[ccp4bb] offtopic: effect of compound impurities on ITC?
Hi All I'm curious the effect of small impurities in commercially synthesized compounds on ITC and its analysis. Say if compound Y is the high affinity binder, but you make a derivative that differs from a single functional group from Y (you used Y to make this new compound) and you never are able to completely get rid of Y. How does this affect the analysis of determining the derivative's affinity by ITC? References or personal experience is appreciated! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] offtopic: effect of compound impurities on ITC?
Hi, If your are talking about proteins or protein subunits, this means that you are making polymers of nY, and Y becames the monomer. So in this case, I will not consider Y as an impurity. If I get you right, then size exclusion chromtography is good option to separate the monomers from the bigger polymers. Another way to do that, in my opinon, is that if you have a good estimate of the stoichometry between the monomers and polymers (and hence concentration of monomer in the cell), then run a refrence ITC with same monomer concetrate and this will automatically subtract the influence of Y component. I hope this give the slightest hint!! Ahmed. --- On Tue, 8/24/10, Francis E Reyes francis.re...@colorado.edu wrote: From: Francis E Reyes francis.re...@colorado.edu Subject: [ccp4bb] offtopic: effect of compound impurities on ITC? To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, August 24, 2010, 11:11 AM Hi All I'm curious the effect of small impurities in commercially synthesized compounds on ITC and its analysis. Say if compound Y is the high affinity binder, but you make a derivative that differs from a single functional group from Y (you used Y to make this new compound) and you never are able to completely get rid of Y. How does this affect the analysis of determining the derivative's affinity by ITC? References or personal experience is appreciated! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
[ccp4bb] Phenix Structure Solution Refinement Webinar
Dear colleagues, I would like to draw your attention to an upcoming educational webinar to be presented by Paul Adams titled Structure Solution and Refinement with Phenix which is scheduled to occur Thursday, August 26th at 10:00 PDT (13:00 PM EST /17:00 UTC/GMT). You can find more information including a registration link at the following site: http://www.rigaku.com/protein/webinars.html Best regards, Angela
[ccp4bb] Data base of sulfur-SAD structures
Hi, I have an undergraduate student collecting information for the development of a database of sulfur-SAD phased structures including data collection and other experimental parameters for his semester project. Since mining the PDB for this information has proven difficult I am asking members of the community that if you have determined a structure by sulfur (or phosphorous) SAD could you please send me a reference to the paper or PDB entry. My goal is to make the data available to the community via a web server. Thanks, John John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 = Phone: 706-542-1750 Fax:706-542-3077
[ccp4bb] TLSMD Alignments
Hi All, I have a question for those of you familiar with the TLSMD webserver. I am working on a structure with slightly imperfect 3-fold rotational NCS. My most recent .pdb file has been generated using Refmac (followed by a little tinkering in Coot), and during refinement I have been imposing medium main chain and loose side chain NCS restraints, and my R-factors don't really improve if I loosen the restraints further. This is the .pdb file I've also used an input to TLSMD. The results of TLSMD do show that the residuals appear to slowly plateau when breaking the chains into 19 or 20 groups (all three A,B,C seem to converge similarly). When I look at the alignments, the TLS groups created for each chain do not align with each other well. The alignment of groups gets slightly better as more groups are added, which is partially just an issue of the groups being smaller and looking closer I think, but there is still significant stagger between neighboring groups. Is this typical for a structure with NCS-related chains? It seems somewhat counterintuitive to my understanding of how symmetric proteins should work (if the TLS motions reflect actual motions of the molecule). Perhaps the difference in TLS grouping between chains results from differences in Biso for NCS-related atoms that result from crystal packing? Maybe someone can shed some light on the situation? Thanks a lot, Mike Thompson -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
Re: [ccp4bb] TLSMD Alignments
Dear Micheal, As you say, the effect is probably arising from the different packing environment of your NCS-related molecules. Once you've taken TLS groups into account NCS restraints might even perform better. Cheers, Roberto On 24 Aug 2010, at 21:15, Michael Thompson wrote: Hi All, I have a question for those of you familiar with the TLSMD webserver. I am working on a structure with slightly imperfect 3- fold rotational NCS. My most recent .pdb file has been generated using Refmac (followed by a little tinkering in Coot), and during refinement I have been imposing medium main chain and loose side chain NCS restraints, and my R-factors don't really improve if I loosen the restraints further. This is the .pdb file I've also used an input to TLSMD. The results of TLSMD do show that the residuals appear to slowly plateau when breaking the chains into 19 or 20 groups (all three A,B,C seem to converge similarly). When I look at the alignments, the TLS groups created for each chain do not align with each other well. The alignment of groups gets slightly better as more groups are added, which is partially just an issue of the groups being smaller and looking closer I think, but there is still significant stagger between neighboring groups. Is this typical for a structure with NCS-related chains? It seems somewhat counterintuitive to my understanding of how symmetric proteins should work (if the TLS motions reflect actual motions of the molecule). Perhaps the difference in TLS grouping between chains results from differences in Biso for NCS-related atoms that result from crystal packing? Maybe someone can shed some light on the situation? Thanks a lot, Mike Thompson -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu --- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail roberto.stei...@kcl.ac.uk
[ccp4bb] Senior Scientist/ Principal Scientist Membrane Protein Chemistry (Takeda San Diego)
Senior Scientist/ Principal Scientist Membrane Protein Chemistry (Takeda San Diego) https://takedapharm.taleo.net/servlets/art.product.recruiterwebtop.Main OperatorServlet?art_ip_action=RequisitionListnextFrame=JRLList# If there is an interest in being considered further for the attached employment opportunities with Takeda San Diego, please feel free to apply directly at www.takedasd.com http://www.takedasd.com/ or for immediate consideration please send your resume directly to jtat...@tpna.com mailto:jtat...@tpna.com , as well as apply directly. Senior Scientist, Membrane Protein Chemistry (Takeda San Diego) Ph.D. in life science with thesis, publication(s) and minimum 5 years of relevant experience in membrane protein chemistry, OR - MS in life science with minimum 11+ years of relevant experience, OR - BS in life science with minimum 14+ years of relevant experience - Proven track record in membrane protein structural biology with 5years of expert knowledge and hands-on experience in successful expression, purification, bioanalytical and biochemical characterization of membrane proteins using state-of-the art technologies Principal Scientist, Membrane Protein Chemistry (Takeda San Diego) * Ph.D. in life science with thesis, publication(s), and minimum of 8years of relevant experience OR * MS in life science with minimum 14+ years of relevant membrane protein chemistry experience, OR * BS in life science with minimum17+ years of relevant membrane protein chemistry/structural biology experience * Proven leadership in membrane protein structural biology with a track record with 5years of expert knowledge and hands-on experience in successful expression, purification, preferably crystallization, bioanalytical and biochemical characterization of membrane proteins using state-of-the art technologies Please Note: Industry experience is strongly preferred Josie Tatone Takeda Pharmaceuticals North America, Inc. Sr. Talent Acquisition Specialist Phone: 224-554-3422 Fax: 224-554-7853 E-mail: jtat...@tpna.com ### This message is for the designated recipient only and may contain privileged or confidential information. If you have received it in error, please notify the sender immediately and delete the original. Any other use of the email by you is prohibited. ###
