e-Newsletter

NMRFAM eNewsletter – September 2019

  • October 2019 time requests: This is a reminder that September19th 2pm CST is the deadline to have spectrometer time reserved for you for October 2019; 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 September 20th, by logging into Sundial and following the requests process.
  • Chicago Area NMR Discussion Group (CANMRDG) will be held on Saturday, November 2nd 2019 in Madison, WI. An added feature for this year’s meeting is a workshop on NMRbox on Friday, November 1st, 2019. Registration and more information – https://www.chem.purdue.edu/canmrdg/. Register today!
  • Devon (500MHz II) – Default probe on Devon will be 4mm CP-MAS (solid probe).
  • 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 

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). Please email Paulo F. Cobra when you drop off your samples.

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 Lai Bergeman, 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)
  • Bruker Nanostar SAXS (small angle X-ray scattering) instrument is operational. For more information about SAXS, please email Paulo F. Cobra.

NMRFAM Software News:

  • GISSMO.nmrfam.wisc.edu:GISSMO enables the efficient calculation and refinement of spin system matrices (chemical shift and coupling constants) against experimental 1D-1H NMR spectra of small molecules. The library of compounds parameterized by GISSMO contains more than 1286 compounds, including many key mammalian metabolites and a library of drug-like molecular fragments used in ligand screening.
  • ALATIS.nmrfam.wisc.edu:Unique and reproducible molecule and atom identifiers are required to ensure the correct cross-referencing of properties associated with compounds archived in databases. The best approach to this requirement is the International Chemical Identifier (InChI). ALATIS is an adaptation of InChI that provides unique and reproducible atom numbering for all atoms including hydrogens.

            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 

600 II

c-tr

OK – cold probe

Bruker AV III 600

Vosges  

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:

Markley JL, Dashti H, Wedell JR, Westler WM, Eghbalnia HR. Tools for Enhanced NMR-Based Metabolomics Analysis. Methods Mol Biol. 2019. PMID:31463858

Lee W, Bahrami A. Dashti Ht, Eghbalnia HR, Tonelli M, Westler WM, Markley JL. I-PINE web server: an integrative probabilistic NMR assignment system for proteins. J Biomol NMR. 2019 May. PMCID:PMC6579641

Tsvetkov P, Detappe A, Cai K, Keys HR, Brune Z, Ying W, Thiru P, Reidy M, Jugener G, Rossen J, Kocak M, Kory N, Tsherniak A, Santagata S, Whitesell L, Ghobrial IM, Markley JL, Lindquist S, Golub TR. Mitochondrial metabolism promotes adaptation to proteotoxic stress. Nat Chem Biol. 2019 Jul. PMID:31133756

Dashti H, Wedell JR, Westler WM, Markley JL, Eghbalnia HR.Automated evaluation of consistency within the PubChem Compound database. Sci Data. 2019 Feb. PMCID:PMC6380220

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