[ccp4bb] Isothermal titration calorimetry
Dear All, I am sorry for the off topic question. I am going to buy ITC to study protein-protein protein-ligand interactions I am comparing microcal, GE and nanoITC, TA instrument.. any suggestions, recommendations, good experiences or bad experiences. is there a better system. Thank in advance for the help. Regards Sameh -- Sameh Soror Postdoc. fellow
Re: [ccp4bb] Isothermal titration calorimetry
I would recommend the Microcal ITC 200, hands down. Not only is it an amazing instrument with the optional automated sample loader (which is worth every penny), but we were able to do experiments (multiple) using FULL-LENGTH p53 binding to a weak cognate protein. I believe this was the first time ITC was ever used with full length p53, as it is so labile and just loves immediately to oligomerize. Sample sizes pay for the instrument. Best, John John Fisher, M.D./PhD St. Jude Children's Research Hospital Department of Oncology Department of Structural Biology W: 901-595-6193 C: 901-409-5699 On Mar 23, 2013, at 4:45 AM, Sameh Soror shamd...@googlemail.com wrote: Dear All, I am sorry for the off topic question. I am going to buy ITC to study protein-protein protein-ligand interactions I am comparing microcal, GE and nanoITC, TA instrument.. any suggestions, recommendations, good experiences or bad experiences. is there a better system. Thank in advance for the help. Regards Sameh -- Sameh Soror Postdoc. fellow
[ccp4bb] Postdoctoral position in Membrane Protein Crystallography - Structural Glycobiology Group, Unit of Biophysics, The Basque Country, Spain
A 2-years postdoctoral research position is available at the Structural Glycobiology Group, Unit of Biophysics (UBF), The Basque Country, Spain. The UBF is a research center located nearly Bilbao, and is equipped with state-of-the-art research facilities including X-ray protein crystallography and membrane/protein biochemistry/biophysics. We are seeking a highly motivated candidate, interested to investigate on the field of cell wall/membrane biogenesis in bacteria. The ideal candidate must hold a Ph.D. in biochemistry, biophysics, structural biology or related fields, with a strong background/working experience in biochemistry, biophysics and structural biology of membrane proteins. The candidate should have a strong publication record in quality peer-reviewed journals, be able to work independently as well to have the ability to work collaboratively in a laboratory environment. Applicants should send a cover letter, CV, and names/contact information of 2/3 references to: Marcelo E. Guerin Head Structural Glycobiology Group Unit of Biophysics - Barrio Sarriena S/N, 48940, Leioa, Bizkaia, SPAIN. E-mail: mrcgue...@gmail.com Closing date: May 30, 2013 or until position is filled. Best regards, Marcelo -- Marcelo E. Guerin, Ph.D. Ikerbasque Research Professor Structural Glycobiology Group Unidad de Biofisica (CSIC-UPV/EHU) Barrio Sarriena s/n - 48940, Leioa, Vizcaya - SPAIN Tel: +34 94 601 8052 - Fax: +34 94 601 3360 Web: http://www.unidaddebiofisica.org/member.aspx?member=60
Re: [ccp4bb] Isothermal titration calorimetry
It might be worth to consider the question more in detail. Do you want to study thermodynamics of the interaction, or a KD would do? If the former, you need ITC. If the latter, and you want to study things at the level of KD only, maybe investing on a plate reader, thermophoresis, or some biosensor technology (spr or interferometry based systems) should be considered. Then, what interactions will you study with the ITC? In general, I would agree that the lower sample volume is worth the nano options, but depending on the typical systems under study, sometimes the gain on sample quantity is not worth the money - while many times its worth it. John is if course right that for studying specific systems as the one he describes the 200 is great. A. Sent from my iPhone On 23 Mar 2013, at 11:00, John Fisher johncfishe...@gmail.com wrote: I would recommend the Microcal ITC 200, hands down. Not only is it an amazing instrument with the optional automated sample loader (which is worth every penny), but we were able to do experiments (multiple) using FULL-LENGTH p53 binding to a weak cognate protein. I believe this was the first time ITC was ever used with full length p53, as it is so labile and just loves immediately to oligomerize. Sample sizes pay for the instrument. Best, John John Fisher, M.D./PhD St. Jude Children's Research Hospital Department of Oncology Department of Structural Biology W: 901-595-6193 C: 901-409-5699 On Mar 23, 2013, at 4:45 AM, Sameh Soror shamd...@googlemail.com wrote: Dear All, I am sorry for the off topic question. I am going to buy ITC to study protein-protein protein-ligand interactions I am comparing microcal, GE and nanoITC, TA instrument.. any suggestions, recommendations, good experiences or bad experiences. is there a better system. Thank in advance for the help. Regards Sameh -- Sameh Soror Postdoc. fellow
[ccp4bb] Crystallization hotel
Dear colleagues, We are planning to replace our crystallisation hotel, a CrystalPro system that has already done its job. We are undecided about what new system to choose and would much appreciate hearing your experiences with your own systems. We are looking for a unit with a capacity of no less than 100 plates (more if possible). The reliability and robustness of the system is the most important consideration for us (we hear some horror stories about grippers dropping plates, motors getting stuck, etc, that we are very keen to avoid). Although ours is a managed crystallisation facility, users have direct access to the equipment and run their own projects after an initial training period. Thus, we need a system that is relatively user friendly. We also need good technical support at this side of the Atlantic (UK/EU). If you have any recommendations pro or against given hotels, we will be most grateful to hear. Please email me off the list at olga.may...@liv.ac.uk and I will post a summary to the BB after collecting all replies. Many thanks in advance, Olga Olga Mayans Institute of Integrative Biology University of Liverpool, UK olga.may...@liv.ac.uk
[ccp4bb] ionic interaction inside a protein
Dear all I am working on a thermostable protein and i have read that the stability to high temperature is due to various ionic interactions among the amino acid residues of the protein itself..I request you all to tell me any web server which can show all the ionic interactions between amino acid residues in my protein structure by just uploading its coordinate file.ina nut shell i want to identify those residues in my protein which are taking part in ionic interaction. -- Regards Faisal School of Life Sciences JNU
[ccp4bb] Map Alignment
Dear Chen you can use the Matrix Copy command in pymol to align maps. Check the pymol wiki for details and an example how to use: http://pymolwiki.org/index.php/Matrix_copy. Best regards Florian Date:Thu, 21 Mar 2013 23:29:31 -0400 From:Chen Zhao chenzhaoh...@gmail.com Subject: Map Alignment Dear all, Does anybody know some softwares for aligning electron density maps? I tried transforming map by SQL model fit extension in COOT, which turned out to be not working: the map it transformed is the one supposed to be fixed. If I switch the moving model with the reference model, I only got some error messages. I also tried the Superpose maps utility in PHENIX, however, since they are nucleic acid structures, it seems that the sequences cannot be recognized. Thank you very much! Best, Chen - Dr. Florian Brückner Laboratory of Biomolecular Research (LBR) OFLG/102 Paul Scherrer Institut CH-5232 Villigen PSI Switzerland Tel.: +41-(0)56-310-2332 Email: florian.brueck...@psi.ch
Re: [ccp4bb] Isothermal titration calorimetry
Keep in mind that output files from nanoITC, TA instrument cannot be red by Origin. At some point you will need to analyse your data further. George -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anastassis Perrakis Sent: Saturday, March 23, 2013 12:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Isothermal titration calorimetry It might be worth to consider the question more in detail. Do you want to study thermodynamics of the interaction, or a KD would do? If the former, you need ITC. If the latter, and you want to study things at the level of KD only, maybe investing on a plate reader, thermophoresis, or some biosensor technology (spr or interferometry based systems) should be considered. Then, what interactions will you study with the ITC? In general, I would agree that the lower sample volume is worth the nano options, but depending on the typical systems under study, sometimes the gain on sample quantity is not worth the money - while many times its worth it. John is if course right that for studying specific systems as the one he describes the 200 is great. A. Sent from my iPhone On 23 Mar 2013, at 11:00, John Fisher johncfishe...@gmail.com wrote: I would recommend the Microcal ITC 200, hands down. Not only is it an amazing instrument with the optional automated sample loader (which is worth every penny), but we were able to do experiments (multiple) using FULL-LENGTH p53 binding to a weak cognate protein. I believe this was the first time ITC was ever used with full length p53, as it is so labile and just loves immediately to oligomerize. Sample sizes pay for the instrument. Best, John John Fisher, M.D./PhD St. Jude Children's Research Hospital Department of Oncology Department of Structural Biology W: 901-595-6193 C: 901-409-5699 On Mar 23, 2013, at 4:45 AM, Sameh Soror shamd...@googlemail.com wrote: Dear All, I am sorry for the off topic question. I am going to buy ITC to study protein-protein protein-ligand interactions I am comparing microcal, GE and nanoITC, TA instrument.. any suggestions, recommendations, good experiences or bad experiences. is there a better system. Thank in advance for the help. Regards Sameh -- Sameh Soror Postdoc. fellow
Re: [ccp4bb] How to convert file format from CNS to CCP4
On 03/23/2013 09:59 AM, Wei Feng wrote: Can you help me to check out why these maps can not be converted by sftools? sftools is not for manipulating map files. Mapman from uppsala software factory would be a good choice. xdlmapman, a gui frontend to it, used to be part of ccp4. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Isothermal titration calorimetry
George, would you please explain your comments? We've found the TA Instruments analysis software very robust and user friendly. We have the low volume nanoITC from TA instruments and get equivalent #'s in our comparison tests to the Microcal instrument. Cheers, Chris -- Christopher L. Colbert, Ph.D. Assistant Professor Department of Chemistry and Biochemistry North Dakota State University P.O. Box 6050 Dept. 2710 Fargo, ND 58108-6050 PH: (701) 231-7946 FAX: (701) 231-8324 On 3/23/13 8:47 AM, George Kontopidis gkontopi...@vet.uth.gr wrote: Keep in mind that output files from nanoITC, TA instrument cannot be red by Origin. At some point you will need to analyse your data further. George -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anastassis Perrakis Sent: Saturday, March 23, 2013 12:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Isothermal titration calorimetry It might be worth to consider the question more in detail. Do you want to study thermodynamics of the interaction, or a KD would do? If the former, you need ITC. If the latter, and you want to study things at the level of KD only, maybe investing on a plate reader, thermophoresis, or some biosensor technology (spr or interferometry based systems) should be considered. Then, what interactions will you study with the ITC? In general, I would agree that the lower sample volume is worth the nano options, but depending on the typical systems under study, sometimes the gain on sample quantity is not worth the money - while many times its worth it. John is if course right that for studying specific systems as the one he describes the 200 is great. A. Sent from my iPhone On 23 Mar 2013, at 11:00, John Fisher johncfishe...@gmail.com wrote: I would recommend the Microcal ITC 200, hands down. Not only is it an amazing instrument with the optional automated sample loader (which is worth every penny), but we were able to do experiments (multiple) using FULL-LENGTH p53 binding to a weak cognate protein. I believe this was the first time ITC was ever used with full length p53, as it is so labile and just loves immediately to oligomerize. Sample sizes pay for the instrument. Best, John John Fisher, M.D./PhD St. Jude Children's Research Hospital Department of Oncology Department of Structural Biology W: 901-595-6193 C: 901-409-5699 On Mar 23, 2013, at 4:45 AM, Sameh Soror shamd...@googlemail.com wrote: Dear All, I am sorry for the off topic question. I am going to buy ITC to study protein-protein protein-ligand interactions I am comparing microcal, GE and nanoITC, TA instrument.. any suggestions, recommendations, good experiences or bad experiences. is there a better system. Thank in advance for the help. Regards Sameh -- Sameh Soror Postdoc. fellow
Re: [ccp4bb] ionic interaction inside a protein
Try PDBSum Jürgen On Mar 23, 2013, at 9:34 AM, Faisal Tarique wrote: Dear all I am working on a thermostable protein and i have read that the stability to high temperature is due to various ionic interactions among the amino acid residues of the protein itself..I request you all to tell me any web server which can show all the ionic interactions between amino acid residues in my protein structure by just uploading its coordinate file.inhttp://file.in/ a nut shell i want to identify those residues in my protein which are taking part in ionic interaction. -- Regards Faisal School of Life Sciences JNU .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
[ccp4bb] molecular replacement problem.
Dear members, I am doing a molecular replacement of a transcription factor whose ligand binding structure(24000 Da) is available in PDB but not for the DNA binding(13000 Da). When i am searching for the two copies from ligand binding domain as a template model, i am getting very good solution but i am not getting any density for the DNA binding domain to build up in density. The space gorup is P 1 21 1 (4) and unit cell parameters are Unit Cell: 57.43 69.36 105.99 90.00 90.00 90.00. Please guide me how to get the complete model structure. Table below show the matthews statistics For estimated molecular weight 37000. Nmol/asym Matthews Coeff %solvent P(2.20) P(tot) _ 1 5.7178.46 0.00 0.01 2 2.8556.91 0.62 0.70 3 1.9035.37 0.37 0.29 4 1.4313.82 0.00 0.00 _ The phaser molecular replacement gives the following table. istogram of relative frequencies of VM values -- Frequency of most common VM value normalized to 1 VM values plotted in increments of 1/VM (0.02) --- relative frequency --- 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 ||||||||||| 10.00 - 8.33 - 7.14 - 6.25 - 5.56 - 5.00 - 4.55 - 4.17 - 3.85 -- 3.57 --- 3.33 -- 3.12 -- 2.94 (COMPOSITION*1) 2.78 --- 2.63 2.50 - 2.38 2.27 -- 2.17 --- 2.08 -- 2.00 -- 1.92 --- 1.85 --- 1.79 --- 1.72 - 1.67 - 1.61 - 1.56 - 1.52 - 1.47 * (COMPOSITION*2) 1.43 - 1.39 - 1.35 - 1.32 - 1.28 - 1.25 - $TABLE : Cell Content Analysis: $SCATTER :N*Composition vs Probability:0|3x0|1:1,2: $$ N*Composition Probability $$ loggraph $$ 1 0.306066 2 0.00141804 $$ Most probable VM for resolution = 2.27817 Most probable MW of protein in asu for resolution = 92664.2 Thank a lot in advance
Re: [ccp4bb] molecular replacement problem.
Dear Appu, I am not sure that I have a complete sense of the issue at hand since some of the information needed to think your issue through is missing in your email. For example, to what high resolution cut-off were the data measured? What resolution limits were used for the MR search? How do the unit cell dimensions and space group in the two cases compare? I am guessing the ligand binding domain in your protein has the identical sequence to that of the published ligand binding domain that you use as a template in your MR search. In any case, here are a couple of my thoughts: (1) It might be worth setting up different runs of MR with different numbers for expected copies (not just two copies but also one copy and three copies just in case you have one of the extreme cases of solvent content)? (2) If the MR solution is correct and there is physical room for a DNA binding domain in your lattice (check by displaying symmetry mates), perhaps the DNA binding domain is disordered. In that case (and if all attempts with current data fail), you may have to crystallize the protein in presence of DNA. Good luck! Raji On Sat, Mar 23, 2013 at 2:26 PM, Appu kumar appu.kum...@gmail.com wrote: Dear members, I am doing a molecular replacement of a transcription factor whose ligand binding structure(24000 Da) is available in PDB but not for the DNA binding(13000 Da). When i am searching for the two copies from ligand binding domain as a template model, i am getting very good solution but i am not getting any density for the DNA binding domain to build up in density. The space gorup is P 1 21 1 (4) and unit cell parameters are Unit Cell: 57.43 69.36 105.99 90.00 90.00 90.00. Please guide me how to get the complete model structure. Table below show the matthews statistics For estimated molecular weight 37000. Nmol/asym Matthews Coeff %solvent P(2.20) P(tot) _ 1 5.7178.46 0.00 0.01 2 2.8556.91 0.62 0.70 3 1.9035.37 0.37 0.29 4 1.4313.82 0.00 0.00 _ The phaser molecular replacement gives the following table. istogram of relative frequencies of VM values -- Frequency of most common VM value normalized to 1 VM values plotted in increments of 1/VM (0.02) --- relative frequency --- 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 ||||||||||| 10.00 - 8.33 - 7.14 - 6.25 - 5.56 - 5.00 - 4.55 - 4.17 - 3.85 -- 3.57 --- 3.33 -- 3.12 -- 2.94 (COMPOSITION*1) 2.78 --- 2.63 2.50 - 2.38 2.27 -- 2.17 --- 2.08 -- 2.00 -- 1.92 --- 1.85 --- 1.79 --- 1.72 - 1.67 - 1.61 - 1.56 - 1.52 - 1.47 * (COMPOSITION*2) 1.43 - 1.39 - 1.35 - 1.32 - 1.28 - 1.25 - $TABLE : Cell Content Analysis: $SCATTER :N*Composition vs Probability:0|3x0|1:1,2: $$ N*Composition Probability $$ loggraph $$ 1 0.306066 2 0.00141804 $$ Most probable VM for resolution = 2.27817 Most probable MW of protein in asu for resolution = 92664.2 Thank a lot in advance -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] ionic interaction inside a protein
you can try the following link: http://pic.mbu.iisc.ernet.in/ Seema Nath
