[ccp4bb] Postdoc position at Washington University
Dear all, We have a postdoc position available at Washington University in St. Louis. The postdoctoral research will focus on elucidating the structural mechanism of membrane proteins as targets of cardiovascular therapy using novel multidisciplinary approaches. Please see attachment for full description of the job, and send your application to wei...@wustl.edu. Regards, Weikai To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ Postdoc Ad 2021.pdf Description: Postdoc Ad 2021.pdf
[ccp4bb] Postdoctoral position at Washington University in St. Louis
One postdoc position is available immediately in Dr. Weikai Li’s lab at Washington University in St. Louis. The medical school has a tradition of excellence in biomedical science. The postdoctoral research will focus on cryo-EM and crystallographic studies of membrane proteins important in cardiovascular biology. Applicants should have a good publication record and strong dedication to scientific research and academic career. Solid training in structural biology techniques and experience with eukaryotic expression systems will be greatly helpful. The Li lab is well equipped for structural, biochemical, mass spectrometry and cellular studies. We have regular and frequent access to APS beamlines and Titan Krios at Washington University. Recent publications of the lab can be found at http://www.biochem.wustl.edu/faculty/li.html. The lab is well funded by four grants from NIH and Keck foundation. Postdocs in lab are supported with generous packages that cover the family living cost in Midwest. Previous trainees have obtained professorship and funding at top universities. Please send a CV with reference information to wei...@wustl.edu. Weikai Li, Ph. D. Associate Professor Department of Biochemistry and Molecular Biophysics Washington University in St. Louis To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Postdoctoral position at Washington University in St. Louis
Applications are invited for a joint postdoctoral position in the Medical School of Washington University in St. Louis. Washington University has a tradition of excellence in medical science and a stimulating academic environment. Weikai Li and Jianmin Cui labs study the structural biology and electrophysiology of various membrane proteins including ion channels. The postdoctoral research will involve the structural determination of these integral membrane proteins using cryo-EM and X-ray crystallography techniques. Applicants should have expertise in membrane protein biology or structural biology. The labs are well funded and have great facilities, including access to a state-of-art Titan Krios, available to support these researches. Please send a CV and reference letters to wei...@wustl.edu<mailto:wei...@wustl.edu>. More information can be found at http://www.biochem.wustl.edu/faculty/li.html and https://research.engineering.wustl.edu/~jcui/index.html.
[ccp4bb] Postdoctoral position at Washington University in St. Louis
Applications are invited for a joint postdoctoral position in the Department of Biomedical Engineering and the Medical School of Washington University in St. Louis. Washington University has a tradition of excellence in medical science and a stimulating academic environment. Weikai Li and Jianmin Cui labs study the structural biology and electrophysiology of various membrane proteins including ion channels. The postdoctoral research will involve the structural determination of these integral membrane proteins using cryo-EM and X-ray crystallography techniques. Applicants should have expertise in membrane protein biology or structural biology. The labs are well funded and have great facilities, including access to a state-of-art Titan Krios, available to support these researches. Please send a CV and reference letters to wei...@wustl.edu<mailto:wei...@wustl.edu>. More information can be found at http://www.biochem.wustl.edu/faculty/li.html and https://research.engineering.wustl.edu/~jcui/index.html.
[ccp4bb] postdoctoral position at Washington University
Applications are invited for a postdoctoral position at Washington University in St. Louis. The NIH supported research will focus on the structure and function of intramembrane enzymes. Studies will use multidisciplinary approaches including macromolecular X-ray crystallography, biochemistry, and cell biology. The candidate would ideally have experience with eukaryotic protein _expression_ systems. The lab website is at http://biochem.wustl.edu/faculty/faculty/weikai-li. Applicants should send their CV with contact information of references to l...@biochem.wustl.edu.
[ccp4bb] Postdoc Position
Applications are invited for a postdoctoral position in the Washington University at St. Louis. The NIH supported research will focus on the structure and function of intramembrane enzymes. Studies will use multidisciplinary approaches including macromolecular X-ray crystallography, biochemistry, membrane biology, and cell biology. Salary commensurates with experience. Applicants should send their CV with contact information of references to l...@biochem.wustl.edu.
[ccp4bb] Postdoc position in Chicago, Illinois, USA
A postdoc position is available in Prof. Constance Jeffery's lab at the University of Illinois at Chicago, starting immediately or within the next few months. While an experienced crystallographer would be strongly preferred, someone with experience in protein expression, purification, and biochemical/biophysical characterization would also be considered. The initial appointment is short-term (approximately 6 months), but might be extended if additional funding or a postdoc fellowship can be obtained. The previous postdoc in the Jeffery lab obtained a tenure-track position and a CAREER award and is now a tenured associate professor! Qualified applicants please send an email and a curriculum vitae to Prof. Jeffery at cjeff...@uic.edu. Due to the need to extend the funding soon, the position can only be offered to someone who has work permission in US.
Re: [ccp4bb] Hampton's adjustable cryoloop
Hi Zhijie,
This loop is good if you have a long unit cell on one dimension and you can
align your crystal in a particular direction. You basically need a beamline
equipped with Kappa, which allows you to directly put the crystal on with the
plastic tube. A normal cryotong does not hold the bent loop.
Regards,
Weikai
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zhijie Li
[zhijie...@utoronto.ca]
Sent: Tuesday, June 07, 2011 5:30 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Hampton's adjustable cryoloop
Hello,
I just noticed that Hampton Research carries this adjustable mounted cryoloop
(HR5-900):
http://hamptonresearch.com/product_detail.aspx?cid=24sid=136pid=385wlmailhtml:{35C92305-260C-4820-B40D-05B0D91A0A8F}mid://0065/!x-usc:http://hamptonresearch.com/product_detail.aspx?cid=24sid=136pid=385
This looks quite interesting to me, as it seems that not every synchrotron
station's configuration can allow the use of an extended arc.
I wonder if somebody here can share some insights or experiences about this
adjustable cryoloop. I once tried to bend my non-hollow stainless steel pin in
liquid nitrogen with tweezers. It didn't work - the pin was too stiff then I
lost my crystal in the end. I wonder if this cryoloop was designed such that
bending it would be easier.
Thanks in advance!
Zhijie
[ccp4bb] crystal bent once open cover slip
Hi Folks, We have some membrane protein crystals that are grown in 30%PEG400, 0.1M Na Citrate pH 4.5, 0.1M LiCl. The protein is purified in DDM. The crystals are long rods and grown under room temperature in a hanging drop set up. But once we open the cover slip, we see the rods start to break and bend in a few seconds. Since it is in high PEG400, we just directly freeze the crystals. The diffraction only goes to 10 Ang at synchrotron. Have anybody had similar problem before and any suggestions? Thanks a lot, Weikai
[ccp4bb] Fwd: [ccp4bb] Summary: measure detergent concentration
Hi Folks, The paper Phil recommended looks very nice. Below is a summary when last time I asked people about this. Regards, Weikai Original Message Subject: [ccp4bb] Summary: measure detergent concentration Date: Wed, 28 Oct 2009 16:49:32 -0400 From: wei...@crystal.harvard.edu To: CCP4BB@JISCMAIL.AC.UK Dear All: Thanks a lot for all the responses. My question was about measuring the detergent concentration after concentrating a membrane protein sample. Here is the summary. 1. The simplest way to control the detergent concentration is to use a higher cut-off concentrator if you protein plus detergent micelle is large enough. Michael Matho: “a 50kDa cutoff withheld a lot of detergent during concentration process and consequently your final concentration might increase significantly. For example we started with 0.25% DES and noticed increases of above 1%. This did not happen when using a 100kDa cutoff, and DES concentration remain pretty much constant.” It is easy enough to test the “maximal cutoff you can use w/o loosing your membrane protein in the flow through”. 2. Patrick Loll, Edward A. Berry and John K. Lee suggested TLC, which seems to have the least requirement for equipments -- “silica gel TLC plates and a chromatography jar”. Patrick: “We've done this as an exercise in NSLS Membrane Protein Crystallization workshop for a few years, and it works like a charm. You can stain in a warm iodine chamber and visualize by scanning the TLC plate on a garden variety scanner (we use an inexpensive Canon LIDE that probably cost less than USD 60 five years ago). We quantify the spot intensity with NIH Image or equivalent, and get lovely linearity down to the CMC, spotting only 1 uL of sample--so we haven't seen any need to concentrate. Edward: “spotting on a TLC plate and running beside standard amounts of the same detergent. From intensity/size of the detergent spot after developing you can bracket the detergent concentration. (And by the way they found that detergents are concentrated by ultrafiltration). To increase sensitivity, speedvac a volume too large to spot on the plate, dissolve the residue in MeOH.” A strategy for identification and quantification of detergents frequently used in the purification of membrane proteins. Laura R. Eriks, June A. Mayor, and Ronald S. Kaplan. Analytical Biochemistry 323 (2003) 234–241 3. For sugar-based detergents (maltosides and glucosides), one can use some traditional chemistry to measure the sugar. Bert Van Den Berg: “do a fehling-type assay” Zhenfeng Liu: ”phenol-sulfuric acid reaction for quantification of sugars.” Biochemistry, vol 36, no. 19, 1997, p. 5887 Hari Jayaram: “sulfuric acid and phenol followed by Absorption measurement; using a standard curve against the same detergent ”. Anal Biochem. 2005 Jan 1;336(1):117-24. A colorimetric determination for glycosidic and bile salt-based detergents: applications in membrane protein research. Urbani A, Warne T. 4. Christopher Law: Use surface tension properties and look at the drop shape (measure contract angle). “A small droplet of the detergent solution is deposited on a piece of Parafilm M and side views are recorded by two orthogonally arranged TV cameras.” A Novel Method for Detergent Concentration Determination. Biophys J. 2006 January 1; 90(1): 310–317. Thomas C. Kaufmann, Andreas Engel, and Hervé-W. Rémigy. 5. Ezra Peisach: by Refractive index. “Refractive index measurements were performed using an OPTILAB DSP instrument (Wyatt Technology) with a P10 cell.” Refractive index-based determination of detergent concentration and its application to the study of membrane proteins Pavel Strop and Axel T. Brunger. Protein Sci. 2005 August; 14(8): 2207–2211. 6. Michael Matho: NMR is the most accurate method “using a high detergent concentration stock solution you can assign resonance peaks to your detergent molecule bonds. Then you can set up a standard curve using different known detergent concentrations (for example from 10% down to 0.1%) by calculating the surface of your peak(s) which is directly related to your detergent concentration. Each time you need to know the concentration of a new sample, you just need to record the peaks, and use the three-click rule to deduct the unknown value.” 7. David Veesler and Kornelius Zeth suggested ATR-FTIR (Fourier transform infrared spectroscopy). “very accurate, fast (10min) and requires as low as 10uL of protein sample.” PVeesler, D. et al. Production and biophysical characterization of the CorA transporter from M. mazei. Analytical Biochem. (2009). 388 :115-121. Regards, Weikai
[ccp4bb] composite omit map in CCP4
Hi Folks, Is there an easy way to generate a composite omit map using CCP4? I know this has been discussed a few times before. But has anybody written some new programs recently? Regards, Weikai
Re: [ccp4bb] analytical ultracentrifugation
Hi: Just a related question. To measure MW of membrane proteins, the density of detergents needs to be matched by D2O/H2O and should be within 1.0 to 1.1. Anyone knows some literature that gives a list of detergents having suitable density? Unfornatatedly, the common ones like Foscholine 12(DPC) and C12E9 do not work with my protein. Regards, Weikai Hi Mike, try the National Analytical Ultracentrifugation Facility in Connecticut. http://www.biotech.uconn.edu/auf/ Cheers, Petra Dear colleagues, does anyone know of a faciltiy for analytical ultracentrifugation? Thanks. Mike Colaneri -- Petra Verdino, PhD Research Associate The Scripps Research Institute, BCC206 10550 North Torrey Pines Road CA 92037 La Jolla, USA tel:1-858-784-2945 fax:1-858-784-2980 http://www.scripps.edu/~verdino/homepage.htm
[ccp4bb] [Fwd: Re: [ccp4bb]: self rotation function matrix NCS matrix]
Hi Eleanor and others: This is a little too late to follow up on this thread. But here is a similar question concerning MR and self-rotation. Without going into the translational part of MR, is it possible to tell the orientation of a 2-fold axis directly from the cross-rotation peaks? e.g. I have 2 top peaks from the cross-rotation function. There is also a strong 2-fold axis shown in self-rotation (kappa=180). Persumbaly then the two cross-rotation peaks are related by this 2-fold axis. From the angles of the two cross-rotation peaks, can I already tell the direction of the 2-fold axis? Regards, Weikai ÍúÍú wrote: I calculated the self-rotation function matrix with POLARRFN (named 1), and also got the molecular replacement solution with phaser, and used CNS's get_ncs_matrices to acquire the NCS matrix (named 2). Now what I wanted to do is to compare the results of 1 and 2. Are they the same or not, or which self-rotation function matrix is the right one of true NCS. Could you give me some suggestions? By the way, if I have got one molecule's PDB, and the rotation function matrix, are there any softwares on acquiring the other molecule's PDB? Many thanks POLARRFN will give you ALL symmetry equivalent rotations for your point group. Only one of these will relate your molecule A to B, and its inverse should relate B to A. Both will be listed in the POLARRFN output, plus probably many others depending on your point group.. I do not know the CNS convention now but it certainly used to be different from the CCP4 one. Hwever if you use he GUI cordinarte utilities superpose molecules select superpose by numbered residues then match A to B the log file will give you the ALPHA BETA GAMMA and the polar angles nt e same convention as POLARRFN. Eleanor
