jiahong Shao : Graduate student : Dept. of Botany : Univ. of Florida Try contacting Amersham life sciences (UK), they do a few antibodies of this type. From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!agate!newsgate.duke.edu!news-server.ncren.net!concert!news.wfu.edu!usenet From: taguebw@wfu.edu Newsgroups: bionet.molbio.proteins,bionet.cellbiol Subject: Re: Enzymatic Product release question Date: Tue, 10 Sep 1996 17:48:48 -0500 Organization: Wake Forest University Lines: 36 Message-ID: <3235F050.200A@wfu.edu> References: <511mpi$ika@newsgate.duke.edu> NNTP-Posting-Host: taguebw.bio.wfu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; PPC) To: "William P. Tschantz" Xref: biosci bionet.molbio.proteins:8712 bionet.cellbiol:5439 William P. Tschantz wrote: > I am looking for examples of any proteins that the product does not > dissociate from the enzyme till either new substrate binds or someother > protein accepts the product from the enzyme. > > I am not aware of anything out in the literature, but then i do not know > what type of search words to use in a literature search of the above > topic. Any help greatly apprecieated. > You might try searching for "channelling" -- referring to the process by which products are passed along or "channeled" to the next enzyme. Try these references: Negrutskii, Boris S. and Murray P. Deutscher (1991) Channeling of aminoacyl-tRNA for protein synthesis in vivo. PNAS 88:4991-4995. Negrutskii, Boris S. and Murray P. Deutscher. (1992) A sequestered pool of aminoacyl-tRNA in mammalian cells. PNAS 89::3601-3604. Negrutskii, Boris S. , Romualdas Stapulionis and Murray P. Deutscher. (1994) Supramolecular organization of the mammalian translation system. PNAS 91:964-968. Also: Hrazdina and Hensen 1992. Spatial organization of enzymes in plant metabolic pathways. Ann Rev. Plant Physiol. Molec. Biol. 43:241-267. Srere. 1987. Complexes of sequential metabolic enzymes. Ann. Rev. Biochem. 56:21-56 Brian From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!agate!news.ucdavis.edu!info.ucla.edu!csulb.edu!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!munnari.OZ.AU!news.unimelb.EDU.AU!wehi.edu.au!wehi!stanyon From: stanyon@wehi.edu.au Newsgroups: bionet.molbio.proteins Subject: Protein Interactions Date: 11 Sep 96 16:47:02 +1000 Organization: Walter & Eliza Hall Institute Lines: 33 Message-ID: <1996Sep11.164702@wehi> NNTP-Posting-Host: wehiw.wehi.edu.au A question for Protein Chemists. With what sort of frequency might a protein oscillate or vibrate between two or more shapes, when one of these shapes usually requires some post-translational modification such as phosphorylation to have occurred before it becomes the dominant form? As background to this question, I should add that I am studying protein-protein interactions in the Yeast Two-hybrid system. A recurrent observation is that interactions - as assessed by transcription of a gene which confers prototrophy upon the yeast - do not give an all-or-nothing readout. Although the DNA required to produce the proteins may be present in the yeast, the frequncy at which this causes the observed phenotype ranges from 50-60% in the case of strongly interacting proteins such as fos & jun, down to less than 1% in the case of "weakly" interacting proteins. This correlates with the activity of b-galactosidase in some reports. In effect, the degree of penetrance of the observable phenotype appears to vary considerably. The other interesting observation is that even though the frequency may differ considerably, the size of colonies does not appear to be affected. Thus, fos-jun pairings will give colonies of similar size to "weaker" pairings, though the numbers of colonies may be 10-fold apart when compared to the number carrying the necessary DNA. I am attempting to find out whether there are any recommendable methods for studying the stability of protein complexes with a view to establishing whether or not complexes between non-post-translationally modified proteins are stable, even though the complex formation may be quite infrequent. Essentially, a quantitative measure would be necessary, in terms of both frequency and stability. Feel free to mail me directly, and thank-you in advance. Clem Stanyon From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!usc!usc!not-for-mail From: separk@pollux.usc.edu (separk) Newsgroups: bionet.molbio.proteins Subject: help: references for substructure matching Date: 11 Sep 1996 04:29:34 -0700 Organization: University of Southern California, Los Angeles, CA Lines: 11 Sender: separk@pollux.usc.edu Message-ID: <5167qu$mia@pollux.usc.edu> NNTP-Posting-Host: pollux.usc.edu Hello, I am looking for references about protein substructure matching. Survey papers about existing methods would be perfect, but any reference that deals with the subject would be helpful as well. Thank you very much for your time! Regards, Seongbin Park (separk@pollux.usc.edu) From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!agate!news.ucdavis.edu!info.ucla.edu!csulb.edu!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!in2.uu.net!news.sojourn.com!condor.ic.net!news2.acs.oakland.edu!cwis-20.wayne.edu!cms.cc.wayne.edu!gkrause From: gkrause@cms.cc.wayne.edu (Gary Krause) Newsgroups: bionet.molbio.proteins Subject: Pest program location Date: Wed, 11 Sep 1996 11:20:06 UNDEFINED Organization: Wayne State University Lines: 8 Message-ID: NNTP-Posting-Host: 146.9.12.243 X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] Does anyone one know what happened to the Pest sequence program at http://www.biu.icnet.uk/projects/pest ? It now is off limits. Any suggestions would be appreciated. Thanks. Gary Krause (gkrause@cms.cc.wayne.edu) Department of Emergency Medicine Wayne State University, Detroit, MI USA From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!agate!newsgate.duke.edu!usenet From: Mara Casar Newsgroups: bionet.molbio.proteins Subject: purifying translation products Date: Wed, 11 Sep 1996 11:54:54 -0500 Organization: Duke University, Durham, NC, USA Lines: 18 Message-ID: <3236EEDE.F8B@acpub.duke.edu> NNTP-Posting-Host: blackshear07.mc.duke.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; 68K) Hi- I'm trying to do an in vitro translation using BMB's biotinylated lysine-tRNA reagents (instead of 35-S labeling). When I do the translation in reticulocyte lysate and run an aliquot on a gel, transfer to nitrocellulose, and then detect with streptavidin-HRP and ECL, I get a lot of other bands lighting up. Retic. lysate supposedly has only a few endogenous biotinylated proteins, though. Has anyone out there in Internet-land (a) used biotinylated lysine in in vitro translations or (b) had a similar problem and can offer advice? I'm not able to see any difference between my control translations without RNA and any of my samples. Thanks in advance! -Mara Casar Department of Biochemistry Duke University From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!csulb.edu!drivel.ics.uci.edu!news.service.uci.edu!design.eng.uci.edu!cskim From: "Craig S. Kim" Newsgroups: bionet.molbio.proteins Subject: Software Info Needed Date: Wed, 11 Sep 1996 14:08:45 -0700 Organization: University of California, Irvine Lines: 26 Message-ID: NNTP-Posting-Host: design.eng.uci.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I've recently been authorized to go on a spending spree for molecular bio/biochemistry type software. Can anyone tell me where I can get information on the following for a Macintosh PowerPC? * The latest version of DNA strider * A program to design oligos for PCR (prevent dimerization and hairpins) * A program which will find degree of homology between different DNA sequences * A graphical program to visualize different chemical structures (HyperChem or others?) If any of you use any of this type of software, I would really appreciate your opinions of any of the packages out there. Thanks in advance for your help, Craig S. Kim Dept. of Chemical and Biochemical Engineering University of California, Irvine Irvine, CA 92697-2575 From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-peer.gsl.net!news.gsl.net!portc01.blue.aol.com!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: browec@aol.com (BroweC) Newsgroups: bionet.molbio.proteins Subject: Request info on semi-dry blotters :) Date: 11 Sep 1996 08:02:39 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 10 Sender: root@newsbf02.news.aol.com Message-ID: <5169ov$ge4@newsbf02.news.aol.com> Reply-To: browec@aol.com (BroweC) NNTP-Posting-Host: newsbf02.mail.aol.com Dear Group, Does anyone have any experiences using a semi-dry blotter? How do the various companies compare (Bio-rad, Hoeffer, etc.)? How does semi-dry compare with standard blotting? Is stacking the gel sandwiches on top of one another to do multiple blots at once a problem? Thanks for helping, Chris Browec@aol.com From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!agate!nature.berkeley.edu!lhom From: lhom@nature.berkeley.edu (Louis Hom) Newsgroups: alt.bio.hackers,bionet.molbio.proteins Subject: Re: light-sensitive peptidase Date: 12 Sep 1996 05:16:44 GMT Organization: University of California, Berkeley Lines: 16 Message-ID: <5186bt$s0t@agate.berkeley.edu> References: <517qvs$p3h@tor-nn1-hb0.netcom.ca> NNTP-Posting-Host: nature.berkeley.edu In article <517qvs$p3h@tor-nn1-hb0.netcom.ca>, Serban San-Marina wrote: >Dear biologists, > >Does anyone have information on peptidases that can be either activated >or inactivated by light? I would appreciate any leads. Thanks! I don't know of any light-activated/inactivated peptidases, but it's neat to think about. It seems likely that there are caging processes out there for making photo-activatable nucleophilic serines or cysteines. Well, maybe. -- _______________________________________________________________________________ Lou Hom >K '93 "Into each life a little rain lhom@nature.berkeley.edu must fall, even in San Diego." http://www.ocf.berkeley.edu/~lhom -- from "My Blue Heaven" From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in3.uu.net!EU.net!Austria.EU.net!01-newsfeed.univie.ac.at!02-newsfeed.univie.ac.at!paladin.american.edu!news.jhu.edu!news From: Reggie Aurora Newsgroups: bionet.molbio.proteins Subject: Re: Primary structure of proteins Date: Tue, 10 Sep 1996 15:58:20 -0400 Organization: HCF - Johns Hopkins University, Baltimore, Maryland, USA Lines: 45 Message-ID: <3235C85C.41C6@grserv.med.jhu.edu> NNTP-Posting-Host: 128.220.138.234 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP20) > In article <32281FA9.484D@chem.ut.ee>, Andres Kreegipuu writes: >Hi, > >I am looking for information about the average occurence frecuency of >the 20 natural amino acids in proteins. Are these data available >anywhere? > >Andres Kreegipuu Andres - Here is the freq. of 20 aa from March 1995 PDB using non-homologous proteins (<25% homology): (PDB is the Brookhaven structure database, just in case you didn't know) Total number of aa counted: 200995 Residue Counts %age ----------------------------------- 1 G 16812 8.36 2 A 17288 8.60 3 V 14591 7.26 4 I 10526 5.24 5 L 16290 8.10 6 F 7494 3.73 7 P 8966 4.46 8 M 3744 1.86 9 W 2919 1.45 10 C 4137 2.06 11 S 15075 7.50 12 T 12900 6.42 13 N 10007 4.98 14 Q 7248 3.61 15 Y 7069 3.52 16 H 4629 2.30 17 D 11221 5.58 18 E 10248 5.10 19 K 11802 5.87 20 R 8029 3.99 ---------------- **** ---------------- Reggie Aurora Dept of Biophysics, WBSB 701, Johns Hopkins School of Medicine 725 N. Wolfe St., Baltimore, MD 21205 From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.compuserve.com!ix.netcom.com!tor-nn1.netcom.ca!news From: serban@netcom.ca(Serban San-Marina ) Newsgroups: bionet.molbio.proteins Subject: light-sensitive peptidase Date: 12 Sep 1996 02:02:36 GMT Organization: Netcom Canada Lines: 6 Message-ID: <517qvs$p3h@tor-nn1-hb0.netcom.ca> NNTP-Posting-Host: trt-on8-18.netcom.ca X-NETCOM-Date: Wed Sep 11 10:02:36 PM EDT 1996 Dear biologists, Does anyone have information on peptidases that can be either activated or inactivated by light? I would appreciate any leads. Thanks! Serban From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!agate!nature.berkeley.edu!lhom From: lhom@nature.berkeley.edu (Louis Hom) Newsgroups: bionet.molbio.proteins Subject: Re: Request info on semi-dry blotters :) Date: 11 Sep 1996 21:53:46 GMT Organization: University of California, Berkeley Lines: 22 Distribution: usa Message-ID: <517cda$eep@agate.berkeley.edu> References: <5169ov$ge4@newsbf02.news.aol.com> NNTP-Posting-Host: nature.berkeley.edu I actually was asking these same questions earlier this year; you might be able to find some of the responses in the www.bio.net archives. I believe semi-dry blotters run *hotter* (higher current) than tank systems, not colder as suggested by someone else. In fact, some setups require high amp power sources (Bio-Rad, e.g., pairs their transfer unit with a 2 amp source) that you might not have on hand. The biggest problems I've heard about are 1) deterioration of graphite plates after extensive use (on the order of years), 2) blotters that require a mylar mask (if any are still around) can be a royal pain, 3) if you work with labeled proteins, make sure the unit is easy to clean (IMHO, the Bio-Rad unit fails horribly on this point), and 4) try to find a blotter with an electrode orientation you're comfortable with -- most blotters out there require you to lay the gel on top of the membrane; I happen to prefer laying the more rigid and manageable membrane on top of the gel. In the end, our lab decided to get the semi-dry blotter manufactured by Owl Scientific. It's about $600. -- _______________________________________________________________________________ Lou Hom >K '93 "Into each life a little rain lhom@nature.berkeley.edu must fall, even in San Diego." http://www.ocf.berkeley.edu/~lhom -- from "My Blue Heaven" From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!agate!spool.mu.edu!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!info.ucla.edu!humc.edu!news.cerf.net!news1.ni.net!usenet Newsgroups: bionet.molbio.proteins Subject: Re: Source for P4501A? Message-ID: <3236F30E.4567@sccwrp.org> From: Jeff Brown Date: Wed, 11 Sep 1996 10:12:46 -0700 References: <3235BE60.642D@sccwrp.com> Organization: Southern California Coastal Water Research Project NNTP-Posting-Host: 206.183.213.134 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; U) Lines: 4 SCCWRP is now a .org instead of a .com for those kind soles trying to reach me by e-mail. Sorry for the inconvenience, Jeff From owner-proteins@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.sgi.com!spool.mu.edu!newshub.tc.umn.edu!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Request info on semi-dry blotters :) Date: 11 Sep 1996 15:19:30 GMT Organization: University of Wuerzburg, Germany Lines: 24 Message-ID: <516la2$8a@winx03.informatik.uni-wuerzburg.de> References: <5169ov$ge4@newsbf02.news.aol.com> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] BroweC (browec@aol.com) wrote: > How do the > various companies compare (Bio-rad, Hoeffer, etc.)? We happen to have a BioRad model, and I am satisfied with it. > How does semi-dry > compare with standard blotting? Some people claim that tank blotting is more sensitive. IMO a large advantage of semi-dry blotting is that you need only a fraction of the buffer, since preparing of buffers is not one of my favourites :-) > Is stacking the gel sandwiches on top of > one another to do multiple blots at once a problem? Never tried this -- actually I never thought of this :-) --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Tue Sep