From owner-proteins@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!biosci!not-for-mail From: ouzounis@embl-heidelberg.de (Christos Ouzounis) Newsgroups: bionet.announce,bionet.molbio.proteins,bionet.general,bionet.biophysics,bionet.biology.computational Subject: protein design course in madrid, 18-22 Jul 1994 Date: 2 Jun 1994 20:35:03 -0700 Organization: European Molecular Biology Laboratory Lines: 32 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: bionet Message-ID: <1994Jun2.161050.171252@eros.embl-heidelberg.de> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:1180 bionet.molbio.proteins:2027 bionet.general:9570 bionet.biophysics:288 bionet.biology.computational:547 Protein Design: From Experiments To Computers 18-22 July 1994, El Escorial, Espan~a "Curso de Verano de la Universidad Complutense" Lectures: 18th, De novo protein design L. Regan (Yale), A. Tramontano (IRBM, Roma) 19th, Protein Engineering L. Serrano (EMBL, Heidelberg), F. Gago (U. Alcala), F.X. Aviles (U. Autonoma, Barcelona) 19th, Tools for protein design C. Sander (EMBL, Heidelberg) 21th, Sequence-Structure space A. Valencia (EMBL, Heidelberg), C. Orengo (University College, London), C. Ouzounis (EMBL, Heidelberg) 22th, Computational approaches to struture determination A. Rey (U. Complutense), I. Fita (U. Politecnica Catalunya, CSIC) Round tables: 19th, Prospects in protein engineering 21th, Biologia Estructural en Espana Practicals: 18th, Visualization of protein structures on computers 20th, Protein design on computers Application forms from: CURSOS DE VERANO, c) Donoso Cortes 63 Madrid 28015, Espan~a tel +34 1 394 64 30, fax +34 1 394 64 33 Deadline for applications, 10 June. From owner-proteins@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!MERCK.BCH.UMONTREAL.CA!lemireis From: lemireis@MERCK.BCH.UMONTREAL.CA (Isabelle LEMIRE) Newsgroups: bionet.molbio.proteins Subject: Re: inclusion bodies Date: 2 Jun 1994 13:22:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <9406021511.AA69918@acs4.acs.ucalgary.ca> NNTP-Posting-Host: net.bio.net On 2 Jun 1994, Soheil Seyed Mahmoud wrote: > I have a protein fused to GST (part of P-GEX bacterial expression > vectors). The fusion protein forms inclusion bodies when > expressed in E.coli. I am having problems solubilizing the > protein in a stable form. This means I can solubilize it in > solutions like 8M urea but, as I dialyze the urea out the > proteins go back to precipitated form. Any ideas about my > problem? Thanks in advance. > Soheil S. Mahmoud > You can try sarcosyl Good luck See: Frankel et al., PNAS, February, 1991, vol. 88 pp. 1192-1196. Frangioni and Neel, Anal. Biochem., 210, pp 179-187. From owner-proteins@net.bio.net Wed Jun 01 23:00:00 1994 Newsgroups: bionet.molbio.proteins From: steve@gardner.demon.co.uk (Steve & Rowan Gardner) Path: biosci!daresbury!trane.uninett.no!sunic!pipex!demon!gardner.demon.co.uk!steve Subject: Re: amino acid residue volumes References: <2siir3$5gg@nic.umass.edu> Distribution: world Organization: Myorganisation Reply-To: steve@gardner.demon.co.uk X-Newsreader: Newswin Alpha 0.4 Lines: 32 Date: Thu, 2 Jun 1994 18:34:43 +0000 Message-ID: <471626061wnr@gardner.demon.co.uk> Sender: usenet@demon.co.uk In article: <2siir3$5gg@nic.umass.edu> ECANTOR@UCSVAX.UCS.UMASS.EDU (ERIC J CANTOR) writes: > > Hello. I was wondering if anyone could direct me to a good resource for info > about the physical volume that the different amino acids fill. I have heard > this property called the "residue volume". I am especially interested in the > van der waals radius of the different side chains. I have looked in "typical" > sources such as the "Handbook of Chemistry and Physics" as well as the > "Handbook of Biochemistry and Molecular Biology" but have been unsuccessful. > Any help would be greatly appreciated. Thanks. > > > This is an interesting request - I wonder what you are trying to do ? One good reason that you may be having difficulty is that the volume occupied by a residue in a protein will vary with the conformation in which the amino acid occurs (because the van der Waals radii of the atoms in the sidechain overlap to a greater or lesser extent depending on conformation). As to the choice of van der Waals radii for the atoms of the sidechains, this will make quite a bit of difference to any calculation you want to make. Unfortunately since it is not always clear what the radii should of the hard sphere used to represent each atom, there are several lists of atomic radii for protein atoms available. The best I can suggest is that the values in the Richards paper (Richards, F.M. (1977) Ann. Rev. Biophys. Bioeng., 6, 151-176) and the Connolly paper (Connolly, M.L., (1983) J. Appl. Cryst., 16, 548-558) are widely used in the calculation of accessible surface area, which is a somewhat similar problem. Steve Gardner From owner-proteins@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!BCRSSU.AGR.CA!RAMPITSCH From: RAMPITSCH@BCRSSU.AGR.CA Newsgroups: bionet.molbio.proteins Subject: Peptide purification summary Date: 2 Jun 1994 11:11:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 117 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HD2IFLUKRM004PK4@GW.AGR.CA> NNTP-Posting-Host: net.bio.net OK, here's the summary for PURIFICATION OF A SMALL PEPTIDE. Be warned that its a long message... Here's the original posting: >I have a peptide query: > I'm trying to isolate a peptide about 1000 to 1500 Da (best guess) >and probably cyclic. Initial purification steps are: acid precipitation >(very inefficient) followed by ion exchange chromatography (which >works well). I want to make polyclonals against the peptide and need >more purification steps so I've set up a gel filtration column. Now I >need to concentrate the sample before loading the column. The sample is >about 20 ml in volume and contains approx 0.4M NaCl and 10 mM Tris buffer >pH 7.5. The peptide is reasonably easy to produce, so we can tolerate >some loss. > > We're considering trying: >1) Ultrafiltration (but can't find any appropriate columns) >2) Ammonium sulphate precipitation (the peptide appears to be quite soluble) >3) Phenol (will the peptide go into the phenol? and how do we get it back?) >4) ????? >Thanks for any suggestions or protocols... ___________________________________________________________________________ Keith Rickert Um...with peptides this size, you dont need to keep them in buffered saline solutions, at least most of them you dont. We routinely purify peptides of about this weight via rather more chemical means - reverse phase HPLC, solid-phase extraction, trituation from methanol with ether, etc. I'd suggest using something like SPE for desalting, then lyophilize away the solvent (probably mostly water, some methanol or acetonitrile), then retake up the solid in the relevant buffer solution. -------------------------------------------------------------------------- From John E. Fox How about trying the following:- 1. Initial clean up by ultrafiltration instead of acid precipitation. This should give better recovery. 2. Purify by HPLC on a reverse phase column e.g. Vydac using gradient of water/MeCN with 0.05% TFA. 3. This should give peptide without any salts. 4. If you want to keep the ion exchange, try removing salts with a small column of Sephadex G10. You could also concentrate on a Sep-Pak column. -------------------------------------------------------------------------- John Markwell Jeff, I would suggest that you might try a C-18 cartridge-type filter at this point. With your sample containing a lot of salt, binding should be no problem. Then try lowering the salt and elute in sometihing like 95% water:5% acetonitrile:0.1% TFA. This can be done with a syringe and does not need an HPLC. Try increasing the proportion of acetonitrile until your peptide elutes. We have used this with basic peptides and phosphopeptides with much success. Our proteins elute at about 50% acetonitrile. We use the Maxi-Clean cartridges from Alltech, but they are available from a variety of companies. THe solvent is then removed from the eluted sample in a speedvac. I hope this helps ------------------------------------------------------------------------- Chris If you can find a dialysis membrane that is small enough (they have 1000 MWCO, I believe) put your 20mls into a bag and lay it on dry PEG-8000 wrapped in Saran Wrap and foil. Pop it into the fridge for a few hours and let the PEG suck out the water. Not sure what it'll do in terms of the salt, but you could always just then dialyze it against some buffer for your next step. Why not use HPLC? If it is that small, you might be able to take advantage of a size-exclusion column or C18... Have fun, ------------------------------------------------------------------------ Stephen Lister Jeff, Have you tried putting the peptide/buffer soln. in dialysis tubing (MWCO 1000 or lower), then placing the bag into a 18% PEG 8000/buffer soln. The PEG decreases the volume in the bag within a few hours. This method works a treat on my protein from 0.01mg/ml to 12mg/ml within 8 hours. Good Luck, Steve. ------------------------------------------------------------------------ Michael Rasmussen Jeff What about hydrophobic interaction chromatography (HIC) or RPHPLC. You could try: Precipitation Ion exchange elution with (NH4)2SO4 HIC elution with (NH4)2SO4 RPHPLC on a C4-column I have only tried this with a protein about 50kD. ======================================================================== Looks like reverse phase HPLC is the way to go! I'll probably do that eventually; currently using a g-15 column though. Thanks for all of the input, there were some other messages to but only reiterations of the above. Thanks, Jeff From owner-proteins@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!doc.ic.ac.uk!bay.cc.kcl.ac.uk!bay.cc.kcl.ac.uk!udbl119 Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: High MWt Markers Message-ID: From: udbl119@bay.cc.kcl.ac.uk (Mandy Johnstone) Date: Thu, 2 Jun 1994 18:37:22 Organization: King's College London Nntp-Posting-Host: pgw2.rai.kcl.ac.uk X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 21 Xref: biosci bionet.molbio.methds-reagnts:14865 bionet.molbio.proteins:2023 Hi Folks, I am working on a protein with a molecular weight of 320kD and routinely do Westerns to probe for this protein. My concern however is that I use both Bio-rad and Sigma Broad range markers of which the largest protein is rabbit skeletal muscle myosin which has a mwt of 200kD, and so when it comes to determining the mwt I have to extrapolate back to determine the molecular weight which isn't terribly accurate!. I am therefore looking for a protein with a mwt greater than 300kD that I can add to my markers. Does anyone know of a commercially available protein that has a mwt greater than 300kD I could add to my markers. Alternatively do you know of prepared mwt markers that I could buy that have greater range. Cheers. Mandy. _______________ Mandy Johnstone (M.Johnstone@bay.cc.kcl.ac.uk) King's College, London. From owner-proteins@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!agate!headwall.Stanford.EDU!hkibak From: hkibak@leland.Stanford.EDU (Henrik Kibak) Newsgroups: bionet.molbio.proteins Subject: Total Digest of Proteins Date: 2 Jun 1994 17:40:19 GMT Organization: Stanford University, CA 94305, USA Lines: 15 Message-ID: <2sl5i3$r02@nntp2.Stanford.EDU> NNTP-Posting-Host: elaine38.stanford.edu In order to determine if the molecule I am interested in is a peptide, I would like to determine if protease digestion will abolish activity. I have tried digesting my crude (animal tissue) homogenate with 1 mg/ml pronase (24 hr, room temperature), but this enzyme alone does not completely digest all proteins to amino acids. Can anyone suggest a protease or combination of proteases which will do the job? Thanks, -Beth Schomer POSTED BY hkibak@leland.stanford.edu FOR schomer@leland.stanford.edu Please respond by posting to this newsgroup or by e-mail to: schomer@leland.stanford.edu From owner-proteins@net.bio.net Wed Jun 01 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: inclusion bodies Date: 2 Jun 1994 08:34:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <9406021511.AA69918@acs4.acs.ucalgary.ca> NNTP-Posting-Host: net.bio.net On 2 Jun 1994, Soheil Seyed Mahmoud wrote: > I have a protein fused to GST (part of P-GEX bacterial expression > vectors). The fusion protein forms inclusion bodies when > expressed in E.coli. I am having problems solubilizing the > protein in a stable form. This means I can solubilize it in > solutions like 8M urea but, as I dialyze the urea out the > proteins go back to precipitated form. Any ideas about my > problem? Thanks in advance. > Soheil S. Mahmoud > > You choiced a bad fusion protein ssince it seem that it is interacting with your protein in a way that the folded fused hibrid protein retains a lot of hydrophobic residues at the surface. I'm not sure on what to do but I supose you have two alteernatives: 1. change your fussion protein. 2. try to chemically break the bond between the fussion protein and your protein in an enviroment where your hibrid is denaturated. These are my oppinions. I may say that I don't work with this. Rafael Najmanovich From owner-proteins@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!ACS.UCALGARY.CA!msseyed From: msseyed@ACS.UCALGARY.CA ("Soheil Seyed Mahmoud") Newsgroups: bionet.molbio.proteins Subject: inclusion bodies Date: 2 Jun 1994 08:07:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406021511.AA69918@acs4.acs.ucalgary.ca> NNTP-Posting-Host: net.bio.net I have a protein fused to GST (part of P-GEX bacterial expression vectors). The fusion protein forms inclusion bodies when expressed in E.coli. I am having problems solubilizing the protein in a stable form. This means I can solubilize it in solutions like 8M urea but, as I dialyze the urea out the proteins go back to precipitated form. Any ideas about my problem? Thanks in advance. Soheil S. Mahmoud From owner-proteins@net.bio.net Wed Jun 01 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!ihnp4.ucsd.edu!swrinde!pipex!uknet!festival!leeds.ac.uk!news From: gends@leeds.ac.uk (SCOTT D.) Subject: Cross-linking Message-ID: Sender: news@leeds.ac.uk Organization: University of Leeds Date: Thu, 2 Jun 1994 15:32:36 GMT X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 13 Hia, Anyone know a fast method for chemically crosslinking proteins....i.e. within seconds????Most methods appear to take minutes. Needed for a kinetic study. yours in anticipation, Dave Scott. p.s. already got the gluteraldeyhde method on LDH from 1981 gends%south-01.novell.leeds.ac.uk@gps.leeds.ac.uk or scott@uk.ac.leeds.bio.vax From owner-proteins@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!zip.eecs.umich.edu!umn.edu!newsdist.tc.umn.edu!mayonews.mayo.edu!Mayo.EDU!eberhard From: eberhard@Mayo.EDU (norm eberhardt) Newsgroups: bionet.molbio.proteins Subject: Re: amino acid residue volumes Date: 2 Jun 1994 13:45:40 GMT Organization: Mayo Foundation, Rochester, Minnesota Lines: 44 Distribution: world Message-ID: <2sknq4$kpt@fermat.mayo.edu> References: <2siir3$5gg@nic.umass.edu> NNTP-Posting-Host: feynman.mayo.edu In article <2siir3$5gg@nic.umass.edu>, ECANTOR@UCSVAX.UCS.UMASS.EDU (ERIC J CANTOR) writes: |> Hello. I was wondering if anyone could direct me to a good resource for info |> about the physical volume that the different amino acids fill. I have heard |> this property called the "residue volume". I am especially interested in the |> van der waals radius of the different side chains. I have looked in "typical" |> sources such as the "Handbook of Chemistry and Physics" as well as the |> "Handbook of Biochemistry and Molecular Biology" but have been unsuccessful. |> Any help would be greatly appreciated. Thanks. |> I found this somewhere via WWW and can't remember where. Even more disturbing than that, I haven't been able to relocate it using a hopefully similar search paradigm that yielded the original. I therefore reproduced it with the reference below: (If it is garbled I will send by e-mail). RESIDUE SYMBOL SYMBO LMASS(Da) VOLUME(A3) ALANINE ALA A 71.09 67 ARGININE ARG R 156.19 148 ASPARAGINE ASN N 114.11 96 ASPARTATE ASP D 115.09 91 CYSTEINE CYS C 103.15 86 GLUTAMATE GLU E 129.12 109 GLUTAMINE GLN Q 128.14 114 GLYCINE GLY G 57.05 48 HISTIDINE HIS H 137.14 118 ISOLEUCINE ILE I 113.16 124 LEUCINE LEU L 113.16 124 LYSINE LYS K 128.17 135 METHIONINE MET M 131.19 124 PHENYLALANINE PHE F 147.18 135 PROLINE PRO P 97.12 90 SERINE SER S 87.08 73 THREONINE THR T 101.11 93 TRYPTOPHAN TRP W 186.21 163 TYROSINE TYR Y 163.18 141 VALINE VAL V 99.14 105 Data after Table 1.1 from T. E. Creighton, Proteins, 2nd ed., W. H. Freeman and Company, New York, 1993. norman eberhardt eberhardt@mayo.edu From owner-proteins@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!MODEL.PHR.UTEXAS.EDU!rhodes From: rhodes@MODEL.PHR.UTEXAS.EDU ("David G. Rhodes") Newsgroups: bionet.molbio.proteins Subject: Re: 1000 Da marker required Date: 2 Jun 1994 05:11:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406020711.ZM9014@model.phr.utexas.edu> NNTP-Posting-Host: net.bio.net On Jun 1, 9:48am, RAMPITSCH@BCRSSU.AGR.CA wrote: > Subject: 1000 Da marker required > Hi: just a quick question. I'm looking for MW markers > to calibrate a G-15 column; I've used polymyxin (1280 Da), > bacitracin (1400 Da) and bromo cresol green (700 Da). Something > in the 1000 Da range would be nice. We can't find any > bradykinin (1050 Da). Any ideas?? > BTW thanks to all of you who responded to the "small > peptide blues query"; is there enough interest for me to make a > summary and post it? ----- Yes, please do ---- > > Jeff >-- End of excerpt from RAMPITSCH@BCRSSU.AGR.CA What is the objective of the calibration? Are you trying to measure the MW of an unknown protein? If so, aren't you concerned that in this MW range the approximations and assumptions involved in going from elution volume (oops - I meant "time") to size to MW are very shaky? There are other methods available for MW determination that might be more appropriate for this system. -- _______________________________________________________________________________ | David G. Rhodes | Internet: RHODES@MODEL.PHR.UTEXAS.EDU | | Pharmaceutics Division | (or: RHODES@VAX.PHR.UTEXAS.EDU) | | College of Pharmacy | | | The University of Texas at Austin | Phone: (512)471-4681 | | Austin, TX 78712-1074 | Fax : (512)471-7474 }:) | |_____________________________________|_______________________________________| From owner-proteins@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!gumby!wupost!waikato!waikato.ac.nz!pjc From: pjc@waikato.ac.nz (Peter Charlton) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Which protein seq. lab service?? Message-ID: <1994Jun3.162122.29268@waikato.ac.nz> Date: 3 Jun 94 16:21:22 +1200 Organization: University of Waikato, Hamilton, New Zealand Lines: 7 Xref: biosci bionet.molbio.proteins:2028 bionet.molbio.methds-reagnts:14879 I urgently need suggestions for commercial protein sequencing laboratories which you have found to provide good results with low to average amounts of protein (~10 pmol) Many thanks, Peter. (worried MSc student) From owner-proteins@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!warwick!bham!usenet From: altabios@bham.ac.uk (John E. Fox) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: Which protein seq. lab service?? Date: 3 Jun 1994 09:51:37 GMT Organization: The University of Birmingham, UK Lines: 22 Message-ID: <2smuf9$icv@sun4.bham.ac.uk> References: <1994Jun3.162122.29268@waikato.ac.nz> NNTP-Posting-Host: bcs119.bham.ac.uk X-Newsreader: WinVN version 0.80 Xref: biosci bionet.molbio.proteins:2029 bionet.molbio.methds-reagnts:14887 In article <1994Jun3.162122.29268@waikato.ac.nz>, pjc@waikato.ac.nz (Peter Charlton) says: > >I urgently need suggestions for commercial protein sequencing laboratories >which you have found to provide good results with low to average amounts of >protein (~10 pmol) > >Many thanks, >Peter. >(worried MSc student) I run a core laboratory which among other things, includes protein sequencing. Our record is 10 amino acids off 800 femtomole of sample, although this is at the extreme edge of the technique when using an ABI 473. We can work with either free proteins or blots on PVDF. Just give the blots a light stain with amido black or similar. We run the sequencing to GLP (Good laboratory practice) standards Director Dr. John Fox tel UK 021 414 5450 fax UK 021 414 3376 Email altabios@uk.ac.bham From owner-proteins@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!VM.CC.PURDUE.EDU!ERNESTO From: ERNESTO@VM.CC.PURDUE.EDU Newsgroups: bionet.molbio.proteins Subject: PME sequence Date: 3 Jun 1994 19:31:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406040231.TAA02478@net.bio.net> NNTP-Posting-Host: net.bio.net Do somebody know how can I find the aminoacid sequence of pectin methyl esteras es from different sources? Thanks Martin. E-mail: ernesto@vm.cc.purdue.edu From owner-proteins@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!umd5.umd.edu!yorick.umd.edu!cabirac From: cabirac@yorick.umd.edu (Daniel M. Cabirac) Newsgroups: bionet.molbio.proteins Subject: Ag Biotech Info Available via Internet! Date: 3 Jun 1994 18:40:01 GMT Organization: University of Maryland, College Park Lines: 80 Message-ID: <2snte1$fd0@umd5.umd.edu> NNTP-Posting-Host: yorick.umd.edu X-Newsreader: TIN [version 1.2 PL1] ** NEW BIOTECH BIBLIOGRAPHY AVAILABLE ** The Biotechnology Information Center (BIC) with the Plant Genome Information Center has released a new bibliography entitled: "BIOTECHNOLOGY: COMMERCIALIZATION AND ECONOMIC ASPECTS" Contains 209 references dealing with economic aspects of agricultural biotechnology from market research and forecasts to commercialization issues. For a free copy (print or electronic) see details below. ************************************************************** AGRICULTURAL BIOTECHNOLOGY INFORMATION AVAILABLE VIA INTERNET! ************************************************************** **LEGISLATION AND REGULATION(newly updated)** **CURRENT GENE MAPPING PROJECTS** **PATENTING ISSUES** **TRANSGENIC TOMATO** **BST-BOVINE GROWTH HORMONE** **BIOTECHNOLOGY OF ALGAE** **BIOTECH VIDEOS** **BIOTECH NEWSLETTERS** **AND many more files, and links to 12 other Ag Biotech Gophers The Biotechnology Information Center, an information center of the USDA-National Agricultural Library, has developed a rich source of current Biotechnology-related information available via Internet. The files at the site include bibliographies composed primarily of citations from scientific journals and some popular periodicals (many with abstracts), on subjects ranging from public perception to gene expression in crops and fungi. In addition, several miscellaneous publications dealing with biotechnology meetings, directories and audio-visuals are also available. Numerous links to other biotechnology-related gophers have also been included. In addition to the documents prepared by the Biotechnology Information Center are files created by the Plant Genome and Data Information Center, dealing with gene mapping in a range of plant species. The gopher site already contains more than 70 files, and new files are being added every week. To access these files via Gopher: telnet inform.umd.edu OR gopher inform.umd.edu -Educational Resources -Biotechnology_Information_Center If you prefer to access the documents via FTP, follow the same path as the one listed above. If you have only email access, talk to your Internet provider about "FTPmail," a method of accessing these files via email. Many of the current books about Internet also describe FTPmail. Please send us your questions and comments. Complimentary copies of the printed bibliographies are avialable from BIC by contacting us at the address below. +---------------------------------------------------------------------------+ | Biotechnology Information Center (BIC) voice1: (301)-504-5947 | | National Agricultural Library - USDA voice2: (301)-504-5340 | | 10301 Baltimore Blvd. fax: (301)-504-7098 | | Beltsville, MD 20705-2351 USA e-mail:biotech@nalusda.gov | +---------------------------------------------------------------------------+ | Daniel Cabirac biotech@nalusda.gov | | Ray Dobert rdobert@nalusda.gov | +---------------------------------------------------------------------------+ From owner-proteins@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!darwin.sura.net!fconvx.ncifcrf.gov!fcs260c!tobin From: tobin@fcs260c.ncifcrf.gov (Greg Tobin) Newsgroups: bionet.molbio.proteins Subject: Re: Total Digest of Proteins Message-ID: Date: 3 Jun 94 17:20:11 GMT References: <2sl5i3$r02@nntp2.Stanford.EDU> Sender: usenet@ncifcrf.gov (C News) Organization: Frederick Cancer Research and Development Center Lines: 23 Nntp-Posting-Host: fcs260c.ncifcrf.gov A poster is studying a catalytic activity and wants to digest proteins with a protease to determine whether this activity is associated with a protein or not. Let's assume that the activity is associated with either a protein, DNA or RNA molecule (probably not DNA). Digestion with Proteinase K should abolish most of the activity of a protein. However, prions were originally isolated from Proteinase K digested culture cells. Phenol extraction should remove proteins not covalently linked to nucleic acids. The material can then be ethanol precipitated prior to assay. Most RNA molecules are very sesensitive to RNAae A digestion. Repeated heating and cooling should relax some of the RNAse-resistent secondary structures to permit additional digestion. RNA is also alkaline-sensitive. The original poster (Beth Schomer) should give us some more details concerning the origin of the molecule and the putative activity. We could then give more relevant assistance. -- Greg Tobin, Ph.D. tobin@lcms-1.ncifcrf.gov LCMS PO Box B Frederick, MD 21702 From owner-proteins@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!vincent2.iastate.edu!adwright From: adwright@iastate.edu () Newsgroups: bionet.molbio.proteins Subject: Re: Total Digest of Proteins Date: 3 Jun 94 15:02:12 GMT Organization: Iowa State University, Ames, Iowa Lines: 44 Message-ID: References: <2sl5i3$r02@nntp2.Stanford.EDU> <1994Jun3.110642.171259@eros.embl-heidelberg.de> NNTP-Posting-Host: vincent2.iastate.edu In <1994Jun3.110642.171259@eros.embl-heidelberg.de> houthaeve@embl-heidelberg.de (Tony Houthaeve) writes: >In article <2sl5i3$r02@nntp2.Stanford.EDU>, hkibak@leland.Stanford.EDU (Henrik Kibak) writes: >> In order to determine if the molecule I am interested in is a peptide, >> I would like to determine if protease digestion will abolish activity. >> I have tried digesting my crude (animal tissue) homogenate with 1 mg/ml >> pronase (24 hr, room temperature), but this enzyme alone does not >> completely digest all proteins to amino acids. Can anyone suggest >> a protease or combination of proteases which will do the job? >> >If you want to know whether you really have a peptide/protein, make an >Amino Acid Analysis. By hydrolyzing 1 h at 156 d C 'every' peptidebond >breaks and by subsequent analysis you might even determine which amino >acids are really in the peptide. >Good Luck >Tony Houthaeve >EMBL-Heidelberg Maybe its the temp? We routinely digest corn kernel samples. I use pronase at 1 mg/ml. but do it at 37 to 40 degrees C. I put it in 0.1 N phosphate buffer, pH 7.6. Pronase still is active after 48h in case you want to react longer. I use a mixture of nystatin and erythromycin to control microbes. I have also found that thermolysin at 0.25 mg/ml at 47 to 50 C for 48 hours followed by pronase as described above for, say 72 hours does a really good job. If you can agitate the solution during proteolysis, so much the better. BTW I would like to learn of any other tips, experiences. Allen -- From owner-proteins@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!doc.ic.ac.uk!daresbury!bioftp.unibas.ch!embl-heidelberg.de!houthaeve From: houthaeve@embl-heidelberg.de (Tony Houthaeve) Newsgroups: bionet.molbio.proteins Subject: Re: Total Digest of Proteins Message-ID: <1994Jun3.110642.171259@eros.embl-heidelberg.de> Date: 3 Jun 94 11:06:42 +0100 References: <2sl5i3$r02@nntp2.Stanford.EDU> Organization: European Molecular Biology Laboratory Lines: 19 In article <2sl5i3$r02@nntp2.Stanford.EDU>, hkibak@leland.Stanford.EDU (Henrik Kibak) writes: > In order to determine if the molecule I am interested in is a peptide, > I would like to determine if protease digestion will abolish activity. > I have tried digesting my crude (animal tissue) homogenate with 1 mg/ml > pronase (24 hr, room temperature), but this enzyme alone does not > completely digest all proteins to amino acids. Can anyone suggest > a protease or combination of proteases which will do the job? > If you want to know whether you really have a peptide/protein, make an Amino Acid Analysis. By hydrolyzing 1 h at 156 d C 'every' peptidebond breaks and by subsequent analysis you might even determine which amino acids are really in the peptide. Good Luck Tony Houthaeve EMBL-Heidelberg From owner-proteins@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!psuvax1!rutgers!mbcl!babcock From: babcock@mbcl.rutgers.edu Newsgroups: bionet.molbio.proteins Subject: Nucleic Acid Structure Analysis Program Release Message-ID: <3479.2deb7a1a@mbcl.rutgers.edu> Date: 31 May 94 21:55:38 GMT Lines: 97 Please: if you know someone who can use the program, forward a copy of this message to them. ANNOUNCING THE RELEASE OF A PROGRAM WHICH ANALYSES NUCLEIC ACID CRYSTALLOGRAPHIC COORDINATE DATA ACCORDINATE TO THE EMBO GUIDELINES OF 1988. This program can be used to analyze the nucleic acid part of a protein-NA co-crystal. Several years ago, the European Molecular Biology Organization published guidelines defining how nucleic acid duplex structures can be examined. The guidelines defined three rotational and three translational parameters between the bases comprising a base pair as well as from one base pair to the next. There are five programs readily distributed in order to perform the calculations. We are releasing a sixth which was created to be able to handle not only the calculations of normal duplexes, but also comparably examine mispaired bases, hoogstein base pairs, looped out bases, a single base adjacent to a base pair, intercalated drugs for which a coordinate frame has been defined, etc. The nucleic acid structure analysis program is written in Fortran and runs in a UNIX or VMS environment (please specify preference). The program calculates all of the rotational and translational parameters for complementary base pairs, neighboring base pairs in Cartesian and helical coordinate frames, and base to base Cartesian and helical parameters along each strand. A simple interactive user interface allows for one to specify what file is examined and which parameters to calculate. The program was designed so that the user needs to spend a minimal time reading the documentation in order for the program to run. Full disclosure of the mathematics has been made and published so that the user can readily understand what their parameters mean. The mathematics are unique for this type of calculation and aviod many of the problems previously encountered. In particular, the calculations are performed by a single rotation not sequential rotations avoiding the use of a midway coordinate frame for rotational parameter calculations. This ensures that the magnitude of the rotational parameters is strand free and direction free. Because a single rotation is used, the equations for each rotational parameter are equivalent, therefore, a 5 degree rotation about the X axis is equivalent to a 5 degree rotation about either the Y or the Z axis. This is not always true of other mathematical formulations presently being used. The mathematics used for calculating the complementary base parameters is identical to the math used to calculate the neighboring base/base pair parameters except that different axes are involved. This is not generally the case of the other available programs. In addition, since the calculations are bases upon local considerations, the value of the parameter depends on only the bases involved and are independent of adjacent bases. This allows for more accurate comparison of parameters from one structure to another. Copies of the code can be acquired by e-mailing me at: Marla@Rutchm.Rutgers.edu. Dr. Marla Babcock Dept of Chemistry Rutgers University P.O. Box 939 Piscataway, N.J. U.S.A 08855 Useful References: A users guide to the programs is provided in the paper: Babcock, M.S., Pednault, E.P.D, and Olson, W.K., "Nucleic Acid Structure Analysis: A Users Guide to a Collection of New Analysis Programs," Journal of Biomolecular Structure and Dynamics, Vol. 11, No. 3, pp 597-628, 1993. The issues surrounding the definition of nucleic acid structure parameters and how we address these issues are discussed in: Babcock, M.S., and Olson, W.K., "A New Program for the Analysis of Nucleic Acid Structure Interpretation," in Computation of Biomolecular Structures: Achievements, Problems, and Perspectives, Soumpasis, D.M., and Jovin, T.M., Eds., Springer-Verlag, Heidelberg, pp 65-85, 1993. The mathematical definitions of the nucleic acid structure parameters and the methods used to calculate them are presented in: Babcock, M.S., Pednault, E.P.D, and Olson, W.K., "Nucleic Acid Structure Analysis: Mathematics for Local Cartesian and Helical Structure Parameters That are Truly Comparable Between Structures," Journal of Molecular Biology, Vol. 237, pp 125-156, 1994. In order to take into account base-stacking effects and other physical constraints, the mathematical definitions we have developed contain parameters called "pivot points", which are the points about which the bases in a structure buckle, propeller twist, and open. The statistical analyses that were performed to determine the optimum positions of the pivot points are presented in: Babcock, M.S., and Olson, W.K., "The Effect of Mathematics and Coordinate System on Comparability and 'Dependencies' of Nucleic Acid Structure Parameters," Journal of Molecular Biology, Vol. 237, pp 98-125, 1994. From owner-proteins@net.bio.net Fri Jun 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: Ig-germline Date: 4 Jun 1994 12:46:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406041954.AA17801@speedy.speedy.coacade.uv.mx> NNTP-Posting-Host: net.bio.net Hi! I am interested to obtain updated versions of directories of germline genes and pseudogenes of Ig-Vh and Ig-Vl for human and mouse (translated to aminoacids) like that published for Ig-Vh by Tomlinson et al. in J. Mol. Biol. (1992) 227,776-798. Does somebody could provide to me some or all of these directories? Thanks in advance, ******************************************************************************* * Enrique Vargas-Madrazo * evargas@speedy.coacade.uv.mx * * * optional: salazar@redvax1.dgsca.unam.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 Fri Jun 03 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.ans.net!newstf01.cr1.aol.com!search01.news.aol.com!not-for-mail From: jfrank777@aol.com (JFrank777) Newsgroups: bionet.molbio.proteins Subject: Stable Isotope Growth Mediums for Protein Structure Work Date: 4 Jun 1994 04:46:03 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 9 Sender: news@search01.news.aol.com Message-ID: <2spf0b$m1i@search01.news.aol.com> NNTP-Posting-Host: search01.news.aol.com Hi everyone, I was wondering if anybody had some suggestions on commercially available stable isotope growth mediums. Are there any drawbacks we should be aware of in using these mediums? We are planning on using them in E.Coli cultures and mammalian cell cultures. Thanks. J. Frank UCSD From owner-proteins@net.bio.net Sun Jun 05 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!gdt!bspahh From: bspahh@midge.bath.ac.uk (A H Henry) Subject: Re: Ig-germline Message-ID: Organization: School of Biological Sciences, University of Bath, UK References: <9406041954.AA17801@speedy.speedy.coacade.uv.mx Date: Mon, 6 Jun 1994 09:51:14 GMT Lines: 32 In the referenced article, evargas@SPEEDY.COACADE.UV.MX (Enrique Vargas) writes: Hi! >I am interested to obtain updated versions of directories of germline >genes and pseudogenes of Ig-Vh and Ig-Vl for human and mouse >(translated to aminoacids) like that published for Ig-Vh by Tomlinson >et al. in J. Mol. Biol. (1992) 227,776-798. Does somebody could >provide to me some or all of these directories? You can get the Kabat database of sequences by anonymous ftp from ncbi.nlm.nih.gov in /repository/kabat. It will take a bit of fiddling to pull out the germline sequences as I don't think it is flagged in the database. Look for the sequences which stop just after the second Cysteine. I have got a file with the human VH germline sequences as quoted in the Tomlinson paper. I have sent these by e-mail. The Tomlinson paper didn't have anything about mouse sequences or VL sequences. I'd be interested in those if you find them. I might as well put in a plug for a paper by our group in Bath which had some analysis of the human VH germline sequences. It was Pedersen et al., J. Mol. Biol. (1994), 235, 959-973. Comparison of Surface Accessible Residues in Human and Murine Immunoglobulin Fv Domains. -- Andrew Henry | Read the rec.autos.sport List of Frequently A.H.Henry@bath.ac.uk | Asked Questions v0.1 available by anonymous University of Bath, UK | ftp at mgu.bath.ac.uk _/Sempre Gilles From owner-proteins@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Germany.EU.net!netmbx.de!zib-berlin.de!news.belwue.de!news.uni-freiburg.de!bio5.chemie.uni-freiburg.de!bio6.chemie.uni-freiburg.de!vonrhein From: vonrhein@bio6.chemie.uni-freiburg.de (Clemens Vonrhein) Newsgroups: bionet.molbio.proteins Subject: Re: amino acid residue volumes Date: 6 Jun 1994 12:25:43 GMT Organization: Inst. f. Organische Chemie u. Biochemie, Freibu Lines: 29 Distribution: world Message-ID: <2sv4k7INN13fk@bio5.chemie.uni-freiburg.de> References: <2siir3$5gg@nic.umass.edu> <471626061wnr@gardner.demon.co.uk> NNTP-Posting-Host: bio6.chemie.uni-freiburg.de |> In article: <2siir3$5gg@nic.umass.edu> ECANTOR@UCSVAX.UCS.UMASS.EDU (ERIC J CANTOR) writes: |> > |> > Hello. I was wondering if anyone could direct me to a good resource for info |> > about the physical volume that the different amino acids fill. I have heard |> > this property called the "residue volume". I am especially interested in the |> > van der waals radius of the different side chains. I have looked in "typical" |> > sources such as the "Handbook of Chemistry and Physics" as well as the |> > "Handbook of Biochemistry and Molecular Biology" but have been unsuccessful. |> > Any help would be greatly appreciated. Thanks. |> > |> > |> > Try M. Gerstein, E.L.L.Sonnhammer & C.Chothia (1994), J. Mol. Bio. 236, 1067-1078 Clemens -- ***************************************************************** * Clemens Vonrhein email:vonrhein@bio5.chemie.uni-freiburg.de * * * * Institut f"ur Organische Chemie * * und Biochemie * * Abt. Prof. G.E.Schulz * * Albertstr.21 * * D-79104 Freiburg i.Br., Germany * ***************************************************************** From owner-proteins@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!swrinde!pipex!lyra.csx.cam.ac.uk!bjd12 From: bjd12@cus.cam.ac.uk (Ben Davis) Newsgroups: bionet.molbio.proteins Subject: Re: Stable Isotope Growth Mediums for Protein Structure Work Date: 6 Jun 1994 11:08:51 GMT Organization: University of Cambridge, England Lines: 28 Message-ID: <2sv043$gv1@lyra.csx.cam.ac.uk> References: <2spf0b$m1i@search01.news.aol.com> NNTP-Posting-Host: grus.cus.cam.ac.uk X-Newsreader: TIN [version 1.2 PL2] JFrank777 (jfrank777@aol.com) wrote: : Hi everyone, : I was wondering if anybody had some suggestions on commercially : available stable isotope growth mediums. Are there any drawbacks we : should be aware of in using these mediums? We are planning on using : them in E.Coli cultures and mammalian cell cultures. Thanks. Which stable isotopes do you mean ? I've grown coli in 13C and 15N labelled media, but I've never tried mammalian cells. My experience with coli is that its worth trying both minimal and rich media, and several different strains of coli - can get big differences between them. I've ended up going for minimal media (M9) using 15N ammonium chloride, and 13C glucose; tried out different C sources as well. In the rich media we tried, there seemed to be quite a bit of batch variation. : J. Frank : UCSD Ben ______________________________________________________________________________ Ben Davis, MRC Protein Function and Design, Cambridge, UK ______________________________________________________________________________ "They can make me do it, but they can't make me do it with dignity." From owner-proteins@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!uunet!newstf01.cr1.aol.com!search01.news.aol.com!not-for-mail From: lot49@aol.com (Lot49) Newsgroups: bionet.molbio.proteins Subject: Re: Small peptide purification blues Date: 6 Jun 1994 21:34:01 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 26 Sender: news@search01.news.aol.com Message-ID: <2t0iq9$cef@search01.news.aol.com> References: <01HCSQ4FBJAQ003YA5@GW.AGR.CA> NNTP-Posting-Host: search01.news.aol.com In article <01HCSQ4FBJAQ003YA5@GW.AGR.CA>, RAMPITSCH@BCRSSU.AGR.CA writes: >I'm trying to isolate a peptide about 1000 to 1500 Da (best guess) >and probably cyclic. Initial purification steps are: acid precipitation >(very inefficient) followed by ion exchange chromatography (which >works well). I want to make polyclonals against the peptide and need >more purification steps so I've set up a gel filtration column. Now I >need to concentrate the sample before loading the column. The sample is >about 20 ml in volume and contains approx 0.4M NaCl and 10 mM Tris >buffer >pH 7.5. The peptide is reasonably easy to produce, so we can tolerate >some loss. Try bumping up the pH a bit - say 8.3 (you're pushing Tris right now) and reloading onto your re-equilibrated ion-exchange column. Hit it with 1 M NaCl in a reverse flow (if possible). You should be able to get it down to a mL or so. Salt concentration is irrelevant for your next step, gel filtration. Hope this helps. shawn PS Make sure you use one of those great Pharmacia products! From owner-proteins@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!usenet.ufl.edu!maple.circa.ufl.edu!KDLST1 From: kdlst1@maple.circa.ufl.edu Newsgroups: bionet.molbio.proteins Subject: amino acid - silica binding Date: 7 Jun 1994 06:03:37 GMT Organization: University of Florida - CIRCA Lines: 21 Message-ID: <2t12jpINNmmt@no-names.nerdc.ufl.edu> Reply-To: kdlst1@maple.circa.ufl.edu NNTP-Posting-Host: maple.circa.ufl.edu Netters, Due to the absence of a chromatography thread, I'm asking this question here. There has been much controversy within my research group on exactly how an amino acid binds with a pure silica substrate. Given an AA with a relatively unreactive R group (ie. glycine, alanine) which end of the AA (ie. carboxyl or amine) will bind with silica, and how? As you may guess, biochemistry is getting out of my group's field (materials engineering). I'm sure these interactions have been thoroughly studied, but have been unable to locate any good reference that directly addresses the issue. Replies giving references of such would be EXTREMELY helpful. Any comments addressing the question are also requested. Thanks for your tolerance in helping a man that's out of his field wanting to consume your time with "the basics". Sincerely, Keith KDLST1@ufcc.ufl.edu From owner-proteins@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!think.com!hsdndev!dartvax.dartmouth.edu!Nicholas.J.Morris From: Nicholas.J.Morris@dartmouth.edu (Nicholas J. Morris) Newsgroups: bionet.cellbiol,bionet.general,bionet.immunology,bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.neuroscience Subject: Antibodies to G-protein beta subunits Date: 6 Jun 1994 19:58:40 GMT Organization: Dartmouth College, Hanover, NH Lines: 18 Message-ID: <2svv5g$ph0@dartvax.dartmouth.edu> NNTP-Posting-Host: at-sn-302.dartmouth.edu X-Posted-From: InterNews 1.0@dartmouth.edu Xref: biosci bionet.cellbiol:585 bionet.general:9695 bionet.immunology:1493 bionet.molbio.methds-reagnts:14983 bionet.molbio.proteins:2041 bionet.neuroscience:3509 Dear Fellow Netters, At present I am working on a project in which I need an antibody that recognizes guanine nucleotide binding protein (G-protein) beta subunits. Preferably the antibody should recognize all the different beta subunits both in Western blots and immunoprecipitations (Yes I know that I am asking a lot!). I have tried several of the commercially available antibodies and have had mixed results. If anybody has any experience or knowledge of any antibodies that may be of use I would be grateful if you could take the time to e-mail the details. Thank you for your time in considering these matters. Nick Morris e-mail address: Nicholas.J.Morris@Dartmouth.Edu From owner-proteins@net.bio.net Mon Jun 06 23:00:00 1994 Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!darwin.sura.net!fconvx.ncifcrf.gov!fcs260c2!pnh From: pnh@fcs260c2.ncifcrf.gov (Paul N Hengen) Subject: Re: Which protein seq. lab service?? Message-ID: Summary: Protein from a polyacrylmide gel slice? Sender: Paul N. Hengen Nntp-Posting-Host: fcs260c2.ncifcrf.gov Organization: Frederick Cancer Research and Development Center References: <1994Jun3.162122.29268@waikato.ac.nz> <2smuf9$icv@sun4.bham.ac.uk> Date: Tue, 7 Jun 1994 16:56:29 GMT Lines: 29 Xref: biosci bionet.molbio.proteins:2049 bionet.molbio.methds-reagnts:15011 In article <2smuf9$icv@sun4.bham.ac.uk> altabios@bham.ac.uk (John E. Fox) writes: : I run a core laboratory which among other things, includes protein sequencing. : Our record is 10 amino acids off 800 femtomole of sample, although this is at : the extreme edge of the technique when using an ABI 473. We can work with : either free proteins or blots on PVDF. Just give the blots a light stain with : amido black or similar. We run the sequencing to GLP (Good laboratory : practice) standards : : Director Dr. John Fox : tel UK 021 414 5450 : fax UK 021 414 3376 : Email altabios@uk.ac.bham Dear John: I'm thinking of detecting proteins using a dye such as Nile Red or SYBR Red from Molecular Probes and then slicing the protein band directly from the gel. Is it possible to sequence a protein directly from a polyacryamide gel without blotting onto PVDF? Do you foresee any problems with the red dye blocking the microsequencing? What is the minimum amount of protein needed for sequencing? ******************************************************************************* * Paul N. Hengen, Ph.D. /--------------------------/* * National Cancer Institute |Internet: pnh@ncifcrf.gov |* * Laboratory of Mathematical Biology | Phone: (301) 846-5581 |* * Frederick Cancer Research and Development Center| FAX: (301) 846-5598 |* * Frederick, Maryland 21702-1201 USA /--------------------------/* ******************************************************************************* From owner-proteins@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!jhunix.hcf.jhu.edu!NewsWatcher!user From: basheer@welchlink.welch.jhu.edu (basheer) Newsgroups: bionet.molbio.proteins Subject: Eukaryotic expression Followup-To: bionet.molbio.proteins Date: Mon, 06 Jun 1994 11:39:42 -0500 Organization: Johns Hopkins School of Med Lines: 5 Distribution: world Message-ID: NNTP-Posting-Host: 128.220.56.33 Has anybody tried Baculovirus-GST fusion protein vector system for eukaryotic expression. Thanks Basheer From owner-proteins@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!gatech!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!news.amherst.edu!news.umass.edu!nic.umass.edu!umassmed.UMMED.EDU!achern From: achern@umassmed.UMMED.EDU (Andrew Cherniack) Newsgroups: bionet.molbio.proteins Subject: Radio-sequencing Date: 7 Jun 1994 22:08:13 GMT Organization: University of Massachusetts Medical Center, Worcester Lines: 9 Distribution: world Message-ID: <2t2r4d$mgo@nic.umass.edu> NNTP-Posting-Host: umassmed.ummed.edu Does anybody know a lab or facility that does radio sequencing of 32P labeled peptides in New England, preferably in the greater Boston area. Andrew Cherniack achern@umassmed.ummed.edu From owner-proteins@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!agate!ames!elroy.jpl.nasa.gov!swrinde!gatech!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!news.amherst.edu!news.umass.edu!nic.umass.edu!umassmed.UMMED.EDU!achern From: achern@umassmed.UMMED.EDU (Andrew Cherniack) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Radio-sequencing Date: 7 Jun 1994 21:42:56 GMT Organization: University of Massachusetts Medical Center, Worcester Lines: 9 Distribution: world Message-ID: <2t2pl0$i9a@nic.umass.edu> NNTP-Posting-Host: umassmed.ummed.edu Xref: biosci bionet.molbio.methds-reagnts:15025 bionet.molbio.proteins:2051 Does anybody know a lab or facility that does radio sequencing of 32P labeled peptides in New England, preferably in the greater Boston area. Andrew Cherniack achern@umassmed.ummed.edu From owner-proteins@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!BROWNVM.BROWN.EDU!KMILLER From: KMILLER@BROWNVM.BROWN.EDU (Ken Miller) Newsgroups: bionet.molbio.proteins Subject: Help needed on oligo secondary structure Date: 7 Jun 1994 10:27:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406071727.KAA29002@net.bio.net> NNTP-Posting-Host: net.bio.net I'm currently planning several oligonucleotide primers to use in Polymerase Chain Reaction and I'm concerned that the primers might have secondary structure that may inhibit the reaction. A primer may fold upon itself in such a way as to inhibit binding to the template or 3' end amplification of the product. Does anyone have any suggestions as to a good method to address this issue either manually or via computer? Any and all suggesstions welcome. Thanks! Ben Greenfield From owner-proteins@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!warwick!bham!usenet From: altabios@bham.ac.uk (John E. Fox) Newsgroups: bionet.molbio.proteins Subject: Proteins and sodium borohydride Date: 7 Jun 1994 11:13:37 GMT Organization: The University of Birmingham, UK Lines: 3 Message-ID: <2t1kp1$k5p@sun4.bham.ac.uk> NNTP-Posting-Host: bcs118.bham.ac.uk X-Newsreader: WinVN version 0.80 Has anyone got any references to the use of sodium borohydride to reduce proteins? Apart from the reduction of Cys does anyone know of any side reactions? From owner-proteins@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!agate!headwall.Stanford.EDU!kksng From: kksng@leland.Stanford.EDU (Kenneth Kai-Sing Ng) Newsgroups: bionet.molbio.proteins Subject: selenomethionine and tfa Date: 7 Jun 1994 15:17:41 GMT Organization: Stanford University, CA 94305, USA Lines: 23 Message-ID: <2t232l$cjd@nntp2.Stanford.EDU> NNTP-Posting-Host: elaine1.stanford.edu I am purifying a protein containing selenomethionines in place of the methionines. One of the purification steps for my native, methionine containing protein involves HPLC purification with 0.1% trifluoroacetic acid (TFA) as a modifier (in 0-50% acetonitrile/100-50% water). I have heard that selenomethionine is more sensitive to oxidation and acid hydrolysis than methionine. Has anyone out there had experience with TFA/acetonitrile and selenomethionine? Thanks in advance. Ken Ng kksng@leland.stanford.edu Department of Cell Biology Stanford University -- kksng@leland.stanford.edu Ken Ng Department of Cell Biology Stanford University From owner-proteins@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!doc.ic.ac.uk!news.lif.icnet.uk!mac034006.edin.icnet.uk!user From: k_wilson@icrf.icnet.uk (kate wilson) Newsgroups: bionet.molbio.proteins Subject: Tenascin. Can someone help. Followup-To: bionet.molbio.proteins Date: 7 Jun 1994 11:55:05 GMT Organization: Imperial Cancer Research Fund \ Lines: 9 Message-ID: NNTP-Posting-Host: mac034006.edin.icnet.uk I've Just started my PhD and I'm looking at the ecm molecule tenascin. No one else in my lab knows much about it and I'd really appreciate talking with someone who does. I'm having real difficulty with immunohistochemistry. I'd also like to know about any relevent meetings that are coming up. I'll be eternally grateful for any help given. Please E-mail me Kate (edinburgh,UK) From owner-proteins@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!comlab.ox.ac.uk!oxuniv!dnicker From: dnicker@vax.oxford.ac.uk (Darren Nickerson) Newsgroups: bionet.molbio.proteins Subject: Optical Difference Spectroscopy?? Ref? Message-ID: <1994Jun7.100738.23482@oxvaxd> Date: 7 Jun 94 10:07:38 BST Organization: Oxford University VAX 6620 Lines: 23 In Biochemistry, Vol. 15, No. 24, 1976 5399-5406, Stephen J. Sligar discusses the determination of equilibrium constants (substrate binding) and thermodynamic parameters describing the spin transition. The method is quoted as optical difference spectroscopy, and consists of having an identical sample as the reference, held at constant temperature, while the other sample is taken taken through a range of temperatures, with the optical spectrum being recorded at each temperature. Sligar makes repeated reference to a paper in Methods in Enzymology, in which the methodology is described, but I have as yet been unable to locate this paper, for which a precise reference is never given. Not being a protein chemist myself, I was wondering if anyone was familiar with this technique, and could perhaps supply a reference? Thanks in advance, e-mail replies preferred, and if there is sufficient interest I will post a summary to the list. -Darren Nickerson New Chemistry Laboratory University of Oxford From owner-proteins@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!ub4b!idefix.CS.kuleuven.ac.be!rc1.vub.ac.be!is3e!philstas From: philstas@vub.ac.be (Stas Philippe) Newsgroups: bionet.general,bionet.software,bionet.molbio.proteins,bionet.xtallography,sci.techniques.xtallography Subject: 2ND AND FINAL CALL FOR VOTES: MOLECULAR-MODELLING Date: 7 Jun 1994 08:34:00 GMT Organization: Brussels Free Universities (VUB/ULB), Belgium Lines: 49 Distribution: bionet Message-ID: <2t1bdo$q34@rc1.vub.ac.be> References: <2t064k$nj3@net.bio.net> NNTP-Posting-Host: is3e.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.general:9711 bionet.software:8422 bionet.molbio.proteins:2044 bionet.xtallography:957 sci.techniques.xtallography:405 This is the second and final call for votes on the proposed MOLECULAR-MODELLING/bionet.molec-model newsgroup. We are running several votes simultaneously, so please be certain to follow the directions further below *carefully*! Thanks! The complete charter can be found in Bionet.announce. All molecular modelling techniques will be discussed in this group, esspecially the methodology and implications, rather than the underlying software. Xtallography and NMR refinenment techniques are excluded from the group. Philippe Stas, discussion leader ---------------------------------------------------------------------- : Voting is open on the MOLECULAR-MODELLING/bionet.molec-model newsgroup : and will run through 24:00 hrs Pacific Time on 21 June 1994. Please : send your vote to either of the following addresses: : Address Location Network : ------- -------- ------- : biovote@daresbury.ac.uk U.K. JANET : biovote@net.bio.net U.S.A. Internet/BITNET : PLEASE BE SURE TO FOLLOW THE FORMAT BELOW - WE OFTEN RUN MORE THAN ONE : VOTE AT A TIME SO A SIMPLE "YES" OR "NO" MESSAGE WITHOUT THE NEWSGROUP : NAME MAY BE AMBIGUOUS. Your vote should contain a single line: : YES on MOLMODEL : if you favor creation of the newsgroup above or : NO on MOLMODEL : if you think that the creation of this newsgroup will adversely affect : the BIOSCI system. If you are simply not interested in participating : in this newsgroup, please don't cast a NO vote, but instead just don't : vote at all. : The newsgroup proposal must receive at least 80 YES votes to pass and : the number of YES votes must be greater than the number of NO votes by : at least 40. Discussion of the newsgroup proposal is now closed and : we strongly discourage posting any messages in other forums about the : fact that a CALL FOR VOTES has been issued. : Sincerely, : Dave Kristofferson : BIOSCI/bionet Manager : biosci-help@net.bio.net From owner-proteins@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!munnari.oz.au!ariel.ucs.unimelb.EDU.AU!ucsvc.ucs.unimelb.edu.au!ipx1.agvic.gov.au!news Newsgroups: bionet.molbio.proteins Subject: Cleaving fusion proteins Message-ID: <2t5jjk$bri@ipx1.agvic.gov.au> From: reedm@woody.agvic.gov.au Date: 8 Jun 1994 23:18:12 GMT Organization: Department of Agriculture. Victoria, Australia NNTP-Posting-Host: 202.12.40.45 X-Newsreader: Lines: 3 I am having difficulties cleaving a pMAL fusion protein. I have tried varying the salt and detergent concentrations without any positive results. Is there anyone out there who has got any tricks to try? Quisling Desperate From owner-proteins@net.bio.net Tue Jun 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!warwick!bham!usenet From: altabios@bham.ac.uk (John E. Fox) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: Which protein seq. lab service?? Date: 8 Jun 1994 12:21:30 GMT Organization: The University of Birmingham, UK Lines: 29 Message-ID: <2t4d4a$d22@sun4.bham.ac.uk> References: <1994Jun3.162122.29268@waikato.ac.nz> <2smuf9$icv@sun4.bham.ac.uk> NNTP-Posting-Host: bcs118.bham.ac.uk X-Newsreader: WinVN version 0.80 Xref: biosci bionet.molbio.proteins:2055 bionet.molbio.methds-reagnts:15047 In article , pnh@fcs260c2.ncifcrf.gov (Paul N Hengen) says: > >Dear John: > >I'm thinking of detecting proteins using a dye such as Nile Red or SYBR Red >from Molecular Probes and then slicing the protein band directly from the gel. >Is it possible to sequence a protein directly from a polyacryamide gel without >blotting onto PVDF? Do you foresee any problems with the red dye blocking the >microsequencing? What is the minimum amount of protein needed for sequencing? > >******************************************************************************* >* Paul N. Hengen, Ph.D. /--------------------------/* >* National Cancer Institute |Internet: pnh@ncifcrf.gov |* >* Laboratory of Mathematical Biology | Phone: (301) 846-5581 |* >* Frederick Cancer Research and Development Center| FAX: (301) 846-5598 |* >* Frederick, Maryland 21702-1201 USA /--------------------------/* >******************************************************************************* Dear Paul, I haven't used the particular two dyes you had in mind, but all the other standard dyes such as Coomassie, Amido black, Ponceau, etc. all work OK and don't seem to interfere. You can avoid blotting, by cutting out the band, and extracting the protein using a 'Microcon' filter as supplied by Amicon. (Amicon Inc tel USA 508-777-3622 Beverly MA.) I haven't used one of these yet but I have just had some free samples to try out. Amicon supply the protocol, their publication number is 311. Our record for sequencing is 800 femto mole, 10 amino acids, but this is right at the edge for our machine, ABI473A. 10 pico mole is fairly easy. From owner-proteins@net.bio.net Tue Jun 07 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!mozo.cc.purdue.edu!mace.cc.purdue.edu!b35 From: b35@mace.cc.purdue.edu (Vic Ilag) Subject: Peptide synthesis incorporating Selenomethionine Sender: news@mozo.cc.purdue.edu (USENET News) Message-ID: Date: Wed, 8 Jun 1994 19:30:22 GMT Organization: Purdue University Lines: 6 Is it possible to synthesize a peptide incorporating selenomethionine or any modified amino acid? Please email me at b35@mace.cc.purdue.edu. Thanks in advance. vic From owner-proteins@net.bio.net Tue Jun 07 23:00:00 1994 Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!darwin.sura.net!fconvx.ncifcrf.gov!fcsparc6!pnh From: pnh@fcsparc6.ncifcrf.gov (Paul N Hengen) Subject: Re: Nile red. Message-ID: Summary: alternative to PVDF transfer? Sender: Paul N. Hengen Nntp-Posting-Host: fcsparc6.ncifcrf.gov Organization: Frederick Cancer Research and Development Center References: <2smuf9$icv@sun4.bham.ac.uk> <1994Jun8.192936.171297@eros.embl-heidelberg.de> Distribution: bionet Date: Wed, 8 Jun 1994 23:01:47 GMT Lines: 36 Xref: biosci bionet.molbio.proteins:2059 bionet.molbio.methds-reagnts:15072 In article <1994Jun8.192936.171297@eros.embl-heidelberg.de> houthaeve@embl-heidelberg.de (Tony Houthaeve) writes: > I'm thinking of detecting proteins using a dye such as Nile Red or SYBR Red > from Molecular Probes and then slicing the protein band directly from the gel. > Is it possible to sequence a protein directly from a polyacryamide gel without > blotting onto PVDF? Do you foresee any problems with the red dye blocking the > microsequencing? What is the minimum amount of protein needed for sequencing? | It is not possible to sequence a protein within a polyacrylamide gel, so you | first have to elute the protein out of their or blot it onto PVDF (nitrocellulo | se does not work). Nile red is a good stain, it has hydrophobic properties and | in only a few minutes a high fluorescence in protein bands in gels is seen. | More it is possible to first stain your gel with Nile red and then additionally | blot onto PVDF. Subsequent sequencing can then be performed, Nile red does not | block. see : Biotechniques vol 16, No 4 (1994) p 621-624 An article from | Bermudez, A, et al. Yes. That's where I got the idea from, but it doesn't make sense to me. In that paper, the authors first stain with Nile Red, then electrotransfer to PVDF, then stain with Coomassie Blue before removing the protein for micro- sequencing. They further say that individual bands could be excised and electroblotted onto PVDF in a mini-sandwich. Since the level of detection with Nile Red is a banded protein of about 20 pg, I don't see why you can't just remove the band directly from the gel for sequencing. I'm looking for the best way to recover the band for sequence analysis without transfer to PVDF. Which should I use? electroelution? freeze and squeeze? Centricon? Which works best for maximum yield of protein and sequence data? Or is PVDF the only way to fly? ******************************************************************************* * Paul N. Hengen, Ph.D. /--------------------------/* * National Cancer Institute |Internet: pnh@ncifcrf.gov |* * Laboratory of Mathematical Biology | Phone: (301) 846-5581 |* * Frederick Cancer Research and Development Center| FAX: (301) 846-5598 |* * Frederick, Maryland 21702-1201 USA /--------------------------/* ******************************************************************************* From owner-proteins@net.bio.net Tue Jun 07 23:00:00 1994 Path: biosci!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!athena.mit.edu!gschinni From: gschinni@athena.mit.edu (Ranganathan S Godavarti) Newsgroups: bionet.molbio.proteins Subject: HOMOLOGY SEARCHES IN PROTEINS. Date: 8 Jun 1994 20:54:38 GMT Organization: Massachusetts Institute of Technology Lines: 15 Distribution: world Message-ID: <2t5b6e$79h@senator-bedfellow.MIT.EDU> NNTP-Posting-Host: lancaster.mit.edu Keywords: HOMOLOGY, SEARCH HI, I have the gene sequences and the amino acid sequences of two proteins made by the same organism and these enzymes cleave the same substrate. I looked for homology with other proteins in the databases like genbank etc and found no homology. With software available in Macvector I found very little ,if nothing, in terms of homology. But since they cleave similar substrates I feel that there must be some way to align these proteins and look for hom ology or conserved amino acid residues. Or maybe look for 3 dimensional homology in terms of hydrophobic patches etc. Does anyone know of any software that can do good homology searches?Especially if I am looking to see if the 2 proteins have similar folding or 3D structures...can any molecular modeling software compare the 2 2 sequences and tell me if they are similar? I appreciate your help...thanks in advance. Ranga From owner-proteins@net.bio.net Tue Jun 07 23:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!houthaeve From: houthaeve@embl-heidelberg.de (Tony Houthaeve) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: Nile red. Message-ID: <1994Jun8.192936.171297@eros.embl-heidelberg.de> Date: 8 Jun 94 19:29:36 +0100 References: <1994Jun3.162122.29268@waikato.ac.nz> <2smuf9$icv@sun4.bham.ac.uk> Organization: European Molecular Biology Laboratory Lines: 27 Xref: biosci bionet.molbio.proteins:2058 bionet.molbio.methds-reagnts:15066 In article , pnh@fcs260c2.ncifcrf.gov (Paul N Hengen) writes: > > I'm thinking of detecting proteins using a dye such as Nile Red or SYBR Red > from Molecular Probes and then slicing the protein band directly from the gel. > Is it possible to sequence a protein directly from a polyacryamide gel without > blotting onto PVDF? Do you foresee any problems with the red dye blocking the > microsequencing? What is the minimum amount of protein needed for sequencing? > > *************************************************************************** It is not possible to sequence a protein within a polyacrylamide gel, so you first have to elute the protein out of their or blot it onto PVDF (nitrocellulo se does not work). Nile red is a good stain, it has hydrophobic properties and in only a few minutes a high fluorescence in protein bands in gels is seen. More it is possible to first stain your gel with Nile red and then additionally blot onto PVDF. Subsequent sequencing can then be performed, Nile red does not block. see : Biotechniques vol 16, No 4 (1994) p 621-624 An article from Bermudez, A, et al. Good Luck Tony Houthaeve EMBL -Protein & Peptide Group From owner-proteins@net.bio.net Wed Jun 08 23:00:00 1994 Path: biosci!agate!headwall.Stanford.EDU!hkibak From: hkibak@leland.Stanford.EDU (Henrik Kibak) Newsgroups: bionet.molbio.proteins Subject: Re: HOMOLOGY SEARCHES IN PROTEINS Date: 9 Jun 1994 17:18:08 GMT Organization: Stanford University, CA 94305, USA Lines: 27 Message-ID: <2t7isg$dac@nntp2.Stanford.EDU> References: <1994Jun9.080552.9358@news.uit.no> NNTP-Posting-Host: elaine38.stanford.edu In article <1994Jun9.080552.9358@news.uit.no>, Oyvind Edvardsen wrote: >Greetings, > >In 1987 an excellent 1 page letter was published in Cell [1], entitled >"Homology" in proteins and nucleic acids: A terminology muddle and >a way out of it > >[1] Reek et al. (1987) Cell 50:667 > Agreed, "similarity" is the word people mean 90% of the time. To look at similarities between two protein sequences the finest approach is a dot matrix comparison. Bill Pearson used to supply a public domain program called "plfasta" for IBMpc's that I still use, and I am sure that there are plenty of programs out there that do the same. Looking through my list of software available from the EMBL Data Library I see, for example, "dotplot$.exe" by R. Nakisa which you can ftp, and it probably does the same as Pearson's program. *================================= ====================================* || Henrik Kibak, Ph.D. || Email: hkibak@leland.stanford.edu || || Stanford University || Telephone: 408.655.6227 || || Hopkins Marine Station || Fax: 408.375.0793 || || Pacific Grove CA 93950 USA || Laboratory: David Epel || *================================= ====================================* From owner-proteins@net.bio.net Wed Jun 08 23:00:00 1994 Path: biosci!biosci!not-for-mail From: RasMol Molecular Graphics Newsgroups: bionet.software,bionet.xtallography,bionet.molbio.proteins,bionet.announce Subject: RasMol 2.4 Molecular Graphics Package Available Followup-To: bionet.software Date: 9 Jun 1994 14:41:05 -0700 Organization: Department of Computer Science, University of Edinburgh Lines: 122 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: bionet Message-ID: NNTP-Posting-Host: net.bio.net Summary: Announcing the next anonymous FTP release of the RasMol package. Keywords: RasMol, RasWin, Molecular Graphics, Protein Structure, PDB Xref: biosci bionet.software:8467 bionet.xtallography:965 bionet.molbio.proteins:2066 bionet.announce:1202 RasMol 2.4 Molecular Graphics Visualisation tool. Roger Sayle BioMolecular Structures Group Glaxo Research & Development Greenford, Middlesex, UK. June 1994 This posting is to announce the release of RasMol version 2.4. RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at teaching, display and generation of publication quality images. The program has been developed at the University of Edinburgh's Biocomputing Research Unit and recently with financial assistance from the Biomolecular Structures Group at Glaxo Research and Development, Greenford, UK. This latest version has a significant number of improvements over RasMol 2.3. Most of these enhancements are described at the end of this message. For a complete list of additions, bug fixes and acknowledgements, refer to the distribution's "ChangeLog". RasMol reads in molecular co-ordinate files in a number of formats and interactively displays the molecule on the screen in a variety of colour schemes and representations. Currently supported input file formats include Brookhaven Protein Databank (PDB), Tripos' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XMol XYZ format and CHARMm format files. If connectivity information and/or secondary structure information is not contained in the file this is calculated automatically. The loaded molecule may be shown as wireframe, cylinder (drieding) stick bonds, alpha-carbon trace, spacefilling (CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface. Different parts of the molecule may be displayed and coloured independently of the rest of the molecule or shown in different representations simultaneously. The spacefilling spheres can even be shadowed. The displayed molecule may be rotated, translated, zoomed, z-clipped (slabbed) interactively using either the mouse, the scroll bars, the command line or an attached dials box. RasMol can read a prepared list of commands from a `script' file (or via interprocess communication) to allow a given image or viewpoint to be restored quickly. RasMol can also be used to create script files containing the commands required to regenerate the current image. Finally the rendered image may be written out in a variety of formats including both raster and vector PostScript, GIF, PPM, BMP, Sun rasterfile or as a MolScript input script. RasMol will run on a wide range of architectures and systems including sun3, sun4, sun386i, SGI, DEC, HP and E&S workstations, IBM RS/6000, Cray, Sequent, DEC Alpha (OSF/1, OpenVMS and Windows NT), VAX VMS (under DEC Windows), IBM RS/6000, HP and IBM PC (under Microsoft Windows, Windows NT, OS/2, Linux, BSD386 and *BSD). Support for an Apple Machintosh version is planned for October '94. UNIX and VMS versions require an 8bit, 24bit or 32bit X Windows frame buffer (X11R4 or later). The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory rendering (via the XInput and MIT-SHM extensions) if available. The source code is public domain and freely distributable provided that the original author is suitably acknowledged. The complete source code and user documentation may be obtained by anonymous FTP from ftp.dcs.ed.ac.uk [129.215.160.5] in the directory /pub/rasmol. The source code, documentation and Microsoft Windows executables are stored in several files appropriate for the receiving operating system. Please read the "README" file in the distribution directory. UNIX and VAX systems should retreive either RasMol2.tar.Z, RasMol2.tar.gz or rasmol2.zip. Microsoft Windows users should retrieve RasWin.zip and optionally the Visual Basic package RasMenu.zip both of which contain executable .EXE files. All these files include source code, on-line help, user manual and reference card. Please remember to use "binary" mode when transferring these files between systems. Check that the file size is the same before and after transfer. Any comments, suggestions or questions about the package may be directed to either "rasmol@dcs.ed.ac.uk" or "rasmol@ggr.co.uk". Enhancements since Version 2.3 [February 1994] o Developed an extensive Graphical Uer Interface (GUI) to the Microsoft Windows version of the program. This Visual Basic application will shortly be rewritten and integrated into RasMol on MS Windows, X Windows and Apple Mac platforms. o Added the ability to store the current representation and transformation of the molecule in a RasMol script file using the "write script" command. These script files are also edittable by hand and allow presentations and databases of `interactive protein images' to be constructed. o Added support for molecular dot surfaces. Dot surfaces may currently be displayed on a Van der Waal's or fixed radius surface on the molecule with a specified point density. A partial implementation of solvent accessible dots surfaces initial attempt has been made at supporting solvent accessible surfaces using the "set solvent" command. o Allow the simultaneous display of biomolecular ribbons as both smooth solid surfaces and as parallel depth-cued strands. Solid ribbons are now Gouraud rather than flat (normal) shaded. Allow the central and outermost strands of a ribbon to be displayed in different colours. o Support for a number of small molecule file formats including CHARMm, MDL Mol files, Sybyl Mol2 and MSC's (XMol) XYZ format. Smaller default bond radius for stick models of small molecules and unadjusted Van der Waals radii of atoms in molecules containing explicit hydrogen atoms. o Improved the quality of MolScript script file output. In addition to rotation and secondary structure, RasMol now also passes zooming, translation and z-clipping information to MolScript. o Improved the methods used to determine molecule bonding. RasMol now honours connectivity records stored in co-ordinate files if included. o RasMol can now also display the cartesian co-ordinate axes, bounding box and crystallographic unit cell of the displayed molecule. o Improved the resizing of the Microsoft Windows command line window and added a scroll bar to redisplay text past the top of the screen. -- Roger Sayle, INTERNET: ras32425@ggr.co.uk Glaxo Research & Development (GRD) ros@dcs.ed.ac.uk Greenford Road, Greenford Tel: (+44) 081 966 3567 (direct line) Middlesex UB6 0HE, UK. Fax: (+44) 081 966 4476 From owner-proteins@net.bio.net Wed Jun 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!comlab.ox.ac.uk!oxuniv!dnicker From: dnicker@vax.oxford.ac.uk (Darren Nickerson) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Equilibrium Dialysis? Apparatus/method? Message-ID: <1994Jun9.161540.23600@oxvaxd> Date: 9 Jun 94 16:15:40 BST Organization: Oxford University VAX 6620 Lines: 12 Xref: biosci bionet.molbio.proteins:2065 bionet.molbio.methds-reagnts:15111 In our continuing quest to investigate substrate-binding equilibria (see previous post requesting info on optical difference spectroscopy), we would be very happy to hear from anyone who might have any direct experience with a technique called "equilibrium dialysis", especially in terms of the equipment required, and the experimental technique involved. Any references would be most helpful, e-mail replies are preferred, and I will summarize if there are any/many replies :). Darren Nickerson University of Oxford. From owner-proteins@net.bio.net Wed Jun 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!xlink.net!scsing.switch.ch!elna.ethz.ch!usenet From: MGCASEY@AEOLUS.VMSMAIL.ETHZ.CH (Michael Casey) Newsgroups: bionet.molbio.proteins Subject: Re: Total Digest of Proteins Date: 9 Jun 1994 14:56:45 GMT Organization: ETH ZUERICH Lines: 34 Distribution: world Message-ID: <2t7ajd$66p@elna.ethz.ch> References: <2sl5i3$r02@nntp2.Stanford.EDU> NNTP-Posting-Host: aeolus-fddi.ethz.ch X-News-Reader: VMS NEWS 1.24 In-Reply-To: hkibak@leland.Stanford.EDU's message of 2 Jun 1994 17:40:19 GMT In <2sl5i3$r02@nntp2.Stanford.EDU> hkibak@leland.Stanford.EDU writes: > > > In order to determine if the molecule I am interested in is a peptide, > I would like to determine if protease digestion will abolish activity. > I have tried digesting my crude (animal tissue) homogenate with 1 mg/ml > pronase (24 hr, room temperature), but this enzyme alone does not > completely digest all proteins to amino acids. Can anyone suggest > a protease or combination of proteases which will do the job? > > Thanks, > -Beth Schomer > > POSTED BY hkibak@leland.stanford.edu FOR schomer@leland.stanford.edu > Please respond by posting to this newsgroup or > by e-mail to: schomer@leland.stanford.edu We use Proteinase K to hydrolyse milk proteins. The proteins may first be denatured with SDS and then treated with Proteinase K. SDS does not inhibit the activity of this enzyme. Mike. //////////////////////////////////////////////////////////////////// Michael Casey ^ Swiss Federal Dairy ^ e-mail: mgcasey@aeolus.ethz.ch Research Institute ^ Tel: (+41) 31 970 81 80 3097 Liebefeld-Bern ^ Fax: (+41) 31 970 82 27 Switzerland ^ \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ From owner-proteins@net.bio.net Wed Jun 08 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!trane.uninett.no!ugle.unit.no!news.uit.no!atf1!edvard From: edvard@atf1.uit.no (Oyvind Edvardsen) Subject: Re: HOMOLOGY SEARCHES IN PROTEINS Sender: news@news.uit.no (News admin.) Message-ID: <1994Jun9.080552.9358@news.uit.no> Date: Thu, 9 Jun 1994 08:05:52 GMT Reply-To: edvard@atf1.uit.no Organization: University of Tromsoe, Norway Lines: 44 Greetings, In 1987 an excellent 1 page letter was published in Cell [1], entitled "Homology" in proteins and nucleic acids: A terminology muddle and a way out of it From reading Ranga's posting it is evident that this paper may still be worth reading. Some highlights from the Cell letter: -homology implies "having a common evolutionary origin". Sequences are either homologous or not. -similarity is a quantitative property of the sequences Strict terminology is important in any science, but unfortunately Ranga is not alone in mixing up the terms homology and similarity. The authors of the letter to Cell in 1987 stated that such "muddy" terminology "is clogging the literature", and it still is. E.g. one has the term "homology modeling" which really should have been "similarity modeling". Ranga, it was not my intention to jump on you, but rather use your posting as an opportunity to point to the letter to Cell. I guess your posting really was on similarity? In that case it may perhaps be worthwile to have a look at the HSSP [2] stuff from EMBL-Heidelberg. Best reg'ds -oed. References: [1] Reek et al. (1987) Cell 50:667 [2] Sander & Schneider (1991) Proteins 9:56-68 -o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o- ___ _ | /| _| |_ _| __ _ _| _ _ |/_| \/ \/ | |\| |_| |_ |_| \/ |_|_ | |_| _\ |_' |\| / _____________________________________________________________________________ Dept. of Pharmacology, IMB | University of Tromsoe | TelePhone: +47-77 64 53 42 MH, Breivika | TeleFax: +47-77 64 53 10 N-9037 TROMSOE | Email: edvard@fagmed.uit.no NORWAY | URL: http://atf1.fagmed.uit.no/cgl.html ------------------------------------------------------------------------------ From owner-proteins@net.bio.net Wed Jun 08 23:00:00 1994 Path: biosci!agate!msuinfo!harbinger.cc.monash.edu.au!bunyip.cc.uq.oz.au!harris From: harris@biosci.uq.oz.au (ml harris) Newsgroups: bionet.molbio.proteins Subject: receive this group as email? Date: 9 Jun 1994 22:20:09 GMT Organization: University of Queensland Lines: 13 Message-ID: <2t84ip$fl3@dingo.cc.uq.oz.au> NNTP-Posting-Host: florey.biosci.uq.oz.au Summary: receive this group as email? Keywords: receive this group as email? Was just wondering if it were possible to receive the postings to this group as email. Thanks heaps Michelle ---------------------------------------------------------------------------- Michelle Harris | Centre for Drug Design and Development | Email address: University of Queensland | harris@biosci.uq.oz.au St Lucia, Queensland | ---------------------------------------------------------------------------- From owner-proteins@net.bio.net Wed Jun 08 23:00:00 1994 Newsgroups: bionet.molbio.proteins,sci.bio.technology,bionet.biophysics Path: biosci!agate!overload.lbl.gov!dog.ee.lbl.gov!ihnp4.ucsd.edu!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!EU.net!uknet!festival!leeds.ac.uk!news From: ccdajrfg@leeds.ac.uk (A.J. REBELO FERREIRA GUIOMAR) Subject: conformational studies of immobilised enzymes Message-ID: Sender: news@leeds.ac.uk Organization: University of Leeds Date: Thu, 9 Jun 1994 19:15:28 GMT X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 3 Xref: biosci bionet.molbio.proteins:2064 sci.bio.technology:1263 bionet.biophysics:299 Does anyone know any group working on conformational characterisation of enzymes after being covalently immobilised onto a solid, polymeric support? Thanks! From owner-proteins@net.bio.net Wed Jun 08 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!EU.net!sunic!trane.uninett.no!daresbury!bioftp.unibas.ch!hubi.abc.hu!hegyi From: hegyi@hubi.abc.hu (Hedvig Hegyi) Subject: Re: HOMOLOGY SEARCHES IN PROTEINS Message-ID: Organization: ABC-Hungary References: <1994Jun9.080552.9358@news.uit.no> Date: Thu, 9 Jun 1994 17:07:52 GMT Lines: 61 edvard@atf1.uit.no (Oyvind Edvardsen) writes: >Greetings, >In 1987 an excellent 1 page letter was published in Cell [1], entitled >"Homology" in proteins and nucleic acids: A terminology muddle and >a way out of it >From reading Ranga's posting it is evident that this paper may still be >worth reading. Some highlights from the Cell letter: >-homology implies "having a common evolutionary origin". Sequences are >either homologous or not. >-similarity is a quantitative property of the sequences >Strict terminology is important in any science, but unfortunately >Ranga is not alone in mixing up the terms homology and similarity. The >authors of the letter to Cell in 1987 stated that such "muddy" terminology >"is clogging the literature", and it still is. E.g. one has the term >"homology modeling" which really should have been "similarity modeling". >Ranga, it was not my intention to jump on you, but rather use your posting >as an opportunity to point to the letter to Cell. I guess your posting >really was on similarity? In that case it may perhaps be worthwile to have >a look at the HSSP [2] stuff from EMBL-Heidelberg. >Best reg'ds >-oed. ... In my opinion anybody who has ever heard the terminology "sequence homology", or "homologous sequences" exactly knows, what it means. Nobody will mix up two homologous sequences with two homologous proteins (ie. of common evolutionary origin). The fact that this terminology still survives justifies itself. The word 'homologous' in this context is used for 'significantly similar', not simply for 'similar'. But let us leave play with words to Wittgenstein. It is rather his privilege. Returning to the original questions: 1/ There are a lot of tools and facilities for looking for sequences that are homologous for a certain sequence. If you are particularly interested in protein sequences then you can try our server, that is a BLAST server and concentrates on protein domain HOMOLOGIES. Send a message to the address: domain@hubi.abc.hu containing the word 'help' in the body of the message and you will get a description of it. 2/ Prediction of 3D structure from sequence is a rather difficult and (mostly) yet unresolved problem. But there have been a lot of developments lately in this field. I read for example an excellent paper (Jones et al., Nature, Vol. 358:86-89, 1992) that tries to derive a 3D structure from a protein sequence based on fitting sequence 'directly onto the backbone coordinates of known protein sequences'. Hope this helps. Hedvig Hegyi From owner-proteins@net.bio.net Thu Jun 09 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!xlink.net!scsing.switch.ch!swidir.switch.ch!univ-lyon1.fr!taloa.unice.fr!ws41.cnusc.fr!ciril.fr!thot.u-strasbg.fr!praline.u-strasbg.fr!hubert From: Pierre Hubert Newsgroups: bionet.molbio.proteins Subject: Help: EGF-receptor purification Date: 10 Jun 1994 09:57:52 GMT Organization: INSERM U-338 Lines: 19 Distribution: world Message-ID: <2t9df0$78i@thot.u-strasbg.fr> NNTP-Posting-Host: praline.u-strasbg.fr X-UserAgent: Version 1.1.3 X-XXMessage-ID: X-XXDate: Fri, 10 Jun 94 10:59:08 GMT We are trying to prepare solubilized lectin-purified EGF receptors from A-431 cells for binding and kinase studies. From the litterature we picked up a method involving solubilization in Triton X-100, chromatography on Wheat Germ Agglutinin-agarose, and elution in acetylglucosamine + MgCl2 + glycerol. On the day of purification, EGF binding and EGF stimulation of receptor autophosphorylation work OK. Our big problem is that after a few days in the -80! freezer, EGF binding and kinase stimulation decrease and eventually are completely lost. We can still detect autophosphorylation, but no stimulation by EGF, and autophosphorylated receptors appear as oligomers upon non-denaturating electrophoresis analysis, with very little monomer. Are there any tricks to allow for conservation of active EGF-receptors for a few weeks ? Is there a better partial purification procedure ? Or is it better use freshly prepared receptors for each experiment ? (quite tedious...) Thanks a lot for any tips. From owner-proteins@net.bio.net Thu Jun 09 23:00:00 1994 Path: biosci!agate!spool.mu.edu!nigel.msen.com!zib-berlin.de!news.belwue.de!news.uni-freiburg.de!sun2.ruf.uni-freiburg.de!eschiltz From: eschiltz@sun2.ruf.uni-freiburg.de (Emile Schiltz) Newsgroups: bionet.molbio.proteins Subject: Re: Proteins and sodium borohydride Date: 10 Jun 1994 15:36:40 GMT Organization: Rechenzentrum der Universitaet Freiburg, Germany Lines: 18 Message-ID: <2ta1a8$p0e@sun2.ruf.uni-freiburg.de> References: <2t1kp1$k5p@sun4.bham.ac.uk> NNTP-Posting-Host: sun2.ruf.uni-freiburg.de X-Newsreader: TIN [version 1.2 PL1] John E. Fox (altabios@bham.ac.uk) wrote: : Has anyone got any references to the use of sodium borohydride to reduce : proteins? : Apart from the reduction of Cys does anyone know of any side reactions? this was done by many people that wanted to fix the PLP-Lys bond in enzymes. it works fine , no particular side-effects, except that the solution produces hydrogen for a while. I have no reference at hand but just look for pyridoxyl-phosphate binding sites in enzymes or in Methods of Enzymology. Bye -- Emile Schiltz or Institute of Organic Chemistry and Biochemistry Albertstrasse 21, D-79104 Freiburg, Germany phone: +49 761 203 6090 From owner-proteins@net.bio.net Thu Jun 09 23:00:00 1994 Path: biosci!agate!ames!elroy.jpl.nasa.gov!usc!howland.reston.ans.net!EU.net!sunic!columba.udac.uu.se!onyx.bmc.uu.se!dunten From: dunten@onyx.bmc.uu.se (Pete Dunten) Newsgroups: bionet.molbio.proteins Subject: Re: Proteins and sodium borohydride Date: 10 Jun 1994 17:55:20 GMT Organization: Uppsala University Lines: 3 Distribution: world Message-ID: <2ta9e8$j14@columba.udac.uu.se> References: <2t1kp1$k5p@sun4.bham.ac.uk> <2ta1a8$p0e@sun2.ruf.uni-freiburg.de> NNTP-Posting-Host: onyx.bmc.uu.se Phosphorylated aspartate is also reduced by borohydride. See JBC Vol. 264, 21770 ('89) for a protocol and possibly further references to the use of borohydride. From owner-proteins@net.bio.net Thu Jun 09 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!xlink.net!zib-berlin.de!news.th-darmstadt.de!hrz-ws11.hrz.uni-kassel.de!newsserver.rrzn.uni-hannover.de!deimos.rz.Uni-Osnabrueck.DE!ax3301.biologie.uni-osnabrueck.de!engel From: engel@ax3301.biologie.uni-osnabrueck.de (Siggi Engelbrecht) Newsgroups: bionet.molbio.proteins Subject: ******** Date: 9 Jun 1994 11:28:32 GMT Organization: Universitaet Osnabrueck, Biophysik Lines: 6 Distribution: world Message-ID: <2t6ud0$g09@deimos.rz.Uni-Osnabrueck.DE> Reply-To: engel@zeder.biologie.uni-osnabrueck.de NNTP-Posting-Host: ax3301.biologie.uni-osnabrueck.de I am looking for executables for xv and ghostscript running on the Evans and Sutherland ESV workstation. gs _MUST_ include the hp 550c driver device cdj550. Alternatively I am looking for somebody who is willing to compile the gs261 gdevmem1.c file on a SGI RS3000 for me. From owner-proteins@net.bio.net Thu Jun 09 23:00:00 1994 Path: biosci!agate!ames!elroy.jpl.nasa.gov!swrinde!gatech!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!unixg.ubc.ca!quartz.ucs.ualberta.ca!uapc.biology.ualberta.ca!wgallin From: wgallin@gpu.srv.ualberta.ca (Warren Gallin) Newsgroups: bionet.molbio.proteins Subject: X-gal reaction product solubility Followup-To: bionet.molbio.proteins Date: Fri, 10 Jun 94 22:04:46 GMT Organization: University of Alberta Lines: 15 Message-ID: NNTP-Posting-Host: uapc.biology.ualberta.ca X-Newsreader: VersaTerm Link v1.1.4 Greetings, We have been staining wholemounts of embryos that we hope have a transgene for lacZ, with the enzyme directed to the nuclei. To see whether the blue stuff that we see is legitimate (i.e. present in the nuclei and therefore a product our transgene) we want to embed and section the embryos. Does anyone know if the X-gal reaction product will stay in place through an ethanol dehydration series and clearing in either xylene or chloroform followed by impregnation in hot paraffin? Do we need to post-fix the embryos before we go through the embedding? All comments and suggestions would be appreciated. Warren Gallin, Department of Zoology, University of Alberta wgallin@gpu.srv.ualberta.ca From owner-proteins@net.bio.net Sat Jun 11 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!ihnp4.ucsd.edu!usc!cs.utexas.edu!howland.reston.ans.net!xlink.net!wega.fibronics.de!neutron!jui From: jui@neutron.nacamar.de (Uwe Harmening) Subject: PDB-Files Message-ID: <1994Jun12.125420.20816@neutron.nacamar.de> Organization: N.A.C.A.M.A.R. HQ and Development Center Date: Sun, 12 Jun 1994 12:54:20 GMT X-Newsreader: TIN [version 1.2 PL2] Lines: 19 Hallo, we just got the Rasmol-Software for Windows, which is excellent and available thru ftp.dcs.ed.ac.uk! (raswin.zip in pub/rasmol) But, because I am new to the matter, there is a question. Where can I get standard pdb-structured files? I would need HSFs or other transcription-factors. Thanx -- Bye and cu Jui ------ Fidonet: 2:244/1370.11 Internet: jui@neutron.nacamar.de Snailnet: no way! From owner-proteins@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!agate!library.ucla.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!EU.net!Germany.EU.net!nntp.gmd.de!dearn! barilvm!vms.huji.ac.il!wisipc.weizmann.ac.il!inherit4.weizmann.ac.il! lsprilus Newsgroups: bionet.molbio.proteins Subject: Re: PDB-Files Message-ID: <1994Jun14.044123.21213@wisipc.weizmann.ac.il> From: Jaime Prilusky Date: Tue, 14 Jun 1994 04:41:23 GMT Sender: news@wisipc.weizmann.ac.il (News User) References: <1994Jun12.125420.20816@neutron.nacamar.de> Organization: Weizmann Institute of Science X-Xxmessage-Id: X-Xxdate: Tue, 14 Jun 1994 05:40:22 GMT X-Newsreader: Nuntius Version 1.2 Lines: 31 Uwe Harmening, jui@neutron.nacamar.de writes: >we just got the Rasmol-Software for Windows, which is excellent and >available thru ftp.dcs.ed.ac.uk! (raswin.zip in pub/rasmol) >But, because I am new to the matter, there is a question. Where can I get >standard pdb-structured files? ... Jonathan B. Marder, MARDER@agri.huji.ac.il writes: >GDB files can be got from NIH via gopher. I don't have the exact pointer and >right now, our connections are down. One way in is to go via gopher at >merlot.gdb.org - you should eventually find an item to search the NIH database >for what you seek. Please note: PDB <> GDB Name : PDB e-mail file server Organism : Protein Data Bank / Brookhaven National Laboratory / USA Type : RETRIEVAL Description: Provides PDB general information and documentation files. Address : fileserv@pb1.pdb.bnl.gov Note : To get help send a message containing the following type of line: send info your_e-mail_address. Contact : To report problems: skora@bnl.gov Dr Jaime Prilusky, Head Bioinformatics Unit ! LSPRILUS@WEIZMANN.WEIZMANN.AC.IL Weizmann Institute of Science ! fax: 972-8-344113 From owner-proteins@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!xlink.net!nntp.gmd.de!dearn!barilvm!vms.huji.ac.il!marder.agri.huji.ac.il!MARDER Newsgroups: bionet.molbio.proteins Subject: Re: PDB-Files Message-ID: From: MARDER@agri.huji.ac.il (Jonathan B. Marder) Date: Mon, 13 Jun 1994 16:03:43 GMT References: <1994Jun12.125420.20816@neutron.nacamar.de> Distribution: world Organization: The Hebrew University of Jerusalem Nntp-Posting-Host: marder.agri.huji.ac.il X-Newsreader: Trumpet for Windows ÝVersion 1.0 Rev B¨ Lines: 26 In article <1994Jun12.125420.20816@neutron.nacamar.de> jui@neutron.nacamar.de (Uwe Harmening) writes: >Subject: PDB-Files >From: jui@neutron.nacamar.de (Uwe Harmening) >Date: Sun, 12 Jun 1994 12:54:20 GMT >Hallo, >we just got the Rasmol-Software for Windows, which is excellent ... I agree - it certainly is! I have been looking at photosynthetic centres with it. >But, because I am new to the matter, there is a question. Where can I get >standard pdb-structured files? I would need HSFs or other >transcription-factors. GDB files can be got from NIH via gopher. I don't have the exact pointer and right now, our connections are down. One way in is to go via gopher at merlot.gdb.org - you should eventually find an item to search the NIH database for what you seek. __ Jonathan B. Marder ' Department of Agricultural Botany | Internet: MARDER@agri.huji.ac.il The Hebrew University of Jerusalem | /\/ Bitnet: MARDER@HUJIAGRI Faculty of Agriculture |/ \ Phone: (08 or +9728) 481918 P.O.Box 12, Rehovot 76100, ISRAEL / Fax: (08 or +9728) 467763 From owner-proteins@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!duong From: duong@chestnut.chem.upenn.edu (Duc Duong) Newsgroups: bionet.molbio.proteins,bionet.molbio.gdb Subject: how to calculate H coordinates of NH bond with pdb file Date: 13 Jun 1994 16:11:51 GMT Organization: NMR Biochemistry Graduate Research Lab Lines: 9 Message-ID: <2ti0g7$pmu@netnews.upenn.edu> NNTP-Posting-Host: chestnut.chem.upenn.edu Xref: biosci bionet.molbio.proteins:2075 bionet.molbio.gdb:204 hi.. I tried to calculate the Hydrogen coordinates of the N-H bond in the pdb file (no need for the side chain Hydrogen, or OH).. I looked thru Quanta4.0 and it does it nicely thru CHARM Energy.. so Is there an algorithm available out there?? This one seems very useful so anyone has any reference or suggestion?? Thank you. dduc From owner-proteins@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!rsaldanh From: rsaldanh@magnus.acs.ohio-state.edu (Roland J Saldanha) Newsgroups: bionet.molbio.proteins Subject: Re: antibody probe solution Date: 13 Jun 1994 21:48:32 GMT Organization: The Ohio State University Lines: 26 Message-ID: <2tik7g$8dr@charm.magnus.acs.ohio-state.edu> References: NNTP-Posting-Host: beauty.magnus.acs.ohio-state.edu X-ORIGINAL-NEWSGROUPS: bionet.molbio.proteins In article , Hanson Lab wrote: >Hello Protein People-- >We are having a lab discussion regarding the number of times one can use a >primary antibody probe solution. Like, can it be used indefinitely? Or is >more than once a dangerous precedent? Are there any general >recommendations from this group? Any ideas would be most welcome. Any >hints on when a solution has been used once-too-many times, and what the >Western would look like (slow to develop, or weak bands disappearing). >thanks for any input, > Claudia Sutton >cas9@cornell.edu >Cornell University >Ithaca,NY >hey, it's hot here today! We have repeatedly used Antibodies upto 10 times or longer. We store the antibodies in TBS with BSA and add sodium azide. The diagnostic characteristics that you mention (slow development) is what we use to judge whether its time to replenish the stock. If the antibody is very precious we merely spike the pool with a smaller amount of the original antibody (say a 1;20,000 dilution if the original dilution was 1:2500 etc). Roland Saldanha From owner-proteins@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!rsaldanh From: rsaldanh@magnus.acs.ohio-state.edu (Roland J Saldanha) Newsgroups: bionet.molbio.proteins Subject: Solubilization of a Nucleic Acid Binding protein Date: 14 Jun 1994 04:11:37 GMT Organization: The Ohio State University Lines: 13 Message-ID: <2tjalp$9im@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: beauty.magnus.acs.ohio-state.edu I am working with a reverse transcriptase that is very tightly attached to its cognate template. On freeing the enzyme from nucleic acids (say by micrococcal nuclease digestion) the protein has a tendency to immediately aggregate and come out of solution though it retains some activity in this precipitated form. I am looking for means to solubilise the protein to facilitate purification and would welcome suggestions from this group. I have tried detergents (non-ionic) and an array of monovalent salts at concentrations from 0.5 to 2.5 M. The protein is very basic with a calculated pI of 10.3! Roland Saldanha From owner-proteins@net.bio.net Sun Jun 12 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!swrinde!ihnp4.ucsd.edu!library.ucla.edu!news.ucdavis.edu!Dave.Bates From: dobates@ucdavis.edu (Dave Bates) Subject: Re: X-gal reaction product solubility Message-ID: X-Posted-From: InterNews 1.0@rocky.ucdavis.edu. Sender: -Not-Authenticated-[1543] Organization: University of California, Davis References: Date: Mon, 13 Jun 1994 22:20:54 GMT Xdisclaimer: No attempt was made to authenticate the sender's name. Lines: 39 In article wgallin@gpu.srv.ualberta.ca (Warren Gallin) writes: > Greetings, > > We have been staining wholemounts of embryos that we hope have a > transgene for lacZ, with the enzyme directed to the nuclei. To see whether > the blue stuff that we see is legitimate (i.e. present in the nuclei and > therefore a product our transgene) we want to embed and section the embryos. > Does anyone know if the X-gal reaction product will stay in place through an > ethanol dehydration series and clearing in either xylene or chloroform > followed by impregnation in hot paraffin? Do we need to post-fix the > embryos before we go through the embedding? All comments and suggestions > would be appreciated. > > Warren Gallin, > Department of Zoology, University of Alberta > wgallin@gpu.srv.ualberta.ca I was transfecting cells in vivo with an LacZ expression vector, and having problems mounting the tissue in glycerol, so I took a precious transfected organ, stained with X-Gal which looked beautiful, and dehdrated it in alcohol and mounted in methyl salycilate to get a good picture, and BAM, the blue colouration had gone. I nearly had a fit. I posted exactly this question to Methds&Reagnts newsgroup and got a very useful reply from Sean May at Warwick, saying that the blue product was soluble in al;cohol, and in order to keep it there you need to post-fix. Needless to say I never tried it again, and now mount in Vectastain mounting medium from Vector Labs on the advice of Ann Baldwin from Arizona. Great stuff, clear as a bell, stops bleaching of fluorescence, and don't need dehydration. Good luck ---------------------------------------------------------------------- Dave Bates, dobates@ucdavis.edu Department of Human Physiology, University of California at Davis No I don't have a sense of humour, now buy me a beer ---------------------------------------------------------------------- From owner-proteins@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!NewsWatcher!user From: Lab_Mac_Hanson@QMrelay.mail.cornell.edu (Hanson Lab) Newsgroups: bionet.molbio.proteins Subject: antibody probe solution Followup-To: bionet.molbio.proteins Date: 13 Jun 1994 15:33:35 GMT Organization: Cornell University Lines: 13 Sender: cas9@cornell.edu (Verified) Message-ID: NNTP-Posting-Host: 128.84.203.227 Hello Protein People-- We are having a lab discussion regarding the number of times one can use a primary antibody probe solution. Like, can it be used indefinitely? Or is more than once a dangerous precedent? Are there any general recommendations from this group? Any ideas would be most welcome. Any hints on when a solution has been used once-too-many times, and what the Western would look like (slow to develop, or weak bands disappearing). thanks for any input, Claudia Sutton cas9@cornell.edu Cornell University Ithaca,NY hey, it's hot here today! From owner-proteins@net.bio.net Mon Jun 13 23:00:00 1994 Path: biosci!agate!spool.mu.edu!torn!news.unb.ca!UNBVM1.CSD.UNB.CA From: MCCORMICK M Newsgroups: bionet.virology,bionet.jobs,bionet.general,bionet.molbio.proteins Subject: looking for advice Date: 14 JUN 94 13:38:55 AST Organization: The University of New Brunswick Lines: 16 Sender: usenet@UNB.CA Message-ID: <14JUN94.14740739.0094@UNBVM1.CSD.UNB.CA> NNTP-Posting-Host: unbvm1.csd.unb.ca Xref: biosci bionet.virology:632 bionet.jobs:4485 bionet.general:9890 bionet.molbio.proteins:2082 Hi! I have just completed the 3rd year of my BSc in Bio-Chemistry at UNB(Fredericton), and I am interested in persuing a Masters/PhD after I graduate. This summer I am working in the Molecular Virology research lab here at UNB on an NSERC scholarship (which I was damn lucky to get!), and plan to do an honours in the fall. I would like to know some of the inside stuff on (Molecular/Bio- Chem) Graduate Programs in Canada. Who is doing really good research? Who is good to work with? Also, I have heard that it is smart to start with a Masters, and if things are going well, to apply for PhD after the first six months or so. Is this true? Thanx Craig (w332@unb.ca) From owner-proteins@net.bio.net Mon Jun 13 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!xmission!u.cc.utah.edu!collagen.med.utah.edu!reese From: reese@msscc.med.utah.edu (Van R. Reese) Newsgroups: bionet.molbio.proteins Subject: Collagen peptides Date: 14 Jun 1994 14:41:45 GMT Organization: Univ. of Utah, Div. of rheumatology Lines: 2 Distribution: usa Message-ID: NNTP-Posting-Host: collagen.med.utah.edu I am working with collagen peptides and would be interested in any suggestions for separating them. From owner-proteins@net.bio.net Mon Jun 13 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!nac.no!eunet.no!nuug!EU.net!howland.reston.ans.net!cs.utexas.edu!not-for-mail From: mcdonald@bsm.biochemistry.ucl.ac.uk (Ian McDonald) Newsgroups: bionet.molbio.proteins Subject: Re: how to calculate H coordinates of NH bond with pdb file Followup-To: poster Date: 14 Jun 1994 17:34:32 -0500 Organization: University College London Lines: 151 Sender: nobody@cs.utexas.edu Message-ID: <1994Jun14.092139.43360@ucl.ac.uk> References: <2ti0g7$pmu@netnews.upenn.edu> NNTP-Posting-Host: news.cs.utexas.edu I don't know about the Charmm algorithm, but the HBPLUS program is capable of positioning Hs according to preset positions. HBPLUS v 2.25 - Free Hydrogen Bond Calculator --------------------------------------------- HBPLUS is a hydrogen bond calculation program that has been developed in-house over the course of over four years and has been used in countries as distant as the USA, Taiwan and South Africa. It calculates positions for polar hydrogens, which it can output in PDB format. It can also be used to generate a list of neighbour interactions. In the process of the algorithm, it calculates the angles at the hydrogen and the acceptor as well as the donor-acceptor and hydrogen-acceptor distances. It also calculates the positions of polar hydrogens. All the hydrogen bond criteria, including which atoms do or do not hydrogen bond, are customisable. The program inputs a Brookhaven protein database format file, and outputs a list of hydrogen bonds, including geometries. It can also output a Brookhaven format file with the polar hydrogen positions included. It is written in ANSI C and has been checked on several UNIX systems as well as VAX/VMS. It requires too much memory to run on an IBM PC. If you would like a copy of HBPLUS, simply snailmail me a signed copy of the confidentiality agreement at the bottom of this post and I shall email you the source code and documentation. The agreement boils down to you promising not to give anyone outside your lab copies, and to reference us if you use HBPLUS' results in a paper. HBPLUS is free to academic users. HBPLUS is (c) IK McDonald, D Naylor, D Jones and JM Thornton 1993 ----------------------------------------------->8-CUT HERE--- Correspondence to: Ian McDonald (PG) Biological Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London Gower Street LONDON WC1E 6BT UK / EC Email mcdonald@uk.ac.ucl.biochemisty.bsm HBPLUS - Hydrogen Bond Calculation ---------------------------------- CONFIDENTIALITY AGREEMENT ------------------------- In regard to the HBPLUS program, specified in Appendix 1 herewith (the Software) supplied to us, the copyright and other intellectual property rights to which belong to the authors, we __________________________________________________________________ undertake to the authors that we shall be bound by the following terms and conditions:- 1. We will receive the Software and any related documentation in confidence and will not use the same except for the purpose of the department's own research. The Software will be used only by such of our officers or employees to whom it must reasonably be communicated to enable us to undertake our research and who agree to be bound by the same confidence. The department shall procure and enforce such agreement from its staff for the benefit of the authors. 2. The publication of research using the Software must reference "McDonald IK, Naylor DN, Jones DT & Thornton J M (1993), 'HBPLUS', Computer Program, Department of Biochemistry and Molecular Biology, University College London." or successor references as defined by the authors. 3. Research shall take place solely at the department's premises at __________________________________________________________________ 4. All forms of the Software will be kept in a reasonably secure place to prevent unauthorised access. 5. Each copy of the Software or, if not practicable then, any package associated therewith shall be suitably marked (and such marking maintained) with the following copyright notice: "Copyright 1991-3 Ian McDonald, Dorica Naylor, David Jones and Janet M Thornton All Rights Reserved". 6. The Software may be modified but any changes made shall be made available to the authors. 7. The Software shall be used exclusively for academic teaching and research. The Software will not be used for any commercial research or research associated with an industrial company. 8. The confidentiality obligation in paragraph one shall not apply: (i) to information and data known to the department at the time of receipt hereunder (as evidenced by its written records); (ii) to information and data which was at the time of receipt in the public domain or thereafter becomes so through no wrongful act of the department; (iii) to information and data which the department receives from a third party not in breach of any obligation of confidentiality owed to the authors. Please sign this Undertaking and return a copy of it to indicate that you have read, understood and accepted the above terms. For and on behalf of _____________________________ _________________________________________________ .................................................. Email ............................................ Dated ............................................ APPENDIX 1 - DETAILS OF THE HBPLUS PROGRAM PROVIDED --------------------------------------------------- Files to be included -------------------- 1. hbplus.c } Source program file 2. hbplus.man } Documentation From owner-proteins@net.bio.net Mon Jun 13 23:00:00 1994 Path: biosci!agate!lhom From: lhom@OCF.Berkeley.EDU (Louis Hom) Newsgroups: bionet.molbio.proteins Subject: Factorial Method Ref? Date: 14 Jun 1994 17:02:56 GMT Organization: U.C. Berkeley Open Computing Facility Lines: 7 Distribution: ca Message-ID: <2tkns0$fnp@agate.berkeley.edu> NNTP-Posting-Host: earthquake.berkeley.edu Can anyone direct me to a reference for the factorial method of determining crystallization conditions for proteins? -- **************************************************************************** * Lou Hom * "All folks are family." * * lhom@ocf.berkeley.edu * -- John Saponara * **************************************************************************** From owner-proteins@net.bio.net Tue Jun 14 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!swrinde!ihnp4.ucsd.edu!sdcc12!jeeves!wsun From: wsun@jeeves.ucsd.edu (Fiberman) Newsgroups: bionet.molbio.proteins Subject: thrombin cleavage site Message-ID: <69376@sdcc12.ucsd.edu> Date: 16 Jun 94 00:37:35 GMT Sender: news@sdcc12.ucsd.edu Organization: University of California, San Diego Lines: 9 Nntp-Posting-Host: jeeves.ucsd.edu Hello, Does anyone out there know the consensus cleavage site for thrombin? I am using thrombin to cleave a glutathione-S-transferase fusion protein. I want to make sure there is no internal cleavage sites on the GST protein. -fm From owner-proteins@net.bio.net Tue Jun 14 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!swrinde!emory!darwin.sura.net!fconvx.ncifcrf.gov!mack From: mack@ncifcrf.gov (Joe Mack) Subject: Re: measuring O-acetylserine Message-ID: Organization: Frederick Cancer Research and Development Center References: <2tnag7$j0@mserv1.dl.ac.uk> Distribution: bionet Date: Wed, 15 Jun 1994 20:48:43 GMT Lines: 27 In article <2tnag7$j0@mserv1.dl.ac.uk> Malcolm Hawkesford writes: >Does anyone know how to seperate and detect (and therefore measure) O-acetyl >serine (OAS) in plant extracts. This is a precursor in cysteine synthesis. > >In preference we would like some kind of HPLC or GC based method. One >particular problem is the rapid spontaneous conversion to the N-acetylated form >that occurs in solution, at alkaline pH. I've worked with these type of compounds before and the anchimerically assisted isomerisation will get you every time. Is it acceptable to make sure all is converted to the N-Ac form and measure it? Joe Mack mack@ncifcrf.gov (NIH, Bethesda MD) > >Thanks, Malcolm > > ------------------------------------------------------------------------------ > RFC-822 : malcolm.hawkesford@BBSRC.AC.UK University of Bristol, > X400 : G=MALCOLM; S=HAWKESFORD; O=BBSRC; P=UK; C=GB Long Ashton Research > Tel : 0275-392181 ext:252 Station, Long Ashton, > Fax : 0275-394281 Bristol, BS18 9AF, UK. > ------------------------------------------------------------------------------ From owner-proteins@net.bio.net Tue Jun 14 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!zip.eecs.umich.edu!umn.edu!maroon!rosto001 From: rosto001@maroon.tc.umn.edu (Alexander P Rostovtsev) Subject: Re: Basic protein for blocking? Message-ID: Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: maroon1.tc.umn.edu Organization: University of Minnesota, Twin Cities References: <2tndtn$48u@gazette.bcm.tmc.edu> Date: Wed, 15 Jun 1994 20:06:15 GMT Lines: 15 In <2tndtn$48u@gazette.bcm.tmc.edu> hdang@cns.neusc.bcm.tmc.edu (Hong Dang) writes: >Dear Netters, >Can anybody suggest a cheap basic protein for blocking DE-81 filters? >We are trying to do filter binding assay using small protein ligands to receptors. >Thank you in advance. >Hong the only one relatively cheap and pure basic protein I know about - cytochrome c. I'm not so sure about histones. May be you should try poly-Lys. Good luck. Alexander Rostovtsev U of Minnesota From owner-proteins@net.bio.net Tue Jun 14 23:00:00 1994 Path: biosci!bcm!cns.neusc.bcm.tmc.edu!hdang From: hdang@cns.neusc.bcm.tmc.edu (Hong Dang) Newsgroups: bionet.molbio.proteins Subject: Basic protein for blocking? Date: 15 Jun 1994 17:31:35 GMT Organization: Baylor College of Medicine, Houston,Tx Lines: 8 Distribution: world Message-ID: <2tndtn$48u@gazette.bcm.tmc.edu> NNTP-Posting-Host: cns.neusc.bcm.tmc.edu Dear Netters, Can anybody suggest a cheap basic protein for blocking DE-81 filters? We are trying to do filter binding assay using small protein ligands to receptors. Thank you in advance. Hong From owner-proteins@net.bio.net Tue Jun 14 23:00:00 1994 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!wupost!monsanto.com!rcwieg.monsanto.com!user From: rcwieg@ccmail.monsanto.com (Roger Wiegand) Subject: Re: antibody probe solution Message-ID: Followup-To: bionet.molbio.proteins Sender: news@tin.monsanto.com (USENET News System) Organization: Searle Molecular Biology References: Date: Wed, 15 Jun 1994 16:23:14 GMT Lines: 29 In article , Lab_Mac_Hanson@QMrelay.mail.cornell.edu (Hanson Lab) wrote: > Hello Protein People-- > We are having a lab discussion regarding the number of times one can use a > primary antibody probe solution. Like, can it be used indefinitely? Or is > more than once a dangerous precedent? Are there any general > recommendations from this group? Any ideas would be most welcome. Any > hints on when a solution has been used once-too-many times, and what the > Western would look like (slow to develop, or weak bands disappearing). > thanks for any input, > Claudia Sutton > cas9@cornell.edu > Cornell University > Ithaca,NY > hey, it's hot here today! We've used them 10-20 times. Background can actually improve significantly with re-use. I've not yet re-used a solution often enough to see any serious degradation in signal strength. Bugs do like to grow in the solutions on storage, so I filter through a 0.2 micron filter periodically. Adding azide would also be a good idea. -- Thanks, Roger rcwieg@ccmail.monsanto.com "If you push it hard enough, it *will* fall over" From owner-proteins@net.bio.net Tue Jun 14 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: Malcolm Hawkesford Newsgroups: bionet.molbio.proteins Subject: measuring O-acetylserine Date: 15 Jun 1994 17:33:11 +0100 Lines: 15 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2tnag7$j0@mserv1.dl.ac.uk> Sensitivity: Company-Confidential Original-To: proteins@dl.ac.uk (Non Receipt Notification Requested) (IPM Return Requested) (Reply Requested) Does anyone know how to seperate and detect (and therefore measure) O-acetyl serine (OAS) in plant extracts. This is a precursor in cysteine synthesis. In preference we would like some kind of HPLC or GC based method. One particular problem is the rapid spontaneous conversion to the N-acetylated form that occurs in solution, at alkaline pH. Thanks, Malcolm ------------------------------------------------------------------------------ RFC-822 : malcolm.hawkesford@BBSRC.AC.UK University of Bristol, X400 : G=MALCOLM; S=HAWKESFORD; O=BBSRC; P=UK; C=GB Long Ashton Research Tel : 0275-392181 ext:252 Station, Long Ashton, Fax : 0275-394281 Bristol, BS18 9AF, UK. ------------------------------------------------------------------------------ From owner-proteins@net.bio.net Tue Jun 14 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: Marjory.Barnes@PEBT.PHARMA.sandoz.ch Newsgroups: bionet.molbio.proteins Subject: - Date: 15 Jun 1994 17:00:48 +0100 Lines: 33 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2tn8jg$s1l@mserv1.dl.ac.uk> Original-To: proteins ******************************************************************************** GLOBAL NETWORK FOR GMP PROTEIN SEQUENCING LABORATORIES ******************************************************************************** 20 April, 1994 Dear Colleagues, We announce the opening of an information exchange network for laboratories which do N-terminal Edman sequence analysis of proteins and peptides to GMP, GLP, or ISO standards. Initially, the network will provide contact addresses of other laboratories working in this field. If you wish to participate, please contact M.Barnes Internet BARNES@PEBT.PHARMA.SANDOZ.CH Technical Research and Development - Biotechnology Sandoz Pharma AG Building 360, Laboratory 1124 4002 Basel, Switzerland 041-61-324-4137 Languages: English, German, French From owner-proteins@net.bio.net Tue Jun 14 23:00:00 1994 Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.immunology Path: biosci!agate!howland.reston.ans.net!noc.near.net!usenet.elf.com!rpi!news.crd.ge.com!maxwell!ebstokes From: ebstokes@maxwell.crd.ge.com (Ed Stokes) Subject: antibodies to chemicals ? Message-ID: Sender: usenet@crdnns.crd.ge.com (USENET News System) Nntp-Posting-Host: maxwell.crd.ge.com Organization: GE Corp. Research & Development, Schenectady, NY Date: Wed, 15 Jun 1994 14:31:39 GMT Lines: 16 Xref: biosci bionet.molbio.methds-reagnts:15266 bionet.molbio.proteins:2088 bionet.immunology:1532 I am interested in the application of antibodies to immunoassays for relatively small organic molecules. Is there a database somewhere which summarizes what antibodies are available which respond selectively to, say, PAH's, or monomers such as styrene ? Looking through the catalogs and the literature, it seems that most antibodues are raised against other proteins. However, there are cases (PCB's, for example) where immunoassays have been implemented for non-biological analytes. Is there a vendor which specializes in these types of "anti-industrial" antibodies ? Thanks Ed Stokes ebstokes@crd.ge.com From owner-proteins@net.bio.net Tue Jun 14 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!swrinde!pipex!uknet!daresbury!not-for-mail From: yduroche@cri.ens-lyon.fr (Yves Durocher) Newsgroups: bionet.molbio.proteins Subject: MW of myelin basic protein (bovine) Date: 15 Jun 1994 16:20:39 +0100 Lines: 8 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2tn687$pl7@mserv1.dl.ac.uk> content-length: 179 Original-To: proteins@dl.ac.uk Is somebody knows the apparent molecular weight of MBP (bovine brain) on SDS-PAGE gels ? Please answer me directly to my E-mail address. Thank you Yves yduroche@cri.ens-lyon.fr From owner-proteins@net.bio.net Tue Jun 14 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!news.funet.fi!news.csc.fi!convex!harper From: harper@convex.csc.FI (Rob Harper) Newsgroups: bionet.molbio.proteins Subject: Re: PDB-Files Date: 15 Jun 1994 09:54:27 GMT Organization: CSC - Tieteellinen laskenta Lines: 27 Message-ID: <2tmj4j$gic@pobox.csc.fi> References: <1994Jun12.125420.20816@neutron.nacamar.de> NNTP-Posting-Host: convex.csc.fi In MARDER@agri.huji.ac.il (Jonathan B. Marder) writes: >GDB files can be got from NIH via gopher. I don't have the exact pointer and >right now, our connections are down. One way in is to go via gopher at >merlot.gdb.org - you should eventually find an item to search the NIH database >for what you seek. You might like to try the WWW and mosaic to the following site. http://www.nih.gov/pdb and if you have Rasmol installed and create a .mailcap file in your home directory like chemical/x-pdb; /p/appl/bin/rasmol %s (your path to boot the Rasmol programme would most likely be different) Then you can search the PDB database for molecules and DISPLAY and ROTATE them online. RGDS -=ROB=- -- R. Andrew Harper E-mail: harper@convex.csc.fi Center for Scientific Computing Molbio/software: harper@nic.funet.fi Tietotie 6, P.O. Box 405 Telephone: +358 0 457 2076 SF-02101 Espoo Finland Fax: +358 0 457 2302 From owner-proteins@net.bio.net Tue Jun 14 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: GAED6043@VAX1.AGRICULTURE.QUEENS-BELFAST.AC.UK Newsgroups: bionet.molbio.proteins Subject: 2-D electrophoresis Date: 15 Jun 1994 10:14:28 +0100 Lines: 2 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2tmgpk$5kh@mserv1.dl.ac.uk> Original-To: PROTEINS Help! Has anyone an idiot proof method for bacterial protein extraction and sample prep. for 2-d page. thanks in anticipation Kim Barr e-mail gaed6043