[ccp4bb] Crystallography Job Vacancy at Argenta
Crystallography Job Vacancy at Argenta (Canterbury, UK) I would like to draw your attention to a full time position for a Crystallographer within the Argenta Structural Biology Group based in Canterbury, KENT UK. Argenta (a Galapagos company) is a successful and expanding contract Drug Discovery organisation with projects spanning a range of disease areas. As part of this continuing expansion we have a vacancy for a crystallographer. Please apply via the company website using the link below. http://www.argentadiscovery.com/careers/current-opps.htm#cryst Dave Brown Director of Structural Biology at Argenta
[ccp4bb] Fwd: DNA sequence from amino acid
-- Forwarded message -- From: Sumita Karan karansumit...@gmail.com Date: Mon, Jan 13, 2014 at 1:00 PM Subject: DNA sequence from amino acid To: CCP4BB@jiscmail.ac.uk Dear all, I am working on eukaryotic protein and have the amino acid sequence of the protein but do no know the sequence of cloned gene. Does anybody know how to get DNA sequence from the amino acid sequence using exprasy or other server?
Re: [ccp4bb] Fwd: DNA sequence from amino acid
reverse translation from protein to nucleotide does not yield a unique sequence. Your best bet is to use the BLAST feature that searches your protein sequence against the entire genbank DNA database translated into protein: http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?PROGRAM=tblastnPAGE_TYPE=BlastSearchLINK_LOC=blasthome This will find the natural genes (and the closest homologues).
[ccp4bb] Assays for protein-ligand interaction?
Sorry for the off topic. I'm looking for a way to monitor protein-(potential) ligand interaction. The ligand is small molecule (mw~250) and we're looking for its potential interaction with couple human proteins. (We do not know this small molecule interacts with these human protein or not.) Is there any efficient way to quickly identify whether this ligand interacts with those human protein? We can buy some protein, but the amount of commercially available purified proteins is very little, making them hard to be analyzed by some good methods (e.g. ITC). That would be really great if anyone suggest any idea. Sorry for the off topic question again. Thanks!
Re: [ccp4bb] Assays for protein-ligand interaction?
Ho Jun Lee, Have you thought about differential scanning fluorimetry (Thermofluor)? With this biophysical technique you can characterize protein-ligand interactions and screen a wide variety of ligands using minimal concentration of ligand and protein. All you need is a quantitative PCR machine (qPCR). Here is a reference for you https://chemistry.osu.edu/~magliery/pdfs/LavinderMagliery2009JACS.pdf Lorenzo Ihsan Finci, Ph.D.Postdoctoral Scientist, Wang LaboratoryHarvard Medical SchoolDana-Farber Cancer InstituteBoston, MA Peking UniversityCollege of Life SciencesBeijing, China Date: Mon, 13 Jan 2014 21:50:07 +0900 From: hojunle...@gmail.com Subject: [ccp4bb] Assays for protein-ligand interaction? To: CCP4BB@JISCMAIL.AC.UK Sorry for the off topic. I'm looking for a way to monitor protein-(potential) ligand interaction. The ligand is small molecule (mw~250) and we're looking for its potential interaction with couple human proteins. (We do not know this small molecule interacts with these human protein or not.) Is there any efficient way to quickly identify whether this ligand interacts with those human protein? We can buy some protein, but the amount of commercially available purified proteins is very little, making them hard to be analyzed by some good methods (e.g. ITC). That would be really great if anyone suggest any idea. Sorry for the off topic question again. Thanks!
Re: [ccp4bb] Assays for protein-ligand interaction?
FRET， CD， Fluorescence， NMR chemical shift assay, isotope-labelled ligand interaction assay, protein melting temperature assay, gel filtration retention assay, gyration radius assay by Malls, native page gel analysis, etc. Acoot On Monday, 13 January 2014 8:51 PM, HJ Lee hojunle...@gmail.com wrote: Sorry for the off topic. I'm looking for a way to monitor protein-(potential) ligand interaction. The ligand is small molecule (mw~250) and we're looking for its potential interaction with couple human proteins. (We do not know this small molecule interacts with these human protein or not.) Is there any efficient way to quickly identify whether this ligand interacts with those human protein? We can buy some protein, but the amount of commercially available purified proteins is very little, making them hard to be analyzed by some good methods (e.g. ITC). That would be really great if anyone suggest any idea. Sorry for the off topic question again. Thanks!
Re: [ccp4bb] Assays for protein-ligand interaction?
Specifically for fluorescence does your ligand fluoresce? It is possible if it has indol group or some aromatic organic compound Does your protein has a tryptophan or tyrosines in the binding site? If yes may be a fluorescence titration experiment could be the solution. Also fluorescence needs very low concentration of protein (nM to microM) george From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Acoot Brett Sent: Monday, January 13, 2014 3:09 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Assays for protein-ligand interaction? FRET， CD， Fluorescence， NMR chemical shift assay, isotope-labelled ligand interaction assay, protein melting temperature assay, gel filtration retention assay, gyration radius assay by Malls, native page gel analysis, etc. Acoot On Monday, 13 January 2014 8:51 PM, HJ Lee mailto:hojunle...@gmail.com hojunle...@gmail.com wrote: Sorry for the off topic. I'm looking for a way to monitor protein-(potential) ligand interaction. The ligand is small molecule (mw~250) and we're looking for its potential interaction with couple human proteins. (We do not know this small molecule interacts with these human protein or not.) Is there any efficient way to quickly identify whether this ligand interacts with those human protein? We can buy some protein, but the amount of commercially available purified proteins is very little, making them hard to be analyzed by some good methods (e.g. ITC). That would be really great if anyone suggest any idea. Sorry for the off topic question again. Thanks!
[ccp4bb] Announcement: Standardization of Amino Acid Nomenclature
Announcement: Standardization of Amino Acid Nomenclature The wwPDB is transitioning to use the nomenclature for pyrrolysine and selenocysteine as recommended by the joint nomenclature committee of IUPAC/IUBMB. Starting in January, PYL (for pyrrolysine) and SEC (for selenocysteine) will be used where three-letter codes appear for amino acids in new releases and updated in entries currently in the archive (50 entries). In April, the letter O (for pyrrolysine) and U (for selenocysteine) will be used where one-letter codes appear for amino acids in new releases and updated in entries currently in the archive. Questions and comments should be sent to i...@wwpdb.org.
[ccp4bb] Cryo-EM 3D Image Analysis Symposium 2014 - early registration ends Jan 31, 2014
Message below forwarded at the request of the conference organizers. From: Dorit Hanein do...@sanfordburnham.org Subject: [3dem] Reminder - Cryo-EM 3D Image Analysis Symposium 2014 - early registration ends Jan 31, 2014 Date: January 13, 2014 11:02:14 AM EST To: 3...@ncmir.ucsd.edu 3...@ncmir.ucsd.edu Reminder - The early registration fare for this workshop ends Jan 31, 2014. So please register soon (http://blake.bcm.edu/tahoe2014). _ We are pleased to announce the first International Conference on Image Analysis in Three-dimensional Cryo-EM, to be held at Granlibakken Conference Center, Lake Tahoe, California, March 12 to March 15, 2014 (http://blake.bcm.edu/tahoe2014) . Dorit Hanein, Chair Steven Ludtke, Co-Chair ORGANIZING COMMITTEE : Wah Chiu, Ed Egelman, Ben Hankamer, Masahide Kikkawa, David Mastronade, Pawel Penczek, Henning Stahlberg, Fei Sun, Niels Volkmann The goal of the Symposium is to discuss state of the art image analysis approaches to tackle challenging biological problems and to identify current limitations and remaining problems in the field as currently practiced. The goal will be for developers in this area, both established as well as students/postdocs to discuss the detailed algorithms and methodologies in this field in greater technical detail than is possible at more general meetings like the GRC. The central premise is that gaining a comprehensive and quantitative understanding of highly sophisticated machines, complexes, and organelles of the cell requires the active, timely and coordinated development of complementary image analysis and data mining algorithm and approaches. We have recruited an outstanding panel of speakers; including an outstanding keynote speaker and the leading algorithm developers in the field (http://ncmi.bcm.edu/ncmi/events/workshops/workshops_139/workshop_schedule_html ). Sessions: * Map Validation * Single Particle Approaches to Helical Symmetry and 2-D Crystals * Direct Detector Movie Processing * Tomogram Segmentation, Annotation and Filtration * Factors Limiting Resolution in Single Particle Analysis/Tomography * Heterogeneous Data in 2-D and 3-D All session will focus on interactive discussions with plenty of time for questions. We will also have a poster session, and selected posters will be invited to give short-format talks. _ Dorit Hanein, PhD
[ccp4bb] skin on crystal
We crystallized a protein at 4 and 22 deg C in different conditions: from ammonium sulfate in acetate buffer pH 5 and PEG4000 in Hepes buffer at pH 7.5 In both cases the drops have a slimy skin (almost feels like DNA). We therefore think that the skin is generated from the protein. I am sure some of you have had similar experiences. I would like your suggestions about how to avoid the skin. Please note that we are not asking for suggestions on how to handle the skin (such as using various tools) we are only interested in knowing if there is a way to prevent the formation of the skin. Thank you so much Debasish Ph: (205)934-0124; Fax: (205)934-0480
Re: [ccp4bb] skin on crystal
Usually the skin is precipitated protein when it comes into contact with air. In this case, avoiding contact with air may be the only way to avoid the skin, i.e. crystallise using a technique that is not vapour diffusion, but for instance microbatch, microdialysis or free interface diffusion. On 13 Jan 2014, at 21:02, Debasish Chattopadhyay wrote: We crystallized a protein at 4 and 22 deg C in different conditions: from ammonium sulfate in acetate buffer pH 5 and PEG4000 in Hepes buffer at pH 7.5 In both cases the drops have a slimy skin (almost feels like DNA). We therefore think that the skin is generated from the protein. I am sure some of you have had similar experiences. I would like your suggestions about how to avoid the skin. Please note that we are not asking for suggestions on how to handle the skin (such as using various tools) we are only interested in knowing if there is a way to prevent the formation of the skin. Thank you so much Debasish Ph: (205)934-0124; Fax: (205)934-0480
Re: [ccp4bb] skin on crystal
Do you use any Dnase while purifying your protein? if not try that and set up new drops to check again. Sent from my iPhone On 13.01.2014, at 21:02, Debasish Chattopadhyay debas...@uab.edu wrote: We crystallized a protein at 4 and 22 deg C in different conditions: from ammonium sulfate in acetate buffer pH 5 and PEG4000 in Hepes buffer at pH 7.5 In both cases the drops have a slimy skin (almost feels like DNA). We therefore think that the skin is generated from the protein. I am sure some of you have had similar experiences. I would like your suggestions about how to avoid the skin. Please note that we are not asking for suggestions on how to handle the skin (such as using various tools) we are only interested in knowing if there is a way to prevent the formation of the skin. Thank you so much Debasish Ph: (205)934-0124; Fax: (205)934-0480
