[NMRFAM enews] Monthly newsletter - May 2014

Rita Hannah rhannah at wisc.edu
Fri May 16 13:34:13 CDT 2014


 <http://www.nmrfam.wisc.edu/wp-content/uploads/2009/09/enews_header.gif> 

National Magnetic Resonance Facility at Madison

 

2014 NMRFAM "1st NMRFAM Advanced Structure Refinement Workshop"

Announcing the Advanced workshop to be held from August 17th until August
20th.

A hands-on workshop: Vignettes on the use of various restraint types in NMR
structure determination. 

A series of lectures and hands-on use of Xplor-NIH for the determination and
refinement of NMR based structures.

Topics:

. Xplor-NIH introduction and overview

. Basic structure calculations

. Generation of structures for a toy peptide

. NOE distance & dihedral angle restraints

. Structure calculation and evaluation of results

. Refinement (RDC, PRE, SAXS,.)

. Complexes (Protein, Nucleic acid, small ligand)

. Validation/deposition

Software:

. XPLOR-NIH / Python

. Pymol

. MolProbity

. Linux platform - VNC

More details on the workshop will follow soon and will be available on our
website

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2014 NMRFAM Protein Structure determination Workshop

This is a reminder that the workshop will be held from June 1st until June
6th. Registration and housing details can be found on our website:
<http://www.nmrfam.wisc.edu/home/workshops/2014-nmrfam-protein-structure-det
ermination-workshop/>
http://www.nmrfam.wisc.edu/home/workshops/2014-nmrfam-protein-structure-dete
rmination-workshop/

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June 2014 time requests:

This is a reminder that May 19th 4pm CST, is the deadline for requesting
spectrometer time in June 2014 at NMRFAM. You may schedule your request in
yourself as soon as the calendar is open (green in color) which is after I
have finished scheduling requests for the next month.

To sign up for time: Use Sundial at

 <http://www.nmrfam.wisc.edu/home/schedule-nmr-time-sundial-2/>
http://www.nmrfam.wisc.edu/home/schedule-nmr-time-sundial-2/

Contact Rita Hannah ( <mailto:rhannah at nmrfam.wisc.edu>
rhannah at nmrfam.wisc.edu, 608-262-3173) for assistance. For scientific
questions/discussions contact Milo Westler ( <mailto:milo at nmrfam.wisc.edu>
milo at nmrfam.wisc.edu)

Please visit the  <http://www.nmrfam.wisc.edu/> NMRFAM website for more
information.

Other NMRFAM capabilities:

*	LC/MS micrOTOF Q II is now available for collaboration. Contact the
facility for more information or please e-mail Dr. Jaime Stark (
<mailto:jstark at wisc.edu> jstark at wisc.edu).
*	Small Angle X-ray Scattering (SAXS): The BrukerNanostar SAXS
instrument is available for requesting time. For information about SAXS,
please email Dr. Jameson Bothe ( <mailto:bothe at wisc.edu> bothe at wisc.edu)

Other News:

*	The cryogenic probe for the Bruker 750 (Telemark) has been sent back
for repair and upgrade to allow for automatic orientation of slotted tubes,
which are used to reduce the effects of high salt concentrations.
*	Agilent/Varian 800 (Gelbvieh) is currently without a cryogenic probe
and is running with an RT probe.

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Spectrometers at NMRFAM:

*	Status of spectrometers can be determined at any time as follows: In
Sundial after login, go to "Options"----->"Site
Resources"----->"Spectrometers" A new set of Options open on the Sundial
Board. Go to "Search"------>"By Owner". A new window pops up in the second
section (Manufacturer), type/write in either "Bruker" or "Varian". A listing
of the spectrometers will be displayed. Select the one of interest and check
on its status, probes available etc.

NMRFAM instrumentation:

*	Spectrometer status:

 


Instrument

 <http://www.nmrfam.wisc.edu/?page_id=500> Cow name

Shortcut name

Probe(a)

Status


Agilent VNS 900

Fleckvieh

900

c-tr

OK-cold 1H and 13C preamps


Agilent VNS 800

Gelbvieh

800

ct-tr

RT probe- cold probe under repair


Bruker AV III 750

Telemark

750

c-tr

RT probe - cold probe under repair


Bruker AV III 600

Dexter

600 I

c-qr1H{13C,15N,31P}

OK-SampleJet


Agilent VNS 600

Jaulan

600 II

c-tr

OK


Agilent VNS 600

Vosges

600 III

c-tr

OK


Bruker AV III 600

Kurgan

600 IV

c-tr-(1.7mm)

              OK-SampleJet(cooled)


Bruker AV III 500

Kerry

500 I

c-tr(13C/15N)

OK-all cold preamp; Samplejet


Bruker AV III 500

Devon

500 II

c-tr

/hrmas/BBFO/cpmas

OK - swappable CP (solids capability)


Bruker DMX 400

Pisa

400

Multiple

OK


BrukerNanostar

 

SAXS

N/A

Ok - temperature control available


(a)rt - room temperature; c - cryogenic; tr - 1H{13C,15N} triple resonance;
qr - 1H{13C,15N,31P} quadruple resonance ; multiple - multiple probes; VNS-
Varian Direct Drive console; AV- BrukerAvance III console

 

 

*	Below is a listing of the available software on our website that you
are free to use or download and some associated publications :
*	 

*	NMRbot  
*	HIFI-NMR
*	LACS / PECAN 
*	PINE 
*	PINE-Sparky 
*	ADAPT-NMR 
*	ADAPT-NMR Enhancer
*	Newton
*	PACSY   
*	PONDERSOSA  
*	SPIDER          
*	RNA-PAIRS      
*	NMR Structure Tools
*	rNMR

Please visit the  <http://www.nmrfam.wisc.edu/software/> NMRFAM software
website for more information on the above listed software.

References for some publications are:

Tonelli, M., Eller, C., Singarapu, K., Lee, W., Bahrami, A., Westler, W.M.,
Raines, R.T. &Markley, J.L. (2014) Assignments of RNase A by ADAPT-NMR and
enhancer, Biomol. NMR Assign.

Whigham, L., Butz, D., Dashti, H., Tonelli, M., Johnson, L., Cook, M.,
Porter, W., Eghbalnia, H., Lindheim, S., Scholler, D., Abbott, D.
&Assadi-Porter, F. (2014) Metabolic Evidence of Diminished Lipid Oxidation
in Women WithPolycystic Ovary Syndrome, Curr. Metabol.2, 269-278. (PMCID:
PMC3994884)

Markley JL, Kim JH, Dai Z, Bothe JR, Cai K, Frederick RO&Tonelli M. (2013)
Metamorphic protein IscU alternates conformations in the course of its role
as the scaffold protein for iron-sulfur cluster biosynthesis and
delivery.FEBS Lett.587, 1172-1179. 

Poplawski, A., Hu, K., Lee, W., Natesan S., Peng, D., Carlson, S., Shi, X.,
Balaz, S, Markley, J. L. & Glass, K. C. (2013) Molecular Insights into the
Recognition of N-Terminal Histone Modifications by the BRPF1 Bromodomain, J.
Mol. Biol. ePub Dec12, 2013 (NIHMSID: NIHMS559160).

Cornilescu, C. C., Cornilescu, G., Brugie E. S., marley, J. L., Ulijasz, A.
T. &Vierstra, R. D. (2013) Dynamic structural changes underpin
photoconversion of a blue/green cyanobacteriochrome between its ground and
photoactivated states, J. Biol. Chem. ePub Dec11, 2013 (PMCID: PMC Journal
-- In Process)

Lee, W., Hu, K., Tonelli, M., Bahrami, A., Neuhardt, E., Glass, K. C. &
Markley, J. L. (2013) Fast automated protein NMR data collection and
assignment by ADAPT-NMR  on Bruker spectrometers, J. Magn. Reson., 236,
83-8. (PMCID:PMC3858185).

Cornilescu, C. C., Cornilescu, G., Rao, H., Porter, S. F., Tonelli, M.,
DeRider, M. L., Markley, J. L. &Assadi-Porter, F. M. (2013)
Temperature-dependent conformational change affecting Tyr11 and sweetness
loops of brazzein, Proteins: Structure, Function & Bioinformatics, 81, 6,
919-25. (NIHMSID:NIHMS556701).

Hsueh, K.-L., Tonelli, M., Cai, K., Westler, W. M. & Markley, J. L. (2013)
Electron Transfer Mechanism of the Rieske Protein from Thermusthermophilus
from Solution Nuclear Magnetic Resonance Investigations, Biochemistry, 52,
17, 2874-87. (PMCID:PMC3686548).

Kim, J-H, Frederick, R. O., Reinen, N. M., Troupis, A. T. & Markley, J. L.
(2013) [2Fe-2S]-Ferredoxin Binds Directly to Cysteine Desulfurase and
Supplies an Electron for Iron-Sulfur Cluster Assembly but Is Displaced by
the Scaffold Protein or Bacterial Frataxin, J. Am. Chem. Soc. 135, 22,
8117-20. (PMCID: PMC3677232).

Lee, W., Bahrami, A. & Markley, J. L. (2013) ADAPT-NMR Enhancer: complete
package for reduced dimensionality in protein NMR spectroscopy,
Bioinformatics. 29, 4, 515-7. [PMCID:PMC23220573]

Clos II, L.J., Jofre, M.F., Ellinger, J.J., Westler, W.M., Markley, J.L.
(2012). NMRbot: Python scripts enable high-throughput data collection on
current BrukerBioSpin NMR spectrometers. Metabolomics (PMCID:PMC3651530).

Bahrami, A., Clos, L. J. II, Markley, J. L., Butcher, S. E. &Eghbalnia, H.
R. (2012) RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts,
J. Biol. NMR. 52, 289-302. [PMCID:PMC3480180]

Bahrami, A., Tonelli, M., Sahu, S. C., Singarapu, K. K., Eghbalnia, H. R. &
Markley, J. L. (2012) Robust, Integrated Computational Control of NMR
Experiments to Achieve Optimal Assignment by ADAPT-NMR, PLoS One.7, 233175.
[PMCID:PMC3299752]

Lee, W., Yu, W., Kim, S. Chang, I., Lee, W. & Markley, J. L. (2012) PACSY, a
relational database management system for protein structure and chemical
shift analysis, J. Biomol. NMR, 154, 169-79.

Chylla, R. A., Hu, K., Ellinger, J. J. & Markley, J. J. (2011) Deconvolution
of two-dimensional NMR spectra by fast Maximum Likelihood Reconstruction:
application to quantitative metabolomics, Anal. Chem, 83, 4871-80. [PMCID:
PMC3114465]

Lee, W., Kim, J. H., Westler, W. M. & Markley, J. L. (2011) PONDEROSA, an
automated 3D-NOESY peak picking program, enables automated protein structure
determination, Bioinform. 27, 1727-8. [PMCID: PMC3106192]

Lewis, I. A., Schommer, S. C. & Markley, J. L. (2009) rNMR open source
software for identifying and quantifying metabolites in NMR spectra, Magn.
Reson.Chem., 47, (S 1), S123-S126. [PMCID: PMC2798074]

Lee, W., Westler, W. M., Bahrami, A., Eghbalnia, H. & Markley, J. L. (2009)
PINE-SPARKY: graphical interface for evaluating automated probabilistic peak
assignments in protein NMR spectroscopy. Boinformatics.25, 2085-7.
[PMCID:PMC2723000]

Bahrami, A., Assadi, A. H., Markley, J. L. &Eghbalnia, H. R. (2009)
Probabilistic interaction network of evidence algorithm and its application
to complete labeling of peak lists from protein NMR spectroscopy. PLoSComput
Biol., 5(3):e1000307. [PMCID:PMC2645676]

Cornilescu, G. Bahrami, A. Tonelli, M., Markley, J. L. &Eghbalnia, H. R.
(2007) HIFI-C: a robust and fast method for determining NMR couplings from
adaptive 3D to 2D projections, J Biomol.NMR.38, 341-51.

Wang L., Eghbalnia, H. R., Bahrami, A. & Markley, J. L. (2005) Linear
analysis of carbon-13 chemical shift differences and its application to the
detection and correction of errors in referencing and spin system
identifications. J Biomol. NMR, 32 (1):13-22.

Eghbalnia, H. R., Wang, L., Bahrami, A. Assadi, A. & Markley, J. L. (2005)
Protein energetic conformational analysis from NMR chemical shifts (PECAN)
and its use in determining secondary structural elements., J Biomol. NMR, 32
(1) 71-81.

Eghbalnia, H. R., Bahrami, A. Tonelli, M., Hallenga, K. &markley, J. L.
(2005) High-resolution iterative frequency identification for NMR as a
general strategy for multidimensional data collection.J Am. Chem. Soc. 127,
12528-36.

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Rita Hannah, Ph.D.

NMRFAM

University of Wisconsin - Madison

Madison, WI - 53706

e-mail:  <mailto:rhannah at nmrfam.wisc.edu> rhannah at nmrfam.wisc.edu

Phone; (608) 262-3173

FAX: (608) 262-3759

 

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