[NMRFAM enews] Newsletter - August 2013

Rita Hannah rhannah at wisc.edu
Wed Aug 14 12:23:36 CDT 2013


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

National Magnetic Resonance Facility at Madison

September 2013 time requests:

This is a reminder that August 19th @ 4pm CST, is the deadline for
requesting spectrometer time in September 2013 at NMRFAM.

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)

For SAXS information and scheduling contact Samuel Butcher (
<mailto:sebutcher at wisc.edu> sebutcher at wisc.edu)

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

We are still planning an advanced structure determination workshop focused
on structure refinement with more diverse restraints, e.g. RDCs, PREs, water
refinement, etc. This workshop will be offered in 2014 and we would love to
have  your input about general interest and suggestions for topics to
include. Kindly write to  <mailto:%20milo at nmrfam.wisc.edu> Milo Westler as
your input will be invaluable.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++++++++++

o  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 of the publications are:

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.

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

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.

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 Bruker BioSpin NMR spectrometers. Metabolomics (epublished Jan. 4,
2013).

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 Likelihiid 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. PLoS
Comput 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.

 

.    Gelbvieh (800 MHz) spectrometer is on the triple resonance - room
temperature probe.

.    LC/MS micrOTOF Q II is now available for collaboration. Contact the
facility for more information.

.    Small Angle X-ray Scattering (SAXS):

.         The Bruker Nanostar SAXS instrument is currently available by
appointment only.  Prior to signing up for the instrument, please email
Prof. Sam Butcher ( <mailto:butcher at biochem.wisc.edu>
butcher at biochem.wisc.edu) and indicate "SAXS TIME" in the subject line of
your email.  Prof. Butcher will help you to schedule a time when someone
from the facility will be available to assist you with SAXS data collection.
Please note the rate for academic/collaboration use is $5/hr. and $100/hr.
for commercial users.

.    A loaner 4mm 1H{X} cpmas probe (15,000 rpm max) has been installed on
the Bruker 500II (Devon) and is available by special request. This
instrument has solids amplifiers and is capable of many modern solids
experiments. A low-e 1H13C15N cpmas probe (24,000 rpm max) has now been
installed on 500II.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++++++++++

Spectrometers at NMRFAM:

.    Status of spectrometers can be determined at anytime 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 it's status, probes available etc.

.    NMRFAM instrumentation

Spectrometer status:


Instrument

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

Shortcut name

Probe(a)

Status


Varian VNS 900

Fleckvieh

900

c-tr

OK-cold 1H and 13C preamps


Varian VNS 800

Gelbvieh

800

rt-tr

Ok


Bruker AV III 750

Telemark

750

c-tr

Ok


Bruker AV III 600

Dexter

600 I

c-qr 1H{13C,15N,31P}

OK-SampleJet


Varian VNS 600

Jaulan

600 II

c-tr

OK


Varian 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)H{X}cp-mas is currently not available


Bruker DMX 400

Pisa

400

Multiple

OK


Bruker Nanostar

 

SAXS

N/A

Ok


(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- Bruker Avance III console

 

 

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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