From graceacc from gmail.com Tue Mar 3 10:15:33 2009 From: graceacc from gmail.com (Li Xiaoli) Date: Tue Mar 3 15:24:01 2009 Subject: [Protein-analysis] Call for Paper: International Journal of Knowledge Discovery in Bioinformatics Message-ID: <7563e84c-b676-40dc-9a60-e7a1b9789ecd@p36g2000prp.googlegroups.com> Dear Colleagues, We are writing to invite you to submit an article to the new International Journal of Knowledge Discovery in Bioinformatics (IJKDB): http://www.igi-global.com/ijkdb. The mission of IJKDB is to increase awareness of interesting and challenging biomedical problems and to inspire new knowledge discovery solutions which can be translated into further biological and clinical studies. IJKDB provides a rapid forum for the dissemination of original research articles on computational knowledge discovery methods as well as discovery notes that report newly found biological discoveries using computational techniques. In addition to the original research articles, IJKDB emphasizes software and tools that exploit the knowledge discovery techniques for biological problems, and databases that contain useful biomedical data for the community. The journal also encompasses reviews and tutorials on relevant computational and experimental techniques for translational research and knowledge discovery in life sciences. We seek well-motivated, cross-disciplinary papers useful for researchers, practitioners, and academicians, mathematicians, statisticians, and computer scientists involved in the many facets of bioinformatics and translational research. Proposals for special issues, especially on emerging topics, are also welcome. IJKDB is available in both print and electronic form to subscribers of the journal. The International Editorial Review Board of the journal consists of well-known experts in various areas of bioinformatics, with broad international representation. Please refer the attached Call for Papers and journal web site (http://www.igi-global.com/ijkdb) for more information. We look forward to your submissions, and we hope that you will also encourage your colleagues and students to contribute to the journal. Sincerely, Xiao-Li Li and See-Kiong Ng Editors-in-Chief International Journal of Knowledge Discovery in Bioinformatics (IJKDB) E-mail: xlli@i2r.a-star.edu.sg; skng@i2r.a-star.edu.sg From piejem from hotmail.com Wed Mar 4 06:49:46 2009 From: piejem from hotmail.com (PM) Date: Wed Mar 4 12:04:31 2009 Subject: [Protein-analysis] Re: proteins that don't ionize In-Reply-To: <864ce66f-5dcc-4240-b110-31976e57bb31@q25g2000vbn.googlegroups.com> References: <864ce66f-5dcc-4240-b110-31976e57bb31@q25g2000vbn.googlegroups.com> Message-ID: <49ae6ada$0$31366$8a7afdce@news4.usenet4u.nl> jps wrote: > Recently purified an unknown protein with a partial N-terminal > sequence match to a bacterial outermembrane protein. Oddly this > protein does not react with DTNB, does not seem to ionize when mixed > with sinnapinic acid and placed in a MALDI-ToF, and has a molecular > weight of 33kDa as judged by SDS PAGE analysis. > > Curious to know if anybody thinks that membrane proteins would have > more difficulty interacting with MALDI matrices than other proteins? Maybe trie a batch of matrices? Not all substrates wil "fly" with sinnapinic acid. DHBA? maybe or use electrospray (TOF) MS. From sarwat_bqau from yahoo.co.uk Thu Mar 5 05:45:55 2009 From: sarwat_bqau from yahoo.co.uk (Sarwat Ahmad) Date: Thu Mar 5 12:57:36 2009 Subject: [Protein-analysis] Recepie for precipitants Message-ID: <753232.54933.qm@web24201.mail.ird.yahoo.com> I am completely new to crystallization. I want to play with lysozyme. I obtained some crystal with 15% NACL but I want to know which other precipitants I can used for this. How to make a good receipe for the precipitants. regards ? From engelbert_buxbaum from hotmail.com Fri Mar 6 12:35:00 2009 From: engelbert_buxbaum from hotmail.com (Dr Engelbert Buxbaum) Date: Fri Mar 6 14:21:43 2009 Subject: [Protein-analysis] Re: Recepie for precipitants References: Message-ID: Am 05.03.2009, 06:45 Uhr, schrieb Sarwat Ahmad : > I am completely new to crystallization. I want to play with lysozyme. I > obtained some crystal with 15% NACL but I want to know which other > precipitants I can used for this. > How to make a good receipe for the precipitants. > regards If you find a good answer to that question they'll probably pay you a trip to Stockholm. Until then it is trial and error, using "sparse matrices" of precipitants that work with other proteins. From breneman from Princeton.EDU Tue Mar 10 11:51:41 2009 From: breneman from Princeton.EDU (Emily A Breneman (breneman@Princeton.EDU)) Date: Tue Mar 10 20:07:16 2009 Subject: [Protein-analysis] Re: lysozyme crystallization In-Reply-To: <200903071703.n27H3nG29607@net.bio.net> References: <200903071703.n27H3nG29607@net.bio.net> Message-ID: Hampton research provides two different recipes for lysozme crystallization on their website: http://hamptonresearch.com/experiments.aspx From melissa.mazan from tufts.edu Mon Mar 16 16:37:39 2009 From: melissa.mazan from tufts.edu (mmazan01) Date: Mon Mar 16 18:52:19 2009 Subject: [Protein-analysis] sca-1 Message-ID: <22548009.post@talk.nabble.com> Hi - I am trying to detect Ly6 A/E (sca-1) from mouse lung on western blot. I am using a monoclonal rat anti-mouse from ebiosciences. I have very clean bands, no background, but at 75 kd instead of the expected 18 kd. Can anyone shed light on this? Melissa -- View this message in context: http://www.nabble.com/sca-1-tp22548009p22548009.html Sent from the Bio.net - Proteins mailing list archive at Nabble.com. From gawak_momo from msn.com Tue Mar 17 09:35:45 2009 From: gawak_momo from msn.com (M O) Date: Tue Mar 17 13:45:16 2009 Subject: [Protein-analysis] Analysis of small peptides: voltage & acrylamide Message-ID: Hi everyone, I am trying to separate 3 smalls peptides (15kDa, 9kDa and 7kDa) , I am using the technic of "tricine sds-page" by schagger H. et al. of Nature protocols The difference between the 9kDa and 7 kDa is visible but I want to increase it, the problem is that the system of detection ( fluorescence) cannot work with gel of 16% of acrylamide so i am working on gel 10%, and i am going to see if i can go further in the percentage of acrylamide.But my problem is about the voltage that I apply to the gel: On the net i can't find any informations about " how to determine the best voltage/current in a sds-page gel" So how can I determine the best voltage/current to apply to my gel? And in lab there's three types of acrylamide: Acrylamide -Bisacrylamide 40% 19:1 Sigma Acrylamide -Bisacrylamide 40% 37.5:1 Merck Acrylamide -Bisacrylamide 40% 19:1 Merck I am using the last one, will I increase the resolution by using the 37.5:1? i don t know much about the difference between 19:1 & 37.5:1 Thanks for paying attention to this post _________________________________________________________________ T?l?phonez gratuitement ? tous vos proches avec Windows Live Messenger? !? T?l?chargez-le maintenant ! http://www.windowslive.fr/messenger/1.asp From adamsmith from econ.com Thu Mar 19 09:28:02 2009 From: adamsmith from econ.com (Adam Smith) Date: Thu Mar 19 10:45:11 2009 Subject: [Protein-analysis] ab initio folding protein SW Message-ID: Hello, What is an estimated value of an ab initio folding protein software to the community? From engelbert_buxbaum from hotmail.com Mon Mar 23 07:10:18 2009 From: engelbert_buxbaum from hotmail.com (Dr Engelbert Buxbaum) Date: Mon Mar 23 09:58:19 2009 Subject: [Protein-analysis] sca-1 References: Message-ID: Am 16.03.2009, 17:37 Uhr, schrieb mmazan01 : > > Hi - I am trying to detect Ly6 A/E (sca-1) from mouse lung on western > blot. > I am using a monoclonal rat anti-mouse from ebiosciences. I have very > clean > bands, no background, but at 75 kd instead of the expected 18 kd. Can > anyone shed light on this? Melissa Sounds like you are looking at a tetramer. 18 kDa x 4 = 72 kDa, the difference is within the expected error margin. Did you heat the sample with DTT and SDS? What does the manufacturer of the antibody and the literature say about what you should find? From sumida from bbri.org Tue Mar 24 09:30:56 2009 From: sumida from bbri.org (jps) Date: Tue Mar 24 11:09:33 2009 Subject: [Protein-analysis] zwitter ionic "Good" buffers Message-ID: <28d9a738-990d-41a1-a4ae-168069346a34@f19g2000yqh.googlegroups.com> How does one calculat the ionic strength of zwitter ionic "Good" buffers such as MOPS or HEPES at their respective pKa values? Is the zitterionic species really equivalent to an uncharged species? From nir from rosettadesigngroup.com Wed Mar 25 11:12:26 2009 From: nir from rosettadesigngroup.com (Nir London) Date: Wed Mar 25 11:45:53 2009 Subject: [Protein-analysis] Rosetta Academic Training Webinar Message-ID: <8B35E726-1A96-4E93-BEB5-9B265BA1A748@rosettadesigngroup.com> The Rosetta Design Group is proud to present the first webinar in the Rosetta Academic Workshop Series. For the first webinar, we have selected to focus on Protein-Protein Docking based on the answers to the interest poll. We hope this will be the first in a line of helpful and inspiring webinars to kick-off our Rosetta Academic Workshop Series. What: Protein-Protein Docking When: May 4th 2009, 0800-1000 AM EST Where: Your office! Click here for more details and registration (For non html emails: http://rosettadesigngroup.com/RDGLS/index.php?sid=54479&lang=en) Pleas note: This is not a promotional webinar. Rosetta is open-source and freeware for academic and non-profit organizations and can be downloaded here from University of Washington's TechTransfer Digital Ventures. The majority of the webinar is concerned with Rosetta 2.3.0. Rosetta 3.0 is still a beta version. Hope to see you there, Nir London. Rosetta Design Group | http://rosettadesigngroup.com/ From zhjwmy from yahoo.com Wed Mar 25 19:02:14 2009 From: zhjwmy from yahoo.com (zhjwmy@yahoo.com) Date: Wed Mar 25 22:07:03 2009 Subject: [Protein-analysis] antibody affinity chromatography question Message-ID: <509304.21260.qm@web39703.mail.mud.yahoo.com> Hi there, anyone here in biology has experience with affinity chromatography? I'm having problem with my columns recently. my columns worked all right before, but suddenly didn't enrich proteins. I confirmed the starting and eluting conditions, and it should be always the same. I heard before that these antibody columns have a definite life, such as a number of cycles it can run, but it's unlikely two of my columns stop working at the same time---one column was very new, and only ran a few times. anybody can give a clue? I'm not a prof bio and this topic is hard to google out. hope some expert friends can share me your valuable opinions and suggestions (why this happens... solutions...). much appreciated!