From owner-proteins@net.bio.net Fri Apr 01 23:00:00 1994 Newsgroups: bionet.molbio.proteins From: Duncan@genesys.demon.co.uk (Duncan Clark) Path: biosci!agate!howland.reston.ans.net!pipex!uknet!demon!genesys.demon.co.uk!Duncan Subject: Re: protein concentration Distribution: world References: Organization: GeneSys Ltd. Reply-To: Duncan@genesys.demon.co.uk X-Newsreader: Simple NEWS 1.90 (ka9q DIS 1.21) Lines: 9 Date: Sat, 2 Apr 1994 13:11:39 +0000 Message-ID: <765292299snz@genesys.demon.co.uk> Sender: usenet@demon.co.uk Although I am starting with volumes of a couple of hundred ml I concentrate using dialysis tubing against solid PEG6000. I can get down to a ml or so. Duncan -- ----------------------------------------------------------------------------- Duncan Clark | Internet: duncan@genesys.demon.co.uk GeneSys Ltd. | Compuserve: 100015.1406@compuserve.com ----------------------------------------------------------------------------- From owner-proteins@net.bio.net Sat Apr 02 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!pipex!sunic!EU.net!sun4nl!tudelft.nl!draconis.cp.tn.tudelft.nl!flohil From: flohil@cp.tn.tudelft.nl (Jaap Flohil) Subject: convergence 99% secondary structure predictions Message-ID: Summary: Experiment with different neural networks based on Qian and Sejnowski Keywords: neural networks protein secondary structure Lines: 16 Sender: news@news.tudelft.nl (UseNet News System) Nntp-Posting-Host: scorpius.cp.tn.tudelft.nl Organization: Delft University of Technology Date: Sun, 3 Apr 1994 18:59:51 GMT Hi, To verify the possibility of handling a large data set for the Intel Neurochip system (80170NX ETANN) I used a data set for secondary structure prediction of proteins from Qian and Sejnowski. After some manipulations with the IO-files and different networks I reached a convergence of 99%, both on the Test set and Training set. I 'm looking for somebody who's interested in this result and can help me with further investigation (I'm physicist, not a biologist) To prove generalization I need an extended dataset, which contains linear sequence of amino acids. Who can help ? From owner-proteins@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!agate!ucbvax!dog.ee.lbl.gov!ihnp4.ucsd.edu!galaxy.ucr.edu!galaxy.ucr.edu!not-for-mail From: joyce@galaxy.ucr.edu (joyce setsuda) Newsgroups: bionet.molbio.proteins Subject: Chitinases Message-ID: <2npmvs$rbc@galaxy.ucr.edu> Date: 4 Apr 94 18:41:00 GMT Organization: University of California, Riverside Lines: 17 NNTP-Posting-Host: galaxy.ucr.edu Hi, Does anyone out there work on plant chitinases? I'm trying to clone a protein that seems to have a high degree of homology to a chitinase and I can't seem to get any plasmid to replicate. All of the controls work so that I believe it is the insert and not the cells or the vector I'm working with. It makes sense that the cells lyse if it is a chitinase and I have a leaky promoter. All of the papers I've read don't mention this problem. This is a cDNA clone in Lambda zap II. Thanks for any ideas. Joyce From owner-proteins@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!SPEEDY.COACADE.UV.MX!evargas From: evargas@SPEEDY.COACADE.UV.MX (Enrique Vargas) Newsgroups: bionet.molbio.proteins Subject: India Congress Date: 4 Apr 1994 10:16:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404041723.AA02302@speedy.speedy.coacade.uv.mx> NNTP-Posting-Host: net.bio.net Hi! Can somebody tell me the (Internet) E-mail of the Secretary General of the XVI IUBMB Congress at India? Your help will be greatly appreciated. ******************************************************************************* * Enrique Vargas-Madrazo * evargas@speedy.coacade.uv.mx * ******************************************************************************* * Laboratorio de Biologia Molecular * Phone number: (28)125757 * * e Inmunologia Teorica. * FAX number: (28)125757 * ******************************************************************************* * Instituto de Investigaciones Biologicas * Universidad Veracruzana * * * Xalapa, Veracruz; Mexico. * ******************************************************************************* * POSTAL ADRESS: * * Juan de la Barrera 54, * * Col. Electricistas, C.P. 91000 * * Xalapa, Veracruz; Mexico. * *************************************** From owner-proteins@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!SPEEDY.COACADE.UV.MX!evargas From: evargas@SPEEDY.COACADE.UV.MX (Enrique Vargas) Newsgroups: bionet.molbio.proteins Subject: India Congress Date: 4 Apr 1994 10:03:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404041711.AA02179@speedy.speedy.coacade.uv.mx> NNTP-Posting-Host: net.bio.net Hi! Can somebody tell me the (Internet) E-mail of the Secretary General of the XVI IUBMB Congress at India? Your help will be greatly appreciated. ******************************************************************************* * Enrique Vargas-Madrazo * evargas@speedy.coacade.uv.mx * ******************************************************************************* * Laboratorio de Biologia Molecular * Phone number: (28)125757 * * e Inmunologia Teorica. * FAX number: (28)125757 * ******************************************************************************* * Instituto de Investigaciones Biologicas * Universidad Veracruzana * * * Xalapa, Veracruz; Mexico. * ******************************************************************************* * POSTAL ADRESS: * * Juan de la Barrera 54, * * Col. Electricistas, C.P. 91000 * * Xalapa, Veracruz; Mexico. * *************************************** From owner-proteins@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!agate!usenet.ins.cwru.edu!cleveland.Freenet.Edu!ep163 From: ep163@cleveland.Freenet.Edu (Patrick D Moss) Newsgroups: bionet.molbio.proteins Subject: TEST Date: 5 Apr 1994 06:06:50 GMT Organization: Case Western Reserve University, Cleveland, Ohio (USA) Lines: 2 Message-ID: <2nqv5q$bmo@usenet.INS.CWRU.Edu> NNTP-Posting-Host: kanga.ins.cwru.edu TEST TEST From owner-proteins@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!agate!ames!elroy.jpl.nasa.gov!swrinde!gatech!usenet.ufl.edu!oak.circa.ufl.edu!KDLST1 From: kdlst1@oak.circa.ufl.edu Newsgroups: bionet.molbio.proteins Subject: Cambridge PDB FTP address? Date: 5 Apr 1994 01:25:21 GMT Organization: University of Florida - CIRCA Lines: 12 Message-ID: <2nqem1INNhgp@no-names.nerdc.ufl.edu> Reply-To: kdlst1@oak.circa.ufl.edu NNTP-Posting-Host: oak.circa.ufl.edu Hi there. I recently became aware of the existence of protein data bases. I have an FTP address for Brookhaven's (pdb.pdb.bnl.gov), and understand there is another in Cambridge. Would anyone happen to know what that FTP address is? Addresses for any other protein data banks that I'm not aware of would also be great. Thanks! Keith Lobel University of Florida KDLST1@ufcc.ufl.edu From owner-proteins@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!news.intercon.com!uhog.mit.edu!news.mtholyoke.edu!news.smith.edu!science.smith.edu!sscordil From: sscordil@science.smith.edu (Stylianos P. Scordilis) Newsgroups: bionet.molbio.proteins Subject: ADP-ribosylation of Proteins Date: Mon, 4 Apr 1994 13:39:40 Organization: SMith College Lines: 12 Message-ID: NNTP-Posting-Host: 131.229.114.2 X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] We are interested in determining whether some proteins we have are ADP-ribosylated. Does anyone have or know of an antibody to ADP-ribose. Initially, only enough would be needed to run some Western blots. Please reply to me directly at Scordilis@smith.edu. Thank you. Stylianos P. Scordilis Dept. Biol. Sci. Smith College Northampton, MA 01063 From owner-proteins@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!EU.net!chsun!elna.ethz.ch!usenet From: tan@aeolus.vmsmail.ethz.ch Newsgroups: bionet.molbio.proteins Subject: Re: Dynamic Light Scattering of Proteins Date: 4 Apr 1994 12:08:17 GMT Organization: ETH-Honggerberg (Swiss Federal Institute of Technology) Lines: 40 Distribution: world Message-ID: <2novvh$cm@elna.ethz.ch> References: <2mvfng$hve@server.st.usm.edu> Reply-To: tan@aeolus.vmsmail.ethz.ch NNTP-Posting-Host: smac.ethz.ch In article <2mvfng$hve@server.st.usm.edu> richard@whale.st.usm.edu (Michael Frederi Richardson) writes: > Is there anyone available who can provide me with some information >about the use of dynamic light scattering of proteins in solution? > >(stuff deleted) > > Michael Richardson > richard@whale.st.usm.edu > and in a followup Andrew wrote: >There is a US company called Wyatt Instruments (sorry, don't know their >address or phone #) which makes a laser-based device which can measure the >dynamic radius of macromolecules in solution. > >(stuff deleted) > >2) Despite obtaining some interesting-looking data, we had no idea how to > interpret it and, it seemed, neither did Wyatt's rep. They appeared to be > aiming the instrument at the industrial polymer chemistry market and > apparently didn't have much experience on handling protein data. > >(more stuff deleted)> Another company which manufactures a device for dynamic light scattering, but which is dedicated to the analysis of biological macromolecules is Protein Solutions Inc (1500 Avon St Extended, Charlotteville, VA 22902, tel: 804-979-2319). Song Tan Institute for Molecular Biology and Biophysics ETH-Honggerberg (Swiss Federal Institute of Technology) 8093 Zurich, Switzerland email: tan@aeolus.vmsmail.ethz.ch From owner-proteins@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!agate!doc.ic.ac.uk!lyra.csx.cam.ac.uk!pipex!uknet!EU.net!chsun!elna.ethz.ch!usenet From: tan@aeolus.vmsmail.ethz.ch Newsgroups: bionet.molbio.proteins Subject: Re: Determining Fab CONCENTRATION accurately Followup-To: bionet.molbio.proteins Date: 4 Apr 1994 11:43:51 GMT Organization: ETH-Honggerberg (Swiss Federal Institute of Technology) Lines: 51 Distribution: world Message-ID: <2nouhn$cm@elna.ethz.ch> References: <01HAICY6CW1CCIQSIE@WISTB.WISTAR.UPENN.EDU> Reply-To: tan@aeolus.vmsmail.ethz.ch NNTP-Posting-Host: smac.ethz.ch In article <01HAICY6CW1CCIQSIE@WISTB.WISTAR.UPENN.EDU> WILLARD@MVAX.WISTAR.UPENN.EDU writes: >I have generated Fab fragments using Papain cleavage of three different >antibodies: one is an IgG2b and the other two are IgG1's. Does anyone >know of an assay to accurately determine the concentration of the Fab >fragment? Note that this is the only product in solution (I purifies the Fab >using protein A and FPLC). > >(I mean, purifieD) > >I have been using an equation I got out of a crystallography text based on the >amino acid sequence and the A280 reading (you count Trp and Tyr residues and, >based on A280, come up with a mg/ml concentration). But I don't know how >accurate this is. > >Can someone tell me of a better way, or is what I'm doing ok? Also, is using >an IgG standard (such as from Biorad) and doing a standard curve going to >be accurate? I mean, since the standard is a whole antibody and I'm using >Fab, is the use of IgG as a standard really comparable? > >Any suggestions would be appreciated. > >Rob Willard >The Wistar Institute of Anatomy and Biology >The University of Pennsylvania >Dept. of Chemistry > Dear Rob, I think what you're doing is o.k.. I use the method of Gill and von Hippel (Anal. Biochem., vol 182, pp 319-326, 1989), which is essentially what you described. The Gill and von Hippel paper presents comparisons of calculated vs measured extinction coefficients to justify the approach and their data does look convincing. If you really want to be sure, you could have your sample amino acid analyzed to determine exactly how much protein is present and then work out the extinction coefficient from that. In the couple of times I've done this, I got back very similar numbers to what the Gill and von Hippel formula came up with. One last note: if you have access to GCG, the command PEPTIDESORT will calculate the molar extinction coefficent based on the Gill and von Hippel formula. Hope this helps. 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 Mon Apr 04 23:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!ihnp4.ucsd.edu!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!ee.und.ac.za!ucthpx!uctvax.uct.ac.za!schren13 From: schren13@uctvax.uct.ac.za Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Protease Inhibitors Message-ID: <1994Mar30.121045.206379@uctvax.uct.ac.za> Date: 30 Mar 94 12:10:45 +0200 Organization: University of Cape Town Lines: 11 Xref: biosci bionet.molbio.methds-reagnts:13006 bionet.molbio.proteins:1686 ANY ADVICE? I am working on a system in which a membrane-bound protein is solubilized by a membrane protease. In order to classify the protease, I treated it with various protease inhibitors. To my surprise I repeatedly get an increased protease activity when the serine-protease inhibitor "3,4-dichloroisocoumarin" is used. Is there anyone out there who has an explanation? Please send any replies by e-mail to rscholle@physio.uct.ac.za. Thanks a lot. From owner-proteins@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!SHIVA.PSU.EDU!zauhar From: zauhar@SHIVA.PSU.EDU (Dr. Randy Zauhar) Newsgroups: bionet.molbio.proteins Subject: Re: convergence 99% secondary structure predictions Date: 5 Apr 1994 12:05:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404051906.AA04067@shiva.psu.edu> NNTP-Posting-Host: net.bio.net > > >>>>> "Jaap" == Jaap Flohil writes: > In article flohil@cp.tn.tudelft.nl (Jaap Flohil) writes: > > Jaap> I used a data set for secondary structure prediction of > Jaap> proteins from Qian and Sejnowski. After some manipulations > Jaap> with the IO-files and different networks I reached a > Jaap> convergence of 99%, both on the Test set and Training set. > > If you have really achieved 99% accuracy in the prediction of secondary > structure it would be a spectacular result that would attract the interest What does "convergence" mean in this context? In Qian and Sejnowski's paper they show that they can achieve spectacular results within a given training set by using a large enough number of cell bodies, but it only demonstrates that there are enough degrees of freedom in the network to allow it "memorize" lots of details of the training set. If my "memory" serves, they actually got _poorer_ results with a large hidden layer when they tried the network out on a database unrelated to the training set, then they got with a simple perceptron model (no hidden layer). Randy ///////////////////////////////////////////////////////////////////////// \\ Randy J. Zauhar, PhD | E-mail: zauhar@shiva.psu.edu // \\ Center for Computational Biology | Phone: (814) 863-3650 // \\ Penn State University | 865-1098 (after 5)// ///////////////////////////////////////////////////////////////////////// From owner-proteins@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!scripps.edu!bashford From: bashford@griffy.scripps.edu (Don &) Newsgroups: bionet.molbio.proteins Subject: Re: convergence 99% secondary structure predictions Date: 04 Apr 1994 08:13:16 GMT Organization: The Scripps Research Institute, La Jolla, CA, USA Lines: 33 Distribution: world Message-ID: References: NNTP-Posting-Host: griffy.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In-reply-to: flohil@cp.tn.tudelft.nl's message of Sun, 3 Apr 1994 18:59:51 GMT >>>>> "Jaap" == Jaap Flohil writes: In article flohil@cp.tn.tudelft.nl (Jaap Flohil) writes: Jaap> I used a data set for secondary structure prediction of Jaap> proteins from Qian and Sejnowski. After some manipulations Jaap> with the IO-files and different networks I reached a Jaap> convergence of 99%, both on the Test set and Training set. If you have really achieved 99% accuracy in the prediction of secondary structure it would be a spectacular result that would attract the interest of almost everyone who studies proteins. But many of us suspect that it is impossible to reach such levels without also predicting a good deal about tertiary structure at the same time. So if you are going to make such a claim, you had better be sure you are right and you should be prepared for intense skepticism. Regarding the limitations of the neural net approach and the artifacts that are possible, I suggest you look at a paper by Howard Holley (Holly?) et al. from PNAS of 1988 or 1989. (Sorry I don't have the reference on hand here at home.) Jaap> To prove generalization I need an extended dataset, which Jaap> contains linear sequence of amino acids. Who can help? There are periodic postings on the bionet.announce group about access to databanks of protein structure (PDB) and sequence (PIR SWISSPROT) databases. Perhaps someone else knows of similar data in a format more convenient for your purposes. Donald Bashford Department of Molecular Biology The Scripps Research Institute bashford@scripps.edu From owner-proteins@net.bio.net Mon Apr 04 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!ames!elroy.jpl.nasa.gov!swrinde!gatech!newsxfer.itd.umich.edu!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: Re: Protein purification? Message-ID: <1994Apr5.214043.7334@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) References: Date: Tue, 5 Apr 1994 21:40:43 GMT Lines: 55 In article , wcg8744@uxa.cso.uiuc.edu (W. Chen) writes: > >Hi, everyone, > >My friend is trying to purify a protein from plant leaf by the following >procedure: The plant proteins were extracted by grinding the leaf in the >phosphate buffer (pH 5.8). The crude proteins were then applied to a >DEAE-Sephacyel column equilibrated with the phosphate buffer, and the >column was washed with the phosphate buffer but no proteins were eluted >out. It seemed that all of the proteins bound to the column. So the bound >proteins were eluted with a 0-1 M NaCl gradient in the phosphate buffer. It >was found that the total proteins eluted in a single sharp peak at an NaCl >concentration of 0.4 M. The fractions of the peak were pooled and subjected >to SDS-PAGE analysis and got the same pattern as the crude proteins before >DEAE-sephacyel chromatography. We don't undersdand why the proteins were >not separated by the above procedure? If you have any suggestions, please >respond me at this account. Thanks. > > >W. Chen What kind of a plant is he working with? I assumed that the crude extract he obtained with phosphate buffer had some proteins. How many proteins he observed on SDS-PAGE? (probably not too many?). Thus, he might have partially isolated those proteins (e.g. extrinsic photosystem II, 23 kDa) which are easily extractable. To get proteins out of foliage is very problematic. The major problem is the phenolic substances. I had a spent over a year just to develop a suitable method to extract and separate proteins from conifer foliage. In this procedure we could resolve upto 50 proteins by SDS-PAGE and about 800 proteins in 2-D gel electrophorsis. The method (not applicable, if you want to maintain biolgical activity) is outlined in the following two references: 1. Ekramoddoullah, A.K.M. (1991) Analysis of proteins of western white pine (Pinus monticola) needles. In: Y. Hiratsuka, J.K. Samoil, P.V. Blenis, P.E. Crane, and B.L. Laishley, editors. Rusts of Pine. Proc. 3rd IUFRO Rusts of Pine Working Party Conference, Sept 18-22, 1989, Banfd, Alberta. For. Can, Northwest Reg., North. For. Cent., Edmonton, Alberta, Inf. Rep. NOR-X-317. pp 102-108. 2. Ekramoddoullah, A.K.M. (1993) Analysis of needle proteins and the N-terminal amino acid sequence of two photosystem II proteins of western white pine (Pinus monticola). Tree Physiology 12: 101-106 Briefly, foliar samples were lyophilized and ground to powder in liquid nitrogen with a mortar and pestle after which 50 mg of needle powder was extracted with 0.7 ml of ES (4% SDS, 5% sucrose, 5% mercatpoethanol) for 10 min at room temperature with gentle stirring. The extract was centrifuged at 10,000 g, and the clear supernatant was heated at 100 C for 3 min and then cooled at room temperature. Proteins were precipitated by adding cold (-20 C) acetone (8 x volume of the supernatant); precipitation was allowed to continue for 1 h, after which the sample was centrifuged at 10,000 g. The pellet was resuspended in 0.2 mL of ES, cnetrifuged at 10,000 g. 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 Mon Apr 04 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!ames!elroy.jpl.nasa.gov!swrinde!gatech!newsxfer.itd.umich.edu!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: Re: alkaline phosphatase, pH? Message-ID: <1994Apr5.210022.6743@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) References: <1994Mar31.145857.1@sara.cc.utu.fi> Date: Tue, 5 Apr 1994 21:00:22 GMT Lines: 28 In article <1994Mar31.145857.1@sara.cc.utu.fi>, pesusi@sara.cc.utu.fi writes: >Hi everybody > >I have a simple question. Does any of you know the pH optimum for alkaline >phosphatase? Actually I want to know in vitro conditions. Does the protein work >better in diethanolamine than in Tris based buffers? My purpose is to find >suitable conditions for colourdevelopment in immuno-blots. >Thanks. > >P.S I would appreciate answers directly to me. > >Peter > The pH is greater than 9. I used alkaline phosphatase color development reagents kit from Bio-Rad and Immobilon membrane from Millipore very successfully. BCIP (5-bromo, 4-chloro 3-idolylphophate p-toluidine salt) and NBT (p-nitro blue tetrazolium chloride) were two color reagents. 1 mL of NBT solution [30 mg/mL of 70% N,N-dimehtylformamide (DMF)] and 1 mL of the BCIP solution (15 mg/mL of 70% DMF) into 100 mL of the carbonate buffer (0.1 M sodium bicarbonate, 1 mM MgCl, pH 9.8) were mixed. Add the Western blot into this color solution, shake gently until a purple band appears on the blot. Good Luck. -- 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 Tue Apr 05 23:00:00 1994 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Temporary Interruption of Access to PIR Date: 6 Apr 1994 15:28:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <01HAV4DEB9XQ9N3W9W@NBRF.Georgetown.Edu> NNTP-Posting-Host: net.bio.net Announcement of Temporary Interruption of Access to The Protein Identification Resource The National Biomedical Research Foundation anonymous FTP server and guest accounts will be unavailable beginning on Thursday April 7 at 17:00 EDT when maintenance work is begun. While the system will otherwise be accessible on Thursday evening and Friday, it may not be possible to access some or all of the sequence databases. From Friday April 8 beginning at 16:00 EDT through about Sunday April 10 at 16:00 EDT it will not be possible for users to access the Protein Identification Resource Network Server, the On-line System, or contact the PIR staff by electronic mail. We regret any inconvenience this temporary loss of service may cause. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-proteins@net.bio.net Tue Apr 05 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!sun4nl!tudelft.nl!draconis.cp.tn.tudelft.nl!flohil From: flohil@cp.tn.tudelft.nl (Jaap Flohil) Subject: convergence 99% .... Message-ID: Lines: 19 Sender: news@news.tudelft.nl (UseNet News System) Nntp-Posting-Host: scorpius.cp.tn.tudelft.nl Organization: Delft University of Technology Date: Wed, 6 Apr 1994 19:10:56 GMT Dear people, Thanks for all your advices, suggestions, critics and skepticism. I have collected all your information and will evaluate it. I didn't realize the significance of this subject on protein studies. Since I 'm not familiar with this field I have to consider what exactly I have found. However, I said that I found a convergence of 99% on the datasets. What I meant was that the results of the learning processes were at best 99% correct, i.e. the generated outputs matched 99% of the target outputs. I didn't say anything about predictions of secondary structures yet. These are different concepts. I hope to prove with other datasets which don't contain secondary structure parameters, that I can predict secondary structures with very high succes rates. Jaap Flohil From owner-proteins@net.bio.net Tue Apr 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!isgate!news.rhi.hi.is!zjons From: zjons@rhi.hi.is (Zophonias Oddur Jonsson) Newsgroups: bionet.molbio.proteins Subject: Re: convergence 99% secondary structure predictions Date: 6 Apr 1994 10:15:35 GMT Organization: University of Iceland Lines: 28 Message-ID: <2nu247$cs8@eldborg.rhi.hi.is> References: NNTP-Posting-Host: hengill.rhi.hi.is In bashford@griffy.scripps.edu (Don &) writes: >>>>>> "Jaap" == Jaap Flohil writes: >In article flohil@cp.tn.tudelft.nl (Jaap Flohil) writes: > Jaap> I used a data set for secondary structure prediction of > Jaap> proteins from Qian and Sejnowski. After some manipulations > Jaap> with the IO-files and different networks I reached a > Jaap> convergence of 99%, both on the Test set and Training set. >If you have really achieved 99% accuracy in the prediction of secondary >structure it would be a spectacular result that would attract the interest >of almost everyone who studies proteins. But many of us suspect that >it is impossible to reach such levels without also predicting a good >deal about tertiary structure at the same time. So if you are going >to make such a claim, you had better be sure you are right and you should >be prepared for intense skepticism..... [del] By the way! When was the original article posted? April 1st ? Zophonias O. Jonsson University of Iceland intensely skeptic! From owner-proteins@net.bio.net Tue Apr 05 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!agate!ihnp4.ucsd.edu!munnari.oz.au!newshost.anu.edu.au!molbiol.anu.edu.au!user From: crowther@rschp1.anu.edu.au (Jeff) Newsgroups: bionet.molbio.proteins Subject: Re: Resolving LMW proteins Followup-To: bionet.molbio.proteins Date: Wed, 06 Apr 1994 18:24:43 +1000 Organization: Bad at Best Lines: 14 Message-ID: References: <1994Mar28.180207.1@pearl.tufts.edu> NNTP-Posting-Host: 150.203.96.2 In article <1994Mar28.180207.1@pearl.tufts.edu>, ajayaram@pearl.tufts.edu wrote: > I'm trying to run a 8 kd protein on a SDS get but I'm having some problems > getting it to show up due to its small size. I've tried 10, 12 and 15 > percent gels but the but the protein doesn't seem to be there ( the problem is Try 20% gel. Some people here have had some trouble with proteins of that size and the higher % works. Depends on the gel formula (bisacryl/acryl ratio) -- Who knows what the signature says so many people use my computer From owner-proteins@net.bio.net Tue Apr 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!zaphod.crihan.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!elna.ethz.ch!torda From: torda@igc.ethz.ch (Andrew Torda) Newsgroups: bionet.molbio.proteins Subject: Re: convergence 99% secondary structure predictions Date: 6 Apr 1994 07:50:39 GMT Organization: Computational Chemistry, ETH, Zuerich Lines: 16 Message-ID: <2ntpkf$fm2@elna.ethz.ch> References: NNTP-Posting-Host: hermitage.ethz.ch bashford@griffy.scripps.edu (Don &) wrote [... lots deleted ....] >be prepared for intense skepticism. Regarding the limitations of >the neural net approach and the artifacts that are possible, I suggest >you look at a paper by Howard Holley (Holly?) et al. from PNAS of >1988 or 1989. (Sorry I don't have the reference on hand here at home.) Holley, LH, Karplus, M (1989), PNAS, 86, 152-156 "Protein secondary structure prediction with a neural network". -Andrew -- This posting is not merely my opinion. It is the official position of my employer, the Swiss Federal Institute of Technology. (Andrew Torda, Computational Chemistry, ETH, Zurich, torda@igc.ethz.ch) From owner-proteins@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!munnari.oz.au!hippo.ru.ac.za!ucthpx!uctvax.uct.ac.za!schren13 From: schren13@uctvax.uct.ac.za Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Protease inhibitors Message-ID: <1994Apr7.141718.206430@uctvax.uct.ac.za> Date: 7 Apr 94 14:17:18 +0200 Organization: University of Cape Town Lines: 12 Xref: biosci bionet.molbio.methds-reagnts:13074 bionet.molbio.proteins:1696 ANY ADVICE?? I am working on a system in which a membrane-bound protein is solubilized by a membrane protease. In order to classify the protease, I treated it with various protease inhibitors. To my surprise I repeatedly get an increased protease activity when the serine-protease inhibitor "3,4-dichloroisocoumarin" is used. Is there anyone out there who has an explanation?? Please send any replies by e-mail to rscholle@physio.uct.ac.za. Thanks a lot. From owner-proteins@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!UMBC.EDU!srinivas From: srinivas@UMBC.EDU ("Dr. Mohan S. Srinivasan") Newsgroups: bionet.molbio.proteins Subject: subscribe this news group Date: 7 Apr 1994 09:07:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199404071608.MAA22755@umbc7.umbc.edu> NNTP-Posting-Host: net.bio.net I would like to subscribe this newsgroup. Mohan. From owner-proteins@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!nntp.msstate.edu!saimiri.primate.wisc.edu!news.doit.wisc.edu!sweetprotein.ahabs.wisc.edu!user From: ming@ahabs.wisc.edu (Ding Ming) Newsgroups: bionet.molbio.proteins Subject: Re: Trypsin Molecular Weight Followup-To: bionet.molbio.proteins Date: Thu, 07 Apr 1994 09:56:12 -0600 Organization: University of Wisconsin-Madison Lines: 22 Distribution: bionet Message-ID: References: NNTP-Posting-Host: sweetprotein.ahabs.wisc.edu In article , szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) wrote: > Hy All, > I need to know the molecular weight of bovine trypsin. Indeed, I > need a new review about trypsin. The newest I found is in Boyle's Book The > enzymes from 1961. > Thanks in advance, > > Rafael Najmanovich The MW of bovine trypsinogen is 23,990 and the activation of trypsinogen results in three different trypsins: beta- and alpha- form, plus pseudotrypsin. The latest review I think is Rovery, M., (1988)Biochimie 70, 1131. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Ding Ming University of Wisconsin-Madison Telephone: (608)265-3544 Fax: (608)262-7420 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-proteins@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!swrinde!emory!usenet From: clarsen@bimcore.emory.edu (Chris Larsen) Newsgroups: bionet.molbio.proteins Subject: Re: Resolving LMW: Answer Date: 7 Apr 1994 15:12:09 GMT Organization: Biomolecular Computing Resource, Emory University Lines: 14 Distribution: world Message-ID: <2o17s9$bub@emory.mathcs.emory.edu> References: <1994Apr1.232907.7523@alw.nih.gov> Reply-To: clarsen@bimcore.emory.edu NNTP-Posting-Host: bimcore.cc.emory.edu We also have this problem with Ubiquitin (8 kDa). You can get over it by doing three things. Pellet the cells first so that no media proteins are present. Run no less than an 18% SDS PA gel, as the front and the small proteins will comigrate at less acrylamide. You can run up to 24 % acrylamide, in my experience. Add more buffer strength to your gel sep layer. You can substitute 3 M Tris-Cl (8.8) instead of the normal 1.5 M buffer. This increases the sharpness of the bands. Works Great. Chris From owner-proteins@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!EU.net!howland.reston.ans.net!europa.eng.gtefsd.com!emory!usenet From: clarsen@bimcore.emory.edu (Chris Larsen) Newsgroups: bionet.molbio.proteins Subject: Re: alk phos pH: ANSWER Date: 7 Apr 1994 15:05:45 GMT Organization: Biomolecular Computing Resource, Emory University Lines: 7 Distribution: world Message-ID: <2o17ga$bub@emory.mathcs.emory.edu> References: <1994Mar31.145857.1@sara.cc.utu.fi> Reply-To: clarsen@bimcore.emory.edu NNTP-Posting-Host: bimcore.cc.emory.edu Rinse the blot (after the antibodies have been used and rinsed off) uwith 50 mM Tris-Cl pH 9.5 Supplement this with 100 uM MgCl2. Repeat until you see no bubbles from the detergents or blocking agents. (these inhibit good development) I recommend the Sigm Fast color substrate tabs for development: 1 into 10 mls, for 10 minutes. Works Great! Chris From owner-proteins@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!FOX.CCE.USP.BR!szeinfel From: szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) Newsgroups: bionet.molbio.proteins Subject: Trypsin Molecular Weight Date: 7 Apr 1994 06:41:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: bionet Message-ID: NNTP-Posting-Host: net.bio.net Hy All, I need to know the molecular weight of bovine trypsin. Indeed, I need a new review about trypsin. The newest I found is in Boyle's Book The enzymes from 1961. Thanks in advance, Rafael Najmanovich From owner-proteins@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!moe.ksu.ksu.edu!matt.ksu.ksu.edu!not-for-mail From: moosp@matt.ksu.ksu.edu (Philip Joseph Moos) Newsgroups: bionet.molbio.proteins Subject: Amino Acid Composition Comparisons Date: 7 Apr 1994 16:29:48 -0500 Organization: Kansas State University Lines: 11 Message-ID: <2o1u0c$sv1@matt.ksu.ksu.edu> NNTP-Posting-Host: matt.ksu.ksu.edu Hello netters, Does anyone know of a mail-server that can be used to search proteins by amino acid composition? I believe such a program exists but I don't know that it is accessible in some type of general "blast-like" fashion. Thanks in advance, Philip Moos moosp@matt.ksu.ksu.edu From owner-proteins@net.bio.net Thu Apr 07 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!darwin.sura.net!fconvx.ncifcrf.gov!mack From: mack@ncifcrf.gov (Joe Mack) Subject: Re: Isoelectric Point of Proteins Message-ID: Organization: Frederick Cancer Research and Development Center References: Date: Fri, 8 Apr 1994 13:43:32 GMT Lines: 20 In article floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) writes: > >Hi! > >Some colleagues from our laboratory asked me whether there is a program >to calculate the Isoelectric Point for a protein using only the sequence >of the protein. This ought to be part of a FAQ file... A program called ISOELECTRIC, which is part of the GCG suite of programs, will calculate the pI for an unfolded protein of a given sequence. This pI will be pretty close to that for the folded protein. Joe Mack mack@ncifcrf.gov From owner-proteins@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!ACF2.NYU.EDU!changliy From: changliy@ACF2.NYU.EDU (Chang) Newsgroups: bionet.molbio.proteins Subject: leucine-zipper Date: 8 Apr 1994 14:53:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404082153.AA27587@acf2.NYU.EDU> NNTP-Posting-Host: net.bio.net Dear netters: Does anyone know how many leucine repeat is requred in order to determine a leucine zipper motif? at least 3? Can other a,a (e.g. Ile) replace leu? What if my protein has 3 leu repeat but the second cycle is spaced 6 residues instead of 7 residues, is there a leu-zipper motif ? Any respone is highly appreciated. Regards Theresa changliy@acf2.nyu.edu From owner-proteins@net.bio.net Thu Apr 07 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!ihnp4.ucsd.edu!swrinde!gatech!howland.reston.ans.net!pipex!uknet!EU.net!Austria.EU.net!newsfeed.ACO.net!edvz.sbg.ac.at!wst!floeckn From: floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) Subject: Isoelectric Point of Proteins Message-ID: Lines: 21 Sender: floeckn@wst (Floeckner Hannes) Reply-To: floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) Organization: University of Salzburg / Austria Date: Fri, 8 Apr 1994 08:38:58 GMT Hi! Some colleagues from our laboratory asked me whether there is a program to calculate the Isoelectric Point for a protein using only the sequence of the protein. I couldn't answer this question and I even don't know whether this is possible or not. That's why I'de like to ask here: Is there any software to calculate the Isoelectric Point for a protein using only the sequence? Hannes =========================================================================== Floeckner Hannes e-mail: floeckn@wst.edvz.sbg.ac.at Inst.f. Chemie und Biochemie Universitaet Salzburg Jakob-Haringerstr. 1 A-5020 Salzburg AUSTRIA - EUROPE From owner-proteins@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!Viroid.AgMarley.Arizona.EDU!zxiong From: zxiong@arizvm1.ccit.arizona.edu (Zhongguo Xiong) Newsgroups: bionet.molbio.proteins Subject: Re: Isoelectric Point of Proteins Date: Fri, 8 Apr 1994 13:48:01 Organization: University of Arizona Lines: 16 Message-ID: References: NNTP-Posting-Host: viroid.agmarley.arizona.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] In article floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) writes: >Hi! >Some colleagues from our laboratory asked me whether there is a program >to calculate the Isoelectric Point for a protein using only the sequence >of the protein. >I couldn't answer this question and I even don't know whether this is possible >or not. That's why I'de like to ask here: > Is there any software to calculate the Isoelectric Point > for a protein using only the sequence? Use the PEPSORT progrm in GCG package >Hannes From owner-proteins@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!FOX.CCE.USP.BR!szeinfel From: szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) Newsgroups: bionet.molbio.proteins Subject: Re: Isoelectric Point of Proteins Date: 8 Apr 1994 09:35:26 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: bionet Message-ID: References: NNTP-Posting-Host: net.bio.net On Fri, 8 Apr 1994, Floeckner Hannes wrote: > > Hi! > > Some colleagues from our laboratory asked me whether there is a program > to calculate the Isoelectric Point for a protein using only the sequence > of the protein. > > I couldn't answer this question and I even don't know whether this is possible > or not. That's why I'de like to ask here: > Is there any software to calculate the Isoelectric Point > for a protein using only the sequence? > > Hannes > > =========================================================================== > Floeckner Hannes e-mail: floeckn@wst.edvz.sbg.ac.at > Inst.f. Chemie und Biochemie > Universitaet Salzburg > Jakob-Haringerstr. 1 > A-5020 Salzburg > AUSTRIA - EUROPE > > If the isoeletric point of a protein depends on the 3-d structure it's impossible to calculate it from the primary structure. So I ask on what depends the isoeletric point of a protein. Rafael Najmanovich From owner-proteins@net.bio.net Thu Apr 07 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!noc.near.net!news.cs.brandeis.edu!binah.cc.brandeis.edu!DUCA From: duca@binah.cc.brandeis.edu (Karen Duca, a.k.a. Rocky) Subject: GROMOS on UNIX Message-ID: <1994Apr8.153027.1061@news.cs.brandeis.edu> Sender: news@news.cs.brandeis.edu (USENET News System) Reply-To: duca@binah.cc.brandeis.edu Organization: Brandeis University Date: Fri, 8 Apr 1994 15:30:27 GMT Lines: 10 I'm wondering if anybody knows of an ftp site where I can find a version of the MM/MD software package called GROMOS that runs under UNIX. I have a version for the VAX which I'm in the process of modifying to run on an RS/6000 and I've encountered a couple of intractable problems. I'd like to see how others have resolved the problem, as I'm sure it's been ported to most platforms by now. Thanx, Karen Duca duca@binah.cc.brandeis.edu From owner-proteins@net.bio.net Thu Apr 07 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!noc.near.net!news.cs.brandeis.edu!binah.cc.brandeis.edu!DUCA From: duca@binah.cc.brandeis.edu (Karen Duca, a.k.a. Rocky) Subject: GROMOS on UNIX Message-ID: <1994Apr8.152012.652@news.cs.brandeis.edu> Sender: news@news.cs.brandeis.edu (USENET News System) Reply-To: duca@binah.cc.brandeis.edu Organization: Brandeis University Date: Fri, 8 Apr 1994 15:20:12 GMT Lines: 11 I'd like to know if anybody is aware of an ftp site where I can find a version of the MM/MD program GROMOS that runs under UNIX. I'v been porting a version that we have that runs on a VAX over to an RS/6000 and I've encountered a couple of intractable problems. I'd like to see how it's gone for others who have already modified the original program. I'm sure it's been done for a variety of platforms already. Thanx, Karen Duca duca@binah.cc.brandeis.edu From owner-proteins@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!newsxfer.itd.umich.edu!gumby!wupost!news.miami.edu!not-for-mail From: kramer@oj.rsmas.miami.edu (Jack Kramer) Newsgroups: bionet.molbio.proteins Subject: Re: Isoelectric Point of Proteins Date: 8 Apr 1994 17:29:53 -0400 Organization: R.S.M.A.S. Lines: 21 Message-ID: <2o4ich$8g8@oj.rsmas.miami.edu> References: NNTP-Posting-Host: oj.rsmas.miami.edu In article , Zhongguo Xiong wrote: >In article floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) writes: >>Hi! > >>Some colleagues from our laboratory asked me whether there is a program >>to calculate the Isoelectric Point for a protein using only the sequence >>of the protein. > >>I couldn't answer this question and I even don't know whether this is possible >>or not. That's why I'de like to ask here: >> Is there any software to calculate the Isoelectric Point >> for a protein using only the sequence? > >Use the PEPSORT progrm in GCG package > But remain a little skeptical of the answers. The best computed pI's can be off by 4 pH units from actual measured values. From owner-proteins@net.bio.net Fri Apr 08 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!xlink.net!wega.fibronics.de!neutron!jui From: jui@neutron.nacamar.de (Uwe Harmening) Subject: RUBISCO Organization: NACAMAR Development Center Date: Sat, 9 Apr 1994 16:08:48 GMT X-Newsreader: TIN [version 1.2 PL2] Message-ID: <1994Apr9.160848.14053@neutron.nacamar.de> Lines: 18 Hi everybody, looking for the Km-Value of Ribulose-1,5-bisphosphat-carboxylase-oxygenase of higher plants for CO2 at pH 7.2 or 7.5 i found lots of data in different books. The problem is, that they differ from 450micromol CO2/l to 25 micromol/l !? Please, does anybody know a good source for this or even a good value? -- Bye and cu Jui ------ Fidonet: 2:244/1370.11 Internet: jui@neutron.nacamar.de Snailnet: no way! From owner-proteins@net.bio.net Fri Apr 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!wupost!waikato!waikato.ac.nz!pjc From: pjc@waikato.ac.nz (Peter Charlton) Newsgroups: bionet.molbio.proteins Subject: Help with mito protein problem Message-ID: <1994Apr10.175604.27411@waikato.ac.nz> Date: 10 Apr 94 17:56:03 +1200 Organization: University of Waikato, Hamilton, New Zealand Lines: 32 Does anyone have any idea what might be going on here? I am trying to isolate a subunit of Complex-1 from Oenothera (evening primrose) root mitochondria. I am also working in parallel with mitochondria isolated from rat liver, as this is an easy tissue to work from, supposedly. My procedure is as follows: A standard mitochondrial isolation (differential centrifugation of homogenate, purification on Percoll gradient). Then the mitochondria are osmotically- -shocked to produce mitoplasts, which I sonicate, and I collect inner membrane by centrifugation. I solubilise about 100mg of IMb in 7% Triton X-100 at a detergent:protein of 5:1. The soluble supernatant is loaded onto a 3-10% gradient PAGE gel containing Triton X-100, and I can visualise dehydrogenase activities by staining with NBT. The pattern of dehydrogenases I get is very similar to what I would expect, and what others have obtained using Vicia, Arum etc. BUT, under Coomassie stain, I have much less protein than I would expect. In fact, I can only see 1 major band, and 3 or 4 lighter bands. By contrast, lanes containing solubilised liver inner membrane stain well, and I can easily see Complex-I, and about 20 major bands in total. On the other hand, the activity stains of liver and plant are of about equal intensity. Literature suggests I should be loading about 0.6 mg of total protein/gel lane, of which ~5ug should be Complex-I. Many thanks for *any* insights or suggestions, Peter Charlton Dept of Biological Sciences University of Waikato, New Zealand. pjc@waikato.ac.nz From owner-proteins@net.bio.net Fri Apr 08 23:00:00 1994 Newsgroups: bionet.molbio.proteins From: Duncan@genesys.demon.co.uk (Duncan Clark) Path: biosci!headwall.Stanford.EDU!ames!elroy.jpl.nasa.gov!swrinde!gatech!howland.reston.ans.net!pipex!uknet!demon!genesys.demon.co.uk!Duncan Subject: Preparation of phospho-sepharose Distribution: world Organization: GeneSys Ltd. Reply-To: Duncan@genesys.demon.co.uk X-Newsreader: Simple NEWS 1.90 (ka9q DIS 1.21) Lines: 16 Date: Sat, 9 Apr 1994 14:03:41 +0000 Message-ID: <765900221snz@genesys.demon.co.uk> Sender: usenet@demon.co.uk Hi Folks, Has anyone ever tried to make a sepharose equivalent of phosphocellulose? If so how did it behave and how did they make it? I know IBF used to sell a phosphoultragel but in my hands it behaved very poorly compared to phosphocellulose. Why a sepharose derivative? Faster flow rates and no fines. Thanks Duncan -- ----------------------------------------------------------------------------- Duncan Clark | Internet: duncan@genesys.demon.co.uk GeneSys Ltd. | Compuserve: 100015.1406@compuserve.com ----------------------------------------------------------------------------- From owner-proteins@net.bio.net Fri Apr 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!emory!news-feed-2.peachnet.edu!umn.edu!mayonews.mayo.edu!Mayo.EDU!eberhard From: eberhard@Mayo.EDU (norm eberhardt) Newsgroups: bionet.molbio.proteins Subject: Re: Resolving LMW proteins Date: 8 Apr 1994 16:17:39 GMT Organization: Mayo Foundation, Rochester, Minnesota Lines: 23 Distribution: world Message-ID: <2o4033$qae@fermat.mayo.edu> References: <1994Mar28.180207.1@pearl.tufts.edu> NNTP-Posting-Host: feynman.mayo.edu In article , crowther@rschp1.anu.edu.au (Jeff) writes: |> In article <1994Mar28.180207.1@pearl.tufts.edu>, ajayaram@pearl.tufts.edu |> wrote: |> |> > I'm trying to run a 8 kd protein on a SDS get but I'm having some problems |> > getting it to show up due to its small size. I've tried 10, 12 and 15 |> > percent gels but the but the protein doesn't seem to be there ( the problem is |> |> |> Try 20% gel. Some people here have had some trouble with proteins of that |> size |> and the higher % works. Depends on the gel formula (bisacryl/acryl ratio) |> |> -- |> Who knows what the signature says so many people use my computer Also, take a look at Christy et al., Modifications for SDS-PAGE of Proteins. BioTechniques 7: 692-3 (1989). Using the procedure described in this paper, we have been able to resolve protein fragments down to 4 kDa. Norman Eberhardt eberhardt@mayo.edu From owner-proteins@net.bio.net Sat Apr 09 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!zaphod.crihan.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!elna.ethz.ch!torda From: torda@igc.ethz.ch (Andrew Torda) Newsgroups: bionet.molbio.proteins Subject: Re: GROMOS on UNIX Date: 10 Apr 1994 15:51:20 GMT Organization: Computational Chemistry, ETH, Zuerich Lines: 28 Message-ID: <2o979o$aiv@elna.ethz.ch> References: <1994Apr8.153027.1061@news.cs.brandeis.edu> NNTP-Posting-Host: hermitage.ethz.ch duca@binah.cc.brandeis.edu wrote >I'm wondering if anybody knows of an ftp site where I can find >a version of the MM/MD software package called GROMOS that runs >under UNIX. I have a version for the VAX which I'm in the process >of modifying to run on an RS/6000 and I've encountered a couple of >intractable problems. I'd like to see how others have resolved the >problem, as I'm sure it's been ported to most platforms by now. The most generally useful bit of information here is to point out that there is a (very quiet) mailing list for GROMOS problems. Mail to gromos-request@igc.chem.ethz.ch and someone will put you on the mailing list. To mail to the actual mailing list, try gromos@igc.chem.ethz.ch. For anyone interested in Karen's original posting, I suspect the problems can't be that severe. The vax code she mentions compiles without change or problems on the rs/6000's hanging around in this place. -Andrew -- This posting is not merely my opinion. It is the official position of my employer, the Swiss Federal Institute of Technology. (Andrew Torda, Computational Chemistry, ETH, Zurich, torda@igc.ethz.ch) From owner-proteins@net.bio.net Sat Apr 09 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!ihnp4.ucsd.edu!library.ucla.edu!csulb.edu!csus.edu!netcom.com!barbose.slip.netcom.com!barbose From: Jeffrey J Barbose Subject: Protein synthesis texts/refs? Message-ID: X-Xxmessage-Id: X-Xxdate: Sun, 10 Apr 1994 18:51:44 GMT Sender: netnews@netcom.com (USENET Administration) Organization: HowLand Software X-Newsreader: Nuntius Version 1.1.4b2 Date: Sun, 10 Apr 1994 18:58:17 GMT Lines: 13 I was wondering if anyone could give me some references for text books that cover (in excruciating detail, if possible :) molecular mechanics of peptide chain formation at the ribosome surface, continuing on into whatever is currently known about folding dynamics. Thanks in advance, Jeff ----- Jeffrey J Barbose President, HowLand Software From owner-proteins@net.bio.net Sat Apr 09 23:00:00 1994 Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Path: biosci!agate!ihnp4.ucsd.edu!swrinde!sgiblab!sgigate.sgi.com!olivea!decwrl!decwrl!waikato!canterbury.ac.nz!otago.ac.nz!sanger.otago.ac.nz!craigm From: craigm@sanger.otago.ac.nz (Craig Marshall) Subject: Re: Protease Inhibitors Message-ID: Followup-To: bionet.molbio.methds-reagnts,bionet.molbio.proteins Sender: usenet@news.otago.ac.nz (News stuff) Nntp-Posting-Host: sanger.otago.ac.nz Organization: University of Otago X-Newsreader: TIN [version 1.1 PL8] References: <1994Mar30.121045.206379@uctvax.uct.ac.za> Date: Sun, 10 Apr 1994 08:15:40 GMT Lines: 11 Xref: biosci bionet.molbio.methds-reagnts:13159 bionet.molbio.proteins:1715 It is possible that there is present in your extract another protease which attacks the protease you are assayng and which is inhibited by the 3,4-dichloroisocoumarin. Cheers, -- Craig Marshall craigm@sanger.otago.ac.nz Biochemistry Department Phone +64 3 479 7570 University of Otago Fax +64 3 479 7866 P.O. Box 56, Dunedin, New Zealand From owner-proteins@net.bio.net Sat Apr 09 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!darwin.sura.net!fconvx.ncifcrf.gov!mack From: mack@ncifcrf.gov (Joe Mack) Subject: Re: Isoelectric Point of Proteins Message-ID: Organization: Frederick Cancer Research and Development Center References: Distribution: bionet Date: Mon, 11 Apr 1994 02:52:32 GMT Lines: 23 In article szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) writes: > > > If the isoeletric point of a protein depends on the 3-d structure >it's impossible to calculate it from the primary structure. Not exactly true. The pI depends on the pKa of each ionisable group. All those residues facing the solVent with have unaltered pKa's. Those in the hydrophobic core and in salt brindges will have altered pKa's. In the old days kineticists used to look for residues with altered pKas as a window on the structure of the protein. I don't remember many residues with pKa's shifted by more than 1 unit. So some residues will be shifted by 1 unit in pKa and others will not be shifted at all. The pI of the unforlded protein thus is not a bad starting point for the pI of the folded protein. Joe Mack mack@ncifcrf.gov From owner-proteins@net.bio.net Sun Apr 10 23:00:00 1994 Path: biosci!UNIXG.UBC.CA!flo From: flo@UNIXG.UBC.CA Newsgroups: bionet.molbio.proteins Subject: Enzyme Kinetics Question Date: 11 Apr 1994 13:45:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404112046.AA24408@unixg.ubc.ca> NNTP-Posting-Host: net.bio.net Netters, If an enzyme has such an incredibly low activity on a substrate that you need to use equal molar amouts of enzyme to substrate, how does this affect the kinetics ? ie can you still use the Michealis-Menten type equations even though the enzyme concentration is no longer much smaller than the substrate concentration????? Thanx, Roger From owner-proteins@net.bio.net Sun Apr 10 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!ihnp4.ucsd.edu!scripps.edu!usenet From: dbg@scripps.edu Newsgroups: bionet.molbio.proteins Subject: Re: Enzyme Kinetics Question Date: Mon, 11 Apr 94 14:10:56 PDT Organization: The Scripps Research Institute, La Jolla, CA Lines: 35 Message-ID: <2ocgso$fvj@riscsm.scripps.edu> References: <9404112046.AA24408@unixg.ubc.ca> NNTP-Posting-Host: satan.scripps.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Newsreader: NEWTNews & Chameleon -- TCP/IP for MS Windows from NetManage In article <9404112046.AA24408@unixg.ubc.ca>, writes: > > If an enzyme has such an incredibly low activity on a substrate that you > need to use equal molar amouts of enzyme to substrate, how does this > affect the kinetics ? ie can you still use the Michealis-Menten type > equations even though the enzyme concentration is no longer much smaller > than the substrate concentration????? > > Thanx, > > Roger > > > Roger, Hi guy! Haven't heard from you since I left Vancouver... Sounds like you have a nearly dead enzyme. The M-M kinetics may still be ok though. The main reason that [S]/[E] is very large in most cases is that is what it takes to observe saturation of the rate. So make sure that you really can saturate the rate with substrate. You also want [S] to be large enough compared to the absolute rate so that the change in [S] does not change significantly over the measurement time. You may need to be careful about why the enzyme is so slow that [E] must be similar to [S]. If it is because the rate limiting step is the binding of S to E, then kinetics will be determined by what is known as 'pre-equilibrium' and they will not follow M-M kinetics anyway. The might appear to, but then the line will exhibit non-linearity at high [S]. Say hello to flo and send me some E-mail : dbg@scripps.edu Dave Goodin From owner-proteins@net.bio.net Sun Apr 10 23:00:00 1994 Path: biosci!agate!news.Brown.EDU!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!husc10!robison1 Newsgroups: bionet.molbio.proteins Subject: Re: Isoelectric Point of Proteins Message-ID: From: robison1@husc10.harvard.edu (Keith Robison) Date: 11 Apr 94 18:03:16 GMT References: <2o4ich$8g8@oj.rsmas.miami.edu> Organization: Harvard University, Cambridge, Massachusetts NNTP-Posting-Host: husc10.harvard.edu Lines: 46 kramer@oj.rsmas.miami.edu (Jack Kramer) writes: >In article , >Zhongguo Xiong wrote: >>In article floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) writes: >>>Hi! >> >>>Some colleagues from our laboratory asked me whether there is a program >>>to calculate the Isoelectric Point for a protein using only the sequence >>>of the protein. >> >>>I couldn't answer this question and I even don't know whether this is possible >>>or not. That's why I'de like to ask here: >>> Is there any software to calculate the Isoelectric Point >>> for a protein using only the sequence? >> >>Use the PEPSORT progrm in GCG package >> >But remain a little skeptical of the answers. The best computed pI's >can be off by 4 pH units from actual measured values. While it's always good to be skeptical, a colleague of mine has extensively sequenced 2D protein gel spots from E.coli and compared the predicted vs. observed for pI and molecular weight -- and most of the points fall near the 4D diagonal. In eukaryotic systems the answers are more likely to be off due to post-translational processing, as many of these processes derivatize ionizable groups and/or add ionizable groups (e.g. sialic acid). The iso program in my molbio++ C++ suite for UNIX machines will calculate pI, and the source should be clear enough to allow extensions to handle known post-translational processes. It is availabe by aFTP from golgi.harvard.edu in pub/robison/molbio++. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI krobison@nucleus.harvard.edu From owner-proteins@net.bio.net Sun Apr 10 23:00:00 1994 Path: biosci!agate!msuinfo!harbinger.cc.monash.edu.au!bunyip.cc.uq.oz.au!nash From: nash@biosci.uq.oz.au (Kevin Nash -BIOCHEM) Newsgroups: bionet.molbio.proteins Subject: pyrophosphatase assays Date: 12 Apr 1994 06:05:14 GMT Organization: University of Queensland Lines: 8 Message-ID: <2oddmq$m4c@dingo.cc.uq.oz.au> NNTP-Posting-Host: florey.biosci.uq.oz.au Summary: I would like to find out more information on how to performed pyropho Keywords: pyrophosphate would like to find out more information on how to perform pyrophos. assays. As I am ptresently experiencing hydrolysis of my substrate after addition of the colour reagent and thus unable to determine the activity. Any help would be more than greatly appreciated. I am presently using a malachite green method because it gives better sensitivity. Kevin Nash. . ZZ From owner-proteins@net.bio.net Sun Apr 10 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!EU.net!sun4nl!sci.kun.nl!ronsmul From: ronsmul@sci.kun.nl (Ronald Smulders) Subject: HMW calibration proteins Message-ID: Sender: news@sci.kun.nl (News owner) Nntp-Posting-Host: wn2.sci.kun.nl Organization: University of Nijmegen, The Netherlands Date: Mon, 11 Apr 1994 15:57:18 GMT Lines: 15 Hi netters, Our group is interested in eye lens proteins called crystallins. Alpha-crystallin is a very dynamic 800 kDa aggregate of about 40 subunits. We would like to determine the size of this protein under various conditions by gel permiation chromatography (HPLC Superose 6 column). To do these experiments we need some monomeric HMW calibration proteins (700 - 1000 kDa). Does anybody know of the existence of this kind of proteins? At this moment we are using the pharmacia calibration kit but the largest protein in this kit is 669 KDa. Thank you for your attention, Ronald (ronsmul@sci.kun.nl) From owner-proteins@net.bio.net Sun Apr 10 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!kintanar From: kintanar@iastate.edu (Agustin Kintanar) Newsgroups: bionet.molbio.proteins Subject: Re: Isoelectric Point of Proteins Date: 11 Apr 1994 16:34:49 GMT Organization: Iowa State University, Ames, Iowa (USA) Lines: 34 Distribution: bionet Message-ID: <2obu79$a4d@news.iastate.edu> References: NNTP-Posting-Host: pv0a0b.vincent.iastate.edu Originator: kintanar@pv0a0b.vincent.iastate.edu In article , mack@ncifcrf.gov (Joe Mack) writes: |> |> Not exactly true. The pI depends on the pKa of each ionisable group. All those |> residues facing the solVent with have unaltered pKa's. Those in the |> hydrophobic core and in salt brindges will have altered pKa's. In the old days |> kineticists used to look for residues with altered pKas as a window on |> the structure of the protein. I don't remember many residues with pKa's shifted |> by more than 1 unit. |> |> So some residues will be shifted by 1 unit in pKa and others will not |> be shifted at all. The pI of the unforlded protein thus is not a bad starting |> point for the pI of the folded protein. |> |> Joe Mack |> mack@ncifcrf.gov |> Actually, measurements of reaction kinetics are a poor way of measuring pKa's because the results are only indirectly linked to ionization of a *particular amino acid residue*. Nuclear magnetic resonance has had some success in measuring the pKa's of specific individual amino acid residues. From what I've seen in the literature and from my own experience, it is not at all unusual for the pKa's of buried ionizable amino acids to be shifted by 2, 3 or even 4 pH units! In fact, I would go so far as to say that this is the rule rather than the exception. Therefore, use these pI calculations as a first approximation but, as an earlier poster pointed out, take the results with a grain of salt. Agustin Kintanar Department of Biochemistry & Biophysics Iowa State University From owner-proteins@net.bio.net Sun Apr 10 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!isgate!news.rhi.hi.is!zjons From: zjons@rhi.hi.is (Zophonias Oddur Jonsson) Newsgroups: bionet.molbio.proteins Subject: Re: Isoelectric Point of Proteins Date: 11 Apr 1994 16:04:58 GMT Organization: University of Iceland Lines: 35 Distribution: bionet Message-ID: <2obsfa$poq@eldborg.rhi.hi.is> References: NNTP-Posting-Host: hengill.rhi.hi.is In mack@ncifcrf.gov (Joe Mack) writes: >In article szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) writes: >> >> >> If the isoeletric point of a protein depends on the 3-d structure >>it's impossible to calculate it from the primary structure. >Not exactly true. The pI depends on the pKa of each ionisable group. All those >residues facing the solVent with have unaltered pKa's. If I remember correctly the original poster wanted to know whether a program that would calculate pI existed. Someone pointed out the GCG package but for those of you who don't have access to GCG, there is a freeware program called DNAid+ 1.8 by Frederic Dardel. Despite the name it can also do some basic protein analysis, e.g. pattern searching. The program can estimate the pI of proteins by solving the pKa's of the ionisable amino acids. It is crude but might be enough for some purposes. DNAid runs on Mac's and is available by ftp. If memory serves me right I downloaded it from the EMBL archives. I hope this helps! Zophonias ############################################################################ Zophonias O. Jonsson SOME people's talents are so well hidden University of Iceland that you overlook them completely! zjons@rhi.hi.is -Stephen Young ############################################################################ From owner-proteins@net.bio.net Sun Apr 10 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!warwick!uknet!EU.net!Germany.EU.net!netmbx.de!zib-berlin.de!news.th-darmstadt.de!terra.wiwi.uni-frankfurt.de!zeus.rbi.informatik.uni-frankfurt.de!news.dfn.de!scsing.switch.ch!swidir.switch.ch!news.unige.ch!ugsc2a!tanya From: tanya@sc2a.unige.ch Subject: paramyosin Message-ID: <1994Apr11.123611.1@ugsc2a> Lines: 9 Sender: usenet@news.unige.ch Organization: University of Geneva, Switzerland Date: Mon, 11 Apr 1994 10:36:11 GMT Hi, Does somebody know where I could get the antibodies against paramyosin? Or some reactions (properties) specific for paramyosin? Any help would be greatly appreciated. Thanks, Tanya From owner-proteins@net.bio.net Sun Apr 10 23:00:00 1994 Path: biosci!HURRICANE.SEAS.UCLA.EDU!johnoliv From: johnoliv@HURRICANE.SEAS.UCLA.EDU Newsgroups: bionet.molbio.proteins Subject: isoelectric point of beta-Galactosidase (E. coli) Date: 11 Apr 1994 14:03:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404112103.AA15425@hurricane.seas.ucla.edu> NNTP-Posting-Host: net.bio.net Does anyone know the isoelectric point (pI) of E. coli beta-galactosidase? Also, if the information came from a reference or book, could you please include that as well? Thanks in advance. John From owner-proteins@net.bio.net Mon Apr 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.intercon.com!udel!news2.sprintlink.net!news.sprintlink.net!indirect.com!nike From: nike@indirect.com (Laurence Canter) Newsgroups: bionet.molbio.proteins,br.piadas Subject: Green Card Lottery- Final One? Date: 12 Apr 1994 07:44:28 GMT Organization: Canter & Siegel Lines: 34 Message-ID: <2odjgs$2de@herald.indirect.com> NNTP-Posting-Host: id1.indirect.com Green Card Lottery 1994 May Be The Last One! THE DEADLINE HAS BEEN ANNOUNCED. The Green Card Lottery is a completely legal program giving away a certain annual allotment of Green Cards to persons born in certain countries. The lottery program was scheduled to continue on a permanent basis. However, recently, Senator Alan J Simpson introduced a bill into the U. S. Congress which could end any future lotteries. THE 1994 LOTTERY IS SCHEDULED TO TAKE PLACE SOON, BUT IT MAY BE THE VERY LAST ONE. PERSONS BORN IN MOST COUNTRIES QUALIFY, MANY FOR FIRST TIME. The only countries NOT qualifying are: Mexico; India; P.R. China; Taiwan, Philippines, North Korea, Canada, United Kingdom (except Northern Ireland), Jamaica, Domican Republic, El Salvador and Vietnam. Lottery registration will take place soon. 55,000 Green Cards will be given to those who register correctly. NO JOB IS REQUIRED. THERE IS A STRICT JUNE DEADLINE. THE TIME TO START IS NOW!! For FREE information via Email, send request to cslaw@indirect.com -- ***************************************************************** Canter & Siegel, Immigration Attorneys 3333 E Camelback Road, Ste 250, Phoenix AZ 85018 USA cslaw@indirect.com telephone (602)661-3911 Fax (602) 451-7617 From owner-proteins@net.bio.net Mon Apr 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!uts!news.uni-c.dk!virus.fki.dth.dk!engel From: engel@virus.fki.dth.dk (Jacob Engelbrecht) Newsgroups: bionet.molbio.proteins Subject: protein surface Date: 12 Apr 1994 08:52:14 GMT Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 10 Message-ID: <2odnfu$b95@news.uni-c.dk> NNTP-Posting-Host: virus.fki.dth.dk X-Newsreader: TIN [version 1.2 PL1] Can anyone inform me on the which methods (= programs) are available for determing which atoms from a PDB coordinate file are ion the surface. The problem I am pursuing is to find out which atoms are accessible for another protein. Jacob Engelbrecht Center for biological Sequence Analysis From owner-proteins@net.bio.net Mon Apr 11 23:00:00 1994 Path: biosci!agate!msuinfo!deitst.bch.msu.edu From: 21664mgr@msu.edu (Tom Deits) Newsgroups: bionet.molbio.proteins Subject: Re: Enzyme Kinetics Question Date: Tue, 12 Apr 1994 10:14 est Organization: Dept. of Biochemistry, Michigan State U. Lines: 52 Distribution: world Message-ID: <19940412101425.21664mgr@deitst.bch.msu.edu> References: <2ocgso$fvj@riscsm.scripps.edu> <9404112046.AA24408@unixg.ubc.ca> NNTP-Posting-Host: deitst.bch.msu.edu X-Newsreader: FTPNuz (DOS) v1.0 In Article <2ocgso$fvj@riscsm.scripps.edu> "dbg@scripps.edu" says: > > In article <9404112046.AA24408@unixg.ubc.ca>, writes: > > > > > If an enzyme has such an incredibly low activity on a substrate that you > > need to use equal molar amouts of enzyme to substrate, how does this > > affect the kinetics ? ie can you still use the Michealis-Menten type > > equations even though the enzyme concentration is no longer much smaller > > than the substrate concentration????? > > > > Thanx, > > > > Roger > > > > > > > > Roger, > Hi guy! Haven't heard from you since I left Vancouver... > > Sounds like you have a nearly dead enzyme. The M-M kinetics may still be ok > though. The main reason that [S]/[E] is very large in most cases is that > is what it takes to observe saturation of the rate. So make sure that you > really can saturate the rate with substrate. You also want [S] to > be large enough compared to the absolute rate so that the change in [S] > does not change significantly over the measurement time. > You may need to be careful about why the enzyme is so slow that [E] must > be similar to [S]. If it is because the rate limiting step is the binding > of S to E, then kinetics will be determined by what is known as > > 'pre-equilibrium' and they will not follow M-M kinetics anyway. The might > appear to, but then the line will exhibit non-linearity at high [S]. > > Say hello to flo and send me some E-mail : dbg@scripps.edu > > Dave Goodin > This isn't quite correct. Another feature that can invalidate a Michaelis- Menten analysis is when the concentration of free S is significantly reduced by binding to E to form ES. The equilibrium constant for the simplest michaelis scheme is, strictly, Km = [S]free[E]free/[ES]. Most people assume that [S]free = [S]total to a good approximation, and make this substition in the above equation. However, this substitution is likely to be invalid in your case regardless of whether the enzyme appears 'saturated' with substrate (that is, even if Vobs is independent of Stotal). If you do your kinetics without taking this explicitly into account, your results will be actively misleading. For example, Cleland's rules have the opposite interpretation if [S]free does not equal [S]total. Hope this helps. Tom Deits deits@pilot.msu.e From owner-proteins@net.bio.net Mon Apr 11 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!ihnp4.ucsd.edu!scripps.edu!usenet From: dbg@scripps.edu Newsgroups: bionet.molbio.proteins Subject: Re: Enzyme Kinetics Question Date: Tue, 12 Apr 94 12:31:05 PDT Organization: The Scripps Research Institute, La Jolla, CA Lines: 18 Message-ID: <2oete1$89s@riscsm.scripps.edu> References: <19940412101425.21664mgr@deitst.bch.msu.edu> NNTP-Posting-Host: satan.scripps.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Newsreader: NEWTNews & Chameleon -- TCP/IP for MS Windows from NetManage > This isn't quite correct. Another feature that can invalidate a Michaelis- > Menten analysis is when the concentration of free S is significantly reduced > by binding to E to form ES. The equilibrium constant for the simplest > michaelis scheme is, strictly, Km = [S]free[E]free/[ES]. Most people assume > that [S]free = [S]total to a good approximation, and make this substition in > the above equation. Yes, you are right. This is what I was trying to say when I cautioned about why the enzyme was so slow. If ES -> Product is so slow that there is a significant concentration of [ES] compared to [S], then you must be very careful to know [S]free and [S]total. Thanks for clarifying... Dave Goodin From owner-proteins@net.bio.net Mon Apr 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!zaphod.crihan.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!urz.unibas.ch!bickle From: bickle@urz.unibas.ch Newsgroups: bionet.molbio.proteins Subject: Re: Isoelectric Point of Proteins Message-ID: <1994Apr12.084422.43686@urz.unibas.ch> Date: 12 Apr 94 08:44:22 MET References: <2o4ich$8g8@oj.rsmas.miami.edu> Organization: University of Basel, Switzerland Lines: 25 In article , robison1@husc10.harvard.edu (Keith Robison) writes: > > > While it's always good to be skeptical, a colleague of mine has > extensively sequenced 2D protein gel spots from E.coli and compared > the predicted vs. observed for pI and molecular weight -- and most of > the points fall near the 4D diagonal. In eukaryotic systems the ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ True, but the isoelectric focussing step of 2-D electrophoresis is done under denaturing conditions. > Keith Robison > Harvard University > Department of Cellular and Developmental Biology > Department of Genetics / HHMI > > krobison@nucleus.harvard.edu > > > -- Tom Bickle Microbiology Dept, Biozentrum, Basel University Klingelbergstrasse 70, CH-4056 Basel, Switzerland + 41 61 267 21 20 bickle@urz.unibas.ch From owner-proteins@net.bio.net Mon Apr 11 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!swrinde!emory!news-feed-2.peachnet.edu!news-feed-1.peachnet.edu!ukma!news.cuny.edu!cunyvm!cunyvm Organization: City University of New York/ University Computer Center Date: Tue, 12 Apr 1994 16:09:01 EDT From: Message-ID: <94102.160901MRLCC@CUNYVM.CUNY.EDU> Newsgroups: bionet.molbio.proteins Subject: Beta-cyanin? Lines: 11 Hello. I am trying to find a gene which encodes the protein beta-cyanin. This is protein aids in the digestion of the red pigment ffom beets. Can someone please let me know if this is indeed the correct name and if so, where might I find information about the gene. ------- From owner-proteins@net.bio.net Mon Apr 11 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!parc!decwrl!ames!purdue!mozo.cc.purdue.edu!biomac1l.bio.purdue.edu!user From: bheymann@bragg.bio.purdue.edu (Bernard Heymann) Subject: Expression from T7 promotor Sender: news@mozo.cc.purdue.edu (USENET News) Message-ID: Date: Wed, 13 Apr 1994 04:04:22 GMT Organization: Dept. Biol. Sciences, Purdue Univ. Followup-To: bionet.molbio.proteins Lines: 40 For some reason I could not reply by e-mail to Geet, and perhaps this may interest some other of my fellow lost souls. The one protein I'm studying is a membrane protein that seems to hit the ceiling in terms of overexpression, no matter which system. I have had it under a lac promotor, and then cloned it into pT7-7. With both BL21(DE3) and BL21(DE3) LysS I get the same expression from the T7 promotor as from the lac promotor. It also seems that I can add IPTG just about any time and get the same amount of protein (~ 1.2 mg per liter 2YT medium). I give this info as an example of a factor other than the expression system that influences the amount of product obtained. The other protein I just recently cloned into pT7-7 and expressed it in BL21(DE3) LysS. The lysozyme was pretty obvious in the gel, but my protein was only slightly overexpressed. Expressing it in BL21(DE3) then solved that problem, and I got overexpression to the tune of tens of mg per liter. However, if your protein is toxic to the cell, you may have problems in this strain. In terms of adding the IPTG, I have had different experiences with different systems and strains. The lac promotor is fully induced at levels as low as 0.1 mM IPTG in many systems, but I don't know whether this also pertains in DE3. Currently I inoculate a liter of 2YT medium with 1 - 2 ml overnight culture and grow it for 3 hr before adding IPTG, and then grow it for another 3 - 4 hr. I think for the T7 system an A550 of 0.1 - 0.2 is too low (although I never really measure mine - I just go by time). Bottom line: Use BL21(DE3) w/o LysS; try and grow it for longer times. -- Bernard Heymann bheymann@bragg.bio.purdue.edu From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!xlink.net!wega.fibronics.de!neutron!jui From: jui@neutron.nacamar.de (Uwe Harmening) Subject: 3D-prediction Organization: NACAMAR Development Center Date: Wed, 13 Apr 1994 16:27:58 GMT X-Newsreader: TIN [version 1.2 PL2] Message-ID: <1994Apr13.162758.10014@neutron.nacamar.de> Lines: 22 Hallo there, is somebody doing 3D-structure-prediction of proteins on a Silicon Graphics Workstation with the Biosym-software? How do you print your pictures. Biosym told me it is possible to print on a Postscriptprinter, but in a rather bad quality. So many people are taking pictures with a camera (imagine you have hard an software for thousands of dollars and have to take a picture from the screen with your camera!?). Is it possible to export the pictures in Tiff or Gif to a Dos/Win Environment to use it in a textprocessor? Any suggestions will help. Thanx in advance! -- Bye and cu Jui ------ Fidonet: 2:244/1370.11 Internet: jui@neutron.nacamar.de Snailnet: no way! From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!convex!darwin.sura.net!hearst.acc.Virginia.EDU!murdoch!galen.med.Virginia.EDU!jv4s From: jv4s@galen.med.Virginia.EDU (Jay Vasudevan) Subject: Re: Isoelectric Point of Proteins Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia References: <1994Apr12.084422.43686@urz.unibas.ch> Date: Wed, 13 Apr 1994 14:38:51 GMT Lines: 13 In article , Keith Robison wrote: >Good point. It all depends on what you need the estimate for. >Out of curiosity, what else do people use pI for other than estimating >2D gel locations? Purely on a practical application level.....separation in native (non-denaturing) PAGE. Jay Vasudevan Dept. Pathology/Biochem. Univ. of Virginia -- eh eheeh eh he heh eh eh heh heh ehe heh From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!news.mic.ucla.edu!unixg.ubc.ca!nntp.cs.ubc.ca!alberta!quartz.ucs.ualberta.ca!tribune.usask.ca!canopus.cc.umanitoba.ca!norton!frist From: frist@cc.umanitoba.ca () Newsgroups: bionet.molbio.proteins Subject: PIR gripes Date: 13 Apr 1994 18:06:40 GMT Organization: The Univeristy of Manitoba. Lines: 53 Distribution: world Message-ID: <2ohcbh$5ft@canopus.cc.umanitoba.ca> Reply-To: frist@cc.umanitoba.ca NNTP-Posting-Host: norton.cc.umanitoba.ca Hey, folks at PIR: 1) Please announce when updates occur ------------------------------------- The recent anouncement of GenBank Release 82.0 reminded me that I hadn't seen a new release of PIR for a while. Out of curiosity I looked at the PIR directories at ftp.bchs.uh.edu to find that, yes, a new release had come out in February! Is it so hard to post a message to bionet.molbio.proteins or bionet.announce when a new release is issued? I think I might have seen messages like this at one time, but not in at least a year. 2) Please give us ADVANCE warning of format changes --------------------------------------------------- In October when PIR 38.0 came out, none of the documentation files said anyting about upcomming changes. In fact, the CODATA Exchange Format Specification (CXFSD-1091) distributed with this release was Version 2.1, dated Oct. 15 1991, indicating that the format has been stable since them. All of a sudden, when I downloaded Release 39.0, my software no longer worked with PIR. A look at the updated CODATA Specification file lists more than two pages of changes in the format, across 13 different sections! Fortunately, for my software (XYLEM) I was able to make the necessary changes in a couple of hours. Others may not have been so lucky. How can PIR make such drastic changes without providing extensive prior warning? Precise specifications of proposed changes should be published in the documentation at least one release in advance, and the same information posted to the appropriate newsgroup(s). Is that so hard to do? In this case, where a large number of changes were made, I would expect that a prior release of the database should have some sample entries in the new format, so that people can test their software and have it working before the new format appears. This should also not be hard to do. Come on guys. These things should be obvious! =============================================================================== Brian Fristensky | Department of Plant Science | A question is like a knife that slices University of Manitoba | through the stage backdrop and gives us Winnipeg, MB R3T 2N2 CANADA | a look at what lies hidden behind. frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Milan Kundera, THE UNBEARABLE LIGHTNESS FAX: 204-261-5732 | OF BEING =============================================================================== From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Path: biosci!MED.PITT.EDU!bsh From: bsh@MED.PITT.EDU (Basavaraju Shankarappa) Newsgroups: bionet.molbio.proteins Subject: Re: Isoelectric Point of Proteins Date: 13 Apr 1994 06:45:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404131344.AA27616@venus.med.pitt.edu> References: NNTP-Posting-Host: net.bio.net > bickle@urz.unibas.ch writes: > >In article , robison1@husc10.harvard.edu (Keith Robison) writes: > >> While it's always good to be skeptical, a colleague of mine has > >> extensively sequenced 2D protein gel spots from E.coli and compared > >> the predicted vs. observed for pI and molecular weight -- and most of > >> the points fall near the 4D diagonal. In eukaryotic systems the > >True, but the isoelectric focussing step of 2-D electrophoresis is done > >under denaturing conditions. > Good point. It all depends on what you need the estimate for. > Out of curiosity, what else do people use pI for other than estimating > 2D gel locations? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Well, with HIV, it has been shown that the number substitutions resulting in basic amino acids in the envelope gene is related to the pathogenicity of the virus (or the virulence as we measure it!). I am trying to use PI as a measure of this increasing charge of the peptide. If anyone has additional pointers, I would appreciate it too. Raj Shankarappa bsh@med.pitt.edu From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Path: biosci!daresbury!s-crim1!lhb From: lhb@s-crim1.dl.ac.uk (L.H. Bell) Newsgroups: bionet.molbio.proteins,bionet.general Subject: email address to report duplications in databases Date: 13 Apr 1994 12:21:57 GMT Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 38 Sender: lhb@s-crim1 (L.H. Bell) Distribution: world Message-ID: <2ogo55$5et@mserv1.dl.ac.uk> Reply-To: lhb@seqnet.dl.ac.uk NNTP-Posting-Host: s-crim1.dl.ac.uk Keywords: email database duplication Xref: biosci bionet.molbio.proteins:1737 bionet.general:8599 One of our users has reported duplicated entries in the pir3 protein database. We have removed the duplication from our own copy of the database, but would also like to report it by e-mail to the database keepers. Does anyone have an e-mail address for them? Also, if there are specific e-mail addresses for bug reports for the other DNA/protein databases, could you please e-mail me them as well. I'll summarise if there's any need. Thanks in advance for the help, Lachlan Bell The duplicated entries are: P1;S21479 - SOX-4 protein - Human C;Species: Homo sapiens (man) C;Date: 22-Nov-1993; #sequence_revision 22-Nov-1993; #text_change 22-Nov-1993 C;Accession: S21479 R;Denny, P.; Swift, S.; Brand, N.; Dabhade, N.; Barton, P.; Ashworth, A. submitted to the EMBL Data Library, April 1992 A;Reference number: S21475 A;Accession: S21479 P1;S22938 - SOX-4 protein - Human C;Species: Homo sapiens (man) C;Date: 22-Nov-1993; #sequence_revision 22-Nov-1993; #text_change 22-Nov-1993 C;Accession: S22938 R;Denny, P.; Swift, S.; Brand, N.; Dabhade, N.; Barton, P.; Ashworth, A. Nucleic Acids Res. 20, 2887, 1992 A;Title: A conserved family of genes related to the testis determining gene, SRY. A;Reference number: S22935; MUID:92310993 A;Accession: S22938 From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!wupost!waikato!canterbury.ac.nz!chmeds.ac.nz!molpath From: molpath@chmeds.ac.nz Newsgroups: bionet.molbio.proteins Subject: Tyrosine Kinase - source Message-ID: <1994Apr14.173815.473@chmeds.ac.nz> Date: 14 Apr 94 17:38:15 +1200 Lines: 9 Does anybody know of a commercial source of Protein Tyrosine Kinase? Please Email. Thanks in advance. -- Andrew Fellowes Hospital Scientist Canterbury Health Laboratories, PO Box 151, Christchurch, New Zealand Ph: 64 3 364 0550 | Fax: 64 3 364 0525 | Email: molpath@chmeds.ac.nz From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!bnr.co.uk!bnrgate!nott!uotcsi2!usenet From: misrael@grdb.csi.uottawa.ca (Mark Israel) Newsgroups: bionet.molbio.proteins Subject: hardcopy from Biosym Date: 14 Apr 1994 01:42:52 GMT Organization: Dept. of Computer Science, University of Ottawa Lines: 23 Message-ID: <2oi72s$cgo@csi0.csi.uottawa.ca> References: <1994Apr13.162758.10014@neutron.nacamar.de> NNTP-Posting-Host: grdb.csi.uottawa.ca In article <1994Apr13.162758.10014@neutron.nacamar.de>, Uwe Harmening writes: > is somebody doing 3D-structure-prediction of proteins on a Silicon Graphics > Workstation with the Biosym-software? How do you print your pictures. Biosym > told me it is possible to print on a Postscript printer, but in a rather bad > quality. So many people are taking pictures with a camera (imagine you have > hard an software for thousands of dollars and have to take a picture > from the screen with your camera!?). Is it possible to export the pictures > in Tiff or Gif to a Dos/Win Environment to use it in a textprocessor? Do you want raster (shaded) pictures, or vector (line-only) pictures? If you want raster pictures, get what you want on the screen and do a screen dump. (If Biosym doesn't have a command for screen dump, then log in remotely and run the SGI-supplied program called "snapshot" -- say "man snapshot" for details.) Then use the utilities described in /usr/people/4Dgifts/iristools/imgtools/README to convert to GIF or a choice of several other formats. If you want vector pictures, then you'll have to look more closely at what plotting options are available in Biosym. misrael@csi.uottawa.ca Mark Israel From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!ames!sgiblab!darwin.sura.net!fconvx.ncifcrf.gov!mack From: mack@ncifcrf.gov (Joe Mack) Subject: Re: Isoelectric Point of Proteins Message-ID: Organization: Frederick Cancer Research and Development Center References: <1994Apr12.084422.43686@urz.unibas.ch> Date: Wed, 13 Apr 1994 16:56:46 GMT Lines: 21 In article robison1@husc10.harvard.edu (Keith Robison) writes: >bickle@urz.unibas.ch writes: > >>In article , robison1@husc10.harvard.edu (Keith Robison) writes: >>> >Out of curiosity, what else do people use pI for other than estimating >2D gel locations? For a purity check for an otherwise homogeneous (or almost homogeneous) protein and a check for deamidation that has occured during purification. The main limitation for me is that yoou cant do proteins with pI>8.5 as hydrolysis of the ampholytes changes the pH gradient within a half hour of starting the run. Any ideas about protein with high pI's anyone? Joe Mack NIH mack@ncifcrf.gov From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!emory!news-feed-2.peachnet.edu!umn.edu!htlv.med.umn.edu!david-l From: david-l@htlv.med.umn.edu (David LaPorte (Biochem)) Subject: Re: Enzyme Kinetics Question Message-ID: Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: htlv.med.umn.edu Organization: University of Minnesota References: <9404112046.AA24408@unixg.ubc.ca> Distribution: bionet Date: Wed, 13 Apr 1994 14:44:10 GMT Lines: 31 In article <9404112046.AA24408@unixg.ubc.ca> flo@UNIXG.UBC.CA writes: >Netters, > >If an enzyme has such an incredibly low activity on a substrate that you >need to use equal molar amouts of enzyme to substrate, how does this >affect the kinetics ? ie can you still use the Michealis-Menten type >equations even though the enzyme concentration is no longer much smaller >than the substrate concentration????? > My enzyme kinetics is (are?) a little rusty, so don't take the following as gospel. The primary reason that MM derivations assume that [S]tot >> [E]tot is that it allows the simplification [S]free = ca. [S]total. [S]free is the important variable, but cannot be easily measured. If your enzyme is binding a substantial portion of the substrate, then the assumption is violated. Try testing linearity of velocity with [E]. If the enzyme is soaking up a lot of the substrate, then the plot won't be linear. With such a high concentration of enzyme, you should also be concerned about whether your enzyme has really achieved steady state (another assumption of the MM equation). Test this by examining linearity with time. If Mo Cleland reads this, he will probably kill me :-(. Dave LaPorte U. of Minn. david-l@microbe.med.umn.edu From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!news.uoregon.edu!gaia.ucs.orst.edu!news.reed.edu!usenet From: especkma@reed.edu (Erik A. Speckman) Newsgroups: bionet.molbio.proteins Subject: (Q) Dialysis against PEG. Date: 13 Apr 1994 20:16:13 GMT Organization: Hellmouth-Heater Democrat Lines: 19 Message-ID: <2ohjud$jjq@scratchy.reed.edu> NNTP-Posting-Host: reed.edu I am dialysing a sample against buffer overnight to eliminate salt. The problem I am having is that I end up increacing the volume significantly and so I have to spend more time concentrating the sampel before loading it onto a column. I got the idea from this group that I could add PEG to my dialysis buffer to eliminate this bloat and maybe even concentrate my sample durring dialysis. My question is, how much should I use? Thanks. -- ____________________________________________________________________________ By my rough estimation, their are 4,000,000,000,000 cycles of proceessing power within reach of the Internet being wasted every second. My advice: use them to sink the clipper chip. From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!univ-lyon1.fr!ghost.dsi.unimi.it!sun.cisi.unige.it!barbarella!carrara From: carrara@barbarella.cisi.unige.it. (Enrico A. Carrara) Newsgroups: bionet.molbio.proteins Subject: Sphericity of Proteins Date: 13 Apr 1994 18:24:12 GMT Organization: Information Services Center,Univ. of Genoa, Italy Lines: 11 Message-ID: <2ohdcc$t4n@sun.cisi.unige.it> NNTP-Posting-Host: carrara%@barbarella.ibf.unige.it X-Newsreader: TIN [version 1.2 PL2] Anybody knows commonly used numerical indicators of the closeness of a protein shape to a sphere, and the most common thresholds used to discriminate approximately-spherical from non-spherical proteins? I am mainly interested in indicators that can be calculated from the 3D coordinates of the atomic positions of protein structures. Thanks Enrico Carrara carrara@barbarella.ibf.unige.it From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uchinews!apollo!orion.it.luc.edu!gnew From: gnew@orion.it.luc.edu (Geraldine A. New) Newsgroups: bionet.molbio.proteins Subject: AT8 antibody-Alzheimer's Date: 13 Apr 1994 16:30:58 GMT Organization: Loyola University of Chicago Lines: 6 Message-ID: <2oh6o2$f3r@apollo.it.luc.edu> NNTP-Posting-Host: orion.it.luc.edu X-Newsreader: TIN [version 1.2 PL2] We're looking to purchase this antibody, which is reportedly available from a company called Innogenetics S.A., Gent, Belgium. Our problem is that we just don't know how to go about contacting this place. Any suggestions? gerri From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Path: biosci!news.cs.umb.edu!hsdndev!husc-news.harvard.edu!husc.harvard.edu!husc10!robison1 Newsgroups: bionet.molbio.proteins Subject: Re: Isoelectric Point of Proteins Message-ID: From: robison1@husc10.harvard.edu (Keith Robison) Date: 13 Apr 94 03:46:07 GMT References: <2o4ich$8g8@oj.rsmas.miami.edu> <1994Apr12.084422.43686@urz.unibas.ch> Organization: Harvard University, Cambridge, Massachusetts NNTP-Posting-Host: husc10.harvard.edu Lines: 25 bickle@urz.unibas.ch writes: >In article , robison1@husc10.harvard.edu (Keith Robison) writes: >> >> >> While it's always good to be skeptical, a colleague of mine has >> extensively sequenced 2D protein gel spots from E.coli and compared >> the predicted vs. observed for pI and molecular weight -- and most of >> the points fall near the 4D diagonal. In eukaryotic systems the > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >True, but the isoelectric focussing step of 2-D electrophoresis is done >under denaturing conditions. > Good point. It all depends on what you need the estimate for. Out of curiosity, what else do people use pI for other than estimating 2D gel locations? Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI krobison@nucleus.harvard.edu From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!ihnp4.ucsd.edu!usc!howland.reston.ans.net!pipex!zaphod.crihan.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!news.unige.ch!ugsc2a!tanya From: tanya@sc2a.unige.ch Subject: protein surface Message-ID: <1994Apr13.094440.1@ugsc2a> Lines: 9 Sender: usenet@news.unige.ch Organization: University of Geneva, Switzerland Date: Wed, 13 Apr 1994 07:44:40 GMT A programme SURVOL which is a part of BRUGEL molecular modelling pakage allows an analytical computation of accessible surface and volume. As output it gives the list of the accessible surface and volume for each atom. It was written by Philippe Alard and probably has somethimg to do with the algorithm of Connolly and Richmond, but I am not sure. E-mail me if you need more information. Tanya Petrova Department of Biochemistry From owner-proteins@net.bio.net Tue Apr 12 23:00:00 1994 Path: biosci!PORTIA.CALTECH.EDU!EARN From: EARN@PORTIA.CALTECH.EDU Newsgroups: bionet.molbio.proteins Subject: Re: (Q) Dialysis against PEG. Date: 13 Apr 1994 15:46:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <01HB4R4BPCHCAC2XDA@PORTIA.CALTECH.EDU> NNTP-Posting-Host: net.bio.net I routinely use dialysis against 25% PEG 20,0000 (in standard protein buffer) to concentrate protein samples up to 10 or 20 times. Takes 5-15 hours depending on the total volume. A short dialysis versus protein buffer is necessary afterwards to remove PEG breakdown products (smaller PEG). Good luck. - Eric ------------------------------------------------------------------------------ one sorry lobe of the Primordial Undermind "It'd take the mountains' fall to wake you from your dreams" - Crystalized Movements EARN@portia.caltech.edu From owner-proteins@net.bio.net Wed Apr 13 23:00:00 1994 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Re: PIR gripes Date: 14 Apr 1994 14:14:26 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 70 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <01HB689SEAMS8WW1HR@NBRF.Georgetown.Edu> NNTP-Posting-Host: net.bio.net In message <2ohcbh$5ft@canopus.cc.umanitoba.ca> Brian Fristensky (frist@cc.umanitoba.ca) raised several issues. I have discussed them with him privately to be certain I could address all his concerns to his satisfaction. We do apologize for any problems that the recent format enhancements to the PIR-International database may have caused anyone. More than one year ago we realized that the changes then being planned could cause software problems if our users were not given advance notice. For that reason we set up our developers mailing list and began issuing the PIR Technical Development Bulletin. The Bulletin was first announced publicly in the PIR Announcements posted 1 February 1993 with the notice of database Release 35. Subsequent announcements appeared on 13 April 1993 for Release 37 and on 21 October 1993 for Release 38 that both contained information about the Technical Bulletin and how copies could be obtained. The October announcement included an explicit warning about the format changes that were to be anticipated in Release 39. We are sorry if these notices were not prominent enough, but we are gratified only one complaint has been received. Let me take this opportunity to remind our users again about the PIR Technical Development Bulletin. The fourth PIR-International Technical Development Bulletin is available in the file PIRTECH.LIS that can be sent by the PIR Network Request Server or picked up by anonymous FTP from the UH Gene-Server, ftp.bchs.uh.edu, IP address 129.7.2.43. This electronic bulletin provides detailed specifications of the database format and serves as an "early warning system" for software developers and others who are concerned about changes in the format and standards for the PIR databases. The fourth Bulletin documents the changes to be introduced with the Enhanced NBRF Format in Release 39.00. If you are interested in the technical aspects of these database changes and would like to be placed on the mailing list for the Technical Bulletin, send a brief electronic mail note to POSTMAST@GUNBRF on BITNET or to POSTMASTER@NBRF.Georgetown.Edu on Internet. The file CXFSD containing only the CODATA Exchange Format Specification can also be sent by the PIR Network Request Server. The format enhancements were undertaken in order to (1) improve the coverage, accuracy, and completeness of the PIR-International Protein Sequence Database, (2) provide additional data fields and define them more precisely so that conversions to other formats or database systems (RDBMS or OODBMS) can be accomplished more easily (3) make the overall presentation more uniform for human readability and more computer parsable to facilitate automatic checking for correct format, syntax and vocabulary within the database, and (4) make the two flat file distribution formats of the PIR-International, the NBRF format and the CODATA format, more completely interconvertible without any degradation of information. The PIR-International has a regular quarterly update cycle, March 31, June 30, September 30, December 31. Database production has adhered to that schedule rigorously since Release 11 in December 1986. Actual distribution and availability follow two to three weeks after those dates and may vary somewhat if we experience CD-ROM and tape production problems beyond our control. Beginning with the PIR Announcement that was posted on 1 October 1992 for Release 34 we have attempted to announce the availability of the database releases. We understand that some people may have gotten the impression from reading only the "Subject" headers that these announcements concerned our network database services. Therefore, we will probably change the "Subject" header for future PIR announcements to reflect their contents more faithfully. The next PIR Announcement for Release 40 will indeed be posted here soon. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-proteins@net.bio.net Wed Apr 13 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!pipex!sunic!uts!news.daimi.aau.dk!biobase!lho From: lho@biobase.aau.dk (Lars Henrik Oestergaard) Subject: Isoelectric point Message-ID: Keywords: pI, isoelectric point, excel worksheet, Apple, Macintosh Organization: The Danish BioBase Date: Thu, 14 Apr 1994 08:02:36 GMT Lines: 5 In reply to all the fuss about programmes for calculation of the isoelectric point of a protein, I have made an excel worksheet. It is based upon the same calculations as the programme "isoelectric" in the gcg-package. The worksheet is available from sumex-aim.stanford.edu (and mirrors) via ftp, fetch... There may be minor mistakes, but I hope no fatal ones. The isoelectric point is that of the unfolded protein, which also is the one found by isoelectric focusing (normally). Best regards Lars (lho@biobase.aau.dk) From owner-proteins@net.bio.net Wed Apr 13 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!macx16.mrc-lmb.cam.ac.uk!user From: sanz@mrc-lmb.cam.ac.uk (Jesus M. Sanz) Newsgroups: bionet.molbio.proteins Subject: Re: (Q) Dialysis against PEG. Followup-To: bionet.molbio.proteins Date: 14 Apr 1994 07:50:28 GMT Organization: Medical Research Council (Cambridge, UK) Lines: 31 Message-ID: References: <2ohjud$jjq@scratchy.reed.edu> NNTP-Posting-Host: macx16.mrc-lmb.cam.ac.uk In article <2ohjud$jjq@scratchy.reed.edu>, especkma@reed.edu (Erik A. Speckman) wrote: > > I am dialysing a sample against buffer overnight to eliminate salt. > > The problem I am having is that I end up increacing the volume > significantly and so I have to spend more time concentrating the sampel > before loading it onto a column. > > I got the idea from this group that I could add PEG to my dialysis buffer > to eliminate this bloat and maybe even concentrate my sample durring > dialysis. > > My question is, how much should I use? > > Thanks. In the past I just took the dialysis bag and covered it with solid PEG, replacing it with new powder when it was getting wet. It's a very efficient way of concentrating samples, but you have to be very careful and control it since your sample might run dry! -- Jesus M. Sanz Tf. (0223) 402146 Centre for Protein Engineering. Fax.(0223) 402140 Hills Road, e-mail:sanz@mrc-lmb.cam.ac.uk Cambridge CB2 2QH, U.K. "Life is hard and happiness is ephemeral" -- From owner-proteins@net.bio.net Wed Apr 13 23:00:00 1994 Path: biosci!INTNET.UPJ.COM!bmao From: bmao@INTNET.UPJ.COM Newsgroups: bionet.molbio.proteins Subject: Re: Sphericity of Proteins Date: 14 Apr 1994 13:13:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404142010.AA18082@intnet.upj.com> NNTP-Posting-Host: net.bio.net The spherical-ness of a protein can be computed as follows. find the centroid and translate the coordinate axes to it. compute the second moment matrix and find eigenvalues/vectors. the relative magnitudes of the three eigenvalues will give an indication of the spherical-ness. I don't know if there is a collection of such info of proteins in pdb anywhere. Seems to be an interesting project. bmao@upj.com (boryeu mao) From owner-proteins@net.bio.net Wed Apr 13 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!columba.udac.uu.se!sol.bmc.uu.se!dunten From: dunten@sol.bmc.uu.se (Pete Dunten) Newsgroups: bionet.molbio.proteins Subject: Re: Isoelectric Point of Proteins Date: 14 Apr 1994 19:50:46 GMT Organization: Uppsala University Lines: 5 Distribution: world Message-ID: <2ok6qm$i94@columba.udac.uu.se> References: <1994Apr12.084422.43686@urz.unibas.ch> NNTP-Posting-Host: sol.bmc.uu.se Q: what do people use the isoelectric point for? A: crystallographers focus their efforts there, as it is often the point of least solubility. From owner-proteins@net.bio.net Wed Apr 13 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!not-for-mail From: mcdonald@bsm.biochemistry.ucl.ac.uk (Ian McDonald) Newsgroups: bionet.molbio.proteins Subject: Re: Sphericity of Proteins Date: 14 Apr 1994 13:05:56 -0500 Organization: University College London Lines: 66 Sender: daemon@cs.utexas.edu Message-ID: <1994Apr14.005028.64836@ucl.ac.uk> References: <2ohdcc$t4n@sun.cisi.unige.it> NNTP-Posting-Host: cs.utexas.edu In article <2ohdcc$t4n@sun.cisi.unige.it>, carrara@barbarella.cisi.unige.it. (Enrico A. Carrara) writes: |> Anybody knows commonly used numerical indicators of the closeness of a |> protein shape to a sphere, and the most common thresholds used to |> discriminate approximately-spherical from non-spherical proteins? |> I am mainly interested in indicators that can be calculated from the |> 3D coordinates of the atomic positions of protein structures. |> |> Thanks |> |> Enrico Carrara |> carrara@barbarella.ibf.unige.it |> I know a little about this from my work on domains . . . if I can check one of my old reports . . . Several scientists have used measurements of the "globularity" (sphericity) of a putative domain. Wodak and Janin (1981) used accessible surface area relative to "estimated" surface area for a globular protein, but not as a full part of their algorithm. Rashin used buried surface area relative to his estimate, but does not seem to have automated his algorithm. Zehfus (1993) used accessible surface area, relative to a sphere with the same building, but rather than divide the protein into separate domains, he finds often overlapping globular polypeptide sequences. Zuker (pers comm) is devoloping an algorithm to locate domains based on CA calculations. He tries to find a preset number of domains, minimising the (i) maximum or (ii) weighted averages of (a) radius of gyration, (b) diameter and (c) extensity. ========================================================================== Table I Wodak and Janin (1981a) ASA / estimated ASA ASA = accessible surface area estimated ASA = 11.1 * M^(2/3) Zehfus (1993) ASA / minimum ASA minimum ASA = 4.836 V^2/3 (I think) expected value around 1.64+-0.09 Rashin (1981) BSA / estimated BSA BSA = buried surface area estimated BSA = 0.859*M + 0.00000744*(M^2) ASA(BSA) = Accessible (Buried) Surface Area. M = Mass, V = Volume ========================================================================== The references to hand are . . Rashin (1981) Nature V291:85 Zehfus (1987) Proteins: 1987:90 Extensity is the average CA-CA distance within a molecule (I think). I hope this helps. Ian McDonald From owner-proteins@net.bio.net Wed Apr 13 23:00:00 1994 Path: biosci!news.cs.umb.edu!hsdndev!husc-news.harvard.edu!husc.harvard.edu!husc10!robison1 Newsgroups: bionet.molbio.proteins Subject: Re: Isoelectric Point of Proteins Message-ID: From: robison1@husc10.harvard.edu (Keith Robison) Date: 14 Apr 94 12:55:51 GMT References: <1994Apr12.084422.43686@urz.unibas.ch> Organization: Harvard University, Cambridge, Massachusetts NNTP-Posting-Host: husc10.harvard.edu Lines: 24 jv4s@galen.med.Virginia.EDU (Jay Vasudevan) writes: >In article , >Keith Robison wrote: >>Good point. It all depends on what you need the estimate for. >>Out of curiosity, what else do people use pI for other than estimating >>2D gel locations? >Purely on a practical application level.....separation in native >(non-denaturing) PAGE. This was one application I pondered, but isn't the migration some function of size and pI? and is this function known? (is just adding a pI term to a standard size vs. migration equation, or are things messier?). Thanks. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI krobison@nucleus.harvard.edu From owner-proteins@net.bio.net Wed Apr 13 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: PIR gripes Message-ID: <1994Apr14.080033.17569@comp.bioz.unibas.ch> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Nntp-Posting-Host: biox.embnet.unibas.ch Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] References: <2ohcbh$5ft@canopus.cc.umanitoba.ca> Date: Thu, 14 Apr 1994 08:00:33 GMT Lines: 66 In article <2ohcbh$5ft@canopus.cc.umanitoba.ca>, frist@cc.umanitoba.ca () writes: |> |> Hey, folks at PIR: |> |> 1) Please announce when updates occur |> ------------------------------------- |> The recent anouncement of GenBank Release 82.0 reminded me that I hadn't |> seen a new release of PIR for a while. Out of curiosity I looked at |> the PIR directories at ftp.bchs.uh.edu to find that, yes, a new release |> had come out in February! You might be delighted to learn that the CD release 40 was shipped last week. It has NRL_3D 14 (DEC '93), though, and Genbank 81 (indices and headlines/titles only - with the option to coutilize the GENBANK CD). If you were on an abonnement of that (one CD, 1200 DM/year, to be paid in advance, unreadable on VMS without installing separate software) you would get it automatically. Your milage might vary with respect to format and performance on the various supported platforms. There is CARBBANK on there besides the NBRF databases, and an alignment as well as a E.COLI database assembled by PIR staff. Not to forget, the ATLAS Software. Though, you might miss the indeces for XQS as those are no longer supported (the last tape I got last year still included them). I have heard non-too-enthusiastic comments about making releases of PIR available for FREE - I am afraid if you really need data you have no choice but buy their CD? |> |> 2) Please give us ADVANCE warning of format changes |> --------------------------------------------------- I got notified on the changes rather early - there's a mailing list of NBRF which you might want to join. What makes me feel sad is that this release's CD lacks *.lis files to be used in database biocomputing - padd.lis , prev.lis etc. are omitted. Space constraints killed auxiliary files needed by the GCG package - so if you ever desired to run GCG on this CD you need to provide those yourself. There wasn't an announcement on these, and I regret this. On the Tape, there used to be release notes which I couldn't find on the CD either, so some of these omissions might not be intended. Regards Reinhard DISCLAIMER Note that the software mentioned resembles Computer Program(s) which require a license in order to be run unless stated otherwise in a state- ment codistributed with the software. The use of the program(s) was men- tioned within a specific problem or example and must not be used to con- clude that other software products cannot possibly do a similar job. -- +---------------------------+-------------------------------------------+ | Dr. Reinhard Doelz | Tel. x41 61 2672247 Fax x41 61 2672078 | | Biocomputing | electronic Mail doelz@urz.unibas.ch | |Biozentrum der Universitaet+-------------------------------------------+ | Klingelbergstrasse 70 | EMBnet embnet@comp.bioz.unibas.ch | |CH 4056 Basel SWITZERLAND | Switzerland gopher.embnet.unibas.ch | +---------------------------+------------- http://beta.embnet.unibas.ch/ From owner-proteins@net.bio.net Wed Apr 13 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: hardcopy from Biosym Message-ID: <1994Apr14.082856.18322@comp.bioz.unibas.ch> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Nntp-Posting-Host: biox.embnet.unibas.ch Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] References: <1994Apr13.162758.10014@neutron.nacamar.de> <2oi72s$cgo@csi0.csi.uottawa.ca> Date: Thu, 14 Apr 1994 08:28:56 GMT Lines: 79 In article <2oi72s$cgo@csi0.csi.uottawa.ca>, misrael@grdb.csi.uottawa.ca (Mark Israel) writes: |> In article <1994Apr13.162758.10014@neutron.nacamar.de>, Uwe Harmening writes: |> |> > is somebody doing 3D-structure-prediction of proteins on a Silicon Graphics |> > Workstation with the Biosym-software? How do you print your pictures. Biosym |> > told me it is possible to print on a Postscript printer, but in a rather bad |> > quality. So many people are taking pictures with a camera (imagine you have |> > hard an software for thousands of dollars and have to take a picture |> > from the screen with your camera!?). Is it possible to export the pictures |> > in Tiff or Gif to a Dos/Win Environment to use it in a textprocessor? |> |> Do you want raster (shaded) pictures, or vector (line-only) pictures? |> |> If you want raster pictures, get what you want on the screen and do a |> screen dump. (If Biosym doesn't have a command for screen dump, then |> log in remotely and run the SGI-supplied program called "snapshot" -- say |> "man snapshot" for details.) Then use the utilities described in |> /usr/people/4Dgifts/iristools/imgtools/README to convert to GIF or a |> choice of several other formats. |> |> If you want vector pictures, then you'll have to look more closely |> at what plotting options are available in Biosym. |> |> misrael@csi.uottawa.ca Mark Israel (1) There's a BIOSYM Mailing list at dibug@comp.bioz.unibas.ch which is more appropriate (and has a better suited readership) with respect to this issue. Mail dibug-request@comp.bioz.unibas.ch to subscribe. (2) We just had a Biosym User Group meeting last week in Amsterdam where a 2-hour workshop was dedicated to this issue. Too bad that you weren't there. You might want to contact your sales office or rcenter@biosym.com to inquire the handouts of this. (3) I wouldn't neccerarily blame BIOSYM if the reproducing devices don't fit in your quality expectations. The molecular modelling world is 3D whereas a plotter or printer is 2D. This implies that the use of smooth shades is required if depth information is vizualized in smooth ramps. Therefore, solid surface models are difficult to obtain as sufficient printout. Similar issues apply to the camera - if you use a high-speed film the contrasts are fine and the picture is grainy, and a lowspeed film might get you images which are often considered as too dark. It requires experience to make the right choice. There are direct-exposure devices commercialy available which do a very good job for a price. If you go for built-in plotting in BIOSYM you have all features but the solids, i.e. there's lines, line ribbons, line characters. You might want to write out PICT format in the export plot function. My preference is to use a reasonably large screen (i.e. not entry graphics) and the snapshot to dump it into RGB. Then I use standard tools (you might want to use the sgi tools, shareware/public domain (have a look at xv but if you use it please register) or use even commercial tools (Colleagues of mine do fantastic graphics using Photoshop as refinement package for annotation and combination, in combination with a direct-exposure technology). Maybe this helps Regards Reinhard DISCLAIMER Note that the software mentioned resembles Computer Program(s) which require a license in order to be run unless stated otherwise in a state- ment codistributed with the software. The use of the program(s) was men- tioned within a specific problem or example and must not be used to con- clude that other software products cannot possibly do a similar job. -- +---------------------------+-------------------------------------------+ | Dr. Reinhard Doelz | Tel. x41 61 2672247 Fax x41 61 2672078 | | Biocomputing | electronic Mail doelz@urz.unibas.ch | |Biozentrum der Universitaet+-------------------------------------------+ | Klingelbergstrasse 70 | EMBnet embnet@comp.bioz.unibas.ch | |CH 4056 Basel SWITZERLAND | Switzerland gopher.embnet.unibas.ch | +---------------------------+------------- http://beta.embnet.unibas.ch/ From owner-proteins@net.bio.net Wed Apr 13 23:00:00 1994 Path: biosci!UGA.CC.UGA.EDU!GPAZ%UCRVM2.BITNET From: GPAZ%UCRVM2.BITNET@UGA.CC.UGA.EDU Newsgroups: bionet.molbio.proteins Subject: unsuscribe Date: 14 Apr 1994 15:45:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199404142245.PAA26039@net.bio.net> NNTP-Posting-Host: net.bio.net please, delete me of the list. Thanks very much. Mabel. From owner-proteins@net.bio.net Wed Apr 13 23:00:00 1994 Path: biosci!DINO.CONICIT.VE!cramos From: cramos@DINO.CONICIT.VE (Cesar Ramos Cedeno (CEDITEC)) Newsgroups: bionet.molbio.proteins Subject: (none) Date: 14 Apr 1994 23:52:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404150136.AA07512@dino.conicit.ve> NNTP-Posting-Host: net.bio.net unsubscribe proteins cramos@conicit.ve From owner-proteins@net.bio.net Thu Apr 14 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!alberta!quartz.ucs.ualberta.ca!tribune.usask.ca!herald.usask.ca!prabhuv From: prabhuv@herald.usask.ca (Vikram Prabhu) Newsgroups: bionet.molbio.proteins Subject: 14C substrate for DHPS Date: 15 Apr 1994 18:15:31 GMT Organization: University of Saskatchewan Lines: 7 Message-ID: <2omlk3$fbl@tribune.usask.ca> NNTP-Posting-Host: herald.usask.ca X-Newsreader: TIN [version 1.2 PL2] Does any one know of a commercial source for radiolabelled p-aminobenzoic acid, substrate for the enzyme DHPS in the folate pathway? Our current source is not able to supply it. Thanks in advance, Vik Prabhu From owner-proteins@net.bio.net Thu Apr 14 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!tsikar1.life.uiuc.edu!user From: David_Nunn@qms1.life.uiuc.edu (David Nunn) Newsgroups: bionet.molbio.proteins Subject: Protein coupling in SDS? Followup-To: bionet.molbio.proteins Date: 15 Apr 1994 19:05:47 GMT Organization: University of Illinois Lines: 25 Distribution: world Message-ID: NNTP-Posting-Host: tsikar1.life.uiuc.edu Life, ;^) , would be so much easier if it were possible to couple proteins to a solid support in the presence of SDS. I am interested in this for the purpose of coupling SDS-solubilized proteins, that are overexpressed as inclusion bodies, to a solid support for use as an immunoadsorbent. Most of the proteins I am working with are normally cytoplasmic membrane proteins that don't renature without a detergent present. What would be ideal would be to purify these overexpressed proteins on a SDS prep gel and then directly couple them to a column, removing the detergent post-coupling without worrying too much if they precipitate on the column (flow rate problems aside). What I have done so far is blot the proteins to PVDF paper, fragment the paper in a Waring blender, and use this material as an immunoadsorbent to purify specific antibodies. It works alright but not great. Anybody know of a coupling procedure that can be done in the presence of SDS or something comparable to PVDF that doesn't care too much if detergent is around? David Nunn Department of Microbiology University of Illinois Urbana, IL 61801 (217) 333-6131 From owner-proteins@net.bio.net Thu Apr 14 23:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!rc1.vub.ac.be!ub4b!news.sri.ucl.ac.be!NewsWatcher!user From: klosen@bani.ucl.ac.be (Paul Klosen) Newsgroups: bionet.molbio.proteins Subject: Re: AT8 antibody-Alzheimer's Followup-To: bionet.molbio.proteins Date: 15 Apr 1994 11:56:38 GMT Organization: Catholic University of Louvain Lines: 30 Message-ID: References: <2oh6o2$f3r@apollo.it.luc.edu> NNTP-Posting-Host: 130.104.130.1 In article <2oh6o2$f3r@apollo.it.luc.edu>, gnew@orion.it.luc.edu (Geraldine A. New) wrote: > We're looking to purchase this antibody, which is reportedly available > from a company called Innogenetics S.A., Gent, Belgium. Our problem is > that we just don't know how to go about contacting this place. Any > suggestions? > > gerri The adress of Innogenetics is: Innogenetics N.V. Industriepark Zwijnaarde 7, Box 4 B-9052 Zwijnaarde BELGIUM Tel. +32-91-41.07.11 Fax. +32-41.07.99 There should also be a distributor in US according to their catalog BIOSOURCE International Tel. (800)242.0607 Fax. (805)987.3385 However, I didn't find the AT8 antibody. They have an antibody to Alzheimer tangles called MIG-T4. I think you will have to contact directly the belgian adress, because I'm not sure this antibody (AT8) is commercially available. -- Paul Klosen Cell Biology Lab., Catholic University of Louvain klosen@bani.ucl.ac.be From owner-proteins@net.bio.net Thu Apr 14 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.intercon.com!panix!zip.eecs.umich.edu!newsxfer.itd.umich.edu!newsrelay.iastate.edu!hobbes.physics.uiowa.edu!news.uiowa.edu!blue.weeg.uiowa.edu!blue.weeg.uiowa.edu!not-for-mail From: kpmurphy@blue.weeg.uiowa.edu (murphy kenneth p) Newsgroups: bionet.molbio.proteins Subject: Re: 3D-prediction Date: 15 Apr 1994 10:11:30 -0500 Organization: University of Iowa, Iowa City, IA, USA Lines: 40 Distribution: world Message-ID: <2omar2$3vr3@blue.weeg.uiowa.edu> References: <1994Apr13.162758.10014@neutron.nacamar.de> NNTP-Posting-Host: blue.weeg.uiowa.edu In article <1994Apr13.162758.10014@neutron.nacamar.de>, Uwe Harmening wrote: >Hallo there, > >is somebody doing 3D-structure-prediction of proteins on a Silicon Graphics >Workstation with the Biosym-software? How do you print your pictures. Biosym >told me it is possible to print on a Postscriptprinter, but in a rather bad >quality. So many people are taking pictures with a camera (imagine you have >hard an software for thousands of dollars and have to take a picture >from the screen with your camera!?). Is it possible to export the pictures >in Tiff or Gif to a Dos/Win Environment to use it in a textprocessor? >Any suggestions will help. >Thanx in advance! > >-- >Bye and cu > >Jui > >------ > > Fidonet: 2:244/1370.11 >Internet: jui@neutron.nacamar.de >Snailnet: no way! You can use the command snapshot (from a shell) to create a graphics file wqhich will have the name snap.rgb. This file can then be dragged onto an icon in the workspace which will convert it to a TIFF file. Unfortunately, I can't remem