From owner-proteins@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!131.103.1.114!news1.chicago.iagnet.net!iagnet.net!newsspool.doit.wisc.edu!wiscnews.wiscnet.net!news.doit.wisc.edu!default From: klenchin@facstaff.REMOVE_TO_REPLY.wisc.edu (Dima Klenchin) Newsgroups: bionet.molbio.proteins Subject: Re: Triton X-100 in SDS-Page Date: Tue, 02 Dec 1997 18:50:54 GMT Organization: UW-Madison Lines: 18 Message-ID: <661l22$tqi$1@news.doit.wisc.edu> References: <34840A11.E061B216@kfunigraz.ac.at> NNTP-Posting-Host: martinlab.biochem.wisc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=KOI8-R Content-Transfer-Encoding: 8bit X-Newsreader: News Xpress 2.01 X-No-Archive: Yes In article <34840A11.E061B216@kfunigraz.ac.at>, Markus Zettl wrote: :Hi! :I know that Triton X-100 forms micelles in a concentration over the CMC. As all detergents do. The actual problem is that X-100 binds proteins very well and so compets with SDS binding. :These micelles cause difficulties if you want to carry a 12,5% SDS-Page. :Therefore I wannt to know if it+ALQ-s possible to run electrophoresis whith :Triton X-100 if you increase the SDS-concentration of the sample buffer? :Does anyone know other possibilities to run SDS-Page with Triton X-100. :Thanks for helpfull information! No problem. Just increase SDS concentration in your loading buffer 1.5-2--fold. (I actually add 1% SDS to the sample, then mix 1:1 with regular loading buffer). Dima From owner-proteins@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!HWCN.ORG!icurkovic From: icurkovic@HWCN.ORG Newsgroups: bionet.molbio.proteins Subject: Need help! Date: 2 Dec 1997 09:05:25 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712021705.MAA00343@james.freenet.hamilton.on.ca> NNTP-Posting-Host: net.bio.net Hello, I'm not sure I'm in the right newsgroup, but here goes nothing. I am an undergrad taking a biochem course on information molecules (DNA, RNA, proteins). Anyway, our prof believes in problem based learning so he gave us a problem for our exam. He expects us to pick out 10 issues from this problem based on what we've learned this year. He will then ask us 10 questions on our exam. Here is the problem he gave us: Eugene is a 10 yr old boy who has been diagnosed as sufferring from Prader-Willi syndrome. The Prader-Willi syndrome is a genetic disorder characterized by decreased sensitivity to pain, fair, hair and behavioural disturbances including overeating leading to obesity. One of the hypotheses developed to explain the manifestiations of this syndrome is a disturbance to explain the manifestations of this syndrome is a disturbance in the production of the polyprotein, proopiomelanocortin (POMC) or its post-translational modifications. Eugene has been treated with drugs which are intended to cause inhibition of enzymes involved in the proteolysis of the defective POMC. Eugene's mother, who works in an institute for molecular biology and biotechnoloogy, is pregnant and seeks counseling about the risks of her offspring to be affected by the Prader-Willi syndrome. She read a recent report claiming that the gene expression can be manipulated. ------------ THE END------------- I already know that I should study the following: -gene expression -competitive/noncompetitive inhibition -post-translational modifications Any other suggestions on what to watch out for would be appreciated. Thanks, Ivan From owner-proteins@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!vetparas.unizh.ch!ahuelsem From: ahuelsem@vetparas.unizh.ch (Andreas Hulsmeier) Newsgroups: bionet.molbio.proteins Subject: Re: de-glycosylation Date: 2 Dec 1997 06:29:04 -0800 Organization: University of Zurich Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <34841AF8.40855673@vetparas.unizh.ch> NNTP-Posting-Host: net.bio.net There is an enzymatic deglycosylation kit from Bio-Rad. You could try that in case you need complete deglycosylation. Regards, Andreas From owner-proteins@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!news.algonet.se!feed1.news.luth.se!luth.se!news-ge.switch.ch!news-zh.switch.ch!news.belnet.be!alpha.luc.ac.be!pstn14.luc.ac.be!user From: ghermans@luc.ac.be (Guy Hermans) Newsgroups: bionet.immunology,bionet.molbio.proteins,sci.med.immunology Subject: transmembrane sequence of TCRB Date: Tue, 02 Dec 1997 14:53:41 +0200 Organization: Dr. L. Willems-Insitute Lines: 21 Message-ID: NNTP-Posting-Host: pstn14.luc.ac.be Xref: biosci bionet.immunology:12984 bionet.molbio.proteins:11952 Could anyone please help me in finding the exact sequence of the transmembrane region of the T cell receptor beta chain? I've found it for the alpha chain in SWISS PROT but it doesn't give me any specifications for the beta chain If anyone knows of a place to find this sequence please let me know at: hellings@luc.ac.be Niels Hellings Belgium Ignore the following signature please -------------------------------------------- Guy Hermans, PhD student MS research Unit Tel 0032 (0) 11/26.92.07 Dr. L. Willems-Institute Fax 0032 (0) 11/26.92.09 University Campus E-mail ghermans@luc.ac.be B-3590 Diepenbeek Belgium -------------------------------------------- From owner-proteins@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.internetmci.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!sunqbc.risq.qc.ca!newsfeed.ecrc.net!newsfeed.nacamar.de!news.icm.edu.pl!news.nask.pl!01-newsfeed.univie.ac.at!03-newsfeed.univie.ac.at!fstgal00.tu-graz.ac.at!balu.kfunigraz.ac.at!not-for-mail From: Markus Zettl Newsgroups: bionet.molbio.proteins Subject: Triton X-100 in SDS-Page Date: Tue, 02 Dec 1997 14:16:01 +0100 Organization: Karl-Franzens-Universitaet Graz Lines: 7 Message-ID: <34840A11.E061B216@kfunigraz.ac.at> NNTP-Posting-Host: bimk14.kfunigraz.ac.at Mime-Version: 1.0 Content-Type: text/plain; charset=x-UNICODE-2-0-UTF-7 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [de] (Win95; I) X-Priority: 3 (Normal) Hi! I know that Triton X-100 forms micelles in a concentration over the CMC. These micelles cause difficulties if you want to carry a 12,5% SDS-Page. Therefore I wannt to know if it+ALQ-s possible to run electrophoresis whith Triton X-100 if you increase the SDS-concentration of the sample buffer? Does anyone know other possibilities to run SDS-Page with Triton X-100. Thanks for helpfull information! From owner-proteins@net.bio.net Mon Dec 01 22:00:00 1997 From: pxpst2@vms.cis.pitt.delet.edu (Peter) Newsgroups: bionet.molbio.proteins Subject: Re: Need help! Date: Tue, 02 Dec 1997 15:41:35 -0500 Organization: University of Pittsburgh Lines: 60 Distribution: world Message-ID: References: <199712021705.MAA00343@james.freenet.hamilton.on.ca> NNTP-Posting-Host: pelli.pathology.pitt.edu X-Newsreader: MT-NewsWatcher 2.3.5 Path: biosci!agate!ihnp4.ucsd.edu!munnari.OZ.AU!news.Hawaii.Edu!news.lava.net!coconut-wireless!news.flex.com!www.nntp.primenet.com!globalcenter1!news.primenet.com!nntp.primenet.com!news.idt.net!news.voicenet.com!dsinc!pitt.edu!newsfeed.pitt.edu!pxpst2 In article <199712021705.MAA00343@james.freenet.hamilton.on.ca>, icurkovic@HWCN.ORG wrote: > Eugene is a 10 yr old boy who has been diagnosed as sufferring from > Prader-Willi syndrome. The Prader-Willi syndrome is a genetic disorder > characterized by decreased sensitivity to pain, fair, hair and behavioural > disturbances including overeating leading to obesity. One of the > hypotheses developed to explain the manifestiations of this syndrome is a > disturbance to explain the manifestations of this syndrome is a > disturbance in the production of the polyprotein, proopiomelanocortin > (POMC) or its post-translational modifications. > > Eugene has been treated with drugs which are intended to cause inhibition > of enzymes involved in the proteolysis of the defective POMC. > > Eugene's mother, who works in an institute for molecular biology and > biotechnoloogy, is pregnant and seeks counseling about the risks of her > offspring to be affected by the Prader-Willi syndrome. She read a recent > report claiming that the gene expression can be manipulated. > > ------------ THE END------------- > > I already know that I should study the following: > > -gene expression > -competitive/noncompetitive inhibition > -post-translational modifications Ivan Those topics do not directly relate to Prader-Willi syndrome but are good to study. Prader Willi(PWS) has to do with gene imprinting. Pws and Angelman syndrome arise from paternal deletion or maternal disomy and from maternal deletion or paternal disomy of region 15q11-13. Parental imprinting is the expression of certain genes from either the maternal or paternal chromosomes. This is accomplished by epigenic modification of the chromosomes. Hope this is a good start Peter -- "Don't you eat that yellow snow WAtch out where the Huskies go" --------------------------------------------------------------------- Let us not forget those marketing boys from SPAM CENTRAL bestrealtor@marketingmaster.com info@herbchew.com clickthru@timefreedom.com invite@onlinenow.net zippydj@nevwest.com Offer@shire.com empower@empowerlabs.com dynamarket@vaprnet.com root@mail.icongrp.com cashrewards@hotmail.com From owner-proteins@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!news2.chicago.iagnet.net!iagnet.net!newspump.sol.net!sol.net!ix.netcom.com!news From: "Scott Shanes" Newsgroups: bionet.molbio.proteins Subject: US-NJ-JOB OPPORTUNITY WITH G PROTEIN COUPLED RECEPTORS Date: 2 Dec 1997 20:11:32 GMT Organization: Netcom Lines: 16 Message-ID: <01bcff5e$aa1a72c0$7279d6ce@scott-s-armada> NNTP-Posting-Host: trn-nj4-18.ix.netcom.com X-NETCOM-Date: Tue Dec 02 12:11:32 PM PST 1997 X-Newsreader: Microsoft Internet News 4.70.1161 I am looking for a Scientist to work on G Protein Coupled Receptors . This person will be working on Radio Ligand Binding Assays and Second Messenger Assays. The selected candidates' job will be 50% basic science and 50% applied science drug discovery. This person will be a part of a larger group in drug discovery and will be supervising three people. This person should have excellent communication skills and computer skills (word processing, data analysis, excel, etc.). You should possess a PhD in Pharmacology, Biochemistry, Neuroscience or related field with 1 year postdoctoral experience. Our client is a leading pharmaceutical company with research facilities in Northern New Jersey and can provide excellent benefits (health insurance, dental, and vision plan, paid vacation and more). A high impact, high profile position with excellent opportunity for advancement. Please contact Scott Shanes by phone at 609-584-8733 Ext. 218, fax CV and cover letter to 609-584-9575 or E-Mail to sis@diedremoire.com From owner-proteins@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.molbio.proteins Subject: RECOMB98: Call for Posters Date: 2 Dec 1997 17:54:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712030154.RAA08027@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net CALL FOR RECOMB 98 POSTERS Please send a one-page abstract (about 200 words, plain justified text, formatted to fit European Standard A-4: 8.5X11 inch or 21.5X28 cm) of your Poster including title, author(s), affiliation and abstract-text to Martin Vingron DKFZ, Theoretische Bioinformatik (0815) INF 280 69120 Heidelberg Germany The actual poster space will be about 15 pages. A booklet with the accepted poster abstracts will be produced and available at the conference. Deadline for poster abstract submission: January 1, 1998 Notification of acceptance/rejection: January 16, 1998 From owner-proteins@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!news-peer.gip.net!news.gsl.net!gip.net!sunqbc.risq.qc.ca!news.uow.edu.au!metro!metro!unsw.edu.au!tim From: tim@[REMOVETHISTOMAIL]unsw.edu.au (Tim Salmon) Newsgroups: bionet.molbio.proteins Subject: Re: Need help! Date: Wed, 03 Dec 1997 12:18:24 +0100 Organization: School of Microbiology UNSW Lines: 25 Distribution: world Message-ID: References: <199712021705.MAA00343@james.freenet.hamilton.on.ca> NNTP-Posting-Host: 149.171.168.46 X-Newsreader: MT-NewsWatcher 2.3.3 Peter, May I suggest that along with technical issues, your professor may also consider ethical considerations to be of great importance, for example i) screening for genetic defects ii) courses of action after positive identification of genetic defect (abortion/gene therapy) iii) possible premature use of drugs which are implied in the question to have no known in vivo effect on the disease iv) no mention of child's wellbeing - (is he perfectly happy being a fair-headed plump little kid that doesn't cry when he falls over?) or of measures taken to counter this directly, such as counselling. Sorry, not having a clue about Prader-Willi syndrome, this is about all I can come up with Cheers, Tim _____________________________________ Tim Salmon School of Microbiology and Immunology University of New South Wales Australia tim@unsw.edu.au From owner-proteins@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!BOTANY.UQ.EDU.AU!J.Marcus From: J.Marcus@BOTANY.UQ.EDU.AU ("Marcus, Dr J.") Newsgroups: bionet.molbio.proteins Subject: Re: Protein Homology Software Date: 2 Dec 1997 17:10:44 -0800 Organization: Dept of Botany, Univ of Queensland Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <1BB3574329F@botany.uq.edu.au> References: Reply-To: Marcus@tpp.uq.edu.au NNTP-Posting-Host: net.bio.net MS Excel doesn't do too bad a job. You can just put one letter per cell and then format it as you please. If you really want a sequence package, we use MacVector. It does alignments and a host of other things like design of primers etc. Hope that helps. John Marcus _________________________________________________________ John Marcus Marcus@tpp.uq.edu.au (Dr J.Marcus) Cooperative Research Centre for Tropical Plant Pathology 5th Level John Hines Building University of Queensland St. Lucia, QLD 4072 AUSTRALIA Fax: 61-7-3365-4771 Phone: 61-7-3365-4764 From owner-proteins@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!uthct.edu!wu From: wu@uthct.edu (Cathy Wu) Newsgroups: bionet.molbio.proteins Subject: New Release 2.0 - ProClass Protein Family Database Date: 2 Dec 1997 16:29:07 -0800 Organization: The University of Texas Health Center at Tyler Lines: 65 Sender: daemon@net.bio.net Distribution: world Message-ID: <3484859E.C646445E@uthct.edu> Reply-To: wu@uthct.edu NNTP-Posting-Host: net.bio.net The Bioinformatics Research Group of the University of Texas Health Center at Tyler is pleased to announce the Release 2.0 of its ProClass Protein Family Database. The database is available for on-line search at: http://diana.uthct.edu/proclass.html Free copies of the ProClass Database and its query program can be obtained via anonymous FTP to: ftp://diana.uthct.edu/pub/ProClass/ The ProClass Protein Family Database, cited in a recent Science Genome issue (Vol. 278, No. 5338, p. 615, Genome Maps), is a non-redundant database organized according to family relationships as defined collectively by PIR superfamilies and ProSite patterns. The objectives are to facilitate protein family information retrieval, unveil domain and family relationships, and classify multi-domained proteins. This is achieved by combining global and motif sequence similarities into a single classification scheme. The current ProClass release consists of 103,312 sequence entries retrieved from PIR-international (Release 54.0, September 1997) and SwissProt (Release 34.0, November 1996) databases. It has three sub-databases, ProClass_Family (PCFam), ProClass_Sequence (PCSeq) and ProClass_Motif (PCMotif) for the collections of family, sequence and motif entries. Major features of ProClass Release 2.0 are: - Compilation of ProClass_Motif. The data set provides an up-to-date and comprehensive source of motif sequences and alignments for all ProSite patterns. Included are several thousands of new family members which are not catalogued in ProSite (Release 13.0), but identified by our GeneFIND family identification system (version 2.0, December 1997, http://diana.uthct.edu/genefind.html). - Hypertext links to all major family databases. Included are links to the underlying raw databases (PIR, SwissProt and ProSite), family/superfamily alignments (PIR_ALN, MIPS), other family/domain databases (BLOCKS, PRINTS, ProDom, Pfam), and structural class databases (SCOP, CATH, HSSP). References: - Wu, C. H., Zhao, S. and Chen, H. L. (1996). A protein class database organized with ProSite protein groups and PIR superfamilies. Journal of Computational Biology, 3(4), 547-561. - Wu, C. H. and Shivakumar, S. (1998). ProClass protein family database: New version with motif alignments. Proceedings of the Pacific Symposium on Biocomputing '98, (In Press). If you have any questions or comments, please contact me at wu@uthct.edu. -- Cathy H. Wu, Ph.D. Associate Professor of Biomathematics University of Texas Health Center at Tyler P. O. Box 2003, Tyler, TX 75710 E-Mail : wu@uthct.edu Phone : (903) 877-7962 Fax : (903) 877-5914 WWW URL: http://diana.uthct.edu/~wu GeneFIND Web Server: http://diana.uthct.edu From owner-proteins@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!news.misty.com!www.nntp.primenet.com!globalcenter0!news.primenet.com!nntp.primenet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!nntphost.dur.ac.uk!vega.dur.ac.uk!d527bd From: Phil Chapman Newsgroups: bionet.molbio.proteins Subject: Protein Homology Software Date: Tue, 2 Dec 1997 22:22:42 +0000 Organization: University of Durham, Durham, UK. Lines: 11 Message-ID: NNTP-Posting-Host: vega.dur.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Can anyone suggest a piece of free or cheap software for the Mac that enables you to produce protein sequence comparisons like you see in the journals? Doing it by hand using MS Word is starting to annoy me.... Thanks for your help, Phil CHapman (Final year undergraduate in Mol Biol + Biochem at Durham Uni UK) From owner-proteins@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!HWCN.ORG!icurkovic From: icurkovic@HWCN.ORG Newsgroups: bionet.molbio.proteins Subject: Need help! Date: 2 Dec 1997 20:04:45 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 65 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712030405.XAA27918@james.freenet.hamilton.on.ca> NNTP-Posting-Host: net.bio.net >> Eugene is a 10 yr old boy who has been diagnosed as sufferring from >> Prader-Willi syndrome. The Prader-Willi syndrome is a genetic disorder >> characterized by decreased sensitivity to pain, fair, hair and >> behavioural disturbances including overeating leading to obesity. One of >> the hypotheses developed to explain the manifestiations of this >> syndrome is a disturbance to explain the manifestations of this >> syndrome is a disturbance in the production of the polyprotein, >> proopiomelanocortin (POMC) or its post-translational modifications. >> Eugene has been treated with drugs which are intended to cause >> inhibition of enzymes involved in the proteolysis of the defective >> POMC. >> Eugene's mother, who works in an institute for molecular biology and >> biotechnoloogy, is pregnant and seeks counseling about the risks of her >> offspring to be affected by the Prader-Willi syndrome. She read a >> recent report claiming that the gene expression can be manipulated. >> ------------ THE END------------- >> I already know that I should study the following: >> -gene expression >> -competitive/noncompetitive inhibition >> -post-translational modifications > Ivan Those > topics do not directly relate to Prader-Willi syndrome but are > good to study. First of all, thanks for your help! I really appreciate it. I probably wasn't as specific as I wanted to be when I posted this problem in the newsgroup, but we aren't actually supposed to solve the problem. What I wanted to know was exactly what you stated above...good topics to study. > Prader Willi(PWS) has to do with gene > imprinting. Pws and Angelman syndrome arise from paternal > deletion or maternal disomy and from maternal deletion or > paternal disomy of region 15q11-13. Parental imprinting is the > expression of certain genes from either the maternal or > paternal chromosomes. This is accomplished by epigenic > modification of the chromosomes. Hope this is a good start I'm sorry for asking, but what exactly do you mean by epigenic modification of the chromosomes. Does this have anything to do with recombination? If so, then you just gave me one more clue as to what else I could study. I also assume that this syndrome is caused by a mutation. Is this assumption correct? If so, then I should probably go over DNA repair mechanisms as well. If you could answer these questions for me again, it would be of great assistance. I am really looking forward to doing well on this exam! Thanks for your time, ****************************************************************************** * Ivan Curkovic * "If at first you don't succeed, * * McMaster University * try again. Then quit. No use * * Hamilton, Ontario, Canada * being a damn fool about it." * * E-mail: icurkovic@hwcn.org * - Dilbert's Rules of the * * URL: www.hwcn.org/~ae987/Profile.html * Workplace * ****************************************************************************** From owner-proteins@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!INFECT.DMED.IUPUI.EDU!mitchell From: mitchell@INFECT.DMED.IUPUI.EDU (Mitch Krathwohl) Newsgroups: bionet.molbio.proteins Subject: Cleaving peptide tags Date: 3 Dec 1997 12:30:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <3485C178.5F739C54@infect.dmed.iupui.edu> NNTP-Posting-Host: net.bio.net Help! I have been using the Affinity LIC protein purification kit from Stratagene, which has worked well until I tried to cleave the peptide tag using enterokinase. More enzyme does not help, nor does longer incubation times. Does anyone have any suggestions? Thanks. Mitch Krathwohl mkrathwo@mdep.iupui.edu From owner-proteins@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!newscore.univie.ac.at!03-newsfeed.univie.ac.at!fstgal00.tu-graz.ac.at!spaniel From: smith@umes07.avl.co.at (Search Spaniel) Newsgroups: bionet.molbio.proteins Subject: Protein-search the web quickly with Search Spaniel Date: Wed, 03 Dec 97 17:35:21 GMT Organization: Search Spaniel Lines: 4 Message-ID: <250108680@searchspaniel.com> NNTP-Posting-Host: isdn024.tu-graz.ac.at To Protein-search the most search engines in the shortest time, use the internet's newest search engine - Search Spaniel at: http://www.searchspaniel.com/ From owner-proteins@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!synbio.tpgnet.net!saudekv From: saudekv@synbio.tpgnet.net (Vladimir Saudek) Newsgroups: bionet.molbio.proteins Subject: Protein Modeller Date: 3 Dec 1997 09:13:31 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 63 Sender: daemon@net.bio.net Distribution: world Message-ID: <19971203171744789.AAA141@[195.10.9.147]> NNTP-Posting-Host: net.bio.net Synthelabo Biomoleculaire has an immediate opening in the Group of Structural Biology for Protein Modeller The successful candidate will have PhD in structural biology, physical chemistry, theoretical chemistry or chemistry and several years of postdoctoral experience in a well-established protein modelling group. His/her skills will include Analysis of amino and nucleic acid sequences and sequence - function assignment Homology and threading modelling Molecular mechanics and dynamics Docking techniques Use of www modelling and sequence analysis resources Good knowledge of structural biology, familiarity with X-ray crystallography and NMR spectroscopy Ability to collaborate within a specialised protein structure team (X-ray crystallography, NMR and optical spectroscopy) as well as interact with scientists in a multidisciplinary institute (molecular biology, biochemistry, chemistry, genomics, bioinformatics) Excellent communication Integrate in an international team Synthelabo Biomoleculaire, a research institute located in Strasbourg and a subsidiary of the French pharmaceutical company Synthelabo, performs research towards the rapid generation of leads for new therapeutic targets emerging from the human genome. The Group of Structural Biology is equipped with 600, 500 and 360 MHz NMR spectrometers, X-ray diffractometer and a range of optical spectrometers (UV, IR, Raman, CD, fluorescence). The computing environment is based on Silicon Graphics servers and workstations. The group collaborates closely with molecular biology, genomics, bioinformatics, and medicinal and combinatorial chemistry. If you are interested, please send your CV and a letter of interest (preferably by email) to the address below. Vladimir Saudek Structural Biology Synthelabo Biomoleculaire 16, rue d'Ankara Strasbourg 67080 CEDEX, France email: saudekv@synbio.tpgnet.net tel: +33 (0)3 8860 8893 fax: +33 (0)3 8845 9070 ********************************************* Vladimir Saudek Structural Biology Synthelabo Biomoleculaire 16, rue d'Ankara Strasbourg 67080 CEDEX, France email: saudekv@synbio.tpgnet.net tel: +33 (0)3 8860 8893 fax: +33 (0)3 8845 9070 PLEASE NOTE THE NEW TELEPHONE NUMBER ********************************************* From owner-proteins@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!gmorley From: gmorley@hgmp.mrc.ac.uk (Mr. G. Morley) Newsgroups: bionet.molbio.proteins Subject: Protease recognition sites Date: 3 Dec 1997 13:51:57 GMT Organization: MRC Human Genome Mapping Project Resource Centre Lines: 10 Message-ID: <663o5t$31r$1@niobium.hgmp.mrc.ac.uk> NNTP-Posting-Host: tin.hgmp.mrc.ac.uk HI.. I was wondering if anyone out there knew of a web page (or worse coming to worse) a good book which might list known protease recognition sites... I realise that a lot of proteases have very general recognition motifs (ie. XXXR) but if anyone has any info I would be obliqued if they could e-mail me at : gmorley@rpms.ac.uk Thanks in advance, gary morley. From owner-proteins@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.internetmci.com!207.103.147.20!news.voicenet.com!dsinc!pitt.edu!newsfeed.pitt.edu!pxpst2 From: pxpst2@vms.cis.pitt.delet.edu (Peter) Newsgroups: bionet.molbio.proteins Subject: Re: Need help! Date: Wed, 03 Dec 1997 09:06:05 -0500 Organization: University of Pittsburgh Lines: 44 Distribution: world Message-ID: References: <199712030405.XAA27918@james.freenet.hamilton.on.ca> NNTP-Posting-Host: pelli.pathology.pitt.edu X-Newsreader: MT-NewsWatcher 2.3.5 In article <199712030405.XAA27918@james.freenet.hamilton.on.ca>, icurkovic@HWCN.ORG wrote: > First of all, thanks for your help! I really appreciate it. I probably > wasn't as specific as I wanted to be when I posted this problem in the > newsgroup, but we aren't actually supposed to solve the problem. What I > wanted to know was exactly what you stated above...good topics to study. > > > Prader Willi(PWS) has to do with gene > > imprinting. Pws and Angelman syndrome arise from paternal > > deletion or maternal disomy and from maternal deletion or > > paternal disomy of region 15q11-13. Parental imprinting is the > > expression of certain genes from either the maternal or > > paternal chromosomes. This is accomplished by epigenic > > modification of the chromosomes. Hope this is a good start > > I'm sorry for asking, but what exactly do you mean by epigenic > modification of the chromosomes. Does this have anything to do with > recombination? If so, then you just gave me one more clue as to what > else I could study. First off I am not a Molecular biologist so before peaple decide to flame me, I make mistakes. My crude understanding of Gene imprinting in plian english is that one gene is dominantly expressed while the other allele is silenced. What causes the silencing is not known but the silenced gene is ussually hyper-methylated. I think with PWS the gene must come from mom and with AS, the gene is from dad. Maybe you should ask the group more about DNA mthylation and ways that nature silences genes > > I also assume that this syndrome is caused by a mutation. Is this > assumption correct? If so, then I should probably go over DNA repair > mechanisms as well. NO not a mutation per se. It is that a dominant mutant gene gets expsressed. In the case of PWS mom may have good genes so the syndrome does not occur. Mom could have one good one bad and the good is paased on so no PWS but if the bad one is passed then the syndrome PWS shows itself and does not mtter on what genes were passed by the father becaused they are silenced. > Merry Christmas Peter Pedaiditakis From owner-proteins@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!news.idt.net!news1.chicago.iagnet.net!iagnet.net!newsspool.doit.wisc.edu!wiscnews.wiscnet.net!news.doit.wisc.edu!mcmahan From: mcmahan@oncology.wisc.edu (Scott McMahan) Newsgroups: bionet.molbio.proteins Subject: Re: Protease recognition sites Date: Wed, 03 Dec 1997 22:38:05 -0600 Organization: University of Wisconsin-Madison Lines: 26 Message-ID: References: <663o5t$31r$1@niobium.hgmp.mrc.ac.uk> NNTP-Posting-Host: alpha.oncology.wisc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 In article <663o5t$31r$1@niobium.hgmp.mrc.ac.uk>, gmorley@hgmp.mrc.ac.uk (Mr. G. Morley) wrote: :HI.. I was wondering if anyone out there knew of a web page : :(or worse coming to worse) a good book which might list : :known protease recognition sites... I realise that a lot : :of proteases have very general recognition motifs (ie. XXXR) : :but if anyone has any info I would be obliqued if they could : :e-mail me at : gmorley@rpms.ac.uk : :Thanks in advance, : : : :gary morley. Try _Specificity_of_Proteolysis_ by Borivoj Keil (Springer-Verlag publ.) -- Scott McMahan mcmahan@oncology.wisc.edu From owner-proteins@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!HWCN.ORG!icurkovic From: icurkovic@HWCN.ORG Newsgroups: bionet.molbio.proteins Subject: Re: Need help! Date: 3 Dec 1997 21:07:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712040508.AAA22028@james.freenet.hamilton.on.ca> NNTP-Posting-Host: net.bio.net I did a bit more research on PWS and I found out a bit more things about it that should help me to focus on some topics for my biochem exam. I found out (correct me if I'm wrong) that a piece of DNA on chromosome 15 from the father is deleted. I was thinking that with this information, I could look at the following other topics to study for: -recombination (I read that during crossover the chiasma does not line up as it usually should) -DNA replication -DNA repair -transposons -restriction enzymes? Like I said before, I do not have to solve the given problem. Our prof just gave us that problem so that we could pick apart possible topics that he might ask us on our exam. Anyway, thanks for all your help guys. I really appreciate it. This is one undergrad that isn't as nervous anymore about this exam. Happy holidays! Ivan From owner-proteins@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!news.idt.net!news.maxwell.syr.edu!news.syd.connect.com.au!news.mel.connect.com.au!news.mel.aone.net.au!newsfeed-in.aone.net.au!inferno.mpx.com.au!news.unimelb.edu.au!ludwignt-4 From: murphy_r@licre.ludwig.edu.au (Roger Murphy) Newsgroups: bionet.molbio.proteins Subject: chromatography parameters Date: Thu, 04 Dec 97 04:53:44 GMT Organization: Ludwig Institute for Cancer Research Lines: 40 Message-ID: <66596p$mnp$1@izvestia.its.unimelb.edu.au> NNTP-Posting-Host: ludwignt-4.austin.unimelb.edu.au X-Newsreader: News Xpress 2.0 Beta #0 Hello there! This note is addressed to all you chrmoatographers out there..... I recently came across what appears to be a novel use of the HETP parameter for chromatography columns. I hadn't used this paricular instrumentation before (it will remain anonymous, but is widely used for protein purification!) and part of the column assessment protocols involved calculating an HETP based on an unretained peak, i.e. came through at the void volume of the column. This calculation was used as a measure of how well the column was packed, but......my years of chromatography tell me (perhaps mistakenly?) that such a calculation on an unretained peak tells your absolutely nothing about the efficiency of the column, and is not an appropriate measure even of how well it's packed. In their defense, they also calculate an asymmetry factor, which I'd be prepared to accept as a legitimate measure of the packing efficiency, but does anyone else feel as I do that the use of HETP here is quite inappropriate? Pity we don't have a bionet.chromatography newsgroup for this sort of discussion... I'd be interested in any ideas on this, including those who want to tell me I'm an idiot (if I am, then so be it!) Cheers, Roger Roger Murphy, Ph.D. Biological Production Facility Ludwig Institute for Cancer Research Austin & Repatriation Medical Centre Studley Road, Heidelberg, Vic. 3084 Australia. Tel 61-3-94965463 Fax 61-3-94965436 Email murphy_r@licre.ludwig.edu.au From owner-proteins@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!HWCN.ORG!icurkovic From: icurkovic@HWCN.ORG Newsgroups: bionet.molbio.proteins Subject: Re: Need help! Date: 4 Dec 1997 09:21:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712041721.MAA10356@james.freenet.hamilton.on.ca> NNTP-Posting-Host: net.bio.net > -recombination (I read that during crossover the chiasma does not line up as it usually should) - ? not clear on what you mean. A finding suggested that an unequeal crossover occurring in the paternal meoisis at the breakpoint is the mechanism leading to deletion. The authors also noted that asymmetric exchanges between nonsister chromatids in meiosis I have previously been demonstrated. As for the stuff on the chiasma, I tried looking again where I first found it, but I just could not find it again. :-( > None of these topics deal with PWS/As directly. "Classical mendelian > genetics assumes that the parental origin of a gene will not influence > its expression. However, this does not appear to be the case with a > small number of genes which may be involved in embryonic and postnatal > development. This phenomenon is known as gene imprinting." What is known > is that the gene that get silenced is heavily metylated. WHY? I believe heavy methylations are used in some forms of DNA repair. Perhaps the DNA repair system is not working properly, but this is probably highly unlikely. But I do believe that I should focus on this topic as well. > Are there any other ways to insure the dominant expression of a gene? I guess I'll have to look into that. I also read that PWS may also be caused by defects in mRNA processing, but what I read really didn't get into specifics. Ivan From owner-proteins@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!sbphrd.com!Hayley_C_Cordingley From: Hayley_C_Cordingley@sbphrd.com (Hayley_C_Cordingley) Newsgroups: bionet.molbio.proteins Subject: 2D gel electrophoresis equipment Date: 4 Dec 1997 08:36:22 -0800 Organization: SmithKline Beecham Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <34874C4F.6E9B@sbphrd.com> NNTP-Posting-Host: net.bio.net Hello there. We're going to be starting on some 2D gel work and will be buying in the equipment in from scratch. I have no idea who sells the best/easiest/most reproducible set up. I've seen the Pharmacia kit in action and it looks good. Is this a good system to go with or does anyone have any other sources? If so could you please e-mail me at Hayley_C_Cordingley@sbphrd.com Thanks in advance. -- The opinions expressed in this communication are my own, and do not necessarily reflect those of my employer. From owner-proteins@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!BOTANY.UQ.EDU.AU!J.Marcus From: J.Marcus@BOTANY.UQ.EDU.AU ("Marcus, Dr J.") Newsgroups: bionet.molbio.proteins Subject: Re: cation exchange chromat Date: 4 Dec 1997 14:38:14 -0800 Organization: Dept of Botany, Univ of Queensland Lines: 45 Sender: daemon@net.bio.net Distribution: world Message-ID: <1EAF3EC7630@botany.uq.edu.au> References: <665st3$l40$1@lyra.csx.cam.ac.uk> Reply-To: Marcus@tpp.uq.edu.au NNTP-Posting-Host: net.bio.net If there is hydrophobic interaction going on with your column, you could add say 10 to 20% Ethanol or Acetonitrile to your buffers. These would not interfere with the CIEX and should disrupt anyhydrophobic interaction you see. Hoping that helps, John Marcus > Dear All, > > I am having problems with elution of my protein from a Resource S cation > exchange resin. I get an active peak when I elute the column with a > 0-1M NaCl gradient (at about 500mM) I then wash the column in 2M NaCl > and nothing elutes. When I put the column back to 0 salt I get a load of > active protein eluting when the column salt conc is about 500mM (which > is the same protein as elutes from the gradient). Any ideas whats > happening? Am I getting a component of hydrophobic binding at hi > salt concs (ie non specific to the matrix) which is removed > when I once again reduce the salt conc. Could detergents get around > \this and if so which detergents are best (which non ionic > detergents donot interfer with UV absorbance less than 280nm?) > > Thanks in advance > > Robert > > Email rw200@cus.cam.ac.uk > > -- > > _________________________________________________________ John Marcus Marcus@tpp.uq.edu.au (Dr J.Marcus) Cooperative Research Centre for Tropical Plant Pathology 5th Level John Hines Building University of Queensland St. Lucia, QLD 4072 AUSTRALIA Fax: 61-7-3365-4771 Phone: 61-7-3365-4764 From owner-proteins@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!agate!usenet.INS.CWRU.Edu!vncnews!HSNX.wco.com!peerfeed.ncal.verio.net!rill.news.pipex.net!pipex!uunetukout!join.news.pipex.net!pipex!uunetukin!server1.netnews.ja.net!bham!med803.bham.ac.uk!user From: noone@bham.ac.uk (CRC Institute for Cancer Studies) Newsgroups: bionet.molbio.proteins Subject: Re: chromatography parameters Date: Thu, 04 Dec 1997 13:52:00 +0000 Organization: CRC Lines: 40 Message-ID: References: <66596p$mnp$1@izvestia.its.unimelb.edu.au> NNTP-Posting-Host: med803.bham.ac.uk In article <66596p$mnp$1@izvestia.its.unimelb.edu.au>, murphy_r@licre.ludwig.edu.au (Roger Murphy) wrote: > Hello there! > > This note is addressed to all you chrmoatographers out there..... > I recently came across what appears to be a novel use of the HETP parameter > for chromatography columns. I hadn't used this paricular instrumentation > before (it will remain anonymous, but is widely used for protein > purification!) and part of the column assessment protocols involved > calculating an HETP based on an unretained peak, i.e. came through at the void > volume of the column. This calculation was used as a measure of how well the > column was packed, but......my years of chromatography tell me (perhaps > mistakenly?) that such a calculation on an unretained peak tells your > absolutely nothing about the efficiency of the column, and is not an > appropriate measure even of how well it's packed. In their defense, they also > calculate an asymmetry factor, which I'd be prepared to accept as a legitimate > measure of the packing efficiency, but does anyone else feel as I do that the > use of HETP here is quite inappropriate? > > Pity we don't have a bionet.chromatography newsgroup for this sort of > discussion... > > I'd be interested in any ideas on this, including those who want to tell me > I'm an idiot (if I am, then so be it!) > > Cheers, > > Roger > > Isn't the HETP dependent on the diffusion rate of your particle into the pores (we're not talking about Superose columns, by any chance?) which again is dependent on the size of your protein (i.e. the HETP isn't much help)? Peter From owner-proteins@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.direct.ca!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!rw200 From: rw200@cus.cam.ac.uk (R. Woodward) Newsgroups: bionet.molbio.proteins Subject: cation exchange chromat Date: 4 Dec 1997 09:24:51 GMT Organization: University of Cambridge, England Lines: 21 Message-ID: <665st3$l40$1@lyra.csx.cam.ac.uk> NNTP-Posting-Host: ursa.cus.cam.ac.uk X-Newsreader: NN version 6.5.0 #2 (NOV) Dear All, I am having problems with elution of my protein from a Resource S cation exchange resin. I get an active peak when I elute the column with a 0-1M NaCl gradient (at about 500mM) I then wash the column in 2M NaCl and nothing elutes. When I put the column back to 0 salt I get a load of active protein eluting when the column salt conc is about 500mM (which is the same protein as elutes from the gradient). Any ideas whats happening? Am I getting a component of hydrophobic binding at hi salt concs (ie non specific to the matrix) which is removed when I once again reduce the salt conc. Could detergents get around \this and if so which detergents are best (which non ionic detergents donot interfer with UV absorbance less than 280nm?) Thanks in advance Robert Email rw200@cus.cam.ac.uk -- From owner-proteins@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!pitt.edu!newsfeed.pitt.edu!pxpst2 From: pxpst2@vms.cis.pitt.delet.edu (Peter) Newsgroups: bionet.molbio.proteins Subject: Re: Need help! Date: Thu, 04 Dec 1997 10:03:58 -0500 Organization: University of Pittsburgh Lines: 34 Distribution: world Message-ID: References: <199712040508.AAA22028@james.freenet.hamilton.on.ca> NNTP-Posting-Host: pelli.pathology.pitt.edu X-Newsreader: MT-NewsWatcher 2.3.5 In article <199712040508.AAA22028@james.freenet.hamilton.on.ca>, icurkovic@HWCN.ORG wrote: > > I found out (correct me if I'm wrong) that a piece of DNA on chromosome 15 > from the father is deleted. I was thinking that with this information, I > could look at the following other topics to study for: I already told you that the gene responsible is located on chromasome 15 and the region of interest spans from q11.2 - q12. Two loci are believed to be involved. All in all, 4 genes have been Identified as imprinted genes. PWS/AS is one region. the other three regions are where? > > -recombination (I read that during crossover the chiasma does not line up > as it usually should)- ? not clear on what you mean. > -DNA replication.- 5' ------> 3' always. but the ends of the Chromosomes are where life gets interesting. Telomers, natures answer to degenerate replication. > -DNA repair- These guys are important in cancer initiation. If they do not work right, the Life form will have big PROBLEMS. > -transposons- these are mobile elements that can move around the genome. I think the scientist that found them was a corn researcher named Barbara McKormick > -restriction enzymes?- DNA scissors None of these topics deal with PWS/As directly. "Classical mendelian genetics assumes that the parental origin of a gene will not influence its expression. However, this does not appear to be the case with a small number of genes which may be involved in embryonic and postnatal development. This phenomenon is known as gene imprinting." What is known is that the gene that get silenced is heavily metylated. WHY? Are there any other ways to insure the dominant expression of a gene? Peter From owner-proteins@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!GROVE.UFL.EDU!stones From: stones@GROVE.UFL.EDU ("ke wu") Newsgroups: bionet.molbio.proteins Subject: concentrating protein samples Date: 5 Dec 1997 11:59:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712051958.OAA23447%anat67104.anatomy.med.ufl.edu@camphor.grove.ufl.edu> NNTP-Posting-Host: net.bio.net Dear netters: I need to concentrate about 200 ul immunoprecipitation sample into 20 ul volume so that I could load it on a SDS-PAGE. Could anyone suggest any good method to concentrate protein samples without losing significant amount of proteins. Thank you. Ke From owner-proteins@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!rutgers!uwm.edu!newsfeeds.sol.net!news.maxwell.syr.edu!newsfeed.ecrc.net!newsfeed.nacamar.de!news1.isdnet.net!grolier!not-for-mail From: "Thierry Baussant" Newsgroups: bionet.molbio.proteins Subject: Re: cation exchange chromat Date: Fri, 5 Dec 1997 20:51:11 +0100 Organization: Grolier Interactive Europe Lines: 11 Message-ID: <669ijq$6mc$1@newsfeeds.grolier.fr> References: <665st3$l40$1@lyra.csx.cam.ac.uk> NNTP-Posting-Host: ppp-134-22.annecy.club-internet.fr X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 May be your protein precipitate near the salt concentration necessary for elution. Concerning a detergent, I suggest you the use of CHAPS or CHAPSO, a non denaturing detergent easy to eliminate Yours Thierry Baussant From owner-proteins@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!GROVE.UFL.EDU!stones From: stones@GROVE.UFL.EDU ("ke wu") Newsgroups: bionet.molbio.proteins Subject: protein microsequencing resources Date: 5 Dec 1997 12:03:55 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712052003.PAA18562%anat67104.anatomy.med.ufl.edu@camphor.grove.ufl.edu> NNTP-Posting-Host: net.bio.net Dear netters: I will have some protein samples for sequencing. Could you guys share some exprience with some good protein microsequencing providers? Thanks. Ke From owner-proteins@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!IC.COM.PL!PSolarz From: PSolarz@IC.COM.PL ("Piotr Solarz") Newsgroups: bionet.molbio.proteins Subject: Does any one know whre to find "Crystal Structure of human lithostathine" Date: 5 Dec 1997 07:40:18 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712051538.QAA04326@main.ic.com.pl> NNTP-Posting-Host: net.bio.net Dear biochemics My friend asked me for a help in looking for: J.A. BERTRAND, D. PIGNOL, J.P. BERNARD, J.M. VERDIER "Crystal Structure of human lithostathine, the pancreatic inhibitor of = stone formation" EMB J. V15 2678 1996. Does anyone knows in which library this publikation is placed or knows = the e-mail address to the authors of it. In my city there is none library that have got EMB J. publications. Thank you for help. Piotr Solarz PSolarz@IC.COM.PL Wroclaw - POLAND From owner-proteins@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!agate!howland.erols.net!news-peer.gip.net!news.gsl.net!gip.net!streamer1.cleveland.iagnet.net!iagnet.net!news-peer.bt.net!btnet!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.cc.ic.ac.uk!not-for-mail From: Armin Sepp Newsgroups: bionet.molbio.proteins Subject: Re: de-glycosylation Date: Fri, 05 Dec 1997 13:06:58 +0100 Organization: Dept. Immunology, Imperial College School of Medicine, Hammersmith Campus,DuCane Road, London W12 0NN, UK Lines: 32 Message-ID: <3487EE61.4886@rpms.ac.uk> References: <65tfa4$15e$1@izvestia.its.unimelb.edu.au> NNTP-Posting-Host: imm5cwb2.rpms.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Macintosh; I; PPC) > Dear Roger, > How about periodate treatment? I have just read one protocol that they > used sodium periodate (10mM) in PBS for 15 minutes. They should remove > neary all of carbohydrate. > Prachya, CNX, Thailand. > > On Mon, 1 Dec 1997, Roger Murphy wrote: > > > Hi fellow protein chemists! > > > > Does anyone have a quick, simple recipe for removing N- and/or O-linked > > glycans from monoclonal antibodies? We want to determine the protein MW with > > and without post-translational modification of the glycan chain. > > > > Thanks, > > > > Roger Murphy Hi! I would have thought that periodate merely oxidizes adjacent cis-hydroxyls to aldehyde groups with simultaneous cleavage of the C-C bond. This should not result in the removal of the polypeptide chain from the protein. Enzymatic cleavage for both N- and O-linked glycans is an option but it is claimed to be rarely complete. According to the Oxford Glycosystems catalogue the most effective method for complete deglycosylation is anydrous trifluoromethanesulphonic acid while causing little damage to the peptide backbone. Armin Sepp a.sepp@rpms.ac.uk From owner-proteins@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!rutgers!uwm.edu!news-penn.gip.net!news-peer.gip.net!news.gsl.net!gip.net!ais.net!news1.chicago.iagnet.net!iagnet.net!dragonfly.wolfram.com!not-for-mail From: ianb@wolfram.com (Ian Brooks) Newsgroups: bionet.molbio.proteins Subject: Enyzme Handbook (2) For Sale Date: Fri, 5 Dec 1997 16:07:47 -0600 Organization: Wolfram Research, Inc. Lines: 23 Message-ID: NNTP-Posting-Host: ianbpc.wolfram.com X-Newsreader: Anawave Gravity v2.00.753 I have a brand new copy of the Enzyme Handbook vol 2 for sale. List price is $218. I will accept any reasonably offer. Enzyme Handbook 2 : Class 5 : Isomerases, Class 6 : Ligases by D. Schomburg (Editor), M. Salzmann (Editor), D. Stephan Ringbound Edition Hardcover Published by Springer Verlag Publication date: March 1991 ISBN: 0387525807 -- Ian Brooks Ph.D. Applications Developer Wolfram Research, Inc. 100 Trade Center Drive Champaign, IL 61820 217-398-0700 217-398-0747 (fax) ianb@wolfram.com From owner-proteins@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!rutgers!uwm.edu!news-penn.gip.net!news.gsl.net!gip.net!news.belnet.be!newsgate.cistron.nl!het.net!152.158.16.55.MISMATCH!newsfeed2.uk.ibm.net!ibm.net!logbridge.uoregon.edu!newsfeed.internetmci.com!193.174.75.126!news-was.dfn.de!news-kar1.dfn.de!news-stu1.dfn.de!news-mue1.dfn.de!news-nue1.dfn.de!news-lei1.dfn.de!news-ber1.dfn.de!news-ham1.dfn.de!news.mu-luebeck.de!not-for-mail From: Thomas Hettmann Newsgroups: bionet.molbio.proteins Subject: Re: de-glycosylation Date: Fri, 05 Dec 1997 18:17:51 -0100 Organization: Inst. f. Biochemie, Med. Univ. Luebeck Lines: 43 Message-ID: <3488535F.167E@physik.mu-luebeck.de> References: <65tfa4$15e$1@izvestia.its.unimelb.edu.au> <3487EE61.4886@rpms.ac.uk> NNTP-Posting-Host: obelix.biochem.mu-luebeck.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) Armin Sepp wrote: > [...] > > > > On Mon, 1 Dec 1997, Roger Murphy wrote: > > > > > Hi fellow protein chemists! > > > > > > Does anyone have a quick, simple recipe for removing N- and/or O-linked > > > glycans from monoclonal antibodies? We want to determine the protein MW with > > > and without post-translational modification of the glycan chain. > > > > > > Thanks, > > > > > > Roger Murphy > [...] > Enzymatic cleavage for both N- and O-linked glycans is an option but it > is claimed to be rarely complete. According to the Oxford Glycosystems > catalogue the most effective method for complete deglycosylation is > anydrous trifluoromethanesulphonic acid while causing little damage to > the peptide backbone. > > Armin Sepp > a.sepp@rpms.ac.uk I have used the Deglycosylation kit from Oxford Glycosystems with very good success, but this method (using anhydrous trifluoromethane sulfonic acid) is neither quick nor simple. First, it takes quite a lot of time to get the protein sample thoroughly dry, second the incubation step of the deglycosylation protocol takes another 4 hours. IMHO the kit is rather expensive, as well. Thomas -- Thomas Hettmann - Institut fuer Biochemie Medizinische Universitaet zu Luebeck Ratzeburger Allee 160 23538 Luebeck Fax: +49-451-500-4068 E-Mail: hettmann@physik.mu-luebeck.de From owner-proteins@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!GOJACKETS.COM!reck From: reck@GOJACKETS.COM Newsgroups: bionet.molbio.proteins Subject: Georgia Tech Message Board Registration Date: 5 Dec 1997 15:29:02 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712052328.PAA03137@net.bio.net> NNTP-Posting-Host: net.bio.net Your account is active. Username: The G-Man Password: 1928nc You may change your password by visiting the registration page and submitting a password change. Enjoy it! From owner-proteins@net.bio.net Fri Dec 05 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: up@uplinkpro.com Newsgroups: bionet.molbio.proteins Subject: Can't Find Your Web Site Date: 6 Dec 1997 16:31:29 -0000 Lines: 74 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <66bul1$99r@mserv1.dl.ac.uk> Reply-To: up@uplinkpro.com Original-To: proteins@dl.ac.uk Can't find your web site? Uplink will post your site to 50 search engines for $89. We guarantee your satisfaction, or you pay nothing! Millions of people every day use search engines to find web sites. Uplink makes your site easier to find by posting it to the top 50 search engines. Here's how it works: 1. Fill out the form below, and return it to us. 2. We'll post your site to the top 50 search engines within two business days and send you a full promotion report. 3. Pay nothing now. We'll send you a bill for $89 with the promotion report. If you're not completely happy, simply write "cancel" on the bill, and you'll owe nothing. THE SEARCH ENGINES Here's the list of top search engines to which we'll post your site: Alta Vista, Excite, Galaxy, HotBot, Infoseek, Lycos, Magellan, Open Text Web Index, Web Crawler, BizWeb, New Riders WWW Yellow Pages, LinkMonster, True North, Northern Light, YelloWWWeb, The Weekly Bookmark, The Galactic Galaxy, TurnPike, Unlock:The Information Exchange, Your WebScout, Manufacturers Information Network, Net Happenings, Net Mall, Web World Internet Directory, WebVenture Hotlist, What's New, WhatUSeek, JumpLink, Linkcentre Directory, InfoSpace, Jayde Online Directory, BC Internet, BizCardz Business Directory, Net-Announce, New Page ListOne World Plaza, PageHost A-Z, PeekABoo, Project Cool, Scrub The Web, Seven Wonders, Sserv, Starting Point, Web 100, Web Walker, Where2Go, World Wide Business Yellow Pages, Wow! Web Wonders!, WWW Worm, JumpCity. ORDER FORM Hit the REPLY button on your e-mail program and fill out the following information. (This information will be posted to the search engines/indexes): URL: http:// Site Title: Description (250 characters): Key words (250 characters, in descending order of importance): Your name: Company Name: Address: City: State/Prov: Zip/Postal Code: Telephone: Fax: Email address: Contact e-mail address (in case we have questions about this order): If billing a different address, please complete the following: Addressee: Company Name: Address: City: State/Prov: Zip/Postal Code: Telephone: Fax: Email address: TERMS Terms are net 15 days from date of invoice. ______________________________________________________________________ Uplink, Inc. 39B Mill Plain Road Danbury, CT 06811 Phone: (203) 791-7351 Fax: (203) 790-6407 E-mail: up@uplinkpro.com From owner-proteins@net.bio.net Sat Dec 06 22:00:00 1997 Path: biosci!BOTANY.UQ.EDU.AU!J.Marcus From: J.Marcus@BOTANY.UQ.EDU.AU ("Marcus, Dr J.") Newsgroups: bionet.molbio.proteins Subject: Re: INF-Gamma? Date: 7 Dec 1997 22:42:58 -0800 Organization: Dept of Botany, Univ of Queensland Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <23B09251777@botany.uq.edu.au> References: <348B9147.1FE4@iae.syb.ac.cn> Reply-To: Marcus@tpp.uq.edu.au NNTP-Posting-Host: net.bio.net 6M Guanidine-HCl is a stronger chaotrophic agent than 8M Urea. So jobs that Urea can't do, often can be done by Guanidine-HCl. If you want to go stroner than that, I understand that Guanidine thiocyanate is an even stronger chaotrophic(sp?) agent. Hoping that helps, John Marcus > Hello,everyone: > > I want to know why inclusion body of INF-Gamma can not be solve by urea? > I find that almost all of the reference said that INF-Gamma's Inclusion > bodies should be solve by GuCl. But why not 8M urea? Who can give me > some explanation? Thanks! > > Sincerely > > Ji Jianfei > > _________________________________________________________ John Marcus Marcus@tpp.uq.edu.au (Dr J.Marcus) Cooperative Research Centre for Tropical Plant Pathology 5th Level John Hines Building University of Queensland St. Lucia, QLD 4072 AUSTRALIA Fax: 61-7-3365-4771 Phone: 61-7-3365-4764 From owner-proteins@net.bio.net Sat Dec 06 22:00:00 1997 Path: biosci!IAE.SYB.AC.CN!wfwu From: wfwu@IAE.SYB.AC.CN ("wfwu@iae.syb.ac.cn") Newsgroups: bionet.molbio.proteins Subject: INF-Gamma? Date: 7 Dec 1997 22:12:02 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <348B9147.1FE4@iae.syb.ac.cn> Reply-To: wfwu@iae.syb.ac.cn NNTP-Posting-Host: net.bio.net Hello,everyone: I want to know why inclusion body of INF-Gamma can not be solve by urea? I find that almost all of the reference said that INF-Gamma's Inclusion bodies should be solve by GuCl. But why not 8M urea? Who can give me some explanation? Thanks! Sincerely Ji Jianfei From owner-proteins@net.bio.net Sat Dec 06 22:00:00 1997 Path: biosci!UPLINKPRO.COM!up From: up@UPLINKPRO.COM Newsgroups: bionet.molbio.proteins Subject: Can't Find Your Web Site Date: 7 Dec 1997 17:33:36 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 74 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712080134.UAA23588@athena.uplinkpro.com> Reply-To: up@uplinkpro.com NNTP-Posting-Host: net.bio.net Can't find your web site? Uplink will post your site to 50 search engines for $89. We guarantee your satisfaction, or you pay nothing! Millions of people every day use search engines to find web sites. Uplink makes your site easier to find by posting it to the top 50 search engines. Here's how it works: 1. Fill out the form below, and return it to us. 2. We'll post your site to the top 50 search engines within two business days and send you a full promotion report. 3. Pay nothing now. We'll send you a bill for $89 with the promotion report. If you're not completely happy, simply write "cancel" on the bill, and you'll owe nothing. THE SEARCH ENGINES Here's the list of top search engines to which we'll post your site: Alta Vista, Excite, Galaxy, HotBot, Infoseek, Lycos, Magellan, Open Text Web Index, Web Crawler, BizWeb, New Riders WWW Yellow Pages, LinkMonster, True North, Northern Light, YelloWWWeb, The Weekly Bookmark, The Galactic Galaxy, TurnPike, Unlock:The Information Exchange, Your WebScout, Manufacturers Information Network, Net Happenings, Net Mall, Web World Internet Directory, WebVenture Hotlist, What's New, WhatUSeek, JumpLink, Linkcentre Directory, InfoSpace, Jayde Online Directory, BC Internet, BizCardz Business Directory, Net-Announce, New Page ListOne World Plaza, PageHost A-Z, PeekABoo, Project Cool, Scrub The Web, Seven Wonders, Sserv, Starting Point, Web 100, Web Walker, Where2Go, World Wide Business Yellow Pages, Wow! Web Wonders!, WWW Worm, JumpCity. ORDER FORM Hit the REPLY button on your e-mail program and fill out the following information. (This information will be posted to the search engines/indexes): URL: http:// Site Title: Description (250 characters): Key words (250 characters, in descending order of importance): Your name: Company Name: Address: City: State/Prov: Zip/Postal Code: Telephone: Fax: Email address: Contact e-mail address (in case we have questions about this order): If billing a different address, please complete the following: Addressee: Company Name: Address: City: State/Prov: Zip/Postal Code: Telephone: Fax: Email address: TERMS Terms are net 15 days from date of invoice. ______________________________________________________________________ Uplink, Inc. 39B Mill Plain Road Danbury, CT 06811 Phone: (203) 791-7351 Fax: (203) 790-6407 E-mail: up@uplinkpro.com From owner-proteins@net.bio.net Sat Dec 06 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!newsfeed.eerie.fr!newsfeed.nacamar.de!blackbush.xlink.net!news-ge.switch.ch!news-zh.switch.ch!elna.ethz.ch!not-for-mail From: Daniel Bisig Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Protein Elution Behaviour on MonoS Date: Sun, 07 Dec 1997 10:29:33 -0800 Organization: ETHZ Lines: 39 Message-ID: <348AEB0D.41C6@wawona.vmsmail.ethz.ch> NNTP-Posting-Host: bccinema.ethz.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) Xref: biosci bionet.molbio.proteins:11989 bionet.molbio.methds-reagnts:63527 Hi all, I am currently trying to purify a protein for subsequent crystallization trials. Based on SDS gel electrophoresis the protein is pure but when running isoelectric focusing gels my protein sample splits up in three major bands of quite distinct IP. Tritration curve analysis indicated an optimal seperation of these protein bands at a pH of about 4.5 on a kation exchange column. But several purification attempts on a 5 ml MonoS column resulted in rather strange elution behaviour of my protein sample when applying a 0-1M NaCl gradient. The protein elutes in 5-6 different peaks. Analysis of each peak by isoelectric focusing showed that each peak still contains the three major bands althought in quantitatively different amount. Drastically reducing the amount of protein loaded did not change the elution profile and protein content of each peak so no precipitation effects should be involved. The buffering system consists of 50 mM NaAcetate of pH 4.5 and should therefore be strong enough to minimize Donnan effects. Does anybody have an idea who this behaviour can be explained? p.s. Isolating the protein of one single elution peak and subsequently applying it to the MonoS column again results on elution of the protein in the same single peak. So there seems to be no dynamical conversion between (denaturated) protein conformeres (exposing different charged groups) which could be responsible for different elution peaks. Thanks in advance and regards, Daniel -- Daniel A. Bisig _______________________________________ _/_/_/_/_/_/_/ _/ Swiss mailto:bcbisig@wawona.vmsmail.ethz.ch _/ _/ _/ _/ Federal phone: 0041-1-632-3020 _/_/_/ _/ _/_/_/ Institute phone (priv): 0041-1-481-6028 _/ _/ _/ _/ of Fax: 0041-1-632-1121 _/_/_/ _/ _/ _/ Technology __________________________________________________________________ From owner-proteins@net.bio.net Sun Dec 07 22:00:00 1997 Path: biosci!OSU.EDU!foster.281 From: foster.281@OSU.EDU ("Mark P. Foster") Newsgroups: bionet.molbio.proteins Subject: Postdoctoral position in protein biochemistry and heteronuclear NMR Date: 8 Dec 1997 13:23:30 -0800 Organization: OSU/Biochemistry Lines: 39 Sender: daemon@net.bio.net Distribution: world Message-ID: <348C65F2.58ED877F@osu.edu> Reply-To: foster.281@osu.edu NNTP-Posting-Host: net.bio.net Postdoctoral position available in protein biochemistry and heteronuclear NMR spectroscopy. Start date: as early as March 1998. This is a unique training opportunity to learn and conduct state of the art research to tackle a very exciting goal: the structure and function of a catalytic ribonucleoprotein (RNA/protein, RNP) complex. This project will involve the use of molecular biology and biochemical techniques to identify RNA-protein interactions in the RNP complex, as well as heteronuclear NMR spectroscopy and molecular modeling to characterize the solution structure and dynamic behavior of the protein cofactor. The laboratories are well equipped for these studies, with excellent access to biophysical instrumentation, NMR spectrometers (500, 600, 800 MHz), Silicon Graphics workstations and molecular modeling software. This is a multidisciplinary research project, so the desired individual should preferably have a strong background in one or more of the following areas: molecular biology, protein overexpression and purification, enzymology, heteronuclear NMR spectroscopy and molecular modeling. Interested individuals should send a cover letter, CV, and arrange to have three letters of recommendation sent to: Prof. Venkat Gopalan or Prof. Mark P. Foster Department of Biochemistry The Ohio State University 484 West 12th Ave. Columbus, OH 43210 FAX: 614-292-6773 foster.281@osu.edu -- Mark P. Foster Department of Biochemistry (614) 292-1377 The Ohio State University FAX 292-6773 484 West 12th Ave. foster.281@osu.edu Columbus, OH 43221 -------------------------------------------------------------- From owner-proteins@net.bio.net Sun Dec 07 22:00:00 1997 Path: biosci!TC3NET.COM!cola From: cola@TC3NET.COM (Nicolas Bayoff) Newsgroups: bionet.molbio.proteins Subject: hormone purification Date: 8 Dec 1997 12:47:46 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <348C5D02.BDC0AD97@tc3net.com> NNTP-Posting-Host: net.bio.net I would appreciate help with any ideas or methods that would allow me to purify growth hormone from "raw" tissue culture media that I have collected from pituitaries ? Initial westerns using lyophylized sample against polyclonal ab chicken GH did reveal a distinct band near the 22kDa range. I would like to purify this GH in its active state to for further study and help would be greatly appreciated. Thank you Nicolas From owner-proteins@net.bio.net Sun Dec 07 22:00:00 1997 Path: biosci!agate!nature.berkeley.edu!lhom From: lhom@nature.berkeley.edu (Louis Hom) Newsgroups: bionet.molbio.proteins Subject: Ligands & NP-40 Date: 8 Dec 1997 19:38:11 GMT Organization: University of California, Berkeley Lines: 10 Message-ID: <66hib3$ftm$1@agate.berkeley.edu> NNTP-Posting-Host: nature.berkeley.edu I want to try a shot in the dark experiment to see if I can identify which protein on a native gel my fluorescent small-molecule ligand is binding to. Do I need to worry about NP-40 (or other non-ionic detergents) interfering with the binding? My guess is that this is something very specific for each case, but maybe someone can tell me otherwise. Thanks. -- _______________________________________________________________________________ Lou Hom >K '93 lhom@nature.berkeley.edu http://www.ocf.berkeley.edu/~lhom From owner-proteins@net.bio.net Sun Dec 07 22:00:00 1997 Message-ID: <348CA08A.4F66@fc.NO.SPAM.up.pt> Date: Mon, 08 Dec 1997 17:36:10 -0800 From: Pedro SIlva Organization: wau.nl X-Mailer: Mozilla 3.01 (Win16; I) MIME-Version: 1.0 Newsgroups: bionet.molbio.proteins Subject: Blue Sepharose Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: flex077.tran.wau.nl Lines: 5 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!192.87.106.104!surfnet.nl!wau.nl!flex077.tran.wau.nl I am trying to anaerobically purify an iron-sulfur protein w/ a NADPH binding domain. I know that Blue Sepharose specifically binds NAD(P)(H), flavin, etc, and intend to use it. My problem is this: to get rid of O2 traces I use 2 mM dithionite in all my buffers. Does anyone know whether Blue Sepharose is stable in these conditions? From owner-proteins@net.bio.net Sun Dec 07 22:00:00 1997 Path: biosci!TC3NET.COM!cola From: cola@TC3NET.COM (Nicolas Bayoff) Newsgroups: bionet.molbio.proteins Subject: hormone purification method or ideas Date: 8 Dec 1997 12:39:01 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <348C5A8E.58795AA2@tc3net.com> NNTP-Posting-Host: net.bio.net I would appreciate any ideas or suggestions to assist me in purifying a tissue culture in order to extract a growth hormone. I have managed to culture iguana pituitaries and would like to isolate growth hormone. I've run a western blot using chicken abGH and rabbit abGH (both polyclonal) and have only about 250mg of "raw" lyophized sample? Could I just run my sample on HPLC, collect the fractions and then run westerns on these fractions using again abGH chicken and perhaps ab prolactin chicken? Thank you Nicolas From owner-proteins@net.bio.net Mon Dec 08 22:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsxfer3.itd.umich.edu!oleane!jussieu.fr!citi2.fr!federici.cochin.inserm.fr!user From: federici@icgm.cochin.inserm.fr (Federici) Newsgroups: bionet.molbio.proteins Subject: Re: chromatography parameters Date: 9 Dec 1997 08:48:48 GMT Organization: ICGM CNRS UPR415 Lines: 52 Message-ID: References: <66596p$mnp$1@izvestia.its.unimelb.edu.au> NNTP-Posting-Host: federici.cochin.inserm.fr X-Newsreader: Yet Another NewsWatcher F2.0 In article (Dans l'article) <66596p$mnp$1@izvestia.its.unimelb.edu.au>, murphy_r@licre.ludwig.edu.au (Roger Murphy) wrote (écrivait) : > Hello there! > > This note is addressed to all you chrmoatographers out there..... > I recently came across what appears to be a novel use of the HETP parameter > for chromatography columns. I hadn't used this paricular instrumentation > before (it will remain anonymous, but is widely used for protein > purification!) and part of the column assessment protocols involved > calculating an HETP based on an unretained peak, i.e. came through at the void > volume of the column. This calculation was used as a measure of how well the > column was packed, but......my years of chromatography tell me (perhaps > mistakenly?) that such a calculation on an unretained peak tells your > absolutely nothing about the efficiency of the column, and is not an > appropriate measure even of how well it's packed. In their defense, they also > calculate an asymmetry factor, which I'd be prepared to accept as a legitimate > measure of the packing efficiency, but does anyone else feel as I do that the > use of HETP here is quite inappropriate? > > Pity we don't have a bionet.chromatography newsgroup for this sort of > discussion... > > I'd be interested in any ideas on this, including those who want to tell me > I'm an idiot (if I am, then so be it!) > > Cheers, > > Roger > > > > Roger Murphy, Ph.D. > Biological Production Facility > Ludwig Institute for Cancer Research > Austin & Repatriation Medical Centre > Studley Road, > Heidelberg, Vic. 3084 > Australia. > > Tel 61-3-94965463 > Fax 61-3-94965436 > Email murphy_r@licre.ludwig.edu.au Hi! Could you tell me exactly the protocol? maybe the use of void volume is only comparative: If the void volume of a column that is well filled is known (and I think it is...), the comparison with the void volume of a column badly filled, will indicate a decrease of HETP. HETP is dependent of the filling. From owner-proteins@net.bio.net Mon Dec 08 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.direct.ca!news.algonet.se!feed1.news.luth.se!eru.mt.luth.se!luth.se!news.kth.se!gvh-caballo.biokemi.su.se!user From: urbig@biokemi.su.se (Thomas) Newsgroups: bionet.molbio.proteins Subject: Re: Blue Sepharose Date: Tue, 09 Dec 1997 09:51:34 +0200 Lines: 20 Message-ID: References: <348CA08A.4F66@fc.NO.SPAM.up.pt> NNTP-Posting-Host: gvh-caballo.biokemi.su.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit In article <348CA08A.4F66@fc.NO.SPAM.up.pt>, Pedro SIlva wrote: > I am trying to anaerobically purify an iron-sulfur protein w/ a NADPH > binding domain. I know that Blue Sepharose specifically binds NAD(P)(H), > flavin, etc, and intend to use it. My problem is this: to get rid of O2 > traces I use 2 mM dithionite in all my buffers. Does anyone know whether > Blue Sepharose is stable in these conditions? I can't answer your actual question but we used to get our materials anaerob by just rinsing them extensively (overnight) with about 10 vol. of oxygen-free equilib. buffer (was made anaerob by autoklaving and cooling down under a stream of N2, then degassed again under vacuo). This was absolutely sufficient for an enzyme that is killed by traces of oxygen. Thomas -- Thomas Urbig email: urbig@biokemi.su.se From owner-proteins@net.bio.net Mon Dec 08 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!mail.dcs.warwick.ac.uk!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: Protein Elution Behaviour on MonoS Date: Tue, 09 Dec 1997 10:15:45 -0800 Organization: University of Leicester (PCFS User) Lines: 23 Message-ID: <348D8AD1.3677@le.ac.uk> References: <348AEB0D.41C6@wawona.vmsmail.ethz.ch> NNTP-Posting-Host: pc10.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win16; I) Xref: biosci bionet.molbio.proteins:12000 bionet.molbio.methds-reagnts:63567 Daniel Bisig wrote: > > Hi all, > > I am currently trying to purify a protein for subsequent crystallization > trials. Based on SDS gel electrophoresis the protein is pure but when > running isoelectric focusing gels my protein sample splits up in three > major bands of quite distinct IP. Tritration curve analysis indicated an > optimal seperation of these protein bands at a pH of about 4.5 on a > kation exchange column. But several purification attempts on a 5 ml > MonoS column resulted in rather strange elution behaviour of my protein > sample when applying a 0-1M NaCl gradient. The protein elutes in 5-6 > different peaks. Analysis of each peak by isoelectric focusing showed > that each peak still contains the three major bands althought in > quantitatively different amount. Could it be that your protein consists of several similar subunits, may be distinguished only by posttranslational modification? N-terminal sequencing of your IEF bands should answer this question. Another option might be to run your proteins on non-denaturing gels, or do some analytical ultracentrifugation to see whether oligomers exist. Consider also proteolytic digestion of the IEF bands and running the resulting peptide mixtures on a Tricine gel. From owner-proteins@net.bio.net Mon Dec 08 22:00:00 1997 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!news.uoregon.edu!news.u.washington.edu!saul3.u.washington.edu!pearton From: pearton@saul3.u.washington.edu (D. Pearton) Newsgroups: bionet.molbio.proteins Subject: Re: concentrating protein samples Date: 10 Dec 1997 01:39:05 GMT Organization: University of Washington Lines: 26 Distribution: world Message-ID: <66krrp$rtp$1@nntp3.u.washington.edu> References: <199712051958.OAA23447%anat67104.anatomy.med.ufl.edu@camphor.grove.ufl.edu> NNTP-Posting-Host: saul3.u.washington.edu X-Trace: nntp3.u.washington.edu 881717945 28601 (None) 140.142.64.4 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: pearton X-Newsreader: TIN [version 1.2 PL2] ke wu (stones@GROVE.UFL.EDU) wrote: : Dear netters: : I need to concentrate about 200 ul immunoprecipitation sample into 20 ul : volume so that I could load it on a SDS-PAGE. Could anyone suggest any good : method to concentrate protein samples without losing significant amount of : proteins. Thank you. A very simple method is to use an organic solvent as a precipitant. I generally use 5 volumes of ice-cold methanol and leave at -20C overnight, then spin down in a microfuge and dry. You can then resuspend in sample buffer. Alternatively you can use acetone or 5% TCA. Cheers, Dave -- Dave Pearton pearton@u.washington.edu +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Down he sank in a chair-ran his hands through his hair- + And chanted in mimsiest tones + Words whose utter inanity proved his insanity, + While he rattled a couple of bones. + + "The Hunting of the Snark" Lewis Carroll + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-proteins@net.bio.net Mon Dec 08 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.direct.ca!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!mail.dcs.warwick.ac.uk!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.molbio.proteins Subject: Re: Blue Sepharose Date: Tue, 09 Dec 1997 10:19:38 -0800 Organization: University of Leicester (PCFS User) Lines: 11 Message-ID: <348D8BBA.15CF@le.ac.uk> References: <348CA08A.4F66@fc.NO.SPAM.up.pt> NNTP-Posting-Host: pc10.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win16; I) Pedro SIlva wrote: > > I am trying to anaerobically purify an iron-sulfur protein w/ a NADPH > binding domain. I know that Blue Sepharose specifically binds NAD(P)(H), > flavin, etc, and intend to use it. My problem is this: to get rid of O2 > traces I use 2 mM dithionite in all my buffers. Does anyone know whether > Blue Sepharose is stable in these conditions? Blue Sepharose does not bind nucleotides, rather the blue dye is a nucleotide analogue and binds to the nucleotide binding site of proteins. From owner-proteins@net.bio.net Tue Dec 09 22:00:00 1997 Path: biosci!BOTANY.UQ.EDU.AU!J.Marcus From: J.Marcus@BOTANY.UQ.EDU.AU ("Marcus, Dr J.") Newsgroups: bionet.molbio.proteins Subject: fructose-1,6-bisphosphate aldolase Date: 10 Dec 1997 02:08:51 -0800 Organization: Dept of Botany, Univ of Queensland Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <26E75F064CC@botany.uq.edu.au> Reply-To: Marcus@tpp.uq.edu.au NNTP-Posting-Host: net.bio.net Dear Netters, Would any of you happen to know of a commercial or other source of fructose-1,6-bisphophate aldolase. I am particularly interested in obtaining some yeast enzyme if it is available. I would much appreciate any help you could give here as I really do not want to purify it myself if I don't have to. Thanking you in advance, John Marcus _________________________________________________________ John Marcus Marcus@tpp.uq.edu.au (Dr J.Marcus) Cooperative Research Centre for Tropical Plant Pathology 5th Level John Hines Building University of Queensland St. Lucia, QLD 4072 AUSTRALIA Fax: 61-7-3365-4771 Phone: 61-7-3365-4764 From owner-proteins@net.bio.net Tue Dec 09 22:00:00 1997 Path: biosci!daresbury!uninett.no!Norway.EU.net!news-feed.ifi.uio.no!recycled.news.erols.com!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!news.iupui.edu!physics.nmr.iupui.edu!user From: bray@iupui.edu (Bruce D. Ray) Newsgroups: bionet.molbio.proteins, Subject: Re: Enzyme's Molecular Weight Date: Wed, 10 Dec 1997 16:53:49 -0600 Organization: IUPUI Physics Dept. Lines: 25 Distribution: world Message-ID: References: <66n0km$1b5@net.bio.net> NNTP-Posting-Host: physics.nmr.iupui.edu In article <66n0km$1b5@net.bio.net>, Monica Marie Arroyo wrote: > Could someone tell me the molecular weight of creatine phosphokinase or > acid phosphatase? Creatine kinase {ATP:creatine N-phosphotransferase, EC 2.7.3.2} from rabbit muscle is a dimer of molecular weight 81,000 {Noda _et al._ (1954) __J. Biol. Chem.__ __209__, 203}. Acid phosphatase {Orthophosphoric-monoester phosphohydrolase (acid optimum), EC 3.1.3.2} from wheat germ consists of three isozymes of similar molecular weight in the range of 55,000 +/- 5,000 {Verjee, Z.H.M. (1969) __Eur. J. Biochem.__ __9__, 439}. -- Warning to commercial e-mailers {spammers}: The e-mail address provided above is for information purposes only. Do not send un solicited commercial e-mail to this address. From owner-proteins@net.bio.net Tue Dec 09 22:00:00 1997 Path: biosci!biosci!not-for-mail From: Monica Marie Arroyo Newsgroups: bionet.molbio.proteins, Subject: Enzyme's Molecular Weight Date: 10 Dec 1997 13:12:54 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <66n0km$1b5@net.bio.net> NNTP-Posting-Host: net.bio.net Could someone tell me the molecular weight of creatine phosphokinase or acid phosphatase? Thanks, Monica arroyo1@mint.net From owner-proteins@net.bio.net Tue Dec 09 22:00:00 1997 Path: biosci!webtv.net!uunet!in5.uu.net!newsfeed.internetmci.com!128.174.5.49!vixen.cso.uiuc.edu!news.indiana.edu!news.iupui.edu!physics.nmr.iupui.edu!user From: bray@iupui.edu (Bruce D. Ray) Newsgroups: bionet.molbio.proteins Subject: Re: fructose-1,6-bisphosphate aldolase Date: Wed, 10 Dec 1997 10:11:36 -0600 Organization: IUPUI Physics Dept. Lines: 50 Distribution: world Message-ID: References: <26E75F064CC@botany.uq.edu.au> <66m4aq$jok$1@light.nih.gov> NNTP-Posting-Host: physics.nmr.iupui.edu Posted and sent as e-mail since the inquirer is located in Australia and may have need of the material more quickly than my news-server's latency. In <26E75F064CC@botany.uq.edu.au>, J.Marcus@BOTANY.UQ.EDU.AU ("Marcus, Dr J.") writes: >Dear Netters, > Would any of you happen to know of a commercial or >other source of fructose-1,6-bisphophate aldolase. I am >particularly interested in obtaining some yeast enzyme if >it is available. I would much appreciate any help you >could give here as I really do not want to purify it myself >if I don't have to. Sigma carries it. The listing is found under the A's for aldolase and not under the F's for fructose. On pages 89 to 90 of the 1997 Sigma catalog, there is a list of fructose-1,6-bisphosphate aldolases from a number of different sources. The Bakers Yeast variant {Zn metalo enzyme} is listed on page 90 as A9562, From Bakers Yeast, suspension in 4.0 M (NH4)2SO4 - 10 mM mercaptoethanol, 10 mM histidine, and 0.1 M ZnCl2, pH 6.8. Activity: 20-50 units per mg protein. Pricing in US dollars is given as: 200 Units 14.30 1,000 Units 47.55 5,000 Units 158.55 Your Australian Sigma affiliate who should have stock and Australian prices is at: P.O. Box 970 Castle Hill NSW 2154 with the Australian telephone number 1-800-800-097 and the Australian fax of 1-800-800-096 They also list Sidney telephone of 61-2-9841-0555 and a Sidney fax of 61-2-9841-0500 Hope this helps. -- Warning to commercial e-mailers {spammers}: The e-mail address provided above is for information purposes only. Do not send un solicited commercial e-mail to this address. From owner-proteins@net.bio.net Tue Dec 09 22:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsfeed.internetmci.com!207.69.200.61!mindspring!news.mindspring.com!usenet From: "Rick A. Bright" Newsgroups: bionet.molbio.proteins Subject: Kinase Assay Date: Thu, 11 Dec 1997 02:49:24 -0500 Organization: Emory University, Molecular Therapeutics & Toxicology Lines: 7 Message-ID: <348F9B03.4ACB4D0E@emory.edu> NNTP-Posting-Host: user-37kbtl7.dialup.mindspring.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Server-Date: 11 Dec 1997 07:49:36 GMT X-Mailer: Mozilla 4.04 [en] (Win95; I) Could anyone please share with me, or direct me to, a kinase activity assay. Preferably an autophosphorylation (without peptide) protocol. I appreciate your help. Rick Bright Emory University From owner-proteins@net.bio.net Tue Dec 09 22:00:00 1997 From: p.bayliss@utoronto.ca Subject: 2D lipid problem Date: Wed, 10 Dec 1997 19:43:15 -0600 Reply-To: p.bayliss@utoronto.ca Message-ID: <881801992.1112080398@dejanews.com> Newsgroups: bionet.molbio.proteins Organization: Deja News Posting Service Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!128.230.129.106!news.maxwell.syr.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Thu Dec 11 00:59:52 1997 GMT X-Authenticated-Sender: p.bayliss@utoronto.ca X-Http-User-Agent: Mozilla/3.01 (Win95; I) X-Originating-IP-Addr: 142.150.129.30 (sienna.dialin.utoronto.ca) Lines: 22 When I run the first dimension of a 2D gel on this particular sample, something stacks inside the tube (visible by bromophenol blue not getting through it). If left long enough (eg. 4hr) and with less sample, it eventually runs out of the bottom of the tube. It's a nuisance, and may be taking some of my protein with it (especially LMW), and it seems to temporarily shift the pI gradient (bromophenol blue which DOES get past turns yellow, even if it's not near the bottom of the tube). With silver stain, it doesn't stain like normal protein, but stains a very light blue. I haven't stained with coomassie. In the second dimension, it again all runs to more or less the same spot. I'm thinking it's lipid, but I'm not sure. I've tried acetone and also chloroform extraction with minimal success. I'd like to rid myself of it altogether. Has anyone had similar problems, or have any suggestions? Anyone know of a really good way to solubilize proteins and then get rid of lipids? Thanks in advance for your help!! p.bayliss@utoronto.ca -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-proteins@net.bio.net Tue Dec 09 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!news-peer.gip.net!news.gsl.net!gip.net!howland.erols.net!usc!news.isi.edu!usenet From: Jesus Cerquides Newsgroups: bionet.molbio.proteins Subject: Secondary structure prediction Date: Wed, 10 Dec 1997 14:44:02 -0800 Organization: USC Information Sciences Institute Lines: 22 Message-ID: <348F1B32.C3F2DACE@iiia.csic.es> NNTP-Posting-Host: vigor.isi.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (X11; I; SunOS 5.5.1 sun4u) Hello, everybody! I am a computer scientist interested in the problem of protein secondary structure prediction. I have some questions I will like to know: Are there any studies of the locality of the problem? That is, if it can or cannot be determined by seeing the aminoacids in the surroundings what will be the secondary structure of a concrete aminoacid. Has a Bayesian classifier ever been applied to the problem? Which is the best database to use for secondary structure prediction? I guess that is the PDB, but can anybody help me if I am wrong? Thank you Jesus Cerquides IIIA. CSIC Spain From owner-proteins@net.bio.net Tue Dec 09 22:00:00 1997 Path: biosci!webtv.net!uunet!in5.uu.net!newsxfer.itd.umich.edu!newsxfer3.itd.umich.edu!cpk-news-hub1.bbnplanet.com!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!nih.gov!not-for-mail From: jhmiller@helix.nih.gov (Jay Miller) Newsgroups: bionet.molbio.proteins Subject: Re: fructose-1,6-bisphosphate aldolase Date: 10 Dec 1997 13:09:46 GMT Organization: National Institutes of Health Lines: 31 Distribution: world Message-ID: <66m4aq$jok$1@light.nih.gov> References: <26E75F064CC@botany.uq.edu.au> Reply-To: jhmiller@helix.nih.gov NNTP-Posting-Host: ams06057.niams.nih.gov X-Newsreader: IBM NewsReader/2 2.0 Sigma doesn't seem to carry it. I have two suggestions. The first is a web page, www.barryinc.com/bio. This is the National Biotech Register. The second suggestion is a new book, The Source Book of Enzymes,ed. J.S. White and D.C. White. It contains a list of companies that sell enzyme preps. In <26E75F064CC@botany.uq.edu.au>, J.Marcus@BOTANY.UQ.EDU.AU ("Marcus, Dr J.") writes: >Dear Netters, > Would any of you happen to know of a commercial or >other source of fructose-1,6-bisphophate aldolase. I am >particularly interested in obtaining some yeast enzyme if >it is available. I would much appreciate any help you >could give here as I really do not want to purify it myself >if I don't have to. > >Thanking you in advance, >John Marcus > > > > >_________________________________________________________ >John Marcus Marcus@tpp.uq.edu.au (Dr J.Marcus) >Cooperative Research Centre for Tropical Plant Pathology >5th Level John Hines Building >University of Queensland >St. Lucia, QLD 4072 >AUSTRALIA > >Fax: 61-7-3365-4771 >Phone: 61-7-3365-4764 From owner-proteins@net.bio.net Tue Dec 09 22:00:00 1997 Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Path: biosci!daresbury!lyra.csx.cam.ac.uk!server1.netnews.ja.net!server5.netnews.ja.net!server3.netnews.ja.net!ucl.ac.uk!bcc.ac.uk!chen From: chen@bsm.bioc.ucl.ac.uk (Chen Ho An) Subject: Re: Protein Elution Behaviour on MonoS Message-ID: <1997Dec10.123248.73600@ucl.ac.uk> Date: Wed, 10 Dec 1997 12:32:48 GMT References: <348AEB0D.41C6@wawona.vmsmail.ethz.ch> <348D8AD1.3677@le.ac.uk> Organization: University College London X-Newsreader: TIN [version 1.2 PL2] Followup-To: bionet.molbio.proteins,bionet.molbio.methds-reagnts Lines: 25 Xref: biosci bionet.molbio.proteins:12004 bionet.molbio.methds-reagnts:63598 If the protein is expressed in E.coli, the most likely explanation is misincoporation of amino acids due to presence of rare codons or large number of the same codon. MIsincorporation of unnatural amino acids is also known. Do a mass spec using electrospray mass spec (MALDI is not accurate enough?) and you may see different species distinguishable by mass, then you can analyse it to see what the most likely misincorporated amino acids is. Then do a mutagenesis to get rid of this or other codons. Email me if you need reference. -chen -- _________________________________________________________________________ HA Chen tel: 0171 391 1354 Department of Biochemistry chen@bioc.ucl.ac.uk University College London http://www.biochem.ucl.ac.uk/~chen/ Gower Street London WC1E 6BT _________________________________________________________________________ From owner-proteins@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.daimi.aau.dk!not-for-mail From: Per Mygind Newsgroups: bionet.molbio.proteins, Subject: Re: Enzyme's Molecular Weight Date: Thu, 11 Dec 1997 10:40:20 +0000 Organization: DAIMI, Computer Science Dept. at Aarhus University Lines: 25 Message-ID: <348FC314.14CC@medmicro.aau.dk> References: <66n0km$1b5@net.bio.net> NNTP-Posting-Host: majestetix.medmicro.aau.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; SunOS 5.5.1 sun4m) Monica Marie Arroyo wrote: > > Could someone tell me the molecular weight of creatine phosphokinase or > acid phosphatase? > > Thanks, > > Monica > arroyo1@mint.net Is there a WWW-site, where you can look up the molecular weight of a wide range of enzymes ??? -- ************************************************************************ If you are are not part of the solution, you are part of the precipitate ************************************************************************ Per Mygind, Cand.scient Department of Medical Microbiology and Immunology The Bartholin Building University of Aarhus Denmark phone : 89 42 17 47 fax : From owner-proteins@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.131!news-pen-1.sprintlink.net!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!eerie.fr!jussieu.fr!utc.fr!univ-lille1.fr!not-for-mail From: Cyril Ruckebusch Newsgroups: bionet.molbio.proteins Subject: protein secondary structure Date: Thu, 11 Dec 1997 17:59:47 +0100 Organization: Universite des Sciences et Technologies de LILLE, France Lines: 14 Message-ID: <34901C02.1F07953C@univ-lille1.fr> NNTP-Posting-Host: pcirtf4.univ-lille1.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.02 [en] (Win95; I) Hello, I work on a thesis dealing with secondary structure of haemoglobin and I have a problem with the biological interpretation of one infrared spectral result. The protein is in a sodium acetate buffer and to resume, when I reach a certain level of haemoglobin concentration, the absorption peak corresponding to the solvant C=OO- vibration disappear and the very near amide II absorption is shiftted to lower frequencies. Is it possible that amine N-h groups not involved in helical conformation make hydrogen bond with solvant C=OO-? If it is, I believed that it was impossible because of the water environnement? Any kind of help would be very appreciate; Thank you Cyril From owner-proteins@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!wuff.mayn.de!news-nue1.dfn.de!uni-erlangen.de!winx03!wpxx02.toxi.uni-wuerzburg.de!krasel From: Cornelius Krasel Newsgroups: bionet.molbio.proteins Subject: Re: Secondary structure prediction Date: Thu, 11 Dec 1997 11:26:43 +0100 Organization: University of Wuerzburg, Germany Lines: 15 Message-ID: <35fo66.863.ln@wpxx02.toxi.uni-wuerzburg.de> References: <348F1B32.C3F2DACE@iiia.csic.es> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 unoff BETA 970930; i486 Linux 2.0.10] Jesus Cerquides wrote: > Are there any studies of the locality of the problem? That is, if it can > or cannot be determined by seeing the aminoacids in the surroundings > what will be the secondary structure of a concrete aminoacid. Yes: the most famous of these studies has been done by Chou & Fasman and some people still use their prediction. There is a review by them somewhere in an older "Annual Review of Biochemistry" issue. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP4 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-proteins@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!PILOT.MSU.EDU!delgadoi From: delgadoi@PILOT.MSU.EDU (Ivan J Delgado Orlic) Newsgroups: bionet.molbio.proteins Subject: Position available: MICROCOMPUTER HARDWARE/SOFTWARE BIOINFORMATICS SPECIALIST Date: 11 Dec 1997 10:50:56 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <34903789.1976ABFD@pilot.msu.edu> Reply-To: delgadoi@pilot.msu.edu NNTP-Posting-Host: net.bio.net Please forward this message to other networks: MICHIGAN STATE UNIVERSITY _____________________________________________________________________________________________ MSU-DOE PLANT RESEARCH LABORATORY EAST LANSING . MICHIGAN . 48824-1312 . USA TELEPHONE: (517) 353-2270 FAX: (517) 353-9168 MICROCOMPUTER HARDWARE/SOFTWARE BIOINFORMATICS SPECIALIST This position will involve serving as an expert in the area of bioinformatics in the MSU-DOE Plant Research Laboratory and the Department of Botany and Plant Pathology at Michigan State Univ. Although no actual data analyses will be performed for faculty or graduate students, the candidate should have ample experience with both protein and nuclic acid manipulation, with database mining and manipulation, and with the creation of highly curated data sets from mined data. The candidate should be able to teach and communicate these skills to faculty and graduate students in tutorial form and provide related support for courses and curriculum. Other responsibilities include analyzing the needs and making recommendations on microcomputer hardware and software products; occasionally installing complicated software and deal with compatibility issues; provide training on software usage, both one-on-one and in seminar form; assist in setting up and maintain a microcomputerized classroom; perform or supervise the minor repair of microcomputers and peripherals; maintain departmental Windows NT LAN; manage the department computer facility; design and maintain departmental web pages; and supervise student employees. Education and Background Required: The successful candidate should possess a M.Sc. or Ph.D. in plant biology or related discipline, have some interest or experience in bioinformatics, have experience working with commonly used sequence analysis programs, and although this is not a wet lab position, 2-3 years of molecular biology lab experience. The candidate should also have demonstrated work experience with microcomputers, experience working on different computer platforms (DOS, Windows, MacIntosh); internet and WWW experience; web page design experience. Familiarity with graphics software and knowledge of UNIX-based systems are desirable. The position does not involve individual research or involvement in faculty research projects. Salary commensurate with education and experience. To assure consideration, applications should be received by January 19, 1998. Please forward a cover letter specifying your interests, qualifications, curriculum vitae and two letters of recommendation to: Computer Search Committee, c/o Ms. Michelle Baker, Department of Botany and Plant Pathology, Michigan State University, East Lansing, MI 48824-1312. From owner-proteins@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!csir.uni.net.za!und.uni.net.za!und.ac.za!newsadmin From: "brendon" Newsgroups: bionet.molbio.proteins Subject: Re: concentrating protein samples Date: 11 Dec 1997 18:16:14 GMT Organization: University of Natal Lines: 26 Message-ID: <01bd0660$fd060860$df80808f@bchm7.bch.unp.ac.za> References: <199712051958.OAA23447%anat67104.anatomy.med.ufl.edu@camphor.grove.ufl.edu> <66krrp$rtp$1@nntp3.u.washington.edu> NNTP-Posting-Host: bchm6.bchm.unp.ac.za X-Newsreader: Microsoft Internet News 4.70.1155 D. Pearton wrote in article <66krrp$rtp$1@nntp3.u.washington.edu>... > ke wu (stones@GROVE.UFL.EDU) wrote: > : Dear netters: > > : I need to concentrate about 200 ul immunoprecipitation sample into 20 ul > : volume so that I could load it on a SDS-PAGE. Could anyone suggest any good > : method to concentrate protein samples without losing significant amount of > : proteins. Thank you. > Alternatively, you can add about 50 ul of the hydrophobic resin (supplied with some molbiol kits to clean protein away from DNA preps) and spin down. Add reducing buffer to the gel pellet (containing your protein solution), boli, and load. You can concentrate protein solutions as low as 10ng/ml for SDS-PAGE. TCA and other solvents usually cause "smearing" in lanes, so give this a bash. Good Luck. Brendon Price priceb@biochem.unp.ac.za From owner-proteins@net.bio.net Thu Dec 11 22:00:00 1997 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.molbio.proteins Subject: Recomb98: list of accepted papers Date: 12 Dec 1997 10:26:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 168 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712121825.KAA04091@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net The following 38 papers were selected by the RECOMB98 Program Committee for presentations among 123 submissions. For more details please visit our web site: http://www.mssm.edu/biomath/recomb98.html PAPER 001 P. Agarwal, V. Bafna Detecting non-adjoining correlations within signals in DNA. PAPER 002 A. Ben-Dor, B. Chor, D. Graur, R. Ophir, D. Pelleg From four-taxon trees to phylogenies: The case of mammalian evolution. PAPER 003 G. Benson An Algorithm for Finding Tandem Repeats of Unspecified Pattern. PAPER 004 B. Berger, T. Leighton Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete. PAPER 005 M. Bonet, M. Steel, T. Warnow, S. Yooseph Better Methods for Solving Parsimony and Compatiblity. PAPER 006 C. C. Chen, J. P. Singh, R. B. Altman The Hierarchical Organization of Molecular Structure Computations. PAPER 007 P. Crescenzi, D. Goldman, C. Papadimitriou, A. Piccolboni, M. Yannakakis On the Complexity of Protein Folding. PAPER 008 D. Fasulo, T. Jiang, R. M. Karp, N. Sharma Constructing Maps Using the Span and Inclusion Relations. PAPER 009 A. V. Finkelstein, A. Ya. Badretdinov How Fast a Protein Chain Can Fold to Its Most Stable Structure? PAPER 010 R. M. Fye, C. J. Benham A Formally Exact Method to Numerically Analyze Local Denaturation in Superhelical DNA PAPER 011 I. Gelfand, A. Kister, C. Kulikowski, O. Stoyanov Algorithmic Determination of Core Positions in the VL and VH Domains of Immunoglobulin Molecules PAPER 012 R. A. Goldstein, J. M. Koshi, D. P. Mindell Beyond mutation matrices: Physical-Chemistry based evolutionary models. PAPER 013 W. N. Grundy Family-based Homology Detection via Pairwise Sequence Comparison. PAPER 014 I. Holmes, R. Durbin Dynamic Programmimg Alignment Accuracy. PAPER 015 T. Hwa, M. Lassig Optimal Detection of Sequence Similarity by Local Alignment. PAPER 016 R. M. Karp, R.Shamir Algorithms for Optical Mapping. PAPER 017 P. E. Kearney Ordinal Beats Additive. PAPER 018 E. Koonin, R. Tatusov, M.Y. Galperin, M.N. Rozanov Genome analysis using clusters of orthologous groups (COGs). PAPER 019 J. K. Lee, V. Dancik, M. S. Waterman Estimation for restriction sites observed by optical mapping using reversible-jump markov chain monte carlo. PAPER 020 H. Lenhof, K. Reinert, M. Vingron A Polyhedral Approach to RNA Sequence Structure Alignment. PAPER 021 A. M. Lesk Assessment of Ab Initio Protein Structure Prediction. PAPER 022 R. Liu, T. W. Blackwell, D. J. States A structure based similarity measure for nucleic acid sequence comparison. PAPER 023 B. Ma, M. Li, L. Zhang On Reconstructing Species Trees From Gene Trees In Term of Duplications PAPER 024 L. Parida, B. Mishra Partitioning K Clones: Hardness Results and a Practical Solution to the K-Popultaions Problem. PAPER 025 D. G. Politte, D. R. Maffitt, D. J. States Estimaiton of Allele Frequencies From Color-Multiplexed Electropherograms. PAPER 026 M. Regnier A Unified Approach to Word Statistics PAPER 027 B. A. Reva, A. V. Finkelstein, J. Skolnick A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins. PAPER 028 I. Rigoutsos, A. Floratos Motif Discovery in Biological Sequences Without Alignment or Enumeration. PAPER 029 E. Rocke, M. Tompa An Algorithm for Finding Novel Gapped Motifs in DNA sequences. PAPER 030 M. Sagot, E. W. Myers Identifying satellites in nucleic acid sequences. PAPER 031 D. Sankoff, M. Blanchette Multiple genome rearrangement. PAPER 032 F. Sun Modeling DNA shuffling. PAPER 033 S. R. Sunyaev, I. V. Rodchenkov Analysis of the Position Dependent Amino Acid Probabilities and its Application to the Search for Remote Homologues. PAPER 034 A. Vologodskii Maxwell demon and topology simplification by type II topoisomerases. PAPER 035 W. L.Walker, D. S. Goodsell, E. M.Landaw The Theoretical Limits of DNA sequence discrimination of Polyamides. PAPER 036 T. D. Wu, S. C. Schmidler, T. Hastie, D. L. Brutlag Regression Analysis of Multiple Protein Structures PAPER 037 Y. Xu, D. Xu, E. C. Uberbacher A New Method for modeling and solving the protein fold recognition problem. PAPER 038 Z. Zhang, P. Berman, W. Miller Alignments Without Low-Scoring Regions. If you do NOT want to be in our mailing list, please reply with Subject line "Recomb98: remove". Sorry, if you get this mail twice. From owner-proteins@net.bio.net Thu Dec 11 22:00:00 1997 Path: biosci!daresbury!server5.netnews.ja.net!nntp.news.xara.net!xara.net!newsfeed.ecrc.net!news.duesseldorf.ecrc.net!RRZ.Uni-Koeln.DE!news-han1.dfn.de!news-koe1.dfn.de!news.ruhr-uni-bochum.de!news.rhrz.uni-bonn.de!news.rwth-aachen.de!not-for-mail From: Andreas Boesmann Newsgroups: bionet.molbio.proteins Subject: immobilized tranexamic acid ? Date: Fri, 12 Dec 1997 11:47:46 +0100 Organization: Aachen University of Technology Lines: 15 Message-ID: <34911652.1C0A5FC1@post.rwth-aachen.de> NNTP-Posting-Host: fs-chemie.ac.rwth-aachen.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.01 [en] (WinNT; I) X-Priority: 3 (Normal) Can epsilon-caproic acid, tranexamic acid or the like be immobilized on a surface and still be anti-fibrinolytic ? Or is it necessary that the molecule is solved to form the complex with the plasmin ? Can anybody hint me to articles regarding the mechanism of anti-fibrinolysis ? thanks in advance Andreas -- SpamResistant adress ! Please remove the `NOS´ from the name ! From owner-proteins@net.bio.net Thu Dec 11 22:00:00 1997 From: guochen69@hotmail.com Subject: affinity aggregation Date: Fri, 12 Dec 1997 21:21:45 -0600 Message-ID: <881982806.411959305@dejanews.com> Newsgroups: bionet.molbio.proteins Organization: Deja News Posting Service Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Sat Dec 13 03:13:26 1997 GMT X-Authenticated-Sender: guochen69@hotmail.com X-Http-User-Agent: Mozilla/3.0 (Win16; I) X-Originating-IP-Addr: 159.226.63.240 () Lines: 11 Hi, all Does anybody know of any of the reference books and reviews of protein separation by affinity aggregation method. I'm soon to start trying to study affinity separation protein. I am looking forward to hearing from you at your earliest convenience and thank you in advance. Guo chen -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-proteins@net.bio.net Fri Dec 12 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.proteins Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 13 Dec 1997 02:00:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712131000.CAA03806@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-proteins@net.bio.net Sun Dec 14 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.algonet.se!uni-erlangen.de!winx03!news From: s88891@stud-mail.uni-wuerzburg.de (Mathias Holpert) Newsgroups: bionet.molbio.proteins Subject: Re: Georgia Tech Message Board Registration Date: Mon, 15 Dec 1997 16:53:57 GMT Organization: University of Wuerzburg, Germany Lines: 14 Message-ID: <3494e925.418391@news.informatik.uni-wuerzburg.de> References: <199712052328.PAA03137@net.bio.net> NNTP-Posting-Host: wex123.extern.uni-wuerzburg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent 1.5/32.451 On 5 Dec 1997 15:29:02 -0800, reck@GOJACKETS.COM wrote: >Your account is active. > >Username: The G-Man >Password: 1928nc > >You may change your password by visiting the registration page and submitting a password change. >Enjoy it! ... you _should_ change your password after everybody in this newsgroup has seen it... Mathias From owner-proteins@net.bio.net Sun Dec 14 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!128.230.129.106!news.maxwell.syr.edu!rill.news.pipex.net!pipex!uunetukout!server1.netnews.ja.net!lyra.csx.cam.ac.uk!rw200 From: rw200@cus.cam.ac.uk (R. Woodward) Newsgroups: bionet.molbio.proteins Subject: purification of Fab fragments (Ig -likedomains) Date: 15 Dec 1997 17:24:57 GMT Organization: University of Cambridge, England Lines: 21 Message-ID: <673p59$1ga$1@lyra.csx.cam.ac.uk> NNTP-Posting-Host: ursa.cus.cam.ac.uk Keywords: Ig-like domains X-Newsreader: NN version 6.5.0 #2 (NOV) Dear All, I am despirately trying to purify the extracellular domains of tyrosine kinase receptors (PDGF like) which are secreted into my culture media. At present I am using cationic exchange resin (Resource S from Pharmacia) my major problem is that my product does not elute as a sharp peak, rather it appears to elute over a broad salt concentration and is not confined to a single peak. I have tried loading and eluting slowly, decreasing the salt gradient, detergents and glycerol in unsuccessful attempts to cure this problem. Has anyone got ideas as to why I should see this characteristic? Is it due to my protein or the exchanger? Has anyone had similar problems? Two other points has anyone had experience of purifying Ig Fab arms other than by using affinity chromatography? Do you need to add any reducing agents to prevent breakdown of the 2ndry structure. Also is there any milage in using other salts e.g. KCl rather than NaCl when eluting from an ion exchange column? Thenks in advance Robert Email rw200@cus.cam.ac.uk k -- From owner-proteins@net.bio.net Sun Dec 14 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!131.103.1.116!news2.chicago.iagnet.net!iagnet.net!128.255.56.80!news.uiowa.edu!green.weeg.uiowa.edu!akumar From: "A. Kumar" Newsgroups: bionet.molbio.proteins Subject: postranlational modifications Date: Mon, 15 Dec 1997 17:03:05 -0600 Organization: The University of Iowa Lines: 4 Message-ID: NNTP-Posting-Host: green.weeg.uiowa.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: akumar@green.weeg.uiowa.edu Is there a site/server that can help predict the post-tranlational modifications of a primary translation product? From owner-proteins@net.bio.net Mon Dec 15 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!oleane!jussieu.fr!univ-lyon1.fr!newsserver.cilea.it!news.csi.unimi.it!not-for-mail From: paolo.castano@unimi.it (Castano Paolo) Newsgroups: bionet.molbio.proteins Subject: Photomicrography Course Date: Tue, 16 Dec 1997 13:49:47 GMT Organization: Universita' degli Studi di Milano Lines: 31 Message-ID: <349686fa.10370102@news.unimi.it> NNTP-Posting-Host: isdn14.csi.unimi.it X-Newsreader: Forte Free Agent 1.1/32.230 INTERNATIONAL COURSES OF LIGHT MICROSCOPY, PHOTOMICROGRAPHY AND LASER SCANNING CONFOCAL MICROSCOPY GARGNANO (Lake of Garda) October 1998 The Course is a post-graduated theoretical/practical course, with propedeutical lectures and practical stages on microscopy, photomicrography and confocal microscopy. The course will take place in Gargnano (Lake of Garda) in October 1998. Further information and registration details will be found at the following Web address. http://imiucca.csi.unimi.it/endomi/micro.html Thank you Paolo Castano _______________________________________________ Prof. Paolo Castano UNIVERSITY of MILAN Institute of Human Anatomy CHAIR OF HUMAN ANATOMY - FACULTY OF PHARMACY Via Mangiagalli 31 - 20133 Milan (Italy) - Tel. 39.2.26.63.683 Fax 39.2.23.64.082 / 39.2.70.63.54.25 e-mail: clsmteam@imiucca.csi.unimi.it From owner-proteins@net.bio.net Mon Dec 15 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.direct.ca!torn!resunix.sickkids.on.ca!not-for-mail From: Randall C Willis Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.general,sci.bio.technology,bionet.cellbiol,bionet.microbiology Subject: THE NIGHT BEFORE DEFENCE (or A Visit From Citrate) Date: Mon, 15 Dec 1997 19:30:54 -0500 Organization: The Hospital For Sick Children Lines: 86 Message-ID: <3495CBBE.2781@gandalf.psf.sickkids.on.ca> NNTP-Posting-Host: gollum.sickkids.on.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP12) Xref: biosci bionet.molbio.methds-reagnts:63717 bionet.molbio.proteins:12025 bionet.general:28925 bionet.cellbiol:8573 bionet.microbiology:11979 THE NIGHT BEFORE DEFENCE (or A Visit From Citrate) Twas the night before defence, when all through the lab Not a gel box was shaking, with stain or with MAb; The columns were hung in the cold room with care, In hopes that my protein, I soon could prepare; The post-docs were nestled all smug in their beds, While extracts of barley muddled their heads; With the tech in the suburbs and PI the same, I had just settled down to another video game. When out of the fridge there arose such a clatter I sprang from the terminal to see what was the matter. Away to the cold box, I flew like a flash But the stench was o'erpowering and I threw up beef hash. The mould on the dampest of walls which were cold Had the softness of kittens only seven weeks old; When what to my view, a thing I despise But a half eaten sandwich and four tiny mice; With a little old scientist, so lively and galling, I knew at a glance was Linus Pauling. More vapid than undergrads, his charges they came, And he whistled, and shouted, and called them rude names. "Now, Watson! Now Francis! You strange little modellers! On Luria! On Bertani! You stupid old broth'lers! To the top of the bench, to the top of the wall! Purify! Purify! Purify all!" As dry heaves before the commitee meeting, bend A young student's body and his colon distend, So up their earlobes, acytes they grew, With a sack full of antibodies, their skin turning blue. And then, for a second, I heard from the 'fuge, An unbalanced rotor spinning something too huge. Where I put down my hand, to better hear the sound, Came the snapping of sparks from a wire sans ground. Pauling's hair was all wavy, and I thought I must be sick `Cause the curl in his hair looked just like a helix. On an arm load of oranges, he started to snack An I recalled his fetish with citrate, the quack. His eyes were all wrinkled, but the cheeks were yet red; Not too shabby for a man who was several years dead; The leer of his smile was just a tad scary And the snow on his rooftop made his head yet quite hairy; The end of a pipette, he held in his teeth And a pile of kimwipes lay around his big feet. He held a small vial of something quite gel-ly, A mercaptan no doubt, for it make him quite smelly. He changed `round the columns, adding to the confusion And I laughed to spite my own paranoid delusion. A wink of his eye and a rotation of his head, Told me whatever I drank would soon leave me dead. He spoke not a word, just buggered up my work, And dried all my resins, that silly old jerk. And separating his middle finger from first, fourth and third, That crazy, old bugger, just