From Neill.Horley from gmail.com Wed Dec 5 05:30:27 2007 From: Neill.Horley from gmail.com (Albert) Date: Thu Dec 6 19:28:03 2007 Subject: [Protein-analysis] magnesium chloride in microsome buffer Message-ID: <74a206d0-b12e-4b7f-b5fc-a50c0c8fe77c@w40g2000hsb.googlegroups.com> Hi I use a NADPH regenerating system for analysis of my microsomal enzymes. Does any one know if there is a need for EDTA in the original microsomes preparation buffer? It seems odd to have EDTA in the microsome preparation buffer and then to have magnesium chloride in the NADPH regenerating system. Any suggestions would be appreciated. From stellaj from bu.edu Thu Dec 6 11:53:19 2007 From: stellaj from bu.edu (stellaj@bu.edu) Date: Thu Dec 6 19:28:19 2007 Subject: [Protein-analysis] recipe for a Prestained Protein Marker? Message-ID: <20071206115319.oeua1yxr9cw0gwow@www.bu.edu> Dear Moritz, I came across your posting on Bionet about staining an unstained protein weight. Did you receive any helpful responses to your post? I have the same problem... Thank you. Sincerely, Stella --- you wrote: --- Hello, We are looking for a recipe for a self made PRESTAINED protein marker, or a way to prestain an unstained protein weight standard, Anybody out there with a good solution? The commercially available products are quit expensive, and we will need a lot in the next time for a student course. Thanks for Your ideas Moritz From ligongw2004 from yahoo.com Thu Dec 6 13:20:12 2007 From: ligongw2004 from yahoo.com (Ligong Wang) Date: Thu Dec 6 19:28:31 2007 Subject: [Protein-analysis] picomolar Kd or Ki Message-ID: <242648.1010.qm@web52504.mail.re2.yahoo.com> It has been bothering me for quite sometime that my belief/understanding in the Kd/Ki determination does not seems to drive well with what I read in (some) papers. So let me just throw in my question here and hopefully to get some enlightenment from our big community. My question is: Can one get a Kd (or Ki) value from an assay that is lower than the amount (concentration) of protein/enzyme used therein? And I have a follow-up request--if anyone can forward me literatures that claimed to detect picomolar or even femto-molar Kd/Ki? Thanks in advance and I am looking forward to any response. Ligong Wang, Ph.D. Yale University --------------------------------- Never miss a thing. Make Yahoo your homepage. From estelle.hrabak from unh.edu Wed Dec 19 17:01:50 2007 From: estelle.hrabak from unh.edu (Estelle Hrabak) Date: Wed Dec 19 18:07:40 2007 Subject: [Protein-analysis] Proteomics position at New Hampshire Message-ID: College of Life Sciences and Agriculture Department of Cellular, Molecular and Biomedical Sciences Tenure-Track Position in Proteomics The newly-formed Department of Cellular, Molecular and Biomedical Sciences seeks to fill a tenure-track position in Proteomics. The ideal candidate will use a proteomics approach to address questions in any area of biology (e.g. human health, agriculture, environmental or basic cellular biology). The proteomics position will be housed in the Hubbard Center for Genome Studies and join existing research groups in genomics and glycomics with a strong commitment to interdisciplinary research and teaching. Appointment may be at any level. The successful applicant will have a strong publication record, demonstrate the ability to develop/maintain a vigorous independent research program and actively participate in training of students at all levels. For more information go to: http://www.colsa.unh.edu/employment/ The University of New Hampshire is a high research activity institution with over 600 full-time faculty that provides 90 comprehensive undergraduate programs and more than 70 graduate programs to 13,000 students. UNH is located in Durham on a 188-acre campus, 60 miles north of Boston, 8 miles from the Atlantic coast, and convenient to New Hampshire's lakes and mountains. Applicants should submit a curriculum vitae, summary of research accomplishments and objectives, a brief description of teaching philosophy and goals, and the names of three references to: W. Kelley Thomas Ph.D., Chair, Proteomics Search Committee, Hubbard Center for Genome Studies, 35 Colovos Road Durham NH 03824. Review of applications will begin Feb. 1, 2008 and continue until the position is filled. The University actively seeks excellence through diversity among its administrators, faculty, staff and students and prohibits discrimination on the basis of race, color, religion, sex, age, national origin, sexual orientation, gender identity or expression, disability, veteran status, or marital status. Application by members of all underrepresented groups is encouraged. -- Estelle M. Hrabak Associate Professor, Dept. of Plant Biology Co-Chair, Genetics Graduate Program University of New Hampshire 46 College Rd. Durham, NH 03824 Ph. (603) 862-0716 FAX (603) 862-3784 From m.fery51 from gmail.com Wed Dec 19 15:58:05 2007 From: m.fery51 from gmail.com (Fery) Date: Wed Dec 19 19:26:22 2007 Subject: [Protein-analysis] protein concentration in Ethanol Message-ID: <000601c84281$f6675280$300a7352@eagle> Dear Friends I have made a lipid extract from pollen by folch method and dissolve the my lipids in pure Ethanol. I want to measure the percent of protein contamination in my extract. please let me know what is the best method for measurment of protein in ethanol. any comments would be very appreciated Thanking you in advance Fery From ram from public.compbio.washington.edu Wed Dec 19 20:34:04 2007 From: ram from public.compbio.washington.edu (Ram Samudrala) Date: Wed Dec 19 21:09:41 2007 Subject: [Protein-analysis] Re: protein structure prediction References: Message-ID: There are tons of servers to predict protein structure, and some are extremely accurate, depending on your particular protein. In general, you can obtain experimental (x-ray diffraction/NMR spectroscopy) level accuracy for proteins with a high similarity (>50%) to a protein with experimentally determined structure. (This typically is about 0.5-1 angstroem root mean square deviation (RMSD) on average, which BTW is lower than the average RMSD for about 300 IDENTICAL proteins whose structures were solved by/between x-ray diffraction and NMR spectroscopy.) These servers and methods are evaluated at the biennial Critical Assessment of Structure Prediction (CASP) experiments which give you an idea of which servers and algorithms work well and when. There are even some cases where, for small proteins and/or distant homologues, you can approach that level of accuracy. See the CASP web site for http://predictioncenter.org for the servers, their rankings, etc. It's mostly an issue of what you want to use the resulting structures for. --Ram Ram Samudrala, Ph.D. Associate Professor, Computational Biology University of Washington Seattle, WA 98195, USA V: 1-206-732-6122 F: 1-206-732-6055 W: http://compbio.washington.edu Sander Groffen wrote: > Are you all talking about the same type of structure? > If you want the tertiary structure (3D) there is no such thing, as DK > pointed out. > If you want the secondary structure, protein prediction servers might > get you started as Dr Buxbaum pointed out. > If you have no idea what kind of protein you have, a mass spectrometer > can help to identify it. > (If you have no idea what the difference between primary, secondary and > tertiary structure is, go read a textbook on biochemistry). > Sander