From jyothi.jayaram from gmail.com Thu May 1 13:44:42 2008 From: jyothi.jayaram from gmail.com (Jyothi Jayaram) Date: Thu May 1 15:42:09 2008 Subject: [Protein-analysis] Re: Proteins Digest, Vol 36, Issue 1 In-Reply-To: <200805011703.m41H3vQ25488@net.bio.net> References: <200805011703.m41H3vQ25488@net.bio.net> Message-ID: <65d286370805011144i76786f21m4fe139bd2b493268@mail.gmail.com> Thank you! J On Thu, May 1, 2008 at 1:03 PM, wrote: > 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. Re: Protocol needed from study the protein aggregation > (Clement Angkawidjaja) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 30 Apr 2008 09:20:11 +0900 > From: "Clement Angkawidjaja" > Subject: [Protein-analysis] Re: Protocol needed from study the protein > aggregation > To: > Message-ID: <003101c8aa57$f46a1a10$0e00a8c0@CLEMENT> > Content-Type: text/plain; format=flowed; charset="ISO-8859-1"; > reply-type=original > > > Hi all > > Recently i got a mutant gene and showing higher solubility then wild > > type. we are assuming that our mutant preventing the aggregation of the > > protein. > > I would like to study the thermal and chemical protein aggregation. > > i would be happy If any one provide me detailed protocol to study this > > experiment. > > Besides DSC, you can also do CD spectroscopy. Easier and needs smaller > amount of protein (10 mg for far-UV should be sufficient). Similar with > Dr. > Engelbert Buxbaum's comment, you need to collaborate with someone with > appropriate instrument. > > Clement > > > > ------------------------------ > > _______________________________________________ > Proteins mailing list > Proteins@net.bio.net > http://www.bio.net/biomail/listinfo/proteins > > End of Proteins Digest, Vol 36, Issue 1 > *************************************** > -- Jyothi Jayaram Vishnumangalam, 8 Country Club Rd, # 31 Ithaca NY 14850 Tel: 408-691-6115 From sittner from lkb.ens.fr Thu May 15 08:10:37 2008 From: sittner from lkb.ens.fr (assa sittner) Date: Thu May 15 10:50:38 2008 Subject: [Protein-analysis] protein candidate Message-ID: Hi There, I need for some biochemical assay, a simple protein that fulfills the following requirements: 1. very stable (no significant degradation) 2. soluble 3. monomeric 4. Mw > 70 KDa 5. easily expressed and purified from E.coli 6. if possible, has an enzymatic activity that can be quantified is it too much to ask? ideas anyone? (I was thinking beta galactosidase, but couldn't find an article with nice gels that show the purity, and data about stability etc. is there something else?) have a nice day, From nick.theodorakis from gmail.com Fri May 16 07:31:53 2008 From: nick.theodorakis from gmail.com (Nick Theodorakis) Date: Fri May 16 11:13:47 2008 Subject: [Protein-analysis] Re: protein candidate References: Message-ID: On May 15, 9:10 am, "assa sittner" wrote: > Hi There, > I need for some biochemical assay, a simple protein that fulfills the > following requirements: > 1. very stable (no significant degradation) > 2. soluble > 3. monomeric > 4. Mw > 70 KDa > 5. easily expressed and purified from E.coli > 6. if possible, has an enzymatic activity that can be quantified > is it too much to ask? > ideas anyone? > > (I was thinking beta galactosidase, but couldn't find an article with nice > gels that show the purity, and data about stability etc. is there something > else?) > > have a nice day, Beta-gal is, IIRC, a tetramer. Maybe firefly luciferase; it's about 60-ish kDa, though. Don't know how stable it is. Glycogen phosphorylase? Myosin Light Chain Kinase? Gelatinase B? They're all bigger than 70 kDa. Nick -- Nick Theodorakis nick_theodorakis@hotmail.com contact form: http://theodorakis.net/contact.html From sudha.mrig from gmail.com Sun May 18 11:23:51 2008 From: sudha.mrig from gmail.com (sudha.mrig@gmail.com) Date: Sun May 18 12:31:07 2008 Subject: [Protein-analysis] inorganic mol. docking Message-ID: I want to dock an inorganic molecule like ZnSO4, MgOAc etc. with a protein molecule. I could not locate any docking software which can handle in organic molecule. If anyone can help me in this regard. Thanks Sudha From clement from bio.mls.eng.osaka-u.ac.jp Mon May 19 18:59:54 2008 From: clement from bio.mls.eng.osaka-u.ac.jp (Clement Angkawidjaja) Date: Mon May 19 20:25:15 2008 Subject: [Protein-analysis] Re: inorganic mol. docking References: <200805191703.m4JH3OO01925@net.bio.net> Message-ID: <002601c8ba0c$6f937dd0$0e00a8c0@CLEMENT> Do you want to dock with density data or prediction? If you have density, recent versions of COOT can do that without much hassle. If you do simulation, most docking softwares can do that. My favourite is Autodock. it's free for academics. Just generate your ligand as a pdb and follow the online instruction. Most metal ions are present as single ion species. It is very very difficult to precisely predict the binding sites of ions in a protein except for the known motifs (active sites, metal-binding motifs such as Zn finger, beta-roll, etc). These kinds of ion are usually present in the protein structure. no docking needed. Clement ----- Original Message ----- From: To: Sent: Tuesday, May 20, 2008 2:03 AM Subject: Proteins Digest, Vol 36, 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. inorganic mol. docking (sudha.mrig@gmail.com) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 18 May 2008 09:23:51 -0700 (PDT) > From: sudha.mrig@gmail.com > Subject: [Protein-analysis] inorganic mol. docking > To: proteins@net.bio.net > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > I want to dock an inorganic molecule like ZnSO4, MgOAc etc. with a > protein molecule. I could not locate any docking software which can > handle in organic molecule. If anyone can help me in this regard. > Thanks > > Sudha > > > ------------------------------ > > _______________________________________________ > Proteins mailing list > Proteins@net.bio.net > http://www.bio.net/biomail/listinfo/proteins > > End of Proteins Digest, Vol 36, Issue 5 > *************************************** From wajih76 from hotmail.com Fri May 23 21:38:03 2008 From: wajih76 from hotmail.com (wajahat mahmood) Date: Sat May 24 14:45:19 2008 Subject: [Protein-analysis] Ni binding of His tag proteins Message-ID: hi everyone,I am trying to purify a His Tag protein by passing it over the nickel column but too much of the protein actually flows thru and does not bind. there is also non specific binding as i see too many bands in my washings. i am using 10mM imidazole, 8M urea nad 20mM Tris as washing buffer and 500 mM imidazole, 8M urea and 20 mM Tris in my elution buffer. Can anyone plaease tell me about the volume of Ni-NTA to be used for binding a specific volume of proteins in a solution. I would appreciate any ideas and any possible soliutions thanks and regardswaji _________________________________________________________________ Connect to the next generation of MSN Messenger? http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline From jyyoungjimmy from gmail.com Thu May 29 10:24:21 2008 From: jyyoungjimmy from gmail.com (Jim Young) Date: Thu May 29 16:22:03 2008 Subject: [Protein-analysis] Re: Ni binding of His tag proteins (wajahat mahmood) Message-ID: <57f211620805290824g39692ea9y82a0c37dd83ad37@mail.gmail.com> The wash condition is really harsh. If your proteins are sort of insoluble, you may use urea. Otherwise you do not need urea. Regular PBS with 5 or 10 mM imidazole should be enough for your wash. You may try this bead: http://www.genscript.com/product_001/kit/code/L00295/category/kit/Ni_Charged_Magnetic_Beads.html?src=forum By the way you may want to try this anti-His antibody: http://www.genscript.com/anti_his_mab.html?src=forum http://www.genscript.com/western_tech.html?src=forum On Sun, May 25, 2008 at 1:03 PM, wrote: > 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. Ni binding of His tag proteins (wajahat mahmood) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 May 2008 07:38:03 +0500 > From: wajahat mahmood > Subject: [Protein-analysis] Ni binding of His tag proteins > To: > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > > hi everyone,I am trying to purify a His Tag protein by passing it over the > nickel column but too much of the protein actually flows thru and does not > bind. there is also non specific binding as i see too many bands in my > washings. i am using 10mM imidazole, 8M urea nad 20mM Tris as washing > buffer and 500 mM imidazole, 8M urea and 20 mM Tris in my elution buffer. > Can anyone plaease tell me about the volume of Ni-NTA to be used for binding > a specific volume of proteins in a solution. I would appreciate any ideas > and any possible soliutions thanks and regardswaji > _________________________________________________________________ > Connect to the next generation of MSN Messenger > > http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline > > ------------------------------ > > _______________________________________________ > Proteins mailing list > Proteins@net.bio.net > http://www.bio.net/biomail/listinfo/proteins > > End of Proteins Digest, Vol 36, Issue 7 > *************************************** >