From owner-proteins@net.bio.net Mon Oct 04 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!uknet!pipex!howland.reston.ans.net!wupost!udel!news.sprintlink.net!demon!visigoth.demon.co.uk!user From: pettsj@visigoth.demon.co.uk (James Petts) Newsgroups: bionet.molbio.proteins Subject: Phosphorylation of protein by lck Message-ID: Date: 5 Oct 93 15:37:07 GMT Sender: news@demon.co.uk (Usenet Administration) Followup-To: bionet.molbio.proteins Organization: No Affiliation Lines: 10 Nntp-Posting-Host: visigoth.demon.co.uk I have seen in some articles that rabbit skeletal muscle enolase is used as a phosphorylation substrate for lck in some assays. There are 8 tyrosines in the enolase. Does anybody know if these are phosphorylated specifically, or is the protein used *because* there are multiple potential phosphorylation sites? -- -------- James Petts --------- DOSthinkers unbellyfeel netsoc ------------------------------ From owner-proteins@net.bio.net Mon Oct 04 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!nott-cs!macfd.biochem.nott.ac.uk!user From: mbxfd@unicorn.nott.ac.uk (Fergus Doherty) Newsgroups: bionet.molbio.proteins Subject: Antibodies to cytochrome oxidase Message-ID: Date: 5 Oct 93 11:51:42 GMT Sender: news@cs.nott.ac.uk Followup-To: bionet.molbio.proteins Organization: Nottingham University, UK. Lines: 16 Nntp-Posting-Host: macfd Hello Bionetter, I am trying to track down antibodies to cytochrome c oxidase, (to the bovine heart from preferably, or at least mammalian). Anyone know of commercial supplier or of a researcher that would be willing to let me have some? I assume these would be subunit specific, that's OK, as many as possible please! I'm looking at proteolysis of cytochrome oxidase in an in vitro system. Thanks 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 Tue Oct 05 23:00:00 1993 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Announcement of Interruption of BITNET Access to PIR Message-ID: <01H3SEVDXB8A8WX9W9@NBRF.Georgetown.Edu> Date: 6 Oct 93 14:37:23 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 22 Announcement of Temporary Interruption of Access to The Protein Identification Resource The National Biomedical Research Foundation has been notified by CREN that there were some problems in the original domain names list distributed earlier this month. Unfortunately, the CREN notice and the corrected list arrived after the defective list had been installed at our site, and we may not be able to correct the problem immediately. As a result, it may not be possible for users at some locations to access the Protein Identification Resource Network Server by BITNET. The On-line System, Internet communications and most BITNET communications are NOT affected by this problem. We regret any inconvenience this temporary loss of service may cause. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-proteins@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!mcsun!uunet!europa.eng.gtefsd.com!howland.reston.ans.net!noc.near.net!news.Brown.EDU!tsq-183.tsq.brown.edu!joe From: joe@as.tsq.brown.edu (Joe Lucas) Newsgroups: bionet.molbio.proteins Subject: looking for a protein Message-ID: Date: 6 Oct 93 19:17:06 GMT Organization: Advanced Systems Lines: 11 NNTP-Posting-Host: tsq-183.tsq.brown.edu I am trying to find a protein with the following qualifications for a computer modeling project: -translated on the rough ER -not embedded in the ER membrane -not modified post translationaly -relatively small ( < 20 amino acids) -tertiary structure is known from x-ray crystallography I can check on the last two qualifications myself fairly easily, but any help on the first three would be greatly appreciated. -Joe From owner-proteins@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!fconvx.ncifcrf.gov!fcs260c!tobin From: tobin@fcs260c.ncifcrf.gov (Greg Tobin) Newsgroups: bionet.molbio.hiv,bionet.molbio.proteins Subject: Myristic acid and Gag proteins Message-ID: Date: 6 Oct 93 18:44:37 GMT Sender: usenet@ncifcrf.gov (C News) Organization: Frederick Cancer Research and Development Center Lines: 12 Xref: biosci bionet.molbio.hiv:246 bionet.molbio.proteins:905 Nntp-Posting-Host: fcs260c.ncifcrf.gov Can anyone comment on the role of myristic acid modification of the N-termini of retroviral Gag proteins. Earlier experiments suggested that mutation of the N-terminus to prohibit myristoylation inhibits virion assembly. How about some opinions on the mechanisms at work here? All theories with or without experimental support are welcome. Thanks in advance. Greg -- Greg Tobin, Ph.D. tobin@lcms-1.ncifcrf.gov LCMS PO Box B Frederick, MD 21702 From owner-proteins@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!usenet.ins.cwru.edu!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!sangam!vikram!imtech!mrigank From: mrigank@imtech.ernet.in (Dr. Mrigank) Newsgroups: bionet.molbio.proteins,bionet.general Subject: Disulphide bonds and cytoplasmic proteins? Message-ID: <7315@imtech.ernet.in> Date: 6 Oct 93 06:15:26 GMT Organization: Inst. of Microbial Technology, Chandigarh, India Lines: 25 Xref: biosci bionet.molbio.proteins:907 bionet.general:6188 Hi netters, We are looking for an answer for a debate. It started in a group discussion where a statment was made "..Only protein that enter the secretory pathway have disulfide bonds.." This was disputed. We looked up in literature and found ".. Of proteins which never leave the parent cell a very few posses disulfide bridges.." Principle of Protein Structure by S.E.Schultz and Schirmer (1978) Springer-Verlag, p. 54. Now we would like to know if there are any cytoplasmic proteins which have a disufide bonds? If so, what are the examples? Are these bonds in cytoplasmic proteins artifacts (like air oxidation during lysis) ? How are these bonds formed in the cytoplasm? are there any PDI like enzymes ? -- Dr. Mrigank \/Phone +91 172 45004 x216 Institute of Microbial Technology /\Email: mrigank@imtech.ernet.in P O Box 1304, Sector 39A \/UUCP:...!uunet!sangam!vikram!imtech!mrigank Chandigarh 160 014 India. /\ ==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+ -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From owner-proteins@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!mrccrc!nimr.mrc.ac.uk!k-hatric From: k-hatric@nimr.mrc.ac.uk (Kerr Hatrick) Newsgroups: bionet.molbio.proteins Subject: PhD position Message-ID: <1993Oct6.154821.12338@crc.ac.uk> Date: 6 Oct 93 15:48:21 GMT Sender: news@crc.ac.uk Organization: National-Institute-for-Medical-Research Lines: 12 Nntp-Posting-Host: nimsn48.nimr.mrc.ac.uk A PhD position is available (starting as soon as possible) at the National Institute for Medical Research (MRC, Mill Hill London). The project is to use molecular modelling and protein structure prediction methods to investigate the binding of insulin to its receptor. The work will be supervised jointly by Willie Taylor and Guy Dodson. The project would be suitable for someone with a background in biochemistry who is familiar with computers. Anyone interested should contact Willie Taylor on w_taylor@nimr.mrc.ac.uk (replys to this ID will also be forwarded) From owner-proteins@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!relay.the.net!SHAUN%JASON.DECNET From: SHAUN%JASON.DECNET@relay.the.net ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: HPLC Gel Filtration/Size Exclusion Columns Message-ID: <01H3TSEIPEB6000SG4@nic.the.net> Date: 7 Oct 93 16:10:41 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 12 Dear Colleagues: I have occasion to do a series of molecular weight determinations of proteins in the presence and absence of detergents. Years ago I used ToyoSoda PW and SW silica-based columns; the PW bound all of my proteins, and the SW worked fairly well. My question is: what is your experience with HPLC gel filtration columns for proteins presently? What/which are best? Protein binding? Silica vs plastic polymers? Effects of detergent? In advance, please know that I appreciate your thoughts. Cheers, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!MAP.MARC.USDA.GOV!keele From: keele@MAP.MARC.USDA.GOV (John Keele) Newsgroups: bionet.molbio.proteins Subject: Postdoc Position Message-ID: <9310071341.AA26092@map.marc.usda.gov> Date: 7 Oct 93 13:41:52 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 22 Postdoctoral Position: U.S. Department of Agriculture, Agricultural Research Service (ARS), Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE has a Postdoctoral Research Associate position available immediately. Incumbent will develop automated system for building real-time physically anchored genetic linkage maps from a growing database of marker genotypes and physical mapping data. Exploration of alternative technologies will be encouraged. Individuals with experience and interest in computational aspects of genetics are encouraged to apply. Two- year appointment with benefits. Minimum starting salary $33,623. Send C.V. and names, addresses, and telephone numbers of three references to: John W. Keele USDA-ARS Roman L. Hruska U.S. Meat Animal Research Center P. O. Box 166 Clay Center, NE 68933-0166 (keele@map.marc.usda.gov) USDA-ARS is an affirmative action/equal opportunity employer. From owner-proteins@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!utcsri!utnut!torn!nott!emr1!weathere From: weathere@emr1.emr.ca (Carl Weatherell) Newsgroups: bionet.molbio.proteins Subject: Protein-SDS-SEC Message-ID: <1993Oct7.193953.14273@emr1.emr.ca> Date: 7 Oct 93 19:39:53 GMT Organization: Dept. of Energy, Mines, and Resources, Ottawa Lines: 13 X-Newsreader: TIN [version 1.1 PL8] I am examining secondary retention of protein-SDS complexes by different SEC stationary phases. Interpretation of the data would be much simpler if I had access to 3D models of the protein-SDS compplexes. Therefore, I would like to know if; a) PDB or other files of proteins-SDS complexes exist; if so where? b) can these be "calculated" or "modeled" with existing data i.e.: the pure protein and SDS? c) can these secondary structure prediction models be used for this application? Carl Weatherell weathere@emr1.emr.ca From owner-proteins@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!spool.mu.edu!nigel.msen.com!yale.edu!yale!news.wesleyan.edu!wesleyan.edu!rgeha From: rgeha@wesleyan.edu Newsgroups: bionet.molbio.proteins Subject: SKIP/NEWSGROUP Message-ID: <1993Oct7.145304.1@wesleyan.edu> Date: 7 Oct 93 18:53:04 GMT Lines: 9 Nntp-Posting-Host: wesleyan.edu I am a senior biology major at Wesleyan University, Middletown, Connecticut. For my senior research project, I am studying the role of actin in insect oocytes. I am tyring to build an affinity column to bind actin and would appreciate any help on constructing this column. I would also appreciate any suggested readings in this area. Thank you, Rula Geha RGEHA@Eagle.Wesleyan.Edu From owner-proteins@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!emba-news.uvm.edu!brianf From: brianf@med.uvm.edu (Brain Foley) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: cleavable acrylamide cross-linkers? Message-ID: <1993Oct7.174932.14210@emba.uvm.edu> Date: 7 Oct 93 17:49:32 GMT Sender: news@emba.uvm.edu Organization: University of Vermont -- Division of EMBA Computer Facility Lines: 24 Xref: biosci bionet.molbio.methds-reagnts:7990 bionet.molbio.proteins:910 X-Newsreader: TIN [version 1.2 PL1] Hi Bionetters: I need to purify a 210 kDa protein. It need not be 100% pure, but as pure as I can get it. I have been immunoprecipitating and then running the precipitate on a 7.5% acrylamide gel. This works fine except that my recovery by electroelution from the gel nets me only 20% of the band of interest. If I load two lanes with identical ammounts, cut out the band of interest in each lane, electroelute the protein from one and save the other; I find that I only retreive 20% of the CPM in the eluate, the other 80% remains in the gel. I know that there are some other cross-linkers for acrylamide. Are any of them cleavable? I'd think it would be handy to "digest" the gel and thus find it easier to get the protein out of it. Alternatively, perhaps I could use agarose instead of acrylamide, but I have no experience with agarose and proteins. Any help is greatly appreciated. -- ******************************************************************** * Brian Foley * If we knew what we were doing * * Molecular Genetics Dept. * it wouldn't be called research * * University of Vermont * * From owner-proteins@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!rutgers!utcsri!utnut!torn!nott!emr1!weathere From: weathere@emr1.emr.ca (Carl Weatherell) Newsgroups: bionet.molbio.proteins Subject: Re: HPLC Gel Filtration/Size Exclusion Columns Message-ID: <1993Oct8.171726.5912@emr1.emr.ca> Date: 8 Oct 93 17:17:26 GMT References: <01H3TSEIPEB6000SG4@nic.the.net> Distribution: bionet Organization: Dept. of Energy, Mines, and Resources, Ottawa Lines: 38 X-Newsreader: TIN [version 1.1 PL8] Shaun D. Black (SHAUN%JASON.DECNET@relay.the.net) wrote: : Dear Colleagues: : I have occasion to do a series of molecular weight determinations of : proteins in the presence and absence of detergents. Years ago I used : ToyoSoda PW and SW silica-based columns; the PW bound all of my proteins, : and the SW worked fairly well. My question is: what is your experience : with HPLC gel filtration columns for proteins presently? What/which are : best? Protein binding? Silica vs plastic polymers? Effects of detergent? : In advance, please know that I appreciate your thoughts. Cheers, Shaun : =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= : = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = : = Dept. of Biochemistry | University of Texas Health Center, at Tyler = : =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Shaun; I am presently examining secondary retention effects on ToyaSodaPW and SW columns using factorial experimental design and principal component analysis. This is oriented specifically towards characterizing animal glues (collagen based) in zinc electrolytes. What I have found thus far, w.r.t. the 2 stationary phases, are briefly; - the efficiency of the PW phase is much higher than SW - ion exclusion effects on the SW phase are larger than that of the PW phase - the PW phase is extremely hydrophobic thus eliminating high salt concentrations in the eluent (complete retention of all denatured proteins is observed at 0.4M NaCl in 3.5mM SDS, pH=4 or 7) - both phases absorb SDS - a good eluent to achieve optimum resolution with no protein binding to the stationary phase consists of 3.5mM SDS, pH=4 (0.05M PO4 buffer), 0.1M NaCl I hope this useful. Catch y'all later eh! Carl Weatherell Research Chemist B.Sc., C.Chem. M.Sc. (almost) weathere@emr1.emr.ca From owner-proteins@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!sunic!uts!biobase!lho From: lho@biobase.aau.dk (Lars Henrik Oestergaard) Newsgroups: bionet.molbio.proteins Subject: Deglycosylation Summary: How to deglycosylate an antibody? Keywords: Antibody, Glycosidase, Glycoprotein, TFMS Message-ID: Date: 8 Oct 93 09:22:38 GMT Organization: The Danish BioBase Lines: 14 Dear reader, I am desperately needing your assistance please. I have been trying to deglycosylate an antibody using TFMS (refs.: Sojar, Arch.Biochem and Biophys. 259:52-57 (1987) and Edge, Anal. Biochem. 118:131-137 (1981)). These attempts haven't been very succesfull untill now. My problem is that the deglycosylated protein behave strange, when subjected to electrophoresis afterwards. Now I would like to try using enzymes instead. I have a feeling, that this is a more gentle way of doings things. My question for you: Does anyone out there ever have deglycosylated an antibody (with any luck)? What enzymes/deglycosidase did you use? Do you have any refs. to procedures? Thank you. Best wishes Lars Henrik Oestergaard Department of Chemistry Aarhus University Denmark From owner-proteins@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!urz.unibas.ch!bickle From: bickle@urz.unibas.ch Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: cleavable acrylamide cross-linkers? Message-ID: <1993Oct8.094644.43162@urz.unibas.ch> Date: 8 Oct 93 08:46:44 GMT References: <1993Oct7.174932.14210@emba.uvm.edu> Organization: University of Basel, Switzerland Lines: 12 Xref: biosci bionet.molbio.methds-reagnts:8001 bionet.molbio.proteins:913 In article <1993Oct7.174932.14210@emba.uvm.edu>, brianf@med.uvm.edu (Brain Foley) writes: > Hi Bionetters: > > I know that there are some other cross-linkers for acrylamide. > Are any of them cleavable? I'd think it would be handy to "digest" the > gel and thus find it easier to get the protein out of it. Alternatively, > perhaps I could use agarose instead of acrylamide, but I have no > experience with agarose and proteins. > One cleavable crosslinker is a bis analogue containing alcohols on adjacent carbon atoms - cleavable with periodate. Sorry, no ref handy but you will find it catalogues under N, N' diallyl tartardiamide. From owner-proteins@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!rpi!mantell From: mantell@alum01.its.rpi.edu (Abraham S. Mantell) Newsgroups: bionet.molbio.proteins Subject: Books for Sale Message-ID: <294ui3$fgc@usenet.rpi.edu> Date: 8 Oct 93 23:53:39 GMT Organization: Rensselaer Polytechnic Institute, Troy NY Lines: 32 NNTP-Posting-Host: alum01.its.rpi.edu Hello, I found a few more books of mine that I wish to sell... 1. Chemical Synthesis in Molecular Biology: Biological Macromolecules with Natural and Modified Monomer Units, From a Symposium held in Brauschweig, FRG, September 1984. Ed. by Blocker, Frank, and Fritz. 1987, softcover. List Price: $105 I ask: $70 2. Flux Coordinates and Magnetic Field Structure: A Guide to a Fundamental Tool of plasma theory, by D'haeseleer, Callen, and Shohet, 1991, Springer-Verlag. List Price: $98 I ask: $70 3. Elliptic Curves, by Dale Husemoller, 1987, Springer-Verlag GTM v.111. List Price: $49 I ask: $30 4. Series of Irregular Observations: Forecasting and Model Building, by Azencott and Dacunha-Castelle, 1986. List Price: $46 I ask: $30 Please add a few dollars for postage, insurance, and COD (if used). All books are in like-new condition... Abe mantell@rpi.edu From owner-proteins@net.bio.net Sun Oct 10 23:00:00 1993 Path: biosci!rutgers!dziuxsolim.rutgers.edu!uunet!tcsi.tcs.com!agate!han.hana.nm.kr!usenet From: bhkim@kuccnx.korea.ac.kr.korea.ac.kr (Byung-hoon Kim) Newsgroups: bionet.molbio.proteins Subject: protein CIP Message-ID: <1993Oct11.125703.15010@han.hana.nm.kr> Date: 11 Oct 93 12:57:03 GMT Sender: usenet@han.hana.nm.kr (news) Organization: KTRC in Seoul, Korea Lines: 8 X-Newsreader: Tin 1.1 PL3 Dear Netters I'm a novice in this field. Would you tell me how I can dephosphorylate DNA binding proteins, please? Buffer contents, reaction conditions...etc. Thanks in advance. Byung-Hoon Kim bhkim@kuccnx.korea.ac.kr From owner-proteins@net.bio.net Sun Oct 10 23:00:00 1993 Path: biosci!uwm.edu!rpi!mantell From: mantell@alum01.its.rpi.edu (Abraham S. Mantell) Newsgroups: bionet.molbio.proteins Subject: Books for Sale Message-ID: <294ui3$fgc@usenet.rpi.edu> Date: 8 Oct 93 23:53:39 GMT Organization: Rensselaer Polytechnic Institute, Troy NY Lines: 32 NNTP-Posting-Host: alum01.its.rpi.edu Hello, I found a few more books of mine that I wish to sell... 1. Chemical Synthesis in Molecular Biology: Biological Macromolecules with Natural and Modified Monomer Units, From a Symposium held in Brauschweig, FRG, September 1984. Ed. by Blocker, Frank, and Fritz. 1987, softcover. List Price: $105 I ask: $70 2. Flux Coordinates and Magnetic Field Structure: A Guide to a Fundamental Tool of plasma theory, by D'haeseleer, Callen, and Shohet, 1991, Springer-Verlag. List Price: $98 I ask: $70 3. Elliptic Curves, by Dale Husemoller, 1987, Springer-Verlag GTM v.111. List Price: $49 I ask: $30 4. Series of Irregular Observations: Forecasting and Model Building, by Azencott and Dacunha-Castelle, 1986. List Price: $46 I ask: $30 Please add a few dollars for postage, insurance, and COD (if used). All books are in like-new condition... Abe mantell@rpi.edu From owner-proteins@net.bio.net Sun Oct 10 23:00:00 1993 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!sdd.hp.com!vixen.cso.uiuc.edu!howland.reston.ans.net!darwin.sura.net!news.Vanderbilt.Edu!news From: PLANCHAJ@ctrvax.Vanderbilt.Edu (Tony Planchart) Newsgroups: bionet.molbio.proteins Subject: Address for Peter Traub Message-ID: <1993Oct11.212014.25800@news.vanderbilt.edu> Date: 11 Oct 93 21:20:14 GMT Sender: news@news.vanderbilt.edu Organization: Vanderbilt University Lines: 15 Nntp-Posting-Host: ctrvax.vanderbilt.edu X-News-Reader: VMS NEWS 1.24 Hi There, Was wondering if any one might have an e-mail address for Dr. Peter Traub. I believe he is at the Max Planck Institut fur Zellbiologie in Ladenburg, Germany. Any help would be greatly appreciated. Also, if you happen to have an e-mail address for Robert Goldman at Northwestern University in Chicago, IL, it would be appreciated as well. Thanks, Tony Planchart Dept. of Molecular Biology Vanderbilt University Nashville, TN From owner-proteins@net.bio.net Sun Oct 10 23:00:00 1993 Path: biosci!rutgers!cs.utexas.edu!usc!howland.reston.ans.net!newsserver.jvnc.net!netnews.upenn.edu!biochem.dental.upenn.edu!lally From: lally@biochem.dental.upenn.edu (Ned Lally) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: cleavable acrylamide cross-linkers? Message-ID: <153547@netnews.upenn.edu> Date: 10 Oct 93 21:23:12 GMT References: <1993Oct7.174932.14210@emba.uvm.edu> <1993Oct8.094644.43162@urz.unibas.ch> Sender: news@netnews.upenn.edu Followup-To: bionet.molbio.methds-reagnts Organization: University of Pennsylvania Lines: 18 Xref: biosci bionet.molbio.methds-reagnts:8034 bionet.molbio.proteins:917 Nntp-Posting-Host: biochem.dental.upenn.edu In article <1993Oct8.094644.43162@urz.unibas.ch>, bickle@urz.unibas.ch writes: |> In article <1993Oct7.174932.14210@emba.uvm.edu>, brianf@med.uvm.edu (Brain Foley) writes: |> > Hi Bionetters: |> > |> > I know that there are some other cross-linkers for acrylamide. |> > Are any of them cleavable? I'd think it would be handy to "digest" the |> > gel and thus find it easier to get the protein out of it. Alternatively, |> > perhaps I could use agarose instead of acrylamide, but I have no |> > experience with agarose and proteins. |> > |> One cleavable crosslinker is a bis analogue containing alcohols on adjacent |> carbon atoms - cleavable with periodate. Sorry, no ref handy but you will |> find it catalogues under N, N' diallyl tartardiamide. Brian: Dumb question. Why can't you use electroelution? Or did I miss something. Bye, Ned From owner-proteins@net.bio.net Mon Oct 11 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!paladin.american.edu!howland.reston.ans.net!pipex!uknet!bcc.ac.uk!bsm.bioc.ucl.ac.uk!mcdonald From: mcdonald@bsm.bioc.ucl.ac.uk (Ian McDonald) Newsgroups: bionet.molbio.proteins Subject: Domains - elucidating them automatically Message-ID: <1993Oct12.121338.340243@ucl.ac.uk> Date: 12 Oct 93 12:13:38 GMT Organization: Bloomsbury Computing Consortium Lines: 6 I am looking for software that can automatically identify the borders between protein domains if given a 3D structure. Please Email me, and I will post a summary. Ian From owner-proteins@net.bio.net Mon Oct 11 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!uni-heidelberg!rz.uni-karlsruhe.de!xlink.net!howland.reston.ans.net!paladin.american.edu!darwin.sura.net!lhc!azalea!francis From: francis@azalea.nlm.nih.gov (Francis Ouellette) Newsgroups: bionet.molbio.proteins Subject: Re: Address for Peter Traub Message-ID: <1993Oct12.042716.6561@nlm.nih.gov> Date: 12 Oct 93 04:27:16 GMT References: <1993Oct11.212014.25800@news.vanderbilt.edu> Sender: news@nlm.nih.gov Organization: National Library of Medicine Lines: 32 X-Newsreader: Tin 1.1 PL4 PLANCHAJ@ctrvax.Vanderbilt.Edu (Tony Planchart) writes: : Also, if you happen to have an e-mail address for Robert Goldman at : Northwestern University in Chicago, IL, it would be appreciated as well. checking the northwestern phone book from the gopher server at gopher.gdb.org I find: ------------------------------------------------------- alias: r-goldman name: goldman, robert d title: stephen w ranson professor department: cms biology title2: chairperson department2: cms biology office_address: w11145 : ward : ch w129 office_phone: 312-503-4215, 312-503-8249 ------------------------------------------------------- is this the right one? regards, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov From owner-proteins@net.bio.net Mon Oct 11 23:00:00 1993 Path: biosci!relay.the.net!SHAUN%JASON.DECNET From: SHAUN%JASON.DECNET@relay.the.net ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: Heme Oxygenase N-terminus? Message-ID: <01H41JLEDD8Y000T5Z@nic.the.net> Date: 13 Oct 93 05:19:22 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 8 Dear Colleagues, Does anyone know if the microsomal protein, Heme Oxygenase, has a free or blocked N-terminus? If it is blocked, what is the blocking group? Thanks in advance! Cheers, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Mon Oct 11 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!dapsun.lif.icnet.uk!not-for-mail From: js@bison.lif.icnet.uk ( BIU) Newsgroups: bionet.molbio.proteins Subject: Re: Domains - elucidating them automatically Message-ID: <29f86fINNn1p@bison.lif.icnet.uk> Date: 12 Oct 93 21:39:27 GMT References: <1993Oct12.121338.340243@ucl.ac.uk> Organization: Imperial Cancer Research Fund Lines: 13 NNTP-Posting-Host: bison.lif.icnet.uk In article <1993Oct12.121338.340243@ucl.ac.uk> mcdonald@bsm.bioc.ucl.ac.uk (Ian McDonald) writes: >I am looking for software that can automatically identify the borders between >protein domains if given a 3D structure. > >Please Email me, and I will post a summary. I'm looking forward to the results of this - as far as I know this is an unsettled problem. If no results though, try again in a year. -- Jack js@biu.icnet.uk If you only have a hammer, you tend to see every problem as a nail. -- Maslow From owner-proteins@net.bio.net Tue Oct 12 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!athena.mit.edu!dresnick From: dresnick@athena.mit.edu (David I Resnick) Newsgroups: bionet.molbio.proteins Subject: (His)6 tags for protein purification Message-ID: Date: 13 Oct 93 14:26:46 GMT Organization: Massachusetts Institute of Technology Lines: 18 NNTP-Posting-Host: m14s-010-4.mit.edu Hi, Has anyone out there used the Hisx6 tags for purification of recomb. expressed proteins? I'm considering putting it on a fragment of a protein we are studying and expressing it in yeast. However I have the following questions/concerns: 1) Does the His6 tag need to be at the very N or C terminus for the protein for the protein to bind to the Ni2+ column? Or can it be internal as long as it is solvent exposed? 2) Has anyone actually done this in yeast? Would you expect it to affect secretion in any way if this sequence were placed immediately after a signal sequence (e.g. invertases')? Thanks! -- David Resnick dresnick@athena.mit.edu From owner-proteins@net.bio.net Tue Oct 12 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!yeshua.marcam.com!zip.eecs.umich.edu!umn.edu!news From: npv@mani.cbs.umn.edu (Nora Plesofsky-Vig) Newsgroups: bionet.molbio.proteins Subject: Re: transfer proteins from a stained gel Message-ID: Date: 13 Oct 93 17:16:38 GMT References: <1993Oct1.090109.6212@gserv1.dl.ac.uk> Sender: news@news.cis.umn.edu (Usenet News Administration) Reply-To: robert brambl Distribution: bionet Organization: University of Minnesota, Twin Cities Lines: 43 Nntp-Posting-Host: mani.cbs.umn.edu In article <1993Oct1.090109.6212@gserv1.dl.ac.uk> emrasmus@dk.aau.biobase (Erik Michael Rasmussen) writes: > > > > Help!! Does anyone know how to transfer protein from > > a gel to nitrocellulose after it has been stained with > > Coomassie blue? We need to perform a Western > > analysis but do not have any more of the sample. > > > > Thanks > > David Mueller > > Chicago Medical School > > > My guess is that if it is still wet, my suggetion is to equilibrate the gel in > transferbuffer and and run the blotting. If the transfer is succesful you will > see it right away because the comassie will remain on the proteins. > It's just to try. I haven't tried myself, but I will be very interested in if > it is possible, because I could fear that the proteins is too fixed in the > gel. > > Michael > > Erik Michael Rasmussen phone (+45) 35322100 > Department of Genetics E-mail emrasmus@biobase.aau.dk > Institute of Molecular Biology > University of Copenhagen > > This response may be too late for the one valuable gel, but for future trials it may be useful. A colleague in our laboratory uses an alternative method for Coomassie staining of proteins that he wishes to subsequently electroelute from the gel, and it should be applicable to Western blotting as well. The SDS gel is fixed and stained in 0.05% Coomassie blue in propan-2-ol/acetic acid/water (5:2:13) and then destained and stored in 10% acetic acid until further treatment. The reference for the procedure is Biochem. J. 197:591-597 (1981). Nora Plesofsky-Vig Plant Biology Dept. nora@molbio.cbs.umn.edu University of Minnesota St. Paul, Minn 55108 From owner-proteins@net.bio.net Wed Oct 13 23:00:00 1993 Path: biosci!news.cs.umb.edu!hsdndev!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!mcsun!sun4nl!sun2.iend.wau.nl!LConceicao.VenV.WAU.NL!Luis.Conceicao From: Luis.Conceicao@Alg.VenV.WAU.NL (Luis Conceicao) Newsgroups: bionet.molbio.proteins Subject: Phenylalanine hydroxilase mechanism Message-ID: Date: 14 Oct 93 09:29:19 GMT Sender: news@sun2.iend.wau.nl (Newsmanager WAU) Distribution: sci.chem Organization: Wageningen Agricultural University Lines: 13 Hi, I would like to know in detail the catalytic mechanism of the phenylalanine- tyrosine reaction. Info/references are welcome! What I really wan't to know is if this reaction can be affected by using isotopic phenylalanine. Thanks, Luis Conceicao ============================================================================= Luis Eugenio C. da Conceicao Dept. Fish Culture and Fisheries P.O.Box 338, NL-6700 AH Wageningen Wageningen Agricultural University Tel: + 31 8370 84942 The Netherlands E-mail: Luis.Conceicao@alg.venv.wau.nl ============================================================================= From owner-proteins@net.bio.net Wed Oct 13 23:00:00 1993 Path: biosci!QMS1.LIFE.UIUC.EDU!Dan_Szymanski From: Dan_Szymanski@QMS1.LIFE.UIUC.EDU ("Dan Szymanski") Newsgroups: bionet.molbio.proteins Subject: Re: protein CIP Message-ID: <199310141724.AA25410@nicnext.life.uiuc.edu> Date: 14 Oct 93 18:18:22 GMT Sender: news@net.bio.net Distribution: bionet Lines: 40 Reply to: RE>protein CIP no suggestions netters? how about the different enzymatic phospatases? do any companies make a preparation that is more pure or more active at room temperature? can the problem be attacked by inhibiting the kinases, with excess target peptide for example? share your thoughts. -------------------------------------- Date: 10/11/93 8:30 PM To: Dan Szymanski From: Byung-hoon Kim Dear Netters I'm a novice in this field. Would you tell me how I can dephosphorylate DNA binding proteins, please? Buffer contents, reaction conditions...etc. Thanks in advance. Byung-Hoon Kim bhkim@kuccnx.korea.ac.kr ------------------ RFC822 Header Follows ------------------ Received: by qms1.life.uiuc.edu with SMTP;11 Oct 1993 20:30:40 -0600 Received: by net.bio.net (5.65/IG-2.0) id AA03367; Mon, 11 Oct 93 18:14:04 -0700 Received: by net.bio.net (5.65/IG-2.0) id AA03351; Mon, 11 Oct 93 18:13:58 -0700 Message-Id: <9310120113.AA03351@net.bio.net> To: proteins@net.bio.net From: bhkim@kuccnx.korea.ac.kr.korea.ac.kr (Byung-hoon Kim) Subject: protein CIP Date: 11 Oct 93 12:57:03 GMT Sender: usenet@han.hana.nm.kr (news) X-Newsreader: Tin 1.1 PL3 From owner-proteins@net.bio.net Wed Oct 13 23:00:00 1993 Path: biosci!parc!decwrl!decwrl!olivea!charnel!yeshua.marcam.com!zip.eecs.umich.edu!umn.edu!news From: npv@mani.cbs.umn.edu (Nora Plesofsky-Vig) Newsgroups: bionet.molbio.proteins Subject: Re: transfer proteins from a stained gel Message-ID: Date: 13 Oct 93 17:16:38 GMT References: <1993Oct1.090109.6212@gserv1.dl.ac.uk> Sender: news@news.cis.umn.edu (Usenet News Administration) Reply-To: robert brambl Distribution: bionet Organization: University of Minnesota, Twin Cities Lines: 43 Nntp-Posting-Host: mani.cbs.umn.edu In article <1993Oct1.090109.6212@gserv1.dl.ac.uk> emrasmus@dk.aau.biobase (Erik Michael Rasmussen) writes: > > > > Help!! Does anyone know how to transfer protein from > > a gel to nitrocellulose after it has been stained with > > Coomassie blue? We need to perform a Western > > analysis but do not have any more of the sample. > > > > Thanks > > David Mueller > > Chicago Medical School > > > My guess is that if it is still wet, my suggetion is to equilibrate the gel in > transferbuffer and and run the blotting. If the transfer is succesful you will > see it right away because the comassie will remain on the proteins. > It's just to try. I haven't tried myself, but I will be very interested in if > it is possible, because I could fear that the proteins is too fixed in the > gel. > > Michael > > Erik Michael Rasmussen phone (+45) 35322100 > Department of Genetics E-mail emrasmus@biobase.aau.dk > Institute of Molecular Biology > University of Copenhagen > > This response may be too late for the one valuable gel, but for future trials it may be useful. A colleague in our laboratory uses an alternative method for Coomassie staining of proteins that he wishes to subsequently electroelute from the gel, and it should be applicable to Western blotting as well. The SDS gel is fixed and stained in 0.05% Coomassie blue in propan-2-ol/acetic acid/water (5:2:13) and then destained and stored in 10% acetic acid until further treatment. The reference for the procedure is Biochem. J. 197:591-597 (1981). Nora Plesofsky-Vig Plant Biology Dept. nora@molbio.cbs.umn.edu University of Minnesota St. Paul, Minn 55108 From owner-proteins@net.bio.net Wed Oct 13 23:00:00 1993 Path: biosci!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!athena.mit.edu!dresnick From: dresnick@athena.mit.edu (David I Resnick) Newsgroups: bionet.molbio.proteins Subject: (His)6 tags for protein purification Message-ID: Date: 13 Oct 93 14:26:46 GMT Organization: Massachusetts Institute of Technology Lines: 18 NNTP-Posting-Host: m14s-010-4.mit.edu Hi, Has anyone out there used the Hisx6 tags for purification of recomb. expressed proteins? I'm considering putting it on a fragment of a protein we are studying and expressing it in yeast. However I have the following questions/concerns: 1) Does the His6 tag need to be at the very N or C terminus for the protein for the protein to bind to the Ni2+ column? Or can it be internal as long as it is solvent exposed? 2) Has anyone actually done this in yeast? Would you expect it to affect secretion in any way if this sequence were placed immediately after a signal sequence (e.g. invertases')? Thanks! -- David Resnick dresnick@athena.mit.edu From owner-proteins@net.bio.net Thu Oct 14 23:00:00 1993 Path: biosci!relay.the.net!SHAUN%JASON.DECNET From: SHAUN%JASON.DECNET@relay.the.net ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: Help! Need partial specific volumes of heme and flavins! Message-ID: <01H459R3W0GI001448@nic.the.net> Date: 15 Oct 93 21:21:47 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 10 Does anyone know what the partial specific volumes ('nu bar', 20C) of heme (ferriprotoporphyrin IX), FMN (flavin mononucleotide), and FAD (flavin adenine dinucleotide) are? We need them 'yesterday' and a speedy reply would be very much appreciated. In advance, thanks very much! -Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | Bitnet: shaun%jason.decnet@thenic.bitnet = = UT Health Center, Tyler | Phone: (903)877-2806 FAX: (903)877-7558 = = Tyler, TX 75710-2003 | B-) (Start every day with a smile...) = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Thu Oct 14 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!xlink.net!scsing.switch.ch!sun.rediris.es!cnbvx3.cnb.uam.es!sergio From: sergio@cnbvx3.cnb.uam.es Newsgroups: bionet.molbio.proteins Subject: chymotrypsin M.W. Message-ID: <1993Oct15.154311.74@cnbvx3.cnb.uam.es> Date: 15 Oct 93 15:43:11 GMT Organization: C.N.Biotecnologia, CSIC Lines: 3 Hi, we are looking for the molecular weight of the protease: chymotrypsin If someone could tell us we would be very gratefull. Thanks in advance. From owner-proteins@net.bio.net Thu Oct 14 23:00:00 1993 Path: biosci!max.physics.sunysb.edu!psinntp!psinntp!cmcl2!news.ans.net!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!mcsun!sun4nl!sun2.iend.wau.nl!LConceicao.VenV.WAU.NL!Luis.Conceicao From: Luis.Conceicao@Alg.VenV.WAU.NL (Luis Conceicao) Newsgroups: bionet.molbio.proteins Subject: Phenylalanine hydroxilase mechanism Message-ID: Date: 14 Oct 93 09:29:19 GMT Sender: news@sun2.iend.wau.nl (Newsmanager WAU) Distribution: sci.chem Organization: Wageningen Agricultural University Lines: 13 Hi, I would like to know in detail the catalytic mechanism of the phenylalanine- tyrosine reaction. Info/references are welcome! What I really wan't to know is if this reaction can be affected by using isotopic phenylalanine. Thanks, Luis Conceicao ============================================================================= Luis Eugenio C. da Conceicao Dept. Fish Culture and Fisheries P.O.Box 338, NL-6700 AH Wageningen Wageningen Agricultural University Tel: + 31 8370 84942 The Netherlands E-mail: Luis.Conceicao@alg.venv.wau.nl ============================================================================= From owner-proteins@net.bio.net Thu Oct 14 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!agate!headwall.Stanford.EDU!MED.Stanford.EDU!cmgm.stanford.edu!garren From: garren@cmgm.stanford.edu (Ron Garren) Newsgroups: bionet.molbio.proteins Subject: thymidine kinase type 1 half life Summary: send reply to garren@cmgm.stanford.edu. thanks ron Keywords: TK herpes half life Message-ID: Date: 15 Oct 93 07:24:24 GMT Sender: news@medmail.stanford.edu Organization: Stanford University, California, USA Lines: 4 If anyone out there knows the half life of herpes TK protein please let me know. I will be using it Jurkat cells. garren@cmgm.stanford.edu thanks ron From owner-proteins@net.bio.net Thu Oct 14 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!news.doit.wisc.edu!sweetprotein.ahabs.wisc.edu!user From: ming@ahabs.wisc.edu (Ding Ming) Newsgroups: bionet.molbio.proteins Subject: Where to find protein sequence data book? Message-ID: Date: 15 Oct 93 22:55:07 GMT Followup-To: bionet.molbio.proteins Organization: University of Wisconsing-Madison Lines: 13 NNTP-Posting-Host: sweetprotein.ahabs.wisc.edu Hi, there, I know that there are quite a few places we can find the sequences of proteins by either computer search or whatever. Can someone recommend a handy data book in which I can find most sequences of known proteins without too much lengthy legends? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ding Ming Telephone: (608)265-3544 University of Wisconsin-Madison Fax: (608)262-7420 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-proteins@net.bio.net Thu Oct 14 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!pipex!uunet!utcsri!utnut!utgpu!fred From: fred@gpu.utcc.utoronto.ca (P. Knygsman) Newsgroups: bionet.immunology,bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Substrate Assays Message-ID: Date: 15 Oct 93 20:16:12 GMT Organization: UTCC Public Access Lines: 10 Xref: biosci bionet.immunology:630 bionet.molbio.methds-reagnts:8207 bionet.molbio.proteins:937 Are substrate assays your forte? Here is one for you. I want to use an Fmoc...~Na (heptapeptide) substrate in a liquid enzyme assay. I want to make a stock solution of 1.0mM (or greater) and use it at a final concentration of 0.8mM in the assay. I have tried to solubilize it in 20mM and 50mM TRIS, at pH 6.0, 6.5 and 7.0. I have tried the same with 50mM KH2PO4. The results showed higher solubility in both buffers at pH 6.5. I have also tried using DMSO up to a final concentration of 8%, this does not solubilize it either. If you have any input, it would be greatly From owner-proteins@net.bio.net Thu Oct 14 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!sangam!vikram!imtech!raman From: raman@imtech.ernet.in (C.RAMAN SURI) Newsgroups: bionet.molbio.proteins Subject: Insulin binding proteins Message-ID: <7565@imtech.ernet.in> Date: 14 Oct 93 06:27:31 GMT Organization: Inst. of Microbial Technology, Chandigarh, India Lines: 10 Hi friends, I am interested in knowing various INSULIN binding proteins that specifically bind with insulin. Can anyone help me in this regard! Thanks, Raman raman@imtech.ernet.in From owner-proteins@net.bio.net Thu Oct 14 23:00:00 1993 Path: biosci!steele!news From: Ecklab@OHSU.Edu Newsgroups: bionet.molbio.proteins Subject: Re: (His)6 tags for protein purification Message-ID: <1993Oct15.030240.29618@ohsu.edu> Date: 15 Oct 93 03:02:40 GMT References: Sender: news@ohsu.edu Distribution: usa Organization: Oregon Health Sci. Univ. Lines: 74 Nntp-Posting-Host: 137.53.72.135 In article dresnick@athena.mit.edu (David I Resnick) writes: >Hi, > >Has anyone out there used the Hisx6 tags for purification of recomb. >expressed proteins? I'm considering putting it on a fragment of a >protein we are studying and expressing it in yeast. However I have >the following questions/concerns: > >1) Does the His6 tag need to be at the very N or C terminus for the > protein for the protein to bind to the Ni2+ column? Or can > it be internal as long as it is solvent exposed? > >2) Has anyone actually done this in yeast? Would you expect it to > affect secretion in any way if this sequence were placed > immediately after a signal sequence (e.g. invertases')? > >Thanks! >-- > David Resnick dresnick@athena.mit.edu > Hello David, Yes I have used the poly histidine tag to purify an overexpressed protein. I overexpressed a 21 kDa chicken neurotrophic factor in E. coli and purified it in one step over a freshly prepared nickle resin. The system I used was the Qiagen PQE-8 vector (now superceeded by many newer and better vectors form the same company). In general I was very happy with the expression system. I got high levels of expression and the purification worked (roughly) as it claimed it would. In this case I inserted the 6 histidines at the amino terminus, though I could have also did it at the carboxy terminus (PQE-12. This form of the recombinant protein is of lower averall specific activity (30 picograms/ml) than the same protein in a different vector (lacking the histidine tag) (1 pg/ml), but I don't believe that's due to the histidine tag. As to whether or not an internal stretched of histidines would work, my guess is that it probably would, IF you were very careful about where you placed the sequence. It might also be necessary to put a longer stretch than 6 histidines in to get it work well. My recommendation is that it wouldn't be worth trying, because of the time it would take to re-engineer your protein so that it would both bind to the column and remain biologically active. Also, bear in mind that the purification procedure is pretty harsh. The 6 M guanidine hydrochloride and 8 M urea is essential. When I tried to remove my bound protein from the nickle column in the absence of urea (by low pH and detergent), nothing came off. This is probably a function of the histidine becoming buried within the protein when the urea is removed, thus locking it onto the column. The urea is also important to break apart the aggregated protein that resulted from overexpression. An important note about this kind of system is that for the nickle column to work as a one step purification you need to have very high levels of expression. Lots of other proteins do bind to this column and tend to elute with your recombinant protein. From that standpoint, high levels of expression is often the best purification step in and of itself. Judging from what I remember about old signal sequence mutagenesis papers I would think the six charged residues might lower the efficiency, or rate of secretion, but I don't think it would stop secretion altogether, if as you say it was placed immediately after the signal sequence. I would think that the high levels of expression might have a stronger effect on the ability of the protein to be expressed than would the presence of the charged residues. I've never tried this in yeast, but I bet a bacculovirus system would work well. I think trying it in yeast is certainly worth a try. By playing around with a variable or two, such as incuabtion temperatures and levels of induction I bet you could get it to work and be secreted. As an initial attempt you might try expressing it in E. coli and collecting your protein from the periplasmic space. Just a thought. Good luck with your research Tom Finn Internet: Ecklab@OHSU.edu Compuserve: 71360.2662 Fax: 1-503-494-4253 From owner-proteins@net.bio.net Fri Oct 15 23:00:00 1993 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!agate!headwall.Stanford.EDU!MED.Stanford.EDU!cmgm.stanford.edu!garren From: garren@cmgm.stanford.edu (Ron Garren) Newsgroups: bionet.molbio.proteins Subject: thymidine kinase type 1 half life Summary: send reply to garren@cmgm.stanford.edu. thanks ron Keywords: TK herpes half life Message-ID: Date: 15 Oct 93 07:24:24 GMT Sender: news@medmail.stanford.edu Organization: Stanford University, California, USA Lines: 4 If anyone out there knows the half life of herpes TK protein please let me know. I will be using it Jurkat cells. garren@cmgm.stanford.edu thanks ron From owner-proteins@net.bio.net Fri Oct 15 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!newsserver.jvnc.net!netnews.upenn.edu!biochem.dental.upenn.edu!lally From: lally@biochem.dental.upenn.edu (Ned Lally) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: cleavable acrylamide cross-linkers? Message-ID: <153547@netnews.upenn.edu> Date: 10 Oct 93 21:23:12 GMT References: <1993Oct7.174932.14210@emba.uvm.edu> <1993Oct8.094644.43162@urz.unibas.ch> Sender: news@netnews.upenn.edu Followup-To: bionet.molbio.methds-reagnts Organization: University of Pennsylvania Lines: 18 Xref: biosci bionet.molbio.methds-reagnts:8235 bionet.molbio.proteins:940 Nntp-Posting-Host: biochem.dental.upenn.edu In article <1993Oct8.094644.43162@urz.unibas.ch>, bickle@urz.unibas.ch writes: |> In article <1993Oct7.174932.14210@emba.uvm.edu>, brianf@med.uvm.edu (Brain Foley) writes: |> > Hi Bionetters: |> > |> > I know that there are some other cross-linkers for acrylamide. |> > Are any of them cleavable? I'd think it would be handy to "digest" the |> > gel and thus find it easier to get the protein out of it. Alternatively, |> > perhaps I could use agarose instead of acrylamide, but I have no |> > experience with agarose and proteins. |> > |> One cleavable crosslinker is a bis analogue containing alcohols on adjacent |> carbon atoms - cleavable with periodate. Sorry, no ref handy but you will |> find it catalogues under N, N' diallyl tartardiamide. Brian: Dumb question. Why can't you use electroelution? Or did I miss something. Bye, Ned From owner-proteins@net.bio.net Sat Oct 16 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!vixen.cso.uiuc.edu!howland.reston.ans.net!darwin.sura.net!news.Vanderbilt.Edu!news From: PLANCHAJ@ctrvax.Vanderbilt.Edu (Tony Planchart) Newsgroups: bionet.molbio.proteins Subject: Address for Peter Traub Message-ID: <1993Oct11.212014.25800@news.vanderbilt.edu> Date: 11 Oct 93 21:20:14 GMT Sender: news@news.vanderbilt.edu Organization: Vanderbilt University Lines: 15 Nntp-Posting-Host: ctrvax.vanderbilt.edu X-News-Reader: VMS NEWS 1.24 Hi There, Was wondering if any one might have an e-mail address for Dr. Peter Traub. I believe he is at the Max Planck Institut fur Zellbiologie in Ladenburg, Germany. Any help would be greatly appreciated. Also, if you happen to have an e-mail address for Robert Goldman at Northwestern University in Chicago, IL, it would be appreciated as well. Thanks, Tony Planchart Dept. of Molecular Biology Vanderbilt University Nashville, TN From owner-proteins@net.bio.net Sat Oct 16 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!tcsi.tcs.com!agate!han.hana.nm.kr!usenet From: bhkim@kuccnx.korea.ac.kr.korea.ac.kr (Byung-hoon Kim) Newsgroups: bionet.molbio.proteins Subject: protein CIP Message-ID: <1993Oct11.125703.15010@han.hana.nm.kr> Date: 11 Oct 93 12:57:03 GMT Sender: usenet@han.hana.nm.kr (news) Organization: KTRC in Seoul, Korea Lines: 8 X-Newsreader: Tin 1.1 PL3 Dear Netters I'm a novice in this field. Would you tell me how I can dephosphorylate DNA binding proteins, please? Buffer contents, reaction conditions...etc. Thanks in advance. Byung-Hoon Kim bhkim@kuccnx.korea.ac.kr From owner-proteins@net.bio.net Sat Oct 16 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!europa.eng.gtefsd.com!darwin.sura.net!lhc!azalea!francis From: francis@azalea.nlm.nih.gov (Francis Ouellette) Newsgroups: bionet.molbio.proteins Subject: Re: Address for Peter Traub Message-ID: <1993Oct12.042716.6561@nlm.nih.gov> Date: 12 Oct 93 04:27:16 GMT References: <1993Oct11.212014.25800@news.vanderbilt.edu> Sender: news@nlm.nih.gov Organization: National Library of Medicine Lines: 32 X-Newsreader: Tin 1.1 PL4 PLANCHAJ@ctrvax.Vanderbilt.Edu (Tony Planchart) writes: : Also, if you happen to have an e-mail address for Robert Goldman at : Northwestern University in Chicago, IL, it would be appreciated as well. checking the northwestern phone book from the gopher server at gopher.gdb.org I find: ------------------------------------------------------- alias: r-goldman name: goldman, robert d title: stephen w ranson professor department: cms biology title2: chairperson department2: cms biology office_address: w11145 : ward : ch w129 office_phone: 312-503-4215, 312-503-8249 ------------------------------------------------------- is this the right one? regards, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov From owner-proteins@net.bio.net Sat Oct 16 23:00:00 1993 Path: biosci!bcm!TAMUTS.TAMU.EDU!cs.utexas.edu!uunet!pipex!doc.ic.ac.uk!dapsun.lif.icnet.uk!not-for-mail From: js@bison.lif.icnet.uk ( BIU) Newsgroups: bionet.molbio.proteins Subject: Re: Domains - elucidating them automatically Message-ID: <29f86fINNn1p@bison.lif.icnet.uk> Date: 12 Oct 93 21:39:27 GMT References: <1993Oct12.121338.340243@ucl.ac.uk> Organization: Imperial Cancer Research Fund Lines: 13 NNTP-Posting-Host: bison.lif.icnet.uk In article <1993Oct12.121338.340243@ucl.ac.uk> mcdonald@bsm.bioc.ucl.ac.uk (Ian McDonald) writes: >I am looking for software that can automatically identify the borders between >protein domains if given a 3D structure. > >Please Email me, and I will post a summary. I'm looking forward to the results of this - as far as I know this is an unsettled problem. If no results though, try again in a year. -- Jack js@biu.icnet.uk If you only have a hammer, you tend to see every problem as a nail. -- Maslow From owner-proteins@net.bio.net Sat Oct 16 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!darwin.sura.net!news.Vanderbilt.Edu!news From: MCCOOLBA@ctrvx1.Vanderbilt.Edu (MCCOOLBA) Newsgroups: bionet.molbio.proteins Subject: Re: (His)6 tags for protein purification Message-ID: <1993Oct15.142150.1873@news.vanderbilt.edu> Date: 15 Oct 93 14:21:50 GMT Sender: news@news.vanderbilt.edu Organization: Vanderbilt University Lines: 36 Nntp-Posting-Host: ctrvax.vanderbilt.edu In a former article we saw... ---begin former article--- From: Ecklab@OHSU.Edu Subject: Re: (His)6 tags for protein purification Date: Fri, 15 Oct 1993 03:02:40 GMT In article dresnick@athena.mit.edu (David I Resnick) writes: >>Hi, >> >>Has anyone out there used the Hisx6 tags for purification of recomb. >>expressed proteins? I'm considering putting it on a fragment of a >>protein we are studying and expressing it in yeast. However I have >>the following questions/concerns: >> [snip] >Hello David, [snip] >[...] Also bear in mind that the purification procedure is pretty harsh.[...] [snip] and MCCOOLBA@cntrvx1.Vanderbilt.edu (MCCOOLBA) comments... David, As an alternative to the guanidinium/urea step in the purification of a His-tagged protein, one can elute such proteins from the nickel-agarose by using an imidizole gradient. This compound competes efficiently with the bound histidines and the gradient removes non-specifically bound material. Furthermore, since you are interested in doing this in yeast, problems with aggregation etc. that one typically runs into in the E. coli system should be minimal. Hope this helps, Brian A. McCool From owner-proteins@net.bio.net Sat Oct 16 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!news.ucdavis.edu!rocky.ucdavis.edu!ez005528 From: ez005528@rocky.ucdavis.edu (Kevin Morano) Newsgroups: bionet.molbio.proteins Subject: Re: Deglycosylation Message-ID: Date: 16 Oct 93 20:57:55 GMT References: Sender: usenet@ucdavis.edu (News Administrator) Organization: University of California, Davis Lines: 27 X-Newsreader: TIN [version 1.2 PL2] Lars Henrik Oestergaard (lho@biobase.aau.dk) wrote: : Dear reader, : I am desperately needing your assistance please. I have been trying to deglycosylate an antibody using TFMS (refs.: Sojar, Arch.Biochem and Biophys. 259:52-57 (1987) and Edge, Anal. Biochem. 118:131-137 (1981)). These attempts haven't been very succesfu ll untill now. My problem is that the deglycosylated protein behave strange, when subjected to electrophoresis afterwards. : Now I would like to try using enzymes instead. I have a feeling, that this is a more gentle way of doings things. My question for you: Does anyone out there ever have deglycosylated an antibody (with any luck)? What enzymes/deglycosidase did you use? Do you have any refs. to procedures? : Thank you. : Best wishes : Lars Henrik Oestergaard : Department of Chemistry : Aarhus University : Denmark From your description I can't quite tell if you still need functional Ab after your procedure or not. I would expect so, so what I'm about to say is probably irrelevant. I have used EndoH with good success to deglycosylate DENATURED proteins. This is the new stuff from New England Bioloabs and is pretty cheap, as deglycosylating enzymes go. ----------------------------------------------------------------------------- Internet:kamorano@ucdavis.edu "Why does it happen, because it happens..." Bitnet:kamorano@ucdavis N. Peart Section of Microbiology, University of California, Davis From owner-proteins@net.bio.net Sat Oct 16 23:00:00 1993 Path: biosci!news.cs.umb.edu!hsdndev!howland.reston.ans.net!noc.near.net!news.Brown.EDU!tsq-184.tsq.brown.edu!joe From: joe@as.tsq.brown.edu (Joe Lucas) Newsgroups: bionet.molbio.proteins Subject: E. Coli. D-glucose, D-galactose binding protein Message-ID: Date: 16 Oct 93 20:10:22 GMT Organization: Advanced Systems Lines: 4 NNTP-Posting-Host: tsq-184.tsq.brown.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] I am looking for the X-ray crystallography results from a 1987 paper in Nature 327, pg 635-638 by N.K. Vyas, M.N. Vyas, and F.A. Quiocho. I have checked in the protein data bank, but could not find it. Could anyone help me out? -Joe From owner-proteins@net.bio.net Sat Oct 16 23:00:00 1993 Path: biosci!HELIX.MGH.HARVARD.EDU!YEH From: YEH@HELIX.MGH.HARVARD.EDU Newsgroups: bionet.molbio.proteins Subject: (none) Message-ID: <01H489UI4S4Y8WZG5O@HELIX.MGH.HARVARD.EDU> Date: 17 Oct 93 23:56:57 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 1 I would like to cancel the subscription. Thank you very much for your kind help! From owner-proteins@net.bio.net Sat Oct 16 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!biosci!relay.the.net!SHAUN%JASON.DECNET From: SHAUN%JASON.DECNET@relay.the.net ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: Heme Oxygenase N-terminus? Message-ID: <01H41JLEDD8Y000T5Z@nic.the.net> Date: 13 Oct 93 05:19:22 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 8 Dear Colleagues, Does anyone know if the microsomal protein, Heme Oxygenase, has a free or blocked N-terminus? If it is blocked, what is the blocking group? Thanks in advance! Cheers, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Sat Oct 16 23:00:00 1993 Path: biosci!parc!decwrl!ames!agate!doc.ic.ac.uk!daresbury!daresbury!news From: emrasmus@dk.aau.biobase (Erik Michael Rasmussen) Newsgroups: bionet.molbio.proteins Subject: Re: chymotrypsin M.W. Message-ID: <1993Oct16.163039.16169@gserv1.dl.ac.uk> Date: 16 Oct 93 16:29:50 GMT References: <93101518160.~INN-LTAa21189.bionet-news@uk.ac.daresbury>; from "sergio@cnbvx3.cnb.uam.es" at Oct 15, 93 3:43 pm Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 18 Precedence: first-class Original-To: sergio@cnbvx3.cnb.uam.es Original-Cc: Proteins@uk.ac.daresbury X-Mailer: ELM [version 2.3 PL11] > > Hi, we are looking for the molecular weight of the protease: chymotrypsin > If someone could tell us we would be very gratefull. > Thanks in advance. > alpha-chymotrypsin (EC 3.4.21.1) has a molecular weight off about 25.000 D. A reference: Okamoto,Y. and Sekine,T. (1985) J.Biochem., 98, p.1143 By the way! You should get a FLUKA catalogue, because it has some good informations. Michael Erik Michael Rasmussen phone (+45) 35322100 Department of Genetics E-mail emrasmus@biobase.aau.dk Institute of Molecular Biology University of Copenhagen From owner-proteins@net.bio.net Sat Oct 16 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!pipex!uknet!bcc.ac.uk!bsm.bioc.ucl.ac.uk!mcdonald From: mcdonald@bsm.bioc.ucl.ac.uk (Ian McDonald) Newsgroups: bionet.molbio.proteins Subject: Domains - elucidating them automatically Message-ID: <1993Oct12.121338.340243@ucl.ac.uk> Date: 12 Oct 93 12:13:38 GMT Organization: Bloomsbury Computing Consortium Lines: 6 I am looking for software that can automatically identify the borders between protein domains if given a 3D structure. Please Email me, and I will post a summary. Ian From owner-proteins@net.bio.net Sun Oct 17 23:00:00 1993 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!darwin.sura.net!news.Vanderbilt.Edu!news From: MCCOOLBA@ctrvx1.Vanderbilt.Edu (MCCOOLBA) Newsgroups: bionet.molbio.proteins Subject: Re: (His)6 tags for protein purification Message-ID: <1993Oct15.142150.1873@news.vanderbilt.edu> Date: 15 Oct 93 14:21:50 GMT Sender: news@news.vanderbilt.edu Organization: Vanderbilt University Lines: 36 Nntp-Posting-Host: ctrvax.vanderbilt.edu In a former article we saw... ---begin former article--- From: Ecklab@OHSU.Edu Subject: Re: (His)6 tags for protein purification Date: Fri, 15 Oct 1993 03:02:40 GMT In article dresnick@athena.mit.edu (David I Resnick) writes: >>Hi, >> >>Has anyone out there used the Hisx6 tags for purification of recomb. >>expressed proteins? I'm considering putting it on a fragment of a >>protein we are studying and expressing it in yeast. However I have >>the following questions/concerns: >> [snip] >Hello David, [snip] >[...] Also bear in mind that the purification procedure is pretty harsh.[...] [snip] and MCCOOLBA@cntrvx1.Vanderbilt.edu (MCCOOLBA) comments... David, As an alternative to the guanidinium/urea step in the purification of a His-tagged protein, one can elute such proteins from the nickel-agarose by using an imidizole gradient. This compound competes efficiently with the bound histidines and the gradient removes non-specifically bound material. Furthermore, since you are interested in doing this in yeast, problems with aggregation etc. that one typically runs into in the E. coli system should be minimal. Hope this helps, Brian A. McCool From owner-proteins@net.bio.net Sun Oct 17 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!howland.reston.ans.net!spool.mu.edu!olivea!news.bbn.com!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!husc10!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.molbio.proteins Subject: Re: E. Coli. D-glucose, D-galactose binding protein Message-ID: Date: 17 Oct 93 17:05:46 GMT References: Organization: Harvard University, Cambridge, Massachusetts Lines: 12 NNTP-Posting-Host: husc10.harvard.edu According to a BLAST search of the NCBI databases, the PDB accessions 2GBP and 3GBP contain X-ray data for the E.coli periplasmic galactose binding protein (mglB gene product). Hope it helps. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@biosun.harvard.edu From owner-proteins@net.bio.net Sun Oct 17 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!wupost!howland.reston.ans.net!agate!biosci!HELIX.MGH.HARVARD.EDU!YEH From: YEH@HELIX.MGH.HARVARD.EDU Newsgroups: bionet.molbio.proteins Subject: (none) Message-ID: <01H489UI4S4Y8WZG5O@HELIX.MGH.HARVARD.EDU> Date: 17 Oct 93 23:56:57 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 1 I would like to cancel the subscription. Thank you very much for your kind help! From owner-proteins@net.bio.net Sun Oct 17 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!wupost!spool.mu.edu!olivea!news.bbn.com!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!husc10!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.molbio.proteins Subject: Re: E. Coli. D-glucose, D-galactose binding protein Message-ID: Date: 17 Oct 93 17:05:46 GMT References: Organization: Harvard University, Cambridge, Massachusetts Lines: 12 NNTP-Posting-Host: husc10.harvard.edu According to a BLAST search of the NCBI databases, the PDB accessions 2GBP and 3GBP contain X-ray data for the E.coli periplasmic galactose binding protein (mglB gene product). Hope it helps. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@biosun.harvard.edu From owner-proteins@net.bio.net Sun Oct 17 23:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!daresbury!daresbury!news From: emrasmus@dk.aau.biobase (Erik Michael Rasmussen) Newsgroups: bionet.molbio.proteins Subject: Re: chymotrypsin M.W. Message-ID: <1993Oct16.163039.16169@gserv1.dl.ac.uk> Date: 16 Oct 93 16:29:50 GMT References: <93101518160.~INN-LTAa21189.bionet-news@uk.ac.daresbury>; from "sergio@cnbvx3.cnb.uam.es" at Oct 15, 93 3:43 pm Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 18 Precedence: first-class Original-To: sergio@cnbvx3.cnb.uam.es Original-Cc: Proteins@uk.ac.daresbury X-Mailer: ELM [version 2.3 PL11] > > Hi, we are looking for the molecular weight of the protease: chymotrypsin > If someone could tell us we would be very gratefull. > Thanks in advance. > alpha-chymotrypsin (EC 3.4.21.1) has a molecular weight off about 25.000 D. A reference: Okamoto,Y. and Sekine,T. (1985) J.Biochem., 98, p.1143 By the way! You should get a FLUKA catalogue, because it has some good informations. Michael Erik Michael Rasmussen phone (+45) 35322100 Department of Genetics E-mail emrasmus@biobase.aau.dk Institute of Molecular Biology University of Copenhagen From owner-proteins@net.bio.net Sun Oct 17 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!noc.near.net!news.Brown.EDU!tsq-184.tsq.brown.edu!joe From: joe@as.tsq.brown.edu (Joe Lucas) Newsgroups: bionet.molbio.proteins Subject: E. Coli. D-glucose, D-galactose binding protein Message-ID: Date: 16 Oct 93 20:10:22 GMT Organization: Advanced Systems Lines: 4 NNTP-Posting-Host: tsq-184.tsq.brown.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] I am looking for the X-ray crystallography results from a 1987 paper in Nature 327, pg 635-638 by N.K. Vyas, M.N. Vyas, and F.A. Quiocho. I have checked in the protein data bank, but could not find it. Could anyone help me out? -Joe From owner-proteins@net.bio.net Sun Oct 17 23:00:00 1993 Path: biosci!BCRSSU.AGR.CA!RAMPITSCH From: RAMPITSCH@BCRSSU.AGR.CA Newsgroups: bionet.molbio.proteins Subject: Apple Proteins Message-ID: <01H49N36HE6A001LJQ@GW.AGR.CA> Date: 18 Oct 93 23:41:01 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 Hi! I am isolating protein from freshly prepared and centrifuged apple juice. I have two questions: 1) The isolation procedure involves a phenol/chloroform extraction followed by an isopropanol precipitation. I am having trouble redissolving the resulting precipitate for BioRad's Bradford microassay. Any suggestions? 2) I want to know what specific interaction occurs between apple proanthocyanins and glycoproteins, carbohydrates and pure proteins. Any information or references would be appreciated (literature is scarce in this area...) On a related topic: I am desperately seeking apple proanthocyanin standards especially B1, B2, B3 etc. Do you know a source, or have a friend who has these??? Am willing to pay $mall $ums. Thanks for your help Chris R. From owner-proteins@net.bio.net Sun Oct 17 23:00:00 1993 Path: biosci!agate!news.ucdavis.edu!rocky.ucdavis.edu!ez005528 From: ez005528@rocky.ucdavis.edu (Kevin Morano) Newsgroups: bionet.molbio.proteins Subject: Re: Deglycosylation Message-ID: Date: 16 Oct 93 20:57:55 GMT References: Sender: usenet@ucdavis.edu (News Administrator) Organization: University of California, Davis Lines: 27 X-Newsreader: TIN [version 1.2 PL2] Lars Henrik Oestergaard (lho@biobase.aau.dk) wrote: : Dear reader, : I am desperately needing your assistance please. I have been trying to deglycosylate an antibody using TFMS (refs.: Sojar, Arch.Biochem and Biophys. 259:52-57 (1987) and Edge, Anal. Biochem. 118:131-137 (1981)). These attempts haven't been very succesfu ll untill now. My problem is that the deglycosylated protein behave strange, when subjected to electrophoresis afterwards. : Now I would like to try using enzymes instead. I have a feeling, that this is a more gentle way of doings things. My question for you: Does anyone out there ever have deglycosylated an antibody (with any luck)? What enzymes/deglycosidase did you use? Do you have any refs. to procedures? : Thank you. : Best wishes : Lars Henrik Oestergaard : Department of Chemistry : Aarhus University : Denmark From your description I can't quite tell if you still need functional Ab after your procedure or not. I would expect so, so what I'm about to say is probably irrelevant. I have used EndoH with good success to deglycosylate DENATURED proteins. This is the new stuff from New England Bioloabs and is pretty cheap, as deglycosylating enzymes go. ----------------------------------------------------------------------------- Internet:kamorano@ucdavis.edu "Why does it happen, because it happens..." Bitnet:kamorano@ucdavis N. Peart Section of Microbiology, University of California, Davis From owner-proteins@net.bio.net Sun Oct 17 23:00:00 1993 Path: biosci!lhc!biosci!BCRSSU.AGR.CA!RAMPITSCH From: RAMPITSCH@BCRSSU.AGR.CA Newsgroups: bionet.molbio.proteins Subject: Apple Proteins Message-ID: <01H49N36HE6A001LJQ@GW.AGR.CA> Date: 18 Oct 93 23:41:01 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 Hi! I am isolating protein from freshly prepared and centrifuged apple juice. I have two questions: 1) The isolation procedure involves a phenol/chloroform extraction followed by an isopropanol precipitation. I am having trouble redissolving the resulting precipitate for BioRad's Bradford microassay. Any suggestions? 2) I want to know what specific interaction occurs between apple proanthocyanins and glycoproteins, carbohydrates and pure proteins. Any information or references would be appreciated (literature is scarce in this area...) On a related topic: I am desperately seeking apple proanthocyanin standards especially B1, B2, B3 etc. Do you know a source, or have a friend who has these??? Am willing to pay $mall $ums. Thanks for your help Chris R. From owner-proteins@net.bio.net Mon Oct 18 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!usc!howland.reston.ans.net!agate!biosci!QMS1.LIFE.UIUC.EDU!Dan_Szymanski From: Dan_Szymanski@QMS1.LIFE.UIUC.EDU ("Dan Szymanski") Newsgroups: bionet.molbio.proteins Subject: Re: protein CIP Message-ID: <199310141724.AA25410@nicnext.life.uiuc.edu> Date: 14 Oct 93 18:18:22 GMT Sender: news@net.bio.net Distribution: bionet Lines: 36 Reply to: RE>protein CIP no suggestions netters? how about the different enzymatic phospatases? do any companies make a preparation that is more pure or more active at room temperature? can the problem be attacked by inhibiting the kinases, with excess target peptide for example? share your thoughts. -------------------------------------- Date: 10/11/93 8:30 PM To: Dan Szymanski From: Byung-hoon Kim Dear Netters I'm a novice in this field. Would you tell me how I can dephosphorylate DNA binding proteins, please? Buffer contents, reaction conditions...etc. Thanks in advance. Byung-Hoon Kim bhkim@kuccnx.korea.ac.kr ------------------ RFC822 Header Follows ------------------ Received: by qms1.life.uiuc.edu with SMTP;11 Oct 1993 20:30:40 -0600 Received: by net.bio.net (5.65/IG-2.0) id AA03367; Mon, 11 Oct 93 18:14:04 -0700 Received: by net.bio.net (5.65/IG-2.0) id AA03351; Mon, 11 Oct 93 18:13:58 -0700 Message-Id: <9310120113.AA03351@net.bio.net> To: proteins@net.bio.net From: bhkim@kuccnx.korea.ac.kr.korea.ac.kr (Byung-hoon Kim) Subject: protein CIP Date: 11 Oct 93 12:57:03 GMT Sender: usenet@han.hana.nm.kr (news) X-Newsreader: Tin 1.1 PL3 From owner-proteins@net.bio.net Mon Oct 18 23:00:00 1993 Path: biosci!HELIX.MGH.HARVARD.EDU!YEH From: YEH@HELIX.MGH.HARVARD.EDU Newsgroups: bionet.molbio.proteins Subject: T4 gene 32 protein Message-ID: <01H4B8ST4VXU8WW1HZ@HELIX.MGH.HARVARD.EDU> Date: 20 Oct 93 03:03:21 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 3 Does anybody know the binding site and binding constant (to single strand DNA) of T4 gene 32 protein? Jade Leaf From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!pipex!uknet!comlab.ox.ac.uk!oxuniv!oxpath!iwilson From: iwilson@molbiol.ox.ac.uk Newsgroups: bionet.molbio.proteins Subject: Re: Deglycosylation Message-ID: <1993Oct22.130338.1@molbiol.ox.ac.uk> Date: 22 Oct 93 12:03:38 GMT References: Organization: Oxford University Molecular Biology Data Centre Lines: 26 Nntp-Posting-Host: heatly Nntp-Posting-User: iwilson In article , ez005528@rocky.ucdavis.edu (Kevin Morano) writes: > Lars Henrik Oestergaard (lho@biobase.aau.dk) wrote: > : Dear reader, > > : I am desperately needing your assistance please. I have been trying to deglycosylate an antibody using TFMS (refs.: Sojar, Arch.Biochem and Biophys. 259:52-57 (1987) and Edge, Anal. Biochem. 118:131-137 (1981)). These attempts haven't been very succes > ll untill now. My problem is that the deglycosylated protein behave strange, when subjected to electrophoresis afterwards. > > : Now I would like to try using enzymes instead. I have a feeling, that this is a more gentle way of doings things. My question for you: Does anyone out there ever have deglycosylated an antibody (with any luck)? What enzymes/deglycosidase did you use? > you have any refs. to procedures? > > > From your description I can't quite tell if you still need functional Ab > after your procedure or not. I would expect so, so what I'm about to say > is probably irrelevant. I have used EndoH with good success to > deglycosylate DENATURED proteins. This is the new stuff from New England > Bioloabs and is pretty cheap, as deglycosylating enzymes go. > But EndoH is only suitable for certain oigosaccharide structures. Endoglycosidases of course leave a GlcNAc behind and all have distinct glycan specificities. PNGase F is more general. Get the Oxford GlycoSystems catalogue: they operate in the US. (I use their products, but do not work forthem.) It has a wide range of things. Iain Wilson Dyson Perrins Laboratory, University of Oxford iwilson@molbiol.ox.ac.uk From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!bcm!avdms8.msfc.nasa.gov!europa.eng.gtefsd.com!darwin.sura.net!news.gdb.org!dev.gdb.org!danj From: danj@dev.gdb.org (Dan Jacobson) Newsgroups: bionet.molbio.proteins,bionet.software,bionet.molbio.genbank Subject: Re: Message-ID: <1993Oct21.211849.996@news.gdb.org> Date: 21 Oct 93 21:18:49 GMT References: <20OCT93.20423407.0085@VM1.MCGILL.CA> Sender: news@news.gdb.org Organization: Johns Hopkins University Genome Data Base (GDB) Lines: 83 Xref: biosci bionet.molbio.proteins:977 bionet.software:6282 bionet.molbio.genbank:1414 Nntp-Posting-Host: dev.gdb.org In article <20OCT93.20423407.0085@VM1.MCGILL.CA> MDNB000 writes: >Dear networkers, > >Could you please help me to locate the right databases and software >for searching for potential tyrosine and serine/threonine kinases >phosphorylation sites, potential SH2/SH3 domain motifs in proteins, >and other important sequences participating in the phospharylation >and complexing of protein kinases with their substrates and "adaptor" >proteins, respectively. > There's a database and two pieces of software which will do this for you available by gopher or ftp. For Unix or Vax/VMS you can get prosearch2.1 and for the Macintosh there's Macpattern both of which will allow you to scan your sequence against the Prosite database (a database of the wide variety of patterns which indidcate motifs and potential sites for post-translational modifications). You can get the latest version of the Prosite Database, Prosearch, and Macpattern by gopher or by anonymous ftp. Prosite: Gopher: Point your gopher client at merlot.welch.jhu.edu and go to the following directories: --> FTP Sites For Biology/ --> NCBI Repository FTP Archive / --> prosite/ Ftp: anonymous ftp to ncbi.nlm.nih.gov ----- Prosearch: Gopher: --> FTP Sites For Biology/ --> IUBio-Software+Data (Indiana)/ --> molbio/ --> search/ --> prosearch2.1.shar Ftp: anonymous ftp to ftp.bio.indiana.edu ----- Macpattern: Gopher: --> FTP Sites For Biology/ --> EMBL software (Heidelberg)/ --> software/ --> mac/ --> macpattern.hqx Ftp: anonymous ftp to ftp.embl-heidelberg.de Best of luck, Dan Jacobson danj@mail.gdb.org From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!europa.eng.gtefsd.com!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.molbio.proteins Subject: Re: searching for pdb entries Message-ID: Date: 20 Oct 93 23:43:00 GMT References: Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 18 Nntp-Posting-Host: sunflower.bio.indiana.edu Sure, just gopher to pdb.pdb.bnl.gov, and search away... You also can get pictures of the molecules returned from your gopher search, along with the molecule data in text format. For your example: An (almost) full text search of the PDB Bibliographic Headers: pseudomonas ... 17. 1pha : CYTOCHROME P450CAM FROM PSEUDOMONAS PUTIDA CAMPHOR MONOXYGE../ 18. 1phb : CYTOCHROME P450CAM FROM PSEUDOMONAS PUTIDA CAMPHOR MONOXYGE../ 19. 1phc : CYTOCHROME P450CAM FROM PSEUDOMONAS PUTIDA CAMPHOR MONOXYGE../ ... You'll also find the PDB gopher listed under Other-Bio-Gophers/ at IUBio archive as Protein Data Bank, and you will find links to it many of your favorite biogopher holes. -- don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!emory!nigel.msen.com!sdd.hp.com!spool.mu.edu!umn.edu!mayonews.mayo.edu!RICKE@rcf.mayo.edu From: ricke@rcf.mayo.edu Newsgroups: bionet.molbio.proteins Subject: NMDA structure Message-ID: <2a9kjo$crp@fermat.mayo.edu> Date: 22 Oct 93 21:50:48 GMT Reply-To: ricke@rcf.mayo.edu Organization: Research Computing Facility, Mayo Foundation, Rochester MN, USA Lines: 5 NNTP-Posting-Host: newton.mayo.edu Where can I find out the 3-D structure of NMDA (N-methyl-D-aspartate)? I am interested in neurotoxicity of the NMDA receptor. Thanks, Darrell O. Ricke From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!bcm!avdms8.msfc.nasa.gov!sol.ctr.columbia.edu!caen!malgudi.oar.net!news.ysu.edu!psuvm!axc19 From: AXC19@psuvm.psu.edu Newsgroups: bionet.molbio.proteins Subject: protein sequence data base Message-ID: <93294.143248AXC19@psuvm.psu.edu> Date: 21 Oct 93 18:32:48 GMT Organization: Penn State University Lines: 7 I need some guidance on what and where or who to go to ...I finally got the ami no acid sequence of a protein of interest...Now, how can I do an aminoacid comp arison to other proteins and figure out if it has already been isolated. Any h elp will be appreciated. Thanks, Aida Cancel axc19@psuvm.psu.edu From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: jmorriso@uk.ac.crc (Dr. J.R. Morrison) Newsgroups: bionet.molbio.proteins Subject: I have a repeating (x4) "motif" running through a protein Message-ID: <1993Oct21.164202.7968@gserv1.dl.ac.uk> Date: 21 Oct 93 16:41:27 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 3 Precedence: first-class Original-To: proteins@uk.ac.daresbury that I am currently studying. The repeat: Rx(x)PH - which is usual by an alpha-helix. Is this a metal binding site? I'd appeciate any comments on this subject! From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!justus.phs.uiuc.edu!user From: gruebele@aries.scs.uiuc.edu (Martin Gruebele) Newsgroups: bionet.molbio.proteins Subject: help: Trp substitution mutants Message-ID: Date: 21 Oct 93 02:13:47 GMT Followup-To: bionet.molbio.proteins Organization: University of Illinois Lines: 13 NNTP-Posting-Host: justus.phs.uiuc.edu I need as much information as possible on sources and availability of single tryptophan substitution mutants; some examples of proteins with multiple available mutants include E. coli adenylate kinase, rat intestinal retinol binding protein, etc. I am interested mostly in small globular proteins with well-determined X-ray structure, and am interested in mutants where the site directed mutagenesis and purification have been worked out in detail. If you know of a good place to find such information, please let me know. (I am interested in this information to do fluorescence experiments.) Martin Gruebele Beckman Institute for Advanced Science and Technology gruebele@aries.scs.uiuc.edu From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!bcm!avdms8.msfc.nasa.gov!europa.eng.gtefsd.com!howland.reston.ans.net!pipex!sunic!corax.udac.uu.se!zeta.bmc.uu.se!daresbury!daresbury!news From: jmorriso@uk.ac.crc (Dr. J.R. Morrison) Newsgroups: bionet.molbio.proteins Subject: I have a repeating "motif" running through a protein that Message-ID: <1993Oct21.160033.5905@gserv1.dl.ac.uk> Date: 21 Oct 93 16:00:07 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 3 Precedence: first-class Original-To: proteins@uk.ac.daresbury I am currently studying. The repeat: Rx(x)PH - it is repeated 4 X and is a apparently followed by a alpha helix. Any ideas? Is it a metal binding site? I'd appreciate any comments! From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!uwm.edu!wupost!medicine.wustl.edu!msdisk.wustl.edu!wetsel_r From: wetsel_r@msdisk.wustl.edu Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: RE: 35S volatility and incubators... Message-ID: <21OCT93.23034059@msdisk.wustl.edu> Date: 22 Oct 93 04:03:40 GMT References: <2a4bjl$7qd@nnrp.ucs.ubc.ca> Organization: Washington University in St. Louis, Medical Library Lines: 32 Xref: biosci bionet.molbio.proteins:980 bionet.molbio.methds-reagnts:8414 NNTP-Posting-Host: msnews.wustl.edu In a previous article, goldberg@unixg.ubc.ca (Goldberg Andrew) wrote: > >I will shortly be doing metabolic labelling of cells in culture with >35S-cys and 35S-met, and do not wish to frighten/enrage co-workers with > >1) Does anyone employ such a device? >2) Is such a thing available ready-made? >3) Is such a thing really necessary? (I expect to be putting a few > hundred micro-curies into this incubator, potentially overnight) ---- Whether you need such a device will depend on how much or how many metabolic labeling reactions you foresee having to do. We routinely do them in small volumes with small amounts ( less than 200 uCi per group) and we rarely label longer than 4 hours (except for pulse chase experiments). Cys isn't the problem, the Met is. It is volitle and light up your incubator like a Christmas tree if you use a lot of it very often. "Do we employ such a device?" No - at least not yet as decontamination of the incubator has has only been 2-3 times per year. Why? (Is such a thing available?) Yes and they aint cheap! They are air-tight circular 14-16 inch plastic containers that run about $175 a pop. For those that get those "biotechniques action cards", everynow and then there is a advertisment for these containers in that collection of cards - maybe someone could post the pertinent info. They come with a charcoal filter. "Will you need it?" again, you need to determine if this is something you're going to do a lot to justify the cost. If you're only going to label every now and then, you may not need it. Hope this helps, David haviland@kids.wustl.edu From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!howland.reston.ans.net!sol.ctr.columbia.edu!news.mtu.edu!news.mtu.edu!not-for-mail From: plnitz@mtu.edu (PP Nitz) Newsgroups: bionet.molbio.proteins Subject: Information on Acorn Composition? Message-ID: <2a98q5$3if@chem11.chem> Date: 22 Oct 93 18:29:25 GMT Organization: Michigan Technological University Lines: 15 NNTP-Posting-Host: chem11.chem.mtu.edu X-Newsreader: TIN [version 1.2 PL1] I am working on a design project involving acorns. If anyone can give me information about acorn processing, or acorn compostion (such as protein content, etc.), or where to look for such information, I would greatly appreciate your help. Sincerely, Peter L Nitz Michigan Technological University ___ _ ___________________________________ Snapped like a | | | | /__ | Peter L Nitz _ _ __ | |/\| | \_/ , | Operations Supervisor * * | |__ | Chem-Met Computer Labs \ my mind | __| the vacuum! | plnitz@mtu.edu ,_) From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!newsflash.concordia.ca!sifon!VM1.MCGILL.CA From: MDNB@MUSICA.MCGILL.CA (MDNB000) Newsgroups: bionet.molbio.proteins,bionet.software,bionet.molbio.genbank Subject: Message-ID: <20OCT93.20423407.0085@VM1.MCGILL.CA> Date: 20 Oct 93 23:54:38 GMT Sender: usenet@MUSICA.MCGILL.CA Organization: McGill University Lines: 15 Xref: biosci bionet.molbio.proteins:970 bionet.software:6276 bionet.molbio.genbank:1411 Dear networkers, Could you please help me to locate the right databases and software for searching for potential tyrosine and serine/threonine kinases phosphorylation sites, potential SH2/SH3 domain motifs in proteins, and other important sequences participating in the phospharylation and complexing of protein kinases with their substrates and "adaptor" proteins, respectively. Thank you in advance. Nikolai I. Baeff, M.D. Montreal Neurological Institute McGill University mdnb@musica.mcgill.ca From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!news-feed-2.peachnet.edu!emory!nigel.msen.com!sdd.hp.com!vixen.cso.uiuc.edu!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!magnesium.club.cc.cmu.edu!pitt.edu!ache.pharm.pitt.edu!user From: drg@prophet.pharm.pitt.edu (Duke Groebe) Newsgroups: bionet.molbio.proteins Subject: Re: Matrix Prot. Seq. Analysis Message-ID: Date: 22 Oct 93 21:09:39 GMT Sender: news+@pitt.edu Followup-To: bionet.molbio.proteins Organization: University of Pittsburgh Lines: 25 I'm looking for a computer program (Mac preferred) that will do a 2D matrix sequence analysis on a protein. I want to look at amino acid interactions between domains of a protein and compare those interactions with other proteins of the same family. Ideally, I could enter the sequences of a number of proteins (hopefully, database format would be acceptable), the program would do an analysis of the sequences to pair amino acids along the sequences of each protein (a pairing not between different sequences but of the same sequence), then the program would compare the pairings from each protein and look for conserved interactions between similar domains of the proteins. If no such program exists, is there a program I could modify to do something somewhat close to it? Responses by e-mail or post will be greatly appreciated. Duke ****************************************************************************** The opinions expressed here are my own. MY very own and NOBODY else's! I THOUGHT OF THEM FIRST, HA HA, AND YOU DIDN'T!! SEE!? There's my name up there! And the date - Ooohh, the DATE! That's important! HEE HEE, I GONNA BE FAMOUS! DO YOU HERE ME!? FAMOUS!! HA HA!! They're mine...heh, heh, all mine.... GOD! I'm so smart! From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!europa.eng.gtefsd.com!news.ans.net!malgudi.oar.net!news.ysu.edu!psuvm!blb122 From: BLB122@psuvm.psu.edu Newsgroups: sci.bio,bionet.molbio.proteins Subject: Parasporal body proteins Message-ID: <93295.130800BLB122@psuvm.psu.edu> Date: 22 Oct 93 17:08:00 GMT Organization: Penn State University Lines: 10 Xref: biosci sci.bio:5818 bionet.molbio.proteins:982 Is there any recent research into the behavior of parasporal body proteins of Bacillus and Clostridium bacteria? Do these proteins - which act as cidal agents for endosporal protection - disrupt transcription of their target organisms? I know the parasporal body of B. thuringienis contains protein toxins which kill over a hundred species of moths by attacking plasma membranes of epithelial cells - but I am interested to know if any of these parasporal proteins enter cells and bind DNA as inhibiting/steric blocking agents of transcript factors? Any comment would be appreciated - please email me personally. thanks. -BRUCE BOOTH- From owner-proteins@net.bio.net Thu Oct 21 23:00:00 1993 Path: biosci!daresbury!s-crim1!mbarg From: mbarg@s-crim1.dl.ac.uk (A.R. Gargaro) Newsgroups: bionet.molbio.proteins Subject: Re: Deglycosylation Message-ID: <2a90pr$svd@mserv1.dl.ac.uk> Date: 22 Oct 93 16:12:43 GMT References: <1993Oct22.130338.1@molbiol.ox.ac.uk> Sender: mbarg@s-crim1 (A.R. Gargaro) Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 33 NNTP-Posting-Host: s-crim1.dl.ac.uk In article <1993Oct22.130338.1@molbiol.ox.ac.uk>, iwilson@molbiol.ox.ac.uk writes: |> In article , ez005528@rocky.ucdavis.edu (Kevin Morano) writes: |> > Lars Henrik Oestergaard (lho@biobase.aau.dk) wrote: |> > : Dear reader, |> > |> > : I am desperately needing your assistance please. I have been trying to deglycosylate an antibody using TFMS (refs.: Sojar, Arch.Biochem and Biophys. 259:52-57 (1987) and Edge, Anal. Biochem. 118:131-137 (1981)). These attempts haven't been very succes|> |> > ll untill now. My problem is that the deglycosylated protein behave strange, when subjected to electrophoresis afterwards. |> > |> > : Now I would like to try using enzymes instead. I have a feeling, that this is a more gentle way of doings things. My question for you: Does anyone out there ever have deglycosylated an antibody (with any luck)? What enzymes/deglycosidase did you use? |> |> > you have any refs. to procedures? |> > |> > |> > From your description I can't quite tell if you still need functional Ab |> > after your procedure or not. I would expect so, so what I'm about to say |> > is probably irrelevant. I have used EndoH with good success to |> > deglycosylate DENATURED proteins. This is the new stuff from New England |> > Bioloabs and is pretty cheap, as deglycosylating enzymes go. |> > |> But EndoH is only suitable for certain oigosaccharide structures. |> Endoglycosidases of course leave a GlcNAc behind and all have distinct glycan |> specificities. PNGase F is more general. Get the Oxford GlycoSystems |> catalogue: they operate in the US. (I use their products, but do not work |> forthem.) It has a wide range of things. |> |> Iain Wilson |> Dyson Perrins Laboratory, University of Oxford |> iwilson@molbiol.ox.ac.uk |> I would also recommend Oxford Glycosystems and the enzyme we use is called EndoF and is really quite good for deglycosylating proteins and antibodies. Hope this helps, Angelo From owner-proteins@net.bio.net Fri Oct 22 23:00:00 1993 Path: biosci!parc!decwrl!ames!agate!howland.reston.ans.net!pipex!uknet!gdt!bspjtpp From: bspjtpp@midge.bath.ac.uk (J T P Pedersen) Newsgroups: bionet.molbio.proteins Subject: Building sidechains onto Ca coordinates Keywords: Crystal structures with Ca only Message-ID: Date: 23 Oct 93 17:47:21 GMT Sender: Dr Jan T Pedersen bspjtpp@midge.bath.ac.uk Distribution: bionet.molbio.proteins Organization: School of Biological Sciences, University of Bath, UK Lines: 20 I am looking for a program which may help me solve the problem of reconstructing the missing coordinates in protein structure files which have only been deposited with Ca coordinates. Many of the commercial Molecular Modelling programs can build things, but I have not yet seen a smart program which attempts to use recognisab- le parts of secondary structure as the takeoff points for reconstruction. Eg an alpha helix would give you the direction of Cb, and hence the backbone etc. I am interested in a program which is able to solve the problem in a ``smart'' way. If anybody know of such a program, or would like to add to the discussion - let them come forward. Yours Jan T Pedersen MGU (Bath University) bspjtpp@midge.bath.ac.uk From owner-proteins@net.bio.net Fri Oct 22 23:00:00 1993 Path: biosci!SCRI.FSU.EDU!STRELETS From: STRELETS@SCRI.FSU.EDU Newsgroups: bionet.molbio.proteins Subject: Announcement: compact PIR with dialog shell for PC Message-ID: <931023140558.204141b3@scri.fsu.edu> Date: 23 Oct 93 18:05:58 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 189 SAGITTARIUS DataBanks Information ********************************* SAGITTARIUS Automated Sequence Bank is a dialog shell for object-oriented compression, storage and manipulation of sequence database information with orientation on MS DOS PC-compartibles (386 or 486 recommended), with installed hard disk optimizators (like Hyperdisk, Ncache, Smartdrive and others). Currently it's oriented on GENBANK and PIR databases. Dialog data shell includes following main possibilities: - selection of sequnces to bank buffer by - dictionary-defined record for specified informational field (name, source, keyword, feature etc.) - user-defined context in specified informational field (name, source, keyword, feature etc.) - set of dictionary-defined records for different informational fields (source, keyword, superfamily etc.) - SEQ (non)perfect homology with user-defined short sequence - store and retrieve buffer content (SEQ bank numbers and indexes) between sessions - output user-specified (buffer) SEQ data to disk files - fast SEQ homology searches (for user-defined SEQ of length not more 50-100 positions, only 1 hour with full bank on 386/33) - fast subregion-sensitive pairwaise alignments (user-defined sequence with buffer SEQ's or full bank, only some hours with full bank on 386/33) - easy data access from user programs (C) as a support for applications development Data bank files filled out by current available database information (2/4 times in a year) only by distributors. Distributive variant includes ready-for-use informational files and some number of executables - all in ZIP-compressed form. PIR-37 (30 June 1993) variant ***************************** For today PIR-derived compressed databank stores following original database informational fields: - database entry index - accession number(s) - other (non-PIR) database crossreference(s) - protein name - organism name - alternative protein name(s) - keyword(s) - superfamily name - gene name - organism host name - map position - unusual codon(s) - intron(s) placement - reference(s), including for each: -journal or citation -author(s) -title -free-format comment - feature(s) - free-format comment - protein sequence For PIRr37, all bank files takes 31 Mb on hard disk ( 16 Mb in ZIP-compressed form). Each original database informational field is stored in separate files set what allows user to build reduced bank variants. For example, deletion of literature references reduces bank to only 23 Mb. Core (minimal configuration) variant of databank files includes only indexes and sequences. All higher variants produced by adding (depacking from distributive) corresponding file sets. List of distributive files with decompressed files data ------------------------------------------------------- ------------------------------------------------------------------------------- ZipFile ZipSize FilesSize Content Description -------------------------------------------------------\/ Stable config part \/ CORE 9247493 12.672 Mb - sequnces and indexes EXE_FILE 83701 .443 Mb - bank executable -------------------------------------------------------\/ User variable part \/ NAM 796747 1.687 Mb - protein names SOURCE 467121 1.161 Mb - sources KEYWORD 251101 .768 Mb - keywords S_FAMILY 158102 .493 Mb - superfamilies CROSSREF 198241 .500 Mb - crossreferences FEATURE 637868 2.160 Mb - sequence features MAP 21955 .190 Mb - map positions ALT_NAM 148836 .502 Mb - alternative names GENE 107297 .374 Mb - gene names HOST 15944 .149 Mb - host names CODON 6783 .174 Mb - unusual start codons ACC_CODE 740177 1.478 Mb - accession codes COMMENT 244859 .813 Mb - free-format comments INTRON 30182 .214 Mb - introns placement REF_JOU 753918 1.984 Mb - references/journals REF_AUTH 1177044 2.519 Mb - references/authors (needs REF_JOU) REF_TITL 1325438 3.129 Mb - references/titles (needs REF_JOU) REF_COMM 220626 .754 Mb - references/comments (needs REF_JOU) ------------------------------------------------------------------------------- SAGITTARIUS PIR is available by anonymous FTP from: - FTP.SCRI.FSU.EDU, directory /pub/genetics/pir/ Probably SAGITTARIUS PIR is available by anonymous FTP from some of the well-known bio-servers (iubio etc.). ------------------------------------------------------------- Installation ------------ All decompressed SAGITTARIUS databank files must be placed in the directory \PIR on any logical drive. Bank executable BANK.EXE may be placed in any directory on any logical drive. It is highly reccomended to run BANK.EXE from directory (and/or logical drive) other than data location to avoid random bank files structure damage. Bank is oriented on file-server data accession and can find \PIR directory (and test them for correct data configuration) on any logical drive. -------------------------------------------------------------- SAGITTARIUS is a FREE DOMAIN software. This package (with compressed data files) can be redistributed freely without any limitations but only free of charge and for non-commercial usage. No changes in data files and/or executables allowed. You may include compressed SAGITTARIUS datafiles in your application packages freely even in the case of commercial usage - text of C-language interface is available upon request (free of charge). -------------------------------------------------------------- For HELPFUL comments and discussions please contact: Dr. Victor B.Strelets (strelets@scri.fsu.edu) or Dr. Hwa A.Lim (hlim@scri.fsu.edu) Supercomputer Computations Research Institute, Florida State University, B-186, Tallahassee, FL 32306-4052, USA --------------------------------------------------------------- Common SAGITTARIUS information ------------------------------ SAGITTARIUS is a family of free domain application packages for molecular biologists with orientation on MS DOS PC-compartibles: - Compressed sequence databases with dialog shells for fast and easy data manipulation (PIR and GENBANK variants) - Fast programs for cross-bank user SEQ homology searches (short subregion homologies sensitive) (closely connected with compressed SAGITTARIUS databases) - Fast sensitive programs for pairwaise alignments (both aminoacid and nucleotide), including cross-bank user SEQ alignments (closely connected with compressed databases to allow cross-bank user SEQ alignments) - Packages for fast tree-based multiple alignments - Package for sequenation-errors-stable contigs joining (on the base of tree-based multiple alignment) - Automated system for revealing coding regions (exon/intron structure) in new nucleotide sequences (including learning mode access to the nucleotide sequences in compressed SAGITTARIUS GENBANK database) - Personal Reference Database dialog shell for manipulation of data from standard BIO-JOURNALS(BIOSCI), SEQANALREF(Bairoch), JOURNALS-TOC(multiple sources) databases -------------------------------------------------------------- Author(s) will in no way be held liable for any loss of profit or any other commercial damage including but not limited to special, incidental, consequential or other damages from use of this package. You may use them only with the understanding that you use it at your own risk and that your use of the software is your agreement to this disclaimer. From owner-proteins@net.bio.net Sat Oct 23 23:00:00 1993 Path: biosci!bloom-beacon.mit.edu!xlink.net!math.fu-berlin.de!news.dfn.de!news.uni-bielefeld.de!news.uni-essen.de!vm.hrz.uni-essen.de!TPH300 From: TPH300@vm.hrz.uni-essen.de Newsgroups: bionet.molbio.proteins Subject: GIF-files/NIH Message-ID: <16C71C7C8R85.TPH300@vm.hrz.uni-essen.de> Date: 24 Oct 93 13:12:24 GMT Sender: newsadm@uni-essen.de Organization: Universitaet Essen Lines: 14 Nntp-Posting-Host: vm.hrz.uni-essen.de Hi there, I have heard about the possibility to get 3D-structure GIF-pictures (or may be another format) from the NIH. Can anybody tell me where I have to log on for these pictures - GOPHER, FTP or something else ? Are these files for free or do I need to have an account ? Thanks, Markus Laub (TPH300@VM.HRZ.UNI-ESSEN.DE) From owner-proteins@net.bio.net Sat Oct 23 23:00:00 1993 Path: biosci!bloom-beacon.mit.edu!news.kei.com!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.molbio.proteins Subject: Pictures of PDB molecules available by gopher (Re: GIF-files/NIH) Message-ID: Date: 24 Oct 93 17:13:51 GMT References: <16C71C7C8R85.TPH300@vm.hrz.uni-essen.de> Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 36 Nntp-Posting-Host: sunflower.bio.indiana.edu For example, use gopher to ftp.bio.indiana.edu Choose: Other-Bio-Gophers/ Choose: Protein Data Bank gopher/ Or gopher direct to PDB gopher at pdb.pdb.bnl.gov Choose: An (almost) full text search of the PDB Bibliographic Headers ... example search on keyword like ... 5tra : TRANSFER RIBONUCLEIC ACID (YEAST,SER) ($T/RNA$) (MODEL)/ 1. 5tra.biblio. 2. 5tra.full. 3. 5tra.gif <<<<<< THIS IS A PICTURE in GIF format Choose: National Institutes of Health (NIH) Gopher/ Or gopher direct to NIH gopher server at gopher.nih.gov Choose: Molecular Biology Databases/ Choose: Search PDB (Release 63 - With images!) ... example search on keyword like ... 1GSG GLUTAMINYL-T|RNA| SYNTHETASE (GLN|RS|) C M.A.ROULD,J.J.PERO../ 1. 1gsg.README. 2. 1gsg.pdb. 3. 1gsg_cpk.gif <<<<<< THIS IS A PICTURE in GIF format If your gopher client doesn't display the items for these searches, then you need a newer gopher client. Your gopher client probably also needs a helper program to display the GIF picture on your computer. This would be for instance, on Mac: JPEGViewer, GIFfer, QuickGif, or others, on MSWindows: WinGIF or others on XWindows: xv, xloadimage, or others -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-proteins@net.bio.net Sat Oct 23 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.molbio.proteins Subject: IMPORTANT BIOSCI INFORMATION Message-ID: <9310240900.AA11764@net.bio.net> Date: 24 Oct 93 09:00:05 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 243 Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS and waismail access (waismail is our WAIS e-mail server, more below) and will also be available for access via other gopher sites if they wish to permit it. The raw unindexed data is available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.welch.jhu.edu and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIO-SOFTWARE bionet.software CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-proteins@net.bio.net Sat Oct 23 23:00:00 1993 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!husc10.harvard.edu!remeans From: remeans@husc10.harvard.edu (Robert Means) Newsgroups: bionet.molbio.proteins Subject: computer protein modeling Message-ID: <2a9t4u$s4h@scunix2.harvard.edu> Date: 23 Oct 93 00:16:30 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 13 NNTP-Posting-Host: husc10.harvard.edu X-Newsreader: TIN [version 1.2 PL1] Hello, I am interested in doing some limited modeling of protein structure on my mac. I have a three dimensional modeling program which accepts Brookhaven coordinates and I was wondering if there were any good programs which do energy minimizations on the macintosh. I would prefer if I could find a shareware of public domain program first to do some preliminary experiments. Later I might buy a commercial program. Thanks in advance, Robert Means NE Primate Res. Center From owner-proteins@net.bio.net Sun Oct 24 22:00:00 1993 Path: biosci!parc!decwrl!ames!elroy.jpl.nasa.gov!swrinde!cs.utexas.edu!uunet!math.fu-berlin.de!news.belwue.de!news.uni-freiburg.de!sun8.ruf.uni-freiburg.de!eschiltz From: eschiltz@sun8.ruf.uni-freiburg.de (Emile Schiltz) Newsgroups: bionet.molbio.proteins Subject: Re: protein sequence data base Message-ID: <2ag2qu$3ph@sun8.ruf.uni-freiburg.de> Date: 25 Oct 93 08:30:22 GMT References: <93294.143248AXC19@psuvm.psu.edu> Organization: Rechenzentrum der Universitaet Freiburg, Germany Lines: 23 NNTP-Posting-Host: sun8.ruf.uni-freiburg.de X-Newsreader: TIN [version 1.2 PL1] AXC19@psuvm.psu.edu wrote: : I need some guidance on what and where or who to go to ...I finally got the ami : no acid sequence of a protein of interest...Now, how can I do an aminoacid comp : arison to other proteins and figure out if it has already been isolated. Any h : elp will be appreciated. : Thanks, : Aida Cancel : axc19@psuvm.psu.edu hi Aida, like often there are many ways: e.g. send an e-mail to blitz@embl-heidelberg.de having first line: TITLE protein-so-and-so second line: SEQ third line and next lines : your sequence last line: END this should give you an automatic and quick answer hope this helps Mil -- Emile Schiltz,203-4290 From owner-proteins@net.bio.net Sun Oct 24 22:00:00 1993 Path: biosci!parc!decwrl!ames!agate!howland.reston.ans.net!torn!nott!nrcnet0!biologym54.lan.nrc.ca!campbell From: campbell@biologym54.lan.nrc.ca (Robert L. Campbell) Newsgroups: bionet.molbio.proteins Subject: Re: Building sidechains onto Ca coordinates Keywords: Crystal structures with Ca only Message-ID: Date: 25 Oct 93 16:14:17 GMT References: Sender: root@nrcnet0.nrc.ca (Operator) Distribution: bionet.molbio.proteins Organization: National Research Council of Canada Lines: 17 Nntp-Posting-Host: 132.246.164.42 In article bspjtpp@midge.bath.ac.uk (J T P Pedersen) writes: >I am looking for a program which may help me solve the >problem of reconstructing the missing coordinates in >protein structure files which have only been deposited >with Ca coordinates. Many of the commercial Molecular [stuff deleted ...] Jan, Sounds to me like you want "O" from Alwyn Jones. It will build a backbone from Ca coordinates by fitting to a database of structures. The side chains can be built automagically with statistically preferred rotamers. Robert Campbell Institute for Biological Sciences campbell@biologym54.lan.nrc.ca National Research Council Canada From owner-proteins@net.bio.net Sun Oct 24 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!olivea!apple.com!netcomsv!netcom.com!biodata.slip.netcom.com!vern From: vern@BioData.COM (Vernon Keenan) Newsgroups: bionet.virology,bionet.xtallography,bionet.molbio.proteins,bionet.general Subject: Re: VIDEO/ANONYMOUS FTP Message-ID: Date: 25 Oct 93 04:45:19 GMT References: <2a91j2$kiv@news.doit.wisc.edu> Sender: netnews@netcom.com (USENET Administration) Organization: BioData, Inc. Lines: 19 Xref: biosci bionet.virology:265 bionet.xtallography:529 bionet.molbio.proteins:994 bionet.general:6374 X-Xxmessage-Id: X-Xxdate: Sun, 24 Oct 93 05:47:38 GMT X-Useragent: Version 1.1.3 In article <2a91j2$kiv@news.doit.wisc.edu> Jean-Yves Sgro, sgro@rhino.bocklabs.wisc.edu writes: > ANONYMOUS FTP/ VIROLOGY VIDEO I have just downloaded this excellent collection of QuickTime movies! I can't wait to distribute these excellent images to my colleagues. Jean-Yves, many thanks from your fellow biological cybernauts! This is the kind of stuff that makes the information superhighway exciting for the lay person... Vern _______________________________________________________________ | Vernon Keenan | Voice: 415-513-8940 | | President | Fax: 415-312-8086 | | BioData, Inc. | Internet: vern@BioData.COM | | 1826 S. Grant St. Suite 620 | | | San Mateo, California 94402 | | _______________________________________________________________ From owner-proteins@net.bio.net Sun Oct 24 22:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uunet!sangam!vikram!imtech!jawahar From: jawahar@imtech.ernet.in (G.JAWAHAR SWAMINATHAN) Newsgroups: bionet.molbio.proteins Subject: COMPOSER problems, any solutions??? Message-ID: <7765@imtech.ernet.in> Date: 25 Oct 93 11:36:38 GMT Organization: Inst. of Microbial Technology, Chandigarh, India Lines: 27 Hi, We are a group working on the prediction of structure of small peptides of the size of 10 to 15 mers, using a knowledge based computer modelling approach. We recently acquired a new software by the name of ACADEMIC COMPOSER (Blundell et al) which can be used for multiple alignments of PDB solved entries with our peptide. Though this program is supposed to run in a UNIX enviornment, we have had problems right from the beginning in getting the object files to be compiled !! When we checked the same program using the VMS , expecting it to be a VAX version, we had no success. Since the version of UNIX indicated in the manual and the one accepted by the IRIS workstation are the same, we are now at our wits end as to the route to be taken from here. Does anyone what modifications to make in the COMPOSER,or has anyone faced similar problems with COMPOSER ? Any idea to this problem will be appreciated !! Jawahar -X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X-X- G.Jawahar Swaminathan Ph: 91-11-686 3004 to 6863009 Protein Chemistry Lab \ / Extn: 234, 309 National Institute of Immunology, | Gram: IMMUNOLOGY, New Delhi Aruna Asaf Ali Marg, \ / \ / Email: Jawahar@NII.ernet.in New Delhi - 110 067. | | Or Jawahar@imtech.ernet.in Fax: 91-11-686 2125 INDIA UUCP: .uunet!sangam!vikram!nii!jawahar! ======================================================================= From owner-proteins@net.bio.net Mon Oct 25 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!agate!library.ucla.edu!csulb.edu!paris.ics.uci.edu!news.service.uci.edu!orion.oac.uci.edu!mojgan From: mojgan@orion.oac.uci.edu (Mojgan Bonakdar) Newsgroups: bionet.molbio.proteins Subject: alpha-crystallin antibodies Message-ID: <2CCDB817.14979@news.service.uci.edu> Date: 26 Oct 93 23:51:51 GMT Distribution: bionet Organization: University of California, Irvine Lines: 11 Nntp-Posting-Host: orion.oac.uci.edu Are alpha-crystallin antibodies commercially available? If so, who and where? Is anyone working with a-crystallins? Your help will be greatly appreciated. Mo. Dept. Ophthalmology fax: 714-553-9407 From owner-proteins@net.bio.net Mon Oct 25 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!usc!nic.csu.net!eis.CalState.EDU!jng From: jng@eis.calstate.edu (Joseph S. Ng) Newsgroups: bionet.molbio.proteins Subject: ELASTIN SEARCH... Message-ID: Date: 26 Oct 93 00:30:17 GMT Organization: Calif State Univ/Electronic Information Services Lines: 14 To whom it may concern: Literature searches for recent research in elastin has yielded nothing of significance. If anyone out there would like to discuss the ramifications and possibilities of elastin or related bio-polymer research, please do not hesitate to contact me by mail. Ye olde address is as follows: jng@eis.calstate.edu -- JoE Hougang is an address Ng, that is... Aukang is home __________________ *** Forever In HIS hands *** From owner-proteins@net.bio.net Mon Oct 25 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!munnari.oz.au!metro!usage!newt.phys.unsw.edu.au!sjt From: sjt@newt.phys.unsw.edu.au (Sarah Tilley) Newsgroups: bionet.molbio.proteins Subject: m wt of alpha casein fragment needed Message-ID: <1993Oct27.025821.13336@usage.csd.unsw.OZ.AU> Date: 27 Oct 93 02:58:21 GMT Sender: news@usage.csd.unsw.OZ.AU Reply-To: sjt@newt.phys.unsw.edu.au (Sarah Tilley) Organization: School of Physics/University of NSW Lines: 7 Nntp-Posting-Host: newt.phys.unsw.edu.au X-Newsreader: dxrn 6.18-4 -- Does anyone know the approximate molecular weight of this fragment of casein? I found the m wt of beta casein in the 11th ed. of the Merck Index, but that is 4 years out-of-date. I have bought some from Sigma, and they are trying to find the answer from me, but the information has to come from the states. I thought the Net might be faster! ** Sarah Tilley sjt@newt.phys.unsw.edu.au From owner-proteins@net.bio.net Tue Oct 26 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pavo.csi.cam.ac.uk!camcus!bjd12 From: bjd12@cus.cam.ac.uk (Ben Davis) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts,bionet.xtallography Subject: Proline cis/trans isomerisation Keywords: NMR, proline Message-ID: <1993Oct27.105435.9751@infodev.cam.ac.uk> Date: 27 Oct 93 10:54:35 GMT Sender: news@infodev.cam.ac.uk (USENET news) Distribution: bionet Organization: U of Cambridge, England Lines: 22 Xref: biosci bionet.molbio.proteins:1000 bionet.molbio.methds-reagnts:8505 bionet.xtallography:532 Nntp-Posting-Host: grus.cus.cam.ac.uk I'm working on the NMR structure of a 40 residue peptide that contains three prolines. Does anyone know (a) what ratio of cis:trans proline do you expect for a random coil, and (b) how far (typically) does the cis:trans isomerisation affect the chemical shifts observed in other residues Thanks a lot, Ben ______________________________________________________________________________ Ben Davis, MRC Protein Function and Design, Cambridge UK ______________________________________________________________________________ "Even if you do get out its no good, 'cause no matter how far you get, they'll fetch you back here and bust you 'to pieces. Just ask Clara Pandy" The Ballad of Halo Jones From owner-proteins@net.bio.net Tue Oct 26 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!msuinfo!netnews.upenn.edu!duong From: duong@chestnut.chem.upenn.edu (Duc Duong) Newsgroups: bionet.software,bionet.molbio.proteins Subject: Softwares draw peptide planes?? Message-ID: <157767@netnews.upenn.edu> Date: 27 Oct 93 16:45:43 GMT Sender: news@netnews.upenn.edu Followup-To: bionet.software Organization: NMR Biochemistry Graduate Research Lab Lines: 8 Xref: biosci bionet.software:6324 bionet.molbio.proteins:1005 Nntp-Posting-Host: chestnut.chem.upenn.edu hi.. I have a set of alpha and beta angles and I want to draw the peptide planes from it.. Are there any softwares will do this for me?? duc From owner-proteins@net.bio.net Tue Oct 26 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!wupost!gumby!wmichgw!eversole From: eversole@gw.wmich.edu Newsgroups: bionet.molbio.proteins Subject: Looking for rat eosinophil peroxid.Ab Message-ID: <1993Oct27.104012.12120@gw.wmich.edu> Date: 27 Oct 93 15:40:12 GMT Organization: Western Michigan University Lines: 3 Sorry, please see previous message (terrible editor here!) thx From owner-proteins@net.bio.net Tue Oct 26 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!news-feed-2.peachnet.edu!ukma!usenet.ins.cwru.edu!agate!ames!decwrl!decwrl!morrow.stanford.edu!morrow.stanford.edu!not-for-mail From: HF.JSL@forsythe.stanford.edu (Jos