From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!news.ohsu.edu!carterd From: carterd@ohsu.edu (Darrick Carter) Newsgroups: bionet.molbio.proteins Subject: Re: L & D amino acids... Date: 3 Feb 1995 03:36:51 GMT Organization: Oregon Health Sciences University Lines: 31 Message-ID: <3gs8cj$p4@steele.ohsu.edu> References: NNTP-Posting-Host: 137.53.1.40 Keywords: Protein Racemization, D-amino acids In reply to your question: D-amino acids do occur in proteins, not just in the short peptides such as those found in bacterial cell walls. Racemization can occur, and has been documented in a wide spectrum of proteins, especially erythrocyte proteins, which -I guess- were studied first. Not only has it been found that the amino acids do not neccessarily have the "L-form" but can also racemize into the "L-iso-form", a form in which the peptide backbone runs through the sidechain of Asp and the carbonyl of the peptide bond is formed by the carboxyl of the aspartate sidechain. The racemization occurs via the formation of a cyclic structure, a succinimide which is prone to racemization and to attack by a hydroxide which can reopen the structure to either the L,D,L-iso or the D-iso form. In fact racemization seems to have been such a problem to nature that there is an enzyme which utilizes a methylation (S-Adenosylmethionine dependent) process to "repair" racemic damage. Why haven't these changes been seen in X-ray X-tal structures? I I think they have been seen - at least their effects are well known to X-talographers trying to crystallize proteins that have been e.g. heat treated, which sometimes is a step that introduces problems in getting X-tals which is likely to be due to the heterogeneities in stereochemistry introduced by racemization, or due to deamidation which can be introduced via a succinimide in Asn sites. (Try running an IEF gel before and after heat treatment :( ) Anyway, if you want more info on this process I'll be happy to send you references. Darrick (carterd@ohsu.edu) From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!zip.eecs.umich.edu!panix!cmcl2!rockyd!notes From: "Dr. Kent L. Nastiuk" Subject: Re: SDS-PAGE of 32P labelled protein X-Nntp-Posting-Host: nastiuk_pc.rockefeller.edu Message-ID: Sender: notes@rockyd.rockefeller.edu (News Administrator) Organization: Rockefeller University References: Date: Thu, 2 Feb 1995 22:20:22 GMT Lines: 15 williel@uclink3.berkeley.edu (Simon Penson) wrote: > > I'm going to need to run some SDS-PAGE gels of proteins which have been > incubated with 32P-ATP. How can I remove the excess (ie uncomsumed) ATP > from the reaction m,ixture prior to electrophoresis? TCA ppt has been > suggested, as has spin-desalting. > why do you need to remove them before running the gel? i routinely just stop the reaction with 5x stop buffer (which contains pyronin Y as a marker for the free ATP) and then run the gel until the pyroninY is appx 1 cm from the bottom. then just cut off the gel below the pyronin and discard. From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!atlas.rc.m-kasei.co.jp!yao From: yao@atlas.rc.m-kasei.co.jp (Toru YAO) Newsgroups: bionet.molbio.proteins Subject: unsubscribe Date: 2 Feb 1995 19:53:25 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502030353.AA23395@atlas.rc.m-kasei.co.jp> NNTP-Posting-Host: net.bio.net unsubscribe proteins From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!hubcap.clemson.edu!biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!ux1.cso.uiuc.edu!elarson From: elarson@ux1.cso.uiuc.edu (larson eric) Newsgroups: bionet.molbio.proteins Subject: Re: Do proteins self-digest? Date: 30 Jan 1995 23:21:16 GMT Organization: University of Illinois at Urbana Lines: 25 Message-ID: <3gjs9c$krl@vixen.cso.uiuc.edu> References: NNTP-Posting-Host: ux1.cso.uiuc.edu aiyo@uoguelph.ca (Abiye Iyo) writes: >I recently used the GST fusion system to purify my protein (a >cellulase). Everything went fine up to the stage of gel filteration and >I had a nice single band . Now the misery part is that my protein which >is about 57kD degrades to two low molecular weight products which are >still active on zymograms. Does this mean my prep is contaminated with >proteases or I am experiencing some form of self digestion judging from >the fact that my protein was pure initially? And how can I prevent >this? I need help before my patience runs out. ======== Sounds like protease contamination. Try adding inhibitors to the mol. wt. col. buffer -- they can be dialyzed away later. Mol. wt. separation is usually time-intensive, affording ample opportunity for residual proteases to function. Couple this with the absence of other proteins (likely if this is the second step with the first being ion-exchange) and you have perfect conditions for protease problems. Proteolysis on mol. wt. resins has affected me directly. -- Eric Larson | University of Illinois at Urbana-Champaign USDA/Agronomy | 190 PABL; 1201 W. Gregory; Urbana, IL 61801 elarson@ux1.cso.uiuc.edu | Voice 217.244.3079 Fax 217.244.4419 Fidonet: 1:233/4.1 | My opinions are my own, but correct :-) From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!bioc.cam.ac.uk!owde100 From: owde100@bioc.cam.ac.uk (Orhan Ertughrul) Newsgroups: bionet.molbio.proteins Subject: Re: HELP! Protein Graphics!! Sorry, No help available on that topic Followup-To: bionet.molbio.proteins Date: 2 Feb 1995 10:00:12 GMT Organization: Somewhere in the University of Cambridge Lines: 40 Distribution: world Message-ID: <3gqafc$1b@lyra.csx.cam.ac.uk> References: <3ggmdi$5j@mace.cc.purdue.edu> <1995Jan30.201542.18484@alw.nih.gov> <3glegb$56a@lyra.csx.cam.ac.uk> <3go23v$qgo@rugch4.chem.rug.nl> NNTP-Posting-Host: babylon.bioc.cam.ac.uk In article <3go23v$qgo@rugch4.chem.rug.nl>, ronald@rugcbe.chem.rug.nl (Ronald Knegtel) writes: > In article <3glegb$56a@lyra.csx.cam.ac.uk>, owde100@bioc.cam.ac.uk (Orhan Ertughrul) writes: > |> In article <1995Jan30.201542.18484@alw.nih.gov>, johnk@spasm.niddk.nih.gov (John Kuszewski) writes: > |> > In article <3ggmdi$5j@mace.cc.purdue.edu>, barani@mace.cc.purdue.edu (Barani) writes: > |> > |> IMHO crystallographers are more closer to the truths > |> > |> of a biomolecule than anyone else. > |> > > |> > Except, of course, for us NMR people. No packing distotions, > |> > good pictures of flexibility. > > |> And a residue limit of about 250AA even for 4D. NMR is always going to be a > |> technique of restricted use until larger biomolecules can be resolved. > > But then again, any technique is of restricted use (ever tried to crystallize > and solve a G-protein coupled receptor, I guess we'll leave that to the EM > people). Let us not argue about which technique is best, each of them, > including modelling, can give us a new perspective on the complex problems > we are facing: why are proteins folded they way they are and why do they function as they do.. I got my PhD in bio-NMR and modelling and am currently working in a bio-X-ray lab. I feel all three techniques are interesting and useful but not perfect. Let's > try to learn from each other instead of putting > each other down. Surely one of the most constructive ways to determine how best to go forward in any field is a reasoned discussion of the pros and cons of experimental techniques used. I've actually learnt quite a lot that I didn't know about both NMR and X-ray Crystallography from people's postings here. A lack of contention often leads to a lack of imagination. Orhan. ----------------------------------------------------------------------- Orhan W.D. Ertughrul | /\ "It's hard enough to watch University of Cambridge | / \ /\ the news, let alone explain Department of Biochemistry | / / \ it to a child to cast its Tennis Court Road | / / \ eyes on nature over fields Cambridge CB2 1QW |/ / \ of rape and corn, and tell | /\/ \ it without flinching not to owde100@cus.cam.ac.uk | / \ \ fear where its been born" ----------------------------------------------------------------------- WWW : http://nirvana.bioc.cam.ac.uk/~owde100/ ----------------------------------------------------------------------- From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!psgrain!nntp.ski.mskcc.org!nntp.mskcc.org!phil From: phil@xtreme1.mskcc.org (Phil Jeffrey) Newsgroups: bionet.molbio.proteins Subject: Re: HELP!!! Protein Graphics!! Date: 1 Feb 95 17:28:03 Organization: Memorial Sloan-Kettering Cancer Center Lines: 64 Distribution: world Message-ID: References: <3g18fo$no3@bigblue.oit.unc.edu> <1995Jan24.173624.8430@alw.nih.gov> <3g4ku9$83s@news.iastate.edu> <3g5b3v$r68@lyra.csx.cam.ac.uk> <3g6k7d$13uk@columba.udac.uu.se> <3g8f7c$8hv@lyra.csx.cam.ac.uk> <3gc2l3$120o@columba.udac.uu.se> <3gejgo$blo@senator-bedfellow.MIT.EDU> NNTP-Posting-Host: xtreme1.ski.mskcc.org In-reply-to: lluis@aaRS's message of 28 Jan 1995 23:20:56 GMT In article <3gejgo$blo@senator-bedfellow.MIT.EDU> lluis@aaRS (Lluis Ribas) writes: >> This is a lot of baloney !!, typical crystallographer's self-protecting >> speech. The fact of the matter is that if your protein Y is a totally >> new enzyme you can dramatically speed up your biochemical >> characterization if you can model its structure. (caveat - I'm a crystallographer) What you will model is a pseudo-structure of your new protein which may OR MAY NOT have much resemblance, even at low resolution, to the real structure. Which invalidates any conclusions you might extract from such a model. Anyone can rationalize their results in a pseudo-structural way, and just because such a rationalization seems plausible, doesn't mean it is correct. >> Molecular modeling is a low resolution technique by comparision to >> experimental methods, that is implicit in the system. However it can >> provide information several orders of magnitude faster than crystallography. >> To say that a model should provide a good solution to a molecular >> replacement search is also nonsense. That is not what should be >> expected from a model. This is simply a question of accuracy. Sometimes even structures with reasonable structural homology don't behave well in Molecular Replacement (recent bitter experience in this regard), but this can usually be traced to inaccuracies in the model (with 20/20 hindsight and a decent MIR map). >> The RAS structure >> would have been proved wrong by several modeling >> statistical methods had they been used to analyze it. Eisenberg's profile method indeed points up some dubious regions in Ras. Other methods may do the same. But these are statistical methods, and many of us are unlikely to invalidate our structures just because some statistical method doesn't like our structure. Crystallographers are experimentalists, and we like to look at electron density to figure out our structures, aided by a pretty good implicit feel for unlikely features in protein structure. >> Don't you think that part of the crystallographer's despise for modeling >> stems from they anger at loosing the monopoly of structure determination ?. No, we'd just prefer NMR didn't exist :) I have seen modelers make unjustified/unrealistic claims about the accuracy of models over the years, and that is why I sometimes get annoyed at posts that give impressions of accuracy to a very imprecise and inaccurate method (ab initio modeling, homology modeling, whatever). I'm certainly not looking over my shoulder in dread at the advance of modeling as a structure *determination* tool. It's not even close. Incidentally, crystallography and NMR have been relatively good about cleaning up their mistakes, including Ras. We take accuracy and precision seriously. Phil -- ------------------------------------------------------------------------------- | Phil Jeffrey | | | X-ray/Computer Manager, Crystallography Lab | If you lie to the compiler, | | Memorial Sloan-Kettering Cancer Center, NYC | it will get its revenge | | phil@xray2.mskcc.org, p-jeffrey@ski.mskcc.org | - Henry Spencer | | Ph: (212) 639 2189 Fax: (212) 717 3066 | | ------------------------------------------------------------------------------- From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!hubcap.clemson.edu!biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!ux1.cso.uiuc.edu!elarson From: elarson@ux1.cso.uiuc.edu (larson eric) Newsgroups: bionet.molbio.proteins Subject: Re: HPLC Assay Question Date: 31 Jan 1995 02:27:39 GMT Organization: University of Illinois at Urbana Lines: 25 Message-ID: <3gk76r$mk7@vixen.cso.uiuc.edu> References: NNTP-Posting-Host: ux1.cso.uiuc.edu cjhixon@netcom.com (Carl Hixon) writes: >Secondly, I have a protein >suspension containing small protein particles (few microns in diameter) >These particles are constructed of Albumin and Fibrinogen. Would it be >possible to determine the protein concentration of this type of >suspension using HPLC by digesting the particles? I worry about the >different sizes of the protein fragments. ========== The Lowry protein procedure is likely to work fine on these samples if they are first treated to alkaline hydrolysis by NaOH. It's also possible that the pH of the regular Lowry is high enough to cause dissociation of the protein. The Lowry also works in the presence of 1% SDS if the Cu concentration is raised several-fold. Colleagues routinely pre-dissolve their protein in a small volume (10% of final volume) of 0.1 M NaOH -- then do the Lowry as normal. NaOH solubilization also works after Na Deoxycholate ppt.. -- Eric Larson | University of Illinois at Urbana-Champaign USDA/Agronomy | 190 PABL; 1201 W. Gregory; Urbana, IL 61801 elarson@ux1.cso.uiuc.edu | Voice 217.244.3079 Fax 217.244.4419 Fidonet: 1:233/4.1 | My opinions are my own, but correct :-) From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!rutgers!netnews.upenn.edu!dsinc!newsfeed.pitt.edu!gatech!howland.reston.ans.net!news.sprintlink.net!uunet!newsfeed.ACO.net!news.iif.hu!news From: szia@enzim.hu (Andras Szilagyi) Newsgroups: bionet.molbio.proteins,bionet.software Subject: Programs for schematic drawings of proteins? Date: 1 Feb 1995 16:57:59 GMT Organization: somewhere Lines: 21 Message-ID: <3goein$e5i@helka.iif.hu> NNTP-Posting-Host: kalori.enzim.hu Mime-Version: 1.0 X-Newsreader: WinVN 0.93.11 Xref: biosci bionet.molbio.proteins:3638 bionet.software:10911 I am looking for programs that can draw schematic drawings of protein structures. I am interested in the following two types of drawings: (1) schematic representation of the [main chain] hydrogen bonding pattern (based on known 3D structure) (2) schematic representation of the domain structure and disulfide bonding pattern, using a chain of several circles, each circle representing a residue, and the type of the residue written in the circle. This chain of circles is folded in 2D to approximately represent the domain structure and the disulfide bonding pattern. Such drawings often appear in journals but I don't know any program that can easily draw such things. (As to the hydrogen bonding pattern, I heard of a program called HERA but I have no idea how to get it.) Anyone can help? Andras Szilagyi (szia@enzim.hu) Institute of Enzymology, Hungarian Academy of Sciences From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!hubcap.clemson.edu!biosci!rutgers!gatech!howland.reston.ans.net!ix.netcom.com!netcom.com!cjhixon From: cjhixon@netcom.com (Carl Hixon) Subject: HPLC Assay Question Message-ID: Organization: NETCOM On-line Communication Services (408 261-4700 guest) X-Newsreader: TIN [version 1.2 PL1] Date: Tue, 31 Jan 1995 00:15:30 GMT Lines: 10 Does anybody know of literature regarding measuring Human Albumin and Fibrinogen concentration using HPLC? Secondly, I have a protein suspension containing small protein particles (few microns in diameter) These particles are constructed of Albumin and Fibrinogen. Would it be possible to determine the protein concentration of this type of suspension using HPLC by digesting the particles? I worry about the different sizes of the protein fragments. If anybody has literature regarding these issues please forward the references. Thank you! Carl From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!ns1.faseb.org!darwin.sura.net!RBSE.Mountain.Net!jbradb From: jbradb@access.mountain.net (Jonathan "Brad" Bellotte) Newsgroups: bionet.molbio.proteins Subject: Random peptide phage display library Date: 2 Feb 1995 19:27:03 GMT Organization: MountainNet Internet Access Service (304) 594-9080 Lines: 10 Message-ID: <3grbm7$bet@rbse.Mountain.Net> NNTP-Posting-Host: adanet.wvnet.edu X-Newsreader: TIN [version 1.2 PL2] I was wondering if anyone could give me a basic textbook description of (or point me to one) random peptide phage display libraries. For example, what are they, how are they made? Thanks for any help. Please mail replies to: aguappon@wvumbrcc1.hsc.wvu.edu Brad. From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!GUARANY.CPD.UNB.BR!pjpz-007 From: pjpz-007@GUARANY.CPD.UNB.BR (pedro jose portugal zanotta) Newsgroups: bionet.molbio.proteins Subject: re:combinatorial help Date: 2 Feb 1995 09:58:13 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502021854.AA78614@guarany.cpd.unb.br> NNTP-Posting-Host: net.bio.net That is! For you to change the triplet for one aa you would have 3x(3x180)=1620 new DNA's-from that youcould get just 19x60=1140 new proteins (because of the redundance of the genetic code). Zanotta, dept biologia celular, IB, UnB - Brasilia, Brasil . From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!univ-lyon1.fr!cri.ens-lyon.fr!mac-adp.ibcp.fr!user From: lgb@ibcp.fr (lgb@ibcp.fr) Newsgroups: bionet.molbio.proteins Subject: Spring meeting-French Society for Biochemistry & Molecular Biology Followup-To: bionet.molbio.proteins Date: Thu, 02 Feb 1995 17:54:20 +0000 Organization: Institut de Chimie et Biologie des Proteines - France Lines: 282 Message-ID: NNTP-Posting-Host: mac-adp.ibcp.fr Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit CONGRES DE PRINTEMPS DE LA SOCIETE FRANCAISE DE BIOCHIMIE ET BIOLOGIE MOLECULAIRE 1995, March 28 - 29 - 30 SPRING MEETING OF THE FRENCH SOCIETY FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY 28 - 29 - 30 mars 1995 Parc de Expositions de Paris-Porte de Versailles - hall 7 niveau 3 P R O G R A M M E Mardi 28 mars matin 10 h Conference pleniere d'introduction de Axel Kahn : Therapie genique : le gene medicament. Plenary lecture : Axel Kahn : Gene therapy : gene as a drug Cette conference est organisee par le Salon du Laboratoire et ouverte a tous les scientifiques. Il n'est donc pas necessaire de passer a l'accueil de la S.F.B.B.M. avant cette Conference. Vous etes convies a y assister en allant directement a l'amphitheatre 731, hall 7 niveau 3. Mardi 28 mars 1995 apres-midi Colloque 1 (salle A) : Role de la conformation de l'ADN dans ses interactions avec les proteines - Responsables : Christian Marion et Etienne Delain Influence of DNA conformation in its interaction with proteins 14h45 - 14h50 : Christian Marion, Paris : accueil et introduction 14h50 - 15h15 : Bernard Revet, Villejuif Interactions ADN-Proteines : exemple de l'activateur de la glutamyl sunthetase DNA-protein interactions : glutamyl synthase activator as exemple 15h15 - 15h40 : Francoise Culard, Orleans Aspects topologiques de l'interaction de la proteine MC1 des Methanosarcines avec l'ADN Topological aspects of the interaction of methanisarcin MC1 with DNA 15h40 - 16h05 : Eric Le Cam, Villejuif Conformation de l'ADN et interactions ADN-proteines en microscopie electronique : exemple de la Poly(ADP-ribose) polymerase Conformation of DNA and DNA-protein interactions studied by electron microscopy : the example of the poly (ADP-ribose)polymerase 16h05 - 16h30 : Etienne Delain, Villejuif Observations des complexes ADN-proteines a l'aide de differentes techniques de microscopie Observations of DNA-protein interactions using different microscopy techniques 16h45 - 17h10 : Josette Rouviere-Yaniv, Paris Interaction de l'ADN avec la proteine HU DNA-HU protein interaction 17h10 - 17h35 : Marc Leng, Orleans Interaction entre HMG 1 et l'ADN modifie par le cis-platine Interaction between HMG 1 and cis-platine modified DNA 17h35 - 18h : Ariel Prunel, Paris Transition conformationnelle du tetramere (H3-H4)2 et ses implications pour la dynamique du nucleosome in vivo Conformational transition of the (H3-H4)2 tetramer and its implications for the dynamic of nucleosome in vivo olloque II (salle B) : Transduction du signal et regulations metaboliques - Responsables : Alain Lavoinne et Jean-Paul Leroux Signal transduction and regulations 15h - 15h50 : Alain Ktorza, Paris Physiopathologie de la deterioration de secretion d'insuline au cours du diabete de type 2 : mecanismes cellulaires et moleculaires Physiopathology of insulin secretion deficiency in type 2 diabetes : cellular and molecular mechanisms 15h50 - 16h15 : Nathalie Vionnet, Paris Implications fonctionnelles des mutations sur le gene de la glucokinase chez l'Homme Functional implications of mutations in the human glucokinase gene 16h45 - 17h10 : Jean-Francois Tanti, Nice Mecanisme d'action de l'insuline dans deux tissus insulinosensibles, le muscle squelettique et le tissu adipeux Mechanism of insuline action in two insulin sensitive tissues : the skeletal muscle and fat tissue 17h10 - 18h : Assemblee generale constitutive du Groupe d'Etudes des Regulations Metaboliques (ex GERCHIC) Meeting of the Interest Group for the study of metabolic regulations Mercredi 29 mars 1995 matin Colloque II suite (Salle B) : Regulations metaboliques - Responsables : Alain Lavoinne et Jean-Paul Leroux Metabolic regulations 9h - 9h50 : Claire Hivroz, Paris La transduction du signal dans les lymphocytes : rôle des tyrosine-kinases Signal transduction in lymphocytes : role of tyrosine-kinases 9h50 - 10h15 : Muriel Quillard, Rouen Regulation de l'expression du gene de l'ASS (arginino-succinate synthetase) : role de la glutamine et du gonflement cellulaire Regulation of the gene expression of the argino-succinate synthase (ASS) : role of glutamine and of cellular swelling 10h45 - 11h10 : Marie-France Chauvin, Lyon Flux enzymatiques lies au metabolisme du glutamate dans les cellules renales de lapin : etude par spectroscopie RMN du carbone 13 Enzymatic flux related to glutamate metabolism in rabbit kidney cells : study by 13C-NMR spectroscopy 11h10 - 11h35 : Annie Rodolosse, Paris Repression par le glucose de la transcription du gene de la saccharase-isomaltase humaine Repression of the uman saccharase-isomerase gene transcription by glucose 11h35 - 12h : Christophe Depre, bruxelles Adaptation metabolique du coeur a l'ischemie Metabolic adaptation of the heart to ischemy Colloque III (salle A) : Domaines fonctionnels des ARN : Responsables : Chantal Ehresmann et Richard Giege RNA Functional domains 9h - 9h50 : Fritz Ekstein, MPI, Gottingen, Allemagne Les ribozymes en tete de marteau : relations structure-fonction Hammer headed ribozymes : structure-function relationship 9h50 - 10h15 : Christiane Branlant, Universite de Nancy Un exemple rare de la dynamique des interactions ARN : le spliccosome A rare example of RNA interactions dynamic : the spliceosome 10h45 - 11h10 : Alain Jacquier, Institut Pasteur, Paris Les introns de groupe II, modele d'etude des reactions d'epissage Type II introns : a model for splicing reactions 11h10 - 11h35 : Roland Marquet, IBMC, Strasbourg La dimerisation de l'ARN genomique HIV-1 : etudes structurales et fonctionnelles Dimerisation of HIV-1 genomic RNA : structural and functional studies 11h35 - 12h : Frederic Dardel, Ecole Polytechnique, Palaiseau Interactions ARN de transfert et enzymes de l'appareil de traduction Interaction of transfer RNAs with the enzymes of the translation machinery Mercredi 29 mars 1995 apres-midi Assemblee Generale de la SFBBM (de 14h a 15h) Society Meeting Colloque IV (salle A) : Proteines G du systeme nerveux - Responsable : Dominique Aunis G proteins of nervous system 15h - 15h45 : Joel Bockacrt, Montpellier Les proteines G heterotrimeriques : 20 ans de recherche Heterotrimeric G proteins : 20 years of research 15h45 - 16h15 : Vincent Homburger, Montpellier Role de la proteine G heterotrimerique Go dans la poussee neuritique Role of Go heterotrimeric G protein during the neuritic growth 16h45 - 17h15 : Marie-France Bader, Strasbourg Proteines G trimeriques et exocytose dans les cellules neuroendocrines Trimeric G proteins and exocytosis in neuroendocrine cells 17h15 - 17h45 : Jean-Pierre Henry, Paris Controle de l'exocytose par la proteine G monomerique Rab3a Control of exocytosis by the Rab3a monomeric G protein 17h45 - 18h : Discussion generale - General discussion Colloque V (salle B) : Production d'enzymes du metabolisme des medicaments par recombinaison genetique - Responsable : Jacques Magdalou production of drug metabolism enzymes by gene recombination 15h - 15h40 : Conference pleniere : Pr P.L.M. Jansen, University Hospital Groningen, Pays-Bas Bilirubin : UDP-glucuronozyltransferase ; normal function and genetic defects 15h40 - 16h05 : F. Trivin, Service de Biochimie, Hopital Saint-Joseph, Paris Les deficits en activite bilirubine : UDP-glucuronosyltransferase hepatique chez l'Homme. Etude genetique et approche therapeutique Deficiencies of human liver bilirubin : UDP-glucuronosyltransferase activity : genetic study and therapeutic approach 16h05 - 16h25 : S. Fournel-Gigleux, Centre du Medicament, URA CNRS 597, Nancy Developpement de cellules de mammiferes genetiquement modifiees pour l'etude mecanistique de la glucuronoconjugaison Genetically modified mammalian cells for the study of the mechanism of the glucuronoconjugation 16h45 - 17h10 : A. Elass, Centre de Recherche et d'Etudes en Simulation et Modelisation Moleculaire, U.279 INSERM, Universite des Sciences et Technologies, Villeneuve-d'Ascq Approche par "relations quantitatives structure-activite" (Etude QSAR classique et CoMFA) du mecanisme reactionnel de la glucuronoconjugaison des substances phenoliques planes par l'UDP-glucuronosyltransferase humaine recombinante UGT1*6 "Quantitative structure activity relationship" (QSAR an CoMFA) study of the mechanism of the glucuronoconjugation of planar phonotic compounds by the recombinant human UDR-glucuronosyltransferase UGP1*6 17h10 - 17h35 : J.C. Gautier, CHU Necker, INSERM U.75, Paris Simulation du metabolisme humain multi-etapes du benzo(a)pyrene dans la levure Saccharomyces cerevisiae Simulation of the multi-step human metabolism of benzo(a)pyrene in Saccharomyces cerevisiae 17h35 - 18h : D. Werck-Reichhardt, Departement d'Enzymologie Cellulaire et Moleculaire, CNRS-IBMP, Strasbourg Substrats et inhibiteurs specifiques de CYP73, un P450 vegetal obtenu sous une forme isolee et fonctionnelle par expression dans la levure Specific substrates and inhibitors of CYP73, a plant P450 obtained as an isolated and functional form in yeast Jeudi 30 mars 1995 matin Colloque VI (salle A) : Proteines recombinantes et modifications post-traductionnelles - Responsable : Yves Cenatiempo Recombinant proteins and post-translational modifications 9h - 9h25 : A. Martinage, CNRS URA 1309, Institut Pasteur de Lille Les modifications post-traductionnelles des proteines : une grande diversite pour un formidable potentiel d'action Post-translational modifications of proteins : a wide diversity for a wide panel of activity 9h25 - 9h50 : B. Domon, UMR 111, UST Lille Caracterisation de la glycosylation et autres modifications post-traductionnelles des proteines recombinantes Characterisation of glycosylation and other post-translational modifications or recombinant proteins 9h50 - 10h15 : A. Fournier, Rhone-Poulenc Rore, Centre de Recherche de Vitry-Alfortville Etude de la O-glycosylation de proteines secretees chez Kluyveromyces lactis O-glycosylation of secreted proteins in Kluyveromyces lactis 10h45 - 11h10 : G. Devauchelle, CNRS URA 1184, INRA, Saint-Christol-les-Ales Le systeme d'expression Baculovirus - Cellules d'insecte : modification post-traductionnelles Insect cell-Baculovirus expression system : post-translational modifications 11h10 - 11h35 : L. Faye (CNRS URA 203, Universite de Rouen) Adressage de proteines recombinantes dans la cellule vegetale Targetting of recombinant proteins in plant cell 11h35 - 12h : J. Wallach, Laboratoire de Biochimie Analytique, Universite de Lyon Amidation C-terminale de peptides bioactifs recombinants C-terminal amidation of recombinant bioactive peptides Table ronde VII (salleB) : Recherche d'un premier emploi - Responsables : Gilles Guihard et J.P. Levremont First employment Jeudi 30 mars 1995 apres-midi Table ronde VIII (salle A) : Enseignement de la Biochimie - Responsables : Bernard Rossignol et Emmanuel Shechter Teaching biochemistry Communications par affiches (posters) : Le Secretariat General vous enverra sur simple demande le cadre pour la redaction des resumes. Responsables scientifiques : Yves Cenatiempo (institut de Biologie Moleculaire et d'Ingenierie Genetique du CNRS, Poitiers) et Andre Verbert (Universite des Sciences et Technologies de Lille I) Informations : Chantal Gaucherelle, Secretariat de la SFBBM, Centre Universitaire Pharmaceutique, 92296 Chatenay-Malabry Cedex, telephone : (33) 1 46 83 17 31, telecopie : (33) 1 46 83 80 55 From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!agate!kos5mac17.berkeley.edu!user From: williel@uclink3.berkeley.edu (Simon Penson) Newsgroups: bionet.molbio.proteins Subject: SDS-PAGE of 32P labelled protein Date: Thu, 02 Feb 1995 09:10:19 -0800 Organization: UC Berkeley; Plant Biology Lines: 11 Message-ID: NNTP-Posting-Host: kos5mac17.berkeley.edu I'm going to need to run some SDS-PAGE gels of proteins which have been incubated with 32P-ATP. How can I remove the excess (ie uncomsumed) ATP from the reaction m,ixture prior to electrophoresis? TCA ppt has been suggested, as has spin-desalting. Any comments/advice gratefully recieved. Simon. Simon Penson Plant Biology Dept UC Berkeley From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news2.near.net!cat.cis.Brown.EDU!cis-ts3-slip5.cis.brown.edu!user From: Stephen_Lasky@brown.edu (Stephen R. Lasky, Ph.D.) Newsgroups: bionet.molbio.proteins Subject: Re: protease deficient strains Date: 2 Feb 1995 15:08:22 GMT Organization: Roger Williams Hospital/Brown U. Lines: 27 Message-ID: References: <3glq0s$d2b@news.tamu.edu> NNTP-Posting-Host: cis-ts3-slip5.cis.brown.edu In article , ming@ahabs.wisc.edu (Ding Ming) wrote: > In article <3glq0s$d2b@news.tamu.edu>, mary@bio.tamu.edu (Mary Fernandes) wrote: > > > I am experiencing severe degradation problems with the expression of a > > fungal DNA-binding protein in E.coli. I have tried both GST and His tag > > systems and have also tried to make a truncated protein, but the > > problem persists. Does anyone have a strain that is lon- or lon-htpr > > that I could use for this purpose? Any suggestions are welcome. Thanks. > > > The strain supplied with some GST-fusion kits is Lon-. I think that it is BL-2. SRLasky -- ********************************************************************* Stephen R. Lasky, Ph.D. Roger Williams Medical Center/Brown University Phone: 401-456-6572 Fax: 401-456-6569 e-mail: Stephen_Lasky@brown.edu ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ "The speed of a computer is inversly proportional to the legnth of time it has been on your desk." Michael Yablonski, circa 1989 ********************************************************************* From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!MIS.FUHSCMS.EDU!muellerd From: muellerd@MIS.FUHSCMS.EDU ("David Mueller") Newsgroups: bionet.molbio.proteins Subject: Light scattering instrument Date: 2 Feb 1995 07:06:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502021506.HAA00784@net.bio.net> NNTP-Posting-Host: net.bio.net Dear colleagues: I am interested in getting a light scattering instrument to measure hydrodynamic radius, polydispersity, etc. Can anybody recommend a manufacturer? I am looking for a best buy. Thanks David Mueller Dept. Biochemistry Chicago Medical School From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!smb18 From: smb18@mole.bio.cam.ac.uk (Simon Brocklehurst (Bioc)) Newsgroups: bionet.molbio.proteins Subject: Re: HELP! Protein Graphics!! (yuck! this echoes even in bionet.software) Date: 2 Feb 1995 13:24:11 GMT Organization: University of Cambridge, England Lines: 31 Message-ID: <3gqmdr$3a5@lyra.csx.cam.ac.uk> References: <3gostk$noo@mace.cc.purdue.edu> NNTP-Posting-Host: mole.bio.cam.ac.uk barani@mace.cc.purdue.edu (Barani) writes: > In today's world if someone asks for a program to generate a 3D > structure from a sequence, then he needs to be cautioned. Cautioning is not the same thing as telling someone to stop wasting their time! The previous advice was that, unless your protein has greater then 80% sequence identity with another protein of known structure, you shouldn't bother trying to construct a 3-D model by using comparative modelling techniques. As people have written previously, 40%-50% identity can allow you to construct models that is as accurate as medium qualitiy X-ray or NMR structures (if you're lucky with the insertions etc). This happens to be a fact! Incidently, your assessment that NMR structure people are rich leads be to believe that the opposite of your thoughts on the mental states of modellers is likely to the correct view ;-) -- Simon _________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences | \>> | Department of Biochemistry, University of Oxford, | \\, Oxford, UK. | E-mail: smb@bioch.ox.ac.uk |________________________________________________________________________ From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!REO.MED.UPENN.EDU!kao_c From: kao_c@REO.MED.UPENN.EDU (Chih-Ching Kao) Newsgroups: bionet.molbio.proteins Subject: (none) Date: 2 Feb 1995 21:45:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502030539.AA17570@reo.med.upenn.edu> NNTP-Posting-Host: net.bio.net Hello! I am thinking about connecting two DNA fragments to make a fusion protein. Because these two DNA fragments are not in frame, I want to add some interval DNA sequences between them. I also try to prevent these interval amino acids from interving these two proteins' structures so that I can preserve their individual functions. What will be the best choice for such interval amino acids? I am thinking about Gly, Ala, Val, Leu, and Ile. Are they suitable for this purpose? Where can I find some guide for such design? Any suggestion? Thanks in advance! CCK at PA, USA From owner-proteins@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!psgrain!nntp.ski.mskcc.org!nntp.mskcc.org!phil From: phil@xtreme1.mskcc.org (Phil Jeffrey) Newsgroups: bionet.molbio.proteins Subject: Re: HELP! Protein Graphics!! Sorry, No help available on that topic Date: 2 Feb 95 18:18:19 Organization: Memorial Sloan-Kettering Cancer Center Lines: 18 Message-ID: References: <3ggmdi$5j@mace.cc.purdue.edu> <1995Jan30.201542.18484@alw.nih.gov> NNTP-Posting-Host: xtreme1.ski.mskcc.org In-reply-to: johnk@spasm.niddk.nih.gov's message of Mon, 30 Jan 1995 20:15:42 GMT In article <1995Jan30.201542.18484@alw.nih.gov> johnk@spasm.niddk.nih.gov (John Kuszewski) writes: >> are probably meaningless--look at calmodulin for an example of >> how precise but wildly inaccurate a crystal structure can be. Or look at the tetramerization domain of p53 for an example of how precise but wildly inaccurate an NMR structure can be (the NIH version). Phil -- ------------------------------------------------------------------------------- | Phil Jeffrey | | | X-ray/Computer Manager, Crystallography Lab | If you lie to the compiler, | | Memorial Sloan-Kettering Cancer Center, NYC | it will get its revenge | | phil@xray2.mskcc.org, p-jeffrey@ski.mskcc.org | - Henry Spencer | | Ph: (212) 639 2189 Fax: (212) 717 3066 | | ------------------------------------------------------------------------------- From owner-proteins@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Mohamed SAAD ESRF BP 220 38043 GRENOBLE CEDEX Newsgroups: bionet.molbio.proteins Subject: myristoylation Date: 3 Feb 1995 10:21:54 -0000 Lines: 9 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3gt042$61l@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk bonjour, does anyone knows what N-myristoylation site in a proteine is ? this was predicted by the prosite search for a new peptide sequence I have submitted. any reference is welcom Thanks for your help, Mohamed SAAD. From owner-proteins@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!hubcap.clemson.edu!biosci!bcm!cs.utexas.edu!swrinde!pipex!lyra.csx.cam.ac.uk!bioc.cam.ac.uk!owde100 From: owde100@bioc.cam.ac.uk (Orhan Ertughrul) Newsgroups: bionet.molbio.proteins Subject: Re: HELP! Protein Graphics!! Sorry, No help available on that topic Followup-To: bionet.molbio.proteins Date: 31 Jan 1995 13:38:19 GMT Organization: Somewhere in the University of Cambridge Lines: 28 Distribution: world Message-ID: <3glegb$56a@lyra.csx.cam.ac.uk> References: <3ggmdi$5j@mace.cc.purdue.edu> <1995Jan30.201542.18484@alw.nih.gov> NNTP-Posting-Host: eden.bioc.cam.ac.uk In article <1995Jan30.201542.18484@alw.nih.gov>, johnk@spasm.niddk.nih.gov (John Kuszewski) writes: > In article <3ggmdi$5j@mace.cc.purdue.edu>, barani@mace.cc.purdue.edu (Barani) writes: > > > |> IMHO crystallographers are more closer to the truths > |> of a biomolecule than anyone else. > > Except, of course, for us NMR people. No packing distotions, > good pictures of flexibility. > And a residue limit of about 250AA even for 4D. NMR is always going to be a technique of restricted use until larger biomolecules can be resolved. Orhan. ----------------------------------------------------------------------- Orhan W.D. Ertughrul | /\ "It's hard enough to watch University of Cambridge | / \ /\ the news, let alone explain Department of Biochemistry | / / \ it to a child to cast its Tennis Court Road | / / \ eyes on nature over fields Cambridge CB2 1QW |/ / \ of rape and corn, and tell | /\/ \ it without flinching not to owde100@cus.cam.ac.uk | / \ \ fear where its been born" ----------------------------------------------------------------------- WWW : http://nirvana.bioc.cam.ac.uk/~owde100/ ----------------------------------------------------------------------- From owner-proteins@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: myristoylation Date: 3 Feb 1995 22:21:57 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 15 Distribution: bionet Message-ID: <3guaa5$163o@sat.ipp-garching.mpg.de> References: <3gt042$61l@mserv1.dl.ac.uk> NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] Mohamed SAAD ESRF BP 220 38043 GRENOBLE CEDEX (saad@malin.esrf.fr) wrote: > does anyone knows what N-myristoylation site in a proteine is ? N-myristoylation means attachment of a myristoyl chain (a C-14 fatty acid chain) to the NH2 group of your protein. The functional relevance of this modification is being discussed. It has been proposed to be relevant for plasma membrane targeting (the acyl chain serving as membrane anchor) and also for protein-protein interactions. --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "Science is the game you play with God to find out what His rules are." */ From owner-proteins@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: viewing protein structures Date: 3 Feb 1995 22:17:13 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 21 Distribution: world Message-ID: <3gua19$163o@sat.ipp-garching.mpg.de> References: <3gpgo3$4uq@tali.hsc.colorado.edu> NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] Peter Hovland (hovland_P@defiance.hsc.colorado.edu) wrote: > In article Leopold Ilag mbb, leoila@ki.se writes: > >Can anyone out there please tell me what is the best software to use on a > >mac to view images . I am specifically interested in those found in the > >worldwide web. > For viewing protein structures with a mac, try the program called "mage". Although I agree with Peter that Mage is an awesome program, I wouldn't recommend it for viewing PDB files. There are some other programs for this task, notably rasmol (rasmac on the mac) which appears to become a kind of standard for molecular viewers, probably because it is also available for Unix or Windows (raswin). --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "Science is the game you play with God to find out what His rules are." */ From owner-proteins@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!genmac28.biochem.mpg.de!user From: spang@vms.biochem.mpg.de (Anne Spang) Newsgroups: bionet.molbio.proteins Subject: Re: yeast protein extraction Date: 3 Feb 1995 22:12:14 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 14 Message-ID: References: NNTP-Posting-Host: genmac28.biochem.mpg.de Hi! -inocculate a 50 ml culture O/N to early or mid-log phase (too high cell conc.will result in a less efficient lysis) -spin down the cells -remove the supernatant -resuspend the pellet in 1 ml 50 mM Tris-ClpH7.5, 1%SDS, 5 mM EDTA, 10 mM DTT, and proteinase inhibitors -add an equal volume glass beads -vortex ´6x 30´´ with intervalls on ice -check the lysis under the microscope -spin 5 min in a Benchtop centrifuge -take the supernatant. Hope this helps Anne From owner-proteins@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news From: jhp20@cus.cam.ac.uk (Mikpf) Newsgroups: bionet.molbio.proteins Subject: Re: HELP! Protein Graphics!! (yuck! this echoes even in bionet.software) Date: 4 Feb 1995 01:05:12 GMT Organization: Soliptist Lines: 35 Message-ID: <3gujs8$jun@lyra.csx.cam.ac.uk> References: <3gostk$noo@mace.cc.purdue.edu> <3gqmdr$3a5@lyra.csx.cam.ac.uk> NNTP-Posting-Host: sonja.acad.cai.cam.ac.uk Mime-Version: 1.0 X-Newsreader: WinVN 0.93.11 >barani@mace.cc.purdue.edu (Barani) writes: > >> In today's world if someone asks for a program to generate a 3D >> structure from a sequence, then he needs to be cautioned. > > Cautioning is not the same thing as telling someone to stop wasting > their time! > The previous advice was that, unless your protein has greater then > 80% sequence identity with another protein of known structure, you > shouldn't bother trying to construct a 3-D model by using comparative > modelling techniques. As people have written previously, 40%-50% identity > can allow you to construct models that is as accurate as medium > qualitiy X-ray or NMR structures (if you're lucky with the insertions > etc). This happens to be a fact! I think the point of making model should be discussed. If you are interested in just looking at a 3D view of your molecule for any kind of visual que, even 10% 20% homology of sequence is enough to build a model which can be in a right shape in general. However, the problem is models are very very useless if you want to go further than that. Even 90% sequence identity can not assure you anything significantly on your experiment. In this case it is better to rely on low quality X-ray structure than a high quality models. Making fancy pictures which seem to be precise does not mean it can be useful for experimentalist. In modelling, the problem is not how good your model is, but to know how bad your model can be in the worst case. So, models built with 40% sequence homology can easily be absolute garbage. By the way, Modeller 12 is now available at ftp site in Harvard. tammy.harvard.edu , it seems to deal with energy minimization better than previous version. From owner-proteins@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!sol.ctr.columbia.edu!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!news From: jhp20@cus.cam.ac.uk (Mikpf) Newsgroups: bionet.molbio.proteins Subject: Re: unsubscribe Date: 4 Feb 1995 00:53:33 GMT Organization: Soliptist Lines: 7 Distribution: world Message-ID: <3guj6d$jun@lyra.csx.cam.ac.uk> References: <9502030353.AA23395@atlas.rc.m-kasei.co.jp> NNTP-Posting-Host: sonja.acad.cai.cam.ac.uk Mime-Version: 1.0 X-Newsreader: WinVN 0.93.11 subscribe proteins -- _________________________________________________ jong@mrc-lmb.cam.ac.uk Tim Hubbard's student _________________________________________________ From owner-proteins@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!swrinde!sgiblab!uhog.mit.edu!rutgers!umdnj!bawagan From: bawagan@umdnj.edu (Hinayana Bawagan) Subject: cytoskeletal proteins Message-ID: Organization: Univ. of Medicine and Dentistry of NJ Date: Fri, 3 Feb 1995 22:33:23 GMT Lines: 7 Dear netters, Someone in my lab has a vague remembrance of a cytoskeletal protein wherein the null mutation of the gene encoding the protein has the same phenotye as its overexpression. Hope there are cytoskeletal experts out there who can drop me a line. Thank you. From owner-proteins@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: L & D amino acids... Date: 3 Feb 1995 13:49:40 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 34 Distribution: world Message-ID: <3gtc9k$2hbk@sat.ipp-garching.mpg.de> References: NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] Geetha Vasudevan (geetha@HELIX.NIH.GOV) wrote: > I am aware of the fact that the racemic mixtures of L & D > amino acids are synthesised for shorter polypeptides. I don't understand what you mean here. When you go synthesizing a peptide by organic chemistry, you don't use racemic amino acids as the starting material, but the L-amino acid (or its activated derivative). > the basic assumption for the observed protein is that, all > the amino acids are in the L-form. This has been corroborated > with experimental studies like crystallography (which alone > I know something about). This is not an assumption, it is a well established fact. In fact, that proteins consist only of L-amino acids was established long before people could ever think of X-ray structures of proteins. For example, if you purify your protein and subject it to total hydrolysis, you will find that the resulting amino acid mixture contains only L-amino acids. > I remember that the L & D conformers > are away by only a few Kcals. I'm not sure what you mean by "conformers". L and D isoforms cannot be interchanged into each other without breaking and forming bonds. --Cornelius (not a crystallographer, not even a structural biologist :-). -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "Science is the game you play with God to find out what His rules are." */ From owner-proteins@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!swrinde!gatech!rutgers!umdnj!soma!butler From: butler@soma.UMDNJ.EDU (Gary Butler) Subject: Re: SDS-PAGE of 32P labelled protein Message-ID: Sender: news@umdnj.edu () Organization: Univ. of Medicine and Dentistry of NJ References: Date: Fri, 3 Feb 1995 17:20:05 GMT Lines: 56 williel@uclink3.berkeley.edu (Simon Penson) writes: >I'm going to need to run some SDS-PAGE gels of proteins which have been >incubated with 32P-ATP. How can I remove the excess (ie uncomsumed) ATP >from the reaction m,ixture prior to electrophoresis? TCA ppt has been >suggested, as has spin-desalting. >Any comments/advice gratefully recieved. >Simon. >Simon Penson >Plant Biology Dept >UC Berkeley In order of simplicity and usefullness, my suggestions follow: 1.) Why do you need to? Most of the ATP should migrate a lot faster, and could be eluted into the anode tray while the protein's still on the gel, and if any remains in the gel, it may come out with soaking in stain/fix. 2.) Amicon's Centricon 10 or Centricon 30 disposible concentrators will separate low MW molecules from proteins without desalting, and leave your protein in 50 microliters. Bring back to 2 ml and reconcentrate to 50 mcl a few times if you want greater efficiency. 3.) Oligo-dT matrix might be used to absorb it out. 4.) It may be possible to absorb out small molecules with charcoal. There are some old RIA methods around which may employ this, 5.) Dialyse then concentrate by laying bag onto PEG 20k or sucrose to reduce volume. 6.) If you do TCA, you'll have to get rid of the TCA with ethanol so as not to interfere with gel run, and you may have to use carrier protein so as not to lose low concentrations of labelled protein (but never use BSA as carrier). You could do TCA, and collect on a filter, wash with ETOH, dry, and stuff the filter in a well. 7.) Sephadex G25 & collect the void. But you'll probably have to concentrate, so #1 or 2 are better. Good Luck. G. -- Gary H. Butler, Ph.D. Coriell Institute for Medical Research 401 Haddon Ave. Camden, NJ 08103 Tel: (609) 757-9716 Fax: (609) 964 0254 Attn: Butler Email: butler@UMDNJ.edu From owner-proteins@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: lgb@ibcp.fr (lgb@ibcp.fr) Newsgroups: bionet.molbio.proteins Subject: Spring meeting-French Society for Biochemistry & Molecular Biology Date: 3 Feb 1995 18:06:02 -0000 Lines: 285 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3gtraa$2ac@mserv1.dl.ac.uk> Reply-To: lgb@ibcp.fr (lgb@ibcp.fr) Comments: To mail both the group and netnews send to (molmodel@dl.ac.uk) X-Article-Number: bionet.molec-model Msg # 253 X-Listpath: bionet-news Original-To: "bionet.molec-model mail newsgroup" CONGRES DE PRINTEMPS DE LA SOCIETE FRANCAISE DE BIOCHIMIE ET BIOLOGIE MOLECULAIRE 1995, March 28 - 29 - 30 SPRING MEETING OF THE FRENCH SOCIETY FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY 28 - 29 - 30 mars 1995 Parc de Expositions de Paris-Porte de Versailles - hall 7 niveau 3 P R O G R A M M E Mardi 28 mars matin 10 h Conference pleniere d'introduction de Axel Kahn : Therapie genique : le gene medicament. Plenary lecture : Axel Kahn : Gene therapy : gene as a drug Cette conference est organisee par le Salon du Laboratoire et ouverte a tous les scientifiques. Il n'est donc pas necessaire de passer a l'accueil de la S.F.B.B.M. avant cette Conference. Vous etes convies a y assister en allant directement a l'amphitheatre 731, hall 7 niveau 3. Mardi 28 mars 1995 apres-midi Colloque 1 (salle A) : Role de la conformation de l'ADN dans ses interactions avec les proteines - Responsables : Christian Marion et Etienne Delain Influence of DNA conformation in its interaction with proteins 14h45 - 14h50 : Christian Marion, Paris : accueil et introduction 14h50 - 15h15 : Bernard Revet, Villejuif Interactions ADN-Proteines : exemple de l'activateur de la glutamyl sunthetase DNA-protein interactions : glutamyl synthase activator as exemple 15h15 - 15h40 : Francoise Culard, Orleans Aspects topologiques de l'interaction de la proteine MC1 des Methanosarcines avec l'ADN Topological aspects of the interaction of methanisarcin MC1 with DNA 15h40 - 16h05 : Eric Le Cam, Villejuif Conformation de l'ADN et interactions ADN-proteines en microscopie electronique : exemple de la Poly(ADP-ribose) polymerase Conformation of DNA and DNA-protein interactions studied by electron microscopy : the example of the poly (ADP-ribose)polymerase 16h05 - 16h30 : Etienne Delain, Villejuif Observations des complexes ADN-proteines a l'aide de differentes techniques de microscopie Observations of DNA-protein interactions using different microscopy techniques 16h45 - 17h10 : Josette Rouviere-Yaniv, Paris Interaction de l'ADN avec la proteine HU DNA-HU protein interaction 17h10 - 17h35 : Marc Leng, Orleans Interaction entre HMG 1 et l'ADN modifie par le cis-platine Interaction between HMG 1 and cis-platine modified DNA 17h35 - 18h : Ariel Prunel, Paris Transition conformationnelle du tetramere (H3-H4)2 et ses implications pour la dynamique du nucleosome in vivo Conformational transition of the (H3-H4)2 tetramer and its implications for the dynamic of nucleosome in vivo olloque II (salle B) : Transduction du signal et regulations metaboliques - Responsables : Alain Lavoinne et Jean-Paul Leroux Signal transduction and regulations 15h - 15h50 : Alain Ktorza, Paris Physiopathologie de la deterioration de secretion d'insuline au cours du diabete de type 2 : mecanismes cellulaires et moleculaires Physiopathology of insulin secretion deficiency in type 2 diabetes : cellular and molecular mechanisms 15h50 - 16h15 : Nathalie Vionnet, Paris Implications fonctionnelles des mutations sur le gene de la glucokinase chez l'Homme Functional implications of mutations in the human glucokinase gene 16h45 - 17h10 : Jean-Francois Tanti, Nice Mecanisme d'action de l'insuline dans deux tissus insulinosensibles, le muscle squelettique et le tissu adipeux Mechanism of insuline action in two insulin sensitive tissues : the skeletal muscle and fat tissue 17h10 - 18h : Assemblee generale constitutive du Groupe d'Etudes des Regulations Metaboliques (ex GERCHIC) Meeting of the Interest Group for the study of metabolic regulations Mercredi 29 mars 1995 matin Colloque II suite (Salle B) : Regulations metaboliques - Responsables : Alain Lavoinne et Jean-Paul Leroux Metabolic regulations 9h - 9h50 : Claire Hivroz, Paris La transduction du signal dans les lymphocytes : rôle des tyrosine-kinases Signal transduction in lymphocytes : role of tyrosine-kinases 9h50 - 10h15 : Muriel Quillard, Rouen Regulation de l'expression du gene de l'ASS (arginino-succinate synthetase) : role de la glutamine et du gonflement cellulaire Regulation of the gene expression of the argino-succinate synthase (ASS) : role of glutamine and of cellular swelling 10h45 - 11h10 : Marie-France Chauvin, Lyon Flux enzymatiques lies au metabolisme du glutamate dans les cellules renales de lapin : etude par spectroscopie RMN du carbone 13 Enzymatic flux related to glutamate metabolism in rabbit kidney cells : study by 13C-NMR spectroscopy 11h10 - 11h35 : Annie Rodolosse, Paris Repression par le glucose de la transcription du gene de la saccharase-isomaltase humaine Repression of the uman saccharase-isomerase gene transcription by glucose 11h35 - 12h : Christophe Depre, bruxelles Adaptation metabolique du coeur a l'ischemie Metabolic adaptation of the heart to ischemy Colloque III (salle A) : Domaines fonctionnels des ARN : Responsables : Chantal Ehresmann et Richard Giege RNA Functional domains 9h - 9h50 : Fritz Ekstein, MPI, Gottingen, Allemagne Les ribozymes en tete de marteau : relations structure-fonction Hammer headed ribozymes : structure-function relationship 9h50 - 10h15 : Christiane Branlant, Universite de Nancy Un exemple rare de la dynamique des interactions ARN : le spliccosome A rare example of RNA interactions dynamic : the spliceosome 10h45 - 11h10 : Alain Jacquier, Institut Pasteur, Paris Les introns de groupe II, modele d'etude des reactions d'epissage Type II introns : a model for splicing reactions 11h10 - 11h35 : Roland Marquet, IBMC, Strasbourg La dimerisation de l'ARN genomique HIV-1 : etudes structurales et fonctionnelles Dimerisation of HIV-1 genomic RNA : structural and functional studies 11h35 - 12h : Frederic Dardel, Ecole Polytechnique, Palaiseau Interactions ARN de transfert et enzymes de l'appareil de traduction Interaction of transfer RNAs with the enzymes of the translation machinery Mercredi 29 mars 1995 apres-midi Assemblee Generale de la SFBBM (de 14h a 15h) Society Meeting Colloque IV (salle A) : Proteines G du systeme nerveux - Responsable : Dominique Aunis G proteins of nervous system 15h - 15h45 : Joel Bockacrt, Montpellier Les proteines G heterotrimeriques : 20 ans de recherche Heterotrimeric G proteins : 20 years of research 15h45 - 16h15 : Vincent Homburger, Montpellier Role de la proteine G heterotrimerique Go dans la poussee neuritique Role of Go heterotrimeric G protein during the neuritic growth 16h45 - 17h15 : Marie-France Bader, Strasbourg Proteines G trimeriques et exocytose dans les cellules neuroendocrines Trimeric G proteins and exocytosis in neuroendocrine cells 17h15 - 17h45 : Jean-Pierre Henry, Paris Controle de l'exocytose par la proteine G monomerique Rab3a Control of exocytosis by the Rab3a monomeric G protein 17h45 - 18h : Discussion generale - General discussion Colloque V (salle B) : Production d'enzymes du metabolisme des medicaments par recombinaison genetique - Responsable : Jacques Magdalou production of drug metabolism enzymes by gene recombination 15h - 15h40 : Conference pleniere : Pr P.L.M. Jansen, University Hospital Groningen, Pays-Bas Bilirubin : UDP-glucuronozyltransferase ; normal function and genetic defects 15h40 - 16h05 : F. Trivin, Service de Biochimie, Hopital Saint-Joseph, Paris Les deficits en activite bilirubine : UDP-glucuronosyltransferase hepatique chez l'Homme. Etude genetique et approche therapeutique Deficiencies of human liver bilirubin : UDP-glucuronosyltransferase activity : genetic study and therapeutic approach 16h05 - 16h25 : S. Fournel-Gigleux, Centre du Medicament, URA CNRS 597, Nancy Developpement de cellules de mammiferes genetiquement modifiees pour l'etude mecanistique de la glucuronoconjugaison Genetically modified mammalian cells for the study of the mechanism of the glucuronoconjugation 16h45 - 17h10 : A. Elass, Centre de Recherche et d'Etudes en Simulation et Modelisation Moleculaire, U.279 INSERM, Universite des Sciences et Technologies, Villeneuve-d'Ascq Approche par "relations quantitatives structure-activite" (Etude QSAR classique et CoMFA) du mecanisme reactionnel de la glucuronoconjugaison des substances phenoliques planes par l'UDP-glucuronosyltransferase humaine recombinante UGT1*6 "Quantitative structure activity relationship" (QSAR an CoMFA) study of the mechanism of the glucuronoconjugation of planar phonotic compounds by the recombinant human UDR-glucuronosyltransferase UGP1*6 17h10 - 17h35 : J.C. Gautier, CHU Necker, INSERM U.75, Paris Simulation du metabolisme humain multi-etapes du benzo(a)pyrene dans la levure Saccharomyces cerevisiae Simulation of the multi-step human metabolism of benzo(a)pyrene in Saccharomyces cerevisiae 17h35 - 18h : D. Werck-Reichhardt, Departement d'Enzymologie Cellulaire et Moleculaire, CNRS-IBMP, Strasbourg Substrats et inhibiteurs specifiques de CYP73, un P450 vegetal obtenu sous une forme isolee et fonctionnelle par expression dans la levure Specific substrates and inhibitors of CYP73, a plant P450 obtained as an isolated and functional form in yeast Jeudi 30 mars 1995 matin Colloque VI (salle A) : Proteines recombinantes et modifications post-traductionnelles - Responsable : Yves Cenatiempo Recombinant proteins and post-translational modifications 9h - 9h25 : A. Martinage, CNRS URA 1309, Institut Pasteur de Lille Les modifications post-traductionnelles des proteines : une grande diversite pour un formidable potentiel d'action Post-translational modifications of proteins : a wide diversity for a wide panel of activity 9h25 - 9h50 : B. Domon, UMR 111, UST Lille Caracterisation de la glycosylation et autres modifications post-traductionnelles des proteines recombinantes Characterisation of glycosylation and other post-translational modifications or recombinant proteins 9h50 - 10h15 : A. Fournier, Rhone-Poulenc Rore, Centre de Recherche de Vitry-Alfortville Etude de la O-glycosylation de proteines secretees chez Kluyveromyces lactis O-glycosylation of secreted proteins in Kluyveromyces lactis 10h45 - 11h10 : G. Devauchelle, CNRS URA 1184, INRA, Saint-Christol-les-Ales Le systeme d'expression Baculovirus - Cellules d'insecte : modification post-traductionnelles Insect cell-Baculovirus expression system : post-translational modifications 11h10 - 11h35 : L. Faye (CNRS URA 203, Universite de Rouen) Adressage de proteines recombinantes dans la cellule vegetale Targetting of recombinant proteins in plant cell 11h35 - 12h : J. Wallach, Laboratoire de Biochimie Analytique, Universite de Lyon Amidation C-terminale de peptides bioactifs recombinants C-terminal amidation of recombinant bioactive peptides Table ronde VII (salleB) : Recherche d'un premier emploi - Responsables : Gilles Guihard et J.P. Levremont First employment Jeudi 30 mars 1995 apres-midi Table ronde VIII (salle A) : Enseignement de la Biochimie - Responsables : Bernard Rossignol et Emmanuel Shechter Teaching biochemistry Communications par affiches (posters) : Le Secretariat General vous enverra sur simple demande le cadre pour la redaction des resumes. Responsables scientifiques : Yves Cenatiempo (institut de Biologie Moleculaire et d'Ingenierie Genetique du CNRS, Poitiers) et Andre Verbert (Universite des Sciences et Technologies de Lille I) Informations : Chantal Gaucherelle, Secretariat de la SFBBM, Centre Universitaire Pharmaceutique, 92296 Chatenay-Malabry Cedex, telephone : (33) 1 46 83 17 31, telecopie : (33) 1 46 83 80 55 From owner-proteins@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!lhc!nih-csl!loglady.ninds.nih.gov!johnk From: johnk@spasm.niddk.nih.gov (John Kuszewski) Subject: Re: HELP! Protein Graphics!! Sorry, No help available on that topic Message-ID: <1995Feb3.193250.14418@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Reply-To: johnk@spasm.niddk.nih.gov (John Kuszewski) Organization: National Insts. of Health References: <3ggmdi$5j@mace.cc.purdue.edu> <1995Jan30.201542.18484@alw.nih.gov> Date: Fri, 3 Feb 1995 19:32:50 GMT Lines: 31 In article , phil@xtreme1.mskcc.org (Phil Jeffrey) writes: |> In article <1995Jan30.201542.18484@alw.nih.gov> johnk@spasm.niddk.nih.gov (John Kuszewski) writes: |> |> >> are probably meaningless--look at calmodulin for an example of |> >> how precise but wildly inaccurate a crystal structure can be. |> |> Or look at the tetramerization domain of p53 for an example of how |> precise but wildly inaccurate an NMR structure can be (the NIH version). |> Ouch! Well, the p53 fiasco was more of a misapplication of the NMR information, rather than in inherent limitation of the method. The calmodulin crystal structure's problems were caused by the requirement for crystallization, which is of course inherent to crystallography. -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| From owner-proteins@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!hubcap.clemson.edu!biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.belwue.de!news.uni-stuttgart.de!uni-regensburg.de!fauern!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Best E.coli strains for GST-expression (re. minimum proteolysis) Date: 30 Jan 1995 21:34:14 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 18 Distribution: world Message-ID: <3gjm0m$h8a@sat.ipp-garching.mpg.de> References: NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] Jim Litts (jlitts@onyx-pharm.com) wrote: [asking for E. coli strains with protease deletions] BL21 and derivatives are E. coli B strains which are protease-deficient compared to WT E. coli K-12 (e.g. they do not contain outer membrane proteases) There are several lon-negative E. coli K-12 strains. lon is an ATP- dependent protease. K-12 which are deficient in the heat-shock response (sorry, can't recall genotype) are also lon-deficient. Some of these strains are available from NEB. --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "Science is the game you play with God to find out what His rules are." */ From owner-proteins@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!news.itd.umich.edu!usenet From: Rick Neubig Newsgroups: bionet.molbio.proteins Subject: Re: viewing protein structures Date: 4 Feb 1995 13:42:37 GMT Organization: University of Michigan Lines: 16 Message-ID: <3h008d$3r5@lastactionhero.rs.itd.umich.edu> References: <3gpgo3$4uq@tali.hsc.colorado.edu> <3gua19$163o@sat.ipp-garching.mpg.de> NNTP-Posting-Host: warbler.med.umich.edu krasel@alf.biochem.mpg.de (Cornelius Krasel) wrote: > Although I agree with Peter that Mage is an awesome program, I wouldn't > recommend it for viewing PDB files. There are some other programs for > this task, notably rasmol (rasmac on the mac) which appears to become > a kind of standard for molecular viewers, probably because it is also > available for Unix or Windows (raswin). I'd strongly second the motion on rasmol. I've used raswin and a friend downloaded rasmac. You can get it by anonymous FTP from ftp.dcs.ed.ac.uk [129.215.160.5] in the directory /pub/rasmol. Rick Neubig http://www.umich.edu/~rneubig From owner-proteins@net.bio.net Fri Feb 03 22:00:00 1995 Newsgroups: bionet.general,bionet.molbio.proteins Path: biosci!agate!howland.reston.ans.net!pipex!uunet!world!maayan From: maayan@world.std.com (Maayan Aharoni) Subject: Band-Leader Version 2.0 - New version for Gel Image Analysis software Message-ID: Keywords: Gel Image Analysis, Bands, Spots Organization: The World Public Access UNIX, Brookline, MA Date: Sat, 4 Feb 1995 23:39:30 GMT Lines: 75 Xref: biosci bionet.general:13345 bionet.molbio.proteins:3660 Band Leader Shareware distribution notes Band Leader Windows Application Version 2.00 TechKnowledge EMail address: maayan@world.std.com KEYWORDS: molecular biology,genetics,bands,image processig,gel - **************************************************************************** - Intended audience Genetics Molecular Biology What is Band Leader? Band Leader was designed and implemented by TechKnowldege as an application for processing Gel images. Band Leader is software for the PC Windows operating environment. It is very easy to use and requires only basic Windows skills. With Band Leader you process your gel images to extract data arranged in lanes or in spots. You may create graphs representing data along lanes which you may later process to extract band information. You may create Spot documents, representing single spots on the Gel image or use the Grid tool to extract a group of Spots. Band Leader data can be exported as flat text file or as Spreadsheet data. Band Leader is an MDI application, thus you may load more than one set of images to process at a time. - **************************************************************************** - - Getting Band Leader version 2.00 by ftp: 1. Ftp to expasy.hcuge.ch 2. Login as 'anonymous' 3. Go to directory pub/chromozoom 4. Ftp the file BLDIST.EXE as a binary file to your station 5. Ftp the file BLREADME.TXT as a text file to your station 6. Download the files to your PC To install Band Leader read the file BLREADME.TXT, it contains complete installation instructions. - **************************************************************************** - How to contact TechKnowledge: If you wish to get any further information about Band Leader please contact TechKnowledge. To contact TechKnowledge by phone please call: 972-3-5270267 To contact by mail write to: TechKnowledge POB 23881, Tel-Aviv 61231, ISRAEL. To contact by EMail, send mail to: MAAYAN@world.std.com From owner-proteins@net.bio.net Sat Feb 04 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!smb18 From: smb18@mole.bio.cam.ac.uk (Simon Brocklehurst (Bioc)) Newsgroups: bionet.molbio.proteins Subject: Re: HELP! Protein Graphics!! (yuck! this echoes even in bionet.software) Date: 5 Feb 1995 18:15:37 GMT Organization: University of Cambridge, England Lines: 41 Message-ID: <3h34k9$70m@lyra.csx.cam.ac.uk> References: <3gostk$noo@mace.cc.purdue.edu> <3gqmdr$3a5@lyra.csx.cam.ac.uk> <3gujs8$jun@lyra.csx.cam.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk jhp20@cus.cam.ac.uk (Mikpf) writes: > However, the problem is models are very very > useless if you want to go further than that. Even 90% sequence identity >can not assure you anything significantly on your experiment. In this case >it is better to rely on low quality X-ray structure than a high quality >models. Maybe you should explain what you mean by "go further than that". Also if you are talking about two _natural_ proteins with 90% sequence identity (i.e. not an engineered multiple mutant), then everything that I wrote previously stands i.e. these models are not "useless" ;-) Define what you mean by low quality X-ray structure in terms of resolution and R-factor - the statement you make in this regard is by no means _necessarily_ correct. But to fair to you I'm not exactly clear what you meant by the "significantly on your experi..." bit. >Making fancy pictures which seem to be precise does not mean it can be >useful for experimentalist. In modelling, the problem is not how good your >model is, but to know how bad your model can be in the worst case. Are you talking about generating ensembles of models using restraint-based comparative modelling techniques, when you mention precision? No-one has claimed that the precision of an ensemble generated in this way is related to the accuracy of the model have they? Except to say that precision measurements do highlight bits where you _definitely_ don't know much about the structure, or in test cases where the "potential accuracy" of a new method is being assessed. >So, models built with 40% sequence homology can easily be absolute garbage. Perhaps it depends who is doing the modelling ;-) _________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences | \>> | Department of Biochemistry, University of Oxford, | \\, Oxford, UK. | E-mail: smb@bioch.ox.ac.uk |________________________________________________________________________ From owner-proteins@net.bio.net Sat Feb 04 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!newsxfer.itd.umich.edu!agate!news.duke.edu!usenet From: Marius Brouwer Newsgroups: bionet.molbio.proteins Subject: Novel/Unusual form of SOD Date: 5 Feb 1995 20:59:49 GMT Organization: Duke University, Durham, NC, USA Lines: 12 Message-ID: <3h3e85$8ds@news.duke.edu> NNTP-Posting-Host: mbatduml.ml.duke.edu We have recently found that marine decapod crustacea have a novel form of cytosolic superoxide dismutase. The apparent molecular weight of the protein corresponds to that of CuZnSOD, but its activity cannot be inhibited with cyanide, hydrogen peroxide or diethyldithio- carbamate, which would classify the protein as a MnSOD. (enzyme activity was measured using the classical cytochrome c reduction assay in solution and by activity staining of PAA gels). I am puzzled and intrigued by these observations. Does anybody know of CN/H2O2/DDC-resis- tant CuZnSODs or have some suggestions that may explain our "strange" results? From owner-proteins@net.bio.net Sat Feb 04 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!news.starnet.net!wupost!howland.reston.ans.net!agate!news.duke.edu!usenet From: Marius Brouwer Newsgroups: bionet.molbio.proteins Subject: Re: Novel/Unusual form of SOD Date: 5 Feb 1995 22:23:49 GMT Organization: Duke University, Durham, NC, USA Lines: 25 Message-ID: <3h3j5l$aqb@news.duke.edu> References: <3h3e85$8ds@news.duke.edu> NNTP-Posting-Host: mbatduml.ml.duke.edu Marius Brouwer wrote: > > We have recently found that marine decapod crustacea have a novel > form of cytosolic superoxide dismutase. The apparent molecular weight > of the protein corresponds to that of CuZnSOD, but its activity cannot > be inhibited with cyanide, hydrogen peroxide or diethyldithio- > carbamate, which would classify the protein as a MnSOD. (enzyme > activity was measured using the classical cytochrome c reduction assay > in solution and by activity staining of PAA gels). I am puzzled and > intrigued by these observations. Does anybody know of CN/H2O2/DDC-resis- > tant CuZnSODs or have some suggestions that may explain our "strange" > results? Sorry, forgot to add my address, here it is: Marius Brouwer Duke University School of the Environmnet Marine Laboratory Beaufort N.C. 28516 email: mbt@acpub.duke.edu telephone: (919) 504-7619 > > From owner-proteins@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: "Andrew, Tel. +39-6-91093434" Newsgroups: bionet.molbio.proteins Subject: Forwarded mail in reply to phage display question Date: 6 Feb 1995 19:44:44 -0000 Lines: 29 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3h5u7c$s3d@mserv1.dl.ac.uk> Original-To: aguappon@wvumbrcc1.hsc.wvu.edu Dear Brad, I am forwarding this to you on behalf of Brian Kay who responded to your original question. Andrew Wallace (wallace@irbm.it) =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ORIGINAL MESSAGE =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From: SMTP%"KAY@UNCVX1.OIT.UNC.EDU" 3-FEB-1995 21:10:41.66 To: WALLACE CC: Subj: Re: Question Dear Brad, I am in the process of co-editing a book with Jill Winter (Chiron) and John McCafferty (CAT) on phage display. Its title is Phage display of peptides and proteins. It is meant to be a lab manual. I can send a copy of the table of contents if you wish. The writing is nearing completion and will be submitted to the editors at Academic Press by the end of the month. I hope that it will be available 3-6 months after that. If you have any questions, send an email note. Brian Kay University of North Carolina at Chapel Hill From owner-proteins@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!ns1.faseb.org!darwin.sura.net!martha.utk.edu!drnelson.utmem.edu!user From: dnelson@utmem1.utmem.edu (David R. Nelson) Newsgroups: bionet.molbio.proteins Subject: Cytochrome P450 Web server Followup-To: bionet.molbio.proteins Date: 6 Feb 1995 22:44:54 GMT Organization: U. Tennessee, Memphis Lines: 21 Message-ID: NNTP-Posting-Host: drnelson.utmem.edu I am currently building a cytochrome P450 WWW server on my Mac. Currently it has two sequence alignments. The first file has 168 sequences and the second file has 150 additional sequences. These are all publically available sequences. The present alignment of all sequences (including confidential sequences) has over 400 sequences. The two files can be put together on a word processor to get a single alignment of 318 P450s. I will also be posting tables of accession numbers to the P450 sequences and bibilographic information for the entries that are new since the 1993 DNA and Cell Biology nomenclature paper appeared. For those who would like to look the URL address is http://drnelson.utmem.edu/homepage.html This name may be changed in the future, but it should be good for the next few weeks as I continue to put this server together. -- David R. Nelson Assistant Professor Dept. of Biochemistry University of Tennessee, Memphis From owner-proteins@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!uhog.mit.edu!rutgers!gatech!howland.reston.ans.net!news.starnet.net!wupost!waikato!canterbury.ac.nz!chmeds.ac.nz!gjacobs From: gjacobs@chmeds.ac.nz Newsgroups: bionet.molbio.proteins Subject: Re: HELP!!! Protein Graphics!! Message-ID: <1995Feb7.120205.894@chmeds.ac.nz> Date: 7 Feb 95 12:02:05 +1200 References: <3g18fo$no3@bigblue.oit.unc.edu> Distribution: world Lines: 53 First off, I'm not going to join the general argument, because to many folk are arguing solely from their side of the fence... but just a thought about one point: > >>> The RAS structure >>> would have been proved wrong by several modeling >>> statistical methods had they been used to analyze it. > > Eisenberg's profile method indeed points up some dubious regions in Ras. Other > methods may do the same. But these are statistical methods, and many of us > are unlikely to invalidate our structures just because some statistical method > doesn't like our structure. Crystallographers are experimentalists, and we > like to look at electron density to figure out our structures, aided by > a pretty good implicit feel for unlikely features in protein structure. > True crystallographers are experimentalists. But think a bit - David (Eisenberg) is also a crystallographer... I understand you preferring to use the density - its what you know best, but that doesn't make these methods inappropriate or useless. The profile method you mentioned in a least part has its origin in a retracing error made in his lab. This lab has published structures since then, and of course they check them with their theorhetical methods! There are two good reasons for experimentalists to use these type of methods: 1. There are unbiased (ie., not favouring your favour theory about the structure!). Everyone will know the argument for this one. 2. The important thing, in my mind with all these types of methods, is to use them, get their results, THEN EXPLAIN WHY THOSE RESULTS WERE GOTTEN IN TERMS OF THE METHOD. It is "the explanation why" of any theorhetical method that bear fruit (well, at least in my opinon). If the technique is clearly being mislead in some way, you should be able to show that this is the case - then good for you. If on the other hand you find the method indicates the structure is likely to be unreasonable in some region - then also good you (hopefully you did this _before_ publication!) - you've avoided an embarassing mistake. If all looks well, then let it be - and it only took a few minutes of the months get the structure to check, so you might as well... Don't forget that in the former case (the method chosen is being mislead) - the _reason_ it is being mislead may be of interest, eg. unusual geometry, a hydrophobic site on the surface, etc. Given all the months you spend on a structure isn't a day or so of checking worth the effort?? Finally, you're all entitled to your own opinons! Grant (ghj@twizon.chmeds.ac.nz) From owner-proteins@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!dundee.ac.uk!pathol4 From: (k.c.breen@dundee.ac.uk) Newsgroups: bionet.molbio.proteins Subject: Research Studentship Followup-To: bionet.molbio.proteins Date: 6 Feb 1995 17:42:55 GMT Organization: The University, Dundee, DD1 4HN, Scotland, UK. Lines: 34 Distribution: world Message-ID: <3h5n2v$n7p@dux.dundee.ac.uk> NNTP-Posting-Host: pathol4.medschool.dundee.ac.uk POSTGRADUATE STUDENTSHIP IN PHARMACOLOGY Applications are invited for a postgraduate studentship, funded by the Association for International Cancer Research, in a multi-disciplinary neuroglycobiology laboratory located in the Department of Pharmacology, University of Dundee. The 3 year studentship will examine the molecular biology of glycosyltransferase enzymes and the functional results of their altered expression in tumor cell lines. Applications are invited from candidates who expect to gain a first or upper-second class degree and although experience in the techniques of molecular biology would be advantageous, training will be provided where necessary. Ninewells Hospital Medical School is situated on the Tay estuary and is surrounded by beautiful countryside which provides excellent opportunities for a variety of outdoor activities. The cost of living is one of the lowest, and the standard of living one of the highest in the U.K. Applications, in the form of a detailed CV with the names of two referees should be sent as soon as possible to Dr. Kieran Breen, Dept. of Pharmacology and Clinical Pharmacology, University of Dundee, Ninewells Hospital Medical School, Dundee DD1 9SY, Scotland, U.K. from whom further details may be obtained (tel. 01382-633900 ext. 2522; e-mail: k.c.breen@dundee.ac.uk). Kieran Breen, Dept. of Pharmacology, University of Dundee, Ninewells Hospital & Medical School, Dundee DD1 9SY,Scotland, U.K. k.c.breen@dundee.ac.uk From owner-proteins@net.bio.net Sun Feb 05 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!rutgers!rockyd!notes From: sali@tamika.rockefeller.edu (Andrej Sali) Subject: Re: HELP! Protein Graphics!! (yuck! this echoes even in bionet.software) X-Nntp-Posting-Host: tamika.rockefeller.edu Message-ID: Sender: notes@rockyd.rockefeller.edu (News Administrator) Organization: Rockefeller University References: <3gujs8$jun@lyra.csx.cam.ac.uk> Date: Tue, 7 Feb 1995 00:16:52 GMT Lines: 54 In article <3gujs8$jun@lyra.csx.cam.ac.uk> jhp20@cus.cam.ac.uk (Mikpf) writes: > > I think the point of making model should be discussed. If you are interested > in just looking at a 3D view of your molecule for any kind of visual que, even > 10% 20% homology of sequence is enough to build a model which can be > in a right shape in general. However, the problem is models are very very > useless if you want to go further than that. Even 90% sequence identity > can not assure you anything significantly on your experiment. In this case > it is better to rely on low quality X-ray structure than a high quality models. To be honest as a modeller, 10-20% sequence identity is generally not nearly enough to get you an even approximate shape of your protein because you simply cannot align your sequence with a known homolog when the sequence identity is that low (i.e. insignificant). The second part of your statement is an over-generalization. There are many kinds of experiment for which models based on 40% sequence identity are sufficient (e.g. Sali et al., J. Biol. Chem. 268, 9023-9034, 1993). In this paper, the question asked by Rick Stevens, a molecular biologist, was 'We believe that mast cell proteases interact with heparin. We do not want to do 100 mutations to find the binding site. Can you tell us which amino acid residues to mutate to confirm (or reject) the predicted location of the binding site?' Comparative modelling based on slightly less than 40% seq identity combined with electrostatic calculations predicted CORRECTLY 3 His residues important for interaction and 2 His residues that were not important for interaction (the paper with the experimental confirmation of the prediction is submitted). The modelling was done in a few days. So I hope that people will admit that there are applications where modeling can be useful for more than preparing nice color slides. > > Making fancy pictures which seem to be precise does not mean it can be > useful for experimentalist. In modelling, the problem is not how good your > model is, but to know how bad your model can be in the worst case. Model evaluation is part of any modeling by a serious modeller. There are many methods and programs that allow you to do this pretty well. > > So, models built with 40% sequence homology can easily be absolute garbage. Not easily if you know what you are doing and if you spent sufficient time doing it (a few days to a week). They can be garbage in exposed regions close to gaps in the alignment or in incorrectly aligned regions (but those are not many at such a high sequence identity). > > By the way, Modeller 12 is now available at ftp site in Harvard. > tammy.harvard.edu , it seems to deal with energy minimization better than > previous version. > Thanks. If you find problems doing what MODELLER is meant to do, I will be grateful if you email your complaints/suggestions/notes to me. It is only the second release ... I can understand that people are unhappy with modeling because of the unjustified claims made in the past. But please do not generalize this to all the modeling/modelers. Andrej From owner-proteins@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news2.near.net!news3.near.net!noc.near.net!saturn.caps.maine.edu!news.ycc.yale.edu!cadmium.csb.yale.edu!gardner From: gardner@cadmium.csb.yale.edu (Kevin Gardner) Newsgroups: bionet.molbio.proteins Subject: Re: HELP! Protein Graphics!! Sorry, No help available on that topic Date: 6 Feb 1995 15:26:05 GMT Organization: Yale University Lines: 34 Message-ID: <3h5f2d$db4@news.ycc.yale.edu> References: <3ggmdi$5j@mace.cc.purdue.edu> <1995Jan30.201542.18484@alw.nih.gov> <1995Feb3.193250.14418@alw.nih.gov> NNTP-Posting-Host: cadmium.csb.yale.edu X-Newsreader: TIN [version 1.2 PL2] John Kuszewski (johnk@spasm.niddk.nih.gov) wrote: : In article , phil@xtreme1.mskcc.org (Phil Jeffrey) writes: : |> In article <1995Jan30.201542.18484@alw.nih.gov> johnk@spasm.niddk.nih.gov (John Kuszewski) writes: : |> : |> >> are probably meaningless--look at calmodulin for an example of : |> >> how precise but wildly inaccurate a crystal structure can be. : |> : |> Or look at the tetramerization domain of p53 for an example of how : |> precise but wildly inaccurate an NMR structure can be (the NIH version). : |> : Well, the p53 fiasco was more of a misapplication of the NMR : information, rather than in inherent limitation of the method. : The calmodulin crystal structure's problems were caused by : the requirement for crystallization, which is of course inherent : to crystallography. Let's not omit the fact that a corrected version of the p53 tetramerization domain was determined by NMR (Lee et al., Nature Struct. Biol. 1(1994):877), thus backing John's point about the misapplication vs. limitations of NMR. Note that this article also indicates that an unpublished crystal structure agrees with this structure, so we can all have our cake and eat it too.... Kevin -- ************************************************************************* Kevin Gardner Yale University Dept. of Molecular Biophysics and Biochemistry Internet: gardner@zinc.csb.yale.edu Bitnet: gardner@yalemed ***I support the boycott of companies using mass Internet advertising*** From owner-proteins@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ratatosk.yggdrasil.com!news.duke.edu!godot.cc.duq.edu!hudson.lm.com!news.pop.psu.edu!news.cac.psu.edu!howland.reston.ans.net!lamarck.sura.net!darwin.sura.net!martha.utk.edu!drnelson.utmem.edu!user From: dnelson@utmem1.utmem.edu (David R. Nelson) Newsgroups: bionet.molbio.proteins Subject: Cytochrome P450 Web server Followup-To: bionet.molbio.proteins Date: 6 Feb 1995 22:44:54 GMT Organization: U. Tennessee, Memphis Lines: 21 Message-ID: NNTP-Posting-Host: drnelson.utmem.edu I am currently building a cytochrome P450 WWW server on my Mac. Currently it has two sequence alignments. The first file has 168 sequences and the second file has 150 additional sequences. These are all publically available sequences. The present alignment of all sequences (including confidential sequences) has over 400 sequences. The two files can be put together on a word processor to get a single alignment of 318 P450s. I will also be posting tables of accession numbers to the P450 sequences and bibilographic information for the entries that are new since the 1993 DNA and Cell Biology nomenclature paper appeared. For those who would like to look the URL address is http://drnelson.utmem.edu/homepage.html This name may be changed in the future, but it should be good for the next few weeks as I continue to put this server together. -- David R. Nelson Assistant Professor Dept. of Biochemistry University of Tennessee, Memphis From owner-proteins@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!pipex!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!dundee.ac.uk!pathol4 From: (k.c.breen@dundee.ac.uk) Newsgroups: bionet.molbio.proteins Subject: Research Studentship Followup-To: bionet.molbio.proteins Date: 6 Feb 1995 17:42:55 GMT Organization: The University, Dundee, DD1 4HN, Scotland, UK. Lines: 34 Distribution: world Message-ID: <3h5n2v$n7p@dux.dundee.ac.uk> NNTP-Posting-Host: pathol4.medschool.dundee.ac.uk POSTGRADUATE STUDENTSHIP IN PHARMACOLOGY Applications are invited for a postgraduate studentship, funded by the Association for International Cancer Research, in a multi-disciplinary neuroglycobiology laboratory located in the Department of Pharmacology, University of Dundee. The 3 year studentship will examine the molecular biology of glycosyltransferase enzymes and the functional results of their altered expression in tumor cell lines. Applications are invited from candidates who expect to gain a first or upper-second class degree and although experience in the techniques of molecular biology would be advantageous, training will be provided where necessary. Ninewells Hospital Medical School is situated on the Tay estuary and is surrounded by beautiful countryside which provides excellent opportunities for a variety of outdoor activities. The cost of living is one of the lowest, and the standard of living one of the highest in the U.K. Applications, in the form of a detailed CV with the names of two referees should be sent as soon as possible to Dr. Kieran Breen, Dept. of Pharmacology and Clinical Pharmacology, University of Dundee, Ninewells Hospital Medical School, Dundee DD1 9SY, Scotland, U.K. from whom further details may be obtained (tel. 01382-633900 ext. 2522; e-mail: k.c.breen@dundee.ac.uk). Kieran Breen, Dept. of Pharmacology, University of Dundee, Ninewells Hospital & Medical School, Dundee DD1 9SY,Scotland, U.K. k.c.breen@dundee.ac.uk From owner-proteins@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!ceres.fokus.gmd.de!nntp.gmd.de!dearn!barilvm!vms.huji.ac.il!marder Newsgroups: bionet.molbio.proteins Subject: Re: anomalous protein migration SDS-PAGE Message-ID: <1995Feb7.153237.1106@vms.huji.ac.il> From: MARDER@agri.huji.ac.il (Jonathan B. Marder) Date: Tue, 07 Feb 95 13:33:08 GMT References: <3g8d31$t46@israel-info.datasrv.co.il> <1995Jan27.132847.1012@vms.huji.ac.il> <3gbu8s$ghh@vixen.cso.uiuc.edu> Distribution: world Organization: Hebrew University Nntp-Posting-Host: marder.agri.huji.ac.il X-Newsreader: News Xpress Version 1.0 Beta #2.1 Lines: 33 elarson@ux1.cso.uiuc.edu (larson eric) wrote: >MARDER@agri.huji.ac.il (Jonathan B. Marder) writes: > >>lenny@zeus.datasrv.co.il (Lenny Garfinkel) wrote: >>>... I see an apparent >>>INCREASE in molecular weight on SDS-PAGE in the presence of >>>mercaptoethanol (yup, it runs slower). What sort of protein >>>modifications could cause this? Could clipping of a few residues result >>>in less SDS binding? >>> >>Yes, especially if you chop off a bit of positively charged sequence >>======== > >Actually, and I hate to sound like a contrarian, but it's very likely the >slower migration is caused by a cleavage of hydrophobic residues. > Actually, my statement about charge is from experience. Phosphorylation seems to cause a slower migration (true for PSII reaction center proteins). I've also seen consistent results via manipulation of acidic vs. basic residues via point mutation of these proteins. Conclusion is that positive charge increases mobility. Very likely, what you write about hydrophobicity is also true. It is generally true that hydrophobic polypeptides have higher mobilities than hydrophilic polypeptides of the same size. __ Jonathan B. Marder ' Department of Agricultural Botany | Internet: MARDER@agri.huji.ac.il The Hebrew University of Jerusalem | /\/ Faculty of Agriculture |/ \ Phone: (08 or +9728) 481918 P.O.Box 12, Rehovot 76100, ISRAEL / Fax: (08 or +9728) 467763 From owner-proteins@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!u-psud.fr!zaphod.crihan.fr!news.univ-rennes1.fr!irisa.fr!news2.EUnet.fr!EU.net!howland.reston.ans.net!usc!usc!not-for-mail From: william@neuro.usc.edu (Fiberman) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: TCA precipitation Date: 7 Feb 1995 13:46:59 -0800 Organization: University of Southern California, Los Angeles, CA Lines: 11 Sender: william@neuro.usc.edu Message-ID: <3h8poj$bkm@neuro.usc.edu> NNTP-Posting-Host: neuro.usc.edu Xref: biosci bionet.molbio.methds-reagnts:24175 bionet.molbio.proteins:3681 Hello Netters, I am doing a pulse-chase experiment by labelling with 35-S-Met. As I recall, after getting the protein out of the cell, I should precipitate with TCA before putting onto the filter and washing and counting. What is the standard protocol for TCA precipitation of proteins? Thanks for your help. -fm From owner-proteins@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ratatosk.yggdrasil.com!news.duke.edu!godot.cc.duq.edu!newsfeed.pitt.edu!gatech!howland.reston.ans.net!news2.near.net!news3.near.net!noc.near.net!saturn.caps.maine.edu!news.ycc.yale.edu!cadmium.csb.yale.edu!gardner From: gardner@cadmium.csb.yale.edu (Kevin Gardner) Newsgroups: bionet.molbio.proteins Subject: Re: HELP! Protein Graphics!! Sorry, No help available on that topic Date: 6 Feb 1995 15:26:05 GMT Organization: Yale University Lines: 34 Message-ID: <3h5f2d$db4@news.ycc.yale.edu> References: <3ggmdi$5j@mace.cc.purdue.edu> <1995Jan30.201542.18484@alw.nih.gov> <1995Feb3.193250.14418@alw.nih.gov> NNTP-Posting-Host: cadmium.csb.yale.edu X-Newsreader: TIN [version 1.2 PL2] John Kuszewski (johnk@spasm.niddk.nih.gov) wrote: : In article , phil@xtreme1.mskcc.org (Phil Jeffrey) writes: : |> In article <1995Jan30.201542.18484@alw.nih.gov> johnk@spasm.niddk.nih.gov (John Kuszewski) writes: : |> : |> >> are probably meaningless--look at calmodulin for an example of : |> >> how precise but wildly inaccurate a crystal structure can be. : |> : |> Or look at the tetramerization domain of p53 for an example of how : |> precise but wildly inaccurate an NMR structure can be (the NIH version). : |> : Well, the p53 fiasco was more of a misapplication of the NMR : information, rather than in inherent limitation of the method. : The calmodulin crystal structure's problems were caused by : the requirement for crystallization, which is of course inherent : to crystallography. Let's not omit the fact that a corrected version of the p53 tetramerization domain was determined by NMR (Lee et al., Nature Struct. Biol. 1(1994):877), thus backing John's point about the misapplication vs. limitations of NMR. Note that this article also indicates that an unpublished crystal structure agrees with this structure, so we can all have our cake and eat it too.... Kevin -- ************************************************************************* Kevin Gardner Yale University Dept. of Molecular Biophysics and Biochemistry Internet: gardner@zinc.csb.yale.edu Bitnet: gardner@yalemed ***I support the boycott of companies using mass Internet advertising*** From owner-proteins@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!gatech!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!biochem.dental.upenn.edu!ellis From: ellis@biochem.dental.upenn.edu (Ellis Golub) Newsgroups: bionet.molbio.proteins Subject: Re: SDS-PAGE of 32P labelled protein Date: 7 Feb 1995 16:55:39 GMT Organization: University of Pennsylvania Lines: 27 Distribution: world Message-ID: <3h88mb$2gb@netnews.upenn.edu> References: NNTP-Posting-Host: biochem.dental.upenn.edu In article , williel@uclink3.berkeley.edu (Simon Penson) writes: |> I'm going to need to run some SDS-PAGE gels of proteins which have been |> incubated with 32P-ATP. How can I remove the excess (ie uncomsumed) ATP |> from the reaction m,ixture prior to electrophoresis? TCA ppt has been |> suggested, as has spin-desalting. |> An old fashioned, but cheap and effective way to remove nucleotides from solution is to adsorb them onto activated charcoal. That will remove the ATP, but any 32Pi will be left in solution. Hope this helps Ellis Golub -- ============================================================================== Ellis Golub Phone: (215) 898-4629 Biochemistry Department FAX: (215) 898-3695 University of Pennsylvania ellis@biochem.dental.upenn.edu School of Dental Medicine 4001 Spruce Street Philadelphia, PA 19104-6003 =============================================================================== From owner-proteins@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!newsserver.jvnc.net!synapse.bms.com!synapse.bms.com!krystek From: krystek@alcor.bms.com (Stanley Krystek) Newsgroups: bionet.molbio.proteins Subject: Re: HELP!!! Protein Graphics!! Date: 07 Feb 1995 15:51:03 GMT Organization: Bristol-Myers Squibb, Macromolecular Modeling Lines: 32 Distribution: world Message-ID: References: <3g18fo$no3@bigblue.oit.unc.edu> <1995Jan24.173624.8430@alw.nih.gov> <3g4ku9$83s@news.iastate.edu> <3g5b3v$r68@lyra.csx.cam.ac.uk> <3g6k7d$13uk@columba.udac.uu.se> <3g8f7c$8hv@lyra.csx.cam.ac.uk> <3gc2l3$120o@columba.udac.uu.se> <3gejgo$blo@senator-bedfellow.MIT.EDU> NNTP-Posting-Host: alcor.bms.com In-reply-to: phil@xtreme1.mskcc.org's message of 1 Feb 95 17:28:03 Hey Phil I know you don't think too much about us modelers....and I agree that some of the modelers out there make far too much about the model accuracy and may overstate the uses...... But is there no good word you can say about modeling....and don't you think that homology modeling has reached a significant level of accuracy and such models are useful for hypothesis generation in the absence of NMR or x-ray structures. After all, sometimes we get the right answers for the worng reasons...but the bottom line is that we have the answer....a new hypothesis, a drug or understanding of protein function when there are no other options because structures for most proteins are not yet available. I think modelers have to explicitly quailfy the results of the modeling, but sometimes one of us is able to get the model qualitatively correct and that may be enough to guide drug design efforts or SAR studies. Hey on a personal note how are you doing up there?!! see ya! stan . -- Stan Krystek Bristol-Myers Squibb krystek@bms.com From owner-proteins@net.bio.net Mon Feb 06 22:00:00 1995 Newsgroups: bionet.molbio.proteins Path: biosci!galaxy.ucr.edu!ratatosk.yggdrasil.com!news.duke.edu!godot.cc.duq.edu!hudson.lm.com!news.pop.psu.edu!news.cac.psu.edu!howland.reston.ans.net!gatech!rutgers!rockyd!notes From: sali@tamika.rockefeller.edu (Andrej Sali) Subject: Re: HELP! Protein Graphics!! (yuck! this echoes even in bionet.software) X-Nntp-Posting-Host: tamika.rockefeller.edu Message-ID: Sender: notes@rockyd.rockefeller.edu (News Administrator) Organization: Rockefeller University References: <3gujs8$jun@lyra.csx.cam.ac.uk> Date: Tue, 7 Feb 1995 00:16:52 GMT Lines: 54 In article <3gujs8$jun@lyra.csx.cam.ac.uk> jhp20@cus.cam.ac.uk (Mikpf) writes: > > I think the point of making model should be discussed. If you are interested > in just looking at a 3D view of your molecule for any kind of visual que, even > 10% 20% homology of sequence is enough to build a model which can be > in a right shape in general. However, the problem is models are very very > useless if you want to go further than that. Even 90% sequence identity > can not assure you anything significantly on your experiment. In this case > it is better to rely on low quality X-ray structure than a high quality models. To be honest as a modeller, 10-20% sequence identity is generally not nearly enough to get you an even approximate shape of your protein because you simply cannot align your sequence with a known homolog when the sequence identity is that low (i.e. insignificant). The second part of your statement is an over-generalization. There are many kinds of experiment for which models based on 40% sequence identity are sufficient (e.g. Sali et al., J. Biol. Chem. 268, 9023-9034, 1993). In this paper, the question asked by Rick Stevens, a molecular biologist, was 'We believe that mast cell proteases interact with heparin. We do not want to do 100 mutations to find the binding site. Can you tell us which amino acid residues to mutate to confirm (or reject) the predicted location of the binding site?' Comparative modelling based on slightly less than 40% seq identity combined with electrostatic calculations predicted CORRECTLY 3 His residues important for interaction and 2 His residues that were not important for interaction (the paper with the experimental confirmation of the prediction is submitted). The modelling was done in a few days. So I hope that people will admit that there are applications where modeling can be useful for more than preparing nice color slides. > > Making fancy pictures which seem to be precise does not mean it can be > useful for experimentalist. In modelling, the problem is not how good your > model is, but to know how bad your model can be in the worst case. Model evaluation is part of any modeling by a serious modeller. There are many methods and programs that allow you to do this pretty well. > > So, models built with 40% sequence homology can easily be absolute garbage. Not easily if you know what you are doing and if you spent sufficient time doing it (a few days to a week). They can be garbage in exposed regions close to gaps in the alignment or in incorrectly aligned regions (but those are not many at such a high sequence identity). > > By the way, Modeller 12 is now available at ftp site in Harvard. > tammy.harvard.edu , it seems to deal with energy minimization better than > previous version. > Thanks. If you find problems doing what MODELLER is meant to do, I will be grateful if you email your complaints/suggestions/notes to me. It is only the second release ... I can understand that people are unhappy with modeling because of the unjustified claims made in the past. But please do not generalize this to all the modeling/modelers. Andrej From owner-proteins@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news2.near.net!cat.cis.Brown.EDU!poncho-slip7.cis.brown.edu!user From: Stephen_Lasky@brown.edu (Stephen R. Lasky, Ph.D.) Newsgroups: bionet.molbio.proteins Subject: Re: SDS-PAGE of 32P labelled protein Date: 7 Feb 1995 15:19:50 GMT Organization: Roger Williams Hospital/Brown U. Lines: 35 Message-ID: References: NNTP-Posting-Host: poncho-slip7.cis.brown.edu In article , butler@soma.UMDNJ.EDU (Gary Butler) wrote: > williel@uclink3.berkeley.edu (Simon Penson) writes: > > >I'm going to need to run some SDS-PAGE gels of proteins which have been > >incubated with 32P-ATP. How can I remove the excess (ie uncomsumed) ATP > >from the reaction m,ixture prior to electrophoresis? TCA ppt has been > >suggested, as has spin-desalting. > > >Any comments/advice gratefully recieved. > > >Simon. > >Simon Penson > >Plant Biology Dept > >UC Berkeley > > In order of simplicity and usefullness, my suggestions follow: > > 1.) Why do you need to? Most of the ATP should migrate a lot faster, and > could be eluted into the anode tray while the protein's still on the gel, > and if any remains in the gel, it may come out with soaking in stain/fix. This is the key: Why bother removing it? You get a hot lower gel tank and buffer, but you're going to get that anyway. SRLasky -- ********************************************************************* Stephen R. Lasky, Ph.D. Roger Williams Medical Center/Brown University Phone: 401-456-6572 Fax: 401-456-6569 e-mail: Stephen_Lasky@brown.edu ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ "The speed of a computer is inversly proportional to the legnth of time it has been on your desk." Michael Yablonski, circa 1989 ********************************************************************* From owner-proteins@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!agate!uclink2.berkeley.edu!rudeboy From: rudeboy@uclink2.berkeley.edu (Edward Elliot Graves) Newsgroups: bionet.molbio.proteins Subject: Amino acid databases? Date: 7 Feb 1995 21:20:24 GMT Organization: University of California, Berkeley Lines: 10 Message-ID: <3h8o6o$k2n@agate.berkeley.edu> NNTP-Posting-Host: uclink2.berkeley.edu Hello all. I am looking for a database that includes information (particularly thermodynamic data) for L alpha amino acids. As I am not quite familiar with Archie I was wondering if someone could direct me towards an anonymous ftp site where I could finds such data. Thanks in advance! Ted Graves rudeboy@uclink2.berkeley.edu From owner-proteins@net.bio.net Tue Feb 07 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!panix!cmcl2!yale.edu!news.ycc.yale.edu!NewsWatcher!user From: johnson_lab@qm.yale.edu (Wang Min) Newsgroups: bionet.molbio.proteins Subject: Re: myristoylation Date: 8 Feb 1995 22:45:26 GMT Organization: Yale Medical School Lines: 16 Distribution: bionet Message-ID: References: <3gt042$61l@mserv1.dl.ac.uk> NNTP-Posting-Host: 130.132.212.19 In article <3gt042$61l@mserv1.dl.ac.uk>, Mohamed SAAD ESRF BP 220 38043 GRENOBLE CEDEX wrote: > bonjour, > > does anyone knows what N-myristoylation site in a proteine is ? > this was predicted by the prosite search for a new peptide sequence > I have submitted. > > any reference is welcom > > Thanks for your help, Mohamed SAAD. The consensus sequence for myristoylation is MGXXXS at N-terminal of a protein. Some proteins may be myristoylated at internal lys site but very rare. Wang Min. From owner-proteins@net.bio.net Tue Feb 07 22:00:00 1995 Path: biosci!MOL.F.U-TOKYO.AC.JP!akiyama From: akiyama@MOL.F.U-TOKYO.AC.JP Newsgroups: bionet.molbio.proteins Subject: Dissociation of multimeric proteins Date: 8 Feb 1995 19:11:13 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502090311.MAA08191@mol.f.u-tokyo.ac.jp> NNTP-Posting-Host: net.bio.net Hello. This is the first time for me to send a message to bio.net. I study about an enzyme. This enzyme acts as a homodimer. I want to make heterodimers of native and recombinant monomers made by site-directed mutagenesis. Please teach me general methods to dissociate and re-associate multimeric proteins or books or reviews about them. (I will be much pleased if someone teach me Japanese books.) From owner-proteins@net.bio.net Tue Feb 07 22:00:00 1995 Path: biosci!ARSERRC.GOV!CTHOMPSON From: CTHOMPSON@ARSERRC.GOV Newsgroups: bionet.molbio.proteins Subject: BSA Date: 8 Feb 1995 14:09:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HMTBP56A9U000A4W@arserrc.gov> NNTP-Posting-Host: net.bio.net Can anyone point me in the right direction on where to find the amino acid composition of BSA. I'm looking to find the tyrosine composition. From owner-proteins@net.bio.net Tue Feb 07 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!lamarck.sura.net!ra.nrl.navy.mil!news.pop.psu.edu!news.cac.psu.edu!newsserver.jvnc.net!phunn1.sb.com!NewsWatcher!user From: Prichett%PHVAX.dnet@SB.COM (William P. Prichett) Newsgroups: bionet.molbio.proteins Subject: Re: SDS-PAGE of 32P labelled protein Followup-To: bionet.molbio.proteins Date: 8 Feb 1995 17:33:33 GMT Organization: SmithKline Beecham Pharmacueticals Lines: 19 Message-ID: References: NNTP-Posting-Host: 139.136.69.95 With regard to removing un incorperated 32P-ATP. I would not. You will have to be concerned with recovering of sample regardlous of what ever manipulation is used. 32P-ATP will run in the dye front of the gel. Run the gel and when the plates are opened use a scapel knife or other object to cut of the very bottom of the gel. this will minimze waste volume and it can quickly be dried to solid dry waste. There will be minimal chance of spilling if it is not allowed to run into the buffer. In article , butler@soma.UMDNJ.EDU (Gary Butler) wrote: > williel@uclink3.berkeley.edu (Simon Penson) writes: > > >I'm going to need to run some SDS-PAGE gels of proteins which have been > >incubated with 32P-ATP. How can I remove the excess (ie uncomsumed) ATP > >from the reaction m,ixture prior to electrophoresis? TCA ppt has been > >suggested, as has spin-desalting. > > From owner-proteins@net.bio.net Tue Feb 07 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: SDS-PAGE of 32P labelled protein Date: 8 Feb 1995 11:54:58 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 27 Message-ID: <3habei$1id3@sat.ipp-garching.mpg.de> References: NNTP-Posting-Host: alf2.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] Stephen R. Lasky, Ph.D. (Stephen_Lasky@brown.edu) wrote: > In article , butler@soma.UMDNJ.EDU (Gary Butler) wrote: > > williel@uclink3.berkeley.edu (Simon Penson) writes: > > > > >I'm going to need to run some SDS-PAGE gels of proteins which have been > > >incubated with 32P-ATP. How can I remove the excess (ie uncomsumed) ATP > > >from the reaction m,ixture prior to electrophoresis? TCA ppt has been > > >suggested, as has spin-desalting. > > > > Why do you need to? Most of the ATP should migrate a lot faster, and > > could be eluted into the anode tray while the protein's still on the gel, > > and if any remains in the gel, it may come out with soaking in stain/fix. > This is the key: Why bother removing it? You get a hot lower gel tank > and buffer, but you're going to get that anyway. Even better, don't let the gel run until the end, cut off the running front which contains the hot ATP and discard it, and your buffers and tanks won't be contaminated :-) --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "Science is the game you play with God to find out what His rules are." */ From owner-proteins@net.bio.net Tue Feb 07 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!newsfeed.pitt.edu!godot.cc.duq.edu!news.duke.edu!usenet From: mbt@acpub.duke.edu (mb) Newsgroups: bionet.molbio.proteins Subject: Re: BSA Date: 9 Feb 1995 01:40:01 GMT Organization: Your Organization Lines: 10 Message-ID: <3hbrph$d2o@news.duke.edu> References: <01HMTBP56A9U000A4W@arserrc.gov> NNTP-Posting-Host: mbatduml.ml.duke.edu X-Newsreader: WinVN 0.92.6+ In article <01HMTBP56A9U000A4W@arserrc.gov>, CTHOMPSON@ARSERRC.GOV says: > >Can anyone point me in the right direction on where to find the amino >acid composition of BSA. I'm looking to find the tyrosine composition. There is a nice review on BSA by Carter and Ho in Advances in Protein Chemistry (1994) 45: 153-203. Among other things it has a table with the amino acid sequence of human, bovine, equine, ovine, rat, frog and salmon albumin. From owner-proteins@net.bio.net Tue Feb 07 22:00:00 1995 Path: biosci!MOL.F.U-TOKYO.AC.JP!akiyama From: akiyama@MOL.F.U-TOKYO.AC.JP Newsgroups: bionet.molbio.proteins Subject: Expression of bigger protein than expected in E. coli Date: 8 Feb 1995 19:27:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502090327.MAA08204@mol.f.u-tokyo.ac.jp> NNTP-Posting-Host: net.bio.net Has anyone ever experienced the production of bigger polypeptide than expected while expressing protein in E. coli ? I expressed a plant enzyme in E. coli using pET system. I ligated my cDNA into the vector pET-3d just at the point of initiation codon, but E. coli horboring this plasmid produced two different polypeptide. They differ in size by about 1-2 kDa. Both react to the antibody against the original plant protein. First, I thought this was caused by protease (i.e. the bigger one is the native form). But I found that the "smaller" one has catalytic activity and the "bigger" doesn't. Now I assume the presence of additional unexpected amino acid sequence before the N-terminus or after the C-terminus. Has anyone encountered or heard of such situation ? If you have, please give me a good advise. (I am going to determine the N-terminal amino acid sequence of both polypeptide in the near future.) From owner-proteins@net.bio.net Wed Feb 08 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!uunet!world!decwrl!waikato!agresearch.cri.nz!napierj From: napierj@agresearch.cri.nz (Jim Napier) Newsgroups: bionet.molbio.proteins Subject: IGF tracers on PAGE Date: Fri, 10 Feb 1995 14:41:25 Organization: AgResearch Lines: 8 Message-ID: NNTP-Posting-Host: 160.4.128.51 X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Can anyone give info on apparent molecular weights for IGF tracers, and how to fix to nitrocellulose membrane after non-reducing 15% PAGE. We seem to find evidence of increases in apparent MW of both tracers and cold IGFs. Tracer was loaded either directly onto gel in 40%EtOH in 0.01N HCL/0.9% saline, or after evaporating off the EtOH, with same result. From owner-proteins@net.bio.net Wed Feb 08 22:00:00 1995 Path: biosci!rutgers!gatech!newsxfer.itd.umich.edu!jobone!lynx.unm.edu!carina!inkim From: inkim@carina.unm.edu (In C. Kim) Newsgroups: bionet.molbio.proteins Subject: Heat Shock Proteins? Date: 9 Feb 1995 16:57:39 GMT Organization: University of New Mexico, Albuquerque Lines: 8 Message-ID: <3hdhi3$5d0@lynx.unm.edu> NNTP-Posting-Host: carina.unm.edu X-Newsreader: TIN [version 1.2 PL2] Hi all, It appears that heat shock proteins are quite popular proteins. I did not catch up with these stuffs. I wonder somebody could summarize the biological significance of these proteins. I also wonder microorganisms have these proteins. --In C. Kim From owner-proteins@net.bio.net Wed Feb 08 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!ux1.cso.uiuc.edu!brazelto From: brazelto@ux1.cso.uiuc.edu (brazelton anthony d) Newsgroups: bionet.molbio.proteins Subject: IgG purification Date: 9 Feb 1995 21:36:05 GMT Organization: University of Illinois at Urbana Lines: 13 Message-ID: <3he1s5$16o@vixen.cso.uiuc.edu> NNTP-Posting-Host: ux1.cso.uiuc.edu Any preferences on which beads to buy (and from whom?) for Protein A column IgG purification? tony Anthony D. Brazelton Neuronal Pattern Analysis Beckman Institute University of Illinois 61801 From owner-proteins@net.bio.net Wed Feb 08 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!EU.net!ub4b!idefix.CS.kuleuven.ac.be!infoserv.rug.ac.be!news From: Dirk.Vandenberghe@rug.ac.be Newsgroups: bionet.molbio.proteins Subject: PHARMACEUTICAL BIOTECHNOLOGY Date: 9 Feb 1995 12:47:56 GMT Organization: Pharmaceutical Biotech Lines: 49 Distribution: world Message-ID: <3hd2ts$3hc@infoserv.rug.ac.be> NNTP-Posting-Host: farmbiot.rug.ac.be Keywords: biotechnology X-Newsreader: FINAL CALL FOR PAPERS **************************************************************************** *** The 2nd International Pharmaceutical Biotechnology Conference *** **************************************************************************** APRIL, 23 - 27 1995 GHENT, BELGIUM, EUROPE Main topics : Gene Therapy, Vaccines and Monoclonal Antibodies, Drug Delivery Systems, Modification of Plants, Drug Design, Biotechnology in the Treatment of Cancer, Pharmacoeconomics, Human Genome Project, ...... INVITED SPEAKERS: A. Angiuoli (USA) H. Galjaard (NL) H. Moereels (Belgium) G. Bleeker (USA) D. Crommelin (NL) M. Mareel (Belgium) D. Brixner (USA) W. Gibbons (UK) M. Soria (Italy) T. Blundell (UK) J. De Muth (USA) T. Osslund (USA) N. Burnette (USA) L. Hansen (USA) J-P. Osselaere (Belgium) R. Braeckman (USA) W. Fiers (Belgium) H. Robays (Belgium) S. Cohen (USA) I. Hart (UK) M. Van Montagu (Belgium) J. Chamberlain (USA) D. Heyd (Israel) K. Seamon (USA) R. Dobbelaere (Belgium)Ph. Johnson (USA) G. Reeder (USA) J. Cooke (UK) S. Huber (USA) N. Spurr (UK) President: Prof. Dr. E. Van den Eeckhout University of Ghent FFW Harelbekestraat 72 Tel: 32 9 221 99 43 B-9000 GENT Fax: 32 9 220 66 88 BELGIUM, EUROPE !!! Send your mailing (not E-mail) address to Dirk.Vandenberghe@rug.ac.be if you want your name on our mailing list for more information and registration forms, and let me know if you are interested in : # poster session / abstract. # joining the International Association for Pharmaceutical Biotechnology. # exhibitor space (industrial forum). # pre / post - conference tours to beautiful cities in Europe. Dirk Vandenberghe Secretary IAPB University of Ghent Laboratory of Pharmaceutical Biotechnology From owner-proteins@net.bio.net Wed Feb 08 22:00:00 1995 Path: biosci!agate!news.ucdavis.edu!csus.edu!news.starnet.net!wupost!nic.smsu.edu!newsdist.tc.umn.edu!mayonews.mayo.edu!smithrd From: smithrd@bubba.mayo.edu (Reginald Smith) Newsgroups: bionet.molbio.proteins Subject: Re: HPLC Assay Question Date: 8 Feb 1995 18:43:27 GMT Organization: Mayo Foundation Lines: 27 Message-ID: <3hb3cf$e86@fermat.mayo.edu> References: NNTP-Posting-Host: bubba.mayo.edu X-newsreader: xrn 7.01-beta-12 (Motif) In article , cjhixon@netcom.com (Carl Hixon) writes: |> Does anybody know of literature regarding measuring Human Albumin and |> Fibrinogen concentration using HPLC? Secondly, I have a protein |> suspension containing small protein particles (few microns in diameter) |> These particles are constructed of Albumin and Fibrinogen. Would it be |> possible to determine the protein concentration of this type of |> suspension using HPLC by digesting the particles? I worry about the |> different sizes of the protein fragments. If anybody has literature |> regarding these issues please forward the references. Thank you! |> |> Carl If the fibrinogen is accessible to thrombin, you could treat aliquots of the solution/suspension with thrombin and measure the liberated fibrinopeptides by C-18 reverse phase HPLC. I have not done human fibrinopeptides but porcine and bovine work well if the gradient is started at 5% AcN and ramped up to 50% at about 1%/min. -- -Reggie +-------------------------------------------------+ Reginald Smith Mayo Graduate School smithrd@bubba.mayo.edu 200 1st street SW (507) 284-8275 Rochester MN, 55905 +-------------------------------------------------+ From owner-proteins@net.bio.net Wed Feb 08 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.cac.psu.edu!ppp118.cac.psu.edu!axc19 From: axc19@psu.edu (Aida Cancel) Newsgroups: bionet.molbio.proteins Subject: phosphorylation Date: Fri, 10 Feb 1995 01:30:23 GMT Organization: CAC Lines: 16 Message-ID: NNTP-Posting-Host: ppp118.cac.psu.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] Can anyone suggest a method to determine protein phosphorylation in Western blots or 2D SDS=PAGE. I am working with an acidic protein mw 55 pI 4.6-4.8. I know that this protein is highly phosphorylated and glycosylated in other tissues..but the amount of modification varies within species and tissue.When I do Western blots or affinity purification I can detect different molecular weights of what appears to be the same protein (other papers have been published that support this idea...and I am using three different antibodies to the recombinant protein amino and carboxy terminus). I tried tissue culture to determine where was this protein being made...that would allow me to use P-32 and determine phosphorylation of this protein..this did not work because I couldn't find this protein. Right now this is getting to the bottom of my patience...please, anyone out there with good suggestions..will be greatly appreciated. Aida axc19@psu.edu From owner-proteins@net.bio.net Thu Feb 09 22:00:00 1995 Path: biosci!ZOOL.UMD.EDU!GOODE From: GOODE@ZOOL.UMD.EDU ("Dennis Goode") Newsgroups: bionet.molbio.proteins Subject: Re: phosphorylation Date: 10 Feb 1995 15:03:59 -0800 Organization: University of Maryland Zoology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <23C4DE3184F@zool.umd.edu> NNTP-Posting-Host: net.bio.net axc19@psu.edu (Aida Cancel) on Fri, 10 Feb 1995 01:30:23 GMT asked: > Can anyone suggest a method to determine protein phosphorylation in Western > blots or 2D SDS=PAGE. I am working with an acidic protein mw 55 pI 4.6-4.8. > I know that this protein is highly phosphorylated and glycosylated in other > tissues..but the amount of modification varies within species and tissue.When > I do Western blots or affinity purification I can detect different molecular > weights of what appears to be the same protein (other papers have been > published that support this idea...and I am using three different antibodies > to the recombinant protein amino and carboxy terminus). I tried tissue > culture to determine where was this protein being made...that would allow me > to use P-32 and determine phosphorylation of this protein..this did not work > because I couldn't find this protein. Right now this is getting to the bottom > of my patience...please, anyone out there with good suggestions..will be > greatly appreciated. > > Aida > axc19@psu.edu > Aida: Have you tried P32 labeling your cells, homogenizing, centrifuging and immunoprecipitating your protein in the cold in the presence of every protease inhibitor you can get your hands on ( pepstatin, leupeptin, PMSF, etc), then running your immunoprecipitates on SDS-PAGE and detecting with ARG? It works well for us with kinesin but requires at least 4 confluent T75 flasks of cells for every treatment group. -Dennis From owner-proteins@net.bio.net Thu Feb 09 22:00:00 1995 Path: biosci!CAT.CCE.USP.BR!mvainzof From: mvainzof@CAT.CCE.USP.BR (Mariz Vainzof) Newsgroups: bionet.molbio.proteins Subject: Calpain determination Date: 10 Feb 1995 05:08:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502101310.AA23296@cat.cce.usp.br> NNTP-Posting-Host: net.bio.net Hello all, I am looking for a methodology for calpain determination on blood and tissue (muscle) extracts. Thanks Mariz Vainzof mvainzof@cat.cce.usp.br Fro