From owner-proteins@net.bio.net Mon May 03 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!gatech!concert!duke!news.duke.edu!acpub.duke.edu!lees From: lees@acpub.duke.edu (Steve Lee) Newsgroups: bionet.molbio.proteins Subject: pSAAM Message-ID: <14377@news.duke.edu> Date: 4 May 93 22:23:15 GMT Sender: news@news.duke.edu Organization: Duke University; Durham, N.C. Lines: 6 Nntp-Posting-Host: raphael.acpub.duke.edu If anyone out there has used pSAAM before or knows how to use it please contact me... i need help... thanks alot.. STeve From owner-proteins@net.bio.net Tue May 04 23:00:00 1993 Path: biosci!SCRI.FSU.EDU!STRELETS From: STRELETS@SCRI.FSU.EDU Newsgroups: bionet.molbio.proteins Subject: Question about 3d-based multiple alignment data Message-ID: <930505145601.2020dd19@scri.fsu.edu> Date: 5 May 93 18:56:01 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 10 I'm working on the correction methods development for multiple alignment algorithms. Is there anybody know about accessable databases (file compilations) with protein (super)family alignments on the base (or taking into account) 3d-structure information? Any references will be helpful.. Thank in advance, V.Strelets strelets@scri.fsu.edu From owner-proteins@net.bio.net Wed May 05 23:00:00 1993 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Interruption of Internet Access to PIR Network Request Server Message-ID: <01GXUQSYX8WYA3CA6S@NBRF.Georgetown.Edu> Date: 6 May 93 15:59:25 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 20 Announcement of Temporary Interruption of Internet Access to The Protein Identification Resource Due to a recent network reconfiguration which removed redundancy of access to Internet at Georgetown University, the National Biomedical Research Foundation may now experience interruptions of service beyond our control. On Saturday May 8 beginning at 8:00 am EDT until about 4:00 pm EDT it will not be possible for users to access the Protein Identification Resource Network Server via Internet. Access through BITNET and the On-line System should not be affected. We regret any inconvenience this temporary loss of service will cause. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-proteins@net.bio.net Thu May 06 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!gatech!destroyer!cs.ubc.ca!utcsri!newsflash.concordia.ca!nstn.ns.ca!ac.dal.ca!nvett From: nvett@ac.dal.ca Newsgroups: bionet.molbio.proteins Subject: Rev protein Message-ID: <1993May7.094800.13500@ac.dal.ca> Date: 7 May 93 12:48:00 GMT Organization: Dalhousie University, Halifax, Nova Scotia, Canada Lines: 5 Hey kids, Does anybody know if the Rev protein (from HIV) has been crystallized? Nat Vettakkorumakankav From owner-proteins@net.bio.net Thu May 06 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: shi@inf.ethz.ch (Shi Fei) Newsgroups: bionet.molbio.proteins Subject: Pattern Sequences Message-ID: <1993May7.122605.13806@gserv1.dl.ac.uk> Date: 7 May 93 12:22:08 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 37 Content-Identifier: Pattern Seque... Original-To: chrom-22@uk.ac.daresbury, mol-evol@uk.ac.daresbury, proteins@uk.ac.daresbury Dear colleagues, We have designed and implemented an new algorithm which searches a sequence database (such as the EMBL Data Library, Genbank or the Swiss-Prot) to find all such sequences in the database that contain a block (a subsequence) which is very similar to some given pattern sequence in the sense that the differences (according to some distance metric, such as the edit distance) between the block (subsequence) found and the pattern sequence is no more than some given constant. The algorithm is expected to be very efficient theoretically. But we want to know if it is efficient and usefull in biological practice too. For this purpose we need a number of real (DNA, RNA or protein) sequences which can be used as pattern sequences which will make the database searches meaningful. The pattern sequences used for searching a nucleotide sequence database probably should be different from those used for searching a protein sequence database? Could you please send us or point us to some of such pattern sequences (seperately, in order to search nucleotide database and protein database separately) ?! We are pure computer scientists. We need your help, particularly the help from biologists and chemists! Thank you very much in advance! -------------------------------------------------------- Shi Fei Institut fuer Theoretische Informatik ETH-Zentrum Ch-8092 Zurich Switzerland e-mail: shi@inf.ethz.ch Fax: 0041-1-262-3973 Phone: 0041-1-254-7403 -------------------------------------------------------------- From owner-proteins@net.bio.net Fri May 07 23:00:00 1993 Path: biosci!steele!news From: shapirop@ohsu.edu Newsgroups: bionet.molbio.proteins Subject: Quantitative autoradiography Message-ID: <1993May8.200707.22727@ohsu.edu> Date: 8 May 93 20:07:07 GMT Sender: news@ohsu.edu Organization: vollum institute/ohsu Lines: 16 Nntp-Posting-Host: 137.53.73.151 Hi Bionetworkers I am interested in quantitfying numerous autoradiograms using NIH Image software on a MAC. Anybody have experience and suggestions regarding image acquisition using a video camera, still-video camera, graphic-arts flatbed scanner, or other device (other than a dedicated scanning laser densitometer). Thanks, shapirop@ohsu I. Paul Shapiro, Ph.D. Pathology and Vollum Institute Oregon Health Sciences University VOX: (503) 494-6904 FAX: (503) 494-6934 From owner-proteins@net.bio.net Fri May 07 23:00:00 1993 Path: biosci!agate!ames!haven.umd.edu!darwin.sura.net!howland.reston.ans.net!zaphod.mps.ohio-state.edu!news.acns.nwu.edu!uicvm.uic.edu!yang.earlham.edu!davidw From: davidw@yang.earlham.edu Newsgroups: bionet.molbio.proteins Subject: Preservation of cyt. c solns Message-ID: <1993May6.181637.23233@yang.earlham.edu> Date: 6 May 93 23:16:37 GMT Organization: Earlham College, Richmond, Indiana Lines: 27 I am currently studying the redox potential of cytochrome c in aqueous solution. As the stuff is pretty expensive $100/.1g, I am trying to reuse my solutions. The conditions are: 1mM Horse heart cytochrome c in 0.1M KPhos buffer at pH=6. The buffer has been filtered through .22um filter to eliminate bacteria and is stored in a sterile bottle. As I work in a chem lab, we do not have access to alot of sterile glassware, so I do the best I can by rinsing the glassware with EtOH followed by several rinses with the sterile buffer to remove the EtOH. My current storage procedure is to put the solution (aprox 1mL) in a 10mL screw-cap test tube and quick freeze it in liquid N2, it is then stored in a -10C freezer. I thaw the protein by placing the tube in a beaker of cold tap water. My questions are the following: 1. Is bacteria really a threat to the protein? 2. If not bacteria, what will damage the protein? 3. What is the best way to store the solution for short periods of time (a few days at a time)? David Weis davidw@yang.earlham.edu Chemistry Department DAVIDW@EARLHAM Earlham College "Every scientist is half B. F. Skinner and half P. T. Barnum." --The Simpsons "You can't argue with Hess's Law, that's why it's a law." --an anonymous chemistry professor From owner-proteins@net.bio.net Sat May 08 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: PAZST@VAX.CCC.NOTTINGHAM.AC.UK Newsgroups: bionet.molbio.proteins Subject: RSC BMG SPM MEETING Message-ID: <1993May9.142737.13754@gserv1.dl.ac.uk> Date: 9 May 93 14:26:15 GMT Sender: JANET"PAZST@UK.AC.NOTTINGHAM.CCC.VAX" Distribution: bionet Lines: 32 Originally-From: PAZST "SAUL TENDLER" Mailer: Janet_Mailshr V3.5 ( 13-OCT-1989 14:07:27 ) Original-To: PROTEINS@UK.AC.DARESBURY Originally-To: JANET"PROTEINS@DARESBURY" Royal Society of Chemistry Biological Methods Group 2nd UK International Meeting on Biological & Biomedical Applications of SCANNING PROBE MICROSCOPY 2-3 SEPTEMBER 1993 NOTTINGHHAM U.K. This meeting covers biological and biomedical applications of scanning probe microscopy including scanning tunnelling and atomic force microscopy Speakers include Amrein - Munster, Germany Steadman - NPL, UK Thundat - Oak Ridge, USA Miles - Bristol, UK Butt - Max-Plank Inst. Germany Davies - Kodak, UK Heckl - Munich, Germany Morris - AFRC, UK Stabel / Rabe - Max-Plank, Germany Lindsay - Arizona, USA Bowen - Warwick, UK For further details E-mail PAZST@UK.AC.NOTT.VAX or write to The Biological SPM Laboratory Department of Pharmaceutical Sciences University of Nottingham Nottingham NG7 2RD UK Fax +44 602 515102 From owner-proteins@net.bio.net Sun May 09 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!zaphod.mps.ohio-state.edu!uwm.edu!caen!destroyer!cs.ubc.ca!utcsri!newsflash.concordia.ca!nstn.ns.ca!ac.dal.ca!arlin From: arlin@ac.dal.ca Newsgroups: bionet.molbio.proteins Subject: PK crystal structure: need updated info Message-ID: <1993May10.152326.13606@ac.dal.ca> Date: 10 May 93 18:23:26 GMT Organization: Dalhousie University, Halifax, Nova Scotia, Canada Lines: 21 I'm looking for current data for the structure of cat muscle pyruvate kinase. A structure was published in 1979, and appears in the Protein Data Bank (pdb1pyk). However, this structure lacks a large segment that couldn't be resolved. In 1986, a paper with the amino acid sequence appeared from the same laboratory (of Hilary Muirhead, Univ. of Bristol), and included a secondary structure map for all 530 residues of the protein, including the 100 residues that weren't in the original crystal structure. Obviously, the structure has been resolved further by using the sequence, but the data bank entry has not been updated. Does anyone know where I can get this structure? Any useful info (e.g., another database, Muirhead's phone number or E-mail) would be greatly appreciated. I need the alpha-carbon coordinates in order to finish a series of tests of the hypothesis that exons encode discrete structural elements of protein (so far, they don't). A. Stoltzfus Dept Biochemistry From owner-proteins@net.bio.net Sun May 09 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!usc!cs.utexas.edu!uunet!newsflash.concordia.ca!nstn.ns.ca!ac.dal.ca!jopa From: jopa@ac.dal.ca Newsgroups: bionet.molbio.proteins Subject: Re: Preservation of cyt. c solns Message-ID: <1993May10.074530.13597@ac.dal.ca> Date: 10 May 93 10:45:30 GMT References: <1993May6.181637.23233@yang.earlham.edu> Organization: Dalhousie University, Halifax, Nova Scotia, Canada Lines: 29 In article <1993May6.181637.23233@yang.earlham.edu>, davidw@yang.earlham.edu writes: > > 1. Is bacteria really a threat to the protein? > 2. If not bacteria, what will damage the protein? > 3. What is the best way to store the solution for short periods of time > (a few days at a time)? > I work with Cyt c regularly, although mine are yeast derived mutants. We generally just keep the solutions at -20c when we are not using them, I haven't noticed any problems. After doing redox potentials or other assays where the cyt c is recoverable, we regenerate it by lyophilizing and then desalting into 50 mM KPO4. I know that storage at pH 11 can lead to degeneration, but I believe this is more chemical (since the protein is denatured). In general, I just make sure all my solutions are at a reasonable pH (~7) and thawed for as little as possible. Jonathan Parrish Department of Biochemistry Dalhousie University Halifax, N.S., Canada > > David Weis davidw@yang.earlham.edu From owner-proteins@net.bio.net Mon May 10 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!news-feed-1.peachnet.edu!gatech!swrinde!sdd.hp.com!saimiri.primate.wisc.edu!usenet.coe.montana.edu!decwrl!uunet!pipex!uknet!pavo.csi.cam.ac.uk!bjd12 From: bjd12@cus.cam.ac.uk (Ben Davis) Newsgroups: bionet.molbio.proteins Subject: fluoresence Summary: how does charge affect Trp fluoresence ? Keywords: Fluoresence, pH Message-ID: <1993May11.090704.11048@infodev.cam.ac.uk> Date: 11 May 93 09:07:04 GMT Sender: bjd12@cus.cam.ac.uk Distribution: global Organization: U of Cambridge, England Lines: 16 Nntp-Posting-Host: bootes.cus.cam.ac.uk Does anyone know if a Lys in close proximity to a Trp can cause quenching ? I've got a lysine lying along the indole ring of the trp (the only one in the protein), with the NH3+ close to the indole NH. When I unfold the protein, I see a large increase in fluoresence as well as a redshift; the redshift I can understand, the increase in fluoresence is the opposite to normal. There's no other aromatics within 10A, and the trp is not solvent exposed.The lys is part of a salt bridge with a glu and an asp. Any suggestions ? Ben Davis MRC Unit for Protein Function and Design Cambridge, UK From owner-proteins@net.bio.net Tue May 11 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!zaphod.mps.ohio-state.edu!cs.utexas.edu!uunet!newsflash.concordia.ca!nstn.ns.ca!ac.dal.ca!nvett From: nvett@ac.dal.ca Newsgroups: bionet.molbio.proteins Subject: Enzymes as mechanical devices Message-ID: <1993May12.105040.13658@ac.dal.ca> Date: 12 May 93 13:50:40 GMT Organization: Dalhousie University, Halifax, Nova Scotia, Canada Lines: 12 Hi all, I was wondering what everyone out there thinks about the recent article by R.J.P.Williams (TIBS, April 1993) on enzymes as mechanical devices. I did not think that it was an entirely new concept, especially for people who appreciate protein structure, but I think it is a very elegant elaboration of the conformational changes on an enzyme molecule during catalysis. I would like to initiate a discussion on this if anyone is interested--to get a general idea of what you people think. Thanks a lot. Nat Vettakkorumakankav Department of Biochemistry From owner-proteins@net.bio.net Wed May 12 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!usc!elroy.jpl.nasa.gov!news.claremont.edu!ucivax!news.service.uci.edu!unogate!mvb.saic.com!zippy.Telcom.Arizona.EDU!joplin.biosci.arizona.edu!r4938585 From: r4938585@joplin.biosci.arizona.edu (Doug Roberts) Newsgroups: bionet.molbio.proteins Subject: Re: Rev protein Keywords: rev crystallization Message-ID: <1subg8$5o2@zippy.Telcom.Arizona.EDU> Date: 13 May 93 20:36:24 GMT References: <1993May7.094800.13500@ac.dal.ca> Sender: r4938585@joplin.biosci.arizona.edu (Doug Roberts) Organization: University of Arizona, Biotechnology, Tucson Lines: 13 NNTP-Posting-Host: joplin.biosci.arizona.edu In article <1993May7.094800.13500@ac.dal.ca> nvett@ac.dal.ca writes: >Hey kids, >Does anybody know if the Rev protein (from HIV) has been >crystallized? > >Nat Vettakkorumakankav A quick search of current contents shows no successful crystallization of the HIV rev protein. This search is only of the past couple of years or so, but I think it is unlikely that it would have been crystallized before then. Fire up those grant proposals! Cheers! Doug From owner-proteins@net.bio.net Wed May 12 23:00:00 1993 Path: biosci!parc!decwrl!decwrl!uunet!pipex!uknet!pavo.csi.cam.ac.uk!bjd12 From: bjd12@cus.cam.ac.uk (Ben Davis) Newsgroups: bionet.molbio.proteins Subject: CD Keywords: CD, salt, denaturation Message-ID: <1993May13.154220.4559@infodev.cam.ac.uk> Date: 13 May 93 15:42:20 GMT Sender: bjd12@cus.cam.ac.uk Distribution: global Organization: U of Cambridge, England Lines: 10 Nntp-Posting-Host: bootes.cus.cam.ac.uk Does anyone have any good suggestions about doing far UV CD with lots of salt (200mM - 600mM) without the noise being too serious ? I'm working at low pH. Thanks, Ben Davis MRC Unit for Protein Function and Design From owner-proteins@net.bio.net Wed May 12 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!darwin.sura.net!haven.umd.edu!purdue!mentor.cc.purdue.edu!mace.cc.purdue.edu!b35 From: b35@mace.cc.purdue.edu (Vic Ilag) Newsgroups: bionet.molbio.proteins Subject: Program for Analysing CD Spectra Message-ID: Date: 13 May 93 12:17:39 GMT Sender: news@mentor.cc.purdue.edu (USENET News) Organization: Purdue University Lines: 10 Does anyone have any program that could analyse CD spectra of proteins to give quantitative estimates of the different secondary structures present? I will be grateful if you could email me the source code or an executable file in any environment (DOS/Unix/VMS). Thanks. vic b35@mace.cc.purdue.edu From owner-proteins@net.bio.net Thu May 13 23:00:00 1993 Path: biosci!agate!news.ucdavis.edu!othello.ucdavis.edu!ez027854 From: ez027854@othello.ucdavis.edu Newsgroups: bionet.molbio.proteins Subject: C-terminal Analysis Protocol Keywords: C-Terminus, Protocol Message-ID: Date: 14 May 93 19:24:22 GMT Sender: Mike Oda (ez027854@hamlet.ucdavis.edu) Distribution: bionet.molbio.proteins Organization: Biochemistry and Biophysics, UC Davis Lines: 14 Hi, I have recently cloned a c-terminally processed protein and am in the process of analysing both the precursor molecule and the processed product. I am wondering if anyone out there could assist me by sending me a protocol for c-terminal analysis of a peptide. My searches have lead me to relatively "old" protocols from the early 80s and I am wondering if there has been any recent advances in this area that I may have overlooked. The reason I ask is because the results obtained from the use of the protocol I have (exopeptidase, time point cleavage) gives rather dirty results that are nearly unusable beyond two amino acids. Any help in this area would be greatly appreciated. Thanks Michael Oda (ez027854@hamlet.ucdavis.edu) From owner-proteins@net.bio.net Sun May 16 23:00:00 1993 Path: biosci!EMORYU1.CC.EMORY.EDU!genekdw From: genekdw@EMORYU1.CC.EMORY.EDU ("Keith D. Wilkinson") Newsgroups: bionet.molbio.proteins Subject: Re: C-terminal Analysis Protocol Message-ID: <9305171333.AA04309@emoryu1.cc.emory.edu> Date: 17 May 93 13:33:19 GMT Sender: daemon@net.bio.net Reply-To: "Keith D. Wilkinson" Distribution: bionet Lines: 59 In message <9305142052.AA14505@emoryu1.cc.emory.edu> writes: > Received: from STANFORD.BITNET (NJE origin MAILER@STANFORD) by > EMUVM1.CC.EMORY.EDU (LMail V1.1d/1.7f) with BSMTP id 8580; Fri, > 14 May 1993 16:43:54 -0400 > Received: by Forsythe.Stanford.EDU; Fri, 14 May 93 13:43:54 PDT > Received: by net.bio.net (5.65/IG-2.0) > id AA05864; Fri, 14 May 93 12:42:27 -0700 > Received: by net.bio.net (5.65/IG-2.0) > id AA05853; Fri, 14 May 93 12:42:25 -0700 > Message-Id: <9305141942.AA05853@net.bio.net> > To: proteins@net.bio.net > From: ez027854@othello.ucdavis.edu > Subject: C-terminal Analysis Protocol > Date: 14 May 93 19:24:22 GMT > Sender: Mike.Oda@net.bio.net (ez027854@hamlet.ucdavis.edu) > > Hi, > I have recently cloned a c-terminally processed protein and am in > the process of analysing both the precursor molecule and the processed > product. I am wondering if anyone out there could assist me by sending > me a protocol for c-terminal analysis of a peptide. My searches have > lead me to relatively "old" protocols from the early 80s and I am wondering > if there has been any recent advances in this area that I may have > overlooked. > The reason I ask is because the results obtained from the use of the protocol > I have (exopeptidase, time point cleavage) gives rather dirty results that > are nearly unusable beyond two amino acids. > Any help in this area would be greatly appreciated. > Thanks > Michael Oda > (ez027854@hamlet.ucdavis.edu) > > :: C-terminal Analysis Protocol The last time I looked into this, the exopeptidase approach was the only one that worked very well, and as you have discovered, in many cases the kinetic approach breaks down fairly quickly. Consider analyzing your reaction products by electrospray mass spectrosopy. Since you know the sequence, this can provide you with the site of cleavage with great accuracy and doesn't require too much material. Post-translational modifications of the precursor molecule should be identified by this proceedure also. Keith D. Wilkinson genekdw@emoryu1.cc.emory.edu Department of Biochemistry grdbckdw@emuvm1.cc.emory.edu Emory University School of Medicine Voice (404) 727-5980 Atlanta, GA 30322 Fax (404) 727-2738 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* If it's worth doing, it's worth doing to excess! -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* From owner-proteins@net.bio.net Sun May 16 23:00:00 1993 Path: biosci!uwm.edu!wupost!uunet!pipex!uknet!warwick!bham!ibm3090.bham.ac.uk!WOCHNIAP From: WOCHNIAP@IBM3090.BHAM.AC.UK Newsgroups: bionet.molbio.proteins Subject: Isozymes staining info needed Message-ID: <931317111306@ibm3090.bham.ac.uk> Date: 17 May 93 10:13:06 GMT Organization: The University of Birmingham, United Kingdom Lines: 13 NNTP-Posting-Host: ibm3090.bham.ac.uk ============================================================================== HALLO EVERYBODY, I am currently working on Brassica isozymes and need a piece of advice about staining protocols suitable for my subject.Does anybody know a good source of references? Would you be kind enough to send me yours experience with isozymes staining? All tips will be most appreciated!!! If you would like to mail me some articles via s-mail my address is: Piotr Wochniak Univ Birmingham Sch Biol Sci Birmingham 15S 2TT W Midlands,ENGLAND From owner-proteins@net.bio.net Sun May 16 23:00:00 1993 Path: biosci!ZEUS.AHABS.WISC.EDU!ming From: ming@ZEUS.AHABS.WISC.EDU ("Ding Ming") Newsgroups: bionet.molbio.proteins Subject: Re: C-terminal Analysis Protocol Message-ID: Date: 17 May 93 21:45:54 GMT Sender: daemon@net.bio.net Reply-To: ming@zeus.ahabs.wisc.edu Distribution: bionet Organization: Animal Health & Biomedical Sciences Lines: 26 > Any help in this area would be greatly appreciated. > Thanks > Michael Oda > (ez027854@hamlet.ucdavis.edu) > > You can call Mr. Gu, qu-ming @608-262-5765 and he is an expert in this field and he just established a new method for c-terminal sequencing. Good luck! ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Ding Ming (608)265-3544 ming@calshp.cals.wisc.edu Sweet Protein Section ming@zeus.ahabs.wisc.edu Taste Research Lab Department of Animal Health & Biomedical Sciences University of Wisconsin-Madison, 1655 Linden Dr., Madison, WI53706 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Office Location: A215 Babcock Hall ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ From owner-proteins@net.bio.net Sun May 16 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!newsserver.jvnc.net!gmd.de!rrz.uni-koeln.de!news-rhrz!unitas.or.uni-bonn.de!will From: will@unitas.or.uni-bonn.de (Hans-Martin Will) Newsgroups: bionet.molbio.proteins,sci.math Subject: Models of Protein Conformation/Folding/Docking Keywords: protein conformation, discrete mathematics Message-ID: <1993May17.142511.10573@news.rhrz.uni-bonn.de> Date: 17 May 93 14:25:11 GMT Sender: news@news.rhrz.uni-bonn.de Organization: Research Institute for Discrete Mathematics, Bonn Lines: 21 Xref: biosci bionet.molbio.proteins:642 sci.math:11748 Hello world, I'd like to make contact to research groups working on mathematical models concerning protein conformation/folding/docking. In this context I'm especially interested in problems occuring due to discretization (finite elements on diff. eqs., lattice models, matching theory...). So, if you are working on one of the topics mentioned above (or one closely related to, or you know any colleague...), please let me know about it. Thanks alot, Martin Will +-------------------------------+--------------------------------------------+ | Martin Will | | | Research Institute of | "Never theorize before one has data" | | Discrete Mathematics | | | University of Bonn +--------------------------------------------+ | Germany | email: will@marvin.or.uni-bonn.de | +-------------------------------+--------------------------------------------+ From owner-proteins@net.bio.net Mon May 17 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.molbio.proteins Subject: Re: conserved amino acid changes Message-ID: Date: 18 May 93 22:25:03 GMT References: <93138.161249FAGUYD@QUCDN.QueensU.CA> Lines: 34 Nntp-Posting-Host: husc10.harvard.edu David M. Faguy writes: >Hello bionetland >I have a question about conserved amino acid changes. Basically is there > agreement on what can be considered conserved changes? Most papers don't >define or reference what they call a conserved change. Any reference we can cite >would be helpful. Thanks in advance. I suspect you mean _conservative_ amino acid substitutions. The conceptual definition is "a substitution of an amino acid with similar chemical properties", such as Ser<->Thr, Asp<->Glu, small aliphatics with each other, etc. The best operational definition is amino acids with low substitution penalties in whatever scoring matrix you are using. Look up Dayhoff's papers and Henikoff^2's BLOSUM paper (and others). For the cites: gopher to merlot.welch.jhu.edu Menu option: Search Databases at Hopkins... Menu option: Seqanalref Search terms: amino and substitute This will get you started -- Seqanalref is wonderful resource for queries such as this. Happy hunting! Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@biosun.harvard.edu From owner-proteins@net.bio.net Mon May 17 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!wupost!uunet!psgrain!ee.und.ac.za!ford.ee.up.ac.za!hippo.ru.ac.za!pukrs7.puk.ac.za!cs.upe.ac.za!csbep From: csbep@cs.upe.ac.za (Elroy Parkinson) Newsgroups: bionet.molbio.proteins Subject: Anaerobic digestion Message-ID: Date: 18 May 93 10:50:01 GMT Organization: University of Port Elizabeth Lines: 4 NNTP-Posting-Host: 192.96.250.71 I need some information on assays and activities of the enzymes important in the anaerobic process.I would appreciate any info the specificity of these enzymes as well as info on the cofactors and kinetics, of the most recent isolated enzymes. From owner-proteins@net.bio.net Mon May 17 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!torn!news.ccs.queensu.ca!qucdn!faguyd From: FAGUYD@QUCDN.QueensU.CA (David M. Faguy) Newsgroups: bionet.molbio.proteins Subject: conserved amino acid changes Message-ID: <93138.161249FAGUYD@QUCDN.QueensU.CA> Date: 18 May 93 20:12:49 GMT Organization: Queen's University at Kingston Lines: 9 Hello bionetland I have a question about conserved amino acid changes. Basically is there agreement on what can be considered conserved changes? Most papers don't define or reference what they call a conserved change. Any reference we can cite would be helpful. Thanks in advance. David Faguy (faguyd@qucdn.queensu.ca) Queen's University Kingston, Ontario Canada From owner-proteins@net.bio.net Mon May 17 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!torn!watserv2.uwaterloo.ca!peptidarus.UWaterloo.ca!ltaylor From: ltaylor@peptidarus.UWaterloo.ca (Lorne Taylor) Newsgroups: bionet.molbio.proteins Subject: Protein Stuctural Feacture Program Sought Message-ID: Date: 18 May 93 15:09:07 GMT Sender: news@watserv2.uwaterloo.ca Organization: University of Waterloo Lines: 10 This is probably a FAQ but does anyone know of programs to display protein structural elements as arrows, cylinders , tubes etc... preferably FTPable but any info on any programs would be much appreciated! ^^^ ^^^ Thanks in Advance Lorne Taylor Chemistry University of Waterloo Waterloo, CANADA ltaylor@peptidarus.uwaterloo.ca From owner-proteins@net.bio.net Mon May 17 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!pipex!warwick!uknet!comlab.ox.ac.uk!oxuniv!oxpath!rpgrant From: rpgrant@molbiol.ox.ac.uk Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Storage of proteins at -20C/-70C Summary: What glycerol concentrations do I need? Keywords: Glycerol, frozen protein Message-ID: <1993May18.135330.1@molbiol.ox.ac.uk> Date: 18 May 93 12:53:30 GMT Followup-To: bionet.molbiol.proteins Organization: Oxford University Molecular Biology Data Centre Lines: 10 Xref: biosci bionet.molbio.methds-reagnts:5555 bionet.molbio.proteins:648 Nntp-Posting-Host: kasia Nntp-Posting-User: rpgrant Does anyone know what concentration of glycerol I should use when storing protein at -20C and -70C? Reference(s)? Thanks! (followup to bionet.molbiol.proteins) -- Richard P. Grant <>< rpgrant@molbiol.ox.ac.uk Sir William Dunn School of Pathology Fax. +44 865 275556 University of Oxford, UK. Tel. +44 865 275565 "It's easy when you know how" From owner-proteins@net.bio.net Tue May 18 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!sdd.hp.com!nigel.msen.com!math.fu-berlin.de!informatik.tu-muenchen.de!hegel!nmeier From: Christoph.Niedermeier@hegel.physik.uni-muenchen.de (Christoph Niedermeier) Newsgroups: bionet.molbio.proteins Subject: protein data bank Message-ID: <1993May19.120301.14166@Informatik.TU-Muenchen.DE> Date: 19 May 93 12:03:01 GMT Sender: news@Informatik.TU-Muenchen.DE (USENET Newssystem) Reply-To: Christoph.Niedermeier@hegel.physik.uni-muenchen.de Organization: Universitaet Muenchen Lines: 20 Hello, I would like to get lists of typical globular and membrane proteins which are available in the Brookhaven Protein data bank. Each protein considered should represent a large class of similiar proteins. I want to do statistics on some structural and electrostatic features e. g. on the ratio of polar and charged side chain groups. Large proteins (>250 residues) are preferred. Thanx a lot Chris -- Christoph Niedermeier -- Theoretische Biophysik -- Institut fuer medizinische Optik -- Ludwigs-Maximilian-Universitaet Muenchen -- __o Theresienstrasse 37 -- 8000 Muenchen 2 -- Germany _`\<,_ phone: ++49-89/2394-4580, fax: ++49-89/2805248 (_)/ (_) email: Christoph.Niedermeier@Physik.Uni-Muenchen.DE ~~~~~~~~~~~ From owner-proteins@net.bio.net Tue May 18 23:00:00 1993 Path: biosci!relay.the.net!SHAUN%JASON.DECNET From: SHAUN%JASON.DECNET@relay.the.net ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: Re: conserved amino acid changes Message-ID: <01GYD3561O6A000VLW@nic.the.net> Date: 19 May 93 20:55:48 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 21 Dear ProteiNetters, Conservative replacements have been well defined by Margaret Dayhoff in her PAM matrices (see Atlas of Protein Sequences, front of any edition). It shows quantitatively how often each amino acid replaces another. The mentioned conservative replacements (S<->T, D<->E, etc) pop out as high frequency results. It might also be of some interest to point you to our work on amino acid side chain hydrophobicity/hydrophilicity. Essentially, most conservative substitutions are similar in polarity, probably because hydrophobicity is probably the principal driving 'force' in protein folding. We've characterized the standard 20 amino acids and about twenty post- or co-translational modifications of these. The reference is Black, S.D. and Mould, D.R. (1991) Anal. Biochem. 193, 72-82, "Development of Hydrophobicity Parameters to Analyze Proteins Which Bear Post- or Co- translational Modifications". Hope this helps. Cheers. -Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | Bitnet: shaun%jason.decnet@thenic.bitnet = = UT Health Center, Tyler | Phone: (903)877-2806 FAX: (903)877-7558 = = Tyler, TX 75710-2003 | B-) (Start every day with a smile...) = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Tue May 18 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!zaphod.mps.ohio-state.edu!caen!saimiri.primate.wisc.edu!zazen!psl.wisc.edu!news From: roca@macc.wisc.edu (Alberto I Roca) Newsgroups: bionet.molbio.proteins Subject: Re: conserved amino acid changes Message-ID: <1993May19.170722.21082@pslu1.psl.wisc.edu> Date: 19 May 93 17:07:22 GMT References: <93138.161249FAGUYD@QUCDN.QueensU.CA> Sender: news@pslu1.psl.wisc.edu (USENET News System) Organization: Biochemistry, UW-Madison Lines: 33 X-Xxdate: Wed, 19 May 93 12:12:53 GMT X-Useragent: Nuntius v1.1.1d17 these are the references i have regarding conservative amino acid replacements. these methods are based upon chemical functionality: Karlin, S., and Ghandour, G., (1985). Multiple!alphabet amino acid sequence comparison of the immunoglobulin k!chain constant domain. Proceedings of the National Academy of Sciences of the United States of America. 82, 8597-8601. amino acid classes: chemical: acidic (DE), aliphatic (AGILV), amide (NQ), aromatic (FWY), basic (RHK), hydroxyl (ST), imino (P), sulfur (CM); functional: acidic, basic, hydrophobic (AILMFPWV), polar (NCQGSTY); charge: acidic, basic, neutral; structural: ambivalent (ACGPSTWY), external (RNDQEHK), internal (ILMFV) the following paper created Venn diagrams of the different amino acids. This reflects the the overlapping relationships that exist between different amino acid classes. Taylor, W. R., (1986). The classification of amino acid conservation. Journal of Theoretical Biology. 119, 205-218. ================================================================= Alberto I. Roca Internet: roca@macc.wisc.edu Biochemistry Bitnet: roca@wiscmacc 420 Henry Mall University of Wisconsin-Madison Madison, Wisconsin 53706 USA From owner-proteins@net.bio.net Wed May 19 23:00:00 1993 Path: biosci!agate!news.ucdavis.edu!othello.ucdavis.edu!ez027854 From: ez027854@othello.ucdavis.edu Newsgroups: bionet.molbio.proteins Subject: Re: C-terminal Analysis Protocol Message-ID: Date: 20 May 93 19:17:31 GMT Sender: Mike Oda Followup-To: bionet.molbio.proteins Distribution: bionet.molbio.proteins Organization: Department of Biochemistry & Biophysics, UC Davis Lines: 24 To all those folks who replied with helpful suggestion, Thankyou. :) After examining the suggestions received and the literature closely, I decided that the standard carboxy peptidase y approach would yield the best initial results. I came across a few chemical approaches that were recently published utilizing thiohydantoin derivatives but found (through discussion with those more familiar with thiohydantoin chemistry) that this method is still fairly "dirty". This leads me to my next question, which is... Now that I have decided to use carboxy peptidase y which company is the best provider of this enzyme? I have seen it from both Sigma and Boeringer Mannheim, although BM is the only producer I have encountered so far that makes a sequencing grade enzyme. Is it necessary to purchase the sequencing grade as opposed to the analytical grade? Is contaminating proteolytic activity a significant problem in analytical grade preparation of this enzyme? And... I am considering doing the amino acid analysis myself on a C18 reverse phase column. Does anybody out there have a protocol or reference that I may turn to for more precise guidance in this area? Thankyou Mike Oda ez027854@hamlet.ucdavis.edu From owner-proteins@net.bio.net Wed May 19 23:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!pipex!uknet!comlab.ox.ac.uk!oxuniv!dnicker From: dnicker@vax.oxford.ac.uk Newsgroups: bionet.molbio.proteins Subject: Re: Enzymes as mechanical devices Message-ID: <1993May20.204612.14206@vax.oxford.ac.uk> Date: 20 May 93 19:46:12 GMT References: <1993May12.105040.13658@ac.dal.ca> Organization: Oxford University VAX 6620 Lines: 23 In article <1993May12.105040.13658@ac.dal.ca>, nvett@ac.dal.ca writes: > Hi all, > I was wondering what everyone out there thinks about the recent article > by R.J.P.Williams (TIBS, April 1993) on enzymes as mechanical devices. I did > not think that it was an entirely new concept, especially for people who > appreciate protein structure, but I think it is a very elegant elaboration > of the conformational changes on an enzyme molecule during catalysis. I would > like to initiate a discussion on this if anyone is interested--to get a general > idea of what you people think. Thanks a lot. > > > Nat Vettakkorumakankav > Department of Biochemistry Hi there Nat, Is seems response is a bit slow in coming on your proposed discussion. . . if there seems to be interest I have spoken to RJP Williams and he would be interested in participating. Guess we'll wait a few more days eh? :) Darren Nickerson A Canadian in the UK From owner-proteins@net.bio.net Thu May 20 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!zaphod.mps.ohio-state.edu!darwin.sura.net!newsserver.jvnc.net!yale.edu!news.yale.edu!zinc.med.yale.edu!gardner From: gardner@zinc.med.yale.edu (Kevin Gardner) Newsgroups: bionet.molbio.proteins Subject: Diamond coordinate format Message-ID: <1993May21.182330.9482@news.yale.edu> Date: 21 May 93 18:23:30 GMT Sender: news@news.yale.edu (USENET News System) Organization: Dept of Mol. Biophysics & Biochemistry, Yale University Lines: 17 Nntp-Posting-Host: zinc.med.yale.edu Does anyone out there have either: a). a good description (field sizes, contents) for the Diamond format for atomic coordinates -or- b). a good program (Fortran, C, Perl,....) for interchanging Diamond and pdb? Thanks in advance, Kevin -- ************************************************************************* Kevin Gardner Yale University Dept. of Molecular Biophysics and Biochemistry Internet: gardner@zinc.med.yale.edu Bitnet: gardner@yalemed From owner-proteins@net.bio.net Thu May 20 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!noc.near.net!uunet!newsflash.concordia.ca!nstn.ns.ca!ac.dal.ca!nvett From: nvett@ac.dal.ca Newsgroups: bionet.molbio.proteins Subject: Re: Enzymes as mechanical devices Message-ID: <1993May21.101852.13878@ac.dal.ca> Date: 21 May 93 13:18:52 GMT References: <1993May12.105040.13658@ac.dal.ca> <1993May20.204612.14206@vax.oxford.ac.uk> Organization: Dalhousie University, Halifax, Nova Scotia, Canada Lines: 38 Yes response to the discussion appears to be slow. I like prof. William's analogy to the hand in glove while illustrating the "enzymes as mechanical devices" concept. I have a problem, however, in picturing the enzyme as a mechanical device--I mean it is difficult to envision something like a robot moving its "arms". I hope that everyone understands what I am trying to project here. It is here that I would like more input as to what people think. I like to picture an enzyme molecule as a very dynamic system that undergoes conformational changes during the catalytic process but not as a rigid mechanical device. Anyway, I shall wait a little while yet for more input. I would like to hear from Prof. Williams on this. Cheers, Nat. In article <1993May20.204612.14206@vax.oxford.ac.uk>, dnicker@vax.oxford.ac.uk writes: > In article <1993May12.105040.13658@ac.dal.ca>, nvett@ac.dal.ca writes: >> Hi all, >> I was wondering what everyone out there thinks about the recent article >> by R.J.P.Williams (TIBS, April 1993) on enzymes as mechanical devices. I did >> not think that it was an entirely new concept, especially for people who >> appreciate protein structure, but I think it is a very elegant elaboration >> of the conformational changes on an enzyme molecule during catalysis. I would >> like to initiate a discussion on this if anyone is interested--to get a general >> idea of what you people think. Thanks a lot. >> >> >> Nat Vettakkorumakankav >> Department of Biochemistry > > > Hi there Nat, > > Is seems response is a bit slow in coming on your proposed discussion. . . if > there seems to be interest I have spoken to RJP Williams and he would be > interested in participating. Guess we'll wait a few more days eh? :) > > Darren Nickerson > A Canadian in the UK > From owner-proteins@net.bio.net Fri May 21 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!wupost!waikato.ac.nz!comp.vuw.ac.nz!canterbury.ac.nz!news!sanger.otago.ac.nz!craigm From: craigm@sanger.otago.ac.nz (Craig Marshall) Newsgroups: bionet.molbio.proteins Subject: Re: Enzymes as mechanical devices Message-ID: Date: 23 May 93 10:47:47 GMT References: <1993May20.204612.14206@vax.oxford.ac.uk> Sender: usenet@news.otago.ac.nz (News stuff) Organization: University of Otago Lines: 26 Nntp-Posting-Host: sanger.otago.ac.nz X-Newsreader: TIN [version 1.1 PL8] I like the idea very much. The serpins, a group of (mostly) serine protease inhibitors have a number of features that I believe are best explained by a mechanical analogy. They exist in two forms; an intact and active form, and an inactive and cleaved form. Inactivation is associated with interaction with an appropriate protease and the subsequent slow release of the cleaved inhibitor. The two forms show very different thermal stabilities, and most interestingly intact serpins show little helical structure as detected by fourier-transform infrared spectroscopy. After cleavage helical signal is found. X-ray structures of four cleaved (or essentially so) serpins indicate that there are definitely helices in the structure. I have imagined that the helices act as springs and are thus slightly under or over-wound in the intact molecules, and this provides the force that allows the substantial changes in structure believed to be associated with the inhibitory mechanism. Amongst these is the insertion of a further strand into a beta-sheet. I would be interested in any other examples that might support (or refute) the idea of mechanical enzymes. -- Craig Marshall craigm@sanger.otago.ac.nz or Biochemistry Department bioc07@otago.ac.nz University of Otago Phone 64 3 479 7849 P.O. Box 56 Fax 64 3 479 7866 Dunedin, New Zealand From owner-proteins@net.bio.net Sun May 23 23:00:00 1993 Path: biosci!uwm.edu!wupost!kuhub.cc.ukans.edu!parsifal.umkc.edu!SEMOVM.SEMO.EDU From: C741SCB@SEMOVM.SEMO.EDU (C741SCB) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Zwitterionic buffers and strong ion exchangers? Message-ID: <24MAY93.11555533.0077@SEMOVM.SEMO.EDU> Date: 24 May 93 16:41:58 GMT Sender: usenet@SEMOVM.SEMO.EDU Organization: University of Missouri - Kansas City Lines: 11 Xref: biosci bionet.molbio.methds-reagnts:5637 bionet.molbio.proteins:658 NNTP-Posting-Host: semovm.semo.edu Does anybody know anything about the interaction between zwitterionic buffer systems and Q ion exchange resins? I am in the middle of a protein purification that looks as if the next logical step involves an anion exchanger equilibrated at below pH 7. For obvious reasons I don't particularlywant to use a buffer system that will interact with the column. I suspect that a zwitterionic system would pose less of a problem as far as competition between the buffer and the proteins of interest than say phosphate or acetate, but I haven't seen anything in the literature dealing with this. Allen Gathman C741SCB@SEMOVM or C741SCB@SEMOVM.SEMO.EDU From owner-proteins@net.bio.net Sun May 23 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!usc!elroy.jpl.nasa.gov!news.claremont.edu!ucivax!news.service.uci.edu!unogate!mvb.saic.com!zippy.Telcom.Arizona.EDU!joplin.biosci.arizona.edu!droberts From: droberts@joplin.biosci.arizona.edu (Doug Roberts) Newsgroups: bionet.molbio.proteins Subject: Re: Preservation of cyt. c solns Keywords: protein stability, storage, denaturation Message-ID: <1tbqrk$f4r@zippy.Telcom.Arizona.EDU> Date: 18 May 93 23:18:12 GMT References: <1993May6.181637.23233@yang.earlham.edu> <1993May10.074530.13597@ac.dal.ca> Sender: droberts@joplin.biosci.arizona.edu (Doug Roberts) Organization: University of Arizona, Biotechnology, Tucson Lines: 16 NNTP-Posting-Host: joplin.biosci.arizona.edu This reminds me of a discussion/argument that I had with a labmate recently. She argued that the reason for always keeping proteins in the cold was to prevent denaturation. I believe that it must be for some other reason, perhaps to prevent microorganism growth, or to slow down the activity of proteases that may be present in the sample. It seems to me that at room temperature, most proteins will be stable against denaturation. (Most of the melting curves I've seen are quite flat around this temp.) The other point is that we grow up our yeast at 36C and their proteins seem to work just fine. Does anyone have any thoughts on this one? I might very well be wrong. (And no, I don't make a habit of leaving my proteins at RT!) %-). Doug Roberts - "Will crystallize for food!!!" From owner-proteins@net.bio.net Sun May 23 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!news-feed-1.peachnet.edu!umn.edu!limerick.cbs.umn.edu!hiroki From: hiroki@limerick.cbs.umn.edu (Hiroki Morizono) Newsgroups: bionet.molbio.proteins Subject: Re: Enzymes as mechanical devices Message-ID: Date: 24 May 93 20:50:24 GMT References: <1993May20.204612.14206@vax.oxford.ac.uk> Sender: news@news2.cis.umn.edu (Usenet News Administration) Reply-To: hiroki@limerick.cbs.umn.edu Organization: University of Minnesota Lines: 10 Nntp-Posting-Host: limerick.cbs.umn.edu X-Newsreader: Tin 1.1 PL5 Here is an article which may be of interest then, Lumry, R., Biltonen, R., (1969) "Thermodynamic and Kinetic Aspects of Protein Conformation in Relation to Physiological Function," Biological Macromolecules Volume 2 There's a section on rack mechanisms in there. Hiroki hiroki@limerick.cbs.umn.ed From owner-proteins@net.bio.net Mon May 24 23:00:00 1993 Path: biosci!uwm.edu!caen!uunet!newsflash.concordia.ca!nstn.ns.ca!ac.dal.ca!nvett From: nvett@ac.dal.ca Newsgroups: bionet.molbio.proteins Subject: Re: Enzymes as mechanical devices Message-ID: <1993May25.110647.13969@ac.dal.ca> Date: 25 May 93 14:06:47 GMT References: <1993May20.204612.14206@vax.oxford.ac.uk> Organization: Dalhousie University, Halifax, Nova Scotia, Canada Lines: 46 In article , craigm@sanger.otago.ac.nz (Craig Marshall) writes: > I like the idea very much. The serpins, a group of (mostly) serine > protease inhibitors have a number of features that I believe are best > explained by a mechanical analogy. They exist in two forms; an intact > and active form, and an inactive and cleaved form. Inactivation is > associated with interaction with an appropriate protease and the > subsequent slow release of the cleaved inhibitor. The two forms show > very different thermal stabilities, and most interestingly intact > serpins show little helical structure as detected by fourier-transform > infrared spectroscopy. After cleavage helical signal is found. X-ray > structures of four cleaved (or essentially so) serpins indicate that > there are definitely helices in the structure. I have imagined that > the helices act as springs and are thus slightly under or over-wound > in the intact molecules, and this provides the force that allows the > substantial changes in structure believed to be associated with the > inhibitory mechanism. Amongst these is the insertion of a further > strand into a beta-sheet. > > I would be interested in any other examples that might support (or > refute) the idea of mechanical enzymes. > > -- > Craig Marshall craigm@sanger.otago.ac.nz or > Biochemistry Department bioc07@otago.ac.nz > University of Otago Phone 64 3 479 7849 > P.O. Box 56 Fax 64 3 479 7866 > Dunedin, New Zealand I have also visualised alpha helices in enzymes as "springs" and the effect of "unwinding" or over winding these "springs" probably provides the energy for catalysis and regulatory process dependent conformational changes. I think that this is a bit more reasonable than a rigid mechanical device concept. However, in the April 29 issue of Nature (Vol 362, pp814-820) Tilbeurgh et al., describe the crystallization of the lipase-procolipase complex. The lipases have their active site "covered" by a "lid" or a "flap" which moves away as a result of conformational changes induced on the molecule as a result of substrate binding. The flap is a helix and helices are present in both the "open" and "closed" forms of the molecule but the length and the residues in the helices differ(unwinding of the original helix and formation of two new helices). In any case, this opening of the molecule now allows the formation of the oxyanion hole and the orientation of the catalytic triad residues for catalysis. This seems to support the "enzymes as mechanical devices" concept--I think. What do you think? Nat Vettakkorumakankav Department of Biochemistry From owner-proteins@net.bio.net Mon May 24 23:00:00 1993 Path: biosci!enterpoop.mit.edu!spool.mu.edu!uunet!newsflash.concordia.ca!nstn.ns.ca!ac.dal.ca!jopa From: jopa@ac.dal.ca Newsgroups: bionet.molbio.proteins Subject: Re: Preservation of cyt. c solns Message-ID: <1993May25.071613.13966@ac.dal.ca> Date: 25 May 93 10:16:13 GMT References: <1993May6.181637.23233@yang.earlham.edu> <1993May10.074530.13597@ac.dal.ca> <1tbqrk$f4r@zippy.Telcom.Arizona.EDU> Organization: Dalhousie University, Halifax, Nova Scotia, Canada Lines: 29 In article <1tbqrk$f4r@zippy.Telcom.Arizona.EDU>, droberts@joplin.biosci.arizona.edu (Doug Roberts) writes: > > This reminds me of a discussion/argument that I had with a labmate > recently. She argued that the reason for always keeping proteins in the cold > was to prevent denaturation. I believe that it must be for some other reason, > perhaps to prevent microorganism growth, or to slow down the activity of > proteases that may be present in the sample. It seems to me that at room > temperature, most proteins will be stable against denaturation. (Most of the > melting curves I've seen are quite flat around this temp.) The other point > is that we grow up our yeast at 36C and their proteins seem to work just > fine I suspect that there is a case for both. However, the denaturation which may be occurring at room temp. may not be a simple folding- unfolding denaturation, it could be a slow chemical process, ie. some oxidation or auto-proteolytic or, as you mentioned, the presence of additional proteinases. I would say it a question of time...proteins which are ok in yeast at 36C may not be okay in pure or semipure solution at 21C, since the environment is so different. Certainly the presence of microorganisms is a definite concern, I have seen solutions go bad and it is definitely because something is growing in it. Jonathan Parrish Department of Biochemistry Dalhousie University Halifax, N.S., Canada From owner-proteins@net.bio.net Mon May 24 23:00:00 1993 Path: biosci!agate!spool.mu.edu!uunet!pipex!uknet!liv!beynonrj From: beynonrj@liverpool.ac.uk (Dr. R.J. Beynon) Newsgroups: bionet.molbio.proteins Subject: Re: Preservation of cyt. c solns Message-ID: Date: 25 May 93 13:36:07 GMT References: <1993May25.071613.13966@ac.dal.ca> Sender: news@liverpool.ac.uk (News System) Organization: The University of Liverpool Lines: 49 Nntp-Posting-Host: uxb.liv.ac.uk X-Newsreader: TIN [version 1.1 PL8] jopa@ac.dal.ca wrote: : In article <1tbqrk$f4r@zippy.Telcom.Arizona.EDU>, droberts@joplin.biosci.arizona.edu (Doug Roberts) writes: : > : > This reminds me of a discussion/argument that I had with a labmate : > recently. She argued that the reason for always keeping proteins in the cold : > was to prevent denaturation. I believe that it must be for some other reason, : > perhaps to prevent microorganism growth, or to slow down the activity of : > proteases that may be present in the sample. It seems to me that at room : > temperature, most proteins will be stable against denaturation. (Most of the : > melting curves I've seen are quite flat around this temp.) The other point : > is that we grow up our yeast at 36C and their proteins seem to work just : > fine : I suspect that there is a case for both. However, the denaturation : which may be occurring at room temp. may not be a simple folding- : unfolding denaturation, it could be a slow chemical process, ie. : some oxidation or auto-proteolytic or, as you mentioned, the : presence of additional proteinases. I would say it a question : of time...proteins which are ok in yeast at 36C may not be okay : in pure or semipure solution at 21C, since the environment is : so different. : Certainly the presence of microorganisms is a definite concern, I have : seen solutions go bad and it is definitely because something is growing : in it. : Jonathan Parrish : Department of Biochemistry : Dalhousie University : Halifax, N.S., Canada Plus, it is instructive to calculate what the physiological concentration of proteins is in the cell - mM or higher. This must also contribute to stability in vivo. And, all those protective mechanisms - proteinase inhibitors, free radical moppers atc are all working away in vivo. Finally, steady state concentration in vivo does not mean that the proteins are stable, necessarily - they could be turning over at a terrific rate - a mouse, for instance, has a new liver every day! -which as an aside, destroys concepts of nationality. Within days or weeks of moving to a new country, many of your high turnover proteins will have been replaced with new proteins, made locally. Others, like crystallins, will take years. Eventually, you will be 'nationalised' biochemically, if not politically! Just my bit for world peace and harmony! Rob Beynon From owner-proteins@net.bio.net Mon May 24 23:00:00 1993 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Re: C-terminal Analysis Protocol Message-ID: <01GYLNT4872EA5U8AW@NBRF.Georgetown.Edu> Date: 25 May 93 22:13:34 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 25 In message <9305141942.AA05853@net.bio.net> ez027854@othello.ucdavis.edu (Michael Oda) asked > I am wondering if anyone out there could assist me by sending > me a protocol for c-terminal analysis of a peptide. An apparently very sensitive method for C-terminal peptide sequencing adaptable for sequenators was reported in @article{Bailey.Nikfarjam.1992, author = "Jermoe M. Bailey and Firoozeh Nikfarjam and Narmada R. Shenoy and John E. Shively", title = "Automated carboxy-terminal sequence analysis of peptides and proteins using diphenyl phosphoroisothiocyanatidate", year = 1992, journal = "Protein Science", volume = "1", pages = "1622-1633"} ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-proteins@net.bio.net Mon May 24 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!swrinde!network.ucsd.edu!dsmithmac.ucsd.edu!wbstine From: wbstine@ucsd.edu (Blaine Stine) Newsgroups: bionet.molbio.proteins Subject: Physical Size of Proteins??? Message-ID: <1tto9fINN2mn@network.ucsd.edu> Date: 25 May 93 18:24:47 GMT Organization: UCSD Biology Lines: 11 NNTP-Posting-Host: dsmithmac.ucsd.edu X-UserAgent: Nuntius v1.1.1d16 X-XXMessage-ID: X-XXDate: Tue, 25 May 93 11:20:39 GMT I was wondering of any of you could direct me to a good resource that would have the physical statistics of some common proteins. I am looking for approximate dimensions in nanometers of single strand binding protein, EcoRI (and maybe other restriction enzymes) and RecA. The volume in cubic nanometers would be great too. Thank you for your help. W. Blaine Stine Jr.----------------- UCSD Biology - Molecular Genetics |||||||||||||| wbstine@ucsd.edu ----------------- La Jolla CA From owner-proteins@net.bio.net Mon May 24 23:00:00 1993 Path: biosci!parc!decwrl!decwrl!purdue!mentor.cc.purdue.edu!vet.vet.purdue.edu!narayana From: narayana@vet.vet.purdue.edu (Padmakumar Narayanan) Newsgroups: bionet.immunology,bionet.molbio.proteins,sci.bio.technology Subject: Methods to measure Nitric Oxide Message-ID: Date: 25 May 93 16:59:32 GMT Sender: news@mentor.cc.purdue.edu (USENET News) Organization: Purdue University SVM Lines: 14 Xref: biosci bionet.immunology:371 bionet.molbio.proteins:663 sci.bio.technology:341 Hai there!!! I WOULD LIKE TO GET SOME FEED-BACK REGARDING THE MEASUREMENT OF NITRIC OXIDE PRODUCTION IN PHAGOCYTES. I KNOW THAT THERE ARE NO DIRECT METHODS TO QUANTIFY THE PRODUCTION OF NO IN CELLS say for eg., USING FLUORESCENT DYES THAT ARE SPECIFIC FOR NO. MOST OF THE METHODS THAT I HAVE COME ACROSS IN THE LITERATURE ARE USING BLOCKERS AND DCFH-DA. ANY INFORMATION REGARDING THE USE OF ANTIBODIES TO NITRIC OXIDE SYNTHASE ARE MOST WELCOME. I WOULD GREATLY APPRECIATE ANY HELP IN THIS REGARD. THANK YOU, PADMA KUMAR NARAYANAN DEP OF PHYSIOLOGY SVM,PURDUE UNIVERSITY W.L. IN47907 From owner-proteins@net.bio.net Tue May 25 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!usenet.ins.cwru.edu!cleveland.Freenet.Edu!bl275 From: bl275@cleveland.Freenet.Edu (Dan Diaz) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: Zwitterionic buffers and strong ion exchangers? Message-ID: <1u15te$368@usenet.INS.CWRU.Edu> Date: 27 May 93 01:35:42 GMT References: <24MAY93.11555533.0077@SEMOVM.SEMO.EDU> Reply-To: bl275@cleveland.Freenet.Edu (Dan Diaz) Organization: Case Western Reserve University, Cleveland, OH (USA) Lines: 29 Xref: biosci bionet.molbio.methds-reagnts:5691 bionet.molbio.proteins:668 NNTP-Posting-Host: hela.ins.cwru.edu In a previous article, C741SCB@SEMOVM.SEMO.EDU (C741SCB) says: >Does anybody know anything about the interaction between zwitterionic >buffer systems and Q ion exchange resins? I am in the middle of >a protein purification that looks as if the next logical step involves >an anion exchanger equilibrated at below pH 7. For obvious reasons >I don't particularlywant to use a buffer system that will interact >with the column. I suspect that a zwitterionic system would pose less >of a problem as far as competition between the buffer and the proteins >of interest than say phosphate or acetate, but I haven't seen anything >in the literature dealing with this. > You should definitely avoid the use of phosphate, acetate, or any other anionic buffer with anion exchangers such as Q or DEAE. Zwitterionic buffers (like the Good buffers) are fine provided you use them within their buffering range at a strength of 50 mM or so. I dont understand why you mention that running an anion exchanger at pH <7 is indicated. Most of my colleagues and I run strong and weak anion exchangers (such as Q or DEAE) in either Tris or MOPS at pH 7.4 or higher. S, CM, or Heparin (cation exchangers) we typically run in phosphate or MOPS at neutral pH or below. Pharmacia's booklet on Ion exchange on FPLC contains a lot of information useful for all types of chromatography, including recommended buffers for given resins at particular pH ranges. -- Dan Diaz bl275@cleveland.freenet.edu From owner-proteins@net.bio.net Tue May 25 23:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!uknet!pavo.csi.cam.ac.uk!nntp-serv.cam.ac.uk!seb1005 From: seb1005@bio.cam.ac.uk (Steven Brenner) Newsgroups: bionet.molbio.proteins Subject: Re: protein data bank Message-ID: Date: 26 May 93 23:10:46 GMT References: <1993May19.120301.14166@Informatik.TU-Muenchen.DE> Sender: news@infodev.cam.ac.uk (USENET news) Organization: U of Cambridge, England Lines: 45 In-Reply-To: Christoph.Niedermeier@hegel.physik.uni-muenchen.de's message of Wed, 19 May 1993 12:03:01 GMT Nntp-Posting-Host: mbfs.bio.cam.ac.uk In article <1993May19.120301.14166@Informatik.TU-Muenchen.DE>, Christoph.Niedermeier@hegel.physik.uni-muenchen.de (Christoph Niedermeier) writes: > I would like to get lists of typical globular and membrane > proteins which are available in the Brookhaven Protein data bank. > Each protein considered should represent a large class of similiar > proteins. I want to do statistics on some structural and electrostatic > features e. g. on the ratio of polar and charged side chain groups. > Large proteins (>250 residues) are preferred. You might want to have a look at: U. Hobohm, M. Scharf, R. Schneider, C. Sander, "Selection Of Representative Protein Data Sets." _Protein Science_ 1:3 409-417 (1992). HOBO9201090:Y. They present a method which uses a simple graph-theory algorithm to narrow down the database to a set of distinct proteins. The methods presented do have a number of problems, but is useful if you need a list of individual representative proteins. A list of current proteins in their representative set is available by ftp; I believe the address is in the paper. --- However, for collecting statistics, you most likely wish to "merge" similar proteins together rather than eliminate all but one representatives of a certain type of protein. Otherwise, you end up throwing away well-nigh 90% of your data! I have developed a sophisticated system for carrying out this sort of weighting in the generation of statistics about protein structures. If you would be interested in using it, please contact me at the address below. Hope that this is of some help. -Steve -- Steven E. Brenner | Internet seb1005@mbfs.bio.cam.ac.uk Department of Biochemistry | JANET seb1005@uk.ac.cam.bio.mbfs University of Cambridge | Laboratory +44 223 333671 Tennis Court Road | Home +44 223 314964 Cambridge CB2 1QW, UK | Lab Fax +44 223 333345 From owner-proteins@net.bio.net Tue May 25 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!math.ohio-state.edu!zaphod.mps.ohio-state.edu!uwm.edu!caen!nic.umass.edu!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc8.harvard.edu!gisselbr From: gisselbr@husc8.harvard.edu (Stephen Gisselbrecht) Newsgroups: bionet.molbio.proteins Subject: Re: Preservation of cyt. c solns Keywords: protein stability, storage, denaturation Message-ID: <1993May26.113030.24468@husc3.harvard.edu> Date: 26 May 93 15:30:30 GMT References: <1993May6.181637.23233@yang.earlham.edu> <1993May10.074530.13597@ac.dal.ca> <1tbqrk$f4r@zippy.Telcom.Arizona.EDU> Organization: Harvard University Science Center Lines: 18 Nntp-Posting-Host: husc8.harvard.edu In article <1tbqrk$f4r@zippy.Telcom.Arizona.EDU> droberts@joplin.biosci.arizona.edu (Doug Roberts) writes: >It seems to me that at room >temperature, most proteins will be stable against denaturation. (Most of the >melting curves I've seen are quite flat around this temp.) The other point >is that we grow up our yeast at 36C and their proteins seem to work just >fine. Things are very different in vivo. Even if your buffer manages to duplicate the precise ionic conditions in the cell, the protective effects of all that glutathione, and the high total protein concentration, there are still the "molecular chaperones" to consider--the hsp70s and all their little friends. They're always there, presumably looking out for partially denatured proteins, and binding them and helping them back to their minimal energy conformation when they find them. steve gisselbrecht cell & dev. bio. harvard medical school From owner-proteins@net.bio.net Tue May 25 23:00:00 1993 Path: biosci!MSU.EDU!21337MGR From: 21337MGR@MSU.EDU ("Jonathan.Walton") Newsgroups: bionet.molbio.proteins Subject: protease inducers? Message-ID: <9305270201.AA17085@net.bio.net> Date: 27 May 93 02:01:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 12 Dear Protease Experts: We are purifying an extracellular serine protease from a filamentous fungus. It is induced by collagen better than any other protein we have tried, but the collagen appears to be interfering with subsequent purification. Has anyone developed gratuitous inducers for such enzymes along the lines of IPTG for beta-galactosidase? Preferably low MW and easily separated from the protease. I am not a bulletin board subscriber so please post responses directly to me. Thank you in advance for your advice. Jonathan Walton, DOE Plant Research Lab, Michigan State Univ., E. Lansing USA e-mail 21337mgr@ibm.cl.msu.edu From owner-proteins@net.bio.net Wed May 26 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uknet!bnr.co.uk!corpgate!news.utdallas.edu!tamsun.tamu.edu!cs.utexas.edu!usc!howland.reston.ans.net!gatech!emory!emoryu1!emoryu1.cc.emory.edu From: bcresas@emoryu1.cc.emory.edu (Scott Sammons) Newsgroups: bionet.molbio.proteins Subject: Protein Motifs and Profiles Databases Message-ID: <3265@emoryu1.cc.emory.edu> Date: 27 May 93 16:21:16 GMT Sender: news@emory.edu Reply-To: bcresas@emoryu1.cc.emory.edu Organization: Emory University (BIMCORE) Lines: 12 Nntp-Posting-Host: emoryu1.cc.emory.edu Are there other protein motif-type databases available to search besides Prosite? Scott A. Sammons ============================================================================== | Scott A. Sammons (404) 727-2780 | | Emory University FAX: (404) 727-3659 | | Biomolecular Computing Resource Internet: bcresas@unix.cc.emory.edu | | 3025 Rollins Research Center | | Atlanta, GA 30322 | ============================================================================== From owner-proteins@net.bio.net Wed May 26 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uunet!news.crd.ge.com!maxwell!ebstokes From: ebstokes@maxwell.crd.ge.com (Ed Stokes) Newsgroups: bionet.molbio.proteins Subject: protein stability in solution ? Message-ID: Date: 27 May 93 19:33:53 GMT Sender: usenet@crdnns.crd.ge.com (USENET News System) Organization: GE Corp. Research & Development, Schenectady, NY Lines: 32 Nntp-Posting-Host: maxwell.crd.ge.com Hello, I am a physicist involved in development of fiber optic chemical sensors. Part of our work involves using a coating of IgG antibodies on the end of the optical fiber to enhance the selectivity of the probe to particular antigens. My current task is to investigate the luminescence properties of antibodies in solution in the presence (and absence) of antigen. I am looking at native fluorescence only, no tags (so far). The hapten of interest is chlorobiphenyl (antibodies were raised in rabbits to a chlorobiphenyl-tagged-protein antigen). Since chlorobiphenyl is not particularly water soluble, we are using an 80% PBS/20% methanol solution as the media for our measurements. I observed visible precipitation of the IgG in higher concentrations of methanol (~50%), but no visible IgG precipitation in the 20% methanol solution. Does anyone have a feeling for how stable the IgG should be over time in an 80% PBS/20% Methanol solution ? Just because I don't see precipitation, does that necessarily mean that the IgG in solution is not denatured ? I would like to exchange ideas with molecular biologists on these and related topics. Ed Stokes ebstokes@crd.ge.com From owner-proteins@net.bio.net Wed May 26 23:00:00 1993 Path: biosci!parc!decwrl!ames!haven.umd.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Motifs and Profiles Databases Message-ID: <1993May27.213127.26717@welchgate.welch.jhu.edu> Date: 27 May 93 21:31:27 GMT References: <3265@emoryu1.cc.emory.edu> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 165 In article <3265@emoryu1.cc.emory.edu> bcresas@emoryu1.cc.emory.edu writes: >Are there other protein motif-type databases available to search besides Prosite? > > >Scott A. Sammons I'm including some information about the Blocks database at the end of this article. To find more information - point your gopher client at merlot.welch.jhu.edu - if using Unix or Vax client just type: gopher merlot.welch.jhu.edu Select the following: --> 13. Search Databases at Hopkins (Vectors, Promoters, NRL-3D, EST, OMIM../ --> 9. Seqanalref - Sequence Analysis Bibliographic Reference Data Ban.. Now search for motif* +---Seqanalref - Sequence Analysis Bibliographic Reference Data Bank----+ | _____________ | | Words to search for | motif* | | | ------------- | | [Cancel ^G] [Accept - Enter] | | | +-----------------------------------------------------------------------+ And you'll get 85 entries - a sample entry is as follows: ------------ ID GRIM8801 RM 88252899 RA Gribskov M., Homyak M., Edenfield J., Eisenberg D.; RT "Profile scanning for three-dimensional structural patterns in protein RT sequences."; RL Comput. Appl. Biosci. 4:61-66(1988). KW PROTEIN; MATRIX-PROFILE. Profile analysis measures the similarity between a target sequence and a group of aligned sequences (the probe). The probe sequences are used to produce a position-specific scoring table (the profile) that can be aligned with any sequence (the target) using standard dynamic programming methods. We are developing a library of profiles, each describing a different structural motif. This allows any target sequence to be rapidly scanned for the presence of structural motifs. Levels of significance for the comparison of target sequences with the profile are determined in advance, permitting an objective decision to be made as to whether a protein is likely to possess a structural motif. -------------- You might ant to narrow your search down a little bit - so try +---Seqanalref - Sequence Analysis Bibliographic Reference Data Bank----+ | ________________________ | | Words to search for | motif* and database | | | ------------------------ | | [Cancel ^G] [Accept - Enter] | | | +-----------------------------------------------------------------------+ Will yield 21 entries and the following will fill in the gap and yield 13 entries. +---Seqanalref - Sequence Analysis Bibliographic Reference Data Bank----+ | _____________________________ | | Words to search for | motif* and data and bank | | | ----------------------------- | | [Cancel ^G] [Accept - Enter] | | | +-----------------------------------------------------------------------+ You might also try searching the Gentools Bibliographys: --> 14. Search the GenTools Bibliography If you've never heard of gopher don't worry it's free and on the net. Write me a note if you'd like info on hpw to get started. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu ============================================================================ //////////////////////////////////////////////////////////////////////////// ============================================================================ From steveh@sparky.fhcrc.org Fri Jan 8 00:37:12 1993 Subject: BLOCKS E-mail searcher Here's our announcement from last August (It's still in operation): ___________ ___________ ___________ |\ __________\ |___________| /__________ /| | | | | | | | | | | **********| |***********| |********** | | | | * BLOCKS | | E-MAIL | |SEARCHER * | | | | **********| |***********| |********** | | \|___________|___________|___________|___________|___________|/ |\ __________\ /__________ /| | | JC Wallace| | Copyright | | | | S Agus | | Fred | | | |JG Henikoff| | Hutchinson| | | | S Henikoff| | Center | | \|___________| |____1992___|/ As an aid to detection and verification of protein sequence homology, we introduce the BLOCKS e-mail searcher, which compares a protein or DNA sequence to the current database of protein blocks. Blocks are short multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. A database of blocks has been constructed by successive application of the automated PROTOMAT system to individual entries in the PROSITE catalog of protein groups keyed to the SWISS-PROT protein sequence databank. The rationale behind searching a database of blocks is that information from multiply aligned sequences is present in a concentrated form, reducing background and increasing sensitivity to distant relationships. If a particular block scores highly, it is possible that the sequence is related to the group of sequences the block represents. Typically, a group of proteins has more than one region in common and their relationship is represented as a series of blocks separated by unaligned regions. If a second block for a group also scores highly in the search, the evidence that the sequence is related to the group is strengthened, and is further strengthened if a third block also scores it highly, and so on. For a detailed help file, send a blank e-mail message as follows: To: blocks@howard.fhcrc.org Subject: help Or just send a protein or DNA sequence in FASTA, Genepro, GenBank, EMBL, SWISS- PROT, or PIR formats (DNA is automatically translated in all 6 reading frames for searching). Here is an example of a protein query in FASTA format: To: blocks@howard.fhcrc.org Subject: >YCZ2_YEAST Hypothetical 40.1 KD protein in HMR 3' region MKAVVIEDGKAVVKEGVPIPELEEGFVLIKTLAVAGNPTDWAHIDYKVGPQGSILGCDAA GQIVKLGPAVDPKDFSIGDYIYGFIHGSSVRFPSNGAFAEYSAISTVVAYKSPNELKFLG EDVLPAGPVRSLEGAATIPVSLTTAGLVLTYNLGLNLKWEPSTPQRNGPILLWGGATAVG EDVLPAGPVRSLEGAATIPVSLTTAGLVLTYNLGLNLKWEPSTPQRNGPILLWGGATAVG QSLIQLANKLNGFTKIIVVASRKHEKLLKEYGADQLFDYHDIDVVEQIKHKYNNISYLVD CVANQNTLQQVYKCAADKQDATVVELTNLTEENVKKENRRQNVTIDRTRLYSIGGHEVPF GGITFPADPEARRAATEFVKFINPKISDGQIHHIPARVYKNGLYDVPRILEDIKIGKNSG EKLVAVLN From owner-proteins@net.bio.net Thu May 27 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uknet!edcastle!festival!leeds.ac.uk!news From: ecl6gum@gps.leeds.ac.uk (G S Bacchus) Newsgroups: bionet.molbio.proteins Subject: Immunglobulins Message-ID: <1993May28.102730.548@gps.leeds.ac.uk> Date: 28 May 93 10:27:30 GMT References: <9305270201.AA17085@net.bio.net> Sender: nntp@gps.leeds.ac.uk Organization: University of Leeds, England Lines: 13 Hello, I'm trying to gather some information for a colleague who does not have access to any Usenet feed. I've posted this question on sci.med without any luck - can anyone on this group provide me with information on the following: As immnuglobulins are a class of protein, can anyone state what happens to any viruses that may be present in the plasma being used to produce immunoglobulins for intramuscular use? Are viruses inactivated by the manufacturing procedure? Any references to articles etc would be most appreciated, and apologies if this is the wrong newsgroup. Thanks. From owner-proteins@net.bio.net Thu May 27 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!rainer-mac.embl-heidelberg.de!user From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Motifs and Profiles Databases Message-ID: Date: 28 May 93 09:38:43 GMT References: <3265@emoryu1.cc.emory.edu> Followup-To: bionet.molbio.proteins Organization: EMBL Data Library Lines: 14 Nntp-Posting-Host: rainer-mac.embl-heidelberg.de In article <3265@emoryu1.cc.emory.edu>, bcresas@emoryu1.cc.emory.edu (Scott Sammons) wrote: > > Are there other protein motif-type databases available to search besides Prosite? In Protein Engineering 5, 479-488 (1992) Ogiwara et al. describe their dictionary of sequence motifs. When I spoke to Atsushi Ogiwara recently he promised to put his database up for ftp, but nothing seems to have happened since then. You may want to contact him directly, the address is given in the paper. Rainer Fuchs EMBL Data Library Fuchs@EMBL-Heidelberg.DE From owner-proteins@net.bio.net Fri May 28 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!howland.reston.ans.net!darwin.sura.net!news.udel.edu!chopin.udel.edu!daschaff From: daschaff@chopin.udel.edu (Dennis A Schaff) Newsgroups: bionet.molbio.gene-linkage,bionet.molbio.gen-org,bionet.molbio.genome-program,bionet.molbio.proteins Subject: Call for Abstracts MAPMBS meeting Message-ID: Date: 29 May 93 14:14:33 GMT Sender: usenet@news.udel.edu Organization: University of Delaware Lines: 241 Xref: biosci bionet.molbio.gene-linkage:187 bionet.molbio.genome-program:483 bionet.molbio.proteins:675 Nntp-Posting-Host: chopin.udel.edu Call for Abstracts 10th Annual Meeting Mid-Atlantic Plant Molecular Biology Society July 15-16, 1993 University of Delaware, Clayton Hall Newark, Delaware Please return Registration and Abstracts by June 25, 1993. Keynote Address Sheila McCormick, USDA/ARS--Plant Gene Expression Center Molecular analysis of gametogenesis in plants. Gene Regulation Becky Boston--North Carolina State University--Regulation and function of maize ribosome inactivating proteins. Michael Dobres--Drexel University--A transcriptional marker for epidermal differentiation in Pisum sativum. Carroll Vance--USDA/ARS, University of Minnesota--Primary assimilation of nitrogen in alfalfa nodules: Molecular features of the enzymes involved. John Watson--University of Maryland--Photo-regulated expression of protein kinase genes. Plant/Microbe Interactions Jim Carrington--Texas A&M--Replication and movement of a potyvirus that expresses GUS. Dan Roberts--USDA/ARS, Beltsville--Molecular basis of rhizosphere colonization by the plant beneficial bacterium, Enterobacter cloacae. Barbara Valent--Du Pont Co.--Two cloned genes for host specificity in the rice blast fungus, Magnaporthe grisea. Transformation/Techniques Ted Klein--Du Pont Co.--Maize transformation: An industrial perspective. Antoni Rafalski--Du Pont Co.--Technology for molecular breeding: RAPD markers, microsatellites, and machines. Developing Technologies Paul Gilna--Los Alamos--The latest advances in community-based access to sequence data submission and maintenance technologies for GenBank. Post-meeting Tour Friday evening, July 16, 1993. We are planning a tour of Longwood Gardens, Kennett Square, PA (18 miles from the University of Delaware). Tenth Annual Meeting of the Mid-Atlantic Plant Molecular Biology Society Univerity of Delaware, Newark, DE July 15-16, 1993 Registration due by June 25, 1993 The Mid-Atlantic Plant Molecular Biology Society (MAPMBS) was formed to provide a high quality, accessible, and affordable plant molecular biology meeting each year for scientists in the Mid-Atlantic region. The society wishes especially to encourage presentations by postdoctoral fellows and graduate students. Toward this goal, and as a special incentive, the registration fee for students who are presenting short talks or posters (one presenter per abstract please) includes only the cost of food and beverages. This year's keynote address on Thursday July 15 will be given by Dr. Sheila McCormick, USDA, ARS, Plant Gene Expression Center, Albany, CA. Dr. McCormick's lecture will be followed by an informal social hour and dinner. Registration for the conference will open at 8:00 a.m. on Thursday inside Clayton Hall. Talks will begin promptly at 9:00 a.m. Thursday and 8:00 a.m. Friday. Two platform sessions will be held each day. Each platform session consists of two or three 30-minute talks by invited speakers followed by short contributed talks of approximately 15-20 minutes. Poster presentations are also encouraged. Time will be reserved for poster presentation and discussion. To present either a talk or a poster please submit an abstract (see directions for format). If you prefer to give a talk, please indicate the session you feel would be most appropriate. Accommodations for participants requiring overnight lodging can be made at the University of Delaware on-campus housing. A block of rooms has been reserved for participants. Arrangements must be made by participants through the Conference Center at Clayton Hall (housing form enclosed). Lodging will be available for Wednesday and Thursday nights at the conference rate (additional nights may be arranged on an individual basis). Breakfast can be bought at the Cafeteria (breakfast $4.50). If you prefer other accommodations, please make your own arrangements. Pre-registration is strongly encouraged. Please note that this is the only announcement and call for abstracts that will be mailed. For those who register in advance, lunches and dinner will be provided and are included in the pre-registration fees. Ample parking is available in the Conference Center parking lot. Walk-in registration will also be available at the door on Thursday morning July 15. ABSTRACT FORMAT (Abstracts are photocopied without modification) TITLE IN CAPITAL LETTERS: Author(s) Name; Author(s) Affiliation, and Address. Please type your abstract on 8.5" x 11" white paper leaving a 1.5" margin on all sides. Mail the original abstract and one copy to the address listed on the registration form. Be sure to check the appropriate spaces on the registration form to indicate your preference for presentation format (short talk or poster) and session. You will be notified of the session, time, and format for your presentation. Posters should fit within a 4' x 4' area. Please return your abstract by June 25, 1993. Your attendance and participation are essential to the continued growth and productivity of the MAPMBS. We look forward to meeting you in July! For further information, contact: Send Abstracts to: Dennis A. Schaff Ben Matthews Department of Plant and Soil Sciences MAPMBS University of Delaware c/o USDA-ARS, PMBL Newark, Delaware 19717-1303 B-006, BARC-West Phone: (302) 831-2534 10300 Baltimore Avenue FAX: (302) 831-3651 Beltsville, MD 20705-2350 E-mail: daschaff@brahms.udel.edu Registration Form Please return by June 25, 1993 Please photocopy this page and mail the registration and housing forms SEPARATELY; MAPMBS will not guarantee forwarding of housing forms sent to Beltsville. Name _________________________________ I am interested in presenting: Institution __________________________ _____ A short talk Department __________________________ _____ A poster Address ______________________________ (Be sure abstract is enclosed) City ________________________________ State ________________________________ Platform session preference: Zip Code _____________________________ _____ Gene Regulation Telephone ____________________________ _____ Plant/Microbe Interactions FAX __________________________________ _____ Transformation/Techniques E-mail _______________________________ Pre-registration: Late registration (after June 25): Presenting Student.......... $50 N/A Student..................... $65 $75 Regular registration........ $80 $90 Total amount enclosed....... $_______ Make Checks Payable to MAPMBS Pre-registration includes meeting attendance, 2 lunches, social hour, and Thursday banquet. ______ Please check if interested in the post-meeting tour to Longwood Gardens (Friday July 16). ______ Special dietary requirements. Please specify:_____________________ Choice of meals for banquet (check one) ______ Chinese Flank Steak ______ Vegetarian Platter ______ Delaware Combo (Crabcake and Chicken Breast ) Mail Registration Materials to: Ben Matthews MAPMBS Meeting c/o USDA-ARS, PMBL B-006, BARC-West 10300 Baltimore Avenue Beltsville, MD 20705-2350 Housing Reservation Form 10th Annual Meeting: Mid-Atlantic Plant Molecular Biology Society July 15-16, 1993 Name_________________________________ Title/position____________________ Affiliation_____________________________________________________________ Address_________________________________________________________________ City____________________________________State__________Zip______________ Telephone Numbers (work)_________________ (home)_______________________ Housing Christiana Towers Apartments (dormitory) All bedrooms have single/twin beds. Rooms do not have television, radio, or clock. [ ] 1 bedroom, 1 person . . . $30.75 per person per night. [ ] 1 bedroom, 2 people . . . $16.75 per person per night. [ ] 2 bedrooms, 2 people . . $18.00 per person per night. [ ] 2 bedrooms, 3 people . . $13.50 per person per night. [ ] 2 bedrooms, 4 people . . $11.00 per person per night. If you want to share a bedroom with a particular person(s), please indicate name(s). Roommate preference, if any _____________________________________________ If you wish to share a bedroom with any MAPMBS participant, circle your sex (M) or (F). If you select other than single accommodations and do not indicate a roommate preference, you may be assigned and charged a single room if no roommate is available. Arrival Date: ___________ Departure Date: _____________ ________ (nights) x $ ________ (rate). . . . . . . . . . . . . .$ _______ Linen Package (required) . . . . . . . . . . . . . . . . . . . .$ 9.95 Total Housing . . . . . . . . . . . . . . . . . . . . . . . . . $ _______ [ ] Enclosed is my check for $ ________ made payable to the "University of Delaware." [ ] Please charge $________ to my: ____MasterCard; ____VISA; ____Discover Card Number ___________________________ Expiration Date: ________________ Authorized Signature _____________________________________________ Note: If paying by credit card, you may FAX your reservation form to 302-831-2998. Sorry, we cannot accept your FAX if paying by check. Purchase Orders are accepted. Please return no later than July 6 to: Conferences and Centers Continuing Education University of Delaware Newark, DE 19716-7430 Phone: 302-831-2216 From owner-proteins@net.bio.net Mon May 31 23:00:00 1993 Path: biosci!COR-MAIL.BIOCHEM.HMC.PSU.EDU!lxia From: lxia@COR-MAIL.BIOCHEM.HMC.PSU.EDU ("liang xia") Newsgroups: bionet.molbio.proteins Subject: isoelectric focusing Message-ID: <9306012144.AA17844@net.bio.net> Date: 1 Jun 93 21:44:38 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 Dear netters: I have been using isoelectric focusing gel to analyze a herpes immediate-early protein-ICP4. The major problem I encountered was the poor solubility of the protein in urea solubilization buffer. Is there anyway to enhance the solubility of proteins in this buffer or are there any alternative buffers for this purpose? Thanx. Liang lxia@cor-mail.biochem.hmc.psu.edu Hershey Medical Center