[NMRFAM enews] NMRFAM eNewsletter_ May 2019

Lai Bergeman lai.bergeman at wisc.edu
Thu May 9 14:21:37 CDT 2019


NMRFAM eNewsletter – May 2019

  *   2019 NMRFAM Introductory Structure Determination Workshop (June 2-7, 2019).<https://nmrfam.wisc.edu/introductory-workshop/> Popular workshop! Register today!



  *   June 2019 time requests: This is a reminder that May 19th 2pm CST is the deadline to have spectrometer time reserved for you for June 2019; please contact Lai Bergeman<mailto:lai.bergeman at wisc.edu> by e-mail or call 608-262-3173. You may schedule time yourself, as soon as the calendar is open by May 20th, by logging into Sundial and following the requests process.

  *   Devon (500MHz II) – Default probe on Devon will be 4mm CP-MAS (solid probe).
  *   Kurgan (600MHz Bruker) – is operational with 5mm cryoprobe.

  *   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<mailto:paulofcobra at gmail.com> 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<mailto:lai.bergeman.wisc.edu>, coordinator, who will bring it up for review at our weekly staff meeting for approval. Please visit the NMRFAM website<https://nmrfam.wisc.edu/become-a-collaborator/> 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 not operational.
  *   For more information about LC/MS and SAXS, please email Paulo F. Cobra<mailto:paulo at nmrfam.wisc.edu>.
NMRFAM Software News:
GISSMO.nmrfam.wisc.edu<http://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<http://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.
NMRFAM-SPARKY new features:

     *   More colors available (ct, cr)
     *   Move labels to peak centers (lc)
     *   Help manual updates for two-letter codes (hn / hI)
     *   NMRPipe, NMRView, TopSpin files can be directly opened in here.
     *   A new conversion script for importing NMRView to UCSF (nv2ucsf)
     *   Mouse wheel (mw, Win excl.) and/or + - , . arrow key integration
     *   Contour shortcuts added (shift ) ; ' [ ]
     *   Very large data support (>10GB) for 64bits (Linux 64 / Mac)
     *   Triple strip plots and their enhancements (sp / SP / Sp)
     *   Completeness counter (cm)
     *   Chemical shift reference views and versatile assigner (ir / va)
     *   Advanced selection tool (SE) from Rienstra group
     *   PluqIn-Sparky (pq) inspired from Rienstra's plugin and PINE-SPARKY.2
     *   Transfer and simulate (ta) also supports aromatic experiments
     *   Improved APES peak picker (ae)- full automation to I-PINE/PONDEROSA
     *   I-PINE/PINE-SPARKY.2 (ep) also supports some 4D experiments
     *   Improved PONDEROSA structure calculation plugin (c3)
     *   To share the thoughts, visit Sparky user forum (Type SF)
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<mailto:slsaunders2 at wisc.edu>

Spectrometers at NMRFAM:

o   NMRFAM Spectrometers availability (Live Schedule) for current and upcoming month can be view at http://www.nmrfam.wisc.edu/Spectrometer-Live-Calendar.htm
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

c-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

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 (not operational)

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:
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<http://www.nmrfam.wisc.edu/software.htm> for more information on the above listed software.
References for recent publications are:
Dashti H, Wedell JR, Westler WM, Markley JL, Eghbalnia HR. Automated evaluation of consistency within the PubChem Compound database<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380220/>. Sci Data. 2019 Feb. PMCID:PMC6380220
Ulrich EL, Baskaran K, Dashti H, Ioannidis YE, Livny M, Romero PR, Maziuk D, Wedell JR, Yao H, Eghbalnia HR, Hoch JC, Markley JL. NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments<https://www.ncbi.nlm.nih.gov/pubmed/30580387>. J. Biomol NMR. Dec 2018 . PMID:30580387
Windsor IW, Palte MJ, Lukesh JC 3rd, Gold B, Forest KT, Raines RT. Sub-picomolar Inhibition of HIV-1 Protease with a Boronic Acid<https://www.ncbi.nlm.nih.gov/pubmed/30346745>. J Am Chem Soc. Oct 2018. PMID:30346745
Assadi-Porter FM, Radek J. Rao H, Tonelli M. Multimodal Ligand Binding Studies of Human and Mouse G-Coupled Taste Receptors to Correlate Their Species-Specific Sweetness Tasting Properties<https://www.ncbi.nlm.nih.gov/pubmed/30282936>. Molecules. 2018 October. PMID:30282936
Cai K, Markley JL. NMR as a Tool to Investigate the Processes of Mitochondrial and Cytosolic Iron-Sulfur Cluster Biosynthesis.<https://www.ncbi.nlm.nih.gov/pubmed/30200358> Molecules. 2018 Aug. PMID:30200358
Dashti H, Wedell JR, Westler WM, Tonelli M, Aceti D, Amarasinghe GK, markley JL, Eghbalnia HR. Applications of Parametrized NMR Spin Systems of Small Molecules<https://www.ncbi.nlm.nih.gov/pubmed/30125102>. Anal Chem. 2018 Aug. PMID:30125102
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