NMRFAM eNewsletter – January 2018

 

 


 

  • 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:

     

     

    p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica} span.s1 {font-kerning: none}

    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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    Become an NMRFAM User
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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