University of Wisconsin–Madison

e-Newsletter

NMRFAM eNewsletter – March 2018

  • April 2018 time requests: This is a reminder that March 19th 4pm CST is the deadline to have spectrometer time reserved for you for April 2018; please contact Lai Bergeman by e-mail or call 608-262-3173. You may schedule time yourself, as soon as the calendar is open by end-of-day on March 23th, by logging into Sundial and following the requests process.
  • 2018 NMRFAM Introductory Structure Determination Workshop – June 3rd-June 8th , 2018. Don’t miss this popular workshop!

  • YouTube video tutorials and help pages for users of Sundial (creating and submitting time request) –http://www.sesame.wisc.edu/sesame_videos.html and http://www.sesame.wisc.edu/sesame_helppages.html 
  • Vosges (Bruker 600) is not operational. Should be available in April.

NMRFAM offers services such as:

  • collect routine NMR spectra of small molecules, process the data with peak picking and integration, and provide their experimental results in electronic or paper format in order to advance research projects.
  • Users can submit their samples in 3 or 5 mm NMR tubes before 1 pm every Tuesday and Thursday. Their data will be acquired between 1 – 5 pm of the same day on a 500 MHz spectrometer optimized for 13C (no appointment necessary)

New User/Collaborator Information:

Please note that if you would like to collaborate with our facility you will need to submit an abstract providing some detail to Dave Aceti, our coordinator, who will bring it up for review at our weekly staff meeting for approval. Please visit the NMRFAM website for more information.

Other NMRFAM capabilities:

Solid state probes at NMRFAM:

  • 3.2mmEfree CPMAS, 4mm CPMAS and HRMAS probes – 500 MHz (Devon)
  • 3.2mm Efree CPMAS and static BioProbe (PISEMA experiments) –  600 MHz III (Vosges)
  • 3.2mm Efree CPMAS probe and 1.3mm ultrafast CPMAS probe – 900 MHz (Fleckvieh)

 LC/MS micrOTOF Q II is now available for collaboration

Bruker Nanostar SAXS (small angle X-ray scattering) instrument is available. For information about SAXS, please email Paulo F. Cobra.

  •   NMRFAM Software News:

            NMRFAMSPARKY new features:

  •             Improved PINE/PINE-SPARKY 2 (ep)
  •             Hydrophobic core and flexibility detection in PINE-SPARKY 2 (ep)
  •             Sequence entry integration for automated tools (sq)
  •             More colors available (ct,cr)
  •             Move labels to peak centers (lc)
  •             Dummy graph (dg)/ Pine graph assigner (pp) small fix
  •             Explicit buttons in the strip plot (sp/SP)           
  •             Completeness counter (cm)
  •             Improved APES peak picker (ae)

 

  • Donate to NMRFAM

US deductible donations can be made to NMRFAM. Please write check payable to “UW Foundation, Account 112152802” and mail to:
Attn: Sarah Lynn Traver Saunders

                        Associate Administrative Program Specialist 

                        University of Wisconsin – Madison 

                        Department of Biochemistry 

                        433 Babcock Drive 

                        Madison WI 53706

For further information, please contact Ms. Saunders, Tel: 608-265-2507 or email 

 Spectrometers at NMRFAM:

  • NMRFAM Spectrometers availability (Live Schedule) for current and upcoming month can be view at Live Schedule

 

  • NMRFAM instrumentation
    Spectrometer status:

 

Instrument

Cow name

Shortcut name

Probe(a)

 Status

Bruker AV-HD 900

Fleckvieh

900

c-tr

OK – cold 1H and13C preamps

Agilent VNS 800

Gelbvieh

800

ct-tr

OK – cold probe

Bruker AV III 750

Telemark

750

c-tr

OK – cold probe

Bruker AV III 600

Dexter

600 I

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

OK – SampleJet

Agilent VNS 600

Jaulan (not operational) 

600 II

c-tr

OK – cold probe

Bruker AV III 600

Vosges (not operational) 

600 III

c-tr

OK – cold probe

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 – cold probe

BrukerNanostar

Bond

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 consol


Below is a listing of the available software on our website that you are free to use or download and some associated publications:
1 – NMRFAM-SPARKY
2 – NMRbot
3 – HIFI-NMR
4 – LACS / PECAN
5 – PINE
6 – PINE-Sparky
7 – ADAPT-NMR
8 – ADAPT-NMR Enhancer
9 – Newton
10 – PACSY
11 – PONDERSOSA
12- PONDEROSA-C/S
13 – SPIDER
14 – RNA-PAIRS
15 – NMR Structure Tools
16 – rNMR

Please visit the NMRFAM software website for more information on the above listed software.

References for some publications are:

Cai K. Frederick RO, Tonelli M, Markley JL. ISCU(M108I) and ISCU(D39V) differ from wild type ISCU in their failure to form cysteine desulfurase complexes containing both frataxin and ferredoxin. Biochemistry. 2018 Feb PMID: 29406711

Lee, Markley JL. PINE-SPARKY.2 for automated NMR-based protein structure research. Bioinformatics. 2017 Dec PMID:29281006

Fathi F, Brun A, Rott KH, Falco Cobra P, Tonelli M, Eghbalnia HR, Caviedes-Vidal E, Karasov WH, Markley JL. NMR-Based Identification of Metabolites in Polar and Non-Polar Extracts of Avian Liver. Metabolites. 2017 Nov PMID: 29144418

Dashti H, Westler WM, Tonelli M, Wedell JR, Markley JL, Eghbalnia HR. Spin System Modeling of Nuclear Magnetic Resonance Spectra for Applications in Metabolomics and Small Molecule Screening. Anal Chem. 2017 Nov. PMID: 29058410

Schilke BA, Ciesielski SJ, Ziegelhoffer T, Kamiya E, Tonelli M, Lee W, Cornilescu G, Hines JK, Markley JL, Craig EA.  Broadening the functionality of a J-protein/HSP70 molecular chaperone system. PLoS Genet. 2017 Oct. PMID: 29084221

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