From owner-proteins@net.bio.net Tue Mar 01 22:00:00 1994 Path: biosci!FOX.CCE.USP.BR!szeinfel From: szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) Newsgroups: bionet.molbio.proteins Subject: Re: Would a consensus sequence form an active protein? Date: 2 Mar 1994 13:16:06 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: bionet Message-ID: NNTP-Posting-Host: net.bio.net Concerning this discussion I would like to hear from you what you think about the following idea. Instead of making a "consensus sequence protein" making random mutations in one protein you'll have the same result. These brings the advantage that you have the 3d structure (of the protein before mutated) and also that a lot of work was already done with random mutations. Ps. I sent this message yesterday but I had no replays. Rafael Najmanovich From owner-proteins@net.bio.net Tue Mar 01 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!Germany.EU.net!netmbx.de!zib-berlin.de!fauern!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Would a consensus sequence form an active protein? Date: 2 Mar 1994 17:18:34 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 15 Distribution: bionet Message-ID: <2l2hpaINN1148@sat.ipp-garching.mpg.de> References: NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.1 PL8] Rafael N Szeinfeld (szeinfel@FOX.CCE.USP.BR) wrote: : Instead of making a "consensus sequence protein" making random : mutations in one protein you'll have the same result. These brings the : advantage that you have the 3d structure (of the protein before mutated) and : also that a lot of work was already done with random mutations. Isn't that roughly what B. Matthews is doing with lysozyme? --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "People are DNA's way of making more DNA." (Edward O. Wilson, 1975) */ From owner-proteins@net.bio.net Tue Mar 01 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!europa.eng.gtefsd.com!mozart.amil.jhu.edu!blaze.cs.jhu.edu!jhunix.hcf.jhu.edu!NewsWatcher!user From: Neil.Clarke@qmail.bs.jhu.edu (Neil Clarke) Newsgroups: bionet.molbio.proteins Subject: Re: Would a consensus sequence form an active protein? (Cont.) Followup-To: bionet.molbio.proteins Date: 2 Mar 1994 21:01:23 GMT Organization: Johns Hopkins Lines: 16 Message-ID: References: <2kvhqk$cjk@ucunix.san.uc.edu> <94Mar1.190039edt.161@neuron.ai.toronto.edu> NNTP-Posting-Host: 128.220.56.231 >In Article <2kvhqk$cjk@ucunix.san.uc.edu>, naussjl@ucunix.san.uc.edu > >(Jeffrey L Nauss) wrote: > >>I am a molecular modeler here at U. Cincinnati lately doing some > >>structutral homology modeling of proteins. I was recently looking > >>over some sequences making comparisons with the consensus sequence > >>when the question in the subject line struck me. If one synthesized > >>an enzyme by whatever means using a consensus sequence, would the > >>resulting polypeptide fold properly and would it be active? Jeremy Berg's group has made a consensus zinc finger peptide based on the 125 zinc fingers known at the time (several years ago). The consensus sequence behaves in every respect like a "wild type" zinc finger. Actually, in some ways (for example Zn dissociation constant) it is better than any of the wild-type sequences examined. Keep in mind that this is a small peptide that requires metal binding to fold stably. IMHO, this better than wt observation is _not_ going to be generally true. From owner-proteins@net.bio.net Tue Mar 01 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!bnr.co.uk!corpgate!news.utdallas.edu!wupost!howland.reston.ans.net!agate!msuinfo!netnews.upenn.edu!news.cc.swarthmore.edu!news.haverford.edu!s201.haverford.edu!user From: dzuckerm@haverford.edu (David Zuckerman) Newsgroups: bionet.neuroscience,bionet.molbio.gene-linkage,bionet.molbio.proteins,sci.bio,sci.med Subject: Huntington's Disease Followup-To: bionet.neuroscience Date: 3 Mar 1994 05:12:42 GMT Organization: Haverford College Lines: 10 Message-ID: NNTP-Posting-Host: 165.82.1.201 Xref: biosci bionet.neuroscience:2708 bionet.molbio.gene-linkage:294 bionet.molbio.proteins:1479 sci.bio:7157 sci.med:30598 I am in desperate need of information bibliographical or otherwise related to Huntington's Disease, especially current treatment practices. It would be most appreciated. Please send any replies via the internet to my email address below. Thankyou.: -- April Rasch arasch@haverford.edu From owner-proteins@net.bio.net Tue Mar 01 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!sgiblab!news.cs.indiana.edu!babbage.ece.uc.edu!ucunix.san.uc.edu!ucunix.san.uc.edu!not-for-mail From: naussjl@ucunix.san.uc.edu (Jeffrey L Nauss) Newsgroups: bionet.molbio.proteins Subject: Re: Length of peptide and Immunological Resistance Date: 2 Mar 1994 09:23:13 -0500 Organization: University of Cincinnati Lines: 12 Message-ID: <2l27gh$d9d@ucunix.san.uc.edu> References: <2krm3c$pq5@network.ucsd.edu> <2kus6r$9i7@hermod.uio.no> NNTP-Posting-Host: ucunix.san.uc.edu In article genecutl@mendel.berkeley.edu (gc) writes: >I think MHC receptors present peptides of around ten to twelve >amino acids to T cells. A peptide smaller than this can't be >presented and won't be very immunogenic. Class I MHC's present peptides of 8-9 amino acids in length. Class II are variable with lengths in the neighborhood of 12-16 residues. -- Jeff Nauss Texas A&M Class of '77 Department of Chemistry Gig 'em, Aggies! University of Cincinnati From owner-proteins@net.bio.net Tue Mar 01 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!gatech!swrinde!menudo.uh.edu!usenet From: ramin@brain.bchs.uh.edu (ramin homayouni) Newsgroups: bionet.molbio.proteins Subject: Looking for polyclonal antibodies to aldolase Date: 2 Mar 1994 18:55:08 GMT Organization: University of Houston Lines: 13 Message-ID: <2l2nec$eqf@menudo.uh.edu> NNTP-Posting-Host: brain.bchs.uh.edu Hi, I'm wondering if someone could point me to a place (a lab or a commercial source) where I could get a polyclonal antibody to the glycolytic enzyme aldolase. I have identified what appears to be an invertebrate homolog of the human aldolase B and I would like to confirm this by immunoblotting and immunoprecipitation experiments. Any hints or suggestions would be greatly appreciated. Thanks, Ramin Ramin@brain.bchs.uh.edu From owner-proteins@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: ARCIB@BIOTECHNET.COM Newsgroups: bionet.molbio.proteins Subject: antibodies to 2-DNA Date: 3 Mar 1994 08:40:01 -0000 Lines: 15 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2l47p1$mce@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk I am looking for a source of anti-2DNA antibodies. If anyone knows where I can get them from please let me know. Thanks in advance Sunita -- Dr.Sunita de Souza Astra Research Centre India P.B.No. 359, Malleswaram P.O. Bangalore - 560 003. India. Tel: +91-80-3340372 Fax: +91-80-3340449 EM : arcib@biotechnet.com From owner-proteins@net.bio.net Wed Mar 02 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!sun4nl!news.nic.surfnet.nl!wau.nl!LConceicao.VenV.WAU.NL!Luis.Conceicao From: Luis.Conceicao@Alg.VenV.WAU.NL (Luis Conceicao) Subject: Role of amino acidic compounds Message-ID: Lines: 30 Sender: news@news.wau.nl (News Administrator) Organization: Wageningen Agricultural University Date: Thu, 3 Mar 1994 11:30:02 GMT Hi! I am looking for some information and/or references on the roles that the following amino acidic compounds have in the different metabolic processes, as well as their physiological importance. Phosphoserine Taurine Phosphoethanolamine alpha-amino-adipic acid alpha-amino-butyric acid beta-amino-isobutyric acid gamma-amino-butyric acid Cystationine Carnosine 1-Methyl-histidine 3-Methyl-histidine My main interest is fish, and its protein metabolism, but any information is welcome! Thanks, Luis Conceicao ============================================================================= Luis Conceicao Dept. Fish Culture and Fisheries P.O.Box 338, NL-6700 AH Wageningen Wageningen Agricultural University Tel: + 31 8370 84942 The Netherlands E-mail: Luis.Conceicao@alg.venv.wau.nl ============================================================================= From owner-proteins@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!umn.edu!mayonews.mayo.edu!Mayo.EDU!eberhard From: eberhard@Mayo.EDU (norm eberhardt) Newsgroups: bionet.molbio.proteins Subject: Protein Structure Prediction Software Date: 3 Mar 1994 14:36:09 GMT Organization: Mayo Foundation, Rochester, Minnesota Lines: 8 Distribution: world Message-ID: <2l4skp$bur@fermat.mayo.edu> NNTP-Posting-Host: feynman.mayo.edu Keywords: Protein Structure, Amino Acid Sequence, 3-d Structure Prediction I am aware of Chou-Fasman types of programs which predict secondary structure on the basis of amino acid sequence. Are there similar programs available that model tertiary (3-d) structure on the basis of amino acid sequence only? Thanks, Norman L. Eberhardt From owner-proteins@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!ddsw1!news.cic.net!magnus.acs.ohio-state.edu!rsaldanh From: rsaldanh@magnus.acs.ohio-state.edu (Roland J Saldanha) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: determining oligomeric structure of a protein Date: 4 Mar 1994 02:42:04 GMT Organization: The Ohio State University Lines: 15 Message-ID: <2l675s$mna@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: bottom.magnus.acs.ohio-state.edu Xref: biosci bionet.molbio.proteins:1489 bionet.molbio.methds-reagnts:12059 I am working on the mitochondrial tyrosyl synthetase that functions as both a synthetase and as a facilitator of group I intron splicing. In characterizing the protein we find that it elutes from gel filtration columns with an apparent molecular weight of a tetramer (monomer MW=72,000). However the protein crosslinks as a dimer with dimethyl suberimidate and glutaraldehyde. This would suggest a highly elongated structure that has an aberrant mobility (reflecting the elongated size) in gel filtration. I would welcome suggestions for other methods for demonstrating the oligomeric structure of the protein. I am aware that sedimentation analysis is the best method of approaching this problem but do not have access to an analytical ultracentrifuge and would welcome collaborative offers from anyone who has a machine. We would also like to try native page but the protein is very basic (computer calculated pI of 10.3). I would thus welcome suggestions for native gels of basic proteins and suitable standards for basic proteins. From owner-proteins@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!SPLAVA.CC.PLATTSBURGH.EDU!GRAZIAWD From: GRAZIAWD@SPLAVA.CC.PLATTSBURGH.EDU ("William D. Graziadei") Newsgroups: bionet.molbio.proteins Subject: Re: Huntington's Disease Date: 3 Mar 1994 11:20:10 -0000 Organization: SUNY at Plattsburgh, New York, USA Lines: 36 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <01H9IX9XMOVS929NS3@splava.cc.plattsburgh.edu> NNTP-Posting-Host: net.bio.net In a message from April Re: >From: IN%"dzuckerm@haverford.edu" 3-MAR-1994 00:42:30.41 >To: IN%"proteins@net.bio.net" >CC: >Subj: Huntington's Disease > >I am in desperate need of information bibliographical or otherwise >related to Huntington's Disease, especially current treatment practices. >It would be most appreciated. Please send any replies via the internet to >my email address below. -------------------------------------------------------------------------------- Gopher and OMIM at Welch library (Johns Hopkins) is (was) a god source. Search Hunt(ington) use to give a good hit. However, lately I get error messages. Can anybody help April (and me). I've tried Downs as well to no avail. Regards, Bill Signature follows: ____________________________________________________________________ / William D. Graziadei / Department of Biological Sciences /| /==============================/====================================/_/ / US Mail / EMail G / / Beaumont Hall 444 / GRAZIAWD (Local) ___/ / SUNY Plattsburgh / SPLAVA::GRAZIAWD (SUNY Decnet) / / / Plattsburgh, New York 12901 / / / / Tel (518) 564-5165 / GRAZIAWD@SNYPLAVA.BITNET / / / Fax (518) 564-7827 / GRAZIAWD@SPLAVA.CC.PLATTSBURGH.EDU / / /______________________________/____________________________________/ / |_____________________________/\____________________________________|/ From owner-proteins@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!news.cs.indiana.edu!babbage.ece.uc.edu!ucunix.san.uc.edu!ucunix.san.uc.edu!not-for-mail From: naussjl@ucunix.san.uc.edu (Jeffrey L Nauss) Newsgroups: bionet.molbio.proteins Subject: Re: Would a consensus sequence form an active protein? Date: 3 Mar 1994 14:08:07 -0500 Organization: University of Cincinnati Lines: 24 Distribution: bionet Message-ID: <2l5cin$fcg@ucunix.san.uc.edu> References: NNTP-Posting-Host: ucunix.san.uc.edu In article szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) writes: > Instead of making a "consensus sequence protein" making random >mutations in one protein you'll have the same result. These brings the >advantage that you have the 3d structure (of the protein before mutated) and >also that a lot of work was already done with random mutations. Not exactly, what I had in mind. The whole point of the consensus sequence is that here is a sequence that is "in common" to a family of similar proteins. Any critical residues for activity and folding should be accounted for in the consensus sequence. But are they? We'll never know unless someone tries the experiment. The random mutations would have to be numerous and to get the same level of information as I tried to explain above. On the other hand, perhaps mutations as directed by the consensus sequence could be useful. > Ps. I sent this message yesterday but I had no replays. Tried to send you a reply but the message bounced. -- Jeff Nauss Texas A&M Class of '77 Department of Chemistry Gig 'em, Aggies! University of Cincinnati From owner-proteins@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!gatech!swrinde!cs.utexas.edu!geraldo.cc.utexas.edu!folate.cm.utexas.edu!appling From: Dean R. Appling Newsgroups: bionet.molbio.proteins Subject: mitoplasts -large scale Date: 3 Mar 1994 19:43:13 GMT Organization: University of Texas at Austin Lines: 11 Distribution: world Message-ID: <2l5ekh$emp@geraldo.cc.utexas.edu> NNTP-Posting-Host: folate.cm.utexas.edu X-UserAgent: Version 1.1.3 X-XXMessage-ID: X-XXDate: Thu, 3 Mar 94 19:42:22 GMT We are attempting to purify an enzyme from rat liver mitochondria that resides in the matrix. Unfortunately, there is a cytosolic isozyme of identical size that binds to the outer membrane of isolated mitochondria that we are unable to wash off. We thus need to prepare large amounts of mitoplasts for purification purposes. We have successfully used the digitonin procedure to subfractionate mitochondria on a small scale, but have not had much success scaling it up. Pedersen's Methods in Cell Biology chapter (Vol. XX, 1978) mentions a French press method for preparing mitoplasts that might be more amenable to scale up. Does anyone have experience with large scale mitoplast preps, or other ideas? Thanks. From owner-proteins@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!hobbes.physics.uiowa.edu!news.uiowa.edu!blue.weeg.uiowa.edu!blue.weeg.uiowa.edu!not-for-mail From: kpmurphy@blue.weeg.uiowa.edu (murphy kenneth p) Newsgroups: bionet.molbio.proteins Subject: Re: alpha helical coiled coils in proteins Date: 18 Feb 1994 13:22:40 -0600 Organization: University of Iowa, Iowa City, IA, USA Lines: 22 Distribution: bionet Message-ID: <2k34i0$170l@blue.weeg.uiowa.edu> References: <5C2B3F3EA6FF2090DC@JHUIGF.BITNET> NNTP-Posting-Host: blue.weeg.uiowa.edu In article <5C2B3F3EA6FF2090DC@JHUIGF.BITNET>, wrote: > >Hello Netters, >Can anybody help me understand the difference between coiled coils and >supercoils? I believe, the alpha helical coiled coils is a result of >packing interactions between parallel or antiparallel or relatively >staggered axes. It must be something analogous to the twisted beta >sheets then. What are those supercoils? I might be wrong. Pl.help me. > >--Geetha. Generally supercoiling refers to nucleic acids (especially plasmids) while coiled coils are a protein structural motif. Kip -- Dr. Kenneth P. Murphy e-mail: k-murphy@uiowa.edu Department of Biochemistry office: (319)335-8910 Univeristy of Iowa lab: (319)335-7936 Iowa City, IA 52242 FAX: (319)335-9570 From owner-proteins@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: PAPAGEORGIOU GEORGIOS Newsgroups: bionet.molbio.proteins Subject: INVITATION TO GREEK BIOSCIENTISTS Date: 4 Mar 1994 06:18:26 -0000 Lines: 45 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2l6jri$9rs@mserv1.dl.ac.uk> X-Char-Esc: 29 X-Charset: ELOT_928 Original-To: proteins@dl.ac.uk * * * * INVITATION TO GREEK BIOLOGICAL SCIENTISTS * * * * The Institute of Biology of the National Research Center Demokritos in Athens, Greece, is interested in compiling a list of Greek research scientists working in diverse fields of life sciences who might be interested in future staff openings at the Institute. The information will be used to formulate the expansion policy of the Institute. Please send brief memo including name, addresses (postal mail, e-mail, telefax, telephone), present affiliation and research area. A list of publications will be helpful. A rough sketch of research areas in the Institute of Biology includes, but it is not limited to, the following: BASIC BIOSCIENCE Mammalian gene expression; cytokines and oncogenes; human serum growth factors; cell regulation mechanisms; opioid peptides and receptors; transmembrane signals; lectines; photosynthesis (function, regulation, biogenesis); developmental theoretical biology. APPLIED BIOSCIENCE Environmental genotoxicity; radiation induced mutations; primary sea productivity and phytoplanckton; chemical communication of insects (feromones); management of insect populations; insect ecophysiology; insect nutrition; soil microbiology; uptake of radioactive nuclides by plants. Please disseminate this information to other interested scientists you may know. Thank you. Contact person: Dr. George C. Papageorgiou, Director NRC Demokritos, Institute of Biology Athens, Greece 153 10 _______________________________ Telefax : (301) 651 1767 Telephone : (301) 652 2018 E-mail: gcpap@cyclades.nrcps.ariadne-t.gr _______________________________  From owner-proteins@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!FOX.NSTN.NS.CA!ewright From: ewright@FOX.NSTN.NS.CA ("Edwin Wright") Newsgroups: bionet.molbio.proteins Subject: Generic Protein Sequence Date: 3 Mar 1994 23:51:06 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <71476.ewright@fox.nstn.ns.ca> NNTP-Posting-Host: net.bio.net Is it possible to construct a generic protein sequence from the existing protein database? Regards, ------- Edwin Wright 85 Spinnaker Drive, A-602 Halifax, Nova Scotia CANADA B3N 3E3 Telephone: (902) 477-5037 Email: ewright@fox.nstn.ns.ca =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Wed Mar 02 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: lfernand@crc.ac.uk (Miss L.M. Fernandez) Newsgroups: bionet.molbio.proteins Subject: raytide peptide substrate Date: 3 Mar 1994 15:08:08 -0000 Lines: 5 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2l4ugo$ars@mserv1.dl.ac.uk> content-length: 102 Original-To: proteins@dl.ac.uk does anyone know where I can obtain Raytide (peptide substrate for protein tyrosine kinase) from ? From owner-proteins@net.bio.net Thu Mar 03 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!usenet.ins.cwru.edu!lerc.nasa.gov!magnus.acs.ohio-state.edu!cis.ohio-state.edu!news.sei.cmu.edu!bb3.andrew.cmu.edu!cantaloupe.srv.cs.cmu.edu!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!husc10!robison1 Newsgroups: bionet.molbio.proteins Subject: Re: Huntington's Disease Message-ID: From: robison1@husc10.harvard.edu (Keith Robison) Date: 4 Mar 94 06:26:44 GMT References: <01H9IX9XMOVS929NS3@splava.cc.plattsburgh.edu> Distribution: bionet Organization: Harvard University, Cambridge, Massachusetts NNTP-Posting-Host: husc10.harvard.edu Lines: 37 GRAZIAWD@SPLAVA.CC.PLATTSBURGH.EDU ("William D. Graziadei") writes: >In a message from April Re: >>From: IN%"dzuckerm@haverford.edu" 3-MAR-1994 00:42:30.41 >> >>I am in desperate need of information bibliographical or otherwise >>related to Huntington's Disease, especially current treatment practices. >>It would be most appreciated. Please send any replies via the internet to >>my email address below. >-------------------------------------------------------------------------------- >Gopher and OMIM at Welch library (Johns Hopkins) is (was) a >god source. Search Hunt(ington) use to give a good hit. >However, lately I get error messages. Can anybody help April >(and me). I've tried Downs as well to no avail. The GDB gopher seems to be up right now, but I too had some problems recently (probably some re-tooling going on at Hopkins). GDB/OMIM now also has an E-mail server which can both search and retrieve. I believe it is based on the same IRX software used for NCBI's Retrieve server. Send a message with only "help" in the body to mailserv@gdb.org Good luck! Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI krobison@nucleus.harvard.edu From owner-proteins@net.bio.net Thu Mar 03 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!ihnp4.ucsd.edu!munnari.oz.au!news.uwa.edu.au!uniwa!uniwa!not-for-mail From: paulakyu@uniwa.uwa.edu.au (Paula K Yu) Newsgroups: bionet.molbio.proteins Subject: anti-rat's endothelium antibodies Date: 4 Mar 1994 16:46:56 +0800 Organization: The University of Western Australia Lines: 7 Message-ID: <2l6si0$r60@uniwa.uwa.edu.au> NNTP-Posting-Host: uniwa.uwa.edu.au X-Newsreader: TIN [version 1.2 PL2] Hello everyone, I'm looking for an anti-human platelet myosin antibody. If anyone knows where I can get them, please let me know. Thank you. Paula Yu From owner-proteins@net.bio.net Thu Mar 03 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: Generic Protein Sequence Message-ID: <1994Mar4.080609.16230@comp.bioz.unibas.ch> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Nntp-Posting-Host: biox.embnet.unibas.ch Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] References: <71476.ewright@fox.nstn.ns.ca> Distribution: bionet Date: Fri, 4 Mar 1994 08:06:09 GMT Lines: 154 In article <71476.ewright@fox.nstn.ns.ca>, ewright@FOX.NSTN.NS.CA ("Edwin Wright") writes: |> Is it possible to construct a generic protein sequence from the existing |> protein database? As the codon table is ambiguous, you will end up in several possibilities. Most protein database entriues have a crosslink to EMBL or GENBANK. You might want to us SRS (Sequence Retrieval System) from Thure Etzold for this purpose. We are collaborating with Thure and a _preliminary_ version of the GOPHER gateway to SRS is currently in the test phase. This gateway is capable of mapping data entries into other databases. The result is printed in GCG format (GCG Inc, commercial software). If you have Access to GOPHER, you might try the following. >>>> NOTE <<<< The following is DEVELOPMENTAL, and there is NO GUARANTEE that this interface will stay at the same links, location, or format. 1. About Gopher, and this bioftp site/ 2. Biology subject tree in Gopher/ 3. DIBUG [Discover Insight Biosym User Group] Mailing list/ --> 4. EMBNet BioInformation Resource Switzerland/ 5. GCG Software Manual/ 6. Infoservers in European Countries/ 7. and if you have suggestions or problems.... [ 7Jan94, 1kb]. 8. development site of GOPHER (U Minnesota)/ 9. selected USENET News/ 1. About EMBnet/ --> 2. Database/ 3. Hints/ 4. Info on this EMBNet Information Resource [ 7Jan94, 4kb]. 5. Other EMBnet Hosts and Sources of Information/ 6. Software/ 1. About these searches [18Jan94, 1kb]. 2. EMBL/ 3. EMBL updates/ --> 4. Experimental/ 5. FLYBASE / 6. GENBANK (Indiana)/ 7. More DNA searches/ 8. Protein databases (NIH)/ 9. general database searches (HOPKINS)/ --> 1. Experimental SRS gateway/ --> 1. Start to compost query on gopher.embnet.unibas.ch/ 2. Expert mode: Query directly getz at gopher.embnet.unibas.ch 1. Use EMBL (+updates)/ --> 2. Use SWISSPROT / 3. Use PIR International/ 4. Use NRL_3D (Xray structure sequences)/ 5. Use PROSITE / 6. Use PROSITEDOC / 7. Use BLOCKS / --> 1. Search ID in SWISSPROT/ 2. Search Definition in SWISSPROT/ 3. Search Accession Number in SWISSPROT/ 4. Search Author in SWISSPROT/ 5. Search Reference in SWISSPROT/ 6. Search Title in SWISSPROT/ 7. Search Keyword in SWISSPROT/ 8. Search Feature in SWISSPROT/ 1. Report directly from ID in SWISSPROT 2. Report MEDLINE entry from ID in SWISSPROT --> 3. Report EMBL entry from ID in SWISSPROT 4. Report PIR International entry from ID in SWISSPROT 5. Report NRL3D entry from ID in SWISSPROT 6. Report PROSITE entry from ID in SWISSPROT 7. Report PROSITEDOC entry from ID in SWISSPROT 8. Report BLOCKS entry from ID in SWISSPROT lqqqqqqqqqqqqqqqqqqqReport EMBL entry from ID in SWISSPROTqqqqqqqqqqqqqqqqqqqk x x x Words to search for calm_human x x x x [Cancel ^G] [Accept - Enter] x x x mqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqj --> 1. Query result overview. 2. File of Sequence Names . 3. embl:GGCALMA . 4. embl:GGCAM . 5. embl:GGCAM1 . 6. embl:GGCAM2 . 7. embl:GGCAM3 . 8. embl:GGCAM4 . 9. embl:GGCAM5 . 10. embl:GGCAM6 . 11. embl:HSCAM . 12. embl:HSCAMA . 13. embl:RNCAM . 14. embl:RNCAMA . 15. embl:RNCAMI1 . 16. embl:RNCAMI2 . 17. embl:RNCAMI3 . 18. embl:RNCAMII3 . 19. embl:RNCAMIII . 20. embl:RNRCM1 . 21. embl:XLCAMA . 22. embl:XLCAMB . 23. This search produced 20 hits. and the result is, report of query "Q1 = [SWISSPROT-ID:calm_human*]>EMBL" //////////////////////////////////////////////////////////////////////////////// ...searching "CALM_HUMAN*" CALM_HUMAN 1 entries library "swissprot": found 1 entries found "CALM_HUMAN*" in 1 entries retrieved 1 entries from index "id" Mapped to "embl" -> 20 entries //////////////////////////////////////////////////////////////////////////////// set "Q1" has 20 entries of type "Seq-ID" time of query: 4-Mar-1994 .... Maybe this helps. Regards Reinhard DISCLAIMER Note that the software mentioned resembles Computer Program(s) which require a license in order to be run unless stated otherwise in a state- ment codistributed with the software. The use of the program(s) was men- tioned within a specific problem or example and must not be used to con- clude that other software products cannot possibly do a similar job. -- +---------------------------+-------------------------------------------+ | Dr. Reinhard Doelz | Tel. x41 61 2672247 Fax x41 61 2672078 | | Biocomputing | electronic Mail doelz@urz.unibas.ch | |Biozentrum der Universitaet+-------------------------------------------+ | Klingelbergstrasse 70 | EMBnet embnet@comp.bioz.unibas.ch | |CH 4056 Basel SWITZERLAND | Switzerland gopher.embnet.unibas.ch | +---------------------------+------------- http://beta.embnet.unibas.ch/ From owner-proteins@net.bio.net Thu Mar 03 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!bcc.ac.uk!bsm.bioc.ucl.ac.uk!martin From: martin@bsm.bioc.ucl.ac.uk (Andrew Martin) Subject: Re: Protein Structure Prediction Software Message-ID: <1994Mar4.095512.49616@ucl.ac.uk> Date: Fri, 4 Mar 1994 09:55:12 GMT References: <2l4skp$bur@fermat.mayo.edu> Organization: University College London Keywords: Protein Structure, Amino Acid Sequence, 3-d Structure Prediction Lines: 30 In article <2l4skp$bur@fermat.mayo.edu>, eberhard@Mayo.EDU (norm eberhardt) writes: |> I am aware of Chou-Fasman types of programs which predict secondary |> structure on the basis of amino acid sequence. Are there similar programs |> available that model tertiary (3-d) structure on the basis of amino acid sequence |> only? |> |> Thanks, |> Norman L. Eberhardt |> Unfortunately this is a rather simplistic request! If only there were such programs we could put all the crystallographers out of a job :-) Secondary structure prediction rarely does better than 60-70% accurate. However, many people are working on this area using a number of homology based methods and a fairly new technique of sequence threading (trying to find the best tertiary fold to accomodate a sequence), but it will be a good few years before one will get reliable results. Now if you already know pretty much what your structure will look like (i.e. you already have the structure of one, or preferably more, closely related structures), that's a different matter and we can do pretty well. Andrew -- **************************************************************************** Dr. Andrew C.R. Martin, University College London & SciTech Software INTERNET: martin@bsm.bioc.ucl.ac.uk -OR- amartin@scitec.adsp.sub.org JANET: martin@uk.ac.ucl.bioc.bsm UUCP: {uunet|rutgers}!cbmehq!cbmuk!scitec!amartin **************************************************************************** From owner-proteins@net.bio.net Thu Mar 03 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!umn.edu!lynx.unm.edu!dns1.NMSU.Edu!malucero From: malucero@nmsu.edu (Mary Elyse Lucero) Newsgroups: bionet.molbio.proteins Subject: Xenobiotic Nitro-reduction Enzymes Date: 4 Mar 1994 17:55:30 GMT Organization: New Mexico State University, Las Cruces, NM Lines: 16 Message-ID: <2l7smiINNljl@dns1.NMSU.Edu> NNTP-Posting-Host: dante.nmsu.edu X-Newsreader: TIN [version 1.2 PL1] Does anyone out there know of any reviews or other references describing enzymes or classes of enzymes which are responsible for reduction of nitro- groups on nitroaromatics or other xenobiotic compounds? In vivo, these nitro groups are often converted to amino-groups. This has been well documented through radiolabeled metabolite studies. However, these studies rarely examine the enzymes involved. I have read up on nitrate and nitrite reductase enzymes, but so far have found nothing to suggest that these enzymes act on anything other than free nitrate/nitrite. I would very much appreciate any references you can suggest. Thanks! From owner-proteins@net.bio.net Thu Mar 03 22:00:00 1994 Path: biosci!FOX.NSTN.NS.CA!ewright From: ewright@FOX.NSTN.NS.CA ("Edwin Wright") Newsgroups: bionet.molbio.proteins Subject: Protein Sequence Database Date: 4 Mar 1994 10:41:58 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <24145.ewright@fox.nstn.ns.ca> NNTP-Posting-Host: net.bio.net Does anyone know if it is possible to obtain a listing of any protein sequence database sorted by increasing sequence length (i.e. number of residues)? Regards, ------- Edwin Wright 85 Spinnaker Drive, A-602 Halifax, Nova Scotia CANADA B3N 3E3 Telephone: (902) 477-5037 Email: ewright@fox.nstn.ns.ca =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Thu Mar 03 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!gumby!wmichgw!ou_lehrman From: ou_lehrman@wmich.edu (Russ_Lehrman) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: determining oligomeric structure of a protein Message-ID: <1994Mar4.212227.15406@wmichgw> Date: 4 Mar 94 21:22:27 EST References: <2l675s$mna@charm.magnus.acs.ohio-state.edu> Organization: Western Michigan University Lines: 28 Xref: biosci bionet.molbio.proteins:1497 bionet.molbio.methds-reagnts:12104 In article <2l675s$mna@charm.magnus.acs.ohio-state.edu>, rsaldanh@magnus.acs.ohio-state.edu (Roland J Saldanha) writes: > I am working on the mitochondrial tyrosyl synthetase that functions as both a > synthetase and as a facilitator of group I intron splicing. In characterizing > the protein we find that it elutes from gel filtration columns with an apparent > molecular weight of a tetramer (monomer MW=72,000). However the protein > crosslinks as a dimer with dimethyl suberimidate and glutaraldehyde. This > would suggest a highly elongated structure that has an aberrant mobility > (reflecting the elongated size) in gel filtration. It isn't clear from this evidence that the protein is only a dimer. For example, your crosslinking agents are on the short side, it may be that the subunits have functional groups that are placed appropiately apart for reaction. , b > I would welcome suggestions for other methods for demonstrating the oligomeric > structure of the protein. I am aware that sedimentation analysis is the best > method of approaching this problem but do not have access to an analytical > ultracentrifuge and would welcome collaborative offers from anyone who has a > machine. Try dynamic light scatter, if its available. For analytical ultracentrifugation, you may want to talk to Dr. Emory Braswell at University of Conneticut. Good luck/. > We would also like to try native page but the protein is very basic (computer > calculated pI of 10.3). I would thus welcome suggestions for native gels of > basic proteins and suitable standards for basic proteins. From owner-proteins@net.bio.net Thu Mar 03 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!bnr.co.uk!corpgate!news.utdallas.edu!wupost!kuhub.cc.ukans.edu!news.umkc.edu!SEMOVM.SEMO.EDU Newsgroups: bionet.molbio.proteins Subject: Re: Hormone Bovine Somatotropin Message-ID: <03MAR94.20435146.0065@SEMOVM.SEMO.EDU> From: SL64STU Date: 03 MAR 94 18:55:17 CST Sender: usenet@SEMOVM.SEMO.EDU Organization: University of Missouri - Kansas City NNTP-Posting-Host: semovm.semo.edu Lines: 6 INFORMATION ON BST NEEDED AS SOON AS POSSIBLE. IT IS NEEDED FOR AN HONORS RESEARCH PAPER FOR MY PRINCIPLES OF HEREDITY CLASS. PLEASE HELP ME. THE PAPER IS DUE AT THE END OF APRIL, BUT THE ROUGH DRAFT IS DUE AT THE END OF MARCH. I ALSO NEED THE E-MAIL ADDRESS FOR MONSANTO IN ST. LOUIS MISSOURI. THANK YOU FOR YOUR TIME. From owner-proteins@net.bio.net Fri Mar 04 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!athena.mit.edu!dresnick From: dresnick@athena.mit.edu (David I Resnick) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: determining oligomeric structure of a protein Date: 5 Mar 1994 21:23:21 GMT Organization: Massachusetts Institute of Technology Lines: 55 Message-ID: References: <2l675s$mna@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: alfredo.mit.edu In-reply-to: rsaldanh@magnus.acs.ohio-state.edu's message of 4 Mar 1994 02:42:04 GMT Xref: biosci bionet.molbio.proteins:1502 bionet.molbio.methds-reagnts:12133 In article <2l675s$mna@charm.magnus.acs.ohio-state.edu> rsaldanh@magnus.acs.ohio-state.edu (Roland J Saldanha) writes: I am working on the mitochondrial tyrosyl synthetase that functions as both a synthetase and as a facilitator of group I intron splicing. In characterizing the protein we find that it elutes from gel filtration columns with an apparent molecular weight of a tetramer (monomer MW=72,000). However the protein crosslinks as a dimer with dimethyl suberimidate and glutaraldehyde. This would suggest a highly elongated structure that has an aberrant mobility (reflecting the elongated size) in gel filtration. I would welcome suggestions for other methods for demonstrating the oligomeric structure of the protein. I am aware that sedimentation analysis is the best method of approaching this problem but do not have access to an analytical ultracentrifuge and would welcome collaborative offers from anyone who has a machine. Gel filtration gives you elution based on Stokes radius, not really on molecular weight -- unless of course your standards are all the same shape and are the same shape as your protein. You can use the Stokes radius you get from gel filtration and a sedimentation velocity that you can get from a prep ultracentrifuge (use a glycerol or sucrose gradient to prevent convection) to calculate a molecular weight. You also need a partial specific volume for this calculation - if you know the amino acid comp you can calculate this, if not you can determine that as well. This approach is a bit crude, but it works. If the issue is tetramer vs dimer I'd think it would be adequate. Sedimentation equilibrium in an analytical ultracentrifuge is better, assuming you have modest amounts of pure material. As I understand it, there are also methods based on light scattering for such determinations. I'd also go for some different crosslinkers - try long spacer arms, different active groups, and maybe even unspecific photoactivatable ones (see the Pierce catalog). We would also like to try native page but the protein is very basic (computer calculated pI of 10.3). I would thus welcome suggestions for native gels of basic proteins and suitable standards for basic proteins. As far as native electrophoresis, you could try it with agarose. You need a fairly decent seiving though, as the charge-to-mass of your oligomers would of course be the same as your monomers. The only problem with this approach is interpreting the result. Say you do a concentration curve with your protein (labelled with 125I or something) and you see a concentration dependant retardation of mobility. How do you know what has happened? You may get the affinity of the interaction, but it isn't clear that you'd expect to see any intermediates if your final oligomerization state is a tetramer since association could be highly cooperative. Good luck! -- David Resnick dresnick@athena.mit.edu From owner-proteins@net.bio.net Fri Mar 04 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!trane.uninett.no!sunic!pipex!lyra.csx.cam.ac.uk!pavo.csi.cam.ac.uk!macx16.mrc-lmb.cam.ac.uk!user From: sanz@mrc-lmb.cam.ac.uk (Jesus M. Sanz) Subject: Re: determining oligomeric structure of a protein Message-ID: Followup-To: bionet.molbio.proteins,bionet.molbio.methds-reagnts Sender: news@infodev.cam.ac.uk (USENET news) Nntp-Posting-Host: macx16.mrc-lmb.cam.ac.uk Organization: Medical Research Council (Cambridge, UK) References: <2l675s$mna@charm.magnus.acs.ohio-state.edu> Date: Sat, 5 Mar 1994 12:02:07 GMT Lines: 37 In article <2l675s$mna@charm.magnus.acs.ohio-state.edu>, rsaldanh@magnus.acs.ohio-state.edu (Roland J Saldanha) wrote: > I am working on the mitochondrial tyrosyl synthetase that functions as both a > synthetase and as a facilitator of group I intron splicing. In characterizing > the protein we find that it elutes from gel filtration columns with an apparent > molecular weight of a tetramer (monomer MW=72,000). However the protein > crosslinks as a dimer with dimethyl suberimidate and glutaraldehyde. This > would suggest a highly elongated structure that has an aberrant mobility > (reflecting the elongated size) in gel filtration. > I would welcome suggestions for other methods for demonstrating the oligomeric > structure of the protein. I am aware that sedimentation analysis is the best > method of approaching this problem but do not have access to an analytical > ultracentrifuge and would welcome collaborative offers from anyone who has a > machine. > We would also like to try native page but the protein is very basic (computer > calculated pI of 10.3). I would thus welcome suggestions for native gels of > basic proteins and suitable standards for basic proteins. You could also try another crosslinking reagent with a different specificity. For instance, water-soluble carbodiimides are good for crosslinking between carboxylates, and may be useful where dimethyl suberimidate and glutaraldehyde cannot work. You can find a nice review about bifunctional reagents in Methods Enzymology (91), 580 (1983). Cheers -- Dr. Jesus M. Sanz Tf. (0223) 402146 Centre for Protein Engineering. Fax.(0223) 402140 Hills Road, e-mail:sanz@mrc-lmb.cam.ac.uk Cambridge CB2 2QH, U.K. "Life is hard and happiness is ephemeral" -- From owner-proteins@net.bio.net Fri Mar 04 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!agate!ihnp4.ucsd.edu!sdd.hp.com!saimiri.primate.wisc.edu!news.doit.wisc.edu!sweetprotein.ahabs.wisc.edu!user From: ming@ahabs.wisc.edu (Ding Ming) Newsgroups: bionet.molbio.proteins Subject: Re: determining oligomeric structure of a protein Followup-To: bionet.molbio.proteins,bionet.molbio.methds-reagnts Date: Sat, 05 Mar 1994 10:48:38 -0600 Organization: University of Wisconsin-Madison Lines: 23 Message-ID: References: <2l675s$mna@charm.magnus.acs.ohio-state.edu> <1994Mar4.212227.15406@wmichgw> NNTP-Posting-Host: sweetprotein.ahabs.wisc.edu > > > We would also like to try native page but the protein is very basic (computer > > calculated pI of 10.3). I would thus welcome suggestions for native gels of > > basic proteins and suitable standards for basic proteins. Check H. R. Maurer's "Disc Electrophoresis and related techniques of PAGE", 1971. There is an excellent acid system for native page of basic protein and I modified it with a gradient gel and it gave out a reasonable resolution. For protein standard, you may use Thaumatin or Monellin and both of them are very water soluble and available from Sigma. Keep in mind that these standards can only tell you if the system runs ok and nothing else can be concluded from them because they have different m/e or e/m from your sample. Good luck! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Ding Ming University of Wisconsin-Madison Telephone: (608)265-3544 Fax: (608)262-7420 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-proteins@net.bio.net Fri Mar 04 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!usc!yeshua.marcam.com!news.kei.com!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!alfredo.MIT.EDU!mingliu From: mingliu@mit.edu (Minghsun Liu) Newsgroups: bionet.molbio.proteins Subject: Intro to NMR in protein structure determination? Date: 5 Mar 1994 17:57:40 GMT Organization: Massachvsetts Institvte of Technology Lines: 13 Message-ID: <2lah6k$aa1@senator-bedfellow.MIT.EDU> NNTP-Posting-Host: alfredo.mit.edu X-Newsreader: TIN [version 1.2 PL2] Hi, I am wondering if someone can recommend good introductory book(s) on NMR, especially on application of the techniques to protein structure determination. I will summarize responses if there is enough interest. Much thanx in advance! - Minghsun Liu From owner-proteins@net.bio.net Sat Mar 05 22:00:00 1994 Path: biosci!FOX.NSTN.NS.CA!ewright From: ewright@FOX.NSTN.NS.CA ("Edwin Wright") Newsgroups: bionet.molbio.proteins Subject: Structural Prediction Date: 7 Mar 1994 02:34:11 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <81181.ewright@fox.nstn.ns.ca> NNTP-Posting-Host: net.bio.net The following statement appeared in Nature: "There are now many examples, in both functionally similar and dissimilar proteins, where the sequence similarity is statistically insignificant (less than 20%) and yet the same topology is observed." (M. Thornton, T.P. Flores, D.T. Jones, M.B. Swindells, Nature, 354, 105, (1991) - p. 106) If this situation is common, then it seems that notwithstanding functional similarity/dissimilarity, topological similarity is dependent on a meta- sequential order, not readily apparent at the level of independently displayed sequences. Presumably, this meta-sequential order is governed by one of the following possibilities: 1. There is a distinct set of sequences (the basis of which is unknown) responsible for a specific topology. 2. The set of sequences responsible for a specific topology are actually manifesting conserved positions (albeit non-conserved residues) of a single (unknown) meta-sequence. Is anyone aware of any research with respect to the second possibility? Regards, ------- Edwin Wright 85 Spinnaker Drive, A-602 Halifax, Nova Scotia CANADA B3N 3E3 Telephone: (902) 477-5037 Email: ewright@fox.nstn.ns.ca =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Sun Mar 06 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!alberta!quartz.ucs.ualberta.ca!warren.biology.ualberta.ca!wgallin From: wgallin@gpu.srv.ualberta.ca (Warren Gallin) Newsgroups: bionet.molbio.proteins Subject: Re: Shared epitopes prediction? Followup-To: bionet.molbio.proteins Date: Mon, 7 Mar 94 16:40:22 GMT Organization: University of Alberta Lines: 35 Message-ID: References: NNTP-Posting-Host: warren.biology.ualberta.ca X-Newsreader: VersaTerm Link v1.1.4 In Article , mbxfd@unicorn.nott.ac.uk (Fergus Doherty) wrote: >Perhaps someone can help me with a problem. An antibody detects >procarboxypeptidase B in rat pancreas, but the antibody is to an unrelated >protein. Comparing the sequence of the protein to which the ab was raised >(165 aa) versus procarboxypeptidase B (>400 aa) with the GCG BESTFIT >program shows 21% identity, 42% similarity. 21% identity is probably not >significant as the identical aa are spread over the sequence of the smaller >protein, there is no string of identical or non-identical aa that could be >a common epitope. Is there another program that might do this comparison >better, ie look for a small (6-10) run of identical/near identical aa (that >might be the common epitope)? Could it be an epitope that depends on some >secondary structure (retained or regained following SDS-PAGE and Western >blotting) so that the epitope consists of residues close in space but >non-adjacent? What are the chances of this? If so is it possible to check >for this with a suitable algorithm? Any help appreciated. You might consider another possibility, that the antigen used to raise the antibody was contaminated with procarboxypeptidase. What was the antigen and how was it prepared? Were other people working with procarboxypeptidase in the same lab (possible source of contamination)? Is it only the procarboxypeptidase that is reacting, and not the mature carboxypeptidase? That might relaly narrow it down. Does the preimmune serum not react with the procarboxypeptidase? A lot of rabbits have positive sera for different proteins even before they are immunized. This sounds like one of those problems that might be better explained by a technical glitch than by abtruse epitope similarities. On the other hand, with antibodies many things are possible, especially with polyclonal antibodies. I'm afraid this isn't much help in your search for algorithms, but I've seen the kinds of phenomena suggested above actually happen, so you might want to follow them up. Warren Gallin, Department of Zoology, University of Alberta wgallin@gpu.srv.ualberta.ca From owner-proteins@net.bio.net Sun Mar 06 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!zaphod.crihan.fr!univ-lille1.fr!cict.fr!reseau.onecert.fr!marechal From: marechal@reseau.onecert.fr (marechal) Newsgroups: bionet.molbio.proteins Subject: Help! Anti-electroosmotic solvents... Date: 7 Mar 1994 15:14:26 GMT Lines: 16 Distribution: world Message-ID: <2lfgci$hp2@reseau.cict.fr> Reply-To: marechal@reseau.onecert.fr (marechal) NNTP-Posting-Host: 134.212.99.1 Hi everybody! I am currently looking for solvents in electrophorese, which reduce electroosmotic flows... Any suggestion would be welcome, from the best-known to the least, I am only searching for a maximum of ideas... Please, if you have any suggestion, e-mail me (marechal@reseau.onecert.fr), or followup... Thanks for your help!!! CHRIS. marechal@reseau.onecert.fr From owner-proteins@net.bio.net Sun Mar 06 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!bipin From: bipin@iastate.edu (Bipin K Dalmia) Newsgroups: bionet.general,bionet.molbio.proteins Subject: experiences with pET vectors from novagen Date: 7 Mar 1994 13:49:09 GMT Organization: Iowa State University, Ames, Iowa (USA) Lines: 17 Distribution: world Message-ID: <2lfbcl$6r6@news.iastate.edu> NNTP-Posting-Host: class1.iastate.edu Xref: biosci bionet.general:8137 bionet.molbio.proteins:1504 i'm looking for +ve and -ve experiences that you have had with the pET expression vectors from Novagen. more specifically with the N-terminal his.tag systems. i have to overexpress a vareity of proteins and i have chosen this system because it offers the advantage of purification in the presence of denaturants. most proteins overexpressed do form inclusion bodies don't they! also, anyone yet tried the new s.tag system from novagen? bip -- bipin k. dalmia the other night i was lying on my bed, looking bipin@iastate.edu up at the beautiful stars, and i said to myself, n2.bkd@isumvs.iastate.edu 'where the F*CK is my ROOF !!' -- From owner-proteins@net.bio.net Sun Mar 06 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!uknet!warwick!nott-cs!macfd.biochem.nottingham.ac.uk!user From: mbxfd@unicorn.nott.ac.uk (Fergus Doherty) Subject: Shared epitopes prediction? Message-ID: Followup-To: bionet.molbio.proteins Sender: news@cs.nott.ac.uk Nntp-Posting-Host: macfd Organization: Nottingham University, UK. Date: Mon, 7 Mar 94 14:24:58 GMT Lines: 21 Perhaps someone can help me with a problem. An antibody detects procarboxypeptidase B in rat pancreas, but the antibody is to an unrelated protein. Comparing the sequence of the protein to which the ab was raised (165 aa) versus procarboxypeptidase B (>400 aa) with the GCG BESTFIT program shows 21% identity, 42% similarity. 21% identity is probably not significant as the identical aa are spread over the sequence of the smaller protein, there is no string of identical or non-identical aa that could be a common epitope. Is there another program that might do this comparison better, ie look for a small (6-10) run of identical/near identical aa (that might be the common epitope)? Could it be an epitope that depends on some secondary structure (retained or regained following SDS-PAGE and Western blotting) so that the epitope consists of residues close in space but non-adjacent? What are the chances of this? If so is it possible to check for this with a suitable algorithm? Any help appreciated. Fergus Doherty, dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH Tel: 602 709366 FAX 602 422225 Internet: mbxfd@unicorn.nott.ac.uk From owner-proteins@net.bio.net Sun Mar 06 22:00:00 1994 Newsgroups: bionet.molbio.proteins,bionet.general,bionet.molbio.embldatabank,bionet.molbio.gene-linkage,bionet.molbio.swiss-prot,bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!torn!utnut!utcsri!newsflash.concordia.ca!sifon!VM1.MCGILL.CA From: BAEV Subject: Peptide Motif Search by e-mail Message-ID: <07MAR94.17195731.0096@VM1.MCGILL.CA> Lines: 8 Sender: usenet@MUSICA.MCGILL.CA Organization: McGill University Date: Mon, 7 Mar 1994 20:55:19 GMT Xref: biosci bionet.molbio.proteins:1509 bionet.general:8144 bionet.molbio.embldatabank:297 bionet.molbio.gene-linkage:295 bionet.molbio.swiss-prot:1 bionet.software:7502 Dear colleagues...I would appreciate any suggestions on peptide motif search programs available on electronic mail (e-mail) servers around the world. Thank you in advance. Nikolai Baeff, M.D. McGill University, Canada mdnb@musica.mcgill.ca From owner-proteins@net.bio.net Sun Mar 06 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!torn!watserv2.uwaterloo.ca!peptidarus.UWaterloo.ca!ltaylor From: ltaylor@peptidarus.UWaterloo.ca (Lorne Taylor) Subject: Re: Intro to NMR in protein structure... Message-ID: Sender: news@watserv2.uwaterloo.ca Organization: University of Waterloo References: <2D7B568E@coursmtp.nrc.ca> Distribution: bionet Date: Mon, 7 Mar 1994 21:16:17 GMT Lines: 32 In article <2D7B568E@coursmtp.nrc.ca>, Prasad@biologysx.lan.nrc.ca ("Prasad, Krishna") writes: > >I am wondering if someone can recommend good introductory book(s) on NMR, > >especially on application of the techniques to protein structure > >determination. > >-Mingshun Liu > _______________________________ > I would recommend the following: > > (1) "Modern NMR Techniques for Chemistry Research" (Andrew Derome, Pergamon > Press, 1987). ISBN #0-08-32513-0 > > (2) "Biological Applications of Magnetic Resonance" (ed. R.G. Shulman, > Academic Press, 1979). ISBN # 0-12-640750-9 > > (3) Methods in Enzymology, "NMR" Vol. 176 & 177 (Ed. N. J. Oppenheimer & > T. L. James). Academic Press, 1989, 1990. > > These are the books that come to my mind, first. > Good Luck! > > Krishna Prasad, > NRC Institute for Biological Sciences > Ottawa, Ontario K1A 0R6, Canada > Two other books you might think about are 1) "NMR of Proteins and Nucleic Acids" Kurt Wuthrich, Wiley Interscience Press 1986 ISBN #0-471-82893-9 2) "NMR of Macromolecules - A Practical Approach" editor - G.C.K. Roberts IRL Press 1993, ISBN #0-19-963224-3 Hope this helps Lorne From owner-proteins@net.bio.net Sun Mar 06 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!sdd.hp.com!col.hp.com!csn!magnus.acs.ohio-state.edu!bhuang From: bhuang@magnus.acs.ohio-state.edu (Baohua Huang) Newsgroups: bionet.molbio.proteins Subject: Apparent MW of protein on-PAGE gel > real MW? Date: 7 Mar 1994 21:40:08 GMT Organization: The Ohio State University Lines: 12 Message-ID: <2lg6vo$9s7@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: bottom.magnus.acs.ohio-state.edu Hi, everyone. A fusion protein I expressed in E. coli has a apparent MW on SDS-PAGE gel ~5 kd lager than it's calculated MW. This protein is 303 aa residues with a calculated MW of 35 kd but it runs at 40 kd position on SDS-PAGE. The protein has very high content of basic amino acids (32 lysines, 20 arginine and 16 histidines). My question is : does high content of basic residues make a protein run slower? I would apreciate very much any hints to my question. Baohua Huang Ohio state Univ. From owner-proteins@net.bio.net Sun Mar 06 22:00:00 1994 Path: biosci!biologysx.lan.nrc.ca!Prasad From: Prasad@biologysx.lan.nrc.ca ("Prasad, Krishna") Newsgroups: bionet.molbio.proteins Subject: Intro to NMR in protein structure... Date: 7 Mar 1994 16:30:13 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <2D7B568E@coursmtp.nrc.ca> NNTP-Posting-Host: net.bio.net >I am wondering if someone can recommend good introductory book(s) on NMR, >especially on application of the techniques to protein structure >determination. >-Mingshun Liu _______________________________ I would recommend the following: (1) "Modern NMR Techniques for Chemistry Research" (Andrew Derome, Pergamon Press, 1987). ISBN #0-08-32513-0 (2) "Biological Applications of Magnetic Resonance" (ed. R.G. Shulman, Academic Press, 1979). ISBN # 0-12-640750-9 (3) Methods in Enzymology, "NMR" Vol. 176 & 177 (Ed. N. J. Oppenheimer & T. L. James). Academic Press, 1989, 1990. These are the books that come to my mind, first. Good Luck! Krishna Prasad, NRC Institute for Biological Sciences Ottawa, Ontario K1A 0R6, Canada From owner-proteins@net.bio.net Sun Mar 06 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!swrinde!ihnp4.ucsd.edu!library.ucla.edu!news.ucdavis.edu!Dave.Bates From: dobates@ucdavis.edu (Dave Bates) Subject: Protein Kinase peptide inhibitors Message-ID: X-Posted-From: InterNews 1.0@rocky.ucdavis.edu. Sender: -Not-Authenticated-[1543] Organization: University of California, Davis Date: Tue, 8 Mar 1994 04:15:30 GMT Xdisclaimer: No attempt was made to authenticate the sender's name. Lines: 17 Does anyone know of any natural or synthetic peptide inhibitors which are specific for kinases involved in the signal transduction, or cell signalling, or cytoskeltal pathways, eg Myosin Light Chain Kinase, Protein Kinase C, MAP Kinase, etc. They have to be peptides/proteins, preferably which have been sequenced, or which have cDNAs available. The only one like this that I'm aware of, or could find in a library search were cAMPD dependent PKI, and an MLCK inhibitor which also inhibits the phosphatase, and may not be as useful to me as I had hoped. Thanks ---------------------------------------------------------------------- Dave Bates, dobates@ucdavis.edu Department of Human Physiology, University of California at Davis ---------------------------------------------------------------------- From owner-proteins@net.bio.net Sun Mar 06 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!cs.utexas.edu!uunet!kelso.abbott.com!rand!matiasm From: matiasm@rand Newsgroups: bionet.molbio.proteins Subject: Elution of High Affinity PcAb Date: 7 Mar 94 18:27:34 CST Organization: Abbott Laboratories Lines: 11 Message-ID: <1994Mar7.182734.1@rand> NNTP-Posting-Host: randb.abbott.com Hello Netters, I'm a first time user of this medium. I am having a problem eluting off PcAb to p53 (Science Mag's "Molecule of the Year") from an antigen affinity column. I've tried low pH (2.6) glycine, 3 Molar MgCl2, and combinations thereof. I've also tried an electroelution method with no apparent luck. Any suggestions would be welcome. This 'b*#ch' of a protein seems to have a pretty high affinity to our PcAb. Thanks in advance! Matt "AbboGrunt" From owner-proteins@net.bio.net Mon Mar 07 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!zaphod.crihan.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!nedcu0!miostri From: David.Strike@imt.unine.ch Newsgroups: bionet.molbio.proteins Subject: pI values Message-ID: <1994Mar8.133439.2196@nedcu0> Date: 8 Mar 94 13:34:39 MET Organization: University of Neuchatel, Switzerland Lines: 11 8/3/94. Hello everybody, I wonder if anyone can tell me where to find tables of protein solubilities and pI values, particularly for oxidase type enyzmes ? Thanks in advance David Strike (david.strike@neimt1.unine.ch) From owner-proteins@net.bio.net Mon Mar 07 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!umn.edu!msus1.msus.edu!vax1.mankato.msus.edu!vengeance Newsgroups: bionet.molbio.proteins Subject: Omaha Project Message-ID: <1994Mar8.085024.2374@vax1.mankato.msus.edu> From: vengeance@vax1.mankato.msus.edu Date: 8 Mar 94 08:50:24 -0500 Organization: Mankato State University Lines: 9 I am trying to build a list of names and E-Mail addresses of people in the Omaha Nebraska area for a school related project. If you live in Omaha or go to school there or know someone that does and will be around for three months or more, please reply via E-Mail to Vengeance@vax1.mankato.msus.edu. Thank you very much! Ryan Krueger From owner-proteins@net.bio.net Mon Mar 07 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!Germany.EU.net!netmbx.de!zrz.TU-Berlin.DE!cs.tu-berlin.de!zib-berlin.de!tertius.in-berlin.de!mpimg-berlin-dahlem.mpg.de!jaensch Newsgroups: bionet.molbio.proteins Subject: LysC kDa ????????? Message-ID: <1994Mar8.153201.1@mpimg-berlin-dahlem.mpg.de> From: jaensch@mpimg-berlin-dahlem.mpg.de Date: 8 Mar 94 15:32:01 +0100 Distribution: world Organization: MPI f. Molekulare Genetik, Berlin Nntp-Posting-Host: pluto Nntp-Posting-User: jaensch Lines: 4 One short question, is their someone who know the molecular mass of LysC (endo-protease)??? From owner-proteins@net.bio.net Mon Mar 07 22:00:00 1994 Path: biosci!FOX.CCE.USP.BR!szeinfel From: szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) Newsgroups: bionet.molbio.proteins Subject: 3D-lattice protein Date: 8 Mar 1994 22:03:03 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: bionet Message-ID: NNTP-Posting-Host: net.bio.net Hi Netter's I would like to know if there is any program that takes as input a pdb file with atomic coordinates of a protein (let's say from Brokheaven protein databank) and inserts it in a cubic lattice (you define the dimensions of the unit cell) so that as output you have a matrix M(AxBxC) where each element of the matrix M(i,j,k)=1 if the this unit cell is ocuppied by one or more atoms or M(i,j,k)=0 if this unit cell is empty. By adjusting the dimension(l, where V(volume)=l^3) you can select how accurate is your lattice model if your unit cell have the dimensions of an atom, your lattice model will be equal to the atomic coordinates file. I'm not sure if I expressed well my idea but I'll appreciate any comment. Rafael Najmanovich From owner-proteins@net.bio.net Mon Mar 07 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!mentor.cc.purdue.edu!inet.d48.lilly.com!mcvax4.d48.lilly.com!swift Newsgroups: bionet.molbio.proteins Subject: Instant Block for Westerns Message-ID: <1994Mar8.160059.1@mcvax4.d48.lilly.com> From: swift@mcvax4.d48.lilly.com Date: 8 Mar 94 16:00:59 EST Distribution: world Nntp-Posting-Host: mcvax4.d48.lilly.com Lines: 5 Can anyone tell me the concentration and mol wt of the polyvinyl alchohol used in the Anal Biochem paper by Miranda et al "Instantanous Blocking ...". That journal has disappeared from our library. From owner-proteins@net.bio.net Mon Mar 07 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!cix.compulink.co.uk!rtfm From: rtfm@cix.compulink.co.uk ("Peter Smith") Subject: Brookhaven Protein Databank (PDB) Files. Message-ID: Organization: Abort, Retry, Fail Ltd Date: Tue, 8 Mar 1994 19:46:37 GMT X-News-Software: Ameol Lines: 9 Could someone please tell me where I can obtain the above files, presumably from a ftp site. thanks Peter Smith email: rtfm@cix.compulink.co.uk From owner-proteins@net.bio.net Tue Mar 08 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!swrinde!ihnp4.ucsd.edu!library.ucla.edu!news.ucdavis.edu!ALCOR.UCDAVIS.EDU!EZ007215 From: ez007215@ALCOR.UCDAVIS.EDU (ZHAOMIN 'THE VICTIM OF SCIENCE') Subject: Re: Apparent MW of protein on-PAGE gel > real MW? Message-ID: Sender: usenet@ucdavis.edu (News Guru) Reply-To: ez007215@ALCOR.UCDAVIS.EDU Organization: University of California, Davis References: <2lg6vo$9s7@charm.magnus.acs.ohio-state.edu> Date: Wed, 9 Mar 1994 04:16:17 GMT Lines: 19 In article <2lg6vo$9s7@charm.magnus.acs.ohio-state.edu>, bhuang@magnus.acs.ohio-state.edu (Baohua Huang) writes: >Hi, everyone. > >A fusion protein I expressed in E. coli has a apparent MW on SDS-PAGE gel ~5 kd >lager than it's calculated MW. This protein is 303 aa residues with a >calculated MW of 35 kd but it runs at 40 kd position on SDS-PAGE. The protein >has very high content of basic amino acids (32 lysines, 20 arginine and 16 >histidines). My question is : does high content of basic residues make a >protein run slower? >I would apreciate very much any hints to my question. > >Baohua Huang >Ohio state Univ. Is it possible that the protein has been modified posttranslationally, such as phosphorylation etc. Zhaomin UCDavis From owner-proteins@net.bio.net Tue Mar 08 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!news.cso.uiuc.edu!lwalsh From: lwalsh@nemo.life.uiuc.edu (Laura L. Walsh) Newsgroups: bionet.molbio.proteins Subject: Re: Brookhaven Protein Databank (PDB) Files. Date: 9 Mar 94 15:01:06 GMT Organization: University of Illinois at Urbana Lines: 11 Message-ID: References: NNTP-Posting-Host: nemo.life.uiuc.edu rtfm@cix.compulink.co.uk ("Peter Smith") writes: >Could someone please tell me where I can obtain the above files, >presumably from a ftp site. >thanks >Peter Smith >email: rtfm@cix.compulink.co.uk The files are at the ftp site: pdb.pdb.bnl.gov They should not be accessed for a couple of days, however, since they are currently doing an update. Try next week. Laura Walsh lwalsh@silibio.ncsa.uiuc.edu From owner-proteins@net.bio.net Tue Mar 08 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.intercon.com!panix!ddsw1!news.kei.com!newsstand.cit.cornell.edu!NewsWatcher!user From: lab_mac_hanson@qmrelay.mail.cornell.edu (Hanson Lab) Newsgroups: bionet.molbio.proteins Subject: antibody production in 8M urea Followup-To: bionet.molbio.proteins Date: Wed, 09 Mar 1994 09:58:39 -0500 Organization: Cornell University Lines: 15 Sender: dcr7@cornell.edu (Verified) Message-ID: NNTP-Posting-Host: 132.236.171.173 Has anyone ever tried making an antibody with a protein still in an 8M Urea solution? This protein is really insoluble and wound up in the above, and I hesitate to run it over a column or any such procedure for fear of losing it entirely. I would just like to inject as is, in an estimated solution of about 0.5 mg/ml. would appreciate knowing your outcome. thanks. Please reply to David Ruth DCR7@crux2.cit.cornell.edu From owner-proteins@net.bio.net Tue Mar 08 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!jmello1 From: jmello1@umbc.edu (mellott james ( bs bioc)) Newsgroups: bionet.molbio.proteins Subject: cAMP stability Date: 9 Mar 1994 18:01:48 GMT Organization: University of Maryland, Baltimore County Lines: 11 Message-ID: <2ll2uc$m0j@news.umbc.edu> NNTP-Posting-Host: rpc18.gl.umbc.edu X-Newsreader: TIN [version 1.2 PL2] In my biochemistry class , we're talking about glycolysis , TCA , etc., and one of the topics is the regulation of glycogen through a cAMP pathway . It is my understanding that a high concentration of cAMP is needed for the continuous activation of Protein kinase , and to inactivate the kinase , the concentration of cAMP is lowered through the activity of a phosphodiesterase . I recall hearing that caffeine stabilizes the concentration of cAMP in such a pathway , and I was wondering , since caffeine and adenine have similar structures , if caffeine acts as a competitive inhibitor with cAMP for the phosphodiesterase . Thanks in advance for any comments and/or references you can give me . From owner-proteins@net.bio.net Tue Mar 08 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!news-feed-2.peachnet.edu!gatech!birdie-blue.cis.pitt.edu!pitt.edu!ache.pharm.pitt.edu!user From: drg@prophet.pharm.pitt.edu (Duke Groebe) Newsgroups: bionet.molbio.proteins Subject: Re: Generic Protein Sequence Message-ID: Date: 9 Mar 94 14:26:53 GMT References: <71476.ewright@fox.nstn.ns.ca> Sender: news+@pitt.edu Followup-To: bionet.molbio.proteins Distribution: bionet Organization: University of Pittsburgh Lines: 17 In article <71476.ewright@fox.nstn.ns.ca>, ewright@FOX.NSTN.NS.CA ("Edwin Wright") wrote: > > Is it possible to construct a generic protein sequence from the existing > protein database? > Yes. Why would you want to? Duke ****************************************************************************** The opinions expressed here are my own. MY very own and NOBODY else's! I THOUGHT OF THEM FIRST, HA HA, AND YOU DIDN'T!! SEE!? There's my name up there! And the date - Ooohh, the DATE! That's important! HEE HEE, I'M GONNA BE RICH! DO YOU HEAR ME!? RICH!! HA HA!! They're mine...heh, heh, all mine.... GOD! I'm so smart! From owner-proteins@net.bio.net Tue Mar 08 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!gumby!wmichgw!ou_lehrman From: ou_lehrman@wmich.edu (Russ_Lehrman) Newsgroups: bionet.molbio.proteins Subject: Re: Apparent MW of protein on PAGE gel Message-ID: <1994Mar9.202838.15613@wmichgw> Date: 9 Mar 94 20:28:38 EST Organization: Western Michigan University Lines: 16 > A fusion protein I expressed in E. coli has a apparent MW on SDS-PAGE gel ~5 > kdlager than it's calculated MW. This protein is 303 aa residues with > acalculated MW of 35 kd but it runs at 40 kd position on SDS-PAGE. The > proteinhas very high content of basic amino acids (32 lysines, 20 arginine > and 16histidines). My question is : does high content of basic residues make > aprotein run slower?I would apreciate very much any hints to my question. Phosphorylation and other post-translational modifications are not typically observed in E. coli. Elution in a gel is not only a function of molecular weight. Often, reduction causes proteins to have apparently higher MW- even in the presence of SDS. You may be right to suspect the basicity of the protein. I can't address that from my experience but you may want to check papers that discuss the characterization of histones (cytochrome c also). The latter proteins are all highly basic. Russ From owner-proteins@net.bio.net Tue Mar 08 22:00:00 1994 Path: biosci!bcm!news.msfc.nasa.gov!europa.eng.gtefsd.com!howland.reston.ans.net!torn!csd.unb.ca!coranto.ucs.mun.ca!newton.physics.mun.ca!beavis From: beavis@newton.physics.mun.ca (Ron Beavis) Newsgroups: bionet.molbio.proteins Subject: Re: Apparent MW of protein on-PAGE gel > real MW? Date: 9 Mar 1994 19:45:47 GMT Organization: Memorial University of Nfld, St. John's, NF Lines: 22 Message-ID: <2ll91b$pbl@coranto.ucs.mun.ca> References: <2lg6vo$9s7@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: newton.physics.mun.ca In article ez007215@ALCOR.UCDAVIS.EDU writes: >In article <2lg6vo$9s7@charm.magnus.acs.ohio-state.edu>, bhuang@magnus.acs.ohio-state.edu (Baohua Huang) writes: >>Hi, everyone. >> >>A fusion protein I expressed in E. coli has a apparent MW on SDS-PAGE gel ~5 kd >>lager than it's calculated MW. This protein is 303 aa residues with a >>calculated MW of 35 kd but it runs at 40 kd position on SDS-PAGE. The protein >>has very high content of basic amino acids (32 lysines, 20 arginine and 16 >>histidines). My question is : does high content of basic residues make a >>protein run slower? >>I would apreciate very much any hints to my question. >> >>Baohua Huang >>Ohio state Univ. > >Is it possible that the protein has been modified posttranslationally, such as >phosphorylation etc. > >Zhaomin >UCDavis From owner-proteins@net.bio.net Tue Mar 08 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!sol.ctr.columbia.edu!news.kei.com!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!vongole.MIT.EDU!mingliu From: mingliu@mit.edu (Minghsun Liu) Newsgroups: bionet.molbio.proteins Subject: Summary: Intro to NMR in protein structure determination Date: 10 Mar 1994 02:58:53 GMT Organization: Massachvsetts Institvte of Technology Lines: 44 Message-ID: <2lm2dd$m36@senator-bedfellow.MIT.EDU> NNTP-Posting-Host: vongole.mit.edu X-Newsreader: TIN [version 1.2 PL2] Sorry for the delay for posting this summary. Here is the summary of replies to my query about good introductory text to NMR in protein structure determination. Many thanx to those who replied: Mathew Ravington, Kevin Gardner, mbarg@s-crim1.dl.ac.uk, John Cort, Prasad Krishna, Jo Ellen Stein, Lorne Taylor, and Christopher Cilley. The books mentioned by almost everyone is: "NMR of Proteins and Nucleic Acid" by Kurt Wuthrich (1986, Wiley) - general comments seem to be that it's a bit dated; and doesn't cover the newer techniques and the actual details of carrying out experiments to collect the data but is still a good intro. A more recent book mentioned by several is: "NMR of Macromolecues - A Practical Approach" edited by GCK Roberts (1993) - this book is fairly recent. (As a matte of fact, my favorite local tech book dealer, Quantum Books, said it was due out last November but the store hasn't received it yet.) And the three books mentioned in Prishad Krishna's post: (1) "Modern NMR Techniques for Chemistry Research" (Andrew Derome, Pergamon Press, 1987). ISBN #0-08-32513-0 (2) "Biological Applications of Magnetic Resonance" (ed. R.G. Shulman, Academic Press, 1979). ISBN # 0-12-640750-9 (3) Methods in Enzymology, "NMR" Vol. 176 & 177 (Ed. N. J. Oppenheimer & T. L. James). Academic Press, 1989, 1990. Book (1) was recommended to Jo Ellen Stein by someone who taught a grad-level NMR course. And finally, Brandon and Tooze's "Introduction to Protein Structure" was mentioned as one with a brief, one-chapter overview of the application of NMR. And that's pretty much it. Good luck and enjoy! - Ming From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!nntp.uio.no!usenet From: dave.buss@studorg.uio.no (Chuck An) Newsgroups: bionet.molbio.proteins Subject: Re: Structural Prediction Date: 10 Mar 1994 15:47:06 GMT Organization: NASA, Kennedy Space Center Lines: 44 Message-ID: <2lnfdq$otq@hermod.uio.no> References: <81181.ewright@fox.nstn.ns.ca> NNTP-Posting-Host: biotek04.uio.no X-Newsreader: WinVN version 0.80 In article <81181.ewright@fox.nstn.ns.ca>, ewright@FOX.NSTN.NS.CA ("Edwin Wright") says: > >The following statement appeared in Nature: > >"There are now many examples, in both functionally similar and dissimilar >proteins, where the sequence similarity is statistically insignificant (less >than 20%) and yet the same topology is observed." (M. Thornton, T.P. Flores, >D.T. Jones, M.B. Swindells, Nature, 354, 105, (1991) - p. 106) > >If this situation is common, then it seems that notwithstanding functional >similarity/dissimilarity, topological similarity is dependent on a meta- >sequential order, not readily apparent at the level of independently >displayed sequences. Presumably, this meta-sequential order is governed by >one of the following possibilities: > >1. There is a distinct set of sequences (the basis of which is unknown) > responsible for a specific topology. > >2. The set of sequences responsible for a specific topology are actually > manifesting conserved positions (albeit non-conserved residues) of a > single (unknown) meta-sequence. > >Is anyone aware of any research with respect to the second possibility? > >Regards, >------- >Edwin Wright >85 Spinnaker Drive, A-602 >Halifax, Nova Scotia >CANADA B3N 3E3 > >Telephone: (902) 477-5037 > >Email: ewright@fox.nstn.ns.ca >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= I think so. it has been noticed that proteins from different families and with quite big variation in sequences were found having both local ang gobal structural resemblance. they were able to be sort of superimposed on one another. I can't recall the details. I wander whether the 3D structures of proteins are the consequences of the combination of the amino acid residues, but not necessarily the definite permutation of the residues. From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!sdd.hp.com!sgiblab!news.cs.indiana.edu!babbage.ece.uc.edu!ucunix.san.uc.edu!ucunix.san.uc.edu!not-for-mail From: naussjl@ucunix.san.uc.edu (Jeffrey L Nauss) Newsgroups: bionet.molbio.proteins Subject: Re: Brookhaven Protein Databank (PDB) Files. Date: 10 Mar 1994 10:03:20 -0500 Organization: University of Cincinnati Lines: 11 Message-ID: <2lncro$eju@ucunix.san.uc.edu> References: NNTP-Posting-Host: ucunix.san.uc.edu In article rtfm@cix.compulink.co.uk ("Peter Smith") writes: >Could someone please tell me where I can obtain the above files, >presumably from a ftp site. There is an anonymous FTP site at pdb.pdb.bnl.gov. IP address 130.199.144.1 -- Jeff Nauss Texas A&M Class of '77 Department of Chemistry Gig 'em, Aggies! University of Cincinnati From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!gatech!birdie-blue.cis.pitt.edu!toads.pgh.pa.us!peaceful.cs.pitt.edu!user From: ethan+@pitt.edu (Ethan Benatan) Newsgroups: bionet.molbio.proteins Subject: Who called random coil a double misnomer? Followup-To: bionet.molbio.proteins Date: Thu, 10 Mar 1994 07:26:52 -0500 Organization: University of Pittsburgh Lines: 9 Distribution: world Message-ID: NNTP-Posting-Host: peaceful.cs.pitt.edu I'd like to use that quotation ("it's not random and it's not coil!"), and I can't remember where I heard it- if anyone knows who deserves the credit, please let me know so that I can assign it appropriately. Thanks, Ethan Benatan ethan+@pitt.edu From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!gatech!birdie-blue.cis.pitt.edu!toads.pgh.pa.us!peaceful.cs.pitt.edu!user From: ethan+@pitt.edu (Ethan Benatan) Newsgroups: bionet.molbio.proteins Subject: Re: Brookhaven Protein Databank (PDB) Files. Followup-To: bionet.molbio.proteins Date: Thu, 10 Mar 1994 07:19:26 -0500 Organization: University of Pittsburgh Lines: 19 Distribution: world Message-ID: References: NNTP-Posting-Host: peaceful.cs.pitt.edu You may want to try Gopher instead of ftp; it makes for easier access. You can search the header text (down to the cryst1 record) and get a list of hits, then retrieve the file, or even a gif of the protein, easily. You can also browse other files that are available there, and follow links to other related sites. The PDB gopher is at pdb.pdb.bnl.gov, port 70. Happy tunneling- Ethan Benatan ethan+@pitt.edu > Could someone please tell me where I can obtain the above files, > presumably from a ftp site. > > thanks > > Peter Smith From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!uknet!EU.net!chsun!elna.ethz.ch!torda From: torda@igc.ethz.ch (Andrew Torda) Newsgroups: bionet.molbio.proteins Subject: Re: Brookhaven Protein Databank (PDB) Files. Date: 10 Mar 1994 11:49:16 GMT Organization: Computational Chemistry, ETH, Zuerich Lines: 18 Message-ID: <2ln1fs$c8i@elna.ethz.ch> References: NNTP-Posting-Host: hermitage.ethz.ch lwalsh@nemo.life.uiuc.edu (Laura L. Walsh) wrote >rtfm@cix.compulink.co.uk ("Peter Smith") writes: >>Could someone please tell me where I can obtain the above files, >>presumably from a ftp site. [...] >The files are at the ftp site: pdb.pdb.bnl.gov [....] They also have a gopher server at the same address. It is a brilliant service if you want something small and specific. It also seems to be down right now. -Andrew -- This posting is not merely my opinion. It is the official position of my employer, the Swiss Federal Institute of Technology. (Andrew Torda, Computational Chemistry, ETH, Zurich, torda@igc.ethz.ch) From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!nntp.uio.no!usenet From: Dave.Buss@studorg.uio.no (Chuck An) Newsgroups: bionet.molbio.proteins Subject: Re: 3D-lattice protein Date: 10 Mar 1994 15:30:31 GMT Organization: NASA, Kennedy Space Center Lines: 34 Message-ID: <2lneen$otq@hermod.uio.no> References: <2lne9v$otq@hermod.uio.no> NNTP-Posting-Host: biotek04.uio.no X-Newsreader: WinVN version 0.80 In article <2lne9v$otq@hermod.uio.no>, rushing@titan.ksc.nasa.gov (Sam Rushing) says: > >In article , szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) says: >> >> >> Hi Netter's >> I would like to know if there is any program that takes as input >>a pdb file with atomic coordinates of a protein (let's say from Brokheaven >>protein databank) and inserts it in a cubic lattice (you define the >>dimensions of the unit cell) so that as output you have a matrix M(AxBxC) >>where each element of the matrix M(i,j,k)=1 if the this unit cell is >>ocuppied by one or more atoms or M(i,j,k)=0 if this unit cell is empty. >>By adjusting the dimension(l, where V(volume)=l^3) you can select how >>accurate is your lattice model if your unit cell have the dimensions of >>an atom, your lattice model will be equal to the atomic coordinates file. >>I'm not sure if I expressed well my idea but I'll appreciate any comment. >> >> Rafael Najmanovich >> >> >very good idea and it's new, so I think you won't have chance to find out an >existing program. > >however since you've got such a clear idea, it wouldn't take long for people who >has experience to build such a one from sratch. > >best wishes! > >Chuck An > >ps. I'm not sure what you are going to do with this arigorithm. but would you >agree that, since a protein is almost as compact as any crystalls, there won't be >so many zeros in the matrix? regardless what kind of cordinates you are going >to make use of. From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!nntp.uio.no!usenet From: rushing@titan.ksc.nasa.gov (Sam Rushing) Newsgroups: bionet.molbio.proteins Subject: Re: 3D-lattice protein Date: 10 Mar 1994 15:27:59 GMT Organization: NASA, Kennedy Space Center Lines: 32 Message-ID: <2lne9v$otq@hermod.uio.no> References: NNTP-Posting-Host: biotek04.uio.no X-Newsreader: WinVN version 0.80 In article , szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) says: > > > Hi Netter's > I would like to know if there is any program that takes as input >a pdb file with atomic coordinates of a protein (let's say from Brokheaven >protein databank) and inserts it in a cubic lattice (you define the >dimensions of the unit cell) so that as output you have a matrix M(AxBxC) >where each element of the matrix M(i,j,k)=1 if the this unit cell is >ocuppied by one or more atoms or M(i,j,k)=0 if this unit cell is empty. >By adjusting the dimension(l, where V(volume)=l^3) you can select how >accurate is your lattice model if your unit cell have the dimensions of >an atom, your lattice model will be equal to the atomic coordinates file. >I'm not sure if I expressed well my idea but I'll appreciate any comment. > > Rafael Najmanovich > > very good idea and it's new, so I think you won't have chance to find out an existing program. however since you've got such a clear idea, it wouldn't take long for people who has experience to build such a one from sratch. best wishes! Chuck An ps. I'm not sure what you are going to do with this arigorithm. but would you agree that, since a protein is almost as compact as any crystalls, there won't be so many zeros in the matrix? regardless what kind of cordinates you are going to make use of. From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!relay.the.net!SHAUN%JASON.DECNET From: SHAUN%JASON.DECNET@relay.the.net ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: 'Favorite' Misnomers Date: 10 Mar 1994 14:59:07 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <01H9SUY39CV60018A3@nic.the.net> NNTP-Posting-Host: net.bio.net Ethan Benatan's question on 'random coil' protein structure as a 'double misnomer' tickled my fancy. I've got a couple of 'favorite' misnomers and wondered if anyone else did too?! Today's entry is: Primary Sequence Cheers, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!FOX.CCE.USP.BR!szeinfel From: szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) Newsgroups: bionet.molbio.proteins Subject: Re: 3D-lattice protein Date: 10 Mar 1994 20:07:33 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: bionet Message-ID: References: <2lne9v$otq@hermod.uio.no> NNTP-Posting-Host: net.bio.net On 10 Mar 1994, Sam Rushing wrote: > In article , szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) says: > > > > > > Hi Netter's > > I would like to know if there is any program that takes as input > >a pdb file with atomic coordinates of a protein (let's say from Brokheaven > >protein databank) and inserts it in a cubic lattice (you define the > >dimensions of the unit cell) so that as output you have a matrix M(AxBxC) > >where each element of the matrix M(i,j,k)=1 if the this unit cell is > >ocuppied by one or more atoms or M(i,j,k)=0 if this unit cell is empty. > >By adjusting the dimension(l, where V(volume)=l^3) you can select how > >accurate is your lattice model if your unit cell have the dimensions of > >an atom, your lattice model will be equal to the atomic coordinates file. > >I'm not sure if I expressed well my idea but I'll appreciate any comment. > > > > Rafael Najmanovich > > > > > very good idea and it's new, so I think you won't have chance to find out an > existing program. > > however since you've got such a clear idea, it wouldn't take long for people who > has experience to build such a one from sratch. > > best wishes! > > Chuck An > > ps. I'm not sure what you are going to do with this arigorithm. but would you > agree that, since a protein is almost as compact as any crystalls, there won't be > so many zeros in the matrix? regardless what kind of cordinates you are going > to make use of. > > I'm confused about who sent this messsage (Chuck or Sam) anyway, I think this idea is not new since there's a paper (Yuzo Ueda, Hiroshi Taketomi and Nobuhiro Go from Kyushu University, Japan. Biopolymers 17:1531-1548(1978).) where they do these or something aproximate with lysozyme. You're right about the ssmall number of zeros but the inportant is that as you know where's the N-terminus and the C-terminus, this representation is good to perform simulations. By the way, if someone knows the e-mail adress of any autor of the above mentioned paper please let me know. Rafael Najmanovich From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!relay.the.net!SHAUN%JASON.DECNET From: SHAUN%JASON.DECNET@relay.the.net ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: Re: 3D-lattice protein Date: 10 Mar 1994 21:19:32 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <01H9T84TDE8I00196L@nic.the.net> NNTP-Posting-Host: net.bio.net Greetings, To continue this discussion, the general idea is not a new one. This area was nicely reviewed in Tom Creighton's book, "Protein Folding" (W.H. Freeman and Co, 1992), chapter 4, "Protein Folding: Theoretical Studies of Thermodynamics and Dynamics" (M. Karplus & E. Shakhnovich). You might look at '3.2.2 Lattice Models with Full Enumeration' (p.161) and '4.4 Lattice Models of Folding' (p.180). Cheers, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!trane.uninett.no!nac.no!nntp-oslo.uninett.no!usenet From: ragnar.flengsrud@ibf.nlh.no Newsgroups: bionet.molbio.proteins Subject: Reduction of Cu (II) in protein assays Date: 11 Mar 1994 07:29:19 GMT Organization: agricultural univ. of norway Lines: 22 Distribution: world Message-ID: <2lp6kf$htl@ratatosk.uninett.no> NNTP-Posting-Host: biorf.nlh.no Hi protein bionetters !, Could anyone out there answer this ?: The protein assays biuret, Lowry and BCA all involves the reduction of Cu 2+ ti Cu + in alkaline environment, but what is oxidized in the protein ? Where does the electron come from ? In the article where the BCA-method is introduced (ref.: P.K. Smith et al., Anal. Biochem. (1985), 150, 76-85), the following statement is made (p.78): " While the mechanism of the Lowry reaction is not well understood, we have theorized that it involves a reduction of the Cu 2+ to Cu 1+ at the complexation sites within the protein molecule. " Is this as far as the knowledge goes today as well ? Regards, Ragnar Flengsrud, Agricultural University of Norway, Department of Biotechnological Sciences, Section of Chemistry, P.O. box 5040, N-1432 Aas, Norway biorf@nlh10.nlh.no From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!daresbury!keele!uknet!pipex!howland.reston.ans.net!news.cac.psu.edu!psuvm!wvnvm!frist Date: Thu, 10 Mar 1994 19:23:21 EST From: Message-ID: <94069.192321FRIST@wvnvm.wvnet.edu> Newsgroups: bionet.molbio.proteins Subject: Re: Apparent MW of protein on-PAGE gel > real MW? References: <2lg6vo$9s7@charm.magnus.acs.ohio-state.edu> Lines: 17 In article <2lg6vo$9s7@charm.magnus.acs.ohio-state.edu>, bhuang@magnus.acs.ohio-state.edu (Baohua Huang) says: > > My question is : does high content of basic residues make a >protein run slower? (on SDS gels) In a word, Yes. SDS will sequester the native charge of most proteins but if there is a high net charge the migration rate will be off the plot of the standards. Years ago (unpublished) I noticed that succinylated proteins run faster than corresponding unmodified proteins on SDS gels. R. Frist From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!torn!csd.unb.ca!coranto.ucs.mun.ca!newton.physics.mun.ca!beavis From: beavis@newton.physics.mun.ca (Ron Beavis) Newsgroups: bionet.molbio.proteins Subject: Re: Apparent MW of protein on PAGE gel Date: 10 Mar 1994 12:41:13 GMT Organization: Memorial University of Nfld, St. John's, NF Lines: 19 Message-ID: <2ln4h9$c2v@coranto.ucs.mun.ca> References: <1994Mar9.202838.15613@wmichgw> NNTP-Posting-Host: newton.physics.mun.ca In article <1994Mar9.202838.15613@wmichgw> ou_lehrman@wmich.edu (Russ_Lehrman) writes: > > >> A fusion protein I expressed in E. coli has a apparent MW on SDS-PAGE gel ~5 >> kdlager than it's calculated MW. This protein is 303 aa residues with >> acalculated MW of 35 kd but it runs at 40 kd position on SDS-PAGE. The >> proteinhas very high content of basic amino acids (32 lysines, 20 arginine >> and 16histidines). My question is : does high content of basic residues make >> aprotein run slower?I would apreciate very much any hints to my question. > It is not unusual for basic (or acidic) proteins to run on SDS-PAGE with apparent MW's significantly different from their true chemical molecular mass. If you are really concerned about this apparent mass shift, send a sample out for mass spectrometry. Ron Beavis Memorial University of Newfoundland From owner-proteins@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!bipin From: bipin@iastate.edu (Bipin K Dalmia) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: disrupting e. coli cells Date: 10 Mar 1994 22:30:50 GMT Organization: Iowa State University, Ames, Iowa (USA) Lines: 12 Distribution: world Message-ID: <2lo72q$9ur@news.iastate.edu> NNTP-Posting-Host: class1.iastate.edu Xref: biosci bionet.molbio.methds-reagnts:12305 bionet.molbio.proteins:1539 i've never had much success with sonication but since that is the only piece of equipment we have at present, do you have any suggestions for optimizing e. coli disruption with a sonicator? i've heard that some people use lysozyme treatment before sonicating, do you have any experience with this?? any other treatments?? bip -- bipin k. dalmia the other night i was lying on my bed, looking bipin@iastate.edu up at the beautiful stars, and i said to myself, n2.bkd@isumvs.iastate.edu 'where the F*CK is my ROOF !!' -- From owner-proteins@net.bio.net Thu Mar 10 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!trane.uninett.no!sunic!pipex!lyra.csx.cam.ac.uk!pavo.csi.cam.ac.uk!mbfs.bio.cam.ac.uk!smb18 From: smb18@mbfs.bio.cam.ac.uk (Simon Brocklehurst (Bioc)) Subject: Re: Structural Prediction Message-ID: <1994Mar11.164752.1348@infodev.cam.ac.uk> Sender: news@infodev.cam.ac.uk (USENET news) Nntp-Posting-Host: mbfs.bio.cam.ac.uk Organization: U of Cambridge, England References: <81181.ewright@fox.nstn.ns.ca> <2lnfdq$otq@hermod.uio.no> Date: Fri, 11 Mar 1994 16:47:52 GMT Lines: 87 dave.buss@studorg.uio.no (Chuck An) writes: >In article <81181.ewright@fox.nstn.ns.ca>, ewright@FOX.NSTN.NS.CA ("Edwin Wright") says: >> >>The following statement appeared in Nature: >> >>"There are now many examples, in both functionally similar and dissimilar >>proteins, where the sequence similarity is statistically insignificant (less >>than 20%) and yet the same topology is observed." (M. Thornton, T.P. Flores, >>D.T. Jones, M.B. Swindells, Nature, 354, 105, (1991) - p. 106) >> >>If this situation is common, then it seems that notwithstanding functional >>similarity/dissimilarity, topological similarity is dependent on a meta- >>sequential order, not readily apparent at the level of independently >>displayed sequences. Presumably, this meta-sequential order is governed by >>one of the following possibilities: >> >>1. There is a distinct set of sequences (the basis of which is unknown) >> responsible for a specific topology. >> >>2. The set of sequences responsible for a specific topology are actually >> manifesting conserved positions (albeit non-conserved residues) of a >> single (unknown) meta-sequence. >> >>Is anyone aware of any research with respect to the second possibility? >> >>Regards, >>------- >>Edwin Wright >>85 Spinnaker Drive, A-602 >>Halifax, Nova Scotia >>CANADA B3N 3E3 >> >>Telephone: (902) 477-5037 >> >>Email: ewright@fox.nstn.ns.ca >>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= >I think so. it has been noticed that proteins from different families and with quite >big variation in sequences were found having both local ang gobal structural >resemblance. they were able to be sort of superimposed on one another. I can't >recall the details. >I wander whether the 3D structures of proteins are the consequences of >the combination of the amino acid residues, but not necessarily the definite > permutation of the residues. Er.... I'm not sure _exactly_ what either of you are getting at... What is a "meta-sequential order" ? What is "the definite permutation of the residues" ? Notwithstanding this... The discovery of structural/functional similarities between proteins that have long been thought to be unrelated, continues to be one of the most interesting aspects of structural biology. These discoveries are increasingly being made as new structures are elucidated experimentally, but the protein databank probably still holds a number of surprises. As to what governs the topology of the protein, obviously it is the sequence. Most of the research going into recognising common folds for proteins that share little or no sequence similarity is based on so-called sequence-structure comparison. That is, we need a trial fold before we can say that two dissimilar sequences will adopt the same fold. This is thought not to be a bad idea, because it seems likely that Nature makes use of only a limited number of protein folds. Thus, we will probably soon have an example of most folds. How well existing methods work is is open to debate... There is no consensus view about which sequence-structure comparison approach is the best at the moment. It should be an interesting twelve months in the literature. A LOT of people from different fields (computer science, mathematicians, biologists) have been working on this kind of stuff. !----------------------------------------------------------------------- Simon M. Brocklehurst Cambridge Centre for Molecular Recognition Department of Biochemistry University of Cambridge Cambridge UK E-mail: s.m.brocklehurst@bioc.cam.ac.uk From owner-proteins@net.bio.net Thu Mar 10 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!fnnews.fnal.gov!att-in!news.bu.edu!rocket1 From: rocket1@bu.edu (Richard Near) Newsgroups: bionet.molbio.proteins Subject: Re: Prestaining Proteins Date: 12 Mar 1994 06:15:44 GMT Organization: Boston University Lines: 6 Message-ID: <2lrmmg$2s8@news.bu.edu> References: <2lqs2r$hdl@news.bu.edu> NNTP-Posting-Host: acs3.bu.edu X-Newsreader: TIN [version 1.2 PL0] Because it's far cheaper to make them than buy them. Rick rocket1@bu.edu From owner-proteins@net.bio.net Thu Mar 10 22:00:00 1994 Path: biosci!FOX.NSTN.NS.CA!ewright From: ewright@FOX.NSTN.NS.CA ("Edwin Wright") Newsgroups: bionet.molbio.proteins Subject: Protein Abbreviation Reference Date: 11 Mar 1994 23:15:42 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <69378.ewright@fox.nstn.ns.ca> NNTP-Posting-Host: net.bio.net Does anyone know where I can obtain a handy reference for the protein abbreviations/codes used in the protein database listings? Regards, ------- Edwin Wright 85 Spinnaker Drive, A-602 Halifax, Nova Scotia CANADA B3N 3E3 Telephone: (902) 477-5037 Email: ewright@fox.nstn.ns.ca =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Thu Mar 10 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!wbecktel From: wbecktel@magnus.acs.ohio-state.edu (Wayne J Becktel) Newsgroups: bionet.molbio.proteins Subject: Re: Apparent MW of protein on-PAGE gel > real MW? Date: 11 Mar 1994 13:50:48 GMT Organization: The Ohio State University Lines: 12 Message-ID: <2lpsvo$51l@charm.magnus.acs.ohio-state.edu> References: <2lg6vo$9s7@charm.magnus.acs.ohio-state.edu> <94069.192321FRIST@wvn NNTP-Posting-Host: bottom.magnus.acs.ohio-state.edu Globular proteins have, on average, approximately the same number of negatively and positively charged groups with the population being roughly 12% of the total number of amino acids for each. SDS binds, again on average, one molecule of the detergent for every two amino acids. Thus, for a 100 residue globular protein, one might expect to find 12 positively and 12 negatively charged amino acids and about 50 SDS molecules associated with the protein. Very basic proteins, such as histones, do not have an "average" composition of charged amino acids and run slow on SDS/PAGE gels. On the other hand, chemical modification of proteins containing Cys residues with iodo acetic acid will increase the negative charge and cause those proteins to have lower apparent molecular weights. From owner-proteins@net.bio.net Thu Mar 10 22:00:00 1994 Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!pipex!uknet!lyra.csx.cam.ac.uk!pavo.csi.cam.ac.uk!camcus!bjd12 From: bjd12@cus.cam.ac.uk (Ben Davis) Subject: Re: disrupting e. coli cells Message-ID: <1994Mar11.080751.6733@infodev.cam.ac.uk> Sender: news@infodev.cam.ac.uk (USENET news) Nntp-Posting-Host: grus.cus.cam.ac.uk Organization: U of Cambridge, England References: <2lo72q$9ur@news.iastate.edu> Date: Fri, 11 Mar 1994 08:07:51 GMT Lines: 48 Xref: biosci bionet.molbio.methds-reagnts:12311 bionet.molbio.proteins:1542 In article <2lo72q$9ur@news.iastate.edu>, bipin@iastate.edu (Bipin K Dalmia) writes: |> i've never had much success with sonication but since that is the only |> piece of equipment we have at present, do you have any suggestions for |> optimizing e. coli disruption with a sonicator? i've heard that some |> people use lysozyme treatment before sonicating, do you have any |> experience with this?? any other treatments?? |> |> bip |> -- |> bipin k. dalmia the other night i was lying on my bed, looking |> bipin@iastate.edu up at the beautiful stars, and i said to myself, |> n2.bkd@isumvs.iastate.edu 'where the F*CK is my ROOF !!' |> -- I've used sonication, with and without lysozyme, and also freeze-thawing to lyse coli (freeze-thawing as in multiple cycles of flash freezing in liquid N2, then rapid thawing in a warm water bath (we use 65C, but do't let the samples get to 65, or much above 30 really, and only invert gently) I've had a _lot_ more sucess with sonication than with freeze- thawing, and found that adding lysozyme wasn't really worth it (you're contaminating your prep with another protein, to start with). A couple of good things to do when you're sonicating are tune the probe first (Does make a difference) do everything on ice, and let it cool down for 10min between cycles resuspend the cell debris after centrifugation, and resonicate it (basically the same as if it was fresh cells, just maybe a little more gently) - can get another 20% yield easy wdoing this. The only other peice of advice I can think of is to keep sonicating, spinning and sonicating, and check by gel to see whether the cell debris still contains intact cells. Should be able to tell farily easily. Good luck (cells that won't lyse are a pain - I sympathise) Ben -- ______________________________________________________________________________ Ben Davis, MRC Protein Function and Design, Cambridge, UK ______________________________________________________________________________ "They can make me do it, but they can't make me do it with dignity." From owner-proteins@net.bio.net Thu Mar 10 22:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!sdd.hp.com!saimiri.primate.wisc.edu!news.doit.wisc.edu!sweetprotein.ahabs.wisc.edu!user From: ming@ahabs.wisc.edu (Ding Ming) Newsgroups: bionet.molbio.proteins Subject: Re: Prestaining Proteins Followup-To: bionet.molbio.proteins Date: Fri, 11 Mar 1994 22:33:36 -0600 Organization: University of Wisconsin-Madison Lines: 21 Message-ID: References: <2lqs2r$hdl@news.bu.edu> NNTP-Posting-Host: sweetprotein.ahabs.wisc.edu In article <2lqs2r$hdl@news.bu.edu>, rocket1@bu.edu (Richard Near) wrote: > I am interested in prestaining some proteins to > serve as markers in sds gels and/or chromatography. > I realize that this will affect the apparent Mwt, bu > t, for my crude applications (at least for now), it will > serve it's purpose. MY Question: does anyone have a > simple protocol for prelableling proteins that should > be stable in sds and/or urea. > Sigma, Bio-Rad, and quite a few biochemical vendors sell Prestained SDS-MW Markers. They are not terribly expensive and pretty neat in Western. Why do you bother to make them by yourself? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Ding Ming University of Wisconsin-Madison Telephone: (608)265-3544 Fax: (608)262-7420 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-proteins@net.bio.net Thu Mar 10 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!usenet.ins.cwru.edu!lerc.nasa.gov!purdue!news.bu.edu!rocket1 From: rocket1@bu.edu (Richard Near) Newsgroups: bionet.molbio.proteins Subject: Prestaining Proteins Date: 11 Mar 1994 22:41:31 GMT Organization: Boston University Lines: 13 Message-ID: <2lqs2r$hdl@news.bu.edu> NNTP-Posting-Host: acs4.bu.edu X-Newsreader: TIN [version 1.2 PL0] I am interested in prestaining some proteins to serve as markers in sds gels and/or chromatography. I realize that this will affect the apparent Mwt, bu t, for my crude applications (at least for now), it will serve it's purpose. MY Question: does anyone have a simple protocol for prelableling proteins that should be stable in sds and/or urea. Thanks Rick rocket1@bu.edu From owner-proteins@net.bio.net Thu Mar 10 22:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!europa.eng.gtefsd.com!emory!news-feed-1.peachnet.edu!umn.edu!htlv.med.umn.edu!david-l From: david-l@htlv.med.umn.edu (David LaPorte (Biochem)) Subject: Re: cAMP stability Message-ID: Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: htlv.med.umn.edu Organization: University of Minnesota References: <2ll2uc$m0j@news.umbc.edu> Date: Fri, 11 Mar 1994 19:38:51 GMT Lines: 20 jmello1@umbc.edu (mellott james ( bs bioc)) writes: > In my biochemistry class , we're talking about glycolysis , TCA , etc., >and one of the topics is the regulation of glycogen through a cAMP pathway . It >is my understanding that a high concentration of cAMP is needed for the >continuous activation of Protein kinase , and to inactivate the kinase , the >concentration of cAMP is lowered through the activity of a phosphodiesterase . >I recall hearing that caffeine stabilizes the concentration of cAMP in such a >pathway , and I was wondering , since caffeine and adenine have similar >structures , if caffeine acts as a competitive inhibitor with cAMP for the >phosphodiesterase . Caffeine, theophiline and related compounds are, indeed, inhibitors of phosphodiesterase. As I recall, however, that is not their biological site of action. The concentrations required to produce a physiological effect are too low to inhibit PDE. Dave LaPorte U. of Minn. david-l@microbe.med.umn.edu From owner-proteins@net.bio.net Sat Mar 12 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!zaphod.crihan.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!zeus.rbi.informatik.uni-frankfurt.de!terra.wiwi.uni-frankfurt.de!news.th-darmstadt.de!fauern!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Prestaining Proteins Date: 12 Mar 1994 12:11:22 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 15 Message-ID: <2lsbhaINNnp8@sat.ipp-garching.mpg.de> References: <2lrmmg$2s8@news.bu.edu> NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.1 PL8] [Why make prestained proteins on yourself when you can buy them?] Richard Near (rocket1@bu.edu) wrote: : Because it's far cheaper to make them than buy them. Write to BioRad and ask kindly for an aliquot to test it out. You will receive (at least here in Germany) about 50 ul for free, enough for 10 gels. --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "People are DNA's way of making more DNA." (Edward O. Wilson, 1975) */ From owner-proteins@net.bio.net Sat Mar 12 22:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!network.ucsd.edu!tpillay.extern.ucsd.edu!tpillay From: T. S. Pillay Newsgroups: bionet.molbio.proteins Subject: Re: Prestaining Proteins Date: 13 Mar 1994 21:32:07 GMT Organization: Endocrinology & Metabolism, UCSD Lines: 38 Distribution: world Message-ID: <2m00on$3vg@network.ucsd.edu> References: <2lqs2r$hdl@news.bu.edu> <2lstd7$kim@columba.udac.uu.se> NNTP-Posting-Host: tpillay.extern.ucsd.edu X-UserAgent: Version 1.1.3 X-XXMessage-ID: X-XXDate: Mon, 14 Mar 94 13:30:16 GMT Subject: Prestaining Proteins From: Richard Near, rocket1@bu.edu Date: 11 Mar 1994 22:41:31 GMT In article <2lqs2r$hdl@news.bu.edu> Richard Near, rocket1@bu.edu writes: >I am interested in prestaining some proteins to >serve as markers in sds gels and/or chromatography. >I realize that this will affect the apparent Mwt, bu >t, for my crude applications (at least for now), it will >serve it's purpose. MY Question: does anyone have a >simple protocol for prelableling proteins that should >be stable in sds and/or urea. > >Thanks >Rick >rocket1@bu.edu > Here's the goods: When I was a graduate student at Cambridge University a few years ago- I used to make my own prestained standards before they became commercially available (rainbow markers; kaleidoscope and the rest). The biggest problem with commercially available markers is the slight batch to batch variation in apparent MW. You can avoid this by making your own in bulk ( Does this answer the question of why make your own?) The protocol is as follows: You can choose the colour by using Remazol dyes which come in various colours- you can make your own "rainbow" (sorry Amersham !!! - disclaimer: "Rainbow" is a trademark of Amersham International etc .....blah, blah!!) I used Remazol Blue(Sigma), but it can be adapted to other remazol dyes. Coupling buffer: 50 mM Tris/0.38 M glycine pH8.3 Dissolve Remazol Blue in buffer above at 100 mg/ml. Make up protein in coupling buffer at 40 mg/ml. Mix with dye in 1: 1 ratio (v/v). Incubate at room Temp for 2 hours and hey presto your protein is prestained. Can be used directly without purification or you might want to remove the excess dye by dialysis or gel filtration. Try it and let me know how it works. From owner-proteins@net.bio.net Sat Mar 12 22:00:00 1994 Path: biosci!FOX.NSTN.NS.CA!ewright From: ewright@FOX.NSTN.NS.CA ("Edwin Wright") Newsgroups: bionet.molbio.proteins Subject: Protein Classification Date: 13 Mar 1994 20:54:55 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <60923.ewright@fox.nstn.ns.ca> NNTP-Posting-Host: net.bio.net Does anyone know of a comprehensive reference on protein classification? Regards, ------- Edwin Wright 85 Spinnaker Drive, A-602 Halifax, Nova Scotia CANADA B3N 3E3 Telephone: (902) 477-5037 Email: ewright@fox.nstn.ns.ca =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Sat Mar 12 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!europa.eng.gtefsd.com!emory!news-feed-1.peachnet.edu!concert!bdrc!cbio6.bdrc.bd.com!beyer From: beyer@bdrc.bd.com (Wayne Beyer) Newsgroups: bionet.molbio.proteins Subject: 2d gel apparatus Message-ID: Date: 12 Mar 94 13:37:11 GMT Sender: news@bdrc.bdrc.bd.com Organization: Becton Dickinson Research Center Lines: 5 Nntp-Posting-Host: cbio6.bdrc.bd.com X-Newsreader: Trumpet for Windows [Version 1.0 Rev Final Beta #9] Can anyone suggest a good commerical supplier for easy to use 2D gel electrophoresis? Thanks! WB From owner-proteins@net.bio.net Sat Mar 12 22:00:00 1994 Path: biosci!FOX.NSTN.NS.CA!ewright From: ewright@FOX.NSTN.NS.CA ("Edwin Wright") Newsgroups: bionet.molbio.proteins Subject: Protein Reference Guide Date: 12 Mar 1994 20:07:53 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <58132.ewright@fox.nstn.ns.ca> Does anyone know of an up-to-date comprehensive reference guide to proteins (similar to a CRC Handbook)? Regards, ------- Edwin Wright 85 Spinnaker Drive, A-602 Halifax, Nova Scotia CANADA B3N 3E3 Telephone: (902) 477-5037 Email: ewright@fox.nstn.ns.ca =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Sat Mar 12 22:00:00 1994 Path: biosci!KKU1.KKU.AC.TH!chaisiri From: chaisiri@KKU1.KKU.AC.TH (Chaisiri Wongkham) Newsgroups: bionet.molbio.proteins Subject: Enzyme database Date: 12 Mar 1994 11:19:11 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: bionet Message-ID: Hi! netters, Does anyone know where there is an enzyme database which I can search for informations, such as inhibitors, optimum pH, substrates? Many thanks, Chaisiri Wongkham Internet: chaisiri@kku1.kku.ac.th Biochemistry, Medicine, Khon Kaen University, Khon Kaen 40002, THAILAND From owner-proteins@net.bio.net Sat Mar 12 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!swrinde!ihnp4.ucsd.edu!network.ucsd.edu!tpillay.extern.ucsd.edu!tpillay From: T. S. Pillay Newsgroups: bionet.molbio.proteins Subject: Re: p53 protein sequences Date: 13 Mar 1994 21:41:58 GMT Organization: Endocrinology & Metabolism, UCSD Lines: 32 Distribution: world Message-ID: <2m01b6$3vg@network.ucsd.edu> References: <2lvtks$nge@spool.cs.wisc.edu> NNTP-Posting-Host: tpillay.extern.ucsd.edu X-UserAgent: Version 1.1.3 X-XXMessage-ID: X-XXDate: Mon, 14 Mar 94 13:40:08 GMT Subject: p53 protein sequences From: John-Luke Picard, jons@picard.cs.wisc.edu Date: 13 Mar 1994 20:38:52 GMT In article <2lvtks$nge@spool.cs.wisc.edu> John-Luke Picard, jons@picard.cs.wisc.edu writes: >Hi There: > > I'm interested in knowing both the protein sequences and structure > of the p53 tumor suppressor gene. I'm having problem in searching > all these information form the Medline. If you have information > concerning this ...please email me . Besides, information > concerning the post transcription mRNA regulation will be > helpful as well... > > Thanks.... > > email address: jons@picard.cs.wisc.edu You can access sequences by tel netting to various fileservers which carry Genbank sequences or you can get the sequence Emailed to you by sending an Email message to Genbank at NIH. In order to get full instructions on how to use the RETRIEVE Email server send an Email message to retrieve@ncbi.nlm.nih.gov with the word "help" in the message. Example of a search: (Send this message as is from your Email link): DATALIB genbank BEGIN p53 [key] address it to retrieve@ncbi.nlm.nih.gov From owner-proteins@net.bio.net Sat Mar 12 22:00:00 1994 Path: biosci!CC.IITB.ERNET.IN!chyusia From: chyusia@CC.IITB.ERNET.IN Newsgroups: bionet.molbio.proteins Subject: pr Date: 13 Mar 1994 11:35:18 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <940313152855843-MTACYBER*chyusia@cc.iitb.ernet.in> NNTP-Posting-Host: net.bio.net dear netters, we are currently interested in the conformational analysis of peptides. we are looking for programs like ECEPP, molecular dynamics programs etc which can be run on PC 486 either in DOS or UNIX (windows too) environment. are these programs available in public domain (ftp sites). if so please let us know the source of availability of these programs. THANKS IN ADVANCE -SASIDHAR asst.prof chemistry dept. I.I.T., Bombay india 400 0476 From owner-proteins@net.bio.net Sat Mar 12 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!columba.udac.uu.se!sol.bmc.uu.se!dunten From: dunten@sol.bmc.uu.se (Pete Dunten) Newsgroups: bionet.molbio.proteins Subject: Re: Prestaining Proteins Date: 12 Mar 1994 17:16:23 GMT Organization: Uppsala University Lines: 22 Distribution: world Message-ID: <2lstd7$kim@columba.udac.uu.se> References: <2lqs2r$hdl@news.bu.edu> NNTP-Posting-Host: sol.bmc.uu.se Protocol for labeling standards Dissolve stds in 50 mM phosphate buffer, pH 7.5, 4% SDS. Add excess dansyl chloride (soluble in acetone). Heat, 5 min at 100 deg. Add excess bme. Heat, 5 min at 100 deg. Load on Pasteur pipette mini-column containing G10 in 2% SDS and your gel stacking buffer. Wash off the column in the same buffer. First off are the dansylated stds, then dansyl-OH. Viola, labeled stds (yellow under UV). From owner-proteins@net.bio.net Sat Mar 12 22:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!sdd.hp.com!vixen.cso.uiuc.edu!uwm.edu!daffy!uwvax!picard.cs.wisc.edu!jons From: jons@picard.cs.wisc.edu (John-Luke Picard) Newsgroups: bionet.molbio.proteins Subject: p53 protein sequences Date: 13 Mar 1994 20:38:52 GMT Organization: U of Wisconsin CS Dept Lines: 13 Message-ID: <2lvtks$nge@spool.cs.wisc.edu> NNTP-Posting-Host: picard.cs.wisc.edu X-Newsreader: TIN [version 1.2 PL0] Hi There: I'm interested in knowing both the protein sequences and structure of the p53 tumor suppressor gene. I'm having problem in searching all these information form the Medline. If you have information concerning this ...please email me . Besides, information concerning the post transcription mRNA regulation will be helpful as well... Thanks.... email address: jons@picard.cs.wisc.edu From owner-proteins@net.bio.net Sat Mar 12 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!columba.udac.uu.se!sol.bmc.uu.se!dunten From: dunten@sol.bmc.uu.se (Pete Dunten) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: disrupting e. coli cells Date: 12 Mar 1994 17:07:27 GMT Organization: Uppsala University Lines: 7 Distribution: world Message-ID: <2lsssf$kim@columba.udac.uu.se> References: <2lo72q$9ur@news.iastate.edu> NNTP-Posting-Host: sol.bmc.uu.se Xref: biosci bionet.molbio.methds-reagnts:12367 bionet.molbio.proteins:1552 3 volumes buffer to 1 gram (wet) cells works pretty well. You can see the cell suspension change color when the cells break. Or you can put a few microliters on a slide, cover with a coverslip, and take a look under a microscope. Intact cells and broken cell envelopes can be distinguished, so you can decide when to stop sonicating. From owner-proteins@net.bio.net Sun Mar 13 22:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!sdd.hp.com!saimiri.primate.wisc.edu!news.crd.ge.com!sarah!psinntp!psinntp!alsys1!gottfrie From: gottfrie@aecom.yu.edu (David S. Gottfried) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Reference Guide Message-ID: <2711@alsys1.aecom.yu.edu> Date: 14 Mar 94 14:26:00 GMT References: <58132.ewright@fox.nstn.ns.ca> Sender: news@alsys1.aecom.yu.edu Organization: Albert Einstein College of Medicine Lines: 21 Nntp-Posting-Host: marcus.aecom.yu.edu X-Posted-From: InterNews 1.0@alsys1.aecom.yu.edu. In article <58132.ewright@fox.nstn.ns.ca> ewright@FOX.NSTN.NS.CA ("Edwin Wright") writes: > Does anyone know of an up-to-date comprehensive reference guide to > proteins (similar to a CRC Handbook)? I have an advertisement for a book (which I do not own) called "Handbook of Proteins" by Ajit Bhown and published by A & M Publications (205-970-0960). I don't know how up to date the book is, but it claims to have 2000 animal and plant proteins and 1269 references. It includes data such as molecular weight, pI, extinction coefficient, solubility, sequence etc. This sounds like the "CRC" model. =================================== David S. Gottfried Physiology and Biophysics Albert Einstein College of Medicine gottfrie@aecom.yu.edu =================================== From owner-proteins@net.bio.net Sun Mar 13 22:00:00 1994 Path: biosci!FOX.CCE.USP.BR!szeinfel From: szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) Newsgroups: bionet.molbio.proteins Subject: Re: Simulationsof protein packing in crystals (fwd) Date: 14 Mar 1994 14:44:57 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: bionet Message-ID: NNTP-Posting-Host: net.bio.net I tried to send directly to you Enrico but the mail returned as host unknown. ---------- Forwarded message ---------- Date: Mon, 14 Mar 1994 11:37:14 -0300 (BDT) From: Rafael N Szeinfeld To: "Enrico A. Carrara" Subject: Re: Simulationsof protein packing in crystals Hi Enrico, I'll send you a big list of references, at most tomorrow, which deals with monte carlo simulations and computational approaches to protein conformation/folding of proteins. Rafael Najmanovich On 14 Mar 1994, Enrico A. Carrara wrote: > > > Could anybody send me references on works done on the simulation/ > prediction of protein packing in 3D or 2D crystals made by Molecular > Mechanics, MonteCarlo simulations or any other computational approach? > > Thanks in advance > > > Enrico Carrara > carrara @ barbarella.ibf.unige.it > > From owner-proteins@net.bio.net Sun Mar 13 22:00:00 1994 Path: biosci!biosci!not-for-mail From: ksuzuki@nih.go.jp (Kazuo Suzuki) Newsgroups: bionet.announce,bionet.cellbiol,bionet.general,bionet.molbio.proteins Subject: Submission for Bioimages (Journal) Date: 14 Mar 1994 12:46:52 -0800 Organization: National Institutes of Health (NIH) Tokyo, Japan Lines: 205 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: bionet Message-ID: Reply-To: bioimage@nih.go.jp NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:1006 bionet.cellbiol:359 bionet.general:8213 bionet.molbio.proteins:1564 Welcome to Bioimages INSTRUCTIONS TO AUTHORS ======================= This text is formatted in setext. Information on setext may be requested by sending "setext" alone on the subject line, no quotes, to . General infomation will be requested to "bioimage@nih.go.jp". ---------------------------------------------------------------------- Scope and Policy of Bioimages ============================= Bioimages is the official journal of the Bioimaging Society, and publishes original articles semiannually on a broad range of bioimaging topics in molecular and cellular biology, biochemistry, biophysics, physiology, medical science and computer science. The jounal is devoted to the publication of practical and theoretical papers on the development of imaging methods and/or their application to the field of biological sciences. All the manuscripts must be written in English. The results presented in manuscripts submitted for publication should not have been previously published or submitted for publication to another journal. 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Results This section should contain the new observations and advances made in the study, presented in a logical fashion with evidence to support any conclusions drawn. Do not repeat material presented in the Introduction or in Materials and Methods. Discussion The Discussion should be concise and deal with the interpretation of results. Models or hypotheses may be proposed in this section only when they are newly s