From owner-proteins@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!news.starnet.net!wupost!howland.reston.ans.net!news.sprintlink.net!demon!genesys.demon.co.uk!Duncan From: Duncan Clark Newsgroups: bionet.molbio.proteins Subject: Re: Image software for PC Date: 2 Jun 1995 09:40:15 +0100 Organization: GeneSys Ltd. Lines: 39 Sender: news@news.demon.co.uk Message-ID: <587761366wnr@genesys.demon.co.uk> References: <3ql31g$cb3@inkblot.med.cornell.edu> Reply-To: Duncan@genesys.demon.co.uk NNTP-Posting-Host: dispatch.demon.co.uk X-Newsreader: Newswin Alpha 0.7 X-Posting-Host: genesys.demon.co.uk In article: <3ql31g$cb3@inkblot.med.cornell.edu> mjbroek@mail.med.cornell.edu (M.Johan Broekman) writes: > > Hi Netters: > > I am interested in purchasing a scanner and software to process gels, > including Northerns and sequencing gels. Is there an equivalent > (however rough) to the NIH Image software, which appears to be only > available for the Mac? What other software do you use on the PC? It is possible to use NIH Image on a PC. You just have to convert your PC temporarily into a MAC. This is quite easy. There is available a MAC emulator for both UNIX and DOS. It can be found on any SIMTEL mirror. Look for the files Exkdisk1.zip and Exkdisk2.zip or contact the suppliers direct: > We are in receipt of your fax dated March 17, 1995 in which you are > ordering Executor 1.99k. We have version 1.99k for Executor/DOS > and Executor/Linux. > > 1.99k for Executor/DOS would cost $99.00 + $15.00 international > shipping charge. There are diskettes and a manual that are shipped > with your order. > > Vaune Fischer > Technical Support > ARDI > vjf@ardi.com I run it quite happily on a 66Mhz 486 16mb RAM. Duncan - ----------------------------------------------------------------------------- My mind's made up. Don't confuse me with the facts! From owner-proteins@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!torn!ccshst05.cs.uoguelph.ca!ccshst01.cs.uoguelph.ca!chouse From: chouse@uoguelph.ca (Chris J House) Newsgroups: bionet.molbio.proteins Subject: RPA,ssb,XPG, Nucl. Excis. Repair Date: 2 Jun 1995 01:58:11 GMT Organization: University of Guelph Lines: 22 Message-ID: <3qlr7j$qfa@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: ccshst01.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] Well, hope someone can shed some light on this for me. What exactly is RPA? According to all the older stuff (we're not talking too old, just 1994 and back.. ;) ) .. reads RPA is an ssb in the NER process. According to a new 1995 article from Cell they say their experimental info concludes that is is used in the incision process. Frankly I am having difficulty seeing the same conclusions from what they wrote and thought if someone else would confirm what RPA is either way I might be able to get this mess straightened out. If anyone has some insight into what RPA is (especially if they have reference to one or the other above) I would love some email from you. I can also discuss with you the ideas I have in how their experimentation is both flawed and could be improved. Thanks for the time. C. House From owner-proteins@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!gwen.pcug.co.uk!kate.ibmpcug.co.uk!redmoth!sdyer Newsgroups: bionet.molbio.proteins Message-ID: <12@redmoth.win-uk.net> Reply-To: sdyer@redmoth.win-uk.net (Sarah Dyer) From: sdyer@redmoth.win-uk.net (Sarah Dyer) Date: Fri, 02 Jun 1995 17:44:59 GMT Subject: A blood disorder called protein C deficiency Lines: 23 Hello! I'm a brand new user, searching for information about protein C deficiency. I've only been on the net three weeks, but so far have had little luck in finding any information through the various search engines on the www. I noticed your newsgroup recently and hope I'm not wasting your time by asking for info that isn't pertinent to you all, but it's difficult to know where to start! I'm researching on behalf of my sister-in-law who suffers from protein C deficiency and has been unable to find satisfactory info through the normal medical channels. If anyone can help me, or perhaps point me in the direction of a more relevant newsgroup or website, I would be very grateful indeed (and it might make my sister-in-law believe the net does have some use after all!) Thankyou, Sarah Dyer sdyer@redmoth.win-uk.net From owner-proteins@net.bio.net Thu Jun 01 23:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bloom-beacon.mit.edu!gatech!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!univ-lyon1.fr!jussieu.fr!oleane!pipex!sunic!sunic.sunet.se!news.chalmers.se!news.gu.se!news From: Anne Farewell Subject: Re: IEF gels Message-ID: Sender: news@news.gu.se (USENET News System) Nntp-Posting-Host: mac36.gmm.gu.se Organization: Gothenburg University References: <355061120wnr@genesys.demon.co.uk> Date: Fri, 2 Jun 1995 14:53:59 GMT Lines: 26 Duncan Clark wrote: > > Hi Folks, > > I've been running IEF gels of various recombinant thermophilic DNA > pols but keep finding that some refuse to run as single bands. The > enzymes are homogeneous on SDS gels with silver staining. On IEF > gels, either native or denaturing with 8M Urea I get one main band > and several others (10% intensity each) over roughly 0.5 pI units > either side (staining with coomassie blue). I am discounting > proteolysis in that the known effect of E.coli proteases on these > pols would show up on SDS gels. Any proteolysis would also have a > marked effect on activity which I'm not seeing. > > Could it be some sort of aggregation? I've thought of treating > the samples with an SDS cracking buffer as per SDS PAGE before > loading onto a denaturing IEF but have yet to try it. What happens if > one puts SDS in an IEF gel, concn of SDS? > I've never tried it, but I think that SDS would affect the charge and thus pI of your protein. Usually, isoelectric varients are modified- phosphorylated for example. Those modifications don't change the size (PAGE remains the same) but can change the pI quite a bit. From owner-proteins@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!usenet.eel.ufl.edu!news.uoregon.edu!ntuix.ntu.ac.sg!raffles.technet.sg!nuscc.nus.sg!mcbrp From: mcbrp@leonis.nus.sg (Philp Robin John) Newsgroups: bionet.molbio.proteins Subject: Micro LC ? Date: 2 Jun 1995 07:55:36 GMT Organization: National University of Singapore Lines: 15 Message-ID: <3qmg5o$8k0@nuscc.nus.sg> NNTP-Posting-Host: mcbrp@leonis.nus.sg X-Newsreader: TIN [version 1.2 PL2] Greetings, I am considering the purchase of an LC Packings micro flow cell to install in an old but not much used Waters 484 detector. This would then be used for monitoring high sensitivity peptide separations. Is there anybody out there who is currently using this combination of detector/flow cell and would comment on the performance? Replies could be direct to me and I will post a summary if anybody is interested. Many thanks, Robin J. Philp Institute of Molecular and Cell Biology Singapore, 0511 From owner-proteins@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!agate!sunsite.doc.ic.ac.uk!warwick!griffin.nott.ac.uk!macbsav2.biochem.nottingham.ac.uk!user From: mbzjwk@unicorn.nott.ac.uk (John Keyte) Newsgroups: bionet.molbio.proteins Subject: triton rtx100 Followup-To: bionet.molbio.proteins Date: Thu, 01 Jun 1995 16:31:51 +0000 Organization: University of Nottingham Lines: 1 Message-ID: NNTP-Posting-Host: macbsav2.biochem.nottingham.ac.uk Triton X-100 in its reduced form is available from Calbiochem and Fluka From owner-proteins@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.belwue.de!news.belwue.de!News.Uni-Marburg.DE!news.th-darmstadt.de!bc3 From: dh7y@pop.thdarmstadt.de (Institute for Biochemistry) Newsgroups: bionet.molbio.proteins Subject: Need antibody to SV40 small, large T Ag and Polyoma large T Ag! Date: 2 Jun 1995 13:10:24 GMT Organization: TH Darmstadt Lines: 12 Message-ID: <3qn2k0$srd@rs18.hrz.th-darmstadt.de> NNTP-Posting-Host: bc3.bc.chemie.th-darmstadt.de X-Newsreader: News Xpress Version 1.0 Beta #3 Hello there! I'm desperately seeking antibodies to SV40 large and/or small T antigen and to Polyoma large T antigen! I need the antibodies for detection of these antigens in immortalized cell lines! Is there anyone who can supply me with the antibodies or who can tell me were to get them? Thanks in advance, Michael Internet: dh97@pop.th-darmstadt.de From owner-proteins@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!emory!sol.ctr.columbia.edu!news.mindlink.net!vanbc.wimsey.com!unixg.ubc.ca!hoekstra From: hoekstra@unixg.ubc.ca (Sucking Gippy) Newsgroups: bionet.molbio.proteins Subject: Immunohistochemical techniques Date: 2 Jun 1995 21:41:36 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 10 Message-ID: <3qo0ig$7kp@nnrp.ucs.ubc.ca> NNTP-Posting-Host: interchg.ubc.ca X-Newsreader: TIN [version 1.2 PL2] Hi. If anyone uses immunohistochemical techniques for location and presence of specific proteins, could you please direct me to a COMPLETE methodology...in a journal or a well written book which you have personally used and like. Thanks -- \|||||/ Ken Hoekstra, Veterinary Technician, B.Sc. O O University of British Columbia o Graduate Student \_/ Ken.Hoekstra@deepcove.com\\\///hoekstra@unixg.ubc.ca From owner-proteins@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!UQTR.UQuebec.ca!Mario_Fragata From: Mario_Fragata@UQTR.UQuebec.ca Newsgroups: bionet.molbio.proteins Subject: Re: Proteolysis of extracellular enzyme Date: 2 Jun 1995 06:03:15 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9506021302.AA09099@neptune.UQTR.UQuebec.ca> NNTP-Posting-Host: net.bio.net D From owner-proteins@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!msunews!netnews.upenn.edu!obgynjm25.obgyn.upenn.edu!user From: ggerton@obgyn.upenn.edu (George L. Gerton) Newsgroups: bionet.molbio.proteins Subject: Re: Public Domain Densitometry Software for Mac? Date: Fri, 02 Jun 1995 07:56:31 -0500 Organization: University of Pennsylvania Lines: 32 Message-ID: References: NNTP-Posting-Host: obgynjm25.obgyn.upenn.edu In article , cam@rschp1.anu.edu.au (Biological User) wrote: > I was wondering whether anybody knows of any public domain software which > will allow me to do densitometry on a scanned image. I just want to do > a quick analysis on two bands on an SDS-PAGE gel which were not evenly > loaded rather than guess which one has more protein in it :-) > > I was hoping to be able to scan a photo of the gel using photoshop and > work with the scanned image. Does any such software exist. I have only > discovered commercial software so far. Is there anyhting else around? > > email me at cam@rschp1.anu.edu.au unless you think the information is > of great interest to the members of the group :-) > > Thanks > > -- > Cameron Neylon +61 6 251 1118 (Home) > Research School of Chemistry +61 6 249 4181 (Lab) > Australian National University or more likely cam@rsc.anu.edu.au Yes. Get NIH-IMAGE from ftp://zippy.nimh.nih.gov/pub/nih-image/ This program is set up to use Photshop plug-ins and is written expressly for the Mac. -- George L. Gerton ggerton@obgyn.upenn.edu From owner-proteins@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news2.near.net!das-news2.harvard.edu!oitnews.harvard.edu!news.dfci.harvard.edu!usenet From: ming@mbcrr.harvard.edu (Ding Ming) Newsgroups: bionet.molbio.proteins Subject: Re: IEF gels Date: 2 Jun 1995 13:06:34 GMT Organization: Dana Farber Cancer Institute Lines: 4 Sender: -Not-Authenticated-[3542] Message-ID: <3qn2cq$pgj@cisunix1.dfci.harvard.edu> References: <355061120wnr@genesys.demon.co.uk> NNTP-Posting-Host: 155.52.84.83 X-Posted-From: InterNews 1.0.6@155.52.84.83 Xdisclaimer: No attempt was made to authenticate the sender's name. I think what you get is so-called "pI forms" of the p[rotein. This is caused by minor heterogeneity of your protein moleculaes and you should not worry about it at all. :) From owner-proteins@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!univ-lyon1.fr!jussieu.fr!oleane!pipex!warwick!griffin.nott.ac.uk!usenet From: stewart.martin@nott.ac.uk (Stewart G Martin) Newsgroups: bionet.molbio.proteins Subject: Adenovirus vectors Date: Fri, 02 Jun 95 17:21:22 GMT Organization: University of Nottingham Lines: 19 Distribution: world Message-ID: <3qmvnl$ls7@griffin.ccc.nottingham.ac.uk> NNTP-Posting-Host: pmmpwh.nottingham.ac.uk Keywords: Adenovirus, Vectors, Transfection X-Newsreader: News Xpress Version 1.0 Beta #2.1 Does anyone out there have access to any adenovirus or adeno-associated virus (AAV) vectors that they could supply me with or know of a source where I could get some from ? I have the 293 cells but don't want to have to go to all the hassle of making suitable vectors from wild type Ad5. Also, from a gene therapy point of view, is there any advantage of using one particular adenovirus type over another? Since some types are more prevalent in the environment than others might not the hosts immune response be greater against them? Thanks in advance Stewart Martin CRC Department of Clinical Oncology University of Nottingham stewart.martin@nott.ac.uc From owner-proteins@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!idefix.CS.kuleuven.ac.be!chaos.kulnet.kuleuven.ac.be!fysiologie-1.med.kuleuven.ac.be!user From: Jan.Eggermont@med.kuleuven.ac.be (Jan Eggermont) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: detergents in gel filtration Date: Fri, 02 Jun 1995 11:20:59 +0100 Organization: Laboratorium voor Fysiologie - KU Leuven Lines: 25 Message-ID: NNTP-Posting-Host: fysiologie-1.med.kuleuven.ac.be Xref: biosci bionet.molbio.methds-reagnts:29131 bionet.molbio.proteins:4710 Hello, I am currently investigating the oligomeric nature of a purified protein. On a Superose 12 FPLC colum with a 150 mM NaCl buffer the protein migrates with a Mr of around 100k whereas the predicted molecular mass from the amino acid sequence is 28k suggesting it may form a trimer. I now want to find out what type of interactions (hydrophobic/hydrophilic/S-S bridges...) are going on. I presume raising the salt concentration will unmask hydrophilic interactions and adding a reducing agent such as DTT will break up S-S bridges. However, I am not sure about the best way to tackle the hydrophobic interactions. At first I wanted to use Triton-X100 but this will interfere with the UV recording at 280 nm. In addition I was told that because of the low critical micellar concentration (cmc) of Tx100, some of the protein may be incorporated into micelles. So any ideas out there on a detergent that does not absorb at 280 nm and that has a rather high cmc? thanks in advance. Jan -- Jan Eggermont Jan.Eggermont@med.kuleuven.ac.be Laboratorium voor Fysiologie - KU Leuven Campus Gasthuisberg tel 32-16-34 59 38 3000 Leuven Belgium fax 32-16-34 59 91 From owner-proteins@net.bio.net Fri Jun 02 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!news.bu.edu!news3.near.net!yale!news.wesleyan.edu!news.wesleyan.edu!news Newsgroups: bionet.molbio.proteins Subject: Re: gel shift using hot protein as a probe? Message-ID: <1995Jun3.132052.1686@news.wesleyan.edu> From: "R.Visvanathan" Date: 3 Jun 95 13:20:51 -0400 References: <3qf1g2$1b9@netnews.upenn.edu> Organization: Wesleyan University Nntp-Posting-Host: doliver2.bio.wesleyan.edu X-Mailer: Mozilla 1.1N (Macintosh; I; 68K)MIME-Version: 1.0X-URL: news:Pine.A32.3.91.950531140410.57514A-100000@parisContent-Type: multipart/mixed;boundary="-------------------------------74402679019475"Lines: 60 Lines: 60 This is a multi-part message in MIME format. ---------------------------------74402679019475 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Why not biotinylate (Variety of biotin available from Pierce) the purified protein of interest (instead of I-125) and use ECL to detect the protein's after crosslinking. I haven't tried this. Just a suggestion. Good luck, Vishy ---------------------------------74402679019475 Content-Transfer-Encoding: 7bit Content-Type: text/plain From: hroychow@NMSU.EDU (Hiranya Roychowdhury) Newsgroups: bionet.molbio.proteins Subject: Re: gel shift using hot protein as a probe? Date: 31 May 1995 13:11:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Message-ID: References: <3qf1g2$1b9@netnews.upenn.edu> On 30 May 1995, Aron B. Jaffe wrote: > I would like to look at protein-protein interactions on a non- > denaturing gel using an 35S-labeled protein as my probe. Can I > do this? Does anyone know of a reference? > > thanks > > aron> Surely, if you have the specific mRNA for the protein that you want to label you could simply do in vitro translation (using 35S-met), purify the protein of your interest and use it as the probe. However, labeling the pure protein with 125I may be a better and easier alternative. Iodination protocols can be had from any protein protocol book or from the Meth. Enzymol. volumes. Protein-protein crosslinking is achieved by uv-irradiation, and this needs to be standardized for each system and the protein pairs. >>>>>>>>>>>>>>>>>>>>>>>>>>> Hiranya S. Roychowdhury Plant Genetic Engineering Lab. Box 3GL, NM State Univ. Las Cruces, NM 88003 Phone: (505) 646-5785 hroychow@nmsu.edu <<<<<<<<<<<<<<<<<<<<<<<<<<< ---------------------------------74402679019475-- From owner-proteins@net.bio.net Fri Jun 02 23:00:00 1995 Path: biosci!scruz.uucp.netcom.com!osvaldo.montano From: osvaldo.montano@scruz.uucp.netcom.com (Osvaldo Montano) Newsgroups: bionet.molbio.proteins Subject: help me Date: 3 Jun 1995 04:00:35 -0700 Organization: Santa Cruz BBS - BOLIVIA - (591) (3) 36-7046 Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <18e.8538.33@scruz.uucp.netcom.com> NNTP-Posting-Host: net.bio.net Dear Sr. I am studing Chemistry here, in Santa Cruz-Bolivia and I need some information about INTERATION OF HEAVY METALS WITH CHITIN and CHITOSAN / "JOURNAL OF POLYMER SCIENCES". If you don't know it, then please let me other addresses where I can ask for it. Especially addresses (e-mail) for journal of Chemical or Bio-Chemical in your country or other country. Yours sincerelly, Osvaldo Montaņo. Please answer if my message was received. I need your help please. Pd. Excuse my English ----------------------------------------------------------------------------- Internet: osvaldo.montano@scruz.uucp.netcom.com (Osvaldo Montano) This message was processed by NetXpress from Merlin Systems Inc. ----------------------------------------------------------------------------- From owner-proteins@net.bio.net Sat Jun 03 23:00:00 1995 Path: biosci!agate!msunews!harbinger.cc.monash.edu.au!lindblat.cc.monash.edu.au!eln118w From: eln118w@lindblat.cc.monash.edu.au (Mr YC Yap) Newsgroups: bionet.molbio.proteins,bionet.molec-model Subject: Locating atoms from angles-Help! Date: 5 Jun 1995 02:51:41 GMT Organization: Monash University Lines: 21 Message-ID: <3qtrft$hc8@harbinger.cc.monash.edu.au> NNTP-Posting-Host: lindblat.cc.monash.edu.au X-NNTP-Posting-User: eln118w X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.proteins:4722 bionet.molec-model:414 Hi there, I wonder if someone can help me with a problem. I'm writing a protein folding program that uses a simplified representation storing only the amino acid sequence, C-alpha coordinates and the Phi and Psi dihedral angles. At the end of the program, I need to reconstruct a detailed atomic model of the molecule. With the dihedral angles, I know the relative orientation of the backbone C, N and O atoms between one residue and its neighbour. But how do I get the starting coordinates of the FIRST N atom? Once I get that, I can work out the rest of the atoms. Any ideas will be greatly appreciated. Thanks in advance. Alexander. From owner-proteins@net.bio.net Sun Jun 04 23:00:00 1995 Newsgroups: bionet.molbio.proteins,bionet.molec-model Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!news.sprintlink.net!demon!uknet!bcc.ac.uk!rmiller From: rmiller@bsm.bioc.ucl.ac.uk (Rob Miller) Subject: Re: Locating atoms from angles-Help! Message-ID: <1995Jun5.164402.74285@ucl.ac.uk> Date: Mon, 5 Jun 1995 16:44:02 GMT References: <3qtrft$hc8@harbinger.cc.monash.edu.au> Organization: University College London X-Newsreader: TIN [version 1.2 PL2] Followup-To: bionet.molbio.proteins,bionet.molec-model Lines: 70 Xref: biosci bionet.molbio.proteins:4725 bionet.molec-model:415 Mr YC Yap (eln118w@lindblat.cc.monash.edu.au) wrote: : Hi there, : I wonder if someone can help me with a problem. : I'm writing a protein folding program that uses : a simplified representation storing only the amino : acid sequence, C-alpha coordinates and the Phi and : Psi dihedral angles. : At the end of the program, I need to reconstruct : a detailed atomic model of the molecule. With the : dihedral angles, I know the relative orientation : of the backbone C, N and O atoms between one residue : and its neighbour. But how do I get the starting : coordinates of the FIRST N atom? Once I get that, : I can work out the rest of the atoms. (1) I think I may be misunderstanding your question, but how about putting the first N atom at the origin (0,0,0) ? If you mean the initial backbone N of each residue, that is of course specified by the dihedral angles of the preceding residue. Also, from your posting, don't forget to spec the omega angle, unless that will always be 180 for your system. (2) From my experience writing this same code, you will find that you need to specify all bond lengths and bond angles if you intend to create a structure which will be super-imposable on a real structure. That is, if you try building a real protein from its dihedral angles alone, you can do all the code correctly and still have a result that is a *long* way off in terms of RMS deviation. If you're trying to do something that iteratively improves a model structure by some other measure, like getting good pairwise distances (PMF), and aren't worried about actually reproducing coords from a crystal structure, this doesn't apply. You *can* get 0.00 rmsd to a real structure by building from scratch if you spec everything. : Any ideas will be greatly appreciated. : Thanks in advance. : Alexander. cheers, rob. -- ------------------------------------------------------- Rob Miller, Ph.D. Biomolecular Structure and Modelling Unit (BSM), Department of Biochemistry and Molecular Biology, University College / Gower Street / London WC1E 6BT. United Kingdom. Tel: +44 171419 3896 Fax: +44 171380 7193 Internet: rmiller@bsm.bioc.ucl.ac.uk http://www.biochem.ucl.ac.uk/~rmiller ------------------------------------------------------- From owner-proteins@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!gatech!news.sprintlink.net!uunet!cis.ohio-state.edu!nntp.sei.cmu.edu!bb3.andrew.cmu.edu!casaba.srv.cs.cmu.edu!das-news2.harvard.edu!oitnews.harvard.edu!news.dfci.harvard.edu!mbcrr!schmidt From: schmidt@jimmy.harvard.edu (Bill Schmidt) Newsgroups: bionet.molbio.proteins Subject: Protein Structure Prediction Using Web E-Mail Server Date: 5 Jun 1995 17:54:32 GMT Organization: Dana-Farber Cancer Institute Lines: 48 Distribution: world Message-ID: <3qvgco$sml@cisunix1.dfci.harvard.edu> NNTP-Posting-Host: mbcrr.harvard.edu Originator: schmidt@mbcrr ANNOUNCING NEW WEB INTERFACE FOR PROTEIN SEQUENCE ANALYSIS The previously announced Protein Sequence Analysis (PSA) e-mail server now has a Web interface. The URL is http://bmerc-www.bu.edu/psa/ The PSA server analyzes your protein sequence and determines which of 209 sequence-structure models, spanning 15 different protein folding classes, are the most probable explanations of your sequence. The analysis results (PostScript files depicting the folding-class probabilities and secondary-structure probabilities) are returned to you by e-mail. The PSA e-mail server is particularly suited for analyzing novel sequences that are unlike any others in the sequence databanks. Currently, the PSA is based on a set of probabilistic Discrete State-space Models (DSMs) that are intended to represent the major folding classes in J. Richardson's taxonomy of tertiary structural domains. The PSA e-mail server is maintained at the BioMolecular Engineering Research Center of Boston University. If you don't have a forms-capable Web browser (e.g., Netscape), you may obtain usage information by sending an empty email message to psa-request@darwin.bu.edu with the word "help" in the subject field. The PSA analysis algorithm is based on optimal filtering and smoothing algorithms as described in the paper "Structural analysis based on state-space modeling" by C.M. Stultz, J.V. White, and T.F. Smith, Protein Science (1993), 2, 305-314. The mathematical basis for the models and algorithms is presented in "Protein Classification by Stochastic Modeling and Optimal Filtering of Amino-Acid Sequences," by J.V. White, C.M. Stultz, and T.F. Smith, Mathematical Biosciences (1994), 119, 35-75. Bill Schmidt Interface Specialist BioMolecular Engineering Research Center schmidt@darwin.bu.edu From owner-proteins@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!uunet!newsflash.concordia.ca!canopus.cc.umanitoba.ca!nazar.dent.umanitoba.ca!user From: egreif@ccu.umanitoba.ca (Elke Greif) Newsgroups: bionet.molbio.proteins Subject: 2D-page and Coomassie staining Followup-To: bionet.molbio.proteins Date: 5 Jun 1995 15:05:41 GMT Organization: University of Manitoba Lines: 16 Distribution: world Message-ID: NNTP-Posting-Host: nazar.dent.umanitoba.ca Hi! I am trying to perfect the staining techniques of 2-dimensional gels. At first, we didn't get enough spots on our gels to analyse(70-80 spots where we expect 200-300 spots.) This was done when we silver stained (using our own solutions). Then we increased our protein concentration, ran the whole shebang again and still didn't get enough, though a little more. If we were to increase our protein again, th IEF would then be overloaded, so we are stuck with a concentration of 100-150ug. We would like to quantitate the proteins by using Coomassie but we are getting less than with silver staining. So, the more spots the better, right? This is just a small dilemma that's just a matter of figuring it out. Any help would be grandly appreciated! Thanks in advance. Please e-mail anything. egreif@ccu.umanitoba.ca From owner-proteins@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!NMSU.EDU!hroychow From: hroychow@NMSU.EDU (Hiranya Roychowdhury) Newsgroups: bionet.molbio.proteins Subject: Re: 2D-page and Coomassie staining Date: 5 Jun 1995 14:23:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On 5 Jun 1995, Elke Greif wrote: > > > Hi! I am trying to perfect the staining techniques of 2-dimensional gels. > At first, we didn't get enough spots on our gels to analyse(70-80 spots > where we expect 200-300 spots.) This was done when we silver stained (using > our own solutions). Then we increased our protein concentration, ran the > whole shebang again and still didn't get enough, though a little more. If > we were to increase our protein again, th IEF would then be overloaded, so > we are stuck with a concentration of 100-150ug. We would like to quantitate > the proteins by using Coomassie but we are getting less than with silver > staining. So, the more spots the better, right? This is just a small > dilemma that's just a matter of figuring it out. Any help would be grandly > appreciated! > Thanks in advance. > > Please e-mail anything. egreif@ccu.umanitoba.ca The amount of protein you are loading on the IEF is suffient. I believe that the entire amount is not entering. There has been a lot of discussion a while back about the use of SDS etc to solubilize the protein sample prior to loading on the IEF gel. Some tend to think that the inclusion of SDS will defeat the IEF. Well, according to my experience (and those of others in this lab and elsewhere) a short (1 - 2min) SDS treatment is all it takes to solubilize difficult crude and membrane proteins, and it does not interfere in any significant way with the IEF. Try it, if you have not already, and see if you have enough spots staining in the 2nd-dimension. > >>>>>>>>>>>>>>>>>>>>>>>>>>> Hiranya S. Roychowdhury Plant Genetic Engineering Lab. Box 3GL, NM State Univ. Las Cruces, NM 88003 Phone: (505) 646-5785 hroychow@nmsu.edu <<<<<<<<<<<<<<<<<<<<<<<<<<< From owner-proteins@net.bio.net Sun Jun 04 23:00:00 1995 Newsgroups: bionet.molbio.proteins,bionet.molec-model Path: biosci!ns1.faseb.org!darwin.sura.net!nih-csl!rvenable From: rvenable@deimos.cber.nih.gov (Rick Venable) Subject: Re: Locating atoms from angles-Help! Message-ID: <1995Jun5.195408.152@alw.nih.gov> Followup-To: bionet.molbio.proteins,bionet.molec-model Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: deimos.cber.nih.gov Organization: FDA/CBER Biophysics Lab X-Newsreader: TIN [version 1.2 PL2] References: <3qtrft$hc8@harbinger.cc.monash.edu.au> Date: Mon, 5 Jun 1995 19:54:08 GMT Lines: 34 Xref: biosci bionet.molbio.proteins:4727 bionet.molec-model:417 On 5 Jun 1995 02:51:41 GMT Mr YC Yap pontificated: > I wonder if someone can help me with a problem. > I'm writing a protein folding program that uses > a simplified representation storing only the amino > acid sequence, C-alpha coordinates and the Phi and > Psi dihedral angles. > At the end of the program, I need to reconstruct > a detailed atomic model of the molecule. With the > dihedral angles, I know the relative orientation > of the backbone C, N and O atoms between one residue > and its neighbour. But how do I get the starting > coordinates of the FIRST N atom? Once I get that, > I can work out the rest of the atoms. Assign the first atom to 0,0,0 Place the second atom along the positive X axis (X= N-CA bond, Y=0, Z=0) Place the third atom in XY plane (Z=0); use CA-C bond and N-CA-C angle Once the first 3 atoms are placed, the rest can be determined from bond lengths, bond angles, and the dihedral angles. The next step is often to align the molecular axes with the Cartesian axes, so that the molecule's center of mass or geometry is at 0,0,0 and perhaps the molecular long axis aligned with a Cartesian axis. N.B. I tried e-mail, but your addressed got garbled somewhere along the way to my newsfeed. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| / Not an official statement \ rvenable@deimos.cber.nih.gov \/ |=| \ or position of the FDA. / From owner-proteins@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!newsfeed.pitt.edu!godot.cc.duq.edu!ddsw1!vanbc.wimsey.com!unixg.ubc.ca!news.bc.net!info.ucla.edu!library.ucla.edu!news.ucdavis.edu!modem68.ucdavis.edu!user From: DDunlap@ucdavis.edu (Matsumura lab) Newsgroups: bionet.molbio.proteins Subject: Help with Immunoprecipitations! Date: Fri, 02 Jun 1995 23:41:10 -0500 Organization: University of California Davis Lines: 11 Message-ID: NNTP-Posting-Host: modem68.ucdavis.edu I'm having problems getting my immunoprecipitated protein band to line up with the non-immunoprecipitated protein band in an SDS-PAGE gel. I have three proteins of interest 97, 105 &115 kDa and have specific antibodies to the 97 & 105 proteins. My problem is after I immunoppt them and run in same gel with whole cytosol (showing the 3 bands) the 97 kDa band lines up well but the 105 seems to be "wider/fuzzy" and HIGHER so it looks like it is between the 105 & 115 bands. These proteins are crosslinked to a BrdU-32P-oligo if that makes any difference. I can get nice separation of the 3 complexes in a gradient gel without the immunoppt. I'd appreciate any help/suggestions/advice from any protein guru out there. Thanks -Kate From owner-proteins@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news-e1a.megaweb.com!newstf01.news.aol.com!uunet!newsflash.concordia.ca!nstn.ns.ca!news.cs.indiana.edu!lynx.unm.edu!SantaFe!chimayo!rice From: rice@chimayo.santafe.edu (Kenneth Rice) Newsgroups: bionet.molbio.proteins,bionet.molbio.evolution Subject: TIM Barrel Alignment Date: 6 Jun 1995 18:21:00 GMT Organization: /network/software/packages/news/lib/organization Lines: 8 Distribution: world Message-ID: <3r26ac$mkc@tierra.santafe.edu> NNTP-Posting-Host: sfi19.santafe.edu Xref: biosci bionet.molbio.proteins:4737 bionet.molbio.evolution:2955 I'm looking for some aligned AA sequences of TIM barrel proteins as test data for a tree reconstruction program that I'm writing. Any alignments or pointers to same would be greatly appreciated. Thanks, Ken Rice From owner-proteins@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news-e1a.megaweb.com!newstf01.news.aol.com!uunet!in1.uu.net!news.uiowa.edu!news From: kpmurphy@blue.weeg.uiowa.edu (murphy kenneth p) Newsgroups: bionet.molbio.proteins Subject: Re: Association of protein dimer as function of temperature Date: 6 Jun 1995 20:27:00 GMT Organization: University of Iowa, Iowa City, IA, USA Lines: 38 Distribution: world Message-ID: <3r2dmk$g0j@nexus.uiowa.edu> References: <3r244l$9i0@helka.iif.hu> NNTP-Posting-Host: red.weeg.uiowa.edu In article <3r244l$9i0@helka.iif.hu>, wrote: >We would like to study the association-dissociation equilibrium of a >homodimeric protein as a function of temperature. > >The protein consists of two identical subunits and there is an equilibrium >between the monomeric and dimeric forms of this protein. It is an enzyme >and we do not know if the monomeric form also has an enzymatic activity >(the dimeric form is known to be active). We would like to know the >relative population of the dimeric and monomeric forms as a function of >temperature. The dimeric form has a molecular weight of cca. 70 kDa. > >Any idea what technique can be used to this problem? We have all kinds of >spectroscopic techniques, and of course chromatographic and >electrophoresis methods. > >Any help would be greatly appreciated. > >Andras Szilagyi (szia@enzim.hu) >Institute of Enzymology, Hungarian Academy of Sciences > > > Two techniques come to mind, isothermal titration calorimetry, for measuring heats of dilution, and analytical ultracentrifugation for measuring the weight- averaged molecular weight. See Burrows, S. D., Doyle, M. L., Murphy, K. P., Franklin, S. G., White, J. R.,Brooks, I., McNulty, D. E., Scott, M. O., Knutson, J. R., Porter, D., Young, P. R. & Hensley, P. (1994) Biochemistry 33, 12741. for an example looking at IL-8 dimerization. Regards, Kip -- Dr. Kenneth P. Murphy e-mail: k-murphy@uiowa.edu Department of Biochemistry office: (319)335-8910 University of Iowa lab: (319)335-7936 Iowa City, IA 52242 FAX: (319)335-9570 From owner-proteins@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!elroy.jpl.nasa.gov!sdd.hp.com!spool.mu.edu!bloom-beacon.mit.edu!cambridge-news.cygnus.com!news3.near.net!yale!usenet From: abonvin@volta.csb.yale.edu ("Alexandre Bonvin") Newsgroups: bionet.molbio.proteins Subject: Re: Locating atoms from angles-Help! Date: 6 Jun 1995 15:51:59 GMT Organization: Yale University, Department of Computer Science, New Haven, CT Lines: 21 Message-ID: <3r1tiv$kvu@babyblue.cs.yale.edu> References: <3qtrft$hc8@harbinger.cc.monash.edu.au> NNTP-Posting-Host: volta.csb.yale.edu In article <3qtrft$hc8@harbinger.cc.monash.edu.au> eln118w@lindblat.cc.monash.edu.au (Mr YC Yap) writes: > ... > At the end of the program, I need to reconstruct > a detailed atomic model of the molecule. With the > dihedral angles, I know the relative orientation > of the backbone C, N and O atoms between one residue > and its neighbour. But how do I get the starting > coordinates of the FIRST N atom? Once I get that, > I can work out the rest of the atoms. > Does the position of your molecule in space matter? I guess not, so just put your first atom wherever you want! Alexandre ========================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Mol. Biophys. & Biochemistry | Fax: (203) 432-6946 | | Yale University | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06520-8114, USA | | ========================================================================== From owner-proteins@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!MANI.CBS.UMN.EDU!npv From: npv@MANI.CBS.UMN.EDU (Nora Plesofsky-Vig) Newsgroups: bionet.molbio.proteins Subject: re:help with immunoprecipitations Date: 6 Jun 1995 09:06:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9506061706.AA00884@mani.cbs.umn.edu> Reply-To: nora@biosci.cbs.umn.edu NNTP-Posting-Host: net.bio.net The IgGs that are in the immunoprecipitated sample can distort bands. I have heard that leaving 2-mercaptoethanol (or DTT) out of the sample buffer can keep the IgGs from entering the gel and causing problems. If your proteins do not have disulfide bonds, you might try this. Nora Plesofsky-Vig nora@biosci.cbs.umn.edu From owner-proteins@net.bio.net Mon Jun 05 23:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!daresbury!trane.uninett.no!nac.no!Norway.EU.net!EU.net!uknet!bcc.ac.uk!martin From: martin@bsm.bioc.ucl.ac.uk (Andrew Martin) Subject: Re: software:3D structure Message-ID: <1995Jun6.110122.15541@ucl.ac.uk> Date: Tue, 6 Jun 1995 11:01:22 GMT References: <1995May29.184217.1@hkucc.hku.hk> Organization: University College London X-Newsreader: TIN [version 1.2 PL2] Lines: 18 vldnaseq@hkucc.hku.hk wrote: : I am seeking a software if possible, for PC, that can show a 3D structure of : the protein whose peptide sequences only be known. Any suggestions are wellcome : Thank you. : Shannon :-) If only!!! (But I suppose a lot of us would be out of a job!) Andrew -- **************************************************************************** Dr. Andrew C.R. Martin, University College London & SciTech Software EMAIL: martin@biochem.ucl.ac.uk Tel:(Work) +44(0)171 419 3284 URL: http://www.biochem.ucl.ac.uk/~martin (Home) +44(0)1372 275775 **************************************************************************** From owner-proteins@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!NMSU.EDU!hroychow From: hroychow@NMSU.EDU (Hiranya Roychowdhury) Newsgroups: bionet.molbio.proteins Subject: Re: Association of protein dimer as function of temperature Date: 6 Jun 1995 13:29:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3r244l$9i0@helka.iif.hu> NNTP-Posting-Host: net.bio.net On 6 Jun 1995 szia@hanga.enzim.hu wrote: > We would like to study the association-dissociation equilibrium of a > homodimeric protein as a function of temperature. > > The protein consists of two identical subunits and there is an equilibrium > between the monomeric and dimeric forms of this protein. It is an enzyme > and we do not know if the monomeric form also has an enzymatic activity > (the dimeric form is known to be active). We would like to know the > relative population of the dimeric and monomeric forms as a function of > temperature. The dimeric form has a molecular weight of cca. 70 kDa. > > Any idea what technique can be used to this problem? We have all kinds of > spectroscopic techniques, and of course chromatographic and > electrophoresis methods. > > Any help would be greatly appreciated. > > Andras Szilagyi (szia@enzim.hu) > Institute of Enzymology, Hungarian Academy of Sciences > Although I do not have any reference handy, one of the summer students in my PhD lab used flourimetry to similar studies. Try searching the citation index or the SilverPlatter with the key words: Fluorimetry, protein, oligomerization, interaction etc. >>>>>>>>>>>>>>>>>>>>>>>>>>> Hiranya S. Roychowdhury Plant Genetic Engineering Lab. Box 3GL, NM State Univ. Las Cruces, NM 88003 Phone: (505) 646-5785 hroychow@nmsu.edu <<<<<<<<<<<<<<<<<<<<<<<<<<< From owner-proteins@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!uunet!newsfeed.ACO.net!news.iif.hu!news From: szia@hanga.enzim.hu Newsgroups: bionet.molbio.proteins Subject: Association of protein dimer as function of temperature Date: 6 Jun 1995 17:43:49 GMT Organization: IIF Lines: 21 Distribution: world Message-ID: <3r244l$9i0@helka.iif.hu> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: S-Lang: slrn (0.5.2.0) We would like to study the association-dissociation equilibrium of a homodimeric protein as a function of temperature. The protein consists of two identical subunits and there is an equilibrium between the monomeric and dimeric forms of this protein. It is an enzyme and we do not know if the monomeric form also has an enzymatic activity (the dimeric form is known to be active). We would like to know the relative population of the dimeric and monomeric forms as a function of temperature. The dimeric form has a molecular weight of cca. 70 kDa. Any idea what technique can be used to this problem? We have all kinds of spectroscopic techniques, and of course chromatographic and electrophoresis methods. Any help would be greatly appreciated. Andras Szilagyi (szia@enzim.hu) Institute of Enzymology, Hungarian Academy of Sciences From owner-proteins@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!sunic!sunic.sunet.se!columba.udac.uu.se!albireo!b93pca From: b93pca@albireo.tdb.uu.se (Peter Carlsson) Newsgroups: bionet.molbio.proteins Subject: www-/ftp-site with protein-info? Date: 6 Jun 1995 17:47:31 GMT Organization: Uppsala University Lines: 23 Message-ID: <3r24bj$ptn@columba.udac.uu.se> NNTP-Posting-Host: albireo.tdb.uu.se X-Newsreader: TIN [version 1.2 PL2] Hi! Is there anyone who knows if there is a www- or ftp-site where I can find a list of (preferably human) proteins? I have seen such lists in some books but I would like to have a computerbased version which can be sorted in an arbitrary way, i.e. by molecular mass. At the moment, such a list may be an 'over-kill' since I'm only looking for a single protein, but it could certainly be useful in the future. Are there BTW any suggestions for a replacer for erythropoietin, in the same size (about 30-35 kD) and considerable cheaper to experiment with? Thanks in advance, Peter -- ============================================================================== = = = Peter Carlsson, Uppsala University School of Engineering, Sweden = = E-mail address: b93pca@student.tdb.uu.se = = = ============================================================================== From owner-proteins@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!news.cerf.net!newsserver.sdsc.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!NewsWatcher!user From: pts3@cornell.edu (phil) Newsgroups: bionet.molbio.proteins Subject: Help!! Paper Wasps Needed Followup-To: bionet.molbio.proteins Date: 7 Jun 1995 02:52:37 GMT Organization: cornell Lines: 24 Sender: pts3@cornell.edu (Verified) Message-ID: NNTP-Posting-Host: cu-dialup-0615.cit.cornell.edu Hello. My name is Phil Starks. I am a graduate student at Cornell University in the field of NeuroBiology and Behavior. I am currently examining paper wasps, specifically Polistes dominulus. I am evaluating their nesting behavior and population genetics. I want to compare animals from different regions -- mostly from the Northeast in areas between Boston, MA and Ithaca, NY. My problem is finding these critters. They tend to congregate in the eves of man-made structures. I have searched state parks and some universities but have only found 4 usable sites. A usable site is one that has been relatively undisturbed (not sprayed with insecticides) for a few years and contains 18 or more colonies. These wasps make un-enveloped nests -- you can plainly see the cells of the comb (it looks much like a gray honeycomb). P. dominulus is the more yellow and smaller of the 2 Polistes species in this region (P. fuscatus is dark brown and the larger of the two animals). At this time of year you may see colonies with anywhere from 1 to 10 individuals, and nests that may contain 8 to 100 cells. If you know of any potential sites please email me. I am offering a $20.00 finder fee for useful sites. Thanks for reading this message Phil Starks (pts3@cornell.edu) From owner-proteins@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!sunic.sunet.se!news.funet.fi!news.csc.fi!news.helsinki.fi!kruuna!kstenber From: kstenber@cc.Helsinki.FI (Kaj Stenberg) Newsgroups: bionet.molbio.proteins,bionet.molbio.evolution Subject: Re: TIM Barrel Alignment Followup-To: bionet.molbio.proteins,bionet.molbio.evolution Date: 7 Jun 1995 09:30:52 GMT Organization: University of Helsinki Lines: 25 Distribution: world Message-ID: <3r3rkc$7t6@oravannahka.Helsinki.FI> References: <3r26ac$mkc@tierra.santafe.edu> NNTP-Posting-Host: kruuna.helsinki.fi Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL0] Xref: biosci bionet.molbio.proteins:4739 bionet.molbio.evolution:2957 Kenneth Rice (rice@chimayo.santafe.edu) wrote: > I'm looking for some aligned AA sequences of TIM barrel proteins as > test data for a tree reconstruction program that I'm writing. > Any alignments or pointers to same would be greatly appreciated. > Thanks, > Ken Rice Try starting from Bork & al. Protein Science(1995) 4:268-274 _____________________________________________________________________________ Kaj Stenberg tel: +46-18174288 Dep. Mol. Biol. fax: +46-18-536971 Swedish University for e-mail: Kaj@xray.bmc.uu.se Agricultural Sciences Kstenber@plootu.helsinki.fi Box 590 URL: http://onyx.bmc.uu.se/~kaj/ 75124 Uppsala, Sweden ______________________________________________________________________________ From owner-proteins@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!biosci!not-for-mail From: Michael Tor Klawansky Newsgroups: bionet.announce,bionet.molec-model,bionet.molbio.proteins,bionet.cellbiol Subject: CCL:METHODS OF MOLECULAR MECHANICS WORKSHOP Date: 7 Jun 1995 18:07:31 -0700 Organization: Sponsored account, Pittsburgh Supercomputing Center, Carnegie Mellon, Pittsburgh, PA Lines: 112 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: <4jpPm2W00YUqI6gbJ_@andrew.cmu.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:2169 bionet.molec-model:424 bionet.molbio.proteins:4750 bionet.cellbiol:2388 ***** NOTE:When replying please reply to ropelews@slave.psc.edu ***** "METHODS OF MOLECULAR MECHANICS AND DYNAMICS OF BIOPOLYMERS" WORKSHOP Pittsburgh Supercomputing Center August 16-19, 1995 The Pittsburgh Supercomputing Center (PSC) is hosting a workshop on "Methods of Molecular Mechanics and Dynamics of Biopolymers," August 16-19, 1995. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in molecular mechanics. Practical experience on our supercomputers will be gained in the application to: (1) the theory and practice of molecular mechanics and dynamics; (2) the development and refinement of molecular mechanics force fields; (3) the problem of conformation mapping and analysis of polypeptide structures, including the refinement of structure from measured NMR data; and (4) computation of interaction energies and free energies for protein-drug interactions and conformational thermodynamics. Workshop leaders are Dr. Charles L. Brooks III, The Scripps Research Institute and Dr. Alexander D. MacKerell Jr., University of Maryland at Baltimore. The worskhop will consist of lectures and extensive hands-on sessions. General aspects of molecular mechanics software will be discussed and a number of packages are available for use at the PSC. However, the programs CHARMM and QUANTA will be utilized most extensively in demonstrations. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. TRAVEL, MEALS AND HOTEL ACCOMMODATIONS FOR RESEARCHERS AFFILIATED WITH U.S. ACADEMIC INSTITUTIONS ARE SUPPORTED BY THIS GRANT. Enrollment is limited to 20. An application form is included. Deadline for applications is: June 22, 1995. Please direct inquires or send the following application form to blankens@psc.edu. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE ************************************** August 16-19, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by June 22, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From owner-proteins@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nac.no!Norway.EU.net!EU.net!Germany.EU.net!howland.reston.ans.net!news.sprintlink.net!noc.netcom.net!ix.netcom.com!netnews From: rolland@ix.netcom.com (Rolland S. Going) Newsgroups: bionet.molbio.proteins Subject: Kombucha fungi Date: 7 Jun 1995 20:22:15 GMT Organization: Netcom Lines: 2 Distribution: world Message-ID: <3r51pn$4hg@ixnews3.ix.netcom.com> NNTP-Posting-Host: ix-la5-14.ix.netcom.com Looking for serious information (Pro&Con) on the Kombucha fungi. Can anyone provide. Please respond to rolland@ix.netcom.com Thank you. From owner-proteins@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nac.no!Norway.EU.net!EU.net!news.sprintlink.net!uunet!in1.uu.net!newsfeed.pitt.edu!NewsWatcher!user From: GAW1+@pitt.edu (Gary Walker) Newsgroups: bionet.molbio.proteins Subject: Re: Protein assay of cell-extracts Date: 7 Jun 1995 19:42:37 GMT Organization: University of Pittsburgh Lines: 35 Message-ID: References: <3r4419$lsr@rs18.hrz.th-darmstadt.de> NNTP-Posting-Host: db.bio.pitt.edu In article <3r4419$lsr@rs18.hrz.th-darmstadt.de>, dh7y@pop.th-darmstadt.de (Inst. f. Biochemie) wrote: > Hy everybody, > > I had lysed my cells with a buffer containing 2-ME and NP-40 so there`s no > chance to test the concentration with BCA (because i got high extinction in > the control with 2-ME !! ), Bradford or OD (NP 40). > > What assay should i do ??? > > Patrick Baer > Institut fuer Biochemie > TH Darmstadt > e-mail: dh7y@pop.th-darmstadt.de Here is a reference for a protein assay designed for SDS-PAGE samples (2%SDS and 2-ME) that I have had great luck with. It is a filter-binding / coomassie staining based assay. Miniamide and Bamburg, Analytical Biochemistry, Vol 90; 66-70, 1990 If you have any trouble finding this protocol or using it you can contqact me. Gary Walker E-mail= GAW1+@pitt.edu -- GARY WALKER gaw1+@pitt.edu From owner-proteins@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!moonbeam.aecom.yu.edu!usenet From: wzhang@alsys1.aecom.yu.edu (wzhang) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: detergents in gel filtration Date: 7 Jun 1995 18:22:12 GMT Organization: Albert Einstein College of Medicine Lines: 2 Message-ID: <3r4qok$nb@moonbeam.aecom.yu.edu> References: <3r3r2l$1eef@rs18.hrz.th-darmstadt.de> NNTP-Posting-Host: sgn.aecom.yu.edu X-Posted-From: InterNews 1.0.1@sgn.aecom.yu.edu X-Authenticated: wzhang on POP host alsys1.aecom.yu.edu Xref: biosci bionet.molbio.methds-reagnts:29389 bionet.molbio.proteins:4747 CHAPS would be a very good choice. It does not have absorbance at 280 nn and has a high cmc. The concentration to be used is about 0.5%-1.0% From owner-proteins@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!MANI.CBS.UMN.EDU!npv From: npv@MANI.CBS.UMN.EDU (Nora Plesofsky-Vig) Newsgroups: bionet.molbio.proteins Subject: re:CNBr cleavage of proteins in PA gel slices? Date: 7 Jun 1995 10:58:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9506071858.AA00266@mani.cbs.umn.edu> Reply-To: nora@biosci.cbs.umn.edu NNTP-Posting-Host: net.bio.net Here are some references to CNBr digestion in gel slices: Analytic Biochem 97:382-386 (1979) Biochem J 197:591-597 (1981) Biochem Biophys Res Comm 166:139-145 (1990) I can't claim success myself, but it seems to me that the technique works better with thin gel slices, high amounts of CNBr, and long (overnight) incubation times. Hope this helps. Nora Plesofsky-Vig nora@biosci.cbs.umn.edu From owner-proteins@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nac.no!Norway.EU.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!fysiologie-1.med.kuleuven.ac.be!user From: Jan.Eggermont@med.kuleuven.ac.be (Jan Eggermont) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Edman degradation of bacterial proteins Date: Wed, 07 Jun 1995 18:49:22 +0100 Organization: Laboratorium voor Fysiologie - KU Leuven Lines: 15 Message-ID: NNTP-Posting-Host: fysiologie-1.med.kuleuven.ac.be Xref: biosci bionet.molbio.methds-reagnts:29379 bionet.molbio.proteins:4745 Hello, A small question for protein sequencers who have experience with Edman degradation of bacterial proteins: is the N-formyl-methionine, i.e. the modified start methione of bacterial proteins, derivatised in one single cycle or in two, i.e. first the formyl and then the methionine? Thanks, Jan -- Jan Eggermont Jan.Eggermont@med.kuleuven.ac.be Laboratorium voor Fysiologie - KU Leuven Campus Gasthuisberg tel 32-16-34 59 38 3000 Leuven Belgium fax 32-16-34 59 91 From owner-proteins@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!swrinde!emory!news-feed-1.peachnet.edu!news.duke.edu!djk From: djk@galactose.mc.duke.edu (Dan Kenan) Newsgroups: bionet.molbio.proteins Subject: CNBr cleavage of proteins in PA gel slices? Date: 7 Jun 1995 15:00:42 GMT Organization: Duke University, Durham, NC, USA Lines: 16 Message-ID: <3r4euq$eoq@news.duke.edu> NNTP-Posting-Host: galactose.mc.duke.edu X-Newsreader: TIN [version 1.2 PL2] I want to CNBr cleave a crosslinked protein RNA complex and determine which peptides form the site(s) of protein-RNA crosslinking. The best way for me to isolate the crosslinked complexes is to run mobility-shift gels with 32P-RNA and protein, then UV crosslink in the gel, then cut out the hot crosslinked complex. Since I will have a relatively small amount of material in the gel slice, it would be simplest for me to cleave directly in the polyacrylamide gel slice with CNBr in 70% formic acid. I can't find anything in the literature remotely similar to this technique. Is there anything in TBE/polyacrylamide gels that would inhibit the CNBr? Any suggestions about subsequent recovery of the cleaved products from the gel? The next step will be to load this treated sample onto an analytical gel such as that of Schagger and von Jagow, so I would probably need to desalt my treated sample, at least. Any suggestions or hints would be welcome. -Dan Kenan From owner-proteins@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!EU.net!Portugal.EU.net!news.rccn.net!scsing.switch.ch!news.belwue.de!news.belwue.de!News.Uni-Marburg.DE!news.th-darmstadt.de!news From: dh7y@pop.th-darmstadt.de (Inst. f. Biochemie) Newsgroups: bionet.molbio.proteins Subject: Protein assay of cell-extracts Date: Wed, 7 Jun 1995 13:55:09 -400 Organization: TH Darmstadt Lines: 17 Message-ID: <3r4419$lsr@rs18.hrz.th-darmstadt.de> NNTP-Posting-Host: bc3.bc.chemie.th-darmstadt.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-NewsReader: QNews v0.9b3 Beta 14 Apr 1994 Evaluation copy. Hy everybody, i have a problems with my protein-assay in a whole cell-extract from endothelial cells. I had lysed my cells with a buffer containing 2-ME and NP-40 so there`s no chance to test the concentration with BCA (because i got high extinction in the control with 2-ME !! ), Bradford or OD (NP 40). What assay should i do ??? Thanks in advance Patrick Baer Institut fuer Biochemie TH Darmstadt e-mail: dh7y@pop.th-darmstadt.de From owner-proteins@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!swrinde!pipex!gwen.pcug.co.uk!kate.ibmpcug.co.uk!redmoth!sdyer Newsgroups: bionet.molbio.proteins Message-ID: <14@redmoth.win-uk.net> Reply-To: sdyer@redmoth.win-uk.net (Sarah Dyer) From: sdyer@redmoth.win-uk.net (Sarah Dyer) Date: Wed, 07 Jun 1995 13:54:15 GMT Subject: Re: protein C deficiency Lines: 11 Re: a blood disorder called protein C deficiency Thankyou to all those helpful people who gave me a lot of valuable advice and pointed me in the right direction! sdyer@win-uk.net From owner-proteins@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!EU.net!Portugal.EU.net!news.rccn.net!scsing.switch.ch!news.belwue.de!news.belwue.de!News.Uni-Marburg.DE!news.th-darmstadt.de!news From: di58@pop.th-darmstadt.de (P. Friedl) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: detergents in gel filtration Date: 7 Jun 1995 09:21:25 GMT Organization: TH Darmstadt Lines: 36 Message-ID: <3r3r2l$1eef@rs18.hrz.th-darmstadt.de> References: NNTP-Posting-Host: friedl.bc.chemie.th-darmstadt.de X-Newsreader: WinVN 0.92.6+ Xref: biosci bionet.molbio.methds-reagnts:29362 bionet.molbio.proteins:4741 In article , Jan.Eggermont@med.kuleuven.ac.be (Jan Eggermont) says: > >Hello, > >I am currently investigating the oligomeric nature of a purified protein. >On a Superose 12 FPLC colum with a 150 mM NaCl buffer the protein migrates >with a Mr of around 100k whereas the predicted molecular mass from the >amino acid sequence is 28k suggesting it may form a trimer. I now want to >find out what type of interactions (hydrophobic/hydrophilic/S-S >bridges...) are going on. I presume raising the salt concentration will >unmask hydrophilic interactions and adding a reducing agent such as DTT >will break up S-S bridges. However, I am not sure about the best way to >tackle the hydrophobic interactions. At first I wanted to use Triton-X100 >but this will interfere with the UV recording at 280 nm. In addition I was >told that because of the low critical micellar concentration (cmc) of >Tx100, some of the protein may be incorporated into micelles. So any ideas >out there on a detergent that does not absorb at 280 nm and that has a >rather high cmc? >thanks in advance. > >Jan > >-- >Jan Eggermont Jan.Eggermont@med.kuleuven.ac.be >Laboratorium voor Fysiologie - KU Leuven >Campus Gasthuisberg tel 32-16-34 59 38 >3000 Leuven Belgium fax 32-16-34 59 91 Hello, you could try chaotropic reagents at moderate concentrations as for example 1-2.5 M KSCN. Another approach could be the inclusion of methanol (10-30%) although this strengthens ionic interactions. good luck P.F. From owner-proteins@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news.sprintlink.net!uunet!in1.uu.net!newsfeed.ACO.net!fuw.edu.pl!news.nask.org.pl!ci.pwr.wroc.pl!was386.ch.pwr.wroc.pl!studks48 From: studks48@was386.ch.pwr.wroc.pl Newsgroups: bionet.molbio.proteins Subject: Carcinoembrionic Antigen Date: Wed, 7 Jun 1995 13:16:00 +0000 Organization: Technical Univeristy of Wroclaw Lines: 5 Message-ID: NNTP-Posting-Host: was386.ch.pwr.wroc.pl Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Please send me some information about Carcinoembrionic Antigen. Please send me addresses where I will find information about that protein. My e-mail: studks48@kchk.ch.pwr.wroc.pl Thanks in advance. Joanna Zapala From owner-proteins@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!sunic.sunet.se!news.uni-c.dk!news.daimi.aau.dk!biobase!wind From: wind@biobase.dk (Troels Wind) Newsgroups: bionet.molbio.proteins Subject: Re: Protein adsorption Date: 8 Jun 1995 11:40:38 GMT Organization: The Danish BioBase Lines: 23 Message-ID: <3r6njm$pg9@biovax.biobase.dk> References: NNTP-Posting-Host: biobase.dk X-Newsreader: TIN [version 1.2 PL2] Proteins in genenral do bind to glass as well as plastic, so switching to plastic probably wouldnt help you. Maybe you can get some ideas from "How to Prevent Losses of Protein by Adsorbtion to Glass and Plastic", Analytical Biochemistry 135, pp 112-119 (1983). I havent done any experiments analyzing these problems though, but I hope the ref can help :) If you want to see the paper, but dont have acces to it, let me know and I'll fax it to you. Troels Wind pharmscience@gandalf.otago.ac.nz wrote: : In our lab we have had a continiung problem with peptides adsorbing to glass- : ware. Suggestions to overcome have included washing the containers with a : surfactant, adding a competing protein (eg 2% BSA), or working at : (higher) concentrations where losses that do occur are negligible. : None of these suggestions however are satisfactory for the system we are : using. : Could anyone help us with other suggestions? : Reply to leo.schep@stonebow.otago.ac.nz From owner-proteins@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!ARSERRC.GOV!CTHOMPSON From: CTHOMPSON@ARSERRC.GOV Newsgroups: bionet.molbio.proteins Subject: collagen crosslink problems Date: 8 Jun 1995 07:19:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HRGK13KSAA0002XR@ARSERRC.Gov> NNTP-Posting-Host: net.bio.net We need some serious help. Here's a little background. 1. Goal- to find out what happens to the lysine groups when collagen is crosslinked with paraformaldahyde. 2. Problem only have one week to analyze the product. 3. Tried TNBS method (but after we filter the solution the membrane is put into the mixture because we need a very quantative transfer) 4. We also need to determine the soluble protein concentration in the filtrate 5. Problem- using BCA method paraformaldyhde and sodium cyanoborohydride complex with copper to throw off the results need help- in finding protien concentraion of filtrate and determine free lysine in the crosslinked collagen please help Craig Thompson cthompson@arserrc.gov From owner-proteins@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!sdd.hp.com!news.cs.indiana.edu!lynx.unm.edu!bubba.NMSU.Edu!dkim From: dkim@nmsu.edu (Daniel Kim) Newsgroups: bionet.molbio.proteins Subject: Re: Protein assay of cell-extracts Date: 8 Jun 1995 16:29:54 GMT Organization: New Mexico State University, Las Cruces, NM Lines: 52 Sender: dkim@nmsu.edu Message-ID: <3r78i2$qar@bubba.NMSU.Edu> References: <3r4419$lsr@rs18.hrz.th-darmstadt.de> NNTP-Posting-Host: verdi.nmsu.edu In article GAW1+@pitt.edu (Gary Walker) writes: >In article <3r4419$lsr@rs18.hrz.th-darmstadt.de>, dh7y@pop.th-darmstadt.de >(Inst. f. Biochemie) wrote: > >> Hy everybody, >> > >> I had lysed my cells with a buffer containing 2-ME and NP-40 so there`s no >> chance to test the concentration with BCA (because i got high extinction in >> the control with 2-ME !! ), Bradford or OD (NP 40). >> >> What assay should i do ??? >> >> Patrick Baer >> Institut fuer Biochemie >> TH Darmstadt >> e-mail: dh7y@pop.th-darmstadt.de > > >Here is a reference for a protein assay designed for SDS-PAGE samples >(2%SDS and 2-ME) that I have had great luck with. It is a filter-binding / >coomassie staining based assay. I have just started using a protein assay called dotMETRIC, sold by: Geno Technology, Inc. (314) 534-0075 This assay is based on diffusion of protein into a membrane strip of some sort. The amount of total protein is proportional to the diameter of the protein "spot" formed by spotting one microliter of a protein solution onto the strip. This method claims to be insensitive to detergents that may be in the protein solutions, and will detect down to a detection limit of 0.3 ng. After applying protein solutions, the detection takes about 5 - 10 minutes. A kit costs about $130 U.S. and will do over 100 assays. The company has a rather liberal definition of an "assay", allowing 4 independent spots per assay (to give duplicate samples or a dilution series for greater accuracy). The method does not require a protein standard. The diameter of a spot is independent of the nature of the protein applied, they say. I have had good luck with the kit so far. It is as easy and quick as advertised. I have not done a formal examination of its accuracy, however, but the results so far are in the "ballpark" that I expect. I hope this is of some help. Daniel Kim From owner-proteins@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!vector.nsk.su!eroshkin From: eroshkin@vector.nsk.su (Alexy Eroshkin) Newsgroups: bionet.molbio.proteins Subject: ANNOUNCEMENT: Protein Structure-Activity Analysis Software Date: 8 Jun 1995 03:11:43 -0700 Organization: NPO Vector Lines: 85 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net New software package PROANAL version 2 is freely available thru: IuBio archive, EBI ftp and email server, NIG (Japan) ftp server. PROANAL version 2.0 ------------------- Enhanced version of the program PROANAL (CABIOS, 9, 491-497, 1993) Purposes: * investigation of relationships between structure and activity in a family of evolutionary related (or/and artificially mutated) proteins/peptides (searching relations between data on activity and various physico- chemical characteristics of different regions in primary structures); * analysis of multiple protein alignments; * studying protein structure-function relationships; * comparative analysis of sequences; * protein-engineering experiment planning. PROANAL may be used to predict protein secondary structures, functionally or structurally important regions, antigenic determinants (B- and T-call epitopes), transmembrane regions. Input data: * aligned protein amino acid sequences with the data on their activity (pK, Km, ED50 or any other, if available). New options: * converts alignments from CLUSTAL output files to PROANAL input files; * plots individual and average profiles (10 different profiles, including alpha-helical and beta-strand moments) for entire protein family; * searching physico-chemically variable and conservative regions (e.g., regions with low dispersion of alpha-helical moments of hydrophobicity); * searching sites with high and low physico-chemical properties; * sequence editing (for mutagenesis planning); * database of about 100 amino acid physico-chemical properties; * examples, extensive manual and help system. Requirements: DOS 3.30 or later, EGA/VGA video card, 500 KB RAM. How to get PROANAL ver 2 ------------------------- 1. From IuBio archive as ftp://iubio.bio.indiana.edu/molbio/ibmpc/proanal2.exe (and proanal2.readme) IUBio archive files are now all available by e-mail to users. This is thru a network Gopher to Email gateway. To start, send mail to gophermail@iubio.bio.indiana.edu 2. From EBI ftp and email server: ftp.ebi.ac.uk /pub/software/dos/proanal$.exe This is the self-extracting archive, so it should before transferring, ftp should be set to binary transfer. Or by sending an email message containing: GET DOS_SOFTWARE:PROANAL.UAA to netserv@ebi.ac.uk Which will return the 6 files. Running UUDECODE you'll get self-extracting archive with the program. 3. From NIG (Japan) ftp server ftp.nig.ac.jp directory: /pub/dos/proanal file: proanal$.exe URL: gopher://gopher.nig.ac.jp:70/59/pub/dos/proanal/proanal$ ftp://ftp.nig.ac.jp/pub/dos/proanal/proanal$.exe ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Alexey Eroshkin Research Institute of Molecular Biology E.mail: eroshkin@vector.nsk.su State Research Center of Virology and Tel: +7 (3832) - 647774 Biotechnology "Vector" Fax: +7 (3832) - 328831 Koltsovo, Novosibirsk Region 633159 Russia +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-proteins@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.tamu.edu!mac2wild2.tamu.edu!user From: Yasha@bioch.tamu.edu (Yasha Hartberg) Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Glycosylation Signal Sequences? Date: 8 Jun 1995 19:47:56 GMT Organization: Texas A&M University Lines: 9 Message-ID: NNTP-Posting-Host: mac2wild2.tamu.edu Xref: biosci bionet.molbio.proteins:4757 bionet.molbio.methds-reagnts:29457 I was wondering if there are known amino acid recognition sequences for O-linked or N-linked glycosylation. Any references would be greatly appreciated. Thanks, Yasha Hartberg Texas A&M University "The most beautiful thing in Tokyo is McDonald's." Andy Warhol From owner-proteins@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!HELIX.NIH.GOV!geetha From: geetha@HELIX.NIH.GOV (Geetha Vasudevan) Newsgroups: bionet.molbio.proteins Subject: Re: www-/ftp-site with protein-info? Date: 8 Jun 1995 10:55:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <9506081755.AA15239@helix.nih.gov> NNTP-Posting-Host: net.bio.net You could try SCOP (structural classification of proteins) or point your browser to the molecular modeling home page of NIH (http://www.nih.gov). Hope this helps. | GEETHA VASUDEVAN Ph.#: (301)-402-0506 (w) | | Post Doctoral Visiting Fellow Fax#: (301)-496-2172 (w) | | Anal.Bio.Sec., Lab.of Str.Biol. E-mail: geetha@helix.nih.gov | | Bldg.12A/Room 2041,DCRT, NIH, Bethesda, MD 20892 | From owner-proteins@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!news-feed-1.peachnet.edu!news.duke.edu!usenet From: Shaojie Wang Newsgroups: bionet.molbio.proteins Subject: peptide mapping Date: 9 Jun 1995 03:57:31 GMT Organization: Duke University, Durham, NC, USA Lines: 4 Message-ID: <3r8grb$3hg@news.duke.edu> NNTP-Posting-Host: shaojie.mc.duke.edu I have used several different proteases to peptide map receptors. However, I got conflicting digestion patterns for trypsin and LysC. Does anybody have experiences with nonspecific cut of trypsin or LysC? Theoretically, if there is a Lysine-Lysine fragment without any Arginine in between, There should be a same trypsin digestion fragment. My data does not show the identical fragment. Any suggestions? Thanks in advance. Jenny Wang From owner-proteins@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!post.its.mcw.edu!not-for-mail From: fpark@post.its.mcw.edu (Frank Park) Newsgroups: bionet.molbio.proteins Subject: Help with Immunoblots Date: 8 Jun 1995 22:06:26 -0500 Organization: Medical College of Wisconsin; Milwaukee Wisconsin Lines: 14 Message-ID: <3r8dri$sto@post.its.mcw.edu> NNTP-Posting-Host: post.its.mcw.edu X-Newsreader: TIN [version 1.2 PL2] I have had recent problems lately with Western Blots. I have been running a 12% polyacrylamide gel but I cannot seem to get the molecular weight markers (sizes 40 kD and down) to separate from the leading dye. Also, I have had problems with the transfer of the proteins from the gel to the nitrocellulose membrane. When I stain the membranes with Ponceau S after the transfer (at 100V for 1 hr), there are splotchy areas on the membrane due to seemingly overtransfer. Please help on this matter with any suggestions. Thank You. Frank Park fpark@post.its.mcw.edu From owner-proteins@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!MIS.FINCHCMS.EDU!muellerd From: muellerd@MIS.FINCHCMS.EDU ("Dr. David Mueller") Newsgroups: bionet.molbio.proteins Subject: His for Glu/ General Base Catalysis Date: 8 Jun 1995 13:36:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi protein@net: I am looking for a reference where a residue that acts as a general base catalyst, such as Glu, is replaced with another residue that can act as a general base catalyst, such as His, but with different properties. Thanks in advance. David Mueller Chicago Medical School muellerd@mis.finchcms.edu From owner-proteins@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!reuter.cse.ogi.edu!engr.orst.edu!gaia.ucs.orst.edu!ava.bcc.orst.edu!vergink From: vergink@ava.bcc.orst.edu (_Kevin Vergin) Newsgroups: bionet.molbio.proteins Subject: Iodoacetamide to block cysteines in SDS-PAGE Date: 8 Jun 1995 14:55:33 GMT Organization: Oregon State University, Corvallis, Oregon Lines: 5 Distribution: na Message-ID: <3r7315$2au@gaia.ucs.orst.edu> NNTP-Posting-Host: ava.bcc.orst.edu In order to fully reduce a protein which I am studying by SDS-PAGE, I need to reduce with DTT and then block the cysteine residues with iodoacetamide to prevent re-formation of disulfide bonds. Does anyone know of a protocol for using iodoacetamide with DTT? Any help would be much appreciated. Thanks in advance. From owner-proteins@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!EU.net!sun4nl!uva.nl!amc!news From: seppen@amc.uva.nl Newsgroups: bionet.molbio.proteins Subject: RE: Protein assay of cell-extracts Date: Thu, 8 Jun 95 16:48:52 -100 Organization: Central Computer Organization AMC/UvA Lines: 27 Message-ID: <3r72kp$ki9@amcnix.amc.uva.nl> References: <3r4419$lsr@rs18.hrz.th-darmstadt.de> NNTP-Posting-Host: amccca.amc.uva.nl In Article <3r4419$lsr@rs18.hrz.th-darmstadt.de> dh7y@pop.th-darmstadt.de (Inst. f. Biochemie) writes: >Hy everybody, > >i have a problems with my protein-assay in a whole cell-extract from >endothelial cells. > >I had lysed my cells with a buffer containing 2-ME and NP-40 so there`s no >chance to test the concentration with BCA (because i got high extinction in >the control with 2-ME !! ), Bradford or OD (NP 40). > >What assay should i do ??? > >Thanks in advance > >Patrick Baer >Institut fuer Biochemie >TH Darmstadt >e-mail: dh7y@pop.th-darmstadt.de You could use fluorescamin, providing that you do not use a Tris or glycine buffer. Fluorescamin reacts with free amines. Email me for a protocol. Hope this helps, Jurgen Seppen, Amsterdam, The Netherlands SEPPEN@AMC.UVA.NL From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!ns1.faseb.org!darwin.sura.net!haven.umd.edu!purdue!yuma!usenet From: Jonathan Wisson Newsgroups: bionet.molbio.proteins Subject: (no subject) Date: 9 Jun 1995 05:28:59 GMT Organization: Colorado State University Lines: 7 Message-ID: <3r8m6r$2u3s@yuma.ACNS.ColoState.EDU> NNTP-Posting-Host: slip216x.slip.colostate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.molbio.proteins Is anyone aware where antibodies to rat angiotensinogen can be bought? To avoid developing antibodies ourselves, any help would be appreciated. jwisson@vth1.vth.colostate.edu jawiss@lamar.colostate.edu From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!rutgers!gatech!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!cdw1000 From: cdw1000@mole.bio.cam.ac.uk (Christopher Walentas (Bioc)) Newsgroups: bionet.molbio.proteins Subject: Trp specific cleavage reagents Date: 9 Jun 1995 23:19:53 GMT Organization: University of Cambridge, England Lines: 18 Message-ID: <3rakup$f10@lyra.csx.cam.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk Hi. I've managed to track down a few different chemicals that will cut at Trp, but am finding out what the difference is between them all or are they by chance all pretty much the same? So far the list consists of o-iodosobenzoic acid, N-chloro- succinimide and BNPS-skatole. I'm trying to follow the formation of some disulphides and a peptide map seemed like the most straightforward route. I'm not sure if o-IBA would therefore be any good if per chance it could exchange with thiols/ disulphides. If anyone knows of a review of these agents or papers which are more comprehensive than the late 70's- early 80's ones I've been able to find through Pierce and BDH, please drop me a line. Thanks again! Tripp From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!noc.netcom.net!netcomsv!uu3news.netcom.com!netcomsv!uucp3.netcom.com!www1.chiron.com!chiremv!larryc From: larryc@chiremv.chiron.com (Larry Cousens) Newsgroups: bionet.molbio.proteins Subject: Re: Iodoacetamide to block cysteines in SDS-PAGE Date: 9 Jun 95 23:17:57 GMT Organization: Chiron Corp. Lines: 15 Distribution: na Message-ID: References: <3r7315$2au@gaia.ucs.orst.edu> NNTP-Posting-Host: chiremv.chiron.com vergink@ava.bcc.orst.edu (_Kevin Vergin) writes: >In order to fully reduce a protein which I am studying by SDS-PAGE, I >need to reduce with DTT and then block the cysteine residues with >iodoacetamide to prevent re-formation of disulfide bonds. Does anyone >know of a protocol for using iodoacetamide with DTT? Any help would be >much appreciated. Thanks in advance. See Lane (1986) Analytical Biochemistry vol86, pp655-664. It describes IAM treatment for SDS PAGE and it works very well. Good luck, Larry Cousens From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!warwick!usenet From: JC Newsgroups: bionet.molbio.proteins Subject: Re: fine resolution on SDS-PAGE Date: 9 Jun 1995 14:26:17 GMT Organization: University of Warwick, Coventry, UK Lines: 17 Message-ID: <3r9lm9$698@violet.csv.warwick.ac.uk> References: <3r9bhr$pig@lyra.csx.cam.ac.uk> NNTP-Posting-Host: holly-fddi.csv.warwick.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.4 sun4m) To: rw200@cus.cam.ac.uk X-URL: news:3r9bhr$pig@lyra.csx.cam.ac.uk Dear Robert, I have a recollection of being told that altering the concentration of Bisacrylamide in the stock solution could help with your problem. I think it was dropped from 0.8 - 0.3% but unfortunately I can't be absolutely certain on this. Anyway hope something works, Yours Jonathan Cook Dept. Biological Sciences University of Warwick Coventry lsrcp@csv.warwick.ac.uk From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!ns1.faseb.org!darwin.sura.net!nih-csl!loglady.ninds.nih.gov!johnk From: johnk@spasm.niddk.nih.gov (John Kuszewski) Subject: Re: fine resolution on SDS-PAGE Message-ID: <1995Jun9.190648.3827@alw.nih.gov> Keywords: SDS-PAGE Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: spasm.niddk.nih.gov Reply-To: johnk@spasm.niddk.nih.gov (John Kuszewski) Organization: National Insts. of Health References: <3r9bhr$pig@lyra.csx.cam.ac.uk> Date: Fri, 9 Jun 1995 19:06:48 GMT Lines: 23 In article <3r9bhr$pig@lyra.csx.cam.ac.uk>, rw200@cus.cam.ac.uk (R. Woodward) writes: |> Dear all, |> I am having problems resolving two proteins of similar Mw on SDS-PAGE, I have tried 7.5 and 12.5% gels but the resolution is not as good as I would like . The sizes of the two proteins are ~55 and 52kD which are radiolabelled in an IVT and then immunopre|> cipitated before SDS-PAGE and flourography. Am I expecting too much or are there any tips to resolve these two bands. Thanks v.much Have you tried cappilary zone electrophoresis instead of SDS-PAGE? CZE has better resolution, from what I understand. -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| "Biophysics has driven me to an attitude of apocalyptic doom" --Frank Delaglio From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!swrinde!pipex!uknet!lyra.csx.cam.ac.uk!rw200 From: rw200@cus.cam.ac.uk (R. Woodward) Newsgroups: bionet.molbio.proteins Subject: fine resolution on SDS-PAGE Date: 9 Jun 1995 11:33:15 GMT Organization: University of Cambridge, England Lines: 13 Message-ID: <3r9bhr$pig@lyra.csx.cam.ac.uk> NNTP-Posting-Host: bootes.cus.cam.ac.uk Keywords: SDS-PAGE X-Newsreader: NN version 6.5.0 #2 (NOV) Dear all, I am having problems resolving two proteins of similar Mw on SDS-PAGE, I have tried 7.5 and 12.5% gels but the resolution is not as good as I would like . The sizes of the two proteins are ~55 and 52kD which are radiolabelled in an IVT and then immunoprecipitated before SDS-PAGE and flourography. Am I expecting too much or are there any tips to resolve these two bands. Thanks v.much Robert R.Woodward Dept Pharmacol University of Cambridge Tennis Court Rd Cambridge U.K. Email rw200@cus.cam.ac.uk an From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!newsfeed.ACO.net!mail.boku.ac.at!news From: Iain Wilson Newsgroups: bionet.molbio.proteins,bionet.molbio.methds-reagnts Subject: Re: Glycosylation Signal Sequences? Date: 9 Jun 1995 10:49:13 GMT Organization: BOKU Wien Lines: 23 Message-ID: <3r98v9$oh2@mail.boku.ac.at> References: NNTP-Posting-Host: 141.244.58.101 Xref: biosci bionet.molbio.proteins:4763 bionet.molbio.methds-reagnts:29494 Yasha@bioch.tamu.edu (Yasha Hartberg) wrote: > > I was wondering if there are known amino acid recognition sequences for > O-linked or N-linked glycosylation. Any references would be greatly > appreciated. > > Thanks, > > Yasha Hartberg > Texas A&M University > "The most beautiful thing in Tokyo is McDonald's." Andy Warhol There is the standard N-glycosylation consensus Asn-X-Ser/Thr look at Gavel and von Heijne (1990) Protein Engineering 3:433-442. However not all Asn-X-Ser/Thr sites get glycosylated even if they are lumenally/extracellular facing. For O-links there are no obvious rules. See for instance Wilson, Gavel and von Heijne (1991) Biochem. J. 275:529-534 Iain wilson@edv1.boku.ac.at From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.molbio.proteins Subject: ?? Labsystems adress? Date: 9 Jun 1995 10:14:51 +0100 Lines: 13 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3r93eb$bsq@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk Hi, who could help me with the adress of Labsystems? They make ELISA type fluorimete rs and the corresponding software. Thanks Tilman ********************************************************* Tilman Voss Ph.D. Protein Chemistry Group Bender+Co Vienna, Austria Tel: xx43-1-80105 351 Tel: xx43-1-80105 351Fax: xx43-1-80105 366 Email: VOSS@AIMP.UNA.AC.AT ********************************************************* From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!news.sprintlink.net!grape.epix.net!sc2c526a.ra.osd.mil!nova.sti.nasa.gov!lerc.nasa.gov!purdue!mozo.cc.purdue.edu!rhphmac8.cc.purdue.edu!user From: (S. Firestine) Newsgroups: bionet.molbio.proteins Subject: Re: fine resolution on SDS-PAGE Followup-To: bionet.molbio.proteins Date: 9 Jun 1995 18:02:06 GMT Organization: Purdue University Lines: 7 Distribution: world Message-ID: <3ra2au$ira@mozo.cc.purdue.edu> References: <3r9bhr$pig@lyra.csx.cam.ac.uk> NNTP-Posting-Host: rhphmac8.cc.purdue.edu You can try to run a gradient gel in which the gradient is not very steep. This should give your greater resolution. I have gotten very good resolution with low molecular weight proteins by increasing the concentration of acrylamide up to 20%. This may be too severe for your size and you will have to guess at the time since the dye front runs off the gel long before the protein has migrated far into the gel. Hope that this helps. From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!NMSU.EDU!hroychow From: hroychow@NMSU.EDU (Hiranya Roychowdhury) Newsgroups: bionet.molbio.proteins Subject: Re: behaviour of protein on gels Date: 9 Jun 1995 13:27:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3r9mo6$qoq@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net On 9 Jun 1995, A.S.McAlpine wrote: > Someon in our lab has been purifying his protein and has come across a strange > phenomenon (to us at least) as regards its behaviour on SDS PAGE. Origianlly > he believed that his protein was infact impure. One day when he ran an identical > sample on a gel it showed a very clean and tight band. This was confusing. > After much playing around with sample conditions SDS concentrations etc, we > pinned it down to when the gels had been set. When a gel was set up and left overnight in the fridge, it gave a very clean gel with tight bands of his protein. If the samples were run on the gel the same day, ie. just after it had > been set, it gave a smeared band (so less intense than the overnight one) and > what we now believe to be aggregates further up the gel., which we had beleived to originally be contamination. We know that the protein is quite hydrophobic in nature and does form aggregates. Why though do we get a nice gel if we leave it overnight? If anyone else has had this problem and has an explanation as to why it happens please let us know. > > thanks > As a matter of fact, you should trust the gel that was allowed to polymerize overnight. Polymerization of the acrylamide, depending on the freshness of the reagents, temp. etc, may take anywhere between 30min to a few hours. While the top of the gel may look nice and flat and solid an hour after it was poured, there may still be some partially polymerized monomers between the two plates. As a result the polypeptides do not migrate as tight bands and sometimes a single band may show a shadow (usually above it). Freshly made monomer solution will effectively polymerize and be ready to run in a couple of hours. As the solution gets older, the gel should be allowed to polymerize longer, ideally overnight. Under no circumstances should the monomer solution be stored more than four weeks. I almost never run my gels the same day they are poured. >>>>>>>>>>>>>>>>>>>>>>>>>>> Hiranya S. Roychowdhury Plant Genetic Engineering Lab. Box 3GL, NM State Univ. Las Cruces, NM 88003 Phone: (505) 646-5785 hroychow@nmsu.edu <<<<<<<<<<<<<<<<<<<<<<<<<<< From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!Germany.EU.net!nntp.gmd.de!news.rwth-aachen.de!news.rhrz.uni-bonn.de!news.uni-stuttgart.de!news.belwue.de!news.belwue.de!fu-berlin.de!160.45.28.9!not-for-mail From: strecker@chemie.fu-berlin.de (Andreas Strecker) Newsgroups: bionet.molbio.proteins Subject: Re: peptide mapping Date: Fri, 09 Jun 95 20:29:29 GMT Organization: FU Berlin Lines: 29 Message-ID: <3r9m4a$b6r@fu-berlin.de> References: <3r8grb$3hg@news.duke.edu> NNTP-Posting-Host: 160.45.28.9 X-Access: 16 19 X-Newsreader: News Xpress Version 1.0 Beta #3 In article <3r8grb$3hg@news.duke.edu>, Shaojie Wang wrote: >I have used several different proteases to peptide map receptors. However, I got conflicting digestion patterns for trypsin and LysC. Does anybody have experiences with nonspecific cut of trypsin or LysC? >Theoretically, if there is a Lysine-Lysine fragment without any Arginine in between, There should be a same trypsin digestion fragment. My data does not show the identical fragment. Any suggestions? Thanks in advance. > Dear Jenny! There are unspecific cleavage positions of trypsin, namely large hydrophobic aa like ile, leu or even tyr. The exact circumstances under which they are used are to my knowledge unknown, but I experienced they become very (!) prominent when you don't stop the digest subsequent the incubation with either trypsin inhibitor (e.g. soybean, stoichiometric amount to the trypsin used) or 1mM PMSF. Especially if you freeze your sample without these inhibitors, you will get mainly "unspecific" cleavage, at least with the proteins I digested. Generally if there is a sequence of two or more basic aa's you should expect incomplete cleavage since the protease usually needs a couple of aa's to hold tight to its substrate. I don't know about uunspecific cleavage patterns with lysC, but probably the same phenomena should be expected. Good luck! Andreas (further questions? please e-mail me!) From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news-e1a.megaweb.com!newstf01.news.aol.com!uunet!rose.uthscsa.edu!news.cc.geneseo.edu!newserve!ub!dsinc!netnews.upenn.edu!elmo.tju.edu!usenet From: MELONI1@JEFLIN.TJU.EDU (Frank Meloni) Newsgroups: bionet.molbio.proteins Subject: Re: Help with Immunoblots Followup-To: bionet.molbio.proteins Date: 9 Jun 1995 15:46:12 GMT Organization: Thomas Jefferson University Lines: 27 Distribution: world Message-ID: <3r9qc4$4mn@elmo.tju.edu> References: <3r8dri$sto@post.its.mcw.edu> NNTP-Posting-Host: meloni1.tjh.tju.edu X-Newsreader: News Xpress Version 1.0 Beta #3 In article <3r8dri$sto@post.its.mcw.edu>, fpark@post.its.mcw.edu (Frank Park) wrote: >I have had recent problems lately with Western Blots. I have been running a >12% polyacrylamide gel but I cannot seem to get the molecular weight markers >(sizes 40 kD and down) to separate from the leading dye. Also, I have had >problems with the transfer of the proteins from the gel to the >nitrocellulose membrane... It would seem that you have several problems. If your 40 KDa marker runs at the bottom of the gel it is very likely that your acrylamide stock is not accurate. A 7 - 8 % gel will not separate a 40 kDa protein from the dye front, but clearly a 12% will. Check the Bio-Rad Catalog and look at the chart they have of their blotting standards for a good picture of the separation you should get. My suggestion is to replace the acrylamide stock, perhaps it is too old and prepare fresh APS while you are at it. You don't mention what method you use for transfer, semi-dry transfers for 1 hr are OK, but wet transfers take longer (I don't care what the companies say) and I have gotten optimal results using a low voltage (30-40 V) overnight transfer. High intensity transfers are inefficient and some protein will remain on the gel and higher percentage gels do require more time. I hope this helps. Frank J. Meloni, Ph.D. Meloni1@jeflin.tju.edu Cardeza Foundation for Hematologic Research Thomas Jefferson University Philadelphia, PA From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!cdw1000 From: cdw1000@mole.bio.cam.ac.uk (Christopher Walentas (Bioc)) Newsgroups: bionet.molbio.proteins Subject: iodosobenzoic acid cleavage of proteins Date: 9 Jun 1995 17:29:13 GMT Organization: University of Cambridge, England Lines: 30 Message-ID: <3ra0d9$2bu@lyra.csx.cam.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk Hi. I was wondering if anyone had a reference for the cleavage of proteins with o-iodosobenzoic acid that is later than the 1981 Fontana et al. and Mahoney et al. From gcg, it looks like it's the reagent of choice, but I've no protocol save the two aforementioned. >From the gcg plot, IBA cuts at Trp residues, but the two refs. I have swear up and down that Tyr is susceptible as well. Has there been a protocol worked out to specifically cleave at Trp only or does another, more reliable reagent exist. Most of the really useful methods texts get locked up at the weekend so I'm pretty well stuck on this front till Monday. Any thoughts (and refs!) on the matter would be greatly appreciated. Cheers, Tripp ------------------------------------------------------------------------------- C. D. Walentas Cambridge Centre for Molecular Recognition, University of Cambridge, Cambridge, England CB2 1QW Phone: 0223 333 662 Fax: 0223 333 345 email: c.d.walentas@bioc.cam.ac.uk From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!news.voicenet.com!philly22.voicenet.com!user From: wetzelrb@omni.voicenet.com (Ron Wetzel) Newsgroups: bionet.molbio.proteins Subject: Radiolysis of 32P-ATP Date: Fri, 09 Jun 1995 22:44:29 -0500 Organization: Voicenet - Internet Access - (215)674-9290 Lines: 51 Message-ID: NNTP-Posting-Host: philly22.voicenet.com > Path: news.voicenet.com!news.sprintlink.net!howland.reston.ans.net!agate!kos5mac7.berkeley.edu!user > From: jlonsdal@nature.berkeley.edu (Jen Lonsdale) > Newsgroups: bionet.molbio.proteins > Subject: Radiolysis of 32P-ATP > Date: 9 Jun 1995 16:15:55 GMT > Organization: Department of Plant Biology; University of California > Lines: 11 > Message-ID: > NNTP-Posting-Host: kos5mac7.berkeley.edu > > Dear All, > > Does anyone know about radiolysis of 32P-ATP during storage? I know that > the time-frame of usefulness for 32P-labelled substrates may eliminate > this as a problem, but I'm still curious! I'm working with a protein > kinase system which may be sensitive to ATP breakdown/isomerization > products. > > Thanks, > > Simon. Dear Simon, This is going back a ways, but when I was in Dieter Soll's lab in the late 70s I was making and storing very hot gamma-32P-ATP for end labelling of RNA fragments for wandering spot sequencing of tRNA. I noticed that autoradiograms of thin layer chromatograms of the ATP after storage (weeks) even in the freezer looked terrible - lots of hot decay products everywhere. Reasoning it was a free radical process I added mercaptoethanol to the next prep and it worked great at stabilizing labelled ATP. Later when buying some commercial 32P-ATP I noticed a distinct mercaptan smell on opening the vial so at least some suppliers at that time were aware of the problem, although I never saw it mentioned in product literature. I suppose you could ask your supplier, if you buy commercial stuff, whether they add a stabilizer. Even if they do stabilize with mercaptoethanol, it might not be a bad idea to add some fresh on delivery. I think at least some of the chemical fragmentation involves free radical chemistry initiated by hydrogen abstraction at the ribose 2' or 3'. I'm a little fuzzy on the chemistry but I bet you can generate some molecules that would be pretty good at chemically modifying proteins. If you're interested, look up some of Joanne Stubbe's papers on ribonucleotide reductase enzymology studies starting in the late 70s - I think she characterized very similar chemistry. Hope this helps. Ron Wetzel From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!agate!kos5mac7.berkeley.edu!user From: jlonsdal@nature.berkeley.edu (Jen Lonsdale) Newsgroups: bionet.molbio.proteins Subject: Radiolysis of 32P-ATP Date: 9 Jun 1995 16:15:55 GMT Organization: Department of Plant Biology; University of California Lines: 11 Message-ID: NNTP-Posting-Host: kos5mac7.berkeley.edu Dear All, Does anyone know about radiolysis of 32P-ATP during storage? I know that the time-frame of usefulness for 32P-labelled substrates may eliminate this as a problem, but I'm still curious! I'm working with a protein kinase system which may be sensitive to ATP breakdown/isomerization products. Thanks, Simon. From owner-proteins@net.bio.net Thu Jun 08 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!daresbury!dlpx1!asm From: asm@dl.ac.uk (A.S.McAlpine) Newsgroups: bionet.molbio.proteins Subject: behaviour of protein on gels Date: 9 Jun 1995 14:44:22 GMT Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 28 Sender: asm@dlpx1 (A.S.McAlpine) Distribution: world Message-ID: <3r9mo6$qoq@mserv1.dl.ac.uk> NNTP-Posting-Host: dlpx1.dl.ac.uk Someon in our lab has been purifying his protein and has come across a strange phenomenon (to us at least) as regards its behaviour on SDS PAGE. Origianlly he believed that his protein was infact impure. One day when he ran an identical sample on a gel it showed a very clean and tight band. This was confusing. After much playing around with sample conditions SDS concentrations etc, we pinned it down to when the gels had been set. When a gel was set up and left overnight in the fridge, it gave a very clean gel with tight bands of his protein. If the samples were run on the gel the same day, ie. just after it had been set, it gave a smeared band (so less intense than the overnight one) and what we now believe to be aggregates further up the gel., which we had beleived to originally be contamination. We know that the protein is quite hydrophobic in nature and does form aggregates. Why though do we get a nice gel if we leave it overnight? If anyone else has had this problem and has an explanation as to why it happens please let us know. thanks -- \\|// (o o) --------------------------ooO---(_)---Ooo-------------------------- Protein Crystallography ----------------------- Alan McAlpine | SRR Division Daresbury Laboratories | Daresbury | Warrington WA4 4AD | Tel: 01925 603606 England | Fax: 01925 603124 UK | E-Mail: a.s.mcalpine@dl.ac.uk ------------------------------------------------------------------- From owner-proteins@net.bio.net Fri Jun 09 23:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!pipex!warwick!bsmail!zeus!bijt From: bijt@zeus.bris.ac.uk (J. Takei) Subject: help: Dialysis tubes Message-ID: Sender: usenet@uns.bris.ac.uk (Usenet news owner) Nntp-Posting-Host: zeus.bris.ac.uk Organization: University of Bristol, England X-Newsreader: TIN [version 1.2 PL2] Date: Sat, 10 Jun 1995 13:11:32 GMT Lines: 14 Dear protein scientists: I'm looking for a low molecular weight cutting dialysis tube, something like 3kDa cut off one. Do you know any manufacturers or distributors? Thanks in advance. Jiro Dept. of Biochemistry University of Bristol UK j.takei@bris.ac.uk From owner-proteins@net.bio.net Fri Jun 09 23:00:00 1995 Path: biosci!NMSU.EDU!hroychow From: hroychow@NMSU.EDU (Hiranya Roychowdhury) Newsgroups: bionet.molbio.proteins Subject: Re: help: Dialysis tubes Date: 10 Jun 1995 09:26:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On Sat, 10 Jun 1995, J. Takei wrote: > Dear protein scientists: > > I'm looking for a low molecular weight cutting dialysis tube, something like > 3kDa cut off one. Do you know any manufacturers or distributors? Thanks in > advance. > > Jiro > > Dept. of Biochemistry > University of Bristol > UK > > j.takei@bris.ac.uk > > Have you tried SPECTRAPOR? >>>>>>>>>>>>>>>>>>>>>>>>>>> Hiranya S. Roychowdhury Plant Genetic Engineering Lab. Box 3GL, NM State Univ. Las Cruces, NM 88003 Phone: (505) 646-5785 hroychow@nmsu.edu <<<<<<<<<<<<<<<<<<<<<<<<<<< From owner-proteins@net.bio.net Fri Jun 09 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!baker From: baker@iastate.edu (Wayne R. Baker) Newsgroups: bionet.molbio.proteins Subject: Re: help: Dialysis tubes Date: 10 Jun 1995 20:54:53 GMT Organization: Biochemistry & Biophysics, Iowa State University Lines: 14 Message-ID: <3rd0qt$pa4@news.iastate.edu> References: NNTP-Posting-Host: pv0a05.vincent.iastate.edu In bionet.molbio.proteins, Hiranya Roychowdhury wrote :On Sat, 10 Jun 1995, J. Takei wrote: : :> I'm looking for a low molecular weight cutting dialysis tube, something like :> 3kDa cut off one. Do you know any manufacturers or distributors? Thanks in :> advance. :> :Have you tried SPECTRAPOR? Best bet is Fisher, which sells SpectraPor tubing. Wayne Baker (baker@iastate.edu) Maybe a great magnet pulls Biochemistry & Biophysics All souls towards truth Iowa State University -- k. d. lang, "Constant Craving" From owner-proteins@net.bio.net Fri Jun 09 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!xmission!news.cc.utah.edu!zifi.genetics.utah.edu!zinc From: zinc@zifi.genetics.utah.edu (zinc) Newsgroups: bionet.molbio.proteins Subject: Re: fine resolution on SDS-PAGE Date: 9 Jun 1995 19:47:16 GMT Organization: assorted dsRNAs and lotsa zinc Lines: 39 Message-ID: <3ra8g4$jqs@news.cc.utah.edu> References: <3r9bhr$pig@lyra.csx.cam.ac.uk> NNTP-Posting-Host: zifi.genetics.utah.edu Keywords: SDS-PAGE -----BEGIN PGP SIGNED MESSAGE----- In article <3r9bhr$pig@lyra.csx.cam.ac.uk>, R. Woodward wrote: > Dear all, > I am having problems resolving two proteins of similar Mw > on SDS-PAGE, I have tried 7.5 and 12.5% gels but the resolution is not > as good as I would like . The sizes of the two proteins are ~55 and > 52kD which are radiolabelled in an IVT and then immunoprecipitated > before SDS-PAGE and flourography. Am I expecting too much or are > there any tips to resolve these two bands. Thanks v.much > Robert well, i would try a gradient gel. something like 7.5% -> 17% might work out well. we used these all the time when i was tech and the resolution is really quite nice. they're not that hard to pour either if you have a gradient maker... good luck... another thing, it would be easier to reply to your mesgs if they weren't all one line, the text above had no newline chars at all... - -pjf -----BEGIN PGP SIGNATURE----- Version: 2.6.2 iQCVAwUBL9imIk3Qo/lG0AH5AQHIqwP/U5MBz4gcQ3j4RLd0Wwfni6HdgBu6Zj7f BfL3GNKx6G3QLAq7sqUAwBMy1EOmZO+eY1DEJG3lZsJQjp+VOCvKmYBXwC67Azjp IiOAvWfIyrC6/XppHklvaFvwri/CLhqVh9JKujwftKVyzWaRm6KkUnrDk5vtAikA 3TyUksJuOwU= =lKmN -----END PGP SIGNATURE----- -- patrick finerty = zinc@zifi.genetics.utah.edu = pfinerty@nyx.cs.du.edu U of Utah biochem grad student in the Bass lab - zinc fingers + dsRNA! ** FINGER ME for my pgp public key ** CRYPTO FOR THE MASSES! zifi is a 486 DX4-100 running LINUX 1.2.9, send me all of your RAM now! From owner-proteins@net.bio.net Fri Jun 09 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!news.u.washington.edu!saul4.u.washington.edu!bassuk From: James Bassuk Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: Edman degradation of bacterial proteins Date: Sat, 10 Jun 1995 19:17:20 -0700 Organization: University of Washington Lines: 33 Message-ID: References: NNTP-Posting-Host: saul4.u.washington.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII NNTP-Posting-User: bassuk In-Reply-To: Xref: biosci bionet.molbio.methds-reagnts:29553 bionet.molbio.proteins:4783 The N-f-Met will be cleaved by a bacterial peptidase before you have a chance to isolate it. It should not be a consideration. ******************************************************** Jim Bassuk, Ph.D. Dept. Biological Structure, Univ. of Washington NetworkAddress: Bassuk@U.Washington.Edu 'Did I say what I meant or did I mean what I said?' ******************************************************** On Wed, 7 Jun 1995, Jan Eggermont wrote: > Hello, > > A small question for protein sequencers who have experience with Edman > degradation of bacterial proteins: is the N-formyl-methionine, i.e. the > modified start methione of bacterial proteins, derivatised in one single > cycle or in two, i.e. first the formyl and then the methionine? > Thanks, > > Jan > > -- > Jan Eggermont Jan.Eggermont@med.kuleuven.ac.be > Laboratorium voor Fysiologie - KU Leuven > Campus Gasthuisberg tel 32-16-34 59 38 > 3000 Leuven Belgium fax 32-16-34 59 91 > > From owner-proteins@net.bio.net Fri Jun 09 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!news.u.washington.edu!saul4.u.washington.edu!bassuk From: James Bassuk Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: Re: detergents in gel filtration Date: Sat, 10 Jun 1995 19:16:00 -0700 Organization: University of Washington Lines: 55 Message-ID: References: <3r3r2l$1eef@rs18.hrz.th-darmstadt.de> NNTP-Posting-Host: saul4.u.washington.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII NNTP-Posting-User: bassuk In-Reply-To: <3r3r2l$1eef@rs18.hrz.th-darmstadt.de> Xref: biosci bionet.molbio.methds-reagnts:29552 bionet.molbio.proteins:4782 Octylthiogalactoside is a detergent from Boehringer Mannheim that does not absorb UV light, has a very low CMC, dialyzes well, and will be worth the $145 investment. ******************************************************** Jim Bassuk, Ph.D. Dept. Biological Structure, Univ. of Washington NetworkAddress: Bassuk@U.Washington.Edu 'Did I say what I meant or did I mean what I said?' ******************************************************** On 7 Jun 1995, P. Friedl wrote: > In article , Jan.Eggermont@med.kuleuven.ac.be (Jan Eggermont) says: > > > >Hello, > > > >I am currently investigating the oligomeric nature of a purified protein. > >On a Superose 12 FPLC colum with a 150 mM NaCl buffer the protein migrates > >with a Mr of around 100k whereas the predicted molecular mass from the > >amino acid sequence is 28k suggesting it may form a trimer. I now want to > >find out what type of interactions (hydrophobic/hydrophilic/S-S > >bridges...) are going on. I presume raising the salt concentration will > >unmask hydrophilic interactions and adding a reducing agent such as DTT > >will break up S-S bridges. However, I am not sure about the best way to > >tackle the hydrophobic interactions. At first I wanted to use Triton-X100 > >but this will interfere with the UV recording at 280 nm. In addition I was > >told that because of the low critical micellar concentration (cmc) of > >Tx100, some of the protein may be incorporated into micelles. So any ideas > >out there on a detergent that does not absorb at 280 nm and that has a > >rather high cmc? > >thanks in advance. > > > >Jan > > > >-- > >Jan Eggermont Jan.Eggermont@med.kuleuven.ac.be > >Laboratorium voor Fysiologie - KU Leuven > >Campus Gasthuisberg tel 32-16-34 59 38 > >3000 Leuven Belgium fax 32-16-34 59 91 > > > > Hello, > you could try chaotropic reagents at moderate concentrations as > for example 1-2.5 M KSCN. Another approach could be the inclusion of > methanol (10-30%) although this strengthens ionic interactions. > good luck > P.F. > > From owner-proteins@net.bio.net Sat Jun 10 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!bhamcs!news.ox.ac.uk!topaz!chan From: chan@bioch.ox.ac.uk () Newsgroups: bionet.molbio.proteins Subject: protein ligands Date: 11 Jun 1995 14:53:50 GMT Organization: Department of Biochemistry, Oxford University Lines: 34 Message-ID: <3rf01u$ft1@news.ox.ac.uk> NNTP-Posting-Host: bioch.ox.ac.uk X-Newsreader: TIN [version 1.2 PL2] -- Hi there, I need help on findind out how good is a ligand. I want to know the relative stability of certain ligands to transition metal. The transition metal of interest are: Cu(I),Cu(II), Zn(II),Cd(II),Hg(II),Ni(II) and Co(II) The ligands are interest are: The delta1-N of His, delta5-N of His, S of Met, O of Gln, N of Gln, , S of Cys, S of the disulphide bridge I would apperciate if someone can tell me where can I find any info about the above ligands. Thanks in advance, Christopher Chan ********************************************************************** * 2 * Christopher Chan * * CCCCC * Dept. of Biochemistry * * C * University of Oxford * * C * Oxford * * C * U.K. * * CCCCC * Tel.: 0865-(2)75239 * * * E-mail: chan@bioch.ox.ac.uk * ********************************************************************** ----- PGP public key available upon request ----- From owner-proteins@net.bio.net Sat Jun 10 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!gryphon.phoenix.net!dial23.phoenix.net!user From: kinase@phoenix.net (Enrico Cantu) Newsgroups: bionet.molec-model,bionet.molbio.proteins,bionet.biophysics Subject: Mitchondrial VDAC Date: Sun, 11 Jun 1995 13:18:18 -0500 Organization: University of Houston Lines: 12 Message-ID: NNTP-Posting-Host: dial23.phoenix.net X-Newsreader: Value-Added NewsWatcher 2.0b24.0+ Xref: biosci bionet.molec-model:436 bionet.molbio.proteins:4786 bionet.biophysics:988 Hello. Is anyone familiar w/any NMR studies of mitochondrial VDAC (voltage-dependent anion channel)? I am doing some homology studies of this protein to determine structure using some bacterial porins as homologous models. I have come across a program that could use NOE and/or COSY data to help in this determination, but I see nothing at brookhaven or a couple of other sources. Any info on this or anything related to VDAC structure would be helpful. Regards, Enrico Cantu University of Houston Department of Biochemical and Biophysical Sciences From owner-proteins@net.bio.net Sat Jun 10 23:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!agate!spool.mu.edu!usenet.eel.ufl.edu!noc.netcom.net!news.sprintlink.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!rzusuntk.unizh.ch!rmf From: rmf@ikc.unizh.ch (Roman Fried) Subject: Re: Help with Immunoblots Message-ID: <1995Jun11.081314.15722@rzu-news.unizh.ch> Sender: newsadm@rzu-news.unizh.ch (CNEWS ADMINISTRATION) Organization: University of Zurich, Switzerland X-Newsreader: TIN [version 1.2 PL2] References: <3r8dri$sto@post.its.mcw.edu> Date: Sun, 11 Jun 1995 08:13:14 GMT Lines: 27 Frank Park (fpark@post.its.mcw.edu) wrote: : I have had recent problems lately with Western Blots. I have been running a : 12% polyacrylamide gel but I cannot seem to get the molecular weight markers : (sizes 40 kD and down) to separate from the leading dye. Also, I have had : problems with the transfer of the proteins from the gel to the : nitrocellulose membrane. When I stain the membranes with Ponceau S after : the transfer (at 100V for 1 hr), there are splotchy areas on the membrane : due to seemingly overtransfer. Please help on this matter with any : suggestions. : Thank You. : Frank Park : fpark@post.its.mcw.edu I would recommend the mw-markers from Biorad (they have coloured proteins). Using this "rainbow" markers, you can check your gel- electrophoresis directly while it is running. It even works with blotting! If you open your sandwich and there are still spots on your gel, just close the sandwich again and continue blotting I hope this helps Roman Fried rmf@ikc.unizh.ch From owner-proteins@net.bio.net Sat Jun 10 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!news.moneng.mei.com!howland.reston.ans.net!xlink.net!rz.uni-karlsruhe.de!news.uni-ulm.de!news.belwue.de!news.belwue.de!volle.slip.rz.fht-esslingen.de!user From: 653265@rshx01.rz.fht-esslingen.de (Volker Scheib) Newsgroups: bionet.cellbiol,bionet.molbio.proteins Subject: Info about cytoskeletons - HELP! Date: 11 Jun 1995 11:26:04 GMT Organization: InterNetNews at News.BelWue.DE (Stuttgart, Germany) Lines: 32 Message-ID: <653265-1106951325100001@volle.slip.rz.fht-esslingen.de> NNTP-Posting-Host: volle.slip.rz.fht-esslingen.de Xref: biosci bionet.cellbiol:2402 bionet.molbio.proteins:4787 Hello! We are a group of students examining for our dissertation human cells by computer simulation (finit element computing using Ansys). We have some intersting cytoskeleton/cell models based on a white blood cell. Our model seems to be very exact compared with a published experiment. Our aim is to destroy cancer cells using oscillation so we also simulate dynamical experiments. We urgently need informations about the mechanical properties and attributes of livercells (or others) with and without cancer. * The average nucleus mass and size * The constitution of the cytoskeleton * The module of elasticity of the cytoskeleton * The average osmotic pressure * The viscosity of the cytoplasm * The elasticity of the membrane of the cell * The constitution of the intercellular cytoskeleton * The viscosity and elasticity of the inter(intra)cellular cytoskeleton We would very much appreciate any direct informations, bibliographical data or e-mail adresses of specialists. Our Professor is Prof. Dr. Ing. E. Theuer. He has done lots of interesting work concerning the computer simulation. Thanks for your help e-mail: 653265@rshx01.rz.fht-esslingen.de Volker Scheib, Mike Baehrle, Oliver Sauter, Ralf Amler -- Volker Scheib e-mail: 653265@rshx01.rz.fht-esslingen.de From owner-proteins@net.bio.net Sat Jun 10 23:00:00 1995 Path: biosci!ns1.faseb.org!darwin.sura.net!nntp.usm.edu!usenet From: richard@whale.st.usm.edu (Dieter) Newsgroups: bionet.molbio.proteins Subject: Help with Information about a Spectra-Physics Laser Date: Mon, 12 Jun 1995 05:06:43 GMT Organization: University of Southern Mississippi Lines: 15 Message-ID: <3rge48$hch@server.st.usm.edu> NNTP-Posting-Host: 131.95.96.32 X-Newsreader: Forte Free Agent v0.55 I am looking for information about a Spectra-Physics Model 2020-05 Argon Ion laser. Particularly, I would like to know the wavelength of this laser. If you have any idea or where I can get the information (friend or colleague) please mail me at the address below. I have tried Spectra-Physics' tech line but they didn't call back. I will try again (toll call...I'm a poor grad student) if there is no help here. Note: this is not a cross-post, I am characterizing protiens by dynamic light scattering and need this information. Thanks in advance Michael F. Richardson richard@whale.st.usm.edu From owner-proteins@net.bio.net Sun Jun 11 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news.sprintlink.net!Sunserver.insinc.net!news.Direct.CA!news.cyberstore.ca!vanbc.wimsey.com!unixg.ubc.ca!news.bc.net!rover.ucs.ualberta.ca!tribune.usask.ca!canopus.cc.umanitoba.ca!newsflash.concordia.ca!news.mcgill.ca!clouso.crim.ca!athena.ulaval.ca!eukaryota!genegin From: genegin@eukaryota (Genevieve Breton-Gingras) Newsgroups: bionet.molbio.proteins Subject: c3 transferase Date: 12 Jun 1995 15:55:11 GMT Organization: Universite Laval Lines: 10 Message-ID: <3rho0v$dr3@athena.ulaval.ca> NNTP-Posting-Host: eukaryota.rsvs.ulaval.ca X-Newsreader: TIN [version 1.2 PL2] Hello, I am looking for the inhibitor of small GTP-protein of the rho subfamilly called c3 exotransferase. I know it is commercially available but i dont know wich company is making it. You can send me info at my email. Thank you. Gene genegin@eukaryota.rsvs.ulaval.ca From owner-proteins@net.bio.net Sun Jun 11 23:00:00 1995 Path: biosci!rutgers!uwm.edu!spool.mu.edu!howland.reston.ans.net!news.starnet.net!wupost!kuhub.cc.ukans.edu!kuhub.cc.ukans.edu!nntp Newsgroups: bionet.molbio.proteins Subject: animal hemoglobin Message-ID: <1995Jun12.204451.95051@kuhub.cc.ukans.edu> From: campbell@kuhub.cc.ukans.edu@cc.ukans.edu Date: 12 Jun 95 20:44:51 CDT Reply-To: campbell@kuhub.cc.ukans.edu@cc.ukans.edu Nntp-Posting-Host: kuts3p10.cc.ukans.edu X-Newsreader: IBM NewsReader/2 v1.09 Lines: 14 My dad says he has heard that someone has found a way to alter animal hemoglobin to make it useable in humans. I don't know what species of animal specifically. (I'm assuming that you can't just come up with a way to turn change all hemoglobin types uniformly.) If anyone knows about this please post some info or tell me where I should go to find the info. Thanks, Chad Campbell CS and Pre-Med undergrad University of Kansas "Crime wouldn't pay if the government ran it." From owner-proteins@net.bio.net Sun Jun 11 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news.sprintlink.net!uunet!in1.uu.net!nctuccca.edu.tw!news.cc.nctu.edu.tw!news.csie.nctu.edu.tw!dragon.nchu.edu.tw!cyyk From: cyyk@dragon.nchu.edu.tw (Chiou-Ying Y. Kao) Newsgroups: bionet.molbio.proteins Subject: faculty position opened in NCHU zoology, Taiwan Date: Tue, 13 Jun 1995 09:55:01 UNDEFINED Organization: NCHU Lines: 7 Message-ID: NNTP-Posting-Host: @140.120.113.100 X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] The Department of Zoology, National Chung Hsing Univ. Taichung, Taiwan, has a faculty position opened for applicants with a Ph.D. degree and expertise in animal histology. The applicants must have a citizenship of Taiwan. and fluent in mandarin. Prior to June 31, 1995, applicants should submit a curriculum vitae, a statement of research interests, teaching experience, and course offerings to: Dr. Chiou-Ying Yang Kao via email at " cyyang@dragon.nchu.edu.tw" or fax to 886-4-285-1797. From owner-proteins@net.bio.net Sun Jun 11 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.starnet.net!wupost!waikato!waikato.ac.nz!hst From: hst@waikato.ac.nz Newsgroups: bionet.molbio.proteins Subject: Re: Protein assay of cell-extracts Message-ID: <1995Jun13.135835.38930@waikato.ac.nz> Date: 13 Jun 95 13:58:35 +1200 References: <3r4419$lsr@rs18.hrz.th-darmstadt.de> Organization: University of Waikato, Hamilton, New Zealand Lines: 40 In article <3r4419$lsr@rs18.hrz.th-darmstadt.de>, dh7y@pop.th-darmstadt.de (Inst. f. Biochemie) writes: > Hy everybody, > > i have a problems with my protein-assay in a whole cell-extract from > endothelial cells. > > I had lysed my cells with a buffer containing 2-ME and NP-40 so there`s no > chance to test the concentration with BCA (because i got high extinction in > the control with 2-ME !! ), Bradford or OD (NP 40). > > What assay should i do ??? > > Thanks in advance > > Patrick Baer > Institut fuer Biochemie > TH Darmstadt > e-mail: dh7y@pop.th-darmstadt.de The technique I use to determine protein concentration of solutions containing interfering substance is the modified Lowry procedure described in the following reference: Peterson, G.L. (1983) Determination of Total Protein. in Methods in Enzymology Vol 91 pp 95-119. This method involves a pretreatment of the sample which removes the interfering substances, followed by the standard Lowry assay. This pretreatment involves a precipitation of the protein with either DOC-TCA (preferred) or RNA-TCA. I modify this method by including two washing steps with 6% TCA to ensure highly-interfering substances are removed. I find this method is useful even for solutions containing substances that the Lowry assay is extremely sensitive to (e.g. HEPES buffer or His). Helen Toogood Thermophile Research Unit University of Waikato New Zealand From owner-proteins@net.bio.net Sun Jun 11 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!news From: Tim Hubbard Newsgroups: bionet.molbio.proteins Subject: ANNOUNCEMENT: have you a protein to predict? Call for prediction Date: 12 Jun 1995 18:46:02 GMT Organization: Centre for Protein Engineering Lines: 24 Message-ID: <3ri21a$acg@lyra.csx.cam.ac.uk> NNTP-Posting-Host: ccpeshiva1-mac2.mrc-lmb.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.molbio.proteins Announcement: Call prediction targets ===================================== The previous mail to this list announced the IRBM practical course: frontiers of protein structure prediction. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. If you are interested in a structure prediction being made on a protein for which there is no sign of an experimental structure and does not appear to be homologous to any known structure, please consider submitting it as a target for this course. For further information and on-line target submission forms see: http://www.mrc-cpe.cam.ac.uk/predict/ Tim Hubbard, (CPE, MRC) Anna Tramontano, (IRBM) From owner-proteins@net.bio.net Sun Jun 11 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news.sprintlink.net!pipex!lyra.csx.cam.ac.uk!news From: Tim Hubbard Newsgroups: bionet.molbio.proteins Subject: ANNOUNCEMENT: IRBM practical course: frontiers of protein structure Date: 12 Jun 1995 18:45:22 GMT Organization: Centre for Protein Engineering Lines: 58 Message-ID: <3ri202$acg@lyra.csx.cam.ac.uk> NNTP-Posting-Host: ccpeshiva1-mac2.mrc-lmb.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.molbio.proteins Announcement: Call for applications =================================== IRBM practical course: frontiers of protein structure prediction *** NOTE: Deadline for applications: 1st July 1995 *** The course is directed at young scientists with some experience and a strong interest in protein structure and structure prediction who wish to learn about the latest developments in the field. The aim of the workshop is to predict as much as possible about the structure of a number of proteins of biological interest, taking advantage of the most recent methodologies for fold recognition and ab initio prediction. The participants will be divided into working groups assisted by an instructor. Each group will be equipp