From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!uunet!in1.uu.net!hodes.com!netcomsv!gatekeeper.genencor.com!usenet From: Joanne Petithory jpetithory@genencor.com Newsgroups: bionet.molbio.proteins Subject: Peptides on the head of a Pin? Date: 28 Feb 1995 03:34:48 GMT Organization: Genencor International, South San Francisco, CA Lines: 19 Message-ID: <3iu5ko$eoh@gatekeeper.genencor.com> NNTP-Posting-Host: 10.1.1.19 X-Newsreader: AIR News 3.X (SPRY, Inc.) I'm looking for information on commercial suppliers of epitope mapping kits based on the 'pin' peptide synthesis technique of Geysen and coworkers (J. Immunol. Methods 102:259, 1987). I know that at one point Cambridge Research Biochemicals in Delaware sold an 'Epitope Scanning Kit', but the person who answered their 800 number informed me that they no longer sell this kit in the US, and could not/ would not tell me what company did sell a kit in the US based on the "pin" peptide synthesis technology. Thanks, Joanne Petithory Genencor International jpetithory@genencor.com From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!news.amherst.edu!news.umass.edu!umassd.edu!ulowell.uml.edu!vtc.tacom.army.mil!news1.oakland.edu!cms.cc.wayne.edu!gkrause From: gkrause@cms.cc.wayne.edu (Gary Krause) Newsgroups: bionet.molbio.proteins Subject: Re: Q2: TCA precipitation Date: Tue, 28 Feb 1995 13:50:05 est Organization: Wayne State University Lines: 28 Message-ID: References: <3il2h3$hp4@violet.csv.warwick.ac.uk> NNTP-Posting-Host: 146.9.12.243 X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] In article <3il2h3$hp4@violet.csv.warwick.ac.uk> Dr J P Cook writes: >From: Dr J P Cook >Subject: Q2: TCA precipitation >Date: 24 Feb 1995 16:46:27 GMT >Dear All >This may have already been asked but I'm new here so... >Does anyone know what the maximum size a peptide can be >before it is precipitated by TCA? >Yours, >Jonathan Cook >lsrcp@csv.warwick.ac.uk Depends on the percentage of TCA. Higher percentages precipitate lower molecular weights (and everything above that molecular weight). Gary ------------------------------------------- Gary Krause (gkrause@cms.cc.wayne.edu) Department of Emergency Medicine Wayne State University, Detroit, MI USA From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!news.amherst.edu!news.umass.edu!umassd.edu!ulowell.uml.edu!vtc.tacom.army.mil!news1.oakland.edu!cms.cc.wayne.edu!gkrause From: gkrause@cms.cc.wayne.edu (Gary Krause) Newsgroups: bionet.molbio.proteins Subject: Re: Anti phosphoserine/theonine Antibodies Date: Tue, 28 Feb 1995 13:48:20 est Organization: Wayne State University Lines: 40 Distribution: world Message-ID: References: <01HNKCNINJZ6A5U6L6@MPGARS.DESY.DE> NNTP-Posting-Host: 146.9.12.243 X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] In article <01HNKCNINJZ6A5U6L6@MPGARS.DESY.DE> DREWES@MPASMB.DESY.DE writes: >From: DREWES@MPASMB.DESY.DE >Subject: Re: Anti phosphoserine/theonine Antibodies >Date: 27 Feb 1995 16:37:29 -0800 >Subject: Anti- phospho serine/ threonine Antibodies >in <1995Feb27.203818.29299@oxvaxd> >golding@sable.ox.ac.uk (Dr Simon Golding) wrote: >> I am currently using an antiphosphotyrosine - HRP conjugated antibody >> in Western blots which is supplied by Transduction Labs. Does anybody >> know of a source of anti-phospho- serine/threonine antibodies >> (HRP/AP conjugated or not)? >> Thanks for your help, Simon. >Anti P-Ser and P-Thr antibodies are available from Sigma. However, they are >quite new and I have not used them yet. It would be very interesting to know >if they are comparable in specifity and affinity to the very good anti P-Tyr >antibodies which are now commercially available from different companies. >Maybe anybody else can comment on this? >Gerard Drewes >Max Planck Unit for Structural Molecular Biology >DESY, Hamburg 22603, Germany We are using the Sigma anti-phosphoserine on nitrocellulose blots. Horrible backgrounds. You can't use Blotto or nonfat dry milk to block since they both contain serine-phosphorylated proteins. 5% Tween 20 is ineffectual as is 10% BSA. I would love to hear if anybody has solved this problem. Gary ------------------------------------------- Gary Krause (gkrause@cms.cc.wayne.edu) Department of Emergency Medicine Wayne State University, Detroit, MI USA From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!agateau From: agateau@ebi.ac.uk (Alain Gateau) Subject: Initial methionin removal ? Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Wed, 1 Mar 1995 18:10:37 GMT Lines: 7 Reply-To: agateau@ebi.ac.uk Organization: European Bioinformatics Institute (EMBL) - UK X-Newsreader: mxrn 6.18-16 I'd like to know the percentage of proteins in which the initial methionin is cleaved in the mature peptide. Is the enzyme responsible for that identified ? What kind of signal does it need? thanks, Alain From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ratatosk.yggdrasil.com!news.duke.edu!godot.cc.duq.edu!hudson.lm.com!newsfeed.pitt.edu!gatech!swrinde!cs.utexas.edu!uunet!nntp.cac.washington.edu!miza From: miza@u.washington.edu (Miguel Zamora) Newsgroups: bionet.molbio.proteins Subject: Northwestern Date: 2 Mar 1995 20:32:51 GMT Organization: University of Washington, Seattle Lines: 24 Message-ID: <3j5a1j$nj0@news.u.washington.edu> NNTP-Posting-Host: nntp2.u.washington.edu Newsgroups: bionet.molbio.proteins Subject: NorthWestern Summary: Expires: Sender: Followup-To: Distribution: Organization: University of Washington, Seattle Keywords: Cc: I have posted this before but I didn't get any comments. Let me try again. I would like to contact someone who has experience in Northwestern blots. I have run 3 or 4 of these blots and I am not getting any signal. As an alternative method, I would like to use a ssRNA-binding assay to detect this RNA-binding protein. Does anyone have an idea of how sensitive/ efficient this method is? Thanks. Miguel From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!uunet!in1.uu.net!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!pmacrz2.biochem.mpg.de!user From: riesle@vms.biochem.mpg.de (jr) Newsgroups: bionet.molbio.proteins Subject: RE dialysis problems Followup-To: bionet.molbio.proteins Date: 2 Mar 1995 18:26:42 GMT Organization: mpg Lines: 7 Message-ID: NNTP-Posting-Host: pmacrz2.biochem.mpg.de hey sylvie, in addition to the hint not to completely fill the dialysis bags try multiple step dialyis, first with about 6 M urea in the outside compartment, and then stepwise lowering the urea concentration. good luck patrik From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!EU.net!uknet!daresbury!not-for-mail From: "Andrew, Tel. +396-91093434" Newsgroups: bionet.molbio.proteins Subject: "Pin" peptide technology Date: 2 Mar 1995 20:56:02 -0000 Lines: 32 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3j5bd2$6rn@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk In reply to: bionet.molbio.proteins Msg # 3427 > I'm looking for information on commercial suppliers of epitope mapping kits >based on the 'pin' peptide synthesis technique of Geysen and coworkers (J. >Immunol. Methods 102:259, 1987). I know that at one point Cambridge Research >Biochemicals in Delaware sold an 'Epitope Scanning Kit', but the person who >answered their 800 number informed me that they no longer sell this kit in the >US, and could not/ would not tell me what company did sell a kit in the US >based on the "pin" peptide synthesis technology . > > Thanks, > > Joanne Petithory > Genencor International > jpetithory@genencor.com If I remember correctly one other company which sells this technology is Chiron Mimotopes. I don't have a phone number or email address for them but I'm sure your purchasing department can track them down. Mario Geysen used to work for Chiron but I heard that he has moved to Glaxo; perhaps he could give you some advice. Andrew =============================================================================== Andrew Wallace, IRBM P. Angeletti, Pomezia, Italy. Voice: +39-6-91093434 Fax: +39-6-91093225 Email: wallace@irbm.it "IRBM - The home of the Minibody" From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!howland.reston.ans.net!agate!msunews!netnews.upenn.edu!sanger.bcm.tju.edu!tromp From: tromp@sanger.bcm.tju.edu (Gerard Tromp) Newsgroups: bionet.molbio.proteins Subject: Circular Dichroism (CD) reference values Date: 2 Mar 1995 15:05:03 GMT Organization: Biochemistry Lines: 27 Distribution: world Message-ID: <3j4mqv$ld5@netnews.upenn.edu> NNTP-Posting-Host: sanger.bcm.tju.edu Keywords: Circular Dichroism, alpha helix, beta sheet, random coil, reference tables. Greetings, Does anyone know where to find the molar ellipticity tables for circular dichroism of the three elementary secondary structures: alpha helix, beta sheet, random coil ? Alternatively does anybody know where to find mathematical functions that describe the curves: y=f(x), where x is wavelength and y is molar ellipticity, ? Thanks in advance Gerard -- ======================================================================= Gerard Tromp, Ph.D. Research Assistant Professor Vox: 215-955-4487 Department of Biochemistry 215-955-4488 and Molecular Biology Fax: 215-955-5393 Thomas Jefferson University 233 South Tenth Street, Room 328 E-mail: tromp@sanger.bcm.tju.edu Philadelphia, PA 19107 U.S.A. From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!reuter.cse.ogi.edu!netnews.nwnet.net!news.pfc.forestry.ca!PFC.Forestry.CA!AEKRAMODDOUL From: aekramoddoul@PFC.Forestry.CA (Ekramoddoullah, Abul Kalam M.) Subject: Re: Peptide synthesis recommendations sought X-Nntp-Posting-Host: pfc.pfc.forestry.ca Message-ID: Sender: news@news.pfc.forestry.ca (Usenet News) Reply-To: aekramoddoul@PFC.Forestry.CA Organization: Forestry Canada (Pacific Forestry Centre) References: <3i2u1f$4f4@mark.ucdavis.edu> Date: Mon, 27 Feb 1995 19:25:22 GMT Lines: 31 In article <3i2u1f$4f4@mark.ucdavis.edu>, ez001427@dale.ucdavis.edu (Marc Goldstein) writes: >Hi All, > > I'm looking into using a synthetic peptide as an antigen for the >production of an antibody in rabbits. The protein I'm working on is >difficult to purify in sufficient amounts for immunological purposes. > > My question is this: to get a good immune response, are there any >guidelines about optimal lengths of a synthetic peptide, hydrophobic/ >hydrophilic nature, etc... > > Also, I'm asking about which companies can be relied on as a good >value in synthesis of the peptide. > > Thanks for your help. Responses by email or followup would be >appreciated. > >Marc Goldstein >Section of Plant Biology >UC. Davis >magoldstein@ucdavis.edu > Hi Marc! try CHIRON MIMOTOPES PEPTIDE SYSTEMS: 3550 General Atomics Court, San Diego, CA 92121 USA Tel: 800-338-4965 Fax: 800-654-5592 Over the years I have used their service of synthesizing peptides and also producing antibodies to the synthetic peptides. I hope this was help. Abul EKRAMODDOULLAH, ABUL KALAM M. Title: Research Scientist Forestry Canada Phone: (604) 363-0600 Victoria, B.C. Internet: AEKRAMODDOUL@A1.PFC.Forestry.CA From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!SCRI.FSU.EDU!STRELETS From: STRELETS@SCRI.FSU.EDU ("VICTOR B. STRELETS") Newsgroups: bionet.molbio.proteins Subject: Where to find PDB-like datafiles for misfolded structures? Date: 2 Mar 1995 09:05:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <950302120507.2020204f@scri.fsu.edu> Hi Netters, I'm working on the evaluation of preliminary protein structure models by hydrophobicity-like plots (in correlation with some structure-derived profiles) and by analysis of hydrophobic core packing. To test corresponding methods performance in some extremal cases, I need to use PDB files for misfolded and/or incorrectly refined structures. Some information about such structures was published (for example: Nature 1992, 356:83-85; J.Mol.Biol. 1992, 225:93-105) in last years, but corresponding datafiles appeared to be unavailable on the net... PDB simply does not contain previously submitted wrong models (deleted?). Info about misfolded proteins from Sander (J.Mol.Biol.) was presented in a very accurate (due to implemented pair comparison approach) manner: pairs of potentially misfolded entries without exact reference which one of them is wrong (in addition, some of listed entries are absent in current PDB). So, how to find PDB (or similar) datafiles for knowlingly misfolded structures (or partially misfolded, with some wrong chain placement or domain structure)? Any references and comments will be greatly appreciated. Thanks, V.Strelets From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!ns1.faseb.org!darwin.sura.net!fconvx.ncifcrf.gov!mack From: mack@ncifcrf.gov (Joe Mack) Subject: Re: Initial methionin removal ? Message-ID: Organization: Frederick Cancer Research and Development Center References: Date: Thu, 2 Mar 1995 23:22:20 GMT Lines: 17 In article agateau@ebi.ac.uk writes: > >I'd like to know the percentage of proteins in which the initial methionin >is cleaved in the mature peptide. >Is the enzyme responsible for that identified ? >What kind of signal does it need? >thanks, >Alain It depends mainly on the residue immediately following the Met. I don't know what they are but they're listed in the papers on the Methionine amino peptidases (MAP) - a literature search should find them. Joe Mack mack@ncifcrf.gov . From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!biosci!not-for-mail From: "Alexander J. Ropelewski" Newsgroups: bionet.announce,sci.techniques.mag-resonance,bionet.molec-model,bionet.molbio.proteins,bionet.cellbiol,sci.research,sci.techniques.spectroscopy,sci.bio.technology Subject: Molecular Mechanics and Dynamics workshop Annoucement Date: 2 Mar 1995 14:18:21 -0800 Organization: Pittsburgh Supercomputing Center, Carnegie Mellon, Pittsburgh, PA Lines: 113 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: <0jJ=MW600WB5M6cHlQ@andrew.cmu.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:1862 sci.techniques.mag-resonance:715 bionet.molec-model:280 bionet.molbio.proteins:3877 bionet.cellbiol:1718 sci.research:4025 sci.techniques.spectroscopy:1372 sci.bio.technology:2393 "METHODS OF MOLECULAR MECHANICS AND DYNAMICS OF BIOPOLYMERS" WORKSHOP Pittsburgh Supercomputing Center August 16-19, 1995 The Pittsburgh Supercomputing Center (PSC) is hosting a workshop on "Methods of Molecular Mechanics and Dynamics of Biopolymers," August 16-19, 1995. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in molecular mechanics. Practical experience on our supercomputers will be gained in the application to: (1) the theory and practice of molecular mechanics and dynamics; (2) the development and refinement of molecular mechanics force fields; (3) the problem of conformation mapping and analysis of polypeptide structures, including the refinement of structure from measured NMR data; and (4) computation of interaction energies and free energies for protein-drug interactions and conformational thermodynamics. Workshop leaders are Dr. Charles L. Brooks III, The Scripps Research Institute and Dr. Alexander D. MacKerell Jr., University of Maryland at Baltimore. The worskhop will consist of lectures and extensive hands-on sessions. General aspects of molecular mechanics software will be discussed and a number of packages are available for use at the PSC. However, the programs CHARMM and QUANTA will be utilized most extensively in demonstrations. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. Travel, meals and hotel accommodations for researchers affilated with U.S. academic institutions are supported by this grant. Enrollment is limited to 20. An application form is included. Deadline for applications is: June 22, 1995. Please direct inquires or send the following application form to blankens@psc.edu. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE ************************************** August 16-19, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by June 22, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!biosci!not-for-mail From: "Alexander J. Ropelewski" Newsgroups: bionet.announce,bionet.molbio.proteins,bionet.molbio.embldatabank,bionet.molbio.genbank,bionet.molbio.evolution,sci.research,sci.bio.technology Subject: Sequencing Analysis workshop Annoucement Date: 2 Mar 1995 14:17:48 -0800 Organization: Pittsburgh Supercomputing Center, Carnegie Mellon, Pittsburgh, PA Lines: 114 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:1861 bionet.molbio.proteins:3876 bionet.molbio.embldatabank:460 bionet.molbio.genbank:1962 bionet.molbio.evolution:2508 sci.research:4024 sci.bio.technology:2392 NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS Pittsburgh, Pennsylvania June 4-9, 1995 Pittsburgh Supercomputing Center (PSC) is again offering a five-day workshop on "Nucleic Acid and Protein Sequence Analysis," June 4-9, 1995. It is funded by a grant from the National Center for Human Genome Research of the National Institutes of Health. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in macromolecular sequence analysis. Emphasis will be on alignment of and pattern extraction from multiple sequences. Participants will gain practical experience on PSC's Cray C-90 and T3D in (1) comparing and aligning sequences, (2) identifying informative patterns in a set of sequences; and (3) using extracted informative patterns to identify related sequences. Researchers will also learn several approaches to database searching and multiple sequence alignment, how to use profile analysis effectively, and how to identify patterns in their sequences. Participants are encouraged to bring sequence analysis problems from their current research. Extensive documentation will be given at the outset on the PSC computing environment as well as on the specific programs to be employed in the workshop. No prior supercomputing experience is required. Workshop leaders are Dr. Gary Churchill, Cornell University, Dr. Michael Gribskov, San Diego Supercomputing Center, and Dr. Hugh Nicholas, PSC. A limited number of grants to cover travel and hotel accommodations are available for U.S. academic participants. ALL PARTICIPANTS ARE REQUIRED TO PAY A $135 REGISTRATION FEE, IN ADVANCE, UPON ACCEPTANCE INTO THE WORKSHOP. The deadline for submitting applications is April 17, 1995. Enrollment is limited to 20 participants. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html * * * * * PITTSBURGH SUPERCOMPUTING CENTER NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS June 4-9, 1995 APPLICATION Name: ________________________________________________________________ Affiliation: ________________________________________________________________ Address: ________________________________________________________________ (Business) ________________________________________________________________ ________________________________________________________________ (Home) ________________________________________________________________ Telephone: ____________________________ ______________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_______________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) In order to attend the workshop, will you need funds for travel?___ lodging?___ Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:_________________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. If you have requested travel funds, please include the cost of roundtrip air fare from your home to Pittsburgh and indicate the amount of travel funds you will need. ALL PARTICIPANTS WILL BE REQUIRED TO PAY A $135 ADVANCE REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Please return all application materials by APRIL 17, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From owner-proteins@net.bio.net Wed Mar 01 22:00:00 1995 Path: biosci!ns1.faseb.org!darwin.sura.net!blaze.cs.jhu.edu!jhunix1.hcf.jhu.edu!welchlink.welch.jhu.edu!dshumake From: dshumake@welchlink.welch.jhu.edu (DALE KENDRICK SHUMAKER) Newsgroups: bionet.molbio.proteins Subject: cold denaturation Date: 3 Mar 1995 05:02:34 GMT Organization: Johns Hopkins University, Welch Medical Library Lines: 11 Distribution: world Message-ID: <3j67ta$rpa@jhunix1.hcf.jhu.edu> NNTP-Posting-Host: 128.220.59.78 I was wondering whether someone could give me a good description of how proteins can cold denature. Specifically I am wondering how a protein that is not involved in self assembly of fibers, polymers, or other supermolecular structures can cold denature. Note, I am not refering to actually freezing the protein but just holding the protein at a cold temperature above 0 Celsius. Thank you for your help. Dale From owner-proteins@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!sol.ctr.columbia.edu!news.mindlink.net!agate!edwardg From: edwardg@OCF.Berkeley.EDU (Edward Graves) Newsgroups: bionet.molbio.proteins Subject: AMINODB, BMCD Date: 3 Mar 1995 23:08:51 GMT Organization: U. C. Berkeley Open Computing Facility Lines: 20 Message-ID: <3j87i3$i2c@agate.berkeley.edu> NNTP-Posting-Host: lightning-ether.berkeley.edu To all: Hi, I am an undergrad at UCB working with a professor on the standard molal thermodynamic properties of biomolecules, particularly amino acids and proteins. In surfing the net, I came across a reference in the List of Molecular Biology Databases (LiMB) to two databases, the Amino Acid Database, run by a Dr. Froemmel in Berlin, and the Biological Macromolecule Crystallization Database, run by Joan Sauerwein at NIST. These both sound very useful, unfortunately I was unable to deduce exactly where I could download them from. Does anyone have any suggestions? The LiMB provides references to the databases (and even gave an email address for Dr. Froemmel, which i was unable to reach), but does not explain where on the net (if at all) the databases are located. Thanks in advance! Ted Graves edwardg@ocf.berkeley.edu From owner-proteins@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!EU.net!Germany.EU.net!zib-berlin.de!uni-duisburg.de!RRZ.Uni-Koeln.DE!news.dfn.de!uni-muenster.de!ifimac02.uni-muenster.de!user From: @uni-muenster.de Newsgroups: bionet.molbio.proteins Subject: Re: Slow running SDSPAGE gels Date: Thu, 02 Mar 1995 10:56:03 +0100 Organization: ZMBE - Institut fuer Infektiologie Lines: 29 Message-ID: <-0203951056030001@ifimac02.uni-muenster.de> References: NNTP-Posting-Host: ifimac02.uni-muenster.de In article , mbxfd@unicorn.nott.ac.uk (Fergus Doherty) wrote: > Every so often we are hit by very slow running SDSPAGE gels, I mean all day > to run a 10% minigel!!! Anyone any ideas of what the problem is? I > thought it might be a problem with stored gels at first but now even gels a > few days old run slow, made with fresh buffers (UltraPure Tris).. Could it > be the water? I'm lost. > > Fergus Doherty, > dept. Biochemistry, > University Medical School, > Queen's Medical Centre, > Nottingham NG7 2UH > Tel: 602 709366 FAX 602 422225 Internet: mbxfd@unicorn.nott.ac.uk Hi, perhaps it is a problem of the composition of your SDS running buffer system. In our lab it takes one hour to run a minigel. I have tried several buffer systems and my experience showed me that the running time depends on the ions present in the system. Now i use the Laemmli-system that means 0.025 M Tris-HCl, 0.192 M glycine, 0.1 % SDS. Bye. Martin Suhr ZMBE, Von-Esmarch-Straße 56, D-48149 Muenster e-mail: suhr@wwupop.uni-muenster.de From owner-proteins@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.rediris.es!diable.upc.es!lilith.uab.es!farmacia.far.ub.es!perez From: perez@farmacia.far.ub.es (Angel Pérez Beroy) Newsgroups: bionet.molbio.proteins Subject: Re: InsightII Date: Fri, 3 Mar 1995 19:20:58 Organization: Universitat de Barcelona - Dept Farmàcia. U. Fisicoquímica Lines: 17 Distribution: inet Message-ID: References: <3j1leh$lf9@oravannahka.Helsinki.FI> NNTP-Posting-Host: 161.116.93.75 X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] In article <3j1leh$lf9@oravannahka.Helsinki.FI> tweckrot@cc.Helsinki.FI (Tero T Weckroth) writes: >Subject: InsightII >From: tweckrot@cc.Helsinki.FI (Tero T Weckroth) >Date: 1 Mar 1995 11:22:57 GMT > So, now with a better success... >Is there any Insight II users around? If there is, would you please mail me? >Tero Weckroth >tweckrot@helsinki.fi I also use insightII. perez@farmacia.far.ub.es From owner-proteins@net.bio.net Thu Mar 02 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!rutgers!gatech!swrinde!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!univ-lyon1.fr!ghost.dsi.unimi.it!genes!karami From: karami@genes.icgeb.trieste.it (Ali Karami) Subject: Mab for OspA of Borrelia???? Message-ID: <1995Mar3.180312.5332@genes.icgeb.trieste.it> Organization: ICGEB X-Newsreader: TIN [version 1.2 PL2] Date: Fri, 3 Mar 1995 18:03:12 GMT Lines: 27 From karami Fri Mar 3 18:58:51 1995 Return-Path: Received: by icgeb.trieste.it (AA05218); Fri, 3 Mar 95 18:58:50 +0100 Date: Fri, 3 Mar 95 18:58:50 +0100 From: Ali Karami Message-Id: <9503031758.AA05218@icgeb.trieste.it> To: karami@icgeb.trieste.it (Ali Karami) Subject: Re: Mab for OspA of Borrelia???? Newsgroups: bionet.immunology Organization: ICGEB X-Newsreader: TIN [version 1.2 PL2] Status: OR In article <1995Mar3.174607.5025@genes.icgeb.trieste.it> you wrote: I need Monoclonal Ab against OspA of Borrelia burgdorferi ? How can I find it ? I want to do few Immuno blotting with mY protein. I would appreciate Any help. Thank you Ali Karami Ali@biobase.dk From owner-proteins@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!JASON.UTHCT.EDU!SHAUN From: SHAUN@JASON.UTHCT.EDU ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: Re: cold denaturation Date: 3 Mar 1995 07:29:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <950303093244.2f33@jason.uthct.edu> NNTP-Posting-Host: net.bio.net dshumake@welchlink.welch.jhu.edu (DALE KENDRICK SHUMAKER) asked about good references on cold protein denaturation. The best reference that I know of is Privalov's discussion in Tom Creighton's book, "Protein Folding". The chapter I'm referring to is chapter 3 (pp. 83-126). IMHO, it is a remarkable chapter because the discussion is quite physical-chemical, but it is understandable and intuitively satisfying. Other chapters in the book touch on cold denatura- tion as well, but this is definitely the most concentrated treatment. Finally, the publisher is Freeman and the date is 1992. Most libraries should have it. Best regards, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet address: shaun@jason.uthct.edu = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = = World Wide Web: http://pegasus.uthct.edu/UTHCT-Home/Welcome.html = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!scripps.edu!NewsWatcher!user From: Bibbs@scripps.edu (Lisa) Newsgroups: bionet.molbio.proteins Subject: C-terminal seq Date: 4 Mar 1995 00:48:02 GMT Organization: The Scripps Research Institute, La Jolla, CA Lines: 3 Message-ID: NNTP-Posting-Host: bertha.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I heard from a friend that HP is now sellin a C-terminal sequencer. Does anyone have any information? Lisa Bibbs From owner-proteins@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!CS.Arizona.EDU!ruby.ucc.nau.edu!news From: porter@warp.phy.nau.edu Newsgroups: bionet.molbio.proteins Subject: Microtubules Date: 3 Mar 1995 16:41:06 GMT Organization: Northern Arizona University Lines: 5 Message-ID: <3j7gr2$k3p@ruby.ucc.nau.edu> Reply-To: porter@warp.phy.nau.edu NNTP-Posting-Host: warp.phy.nau.edu X-Newsreader: IBM NewsReader/2 v1.03 I am looking for a source of MTP (microtubule protein) or tubulin dimer. We wish to polymerize the protein into microtubles for high resolution imaging in an atomic force microscope. We have several recepies for this polymerization process, but we are lacking the MTP or tubulin dimer. Any help in obtaining this material would be greatly appreciated. From owner-proteins@net.bio.net Thu Mar 02 22:00:00 1995 Path: biosci!JWCI.ORG!dale From: dale@JWCI.ORG ("Dale Yuzuki's Work Account") Newsgroups: bionet.molbio.proteins Subject: Re: Peptides on the head of a Pin? Date: 3 Mar 1995 17:56:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503030914.aa01708@jwi-adm.jwci.org> NNTP-Posting-Host: net.bio.net I've used the Chiron Mimotopes pin-based peptide synthesis for a few years now, with good success (according to my T-cell people). They are based in Australia and have recently been taken over by Multiple Peptide Systems in San Diego. 800 338-4965 fax619 455-3713. No connection with said company. Penny Rogers, a technical support person, is extremely helpful with any questions you may have. Regards - Dale Yuzuki M.A. M.Ed. - John Wayne Cancer Inst. - dale@jwci.org - __@ - 2200 Santa Monica Blvd - Santa Monica CA 90404 - (310) 449-5267 _ -\<'_ - I cannot live without books. Thomas Jefferson (_)-/-(_) From owner-proteins@net.bio.net Fri Mar 03 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!msunews!netnews.upenn.edu!mscf.med.upenn.edu!pathology From: pathology@mscf.med.upenn.edu Newsgroups: bionet.molbio.proteins Subject: Re: HELP: dialysis of protein Date: 4 Mar 95 18:23:21 -0500 Organization: UPENN - Med School Computer Facility Lines: 29 Distribution: world Message-ID: <1995Mar4.182321.1@mscf.med.upenn.edu> References: <1995Feb24.080009.42766@cc.usu.edu> <3jaa0j$jfd@news.duke.edu> NNTP-Posting-Host: mscf.med.upenn.edu >> NAME RAVI PRAKASH .D (sl16s@cc.usu.edu) wrote: >> : Dear Netters, >> : I have attempted to dialyse a recombinant protein (in 0.5M NaCl, 300mM >> : imidazole, 6M urea) into buffer with 150mM NaCl, 20mM tris, 2.5mM CaCl2. Within >> : few minutes of dialysis there is a precipitate formation in my dialysis bag. >> : Can anyone have any suggestions as to how I can rescue my protein from the >> : precipitate? Or any better way to dialyse the protein in future? >> : Thankyou in advance for any suggestions or comments. > I suggest that you vary the ionic strength of your refolding buffer. In other words, increase or reduce or eliminate the NaCl and/or CaCl2. Your protein may remain soluble in higher or lower ionic strength buffer. A recombinant protein that I am working with stays in solution with stepwise dialysis from 6M, 4M, 2M, 0M urea when in 40mM Tris, pH 8, as the buffering solvent; whereas it precipitates when I put it through the same dialysis step with decrements of urea concentration with PBS as the buffering solvent (100mM NaCl and 10mM sodium phosphate, pH 7.5). pH and the type of buffering chemicals can be important, too. The calcium may or may not interfere with solubility. Don't give up hope yet. Gregg Wells Department of Pathology University of Pennsylvania Philadelphia, PA 19104-4283 email: pathology@a1.mscf.upenn.edu From owner-proteins@net.bio.net Fri Mar 03 22:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!gatech!news-feed-1.peachnet.edu!news.duke.edu!usenet From: hughe014@mc.duke.edu (Christine Hughes) Newsgroups: bionet.molbio.proteins Subject: Re: Determining Calmodulin Concentration Date: 4 Mar 1995 18:09:33 GMT Organization: Dept. of Biochemistry, Duke University Lines: 10 Sender: -Not-Authenticated-[7629] Message-ID: <3jaact$jfd@news.duke.edu> References: <95059.080316RJC8@psuvm.psu.edu> NNTP-Posting-Host: bennett02.mc.duke.edu X-Posted-From: InterNews 1.0.5@bennett02.mc.duke.edu Xdisclaimer: No attempt was made to authenticate the sender's name. In article <95059.080316RJC8@psuvm.psu.edu> Richard Cyr writes: > Does anyone know of a reference wher > e the extinction coefficient of CaM was determined? The Merck index gives the extinction coefficient(1%) at A280 to be 2.1 Christine Dept. of Biochemistry hughe014@mc.duke.edu From owner-proteins@net.bio.net Fri Mar 03 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!news.duke.edu!usenet From: hughe014@mc.duke.edu (Christine Hughes) Newsgroups: bionet.molbio.proteins Subject: Re: HELP: dialysis of protein Date: 4 Mar 1995 18:02:59 GMT Organization: Dept. of Biochemistry, Duke University Lines: 20 Sender: -Not-Authenticated-[7629] Message-ID: <3jaa0j$jfd@news.duke.edu> References: <1995Feb24.080009.42766@cc.usu.edu> <3isvc7$d8m@nic.umass.edu> NNTP-Posting-Host: bennett02.mc.duke.edu X-Posted-From: InterNews 1.0.5@bennett02.mc.duke.edu Xdisclaimer: No attempt was made to authenticate the sender's name. In article <3isvc7$d8m@nic.umass.edu> nzheng@titan.oit.umass.edu (NZ) writes: > NAME RAVI PRAKASH .D (sl16s@cc.usu.edu) wrote: > : Dear Netters, > : I have attempted to dialyse a recombinant protein (in 0.5M NaCl, 300mM > : imidazole, 6M urea) into buffer with 150mM NaCl, 20mM tris, 2.5mM CaCl2. Within > : few minutes of dialysis there is a precipitate formation in my dialysis bag. > : Can anyone have any suggestions as to how I can rescue my protein from the > : precipitate? Or any better way to dialyse the protein in future? > : Thankyou in advance for any suggestions or comments. You could try dialyzing away the urea over 1-2 days in a stepwise fashion, maintaining high salt (1M NaCl) and 10-20% sucrose through each of the urea conditions -- you can dialyze away the salt and sucrose after the urea is gone Christine Dept of Biochemistry hughe014@mc.duke.edu From owner-proteins@net.bio.net Fri Mar 03 22:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!gatech!udel!news.sprintlink.net!EU.net!Germany.EU.net!news.dfn.de!uni-muenster.de!asterix.uni-muenster.de!borcher From: borcher@asterix.uni-muenster.de (Torsten Borchers) Newsgroups: bionet.molbio.proteins Subject: Re: Initial methionin removal ? Date: 4 Mar 1995 22:30:24 GMT Organization: Westfaelische Wilhelms-Universitaet Muenster, Germany Lines: 33 Message-ID: <3japm0$rkk@majestix.uni-muenster.de> References: NNTP-Posting-Host: asterix.uni-muenster.de X-Newsreader: TIN [version 1.2 PL2] Joe Mack (mack@ncifcrf.gov) wrote: : In article agateau@ebi.ac.uk writes: : > : >I'd like to know the percentage of proteins in which the initial methionin : >is cleaved in the mature peptide. : >Is the enzyme responsible for that identified ? : >What kind of signal does it need? : >thanks, : >Alain : It depends mainly on the residue immediately following the Met. I don't : know what they are but they're listed in the papers on the Methionine : amino peptidases (MAP) - a literature search should find them. : Joe Mack : mack@ncifcrf.gov : . I would like to add that besides for "normal" eucaryotic proteins this behaviour is a problem in production of recombinant proteins in bacteria. Since even for one protein not just clear cleavage or no cleavage occurs very often N-terminal heterogeneity is the result. This is only rarely addressed in the literature. A tool to quickly look at this heterogeneity and that caused by incomplete deformylation is to run isoelectric focusing. -------------------------------------------------------------------- Torsten Boerchers Phone: +49-251-980 2876 Institute for Chemical and Fax: +49-251-980 2890 Biochemical Sensor Research (ICB) Mendelstr. 7 D-48149 Muenster Germany E-Mail: borcher@uni-muenster.de -------------------------------------------------------------------- From owner-proteins@net.bio.net Fri Mar 03 22:00:00 1995 Path: biosci!agate!library.ucla.edu!psgrain!nntp.ski.mskcc.org!mac-175.rrl-g4.ski.mskcc.org!user From: h-kiong@ski.mskcc.org (Kiong Ho) Newsgroups: bionet.molbio.proteins Subject: Re: Northwestern Date: 4 Mar 1995 22:28:21 GMT Organization: MSKCC Lines: 27 Message-ID: References: <3j5a1j$nj0@news.u.washington.edu> NNTP-Posting-Host: mac-175.rrl-g4.ski.mskcc.org In article <3j5a1j$nj0@news.u.washington.edu>, miza@u.washington.edu (Miguel Zamora) wrote: > Newsgroups: bionet.molbio.proteins > Subject: NorthWestern > I have posted this before but I didn't get any comments. Let me try again. > > I would like to contact someone who has experience in Northwestern blots. > I have run 3 or 4 of these blots and I am not getting any signal. > > As an alternative method, I would like to use a ssRNA-binding assay to > detect this RNA-binding protein. Does anyone have an idea of how > sensitive/ efficient this method is? > Dear Miguel, yes, I perform northwestern, with both ds and ssRNA. From what I read from your comment, I cannot give much suggestion what is going wrong. Are you running a SDS PAGE and transfering to the membrene? How is the transfer efficency of your protein (if you can determine). What specific activity are you probing. And what is the probe (homopolymer like poly rC or poly rI should do good). Reply to me if you need more info. Kiong Ho hkiong@ski.mskcc.org. From owner-proteins@net.bio.net Fri Mar 03 22:00:00 1995 Path: biosci!agate!library.ucla.edu!psgrain!nntp.ski.mskcc.org!mac-175.rrl-g4.ski.mskcc.org!user From: h-kiong@ski.mskcc.org (Kiong Ho) Newsgroups: bionet.molbio.proteins Subject: Re: Northwestern Date: 4 Mar 1995 22:30:05 GMT Organization: MSKCC Lines: 27 Message-ID: References: <3j5a1j$nj0@news.u.washington.edu> NNTP-Posting-Host: mac-175.rrl-g4.ski.mskcc.org In article <3j5a1j$nj0@news.u.washington.edu>, miza@u.washington.edu (Miguel Zamora) wrote: > Newsgroups: bionet.molbio.proteins > Subject: NorthWestern > I have posted this before but I didn't get any comments. Let me try again. > > I would like to contact someone who has experience in Northwestern blots. > I have run 3 or 4 of these blots and I am not getting any signal. > > As an alternative method, I would like to use a ssRNA-binding assay to > detect this RNA-binding protein. Does anyone have an idea of how > sensitive/ efficient this method is? > Dear Miguel, yes, I perform northwestern, with both ds and ssRNA. From what I read from your comment, I cannot give much suggestion what is going wrong. Are you running a SDS PAGE and transfering to the membrene? How is the transfer efficency of your protein (if you can determine). What specific activity are you probing. And what is the probe (homopolymer like poly rC or poly rI should do good). Reply to me if you need more info. Kiong Ho hkiong@ski.mskcc.org. From owner-proteins@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!pipex!oleane!jussieu.fr!univ-lyon1.fr!fdn.fr!uunet!munnari.oz.au!newshost.anu.edu.au!rschp1.anu.edu.au!chrisp From: chrisp@rschp1.anu.edu.au (Chris Penington) Newsgroups: bionet.molbio.proteins Subject: Re: Glutathione sequence Date: 6 Mar 1995 04:29:35 GMT Organization: Australian National University Lines: 43 Message-ID: <3je33f$q9r@manuel.anu.edu.au> NNTP-Posting-Host: 150.203.35.20 In article writes: >fdn.fr!jussieu.fr!univ-lyon1.fr!ghost.dsi.unimi.it!ictpsp10.ictp.trieste.it!genes.icgeb.trieste.it!buratti >From: buratti@genes.icgeb.trieste.it (Emanuele Buratti) >Newsgroups: bionet.molbio.proteins >Subject: Glutathione sequence >Date: 1 Mar 1995 12:20:52 GMT >Organization: ICGEB >Lines: 15 >Message-ID: <3j1or4$ke5@ictpsp10.ictp.trieste.it> >NNTP-Posting-Host: base.icgeb.trieste.it >X-Newsreader: TIN [version 1.2 PL2] > >Hi all, > my question is: the glutathione that is used to elute any GST >fusion protein from the glutathine-derivatized affinity column has the >sequence (GAMMA)Glu-Cys-Gly. > Does anybody know whether the sequence (BETA)Glu-Cys-Gly present >in the primary structure of a protein can also interact in the active site >of the enzyme?. I seem to remember that it is the -SH part of the >tripeptide that does most of the docking, does the way the glutamic acid >is bound to the cysteine affect this interaction?. I think this is fairly unlikely. In the various structures of vertebrate GSTs that have been published there are about 15 contacts between enzyme and substrate. The cysteine thiol is important for conjugation reactions, but is not critical for binding of GSH to GST ( you can substitute it with a hydroxyl group and still get quite good binding). Adang's group has published a series of papers looking at a variety of GSH analogs and found that the gamma glutamyl group is the least tolerant to substitution and appears to play a critical role in binding of GSH to the enzyme. The crystallographic data supports this conclusion: the enzymes make numerous contacts with the gamma-glutamyl group. Chris -- Chris Penington The opinions expressed are mine. NOT Research School of Chemistry, those of the school *or* the university Australian National University, Canberra, ACT 0200 chrisp@rschp1.anu.edu.au From owner-proteins@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!FOX.NSTN.CA!ewright From: ewright@FOX.NSTN.CA ("Edwin Wright") Newsgroups: bionet.molbio.proteins Subject: (none) Date: 5 Mar 1995 05:52:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <49018.ewright@fox.nstn.ca> Reply-To: NNTP-Posting-Host: net.bio.net test -- Edwin Wright ewright@fox.nstn.ca From owner-proteins@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!galaxy.ucr.edu!library.ucla.edu!agate!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!reuter.cse.ogi.edu!henson!news.clark.edu!sun.lclark.edu!news.reed.edu!usenet From: amackey@reed.edu (Aaron J Mackey) Newsgroups: bionet.general,bionet.metabolic-reg,bionet.microbiology,bionet.molbio.hiv,bionet.molbio.proteins,bionet.virology,bionet.jobs,bionet.jobs.wanted,bionet,bionet.immunology,bionet.cellbiol,sci.med.immunology,sci.bio.microbiology, Subject: Looking for European work in Immunology or ? Date: 2 Mar 1995 01:05:00 GMT Organization: Reed College, Portland, Oregon Lines: 38 Message-ID: <3j35js$i2i@scratchy.reed.edu> NNTP-Posting-Host: reed.edu Xref: biosci bionet.general:13978 bionet.metabolic-reg:421 bionet.microbiology:1573 bionet.molbio.hiv:954 bionet.molbio.proteins:3896 bionet.virology:1789 bionet.jobs:8189 bionet.jobs.wanted:857 bionet.immunology:3353 bionet.cellbiol:1745 sci.med.immunology:1045 sci.bio.microbiology:473 Dear M.D.'s, Ph.D.'s, D.V.M.'s, etc. in the UK and EC, I am an undergraduate at Reed College in Portland Oregon, USA, about to graduate with a B.A. in Biochemistry and Molecular Biology. I plan to attend graduate school at Washington University in St. Louis, Missouri, in the Department of Immunology, to obtain my Ph.D. Currently, however, I am attempting to find a lab job in the UK or at any other english-speaking European laboratory for the coming year, and defer my admission to grad school for this period. My reasons for this job search are simple; I wish to take a year off from my studies and have an international experience, but would like to maintain my involvement in science. This is the one time in my life when I will have the opportunity for a year to live in a foreign country, so I'm trying to arrange full time employment abroad. My research experience is extensive and includes knowledge of most standard biochemical techniques, as well as some genetic and cellular work (PCR, FACS, etc.) I am currently working on my undergraduate thesis project, the complete synthesis of a putative enzyme inhibitor, so my chemistry background is solid as well. I would love the chance to work in an immunology-related field, but I would be happy for any opportunity. I won't bother with a full c.v. here, but one is obviously available, as well as excellent letters of recommendation from current and past research advisors. I ask that any of you who either have or know of, an available research or lab tech position, in academia or industry, beginning around next September and lasting for about a year, PLEASE respond via email to the address below. Thank you for your time. Aaron J Mackey #422 Reed College 3203 SE Woodstock Blvd. Portland, OR 97202-8199 (503) 775-1523 email: amackey@reed.edu From owner-proteins@net.bio.net Sat Mar 04 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!rutgers!umdnj!njmsa!upperman From: upperman@njmsa.UMDNJ.EDU (Jeffrey Upperman) Subject: rat TNFa cross react with human endo./or neutrophil Message-ID: Summary: does rat TNFa cross react with human endo. or neutrophil Keywords: rat TNFa, endothelial cells, neutrophil Sender: news@umdnj.edu () Organization: Univ. of Medicine and Dentistry of NJ Date: Sun, 5 Mar 1995 22:28:30 GMT Lines: 13 does anybody know if rat tumor necrosis alpha cross reacts with human endothelial cells or neutrophils? thanks -- Jeffrey S. Upperman,MD Internet: upperman@umdnj.edu Research Fellow Voice: (201) 982-4474 Dept. Anatomy, Cell Biology & Injury Fax: (201) 982-6803 Dept. of Surgery Beeper: (201) 708-4150 New Jersey Medical School Office: (201) 982-5045 185 S. Orange Ave., G606 Lab: (201) 982-5404 Newark, NJ 07103 From owner-proteins@net.bio.net Sat Mar 04 22:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!caen!msunews!harbinger.cc.monash.edu.au!news.uwa.edu.au!newsman.csu.murdoch.edu.au!newsman.csu.murdoch.edu.au!usenet From: Jim Cummins Newsgroups: bionet.molbio.proteins Subject: Oxidoreductase on sperm? Date: 6 Mar 1995 06:32:53 GMT Lines: 10 Message-ID: <3jeaalINNi8m@newsman.murdoch.edu.au> NNTP-Posting-Host: vetmac3.murdoch.edu.au Current ideas about the role of reactive oxygen species in mediating (human) sperm dysfunction seem to centre on excess sperm cytoplasm and membrane-bound NADH-dependant oxidoreductase. PMOR has been found in all eukaryotic cells studied so far (see Larm et al 1994 J Biol Chem 269: 30097-30100). However, has anyone yet demonstrated that this enzyme exists on the sperm? From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!warwick!bham!usenet From: altabios@bham.ac.uk (John E. Fox) Newsgroups: bionet.molbio.proteins Subject: Re: Peptides on the head of a Pin? Date: 6 Mar 1995 13:06:32 GMT Organization: Alta Bioscience Lines: 26 Message-ID: <3jf1co$2m7@sun4.bham.ac.uk> References: <3iu5ko$eoh@gatekeeper.genencor.com> NNTP-Posting-Host: bcs118.bham.ac.uk X-Newsreader: WinVN 0.90.6 In article <3iu5ko$eoh@gatekeeper.genencor.com>, Joanne Petithory jpetithory@genencor.com says: > > > > > > I'm looking for information on commercial suppliers of epitope mapping kits based on the 'pin' > peptide synthesis technique of Geysen and coworkers (J. Immunol. Methods 102:259, 1987). > I know that at one point Cambridge Research Biochemicals in Delaware sold an > 'Epitope Scanning Kit', but the person who answered their 800 number informed me > that they no longer sell this kit in the US, and could not/ would not tell me what company > did sell a kit in the US based on the "pin" peptide synthesis technology. > > Thanks, > > Joanne Petithory > Genencor International > jpetithory@genencor.com > > > I think this has been bought up by Genosys Biotechnologies Inc. Texas. have got this as an email 100140.2401@compuserve.com John Fox From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!uunet!world!rbb From: rbb@world.std.com (robert b burrows) Subject: disulfide-linked proteins Message-ID: Organization: The World Public Access UNIX, Brookline, MA Date: Tue, 7 Mar 1995 02:33:24 GMT Lines: 9 We are curious as to how often different gene products are covalently linked. Collagen and immunoglobins are examples, and I think skin keratins are, too. Can anyone think of other examples? -- Robert Burrows rbb@world.std.com From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!oleane!jussieu.fr!univ-lyon1.fr!ghost.dsi.unimi.it!news.unige.it!nikita.ibf.unige.it!user From: vakula@ibf.unige.it (Sergei Vakula) Newsgroups: bionet.molbio.proteins Subject: Re: Stability of proteins... Date: Sat, 04 Mar 1995 12:39:55 +0100 Organization: Institute of Biophysics Lines: 22 Message-ID: References: NNTP-Posting-Host: 130.251.105.50 > I am looking for any and all info/references on the stability of proteins on > transferral from aqueous to apolar solvents.... Apart from Klibanov, check also all the works of the group he worked with before leaving for the States - the group of Martinek, Levashov A.V., Klyachko N.L., Khmelnitskii, Kabanov A.V. (beware - not Kabanov V.A., that's his Dad!), and some others, mostly Mozhaev V.V. However, these key-names should be enough to do some search. They worked on proteins in apolar solvents, in water and water-organic solvent containing reversed micelles. Also check the group of Luisi P.-L. at the ETH of Zurich, the group of Drost-Hansen in Florida, the work of Hutton T. (don't remember his whereabouts!) If it is not enough to keep you working for a week, get in touch with me, maybe I'll be able to remember some others. Cheers, S. Vakula vakula@ibf.unige.it From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!rutgers!gatech!newsxfer.itd.umich.edu!news.itd.umich.edu!174.52.med.umich.edu!user From: Daniel.L.Burgess@um.cc.umich.edu (Daniel L. Burgess) Newsgroups: bionet.molbio.proteins Subject: Antigenicity? Date: Mon, 06 Mar 1995 18:10:42 +0000 Organization: University of Michigan, Dept. of Human Genetics Lines: 29 Message-ID: NNTP-Posting-Host: 174.52.med.umich.edu Greetings, I'm trying to choose regions of a new cDNA/protein we've cloned to put into pMAL (MBP-fusion vector) as a prelude to making pABs. It's a member of a large and VERY (sigh) conserved gene superfamily so there are only a few regions I've identified that are likely to be specific and not cross-react. There is one region of about 62 aa and a handful of from 20-30 aa. My questions are these: (1) Are there any programs (or servers) available that will determine whether the regions I've chosen are likely to be antigenic? Free ones preferably. (2) Are there any feelings on smaller size limits for antigenic peptides (ie. will 20-30 aa work often/sometimes/never in this system)? (3) Are there any other hints or suggestions on how to proceed in such cases, where you need specific pABs to differentiate between members of large, conserved gene families. I'm new to protein work and would greatly appreciate any suggestions. Please respond to my E-mail and I will post a summary of the responses. Thanks in advance. Dan Burgess Univ. of Michigan Dept. of Human Genetics Daniel.L.Burgess@um.cc.umich.edu -- Positional cloning...it's not the kill, it's the thrill of the chase. From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!ns1.faseb.org!darwin.sura.net!mother.usf.edu!com1!acannons From: acannons@com1.med.usf.edu (Andrew Cannons) Newsgroups: bionet.molbio.proteins Subject: FAD Date: 6 Mar 1995 22:01:28 GMT Organization: University of South Florida Lines: 7 Message-ID: <3jg0no$pq0@mother.usf.edu> NNTP-Posting-Host: com1.med.usf.edu X-Newsreader: TIN [version 1.2 PL2] Hi: Does anyone have a direct method to identify bacteria on a plate that are over expressing a protein containing FAD? That is to be able to visualize the FAD directly? Thanks From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!msunews!netnews.upenn.edu!netaxs.com!osias From: osias@netaxs.com (Brian Osias) Newsgroups: bionet.molbio.proteins Subject: DUCKWEED, PROTEIN SYNTHESIS Date: 6 Mar 1995 21:42:15 GMT Organization: Netaxs Internet BBS and Shell Accounts Lines: 14 Message-ID: <3jfvjn$5oj@netaxs.com> NNTP-Posting-Host: unix1.netaxs.com X-Newsreader: TIN [version 1.2 PL2] Dear Reader, My name is Daniel Osias and I am a ninth grade student participating in Science Fair. My project is the effect of different pH environments on Lemna minor. I am having trouble finding information on the topics of duckweed, protein synthesis, and the pH scale. It would be deeply appreciated if you could send me information. Sincerely, Daniel Osias -- --- Daniel Osias * osias@netaxs.com From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!uunet!in1.uu.net!ftpbox!news.acns.nwu.edu!uicvm.uic.edu!u12201 Organization: University of Illinois at Chicago, ADN Computer Center Date: Mon, 6 Mar 1995 12:30:19 CST From: Message-ID: <95065.123019U12201@uicvm.uic.edu> Newsgroups: bionet.molbio.proteins Subject: Companies with E-mail / Gopher / WWW Lines: 2 Is there a list of companies that have E-mail/Gopher/WWW anywhere ? preferably searchable. From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!ZOOL.UMD.EDU!GOODE From: GOODE@ZOOL.UMD.EDU ("Dennis Goode") Newsgroups: bionet.molbio.proteins Subject: Re: Microtubules Date: 6 Mar 1995 12:11:55 -0800 Organization: University of Maryland Zoology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <16AC5273047@zool.umd.edu> NNTP-Posting-Host: net.bio.net porter@warp.phy.nau.edu wrote on the Subject: Microtubules > Date: 3 Mar 1995 16:41:06 GMT : <3j7gr2$k3p@ruby.ucc.nau.edu> > I am looking for a source of MTP (microtubule protein) or tubulin dimer. We wish > to polymerize the protein into microtubles for high resolution imaging in an atomic force > microscope. We have several recepies for this polymerization process, but we are > lacking the MTP or tubulin dimer. Any help in obtaining this material would be > greatly appreciated. > Porter: Tubulin or MT protein is usually purified from calf or pig brains and is not a simple procedure for the uninitiated. I suggest you collaborate with a microtubule lab in your area so they can do the preparation. Where are you located? -Dennis Goode> From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!nntp-ucb.barrnet.net!onyx-pharm.com!dbl.onyx-pharm.com!user From: jlitts@onyx-pharm.com (Jim Litts) Newsgroups: bionet.molbio.proteins Subject: Re: HELP: dialysis of protein Followup-To: bionet.molbio.proteins Date: Mon, 06 Mar 1995 09:38:06 -0700 Organization: Onyx Pharmaceuticals Lines: 34 Distribution: world Message-ID: References: <1995Feb24.080009.42766@cc.usu.edu> <3jaa0j$jfd@news.duke.edu> <1995Mar4.182321.1@mscf.med.upenn.edu> NNTP-Posting-Host: dbl.onyx-pharm.com In article <1995Mar4.182321.1@mscf.med.upenn.edu>, pathology@mscf.med.upenn.edu wrote: > >> NAME RAVI PRAKASH .D (sl16s@cc.usu.edu) wrote: > >> : Dear Netters, > >> : I have attempted to dialyse a recombinant protein (in 0.5M NaCl, 300mM > >> : imidazole, 6M urea) into buffer with 150mM NaCl, 20mM tris, > 2.5mM CaCl2. Within > >> : few minutes of dialysis there is a precipitate > formation in my dialysis bag. > >> : Can anyone have any suggestions as to how I can rescue my protein from the > >> : precipitate? Or any better way to dialyse the protein in future? > >> : Thankyou in advance for any suggestions or comments. > > > We have experienced similar problems with our proteins and have currently adopted a general approach that has been successful in the two instances we've tried so far. That is to set up a series of dialysis solutions from pH 6 to 9, with salt from 0 to 0.5 M, and plus or minus a detergent (usually NP40, but octyl glucoside is generally better in dialysis) and place 1 ml aliquots of our sample in each. This approach has allowed us to "map" a proteins "solubility space" quickly while only exposing a relatively small amount to precipitation. We have also taken samples that precipitate and returned them to a non-precipitating condition to test for reversibility of the precipitation. The little 'slide-alyzer' dialysis chambers from Pierce have been useful in this protocol, though I'm sure a series of bags would be just as effective. This approach takes some of the guess work out of the experiment, and I have found it very difficult to predict how a protein is going to behave based upon the behavior of other proteins. They're all so individual, you know... ;-) Good luck! Jim From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!sunsite.doc.ic.ac.uk!sunews!suma1!abskhuri From: abskhuri@reading.ac.uk (S. Khuri) Newsgroups: bionet.molbio.proteins Subject: native PAGE gels Date: 6 Mar 1995 17:30:38 GMT Organization: University of Reading, U.K. Lines: 7 Message-ID: <3jfgru$ddm@susscsc1.rdg.ac.uk> NNTP-Posting-Host: suma1.reading.ac.uk X-Newsreader: TIN [version 1.2 PL2] Does anyone out there have any information about native PAGE gels? The books only seem to skim over the subject, are there any Idiot's Guides out there that I could have a look at? Thanks!! Sawsan Khuri From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!sunic!trane.uninett.no!daresbury!bioftp.unibas.ch!citi2.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.rwth-aachen.de!newsserver.rrzn.uni-hannover.de!deimos.rz.Uni-Osnabrueck.DE!zeder.biologie.Uni-Osnabrueck.DE!engel From: engel@zeder.biologie.Uni-Osnabrueck.DE (Siggi Engelbrecht) Newsgroups: bionet.molbio.proteins Subject: chloroplast chaperones Date: 6 Mar 1995 14:49:19 GMT Organization: Uni Osnabrueck, Germany Lines: 5 Distribution: world Message-ID: <3jf7df$6ma@deimos.rz.Uni-Osnabrueck.DE> Reply-To: engel@zeder.biologie.Uni-Osnabrueck.DE NNTP-Posting-Host: zeder.biologie.uni-osnabrueck.de Keywords: cpn60, cpn24, hcsp70 X-Newsreader: mxrn 6.18-24 I wonder whether there is a commercial source for the spinach chloroplast chaperones cpn60/24 and the spinach chloroplast hsp70? Addresses where one could get expression vectors coding for one or several of the above are also most welcome. Thanks. Sig From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!warwick!griffin.nott.ac.uk!unicorn.nott.ac.uk!macfd.biochem.nottingham.ac.uk!user From: mbxfd@unicorn.nott.ac.uk (Fergus Doherty) Newsgroups: bionet.molbio.proteins Subject: Slow running SDSPAGE gels answered Followup-To: bionet.molbio.proteins Date: 6 Mar 1995 14:35:36 GMT Organization: Nottingham University, UK. Lines: 26 Distribution: world Message-ID: NNTP-Posting-Host: macfd.biochem.nottingham.ac.uk Many thanks to all those who replied to my question about our problem with slow running SDS mini-gels. I think the problem is solved and is embarassing to explain - but what the heck. I use the Hoeffer mini-gel system. The problem occurred mostly when my technician ran the gels (honestly!), and he made up more electrode buffer than me and poured any excess after filling the upper chamber into the lower chamber. If there is only one gel on the rig then the unused upper chamber electrode (which actually goes down to the bottom of the core) can be covered with buffer from the lower compartment! Running at constant current this must mean that the current actually passing through the gel is very small (presumably teh voltage is low, we never check that). Anyway, if you just put a glass plate where the second gel should go and hide the spare electrode then the gels run much quicker. OK, so I haven't experimented with it yet to check this all out, but so far all the gels have run in the normal time. Someone did suggest this - (thanks AG Goetz, thanks to all). What a twit I am. BTW storing home-made gels is definitely not the problem. We store them wrapped in cling film in a moist box in the fridge. Fergus Doherty, dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH Tel: 602 709366 FAX 602 422225 Internet: mbxfd@unicorn.nott.ac.uk From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!pipex!uknet!daresbury!not-for-mail From: HERNDZA Newsgroups: bionet.molbio.proteins Subject: Help needed with Ca-Transport assays Date: 6 Mar 1995 14:19:30 -0000 Lines: 14 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3jf5li$52v@mserv1.dl.ac.uk> Sensitivity: Company-Confidential Original-To: proteins@dl.ac.uk (Non Receipt Notification Requested) (IPM Return Requested) Hi I am working on Ca-transport across plasma membrane in fungi. I have, so far, found a 'P'-Type Ca-ATPase of which I should like to determine its kinetic parameters (Km, Vmax, Ki's). However, I am encountering some problems when I vary the conc. of Ca or ATP in the assay, although I think I am taking into account the changes in ionic strength etc. and I vary the Ca/EGTA buffer accordingly. Is there anyone in the net that have done such experiments in other systems?. Any help would be much appreciated. Agustin Hernandez e-mail: Agustin.Hernandez@BBSRC.ac.uk From owner-proteins@net.bio.net Sun Mar 05 22:00:00 1995 Path: biosci!rutgers!gatech!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!msunews!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!unsw.edu.au!newt.phys.unsw.edu.au!sjt From: sjt@newt.phys.unsw.edu.au (Sarah Tilley) Newsgroups: bionet.molbio.proteins Subject: Lysozyme molar absorption coefficient? Date: 6 Mar 1995 23:40:17 GMT Organization: School of Physics/University of NSW Lines: 10 Distribution: world Message-ID: <3jg6h1$5nl@mirv.unsw.edu.au> Reply-To: sjt@newt.phys.unsw.edu.au (Sarah Tilley) NNTP-Posting-Host: newt.phys.unsw.edu.au X-Newsreader: dxrn 6.18-4 -- Hi, I want to check some spurious results I am getting when trying to determine my protein's concentration at 280nm. I want to use a Lyzozyme standard to check the spec but I can't find the molar absorption coefficient anywhere. Does anyone happen to know what it is? Thanks, ** Sarah Tilley sjt@newt.phys.unsw.edu.au From owner-proteins@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!rgs From: rgs@mole.bio.cam.ac.uk (Robert Solomon (Bioc)) Newsgroups: bionet.molbio.proteins Subject: Re: native PAGE gels Date: 7 Mar 1995 11:17:09 GMT Organization: U. of Cambridge, England Lines: 22 Message-ID: <3jhfbl$5ai@lyra.csx.cam.ac.uk> References: <3jfgru$ddm@susscsc1.rdg.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk abskhuri@reading.ac.uk (S. Khuri) writes: > >Does anyone out there have any information about native PAGE gels? >The books only seem to skim over the subject, are there any Idiot's Guides >out there that I could have a look at? >Thanks!! >Sawsan Khuri Well, there's always "An Idiot's Guide To Native PAGE Gels", normally carrying the title.. "Gel Electrophoresis; A Practical Approach", edited by B.D. Hames. Note that the 'normal' stack at pH6.8, resolve at pH8.8, tris-Glycine running buffer system actually stacks at ca. pH8.3 and separates at nearer pH9.5, which may not be "native" for your particular protein, but alternative buffering systems are mentioned. Good luck Rob Solomon From owner-proteins@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!rutgers!gatech!newsxfer.itd.umich.edu!news.itd.umich.edu!133.233.med.umich.edu!cascas From: Luis Diaz Newsgroups: bionet.molbio.proteins Subject: Protein Homology Date: 8 Mar 1995 01:35:55 GMT Organization: University of MIchigan Lines: 12 Distribution: world Message-ID: <3jj1lr$k15@lastactionhero.rs.itd.umich.edu> NNTP-Posting-Host: 133.233.med.umich.edu X-UserAgent: Version 1.1.3 X-XXMessage-ID: X-XXDate: Tue, 7 Mar 95 20:39:19 GMT I am looking for a computer program for the Macintosh, that will allow me to compare protein sequences. I've used Entrez to identify proteins with homology to the one I am studying, but it does not show where in the sequence this homology exists. Thanks for the help. Luis Diaz Graduate Student Univ. of Michigan cascas@umich.edu From owner-proteins@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!psuvax1!news.cc.swarthmore.edu!netnews.upenn.edu!dsinc!ub!netfs.dnd.ca!dgbt!nott!nrcnet0.nrc.ca!nrcbsa!phi From: phi@nrcbsa.bio.nrc.ca (Dr. Barry Phipps) Newsgroups: bionet.molbio.proteins Subject: test2 - please ignore Date: 7 Mar 1995 13:48:50 GMT Organization: National Research Council, Canada Lines: 17 Message-ID: <3jho82$k3i@nrcnet0.nrc.ca> NNTP-Posting-Host: nrcbsa.bio.nrc.ca X-Newsreader: TIN [version 1.2 PL2] This is a test - please ignore. -- --------------------------------- Barry M. Phipps Institute for Biological Sciences National Research Council Building M-54, Montreal Road Ottawa, Ontario CANADA K1A 0R6 E-mail: phi@nrcbsa.bio.nrc.ca Phone: (613) 990-0889 Fax: (613) 941-4475 --------------------------------- From owner-proteins@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!agate!usenet.hana.nm.kr!xpat.postech.ac.kr!news.kreonet.re.kr!sorak.kaist.ac.kr!cojoe From: cojoe@sorak.kaist.ac.kr (doo yeon kim) Newsgroups: bionet.molbio.proteins Subject: Connexin 26 antibody Date: 8 Mar 1995 05:55:20 GMT Organization: Korea Research Environment Open Network (KREONet) Lines: 5 Message-ID: <3jjgs8$mnk@news.kreonet.re.kr> NNTP-Posting-Host: sorak.kaist.ac.kr X-Newsreader: TIN [version 1.2 PL2] I need connexin 26 antibodies to explore the differentiation-stage-specific expresstion of gap junction protein. Where can I get these antibodies ? Any information regarding these antibodies will be greatly appreciated. Kaist. dpt of biological science From owner-proteins@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!rutgers!gatech!news-feed-1.peachnet.edu!insosf1.infonet.net!news.kreonet.re.kr!worak.kaist.ac.kr!usenet From: jylee Newsgroups: bionet.molbio.proteins Subject: demethylation activity Date: 8 Mar 1995 04:14:22 GMT Organization: Korea Advanced Institute of Science and Technology Lines: 31 Message-ID: <3jjauu$2bh@worak.kaist.ac.kr> NNTP-Posting-Host: hskim.kaist.ac.kr Hi Bionetters I am not sure whether this is right place to post this. If this is not, please forgive me. Recently, I am studying on the *** enzyme from Pseudomonas. What I feel interested most is that this enzyme shows demethylation activity in vivo in addition to its original activity. But upon purification, demethylation activity was completely lost, only its original activty was left. I checked this out by LC/MS. I know that biological demethylation by an enzyme itself is hard to occur due to the chemical inertness of methyl moiety. Any information regarding the enzyme able to methylate/demethylate substrate would be apprecited. Personal communication at jylee@chiak.kaist.ac.kr is especially appreciated. I am looking forwared to hearing your reply. Thanks. Jang Young Lee ,Dept.Biotech.KAIST Tel) 82-42-869-2656 Fax) 82-42-869-2610 E-mail) jylee@chiak.kaist.ac.kr From owner-proteins@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!imb.lan.nrc.ca!RossN From: RossN@imb.lan.nrc.ca Newsgroups: bionet.molbio.proteins Subject: Re-Lysozyme molar absorption coefficient Date: 7 Mar 1995 04:44:51 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 38 Sender: daemon@net.bio.net Distribution: world Message-ID: <2F5C5539@coursmtp.nrc.ca> CRC's Practical handbook of Biochemistry and Molecular Biology (Fasman, GE, Ed) (1989 or 1990) has molar extinction coefficients for several proteins, including different forms of lysozyme. Molar extinction coefficient for egg white lysozyme ranges from 36,000 to 39,000 M-1 cm-1 (or A(1%) = 24.7 - 26.5 cm-1) depending on buffer. Hope this is helpful, Neil W. Ross, Ph.D. National Research Council Canada Institute for Marine Biosciences 1411 Oxford St., Halifax, NS B3H 3Z1 (902)426-8402 FAX (902) 426-9413 Email: ROSSN@imb.lan.nrc.ca ------------------------------------------------------------------------------ FORWARDED FROM: Ross, Neil W. Return-Path: To: proteins@net.bio.net From: sjt@newt.phys.unsw.edu.au (Sarah Tilley) Subject: Lysozyme molar absorption coefficient? Date: 6 Mar 1995 23:40:17 GMT Message-Id: <3jg6h1$5nl@mirv.unsw.edu.au> Reply-To: sjt@newt.phys.unsw.edu.au (Sarah Tilley) Nntp-Posting-Host: newt.phys.unsw.edu.au X-Newsreader: dxrn 6.18-4 -- Hi, I want to check some spurious results I am getting when trying to determine my protein's concentration at 280nm. I want to use a Lyzozyme standard to check the spec but I can't find the molar absorption coefficient anywhere. Does anyone happen to know what it is? Thanks, ** Sarah Tilley sjt@newt.phys.unsw.edu.au From owner-proteins@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!uunet!world!decwrl!tribune.usask.ca!duke.usask.ca!prabhuv From: prabhuv@duke.usask.ca (Vikram Prabhu) Newsgroups: bionet.molbio.proteins Subject: Re: native PAGE gels Date: 7 Mar 1995 14:41:22 GMT Organization: University of Saskatchewan Lines: 27 Message-ID: <3jhrai$fo3@tribune.usask.ca> References: <3jfgru$ddm@susscsc1.rdg.ac.uk> <3jhfbl$5ai@lyra.csx.cam.ac.uk> NNTP-Posting-Host: duke.usask.ca X-Newsreader: TIN [version 1.2 PL2] Robert Solomon (Bioc) (rgs@mole.bio.cam.ac.uk) wrote: : abskhuri@reading.ac.uk (S. Khuri) writes: : > : >Does anyone out there have any information about native PAGE gels? : >The books only seem to skim over the subject, are there any Idiot's Guides : >out there that I could have a look at? : >Thanks!! : >Sawsan Khuri : Well, there's always "An Idiot's Guide To Native PAGE Gels", normally : carrying the title.. : "Gel Electrophoresis; A Practical Approach", edited by B.D. Hames. : Note that the 'normal' stack at pH6.8, resolve at pH8.8, tris-Glycine : running buffer system actually stacks at ca. pH8.3 and separates at : nearer pH9.5, which may not be "native" for your particular protein, : but alternative buffering systems are mentioned. : Good luck : Rob Solomon In addition to the above book, I had earlier posted this ref: "Protein Methods" Bollag and Edelstein which has chapters on PAGE, practical I might add. What PAGE equipment are you using, a minigel? Vik Prabhu From owner-proteins@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!uunet!ftpbox!news.acns.nwu.edu!uicvm.uic.edu!u12201 Organization: University of Illinois at Chicago, ADN Computer Center Date: Tue, 7 Mar 1995 12:00:27 CST From: Message-ID: <95066.120027U12201@uicvm.uic.edu> Newsgroups: bionet.molbio.proteins Subject: Re: HELP: dialysis of protein Distribution: world References: <1995Feb24.080009.42766@cc.usu.edu> <3jaa0j$jfd@news.duke.edu> <1995Mar4.182321.1@mscf.med.upenn.edu> Lines: 5 I have used the Pierce Slide-A-Lyzers that JLItts recommend also, with good results. I can not E-mail JLitts on this address, or at least I get error messages of undeliverability. Pierce has E-mail: PierceChem@mcimail.com **** From owner-proteins@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!ix.netcom.com!netcomsv!netcomsv!gatekeeper.genencor.com!usenet From: Joanne Petithory jpetithory@genencor.com Newsgroups: bionet.molbio.proteins Subject: Re: Peptides on the head of a Pin? Date: 6 Mar 1995 20:40:12 GMT Organization: Genencor International, South San Francisco, CA Lines: 15 Message-ID: <3jfrvc$obq@gatekeeper.genencor.com> References: <3iu5ko$eoh@gatekeeper.genencor.com> NNTP-Posting-Host: 10.1.1.19 X-Newsreader: AIR News 3.X (SPRY, Inc.) > Joanne Petithory jpetithory@genencor.com writes: > > I'm looking for information on commercial suppliers of epitope mapping kits based on the 'pin' > peptide synthesis technique of Geysen and coworkers (J. Immunol. Methods 102:259, 1987). Thanks to the many who have responded! Here is what I have found out, in case anyone else needs this info: ICN/Cambridge Research Biochemicals used to carry kits both for the PIN method, and for a SPOTS method where the peptides are synth'd on a membrane. In the latter case the peptides cannot be cleaved from the membrane support. Chiron Mimetopes in San Diego (619-455-3710) now carries the PIN kit, & the SPOTS kit is now being marketed by Genosys in Texas (1-800-234-5362). From owner-proteins@net.bio.net Mon Mar 06 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!nova.puug.pt!news.rccn.net!ciup2.ncc.up.pt!khyber.ncc.up.pt!fc1!pbalexan From: pbalexan@fc1.fc.up.pt (Paulo Barros Alexandrino) Newsgroups: bionet.molbio.proteins Subject: Immunobloting of Albumin... Date: 7 Mar 1995 13:22:08 GMT Organization: Universidade do Porto Lines: 9 Message-ID: <3jhmm0$ndb@khyber.ncc.up.pt> NNTP-Posting-Host: fc1.fc.up.pt X-Newsreader: TIN [version 1.2 PL2] : Dear All : I would like to know what kind of blocking agent would be advisable : to employ for immunological probing of albumin after transfering the : protein to a nitrocellulose matrix. Use of gelatin or non-fat milk : is yelding a too undesirable background. : Thanking in advance any answers... : Paulo Alexandrino : University of Porto, PORTUGAL : E-mail: pbalexan@fc1.fc.up.pt From owner-proteins@net.bio.net Tue Mar 07 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!msunews!netnews.upenn.edu!news.amherst.edu!news.mtholyoke.edu!world!news.bu.edu!rmandel From: rmandel@bu.edu (Richard Mandel) Newsgroups: bionet.molbio.proteins Subject: Re: HELP: dialysis of protein Date: 8 Mar 1995 16:39:54 GMT Organization: Boston University Lines: 30 Message-ID: <3jkmkq$snr@news.bu.edu> References: <1995Feb24.080009.42766@cc.usu.edu> NNTP-Posting-Host: acs.bu.edu X-Newsreader: TIN [version 1.2 PL0] NAME RAVI PRAKASH .D (sl16s@cc.usu.edu) wrote: : Dear Netters, : I have attempted to dialyse a recombinant protein (in 0.5M NaCl, 300mM : imidazole, 6M urea) into buffer with 150mM NaCl, 20mM tris, 2.5mM CaCl2. Within : few minutes of dialysis there is a precipitate formation in my dialysis bag. : Can anyone have any suggestions as to how I can rescue my protein from the : precipitate? Or any better way to dialyse the protein in future? : Thankyou in advance for any suggestions or comments. You could try using a linear gradient for the dialysis to more slowly remove the urea from the buffer. Use two beakers, the first with the final buffer the second with the starting buffer with a filled tube connecting them. Place the second buffer on a stirrer but have the levels of the two beakers equal. Finally hook up a tube from the second beaker to a small flask containing the dialysis bag and a small volume of the starting buffer. Seal the top of the flask with a two hole stopper, having an input and outlet and control the rate of throughput to give a gradual change in the solution that bathes the dialysis bag. I hope that is comprehensible. -- Ciao, Rich --------------------------------------------------------------------------- Richard Mandel | E-mail address: rmandel@acs.bu.edu Boston Univ. School of Medicine | Phone No. 617-638-4512 Boston, MA 02118 | Fax No. 617-638-4085 ----------------------------------------------------------------------------- From owner-proteins@net.bio.net Tue Mar 07 22:00:00 1995 Path: biosci!rutgers!gatech!newsxfer.itd.umich.edu!agate!usenet.hana.nm.kr!xpat.postech.ac.kr!news.kreonet.re.kr!sorak.kaist.ac.kr!cojoe From: cojoe@sorak.kaist.ac.kr (Yoosik Yoon) Newsgroups: bionet.molbio.proteins Subject: poly(ADP-ribose)polymerase antibody Date: 8 Mar 1995 13:11:28 GMT Organization: Korea Research Environment Open Network (KREONet) Lines: 4 Message-ID: <3jkae0$8ad@news.kreonet.re.kr> NNTP-Posting-Host: sorak.kaist.ac.kr X-Newsreader: TIN [version 1.2 PL2] I have an interest in the role of poly(ADP-ribosylation) during apoptosis induced by radiation or anticancer drugs. I want to get some antibody against poly(ADP-ribose)polymerase. If any of you would kindly provide the antibody, I will be greatly appreciated. Any information about the antibody will be wellcomed. Yoo Sik Yoon KAIST From owner-proteins@net.bio.net Tue Mar 07 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!uunet!ftpbox!news.acns.nwu.edu!uicvm.uic.edu!u12201 Organization: University of Illinois at Chicago, ADN Computer Center Date: Wed, 8 Mar 1995 09:19:13 CST From: Message-ID: <95067.091913U12201@uicvm.uic.edu> Newsgroups: bionet.molbio.proteins Subject: Re: Immunobloting of Albumin... References: <3jhmm0$ndb@khyber.ncc.up.pt> Lines: 2 I have succesfully used "SuperBlock" from Pierce Chemical. They are distributed in Portugal by Quimigranel From owner-proteins@net.bio.net Tue Mar 07 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!news.itd.umich.edu!usenet From: Rick Neubig Newsgroups: bionet.molbio.proteins.7tms_r,bionet.molbio.proteins Subject: Ultracold storage Date: 9 Mar 1995 00:01:21 GMT Organization: University of Michigan Lines: 15 Message-ID: <3jlggi$41c@lastactionhero.rs.itd.umich.edu> NNTP-Posting-Host: pm002-24.dialip.mich.net Xref: biosci bionet.molbio.proteins.7tms_r:199 bionet.molbio.proteins:3929 We just got a new freezer that can go to -86 C and I wondered if anybody had personal experience with storage of G proteins and/or 7tm receptors/membranes at different temperatures. We've always stored them at -70. Do they remain more stable at lower temps (e.g. -80 or -86). My initial reaction was "put it as cold as it gets" but apparently that leads to more problems with frosting up and more stress on motors and compressors. So - at what temperature do you all store your precious G proteins and 7tms_r's and is there any rational basis for the choice? Rick Neubig http://www.umich.edu/~rneubig From owner-proteins@net.bio.net Tue Mar 07 22:00:00 1995 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!chuck.biosci.arizona.edu!user From: Dress@biosci.arizona.edu (Virginia Dress) Newsgroups: bionet.molbio.proteins Subject: Re: Microtubules Followup-To: bionet.molbio.proteins Date: 8 Mar 1995 22:10:42 GMT Organization: University of Arizona Lines: 32 Distribution: world Message-ID: References: <16AC5273047@zool.umd.edu> NNTP-Posting-Host: chuck.biosci.arizona.edu In article <16AC5273047@zool.umd.edu>, GOODE@ZOOL.UMD.EDU ("Dennis Goode") wrote: > > porter@warp.phy.nau.edu wrote on the > Subject: Microtubules > > Date: 3 Mar 1995 16:41:06 GMT > : <3j7gr2$k3p@ruby.ucc.nau.edu> > > > I am looking for a source of MTP (microtubule protein) or tubulin dimer. We wish > > to polymerize the protein into microtubles for high resolution imaging in an atomic force > > microscope. We have several recepies for this polymerization process, but we are > > lacking the MTP or tubulin dimer. Any help in obtaining this material would be > > greatly appreciated. > > > Porter: > > Tubulin or MT protein is usually purified from calf or pig brains > and is not a simple procedure for the uninitiated. I suggest you > collaborate with a microtubule lab in your area so they can do the > preparation. Where are you located? > > -Dennis Goode> I got a flyer/catalog from a new company that will sell you tubulin and MAPs. I can try to find the info if you are not willing to make your own tubulin or can't find anyone that will just give you some. It's not that hard to make. How much tubulin do you need? Ginnie Dress@biosci.arizona.edu From owner-proteins@net.bio.net Tue Mar 07 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!swiss.ans.net!paperboy.amoco.com!cronkite!usenet From: rkdukor@amoco.com@amoco.com (Rina K. Dukor) Newsgroups: bionet.molbio.proteins Subject: ACS Bioinformatics Symposium Date: 8 Mar 1995 15:37:59 GMT Organization: Amoco Corporation Lines: 7 Distribution: world Message-ID: <3jkj0n$5rm@cronkite.amoco.com> Reply-To: rkdukor@amoco.com@amoco.com Keywords: symposium announcement The Computers In Chemistry Division of the American Chemical Society will be holding a symposium on "Bioinformatics" at its national meeting to be held in Chicago, Aug 20-24, 1995. This symposium is directed at presenting the broad view of Bioinformatics as an integration of experiment and computation from biological, biochemical and biophysical studies to solve complex problems. Abstracts for presentations are being solicited which described tools and/or applications of these approaches in areas which may range from therapeutic and diagnostic development in pharmaceuticals and agriculture, to rational protein engineering, biological pathway analysis, genome linkage to disease, etc. For more information, or to submit an abstract, please contact Dr. Michael N. Liebman, Director of Bioinformatics, Vysis, Inc., 3100 Woodcreek Drive, Downers Grove, IL 60515 (708) 271-7190 office; (708) 271-7008 fax or mliebman@amoco.com From owner-proteins@net.bio.net Tue Mar 07 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!rutgers!gatech!howland.reston.ans.net!torn!utnut!oci!news From: Dawn Gray Subject: Re: Northwestern In-Reply-To: <3j5a1j$nj0@news.u.washington.edu> X-Sender: gray@pip Content-Type: TEXT/PLAIN; charset=US-ASCII Message-ID: Sender: news@oci.utoronto.ca Organization: Ontario Cancer Institute - U of Toronto References: <3j5a1j$nj0@news.u.washington.edu> Mime-Version: 1.0 Date: Tue, 7 Mar 1995 20:32:11 GMT Lines: 2 I have only run southwesterns. Have you renatured the protein on your blot? How much protein do you run? (I run 100ug to 200ug per lane). From owner-proteins@net.bio.net Wed Mar 08 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!agate!usenet.hana.nm.kr!news.kreonet.re.kr!sorak.kaist.ac.kr!cojoe From: cojoe@sorak.kaist.ac.kr (Dooyeon Kim) Newsgroups: bionet.molbio.proteins Subject: Need connexin 26 antibody Date: 9 Mar 1995 13:17:39 GMT Organization: Korea Research Environment Open Network (KREONet) Lines: 4 Message-ID: <3jmv5k$m1b@news.kreonet.re.kr> NNTP-Posting-Host: sorak.kaist.ac.kr X-Newsreader: TIN [version 1.2 PL2] I need connexin 26 antibody. Where can I get this antibody. Any information regarding this antibody will be greatly appreciated. Please help me. Doo yeon kim, Dpt of Biological science, KAIST, KOREA From owner-proteins@net.bio.net Wed Mar 08 22:00:00 1995 Path: biosci!rutgers!gatech!swrinde!cs.utexas.edu!news.sprintlink.net!uunet!news.iij.ad.jp!wnoc-tyo-news!news.u-tokyo.ac.jp!t-server!mech.t.u-tokyo.ac.jp!mech.t!yokada From: yokada@kinesin.kaibo1.m.u-tokyo.ac.jp (Yasushi OKADA) Newsgroups: bionet.molbio.proteins Subject: Re: Microtubules Followup-To: bionet.molbio.proteins Date: 9 Mar 1995 11:59:55 GMT Organization: Dept. Anatomy & Cell Biol. Facul. Med. Univ. Tokyo. Lines: 22 Distribution: world Message-ID: References: <16AC5273047@zool.umd.edu> NNTP-Posting-Host: kinesin.kaibo1.m.u-tokyo.ac.jp In-reply-to: Dress@biosci.arizona.edu's message of 8 Mar 1995 22:10:42 GMT In article Dress@biosci.arizona.edu (Virginia Dress) writes: I got a flyer/catalog from a new company that will sell you tubulin and MAPs. I can try to find the info if you are not willing to make your own tubulin or can't find anyone that will just give you some. It's not that hard to make. How much tubulin do you need? Ginnie Dress@biosci.arizona.edu Cytoskeleton and Molecular Probes sell tubulin. Cytoskeleton also sells MAPs, kinesin and actin. But I do not think the purification of tubulin and MAPs is not very difficult. Hope this helps. -- ****************************************************************************** * Yasushi Okada, MD. | Email:yokada@kinesin.kaibo1.m.u-tokyo.ac.jp * * Dept. Anatomy & Cell Biology | Tel:81-3-3812-2111 ext.3336 * * Univ. Tokyo JAPAN | Fax:81-3-5689-4856 * ****************************************************************************** From owner-proteins@net.bio.net Wed Mar 08 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!rzusuntk.unizh.ch!rmf From: rmf@ikc.unizh.ch (Roman Fried) Subject: Re: Immunobloting of Albumin... Message-ID: <1995Mar9.174101.24279@rzu-news.unizh.ch> Sender: newsadm@rzu-news.unizh.ch (CNEWS ADMINISTRATION) Organization: University of Zurich, Switzerland X-Newsreader: TIN [version 1.2 PL2] References: <3jhmm0$ndb@khyber.ncc.up.pt> Date: Thu, 9 Mar 1995 17:41:01 GMT Lines: 48 Paulo Barros Alexandrino (pbalexan@fc1.fc.up.pt) wrote: : : Dear All : : I would like to know what kind of blocking agent would be advisable : : to employ for immunological probing of albumin after transfering the : : protein to a nitrocellulose matrix. Use of gelatin or non-fat milk : : is yelding a too undesirable background. : : Thanking in advance any answers... : : Paulo Alexandrino : : University of Porto, PORTUGAL : : E-mail: pbalexan@fc1.fc.up.pt Dear Paulo In our lab we use the following protocol 1. incubate the nc membrane 1 h in tween-tbs (tris 20mM, NaCl 0.5M, pH 7.5 and 0.3% tween-20 2. 1. antibody over night (in tbs-tween) 3. 2 x 10 min tween-tbs 4. 2. antibody 1h (in tbs-tween) 5. 2 x 10 min tbs (no tween!) 6. detection with chloronaphtol 7. after detection you can do an overall staining using colloidal gold solution i hope this helps regards roman Roman Fried Institut fuer Klinische Chemie Universitaetsspital Zuerich 8091 Zuerich mail rmf@ikc.unizh.ch From owner-proteins@net.bio.net Wed Mar 08 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news2.near.net!news.delphi.com!usenet From: H. David Fischer Newsgroups: bionet.molbio.proteins Subject: Re: Myc Antibody Date: Thu, 9 Mar 95 08:14:52 -0500 Organization: Delphi (info@delphi.com email, 800-695-4005 voice) Lines: 7 Message-ID: References: <199503012044.OAA28447@sequencer.wustl.edu> NNTP-Posting-Host: bos1b.delphi.com X-To: writes: >Does anybody know a commercial source for Myc antibody? Try Berkeley Antibody Company in Richmond, CA (phone 800-92-babco; fax 510-222-1867). Their catalog lists the 9E10 anti-c-myc mAb that recognizes the EQKLISEEDL epitope. From owner-proteins@net.bio.net Wed Mar 08 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!uwvax!uchinews!apollo!usenet From: "William J. Wasserman" Newsgroups: bionet.molbio.proteins Subject: WANTED ACTIVE MAP KINASE KINASE!! Date: 9 Mar 1995 19:00:08 GMT Organization: Loyola University of Chicago Lines: 2 Message-ID: <3jnj7o$do5@apollo.it.luc.edu> NNTP-Posting-Host: pc--5.ls.luc.edu Does anybody have active MAP Kinase Kinase for microinjection into Xenopus oocytes? From owner-proteins@net.bio.net Wed Mar 08 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!quagga.ru.ac.za!nntp.und.ac.za!pc099.cc.unp.ac.za!Berry From: Berry@biochem.unp.ac.za (Ronald.Berry) Newsgroups: bionet.molbio.proteins Subject: Alternative to Starch Gel Electrophoresis? Date: Thu, 9 Mar 1995 10:09:12 GMT Organization: University of Natal , Pietermaritzburg, South Africa Lines: 30 Message-ID: NNTP-Posting-Host: pc099.cc.unp.ac.za Hello Bionetters We routinely do PAGE gels on proteins (usually Hoeffer Mighty Small gels), using traditional Tris/Glycine, and also Tricene buffers. I have had a request from a non-biochemist to do starch gels electrophoresis on plant proteins, with the object of using zymograms to do genetic linkage analysis. Surely starch gels have been superceded by more modern polyacrylamide protocols? Has anyone a protocol for "transfering" a starch gel method to PAGE? Thanks Ron Berry Biochemistry Dept University of Natal PIETERMARITZBURG South Africa Ron Berry Biochemistry Department, University of Natal, Pietermaritzburg. South Africa From owner-proteins@net.bio.net Wed Mar 08 22:00:00 1995 Path: biosci!atlas.rc.m-kasei.co.jp!yao From: yao@atlas.rc.m-kasei.co.jp (Toru YAO) Newsgroups: bionet.molbio.proteins Subject: (none) Date: 9 Mar 1995 14:56:53 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9503092256.AA03546@atlas.rc.m-kasei.co.jp> NNTP-Posting-Host: net.bio.net Unsubscribe From owner-proteins@net.bio.net Thu Mar 09 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!EU.net!Belgium.EU.net!idefix.CS.kuleuven.ac.be!reks.uia.ac.be!news From: bone@reks.uia.ac.be (Darth Vader) Subject: Re: IMPORTANT OPPORTUNITY Message-ID: <1995Mar10.082709.12113@reks.uia.ac.be> Sender: news@reks.uia.ac.be (USENET News System) Organization: University of Antwerp X-Newsreader: Date: Fri, 10 Mar 1995 08:27:09 GMT Lines: 2 ..another one. Cutting access to internet is not enough, I am afraid. This calls for a post-natal abortion... From owner-proteins@net.bio.net Thu Mar 09 22:00:00 1995 Newsgroups: bionet.software,bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!newsxfer.itd.umich.edu!zip.eecs.umich.edu!caen!hearst.acc.Virginia.EDU!murdoch!reed0.med.Virginia.EDU!wrp From: wrp@reed0.med.Virginia.EDU (Bill Pearson) Subject: FASTA 2.0x avaiable X-Nntp-Posting-Host: reed0.med.virginia.edu Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia Date: Fri, 10 Mar 1995 15:45:29 GMT Lines: 41 Xref: biosci bionet.software:11426 bionet.molbio.genbank:1970 bionet.molbio.embldatabank:467 bionet.molbio.proteins:3942 A new (experimental) release of the FASTA program package is now available from virginia.edu in pub/fasta/fasta20x.shar(.Z). Version 2.0x incorporates several major improvements in the FASTA and SSEARCH (Smith-Waterman) sequence searching programs: (1) Explicit statistical estimates are now available from FASTA, TFASTA, and SSEARCH. Expectation values (a la BLAST) are provided for library similarity scores. In addition, raw similarity scores are normalized to correct for the expected length-dependence of similarity scores. The statistical estimates are very accurate for SSEARCH and for FASTA if the "-o" option is used. The "-o" option improves dramatically the performace of FASTA - at a cost in execution time - I recommend strongly that you use it as often as possible for proteins. For DNA it serves no purpose. (2) FASTA now uses the rigorous Smith-Waterman algorithm to produce alignments. Thus, there is no limit to length size in alignments. (3) The BLOSUM50 matrix is now used by default. (4) It is easy to change the penalties for the first residue (now -12 by default) and additional residue (-2) in a a gap. (5) A new alignment option "-m 4", makes it easy to display the part of the query sequence that is aligned to the library sequence. For many protein families, one expects for the alignment to extend from one end of the sequence to the other. This display makes it easy to see when the alignments become much shorter. This version has only been tested for a few weeks, thus the version number 2.0x. Please let me know if you have any problems with it. Bill Pearson wrp@virginia.edu -- wrp@virginia.EDU Dept. of Biochemistry #440 U. of Virginia Charlottesville, VA 22908 From owner-proteins@net.bio.net Thu Mar 09 22:00:00 1995 Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!cc.usu.edu!sl16s From: sl16s@cc.usu.edu (NAME RAVI PRAKASH .D) Newsgroups: bionet.molbio.proteins Subject: SDS PAGE and UREA in sample Message-ID: <1995Mar8.162256.44047@cc.usu.edu> Date: 8 Mar 95 16:22:56 MDT Organization: Utah State University Lines: 6 Dear Netters, Does the presence of Urea in the sample for SDS PAGE have any effect on the migration of the protein samples in the gel? The urea concentration is 5M in my protein and I loaded 15ul of this along with 5ul of 4X sample buffer(Laemli). Any suggestions will be helpfull. From owner-proteins@net.bio.net Thu Mar 09 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!ns1.faseb.org!darwin.sura.net!nih-csl!loglady.ninds.nih.gov!johnk From: johnk@spasm.niddk.nih.gov (John Kuszewski) Subject: Re: IMPORTANT OPPORTUNITY Message-ID: <1995Mar10.165524.26949@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: spasm.niddk.nih.gov Reply-To: johnk@spasm.niddk.nih.gov (John Kuszewski) Organization: National Insts. of Health References: <1995Mar10.082709.12113@reks.uia.ac.be> Date: Fri, 10 Mar 1995 16:55:24 GMT Lines: 19 In article <1995Mar10.082709.12113@reks.uia.ac.be>, bone@reks.uia.ac.be (Darth Vader) writes: |> ..another one. Cutting access to internet is not enough, I am afraid. This |> calls for a post-natal abortion... Actually, the therm you want is "retroactive abortion." 'Twould be appropriate in this case. :-/ -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| From owner-proteins@net.bio.net Thu Mar 09 22:00:00 1995 Path: biosci!ns1.faseb.org!darwin.sura.net!martha.utk.edu!drnelson.utmem.edu!user From: dnelson@utmem1.utmem.edu (David R. Nelson) Newsgroups: bionet.molbio.proteins Subject: mitochondrial carriers Followup-To: bionet.molbio.proteins Date: 10 Mar 1995 16:47:33 GMT Organization: U. Tennessee, Memphis Lines: 18 Message-ID: NNTP-Posting-Host: drnelson.utmem.edu For those interested in mitochondrial carriers, or mitochondrial inner membrane proteins generally, I have included a list of all the mito carriers I could find by blast searching with multiple carriers against the yeast database and against the non-redundant NCBI blast server database. There is also an alignment of mitochondrial carriers (80 sequences) with more to be added soon. There are 20 yeast carriers so far, but only a few have their function identified. The lists and the alignment are available on the World Wide Web at The Dept. of Biochemistry Web server http://drnelson.utmem.edu/homepage.html I am currrently working on assembling this data and it may change frequently, so you might want to check it again in a month or so. -- David R. Nelson Assistant Professor Dept. of Biochemistry University of Tennessee, Memphis From owner-proteins@net.bio.net Thu Mar 09 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!uunet!psinntp!news.worldlink.com!usenet From: "Jim Chinnis" Newsgroups: bionet.molbio.proteins Subject: Type II Collagen Source Date: Fri, 10 Mar 95 17:47:48 -0400 Organization: Decision Science Associates, Inc. Lines: 8 Distribution: world Message-ID: <3003961306.1.p00511@psilink.com> NNTP-Posting-Host: worldlink.com X-Mailer: PSILink-DOS (3.6.2) I am a non-biological scientist who is looking for a simple source of dietary type II collagen for experimentation on myself. I am interested in its impact, if any, on cochlear symptoms (aka Meniere's disease) that I believe may--in my case--represent autoimmune response to type II and possibly type IX collagen. Do I grind up chicken bones, or what? Thanks. From owner-proteins@net.bio.net Thu Mar 09 22:00:00 1995 Path: biosci!FREENET.UFL.EDU!afn08460 From: afn08460@FREENET.UFL.EDU ("Brian A. Hollander") Newsgroups: bionet.molbio.proteins Subject: Re: SDS PAGE and UREA in sample Date: 10 Mar 1995 13:07:36 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <1995Mar8.162256.44047@cc.usu.edu> NNTP-Posting-Host: net.bio.net In my experience it does not as long as you *do not heat* your samples. If you heat them the proteins in your samples will becone carbamylated due to the ionized urea. This probably happens to some extent even without boiling, but It hasn't seemed to affect migration if the samples are processed and loaded at room temp. at least in my hands. BAH On 8 Mar 1995, NAME RAVI PRAKASH .D wrote: > Dear Netters, > Does the presence of Urea in the sample for SDS PAGE have any effect on the > migration of the protein samples in the gel? > The urea concentration is 5M in my protein and I loaded 15ul of this along > with 5ul of 4X sample buffer(Laemli). Any suggestions will be helpfull. > > > From owner-proteins@net.bio.net Thu Mar 09 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news2.near.net!news.delphi.com!news2.delphi.com!not-for-mail From: XYZZYX@news.delphi.com (XYZZYX@DELPHI.COM) Newsgroups: bionet.molbio.proteins Subject: Re: Wanted Lectin A of Lens culinary Date: 11 Mar 1995 01:12:36 -0500 Organization: Delphi Internet Services Corporation Lines: 29 Message-ID: <3jrf0k$j2q@news2.delphi.com> References: NNTP-Posting-Host: news2.delphi.com pcomm@cismibm.univ-lyon1.fr (Pierre Commercon) writes: >Hello >Help, help ! >I need Lens culinaris Lectin A for affinity electrophoresis of a blood protein. >I found only A+B Lectin which is not not good for our use >Can you tell me the company able to sell me this lectin A >Thanks >Pierre >pcomm@cismibm.univ-lyon1.fr I think that Sigma Chemical, USA sells this, they have a huge selection of lectins. Alternatively, you can prepare your own from common lentils by extraction into normal saline or PBS followed by centrifugation to remove debris and lipids. Ammonium Sulfate precipitation will pull down the proteins. Dialyze into PBS and centrifuge out debris, then load onto a column of the appropriate sugar immobilized ontoagarose. I can't recall the specificity at the moment. Elute with more of the same sugar and then dialyze it off. I did this kind of thing about ten years ago, the details are sketchy. If you are interested, I can look into it. George Trager From owner-proteins@net.bio.net Fri Mar 10 22:00:00 1995 Path: biosci!imb.lan.nrc.ca!RossN From: RossN@imb.lan.nrc.ca Newsgroups: bionet.molbio.proteins Subject: Re: Wanted Lectin A of Lens culinary Date: 11 Mar 1995 08:12:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 51 Sender: daemon@net.bio.net Distribution: world Message-ID: <2F61CBE7@coursmtp.nrc.ca> NNTP-Posting-Host: net.bio.net E.Y Laboratories also sells Lens culinaris A lectin as well. Address: P.O. Box 1787, 107 North Amphlett Blvd, San Mateo, CA 94401 USA (415) 342-3296 FAX (415) 342-2648 They also have a good selection of Lectins. Neil W. Ross, Ph.D. National Research Council Canada Institute for Marine Biosciences 1411 Oxford St., Halifax, NS B3H 3Z1 (902)426-8402 FAX (902) 426-9413 Email: ROSSN@imb.lan.nrc.ca ------------------------------------------------------------------------------ FORWARDED FROM: Ross, Neil W. Return-Path: To: proteins@net.bio.net From: XYZZYX@news1.delphi.com (XYZZYX@DELPHI.COM) Subject: Re: Wanted Lectin A of Lens culinary Date: 11 Mar 1995 01:12:36 -0500 Message-Id: <3jrf0k$j2q@news2.delphi.com> Nntp-Posting-Host: news2.delphi.com pcomm@cismibm.univ-lyon1.fr (Pierre Commercon) writes: >Hello >Help, help ! >I need Lens culinaris Lectin A for affinity electrophoresis of a blood protein. >I found only A+B Lectin which is not not good for our use >Can you tell me the company able to sell me this lectin A >Thanks >Pierre >pcomm@cismibm.univ-lyon1.fr I think that Sigma Chemical, USA sells this, they have a huge selection of lectins. Alternatively, you can prepare your own from common lentils by extraction into normal saline or PBS followed by centrifugation to remove debris and lipids. Ammonium Sulfate precipitation will pull down the proteins. Dialyze into PBS and centrifuge out debris, then load onto a column of the appropriate sugar immobilized ontoagarose. I can't recall the specificity at the moment. Elute with more of the same sugar and then dialyze it off. I did this kind of thing about ten years ago, the details are sketchy. If you are interested, I can look into it. George Trager From owner-proteins@net.bio.net Fri Mar 10 22:00:00 1995 Path: biosci!biosci!not-for-mail From: Bill Pearson Newsgroups: bionet.software,bionet.molbio.embldatabank,bionet.molbio.genbank,bionet.announce,bionet.molbio.proteins Subject: FASTA 2.0x available Date: 11 Mar 1995 07:30:55 -0800 Organization: University of Virginia Lines: 40 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:11434 bionet.molbio.embldatabank:468 bionet.molbio.genbank:1972 bionet.announce:1887 bionet.molbio.proteins:3949 A new (experimental) release of the FASTA program package is now available from virginia.edu in pub/fasta/fasta20x.shar(.Z). Version 2.0x incorporates several major improvements in the FASTA and SSEARCH (Smith-Waterman) sequence searching programs: (1) Explicit statistical estimates are now available from FASTA, TFASTA, and SSEARCH. Expectation values (a la BLAST) are provided for library similarity scores. In addition, raw similarity scores are normalized to correct for the expected length-dependence of similarity scores. The statistical estimates are very accurate for SSEARCH and for FASTA if the "-o" option is used. The "-o" option improves dramatically the performace of FASTA - at a cost in execution time - I recommend strongly that you use it as often as possible for proteins. For DNA it serves no purpose. (2) FASTA now uses the rigorous Smith-Waterman algorithm to produce alignments. Thus, there is no limit to length size in alignments. (3) The BLOSUM50 matrix is now used by default. (4) It is easy to change the penalties for the first residue (now -12 by default) and additional residue (-2) in a a gap. (5) A new alignment option "-m 4", makes it easy to display the part of the query sequence that is aligned to the library sequence. For many protein families, one expects for the alignment to extend from one end of the sequence to the other. This display makes it easy to see when the alignments become much shorter. This version has only been tested for a few weeks, thus the version number 2.0x. Please let me know if you have any problems with it. Bill Pearson wrp@virginia.edu -- wrp@virginia.EDU Dept. of Biochemistry #440 U. of Virginia Charlottesville, VA 22908 From owner-proteins@net.bio.net Fri Mar 10 22:00:00 1995 Path: biosci!news.cs.umb.edu!hsdndev!purdue!mozo.cc.purdue.edu!macg203d.bio.purdue.edu!user From: shall@bilbo.bio.purdue.edu (Stephen Hall) Newsgroups: bionet.molbio.proteins Subject: Re: IMPORTANT OPPORTUNITY Date: Sat, 11 Mar 1995 14:29:56 -0800 Organization: Purdue University Lines: 18 Message-ID: References: <1995Mar10.082709.12113@reks.uia.ac.be> <1995Mar10.165524.26949@alw.nih.gov> NNTP-Posting-Host: macg203d.bio.purdue.edu In article <1995Mar10.165524.26949@alw.nih.gov>, johnk@spasm.niddk.nih.gov (John Kuszewski) wrote: > In article <1995Mar10.082709.12113@reks.uia.ac.be>, bone@reks.uia.ac.be (Darth Vader) writes: > |> ..another one. Cutting access to internet is not enough, I am afraid. This > |> calls for a post-natal abortion... > > Actually, the therm you want is "retroactive abortion." > 'Twould be appropriate in this case. :-/ > -- > One responded that this type of posting is evidence that brothers and sisters shouldn't mate. But people like Mr. Haythorn, one of the originators of this posting, and their families have worked at inbreeding for many generations. I mean they should feel a real sense of accomplishment that they have managed to bring the recessive mutation for idiocy into the homozygous state. From owner-proteins@net.bio.net Fri Mar 10 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!agate!newsxfer.itd.umich.edu!gatech!news.Gsu.EDU!news-feed-1.peachnet.edu!news.duke.edu!convex!cs.utexas.edu!news.sprintlink.net!uunet!world!ksm From: ksm@world.std.com (Kris S Moorthi) Subject: 3d map of protein Message-ID: Organization: The World Public Access UNIX, Brookline, MA X-Newsreader: TIN [version 1.2 PL2] Date: Sun, 12 Mar 1995 04:19:03 GMT Lines: 10 I am writing a research paper on a molecular biology project I am working on... I was wondering if anyone might have any idea where I might get an image of a 3d representation of an actin, spectrin, myosin, ankyrin, or related RBC protein. please email me: Jay Moorthi Thanks From owner-proteins@net.bio.net Fri Mar 10 22:00:00 1995 Newsgroups: bionet.software,bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.proteins Path: biosci!rutgers!rockyd!notes From: "Dr. Kent L. Nastiuk" Subject: Re: FASTA 2.0x avaiable X-Nntp-Posting-Host: nastiuk_pc.rockefeller.edu Message-ID: Sender: notes@rockyd.rockefeller.edu (News Administrator) Organization: Rockefeller University References: Date: Sat, 11 Mar 1995 18:53:47 GMT Lines: 14 Xref: biosci bionet.software:11437 bionet.molbio.genbank:1973 bionet.molbio.embldatabank:470 bionet.molbio.proteins:3952 wrp@reed0.med.Virginia.EDU (Bill Pearson) wrote: > > > A new (experimental) release of the FASTA program package is now > available from virginia.edu in pub/fasta/fasta20x.shar(.Z). Version > 2.0x incorporates several major improvements in the FASTA and SSEARCH > (Smith-Waterman) sequence searching programs: > i tried to login to 'virginia.edu' and 'reed0...', but could access neither could you provide better ftp site information, including how to login (ie guest, anonymous, or whatever? thanks From owner-proteins@net.bio.net Fri Mar 10 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!rutgers!rockyd!notes From: sali@tamika.rockefeller.edu (Andrej Sali) Subject: ANNOUNCE: MODELLER new version (homology protein modeling) X-Nntp-Posting-Host: tamika.rockefeller.edu Message-ID: Keywords: homology comparative protein modeling Sender: notes@rockyd.rockefeller.edu (News Administrator) Organization: Rockefeller University Date: Sun, 12 Mar 1995 03:38:00 GMT Lines: 83 ANNOUNCE: MODELLER new version (homology protein modeling) MODELLER PROTEIN MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS MODELLER 12, December 31, 1994 Copyright(c) 1989-1994 Andrej Sali All Rights Reserved Written by Andrej Sali Birkbeck College, University of London, London, UK Imperial Cancer Research Fund, London, UK Harvard University, Cambridge, USA Andrej Sali, Box 270, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. Tel: (212) 327 7550. Fax: (212) 327 7540. E-mail: sali@rockvax.rockefeller.edu. ** DESCRIPTION: MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints (A. Sali & T.L. Blundell. J.Mol.Biol. 234, 779-815, 1993). In principle, the restraints can be derived from a number of different sources. These include homologous structures (comparative modeling), NMR experiments (NMR refinement), rules of secondary structure packing (combinatorial modeling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue-residue and atom-atom potentials of mean force, etc. The output of MODELLER is a 3D structure of a protein that satisfies these restraints as well as possible. The optimization is carried out by the variable target function procedure employing methods of conjugate gradients and molecular dynamics with simulated annealing. MODELLER can also do several other tasks, including multiple comparison of protein sequences and/or structures, clustering, and searching of sequence databases. The program is described in a 120-page manual. MODELLER is written in Fortran and is meant to run on a UNIX system. ** DISTRIBUTION: MODELLER is available free of charge to academic non-profit institutions. First, please use the anonymous ftp account on tammy.harvard.edu (IP 128.103.96.19) to copy at least the following files from the pub/modeller directory to your computer: the license form (PostScript file academic-license.ps), the encrypted distribution file that contains the data files necessary to run MODELLER (modeller12-data.tar.Z.cr), and an executable for each machine type and memory size that you need (described in file INSTALLATION). Next, print, sign, and mail or fax the license form to Andrej Sali. You will then receive the encryption key (MODELLER_KEY) with which you will be able to unpack the encrypted distribution file. See file INSTALLATION for installation instructions. An interface to MODELER is available as part of QUANTA, an interactive molecular modeling program with many tools for protein modeling and structural analysis. QUANTA also includes interfaces to CHARMm for molecular dynamics simulations and X-PLOR for NMR and X-ray structure determination. QUANTA provides a useful graphical interface to MODELLER that facilitates preparation of input files for MODELLER as well as analysis of the results produced by MODELLER; in particular, the preparation of an alignment and evaluation of the models are made much easier by QUANTA/MODELLER combination. If you are interested in QUANTA, please contact Ms. Jo Ellen Collins at Molecular Simulations Inc, 16 New England Executive Park, Burlington, MA 01803-5297, tel: (617) 229 9800, fax: (617) 229 9899, email: jcollins@msi.com. ** CONTENTS: src\ sources or executables for MODELLER; modlib\ libraries and data files for the programs; scripts\ script files used to compile and use MODELLER; doc\ MODELLER documentation; Makefile Makefile for compiling/installing MODELLER modules; modeller12.README this file; INSTALLATION how to install MODELLER; Install compilation and installation script relying on Makefile; tests\ tests and examples; From owner-proteins@net.bio.net Sat Mar 11 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!sunic.sunet.se!news.funet.fi!nntp.utu.fi!sara.cc.utu.fi!pekrappu From: pekrappu@sara.cc.utu.fi (Pekka Rappu) Subject: Human b-galactosidase properties Message-ID: <1995Mar10.153521.1@sara.cc.utu.fi> Lines: 1 Sender: news@utu.fi (Usenet News admin) Nntp-Posting-Host: sara.cc.utu.fi Organization: University of Turku, Finland Date: Fri, 10 Mar 1995 13:35:21 GMT -- From owner-proteins@net.bio.net Sat Mar 11 22:00:00 1995 Newsgroups: bionet.software,bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.proteins Path: biosci!lhc!borduas!francis From: francis@borduas.nlm.nih.gov (Francis Ouellette) Subject: Re: FASTA 2.0x avaiable Message-ID: <1995Mar12.220021.15425@nlm.nih.gov> Followup-To: bionet.software,bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.proteins Sender: news@nlm.nih.gov Organization: National Library of Medicine X-Newsreader: TIN [version 1.2 PL2] References: Date: Sun, 12 Mar 95 22:00:21 GMT Lines: 50 Xref: biosci bionet.software:11444 bionet.molbio.genbank:1974 bionet.molbio.embldatabank:471 bionet.molbio.proteins:3956 Dr. Kent L. Nastiuk (nastiuk@rockvax.rockefeller.edu) wrote: > wrp@reed0.med.Virginia.EDU (Bill Pearson) wrote: > > > > > > A new (experimental) release of the FASTA program package is now > > available from virginia.edu in pub/fasta/fasta20x.shar(.Z). Version > > 2.0x incorporates several major improvements in the FASTA and SSEARCH > > (Smith-Waterman) sequence searching programs: > > > i tried to login to 'virginia.edu' and 'reed0...', but could access neither > could you provide better ftp site information, including how to login > (ie guest, anonymous, or whatever? If you look in Amos Bairoch's 'serv_ftp.txt' document, you will find these coordinates (login anonymous, use your e-mail address as password. -------------------------------------------------------------------- Organiz.: University of Virginia / USA Address : uvaarpa.virginia.edu (128.143.2.7) Programs: Name=FASTA; Desc=database search program; OS=UNIX and DOS; Directory= /pub/fasta Contact : William Pearson; wrp@virginia.edu Status : Tested (30 Sep 1992). -------------------------------------------------------------------- I went to check, and all the files where in the right place ... so if Amos sees this mail, he can update the 'Status' to >> Status : Tested (12 Mar 1995). The latest version of Amos' document is available by anonymous FTP from expasy.hcuge.ch (IP address 129.195.254.61) in the /database/info directory as 'serv_ftp.txt'. This (and many others) is also available from the WWW at this URL: http://expasy.hcuge.ch/info/serv_ftp.txt regards, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov From owner-proteins@net.bio.net Sat Mar 11 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!adam.cc.sunysb.edu!news.nysernet.net!news.sprintlink.net!howland.reston.ans.net!pipex!sunic!sunic.sunet.se!news.funet.fi!nntp.utu.fi!sara.cc.utu.fi!pekrappu From: pekrappu@sara.cc.utu.fi (Pekka Rappu) Subject: Human b-galactosidase properties Message-ID: <1995Mar10.154700.1@sara.cc.utu.fi> Lines: 13 Sender: news@utu.fi (Usenet News admin) Nntp-Posting-Host: sara.cc.utu.fi Organization: University of Turku, Finland Date: Fri, 10 Mar 1995 13:47:00 GMT What are the optimal reaction conditions for human beta-galactosidase? I have been wondering if the activity of the enzyme is considerably lower in processed (i.e. homogenized & pasteurized) milk than in "native" milk. If this is the case, could it be a reason for a fact that there is all the sudden so many people having hypolactasia among the Finnish and other "lactose tolerant" people. Please tell me if I am totally wrong with my ideas. Hypolactasia patient & Post graduate student Pekka Rappu University of Turku Finland -- From owner-proteins@net.bio.net Sun Mar 12 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!ra.nrl.navy.mil!usenet From: Jonathan Walker Newsgroups: bionet.molbio.proteins Subject: How to calculate Protein & Lipid molecules Date: 13 Mar 1995 14:21:38 GMT Organization: Naval Research Laboratory Lines: 30 Message-ID: <3k1kdi$sq5@ra.nrl.navy.mil> NNTP-Posting-Host: kraken.nrl.navy.mil Hello, My background in Lipid, Protein, & Bilayers in Red Cells is not well versed. However, I'm trying to calculate the following: 1) I have a (human) red cell membrane approx. 8nm thick 2) The cell contains 5.2 x 10^-13 grams of lipid (10^-13 = ten to the minus thirteen) 3) Also, the cell contains 6.0 x 10^-13 grams of protein. 4) The lipid has primarily phospholipid (MW 800) & cholestrol (MW386) in a 1:1 molar ratio. 5) Each phospholipid occupies a surface area of 0.55nm^2 per molecules 6) While, the cholesterol occupies a surface area of 0.38nm^2 per molecules 7) The red cell has a surface area of 145um^2. Questions: 1) If we assume an average protein has a molecular weight of 50,000, how many molecules of protein are in a single red cell membrane? 2) What is the ratio of lipid molecules to protein molecules in the red cell membrane?? 3) What proportion of the total surface area of the membrane is occupied by a lipid bilayer??? Thanks in Advance From owner-proteins@net.bio.net Sun Mar 12 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!uhog.mit.edu!rutgers!gatech!swrinde!howland.reston.ans.net!nntp.crl.com!crl2.crl.com!not-for-mail From: labware@crl.com (John Brookes) Newsgroups: bionet.molbio.proteins Subject: For Sale: Discount Lab Glasswa Date: 13 Mar 1995 17:52:27 -0800 Organization: CRL Dialup Internet Access Lines: 9 Message-ID: <3k2ssr$1mf@crl2.crl.com> NNTP-Posting-Host: crl2.crl.com X-Newsreader: TIN [version 1.2 PL2] CyberGlass is offering Laboratory Glassware of all types for sale at discount prices: New............................30% off list price Used (like new condition)......40% off list price Please e-mail us for details! John Brookes From owner-proteins@net.bio.net Sun Mar 12 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!ukc!kiwi.ukc.ac.uk!int From: int@ukc.ac.uk (I.N.Taylor) Newsgroups: bionet.molbio.proteins Subject: Isoelectric focusing gels Date: Mon, 13 Mar 95 09:15:18 GMT Organization: University of Kent at Canterbury, UK. Lines: 29 Sender: int@ukc.ac.uk Distribution: world Message-ID: <738@kiwi.ukc.ac.uk> NNTP-Posting-Host: kiwi.ukc.ac.uk Hello, I'm having a few problems with isoelectric focusing gels. The recipe I use is from the Hoeffer Mighty small tube gel adapter kit. This allows tube IEF gels to be run on a midget SDS-PAGE unit. I have great difficulty in extracting these gels from the tube and keeping them whole. Because of this I am trying to use the same recipe and run vertical slab gels. The gels do not appear to set in the vertical format,they do in the tube gels but I'm wondering wether this has anything to do with capillary action. The recipe is; Total volume 3.5ml contains 1.9g (9.0M) Urea, .175ml 40%ampholytes, .29ml 30% (3.3%) acrylamide, 1,2ml water, .35ml 20% Nonidet P40, .025ml 10% APS and .025ml TEMED. I am going to try and improve the gel by using bind silane on the glass plates to stabilise the gel. Does anybody have any advice on preparing vertical IEF slab gels? Please feel free to repond by email or on the net. Thanks in advance Ian . From owner-proteins@net.bio.net Sun Mar 12 22:00:00 1995 Path: biosci!biosci!not-for-mail From: Bill Pearson Newsgroups: bionet.software,bionet.molbio.embldatabank,bionet.molbio.genbank,bionet.announce,bionet.molbio.proteins Subject: Re: FASTA 2.0x available Date: 13 Mar 1995 15:21:20 -0800 Organization: University of Virginia Lines: 30 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:11456 bionet.molbio.embldatabank:476 bionet.molbio.genbank:1976 bionet.announce:1891 bionet.molbio.proteins:3964 In article , Bill Pearson wrote: >A new (experimental) release of the FASTA program package is now >available from virginia.edu in pub/fasta/fasta20x.shar(.Z). Version >2.0x incorporates several major improvements in the FASTA and SSEARCH >(Smith-Waterman) sequence searching programs: >(2) FASTA now uses the rigorous Smith-Waterman algorithm to produce >alignments. Thus, there is no limit to gap size in alignments. ^^^ Several people have reported problems in compiling the programs due to oversights on my part. I believe that those problems have been fixed. Another person reported some problem downloading the programs. They are available via anonymous ftp from the machine "uvaarpa.virginia.edu", also known as "virginia.edu" and "128.143.2.7". FTP in as anonymous using your email address as the password. Keep those cards and letters coming. (If you have problems, an email message is more likely to get a prompt response than a newsgroup posting). Bill Pearson -- wrp@virginia.EDU Dept. of Biochemistry #440 U. of Virginia Charlottesville, VA 22908 From owner-proteins@net.bio.net Sun Mar 12 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!uunet!ftpbox!news.acns.nwu.edu!uicvm.uic.edu!u12201 Organization: University of Illinois at Chicago, ADN Computer Center Date: Mon, 13 Mar 1995 13:42:23 CST From: Message-ID: <95072.134223U12201@uicvm.uic.edu> Newsgroups: bionet.molbio.proteins Subject: Signal Transduction Lines: 2 Any good leads on discussion groups on signal transduction and protein kinases etc etc. ?? From owner-proteins@net.bio.net Sun Mar 12 22:00:00 1995 Path: biosci!NETAXS.COM!gheavner From: gheavner@NETAXS.COM Newsgroups: bionet.molbio.proteins Subject: 3d map of protein Date: 13 Mar 1995 09:48:18 -0800 Organization: BIOSC