From sticher from bioc.uzh.ch Fri Aug 14 09:33:37 2009 From: sticher from bioc.uzh.ch (Patrick Sticher) Date: Fri Aug 14 10:49:25 2009 Subject: [Protein-analysis] Practical Course in Biomolecular Modelling Message-ID: <4A8575C1.7010909@bioc.uzh.ch> Dear colleagues, please be informed that online applications are accepted for the following course: 8TH NCCR PRACTICAL COURSE IN BIOMOLECULAR MODELLING January 10 - 15, 2010 Kandersteg, Switzerland http://www.structuralbiology.uzh.ch/course2010.asp Course topics include Simulation techniques, force-field development, conformational search, computation of free energy and entropy, treatment of electrostatic forces, simulation of folding, comparison of simulation with experiment This course is primarily directed to PhD students and postdocs from experimental structural biology groups wishing to learn more on biomolecular modelling. The course format will include morning lectures and late-afternoon/early evening tutorials, and provide ample opportunities for discussions with experts and fellow participants. Participants will be invited to bring own problems for tutorials and/or discussion. The course will be organized as a winter retreat in the Swiss Alps offering a stimulating learning atmosphere with the afternoons available for informal participation in discussions, reading and self-study or recreational activities in the area. Interested candidates are encouraged to apply online on http://www.structuralbiology.uzh.ch/course2010_application.asp. Application deadline will be October 16, 2010. We will be able to accept 20 participants to this course. Best regards, Patrick Sticher -- _________________________________ Visit the NCCR on the Internet www.structuralbiology.uzh.ch Dr. Patrick Sticher Moser NCCR Scientific Officer Institute of Biochemistry University of Z?rich Winterthurerstrasse 190 CH - 8057 Z?rich Phone +41 / (0)44 / 635 54 84 Fax +41 / (0)44 / 635 59 08 Mail sticher@bioc.uzh.ch From Laura.Oesterle from ARS.USDA.GOV Mon Aug 17 15:58:58 2009 From: Laura.Oesterle from ARS.USDA.GOV (Oesterle, Laura) Date: Mon Aug 17 17:44:33 2009 Subject: [Protein-analysis] Help: Manual for Speed Vac Concentrator SVC-100H Message-ID: Dear Jim, I realize your posting was over 3 years ago, but... for others with this need too. I just talked to John Olson at GMI (763-712-8717 USA), a distributer for Savant items (mostly used), and he had an in-house version of of the manual he could send you via an e-mail attachment. His e-mail is jolson@gmi-inc.com. The biggest reason speed vacs stop working, in terms of evaporative power, is due to dirty pump oil. Get a gauge and check the amount of vacuum it really provides. Or, more pragmatically, just change your vac pump oil. Yah, it's a pain. If you have something more volatile than water to evaporate, get dry ice onto your cold trap to get the vapor coming off of your sample into liquid phase so you can drive more vapor off of you sample. Good Luck, Laura From gayers07 from cogeco.ca Sun Aug 23 17:27:49 2009 From: gayers07 from cogeco.ca (gord) Date: Sun Aug 23 18:11:41 2009 Subject: [Protein-analysis] protein biosynthesis Message-ID: Hello All I would like to know to which end of the elongating protein chain, during biosysnthesis, is the next amino acid attached. Amino or carboxyl. Thank you. Gord From DBienvenue from vlstcorp.com Mon Aug 24 12:36:04 2009 From: DBienvenue from vlstcorp.com (David Bienvenue) Date: Mon Aug 24 15:03:09 2009 Subject: [Protein-analysis] RE: Protein biosynthesis In-Reply-To: <200908241704.n7OH4Tp22430@net.bio.net> References: <200908241704.n7OH4Tp22430@net.bio.net> Message-ID: <31DC70432F629F4CA4E593E98373B59B2162DD5CA2@VLSTMAIL1.vlstcorp.loc> Protein biosynthesis starts at the N-terminus. David Bienvenue, Ph.D. Senior Principal Scientist VLST Corporation Seattle, WA 98109 -----Original Message----- From: proteins-bounces@oat.bio.indiana.edu [mailto:proteins-bounces@oat.bio.indiana.edu] On Behalf Of proteins-request@oat.bio.indiana.edu Sent: Monday, August 24, 2009 10:04 AM To: proteins@magpie.bio.indiana.edu Subject: Proteins Digest, Vol 51, Issue 3 Send Proteins mailing list submissions to proteins@net.bio.net To subscribe or unsubscribe via the World Wide Web, visit http://www.bio.net/biomail/listinfo/proteins or, via email, send a message with subject or body 'help' to proteins-request@net.bio.net You can reach the person managing the list at proteins-owner@net.bio.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Proteins digest..." Today's Topics: 1. protein biosynthesis (gord) ---------------------------------------------------------------------- Message: 1 Date: Sun, 23 Aug 2009 18:27:49 -0400 From: "gord" Subject: [Protein-analysis] protein biosynthesis To: proteins@net.bio.net Message-ID: Hello All I would like to know to which end of the elongating protein chain, during biosysnthesis, is the next amino acid attached. Amino or carboxyl. Thank you. Gord ------------------------------ _______________________________________________ Proteins mailing list Proteins@net.bio.net http://www.bio.net/biomail/listinfo/proteins End of Proteins Digest, Vol 51, Issue 3 *************************************** From gayers07 from cogeco.ca Mon Aug 24 17:14:56 2009 From: gayers07 from cogeco.ca (gord) Date: Mon Aug 24 17:39:13 2009 Subject: [Protein-analysis] Re: Protein biosynthesis References: <200908241704.n7OH4Tp22430@net.bio.net> Message-ID: Thank you very much for your reply Gord "David Bienvenue" wrote in message news:mailman.836.1251144189.21502.proteins@net.bio.net... > > Protein biosynthesis starts at the N-terminus. > > > > David Bienvenue, Ph.D. > Senior Principal Scientist > VLST Corporation > Seattle, WA 98109 > > > -----Original Message----- > From: proteins-bounces@oat.bio.indiana.edu > [mailto:proteins-bounces@oat.bio.indiana.edu] On Behalf Of > proteins-request@oat.bio.indiana.edu > Sent: Monday, August 24, 2009 10:04 AM > To: proteins@magpie.bio.indiana.edu > Subject: Proteins Digest, Vol 51, Issue 3 > > Send Proteins mailing list submissions to > proteins@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bio.net/biomail/listinfo/proteins > or, via email, send a message with subject or body 'help' to > proteins-request@net.bio.net > > You can reach the person managing the list at > proteins-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Proteins digest..." > > > Today's Topics: > > 1. protein biosynthesis (gord) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 23 Aug 2009 18:27:49 -0400 > From: "gord" > Subject: [Protein-analysis] protein biosynthesis > To: proteins@net.bio.net > Message-ID: > > Hello All > > I would like to know to which end of the elongating protein chain, > during biosysnthesis, is the next amino acid attached. Amino or carboxyl. > > Thank you. > > Gord > > > > > ------------------------------ > > _______________________________________________ > Proteins mailing list > Proteins@net.bio.net > http://www.bio.net/biomail/listinfo/proteins > > End of Proteins Digest, Vol 51, Issue 3 > *************************************** > From kaj.stenberg from helsinki.fi.invalid Tue Aug 25 02:48:55 2009 From: kaj.stenberg from helsinki.fi.invalid (kaj.stenberg@helsinki.fi.invalid) Date: Tue Aug 25 13:20:58 2009 Subject: [Protein-analysis] Re: Protein biosynthesis References: <200908241704.n7OH4Tp22430@net.bio.net> Message-ID: David Bienvenue wrote: > Protein biosynthesis starts at the N-terminus. However, this means that each new amino acid is attached to the C-terminus of the growing peptide. -- Kaj From Victor_Morales from URMC.Rochester.edu Tue Aug 25 08:49:11 2009 From: Victor_Morales from URMC.Rochester.edu (Morales, Victor) Date: Tue Aug 25 13:21:04 2009 Subject: [Protein-analysis] RE: Proteins Digest, Vol 51, Issue 3 In-Reply-To: <200908241704.n7OH4bp22451@net.bio.net> References: <200908241704.n7OH4bp22451@net.bio.net> Message-ID: For ribosomal protein synthesis: The aminogroup of the next amino acid is linked to the carboxyl group of the previous amino acid. Victor -----Original Message----- From: proteins-bounces@oat.bio.indiana.edu [mailto:proteins-bounces@oat.bio.indiana.edu] On Behalf Of proteins-request@oat.bio.indiana.edu Sent: Monday, August 24, 2009 1:05 PM To: proteins@magpie.bio.indiana.edu Subject: Proteins Digest, Vol 51, Issue 3 Send Proteins mailing list submissions to proteins@net.bio.net To subscribe or unsubscribe via the World Wide Web, visit http://www.bio.net/biomail/listinfo/proteins or, via email, send a message with subject or body 'help' to proteins-request@net.bio.net You can reach the person managing the list at proteins-owner@net.bio.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Proteins digest..." Today's Topics: 1. protein biosynthesis (gord) ---------------------------------------------------------------------- Message: 1 Date: Sun, 23 Aug 2009 18:27:49 -0400 From: "gord" Subject: [Protein-analysis] protein biosynthesis To: proteins@net.bio.net Message-ID: Hello All I would like to know to which end of the elongating protein chain, during biosysnthesis, is the next amino acid attached. Amino or carboxyl. Thank you. Gord ------------------------------ _______________________________________________ Proteins mailing list Proteins@net.bio.net http://www.bio.net/biomail/listinfo/proteins End of Proteins Digest, Vol 51, Issue 3 *************************************** From engelbert_buxbaum from hotmail.com Tue Aug 25 09:27:19 2009 From: engelbert_buxbaum from hotmail.com (Dr Engelbert Buxbaum) Date: Tue Aug 25 13:21:15 2009 Subject: [Protein-analysis] Re: Protein biosynthesis References: <200908241704.n7OH4Tp22430@net.bio.net> Message-ID: Am 25.08.2009, 03:48 Uhr, schrieb : > David Bienvenue wrote: > >> Protein biosynthesis starts at the N-terminus. > > However, this means that each new amino acid is attached to the > C-terminus of the growing peptide. And note that above is true only for biological protein synthesis, chemists do it the other way round (Merrifield peptide synthesis). In case of daubt, it is worthwhile to write peptides like NH2-XXXXX-COOH (I have been burned!) From sanchayita_kar from yahoo.com Tue Aug 25 20:27:50 2009 From: sanchayita_kar from yahoo.com (Sanchayita Kar) Date: Wed Aug 26 11:05:26 2009 Subject: [Protein-analysis] Seeking collaboration Message-ID: <871349.32061.qm@web50005.mail.re2.yahoo.com> Seeking collaboration for studying interaction between proteins and different inorganic surfaces.?For details:?http://tinyurl.com/m2bjof From elham.rastegar from gmail.com Wed Aug 26 11:44:41 2009 From: elham.rastegar from gmail.com (elham rastegari) Date: Wed Aug 26 12:30:57 2009 Subject: [Protein-analysis] plant proteomics Message-ID: Dear all, My project is protein extraction and identification of Curculigo latifolia fruit(somehow protein profiling). i already extracted all the proteins through TCA-aceton methanol washes phenol precipitation. and i plan to do two dimensional gel electrophoresis to get spots and then send the spots to Ms/MS to sequence, but it would be very expensive to apply for all spots.So would you tell me if you were me, which kind of spots you would choose? please help me narrow my identification. cheers Eli From conf from topaz.gatech.edu Wed Aug 26 14:13:06 2009 From: conf from topaz.gatech.edu (Georgia Tech Conference Announcement) Date: Wed Aug 26 19:18:37 2009 Subject: [Protein-analysis] 7th Georgia Tech - ORNL Conference on Bioinformatics Message-ID: <20090826191306.E04B06C2D49@topaz.gatech.edu> -------------------------------------------- CALL FOR PAPERS Dear Colleagues The 7th Georgia Tech - ORNL Conference on Bioinformatics - In silico Biology: Genome Biology and Bioinformatics will be held in Atlanta, Georgia, November 12-14, 2009 http://www2.isye.gatech.edu/binf2009/ Georgia Tech continues the tradition of organizing bi-annual International Conference on Bioinformatics, bringing together leading researchers in genomics, bioinformatics and genome biology to present recent advances in the field and to discuss open problems. Important Dates Deadline for early registration: October 15, 2009 Deadline for poster abstract subsmission: October 1, 2009 Notification of acceptance of abstracts: October 11, 2009 We invite papers submissions in the following areas * genomics; * transcriptomics; * proteomics; * reconstruction and modeling of gene networks; * evolutionary biology; SPEAKERS Margaret O. Dayhoff lecture David Lipman , NCBI/NIH, Bethesda, MD, USA Plenary Speakers: Vineet Bafna, University of California at San Diego, USA Gill Bejerano, Stanford University, Stanford, CA, USA Jeffrey Bennetzen, University of Georgia, Athens, GA, USA Mark Borodovsky, Georgia Tech and Emory University, Atlanta, GA, USA Nick Grishin, University of Texas, Dallas, TX, USA Curtis Huttenhower, Harvard University, Boston, MA, USA King Jordan, Georgia Tech, Atlanta, GA, USA Igor Jouline (Zhulin), University of Tennessee - ORNL, Oak Ridge, TN, USA Eugene Koonin, NCBI/NIH, Bethesda, MD, USA Nikos Kyrpides, DOE Joint Genome Institute, Walnut Creek, CA, USA Boris Lenhard, University of Bergen, Norway Jian Ma, University of Illinois at Urbana Champaign, Urbana, IL, USA Yael Mandel-Gutfreund, Technion, Israel Insitute of Technology, Haifa, Israel Joanna Masel, University of Arizona, Tucson, AZ, USA Andrey Mironov, Moscow State University, Russia Andrei Osterman, Burnham Institute for Medical Research, La Jolla, CA USA Karen Nelson, J. Craig Venter Institute, Rockville, MD, USA Natasa Przulj, University of California at Irvine, CA, USA John Reinitz, State Uiversity of New York at Stony Brook, NY, USA Pierre Rouze, Gent University, Gent, Belgium CONFERENCE CHAIRS Mark Borodovsky, Georgia Tech and Emory University Eva K. Lee, Georgia Tech and Emory University PROGRAM COMMITTEE Nicholas Bergman, Georgia Tech Dmitrij Frishman, Munich Polytechnic University, Germany Andrey Gorin, Oak Ridge National Laboratory Andrzej M. Kierzek, University of Surrey, UK. Eileen Kraemer, University of Georgia Jun Liu, Harvard University Andrey Rzhetsky, University of Chicago Andre Rogatko, Samuel Oschin Comprehensive Cancer Institute Gary Stormo, Washington University Ying Xu, University of Georgia and Oak Ridge National Laboratory Soojin Yi, Georgia Tech Igor Zhulin, Oak Ridge National Laboratory and University of Tennessee ADMINISTRATION Harry Sharp, Georgia Tech CONFERENCE LOCATION The Georgia Tech Ferst Center for the Arts. The Georgia Tech campus is located in Midtown Atlanta near the center of the 1996 Olympic development, close to the Fox Theatre and Margaret Mitchell house. From darek.kedra from gmail.com Fri Aug 28 01:53:27 2009 From: darek.kedra from gmail.com (darked) Date: Fri Aug 28 08:53:49 2009 Subject: [Protein-analysis] Re: plant proteomics References: Message-ID: On Aug 26, 6:44?pm, elham rastegari wrote: > Dear all, > > My project is protein extraction and identification of Curculigo latifolia > fruit(somehow protein profiling). i already extracted all the proteins > through TCA-aceton methanol washes phenol precipitation. and i plan to do > two dimensional gel electrophoresis to get spots and then send the spots to > Ms/MS to sequence, but it would be very expensive to apply for all spots.So > would you tell me if you were me, which kind of spots you would choose? > please help me narrow my identification. > > ?cheers Eli Hi, there are just few proteins or cDNA sequences for Curculigo latifolia / C. capitulata and Hypoxidaceae in general. So you will be going for de novo protein sequencing. This will make sense if you want to spot a difference, say between ripe / non-ripe fruit . As a method for characterising proteome, de novo protein sequencing is to costly/to low throughput. IMHO it is way easier to go for EST sequencing first, as a stepping stone for proteome characterisation. Best, darked