From sumida from bbri.org Mon Nov 3 13:55:55 2008 From: sumida from bbri.org (jps) Date: Mon Nov 3 15:16:01 2008 Subject: [Protein-analysis] protein nucleation. Message-ID: Salting out proteins is a pretty basic technique in the separation and extraction of native protein. My question has to do with the manner in which one adjusts the salt concentration, specifically whether or not it matters if the salt concentrations are adjusted from med-high salt (where the protein is soluble ~3M KCl) to low salt (50mM KCl) in one step, or if it is actually better to adjust the salt concentration in a graded manner. I suppose the issue here is whether or not one thinks that protein precipitation is a controlled process or not. Thought and comments, and thanks for all input in advance. From vahidchamanara from gmail.com Sun Nov 9 03:26:42 2008 From: vahidchamanara from gmail.com (Vahid Chamanara) Date: Sun Nov 9 13:16:04 2008 Subject: [Protein-analysis] (no subject) Message-ID: <9b7ad5cb0811090026q7d0de892u1e7537b27436051f@mail.gmail.com> Dear *Dr Engelbert Buxbaum* excuse me for my little english language... i am MS.c student of fish processing from agricultural sciences and natural resources university of Gorgan- Iran. i am working toward my MS.c degree.my thesis is about cryoprotectants in fish fillet by actomyosin of frozen-stored farmed fish by some sugars and polyols. i want the true and simple methode to determaine and assay of ATPase activity for fish fillet. i will appreciate you for your help best regards -- For Fine Fresh Fishes For You! From elham.rastegar from gmail.com Wed Nov 12 23:47:51 2008 From: elham.rastegar from gmail.com (elham rastegari) Date: Thu Nov 13 11:10:07 2008 Subject: [Protein-analysis] question Message-ID: Hi I want to extract all the proteins(root,leaf.fruit) of a plant which is almost unknown and determine which part has a high protein content in comparsion with others and then characterizing all the proteins of that part.whould you plz help me with extraction protocol? From ql5 from ualberta.ca Thu Nov 13 12:50:32 2008 From: ql5 from ualberta.ca (Qin Liu) Date: Thu Nov 13 17:11:35 2008 Subject: [Protein-analysis] Re: Proteins Digest, Vol 42, Issue 3 References: <200811131704.mADH4GV16601@net.bio.net> Message-ID: why not do some research first by yourself? Try to search the protocol on the web or read the papers to see how other people did. Qin -------------------------------------------------- From: Sent: Thursday, November 13, 2008 10:04 AM To: Subject: Proteins Digest, Vol 42, 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. question (elham rastegari) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 13 Nov 2008 12:47:51 +0800 > From: "elham rastegari" > Subject: [Protein-analysis] question > To: proteins@magpie.bio.indiana.edu > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi > > I want to extract all the proteins(root,leaf.fruit) of a plant which is > almost > > unknown and determine which part has a high protein content in > > comparsion with others and then characterizing all the proteins of > > that part.whould you plz help me with extraction protocol? > > > ------------------------------ > > _______________________________________________ > Proteins mailing list > Proteins@net.bio.net > http://www.bio.net/biomail/listinfo/proteins > > End of Proteins Digest, Vol 42, Issue 3 > *************************************** > > From k.b.aitken-06 from lboro.ac.uk Fri Nov 14 02:50:17 2008 From: k.b.aitken-06 from lboro.ac.uk (kba) Date: Fri Nov 14 11:55:26 2008 Subject: [Protein-analysis] protein database thanks Message-ID: <8f6891c1-61fe-421a-b8eb-d0c404319204@e1g2000pra.googlegroups.com> Hi. For all those who took the time to complete my online survey on protein database use, many thanks. If you missed the first post and would like to add your perspective regarding the use of these databases the survey is still open for a little while longer. The link is below and the survey should only take 10-15 minutes to fill out. I would appreciate your input. KBA http://www.surveymonkey.com/s.aspx?sm=tNKIQHxUhEven_2fQ4DqiiHA_3d_3d From engelbert_buxbaum from hotmail.com Fri Nov 14 11:28:36 2008 From: engelbert_buxbaum from hotmail.com (Dr Engelbert Buxbaum) Date: Fri Nov 14 11:55:37 2008 Subject: [Protein-analysis] Re: (no subject) References: Message-ID: Am 09.11.2008, 04:26 Uhr, schrieb Vahid Chamanara : > i want the true and simple methode to determaine and assay of ATPase > activity for fish fillet. The most sensitive determination was originally proposed by Neufeld & Levy (1969) and uses gamma-33P (or 32P) labelled ATP. The radioactive phosphate produced is, in the presence of carrier phosphate, converted into phosphomolybdic acid and extracted into organic solvent. A modern (small volume, non-toxic solvents) version of this assay I have described in Eur. J. Biochem. 265 (1999) 54-63. With that assay you can detect fmol of released phosphate in a few ul of sample. If you can not work with radioactivity or if you can afford some loss of sensitivity in exchange for much lower costs, you can use a colorimetric assay. The phosphate released is converted to phosphomolybdic acid, which is reduced to molybdenum blue (Fiske & Subbarov 1925). To increase the sensitivity further you can bind dyes to the molybdenum blue (Ekman & J?ger: Anal. Biochem. 214 (1993) 138; Kagami & Kamya: Meth Cell Biol 47 (1995) 147). A continuous fluorescent assay for phosphate was described by Brune et al in Biochemistry 33 (1994) 8262, but I have never used it. From allicindixvin from gmail.com Sun Nov 16 03:32:06 2008 From: allicindixvin from gmail.com (kyoli) Date: Sun Nov 16 13:43:57 2008 Subject: [Protein-analysis] greening Message-ID: i am extracting protein from algal mat and the problem is that when i run the samples on SDS PAGE it looks greem. what may be the reason From ql5 from ualberta.ca Mon Nov 17 16:44:37 2008 From: ql5 from ualberta.ca (Qin Liu) Date: Mon Nov 17 18:07:29 2008 Subject: [Protein-analysis] Re: Greening- Proteins Digest, Vol 42, Issue 5 References: <200811171703.mAHH3kV05747@net.bio.net> Message-ID: <499E268955714728A8B7992EC8818183@weifeng> PH problem? Qin -------------------------------------------------- From: Sent: Monday, November 17, 2008 10:03 AM To: Subject: Proteins Digest, Vol 42, Issue 5 > 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. greening (kyoli) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 16 Nov 2008 00:32:06 -0800 (PST) > From: kyoli > Subject: [Protein-analysis] greening > To: proteins@net.bio.net > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > i am extracting protein from algal mat and the problem is that when i > run the samples on SDS PAGE it looks greem. what may be the reason > > > ------------------------------ > > _______________________________________________ > Proteins mailing list > Proteins@net.bio.net > http://www.bio.net/biomail/listinfo/proteins > > End of Proteins Digest, Vol 42, Issue 5 > *************************************** > > From lizboyd from uchicago.edu Fri Nov 21 14:53:48 2008 From: lizboyd from uchicago.edu (Elizabeth W. Boyd) Date: Fri Nov 21 16:17:55 2008 Subject: [Protein-analysis] graduate student positions Message-ID: Fully funded positions are available for PhD students in the lab of Prof. Rustem Ismagilov at the University of Chicago, in the Biophysical Sciences or Chemistry graduate programs. We use microfluidics to understand complex systems, and develop tools for research and medicine. Recent projects include 1) development of "chemistrode", a microfluidic device for to deliver, record, and analyze chemical information from cells and tissues; 2) understanding general principles that govern biological dynamics in space and time; 3) using chemistrode and other microfluidic tools to understand biological dynamics and signaling in vivo and in culture; 4) synthetic biology to construct microbial communities; 5) developing technologies for control of crystallization and aggregation of proteins in nanoliter volumes; 6) determining the mechanisms that maintain robustness of early patterning of the Drosophila embryo; 7) understanding how in blood coagulation simple dynamics arises from complexity; and 8) developing new catalysts using genetic algorithms. See http://ismagilovlab.uchicago.edu/publications.html for details. Interests of current lab members span microfluidics, analytical chemistry, organic and physical chemistry, catalysis, biophysics, biochemistry, single-molecule microscopy, microbiology, developmental biology, Alzheimer's, diabetes, and immunology. We welcome candidates from all disciplines, including chemistry, biology, engineering, or physics. Interested applicants should apply to the University of Chicago Chemistry graduate program ( http://chemistry.uchicago.edu/phdapp.shtml) or University of Chicago Biophysical Sciences graduate program ( http://biophysics.uchicago.edu/students/application.html) and mention the Ismagilov group on the application. Contact ismagilovlab@uchicago.edu with questions. From rakuen from gmail.com Sun Nov 23 12:47:01 2008 From: rakuen from gmail.com (Yutong Zhao) Date: Sun Nov 23 14:39:54 2008 Subject: [Protein-analysis] What experiment will let me detect merging of protein folding pathways? Message-ID: Hi guys, I realized that the relax-tighten optimization approach found in most computational chemistry experiments may be ill-suited for the protein folding problem. So I'm developing a new merging-tree iterative deepening search algorithm that will navigate through the protein folding well. However, this algorithm hinges on one key assumption: there are many initial pathways in the protein folding landscape with a SIGNIFICANT amount of pathway convergence as the protein folds. A corollary of this assumption would be intermediates that result from the merges (nodes), which have the unique property of resulting from multiple merges and thus would be found in high frequency no matter how many times you refold a protein. I was looking through experimental techniques in circular dichroism and NMR, ideally something that would permit observation of a rapid decrease in fluctuations of a few, key, residues. Any ideas how I can find these things? Cheers, Yutong Zhao From sumida from bbri.org Mon Nov 24 10:26:04 2008 From: sumida from bbri.org (jps) Date: Mon Nov 24 11:20:49 2008 Subject: [Protein-analysis] Re: What experiment will let me detect merging of protein folding pathways? References: Message-ID: On Nov 23, 12:47?pm, "Yutong Zhao" wrote: > Hi guys, > > I realized that the relax-tighten optimization approach found in most > computational chemistry experiments may be ill-suited for the protein > folding problem. So I'm developing a new merging-tree iterative deepening > search algorithm that will navigate through the protein folding well. > However, this algorithm hinges on one key assumption: there are many initial > pathways in the protein folding landscape with a SIGNIFICANT amount of > pathway convergence as the protein folds. A corollary of this assumption > would be intermediates that result from the merges (nodes), which have the > unique property of resulting from multiple merges and thus would be found in > high frequency no matter how many times you refold a protein. > > I was looking through experimental techniques in circular dichroism and NMR, > ideally something that would permit observation of a rapid decrease in > fluctuations of a few, key, residues. Any ideas how I can find these things? > > Cheers, > Yutong Zhao NMR deuterium exchange, or proteolytic cleavage. See Walter Englender or Susan Marqusee's work. From info from noster-it.com Wed Nov 26 03:55:23 2008 From: info from noster-it.com (Dokorek) Date: Wed Nov 26 11:17:34 2008 Subject: [Protein-analysis] New High Protein Rice Strain Developed Message-ID: <528a45e9-8dc3-41e8-817e-60d144f696f4@w3g2000yqc.googlegroups.com> Scientists in the United States and India are reporting development of a high-protein variety of rice, dietary staple for half the world's population. Researchers have been trying to bolster the protein in rice for five decades. Rice already is a main source of calories as well as protein intake for billions of people, and its enrichment of protein would have a positive impact on millions of poor and malnourished people in developing countries, the report says. Dokorek Portal to share biological information-data between people http://biospace.ethz.ch