[ccp4bb] Postdoctoral position at the University of Pittsburgh, School of Pharmacy
Post for a colleague: We are seeking a highly trained and self-motivated postdoctoral associate/biomedical scientist (PhD or other doctoral degrees) to participate in chemogenomics-based drug research projects ( http://www.cbligand.org/XieLab). To advance our *CELL*-published technology of 3D Cryo-EM Structure of Human Cannabinoid Receptor CB2-Gi Signaling Complex *(*PMID:32004460), we are seeking an individual with the following expertise and qualifications: - must have the expertise and working experience in molecular biology/microbiology (e.g., cloning, site-directed mutagenesis, CRISPR-Cas9, etc.) - working experience in autophagy, cell fate decision-making, and cell signaling studies that can be applied to targeting cannabinoid CB2 receptor, squestosome-1/p62, Ink4c/p18 proteins for drug research projects focusing on the following diseases: immune/inflammatory diseases (e.g., GVHD, IBD), acute myeloid leukemia (AML), multiple myeloma (MM), kidney fibrosis, Alzheimer’s diseases, hematopoietic stem cells, COVID-19, and osteoporosis; - experience working with cells at BSL2/BSL2+ is essential; experience with receptor binding affinity bioassay and cellular functional bioassays is desirable; - experience with *Baculovirus *(sf9) and/or *E coli *expression systems, IMAC, SEC, and other novel purification protocols; as well as AKTA purification and LC-MS/MS systems to provide functional proteins for bioassays and structural characterizations; experience with X-ray crystallographic biophysics and/or CryoEM is a plus; - must have demonstrated independent ability to design and execute experiments, prepare figures of results, analyze & interpret those results, and present them in a professional scientific manner; - must have experience in performing literature searches and can assist with scientific writing (manuscripts and grant proposals); meticulous record-keeping of research work is required; - good verbal and interpersonal skills are also necessary; individuals may be required to assist and guide graduate students and other post-docs in the lab. Salary is commensurate with experience. Please apply through the University of Pittsburgh Talent Center at www.join.pitt.edu. Also, please email your CV, letter, and three references to Prof. Sean Xie, sean@pitt.edu, and his assistant Dr. Terry McGuire t...@pitt.edu with *“Manager-Postdoc*” in the subject line. The University of Pittsburgh is an Affirmative Action/ Equal Opportunity Employer and values equality of opportunity, human dignity, and diversity, EOE, including disability/vets. -- ----- Cheng Zhang 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/
[ccp4bb] Multiple postdoc positions at Icahn School of Medicine, Mount Sinai, New York, USA
%80%9D//www.wpxi.com/news/business/pitt-team-discovers-new-way-find-nanobodies-fight-disease/UHJISHPYNRGW7JWFUEOE7FQIHA/%E2%80%9D%E2%80%9D%E2%80%9D%E2%80%9D%E2%80%9D> -- - Cheng Zhang 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/
[ccp4bb] Postdoc positions at Icahn School of Medicine, Mount Sinai, New York, USA
%80%9D//www.wpxi.com/news/business/pitt-team-discovers-new-way-find-nanobodies-fight-disease/UHJISHPYNRGW7JWFUEOE7FQIHA/%E2%80%9D%E2%80%9D%E2%80%9D%E2%80%9D%E2%80%9D> -- - Cheng Zhang 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/
Re: [ccp4bb] Non-standard amino acids in Coot
I had this issue before and tried several ways to fix it. The best way
that works for me is to edit the PDB and cif files of this unnatural
amino acid for Coot or Phenix. The goal is to allow COOT and Phenix to
recognize it as an 'amino acid', not a random HETATM, so they can add
peptide bonds and apply appropriate geometry restrictions in the real-space
refinement automatically. But I will be interested to learn better ways if
there are any.
Here is how I do it: 1. Make a PDB file with Phenix's elbow based on the
chemical structure of this amino acid. I usually use MDL or SDL files. 2.
Change the names of atoms in the PDB file. You have to name the main chain
atoms of amino acids specifically so COOT can read them as 'amino acids'.
Open a PDB file of any protein and you will see those specific names (C, O,
N, C, CA, CB). 3. Use this PDB file to make a cif file. In the cif file,
you have to define this amino acid as an 'L-peptide' or 'D-peptide' in the
ligand type line. I attached a cif file of L-cysteine. Pay attention to the
ligand definition (' L-peptide') and the names of atoms. 4. Open the PDB
and cif files in Coot. Merge this amino acid into your structure and change
its numbering. Now you should be able to do real space refinement on it as
if it is a natural amino acid.
Also, there are already many unnatural amino acids in COOT or Phenix
database. You just have to find the right 3-letter codes.
Hope it helps.
Cheng
On Mon, Jun 14, 2021 at 10:05 AM Hall, Gareth A.F. (Dr.) <
gh...@leicester.ac.uk> wrote:
> Dear ccp4bb,
>
>
>
> I am having an issue with a non-standard amino acid in Coot. I have a
> cyclic peptide that is stapled using two cysteine residues and a methylene
> bridge. I have prepared a restraints file using ACEDRG for a methyl
> cysteine as a surrogate for one of the cysteine residues and I have fitted
> it into the density in the appropriate space within the peptide where the
> cysteine would have been. I have made LINKs between the appropriate atoms
> of the previous and subsequent amino acids in the peptide chain to the
> methyl cysteine, as well as between the methyl component of the methyl
> cysteine and the bonded cysteine residue to form a methylene bridge. The
> resulting pdb file runs without fault within REFMAC, but when I open the
> refined files in Coot and try to triple refine the methyl cysteine within
> the peptide chain Coot pushes all the residues away from each other.
>
>
>
> Please can someone advise as to what I am missing/doing wrong!
>
>
>
> Many thanks in advance,
>
>
>
> Gareth
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
--
-
Cheng Zhang
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CYS.cif
Description: Binary data
[ccp4bb] Refine modified residues based on cryo-EM maps
Hi everyone, This question must have been asked before but I couldn't find a good answer online. I work on a cryo-EM structure with one serine residue covalently linked with a lipid molecule. The map for the lipid moiety was there but not good enough to unambiguously place each atom. I tried to manually model the lipid moiety to fit the map. But if I refine it in real space, it would move away from the serine residue even though I linked it to the residue in the PDB file. My question is, how to refine such a modified residue in real space without breaking the covalent bond? Is there any way to make a molecular topology file for the lipid moiety that also contains restraints for the covalent bond with the modified residue? Also, let's say there is an unnatural amino acid in the protein, how to define this residue so COOT or Phenix can recognize it as an amino acid and the peptide bond restraints still apply to it? Thanks! Cheng -- - Cheng Zhang 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/
[ccp4bb] Postdoc position at the University of Pittsburgh, protein design and engineering for drug development
Dear Colleagues, I post this for Dr. Yi Shi at the University of Pittsburgh. *Description:* a postdoctoral position is available in the Shi laboratory of antibody biotechnology and proteomics at the Department of Cell Biology, University of Pittsburgh School of Medicine (UPMC). The laboratory is at the forefront of developing transformative new technologies that integrate proteomics, computational biology, and structural approaches for large-scale antibody (especially camelid VHH antibody/ nanobody) discovery and characterization. The lab is also interested in applying these techniques to develop novel nanobody-based therapies for some of the most devastating diseases including COVID-19, cancer, and neurodegeneration. The lab is currently funded by several grants including the NIH, MJFF, and Alzheimer Foundation. More information about our research could be found here at www.shi-lab.org. For the successful incumbent, the initial appointment is 12 months with the possibility of renewal. Compensation will follow standard NIH Post-Doc salary rates and is based on experience. We strongly support the career development of our colleagues and trainees. A listing of Pitt employee benefits is available at https://www.hr.pitt.edu/current-employees/benefits Highly motivated individuals with a background in biochemistry, bioengineering, biophysics or structural biology (especially membrane protein structural biology) are welcome to apply. Successful candidates should have excellent communication skills and the desire to lead research projects. Interested candidates may submit their CV including names and contact information for two-three references, a short description of their research experience, and research goals to Yi Shi at (yi@pitt.edu). For more information about our research visit: https://www.shi-lab.org/ *Pittsburgh:* As the second-largest city in Pennsylvania, Pittsburgh is best known as "the city of Bridges". In 2015, Pittsburgh was listed among the "eleven most livable cities in the world" and has been considered as one of the most livable cities in the United States. *The University of Pittsburgh is an Equal Opportunity Employer**.* -- ----- Cheng Zhang 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/
Re: [ccp4bb] A helix with leucine repeats
Hi Michael, Thanks for the information. It is amphipathic. It follows a transmembrane helical domain of a cell surface receptor and adopts an orientation parallel to the membrane. So it may be associated with the membrane. I am just wondering if such leucine-repeat motif is special among all amphipathic, membrane-associated helical structures. In other words, any other possible functional roles than just membrane association? Best, Cheng On Sat, Mar 3, 2018 at 10:23 PM, R. Michael Garavito <rmgarav...@gmail.com> wrote: > Dear Cheng, > > Chris and Ruud have provided you with the typical interpretation of such a > motif, but you have forgotten to give the CCP4 community the context of > this leucine-repeat helix. Is it amphipathic? Does the protein also have > transmembrane helices (as suggested by the figure provided) which would > provide the membrane anchoring? > > Look up structurally similar membrane proteins (not necessarily homologous > by sequence), such as proteins which have a monotonic-like membrane > interaction, but that also have a transmembrane helix (monoamine oxidase or > some mammalian cyt P450s). If your protein is monotopic, look at that > class of membrane proteins (squalene cyclase, fatty acid hydrolase, > cyclooxygenase, etc.). One structurally undescribed motif is a “reentrant > membrane helix.” In other words, look at context before assigning > function. > > Good luck and hope this helps, > > Michael > > ** > > *R. Michael Garavito, Ph.D.* > > *Professor of Biochemistry & Molecular Biology* > > *513 Biochemistry Bldg. * > > *Michigan State University * > > *East Lansing, MI 48824-1319* > > *Office:* *(517) 355-9724 <(517)%20355-9724> Lab: (517) 353-9125 > <(517)%20353-9125>* > > *FAX: (517) 353-9334 <(517)%20353-9334>Email: > rmgarav...@gmail.com <garav...@gmail.com>* > > ** > > > > On Mar 3, 2018, at 3:51 PM, Cheng Zhang <chengzh1...@gmail.com > <chengzh1...@gmail.com>> wrote: > > Hi all, > > We recently got a structure of a transmembrane protein. There is a helix > that is parallel to the membrane. The function of this helix is not known > and we are trying to make some hypothesis. A unique feature is that there > are repeated leucine residues on this helix facing the lipids. I am > wondering if anyone has seen a similar pattern and could suggest possible > function, e.g. membrane anchoring? > > Thanks! > > Best, > > Cheng > > > > > -- > - > Cheng Zhang > > > -- - Cheng Zhang
Re: [ccp4bb] Regarding Patents
A related question. If you have a crystal structure and found a novel ligand binding site that can be used to regulate protein activity, could you patent such "binding site"? If not, how to make the best use of such findings? Thanks! Cheng On Sat, Nov 4, 2017 at 12:33 AM, James Phillips <phillipsjames...@gmail.com> wrote: > Realistically, if you live in the US and 5 SCOTUS judges agree you can > patent anything. > > On Fri, Nov 3, 2017 at 09:45 Francisco Tenjo <franja...@gmail.com> wrote: > >> Hi. >> >> A mutated DNA or protein molecule can be patented if the mutations are >> not present in nature and they have a technical effect (for example, in the >> case of antibodies, you could have increased affinity for an antigen if you >> make the right mutations of the CDRs). Also, the mutations should not have >> been published before you file your patent application. >> >> Regards, >> >> - Francisco >> >> 2017-11-03 6:26 GMT-04:00 Chris Morris <chris.mor...@stfc.ac.uk>: >> >>> > Sorry for asking out of context question. Can a mutated DNA or protein >>> molecule be patented. >>> >>> Yes and no. A molecule as such cannot be patented. But the use of a >>> molecule for a specific purpose can be. There are many patents for small >>> molecule drugs, and also for engineered antibodies, which are proteins. >>> There are patents for industrial use of enzymes too. >>> >>> regards, >>> Chris >>> >>> Chris Morris >>> chris.mor...@stfc.ac.uk >>> Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 >>> Mobile: 07921-717915 >>> Skype: chrishgmorris >>> http://www.citeulike.org/blog/chrishmorris >>> STFC, Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane, >>> Daresbury, Warrington, WA4 4AD UK >>> >> >> >> >> -- >> Francisco Tenjo >> > -- - Cheng Zhang
[ccp4bb] Questions about antibody in crystallization
Hi all, I have a naive question about antibodies. Many people used Fab fragments in crystallization. I am wondering if it is possible to use the whole IgG molecule with Fc fragment as well. Or it would be too flexible and bad for crystallization? Thanks, Cheng -- - Cheng Zhang
[ccp4bb] Instrument help: any comments on bench-top SPR
Dear colleagues, I would like to ask for asuggestions on bench-top SPR machine. In our lab we study the interaction between membrane proteins and peptide and lipid ligands. Our main focus is the structural study. We also want to use SPR to measure the binding kinetics such as on and off rates. Does anyone have experience with bench-top SPR like openSPR from Nicoya? It seems that it is a quite affordable machine. Just wondering how sensitive it is, how much protein it consumes and how much it costs for the sensors? Any suggestions would be appreciated. Thanks! Cheng Zhang -- - Cheng Zhang
[ccp4bb] Can anyone recommend a good 20 degree incubator?
Hi everyone, We are a new lab and we would like to buy a 20 degree incubator for crystal growth. However there are many choices with a broad range of prices. Can anyone recommend a good one with stable temperature control, minimal vibration, but with a reasonable price, like below $2000? Thanks, Cheng
[ccp4bb] Postdoctoral positions available at the University of Pittsburgh, Pittsburgh, PA, United States - Structural and molecular pharmacology of GPCRs
We have immediate openings for postdoctoral fellows in the lab of Dr. Cheng Zhang in the Department of Pharmacology and Chemical Biology at School of Medicine, University of Pittsburgh at Pittsburgh, PA, United States. Our lab is a newly established lab that focus on the studies of a family of cell surface receptors - G protein-coupled receptors (GPCRs). The aim is to understand the molecular mechanisms of the signal transduction by GPCRs, which represent 30-40% of current drug targets, and to explore the molecular pharmacology to facilitate future drug design. The initial research effort will focus on the structural characterization of several GPCRs that function in inflammation and calcium metabolism in complex with different ligands and signaling effectors. The main approach is X-ray crystallography, complemented by EM and NMR methods. The obtained structural information will be used in the following structure-based drug design to find new chemicals as potential drugs with desired pharmacological properties. Also structure-based development of macro-biomolecules such as antibodies and peptides as potential pharmaceuticals that can modulate the functional properties of GPCRs is another research direction. So far several GPCRs as important drug targets have been successfully prepared in the lab, which are ready for further structural studies. The potential candidates are expected to perform structural studies on these receptors and/or develop other biophysical and cell-based experiments to examine the signaling behaviors of these receptors in respond to different ligands/drugs. Interested candidates should be highly motivated and have a PhD with strong background in one or several of the followings: 1) Molecular cloning and recombinant protein expression and purification. Experienced in protein characterization using various biochemical and biophysical methods such as pull-down, western blot, mass spec, ITC etc. 2) Protein X-ray Crystallography. 3) Recombinant protein expression in mammalian cells. Making stable cell lines. FACS setups. Experience with confocol or TIRF is optional but would be a plus. 4) Antibody production and engineering. Producing antibodies in hybridoma cells. Antibody characterization by ELISA. Experience in phage display or yeast display would be a major plus. We offer a quite exciting and vibrating working environment. There are several laboratories in the department that focus on the studies of GPCRs. You will be working with enthusiastic professionals studying GPCRs from difference perspectives. An competitive salary will be provided based on previous research experience and accomplishments. The initial appointment will be one year with the potential to renew every year depending on the progress of the projects. As for living, Pittsburgh is a very nice city to live. It has been elected as one of the most livable cities in the US for years with a diversity of people and culture. For more information about the lab and the department, please see: http://www.pharmacology.us/Faculty/ChengZhang To apply, please send a CV with cover letter to Dr. Cheng Zhang at chengzh1...@gmail.com. 2-3 reference letters will be requested if you are shortlisted for call interview.
