[ccp4bb] Research / Postdoc Position in Proteostasis Mechanisms

[Tsai, Francis T.F.]

RESEARCH / POSTDOC ASSOCIATE

An NIH-funded research position is available in the Tsai laboratory at Baylor 
College of Medicine to determine the 3D structure, mechanism, and function of 
ATP-dependent protein quality control machines and related stress-response 
proteins using protein crystallography and cryoEM/ET. Applicants with a PhD or 
MSc in biochemistry, molecular/cell biology, or enzymology are encouraged to 
apply. Demonstrated experience with methods used to express and purify proteins 
is essential. Prior experience with site-directed mutagenesis, enzymology, 
mammalian cell culture, and/or model organisms, such as bacteria, fungi, and 
worms, is desired. The successful applicant will join a multi-disciplinary team 
to investigate stress response mechanisms in human diseases (e.g. AD, ALS, T2D 
and related metabolic disorders) and host-microbe interactions (e.g. IDs and 
NTDs). Salary is competitive and is in addition to a generous fringe benefit 
package. To apply, please send a cover letter with research interests and 
experiences, a current CV, and contact information for three referees to Dr. 
Francis Tsai (ft...@bcm.edu).


  *   Experience with protein expression and IEX, HIC, SEC chromatography is 
essential.
  *
  *   Prior experience in enzymology is an advantage (biochemists).
  *
  *   Prior experience with tissue culture or model organisms is an advantage 
(molecular/cell biologists)
  *   Applicants must be able to work independently and as a member of a team.
  *
All applicants with a graduate degree in biochemistry or biological sciences 
(including non-structural biologists) will be considered. Highly motivated 
scientists with excellent communication skills are encouraged to apply. Please 
share this job ad with friends and colleagues. Baylor College of Medicine is an 
equal opportunity employer.



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Re: [ccp4bb] [External] [ccp4bb] Protein's C-terminal neutral

[Srivastava, Dhiraj]

Hi Rohit
 Since you are saying the C terminus in crystal structure is not 
end of your protein in crystal, and you are worried about its charge status, is 
in't a good idea to model few residues beyond the C terminus you see in crystal 
structure using weak electron density and crystal packing as guide and then do 
the electrostatic calculation. Even if you are modeling it as COOH, it's not 
going to be true end anyway. Two or three extra residues should be sufficient 
as ionic interaction is going to be quite weak beyond 8-10 A.

Dhiraj

From: CCP4 bulletin board  on behalf of rohit kumar 

Sent: Wednesday, September 22, 2021 4:29 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [External] [ccp4bb] Protein's C-terminal neutral

Hello Everyone,

Is there any way that I could make my protein's C-terminal neutral using Coot?
Actually, I have a protein-peptide complex structure and my peptide is bound at 
the C-terminal end. While making a surface charge diagram it is negatively 
charged (because of the CO group at the end, which is not the end residue of my 
purified protein)  and I want to make it neutral (possibly a peptide bond in 
solution).

Please let me know if I am clear enough with my question.

Thank you

--
Regards
Dr. Rohit Kumar Singh
Postdoctoral fellow
Aurora CO USA





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Re: [ccp4bb] AW: [ccp4bb] Protein's C-terminal neutral

[Jon Cooper]

You could replace the OXT with a hydrogen, note O-H bond length is about 1 
Angstrom, a la neutron style refinement. Phenix has this sort of thing inbuilt, 
I think.

Sent from ProtonMail mobile

 Original Message 
On 23 Sep 2021, 10:06, Schreuder, Herman /DE wrote:

> Dear Rohit,
>
> Do you mean that the residues after your “C-terminus” have been deleted 
> because there is no convincing electron density for them?
>
> In that case, a charged carboxylate at the N-terminus is incorrect and you 
> should delete the OXT atom. Alternatively, you could add one residue at the 
> C-terminus and delete all atoms except the N. however, you may still have to 
> manually delete the OXT atom.
>
> Best,
>
> Herman
>
> Von: CCP4 bulletin board  Im Auftrag von rohit kumar
> Gesendet: Mittwoch, 22. September 2021 23:29
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [ccp4bb] Protein's C-terminal neutral
>
> Hello Everyone,
>
> Is there any way that I could make my protein's C-terminal neutral using Coot?
>
> Actually, I have a protein-peptide complex structure and my peptide is bound 
> at the C-terminal end. While making a surface charge diagram it is negatively 
> charged (because of the CO group at the end, which is not the end residue of 
> my purified protein) and I want to make it neutral (possibly a peptide bond 
> in solution).
>
> Please let me know if I am clear enough with my question.
>
> Thank you
>
> --
>
> Regards
> Dr. Rohit Kumar Singh
>
> Postdoctoral fellow
>
> Aurora CO USA
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
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>
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[ccp4bb] Professor in Physics of Imaging / Ecole polytechnique fédérale de Lausanne (EPFL) and Head of Mathematics and Physics of Imaging / Paul Scherrer Institut (PSI) ‒ Working ‐ EPFL

[Schertler Gebhard (PSI)]

https://www.epfl.ch/about/working/professor-in-physics-of-imaging-ecole-polytechnique-federale-de-lausanne-epfl-and-head-of-mathematics-and-physics-of-imaging-paul-scherrer-institute-psi/




Prof. Gebhard F.X. Schertler
Structural Biology ETH Zürich D-BIOL

Head of Biology and Chemistry
Division
Paul Scherrer Institut
Laboratory of Biomolecular Research,
LBR
OFLC 109
CH-5232 Villigen PSI
gebhard.schert...@psi.ch
phone +41 56 310 4265



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[ccp4bb] AW: [ccp4bb] Protein's C-terminal neutral

[Schreuder, Herman /DE]

Dear Rohit,

Do you mean that the residues after your "C-terminus" have been deleted because 
there is no convincing electron density for them?
In that case, a charged carboxylate at the N-terminus is incorrect and you 
should delete the OXT atom. Alternatively, you could add one residue at the 
C-terminus and delete all atoms except the N. however, you may still have to 
manually delete the OXT atom.

Best,
Herman

Von: CCP4 bulletin board  Im Auftrag von rohit kumar
Gesendet: Mittwoch, 22. September 2021 23:29
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Protein's C-terminal neutral

Hello Everyone,

Is there any way that I could make my protein's C-terminal neutral using Coot?
Actually, I have a protein-peptide complex structure and my peptide is bound at 
the C-terminal end. While making a surface charge diagram it is negatively 
charged (because of the CO group at the end, which is not the end residue of my 
purified protein)  and I want to make it neutral (possibly a peptide bond in 
solution).

Please let me know if I am clear enough with my question.

Thank you

--
Regards
Dr. Rohit Kumar Singh
Postdoctoral fellow
Aurora CO USA





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