e-Newsletter

NMRFAM eNewsletter – April 2020

  • NMRFAM operations during the COVID-19 pandemic – Essential operations only
  • UW-Madison is currently operating under essential operations ONLY. This means that NMRFAM is not operating under normal procedures.
    • Standard NMR calendars are suspended while research operations are restricted. You will not be charged for time that you have reserved but cannot use because of COVID-19.
    • Limited research operations are ongoing. Samples can be changed only when staff are already in the facility to perform essential operations. No experiments requiring frequent sample changes or hands-on staff time in the facility will be performed. Long-running experiments may be run through remote operations in consultation with NMRFAM staff. If you have a sample already at NMRFAM and wish to collect additional data, this is your chance! Please contact Lai Bergeman (lai.bergeman@wisc.edu) and Milo Westler (milo@nmrfam.wisc.edu) if you would like to discuss experiments that meet these requirements.
    • There will be no entrance to any part of the facility except for essential staff. No staff will be present except during essential procedures (cryogen fills, maintenance, etc.). Staff will be available through email and are happy to discuss project planning, data analysis, etc.
    • Shipping and receiving is currently operating at a very reduced capacity. Please do NOT ship your precious, isotopically-labeled samples to us because we cannot guarantee prompt receipt and proper handling.
    • There will be no drop-off sample service on Tuesdays and Thursdays.
    • For the latest updates on UW Madison operations and support services – please visit https://covid19.wisc.edu/
  • 2020 NMRFAM Introductory Structure Determination Workshop – our popular annual workshop will be held virtually. More information will be posted on the link above by May 1st 2020.

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:

  • 3.2mm 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)

More solid state NMR capability is currently being added in Summer 2020!

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

(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, Markley JL. 2mISCU interacts with NFU1, and ISCU(4Fe-4S) transfers its FE-S cluster to NFU1 leading to the production of holo-NFU1. J Struct Biol. 2020 Mar. PMID:32151725

Barnett BR, Fathi F, Falco Cobra P, Yi SY, Anderson JM, Eghbalnia HR, Markley JL, Yu JJ. Metabolic Changes in Synaptosomes in an Animal Model of Schizophrenia Revealed by 1H and 1H, 13C NMR Spectroscopy. Metabolites. 2020 Feb. PMID: 32102223

Weber DK, Wang S, Markley JL, Veglia G, Lee W. PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins. Bioinformatics. 2020 Jan. PMID:31930377

Tanrikulu IC, Westler WM, Ellison AJ, Markley JL, Raines RT. Templated Collagen “Double Helices” Maintain Their Structure. J Am Chem Soc. 2020 Jan. PMID:31895554

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