NMRFAM eNewsletter – November 2017


  • December 2017 time requests: This is a reminder that November 19th 4pm CST is the deadline to have spectrometer time reserved for you for December 2017; 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 November 20th, by logging into Sundial and following the requests process.
  • Jaulan (Agilent 600) is operational starting December 1st 2017.
  • Vosges (Bruker 600) is not operational. It is in the process of being moved and should be available in 1 month.
  • Devon (500MHZ 11) - Starting from September 1st 2017, default probe on Devon will be 4mm CP-MAS (solid probe). If user would like to use cryoprobe, request has to be submitted on/or before the 19th of the previous month in Sundial for consideration or use Kerry ( 500MHZ I)

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 Mark Anderson.

 ·      NMRFAM Software News:

            NMRFAM-SPARKY 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 athttp://www.nmrfam.wisc.edu/546.htm
  • 400 MHz spectrometer (Pisa) was decommissioned in December 2016.
  • 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:

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Wyche TP, Alvarenga RFR, Piotrowski JS, Duster MN, Warrack SR, Cornilescu G, De Wolfe TJ, Hou Y, Braun DR, Ellis GA, Simpkins SW, Nelson J, Myers CL, Steele J, Mori H, Safdar N, Markley JL, Rajski SR, Bugni TS. Chemical Genomics, Structure Elucidation, and in Vivo Studies of the Marine-Derived Anticlostridial Ecteinamycin. ACS Chem Biol. 2017 Jul. PMID 28708379


Cornilescu G, Ramos Alvarenga RF, Wyche TP, Bugni TS, Gil RR, Cornilescu CC, Westler WM, Markley JL, Schwieters CD. Progressive Stereo Locking (PSL) – A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and other Small Molecules. ACS Chem Biol. 2017 Jun. PMID:28617580 

Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. Methods Mol Biol. 2017. PMID: 28573592


Dashti H, Westler WM, Markley JL, Eghbalnia HR. Unique identifiers for small molecules enable rigorous labeling of their atoms. Sci Data. 2017 May. PMID: 28534867

Markley JL, Westler WM. Biomolecular NMR: Past and future. Arch Biochem Biophys. 2017 May. PMID: 28495511 


Chae YK, Kim SH, Markley JL. Relationship between recombinant protein expression and host metabolome as determined by two-dimensional NMR spectroscopy. PLoS One. 2017 May. PMID:28486539

 Cai K, Tonelli M, Frederick RO, Markley JL, Human Mitochondrial Ferredoxin 1 (FDX1) and Ferredoxin 2 (FDX2) Both Bind Cysteine Desulfurase and Donate Electrons for Iron-Sulfur Cluster Biosynthesis. Biochemistry.2017 Jan. PMID:28001042

Yokochi M, Kobayashi N, Ulrich EL, Kinjo AR, Iwata T, Ioannidis YE, Livny M, Markley JL, Namamura H, Kojima C, Fujiwara T, Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. J Biomed Semantics, 2016 May. PMID 27927232

Cai K., Liu G., Frederick R.O., Xiao R., Montelione G.T., Markley J.L., Structural/Functional Properties of Human NFU1, an Intermediated [4Fe-4S] Carrier in Human Mitochondrial Iron-Sulfur Cluster Biogenesis.  Structure. 2016. PMID 27818104

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Biochemistry 800 - Practical Nuclear Magnetic Resonance Theory 

Biochemistry 801 - Biochemical Applications of Nuclear Magnetic Resonance 

"The Future of NMR-Based Metabolomics, Current Opinion in Biotechnology (2017), pp. 34-40

Documents on the use of the Bruker-Axs Nanostar,SAXS instrument and analysis of SAXS data are now available.

NMRFAM-SPARKY Distribution - the popular NMR analysis program SPARKY recompiled (including updated python and Tcl/Tk) with incorporation of PINE-Sparky, enhancements to import/export to the structural analysis program CYANA, and other useful python extensions.

ADAPT-NMR Enhancer: Complete Package for Reduced Dimensionality in Protein NMR Spectroscopy

RNA-PAIRS: RNA Probabilistic Assignment of Imino Resonance Shifts

PACSY, a Relational Database Management System for Protein Structure and Chemical Shift Analysis 

 

Donate to NMRFAM. US tax-deductible donation 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 
433 Babcock Drive 
Madison, WI 53706 
Tel: 608-265-2507 or email 

 

1st: Lai Bergeman 
Rm 171; Phone 262-3173

2nd: Milo Westler
Rm B160; Phone 263-9599

3rd: Paulo F. Cobra
Rm B224; Phone 265-3303

4th: Marco Tonelli
Rm B160; Phone 263-9493

5th: John Markley
Rm 171A; Phone 263-9349

We welcome your questions and feedback!

NMRFAM Established 1987