From owner-proteins@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!uwm.edu!ogicse!psgrain!ee.und.ac.za!csir.co.za!frcs!linda From: linda@frcs.Alt.ZA (Linda Jacobson) Newsgroups: sci.med,sci.bio.technology,bionet.molbio.proteins Subject: Interspecific endocrine assays Message-ID: <1993Apr2.191707.9049@frcs.Alt.ZA> Date: 2 Apr 93 19:17:07 GMT Organization: Onderstepoort School of Veterinary Science, University of Pretoria Lines: 23 Xref: biosci sci.med:11893 sci.bio.technology:230 bionet.molbio.proteins:574 [Apologies in advance if this lands in places where it is out of context. I don't receive some of the above groups so couldn't check their content first. I'd appreciate e-mail responses unless the reponse is sent to sci.med.] I need to assay canine somatotropin and glucagon. Neither assay is available in this country. We do have human assays, and very likely have bovine somatotropin assays. Are the canine molecules close enough to the human to allow me to use the human assay? Likewise for the bovine assay. If the _assays_ aren't likely to be successful, would _treatment_ be a different issue? I have read that human and bovine somatotropin can be used in dogs, but would like confirmation. I'd appreciate any information, or any literature sources which might help. Linda ------------------------------------------------------------------------- Linda Jacobson Department of Medicine "Only the thing for which you Faculty of Vet Science have struggled will last." Onderstepoort, South Africa (Yoruba proverb) From owner-proteins@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!uwm.edu!spool.mu.edu!agate!dog.ee.lbl.gov!network.ucsd.edu!dlk From: dlk@chem.ucsd.edu (Daniel R. Knighton) Newsgroups: bionet.xtallography,bionet.molbio.proteins Subject: New cAMP-dependent protein kinase structures from UCSD Summary: 1ATP for cAPK:MnATP:PKI(5-24); 1APM for cAPK:PKI(5-24):MEGA-8 Keywords: protein kinase, crystal structure Message-ID: <1phenq$njf@network.ucsd.edu> Date: 2 Apr 93 13:23:06 GMT Organization: University of California San Diego, Chemistry Lines: 56 Xref: biosci bionet.xtallography:242 bionet.molbio.proteins:573 NNTP-Posting-Host: sdchemi3.ucsd.edu Dear cAMP-dependent protein kinase (PKA, cAPK) aficionados, Because confusion exists about what coordinate sets are available from whom, I will list here what *UCSD* prerelease coordinate entries are about to become available by April 2, 1993, from pdb.pdb.bnl.gov: 1ATP (pdb1atp.ent): 2.2-Angstrom refined structure of a recombinant mouse cAMP-dependent protein kinase catalytic subunit complexed with PKI(5-24) and MnATP. 1APM (pdb1apm.ent): 2.0-Angstrom refined structure of a recombinant mouse cAMP-dependent protein kinase catalytic subunit (S139A mutant) complexed with PKI(5-24) and the detergent octanoyl-N-methyl glucamide (MEGA-8), which binds in the same place as the mammalian enzyme's N-terminal myristic acid moiety. Both of these models have R-factors below 0.19 against all F/sigma>2 data and also good geometry, with r.m.s. deviations from ideal bond lengths for both of 0.013 Angstroms, and from ideal bond angles of 2.2 and 2.3 degrees. The structure factors for these two models are on hold until April, 1994. One other UCSD entry that has been available by ftp since Dec. 2, 1992, from the PDB (notice posted here Dec. 4, 1992) and that will still be available, because it is of crystallized mixed-phosphoform catalytic subunit and has a model for phospho-Ser 139, is 2CPK (pdb2cpk.ent). This is still at 2.7 Angstroms and was a 10/92 deposition to correct sequence register errors in two places in our initial 1991 structure model deposited as 1CPK. (If you are still using 1CPK, please discard it immediately and get 1APM for the backbone and 2CPK only if you have interest in Ser 139.) Published articles from UCSD that reflect information from our two high-resolution refinements are the following [two additional articles are also in the press in Acta Cryst. D49 (1993)]: "A template for the protein kinase family," S.S. Taylor, et al., Trends in Biochemical Sciences (TIBS) 18(3), 84-89 (1993). "Crystal Structure of the Catalytic Subunit of cAMP-Dependent Protein Kinase Complexed with MgATP and Peptide Inhibitor," J. Zheng, et al., Biochemistry 32(9), 2154-2161 (1993). I have no information regarding the coordinates of the independently solved porcine heart catalytic subunit structure complexed with PKI(5-24) and MnAMPPNP mentioned as having been deposited in the PDB by D. Bossemeyer, et al., EMBO J. 12(3), 849-859 (1993). However, the coordinates mentioned by Dr. E. Abola of the PDB in posts to bionet.xtallography as being newly available by today from the prerelease directory of pdb.pdb.bnl.gov should include at least the two UCSD entries I have described. As before, if you are unable to get any of the UCSD coordinates from the PDB for whatever reason, I will gladly e-mail any of them to you. Sincerely yours, Daniel R. Knighton dlk@chem.ucsd.edu FAX: 001-619-622-3299 From owner-proteins@net.bio.net Sat Apr 03 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!zaphod.mps.ohio-state.edu!swrinde!gatech!usenet.ins.cwru.edu!agate!headwall.Stanford.EDU!nntp.Stanford.EDU!catalan From: catalan@leland.Stanford.EDU ( Arredondo) Newsgroups: sci.med,sci.bio.technology,bionet.molbio.proteins Subject: Hemophilia Carrier Test? Summary: Is there a test for carriers? Keywords: Hemophilia, female, carrier, assay Message-ID: <1993Apr4.232622.895@leland.Stanford.EDU> Date: 4 Apr 93 23:26:22 GMT Sender: news@leland.Stanford.EDU (Mr News) Organization: DSG, Stanford University, CA 94305, USA Lines: 3 Xref: biosci sci.med:11954 sci.bio.technology:231 bionet.molbio.proteins:575 Does anyone out there know of a reliable test to determine if a daughter of a known carrier is also a carrier? Any information you may have is much appreciated. From owner-proteins@net.bio.net Tue Apr 06 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!natinst.com!news.dell.com!swrinde!zaphod.mps.ohio-state.edu!saimiri.primate.wisc.edu!zazen!psl.wisc.edu!sinchi.biochem.wisc.edu!rapulak From: rapulak@macc.wisc.edu (Rock A Pulak) Newsgroups: bionet.molbio.proteins Subject: missense mutations and protein levels Message-ID: <1993Apr7.202003.7040@pslu1.psl.wisc.edu> Date: 7 Apr 93 20:20:03 GMT Sender: news@pslu1.psl.wisc.edu (USENET News System) Organization: Biochemistry, UW-Madison Lines: 10 X-Xxmessage-Id: X-Xxdate: Wed, 7 Apr 93 21:32:01 GMT X-Useragent: Nuntius v1.1.1d17 Does anyone know of an example or examples where a missense mutation affects the steady-state level of the encoded polypeptide? One rather surprising example of this is described by Befsovec and Anderson (Genes and Development (1988) 2:1307 and Cell (1990) 60:133). I wonder if many missense mutations lead to a mutant phenotype not because the polypeptide is non-functional but because of the low level or amount of polypeptide. Rock A Pulak rapulak@macc.wisc.edu From owner-proteins@net.bio.net Thu Apr 08 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!rc1!dec5.ulb.ac.be!rherzog From: rherzog@dec5.ulb.ac.be (Robert Herzog) Newsgroups: bionet.molbio.proteins Subject: 2D gel databank ? Keywords: 2D protein gel databank Message-ID: <1614@rc1.vub.ac.be> Date: 9 Apr 93 14:24:21 GMT Sender: news@rc1.vub.ac.be Organization: Free University Brussels - Belgium - Department of Molecular Biology Lines: 1 Is there an endeavour to create / maintain a databank of 2D gel patterns somewhere? From owner-proteins@net.bio.net Fri Apr 09 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!agate!ames!network.ucsd.edu!riscsm!anthonyp From: anthonyp@riscsm.scripps.edu (Anthony Pelletier) Newsgroups: bionet.molbio.proteins Subject: Re: 2D gel databank ? Keywords: 2D protein gel databank Message-ID: <1993Apr10.161614.9864@riscsm.scripps.edu> Date: 10 Apr 93 16:16:14 GMT References: <1614@rc1.vub.ac.be> Organization: The Scripps Research Institute, La Jolla, California, USA Lines: 19 In article <1614@rc1.vub.ac.be> rherzog@dec5.ulb.ac.be (Robert Herzog) writes: >Is there an endeavour to create / maintain a databank of 2D gel patterns somewhere? Jim Garrels at was doing this at Cold Spring Harbor 10 years ago. I have no idea what ever became of the project. At the time it was very well funded and looked like it would be going for some time. -tony "Just because a few of us can read and write and do a little math, that doesn't mean we deserve to conquer the Universe" -Kurt Vonnegut in "Hocus Pocus" **************************************************************************** Anthony J. Pelletier Ph.D The Scripp's Research Inst. La Jolla, CA From owner-proteins@net.bio.net Sat Apr 10 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!bogus.sura.net!news-feed-1.peachnet.edu!umn.edu!msus1.msus.edu!TIGGER.STCLOUD.MSUS.EDU!Q00023 From: q00023@TIGGER.STCLOUD.MSUS.EDU Newsgroups: bionet.molbio.proteins Subject: cloning in animals Message-ID: <1993Apr11.161239.3042@msus1.msus.edu> Date: 11 Apr 93 22:12:39 GMT Reply-To: q00023@TIGGER.STCLOUD.MSUS.EDU Organization: ST. CLOUD STATE UNIVERSITY, ST. CLOUD, MN Lines: 8 Nntp-Posting-Host: tigger.stcloud.msus.edu Dear netters, I have a cloning porject lately that I have to gather information of animal cloning. Like methodologies, techniques, instrumentations, purposes, and ethic. I would greatly appreciate anyone who will send me information on this topics. Thanks in advances, Gabriel Cheung SCSU, Biotechnology Q00023@TIGGER.STCLOUD.MSUS.EDU From owner-proteins@net.bio.net Sun Apr 11 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!zaphod.mps.ohio-state.edu!saimiri.primate.wisc.edu!zazen!news From: nmrdb@vms.macc.wisc.edu (BEVERLY SEAVEY) Newsgroups: bionet.molbio.proteins Subject: Re: 2D gel databank ? Message-ID: <1993Apr12.135529.361@macc.wisc.edu> Date: 12 Apr 93 15:52:40 GMT Sender: news@macc.wisc.edu (USENET News System) Organization: University of Wisconsin Academic Computing Center Lines: 9 In article <1614@rc1.vub.ac.be>, rherzog@dec5.ulb.ac.be (Robert Herzog) writes... >Is there an endeavour to create / maintain a databank of 2D gel patterns somewhere? Contact Dr. Richard Simpson Ludwig Institute for Cancer Research P.O. Royal Melbourne Hospital email: simpson%licra.dn.mu.oz.au@uunet.uu.net From owner-proteins@net.bio.net Mon Apr 12 23:00:00 1993 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Announcements of PIR Network Request Service Message-ID: <01GWYUXYCJY69LV03D@NBRF.Georgetown.Edu> Date: 13 Apr 93 19:51:33 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 284 Announcements of the Protein Information Resource Network Request Service Highlights 1. Summaries for PIR-International Release 36, NRL_3D Release 12, ALN Release 4 2. Summary of Database Developments in Release 36.00 3. Second Technical Development Bulletin Available 4. Answer to an FAQ and Changes in PIR Network Request Server Commands 5. PIR Network Request Service Command Summary Announcements 1. Summaries for PIR-International Release 36, NRL_3D Release 12, ALN Release 4 Release 36.00 of the PIR-International database, Release 12.00 of the NRL_3D database (corresponding to Brookhaven Protein Data Bank Release 63), and Release 4.00 of the ALN database of protein sequence alignments are now available through the PIR On-line system and the Network Request Server. The PIR1, PIR2, PIR3 and NRL_3D databases have been distributed on tape; the CD-ROM with those databases and ALN is in production. An appropriate announcement will be made when the CD-ROM is distributed. Database Release Sequences Residues PIR1 36.00 11,252 3,903,802 Classified and Annotated Entries PIR2 36.00 27,383 7,560,531 Annotated Entries PIR3 36.00 13,622 4,021,433 Unverified Entries NRL_3D 12.00 1,630 283,635 Sequences in Brookhaven PDB ALN 4.00 956 (Entries) Protein Sequence Alignments Growth of the PIR databases is documented in the file DBGROWTH.LIS available through the Network Request Server. The following files are also available through the Server: PADD.LIS PIR1 entries added since Release 35.00 PREV.LIS PIR1 entries with revised sequences since Release 35.00 SUPERFAM.LIS superfamiles recorded in PIR1 and PIR2 KEYWORDS.LIS keywords employed in PIR1 and PIR2 FEATURES.LIS features cataloged in PIR1 and PIR2 JOURNALS.LIS recognized journal abbreviations ALNBASE.LIS a description of the ALN database ALNTITLE.LIS titles in the ALN database NRLTITLE.LIS titles in the NRL_3D Database To obtain these and other files from the PIR Network Request Server, follow the instructions in the last section of these announcements. 2. Summary of Database Developments in Release 36.00 The three sections, PIR1, PIR2 and PIR3, of the PIR-International Database now have a uniform format description. Previously some PIR3 entries appeared with an asterisk in the title and included the comment *This entry is not verified. This has been resolved for each entry, or removed and replaced with a new "Status:" comment. The comment Status: preliminary indicates that the sequence and reference information has been verified or extracted automatically from another database. However, the entry may not have been reviewed subsequently by a PIR-International staff scientist. Information extracted from the NCBI Backbone Sequence Database is included in the PIR-International Database. Initially, some information extracted from the NCBI data set may not conform to previous PIR standards or conventions. The database codes "NCBIN:" and "NCBIP:" now appear indicating, respectively, a cross-reference to a nucleic sequence and a cross-reference to a protein sequence (or conceptual translation) from the NCBI Backbone Database. Such cross-references are followed by the comment Note: sequence extracted from NCBI backbone In entries extracted from other databases the comment "Status: preliminary" additionally indicates that the sequence has not been checked by PIR-International personnel. The new molecule type "nucleic acid" has been introduced for those entries where the molecule type could not be determined. As a result of collaborations with Human Genome Data Base (GDB) Center at the Johns Hopkins University Welch Medical Library, the human sequence entries in the PIR-International Database have gene names cross-referenced to GDB gene symbols. In the "Gene name" information the database code "GDB:" before a gene symbol indicates this cross-reference. Human entries with gene names not preceded by "GDB:" and those without gene names will be matched in an on-going joint effort with the Human Genome Data Base. As a result of collaborations with the National Center for Biotechnology Information (NCBI), the bibliographic references in the PIR-International Database have been extensively cross-referenced with the National Library of Medicine MedLine UID's. In the "Reference number" information the database code "MUID:" followed by a reference number indicates the MedLine UID. 3. Second Technical Development Bulletin Available The second PIR-International Technical Development Bulletin is available in the file PIRTECH.LIS that can be sent by the PIR Network Request Server or picked up by anonymous FTP from the UH Gene-Server, ftp.bchs.uh.edu, IP address 129.7.2.43. This electronic bulletin provides detailed specifications of the database format and serves as an "early warning system" for software developers and others who are concerned about changes in the format and standards for the PIR databases. If you are interested in the technical aspects of these database changes and would like to be placed on the mailing list for the Technical Bulletin, send a brief electronic mail note to POSTMAST@GUNBRF on BITNET or to POSTMASTER@NBRF.Georgetown.Edu on Internet. 4. Answer to an FAQ and Changes in PIR Network Request Server Commands One frequently asked question goes something like > What is the longest (or shortest) known human (or some other species) > protein sequence? Fragments, free-amino acids and isopeptides should be eliminated from the contest for shortest. Then there would have to be a caveat that it might not be certain whether a particular di- or tripeptide is genetically coded. Also, for various reasons there is an inherent bias that may limit the shortest to 3 rather than 2 residues. The shortest human sequence in the PIR databases is: length code title 3 GKHU Growth-modulating peptide - Human The current longest sequences for various eukaryotes are: length code title 6805 S20901 Titin - Rabbit 6048 S07571 Twitchin - Caenorhabditis elegans 5147 A41087 Cadherin-related tumor suppressor precursor - Fruit fly (Drosophila melanogaster) 5032 A35041 Ryanodine receptor - Human The PIR Network Request Server will now allow the PIR protein sequence databases to be queried on the basis of length. The commands USE LOWER nnn and USE UPPER nnn will set the sequence length lower and upper limits. For example, the commands USE LOWER 1300 USE UPPER 1600 will restrict the selection to sequences with from 1300 through 1600 residues. The default unrestricted limits can be restored by using the commands USE LOWER * USE UPPER * The USE LOWER, USE UPPER, USE BEFORE, USE AFTER and USE FORMAT commands are applicable only to the PIR1, PIR2, PIR3 and NRL_3D databases; these commands cannot be used with the ALN, GenBank and EMBL databases. It is now anticipated that with Release 37.00, the "Host" information will be eliminated in the PIR databases. When this happens, the HOST command for the PIR Network Request Server will be disabled. 5. PIR Network Request Server Command Summary The National Biomedical Research Foundation Protein Information Resource Network Request Server is a full-function fileserver and database query system. Operating since August 1990 it is capable of handling database queries, sequence searches and sequence submissions, in addition to fileserver requests. To use this server, request commands should be sent to FILESERV@GUNBRF on BITNET or FILESERV@NBRF.Georgetown.EDU on Internet. The server recognizes the following commands sent either in a mail message or (if the sender is on BITNET) in a command message or a file: Command Action ------- ----------------------------------------------- ACCESSION list entry codes and titles by accession number AND combine QUERY commands with Boolean AND AUTHOR list entry codes and titles by author BASES list accessible databases CROSS list PIR entry codes and titles corresponding to a particular nucleic sequence database entry DEPOSIT deposit entry for database submission END DEPOSIT terminate deposit entry FEATURE list entry codes and titles by feature table entry GENE list entry codes and titles for a gene name GET return entry by entry code HELP return HELP instructions HOST list entry codes and titles by host species INDEX list SENDable files JOURNAL list entry codes and titles by journal citation KEYWORD list entry codes and titles by keyword MEMBER list alignments containing entry code as a member NOT combine QUERY commands with Boolean NOT OR combine QUERY commands with Boolean OR QUERY begin collecting QUERY commands END QUERY terminate collecting commands and execute QUERY QUIT ignore the remaining text (E-mail signature blocks) RETURN change return address for gateway mail SEARCH search for matching sequences by FASTA procedure END SEARCH terminate sequence for searching SEND send file SPECIES list entry codes and titles by species SUGGEST leave suggestion or correction for PIR staff END SUGGEST terminate suggestion text SUPERFAMILY list entry codes and titles by superfamily name TAXONOMY report taxonomy for scientific or common name TITLE list entry codes and titles by title USE set databases, dates, lengths or formats to use in limited searches Multiple commands can be sent with one command on each line of a mail message or file. Commands should NOT be sent on the Subject line of a mail message. Receipt of BITNET command messages and files will be acknowledged immediately. Mail messages will be acknowledged by return mail. For help in using any of the commands, send a request of the form HELP topic for example HELP SEARCH In addition to the commands, help instructions are also available on the following topics: Custom_Services Databases FTP Gateway_Access Help_en_Espanol Help_en_francais Hints IBM-VM_BITNET On-Line_Access PIR_Distribution VAX-VMS_BITNET Because of network gateway communication protocols, there are limitations on requests sent through gateways. Users not on BITNET or INTERNET who access the server through local or network gateways should read and carefully follow these instructions before sending requests. Only mail message requests (not command messages or files) can be sent through gateways. Because addresses posted on gateway mail do not always work for the return, before you send requests through network gateways it is strongly recommended that you first contact John S. Garavelli (POSTMAST@GUNBRF on BITNET, POSTMASTER@NBRF.Georgetown.EDU on Internet). We will confirm a return address for you and may instruct you to use the RETURN command to ensure that your request output will reach you. It is not usually necessary to do this if you are on BITNET or INTERNET, unless your system employs a local remailer or your mail program applies a nonstandard return address (for example a personal name on the FROM: line). The BITNET network and the network gateways impose strict limits on file size. Poorly posed database queries may result in output so extensive that it could not be returned by network mail. Therefore, an output limit of 1000 lines for each command and 3000 lines for each request is imposed by the PIR server. The DEPOSIT and QUERY commands, and the SEARCH and SUGGEST commands (in their multiline form) must be followed by their respective END commands after the text appearing on the intervening lines. The DEPOSIT command requires, and the SEARCH command optionally uses, parameters that appear on the same line as the command. Because these four commands are so complex, users should obtain and carefully read the help instructions before attempting to use them. The databases available through the PIR Network Server and their abbreviations for code specification are as follows: Abbreviation Database Update Schedule PIR1 PIR Annotated and Classified Entries approximately biweekly PIR2 PIR Preliminary Entries approximately weekly PIR3 PIR Unverified Entries weekly ALN PIR Alignment Entries quarterly NRL_3D Brookhaven Data Bank Sequences quarterly PATCHX MIPS PIR-Supplementary Database quarterly N NBRF Nucleic GB* GenBank (TM) as received GBNEW GenBank (TM) New Entries weekly EMBL* EMBL as received In the FASTA output of the SEARCH command the abbreviation for PATCHX is shortened to PATX and NRL_3D is shortened to NR3D; the longer abbreviations should be used to retrieve entries with the GET command. Not all commands work with all databases; please read the information returned by the command HELP DATABASES. The GenBank (TM), GB, and EMBL databases are divided into sections corresponding to the sections of their standard releases. These databases may be indivually accessed with the USE BASES command with the database abbreviation and the section abbreviation, for example USE BASES GBPRI or all sections of a given database may be accessed with the database abbreviation and an asterisk, for example USE BASES PIR* or USE BASES GB* ------------------------------------------------------------------------ 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 Apr 12 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!hp4at!news.univie.ac.at!paladin.american.edu!europa.eng.gtefsd.com!emory!emoryu1!mfbalis From: mfbalis@emory.edu (Mitchell F. Balish) Newsgroups: bionet.molbio.proteins Subject: Re: Branched-chain keto acid dehydrogenase Message-ID: <2655@emoryu1.cc.emory.edu> Date: 13 Apr 93 19:40:47 GMT References: <13158@news.duke.edu> Organization: Emory University, Atlanta, GA Lines: 17 X-Newsreader: Tin 1.1 PL3 lees@acpub.duke.edu (Steve Lee) writes: : : I really need information on branched-chain keto acid dehydrogenase. : does anyone know any good review papers out there or books that are : related so I can get background data to help me interpret current : papers? : : I am specifically interested in transcriptional and translational : control of the protein and info on the bkd operon. Are there any : reference books that discuss that specific operon? : : thanks alot, : : steve I can tell you that Dean Danner here at Emory (in pediatrics) studies that complex. You might want to look his stuff up. From owner-proteins@net.bio.net Mon Apr 12 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!haven.umd.edu!darwin.sura.net!udel!gatech!concert!duke!news.duke.edu!acpub.duke.edu!lees From: lees@acpub.duke.edu (Steve Lee) Newsgroups: bionet.molbio.proteins Subject: Branched-chain keto acid dehydrogenase Message-ID: <13158@news.duke.edu> Date: 13 Apr 93 16:51:29 GMT Sender: news@news.duke.edu Organization: Duke University; Durham, N.C. Lines: 13 Nntp-Posting-Host: raphael.acpub.duke.edu I really need information on branched-chain keto acid dehydrogenase. does anyone know any good review papers out there or books that are related so I can get background data to help me interpret current papers? I am specifically interested in transcriptional and translational control of the protein and info on the bkd operon. Are there any reference books that discuss that specific operon? thanks alot, steve From owner-proteins@net.bio.net Tue Apr 13 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!pipex!uknet!warwick!dcs.warwick.ac.uk!mrccrc!dmartin From: dmartin@crc.ac.uk (David Martin x3175) Newsgroups: sci.med,sci.bio.technology,bionet.molbio.proteins Subject: Re: Hemophilia Carrier Test? Keywords: Hemophilia, female, carrier, assay Message-ID: <1993Apr13.111113.7742@crc.ac.uk> Date: 13 Apr 93 11:11:13 GMT References: <1993Apr4.232622.895@leland.Stanford.EDU> Sender: news@crc.ac.uk Organization: MRC Human Genome Resource Centre Lines: 15 Xref: biosci sci.med:12538 sci.bio.technology:242 bionet.molbio.proteins:584 Nntp-Posting-Host: tin There are many tests that can be done. Our lab is an academic setup involved in Haemophilia lineage analysis and has samples referred from all over UK. Write to: Dr. E.G.D. Tuddenham Haemostasis Research Group Clinical Research Centre Watford Road Harrow HA1 3UJ ENGLAND Fax. +44 (0)81 423 1275 He should be able to offer some advice. ....david From owner-proteins@net.bio.net Tue Apr 13 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!darwin.sura.net!haven.umd.edu!purdue!mentor.cc.purdue.edu!mace.cc.purdue.edu!b35 From: b35@mace.cc.purdue.edu (Vic Ilag) Newsgroups: bionet.molbio.proteins Subject: tetrameric alpha-helical protein Message-ID: Date: 14 Apr 93 14:55:25 GMT Sender: news@mentor.cc.purdue.edu (USENET News) Organization: Purdue University Lines: 7 Does anyone know of a protein that is mainly alpha-helical and exists as a tetramer in solution? I am working with a phage scaffolding protein that has these properties and has no apparent sequence homology to any protein in the database. Please e-mail me if you know of any. Thanks in advance. vic ilag From owner-proteins@net.bio.net Wed Apr 14 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!zaphod.mps.ohio-state.edu!howland.reston.ans.net!noc.near.net!news.cs.brandeis.edu!news From: ahouse@hydra.rose.brandeis.edu (Jeremy John Ahouse) Newsgroups: bionet.molbio.proteins Subject: follicle cell specific protein? Message-ID: <1993Apr15.143745.19929@news.cs.brandeis.edu> Date: 15 Apr 93 14:37:45 GMT Sender: news@news.cs.brandeis.edu (USENET News System) Organization: Center for Complex Systems Lines: 19 X-Xxdate: Thu, 15 Apr 93 15: 43:53 GMT X-Useragent: Nuntius v1.1.1d17 ***Does anyone recognize the following palindromic binding site?*** tttattccGCTATCGATAGCatatacac This element occurs upstream of the yolk protein genes 1 and 2 of Drosophila melanogaster. It functions as an activator of transcription in vitro, and boosts follicle cell-specific, but not fat body-specific expression in vivo. I would appreciate any information you might have about related binding sites, or in broader scope, about elements with similar function in other systems. Thanks for your help. Marie Lossky lossky@hydra.rose.brandeis.edu From owner-proteins@net.bio.net Wed Apr 14 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!haven.umd.edu!darwin.sura.net!zaphod.mps.ohio-state.edu!uwm.edu!psuvax1!psuvm!sml108 From: SML108@psuvm.psu.edu Newsgroups: bionet.molbio.proteins Subject: Re: tetrameric alpha-helical protein Message-ID: <93105.003526SML108@psuvm.psu.edu> Date: 15 Apr 93 04:35:26 GMT References: Organization: Penn State University Lines: 5 How about melittin? 26 residue kinked helix which exists as a tetramer in solution I believe. PDB entry 2mlt... From owner-proteins@net.bio.net Wed Apr 14 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!comp.vuw.ac.nz!canterbury.ac.nz!news!sanger.otago.ac.nz!craigm From: craigm@sanger.otago.ac.nz (Craig Marshall) Newsgroups: bionet.molbio.proteins Subject: Re: tetrameric alpha-helical protein Message-ID: Date: 15 Apr 93 22:39:22 GMT References: Sender: usenet@news.otago.ac.nz (News stuff) Organization: University of Otago Lines: 17 Nntp-Posting-Host: sanger.otago.ac.nz X-Newsreader: TIN [version 1.1 PL8] How about haemoglobin? -- Craig Marshall bioc07@otago.ac.nz Biochemistry Department University of Otago Phone 64 3 479 7849 P.O. Box 56 Fax 64 3 479 7866 Dunedin, New Zealand Vic Ilag (b35@mace.cc.purdue.edu) wrote: > Does anyone know of a protein that is mainly alpha-helical and exists as a > tetramer in solution? I am working with a phage scaffolding protein > that has these properties and has no apparent sequence homology to any > protein in the database. Please e-mail me if you know of any. > Thanks in advance. > vic ilag From owner-proteins@net.bio.net Wed Apr 14 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!math.fu-berlin.de!news.belwue.de!softserv.zdv.uni-tuebingen.de!studserv!zxmkr08 From: zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: tetrameric alpha-helical protein Message-ID: Date: 14 Apr 93 22:56:28 GMT References: Organization: InterNetNews at ZDV Uni-Tuebingen Lines: 13 NNTP-Posting-Host: studserv.zdv.uni-tuebingen.de In b35@mace.cc.purdue.edu (Vic Ilag) writes: >Does anyone know of a protein that is mainly alpha-helical and exists as a >tetramer in solution? I am working with a phage scaffolding protein Perhaps hemoglobin? (Sorry, couldn't resist; to be precise, hemoglobin consists of two alpha- and two beta-subunits etc.) --Cornelius :-) -- /* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen */ /* email: krasel@studserv.zdv.uni-tuebingen.de */ /* "People are DNA's way of making more DNA." (R. Dawkins / anonymous) */ From owner-proteins@net.bio.net Wed Apr 14 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!natinst.com!news.dell.com!swrinde!network.ucsd.edu!munnari.oz.au!metro!usage!newt.phys.unsw.edu.au!sjt From: sjt@newt.phys.unsw.edu.au (Sarah Tilley) Newsgroups: bionet.molbio.proteins Subject: Protein Sequence Databases Message-ID: <1993Apr15.011057.18771@usage.csd.unsw.OZ.AU> Date: 15 Apr 93 01:10:57 GMT Sender: news@usage.csd.unsw.OZ.AU Reply-To: sjt@newt.phys.unsw.edu.au (Sarah Tilley) Organization: University of NSW Lines: 9 Nntp-Posting-Host: newt.phys.unsw.edu.au -- Could anyone recommend a database that contains up-to-date amino acid sequences? I would like to transfer the sequence of a particular protein to the machine I work on. Thanks in advance. ** Sarah Tilley sjt@newt.phys.unsw.edu.au From owner-proteins@net.bio.net Wed Apr 14 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!zaphod.mps.ohio-state.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Sequence Databases Message-ID: <1993Apr15.151230.26487@welchgate.welch.jhu.edu> Date: 15 Apr 93 15:12:30 GMT References: <1993Apr15.011057.18771@usage.csd.unsw.OZ.AU> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 18 In article <1993Apr15.011057.18771@usage.csd.unsw.OZ.AU> sjt@newt.phys.unsw.edu.au (Sarah Tilley) writes: > >-- >Could anyone recommend a database that contains up-to-date amino acid sequences? I would like to transfer the sequence of a particular protein to the machine I work on. > The two databases you're looking for are PIR and Swiss-Prot. The easiest way to retrieve sequences from them (and many other databases) is gopher. If you've never heard of gopher don't worry it's free and on the net. There have been quite a few posts about gopher on other bionet groups so I won't post a full description here (unless there's lots of demand :-), write me a note if you need info on how to get started with gopher. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-proteins@net.bio.net Wed Apr 14 23:00:00 1993 Path: biosci!EVOL.HARVARD.EDU!dmw From: dmw@EVOL.HARVARD.EDU (Dan Weinreich) Newsgroups: bionet.molbio.proteins Subject: folding software Message-ID: Date: 15 Apr 93 19:50:21 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 30 I'm an evolutionary biologist (i.e. protein folding neophyte) looking for info/advice/wisdom regarding protein folding software. Implementations of the Garnier/Robson approach are commonly available. But those tables are derived from globular soluble proteins and my study object is an extracellular fibrous protein (Drosophila chorion). What effect on predictive success can be expected in such an application? I just read the Cohen et al. (1986) pattern-matching approach. Does anyone know of a public domain implementation of the system? And again, what effect on predictive success can be expected in the application of an algorithm developed for globular proteins on fibrous proteins? My intent is to test for conservation of higher level structure among homologous, highly diverged proteins. As such I am not particularly wedded to either of these methodologies, and would welcome any suggestions regarding other approaches to predicting protein structure. Thank you. Dan Weinreich email: dmw@mcz.harvard.edu Museum of Comparative Zoology usmail: 26 Oxford St. Harvard University Cambridge, MA 02138 From owner-proteins@net.bio.net Wed Apr 14 23:00:00 1993 Path: biosci!IFQSC.USP.ANSP.BR!RODRIGO From: RODRIGO@IFQSC.USP.ANSP.BR (Rodrigo Neves Romcy Pereira) Newsgroups: bionet.molbio.proteins Subject: H-T-H motif Message-ID: <4EB3586641DF012D2F@USPFSC.IFQSC.USP.ANSP.BR> Date: 16 Apr 93 00:34:35 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 My question is the following : It has been described in many prokaryotic repressors the helix-turn-helix motif and sequence analysis have showed a high conserved glycine (usually with a left-handed conformation- 60 and 40) at the first position of the turn that connects these two helices. However, amino acids like lys, cys,asn,glu,ala,his,met and asp were also found in this position, in other prokaryotic repressors. Among those with 3D structure solved(that I know), the residues that occupy that position are G,N and C. Well,I work on a E.coli repressor, but instead of a glycine residue at the turn I have a glutamine. This sequence has homology with xylose represssors from other bacteria that apparently share a h-t-h motif, but none of them has a Q (neither any H-T-H DNA binding protein I got to found). How can I decide the validity of the hipothesis that my repressor has a H-T-H motif? What is the degree of reliability in using one of the known repressors to model my sequence? From owner-proteins@net.bio.net Thu Apr 15 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!gatech!news-feed-1.peachnet.edu!umn.edu!molbio.cbs.umn.edu!dubear From: dubear@molbio.cbs.umn.edu (Dubear Kroening) Newsgroups: bionet.molbio.proteins Subject: Membrane proteins - specific targeting? Message-ID: Date: 16 Apr 93 22:50:58 GMT Sender: news@news2.cis.umn.edu (Usenet News Administration) Organization: University of Minnesota Lines: 16 Nntp-Posting-Host: molbio.cbs.umn.edu X-Newsreader: Tin 1.1 PL5 Hi, Sorry if this is a FAQ, but I haven't seen it yet. Is there a some type of consensus sequence for targeting a protein to the plasma membranes. I know that there are signals for targeting to mitochondria, peroxisomes, and the nucleus, but what about just plasma membranes. I am specifically interested in yeast (S. cerevisiae) sequences if there is a difference. I have only found some general textbook refs. which really don't say too much. Any info. would be greatly appreciated. Please contact me e-mail to save bandwith. dubear@molbio.cbs.umn.edu Thanks in advance for any and all information, Dubear From owner-proteins@net.bio.net Thu Apr 15 23:00:00 1993 Path: biosci!CUCCFA.CCC.COLUMBIA.EDU!LIJ From: LIJ@CUCCFA.CCC.COLUMBIA.EDU Newsgroups: bionet.molbio.proteins Subject: turn prediction Message-ID: <930416174951.1540@CUCCFA.CCC.COLUMBIA.EDU> Date: 16 Apr 93 21:49:51 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 Dear netters; Does anybody there know the algorithm for the prediction of different types of beta-turn by Wilmot and Thornton (published in JMB 203:221-232,1988)? Are there any ftp or gopher place for this program or can somebody tell me the email address of the authors, so that I can ask them directly ? Thanks for any help and I'll appreciate it very much if the notes can be dropped to my personal email address(lij@cuccfa.bitnet). Jun Li From owner-proteins@net.bio.net Thu Apr 15 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!noc.near.net!uunet!psgrain!ee.und.ac.za!ucthpx!uctvax.uct.ac.za!bbbbre01 From: bbbbre01@uctvax.uct.ac.za (Doon) Newsgroups: bionet.general,bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Clones genes that don't express Message-ID: <1993Apr16.151753.203905@uctvax.uct.ac.za> Date: 16 Apr 93 13:17:53 GMT Organization: Whacko Tower Lines: 42 Xref: biosci bionet.general:4603 bionet.molbio.methds-reagnts:5114 bionet.molbio.proteins:597 Will Bourne and I are working on a theory as to why certain cloned genes that should express in Ecoli don't. If you have a clone that you expected to express, but did not, we would appreciate it if you would tell us the sequence of that clone. ------Included message from Will ------------------------------------> We are conducting some research on codon usage in E.Coli and need to find examples of cloned genes that display certain characteristics that would not normally be reported in the literature. The genes need to have the following features: 1) They must be from organisms other than E.Coli 2) The complete sequence must be known and if possible available on one of the data bases 3) The sequence must have been cloned in E.Coli as an in frame translational fusion, behind an active E.Coli promoter and known E.Coli ribosome binding site 4) When the ORF is cloned as described above it must give bizarre or inexplicable results in that expression of the gene is weak or does not occur at all, when it is reasonable to expect expression to occur. 5) This lack of expression should be alleviated by a change in the growth conditions and work in unexpected ways. For example, if you were working with a DNA damage repair gene from Bacillus and it was cloned as a translation fusion but would only express on minimal medium but not on complex medium (or vice versa) then that is exactly the type of gene we are looking for. We are especially interested in systems where the expression is known to be linked to a particular single compound, eg. glucose or an individual amino acid. We would be very grateful, if you have or know of such genes, if you would send us details such as references, data base accession numbers and unpublished experimental observations that you feel you can pass on. ---------------------------------------------------> From owner-proteins@net.bio.net Sun Apr 18 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!saimiri.primate.wisc.edu!zaphod.mps.ohio-state.edu!uwm.edu!caen!batcomputer!munnari.oz.au!bruce.cs.monash.edu.au!monu6!vaxc.cc.monash.edu.au!mic268a From: mic268a@vaxc.cc.monash.edu.au Newsgroups: bionet.molbio.proteins Subject: helix-turn-helix query Message-ID: <1993Apr19.224009.91701@vaxc.cc.monash.edu.au> Date: 19 Apr 93 12:40:09 GMT Organization: Computer Centre, Monash University, Australia Lines: 10 Hi there, Does anyone know of a computer program that determines if proteins contain a helix-turn-helix? I have a paper that allows you to determine this but it is very cumbersome as you have to do it by eye. Any help would be gratefully appreciated. Thanks Mike L Monash University AUSTRALIA From owner-proteins@net.bio.net Mon Apr 19 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!spool.mu.edu!howland.reston.ans.net!bogus.sura.net!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.proteins Subject: Re: helix-turn-helix query Message-ID: <1993Apr19.223446.23580@welchgate.welch.jhu.edu> Date: 19 Apr 93 22:34:46 GMT References: <1993Apr19.224009.91701@vaxc.cc.monash.edu.au> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 27 In article <1993Apr19.224009.91701@vaxc.cc.monash.edu.au> mic268a@vaxc.cc.monash.edu.au writes: >Hi there, >Does anyone know of a computer program that determines if proteins contain >a helix-turn-helix? I have a paper that allows you to determine this but it is >very cumbersome as you have to do it by eye. >Any help would be gratefully appreciated. > >Thanks >Mike L >Monash University >AUSTRALIA > > You might try Prosearch or Macpattern to see if you pick up one of the many helix-turn-helix motifs present in the Prosite database. You can obtain either program from a variety of ftp and gopher holes including ftp.bio.indiana.edu and felix.embl-heidelberg.de. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-proteins@net.bio.net Mon Apr 19 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!nigel.msen.com!emory!europa.eng.gtefsd.com!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.proteins Subject: Re: helix-turn-helix query Message-ID: <1993Apr20.141354.19295@welchgate.welch.jhu.edu> Date: 20 Apr 93 14:13:54 GMT Organization: Johns Hopkins Univ. Welch Medical Library Lines: 54 >Hi there, >Does anyone know of a computer program that determines if proteins contain >a helix-turn-helix? I have a paper that allows you to determine this but it is >very cumbersome as you have to do it by eye. >Any help would be gratefully appreciated. > >Thanks >Mike L >Monash University >AUSTRALIA As a follow up to my follow up there's another source of information that you might try. Point you gopher client at merlot.welch.jhu.edu and select the following: --> 12. Search Databases at Welchlab (Vectors, Promoters, NRL-3D, EST, OMI../ --> 9. Seqanalref - Sequence Analysis Bibliographic Reference Data Ban.. Now Search for helix and turn and you'll see the following entries (which are litereature citations with abstracts): --> 1. RT "Prediction of the secondary structure of globular proteins b... 2. RT "Hydrophobicity scales and computational techniques for detec... 3. RT "Improved detection of helix-turn-helix DNA-binding motifs in... 4. RT "Conformational preferences of amino acids in globular protei... 5. RT "DNABIND: an interactive microcomputer program searching for ... 6. RT "Amino acid preference for specific locations at the end of a... 7. RT "Automatic definition of recurrent local structure motifs in ... 8. RT "Weak correlation between predictive power of individual sequ... 9. RT "Amino acid template useful for alpha-helix-turn-alpha-helix. 10. RT "Prediction of DNA-recognizing protein supersecondary structu... 11. RT "Acid helix-turn activator motif.";. 12. RT "The helix-turn-helix DNA binding motif.";. 13. RT "The prediction of helix-turn-helix DNA-binding regions in pr... 14. RT "The prediction of helix-turn-helix DNA-binding regions in pr... which you might find helpful. If you've never heard of gopher - don't worry it's free and on the net - write me a note if you need information on how to get started. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-proteins@net.bio.net Mon Apr 19 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!natinst.com!news.dell.com!swrinde!gatech!howland.reston.ans.net!zaphod.mps.ohio-state.edu!saimiri.primate.wisc.edu!usenet.coe.montana.edu!news.u.washington.edu!carson.u.washington.edu!jing From: jing@carson.u.washington.edu (Jing Huang) Newsgroups: bionet.molbio.proteins Subject: Random cutting Proteinase? Message-ID: <1qvi9cINNehp@shelley.u.washington.edu> Date: 20 Apr 93 01:05:48 GMT Organization: University of Washington, Seattle Lines: 9 NNTP-Posting-Host: carson.u.washington.edu Hi, I am interested in studying the conformational changes in proteins after they bind to target DNA sequences. I hope to use a random cutting proteinase to attack my protein of interest so that I can see discrete patterns on and off DNA. Could anybody advice me on what kind of proteinase to use to achieve that? Thanks a lot. -Fred From owner-proteins@net.bio.net Tue Apr 20 23:00:00 1993 Path: biosci!tigr.org!bult From: bult@tigr.org (Carol Bult) Newsgroups: bionet.molbio.proteins Subject: dayhoff's atlas via FTP? Message-ID: <9304211638.AA00493@bengal.tigr.org> Date: 21 Apr 93 16:38:03 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 I'm looking for an FTP site or Gopher hole that has summary information on protein nomenclature (family, superfamily, etc). Is Dayhoff's Atlas of Protein Sequence and Structure available via FTP ? Any clues will be appreciated. I'll post a summary of responses. Carol ___________________________________________________________________ Carol Bult, Ph.D. bult@tigr.org The Institute for Genomic Research 932 Clopper Road voice: 301-869-9056 Gaithersburg, MD 20878 fax: 301-869-9423 ___________________________________________________________________ From owner-proteins@net.bio.net Tue Apr 20 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!nigel.msen.com!emory!europa.eng.gtefsd.com!darwin.sura.net!haven.umd.edu!uunet!comp.vuw.ac.nz!canterbury.ac.nz!news!sanger.otago.ac.nz!craigm From: craigm@sanger.otago.ac.nz (Craig Marshall) Newsgroups: bionet.software,bionet.molbio.proteins Subject: Commercial Mac Modelling Software Message-ID: Date: 23 Apr 93 00:00:12 GMT Sender: usenet@news.otago.ac.nz (News stuff) Organization: University of Otago Lines: 5 Xref: biosci bionet.software:4815 bionet.molbio.proteins:604 Nntp-Posting-Host: sanger.otago.ac.nz X-Newsreader: TIN [version 1.1 PL8] I would appreciate comments from anybody who knows anything about software suitable for displaying protein (and nucleic acid) structures on a Mac. I know there has been quite a lot of discussion on and off about this and so I know about Kinemage, MacModel and Ball-and-Stick, and so forth, but we are particularly interested in commercial software From owner-proteins@net.bio.net Tue Apr 20 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!zaphod.mps.ohio-state.edu!uwm.edu!caen!batcomputer!ghost.dsi.unimi.it!genes!pongor From: pongor@genes.icgeb.trieste.it (Sandor Pongor) Newsgroups: bionet.molbio.proteins Subject: ICGEB/EMBnet Practical Course: Computers in Molecular Biology Keywords: Computer course, Biocomputing, Sequence Databases Message-ID: <1993Apr21.143114.19705@genes.icgeb.trieste.it> Date: 21 Apr 93 14:31:14 GMT Organization: ICGEB Lines: 114 Practical Course "Computer Methods in Molecular Biology" International Centre for Genetic Engineering and Biotechnology 14-23 July 1993, Trieste-Italy Co-sponsored by ICGEB and EMBnet/BRIDGE Organizer: Sandor Pongor, ICGEB Trieste, Italy Faculty: Amos Bairoch, University of Geneva, Geneva, Switzerland Dennis Benson, NCBI-NIH, Bethesda, USA Martin Bishop, Medical Research Council, HGMP, Cambridge, UK Miklos Cserzo, Institute of Enzymology, Budapest, Hungary Reinhard Doelz, Biozentrum, Basel, Switzerland David Judge, University of Cambridge, Cambridge, UK Jack Leunissen, University of Nijmegen, The Netherlands Peter Rice, EMBL, Heidelberg, Germany Cecilia Saccone, University of Bari, Bari, Italy Gyorgy Simon, ICGEB Trieste, Italy Topics: Introduction to Computer Operating Systems Computer Communications, Networking, File Transfer, Electronic Mail, Bulletin Boards Molecular Biology Databases Sequence Homology Searches, Alignments Multiple Alignment, PCR Primer Design Sequence Patterns, Distant Protein Homologies Molecular Evolution: Quantitative and Qualitative Aspects Genome Projects Registration is limited to 30 participants. Prerequisites: Participants must have a basic knowledge of biochemistry and molecular biology, a basic familiarity with computer uses and a need for DNA or protein sequence analysis for their ongoing research. In order to apply, submit the below participation form via e-mail, FAX or normal mail to Ms. Diana Viti, ICGEB, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757333, Fax: +39-40-226555, Telex: 460396 ICGEBT I, Email: viti@icgeb.trieste.it Closing date for applications 31 May 1993. ICGEB will provide accommodation and local hospitality to participants from ICGEB Member Countries. Travel to and from Trieste will normally be borne by the participants. There is no registration fee. ICGEB MEMBER COUNTRIES: Afghanistan, Algeria, Argentina, Bhutan, Bolivia, Brazil, Bulgaria, Chile, China, Colombia, Congo, Costa Rica, Croatia, Cuba, Ecuador, Egypt, Greece, Hungary, India, Indonesia, Iran, Iraq, Italy, Kuwait, Mauritania, Mauritius, Mexico, Morocco, Nigeria, Pakistan, Panama, Peru, Poland, Russia, Senegal, Sri Lanka, Sudan, Syria, Thailand, Trinidad & Tobago, Tunisia, Turkey, Venezuela, Viet Nam, Yugoslavia, Zaire --- Cut here --- ___________________________________________________________________________ INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY MEETINGS * COURSES * WORKSHOPS PARTICIPATION FORM (viti@icgeb.trieste.it) ___________________________________________________________________________ MEETING/COURSE/WORKSHOP.TITLE COMPUTER METHODS IN MOLECULAR BIOLOGY, 14-23 JULY, 1993 ___________________________________________________________________________ DATES............| LOCATION.........| ___________________________________________________________________________ SURNAME..........| FIRSTNAME........| SEX..............| DATE.OF.BIRTH....| AGE..............| COUNTRY.OF.BIRTH.| NATIONALITY......| ___________________________________________________________________________ FULL.BUSINESS.ADDRESS ___________________________________________________________________________ TELEPHONE.NUMBER.| FAX.NUMBER.......| TELEX.NUMBER.....| E-MAIL.ADDRESS...| ___________________________________________________________________________ HOW.WILL.YOUR.RESEARCH.BENEFIT.BY.YOUR.PARTICIPATION.IN.THE.MEETING/COURSE/ WORKSHOP.(NO.MORE.THAN.5.LINES.OF.TEXT) ___________________________________________________________________________ RESEARCH.AREA.OF.INTEREST ___________________________________________________________________________ PRESENT.POSITION ___________________________________________________________________________ ACADEMIC.QUALIFICATIONS.(DEGREE/YEAR/INSTITUTE) ___________________________________________________________________________ INSTITUTES.OF.WORK.SINCE.FORMAL.EDUCATION ___________________________________________________________________________ FELLOWSHIPS.HELD ___________________________________________________________________________ PREVIOUSLY.ATTENDED.ICGEB.MEETINGS/COURSES/WORKSHOPS ___________________________________________________________________________ SHORT.LIST.OF.RELEVANT.PUBLICATIONS ___________________________________________________________________________ From owner-proteins@net.bio.net Wed Apr 21 23:00:00 1993 Path: biosci!parc!decwrl!ames!haven.umd.edu!uunet!pipex!warwick!uknet!newcastle.ac.uk!dbl3nct From: N.C.Thomas@newcastle.ac.uk (N C Thomas) Newsgroups: bionet.molbio.proteins Subject: Conserved sequence functions Message-ID: Date: 22 Apr 93 11:19:37 GMT Organization: University of Newcastle upon Tyne, UK, NE1 7RU Lines: 15 Nntp-Posting-Host: norma.dur.ac.uk X-Newsreader: TIN [version 1.1 PL9] Apologies if this is an FAQ..., I have used a program called BLAST to compile a list of proteins similar in sequence to an enzyme I am investigating. I have noticed several conserved regions amongst the proteins in this list. Is there a database of motifs held anywhere that might help to attribute functions to any of these conserved regions? I have access to the usual databases via Seqnet in the U.K. and a selection of gopher servers. Please send any suggestions to me via email please. Thanks in advance for any advice, Neil Thomas. From owner-proteins@net.bio.net Wed Apr 21 23:00:00 1993 Path: biosci!CHESTNUT.CHEM.UPENN.EDU!duong From: duong@CHESTNUT.CHEM.UPENN.EDU (Duc Duong) Newsgroups: bionet.molbio.proteins Subject: Searching for protein homology using BLAST?? Message-ID: <9304221530.AA20467@chestnut.chem.upenn.edu> Date: 22 Apr 93 16:30:16 GMT References: <9304221204.AA15055@net.bio.net> Sender: daemon@net.bio.net Distribution: bionet Lines: 29 > > Apologies if this is an FAQ..., > > I have used a program called BLAST to compile a list of proteins > similar in sequence to an enzyme I am investigating. > I have noticed several conserved regions amongst the proteins in this list. > Is there a database of motifs held anywhere > that might help to attribute functions to any of these conserved > regions? I have access to the usual databases via Seqnet in the U.K. > and a selection of gopher servers. > Please send any suggestions to me via email please. > > Thanks in advance for any advice, > > > Neil Thomas. > Talking about BLAST.. Does any one know Can BLAST search NRL_3D database for sequence homologies? What I want to do is just specify the number of amino acid (5,6,7,8..etc) then tell BLAST to search for the best match.. Print out the sequence that It found.. No, I don't know my query before the search.. Just tell the program automatically compares all of the sequence in database and print out the result.. Are there any other softwares do this kind of database analysis?? Thank you for all respsonses.. duc From owner-proteins@net.bio.net Wed Apr 21 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!zaphod.mps.ohio-state.edu!news.acns.nwu.edu!uicvm.uic.edu!yang.earlham.edu!davidw From: davidw@yang.earlham.edu Newsgroups: bionet.molbio.proteins Subject: Problem with pH electrode in cyt c Message-ID: <1993Apr22.174136.22908@yang.earlham.edu> Date: 22 Apr 93 22:41:36 GMT Organization: Earlham College, Richmond, Indiana Lines: 19 I am currently working on a project which involves measuring the pH of aprox 1mM cytochrome c solutions. The pH electrode that we use is a micro electrode (Microelectrodes, Inc., I think). The problem that we are now experiencing is that the pH reading drifts over time in our pH 4 and 7 buffers. The electrode was rock steady and really fast until we started working with protein solutions. 1. Could the protein be clogging our electrode? 2. If so, what is the best way to clean it? David Weis davidw@yang.earlham.edu Chemistry Department DAVIDW@EARLHAM Earlham College "Every scientist is half B. F. Skinner and half P. T. Barnum." --The Simpsons "You can't argue with Hess's Law, that's why it's a law." --an anonymous chemistry professor From owner-proteins@net.bio.net Wed Apr 21 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.proteins Subject: Re: Conserved sequence functions Message-ID: <1993Apr22.141748.12146@welchgate.welch.jhu.edu> Date: 22 Apr 93 14:17:48 GMT References: Organization: Johns Hopkins Univ. Welch Medical Library Lines: 40 In article N.C.Thomas@newcastle.ac.uk (N C Thomas) writes: >Apologies if this is an FAQ..., > >I have used a program called BLAST to compile a list of proteins >similar in sequence to an enzyme I am investigating. >I have noticed several conserved regions amongst the proteins in this list. >Is there a database of motifs held anywhere >that might help to attribute functions to any of these conserved >regions? I have access to the usual databases via Seqnet in the U.K. >and a selection of gopher servers. >Please send any suggestions to me via email please. > >Thanks in advance for any advice, > > Prosite is such a database and there are programs designed to compare your sequences to Prosite - Prosearch and Macpattern being the most common ones. You can obtain Prosite and either program from a variety of ftp and gopher holes including ftp.bio.indiana.edu and felix.embl-heidelberg.de. You can also learn more about this type of thing by pointing your gopher client at merlot.welch.jhu.edu and selecting the following: --> 12. Search Databases at Welchlab (Vectors, Promoters, NRL-3D, EST, OMI../ --> 9. Seqanalref - Sequence Analysis Bibliographic Reference Data Ban.. and search for - database and patter* Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-proteins@net.bio.net Fri Apr 23 23:00:00 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: <9304240900.AA08218@net.bio.net> Date: 24 Apr 93 09:00:04 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 Sun Apr 25 23:00:00 1993 Path: biosci!agate!darkstar.UCSC.EDU!orchid.UCSC.EDU!quinones From: quinones@ucsc.edu (Cathy Quinones) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: help! how to pack a sepharose column Message-ID: <1rhso9INNfpb@darkstar.UCSC.EDU> Date: 26 Apr 93 23:54:49 GMT Distribution: usa Organization: Santa Cruz Lines: 19 Xref: biosci bionet.molbio.proteins:612 bionet.molbio.methds-reagnts:5258 NNTP-Posting-Host: orchid.ucsc.edu Originator: quinones@orchid.UCSC.EDU I am about to venture into the world of proteins and am interested in follow- ing a published protocol that is too sketchy for my knowledge. Basically, I need to find a description of how to pack a Concanavalin-A Sepharose column. My source reads:"... a filtrate... was applied to Con A-Sepharose suspended in a buffer of... {description of buffer}" and I need information as to how to do such a thing. Can anyone offer any hints/references as to how to do lectin chromatography? A reference to a source that describes how to pack and run these columns would really make my day! I will appreciate any help you can provide, whether this gets posted on the net or sent directly to me. Thanx Cathy From owner-proteins@net.bio.net Sun Apr 25 23:00:00 1993 Path: biosci!ACC.WUACC.EDU!zzbart From: zzbart@ACC.WUACC.EDU (barton jan) Newsgroups: bionet.molbio.proteins Subject: ph elect Message-ID: <9304261928.AA56773@acc.wuacc.edu> Date: 26 Apr 93 19:28:36 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 38 From root Thu Apr 22 21:29:09 1993 Received: from net.bio.net by acc.wuacc.edu (AIX 3.2/UCB 5.64/4.03) id AA13934; Thu, 22 Apr 1993 21:29:06 -0500 Received: by net.bio.net (5.65/IG-2.0) id AA07154; Thu, 22 Apr 93 18:46:30 -0700 Received: by net.bio.net (5.65/IG-2.0) id AA07148; Thu, 22 Apr 93 18:46:25 -0700 Message-Id: <9304230146.AA07148@net.bio.net> To: proteins@net.bio.net From: davidw@yang.earlham.edu Subject: Problem with pH electrode in cyt c Date: 22 Apr 93 22:41:36 GMT Status: O I am currently working on a project which involves measuring the pH of aprox 1mM cytochrome c solutions. The pH electrode that we use is a micro electrode (Microelectrodes, Inc., I think). The problem that we are now experiencing is that the pH reading drifts over time in our pH 4 and 7 buffers. The electrode was rock steady and really fast until we started working with protein solutions. 1. Could the protein be clogging our electrode? 2. If so, what is the best way to clean it? David Weis davidw@yang.earlham.edu Chemistry Department DAVIDW@EARLHAM Earlham College "Every scientist is half B. F. Skinner and half P. T. Barnum." --The Simpsons "You can't argue with Hess's Law, that's why it's a law." --an anonymous chemistry professor we successfully use soaking in detergent. also electrode should be stored in pH 4 buffer. From owner-proteins@net.bio.net Sun Apr 25 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!agate!doc.ic.ac.uk!uknet!liv!beynonrj From: beynonrj@liverpool.ac.uk (Dr. R.J. Beynon) Newsgroups: bionet.molbio.proteins Subject: Re: Random cutting Proteinase? Message-ID: Date: 26 Apr 93 17:32:34 GMT References: <1qvi9cINNehp@shelley.u.washington.edu> Sender: news@liverpool.ac.uk (News System) Organization: The University of Liverpool Lines: 23 Nntp-Posting-Host: uxb.liv.ac.uk X-Newsreader: TIN [version 1.1 PL8] Jing Huang (jing@carson.u.washington.edu) wrote: : Hi, I am interested in studying the conformational changes in proteins : after they bind to target DNA sequences. I hope to use a random cutting : proteinase to attack my protein of interest so that I can see discrete : patterns on and off DNA. Could anybody advice me on what kind of : proteinase to use to achieve that? : Thanks a lot. : -Fred Fred - there's no such thing! But, you can mimic that a) with a mixture of proteinases (try Sigma Pronase - it's a mixture already :-)) or b) with a low-specificity proteinase such as subtilisin or proteinase K. But for your work, it might be better to use restricted proteinases and look for larger, conformationally sensitive fragments. No-one knows which sites are sensitive in a protein (native) or why, and some trial and error is warranted. Good luck Rob Beynon, Proteolysis Group, Liverpool, UK From owner-proteins@net.bio.net Tue Apr 27 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!tpm-sprl!jbh From: jbh@anat.UMSMED.EDU (James B. Hutchins) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: help! how to pack a sepharose column Message-ID: <1993Apr28.233323.7246@anat.UMSMED.EDU> Date: 28 Apr 93 23:33:23 GMT Organization: Dept. of Anatomy, Univ. of Mississippi Medical Center Lines: 14 Xref: biosci bionet.molbio.proteins:614 bionet.molbio.methds-reagnts:5293 Cathy Quinones, I tried to send you e-mail but it bounced. Please write me, I have (an) answer to your question. All others: sorry about wasted bandwidth... Jim jbh@anat.umsmed.edu -- Jim Hutchins [] E-Mail: jbh@anat.umsmed.edu Dept of Anatomy [] Univ Mississippi Med Ctr [] From owner-proteins@net.bio.net Tue Apr 27 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!isgate!krafla!zjons From: zjons@rhi.hi.is (Zophonias Oddur Jonsson) Newsgroups: sci.bio,sci.bio.technology,bionet.general,bionet.molbio.proteins Subject: Help on htgA gene of E.coli ?? Keywords: htgA E.coli heat shock Message-ID: <6882@krafla.rhi.hi.is> Date: 28 Apr 93 22:27:29 GMT Sender: usenet@rhi.hi.is Followup-To: poster Lines: 22 Xref: biosci sci.bio:3093 sci.bio.technology:276 bionet.general:4717 bionet.molbio.proteins:613 Nntp-Posting-Host: hengill.rhi.hi.is Dear Netters! I am looking for references or any current information about the htgA gene of E.coli. I have the original description: (Dean & James, J.Gen.Microbiol. (1991) 137 ) but nothing more, and I have not been able to find anything else by ploughing through the abstract books and C.C. It is quite likely that nothing more has been published about this gene but if someone is better informed I would be grateful to know. (For those of you who don't know anything about htgA but just read this out of curiosity: htgA is a gene associated with the dnaK heat shock protein and is essential for E.coli at high temperature) Thakns ! Zophonias O. Jonsson Department of Genetics University of Iceland e-mails! : zj@lif.hi.is or zjons@rhi.hi.is From owner-proteins@net.bio.net Wed Apr 28 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!noc.near.net!nic.umass.edu!umassmed.UMMED.EDU!rzottola From: rzottola@umassmed.UMMED.EDU (Ralph Zottola) Newsgroups: bionet.molbio.proteins Subject: Re: pH electrode problem Keywords: pH electrodes, maintenance Message-ID: <1rojnb$fqd@nic.umass.edu> Date: 29 Apr 93 13:03:39 GMT Distribution: usa Organization: University of Massachusetts Medical Center, Worcester Lines: 13 NNTP-Posting-Host: umassmed.ummed.edu David Weis wrote that his Microelectrodes Inc electrode gave a sluggish response after being exposed to protein. I had a similar problem and Microelectrodes was extremely helpful with a solution. They suggest that you soak the electrode in a glass cleaning solution (ie chromic/sulfuric acid available via Fisher) for 1 minute. Then soak in a detergent protein cleaning solution (ie Terg-A-Zyme) for up to an hour daily depending on use. They have sample packs available. -- Ralph J. Zottola Graduate Student UMMC/Prog. Mol. Med. Voice: (508)856-6881 373 Plantation St. FAX: (508)856-4289 Worcester, MA 01605 Internet: rzottola@umassmed.ummed.edu From owner-proteins@net.bio.net Wed Apr 28 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!torn!thunder!flash!mligr From: mligr@flash.LakeheadU.Ca (Martin Ligr) Newsgroups: bionet.molbio.proteins Subject: Programs for gel image analysis? Message-ID: Date: 29 Apr 93 18:39:41 GMT Sender: news@thunder.LakeheadU.Ca Distribution: bionet Lines: 14 Hallo! We are concidering purchase of IBM-PC software for analysis of images of one dimensional protein gels. I would greatly appreciate if you told me about your experince with this kind of software and gave me some recomendations. Are there some shareware programs able to perform this task? Thanks. Martin Ligr Dept. of Biology Lakehead University Thunder Bay, Ontario From owner-proteins@net.bio.net Thu Apr 29 23:00:00 1993 Path: biosci!enterpoop.mit.edu!uhog.mit.edu!news.bbn.com!noc.near.net!howland.reston.ans.net!zaphod.mps.ohio-state.edu!moe.ksu.ksu.edu!interceptor.ksu.ksu.edu!news From: nexus@interceptor.ksu.ksu.edu (hUnix) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: help! how to pack a sepharose column Message-ID: <1rqb3jINNpe1@interceptor.ksu.ksu.edu> Date: 30 Apr 93 04:48:51 GMT References: <1rhso9INNfpb@darkstar.UCSC.EDU> Distribution: usa Organization: Kansas State University Lines: 30 Xref: biosci bionet.molbio.proteins:619 bionet.molbio.methds-reagnts:5315 NNTP-Posting-Host: interceptor.ksu.ksu.edu There's nothing really magic or particularly sophisticated about packing a column. You need to swell the Sepharose beads in the buffer described in the protocol for the prescribed time. You usually end up with a 50% slurry by mixing it really good. Then you take a proper amount of the 50% suspension estimated on the basis of the column bed volume you want to pack. [you can calculate the necessary volume from the data in the supplier sheet, ml suspension of resin, or mg dry weight resin vs. amount of protein to be purified, _bound_ by the active surface of the column beads - this value is always given]. When you estimate the necessary volume, you pick a proper column size that will hold this volume. You put a bit of glasswool at the end-opening of the column and poor the estimated amount of slurry over it. Perform several column washes with the required buffers [there will be an activation step for sure]. Wash with sample buffer and wait for the column to settle. [pack] Don't let the column dry! You should have about 1 cm [~ 1/2" ] buffer layer over the column bed surface when you apply the sample if the column has the standard radius of 1 - 1.5 cm. You apply the sample _carefully_ so that you _don't_ disturb the column bed surface. Hope this helps. -- Arseny Markov Virology/Oncology ex-KSU research fellow -- -human research dept. by Unix, the god From owner-proteins@net.bio.net Thu Apr 29 23:00:00 1993 Path: biosci!enterpoop.mit.edu!gatech!howland.reston.ans.net!usc!sol.ctr.columbia.edu!destroyer!cs.ubc.ca!unixg.ubc.ca!creimer From: creimer@unixg.ubc.ca (Corinne L Reimer) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: help! how to pack a sepharose column Message-ID: <1rpte8INNjon@skeena.ucs.ubc.ca> Date: 30 Apr 93 00:55:36 GMT References: <1rhso9INNfpb@darkstar.UCSC.EDU> Distribution: usa Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 6 Xref: biosci bionet.molbio.proteins:618 bionet.molbio.methds-reagnts:5311 NNTP-Posting-Host: unixg.ubc.ca Pharmacia puts out a nice packet of chromatography handbooks...you could probably phone them up and ask them to send them out to you. They have one specifically on affinity chromatography, and Ifound it very helpful for the basics of column packing. It also has a specific section on Con A-affinity chromatography. Hope this helps. corinne From owner-proteins@net.bio.net Thu Apr 29 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!newsserver.jvnc.net!louie!udel!bogus.sura.net!news-feed-1.peachnet.edu!gatech!swrinde!sdd.hp.com!saimiri.primate.wisc.edu!hp9000.csc.cuhk.hk!wksa05.csc.cuhk.hk!S901718 From: S901718@mailserv.cuhk.hk (Johnson Leung) Newsgroups: bionet.molbio.proteins Subject: Enquiry Message-ID: Date: 30 Apr 93 00:50:12 GMT Sender: usenet@hp9000.csc.cuhk.hk Distribution: World Organization: Computer Services Centre, C.U.H.K. Lines: 9 Nntp-Posting-Host: wksa05.csc.cuhk.hk To whom may concern, I shall work on a project titiled "Transcription regulation in bacteria - the role of binding protein" this summer, and I am now looking for some articles as my introduction. Would you kindly please suggest some articles for me to read? You may e-mail your suggestion to me. Your help would be greatly appreciated. Thank you. Johnson Leung, from CUHK, HK. e-mail: JohnsonLeung@cuhk.hk From owner-proteins@net.bio.net Thu Apr 29 23:00:00 1993 Path: biosci!COR-MAIL.BIOCHEM.HMC.PSU.EDU!lxia From: lxia@COR-MAIL.BIOCHEM.HMC.PSU.EDU Newsgroups: bionet.molbio.proteins Subject: help Message-ID: <9304301727.AA28834@net.bio.net> Date: 30 Apr 93 18:32:19 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 3 HELP How could I subscribe. From owner-proteins@net.bio.net Thu Apr 29 23:00:00 1993 Path: biosci!IFQSC.USP.ANSP.BR!RODRIGO From: RODRIGO@IFQSC.USP.ANSP.BR (Rodrigo Neves Romcy Pereira) Newsgroups: bionet.molbio.proteins Subject: four-helix bundles Message-ID: <42D43AF7A89F00AB10@USPFSC.IFQSC.USP.ANSP.BR> Date: 1 May 93 01:59:51 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 23 In four-helix bundle proteins there are two ways of folding the helices with respect to the handness of the first connection and many ways with respect to their orientations (paralell/anti-paralell). The right-turning way in which the connection is right-handed and the left-turning, similarly, with a left-handed connection. Among all the possibilities of connecting four-helix bundles only 48 correspond to the orientations observed in protein strutuctes and among these 48 connections we have a ratio of 6/48 for anti-parallels. However,in the structures known(about 13) up to now, 12 are anti-parallels while only one parallel. What could be the reasons for this distribution? The small number of 3D-structures solved? Energetically favorable arrangements independent of the probabilities of combinations? I suppose that although the 1/8 probability to anti-parallels, this arrangement is highly energetically favored (I don't know why!) in relation to the parallel and for this reason the equilibrium is displaced in direction to the anti-parallels. Any other suggestion? Rodrigo Neves USP-Sao Paulo Depto.Phisics and Chemistry rodrigo@ifqsc.usp.ansp.br From owner-proteins@net.bio.net Fri Apr 30 23:00:00 1993 Path: biosci!enterpoop.mit.edu!gatech!howland.reston.ans.net!agate!news.ucdavis.edu!chip.ucdavis.edu!ez005587 From: ez005587@chip.ucdavis.edu (David J. Meyer) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: help! how to pack a sepharose column Message-ID: Date: 1 May 93 01:13:09 GMT References: <1rqb3jINNpe1@interceptor.ksu.ksu.edu> Sender: usenet@ucdavis.edu (News Administrator) Distribution: usa Organization: University of California, Davis Lines: 25 Xref: biosci bionet.molbio.proteins:623 bionet.molbio.methds-reagnts:5323 X-Newsreader: Tin 1.1 PL3 nexus@interceptor.ksu.ksu.edu (hUnix) writes: : Don't let the column dry! ^^^^^^^^^^^^^^^^^^^^^^^^^ : : Arseny Markov : Virology/Oncology : ex-KSU research fellow : -- I just thought I would point out the reason why you don't let the column run dry, since this is usually not made clear (although always stated)! If the level of buffer in the column runs below the top of the bed, air will enter in its place. The air between the beads is not usually chased down the column when more buffer is added; instead, the buffer usually follows the easiest path down the column, and this does not necessarily (or usually) involve the entire cross-sectional area of the column. This effectively decreases the bed volume of your column. If the coulumn 'runs dry,' it must be reequilibrated and repacked. Good luck! -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ David J. Meyer djmeyer@ucdavis.edu