From owner-proteins@net.bio.net Mon Feb 01 22:00:00 1993 Path: biosci!uwm.edu!spool.mu.edu!news.nd.edu!mentor.cc.purdue.edu!mace.cc.purdue.edu!b35 From: b35@mace.cc.purdue.edu (Vic Ilag) Newsgroups: bionet.molbio.proteins Subject: NMR labs Message-ID: Date: 2 Feb 93 17:23:30 GMT Sender: news@mentor.cc.purdue.edu (USENET News) Organization: Purdue University Lines: 6 A friend of mine wants to know the addresses of laboratories using NMR for protein structure determination and protein-ligand interactions. Please email their addresses to me at b35@mace.cc.purdue.edu. Thanks in advance. vic From owner-proteins@net.bio.net Tue Feb 02 22:00:00 1993 Path: biosci!BIOTECHNET.COM!MWRAVERA From: MWRAVERA@BIOTECHNET.COM Newsgroups: bionet.molbio.proteins Subject: Integrin-bacterial interactions Message-ID: <01GUAWHHIVWY8WWOCO@delphi.com> Date: 4 Feb 93 04:19:23 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 In doing a literature search on cellular adhesion molecules, I came across several references to bacteria of the genus Yersinia. Several species of Yersinia apparently infect mammalian cells by specifically interacting with cellular integrins (VLA-4, VL A-5, etc.). These bacteria also produce a protein tyrosine phosphatase that is required for infection. I would appreciate any information about how these virulence factors interact with integrins, eventually (with any luck!) finding out more about the functioning of the integrins themselves. I would also be interested in learning about any other pathogens that use adhesion molecules for access to cells. ================================================================= | Mark W. Ravera | | Sandoz Research Institute | | | | 59 Route 10 InterNet: MWRAVERA@BioTechNet.Com | | East Hanover, NJ PhoneNet: 201-503-8427 | | 07936 FaxNet : 201-503-6870 | ================================================================= From owner-proteins@net.bio.net Wed Feb 03 22:00:00 1993 Path: biosci!news.cs.indiana.edu!sgiblab!nec-gw!nec-tyo!wnoc-tyo-news!news.u-tokyo.ac.jp!s.u-tokyo!kuis!kudpc!sakura.kudpc.kyoto-u.ac.jp!c50951 From: c50951@sakura.kudpc.kyoto-u.ac.jp (yukio nagano) Newsgroups: bionet.molbio.proteins Subject: ras or ras-related protein Message-ID: <1993Feb4.054701.11271@kudpc.kyoto-u.ac.jp> Date: 4 Feb 93 05:47:01 GMT Sender: news@kudpc.kyoto-u.ac.jp Organization: Department of Food Science and Technology, Kyoto University, Kyoto, Japan Lines: 12 Originator: c50951@sakura.kudpc.kyoto-u.ac.jp Nntp-Posting-Host: sakura.kudpc.kyoto-u.ac.jp Hello, Is there any difference of the binding efficiency of the GTP between the ras or ras-related protein in the nitrocellulose blots and the protein in solution? ----------------------------------------------------------------------------- - - Yukio Nagano n n Department of Food Science and Technology, Faculty of Agriculture, Kyoto University, " -- " Kyoto 606-01, Japan, E-mail: c50951@sakura.kudpc.kyoto-u.ac.jp From owner-proteins@net.bio.net Wed Feb 03 22:00:00 1993 Path: biosci!daresbury!daresbury!not-for-mail From: mbasd@s-crim1.dl.ac.uk (A. Sheppard) Newsgroups: bionet.molbio.proteins Subject: ECE information... Message-ID: <1kqp1oINN8r3@s-crim1.dl.ac.uk> Date: 4 Feb 93 09:52:56 GMT Organization: Daresbury Lab., Warrington, U.K. Lines: 10 NNTP-Posting-Host: seqnet.dl.ac.uk Dear Netters, I would be grateful for information (references, sequences etc.) for endothelin converting enzyme (ECE). Thanks in advance, Paul mbasd@seqnet.dl.ac.uk From owner-proteins@net.bio.net Thu Feb 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!bogus.sura.net!darwin.sura.net!sgiblab!sgigate!olivea!charnel!sifon!newsflash.concordia.ca!nstn.ns.ca!psinntp!psinntp!vaxa.hofstra.edu!drmljg From: drmljg@vaxa.hofstra.edu Newsgroups: bionet.molbio.proteins Subject: Amino Acid Therapy Message-ID: <1993Feb3.111032.604@vaxc> Date: 3 Feb 93 16:10:32 GMT Reply-To: DRMLJG@VAXC.HOFSTRA.EDU Lines: 13 I am currently under the care of a bio-chemical nutritionist. He has me taking 1 gm. of L-Tyrosine, 2 gms. of L-Glutamine, and 1.5 gms. of Inosine per day. Since I began his program I have had all sorts of cold and flu symptoms. I was wondering if the ingestion of amino acids can trigger a dormant virus into activity? I would very much appreciate an answer to this question as I am concerned that I might be undermining my health. Please respond to me personally. Thanks. Laurence From owner-proteins@net.bio.net Sun Feb 07 22:00:00 1993 Path: biosci!agate!netsys!pagesat!olivea!charnel!sifon!VM1.MCGILL.CA From: B7JP@MUSICT.MCGILL.CA (B7JP) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Looking for anyibody, Help! Message-ID: <08FEB93.19591276.0127@VM1.MCGILL.CA> Date: 8 Feb 93 23:08:24 GMT Sender: usenet@MUSICT.MCGILL.CA Organization: McGill University Lines: 17 Xref: biosci bionet.molbio.methds-reagnts:4191 bionet.molbio.proteins:511 Nntp-Posting-Host: vm1.mcgill.ca Hi Group! I am looking for anti tissue Transglutaminase (tTG) to be used in immunohistochemical staining in limb bud of mice embryo. If anybody knows from where I can get it (a researcher or a company), I would be grateful if he/she could let me know. Thanks a lot. Seyed Moallem Dept. Pharmacology & Therapeutics........E-Mail: B7JP@MUSICB.MCGILL.CA McGill University........................Phone# (514) 398-3634 3655 Drummond St.........................FAX# (514) 398-7120 Montreal, Que., H3G 1Y6 CANADA From owner-proteins@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: Looking for anyibody, Help! Message-ID: <1993Feb9.143947.1687@welchgate.welch.jhu.edu> Date: 9 Feb 93 14:39:47 GMT References: <08FEB93.19591276.0127@VM1.MCGILL.CA> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 55 Xref: biosci bionet.molbio.methds-reagnts:4198 bionet.molbio.proteins:512 In article <08FEB93.19591276.0127@VM1.MCGILL.CA> B7JP@MUSICT.MCGILL.CA (B7JP) writes: >Hi Group! > >I am looking for anti tissue Transglutaminase (tTG) to be used in >immunohistochemical staining in limb bud of mice embryo. > >If anybody knows from where I can get it (a researcher or a company), I >would be grateful if he/she could let me know. > I just announced a gopher search last night which might help you find a lab that can help you. Gopher on down to merlot.welch.jhu.edu and select the following directory: --> 14. Searching For Biologists/ Then select - --> 2. Search for All Researchers funded by NIH A search for - Transglutaminase and immunohistochemical turns up two labs which may be able to help you out or at least point you in the right direction. LOTAN, REUBEN UNIVERSITY OF TEXAS 1515 HOLCOMBE BLVD HOUSTON, TX 77030 PERFORMING ORGANIZATION: UNIVERSITY OF TEXAS SYSTEM CANCER CENTER and SACKS, PETER G SLOAN-KETTERING INSTITUTE 1275 YORK AVENUE NEW YORK, NY 10021 PERFORMING ORGANIZATION: SLOAN-KETTERING INSTITUTE FOR CANCER RESEARCH Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-proteins@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!bio.embnet.se!sunic!uunet!stanford.edu!ames!saimiri.primate.wisc.edu! zaphod.mps.ohio-state.edu!howland.reston.ans.net!ux1.cso.uiuc.edu!news.cso.uiuc.edu!usenet From: feng@lisboa.ks.uiuc.edu (Zhou Feng) Newsgroups: bionet.molbio.proteins Subject: membrane ? Message-ID: Date: 10 Feb 93 20:38:00 GMT Sender: usenet@news.cso.uiuc.edu (Net Noise owner) Organization: University of Illinois at Urbana Lines: 12 How about setting up a new subject in the bionet? Many people are interested in membrane proteins and membranes, especially for many of the molecular biologists who are interested in modeling membrane proteins. Is there anybody who can take care of this -- Feng Zhou +-------------------------------------------------------------------- |Theoretical Biophysics feng@lisboa.ks.uiuc.edu |University of Illinois Tel: (217)-244-3667 |3109 Beckman Institute Fax: (217)-244-8371 From owner-proteins@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: skrshaw@reading.ac.uk Newsgroups: bionet.molbio.proteins Subject: unsubscribe Message-ID: <1993Feb10.104245.12842@gserv1.dl.ac.uk> Date: 10 Feb 93 10:42:17 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 1 Original-To: proteins@uk.ac.daresbury unsubscribe From owner-proteins@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!usenet.ins.cwru.edu!howland.reston.ans.net!usc!sdd.hp.com!caen!umeecs!yale!yale.edu!newsserver.jvnc.net!netnews.upenn.edu!duong From: duong@chestnut.chem.upenn.edu (Duc Duong) Newsgroups: bionet.software,bionet.molbio.proteins Subject: Software to display peptide planes structures? Message-ID: <108912@netnews.upenn.edu> Date: 10 Feb 93 15:16:00 GMT Sender: news@netnews.upenn.edu Followup-To: bionet.software Organization: NMR Biochemistry Graduate Research Lab Lines: 10 Xref: biosci bionet.software:4157 bionet.molbio.proteins:515 Nntp-Posting-Host: chestnut.chem.upenn.edu hi.. I am urgently looking for a software (PD or comercial) that read in the alpha, and beta angles of the peptide planes then display or print it out on the paper as retangular planes.. The structure of the peptides we have determined can of course be hand drawing but We have a punches of them and they are in 3Dimension.. So are there such a software? E-mail please. Thank you.. duc From owner-proteins@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!nigel.msen.com!fmsrl7!lynx.unm.edu!umn.edu!noc.msc.net!news.stolaf.edu!mari.acc-admin.stolaf.edu!bell From: bell@mari.acc-admin.stolaf.edu (David E Bell) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: immuno blot Message-ID: <1993Feb10.151615.28695@news.stolaf.edu> Date: 10 Feb 93 15:16:15 GMT Sender: news@news.stolaf.edu Organization: St. Olaf College; Northfield, MN Lines: 30 Xref: biosci bionet.molbio.methds-reagnts:4215 bionet.molbio.proteins:514 a simple experiment, but not working... who can help ??? I did immunoblots (running ag on a gel, blotted it, incubated blot with positive human serum, developed with anti human POD conjugate ==> no bands !!) Ponceau staining revealed lots of protein on my blot. My substrate reaction is positive, too. After several investigations the problem is bordered in: no binding of the antibodies (or not enough) in the positive patient serum to the on NC membrane presented antigens !! why ?? did anybody experience similar problems ?? in addition it must be said, that i did the same procedure as ELISA (same antigens coated, same human serum, same POD conjugate !!) - and there it was working very well !!! So any ideas what prevents ab binding to NC presented antigens ???? I appreciate every hint, thougt or idea. Thanks. Tom Pasternak Immunology University Aberdeen Internet: ugn4501@aberdeen.ac.uk or as sender: bell@stolaf.edu From owner-proteins@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!saimiri.primate.wisc.edu!usenet.coe.montana.edu!news.uoregon.edu!fp1-molbio-15.uoregon.edu!user From: thomas@molbio.uoregon.edu (Matthew Thomas) Newsgroups: bionet.molbio.proteins Subject: erk2 and mpk? Message-ID: Date: 11 Feb 93 01:47:54 GMT Followup-To: bionet.molbio.proteins Organization: University of Oregon Network Services Lines: 2 NNTP-Posting-Host: fp1-molbio-15.uoregon.edu I've been going crazy trying to figure out if erk2 is the same protein as mpk from sea stars? From owner-proteins@net.bio.net Sun Feb 14 22:00:00 1993 Path: biosci!uwm.edu!psuvax1!psuvm!frmop11!barilvm!vms.huji.ac.il!inna From: inna@vms.huji.ac.il Newsgroups: bionet.molbio.proteins Subject: HELP: search of protein structure Message-ID: <1993Feb14.140001.283@vms.huji.ac.il> Date: 14 Feb 93 14:00:01 GMT Organization: The Hebrew University of Jerusalem Lines: 15 Is there an existing program for searching the Brookhaven protein data bank for a specific sequence of amino acids, in a similar manner to searches of GCG ? I hope that someone can answer this.. Thank you, ---------------------------------------------------------------------- Inna Perlov Phone 972-2-584848 Hebrew University E-Mail Inna@hujivms.bitnet Computation center Inna@vms.huji.ac.il Givat-Ram 91904 Jerusalem FAX 972-2-527349 Israel ---------------------------------------------------------------------- From owner-proteins@net.bio.net Sun Feb 14 22:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!gatech!ee.gatech.edu!cc.gatech.edu!news From: hernan@cc.gatech.edu (Hernan Astudillo R.) Newsgroups: bionet.general,bionet.immunology,bionet.molbio.proteins Subject: Animal bloodtyping Message-ID: <1993Feb16.010043.1064@cc.gatech.edu> Date: 16 Feb 93 01:00:43 GMT Sender: news@cc.gatech.edu Reply-To: hernan@cc.gatech.edu Organization: College of Computing, Georgia Institute of Technology Lines: 23 Xref: biosci bionet.general:4090 bionet.immunology:255 bionet.molbio.proteins:521 Dear netlanders, A friend of mine, who is a biology major and has no access to the net, has been looking for some information that doesn't seem to be readily available (no, the library doesn't have it). We'll be thankful of any help that anybody our there in netland can give. The question is (are): (1) Have blood types been defined for (domestic) animals? (2) If so, what is the process for the blood type analysis? (if it is any different from the human one) (3) Finally, she'll appreciate any summaries and/or references. Thanks a lot!! --hernan -- | Hernan Astudillo R. | "Life is short. Play hard." hernan@cc.gatech.edu | -- Reebok College of Computing, Georgia Tech, Atlanta GA 30332 / (404) 853-9390 From owner-proteins@net.bio.net Sun Feb 14 22:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!rutgers!igor.rutgers.edu!yoko.rutgers.edu!minnam From: minnam@yoko.rutgers.edu (Minnam Sivananda) Newsgroups: sci.bio,bionet.general,bionet.molbio.methds-reagnts,bionet.molbio.evolution,bionet.molbio.proteins,bionet.molbio.gdb,bionet.molbio.embldatabank,bionet.molbio.gene-linkage Subject: Laboratory courses on DNA offered by Cook College of Rutgers-Univ. Message-ID: Date: 15 Feb 93 19:30:58 GMT Followup-To: bionet.general Distribution: usa Organization: Rutgers Univ., New Brunswick, N.J. Lines: 46 Xref: biosci sci.bio:2073 bionet.general:4085 bionet.molbio.methds-reagnts:4262 bionet.molbio.evolution:758 bionet.molbio.proteins:519 bionet.molbio.gdb:38 bionet.molbio.embldatabank:150 bionet.molbio.gene-linkage:152 Rutgers-The State University of New Jersey Campus at New Brunswick Continuing Professional Education Programs in Biotechnology The Cook College of Rutgers- The State University of New Jersey is offering two hands-on Laboratory courses in the field of Biotechnology. Recombinant DNA Techniques: Three sessions: March 16-19,1993 June 8-11,1993 August 9-12,1993 Course description This 4-day hands-on laboratory course introduces the fundamental techniques used in Recombinant DNA research. Emphasis will be placed on the practical aspects of molecular genetics and the acquired techniques and styles needed for successful experimentation. Theoretical background and ideas for troubleshooting will also be presented in a format that integrates lectures and laboratory work, making the most efficient use of time and enhancing the learning experience. Protein Electrophoresis and Western Blotting Two sessions: June 23-24,1993 January 13-14,1994 Course Description This 2-day hands on laboratory course will introduce fundamental techniques used in the separation and analysis of proteins using antibodies. Optimal conditions and limits under which western blotting can be applied will be demonstrated. Detection strategies using various secondary antibodies and reporter molecules will be presented. Emphasis will be placed on the laemmli method and other electrophoresis systems. Theoretical background and ideas for troubleshooting will also be presented in a format tha t integrates lectures and laboratory work, making the most efficient use of time and enhancing the learning experience. For more information : Call Pam at (908)932-9271 or Send mail to : Cook College Office of Continuing Professional Education P.O Box 231 New Brunswick NJ-08903-0231 or Send email to : czesak@gandalf.rutgers.edu or Send Fax to : (908)932-8726 From owner-proteins@net.bio.net Sun Feb 14 22:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!howland.reston.ans.net!wupost!uwm.edu!linac!uchinews!quads!oze3 From: oze3@quads.uchicago.edu (J. Daniel Ozeran) Newsgroups: bionet.molbio.proteins Subject: Re: membrane ? Message-ID: <1993Feb13.191211.22990@midway.uchicago.edu> Date: 13 Feb 93 19:12:11 GMT References: Sender: news@uchinews.uchicago.edu (News System) Reply-To: oze3@midway.uchicago.edu Organization: University of Chicago Lines: 17 In article feng@lisboa.ks.uiuc.edu (Zhou Feng) writes: >How about setting up a new subject in the bionet? Many people are >interested in membrane proteins and membranes, especially for many of the >molecular biologists who are interested in modeling membrane proteins. >Is there anybody who can take care of this > >-- > Feng Zhou > I'd like to second this idea. Dan Ozeran -- J. Daniel Ozeran | Dept. of Biochemistry and dan-ozeran@uchicago.edu | Molecular Biology and oze3@midway.uchicago.edu | The Joseph P. Kennedy Jr. jozeran@biovax.uchicago.edu| Mental Retardation Research Center From owner-proteins@net.bio.net Sun Feb 14 22:00:00 1993 Path: biosci!agate!stanford.edu!rutgers!igor.rutgers.edu!yoko.rutgers.edu!minnam From: minnam@yoko.rutgers.edu (Minnam Sivananda) Newsgroups: bionet.general,bionet.molbio.methds-reagnts,bionet.molbio.proteins,bionet.molbio.gene-linkage,bionet.genome.arabidopsis,misc.education,bionet.neuroscience,fj.sci.chem Subject: Protein purification course offered by Cook College of Rutgers-Univ. Message-ID: Date: 15 Feb 93 19:58:49 GMT Followup-To: bionet.molbio.proteins Distribution: usa Organization: Rutgers Univ., New Brunswick, N.J. Lines: 41 Xref: biosci bionet.general:4086 bionet.molbio.methds-reagnts:4263 bionet.molbio.proteins:520 bionet.molbio.gene-linkage:153 bionet.genome.arabidopsis:918 misc.education:3117 bionet.neuroscience:1015 Rutgers-The State University of New Jersey Campus at New Brunswick Continuing Professional Education Programs in Biotechnology The Cook College of Rutgers- The State University of New Jersey is offering a hands-on Laboratory course in the field of Biotechnology. Protein Purification: Isolation, Analysis and Characterization Three Offerings: March 14-19,1993 June 13-18,1993 July 18-23,1993 Course description This 5- 1/2 day laboratory course covers a wide varietyof conventional methods for protein isolation, purification and characterization. Th course format integrates hands-on laboratory exercises with class room lectures, demonstrations, study breaks and short take-home assignments. A special feature of the course is that all laboratory work will be performed on the same starting sample which will be purified from an exceedingly crude form to near homogenity as judged by HPLC, SDS gel electrophoresis and isoelectric focusing. This feature provides a continuity of purpose , integrating dozens of preparative and analytical protein techniques in a way that few competing courses can match. A problem solving approach will be used throughout the course. Under the guidance of experienced lab instructors, participants will work in groups of three to plan their own protocols, analyze data and interpret results. A student teacher ratio no greater than 8:1 will be maintained and faculty co-ordinators will be present throughout the course. Techniques and Instruments you will use: * Tissue Homogenizers * Filtration devices including Tangential Flow Ultrafiltration * Refrigerated (Sorvall) centrifuges * Recording UV-Vis Spectrophotometers * Filter Fluorometers * Luminescence photometers * Column Chromatography (gel filtration , Ion exchange and Hydrophobic Interaction) * Fraction - Collectors * Column Monitors * Electrophoresis (SDS,native and isoelectric focusing) * Coomassie Blue and Silver Staining * Reverse Phase HPLC * FPLC and Phast System * Amino Acid analysis * Automated Edm an sequencing * DNA Sequence Analysis * Peptide Mapping * Mass Spectral Analysis For more information : Call Pam at (908)932-9271 or Send mail to : Cook College Office of Continuing Professional Education P.O Box 231 New Brunswick NJ-08903-0231 or Send email to : czesak@gandalf.rutgers.edu or Send Fax to : (908)932-8726 From owner-proteins@net.bio.net Mon Feb 15 22:00:00 1993 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Re: search of protein structure Message-ID: <01GUSDBOALOU9EDCA8@NBRF.Georgetown.Edu> Date: 16 Feb 93 16:12:08 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 75 In message <9302160245.AA17810@net.bio.net> Inna Perlov (Inna@vms.huji.ac.il) asks: > Is there an existing program for searching the Brookhaven > protein data bank for a specific sequence of amino acids, > in a similar manner to searches of GCG ? In 1990 Pattabiraman, Namboodiri, Lowrey and Gaber at the Naval Research Laboratory, Washington, DC, described the construction and use of the NRL_3D database. @article{NRL3D, author = "N. Pattabiraman and K. Namboodiri and Alfred Lowrey and Bruce P. Gaber", title = "{NRL\_3D}: a sequence-structure database derived from the protein data bank ({PDB}) and searchable within the {PIR} environment", year = 1990, journal = "Protein Seq.\ Data Anal.", volume = "3", pages = "387-405"} That database is now produced and released on a quarterly basis as part of the Protein Information Resource (PIR-International) Database. Release 35.00 of the PIR-International databases on 31 December 1992 included Release 11.00 of the NRL_3D database (corresponding to Brookhaven Protein Data Bank Release 62) with 1,550 sequences of 272,744 residues. That database can be used like the other PIR-Internation protein sequence databases with search programs that use the NBRF format or after conversion by those programs that do not. The NRL_3D database can be used by any of the protein database programs produced by the PIR, in particular the ATLAS program available in VMS and PC versions. The SCAN command in the program can be used to find particular sequences in the NRL_3D database. The MATCH and SCAN commands in the PSQ program will find sequences in the NRL_3D database and with the /NRL qualifier produce as output a VMS command procedure that will extract the corresponding residue ATOM records from the Brookhaven Protein Data Bank entry files for input to molecular modeling programs. In the Announcements of the Protein Information Resource posted on 3 August 1992 the following appeared. > The NRL_3D Database of sequence information extracted from the Brookhaven > Protein Data Bank (PDB) has been upgraded to release 9.1. This new version > includes feature annotations extracted from PDB HELIX, SHEET, TURN, SITE, and > SSBOND records along with special ATOM and HETATM records. > > The inclusion of this feature information in NRL_3D allows PDB entries to be > recovered through the FEATURE command. For example the commands > USE BASES NRL_3D > FEATURE TURN "TYPE I " > will list all entries in the NRL_3D database with a "type I" turn annotated > in their corresponding PDB entry. From the Announcements posted on 1 October 1992: > Some users had suggested that they wanted to do FASTA sequence searches > only for the sequences with known 3-dimensional structures, the sequences > extracted from the Brookhaven Protein Data Bank in NRL_3D. Normally our > FASTA searches are done against all the protein databases, PIR1, PIR2, PIR3, > the non-redundant PATCHX (described in the August announcement and in part 2 > above) and NRL_3D. Now when the command > USE BASES NRL_3D > is used before a SEARCH command, only the NRL_3D database will be used for > the FASTA search. Otherwise, all the protein databases will be used. More information about the PIR-International databases, NRL_3D and use of the PIR Network Request Server to search for protein sequences can be obtained by sending the electronic mail message HELP to FILESERV@GUNBRF on BITNET or to FILESERV@NBRF.Georgetown.EDU on Internet. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-proteins@net.bio.net Mon Feb 15 22:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!pipex!bnr.co.uk!uknet!comlab.ox.ac.uk!oxuniv!oxpath!rpgrant From: rpgrant@molbiol.ox.ac.uk Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: V8 protease/domain mapping Message-ID: <1993Feb16.094451.1@molbiol.ox.ac.uk> Date: 16 Feb 93 08:44:51 GMT Organization: Oxford University Molecular Biology Data Centre Lines: 14 Xref: biosci bionet.molbio.methds-reagnts:4286 bionet.molbio.proteins:526 Nntp-Posting-Host: newton Nntp-Posting-User: rpgrant Hi all! I'm thinking of using V8 protease to investigate the domain structure of a large-ish protein (280 kDa). Does anyone know of any good protocols/sources? Thanks. -- Richard P. Grant rpgrant@molbiol.ox.ac.uk Chemical Pathology Department Tel. +44 865 275565 Sir William Dunn School of Pathology Fax. +44 865 275556 OXFORD, UK. <>< "I pledge allegiance to Queen Fragg and her mighty state of hysteria!" - Calvin From owner-proteins@net.bio.net Mon Feb 15 22:00:00 1993 Path: biosci!uwm.edu!wupost!usc!rpi!usenet.coe.montana.edu!news.uoregon.edu!fp1-molbio-15.uoregon.edu!user From: thomas@molbio.uoregon.edu (Matthew Thomas) Newsgroups: bionet.molbio.proteins Subject: p90isk Message-ID: Date: 17 Feb 93 03:19:00 GMT Followup-To: bionet.molbio.proteins Organization: University of Oregon Network Services Lines: 12 NNTP-Posting-Host: fp1-molbio-15.uoregon.edu Has the p90ISK protein described in Wolfe etal. (JBC '92) been cloned or sequenced (AA)? Just wondering. Our version of genbank is old and it is not in there. Thanks Matt Thomas It's impossible to make anything foolproof, Because fools are so ingenious. From owner-proteins@net.bio.net Mon Feb 15 22:00:00 1993 Path: biosci!agate!howland.reston.ans.net!wupost!darwin.sura.net!newsserver.jvnc.net!netnews.upenn.edu!rene.med.upenn.edu!pathology From: pathology@a1.mscf.upenn.edu (Gregg Wells) Newsgroups: bionet.molbio.proteins Subject: protein microsequencing Message-ID: <109901@netnews.upenn.edu> Date: 17 Feb 93 01:10:26 GMT Sender: news@netnews.upenn.edu Organization: University of Pennsylvania Lines: 11 Nntp-Posting-Host: rene.med.upenn.edu X-UserAgent: Nuntius v1.1.1d17 X-XXMessage-ID: X-XXDate: Tue, 16 Feb 93 20:15:50 GMT Can anyone recommend a facility for microsequencing of proteins? I have about 10-20 picomoles of the sample. This amount is quite a bit smaller than the minimum amount requested by our local sequencing laboratory. Is this quantity beyond the capability of current technology? Can anyone recommend a laboratory for protein sequencing at this scale? Gregg Wells Department of Pathology University of Pennsylvania Philadelphia, Pennsylvania 19104-4283 USA From owner-proteins@net.bio.net Mon Feb 15 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: SUNDARAM@cmu.unige.ch (Ganesh) Newsgroups: bionet.molbio.proteins Subject: cancel subscription Message-ID: <1993Feb16.221943.21235@gserv1.dl.ac.uk> Date: 16 Feb 93 23:11:26 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 1 X-Envelope-To: proteins@daresbury.ac.uk Content-Identifier: cancel subscr... X-Vms-Cc: SUNDARAM Original-To: proteins@uk.ac.daresbury Content-Transfer-Encoding: 7BIT Mime-Version: 1.0 X-Vms-To: IN%"proteins@daresbury.ac.uk" please cancel subscription From owner-proteins@net.bio.net Mon Feb 15 22:00:00 1993 Path: biosci!agate!howland.reston.ans.net!usc!rpi!utcsri!newsflash.concordia.ca!mizar.cc.umanitoba.ca!hamel From: hamel@ccu.umanitoba.ca (Andre Hamel) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: immuno blot Message-ID: Date: 16 Feb 93 19:11:40 GMT References: <1993Feb10.151615.28695@news.stolaf.edu> Sender: news@ccu.umanitoba.ca Organization: University of Manitoba, Winnipeg, Manitoba, Canada Lines: 113 Xref: biosci bionet.molbio.methds-reagnts:4278 bionet.molbio.proteins:524 Nntp-Posting-Host: antares.cc.umanitoba.ca In article <1993Feb10.151615.28695@news.stolaf.edu> bell@mari.acc-admin.stolaf.edu (David E Bell) writes: > > >a simple experiment, but not working... >who can help ??? > >I did immunoblots (running ag on a gel, blotted it, incubated blot with > positive human serum, developed with anti human POD > conjugate ==> no bands !!) >Ponceau staining revealed lots of protein on my blot. >My substrate reaction is positive, too. >After several investigations the problem is bordered in: > > no binding of the antibodies (or not enough) in the positive > patient serum to the on NC membrane presented antigens !! > >why ?? did anybody experience similar problems ?? > >in addition it must be said, that i did the same procedure as ELISA (same >antigens coated, same human serum, same POD conjugate !!) - and there it was >working very well !!! > >So any ideas what prevents ab binding to NC presented antigens ???? > >I appreciate every hint, thougt or idea. Thanks. > >Tom Pasternak >Immunology University Aberdeen >Internet: ugn4501@aberdeen.ac.uk > >or as sender: bell@stolaf.edu Before I get into further details, I have several questions for you first: 1/ What dilution(s) was your human antisera(um) used at? Was it a pool of antisera? If used diluted, what buffer(s) did you try using to dilute the antisera in? 2/ What buffers did you use to block the western blot? How much, at what temperature and for how long? Also what buffers were used to wash the western blot inbetween steps? Again, how often, at what temperature and for how long? 3/ How "fresh" are your antibodies? (Human antisera and the antihuman conjugate). Are they ever frozen and thawed? 4/ What preservatives (if any) are included in the buffers used? Are the buffers filtered and autoclaved? We had routinely probed western blots of pollen protein extracts against human allergic antisera followed by rabbit antihuman IgE followed by goat antirabbit conjugates (alk phos and HRP conjugates were used). Thus, the human IgE against the pollen allergins were quite dilute compared to IgG. We used human antisera diluted to around 1 in 10. A/ First the blots were blocked at room temp with gentle shaking for 1 to 4 hours in filtered, autoclaved blocking solution (2% gelatin in 50 mM Tris, pH 7.5, 100 mM NaCl and 0.02% sodium azide (azide NOT included if HRP conjugate used, thus for HRP conjugates this solution was made fresh and autoclaved/cooled just prior to use) .. thus we preferred to use alk phos conjugates instead .. more convenient. Use about 50 mL per 10 x 10 cm blot. B/ After blocking, the blots were washed in 50 mM Tris, pH 7.5, 100 mM NaCl, 0.1% NP40, three times 15 minutes with gentle shaking. About 50 mL per 10 x 10 cm blot is used per wash. C/ The human antisera (we used pooled sera) were thawed from -70oC stock 1 mL aliquots then "freshly" diluted in blocking buffer. Likewise, about 50 mL per 10 x 10 cm blot. Blots were incubated for no more than 16 hours at room temp with gentle shaking. We found that longer time did not improve results (at room temp or 4oC cold room), even for more diluted antisera. D/ Repeat step B/ except increase number of washes to 6 instead of only three. E/ Incubate with "freshly" made antihuman antibody (conjugate). Appropriately diluted in blocking buffer. Incubate 1 to 4 hours at room temp with gentle shaking. Much longer than 4 hours likely will lead to increased background signal (especially with alk phos conjugates). F/ Repeat step D. G/ Wash 2 times 15 min in assay buffer (for alk phos conjugates, we use: 100 mM Tris, pH 9.5, 100 mM NaCl, 50 mM MgCl2, 0.02% sodium azide). This buffer is stored at room temp, when first made it is filtered/autoclaved (without azide added yet until after cooled), as are ALL of our alk phos buffers (blocking, washing, and assay buffers). H/ Color development as recommended by manufacturer. We use CSPD by Tropix, the blot is wetted in assay buffer containing CSPD substrate, then sealed, with heated bag sealer, between polyurethane sheet, exposed to Xray film for 5 min up to 48 hours (I routinely develop a film after about 1 hour then decide from there whether shorter or longer exposure is needed). CSPD chemiluminescence lasts for up to 48 hours, peaks at around 2 to 6 hours. Blot can also be placed in assay buffer containing NBT/X-phos color developer. It can then be washed in 50 mM EDTA for at least 1 hour, then stored damp in a sealed bag (color should not fade for years if stored in note book). If you want even more details (there ARE more than what I've just given above) feel free to let me know. Andre Hamel Manitoba Veterinary Virology 545 University Crescent Winnipeg, Manitoba CANADA R3T 5S6 tel: 204-945-7630 FAX: 204-945-8062 email: hamel@ccu.umanitoba.ca From owner-proteins@net.bio.net Tue Feb 16 22:00:00 1993 Path: biosci!uwm.edu!wupost!udel!darwin.sura.net!newsserver.jvnc.net!yale.edu!ira.uka.de!math.fu-berlin.de!tertius.in-berlin.de!mpimg-berlin-dahlem.mpg.de!zabin From: zabin@mpimg-berlin-dahlem.mpg.de Newsgroups: bionet.molbio.proteins Subject: model kit Message-ID: <1993Feb17.173423.1@mpimg-berlin-dahlem.mpg.de> Date: 17 Feb 93 16:34:23 GMT Organization: MPI f. Molekulare Genetik, Berlin Lines: 6 Nntp-Posting-Host: pluto Nntp-Posting-User: zabin Hi. I want to build an alpha-carbon model of a protein, and am looking for a good model-building kit. I did this once before, and used a kit which was very good from England, where the torsion angles were simply "dialed in". I don't remember the name of the company. If anyone can help, I would greatly appreciate it. Thanks, Hal Zabin From owner-proteins@net.bio.net Wed Feb 17 22:00:00 1993 Path: biosci!POST.ITS.MCW.EDU!fgarbrec From: fgarbrec@POST.ITS.MCW.EDU (Frederick Garbrecht) Newsgroups: bionet.molbio.proteins Subject: Re: Protein assay - which one is better? Message-ID: Date: 18 Feb 93 23:03:40 GMT References: <9302182036.AA24793@net.bio.net> Sender: daemon@net.bio.net Distribution: bionet Lines: 29 I have used them both, and they both work well. I think the BCA assay may be more tolerant to the presence of detergents (but I am not positive about this). Interestingly, I have used both to monitor column effluent when separating Ig fragments, and both were non-reactive to different fragments. Don't ask me why! In general, though, I have been happy with them, and I particularly like the BCA because it is easily adaptible to microassay. F Garbrecht Medical college of Wisconsin fgarbrec@post.its.mcw.edu On 18 Feb 1993, Peter M. Muriana wrote: > Date: 18 Feb 93 20:17:13 GMT > From: Peter M. Muriana > To: proteins@net.bio.net > Subject: Protein assay - which one is better? > > > Hi Netters, > We're thinking of using either the BCA protein assay (Pierce) or the > DC protein assay (Bio-Rad) - is one any better than the other? Thanks in > advance. > > Peter > From owner-proteins@net.bio.net Wed Feb 17 22:00:00 1993 Path: biosci!agate!howland.reston.ans.net!wupost!darwin.sura.net!haven.umd.edu!purdue!mentor.cc.purdue.edu!aclcb.purdue.edu!MURIANA From: muriana@aclcb.purdue.edu (Peter M. Muriana) Newsgroups: bionet.molbio.proteins Subject: Protein assay - which one is better? Message-ID: Date: 18 Feb 93 20:17:13 GMT Sender: news@mentor.cc.purdue.edu (USENET News) Reply-To: muriana@aclcb.purdue.edu Organization: Purdue University AIDS Center Lines: 7 Hi Netters, We're thinking of using either the BCA protein assay (Pierce) or the DC protein assay (Bio-Rad) - is one any better than the other? Thanks in advance. Peter From owner-proteins@net.bio.net Wed Feb 17 22:00:00 1993 Path: biosci!agate!howland.reston.ans.net!usc!rpi!utcsri!torn!nott!nrcnet0!biologysx.lan.nrc.ca!deng From: deng@biologysx.lan.nrc.ca (Deng, Dr. Sujun) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: V8 protease/domain mapping Message-ID: Date: 18 Feb 93 17:18:00 GMT References: <1993Feb16.094451.1@molbiol.ox.ac.uk> Sender: root@nrcnet0.nrc.ca (Operator) Organization: National Research Council of Canada Lines: 49 Xref: biosci bionet.molbio.methds-reagnts:4326 bionet.molbio.proteins:530 Nntp-Posting-Host: 132.246.164.32 In article <1993Feb16.094451.1@molbiol.ox.ac.uk> rpgrant@molbiol.ox.ac.uk writes: >From: rpgrant@molbiol.ox.ac.uk >Subject: V8 protease/domain mapping >Date: 16 Feb 93 08:44:51 GMT >Hi all! >I'm thinking of using V8 protease to investigate the domain structure >of a large-ish protein (280 kDa). Does anyone know of any good >protocols/sources? >Thanks. >-- >Richard P. Grant rpgrant@molbiol.ox.ac.uk >Chemical Pathology Department Tel. +44 865 275565 >Sir William Dunn School of Pathology Fax. +44 865 275556 >OXFORD, UK. <>< >"I pledge allegiance to Queen Fragg and her mighty state of hysteria!" >- Calvin From owner-proteins@net.bio.net Thu Feb 18 22:00:00 1993 Path: biosci!agate!howland.reston.ans.net!paladin.american.edu!news.univie.ac.at!blekul11!frmop11.cnusc.fr!barilvm!vms.huji.ac.il!agri!marder From: marder@agri.huji.ac.il Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: V8 protease/domain mapping Message-ID: <1993Feb18.171741.1@agri.huji.ac.il> Date: 19 Feb 93 11:52:58 GMT References: <1993Feb16.094451.1@molbiol.ox.ac.uk> Organization: The Hebrew University of Jerusalem - Faculty of Agriculture Lines: 28 Xref: biosci bionet.molbio.methds-reagnts:4353 bionet.molbio.proteins:533 Nntp-Posting-Host: agri.huji.ac.il In article <1993Feb16.094451.1@molbiol.ox.ac.uk>, rpgrant@molbiol.ox.ac.uk writes: > Hi all! > > I'm thinking of using V8 protease to investigate the domain structure > of a large-ish protein (280 kDa). Does anyone know of any good > protocols/sources? > > Thanks. > -- > Richard P. Grant rpgrant@molbiol.ox.ac.uk > Chemical Pathology Department Tel. +44 865 275565 > Sir William Dunn School of Pathology Fax. +44 865 275556 > OXFORD, UK. <>< A convenient method is by "Cleveland et al. (1977) J. Biol. Chem. 252, 1102-1108." The protein is extracted as a band from a gel, re-equilibrated with buffer, placed directly on a second gel and overlayed with protease. Digestion occurs in the stack of the second gel. I have used this method extensively with V8 protease - it works fine in 0.1% SDS and normal gel conditions. V8 is available from many biochemical companies (sometime called endoproteinase Glu-C). -- ' Jonathan B. Marder Internet: MARDER@AGRI.HUJI.AC.IL | Department of Agricultural Botany Bitnet: MARDER@HUJIAGRI | /\/ The Hebrew University of Jerusalem Phone: (08 or +9728) 481918 |/ \ Faculty of Agriculture Fax: (08 or +9728) 467763 / P.O.Box 12, Rehovot 76100, ISRAEL From owner-proteins@net.bio.net Fri Feb 19 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!usc!sdd.hp.com!nigel.msen.com!fmsrl7!destroyer!cs.ubc.ca!unixg.ubc.ca!kakwa.ucs.ualberta.ca!news From: Chris_Upton@darwin.biochem.ualberta.ca Newsgroups: bionet.molbio.proteins Subject: exons in protiens Message-ID: <1993Feb20.200955.11453@kakwa.ucs.ualberta.ca> Date: 20 Feb 93 20:09:55 GMT Sender: news@kakwa.ucs.ualberta.ca Organization: University of Alberta Lines: 24 Nntp-Posting-Host: mac08.biochem.ualberta.ca Hi, I had a colleague ask this question: How do I find out which parts of proteins correspond to different exons? He was only interested in proteins for which the crystal structure has been solved. And he wants them all!! I'm not even sure how many genes with all the introns/exons mapped there are! Since sequencing a gene, solving the protein structure, and mapping intron/exon boundaries are likely to take place over a long period of time and many sequences are cDNAs, then the references in database enteries may not be current. Any advice on how to be most efficient in this quest appreciated!! I think that if he sticks rigidly to solved structures then there might be quite a small number of these that have the genomic sequences known. Many of the proteins structures must be of bacterial origins!!! Is the Brookhaven database the best place to start? Typing this is even quite useful!! Thanks, Chris Upton Biochem U Alberta From owner-proteins@net.bio.net Fri Feb 19 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!usenet.ins.cwru.edu!cleveland.Freenet.Edu!bl275 From: bl275@cleveland.Freenet.Edu (Dan Diaz) Newsgroups: bionet.molbio.proteins Subject: Re: Protein assay - which one is better? Message-ID: <1m4cktINNlj5@usenet.INS.CWRU.Edu> Date: 20 Feb 93 04:38:53 GMT References: Reply-To: bl275@cleveland.Freenet.Edu (Dan Diaz) Organization: Case Western Reserve University, Cleveland, OH (USA) Lines: 19 NNTP-Posting-Host: slc4.ins.cwru.edu In a previous article, muriana@aclcb.purdue.edu (Peter M. Muriana) says: > Hi Netters, > We're thinking of using either the BCA protein assay (Pierce) or the >DC protein assay (Bio-Rad) - is one any better than the other? Thanks in >advance. Any protein assay short of amino acid analysis can only be considered an estimate. If you want to assay pure protein, then I suggest you have amino acid analysis done on a sample and then determine the 280 or 210 nm extinction coefficients. If you are analyzing a complex mixture, then just use whatever is easiest, since whatever number you arrive at will be an estimate. The point is to be consistent. I am quite happy with the Bradford assay; which I do using a reagent purchased from USB. -- Dizzy Dan ddiaz@cwru.bitnet bl275@cleveland.freenet.edu Department of Molecular Genetics - Albert Einstein College of Medicine "My opinions are my own, and they should be yours as well" From owner-proteins@net.bio.net Sat Feb 20 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: SUNDARAM@cmu.unige.ch (Ganesh) Newsgroups: bionet.molbio.proteins Subject: cancel subscription Message-ID: <1993Feb21.121108.12599@gserv1.dl.ac.uk> Date: 21 Feb 93 13:10:47 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 2 X-Envelope-To: proteins@daresbury.ac.uk Content-Identifier: cancel subscr... X-Vms-Cc: SUNDARAM Original-To: proteins@uk.ac.daresbury Content-Transfer-Encoding: 7BIT Mime-Version: 1.0 X-Vms-To: IN%"proteins@daresbury.ac.uk" Please cancel subscription. thanks From owner-proteins@net.bio.net Sat Feb 20 22:00:00 1993 Path: biosci!agate!howland.reston.ans.net!newsserver.jvnc.net!princeton!phoenix.Princeton.EDU!angelo From: angelo@phoenix.Princeton.EDU (Angelo Gunasekera) Newsgroups: bionet.molbio.proteins Subject: help: Good E.coli host to express fusion proteins with ompA signal peptide Message-ID: <1993Feb20.084529.21178@Princeton.EDU> Date: 20 Feb 93 08:45:29 GMT Sender: news@Princeton.EDU (USENET News System) Distribution: w Organization: Princeton University Lines: 21 Originator: news@nimaster Nntp-Posting-Host: phoenix.princeton.edu I am trying to express a single chain antbody as a fusion protein. I like to use ompA signal sequence as the leader peptide. The problem I have is finding the best E.coli host with mutant repressor gene cI857. Pharmacia sells E.coli N4830-1 strain and I would like to know whether N4830-1 is compatible with pUC8 vector. Any comments, suggestions etc..are greately appreciated. Thanks in advance Angelo o Angelo@hamlet.ucdavis.edu A Gunaseker@gnl2.ucdavis.edu P.S. I already have the single chain antibody as a fusion with the ompA signal peptide in the pUC8 vector. If someone has a better strain to express my protein with signal peptide, I would like to talk to him/her about it. Thanks From owner-proteins@net.bio.net Sat Feb 20 22:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!Germany.EU.net!gmd.de!newsserver.jvnc.net!howland.reston.ans.net!usc!sdd.hp.com!news.cs.indiana.edu!nstn.ns.ca!ac.dal.ca!arlin From: arlin@ac.dal.ca Newsgroups: bionet.molbio.proteins Subject: Re: exons in proteins Message-ID: <1993Feb21.215120.11425@ac.dal.ca> Date: 22 Feb 93 01:51:20 GMT References: <1993Feb20.200955.11453@kakwa.ucs.ualberta.ca> Organization: Dalhousie University, Halifax, Nova Scotia, Canada Lines: 53 In article <1993Feb20.200955.11453@kakwa.ucs.ualberta.ca>, Chris_Upton@darwin.biochem.ualberta.ca writes: > Hi, > I had a colleague ask this question: How do I find out which parts of > proteins correspond to different exons? > He was only interested in proteins for which the crystal structure has been > solved. And he wants them all!! My guess is that he want to investigate possible correlations between gene structure and protein structure. > > Any advice on how to be most efficient in this quest appreciated!! > > I think that if he sticks rigidly to solved structures then there might be > quite a small number of these that have the genomic sequences known. Many of > the proteins structures must be of bacterial origins!!! > Is the Brookhaven database the best place to start? Typing this is even quite > useful!! > > Chris Upton I have been interested in this question myself, though I haven't pursued it very far. There are about 1000 crystal structures in the PDB. Of these, many are repetitive determinations of RNases, lysozymes or cytochromes from different organisms, or of mutant or modified proteins, or of proteins that have been crystallized with several different substrates. I would guess that there are at least 500 distinctly different proteins represented, but this is just a thumbnail estimate. Of these, a large proportion are probably of bacterial origin. In the end, there may be 200-600 different eukaryotic proteins (again, these are just guesses). Since this is certainly smaller than the number of sequenced eukaryotic genes, the most efficient search strategy is the one that you suggested: start with the pdb list. Next, prune away duplicates and bacterial proteins. Then, start searching genbank and EMBL for gene sequences that correspond to the proteins. Make sure that you get gene sequences, as opposed to cDNA sequences (which, of course, never have introns). In the end you may get a few dozen to perhaps 200. You may find that you can only get the gene from organism X, but the protein was crystallized from organism Y. In that case, you will have to do some kind of homology- based structure prediction. If your friend is interested in the type of gene structure/protein structure correlations that are predicted by the introns-early theory of intron origins, then there is no sense in looking at recently evolved proteins (e.g., immunoglobulins), since these do not bear on the question. This will limit the search even futher. Hope this helps. Arlin Stoltzfus Department of biochemistry Dalhousie University Halifax, Nova Scotia From owner-proteins@net.bio.net Sat Feb 20 22:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!Germany.EU.net!gmd.de!ira.uka.de!sol.ctr.columbia.edu!howland.reston.ans.net!agate!ames!network.ucsd.edu!munnari.oz.au!ariel.ucs.unimelb.EDU.AU!ariel.ucs.unimelb.EDU.AU!not-for-mail From: vivien@ariel.ucs.unimelb.EDU.AU (Vivien Bonazzi) Newsgroups: bionet.molbio.proteins Subject: Guanylyl Cyclase Stuff Message-ID: <1m98c1INNelt@ariel.ucs.unimelb.EDU.AU> Date: 22 Feb 93 00:56:33 GMT Organization: University of Melbourne Lines: 20 NNTP-Posting-Host: ariel.ucs.unimelb.edu.au Hi, I was wondering if any nice soul could provide some information on the following questions. Does anyone know the complete structure of soluble guanylyl cyclase, including the haem moeity. Could anyone send me any information on the relationship between the haem moeity and the heterodimer in soluble guanylyl cyclase?. Thanks, Vivien vivien@ariel.ucs.unimelb.edu.au From owner-proteins@net.bio.net Mon Feb 22 22:00:00 1993 Path: biosci!agate!howland.reston.ans.net!newsserver.jvnc.net!netnews.upenn.edu!duong From: duong@chestnut.chem.upenn.edu (Duc Duong) Newsgroups: bionet.molbio.proteins,bionet.molbio.gene-linkage Subject: How a DNA bond with Digoxigenin?? Message-ID: <110919@netnews.upenn.edu> Date: 23 Feb 93 13:21:39 GMT Sender: news@netnews.upenn.edu Followup-To: bionet.molbio.proteins Organization: NMR Biochemistry Graduate Research Lab Lines: 9 Xref: biosci bionet.molbio.proteins:540 bionet.molbio.gene-linkage:155 Nntp-Posting-Host: chestnut.chem.upenn.edu hi.. Does any one know how the Digoxigenin bonds with a DNA?? Specifically is that how does the Negative charge of the phosphate back bone link with the Digoxigenin? There are three OH groups in the digoxigenin structure so which one it will use to bond with DNA?? E-mail please. Thank you.. duc From owner-proteins@net.bio.net Tue Feb 23 22:00:00 1993 Path: biosci!agate!spool.mu.edu!uwm.edu!caen!kuhub.cc.ukans.edu!husc-news.harvard.edu!husc10.harvard.edu!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.molbio.proteins Subject: Re: How a DNA bond with Digoxigenin?? Message-ID: <1993Feb24.094800.20997@husc3.harvard.edu> Date: 24 Feb 93 14:47:58 GMT References: <110919@netnews.upenn.edu> Organization: Harvard University Science Center Lines: 33 Nntp-Posting-Host: husc10.harvard.edu In article <110919@netnews.upenn.edu> duong@chestnut.chem.upenn.edu (Duc Duong) writes: >hi.. > >Does any one know how the Digoxigenin bonds with a DNA?? Specifically >is that how does the Negative charge of the phosphate back bone link >with the Digoxigenin? There are three OH groups in the digoxigenin >structure so which one it will use to bond with DNA?? E-mail please. >Thank you.. > >duc Look in Boehringer Mannheim catalog. The DIG is attached to the nucleotides via a linker that is attached to the base. O O H || || N DIG HN/ \ /\\/\N/ \/\/\/ \ /\ / | || H || O //\ / O O N | Sugar Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@ribo.harvard.edu From owner-proteins@net.bio.net Tue Feb 23 22:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.molbio.proteins Subject: BIOSCI/bionet Frequently Asked Questions Message-ID: <9302241000.AA24951@net.bio.net> Date: 24 Feb 93 10:00:02 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 16 New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-proteins@net.bio.net Wed Feb 24 22:00:00 1993 Path: biosci!agate!howland.reston.ans.net!gatech!udel!gvls1!psuvax1!psuvm!sml108 From: SML108@psuvm.psu.edu Newsgroups: bionet.molbio.proteins Subject: Crytallographic resolution versus R factor Message-ID: <93056.112831SML108@psuvm.psu.edu> Date: 25 Feb 93 16:28:31 GMT Organization: Penn State University Lines: 8 Hi, in the hopes of starting a heated debate I would like to ask the following questions: Which is a better measure of the accuracy of a protein's crystal structure: Its resolution in angstroms or its overall R factor? And what would you consider reasonable cutoffs for each of these? Scott From owner-proteins@net.bio.net Wed Feb 24 22:00:00 1993 Path: biosci!agate!howland.reston.ans.net!usc!sdd.hp.com!caen!saimiri.primate.wisc.edu!usenet.coe.montana.edu!news.u.washington.edu!provolone.bchem.washington.edu!merritt From: merritt@provolone.bchem.washington.edu (Ethan A Merritt) Newsgroups: bionet.molbio.proteins,bionet.xtallography Subject: Re: Crytallographic resolution versus R factor Message-ID: <1mj5c8INNee0@shelley.u.washington.edu> Date: 25 Feb 93 19:06:48 GMT References: <93056.112831SML108@psuvm.psu.edu> Reply-To: merritt@u.washington.edu Followup-To: bionet.xtallography Organization: University of Washington Lines: 60 Xref: biosci bionet.molbio.proteins:544 bionet.xtallography:157 NNTP-Posting-Host: provolone.bchem.washington.edu In article <93056.112831SML108@psuvm.psu.edu>, writes: |> Hi, in the hopes of starting a heated debate I would like to ask the |> following questions: |> |> Which is a better measure of the accuracy of a protein's crystal structure: |> Its resolution in angstroms or its overall R factor? And what would you |> consider reasonable cutoffs for each of these? |> |> Scott (followups redirected to bionet.xtallography) Resolution in Angstroms is a statement of the data collected, not a measure of accuracy in refinement. I.e., you know the resolution when you collect the data, long before you have solved the structure! It is true, however, that the eventual precision of the refined structure is limited by the resolution of the data used in refinement. Generally the resolution is limited by (1) how well the crystals diffract and (2) the amount of time needed to collect higher resolution data. The standard crystallographic R factor is a measure of how well the refined structure predicts the observed data. As such it is not a perfect measure by any means, and in fact it is theoretically possible to have a very low R factor for a totally incorrect model, although in general the "model" in question will not look much like a real protein. More common (though fortunately not _too_ common :-) is a mistake in connectivity or other specific features in what would otherwise be a correct model. This can produce an R factor which looks reasonable, though not as good as the correct model would have produced. Resolution and R factor do interact. One possible rule of thumb is that a reasonable model for the protein in the presence of a minimal solvent model (I'm not going to get into that here) should give an R no greater than (resolution in A)/10. E.g. a 2.4A model with an R factor greater than 0.24 is suspect. In any event the plausibility of the model itself needs to be considered, not just the R factor or resolution. A standard crystallographic paper will report how far the stereochemistry of the model departs from the "ideal" (i.e. most commonly observed) bond lengths, angles, etc for proteins. A related measure is the reported distribution of backbone torsion angles (PHI/PSI), often called Ramachandran plot. The question of evaluating the goodness of a protein structure is one that many people have thought about. I suggest that you check, for instance, the paper: "Stereochemical Quality of Protein Structure Coordinates" by Morris, MacArthyr, Hutchinson & Thornton (1992) Proteins 12:345-364. hope that helps, Ethan A Merritt ------------------------------------------------------------------------ --------- Dept of Biological Structure H510 Health Sciences University of Washington SM-20 (206)543-1421 Seattle, WA 98195 merritt@u.washington.edu ------------------------------------------------------------------------ --------- From owner-proteins@net.bio.net Sat Feb 27 22:00:00 1993 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Re: Searching a sequence in Brookhaven Protein Data Bank... Message-ID: <01GV9E1B8VD29GV5WC@NBRF.Georgetown.Edu> Date: 28 Feb 93 19:49:05 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 47 In message <9302281623.AA22721@net.bio.net> Duc Duong (duong@chestnut.chem.upenn.edu) asks > Could any one show me how to search the Brookhaven Protein Data Bank? > I am trying to search for five or more residues amino acid on all > proteins that the structures have been found. The results then can prove > that "one sequence one structure" is correct or not... (This should qualify as an FAQ.) The following is extracted from the Announcements of the Protein Information Resource Network Request Service published last summer. > 5. FASTA Searches for NRL_3D Only > Some users had suggested that they wanted to do FASTA sequence searches > only for the sequences with known 3-dimensional structures, the sequences > extracted from the Brookhaven Protein Data Bank in NRL_3D. Normally our > FASTA searches are done against all the protein databases, PIR1, PIR2, PIR3, > the non-redundant PATCHX (described in the August announcement and in part 2 > above) and NRL_3D. Now when the command > USE BASES NRL_3D > is used before a SEARCH command, only the NRL_3D database will be used for > the FASTA search. Otherwise, all the protein databases will be used. To do the search Duc wants, he may send an electronic mail message containing the following lines (with the appropiate sequence substitution) USE BASES NRL_3D SEARCH protein_sequence_in_single_letter_code to the PIR Network Request Service address FILESERV@NBRF.Georgetown.EDU on Internet or FILESERV@GUNBRF on BITNET. The server will return the result of a FASTA search through only the protein sequences with reported atomic positions in the Brookhaven Protein Data Bank. The first four characters of the entry codes in the NRL_3D database correspond to the PDB entry codes. Users who have the PIR database access programs, the NRL_3D database and the Brookhaven Protein Data Bank can use the MATCH command to generate a VMS command procedure that will extract the atomic coordinates of all the matched sequences in the PDB for model building and comparison. Addition information can be obtained by sending a HELP request to the PIR Network Request Service address. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-proteins@net.bio.net Sat Feb 27 22:00:00 1993 Path: biosci!agate!howland.reston.ans.net!newsserver.jvnc.net!netnews.upenn.edu!duong From: duong@chestnut.chem.upenn.edu (Duc Duong) Newsgroups: bionet.xtallography,bionet.molbio.proteins Subject: Searching a sequence in Brookhaven Protein Data Bank... Message-ID: <111738@netnews.upenn.edu> Date: 28 Feb 93 14:39:39 GMT Sender: news@netnews.upenn.edu Followup-To: bionet.xtallography Organization: NMR Biochemistry Graduate Research Lab Lines: 8 Xref: biosci bionet.xtallography:162 bionet.molbio.proteins:545 Nntp-Posting-Host: chestnut.chem.upenn.edu Hi.. Could any one show me how to search the Brookhaven Protein Data Bank? I am trying to search for five or more residues amino acid on all proteins that the structures have been found. The results then can prove that "one sequence one structure" is correct or not... duc From owner-proteins@net.bio.net Sat Feb 27 22:00:00 1993 Path: biosci!UNLVM.UNL.EDU!PATH009 From: PATH009@UNLVM.UNL.EDU ("V. Warwar") Newsgroups: bionet.molbio.proteins Subject: Help with immunoprecipitation Message-ID: <930228.234331.CST.PATH009@UNLVM> Date: 1 Mar 93 05:43:31 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 Dear colleges: I am having a terrible problem with an immunoprecipitation experiment. I am immunoprecipitating the protein of my interest with the same antibody that I am using as a primary antibody in the western blot of this protein. As a result, in my secondary antibody used for detection (horseradish peroxidase) is giving me an enourmous background with the heavy and low chain of the antibody used in the immunoprecipitation procedure. Does someone know a way to avoid this this background? Thanks a lot in advance. Please reply to my e-mail adress because I am not in this newsgroup. Vitor Warwar Bitnet: PATH009@UNLVM University of Nebraska, Lincoln