From owner-proteins@net.bio.net Sun Nov 01 22:00:00 1992 Path: biosci!agate!ames!elroy.jpl.nasa.gov!swrinde!cs.utexas.edu!uunet!digex.com!wbrown From: wbrown@access.digex.com (William Brown) Newsgroups: bionet.molbio.proteins Subject: Re: Genetics transposons conventions... Message-ID: Date: 2 Nov 92 17:30:27 GMT References: <1992Nov1.211151.1@uwovax.uwo.ca> Sender: usenet@access.digex.com Organization: Express Access Online Communications, Greenbelt, MD USA Lines: 24 Nntp-Posting-Host: access.digex.com In article <1992Nov1.211151.1@uwovax.uwo.ca> 37_1510@uwovax.uwo.ca writes: >In article , wbrown@access.digex.com (William Brown) writes: >> I hope somebody can help me with this problem. My research is in >> modeling, so I've gotten a little rusty on the genetics end of things. >> I'm reading a paper that includes the following descriptions of >> transposons in its PROCEDURES section, and for the life of me I don't know >> what they are talking about: Hfr::Tn10, zcf::Tn10, and srl::Tn10. I KNOW >> what Tn10 is - a P1 phage-transfer unstable transposon carrying >> tetracycline resistance. I HAVE NO IDEA what the meanings of the >> three-letter prefixes are. >> > >The three letter symbols correspond to the gene where the transposon is >inserted. ie. srl=sorbitol. [...etc.] >Miguel A. Valvano. Microbiology and Immunology, University of Western Ontario, >London, Ontario. Thank you and the others who have replied. The Hfr I figured out, but the other two (epsecially the zcf) had me stumped. Thanks for the help. William Brown, Jr. From owner-proteins@net.bio.net Mon Nov 02 22:00:00 1992 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Announcements of PIR Network Request Service Message-ID: <01GQPXXA18WA8WW08R@NBRF.Georgetown.Edu> Date: 3 Nov 92 19:48:23 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 276 Announcements of the Protein Information Resource Network Request Service Highlights 1. Hints for Retrieving Sequence Database Entries 2. PIR Network Request Service Command Summary 1. Hints for Retrieving Sequence Database Entries The very first thing to appreciate about the sequence databases is that the most commonly sought information for every entry is contained in the title field. The title field contains the protein name, the source organism and the EC number if it's an enzyme. On the other hand, the keyword field contains information that does not necessarily duplicate what is in the title. What the keyword field is designed to do is provide ancillary retrieval information that is not conveyed in a protein name, such information as * disease or resistance states associated with the protein ACQUIRED IMMUNE DEFICIENCY SYNDROME or CYANATE RESISTANCE * metabolic roles or pathways CALCIUM TRANSPORT or PENTOSE PHOSPHATE PATHWAY * posttranslation modification processes HYDROXYLATION * tissues, cell types or subcellular components that are the origin of or the targets of the protein HEART, LEUKOCYTE or MITOCHONDRIAL MATRIX * structural characteristics TRIMER or ZINC FINGER * larger classification schemes the protein may fall in SERINE PROTEASE or STRUCTURAL PROTEIN Most searches are for information contained in the title field. The most common reason for a keyword search failure is that the protein name is what is being used and that can be found in the title, not the keyword list. A list of the keywords found in the current public distribution release of the PIR can be obtained by using the command SEND KEYWORDS The keywords used by the PIR correspond closely to the MESH terms of the National Library of Medicine. When only one field is being searched, all the words that follow the field name must be found in the same entry for there to be a "hit". This means that all the words on one command line form a logical AND; a QUERY that repeats the same field connected by AND is unnecessary. Furthermore since the title combines both the protein name and the source organism, the title and species can be searched in a single command; for example, QUERY TITLE ALPHA AND TITLE HEMOGLOBIN AND SPECIES HUMAN END QUERY can be simply combined as TITLE HUMAN ALPHA HEMOGLOBIN On the other hand OR operations are just equivalent to combining the results of several different searches; for example QUERY TITLE HUMAN ALPHA HEMOGLOBIN OR TITLE HUMAN DELTA HEMOGLOBIN END QUERY would achieve the same result as the two separate TITLE searches. The Boolean operators must be placed on separate lines and not on the line with another command; for example, TITLE CYTOCHROME AND P450 will fail because only entries with the character string "AND" in the title along with "CYTOCHROME" and "P450" will hit. TITLE CYTOCHROME P450 means "search for titles containing both strings 'CYTOCHROME' and 'P450' in either order". Double quotation marks can be used to change the meaning slightly TITLE "CYTOCHROME P450" means "search for titles containing the string 'CYTOCHROME P450' ". The double quotation marks must be used when some part of the search string is less than 3 characters long; for example, TITLE "CYTOCHROME C" The Boolean NOT command can be used most effectively to remove entries with names that are extensions of some shorter name of interest; for example, QUERY TITLE "CYTOCHROME C " NOT TITLE OXIDASE NOT TITLE REDUCTASE END QUERY will pretty much eliminate everything but cytochrome C from the resulting list. (Because the indexing scheme used by the retrieval program lumps together all the nonalphanumeric characters, the space appearing after the "C" and before the double quotation mark eliminates entries like "cytochrome c2" but not "cytochrome c'" from the list.) One very inappropriate type of request is the following. GENE CONCANAVALIN KEYWORD CONCANAVALIN FEATURE CONCANAVALIN TITLE CONCANAVALIN SEARCH CONCANAVALIN Specifically, "concanavalin" is not a gene name, so it will not be found in the gene field. The word "concanavalin" is plain text, not a sequence, so it should not appear after the SEARCH command --- only actual sequences should appear after a SEARCH command. While "concanavalin" might possibly appear in the keyword or feature fields, its use there would be very specialized and not indicative of a concanavalin entry. The only command that makes any sense is TITLE CONCANAVALIN The biggest problem comes when the SEARCH command is used in that way. The futile FASTA search this generates wastes shared computer resources that can be used by others much more fruitfully. The FASTA program has been modified to recognize some occurrences of plain text and print a warning. The USE command is used to restrict searches to particular databases or to entries added or modified within a particular time period. Such restrictions apply to all subsequent search commands in the same request and need not be used only in queries. After a successful search, the GET command should be used to retrieve the actual text of an entry. The format of the GET command is either GET database:code or simply GET code There are no spaces around the colon and only one code may follow each GET command. There are a few special considerations to keep in mind when using the NRL_3D database of sequence information extracted from the Brookhaven Protein Data Bank. Only these fields in NRL_3D are indexed and can be searched through the PIR Server: TITLE, SPECIES, FEATURE and the sequence. At this time the TITLE field consists of the COMPND records from the Brookhaven Protein Data Bank file as well as the species. In most cases your search will be for something in this TITLE or name field. For example, after an initial USE BASES NRL_3D the command TITLE MYOGLOBLIN will retrieve a list of all the myoglobin sequences in the PDB and SPECIES MOUSE will retrieve a list of all the mouse sequences. The SPECIES field is not 100% accurate for the NRL_3D because of some eccentricities in the SOURCE records of the PDB used to construct it. Although there is a KEYWORD field in NRL_3D entries, it is constructed directly from the PDB HEADER record and is not indexed. With release 10.00 of NRL_3D the PIR will cease converting all of each PDB release. Instead only new and modified entries will be converted; the NRL_3D entries will gradually be modified to standardize spelling, capitalization, nomenclature, taxonomy and keywords. With this standardization the KEYWORD field will become more meaningful and probably be indexed within the coming year. 2. PIR Network Request Service Command Summary The National Biomedical Research Foundation Protein Information Resource network request service 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 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 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 Dr. 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 quarterly PIR2 PIR Preliminary Entries approximately monthly PIR3 PIR Unverified Entries weekly ALN PIR Alignment Entries semiannually NRL_3D Brookhaven Data Bank Sequences quarterly PATCHX MIPS PIR-Supplementary Database quarterly N NBRF Nucleic GB GenBank (TM) as received GBSUP GenBank (TM) as received GBNEW GenBank (TM) New Entries weekly EMBL EMBL as received EMBLSUP 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 abbreviation should be used to retrieve an entry with the GET command. Not all commands work with all databases; please read the information returned by the command HELP DATABASES. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMASTER@GUNBRF.BITNET POSTMASTER@NBRF.Georgetown.Edu From owner-proteins@net.bio.net Tue Nov 03 22:00:00 1992 Path: biosci!PB1.PDB.BNL.GOV!ABOLA From: ABOLA@PB1.PDB.BNL.GOV Newsgroups: bionet.molbio.proteins Subject: Protein Data Bank on FTP Message-ID: <921104163102.e46@PB1.PDB.BNL.GOV> Date: 4 Nov 92 21:31:02 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 88 --------------------------------------------------------------------- Protein Data Bank Announcement 11/4/92 --------------------------------------------------------------------- Protein Data Bank via FTP ------------------------- Beginning immediately, all full-release and pre-release coordinate entries will be available from Brookhaven National Laboratory via anonymous ftp and the PDB e-mail server. As we expect a dramatic rise in the number of users downloading entries, we request that users limit the number of files transferred during a given FTP session. Those requiring a substantial number of entries should continue to order the PDB on tape or CD ROM. File Server and Anonymous FTP ----------------------------- At Brookhaven, the PDB has an e-mail file server available for your use. This server provides PDB general information and documentation files. For more information, send an e-mail message to fileserv@pb1.pdb.bnl.gov and include the following text: send info your_e-mail_address. The PDB also has an anonymous FTP account available on the system pdb.pdb.bnl.gov with Internet address 130.199.144.1. It is possible to transfer files to and from this system using "anony- mous" as the FTP user name and your real user name as the pass- word. PDB general information and documentation files, as well as pre-release atomic coordinate entries, are available for down- loading. You also can upload any files that you may wish to send to the PDB. Those using VMS may need to place quotes around file names. Anyone experiencing problems or having questions related to the above network service should send an e-mail message to skora@bnl.gov. Accessing PDB via Gopher ------------------------ The PDB anonymous FTP directories can now be accessed via the gopher service. Those running the Gopher client can access the PDB FTP site by including the following link: Name= Protein Data Bank ftp Site Type=1 Host=pdb.pdb.bnl.gov Port=70 Path=1/ For more information or help in accessing PDB via Gopher, send an e-mail message to oeder@bnl.gov/ To Contact the PDB ------------------ Please include your telephone number, facsimile number, mailing address, and e-mail address in all correspondence. Mail: Protein Data Bank Chemistry Department, Building 555 Brookhaven National Laboratory Upton, NY 11973 USA Phone: +1 516-282-3629 Fax: +1 516-282-5751 e-mail: pdb@bnlchm.bitnet or pdb@chm.chm.bnl.gov --------------------------------------------------------------------- ________________________________________________________________ | enrique e. abola | BITNET: abola1@bnl Protein Data Bank | INTERNET: abola1@bnl.gov Department of Chemistry | (516)-282-4383 Brookhaven National Laboratory | Upton NY 11973 | ________________________________________________________________ From owner-proteins@net.bio.net Sat Nov 07 22:00:00 1992 Path: biosci!agate!spool.mu.edu!uunet!noc.near.net!news.cs.brandeis.edu!binah.cc.brandeis.edu!DUCA From: duca@binah.cc.brandeis.edu Newsgroups: bionet.molbio.proteins Subject: ...looking for just the right peptide... Message-ID: <1992Nov8.133724.28617@news.cs.brandeis.edu> Date: 8 Nov 92 13:37:24 GMT Sender: news@news.cs.brandeis.edu (USENET News System) Reply-To: duca@binah.cc.brandeis.edu Organization: Brandeis University Lines: 17 Hi there all you exquisitely architectured biological (and/or artificial) neural nets, I'm trying to develop a theoretical model of ion channel formation within a lipid bilayer. I've settled on using certain "designer channels" made by Lear and DeGrado at DuPont about 5-7 years ago, but unfortunately no spectroscopy has been done on them and we don't have too clear an idea of their structures. Does anyone know of any serine and leucine rich alpha helical proteins with good structural data available (X-ray or NMR)? Seeing as initial parameter setting is so crucial in these models I want to try to start with some known interatomic distances as first approximations. Can anybody make a suggestion? I'd really appreciate it. Thanx in advance. Karen Duca Dept. of Biophysics Brandeis U. duca@binah.cc.brandeis.edu From owner-proteins@net.bio.net Wed Nov 11 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!convex!constellation!aardvark.ucs.uoknor.edu!bfrank From: bfrank@aardvark.ucs.uoknor.edu (FRANK,BART) Newsgroups: bionet.molbio.proteins Subject: anti-GST antibodies for fusion protein detection Message-ID: <12NOV199215143452@aardvark.ucs.uoknor.edu> Date: 12 Nov 92 21:14:00 GMT Sender: usenet@constellation.ecn.uoknor.edu (Usenet Administrator) Organization: University of Oklahoma - University Computing Services Lines: 9 Originator: usenet@midway.ecn.uoknor.edu News-Software: VAX/VMS VNEWS 1.41 We are attempting to produce a GST fusion protein and either little of it is made or little survives proteolysis. We would like to demonstrate its presence by showing the expected increase in molecular weight on a Western blot with an anti-GST antibody. Can anyone recommend a source for such a reagent? Thanks, Bart Frank Internet: BFRANK@AARDVARK.UCS.UOKNOR.EDU From owner-proteins@net.bio.net Thu Nov 12 22:00:00 1992 Path: biosci!agate!doc.ic.ac.uk!mrccrc!warwick!pavo.csi.cam.ac.uk!cy-mac.welc.cam.ac.uk!cyk10 From: cyk10@cus.cam.ac.uk (C-Y Khoo) Newsgroups: bionet.molbio.proteins Subject: anti-GST antibodies for fusion protein detection Message-ID: <1992Nov13.121349.23095@infodev.cam.ac.uk> Date: 13 Nov 92 12:13:49 GMT References: <12NOV199215143452@aardvark.ucs.uoknor.edu> Sender: news@infodev.cam.ac.uk (USENET news) Organization: Wellcome/CRC Institute, Cambridge Lines: 34 X-Xxmessage-Id: X-Xxdate: Fri, 13 Nov 92 12:13:49 GMT Nntp-Posting-Host: cy-mac.welc.cam.ac.uk X-Useragent: Nuntius v1.1.1d11 I too, have been looking for anti-GST antibodies, but without any success. I called Pharmacia and they said that they are in the process of developing such a reagent, but that it won't be ready for some time yet. There are commercial sources of anti-GST antibodies, but they're raised against the human antigen, and according to Pharmacia, don't cross react with the S. japonicum antigen. Your best bet is to express pGEX, purify GST from the supernatant, and immunize a rabbit with it. Depending on various things, I _may_ have some anti-GST by January next year (I'm currently immunizing with a fusion protein). Ask me later! Regarding your expression problems, I found out that _most_ fusion proteins are insoluble and are found in inclusion bodies, _not_ the supernatant (as stated in Smith and Johnson (or indeed, Current Protocols in Molecular Biology). See Fiona Marston's articles in Biochem J. (1986) 240, 1-12 and an article of the same name in another journal (don't have the reference at hand, unfortunately!). Also, Nagai and Thogersen (1987) Methods Enzymol 153, 461-481 for inclusion body prep. As a first step, you may want to boil some of the pellet to see if the fusion protein is actually being produced, but in an insoluble form. Good luck! ======================================================================= ======= Chong-Yee Khoo E-mail: cyk10@cus.cam.ac.uk Wellcome/CRC Institute Talk: cyk10@cy-mac.welc.cam.ac.uk Tennis Court Road Phone: +44 223 334110 Cambridge Fax: +44 223 334089 CB2 1QR From owner-proteins@net.bio.net Thu Nov 12 22:00:00 1992 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Temporary Interruption of BITNET Access to PIR Message-ID: <01GR3OH7XZYQ94DQ9J@NBRF.Georgetown.Edu> Date: 13 Nov 92 15:50:36 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 25 Announcement of Temporary Interruption of Access to The Protein Information Resource The National Biomedical Research Foundation will not have direct access to BITNET from 17:00 EST Friday 20 November through about 12:00 EST Monday 23 November because of a system upgrade to be performed on a connecting node. Users who normally access the PIR Network Request Server through BITNET channels can expect a delay in response until full channel operation is restored. This interruption will not affect our On-line System users or users who normally access the server through Internet channels. BITNET users may wish to attempt to access our server through a gateway at the Internet address FILESERV@NBRF.GEORGETOWN.EDU We regret any inconvenience this temporary loss of service will cause. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMASTER@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-proteins@net.bio.net Sat Nov 14 22:00:00 1992 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!umn.edu!bru!minsky!raja From: raja@mayo.edu (Raja Muthupillai, BIR Grad Student, Dr. Robb) Newsgroups: bionet.molbio.proteins Subject: Request for info reg. resources In article Message-ID: <1992Nov15.234117.11661@bmw.mayo.edu> Date: 15 Nov 92 23:41:17 GMT References: <12NOV199215143452@aardvark.ucs.uoknor.edu> Sender: newsman@bmw.mayo.edu (/home/bmw/usenet) Reply-To: raja@mayo.edu Organization: Mayo Foundation Lines: 13 Hi, I am new to the newsgroups in the field of molecular biology. I am very much interested in the resources availble in the network, for researchers in molecular biology. I'd greatly appreciate any relevant information. If anyone wants to send it directly, please do so. My email address raja@mayo.edu Thanks, Raja. From owner-proteins@net.bio.net Sun Nov 15 22:00:00 1992 Path: biosci!uwm.edu!rpi!crdgw1!rdsunx.crd.ge.com!maxwell!ebstokes From: ebstokes@maxwell.crd.ge.com (Ed Stokes) Newsgroups: bionet.molbio.proteins Subject: tryp in IgG ? Message-ID: <1992Nov16.162558.20257@crd.ge.com> Date: 16 Nov 92 16:25:58 GMT Sender: usenet@crd.ge.com (Required for NNTP) Organization: GE Corp. Research & Development, Schenectady, NY Lines: 14 Nntp-Posting-Host: maxwell.crd.ge.com I am a physicist investigating the binding and optical properties of antibodies for possible sensor applications. My understanding is that if an IgG antibody contains tryptophan in the binding pocket, then the perturbation of the tryptophan luminescence properties can be used to identify an antigen binding event. Are the sequences of IgG's from various species and for various antigens known ? How can I know whether there are luminescent amino acid residues in the binding pocket of a particular antibody ? Can these properties be engineered ? Thanks Ed Stokes ebstokes@crd.ge.com From owner-proteins@net.bio.net Mon Nov 16 22:00:00 1992 Path: biosci!agate!spool.mu.edu!yale.edu!ira.uka.de!ira.uka.de!news.belwue.de!news.uni-ulm.de!news From: ORTIGAO@rzmain.rz.uni-ulm.de (ORTIGAO FLAVIO) Newsgroups: bionet.molbio.proteins Subject: Solid-phase peptide modification Message-ID: <1992Nov17.190845.19153@wega.rz.uni-ulm.de> Date: 17 Nov 92 19:08:45 GMT Sender: news@wega.rz.uni-ulm.de (News Net) Organization: University of Ulm, Germany Lines: 13 X-News-Reader: VMS NEWS 1.24 Dear collegues: I am looking for methods, compatible wiht Fmoc-chemistry to derivatize a peptide with a handle, which could be used to attach the growing peptide covalently into a different surface. Ideally the handle should be introduced while the peptide is still protected. Even better it should be cleaved from support while still protected, and would be deprotected after the coupling to the new surface. I would appreciate any help. Thanks in advance, Flavio +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. J.F. Ramalho Ortigao University of Ulm Sektion Polymere D-7900 Ulm, Germany From owner-proteins@net.bio.net Mon Nov 16 22:00:00 1992 Path: biosci!BRI.NRC.CA!Carlos.Faerman From: Carlos.Faerman@BRI.NRC.CA (Carlos Faerman) Newsgroups: bionet.molbio.proteins Subject: General Question Message-ID: <9211171928.AA28422@bobino.BRI.NRC.CA> Date: 17 Nov 92 19:28:44 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 8 I would like to find out whether a tabulation of the second-order rate constants for enzymes is available. In other words, I would be very happy to find a Table that lists Kcat/Km for a large set of the known enzymes. I look forward to hearing from you. e-mail: carlos@bri.nrc.ca From owner-proteins@net.bio.net Mon Nov 16 22:00:00 1992 Path: biosci!agate!spool.mu.edu!uunet!seas.gwu.edu!merlot.gwu.edu!danj From: danj@merlot.gwu.edu (Dan Jacobson ) Newsgroups: bionet.molbio.proteins Subject: Re: tryp in IgG ? Message-ID: <1992Nov17.165646.26056@seas.gwu.edu> Date: 17 Nov 92 16:56:46 GMT References: <1992Nov16.162558.20257@crd.ge.com> Sender: news@seas.gwu.edu Organization: George Washington University, Washington, D.C. Lines: 83 In article <1992Nov16.162558.20257@crd.ge.com> ebstokes@maxwell.crd.ge.com (Ed Stokes) writes: >I am a physicist investigating the binding and optical properties >of antibodies for possible sensor applications. My understanding >is that if an IgG antibody contains tryptophan in the binding >pocket, then the perturbation of the tryptophan luminescence >properties can be used to identify an antigen binding event. > >Are the sequences of IgG's from various species and for various >antigens known ? How can I know whether there are luminescent >amino acid residues in the binding pocket of a particular >antibody ? Can these properties be engineered ? > >Thanks >Ed Stokes >ebstokes@crd.ge.com Umm - first off I think you're talking about fluorescence - the emission of or the property of emission of or the property of emitting electromagnetic radiation usu. as visible light resulting from and only during the absorption of radiation from some other source rather than luminescence - an emission of light that is not ascribable directly to incandescence and therefore occurs at low temperatures and that is produced by physiological processes (as in the firefly), by chemical action, by friction, or by electrical action. With that minor clarification aside - yes the sequences for some species and some antigens are known. As a starting point I suggest that you take a look at the sequences that are in the databases - a quick search of Genbank for IgG yeilds the following list. Note that many of these sequences are IgG RECEPTORS etc.. not IgG itself. 1. IIMSG1 IgG1 induction factor precursor - Mouse. 2. QVSAA Protein A precursor - Staphylococcus aureus. 3. A24496 IgG-binding protein - Streptococcus sp. (group G). 4. A26314 Protein G - Streptococcus sp. (fragment). 5. A26555 Ig heavy chain V region (Ger) - Human (fragment). 6. B25521 Ig kappa chain precursor V region (305) - Human. 7. A25521 Ig kappa chain V region (321) - Human (fragment). 8. B26555 Ig kappa chain V-III region (Ger) - Human. 9. S03018 IgG Fc receptor (clone p135) - Human. 10. S03019 IgG Fc receptor (clone p98/X2) - Human. 11. A31932 IgG Fc receptor precursor - Human. 12. JU0284 IgG Fc receptor precursor, type III-1. 13. JL0107 IgG Fc receptor precursor, type III-2 (NK cells) -. 14. JH0429 IgG light chain V region VKIIIb-T14 - Human. 15. S00477 Surface glycoprotein CDw32 precursor (clone PC23) -. 16. S00478 Surface glycoprotein CDw32 precursor (clone TC3) -. 17. S02297 Surface glycoprotein CDw32 precursor - Human. 18. PT0356 IgG kappa chain V region 2B11.1 - Mouse (fragment). 19. PT0358 IgG kappa chain V region 7D2.G12 - Mouse (fragment). 20. PT0357 IgG kappa chain V region C8.5 - Mouse (fragment). 21. PT0359 IgG kappa chain V region R4A.12 - Mouse (fragment). 22. A35902 Fc gamma (IgG) receptor II (low affinity) alpha. 23. S02117 IgG Fc receptor 51K chain precursor - Rat. 24. A33939 *IgG Fc receptor II precursor - Streptococcus sp.. 25. A39041 *IgG-binding protein - Streptococcus sp. (group G). 26. S20760 *IgG heavy chain (5.7S ) - Duck. 27. S20759 *IgG heavy chain (7.8S) - Duck. 28. A39878 *CD64 (high affinity IgG receptor) precursor - Human. 29. B41357 *Fc-gamma (IgG) receptor I (high affinity) - Human. 30. A41357 *Fc-gamma (IgG) receptor I (high affinity) form b -. 31. S06946 *IgG Fc receptor - Human. 32. JL0118 *IgG Fc receptor IIa (CD32) precursor - Human. 33. A32933 *IgG receptor CD16 (clone HL12) - Human (fragment). 34. S13852 *CD4-IgG - Chinese hamster. 35. A40071 *Fc gamma (IgG) receptor II (low affinity) beta-1. 36. B40071 *Fc gamma (IgG) receptor II (low affinity) beta-2. 37. A35944 *IgG heavy chain 2a - Mouse (fragment). Best of luck, Dan Jacobson danj@chablis.gwu.edu From owner-proteins@net.bio.net Mon Nov 16 22:00:00 1992 Path: biosci!QMS1.LIFE.UIUC.EDU!Dan_Szymanski From: Dan_Szymanski@QMS1.LIFE.UIUC.EDU ("Dan Szymanski") Newsgroups: bionet.molbio.proteins Subject: TCA precipitations Message-ID: <199211180207.AA03982@ux1.cso.uiuc.edu> Date: 18 Nov 92 02:05:04 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 10 Subject: Time:7:59 PM OFFICE MEMO TCA precipitations Date:11/17/92 wondering.... does TCA precipitate things in a way similar to ammonium sulfate? who knows the real story? further, what would are the characteristics of a protein that is soluable in low percentage solutions of TCA? highly charged? h-bonding characteristics? stability/solvent acccesiblity? so many questions. thanks for any responses From owner-proteins@net.bio.net Mon Nov 16 22:00:00 1992 Path: biosci!QMS1.LIFE.UIUC.EDU!Dan_Szymanski From: Dan_Szymanski@QMS1.LIFE.UIUC.EDU ("Dan Szymanski") Newsgroups: bionet.molbio.proteins Subject: competitive inhibition Message-ID: <199211180238.AA07191@ux1.cso.uiuc.edu> Date: 18 Nov 92 02:22:03 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 Subject: Time:7:59 PM OFFICE MEMO competitive inhibition Date:11/17/92 to the net: i am looking for a reference that will help in designing an gel mobility shift experiment that will allow me to calculate the equilibrium binding constant of a ligand (dna binding protein) for a competitor (different DNA polymers) knowing the the eq. binding constant for a high affinity site with constrained sequence. i know im looking at around 10 -8 to 10 -9 for the high affinity site, and the competitors will be within an order of magnitude, or two at the most. sincerely, molecular biologist with a cause, dan From owner-proteins@net.bio.net Tue Nov 17 22:00:00 1992 Path: biosci!uwm.edu!cs.utexas.edu!uunet!comp.vuw.ac.nz!am.dsir.govt.nz!lincoln.cri.nz From: srckuxw@lincoln.cri.nz Newsgroups: bionet.molbio.proteins Subject: peptide analysis Message-ID: <2b0b9211.d40@lincoln.cri.nz> Date: 19 Nov 92 00:09:37 GMT Organization: Canty Ag & Science Centre, New Zealand. Lines: 12 Dear colleagues I am interested in the glycosylation of a protein. My idea is to separate a tryptic (or other) digest of my protein on a polyacrylamide gel, blot them on a PVDF Membrane and screen the membrane afterwards for glycosylated peptides. Has anybody experiance with that kind of work. I am manly interested in hints how to bind small peptides (smaller than 10K) on membranes. Thanks in advance Urs Waefler Crop & Food Research Lincoln New Zealand From owner-proteins@net.bio.net Tue Nov 17 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!ub!galileo.cc.rochester.edu!news From: DSCT@db1.cc.rochester.edu (DAVID SCOTT) Newsgroups: bionet.molbio.proteins Subject: Re: TCA precipitations Message-ID: <1992Nov18.215322.4034@galileo.cc.rochester.edu> Date: 18 Nov 92 21:53:22 GMT References: <199211180207.AA03982@ux1.cso.uiuc.edu> Sender: news@galileo.cc.rochester.edu Organization: University of Rochester, Rochester NY Lines: 15 In-Reply-To: Dan_Szymanski@QMS1.LIFE.UIUC.EDU's message of 18 Nov 92 02:05:04 GMT Nntp-Posting-Host: db4.cc.rochester.edu X-News-Reader: VMS NEWS 1.11 In <199211180207.AA03982@ux1.cso.uiuc.edu> Dan_Szymanski@QMS1.LIFE.UIUC.EDU writes: > > Subject: Time:7:59 PM > OFFICE MEMO TCA precipitations Date:11/17/92 > wondering.... does TCA precipitate things in a way similar to ammonium sulfate? > who knows the real story? further, what would are the characteristics of a > protein that is soluable in low percentage solutions of TCA? highly charged? > h-bonding characteristics? stability/solvent acccesiblity? so many questions. > thanks for any responses TCA and ammonium sulfate do not precipitate in the same way. TCA irreversibly denatures proteins whereas amm. sulf. does not. Amm. sulf. ppt.ated proteins can be readily redissolved in physiological buffers. Can't help with the rest. Sorry From owner-proteins@net.bio.net Thu Nov 19 22:00:00 1992 Path: biosci!UH.EDU!Davison From: Davison@UH.EDU (Dan Davison) Newsgroups: bionet.molbio.proteins Subject: Re: Looking for a protein secondary-structure databank Message-ID: <199211201918.AA02210@Menudo.UH.EDU> Date: 20 Nov 92 19:18:38 GMT References: <01GRDFUI6I8I94DSOM@NBRF.Georgetown.Edu> Sender: daemon@net.bio.net Distribution: bionet Lines: 29 POSTMASTER@NBRF.Georgetown.Edu said: > Release 9.1 of NRL_3D is available through the PIR Network Request Server, > through the PIR On-Line Access System and by FTP from the University > of Houston server at ftp.bchs.uh.edu in the files > /pub/gene-server/incoming/pir33/nrl_3d-9.1-vms > /pub/gene-server/incoming/pir33/nrl_3d-9.1-ascii > Our thanks to Bill Pearson and Dan Davison for their efforts in > providing FTP access to the PIR databases. The files are moved; they are in pub/gene-server/pir/pir_rel34/vms or pub/gene-server/pir/pir_rel34/ascii as compressed files (nrl_*.Z). Be sure to use "binary" mode when transferring the files. dan -- dr. dan davison/dept. of biochemical and biophysical sciences/univ. of Houston/4800 Calhoun/Houston,TX 77204-5934/davison@uh.edu/DAVISON@UHOU -----RIP Isaac Asimov 1920-1992 I'll miss him -------------------- Disclaimer: As always, I speak only for myself, and, usually, only to myself. From owner-proteins@net.bio.net Thu Nov 19 22:00:00 1992 Path: biosci!uwm.edu!spool.mu.edu!darwin.sura.net!Sirius.dfn.de!news.uni-bielefeld.de!asl.uni-bielefeld.de!karsten From: karsten@asl.uni-bielefeld.de (Karsten Quast) Newsgroups: bionet.molbio.proteins Subject: Looking for a protein secondary-structure databank Message-ID: Date: 20 Nov 92 11:00:37 GMT Sender: news@hermes.hrz.uni-bielefeld.de (News Administrator) Organization: Universitaet Bielefeld, ASL. Lines: 9 Nntp-Posting-Host: liliasl1.uni-bielefeld.de Hi, I,m looking for a databank which contains protein secondary-structure data. I'd like to implement a neural network which predicts secondary-structure and need very much data for the training. Thanks in advance for any responses Karsten From owner-proteins@net.bio.net Thu Nov 19 22:00:00 1992 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Re: Looking for a protein secondary-structure databank Message-ID: <01GRDFUI6I8I94DSOM@NBRF.Georgetown.Edu> Date: 20 Nov 92 16:18:18 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 53 Karsten Quast in message <9211201109.AA11655@net.bio.net> pleads > I,m looking for a databank which contains protein secondary-structure data. > I'd like to implement a neural network which predicts secondary-structure > and need very much data for the training. The PIR's NRL_3D database is an integrated database of protein sequence and secondary structure information using all of the Brookhaven Protein Data Bank. The caveat is that the annotated secondary structure information is only what appears in the Brookhaven Protein Data Bank. Since that information was provided by the depositors, it is not necessarily complete (not all sequences are annotated for all features, so the absence of a feature for a particular sequence can't be taken as meaning that structure is not present) or consistent (some depositors may interpret what is essentially the same structure in different ways.) The following is a description of the features annotations in the NRL_3D database from one of our recent announcements. The current version of NRL_3D is 10.00 it corresponds to Brookhaven Protein Data Bank Release 61, and contains 1,457 sequences with 244,804 residues. ------------------------------------------------------------------------ 2. NRL_3D Release 9.1 Has Feature Information from Brookhaven Data Bank 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. New algorithms have been implemented to construct and name chains and fragments, to recognize non-standard residues and to discard entries with completely unknown sequence. NRL_3D release 9.1 corresponds to PDB release 60 (May 1992) and contains 1,380 sequences with 229,099 residues. 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. Release 9.1 of NRL_3D is available through the PIR Network Request Server, through the PIR On-Line Access System and by FTP from the University of Houston server at ftp.bchs.uh.edu in the files /pub/gene-server/incoming/pir33/nrl_3d-9.1-vms /pub/gene-server/incoming/pir33/nrl_3d-9.1-ascii Our thanks to Bill Pearson and Dan Davison for their efforts in providing FTP access to the PIR databases. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMASTER@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-proteins@net.bio.net Thu Nov 19 22:00:00 1992 Path: biosci!QMS1.LIFE.UIUC.EDU!Dan_Szymanski From: Dan_Szymanski@QMS1.LIFE.UIUC.EDU ("Dan Szymanski") Newsgroups: bionet.molbio.proteins Subject: TCA precipitations Message-ID: <199211201510.AA15392@ux1.cso.uiuc.edu> Date: 20 Nov 92 15:09:37 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 10 Subject: Time:7:59 PM OFFICE MEMO TCA precipitations Date:11/17/92 wondering.... does TCA precipitate things in a way similar to ammonium sulfate? who knows the real story? further, what would are the characteristics of a protein that is soluable in low percentage solutions of TCA? highly charged? h-bonding characteristics? stability/solvent acccesiblity? so many questions. thanks for any responses From owner-proteins@net.bio.net Sun Nov 22 22:00:00 1992 Path: biosci!uwm.edu!caen!uunet!mcsun!news.funet.fi!hydra!klaava!tolvanen From: tolvanen@klaava.Helsinki.FI (Martti Tolvanen) Newsgroups: bionet.molbio.proteins Subject: New PDB entries Message-ID: <1992Nov23.135345.29653@klaava.Helsinki.FI> Date: 23 Nov 92 13:53:45 GMT Organization: University of Helsinki Lines: 11 I just read in Nature, Nov. 19, (360:232-239) about a crystal structure of CD2 that has been deposited in the Protein Data Bank, and of course I went ahead and checked the prerelease area in their ftp site (pdb.pdb.bnl.gov). Searching for cd2 in the NOTICE.UPDATE file or in the filenames gave nothing, though. Does anyone have an idea how long it takes to process a submitted entry into a prerelease entry? -- Martti Tolvanen, Dept. Biochem., Univ. Helsinki, Finland tolvanen@cc.helsinki.fi From owner-proteins@net.bio.net Mon Nov 23 22:00:00 1992 Path: biosci!lhc!lhc!hunter From: hunter@work.nlm.nih.gov (Larry Hunter) Newsgroups: bionet.molbio.proteins Subject: Re: Looking for a protein secondary-structure databank Message-ID: Date: 24 Nov 92 17:42:47 GMT References: Sender: news@nlm.nih.gov Organization: National Library of Medicine Lines: 42 In-Reply-To: karsten@asl.uni-bielefeld.de's message of Fri, 20 Nov 1992 11:00:37 GMT karsten@asl.uni-bielefeld.de writes: I,m looking for a databank which contains protein secondary-structure data. I'd like to implement a neural network which predicts secondary-structure and need very much data for the training. As noted previously, the NRL-3D dataset (available from the UH server) is one way to get structural information. Another is to get the PDB dataset itself directly from Brookhaven, either by email server (fileserv@pb1.pdb.bnl.gov) or anonymous ftp (pdb.pdb.bnl.gov). I believe there is also a gopher hole at Brookhaven. Write pdb@chm.chm.bnl.gov for more information. If you are going to use these "raw" sources of data, I would strongly recommend getting Laura Lynn Walsh's PDB info file, which has very useful annotation of each structure. It is available from her by writing lwalsh@nemo.life.uiuc.edu. It is also possible to get precisely the same dataset that Qian & Sejnowski used for their neural network secondary structure prediction paper [J. Mol. Bio. (1988) 202:865-884] which is available via the University of California, Irvine machine learning archive. Anonymous ftp to host ics.uci.edu, directory /pub/machine-learning-databases/molecular-biology/protein-secondary-structure/ I believe this archive is mirrored by the hosts cs.dal.ca in Canada, and by src.doc.ic.ac.uk in the UK. You may also want to check Zhang, Mesirov and Waltz's "Hybrid Systems for Protein Secondary Structure Prediction," [J. Mol. Bio. (1992) 225:1049-1063] for the training and test sets that they used, which were quite carefully selected. Best of luck, Larry -- Lawrence Hunter, PhD. National Library of Medicine Bldg. 38A, MS-54 Bethesda. MD 20894 USA tel: +1 (301) 496-9300 fax: +1 (301) 496-0673 internet: hunter@nlm.nih.gov encryption: PGP 2.0 public key via "finger hunter@work.nlm.nih.gov" From owner-proteins@net.bio.net Tue Nov 24 22:00:00 1992 Path: biosci!uwm.edu!caen!uunet!olivea!charnel!sifon!VM1.MCGILL.CA From: EH26005@MUSICA.MCGILL.CA (EH26005) Newsgroups: bionet.molbio.proteins Subject: Molten Globule State of Porin Message-ID: <25NOV92.21918560.0057@VM1.MCGILL.CA> Date: 26 Nov 92 01:17:41 GMT Sender: usenet@MUSICA.MCGILL.CA Organization: McGill University Lines: 15 Nntp-Posting-Host: vm1.mcgill.ca Porins are a family of bacterial outer membrane proteins organized as 16 anti-parallel b-strands that are joined by a salt bridge at the NH2 and COOH terminii to form a transmembrane B-barrel. I would like to know if such a structure can exist in a molten globule state. Any references to studies on the molten-globule state of proteins organized as B-sheets would be helpful. Speculation on the properties of porin in the molten globule state would also be appreciated: would we have a B-barrel that was opened up by breakage of the COOH terminus salt bridge? ; what about the hydrogen bonding between strands? Any ideas would be welcome. Dave Dahan EH26005@MUSICA.MCGILL.CA From owner-proteins@net.bio.net Tue Nov 24 22:00:00 1992 Path: biosci!QMS1.LIFE.UIUC.EDU!Dan_Szymanski From: Dan_Szymanski@QMS1.LIFE.UIUC.EDU ("Dan Szymanski") Newsgroups: bionet.molbio.proteins Subject: TCA????? Message-ID: <199211251621.AA15027@ux1.cso.uiuc.edu> Date: 25 Nov 92 16:10:03 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 10 Subject: Time:7:59 PM OFFICE MEMO TCA????? Date:11/17/92 wondering.... does TCA precipitate things in a way similar to ammonium sulfate? who knows the real story? further, what are the characteristics of a protein that is soluable in low percentage solutions of TCA? highly charged? h-bonding characteristics? stability/solvent acccesiblity? so many questions. thanks for any responses From owner-proteins@net.bio.net Tue Nov 24 22:00:00 1992 Path: biosci!uwm.edu!caen!uunet!utcsri!torn!csd.unb.ca!UNBVM1.CSD.UNB.CA From: E85J@UNB.CA (E85J000) Newsgroups: bionet.molbio.proteins Subject: RSV/Tyler Jacks Message-ID: <25NOV92.21205996.0082@UNBVM1.CSD.UNB.CA> Date: 25 Nov 92 23:38:06 GMT Sender: usenet@UNB.CA Organization: The University of New Brunswick Lines: 10 Has anyone out there seen any recent articles from Tyler Jacks since hisoriginal work with ribosomal frameshifting in RSV's gag-poL? I haven't been able to find anything since the Cell 55(447-458) paper in 1988 on the signals for frameshifting. I've been doing a lot of work recently on a term paper on the subject and haven't been able to find anything, though his work up to '88 seems top notch. Thanks in advance, pat f. (E85J@UNB.CA) From owner-proteins@net.bio.net Tue Nov 24 22:00:00 1992 Path: biosci!XIBALBA.CSHL.ORG!mzhang From: mzhang@XIBALBA.CSHL.ORG (Michael Zhang) Newsgroups: bionet.molbio.proteins Subject: motifs Message-ID: <9211251824.AA06428@xibalba.cshl.org> Date: 25 Nov 92 18:24:42 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 4 Is there any protein or DNA sequence motifs database (or collections) available in the network? -Michael Zhang mzhang@cshl.org From owner-proteins@net.bio.net Wed Nov 25 22:00:00 1992 Path: biosci!uwm.edu!cs.utexas.edu!uunet!pipex!demon!nuntius From: pettsj@visigoth.demon.co.uk (James Petts) Newsgroups: bionet.molbio.proteins Subject: ras/GTP Message-ID: Date: 26 Nov 92 08:06:58 GMT Sender: news@gate.demon.co.uk (Usenet Administration) Organization: No Affiliation Lines: 9 X-Useragent: Nuntius v1.1 Nntp-Posting-Host: visigoth.demon.co.uk Off the top of their head, does anybody have a rough idea of the binding constant for GTP to ras p21, and alsao the intracellular conc. of GTP? James Petts ******************************************************************** * "We use the classical theory on Mondays, Wednesdays and Fridays, * * and the quantum theory on Tuesdays, Thursdays and Saturdays." * ************************************** Wm. Bragg ******************* From owner-proteins@net.bio.net Wed Nov 25 22:00:00 1992 Path: biosci!BIOTECHNET.COM!MWRAVERA From: MWRAVERA@BIOTECHNET.COM Newsgroups: bionet.molbio.proteins Subject: Tryptophan residues in IgG Message-ID: <01GRMKU0D37M8WWNLI@delphi.com> Date: 27 Nov 92 05:29:42 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 26 Recently, a question was asked by Ed Stokes about finding tryptophan residues in the antigen binding pockets of IgG molecules. One suggestion was to pull all of the IgG sequences out of GenBank to see what could be seen. I would like to suggest an alte rnate, admittedly "lower tech" approach. There is a book (now actually in three volumes) published by the US Govt. Printing Office entitled "Sequences of Proteins of Immuno- logical Interest" edited by Kabat et al. The advantage of this book over a collection of GenBank sequences is that the e ditors have layed out the sequences (both DNA and protein) logically and with easy-to-find landmarks. In Ed's case, he would look under the section entitled "Immuno- globin Variable Regions." There, the sequences are laid out with labels for framework and CDR (hypervariable) subregions. While this simplifies finding the CDRs (which are the antigen-bind ing portions of the antibody), it still requires the intrepid researcher to manually look for tryptophan residues. Call it "good news, bad news..." I can only hope that some relational database guru (or some whiz kid working on a senior project) will soon allow us to ask a data-base questions such as "Show Ig sequences that contain tryptophan residues in the CDR regions." Mark ================================================================= | Mark W. Ravera | | Sandoz Research Institute | | | | USMailNet: InterNet: MWRAVERA@BioTechNet.Com | | 59 Route 10 PhoneNet: 201-503-8613 | | East Hanover, NJ FaxNet : 201-503-6870 | | 19406 InterStateNet: I-287, New Joisey | | Exit 30 | | VoiceNet: "Hey, Mark!" | ================================================================= From owner-proteins@net.bio.net Thu Nov 26 22:00:00 1992 Path: biosci!SMITHKLINE.COM!carpenter_dd%frgen.dnet From: carpenter_dd%frgen.dnet@SMITHKLINE.COM Newsgroups: bionet.molbio.proteins Subject: (none) Message-ID: <9211272202.AA09564@smithkline.com> Date: 27 Nov 92 22:02:01 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 2 help From owner-proteins@net.bio.net Sun Nov 29 22:00:00 1992 Path: biosci!UCRVM2.bitnet!GPAZ From: GPAZ@UCRVM2.bitnet (Gisela Mabel Paz) Newsgroups: bionet.molbio.proteins Subject: Suscripcion Message-ID: <9211301951.AA02442@net.bio.net> Date: 30 Nov 92 19:51:57 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 4 Estoy interesada en recibir informacion sobre analisis de proteinas. especificamente de isoenzimas. Gracias. Mabel