[ccp4bb] Structural Biology Faculty Position at Purdue University

[Andrew Mesecar]

* *

Faculty Position in Structural Biology

Purdue University



The Department of Biological Sciences and the Markey Center for Structural
Biology at Purdue University invite applications for a tenure-track faculty
position in Structural Biology. We expect to fill this academic-year
appointment at the Assistant Professor level, but appointment at the
Associate level will also be considered.  Applicants must have a Ph.D. or
equivalent in biology, chemistry, physics or related field and at least 2
years of postdoctoral experience in X-ray crystallography, cryo-EM, NMR or
other relevant field. The successful applicant will be required to
establish a strong and independent research program in structural biology
and to teach at the undergraduate and graduate levels.  Applicants with
research interests in cancer biology, drug discovery, energy & signal
transduction, infectious disease, large macromolecular complexes,
membrane-based transport, molecular pathogenesis, neurobiology, viruses or
viral-host interactions are encouraged to apply.



The Markey Center for Structural Biology at Purdue is recognized worldwide
for its leadership in structural biology of viruses, membrane proteins,
receptors, signaling proteins and enzymes in addition to methods
development in crystallography, NMR and electron microscopy.  The
Department has over 50 faculty members conducting research in a wide range
of fields including those areas listed above, bioinformatics, computational
chemistry and biology, ecology, evolutionary biology and vision research.
The successful candidate will have opportunities to interact with
colleagues in many departments and colleges including Chemistry, Medicinal
Chemistry and Molecular Pharmacology, Computer Science and Physics, and to
join centers such as the Center for Cancer Research and the new Center for
Drug Discovery.  The successful candidate will also have laboratory space
in the newly constructed Hockmeyer Hall of Structural Biology and will have
access to state-of-the-art shared resources across Purdue including a Titan
Krios cryo-TEM, Bruker Avance-III 800 MHz NMR, Rigaku X-ray generators and
detectors, and other advanced biophysical instrumentation available at the
Bindley Bioscience Center and the Birck Nanotechnology Center.



Applications must be submitted electronically to *sea...@bio.purdue.edu* as
a PDF file that includes a detailed curriculum vitae, names and addresses
of three referees, a 2 - 3 page summary of research interests, and a
one-page statement on a vision for teaching.  Inquiries should be directed
to *Structural Biology Search Committee, Department of Biological Sciences,
Purdue University, 915 W. State St., West Lafayette, IN 47907-2054*.  Review
of applications will begin *November 1, 2013 *and continue until the
position is filled. Further information about the Department is available
at http://www.bio.purdue.edu/.



* *

*Purdue University in an Equal Opportunity/Equal Access/Affirmative Action
employer fully committed to achieving a diverse workforce.*

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

[Andrew Mesecar]

Hi Nika,

A couple of other things you could try to improve maps to add to what the
others have suggested.  One, I am assuming that you are refining the
occupancy of the ligand, but if not, that should reduce the negative
density?  2.  Since you mention soaking the ligand, do you have a good
X-ray data set and refined structure of the unliganded protein in the same
space group and about the same resolution?  If so, you could run an
Fo(ligand)-Fo(unliganded) isomorphorous difference map calculation using
the phases of the unliganded structure for a map calculation.  This may
help (or hurt) too.

Best wishes
Andy Mesecar

On Tue, Nov 24, 2020 at 6:30 AM Nika Žibrat  wrote:

> Hello,
>
>
> I have a question about protein-ligand, of which ligand displays an
> ambiguous electron density. I am solving a structure of protein with
> ligand  which was obtained via soaking. Structural characteristics indicate
> the ligand is present however the electron density is quite vague and too
> small for the size of the whole ligand. I did a Polder map which showed
> much larger area of green density. After insertion of my ligand into the
> green density in Polder I ran phenix.refine and there is a lot of red on
> the spot where the ligand is which was to be expected. This leaves me
> wondering how, if even do I incorporate the polder map data into my refine
> input.
>
>
> My question is, how do I continue refining and validating the structure in
> this case?
>
>
> Thank you,
>
>
> Nika Žibrat
>
>
> --
>
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-- 
*Andrew D. Me**secar*
Head, Department of Biochemistry
Walther Professor of Cancer Structural Biology
Deputy Director, Purdue Center for Cancer Research
E-Mail: amese...@purdue.edu
_
*Department of Biochemistry Contact Information:*
175 S. University Street
W. Lafayette, IN 47907-2063
765-494-1607
--
*Research Lab Contact Information:*
Hockmeyer Hall of Structural Biology
Room 311
240 S. Martin Jischke Drive
West Lafayette, IN 47907-1971
765-494-1924
_



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Re: [ccp4bb] unknown density in 1.6 A structure

[Andrew Mesecar]

Dear Peer,

This reminds me of my colleague Michael Rossmann's discovery of a Pocket
Factor which is a fatty acid-like molecule residing in a hydrophobic pocket
underneath the "canyon" in enteroviruses. See
https://link.springer.com/article/10.1007/s13238-014-0092-6.  You likely
have an endogenous ligand that binds and stays bound during purification.
You may want to do some MS on your purified protein to see if you can
identify it.  Your density should provide enough information on a mass
range to look for.

Andy Mesecar

On Thu, Jun 3, 2021 at 6:50 AM Peer Mittl  wrote:

> I'm struggling with the electron density shown in the attachment. The
> substance does not seem to come from the crystallization condition nor
> from the mounting buffer. The 1.6 A maps are rather clear, because the
> compound binds into the hydrophobic core, which seems to be loosely packed.
>
> -Peer
>
>
>
> 
>
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-- 
*Andrew D. Me**secar*
Head, Department of Biochemistry
Walther Professor of Cancer Structural Biology
Deputy Director, Purdue Center for Cancer Research
E-Mail: amese...@purdue.edu
_
*Department of Biochemistry Contact Information:*
175 S. University Street
W. Lafayette, IN 47907-2063
765-494-1607
--
*Research Lab Contact Information:*
Hockmeyer Hall of Structural Biology
Room 311
240 S. Martin Jischke Drive
West Lafayette, IN 47907-1971
765-494-1924
_



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Re: [ccp4bb] Na-Binding Protein?

[Andrew Mesecar]

Dear Jacob,



One of my favorite examples of monovalent cation discrimination is by the
enzyme Pyruvate Kinase.  It prefers K(+), NH4(+), Rb(+) and Tl+ for maximum
catalysis and then activity falls off as the monovalent cation sizes get
larger, Cs(+) or smaller Na(+) >> Li (+).  The conformations of pyruvate
kinase are known to be altered by binding of monovalent cations and it has
been studied for over 50 years by a variety of approaches.  A number of the
X-ray structures are with K(+).  I spent a few years of my life studying
this enzyme a couple of decades ago.  It will hopefully provide some
information for your project.



Best of luck,



Andy Mesecar

On Tue, Jan 9, 2018 at 9:42 AM, Keller, Jacob 
wrote:

> Dear Crystallographers,
>
>
>
> Is anyone aware of a soluble protein which changes large-scale
> conformation +/- Na+, and is specific for Na+ per se, or at least ignores
> K+ and Ca++? E.g., Rb+ or Li+ might be okay. Structural info would be a
> plus, but not a sine qua non.
>
>
>
> Similarly, what about with K+ or Cl- specificities, but oblivious to
> similar common ions?
>
>
>
> All the best,
>
>
>
> Jacob Keller
>
>
>
> +
>
> Jacob Pearson Keller
>
> Research Scientist / Looger Lab
>
> HHMI Janelia Research Campus
>
> 19700 Helix Dr, Ashburn, VA 20147
> 
>
> (571)209-4000 x3159 <(571)%20209-4000>
>
> +
>
>
>
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-- 
*Andrew D. Mesecar*
Head, Department of Biochemistry
Walther Professor of Cancer Structural Biology
Deputy Director, Purdue Center for Cancer Research
E-Mail: amese...@purdue.edu
_
*Department of Biochemistry Contact Information:*
175 S. University Street
W. Lafayette, IN 47907-2063
765-494-1607
--
*Research Lab Contact Information:*
Hockmeyer Hall of Structural Biology
Room 311
240 S. Martin Jischke Drive
West Lafayette, IN 47907-1971
765-494-1924
_