From owner-proteins@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!dh124 From: dh124@cus.cam.ac.uk (D. Hodges) Newsgroups: bionet.molbio.proteins Subject: amino acid frequency Date: 2 Sep 1994 10:55:03 GMT Organization: University of Cambridge, England Lines: 20 Message-ID: <3470a7$orc@lyra.csx.cam.ac.uk> NNTP-Posting-Host: bootes.cus.cam.ac.uk X-Newsreader: TIN [version 1.2 PL2] Hi, I have a feeling that somone may have asked a similar question to this before, unfortunately I have no memory of any answers to it. What I would like is a table of some sort that gives the relative frequencies of the different amino acids in proteins to see how any one amino acid composition compares with the 'norm'. I realise that I would need to be very cautious in any conclusions I made from such a comparison (the table would reflect the choice of proteins used to create it). However it would still be interesting to have a look. Either tables or references to them would be appreciated. Thanks Debbie -- --------------------------------------------------------------------------- Debbie Hodges dh124@cus.cam.ac.uk Fax 0223 217838 Rheumatology Research Unit, Addenbrookes Hospital, Hills Road, Cambridge, UK. ---------------------------------------------------------------------------- I never could get the hang of Thursdays (A.Dent). From owner-proteins@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!BANGOR.AC.UK!BSS169 From: BSS169@BANGOR.AC.UK Newsgroups: bionet.molbio.proteins Subject: Re: Setting up 2D gel. Date: 2 Sep 1994 02:40:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409020940.CAA13545@net.bio.net> NNTP-Posting-Host: net.bio.net A message says: ***************************************************** Does any one have any info on setting 2D gels? What equipment is the easiest to work with?.... ****************************************************************************** You can try the Mini-2D unit from BioRad, Richmond, CA. USA, It is a very good one, easy to use, compatible with other units made by the same company for SDS-PAGE, and Western transfer, it is also relatively inexpensive. Please remember the 'MINI' one, not the big, old one. You can contact to them: Tel. 1-800-424-6723. Fax.1-800-879-2289. Best luck. Dan WU From owner-proteins@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!scsing.switch.ch!elna.ethz.ch!smac.ethz.ch!user From: tan@aeolus.vmsmail.ethz.ch (Song Tan) Newsgroups: bionet.molbio.proteins Subject: Re: Trombin cleavage of fusion proteins Date: Fri, 02 Sep 1994 10:35:38 +0100 Organization: ETH Zurich, Switzerland Lines: 20 Distribution: world Message-ID: References: <9409012138.AA65559@acs4.acs.ucalgary.ca> NNTP-Posting-Host: smac.ethz.ch In article <9409012138.AA65559@acs4.acs.ucalgary.ca>, msseyed@ACS.UCALGARY.CA ("Soheil Seyed Mahmoud") wrote: > Hi there. I have expressed a protein (ca 22kd) as a fusion with > GST in E.coli. I can purify ther fusion protein on agarose bound > glutathione beads. However, as I attempt to add the thrombin > bufer (20mMtris (pH8.3), 5mM CaCl2, with or without 150mMNacl), > the fusion protein precipitates out. Any suggestions how I can > get over this problem? Thanmks a bunch. How about cleaving the fusion protein while it's still bound to the glutathione beads? Pharmacia's "GST Gene Fusion System" booklet on the pGEX expression system describes the procedure for doing this. -- Song Tan Institute for Molecular Biology and Biophysics ETH-Honggerberg (Swiss Federal Institute of Technology) 8093 Zurich, Switzerland email: tan@aeolus.vmsmail.ethz.ch From owner-proteins@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: psansom@hgmp.mrc.ac.uk (Mr. P.A. Sansom) Newsgroups: bionet.molbio.proteins Subject: Query on LYSIS proteolysis database for PC Date: 2 Sep 1994 11:49:54 +0100 Lines: 11 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <34700i$rk@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk Does anybody have experience of the LYSIS proteolysis database for PC, available from Springer-Verlag? We are thinking of purchasing it, but want to know if it is ever updated, and if it will indicate cleavages in a sequence that we define. Thanks in advaance for your help. Paul Sansom The Kennedy Institute of Rheumatology 6 Bute Gardens Hammersmith London From owner-proteins@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!news From: sfm@manduca.neurobio.arizona.edu (Stephen Matheson) Newsgroups: bionet.molbio.proteins Subject: Re: amino acid frequency Date: 2 Sep 1994 16:28:52 GMT Organization: University of Arizona UNIX Users Group Lines: 32 Message-ID: <347js4$6a@organpipe.uug.arizona.edu> References: <3470a7$orc@lyra.csx.cam.ac.uk> NNTP-Posting-Host: manduca.neurobio.arizona.edu From article <3470a7$orc@lyra.csx.cam.ac.uk>, by dh124@cus.cam.ac.uk (D. Hodges): > I have a feeling that somone may have asked a similar question > to this before, unfortunately I have no memory of any answers to it. > What I would like is a table of some sort that gives the relative > frequencies of the different amino acids in proteins to see how any > one amino acid composition compares with the 'norm'. > I realise that I would need to be very cautious in any conclusions I > made from such a comparison (the table would reflect the choice of > proteins used to create it). However it would still be interesting > to have a look. > Either tables or references to them would be appreciated. This information would be fairly readily obtained from a codon usage table. A set of codon usage tables is published every year in Nucleic Acids Research in the supplement. The last one that shows up in my Current Contents search is Wada et al., "Codon usage tabulated from the Genbank genetic sequence data", Nucleic acids research 1992 v.20 S p.2111-2118. At least in the old usage tables, the raw numbers of codons were given, and that would enable you to calculate the number of times each amino acid is used. Also, you could generate your own codon usage table using Genbank data. The major sequence analysis software packages can do this, as can a program that I wrote for this purpose which I am happy to provide to anyone who is interested. -- Steve Matheson Program in Neuroscience University of Arizona sfm@neurobio.arizona.edu From owner-proteins@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!sr120 From: sr120@mole.bio.cam.ac.uk (Steven Russell (Genetics)) Newsgroups: bionet.molbio.proteins Subject: protamines Date: 2 Sep 1994 11:14:09 GMT Organization: University of Cambridge, England Lines: 10 Message-ID: <3471e1$pei@lyra.csx.cam.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk Summary: electrophoresis of protamines Keywords: protamines Hi there I am looking for a good method to separate protamines and histones. help much appreciated. Steve Russell Dept of Genetics University of Cambridge UK SR120@mole.bio.cam.ac.uk From owner-proteins@net.bio.net Thu Sep 01 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!scsing.switch.ch!sun.rediris.es!obelix.cica.es!news From: pmateo@ugr.es (Pedro L. Mateo) Newsgroups: bionet.molbio.proteins Subject: Postdoctoral position Date: 2 Sep 1994 12:25:01 GMT Organization: University of Granada (SPAIN) Lines: 26 Distribution: world Message-ID: <3475it$do9@obelix.cica.es> NNTP-Posting-Host: atri1.ugr.es X-Newsreader: One postdoctoral position is available at the Physical Chemistry Department at Granada University in Spain. The current interest of the Department on the thermodynamics of protein folding, stability and binding are being expanded into structural aspects. The position requires a person with experience and training in protein NMR. Applicants must be citizens of any of the European Union countries (EXCEPT FOR SPAIN) including Austria, Finland, Iceland, Norway, Sweden and Switzerland. The length of the stay could be from 9 to 12 months with a salary ranging from 2000 to 2400 ECU/month, plus round trip to Granada and medical insurance. Starting date for the position could be between October 1994 and March 1995. The University of Granada has recently bought three NMR Bruker instruments (AMX-300, ARX-400 and AMX-500 MHz), located at the Central Services of the University, where FTIR, electron microscopy and other bio-physico-chemical techniques are also available. It is expected that the successful applicant will mainly work with the 500 MHz spectrometer. The Department facilities include high- sensitivity differential scanning and isothermal calorimeters, stopped-flow, spectrophotometer, spectrofluorimeter, HPLC, S.G. workstation and the usual biochemical infrastructure. Interested persons should send a C.V. and names and addresses of two references (or contact for further information) to Prof. Pedro L. Mateo, Department of Physical Chemistry, Faculty of Sciences, University of Granada, 18071 Granada, Spain. Phone: 34-58-243333/1. Fax: 34-58-272879 (or 274258). . ( From owner-proteins@net.bio.net Thu Sep 01 23:00:00 1994 Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.genome-program,bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!darwin.sura.net!fconvx.ncifcrf.gov!fcsparc6!toms From: toms@fcsparc6.ncifcrf.gov (Tom Schneider) Subject: Re: BCM Sequence Annotation Web Server Message-ID: Sender: usenet@ncifcrf.gov (C News) Nntp-Posting-Host: fcsparc6.ncifcrf.gov Organization: Frederick Cancer Research and Development Center References: <1994Aug31.142529.4040@emba.uvm.edu> Date: Fri, 2 Sep 1994 23:59:29 GMT Lines: 46 Xref: biosci bionet.molbio.genbank:1737 bionet.molbio.embldatabank:362 bionet.molbio.genome-program:925 bionet.molbio.proteins:2587 In article rsmith@dot.bcm.tmc.edu (Randall Smith) writes: | : Announcing a new WWW Server: The BCM Sequence Annotation Server | : URL: http://dot.imgen.bcm.tmc.edu:9331/seq-annot/home.html This idea has both good and bad points and I think that they should be considered extremely carefully. First, the idea that individual researchers should be able to update a database directly is wonderful. If everybody were to do that to the data they are experts on, GenBank would quickly become a clean database. However, there are several problems: 1. Corruption of the data either intentionally or inadvertently. The authors already are aware of this possibility. 2. Inconsistency between researchers. The NCBI attempts to make entries uniform by certain standards, but individual researchers cannot know what these are in detail. The only solutions I see are to force the kinds of annotations to follow certain forms or to pass all the changes to experts for editing. The trouble with passing the data to experts is that the number of experts has to grow exponentially along with the growth of the database. Maybe we just have to accept that to avoid a worse mess! 2. Do the data flow into GenBank? There is no indication that it will. This means that if GenBank makes a correction it won't go into this database and vice versa. Since the data are not maintained in one place, it is duplicated and will eventually become inconsistent. Who should or will a researcher believe? A randomly annotated database or the "official" one? How will inconsistencies be resolved? I see this as an experiment. Once the experiment has been shown to work reasonably well, all the data should be passed to NCBI for careful processing along with all new data. That is, the server should be run by NCBI or closely in conjunction with them. For my reasoning behind this posting, see the philosophy paper available from: http://fconvx.ncifcrf.gov:2001/~toms/onlinepapers.html Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov From owner-proteins@net.bio.net Fri Sep 02 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!lhom From: lhom@OCF.Berkeley.EDU (Louis Hom) Newsgroups: bionet.molbio.proteins Subject: Calculating a simple pI Date: 3 Sep 1994 15:12:20 GMT Organization: U.C. Berkeley Open Computing Facility Lines: 10 Distribution: usa Message-ID: <34a3ok$cgi@agate.berkeley.edu> NNTP-Posting-Host: sandstorm.berkeley.edu It's simple enough to calculate the pI for a molecule with one acidic group and one basic group -- you just take the arithmetic mean of the two pKa's (as in Lehninger). But what about systems with, say, two acidic groups and one basic group? Do you still just take the arithmetic mean? -- **************************************************************************** * Lou Hom * "All folks are family." * * lhom@ocf.berkeley.edu * -- John Saponara * **************************************************************************** From owner-proteins@net.bio.net Fri Sep 02 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!lhom From: lhom@OCF.Berkeley.EDU (Louis Hom) Newsgroups: bionet.molbio.proteins Subject: Why does pH denature proteins? Date: 3 Sep 1994 15:17:03 GMT Organization: U.C. Berkeley Open Computing Facility Lines: 6 Distribution: usa Message-ID: <34a41f$ci2@agate.berkeley.edu> NNTP-Posting-Host: sandstorm.berkeley.edu Why do extremes in pH lead to protein denaturation? -- **************************************************************************** * Lou Hom * "All folks are family." * * lhom@ocf.berkeley.edu * -- John Saponara * **************************************************************************** From owner-proteins@net.bio.net Fri Sep 02 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!lhom From: lhom@OCF.Berkeley.EDU (Louis Hom) Newsgroups: bionet.molbio.proteins Subject: Titrating e.g. poly-Glu Date: 3 Sep 1994 15:15:45 GMT Organization: U.C. Berkeley Open Computing Facility Lines: 9 Distribution: usa Message-ID: <34a3v1$chj@agate.berkeley.edu> NNTP-Posting-Host: sandstorm.berkeley.edu What does the pH titration curve look like for something like poly-glutamic acid? Do you have one equiv point for the COOH terminus, one point for the NH2 terminus, and then one very long region for the side chain acids or many small equiv points (one for each acid group)? -- **************************************************************************** * Lou Hom * "All folks are family." * * lhom@ocf.berkeley.edu * -- John Saponara * **************************************************************************** From owner-proteins@net.bio.net Sat Sep 03 23:00:00 1994 Path: biosci!VAXA.WEEG.UIOWA.EDU!cmdrub From: cmdrub@VAXA.WEEG.UIOWA.EDU Newsgroups: bionet.molbio.proteins Subject: zero-length cross-linker Date: 4 Sep 1994 01:37:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <00983ECD.45BDBCA0.3@vaxa.weeg.uiowa.edu> NNTP-Posting-Host: net.bio.net I am trying to use the zero-length cross-linker EDC to crosslink some mutated actin monomers in the filamentous form. Can anyone suggest a good protocol for me to start with? Thanks! Bing From owner-proteins@net.bio.net Sun Sep 04 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!swrinde!pipex!bt!uknet!daresbury!not-for-mail From: JAB5@VAX.YORK.AC.UK Newsgroups: bionet.molbio.proteins Subject: periplasmic coli proteins Date: 5 Sep 1994 16:42:47 +0100 Lines: 10 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <34fe9n$4hc@mserv1.dl.ac.uk> Original-To: PROTEINS@dl.AC.UK Dear Colleagues, Can anyone tell me how to best compile a list of periplasmic coli proteins? Both anchored and free are needed. Many thanks, Jim Brannigan Chemistry dept. University of York York YO1 5DD UK jab5@uk.ac.york.vax jab@uk.ac.york.yorvic From owner-proteins@net.bio.net Sun Sep 04 23:00:00 1994 Path: biosci!KB.USM.MY!asma From: asma@KB.USM.MY (Asma Ismail) Newsgroups: bionet.molbio.proteins Subject: School of tropical medicine Date: 5 Sep 1994 23:39:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Dear netters, Does anyone know the e-mail address for the Registrar of Admission & Records at the London School of Hygiene and Tropical Medicine ( particularly for Mrs Julie Thompson). Thank you in advance!!!!! Zainuddin USM, Malaysia. From owner-proteins@net.bio.net Sun Sep 04 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!holonet!colossus.holonet.net!iat.holonet.net!janyoung From: janyoung@iat.holonet.net (DR. JANIS YOUNG) Subject: peptides Message-ID: Organization: HoloNet National Internet Access System: 510-704-1058/modem Date: Mon, 5 Sep 1994 17:53:27 GMT Lines: 14 This is an inquiry as to whether it's O.K. to post peptide questions in the protein group. As far as I know there isn't a peptide discussion group. Any information here would be appreciated. I am currently interested in the relationship of peptides to Geriactric Medicine and also thinking of writng a third edition of our book Solid Phase Peptide Synthesis by Stewart and Y0ung. I want to get input on both of these areas. Of course I now who to go to directly for the SPPS book but it would be of interest to get more input.I have two e-mail addresses: janyoung@holonet.net and SkylinePep@AOL.com. -- ============================================================================ Janis Dillaha Young, Ph.D. Skyline Peptides Tel.&FAX: (510) 655-5885 6039 Skyline Blvd. #A e-mail: janyoung@holonet.net From owner-proteins@net.bio.net Sun Sep 04 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!pipex!warwick!lyra.csx.cam.ac.uk!bjd12 From: bjd12@cus.cam.ac.uk (Ben Davis) Newsgroups: bionet.molbio.proteins Subject: Re: Why does pH denature proteins? Date: 5 Sep 1994 07:06:42 GMT Organization: University of Cambridge, England Lines: 40 Distribution: usa Message-ID: <34eg22$7hn@lyra.csx.cam.ac.uk> References: <34a41f$ci2@agate.berkeley.edu> NNTP-Posting-Host: grus.cus.cam.ac.uk X-Newsreader: TIN [version 1.2 PL2] Louis Hom (lhom@OCF.Berkeley.EDU) wrote: : Why do extremes in pH lead to protein denaturation? : Couple of general points, then a funny example that I've been working on. Just thinking about low pH (which is what I'm more used to), what tends to happen is that you protonate the vacrious acidic groups in the protein, and eventually, this destablises the protein sufficiently to unfold it. In the case of barnase, this happens when you protonate the acidic partner of a buried salt bridge - the energetic cost of having a buried lone charge is too destablising, and the protein unfolds. As far as I can tell, this is fairly typical, in that one crucial event causes the protein to unfold. The protein that I've been working on, barley CI-2, is different, in that the lowest pKa is 2.7, but the protein is folded to at least pH 2.2 - in other words, there is no titrating sidechain that causes the protein to unfold.One possible explanation may be backbone titration (amide group has pKa of ~-1, so at pH 1 1% of the groups will be protonated, which may be enough to tip the protein to being unfolded), or it may be the increased salt at lower pH (the acid denatured state is very sensitive to salt concentration). :**************************************************************************** : * Lou Hom * "All folks are family." * : * lhom@ocf.berkeley.edu * -- John Saponara * :**************************************************************************** Ben ______________________________________________________________________________ Ben Davis, MRC Protein Function and Design, Cambridge, UK ______________________________________________________________________________ "They can make me do it, but they can't make me do it with dignity." From owner-proteins@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!rgs From: rgs@mole.bio.cam.ac.uk (Robert Solomon (Bioc)) Newsgroups: bionet.molbio.proteins Subject: Re: Trombin cleavage of fusion proteins Date: 6 Sep 1994 09:55:18 GMT Organization: U. of Cambridge, England Lines: 18 Distribution: world Message-ID: <34hea6$8sf@lyra.csx.cam.ac.uk> References: <9409012138.AA65559@acs4.acs.ucalgary.ca> NNTP-Posting-Host: mole.bio.cam.ac.uk In article <9409012138.AA65559@acs4.acs.ucalgary.ca> msseyed@ACS.UCALGARY.CA ("Soheil Seyed Mahmoud") writes: >Hi there. I have expressed a protein (ca 22kd) as a fusion with >GST in E.coli. I can purify ther fusion protein on agarose bound >glutathione beads. However, as I attempt to add the thrombin >bufer (20mMtris (pH8.3), 5mM CaCl2, with or without 150mMNacl), >the fusion protein precipitates out. Any suggestions how I can >get over this problem? Thanmks a bunch. >Soheil You have a number of things to try here - the buffer specificty for thrombin is fairly wide - Ive cut fusions in 50mM (NH4)2SO4, and in 50mM Tris pH 7.6, and others Ive forgotten about. So I suggest as a first attempt you leave out the calcium (it is *not* necessary) which I suspect is your problem, and/or change the pH to something a little lower. Good luck RSol From owner-proteins@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!EU.net!sunic!trane.uninett.no!daresbury!not-for-mail From: Marjory.Barnes@TRDBT.PHARMA.sandoz.ch Newsgroups: bionet.molbio.proteins Subject: GMP PROTEIN SEQUENCING NETWORK Date: 6 Sep 1994 15:13:46 +0100 Lines: 47 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <34hteq$sp4@mserv1.dl.ac.uk> Original-To: proteins ------------------------------ Start of forwarded message 1 Message-ID: <"20115160904991/287457 PHARMAX400*"@MHS> To: list:; Subject: Startup Repeat Date: Tue, 6 Sep 1994 14:11:34 +0000 Sender: Marjory.Barnes@ch.sandoz.PHARMA.TRDBT *************************************************************************** GLOBAL NETWORK FOR GMP PROTEIN SEQUENCING LABORATORIES *************************************************************************** 9 September, 1994 Dear Protein Sequencers, Do you do QC or development work? If so, you may profit from joining our information exchange network of laboratories which do N-terminal Edman sequence analysis to GMP, GLP, or ISO standards. At present, the network provides contact addresses of other laboratories working in this field. If you wish to participate, please contact M.Barnes Internet BARNES@PEBT.PHARMA.SANDOZ.CH Technical Research and Development - Biotechnology Sandoz Pharma AG Building 360, Laboratory 1124 4002 Basel, Switzerland 041-61-324-4137 Languages: English, German, French ------------------------------ End of forwarded message 1 From owner-proteins@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!bolognes From: bolognes@umbc.edu (Ms. Cynthia Bolognese; (BIOL; GRAD)) Newsgroups: bionet.molbio.proteins Subject: westerns w/ HA-tagged proteins Date: 6 Sep 1994 16:25:37 GMT Organization: University of Maryland, Baltimore County Lines: 16 Message-ID: <34i561$cgs@news.umbc.edu> NNTP-Posting-Host: umbc7.umbc.edu X-Newsreader: TIN [version 1.2 PL2] I'd like some input on westerns with HA-tagged proteins. I can't detect my HA-tagged protein on a western, nor can I detect the positive control. I've tried various ab dilutions and have had no luck. Transfer appears to be complete, yet I get no signal from my protein or positive control, while the 14C standard is very strong. Any suggestions? -- ___________________________________________________________________________ Cindy Bolognese | | e-mail address: | Qapla'! (Klingon for Success!) | bolognes@umbc7.umbc.edu | | --------------------------------------------------------------------------- From owner-proteins@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!agate!doc.ic.ac.uk!charlie.lif.icnet.uk!pic.lif.icnet.uk!user From: p_whitehead@icrf.icnet.uk (Phil Whitehead) Newsgroups: bionet.molbio.proteins Subject: HELP WITH Organalles Followup-To: bionet.molbio.proteins Date: Tue, 06 Sep 1994 12:21:08 +0000 Organization: Imperial Cancer Research Fund Lines: 11 Message-ID: NNTP-Posting-Host: 143.65.8.48 I'm trying to purify some subcellular organales with an apparent molecular weight of 600 kD. I'd like to be able to follow the purification bylooking at the intact protein on a gel. Obviously SDSPAGE is out, but occasionaly on the net people have aluded to agarose gels can anyone in the know either post their ideas or E-Mail me a ny proceedures you may have. I'm not desperate (yet) but it would be nice to have a few methods up my sleve thanks in advance Phil Whitehead From owner-proteins@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!agate!kos2mac9.berkeley.edu!user From: insomnia@mendel.berkeley.edu (Shane Albright) Newsgroups: bionet.molbio.proteins Subject: Re: Calculating a simple pI Date: 6 Sep 1994 19:01:38 GMT Organization: MCB Dept., UC Berkeley Lines: 29 Distribution: usa Message-ID: References: <34a3ok$cgi@agate.berkeley.edu> NNTP-Posting-Host: kos2mac9.berkeley.edu In article <34a3ok$cgi@agate.berkeley.edu>, lhom@OCF.Berkeley.EDU (Louis Hom) wrote: > It's simple enough to calculate the pI for a molecule with one acidic group > and one basic group -- you just take the arithmetic mean of the two pKa's > (as in Lehninger). > But what about systems with, say, two acidic groups and one basic group? > Do you still just take the arithmetic mean? > -- Lou - You still take the arithmetic mean of _two_ pKa's. The trick is to decide which two. As the pH is titrated from 0 to 14, the protein accumulates more and more negative charge due to deprotonation. The pI is, by definition, the pH at which the protein has no net charge and is therefore the mean of the two pKa's on either side of this neutral state. In the example you state--two acidic and one basic group--a fully protonated protein will have a charge of +1 (the -NH3+ basic group). When the pH is at the lowest pKa, the charge is +0.5; at the second lowest pKa (the other acidic group), the charge is -0.5. The pI is the pt halfway in-between. Hope this helps. Shane Albright insomnia@mendel.berkeley.edu From owner-proteins@net.bio.net Mon Sep 05 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!genmac14.biochem.mpg.de!user From: spang@vms.biochem.mpg.de (Anne Spang) Newsgroups: bionet.molbio.proteins Subject: Re: HELP WITH Organalles Date: 6 Sep 1994 19:10:36 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 25 Message-ID: References: NNTP-Posting-Host: genmac14.biochem.mpg.de Hi Phil! You could also use a native PAGE. The negative charge is supplied by coomassie blue in the cathode buffer. There is an article from Schaegger and von Jagow about native blue gel electrophoresis, but unfortunatly I cannot find the article now.... good luck Anne GIn article , p_whitehead@icrf.icnet.uk (Phil Whitehead) wrote: > I'm trying to purify some subcellular organales with an apparent molecular > weight of 600 kD. I'd like to be able to follow the purification bylooking > at the intact protein on a gel. > Obviously SDSPAGE is out, but occasionaly on the net people have aluded to > agarose gels can anyone in the know either post their ideas or E-Mail me a > ny proceedures you may have. > I'm not desperate (yet) but it would be nice to have a few methods up my > sleve > thanks in advance > > Phil Whitehead From owner-proteins@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!julienas!news2.fnet.fr!sophia.inria.fr!taloa.unice.fr!ws41.cnusc.fr!ciril.fr!thot.u-strasbg.fr!usenet From: nussbaum@neurochem.u-strasbg.fr Newsgroups: bionet.molbio.proteins Subject: glycorpotein purification Date: 7 Sep 1994 15:25:40 GMT Organization: cnrs Lines: 12 Message-ID: <34km1k$7cc@thot.u-strasbg.fr> NNTP-Posting-Host: noiset.u-strasbg.fr X-Newsreader: I have an antiserum which was obtained by injecting a rabbit with an N-terminal sequence of an until now undescribed protein. this antiserum reacts specifically with a protein present in a wheat germ agglutinin fraction isolated from rat brain. I am loking for ideas or suggestions to go further in the purification of this antigen by another way than that I have used (Western blotting). Note that this protein is solubilized by DOC and probably other detergents. Purification of this antigen by immunoaffinity column chromatography is, in my opinion, not feasible since the antibodies are not strong enough. I am thinking about ion exchange chromatography or similar things. thanks in advance for your help. Nussbaum E-mail: nussbaum@neurochem.u-strasbg.fr From owner-proteins@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!usenet.ins.cwru.edu!po.cwru.edu!slf8 From: slf8@po.cwru.edu Newsgroups: bionet.molbio.proteins Subject: Proteins over 400 KDa Date: 8 Sep 1994 02:09:35 GMT Organization: Case Western Reserve University, Cleveland, Ohio USA Lines: 21 Message-ID: <34lrov$42k@usenet.INS.CWRU.Edu> NNTP-Posting-Host: mae53301.mae.cwru.edu Dear Protein Researchers, Our lab is working with a nuclear protein which is over 400 KDa. We have been running 6% DATD-acrylamide minigels to visualize the protein with minimal success. (It just smears.) I was wondering if anyone else has had experience in working with proteins of this size and what they would suggest as far as gel apparatus. Would horizontal agarose gels be better, and if so, what type of equipment will we need? Thanks in advance. Stephanie L. Fox slf8@po.cwru.edu Graduate Student, Dept. of Genetics Case Western Reserve University -- -- From owner-proteins@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!spool.mu.edu!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!univ-lyon1.fr!ghost.dsi.unimi.it!news.unige.it!barbarella!carrara From: carrara@barbarella (Enrico A. Carrara) Newsgroups: bionet.molbio.proteins,bionet.xtallography Subject: Residues at protein surface Date: 6 Sep 1994 09:15:07 GMT Organization: Univ. of Genoa, Italy Lines: 13 Message-ID: <34hbur$rbv@alpha.cisi.unige.it> NNTP-Posting-Host: barbarella.ibf.unige.it X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.proteins:2604 bionet.xtallography:1143 Does anybody have references on studies about surface composition of proteins (i.e. statistics on the relative frequency of specific residues appearing at the surface of some protein, hopefully made on a large subset of the PDB)? Please answer to me directly, as I not always have a chance to read the news before they are erased. Thanks in advance for the attention Enrico Carrara carrara@barbarella.ibf.unige.it From owner-proteins@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!EU.net!sunic!news.uni-c.dk!rna!hnielsen From: hnielsen@rna (Henrik Nielsen) Newsgroups: bionet.molbio.proteins Subject: Re: periplasmic coli proteins Date: 7 Sep 1994 08:07:57 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 26 Distribution: bionet Message-ID: <34jsct$4aj@news.uni-c.dk> References: <34fe9n$4hc@mserv1.dl.ac.uk> NNTP-Posting-Host: rna.cbs.fki.dth.dk X-Newsreader: TIN [version 1.2 PL1] JAB5@VAX.YORK.AC.UK wrote: : Dear Colleagues, : Can anyone tell me how to best compile a list of periplasmic : coli proteins? Both anchored and free are needed. : Many thanks One possibility is to use SWISS-PROT and search for lines beginning with CC -!- SUBCELLULAR LOCATION: Not every entry has such a line, but it may be enough to compile a list. -- Henrik Nielsen Center for Biological Sequence Analysis (CBS) Department of Physical Chemistry (FKI) The Technical University of Denmark (DTU) Building 206 DK-2800 Lyngby, Denmark phone: +45 4288 2222 ext. 2470 (operator) phone: +45 4593 1222 ext. 2470 (tone) fax: +45 4593 4808 e-mail: hnielsen@cbs.dth.dk From owner-proteins@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!CS.Arizona.EDU!uunet!zib-berlin.de!gs.dfn.de!tubsibr!ws.rz.tu-bs.de!i3080406 From: i3080406@ws.rz.tu-bs.de (Schuetze) Newsgroups: bionet.molbio.proteins Subject: Circular dichroism Date: 7 Sep 1994 11:09:01 GMT Organization: Technische Universitaet Braunschweig, Germany Lines: 17 Sender: i3080406@rz1pht1.rz.tu-bs.de (SchÏtze) Distribution: world Message-ID: <34k70d$c6o@ra.ibr.cs.tu-bs.de> NNTP-Posting-Host: rz1pht1.rz.tu-bs.de Hello out there, imaging you have the possibility to use a tool that messures the circular dichroism (CD). Which experiments can be done ? Which results/informations can be obtained (expected)??? Any comment will be helpful! Thanks in advance Wolfram -- +------------------------------------------------------------+ Wolfram Sch"utze w.schuetze@tu-bs.de Pharmaceutical Technology/University Braunschweig/Germany From owner-proteins@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!ouzounis From: ouzounis@embl-heidelberg.de (Christos Ouzounis) Newsgroups: bionet.molbio.proteins Subject: Re: Proteins - Functional Diversity Message-ID: <1994Sep7.190208.171508@eros.embl-heidelberg.de> Date: 7 Sep 94 19:02:08 +0100 References: <80526.ewright@fox.nstn.ns.ca> <1994Aug24.085427.34379@hulaw1.harvard.edu> Distribution: world Organization: European Molecular Biology Laboratory Lines: 38 In article <1994Aug24.085427.34379@hulaw1.harvard.edu>, robison@lipid.harvard.edu (Keith Robison) writes: > Edwin Wright (ewright@FOX.NSTN.CA) wrote: > : Does anyone know which specific proteins exhibit the greatest functional > : diversity among different species? > > Er. How do you define "specific protein" and how do you define > "functional diversity"? Most definitions of "specific protein" > are probably not independent of their function. > > [...] > > Whether these fit your question depends on your definitions... > > Keith Robison > Harvard University > Department of Cellular and Developmental Biology > Department of Genetics / HHMI > > robison@mito.harvard.edu > Interesting question. Functional diversity is a sloppy term, could be quantified, though. You should have equally represented families, calibrate for rates of change, and then have a way of judging by name whether the function remains the same or changes to some extent. Usually for enzymes, reaction types do not dramatically change, while substrates do. If you think about a hierarchy of structure (topology), function (reaction class) and finally specificity (substrate type), all goverved by sequence changes, then 'function' can be considered to be conserved less than structure does but more than specificity. Too abstract???... ----------------- Christos Ouzounis EMBL Heidelberg Germany ----------------- ouzounis@embl-heidelberg.de ---------------------------------- From owner-proteins@net.bio.net Tue Sep 06 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!scripps.edu!NewsWatcher!user From: lisa@scripps.edu (Lisa Bibbs) Newsgroups: bionet.molbio.proteins Subject: subscribe Followup-To: bionet.molbio.proteins Date: 7 Sep 1994 20:13:05 GMT Organization: TSRI Core Facility Lines: 3 Message-ID: NNTP-Posting-Host: pbfnuts.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I would like to subscribe my co-worker to this net. Her internet address is Sandi@scripps.edu. Thank you From owner-proteins@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!urmel.informatik.rwth-aachen.de!newsserver.rrzn.uni-hannover.de!deimos.rz.Uni-Osnabrueck.DE!ax3301.biologie.uni-osnabrueck.de!engel From: engel@ax3301.biologie.uni-osnabrueck.de (Siggi Engelbrecht) Newsgroups: bionet.molbio.proteins Subject: Re: zero-length cross-linker Date: 8 Sep 1994 11:51:05 GMT Organization: Universitaet Osnabrueck, Biophysik Lines: 3 Distribution: world Message-ID: <34mtra$t47@deimos.rz.Uni-Osnabrueck.DE> References: <00983ECD.45BDBCA0.3@vaxa.weeg.uiowa.edu> Reply-To: engel@zeder.biologie.uni-osnabrueck.de NNTP-Posting-Host: ax3301.biologie.uni-osnabrueck.de Look at Biochim. Biophys.Acta 1101, 97-104 (1992). There you find a pretty good protocol for enhancing the EDC reaction by use of Sulfo-NHS. From owner-proteins@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!library.ucla.edu!europa.eng.gtefsd.com!swiss.ans.net!solaris.cc.vt.edu!uunet!news.iij.ad.jp!sumitomo-chem.co.jp!tziris1!kanaoka From: kanaoka@tziris1.sumitomo-chem.co.jp (Kanaoka Masaharu (Sumitomo Pharmaceuticals)) Newsgroups: bionet.molbio.proteins Subject: Info wanted: American Peptide Sympo Date: 8 Sep 1994 09:54:27 GMT Organization: SUMITOMO CHEMICAL CO., LTD. Lines: 11 Message-ID: <34mn0j$j9s@ohsun01.sumitomo-chem.co.jp> NNTP-Posting-Host: tziris1.sumitomo-chem.co.jp X-Newsreader: TIN [version 1.2 PL0] I would like to know where and when the American Peptide Symposium will be held in 1995. Information such as where to look into or who to contact would be appreciated. +------------------------------------------------------------------+ | Masaharu Kanaoka, Ph.D. TEL +81-6-466-5187 | | Sumitomo Pharmaceuticals FAX +81-6-466-5484 | | Research Center e-mail: kanaoka@sumitomo-chem.co.jp | | Osaka, Japan | +------------------------------------------------------------------+ From owner-proteins@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!ACS.UCALGARY.CA!jbooth From: jbooth@ACS.UCALGARY.CA (Joseph Booth) Newsgroups: bionet.molbio.proteins Subject: concentrating proteins Date: 8 Sep 1994 07:25:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi! I've read that you can concentrate a dilute solution of proteins through the addition of dry G25 Sephadex. I was wondering if anyone who has used this method could comment on how effective it is or if there are any disadvantages (like binding of the protein to the beads) that I should be aware of. Also, any alternative suggestions for a gentle method of concentrating proteins would be appreciated. Thanks. Joe From owner-proteins@net.bio.net Wed Sep 07 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!news.msfc.nasa.gov!europa.eng.gtefsd.com!library.ucla.edu!news.ucdavis.edu!okra.ece.ucdavis.edu!varma From: varma@okra.ece.ucdavis.edu (Hemant Varma) Subject: DSSP like program in FORTRAN? Message-ID: Sender: usenet@ucdavis.edu (News Guru) Organization: University of California, Davis X-Newsreader: TIN [version 1.2 PL2] Date: Thu, 8 Sep 1994 22:54:22 GMT Lines: 25 Hello, Dear Colleagues, I was wondering if anybody knows whether a program similar to DSSP is available anywhere at any ftp site, but written in FORTRAN. As you may know C and Pascal versions of DSSP are available. The C version is nothing but a conversion of the Pascal code to C using a P to C convertor and the resulting code is very hard to understand. As you might know, DSSP is used to assign secondary structures to files of protein structure coordinates. Any pointers would be helpful. I want to write a program that is similar to DSSP but to try and get the coordinates of the the Center of Mass of the side chain atoms output along with the C- alphas. Regards, Hemant From owner-proteins@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!agate!doc.ic.ac.uk!charlie.lif.icnet.uk!pic.lif.icnet.uk!user From: p_whitehead@icrf.icnet.uk (Phil Whitehead) Newsgroups: bionet.molbio.proteins Subject: BIO-RAD fraction collector Followup-To: bionet.molbio.proteins Date: Thu, 08 Sep 1994 11:30:54 +0000 Organization: Imperial Cancer Research Fund Lines: 7 Message-ID: NNTP-Posting-Host: 143.65.8.48 We have had a few problems with a Bio-Rad 2128 fraction collector (New Model). Particularly the***** thing missing fractions. The engineers can't find anything wrong with it . Has anyone else out there had any problems with this hardware? Phil Whitehead From owner-proteins@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!concert!hearst.acc.Virginia.EDU!oduvm!lkm100f Organization: Old Dominion University - Computing & Communications Services Date: Thu, 8 Sep 1994 12:57:12 EDT From: Message-ID: <94251.125712LKM100F@ODUVM.BITNET> Newsgroups: bionet.molbio.proteins Subject: Re: concentrating proteins Distribution: world References: Lines: 8 Joe Booth wrote "I've heard that proteins can be concentrated by the addition of dry Sephadex G-25" I have used this method, but I don't add the Sephadex directly to my protein solution. I put the protein in a dialysis membrane and put the Sephadex on the outside to suck up the water without risking any protein binding. It works OK. I think PEG (polyethylene glycol) works better; so do Amicon pressure cells. Laura Moen LKM100F@ODUVM.cc.odu.edu (U.S.) From owner-proteins@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!bt!uknet!comlab.ox.ac.uk!oxuniv!leppard From: leppard@vax.oxford.ac.uk Newsgroups: bionet.molbio.proteins Subject: Re: Info wanted: American Peptide Sympo Message-ID: <1994Sep8.183647.25844@oxvaxd> Date: 8 Sep 94 18:36:47 BST References: <34mn0j$j9s@ohsun01.sumitomo-chem.co.jp> Organization: Oxford University VAX 6620 Lines: 27 In article <34mn0j$j9s@ohsun01.sumitomo-chem.co.jp>, kanaoka@tziris1.sumitomo-chem.co.jp (Kanaoka Masaharu (Sumitomo Pharmaceuticals)) writes: > I would like to know where and when the American Peptide Symposium > will be held in 1995. Information such as where to look into or > who to contact would be appreciated. > June 18-23, 1995: Ohio State University Columbus, Ohio. c/o Dr. Pravin T.P. Kaumaya Chairman, 14th APS The Ohio State University Suite 302 Comprehensive Cancer Center 410 West Twelfth Avenue Columbus, OH 43210 phone 614-292-0726 fax 614-292-1135 Hope this helps. Rachel. Oxford. DON'T USE REPLY - MY REAL ADDRESS IS quarrell@vax.ox.ac.uk From owner-proteins@net.bio.net Wed Sep 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!NewsWatcher!user From: hm10006@mole.bio.cam.ac.uk (Hemlata Mistry) Newsgroups: bionet.molbio.proteins Subject: unwanted ppt in Biorad assay Followup-To: bionet.molbio.proteins Date: 8 Sep 1994 16:44:32 GMT Organization: Dept of Genetics, University of Cambridge, UK Lines: 8 Message-ID: NNTP-Posting-Host: po-mac1.gen.cam.ac.uk Help! I get a large precipitate in a Biorad protein assay. Maybe my assay conditions are not right. I have been extracting cAMP from Drosophila eggs using 6% TCA or hot 0.1M HCl, and saving the pellets containing protein + eggshell. I resuspend the pellet in deoxycholate, spin down undissolved stuff and try to assay amount of protein in supernatant. All I have got so far are massive blue pptes, whose OD I cannot measure! Any suggestions? From owner-proteins@net.bio.net Wed Sep 07 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!spool.mu.edu!umn.edu!maroon!mcnei002 From: mcnei002@maroon.tc.umn.edu (Kenneth J McNeil) Subject: Recommendations for light level protein detection? Message-ID: Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: maroon1.tc.umn.edu Organization: University of Minnesota, Twin Cities Date: Thu, 8 Sep 1994 14:59:54 GMT Lines: 32 I have been attempting to localize antigens in plant tissue with antibodies using silver enhancement of gold particles and, so far, have had no positive results. Western blots show a strong reaction with a single band (6.5 kD) in tomato anthers. Primary antibody dilution in Western blots is 1:100, secondary antibody (antirabbit-HRP) is 1:2,000. I have tried various dilutions and methods of fixation (paraformaldehyde, glutaraldehyde), as well as fresh tissue. I have made sections of paraffin-embedded tissue as well as OCT-embedded tissue for cryostat sectioning. Section thickness is 10 microM. Detection of antigens with antibodies using light microscopy is with silver enhancement of 4 nM gold particles. Primary antibody dilution is 1:20 up to 1:100 and antirabbit-gold (Jackson ImmunoResearch) is 1:50 (manufacturer recommends 1:20-1:200). Silver enhancement using the method sent by Jackson ImmunoResearch produces no detectable differences in sections when compared to the control (no primary antibody). Some silver particles are seen scattered throughout the control and treated sections, but no specific regions are detected. The Intense kit from Amersham gave similar results. Western blots detected with primary antibody (1:100) and antirabbit-4nM gold (1:200) did show the 6.5 kD band when detected by silver enhancement. High endogenous peroxidase activity has made use of horseradish peroxidase difficult. Treatment of sections with hydrogen peroxide (to inactivate endogenous peroxidase) has not been successful, I still see endogenous peroxidase. We have considered using fluorescent conjugated antibodies, but the autofluorescence of some tissues in the anther may be another problem that I then have to deal with. Any recommendations or suggestions for what to do next? Is there a better method for detection of Abs at the light level? Thanks for your help, Ken kmcneil@molbio.cbs.umn.edu From owner-proteins@net.bio.net Wed Sep 07 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uchinews!kimbark!rslomkow From: rslomkow@kimbark.uchicago.edu (Robin * Slomkowski) Subject: Re: concentrating proteins Message-ID: <1994Sep8.230330.11079@midway.uchicago.edu> Sender: news@uchinews.uchicago.edu (News System) Reply-To: rslomkow@midway.uchicago.edu Organization: uchicago strn fanclub References: Date: Thu, 8 Sep 1994 23:03:30 GMT Lines: 16 For concentrating proteins, we have three major methods for T4 Lysozyme Mainly we use a column sephadex colum 100-200ml goes to 3ml kontex disposiable columns can be reused for this purpose Sometimes we use Centripreps and Centricons they take forever. Loss is less than most other filters. We also use dry sephadex put in a small (smaller than our protein) molecular weight cutoff dialisys tube. We have the protein in some salt so it will not stick to the sephadex. -- Robin * Slomkowski Long Live the Future "Real life is Squared" lONG lIVE THE fUTURE "Squared is OK but square root is a disaster" email-rslomkow@midway.uchicago.edu -Wah, Yau Phd April, 5th 1994 From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!torn!nott!uotcsi2!misrael From: misrael@csi.uottawa.ca (Mark Israel) Newsgroups: bionet.molbio.proteins Subject: Re: DSSP like program in FORTRAN? Date: 9 Sep 1994 17:29:02 GMT Organization: Dept. of Computer Science, University of Ottawa Lines: 19 Message-ID: <34q60u$7uh@csi0.csi.uottawa.ca> References: NNTP-Posting-Host: grdb.csi.uottawa.ca In article , Hemant Varma writes: > I was wondering if anybody knows whether a program similar to DSSP > is available anywhere at any ftp site, but written in FORTRAN. DEFINE_STRUCTURE, by Richards, Kundrot, and Kahn, is in FORTRAN. Like DSSP, it's not public domain, but it's free if you sign a licence. Contact Art Perlo (perlo@csb.yale.edu) to get it. > I want to write a program that is similar to DSSP but to try and > get the coordinates of the the Center of Mass of the side chain > atoms output along with the C-alphas. You might ask DSSP co-author Chris Sander (sander@embl-heidelberg.de) if he'd be willing to make this modification for you. It sounds simple, and he's a helpful man. misrael@csi.uottawa.ca Mark Israel From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!moe.ksu.ksu.edu!news.mid.net!crcnis1.unl.edu!unlinfo.unl.edu!markwell From: markwell@unlinfo.unl.edu (john markwell) Newsgroups: bionet.molbio.proteins Subject: Re: concentrating proteins Date: 9 Sep 1994 14:27:38 GMT Organization: University of Nebraska--Lincoln Lines: 25 Distribution: world Message-ID: <34prcq$81j@crcnis1.unl.edu> References: NNTP-Posting-Host: unlinfo2.unl.edu jbooth@ACS.UCALGARY.CA (Joseph Booth) writes: >Hi! STUFF DELETED. . .. Also, any alternative suggestions for a gentle method of >concentrating proteins would be appreciated. Thanks. >Joe Joe, One trick for concentrating proteins from the dark ages is to freeze a tube of the protein at -20C. After frozen solid, place the tube on the lab bench and let thaw undisturbed. The bottom of the tube will contain concentrated protein and the top of the tube will be water. In between is a gradient. You decide how much to discard from the top and the remaining solution is concentrated protein. I hope this helps. John -- John Markwell Phone: 402-472-2924 Dept. Biochemistry FAX: 402-472-7842 University of Nebraska Internet: markwell@unl.edu Lincoln, NE 68583-0718 From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: "Andrew, Tel. +39-6-91093434" Newsgroups: bionet.molbio.proteins Subject: Peptide workup after Fmoc synthesis Date: 9 Sep 1994 10:12:28 +0100 Lines: 40 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <34p8ts$sag@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk Hello Talha, In reply to your message: >Does anyone know the most recent protocol for extraction of peptides after >Fmoc synthesis on a PEG-PS resin? We would like to know the cocktail >composition. We are currently using a 9050 Millipore Peptide synthesizer. The cocktail you need depends on the linker you have used to attach your peptide and the side-chain protecting groups, but for the common mild acid- labile linkers and groups we routinely use the Reagent B cocktail developed by Barany.(reference: Sole, N.A. & Barany, G. (1992) J. Org. Chem. 57, 5399-5403.) The composition is: Trifluoroacetic acid 88% Water 5% Phenol 5% Triisopropylsilane 2% The nice feature of this is that it doesn't contain thiols so is relatively odourless and more pleasant to handle than other mixtures. We have synthesised many dozens of peptides with this reagent without side-chain deprotection problems or other difficulties attributable to its use. After cleavage we precipitate the peptide with cold (-80 C) tert-butyl methyl ether, wash with the ether, recover the ppt. and dry it under vacuum then dissolve in a volatile aqueous buffer (5% acetic acid for basic peptides, 1% ammonium bicarbonate for acidic peptides) adding some organic solvent e.g. acetonitrile if necessary, then put it on a suitable size-exclusion column (e.g. Fractogel HW-50) to isolate the peptide from small MW species. After this we lyophilise the peptide-contining fractions an purify further by HPLC if necessary. If the peptide is less than 10 aa long and the purity is good then we often lyophilise directly without gel filtration. Hope this helps, Andrew Wallace =============================================================================== Andrew Wallace, IRBM P. Angeletti, Pomezia, Italia. Voice: +39-6-91093434 Fax: +39-6-91093225 Email: wallace@irbm.it "IRBM - The home of the Minibody" From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!swiss.ans.net!solaris.cc.vt.edu!uunet!psinntp!hk.super.net!news.ust.hk!ustsu3.ust.hk!bctalarz From: bctalarz@uxmail.ust.hk (AROOZ) Subject: Peptide synthesis Message-ID: <1994Sep9.055825.10552@uxmail.ust.hk> Sender: usenet@uxmail.ust.hk (usenet account) Organization: Hong Kong University of Science and Technology X-Newsreader: TIN [version 1.2 PL2] Date: Fri, 9 Sep 1994 05:58:25 GMT Lines: 8 Does anyone know the most recent protocol for extraction of peptides after Fmoc synthesis on a PEG-PS resin? We would like to know the cocktail composition. We are currently using a 9050 Millipore Peptide synthesizer. Thanks for any help. Talha From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!pipex!bt!uknet!comlab.ox.ac.uk!oxuniv!oxpath!rhubner Newsgroups: bionet.molbio.proteins Subject: xylose isomerase? Message-ID: <1994Sep9.080619.1@molbiol.ox.ac.uk> From: rhubner@molbiol.ox.ac.uk Date: 9 Sep 94 08:06:19 GMT Organization: Oxford University Molecular Biology Data Centre Nntp-Posting-Host: kasia.path Lines: 4 hi there, does somebody know where one can obtain/buy xylose isomerase? thank you very much for any pointer! kind regards, Roland From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!uunet!dziuxsolim.rutgers.edu!er1.rutgers.edu!not-for-mail From: alkaiser@er1.rutgers.edu (Alan Kaiser) Newsgroups: bionet.molbio.proteins Subject: Re: concentrating proteins Date: 9 Sep 1994 13:53:56 -0400 Organization: Rutgers University Lines: 36 Message-ID: <34q7fk$pcl@er1.rutgers.edu> References: NNTP-Posting-Host: er1.rutgers.edu In jbooth@ACS.UCALGARY.CA (Joseph Booth) writes: > I've read that you can concentrate a dilute solution of proteins through >the addition of dry G25 Sephadex. I was wondering if anyone who has used >this method could comment on how effective it is or if there are any >disadvantages (like binding of the protein to the beads) that I should be >aware of. Also, any alternative suggestions for a gentle method of >concentrating proteins would be appreciated. Thanks. >Joe I'm not sure, but this might be the same thing as using polyethylene glycol (PEG) to concentrate proteins. I use this method on a regular basis and it works fine. Put your dilute protein solution in a dialysis tubing with an appropriate MWCO (less than the MW of the protein) and cover the tubing with PEG. I use Sigma PEG (avg. MW 10,000) but there is also a product available from Calbiochem called Aquacide but it is more expensive. These powers draw the water out of the dilute solution and therefore concentrate the sample. I have eliminated 10-15 ml of water in about 6 hours or so at room temp (I work with very stable peptides). The dry G25 Sephadex may serve the same function since it swells when you add water to it. If this is the case, the PEG or Aquacide would be more efficient than Sephadex since it can absorb more water (I think Aquacide is better than PEG at doing this). You will have to be careful to not contaminate your sample with the PEG. Hope this helps Alan Kaiser Rutgers University New Brunswick, NJ alkaiser@eden.rutgers.edu -- Alan Kaiser Rutgers University, Graduate Program in Microbiology alkaiser@eden.rutgers.edu From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!genmac14.biochem.mpg.de!user From: spang@vms.biochem.mpg.de (Anne Spang) Newsgroups: bionet.molbio.proteins Subject: Re: Proteins over 400 KDa Date: 9 Sep 1994 19:27:21 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 15 Message-ID: References: <34lrov$42k@usenet.INS.CWRU.Edu> NNTP-Posting-Host: genmac14.biochem.mpg.de Hi Stephanie! You could use a simple PAGE with just a modified acrylamid solution (T: 49.5%, C:3%). The final acrylamide concentration should be about 6 to 8 %. To determine the best concentration, I would simply run a gradient gel from 10 to 4%. Hope it helps! Anne > > -- > > -- From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!MACC.WISC.EDU!GOSINK From: GOSINK@MACC.WISC.EDU (Mark Gosink) Newsgroups: bionet.molbio.proteins Subject: Looking for random display peptides. Date: 9 Sep 1994 13:48:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <24090915482917@vms2.macc.wisc.edu> NNTP-Posting-Host: net.bio.net Dear Netters: I'm interested in finding out more information about random display peptides (synthetic peptide libraries, peptide display libraries, what ever you wish to call them). As far as I've been able to discern from the literature, these peptides are primarily used to identify epitopes of monoclonal antibodies. What I'm primarily interested in finding out is instances where peptides have been identified that bind to non-antibody proteins. (So far, I've found reference to peptides that bind S-protein, streptavidin and a few hormone receptors.) Does anyone out there know of any others? Thanks in advance, Mark ************************************************************************* * Dr. Mark Gosink Post-doctoral Fellow * * Department of Horticulture (608) 262-1622 voice * * University of Wisconsin-Madison (608) 262-4743 FAX * * 1575 Linden Dr. * * Madison ,WI 53706 GOSINK@MACC.WISC.EDU * ************************************************************************* From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!cville-srv.wam.umd.edu!jryan From: jryan@wam.umd.edu (Blonde Mentos Guy) Newsgroups: bionet.molbio.proteins Subject: Not really dealing with proteins... Date: 9 Sep 1994 17:34:51 GMT Organization: Zima HQ, Mallorea Lines: 22 Message-ID: <34q6br$e3l@cville-srv.wam.umd.edu> NNTP-Posting-Host: rac6.wam.umd.edu X-Newsreader: TIN [version 1.2 PL0] I was just wondering if anyone out there knew of any articles that they could recommend to me on PNAs. For those who may know the subject but not the name it stands for peptide nucleic acids. I was just curious and wanted to read up more on this topic. My address in below. Thanx. -- What do you think sirs? Joe Tseng ___/| aka Blonde Mentos Guy jryan@Glue.umd.edu \O.-| "Finger me!" jryan@wam.umd.edu NYYANKEES IN 94!!!!! ------oOO =(___)= OOo------------ NYGIANTS IN '94!!!!! ''' U ''' Top Ten Baseball Player Demands: 1. More games against the Mets. ----------------------------------------------------------------------------- #include P: (301) 935-7049 Alpha Phi Omega - Epsilon Mu Pi Kappa Phi - Eta Epsilon END THE STRIKE!!!!!! "Push the button, Frank!" From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!iat.holonet.net!janyoung From: janyoung@iat.holonet.net (DR. JANIS YOUNG) Subject: APS brochures Message-ID: Organization: HoloNet National Internet Access System: 510-704-1058/modem Date: Sat, 10 Sep 1994 05:13:24 GMT Lines: 10 In response to the American Peptide Symposium information: I have quite a few of the brochures. If you send me your address, I will send them to you. Dr. Pravin, the cahir has them but I don't think he has e-mail. Jan Young -- ============================================================================ Janis Dillaha Young, Ph.D. Skyline Peptides Tel.&FAX: (510) 655-5885 6039 Skyline Blvd. #A e-mail: janyoung@holonet.net From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!swiss.ans.net!newstf01.cr1.aol.com!search01.news.aol.com!not-for-mail From: jfrank777@aol.com (JFrank777) Newsgroups: bionet.molbio.proteins Subject: Re: Oxford University press phone number ? Date: 10 Sep 1994 00:50:02 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 4 Sender: news@search01.news.aol.com Message-ID: <34rdtq$a5o@search01.news.aol.com> References: NNTP-Posting-Host: search01.news.aol.com In article , scottb@lsiris2.biology.utah.edu (Scott beeser) writes: Go to your library and ask the research librarian. From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!asuvax!news.asu.edu!asuidme From: asuidme@imap2.asu.edu Newsgroups: bionet.molbio.proteins Subject: Thermostable 3D protein Structure? Date: 9 Sep 1994 19:56:03 GMT Organization: Arizona State University Lines: 16 Message-ID: <34qekj$qoq@news.asu.edu> NNTP-Posting-Host: general2.asu.edu X-Newsreader: TIN [version 1.2 PL2] Proteins that are stable and can fuction at temperatures exceeding 100 degress Celcius have been reported in the hyperthermophiles. My understanding of protein chemistry is that this excessive heat would denature any secondary, tertiary or quaternary structure. If this is so, then how does one reason for enzyme active sites under the 3D lock and key hypothesis? In addition, if anyone is interested in a lab technician with recombinant DNA experience, please E-mail or write. Shaun R. Opie asuidme@imap2.asu.edu 1075 N. Miller Rd, #367 Scottsdale Arizona 85257 From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!ux1.cso.uiuc.edu!elarson From: elarson@ux1.cso.uiuc.edu (larson eric) Newsgroups: bionet.molbio.proteins Subject: Re: unwanted ppt in Biorad assay Date: 10 Sep 1994 06:19:23 GMT Organization: University of Illinois at Urbana Lines: 29 Message-ID: <34rj5b$set@vixen.cso.uiuc.edu> References: NNTP-Posting-Host: ux1.cso.uiuc.edu hm10006@mole.bio.cam.ac.uk (Hemlata Mistry) writes: >Help! >I get a large precipitate in a Biorad protein assay. Maybe my assay >conditions are not right. I have been extracting cAMP from Drosophila eggs >using 6% TCA or hot 0.1M HCl, and saving the pellets containing protein + >eggshell. I resuspend the pellet in deoxycholate, spin down undissolved >stuff and try to assay amount of protein in supernatant. All I have got so >far are massive blue pptes, whose OD I cannot measure! Any suggestions? ============= The DOC is the problem. DOC is a wonderful way to ppt. proteins since it will fall out of solution in the presence of acid. The Biorad reagent is in phosphoric acid, thus the source of your problem. Similarly, the Biorad reagent will react with many detergents giving a blue color. I recommend just doing a Lowry assay with the ppt. protein (or a Larson Lowry :-). You can try resuspending the pellet with a small amount of NaOH and then do a Biorad assay if your protein concentrations are very low. Skip the DOC if you do this. -- Eric Larson | University of Illinois at Urbana-Champaign USDA/Agronomy | 190 PABL; 1201 W. Gregory; Urbana, IL 61801 elarson@ux1.cso.uiuc.edu | Voice 217.244.3079 Fax 217.244.4419 Fidonet: 1:233/4.1 | My opinions are my own, but correct :-) From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!ux1.cso.uiuc.edu!elarson From: elarson@ux1.cso.uiuc.edu (larson eric) Newsgroups: bionet.molbio.proteins Subject: Re: concentrating proteins Date: 10 Sep 1994 06:13:03 GMT Organization: University of Illinois at Urbana Lines: 37 Message-ID: <34ripf$rs3@vixen.cso.uiuc.edu> References: NNTP-Posting-Host: ux1.cso.uiuc.edu jbooth@ACS.UCALGARY.CA (Joseph Booth) writes: >Hi! > I've read that you can concentrate a dilute solution of proteins through >the addition of dry G25 Sephadex. I was wondering if anyone who has used >this method could comment on how effective it is or if there are any >disadvantages (like binding of the protein to the beads) that I should be >aware of. Also, any alternative suggestions for a gentle method of >concentrating proteins would be appreciated. Thanks. ========================== I've use the Sephadex method when I've had to concentrate proteins already within 100% Ammonium Sulfate or when glycerol is present. The method works, but it takes a fair amount of Sephadex to achieve a decent concentration. I'm not sure of the losses, but they must be there (I'm usually working with crude mixtures). The biggest hassel is working out an appliance to do the actual concentrating. I prefer using syringes with polyethylene frits forced to the bottom and spinning them in 15 or 50 mL Falcon tubes (plastic top with a hole cut for the syringe which "floats" above the angled bottom). A somewhat slow, but reliable method, is to dialyze against polyetheylene glycol solutions (7 to 50%). The method is a bit slow, requires dialysis tubing of 12,000 m. wt. or less, but can concentrate into the hundreds of grams/liter range. Be aware that it's best to simply make the buffer you want then add the PEG -- making a 20% PEG solution in 1 liter with other components at nominal concentrations means the dialysis bag will ultimately contain the buffers/salts at 20% elevated levels. -- Eric Larson | University of Illinois at Urbana-Champaign USDA/Agronomy | 190 PABL; 1201 W. Gregory; Urbana, IL 61801 elarson@ux1.cso.uiuc.edu | Voice 217.244.3079 Fax 217.244.4419 Fidonet: 1:233/4.1 | My opinions are my own, but correct :-) From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!KB.USM.MY!asma From: asma@KB.USM.MY (Asma Ismail) Newsgroups: bionet.molbio.proteins Subject: e-mail address to the London School of Hygiene and Tropical Medicine. Date: 9 Sep 1994 22:48:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net > Dear netters, > Recently I have enquired about the above mentioned matter through this > network. > One of the netters has reply to me. Unfortunetly I could not remember > neither the netter's nor the message as well due to accidental > deletion of the pacticular message. That netter have forwarded to > me the e-mail address of the London School of Tropical Medicine. I would > like to forward this again and hope to receive reply > from the netters. Thanking you in advance. > > Details of the institution is...... > > Mrs Julie A Thompson, > Assitant Registrar (Admissioms and Records), > London School of Hygiene and Tropical Medicine , > University of London, > Keppel Street, > London. > From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!umd5.umd.edu!xiao From: xiao@mbisgi.umd.edu (Jinsong Xiao) Newsgroups: bionet.molbio.proteins Subject: About Centriprep Date: 9 Sep 1994 22:25:42 GMT Organization: University of Maryland, College Park Lines: 1 Message-ID: <34qnd7$h28@umd5.umd.edu> NNTP-Posting-Host: mbisgi.umd.edu X-Newsreader: TIN [version 1.2 PL0] From owner-proteins@net.bio.net Thu Sep 08 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!uunet!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!mozart.amil.jhu.edu!blaze.cs.jhu.edu!jhunix1.hcf.jhu.edu!NewsWatcher!user From: blesley.welchlink.welch.jhu.edu (lesley brown) Newsgroups: bionet.molbio.proteins Subject: T4 Lysozyme Followup-To: bionet.molbio.proteins Date: Fri, 09 Sep 1994 17:51:56 +0100 Organization: johns hopkins university Lines: 10 Message-ID: NNTP-Posting-Host: 128.220.56.44 I want to lyse cells and have read a few accounts in which T4 lysozyme was used because it is more active toward E. coli membranes. Does any one know of any suppliers? You can post answers directly to me and I will post a summary. Thanks. Lesley Brown blesley@welchlink.welch.jhu.edu From owner-proteins@net.bio.net Fri Sep 09 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sun4nl!news.nic.surfnet.nl!highway.LeidenUniv.nl!rulsfb.LeidenUniv.nl!SBTNFH From: sbtnfh@rulsfb.LeidenUniv.nl (Flip Hoedemaeker, CvF RUL/TNO, Leiden, The Netherlands) Newsgroups: bionet.molbio.proteins Subject: concentrating proteins Date: 10 Sep 1994 13:51:55 GMT Organization: Biology, Leiden University, The Netherlands Lines: 7 Message-ID: <34sdlr$f04@highway.LeidenUniv.nl> Reply-To: sbtnfh@rulsfb.LeidenUniv.nl NNTP-Posting-Host: rulsfb.leidenuniv.nl Hi, sofar I read a lot of ways to concentrate proteins. Nice, but most methods still use dialysis tubes next to Sephadex etc. etc. If you use dialysis tubes you may just as well dialyze and lyophilize! Isn't that the simplest thing to do? Flip From owner-proteins@net.bio.net Fri Sep 09 23:00:00 1994 Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!swiss.ans.net!newstf01.cr1.aol.com!search01.news.aol.com!not-for-mail From: jfrank777@aol.com (JFrank777) Newsgroups: bionet.molbio.proteins Subject: Stable Isotope Labeled Biochemicals Date: 10 Sep 1994 19:48:01 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 10 Sender: news@search01.news.aol.com Message-ID: <34tgjh$ph6@search01.news.aol.com> NNTP-Posting-Host: search01.news.aol.com Hello. Thanks for everyone's assistance in helping me find a source for stable isotope labeled biochemicals and growth media. Below is a summary of the (useful?) sources I've found: MicroForest, Inc., San Diego, CA 800-806-4276 CDN Isotopes, Vaudreuil, Que, Canada 800-565-4696 Cambridge Isotope Labs, Andover MA 508-749-8000 Omicron, South Bend, IN, 219-631-7807 Have a good day. From owner-proteins@net.bio.net Fri Sep 09 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!uunet!intac!usenet From: Seshadri Narasimhan Newsgroups: bionet.neuroscience,bionet.molbio.proteins Subject: Help in microsequencing & homology detection Date: Sat, 10 Sep 1994 15:32:11 -0400 (EDT) Organization: INTAC Access Corporation - An Internet Service Provider Lines: 103 Message-ID: NNTP-Posting-Host: nile.intac.com Mime-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="1913651362-118358326-779224824=:20939" To: Rajeswari Seshadri Content-ID: Xref: biosci bionet.neuroscience:4232 bionet.molbio.proteins:2639 This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. --1913651362-118358326-779224824=:20939 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-ID: Hi there to everyone in cyber-space!! I am posting the following information from Cancer Research Institute (Bombay, INDIA). Please e-mail responses to: cril@sangra.ncst.ernet.in Attention: Dr. Rajeswari Seshadri ______________________________________________________________________________ Teratocarcinoma-derived neurotrophic factor: We have developed a translatable teratocarcinoma model in C3HJax mice in our lab. This type of tumor, which is equivalent to a developing embryo, is known to produce various growth promoting factors. During our search for such a factor which would promote growth of neural elements, employing the standard method for isolation of Nerve growth factor (Mr 26,000), we observed three (3) bands with Mr 50kD, 60kD and 72kD on SDS-PAGE. All these bands were eluted individually from the gel and their biological activity was tested on cerebellar explant cultures from newborn rats. The neurite extension and proliferation of neuronal cells was maximum in the 60kD protein and we decided to focus our attention on it for further studies. At present we are in the process of producing polyclonal antibody against this 60kD protein with the aim of immunohistochemically localizing it in a variety of normal & cancerous nervous tiisues. The lypophilised powder is available for 1) microsequencing off proteins to as much length of amino acids as possible, 2) comparison of this sequence with already known protein sequences to detect any homology. We would like someone to help us due to our lack of expertise/experience in microsequencing. Please contact us either via e-mail or snail-mail. (The attached file gives additional information regarding the protocol). --1913651362-118358326-779224824=:20939 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII; NAME=protein-cri Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: VGVyYXRvY2FyY2lub21hLWRlcml2ZWQgbmV1cm90cm9waGljIGZhY3RvcjoN Cg0KV2UgaGF2ZSBkZXZlbG9wZWQgYSB0cmFuc2xhdGFibGUgdGVyYXRvY2Fy Y2lub21hIG1vZGVsIGluIEMzSEpheCBtaWNlIGluIG91cg0KbGFiLiBUaGlz IHR5cGUgb2YgdHVtb3IsIHdoaWNoIGlzIGVxdWl2YWxlbnQgdG8gYSBkZXZl bG9waW5nIGVtYnJ5bywgaXMga25vd24NCnRvIHByb2R1Y2UgdmFyaW91cyBn cm93dGggcHJvbW90aW5nIGZhY3RvcnMuIER1cmluZyBvdXIgc2VhcmNoIGZv ciBzdWNoIGENCmZhY3RvciB3aGljaCB3b3VsZCBwcm9tb3RlIGdyb3d0aCBv ZiBuZXVyYWwgZWxlbWVudHMsIGVtcGxveWluZyB0aGUgc3RhbmRhcmQNCm1l dGhvZCBmb3IgaXNvbGF0aW9uIG9mIE5lcnZlIGdyb3d0aCBmYWN0b3IgKE1y IDI2LDAwMCksIHdlIG9ic2VydmVkIHRocmVlICgzKSANCmJhbmRzIHdpdGgg TXIgNTBrRCwgNjBrRCBhbmQgNzJrRCBvbiBTRFMtUEFHRS4gQWxsIHRoZXNl IGJhbmRzIHdlcmUgZWx1dGVkIA0KaW5kaXZpZHVhbGx5IGZyb20gdGhlIGdl bCBhbmQgdGhlaXIgYmlvbG9naWNhbCBhY3Rpdml0eSB3YXMgdGVzdGVkIG9u DQpjZXJlYmVsbGFyIGV4cGxhbnQgY3VsdHVyZXMgZnJvbSBuZXdib3JuIHJh dHMuIFRoZSBuZXVyaXRlIGV4dGVuc2lvbiBhbmQgDQpwcm9saWZlcmF0aW9u IG9mIG5ldXJvbmFsIGNlbGxzIHdhcyBtYXhpbXVtIGluIHRoZSA2MGtEIHBy b3RlaW4gYW5kIHdlIGRlY2lkZWQgDQp0byBmb2N1cyBvdXIgYXR0ZW50aW9u IG9uIGl0IGZvciBmdXJ0aGVyIHN0dWRpZXMuIEF0IHByZXNlbnQgd2UgYXJl IGluIHRoZSANCnByb2Nlc3Mgb2YgcHJvZHVjaW5nIHBvbHljbG9uYWwgYW50 aWJvZHkgYWdhaW5zdCB0aGlzIDYwa0QgcHJvdGVpbiB3aXRoIHRoZSANCmFp bSBvZiBpbW11bm9oaXN0b2NoZW1pY2FsbHkgbG9jYWxpemluZyBpdCBpbiBh IHZhcmlldHkgb2Ygbm9ybWFsICYgY2FuY2Vyb3VzIA0KbmVydm91cyB0aWlz dWVzLg0KDQpQcm90b2NvbCBmb3IgaXNvbGF0aW9uIG9mIDYwa0QgcHJvdGVp bjoNCjEpIDIwIGcgdHVtb3IgaG9tb2dlbml6ZWQgaW4gMTAwIG1sIGRpc3Rp bGxlZCB3YXRlci4NCjIpIENlbnRyaWZ1Z2UgYXQgMTQ1MDAgcnBtIGZvciAx IGhyLg0KMykgVG8gdGhlIHN1cGVybmF0ZW50IDEvOSB2b2x1bWUgb2YgMC41 TSBhY2V0YXRlIGJ1ZmZlciAocEggNC4wKSBhbmQgc29saWQgTmFDbA0KICAg d2EgYWRkZWQgdG8gYnJpbmcgdGhlIGZpbmFsIGNvbmNuLiBvZiBOYUNsIHRv IDAuNE0NCjQpIENlbnRyaWZ1Z2UgYXQgMTQ1MDAgcnBtIGZvciAzMCBtaW5z Lg0KNSkgU3VwZXJuYXRlbnQgbG9hZGVkIG9udG8gYSBjYXJib3h5IG1ldGh5 bCBjZWxsdWxvc2UgY29sdW1uIGVxdWlsaWJyYXRlZCB3aXRoDQogICAwLjA1 TSBhY2V0YXRlIGJ1ZmZlciB3aXRoIDAuNE0gTmFDbCAocEggNC4wKQ0KNikg Tm9uLWFkc29yYmluZyBtYXRlcmlhbCB3YXNoZWQgd2l0aCBzYW1lIGJ1ZmZl cg0KNykgQ29sdW1uIHdhc2hlZCB3aXRoIDAuMDVNIGFjZXRhdGUgYnVmZmVy IChwSCA0LjApICh0aWxsIGFic29yYmFuY2UgYXQgMjgwIG5tIA0KICAgaXMg bGVzcyB0aGFuIDAuMDAxKQ0KOCkgRmluYWwgZWx1dGlvbiB3aXRoIFRyaXMt SENsIGJ1ZmZlciB3aXRoIDAuNE0gTmFDbCAocEggOS4wKQ0KDQpUaGUgZmlu YWwgZWx1YXRlIGlzIHN1YmplY3RlZCB0byBTRFMtUEFHRS4gUHJvdGVpbnMg YXJlIGVsdXRlZCBpbiBhbW1vbml1bSANCmJpY2FyYm9uYXRlIFNEUyBidWZm ZXIgYWZ0ZXIgS0NsIHZpc3VhbGl6YXRpb24gYW5kIGx5cG9waGlsaXNlZC4N Cg0KVGhlIGx5cG9waGlsaXNlZCBwb3dkZXIgaXMgYXZhaWxhYmxlIGZvciAx KSBtaWNyb3NlcXVlbmNpbmcgb2ZmIHByb3RlaW5zIHRvIA0KYXMgbXVjaCBs ZW5ndGggb2YgYW1pbm8gYWNpZHMgYXMgcG9zc2libGUsIDIpIGNvbXBhcmlz b24gb2YgdGhpcyBzZXF1ZW5jZSANCndpdGggYWxyZWFkeSBrbm93biBwcm90 ZWluIHNlcXVlbmNlcyB0byBkZXRlY3QgYW55IGhvbW9sb2d5Lg0KDQpQcmlu Y2lwYWwgaW52ZXN0aWdhdG9yOg0KRHIuIFYuIFMuIExhbGl0aGEgTS5ELCBQ aC5ELg0KSGVhZCwgTmV1cm8gT25jb2xvZ3kgRGl2aXNpb24sDQoNCkNvLWlu dmVzdGlnYXRvcjoNCkRyIFJhamVzd2FyaSBTZXNoYWRyaSBQaC5ELg0KU2Np ZW50aWZpYyBPZmZpY2VyIC0gTmV1cm8gT25jb2xvZ3kgRGl2aXNpb24NCg0K UG9zdGFsIGFkZHJlc3M6DQpjL28gKGVpdGhlciBvZiB0aGUgYWJvdmUpDQpD YW5jZXIgUmVzZWFyY2ggSW5zdGl0dXRlDQpQYXJlbCwgQm9tYmF5IDQwMDAx Mg0KSU5ESUENCg0KZS1tYWlsIGFkZHJlc3M6DQpjcmlsQHNhbmdyYS5uY3N0 LmVybmV0LmluDQoNCg0KV2Ugd291bGQgbGlrZSBzb21lb25lIHRvIGhlbHAg dXMgZHVlIHRvIG91ciBsYWNrIG9mIGV4cGVydGlzZS9leHBlcmllbmNlIGlu IA0KbWljcm9zZXF1ZW5jaW5nLiBQbGVhc2UgY29udGFjdCB1cyBlaXRoZXIg dmlhIGUtbWFpbCBvciBzbmFpbC1tYWlsLg== --1913651362-118358326-779224824=:20939-- From owner-proteins@net.bio.net Fri Sep 09 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!news.uoregon.edu!usenet.eel.ufl.edu!usenet.cis.ufl.edu!usenet.ufl.edu!gnv.ifas.ufl.edu!icbr!rep Newsgroups: bionet.molbio.proteins Subject: isoelectric focusing data Message-ID: <1994Sep10.151538.1@icbr> From: rep@icbr Date: 10 Sep 94 15:15:38 -0500 Organization: ICBR Nntp-Posting-Host: icbr.ifas.ufl.edu Lines: 7 Can anybody tell me a good place to look for the isoelectric focusing point of various proteins, from various animals? I would greatly appreciate any advice. Robert Peterson Whitney Laboratory From owner-proteins@net.bio.net Sat Sep 10 23:00:00 1994 Path: biosci!agate!lhom From: lhom@OCF.Berkeley.EDU (Louis Hom) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Negative Cooperativity Date: 11 Sep 1994 17:49:05 GMT Organization: U.C. Berkeley Open Computing Facility Lines: 9 Distribution: usa Message-ID: <34vfuh$pm0@agate.berkeley.edu> NNTP-Posting-Host: planecrash.berkeley.edu Xref: biosci bionet.molbio.proteins:2642 bionet.molbio.methds-reagnts:18301 For independent ligand binding sites, you have a hyperbola. For positive ligand binding, you get a sigmoidal curve when you plot saturation versus ligand concentration. What about for negative cooperativity? Is it just like the hyperbola but with a lower asymptote? Or maybe stretched out? -- **************************************************************************** * Lou Hom * "All folks are family." * * lhom@ocf.berkeley.edu * -- John Saponara * **************************************************************************** From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!Germany.EU.net!news.dfn.de!urmel.informatik.rwth-aachen.de!news.rhrz.uni-bonn.de!usenet From: allera@mailer.meb.uni-bonn.de Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.genome-program,bionet.molbio.proteins Subject: Re: BCM Sequence Annotation Web Server Date: 12 Sep 1994 15:49:53 GMT Organization: Klin.Biochemie/MEB Lines: 47 Message-ID: <351tb1$3k2@news.rhrz.uni-bonn.de> NNTP-Posting-Host: allera.meb.uni-bonn.de X-Newsreader: Xref: biosci bionet.molbio.genbank:1742 bionet.molbio.embldatabank:363 bionet.molbio.genome-program:935 bionet.molbio.proteins:2653 In article toms@fcsparc6.ncifcrf.gov (Tom Schneider) writes: >In article rsmith@dot.bcm.tmc.edu >(Randall Smith) writes: > >| : Announcing a new WWW Server: The BCM Sequence Annotation Server >| : URL: http://dot.imgen.bcm.tmc.edu:9331/seq-annot/home.html > >This idea has both good and bad points and I think that they should be >considered extremely carefully. > >First, the idea that individual researchers should be able to update a database >directly is wonderful. If everybody were to do that to the data they are >experts on, GenBank would quickly become a clean database. > >However, there are several problems: > >1. Corruption of the data either intentionally or inadvertently. The authors >already are aware of this possibility. > >2. Inconsistency between researchers. The NCBI attempts to make entries >uniform by certain standards, but individual researchers cannot know what these >are in detail. The only solutions I see are to force the kinds of annotations >to follow certain forms or to pass all the changes to experts for editing. The >trouble with passing the data to experts is that the number of experts has to >grow exponentially along with the growth of the database. Maybe we just have >to accept that to avoid a worse mess! > >2. Do the data flow into GenBank? There is no indication that it will. This >means that if GenBank makes a correction it won't go into this database and >vice versa. Since the data are not maintained in one place, it is duplicated >and will eventually become inconsistent. Who should or will a researcher >believe? A randomly annotated database or the "official" one? How will >inconsistencies be resolved? > >I see this as an experiment. Once the experiment has been shown to work >reasonably well, all the data should be passed to NCBI for careful processing >along with all new data. That is, the server should be run by NCBI or closely >in conjunction with them. > >For my reasoning behind this posting, see the philosophy paper available from: >http://fconvx.ncifcrf.gov:2001/~toms/onlinepapers.html > > Tom Schneider > National Cancer Institute > Laboratory of Mathematical Biology > Frederick, Maryland 21702-1201 > toms@ncifcrf.gov From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!urmel.informatik.rwth-aachen.de!news.rhrz.uni-bonn.de!usenet From: allera@mailer.meb.uni-bonn.de Newsgroups: bionet.molbio.proteins Subject: antibody against rat glucocorticoid receptor Date: 12 Sep 1994 15:18:00 GMT Organization: Klin.Biochemie/MEB Lines: 6 Message-ID: <351rf8$2nt@news.rhrz.uni-bonn.de> NNTP-Posting-Host: allera.meb.uni-bonn.de X-Newsreader: Dear Colleagues! I need urgently a good working antibody against the ligand binding domain of the rat glucocorticoid receptor. Who can give me information on where and how to get it. Thanks a lot. Axel Allera, Dpt. of Clinical Biochemistry, University of Bonn, Germany From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sun4nl!news.nic.surfnet.nl!highway.LeidenUniv.nl!rulsfb.LeidenUniv.nl!SBTNFH From: sbtnfh@rulsfb.LeidenUniv.nl (Flip Hoedemaeker, CvF RUL/TNO, Leiden, The Netherlands) Newsgroups: bionet.molbio.proteins Subject: studying dimerisation Date: 12 Sep 1994 15:08:24 GMT Organization: Biology, Leiden University, The Netherlands Lines: 21 Message-ID: <351qt8$s9@highway.LeidenUniv.nl> Reply-To: sbtnfh@rulsfb.LeidenUniv.nl NNTP-Posting-Host: rulsfb.leidenuniv.nl Hello Netters, I'm looking for a sensible and reliable method to find out if a protein is a monomer or a dimer. For gelfiltration analysis you need a reasonable amount of relatively pure protein, which I haven't got. I've mutagenized pea lectin which is a dimer in order to try to get monomers. pea lectin is an all-beta sheet protein, and the two subunits are "zipped" together by combining two sheets. I express both wild type and mutant pea lectin in tobacco. The expression level is something like 1% of the total soluble protein in leaves I've tried to use Dimethyl Suberimidate to cross-link the subunits, so I can see the difference between monomers and dimers on a SDS-PAGE, (reference Davies et al, PNAS 66: 651-656, 1970) but this doesn't work, not even with wild type lectin. Does somebody know of a method to cross-link subunits without having to purify the protein first? Or maybe another method to study the subunit structure? Thanks, Flip p.s. I meant sensitive and not sensible, but I have a lousy editor so I can not go back for typos Sorry From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!unixg.ubc.ca!news.bc.net!news.mic.ucla.edu!hodgkin.mbi.ucla.edu!arne From: arne@hodgkin.mbi.ucla.edu (Arne Elofsson) Newsgroups: bionet.molbio.proteins Subject: Re: Thermostable 3D protein Structure? Date: 12 Sep 1994 15:08:00 GMT Organization: OrgFreeware Lines: 15 Distribution: world Message-ID: <351qsh$s09@news.mic.ucla.edu> References: <34qekj$qoq@news.asu.edu> Reply-To: arne@hodgkin.mbi.ucla.edu (Arne Elofsson) NNTP-Posting-Host: hodgkin.mbi.ucla.edu It is not so. These proteins keep there structure at these temperatures arne -- ****************************************************************************************** ** Arne Elofsson (arne@hodgkin.mbi.ucla.edu) ** ** Molecular Biology Institute, UCLA ** ** 405 Hilgard Avenue, Los Angeles ** ** 90024-1570 California, USA ** ** tel: +1-(310)-825-1402 Fax: +1-(310)-206-3914 ** ** Home: +1-(310)-268-8006 SWE: +46-8-306129 ** ****************************************************************************************** From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!uunet!zib-berlin.de!news.th-darmstadt.de!terra.wiwi.uni-frankfurt.de!zeus.rbi.informatik.uni-frankfurt.de!news.dfn.de!urmel.informatik.rwth-aachen.de!news.rhrz.uni-bonn.de!usenet From: allera@mailer.meb.uni-bonn.de Newsgroups: bionet.molbio.proteins Subject: Re: ppt protiens Date: 12 Sep 1994 14:48:45 GMT Organization: Klin.Biochemie/MEB Lines: 25 Message-ID: <351pod$1rt@news.rhrz.uni-bonn.de> NNTP-Posting-Host: allera.meb.uni-bonn.de X-Newsreader: In article magoldstein@ucdavis.edu (Marc A. Goldstein) writes: >In article , >thomas@molbio.uoregon.edu (matt thomas) wrote: > >> I am planing to do an experiment where I will end up with a large volume. I >> want to run this on a SDS gel and my lanes will not hold the volume the >> experiment will generate. I don't care if the proteins get killed. Does >> anyone have a good meathod they might suggest? > >Dear Thomas, > > What's a large volume, and how large are you're wells? > >Some standard thoughts: > 1. Concentrate the protein by using small-pore-sized spin filters >(millipore, amicon, etc..) > 2. Precipitate the protein with acetone, or ammonium sulfate or the like. > 3. If all else fails, dialyze the salt away and lyophilize the stuff. > >Hope this helps. >________________________ >Marc A. Goldstein >Section of Plant Biology >UC Davis >magoldstein@ucdavis.edu From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!JASON.UTHCT.EDU!SHAUN From: SHAUN@JASON.UTHCT.EDU ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: Re: concentrating proteins Date: 12 Sep 1994 07:32:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <940912093114.a153@jason.uthct.edu> NNTP-Posting-Host: net.bio.net sbtnfh@rulsfb.LeidenUniv.nl on 10-SEP-1994 09:42 writes: > sofar I read a lot of ways to concentrate proteins. Nice, but most methods > still use dialysis tubes next to Sephadex etc. etc. > If you use dialysis tubes you may just as well dialyze and lyophilize! > Isn't that the simplest thing to do? > This is an acceptable strategy for some proteins, but will not work for all. For example, most membrane proteins when lyophilized form intractably insoluble precipitates. Cheers, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet address: shaun@jason.uthct.edu = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!ceylon!news2.near.net!das-news.harvard.edu!husc-news.harvard.edu!lipid!robison Newsgroups: bionet.molbio.proteins Subject: Re: isoelectric focusing data Message-ID: <1994Sep12.090846.34703@hulaw1.harvard.edu> From: robison@lipid.harvard.edu (Keith Robison) Date: 12 Sep 94 09:08:46 EDT References: <1994Sep10.151538.1@icbr> Nntp-Posting-Host: lipid.harvard.edu X-Newsreader: TIN [version 1.2 PL2] Lines: 21 rep@icbr wrote: : Can anybody tell me a good place to look for the isoelectric focusing point : of various proteins, from various animals? I would greatly appreciate any : advice. The ExPASy WWW server will predict the isoelectric point of any protein in SwissProt. Point your WWW Client (such as Mosaic) to http://expasy.hcuge.ch/ pI-predicting programs are also part of most software suites, such as GCG and DNAStar. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@mito.harvard.edu From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!pipex!uknet!gdt!aber!spp From: spp@aber.ac.uk (SIMON PETER PENSON) Subject: Re: concentrating proteins Message-ID: <1994Sep12.121746.11895@aber.ac.uk> Organization: University of Wales - Aberystwyth - Prifysgol Cymru References: <34ripf$rs3@vixen.cso.uiuc.edu> Date: Mon, 12 Sep 1994 12:17:46 GMT Lines: 5 Sorry, I didn't see the original message. However, one method I've found to be quick and effecient is centrifugal ultrafiltration. Amicon do a range of gadgets, from 1ml up to 30ml. Simon. From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!warwick!bham!usenet From: altabios@bham.ac.uk (John E. Fox) Newsgroups: bionet.neuroscience,bionet.molbio.proteins Subject: Re: Help in microsequencing & homology detection Date: 12 Sep 1994 12:00:06 GMT Organization: The University of Birmingham, UK Lines: 24 Message-ID: <351fs6$skg@sun4.bham.ac.uk> References: NNTP-Posting-Host: bcs118.bham.ac.uk X-Newsreader: WinVN version 0.80 Xref: biosci bionet.neuroscience:4239 bionet.molbio.proteins:2645 In article , Seshadri Narasimhan says: > > cril@sangra.ncst.ernet.in > Attention: Dr. Rajeswari Seshadri > >______________________________________________________________________________ I run a laboratory which amongst other things, offers a protein micro sequencing service. The charge is £25 per amino acid residue, with a minimum charge of 5 residues. We can work with either free proteins or proteins on blots. Our record for sensitivity is 800 f.mole. We also do Peptide synthesis Oligo synthesis DNA sequencing. Amino acid analysis Mass Spec. If you want any more info. contact me and I will send our handbook which describes in detail what we do and how it is done. From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!ki.se!kidec.cmb.ki.se!cib From: cib@kidec.cmb.ki.se (Carlos Ibanez) Subject: address Message-ID: Organization: CMB, Karolinska Institutet Date: Mon, 12 Sep 1994 08:21:44 GMT Lines: 7 Hi! I am trying to get in touch with Dr. Eileen Jaffe through the e-mail. If you know her e-mail address, kindly send it to me. Thanks in advance cheers, From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!psgrain!nntp.cs.ubc.ca!news.UVic.CA!spruce.pfc.forestry.ca!PFC.Forestry.CA!AEKRAMODDOUL From: aekramoddoul@PFC.Forestry.CA (Ekramoddoullah, Abul Kalam M.) Subject: POSTDOCTROAL POSITION Message-ID: <1994Sep9.182918.16628@spruce.pfc.forestry.ca> Sender: news@spruce.pfc.forestry.ca Nntp-Posting-Host: pfc.pfc.forestry.ca Reply-To: aekramoddoul@PFC.Forestry.CA Organization: Forestry Canada (Pacific Forestry Centre) Date: Fri, 9 Sep 1994 18:29:18 GMT Lines: 15 Available April 1, 1995 for two years to investigate the anti-freeze properties of a recently discovered conifer protein by employing molecular biological techniques. Specifically, these studies will focus on the synthesis of cDNA, PCR cloning, sequencing and characterization of cDNA clones, purification of the expressed protein, assessment of its anti-freeze function by over expressing the protein in a transgenic plant such as tobacco. Experience in molecular biology is essential. Applicants should send curriculum vitae, description of research experience, and three letters of recommendation to: Abul K.M. Ekramoddoullah, Ph.D., Research Scientist, Canadian Forest Service, Pacific Forestry Centre, 506 West Brunside Road, Victoria, British Columbia, Canada, V8Z 1M5 EKRAMODDOULLAH, ABUL KALAM M. Title: Research Scientist Forestry Canada Phone: (604) 363-0600 Victoria, B.C. Internet: AEKRAMODDOUL@A1.PFC.Forestry.CA From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Andrew, Tel. +39-6-91093434" Newsgroups: bionet.molbio.proteins Subject: Articles on PNAs Date: 12 Sep 1994 17:38:04 +0100 Lines: 25 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <35205c$m5j@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk In reply to the message: > I was just wondering if anyone out there knew of any articles that >they could recommend to me on PNAs. For those who may know the subject [stuff deleted] Try: Mollegaard et al., PNAS (1994) 91, 3892-3895 Wittung et al., Nature (1994) 368, 561-563 Orum et al., Nucl. Acids Res. (1993) 21, 5332-5336 Peffer et al., PNAS (1993) 90, 10648-10652 This is a fairly new field, so it shouldn't be difficult to keep up with it at the moment. One interesting application seems to be in PCR-based diagnostics - apparently the current generation of PNAs don't go into cells very easily. Andrew =============================================================================== Andrew Wallace, IRBM P. Angeletti, Pomezia, Italia. Voice: +39-6-91093434 Fax: +39-6-91093225 Email: wallace@irbm.it "IRBM - The home of the Minibody" From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!ZOOL.UMD.EDU!GOODE From: GOODE@ZOOL.UMD.EDU ("Dr. Dennis Goode") Newsgroups: bionet.molbio.proteins Subject: Re: Recommendations for light level protein detection? Date: 12 Sep 1994 10:38:03 -0700 Organization: University of Maryland Zoology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <40C6D4663D@zool.umd.edu> NNTP-Posting-Host: net.bio.net Often the problem of lack of antibody staining of whole cells or fixed sections is one of antibody penetration, especially with aldehyde fixation. I'd try fixation with cold methanol at -20 C instead of aldehydes, or using a detergent such as 0.2% Triton x-100 after fixation in a low concentration (2% paraformaldehyde or 0.6% glutaraldehyde) of the aldehyde fixative. See Harlow and Lane: Antibodies A Laboratory Manual (CSH lab press). Hope this helps. Dennis Goode Goode@Zool.umd.edu From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!SNFMA1.IF.USP.BR!szeinfel From: szeinfel@SNFMA1.IF.USP.BR (Rafael Iosef Najmanovich Szeinfeld {S) Newsgroups: bionet.molbio.proteins Subject: Protein Isoeletric point calculation Date: 12 Sep 1994 09:17:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi All, I read a recent message about Proteins Isoeletric point (PIP) and the replayer said something about a progam that calculates PIP's so I'll like someone to say something about the method used for such calculations, what are the simplifications an so on. Thanks for your help. Rafael. *----------------------------------------------------- * Rafael Iosef Najmanovich Szeinfeld * Dept. Biochemistry -Chemistry Institute * Dept. Mathematical Physics -Physics Institute * University of Sao Paulo * E-MAIL : szeinfel@snfma1.if.usp.br * * MAIL: Depatartamento de Bioquimica - BLOCO 10 INF. * Universidade de Sao Paulo * Av. Prof. Lineu Prestes 748 * CEP 05508-900 Sao Paulo - SP - Brazil *------------------------------------------------------ From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!network.ucsd.edu!tpillay.extern.ucsd.edu!tpillay From: T. S. Pillay Newsgroups: bionet.molbio.proteins Subject: Re: Proteins over 400 KDa Date: 10 Sep 1994 22:00:14 GMT Organization: Endocrinology & Metabolism, UCSD Lines: 11 Distribution: world Message-ID: <34ta9e$sh9@network.ucsd.edu> References: <34lrov$42k@usenet.INS.CWRU.Edu> NNTP-Posting-Host: tpillay.extern.ucsd.edu X-UserAgent: Version 1.1.3 X-XXMessage-ID: X-XXDate: Sat, 10 Sep 94 15:00:02 GMT Subject: Proteins over 400 KDa From: slf8 Date: 8 Sep 1994 02:09:35 GMT In article <34lrov$42k@usenet.INS.CWRU.Edu> , slf8@po.cwru.edu writes: >Dear Protein Researchers, > Our lab is working with a nuclear protein which is over >400 KDa. etc Take a look at some of the papers on lipoproteins- I can't give you details off the top of my head but I recall a composite agarose-acrylamide gel being used for some lipoproteins. From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!agate!ames!purdue!haven.umd.edu!umd5.umd.edu!ram From: ram@mbisgi.umd.edu (Ram Samudrala) Newsgroups: bionet.molbio.proteins Subject: Protein Structure Prediction Competition Date: 13 Sep 1994 06:13:37 GMT Organization: The Centre for Advanced Research in Biotechnology Lines: 228 Message-ID: <353fuh$h1s@umd5.umd.edu> Reply-To: ram@elan1.carb.nist.gov NNTP-Posting-Host: indigo3.carb.nist.gov X-Newsreader: TIN [version 1.2 PL0] Please feel free to post this to any other newsgroups that are relevant. --Ram ------------------------------------------------------------------------ Meeting on the Critical assessment of Techniques for Protein Structure Prediction December 4 - 8 1994, Asilomar Conference Center, California, USA. Goal: Methods for obtaining information about protein structure from the amino acid sequence have apparently been advancing rapidly. But just what can these methods currently deliver? The goal of the workshop is to provide an indepth and objective assessment of our current abilities and inabilities in this area. To this end, prediction teams are predicting as much as possible about a set of soon to be known structures. Sessions at the meeting will be devoted to presentation of the results and comparison with experiment, and to the description of the methods used. Categories: Prediction methods are divided into three classes: 1) Comparative modeling: where there is a clear sequence relationship between the target structure and one or more known structures. 2) Fold recognition ('threading'): Testing a sequence for compatibility with a library of folds. 3) Ab initio structure prediction: deriving structures, approximate or otherwise, from sequence. Current Status of the Predictions: Details of a total of 25 target structures have so far been received from the experimentalists. Information about these can be found on the anonymous ftp site at iris4.carb.nist.gov. Not all of these structures will be predicted, but with approximately three months prediction time still to go, predictions have been received on eight of them. A total of 10 groups have already made at least one prediction, and a number of other groups have declared a serious intent to take part. The current list is as follows: Geoffrey Barton, Oxford University, UK Steve Benner, ETH, Zurich, Switzerland Tom Blundell, University of London, UK Steve Bryant, NLM, Bethesda, USA David Covell, NCI, Frederick, USA Andrew Coulson, University of Edinburgh, UK David Eisenberg, UCLA, USA Adam Godzik, Scripps, USA Tim Hubbard, MRC, Cambridge,UK Rod Hubbard, MSI, USA. Yo Matsuo, PERI, Japan David Mosenkis, Tripos, USA Chris Sander, EMBL, Germany Harold Scheraga, Cornell University, USA Manfred Sippl, University of Salzburg, Austria Janet Thornton, University of London, UK Gert Vriend, EMBL, Germany Irene Weber, Thomas Jefferson University, USA Peter Wolynes, University of Illinois, USA. Prediction Arrangements: Predictors say which category they intend to submit in, and declare a serious intent to submit. They are provided with the sequences and origins of the structures to be determined as they become available from the experimentalists, and are asked to stop work on a structure and submit their results with (hopefully) at least three weeks notice. Predictions are sent to the independent assessors. Thus there are no fixed time lines, each structure being available for a period dependent on the experimental situation. Those wishing to make predictions should contact: John Moult jmoult@iris4.carb.nist.gov tel: 301-738 6241 Fax: 301-738 6255 Criteria for Assessing the Predictions: A team of independent assessors will evaluate the predicted structures. As far as possible, assessments will be made objectively, using predefined criteria, supplemented where necessary by comments from the assessors. The primary assessors are: Michael James, University of Alberta, Canada (Comparative modeling) Shoshana Wodak, Free University of Brussels, Belgium (Threading) Fred Cohen, UCSF, USA (Ab initio methods). Publication: The proceedings of the meeting will be published, preferably in a refereed journal. Arrangements for publication are nearing completion. Meeting Program: December 4: Afternoon : Arrival and registration Evening : Dinner, Introductory lecture. December 5, 6, 7: One day devoted to each of the three categories of prediction: Comparative modeling, threading and ab initio methods. Each day as follows: Morning: : Overview by the primary assessor in that area. Lectures on the most successful and interesting predictions. Afternoon : Free time Poster session Informal session using workstations Evening : Round table discussion of the implications of the day's results December 8: Morning : Lectures on emerging techniques After lunch: End of meeting. Those wishing to attend the meeting should fill in and return the accompanying application form. Since space is limited applications will be reviewed by the organizing committee. Preference will be given to early applications. Organizing committee: John Moult CARB, University of Maryland Jan T. Pedersen CARB, University of Maryland Krzysztof Fidelis Lawrence Livermore National Laboratory. Rod Balhorn Lawrence Livermore National Laboratory. Richard Judson Sandia National Laboratory Walt Stevens National Institute of Standards and Technology ---------------------------- Cut Here ------------------- Meeting on the Critical assessment of Techniques for Protein Structure Prediction APPLICATION FORM This meeting has a limited attendence of approximately 100. If you wish to attend, please complete the following application. Name:_______________________________________ Affiliation:________________________________ Address:____________________________________ ____________________________________________ ____________________________________________ Phone:_________________ FAX:________________ Email:______________________________________ Status: Student ____ Post-doc ____ Academic Faculty ____ Industry ____ Other (please specify) _______________ Please give a brief description of your research interests: ___________________________________________________________ ___________________________________________________________ ___________________________________________________________ Some financial assistance (i.e. payment for lodging and meals and a waiver of the conference fee) will be available for students and post-docs. Please indicate if you wish to be considered for assistance: ________ Fees: Meeting: Academics $150 Others $300 Lodging and Meals: $250 (double occupancy) NOTE: Most rooms are double occupancy. A very limited number of single rooms will be available. Single room surcharge will be $100. Check here if you are interested in a single room ______ Send application, but no money to: Richard Judson Sandia National Laboratories MS-9214 Livermore, CA 94551-0969. email: rsjuds@ca.sandia.gov FAX: (510) 294-2234 Phone (510) 294-1438 Deadline for application: 1 October, 1994. Preference will be given to early respondents Decisions on attendence will be sent out by October 15 at the latest. -- Ram Samudrala ram@elan1.carb.nist.gov From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!MIS.FUHSCMS.EDU!muellerd From: muellerd@MIS.FUHSCMS.EDU ("David Mueller") Newsgroups: bionet.molbio.proteins Subject: affinity tags Date: 12 Sep 1994 13:55:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <199409122055.NAA09018@net.bio.net> NNTP-Posting-Host: net.bio.net Are there any tags that can be used on the amino end of a protein to aid in its purification - outside the His tag for Ni, the Cys tag for Hg and epitope tags? I need a third tag and fear that an epitope tag would not be aceptable because of the cost of the Ab and the difficulty in removing the Ab from the tag. Thanks in advance. David Mueller Dept. Biochemistry Chicago Medical School From owner-proteins@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!network.ucsd.edu!tpillay.extern.ucsd.edu!tpillay From: T. S. Pillay Newsgroups: bionet.molbio.proteins Subject: Re: glycosylated proteins Date: 10 Sep 1994 21:55:46 GMT Organization: Endocrinology & Metabolism, UCSD Lines: 10 Distribution: world Message-ID: <34ta12$sh9@network.ucsd.edu> References: <1994Aug29.144526.1@leif> NNTP-Posting-Host: tpillay.extern.ucsd.edu X-UserAgent: Version 1.1.3 X-XXMessage-ID: X-XXDate: Sat, 10 Sep 94 14:55:34 GMT Subject: glycosylated proteins From: jgill Date: 29 Aug 94 14:45:26 -0230 In article <1994Aug29.144526.1@leif> , jgill@kean.ucs.mun.ca writes: >Hello fellow netters: > > I need to ask you a question about protein isolation. In >particular glycosylated protein isolation etc. Try washing the pellet with acetone From owner-proteins@net.bio.net Mon Sep 12 23:00:00 1994 Path: biosci!agate!library.ucla.edu!csulb.edu!nic-nac.CSU.net!usc!howland.reston.ans.net!EU.net!sun4nl!news.nic.surfnet.nl!highway.LeidenUniv.nl!rulsfb.LeidenUniv.nl!SBTNFH From: sbtnfh@rulsfb.LeidenUniv.nl (Flip Hoedemaeker, CvF RUL/TNO, Leiden, The Netherlands) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Isoeletric point calculation Date: 13 Sep 1994 09:13:14 GMT Organization: Biology, Leiden University, The Netherlands Lines: 22 Distribution: world Message-ID: <353qfa$gq8@highway.LeidenUniv.nl> References: Reply-To: sbtnfh@rulsfb.LeidenUniv.nl NNTP-Posting-Host: rulsfb.leidenuniv.nl In article , szeinfel@SNFMA1.IF.USP.BR (Rafael Iosef Najmanovich Szeinfeld {S) writes: > Hi All, > I read a recent message about Proteins Isoeletric point (PIP) and the >replayer said something about a progam that calculates PIP's so I'll like >someone to say something about the method used for such calculations... Hi Rafael, I don't want to disappoint you, but pI calculation is very diificult. You have to take into account which amino acids are on the protein surface, becauce their pK's are important for the charge of the protein. I've asked Gert Vriend and the biocomputing group at the EMBL in Heidelberg just the same question about a year ago. He said that at the time they were very busy with a whole team to come up with a suitable algorithm, but that it could take quite some time still. I don't know how far they are now, you'll have to ask him (Gert.Vriend@EMBL-Heidelberg.de) Still you would need the 3D coordinates of your protein. With other methods you'll end up with a pI, but it won't be very reliable. Flip From owner-proteins@net.bio.net Mon Sep 12 23:00:00 1994 Path: biosci!agate!library.ucla.edu!csulb.edu!nic-nac.CSU.net!usc!cs.utexas.edu!swrinde!emory!usenet From: clarsen@bimcore.emory.edu (Chris Larsen) Newsgroups: bionet.molbio.proteins Subject: Re: Circular dichroism Date: 13 Sep 1994 13:57:47 GMT Organization: Biomolecular Computing Resource, Emory University Lines: 12 Distribution: world Message-ID: <354b4r$rbr@emory.mathcs.emory.edu> References: <34k70d$c6o@ra.ibr.cs.tu-bs.de> Reply-To: clarsen@bimcore.emory.edu NNTP-Posting-Host: bimcore.cc.emory.edu Wolfram: You can measure helix content of your protein, and its binding to the substrate, if there is any "pertubation spectra". Check out Curtis Johnson on a medline search. You can also measure for disappearance of secondary structure by denatuaration with heat, guanidine or urea. Chris From owner-proteins@net.bio.net Mon Sep 12 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!uunet!newsflash.concordia.ca!nstn.ns.ca!nstn.ns.ca!nntp-user From: ybou@fox.nstn.ns.ca (Yvon Boudreau) Newsgroups: bionet.molbio.proteins Subject: Important Question About AMINO ACIDS ????? Date: 13 Sep 1994 23:05:53 -0300 Organization: NSTN Windows User Lines: 7 Sender: news@nstn.ns.ca Message-ID: <355lq1$n9c@owl.nstn.ns.ca> NNTP-Posting-Host: owl.nstn.ns.ca X-Newsreader: WinVN version 0.82 1.) Why are the amino acids of the "alpha" type? 2.) Why are they of the "levo" type? These questions were given to me in my grade 12 biology class. Help would be very much appreciated! Thank - you Marc Boudreau. From owner-proteins@net.bio.net Mon Sep 12 23:00:00 1994 Path: biosci!agate!library.ucla.edu!csulb.edu!nic-nac.CSU.net!usc!howland.reston.ans.net!swrinde!cs.utexas.edu!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!genmac14.biochem.mpg.de!user From: spang@vms.biochem.mpg.de (Anne Spang) Newsgroups: bionet.molbio.proteins Subject: Re: affinity tags Date: 13 Sep 1994 16:20:35 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 13 Distribution: world Message-ID: References: <199409122055.NAA09018@net.bio.net> NNTP-Posting-Host: genmac14.biochem.mpg.de Hi David! You may fuse your protein directly to protein A. This makes it very easy to purify! I think you can get vectors from Dr.M. Uhlén Karolinska Institute S-10401 Stockholm SWEDEN Hope this helps! Anne From owner-proteins@net.bio.net Mon Sep 12 23:00:00 1994 Path: biosci!UQTR.UQuebec.ca!Abdelwahab_Ahmed From: Abdelwahab_Ahmed@UQTR.UQuebec.ca Newsgroups: bionet.molbio.proteins Subject: help-protein Date: 13 Sep 1994 19:16:33 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409140215.AA46712@neptune.UQTR.UQuebec.ca> NNTP-Posting-Host: net.bio.net Hi netters! Could someone please post a protocol for various estimations: RNA, DNA and protein on algae cells ? Thanks for any help in advance. From owner-proteins@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!news.funet.fi!news.csc.fi!news.helsinki.fi!ktl.fi!aairaksinen From: aairaksinen@ktl.fi Newsgroups: bionet.molbio.proteins,bionet.molec-model Subject: Recognizing structural conservation Message-ID: <1994Sep14.161812.1843@ktl.fi> Date: 14 Sep 94 16:18:12 EET Organization: National Public Health Institute, Finland Lines: 5 Xref: biosci bionet.molbio.proteins:2668 bionet.molec-model:101 Is there / is anyone aware of a program that can recognize structurally conserved regions in proteins? The input should be something like two PDB files. Thanks, A From owner-proteins@net.bio.net Tue Sep 13 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!rutgers!princeton!berthaw.princeton.edu!micky From: micky@berthaw.princeton.edu (Michael West) Subject: Secondary Structure Message-ID: <1994Sep13.153250.17495@Princeton.EDU> Originator: news@nimaster Sender: news@Princeton.EDU (USENET News System) Nntp-Posting-Host: berthaw.princeton.edu Organization: Princeton University Date: Tue, 13 Sep 1994 15:32:50 GMT Lines: 7 I am looking for a computer program which will determine the secondary structure of a protein from the pdb file. I have been told that the most popular is by Kabsch & Sander. Does anyone have any insight or suggestions as to where I may get further info. on this subject. Thanks. Michael micky@berthaw.princeton.edu From owner-proteins@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!JASON.UTHCT.EDU!SHAUN From: SHAUN@JASON.UTHCT.EDU ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: Re: Secondary Structure Date: 14 Sep 1994 08:01:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <940914100006.c750@jason.uthct.edu> NNTP-Posting-Host: net.bio.net Send e-mail to predictprotein@embl-heidelberg.de with the message HELP. It's a pretty easy server to use. Cheers, Shaun From owner-proteins@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!JASON.UTHCT.EDU!SHAUN From: SHAUN@JASON.UTHCT.EDU ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: Re: Important Question About AMINO ACIDS ????? Date: 14 Sep 1994 07:21:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <940914092051.c750@jason.uthct.edu> NNTP-Posting-Host: net.bio.net ybou@fox.nstn.ns.ca (Yvon Boudreau) on 13 Sep 1994 writes: > > 1.) Why are the amino acids of the "alpha" type? > 2.) Why are they of the "levo" type? > > These questions were given to me in my grade 12 biology class. > Help would be very much appreciated! > My reading of the scientific literature suggests that noone really knows the answer to these questions. Probably the most important thing for a grade 12 biology class to know is that these observations are nearly inviolate throughout all known organisms/proteins in nature. A guess/hypothesis concerning (1) is that beta, gamma, etc. amino acids would impart too much backbone flexibility and thus degrees of freedom to a folding polypeptide chain. In all likelihood non-alpha amino acids in peptide linkage would not fold. As for (2), this has been covered in an extensive thread on Methods-and-Reagents a few months back; check the archives, preferably by a Gopher search. Briefly, polypeptides of L-amino acids form structures with right-handed helices, right-handed twists to beta strands, left-handed twist to beta sheets, etc. Polypeptides of D-amino acids form the same structures but of the _opposite_ handedness. I hope this helps you a bit. Best regards, =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet address: shaun@jason.uthct.edu = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!bcm!mbcr.bcm.tmc.edu!th035681 From: th035681@mbcr.bcm.tmc.edu (Timothy R. Hughes) Newsgroups: bionet.molbio.proteins Subject: Protein degradation Date: 14 Sep 1994 20:56:31 GMT Organization: Baylor College of Medicine, Houston, Tx Lines: 16 Distribution: world Message-ID: <357o1v$229@gazette.bcm.tmc.edu> NNTP-Posting-Host: mbcr.bcm.tmc.edu I'm a grad student working on my qualifying exam. Right now I'm in the first phase, writing one-page research proposal abstracts. One of them is going to involve protein degradation. I would be grateful if someone who is an expert or has some experience in the field would be willing to review my abstract. It involves cellular degradation pathway(s) of abnormal/mutant proteins. There are too many papers to read on the topic overall and I want to make sure what I'm proposing isn't foolhardy and hasn't been disproven/done already. I can't seek help from faculty here at Baylor but outside is OK. Thank you, Tim Hughes th035681@mbcr.bcm.tmc.edu From owner-proteins@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!GIBBS.OIT.UNC.EDU!vaisman From: vaisman@GIBBS.OIT.UNC.EDU (Iosif Vaisman) Newsgroups: bionet.molbio.proteins Subject: Molecular Modeling Conference 1994 Date: 14 Sep 1994 10:19:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 112 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Molecular Modeling Conference 1994 Fundamentals and Applications for the Pharmaceutical Industry 2-4 October 1994 Brunswick Hilton and Towers, East Brunswick, New Jersey Molecular Modeling Conference 1994 is organized by Advanstar Communications, the publishers of Pharmaceutical Technology, BioPharm, LC-GC, and Spectroscopy magazines. * A limited number of discounted registrations are available for * full-time university students and faculty. Conference Moderators: Alexander MacKerell, Assistant Professor, Department of Pharmaceutical Sciences, University of Maryland at Baltimore Alexander Tropsha, Assistant Professor, Director, Laboratory for Molecular Modeling, University of North Carolina at Chapel Hill Herschel J.R. Weintraub, Assistant Director, Medicinal Chemistry, R.W. Johnson Pharmaceutical Research Institute Sunday, 2 October 1994 Afternoon Session: Optional Introductory Workshop - Molecular Modeling Basics Instructors: Warren J. Hehre, Wavefunction, Inc., and University of California, Irvine Alexander Tropsha (Session Organizer), University of North Carolina, Chapel Hill Herschel J.R. Weintraub, R.W. Johnson Pharmaceutical Research Institute Monday, 3 October 1994 Plenary Lecture: Molecular Modeling - For Better, For Worse. For Richer, For Poorer. Peter Goodford, University of Oxford, UK On the Effect of Long-range Interactions on Protein Structure, Specificity, & Ligand Binding Free Energies Arnie Hagler, Biosym Technologies, Inc. Modeling Selectivity in Organic Reactions Warren J. Hehre, Wavefunction, Inc. and University of California, Irvine General Representation and Solution of the QSAR Problem Based Upon Tensor Analysis A. J. Hopfinger, University of Illinois at Chicago Rapid Prediction of Binding Energies Using Continuum Methods Barry Honig, Columbia University Pharmacophore Determination: The Critical Decision in Ligand-Based Design Richard D. Cramer, Tripos, Inc. Overview of 3D-Searching: A Powerful Technique for Computer-Assisted Molecular Design Robert S. Pearlman, University of Texas, Austin Tuesday, 4 October 1994 X-ray Crystallographic Analysis of Macromolecular Structures Wayne A. Hendrickson, Columbia University Free Energy Modeling Monte Pettitt, University of Houston Multidimensional Heteronuclear NMR of Proteins Angela M. Gronenborn, NIDDK, National Institutes of Health Models of G Protein-Linked Receptors: How Do We Get Them and What Can We Do With Them? Charles Hutchins, Abbott Laboratories Comparative Homology Modeling: What Is It Good For and How Well Does It Work? Jonathan Greer, Abbott Laboratories De Novo Predications of Quaternary Protein Structure: Applications to Coiled Coils Jeffrey Skolnick, Scripps Research Institute Computer Assisted Ligand Design I.D. Kuntz, University of California, San Francisco Retrospective and Prospective Successes of Molecular Modeling in the Pharmaceutical Industry Peter Gund, Molecular Simulations Inc. Registration Information To register or to receive a copy of the conference program brochure, please call the Molecular Modeling Conference Registrar at (800) 343-3423 or (503) 343-1200. Fees for Molecular Modeling Conference include all course materials, a copy of the conference proceedings, admission to the Technology Demonstration Room, the Optional Introductory Workshop, and refreshment breaks. Fees Regular (postmarked after 19 August 1994): $645.00 On-Site: $695.00 For more information, contact: Molecular Modeling Conference 1994 859 Willamette Street Eugene, OR 97401-6806 Phone: (800) 343-3423 or (503) 343-1200 Fax: (503) 343-7024 From owner-proteins@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!rutgers!netnews.upenn.edu!news.cc.swarthmore.edu!psuvax1!news.pop.psu.edu!news.cac.psu.edu!howland.reston.ans.net!swiss.ans.net!newstf01.cr1.aol.com!search01.news.aol.com!not-for-mail From: jfrank777@aol.com (JFrank777) Newsgroups: bionet.molbio.proteins Subject: Re: Stable Isotope Labeled Biochemicals Date: 15 Sep 1994 01:50:03 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 11 Sender: news@search01.news.aol.com Message-ID: <358nab$qe@search01.news.aol.com> References: NNTP-Posting-Host: search01.news.aol.com In article , lisa@scripps.edu (Lisa Bibbs) writes: Here are four more suppliers of stable isotopes I've found: Aldrich Chemical, Milwaukee, WI 800-558-9160 Isotec, Miamisburg, OH, 513-859-1808 Martek, Columbia, MD, 410-730-0081 ICON Services, Summit, NJ 908-273-0440 From owner-proteins@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!scripps.edu!NewsWatcher!user From: lisa@scripps.edu (Lisa Bibbs) Newsgroups: bionet.molbio.proteins Subject: Re: Stable Isotope Labeled Biochemicals Followup-To: bionet.molbio.proteins Date: 14 Sep 1994 16:07:11 GMT Organization: TSRI Core Facility Lines: 22 Message-ID: References: <34tgjh$ph6@search01.news.aol.com> NNTP-Posting-Host: pbfnuts.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > Hello. Thanks for everyone's assistance in helping me find a source for > stable isotope labeled biochemicals and growth media. Below is a summary > of the (useful?) sources I've found: > > MicroForest, Inc., San Diego, CA 800-806-4276 > CDN Isotopes, Vaudreuil, Que, Canada 800-565-4696 > Cambridge Isotope Labs, Andover MA 508-749-8000 > Omicron, South Bend, IN, 219-631-7807 > > Have a good day. I notice from bionet.jobs that you work for MicroForest, Inc. ... . . . . . . . . From owner-proteins@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!JASON.UTHCT.EDU!SHAUN From: SHAUN@JASON.UTHCT.EDU ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: Re: Secondary Structure Date: 14 Sep 1994 08:06:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <940914100521.c750@jason.uthct.edu> NNTP-Posting-Host: net.bio.net Send e-mail to predictprotein@embl-heidelberg.de with the message HELP. It's a pretty easy server to use. Cheers, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet address: shaun@jason.uthct.edu = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Tue Sep 13 23:00:00 1994 Path: biosci!MOLBIO.CBS.UMN.EDU!nora From: nora@MOLBIO.CBS.UMN.EDU ("Nora Vig") Newsgroups: bionet.molbio.proteins Subject: dimerization Date: 14 Sep 1994 09:34:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <9409141632.AA10887@molbio.cbs.umn.edu> NNTP-Posting-Host: net.bio.net A possible way to estimate the dimerization of a protein, if cross-linking is unsuccessful, would be to separate a protein mixture on a native gel, using an appropriate acrylamide gradient (e.g. 3-20% for a wide range of sizes). The gel can be run to equilibrium at 200 V for about 18 hr at 4oC. It is best, of course, if you have some way to identify your protein. Gel migration is not the final word on protein size or oligomerization, but it is a reasonable first step and might indicate if there is a difference between the wild-type and mutant proteins. Good luck Nora Plesofsky-Vig Department of Plant Biology University of Minnesota St. Paul, Minn. 55108 nora@molbio.cbs.umn.edu From owner-proteins@net.bio.net Wed Sep 14 23:00:00 1994 Path: biosci!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!athena.mit.edu!dresnick From: dresnick@athena.mit.edu (David I Resnick) Newsgroups: bionet.molbio.proteins Subject: Renaturation of proteins from 8M Urea - references? Date: 15 Sep 1994 17:30:41 GMT Organization: Massachusetts Institute of Technology Lines: 13 Distribution: world Message-ID: NNTP-Posting-Host: m66-080-9.mit.edu Hi, I'm expressing a ~130 amino acid protein fragment in E. coli. After solubilization in 8 M Urea, I purify it using a His6 tag. I then want to get rid of the urea (and pray that it will fold). Everything I've tried so far (not many things, but a few) has resulted in precipitation. Anyone out there know of a comprehensive reference for this sort of thing? Any ideas??? Thanks! -- David Resnick dresnick@athena.mit.edu From owner-proteins@net.bio.net Wed Sep 14 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!sun4nl!news.nic.surfnet.nl!highway.LeidenUniv.nl!rulsfb.LeidenUniv.nl!SBTNFH From: sbtnfh@rulsfb.LeidenUniv.nl (Flip Hoedemaeker, CvF RUL/TNO, Leiden, The Netherlands) Newsgroups: bionet.molbio.proteins Subject: Re: A280 vs. protein assay? Date: 15 Sep 1994 15:04:04 GMT Organization: Biology, Leiden University, The Netherlands Lines: 10 Message-ID: <359np4$8qb@highway.LeidenUniv.nl> References: Reply-To: sbtnfh@rulsfb.LeidenUniv.nl NNTP-Posting-Host: rulsfb.leidenuniv.nl In article , tom@radical.chm.jhu.edu (Tom Tullius) writes: >Could dimerization somehow be "quenching" the >absorbance at 280 nm? Ideas or experience would be appreciated. > >-- Only aromatic amino acids absorb at 280. Do you know if there are some on the dimer interface? That could account for the quenching! I don't know if this has been seen before, but it could be an explanation. Flip From owner-proteins@net.bio.net Wed Sep 14 23:00:00 1994 Path: biosci!rutgers!netnews.upenn.edu!news.amherst.edu!news.mtholyoke.edu!news.umass.edu!news2.near.net!das-news.harvard.edu!husc-news.harvard.edu!lipid!robison Newsgroups: bionet.molbio.proteins Subject: Re: Protein Isoeletric point calculation Message-ID: <1994Sep15.185922.34776@hulaw1.harvard.edu> From: robison@lipid.harvard.edu (Keith Robison) Date: 15 Sep 94 18:59:22 EDT References: <353qfa$gq8@highway.LeidenUniv.nl> Distribution: world Nntp-Posting-Host: lipid.harvard.edu X-Newsreader: TIN [version 1.2 PL2] Lines: 36 Flip Hoedemaeker, CvF RUL/TNO, Leiden, The Netherlands (sbtnfh@rul