NMRFAM eNewsletter - December 2016

  • January 2017 time requests: This is a reminder that December 19th 4pm CST is the deadline to have spectrometer time reserved for you for January 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 December 20th, by logging into Sundial and following the requests process.
  • Contact Lai Bergeman by e-mail or at 608-262-3173 for general assistance. For scientific questions/discussions contact Milo Westler.
  • 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:
  • Currently available solid state probes at NMRFAM
4mm CPMAS and HRMAS probes - 500 MHz (Devon)
  • New solid state probes becoming available at NMRFAM in 2017
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. Contact the facility for more information. 
  • Small Angle X-ray Scattering (SAXS): The Bruker Nanostar SAXS instrument is available. For information about SAXS, please email Mark Anderson.
  • NMRFAM Software News:

New features in the latest version of NMRFAM-SPARKY

- Mouse wheel (and/or +, - keys) to zoom in and out

- Arrow keys to move around in spectrum view

- Better contour level adjustment bar (two-letter-code: vC)

- Updated peak list window (two-letter-code: lt)

  - Peak and assignment numbers in the peak list

  - Data height sorting option in the peak list options

- Extra strip plot window (two-letter-code: sp / SP)

- NMRFAM extensions in the popup menu (right-click)

- Help manual updates for two-letter codes (two-letter-code: hn / hI)

- A new conversion script for importing NMRView to UCSF (nv2ucsf)

  • Other News:
    • The Bruker Avance HD 600 MHz spectrometer a.k.a. "600iii" or "Vosges" now has a cryogenic 1H{13C,15N} probe where the 1H channel can be retuned to 19F.
    • The 900 MHz spectrometer "Fleckvieh" has been converted from an Agilent to a Bruker AV-HD system.
  • 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 instrumentation
      Spectrometer status:
    Instrument

    Cow name

    Shortcut name

    Probe(a)

     Status


    Bruker AV-HD 900

    Fleckvieh

    900

    c-tr

    OK - cold 1H and 13C 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

    Bruker DMX 400

    Pisa

    400

    Multiple

    Under repair

    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 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 
    17 -ARECA

    Please visit the NMRFAM software website for more information on the above listed software.

    References for some publications are :

    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

    Markley J.L, Bruschweiler R., Edison A.S., Eghbalnia H.R., Powers R., Raftery D., Wishart D.S., The future of NMR-based metabolomics. Curr Opin Biotechnol. 2016. PMID:27580257

    Berman H.M., Burley S.K, Kleywegt G.J., Markley J.L., Nakamura H, Velankar S. The archiving and dissemination of biological structure data. Curr Opin Struct Biol. 2016.PMID: 27450113

    Wessel S.R., Cornilescu CC, Cornilescu G, Metz A, Leroux M, Hu K, Sandler S.J., Markley J.L., Keck J.L. Structure and Function of the PriC Replication Restart Protein. J. Biol Chem. 2016. PMID:27382050

    Kim S, Natesan S, Cornilescu G, Carlson S, Tonelli M, McClurg U.L., Binda O, Robson C.N., Markley J.L., Balaz S, Glass K.C. Mechanism of Histone H3K4me3 Recognition by the Plant Homeodomain of Inhibitor of Growth 3. J Biol Chem. 2016 Jun 8.pii:jbc.M115.690651. PMID: 27281824

    Lee W, Petit C.M., Cornilescu G, Stark J.L., Markley J.l., The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data. J Biomol NMR. 2016 May 12 PMID: 27169728

    Adams, P.D., Aertgeerts, K., Bauer, C., Bell, J.A., Berman, H.M., Bhat, T.N., Blaney, J.M., Bolton, E., Bricogne, G., Brown, D., Burley, S.K1, Case, D.A., Clark, K.L., Darden, T., Emsley, P., Feher, V.A., Feng, Z., Groom, C.R., Harris, S.F., Hendle, J., Holder, T., Joachimiak, A., Kleywegt, G.J., Krojer, T., Marcotrigiano, J., Mark, A.E., Markley, J.L., Miller, M., Minor, W., Montelione, G.T., Murshudov, G.1., Nakagawa, A., Nakamura, H., Nicholls, A., Nicklaus, M., Nolte, R.T., Padyana, A.K., Peishoff, C.E., Pieniazek, S., Read, RJ., Shao, C., Sheriff, S., Smart, O., Soisson, S., Spurlino, J., Stouch, T., Svobodova, R., Tempel, W., Terwilliger, T.C., Tronrud, D., Velankar, S., Ward, S.C., Warren, G.L., Westbrook, J.D., Williams, P., Yang, H., Young, J. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure, 2016 Apr 5;24(4):502-8. doi: 10.1016/j.str.2016.02.017.

    Lee W., Cornilescu G., Dashti H., Eghbalnia HR., Tonelli M., Westler WM., Butcher SE., Henzler-Wildman KA.,  Markley JL Integrative NMR for biomolecular research.  J. Biomol NMR 2016 Mar 2.

    Stark, JL., Eghbalnia, HR., Lee W., Westler, WM., Markley JL. NMRmix: A Tool for the Optimization of Compound Mixtures in 1D (1)H NMR Ligand Affinity Screens. J. Proteome Res. 2016 Apr 1;15(4):1360-8. doi: 10.1021/acs.jproteome.6b00121. Epub 2016 Mar 23.

    Dashti, H., Tonelli, M., Westler, W. M., Cornilescu, G., Ulrich, E. L., & Markley, J. L. (2016). Probabilistic validation of protein NMR chemical shift assignments. J. Biomol. NMR 64 (1) 17-25.

    Singarapu, K. K., Otte, M. M., Tonelli, M., Westler, W. M., Escalante-Semerena, J. C., & Markley, J. L. Solution structural studies of GTP:Adenosylcobinamide-phosphateguanylyl transferase (CobY) from Methanococcus jannaschii. PLOS One. doi: 10.1371/journal.pone.0141297.

    Chen, V. B.,  Wedell, J. R., Wenger, R. K., Ulrich, E. L. & Markley, J. L. (2015) MolProbity for the masses-of data. J. Biomol. NMR doi: 10.1007/s10858-015-9969-9.

    Dashti, H., Tonelli, M. & Markley, J. L. (2015) ADAPT-NMR 3.0: utilization of BEST-type triple-resonance NMR experiments to accelerate the process of data collection and assignment. J. Biomol. NMR 62 (3) 247-252.

    Dashti, H., Lee, W., Tonelli, M., Cornilescu,C. C., Cornilescu, G., Assadi-Porter, F. M., Westler, W. M., Eghbalnia, H. R. & Markley, J. L.(2015) NMRFAM-SDF: a protein structure determination framework. J Biomol. NMR Apr 22nd, ahead of print, doi:10.1007/s10858-015-9933-8

    Lee, W., Tonelli, M. &  Markley, J. L. (2015) NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31 (8) 1325-1327. (PMCID: PMC4393527)

    Korasick, David A., Chatterjee ,Srirupa, Tonelli, Marco,  Dashti, Hesam, Lee, Soon Goo, Westfall, Corey S., Fulton, D. Bruce, Andreotti ,Amy H. Amarasinghe, Gaya K., Strader, Lucia C. and  Jez, Joseph M.(2015) Defining a Two-Pronged Structural Model for PB1 Domain Interaction in Plant Auxin Responses. J. Biol. Chem. 290 (20) 12868-12878. (PMCID: PMC4432302)

    Mouzakis K. D.,Dethoff E. A., Tonelli M., Al-Hashimi H., Butcher S. E. (2015) Dynamic Motions of the HIV-1 Frameshift Site RNA. Biophys. J 108(3):644-654. (PMCID: PMC4317556)

    Baßler, J., Paternoga, H., Holdermann, I., Thomas, M., Granneman, S., Barrio-Garcia, C., Nyarko, A., Lee, W., Stier, G., Clark, S. A., Schraivogel, D., Kallas, M., Beckmann, R., Barbar, E., Sinning, I. & Hurt, E. (2014) A network of assembly factors is involved in remodeling rRNA elements during preribosome maturation. J. Cell Biol. 207(4):481-498.(PMCID: PMC4242840)

    Lee, W., Stark, J. L. & Markley, J. L. (2014) PONDEROSA-C/S: client-server based software package for automated 3D structure determination. J. Biomol. NMR 60 (2-3) 73-75. (PMCID: PMC4207954)

    Kim, J. H., Bothe, J. R., Alderson, T. R., & Markley, J. L. (2014) Tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by NMR, SAXS, Chemical crosslinking and functional studies. Biochim. Biophys. Acta. S0167-4889 (14) 00481-2 doi: 10.1016/j.bbamcr.2014.11.020. (PMCID: PMC4390431).

    Kim, J. H.,  Alderson, T. R., Frederick, R. O. & Markley, J. L. (2014) Nucleotide dependent interactions within a specialized Hsp7-/Hsp40 complex involved in Fe-S cluster biogenesis. J. Am. Chem. Soc. 136, 11586-11589. (PMCID: PMC4140450)

    Kim, J. H.,  Bothe, J. R., Frederick, R. O., Holder, J. C. & Markley, J. L. (2014) Role of IscX in iron Sulfur Cluster Biogenesis in Escherichia coli. J. Am. Chem. Soc. 136, 7933-7942. (PMCID: PMC4063190)

    Dai, Z., Kim, J.,  Tonelli, M., Ali, I., & Markley, J. L. (2014) pH induced conformational change of IscU at low pH correlates with protonation/deprotonation of two conserved histidine residues. Biochem. 53 (32) 5290-5297. (PMCID: PMC4139155)

    Singh, S. Peltier-Pain, P., Tonelli, M. & Thorson, J. S. (2014) A General NMR based strategy for the in situ characterization of Sugar-Nucleotide-Dependent Biosynthetic pathways. Org Letts. 16, 3220-3223. (PMCID: PMC4075999)

    Morrison, E. A. & Henzler-Wildman, K. A. (2014) Transported substrate determines exchange rate in the multidrug resistance transporter EmrE. J. Biol. Chem. 289 (10) 6825-6836. (PMCID: PMC394543)

    Lee, W., Watters, K. E., Troupis, A. T., Reinen, N. M., Suchy, F. P., Moyer, K. L., Frederick, R. O., Tonelli, M., Aceti, D. J., palmenberg, A. C. & Markley, J. L. (2014) Solution structure of the 2A protease from a common cold agent human rhinovirus C2 strain W12. PLoS ONE 9, e97198 (PMCID: PMC4061012)

    Cornilescu, C. C., Cornilescu, G., Burgie, E. S., Markley, J. L., Ulijasz, A. T. & Vierstra, R. D. (2014) Dynamic structural changes underpin photoconversion of a blue/green cyanobacteriochrome between its dark and photoactivated states. J. Biol. Chem. 289, 3055-3065 (PMCID: PMC3908435)

    Kim, J. H., Bothe, J. R., Frederick, R. O., Holder, J. C. & Markley, J. L. (2014) Role of IscX in Iron Sulfur cluster biogenesis in Escherichia coli. JACS 136, 7933-7942. (PMCID: PMC4063190)

    Tonelli, M., Eller, C., Singarapu, K., Lee, W., Bahrami, A., Westler, W.M., Raines, R.T. & Markley, J.L. (2014) Assignments of RNase A by ADAPT-NMR and enhancer, Biomol. NMR Assign. 9, 8188. (PMCID: PMC41628551)

    Whigham, L., Butz, D., Dashti, H., Tonelli, M., Johnson, L., Cook, M., Porter, W., Eghbalnia, H., Lindheim, S., Scholler, D., Abbott, D. & Assadi-Porter, F. (2014) Metabolic Evidence of Diminished Lipid Oxidation in Women With Polycystic Ovary Syndrome, Curr. Metabol. 2, 269–278. (PMCID: PMC3994884)

    Markley JL, Kim JH, Dai Z, Bothe JR, Cai K, Frederick RO & Tonelli M. (2013) Metamorphic protein IscU alternates conformations in the course of its role as the scaffold protein for iron-sulfur cluster biosynthesis and delivery. FEBS Lett. 587, (8) 1172-1179.(PMCID: PMC3960074)

    Poplawski, A., Hu, K., Lee, W., Natesan S., Peng, D., Carlson, S., Shi, X., Balaz, S, Markley, J. L. & Glass, K. C. (2013) Molecular Insights into the Recognition of N-Terminal Histone Modifications by the BRPF1 Bromodomain, J. Mol. Biol. ePub Dec12, 2013 (PMCID: PMC3969779).

    Cornilescu, C. C., Cornilescu, G., Brugie E. S., Markley, J. L., Ulijasz, A. T. & Vierstra, R. D. (2013) Dynamic structural changes underpin photoconversion of a blue/green cyanobacteriochrome between its ground and photoactivated states, J. Biol. Chem.  284 (43) 29757-29772. (PMCID: PMC2785607)

    Lee, W., Hu, K., Tonelli, M., Bahrami, A., Neuhardt, E., Glass, K. C. & Markley, J. L. (2013) Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers, J. Magn. Reson., 236, 83-8. (PMCID: PMC3858185).

    Cornilescu, C. C., Cornilescu, G., Rao, H., Porter, S. F., Tonelli, M., DeRider, M. L., Markley, J. L. & Assadi-Porter, F. M. (2013) Temperature-dependent conformational change affecting Tyr11 and sweetness loops of brazzein, Proteins: Structure, Function & Bioinformatics, 81, 6, 919-25. (PMCID: PMC3982881).

    Hsueh, K.-L., Tonelli, M., Cai, K., Westler, W. M. & Markley, J. L. (2013) Electron Transfer Mechanism of the Rieske Protein from Thermus thermophilus from Solution Nuclear Magnetic Resonance Investigations, Biochemistry, 52, 17, 2874-87. (PMCID: PMC3686548).

    Kim, J-H, Frederick, R. O., Reinen, N. M., Troupis, A. T. & Markley, J. L. (2013) [2Fe-2S]-Ferredoxin Binds Directly to Cysteine Desulfurase and Supplies an Electron for Iron–Sulfur Cluster Assembly but Is Displaced by the Scaffold Protein or Bacterial Frataxin, J. Am. Chem. Soc. 135, 22, 8117-20. (PMCID: PMC3677232).

    Lee, W., Bahrami, A. & Markley, J. L. (2013) ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy, Bioinformatics. 29, 4, 515-7. (PMCID: PMC23220573)

    Clos II, L.J., Jofre, M.F., Ellinger, J.J., Westler, W.M., Markley, J.L. (2012). NMRbot: Python scripts enable high-throughput data collection on current Bruker BioSpin NMR spectrometers. Metabolomics (PMCID: PMC3651530).

    Bahrami, A., Clos, L. J. II, Markley, J. L., Butcher, S. E. & Eghbalnia, H. R. (2012) RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts, J. Biol. NMR. 52, 289-302. (PMCID: PMC3480180)

    Bahrami, A., Tonelli, M., Sahu, S. C., Singarapu, K. K., Eghbalnia, H. R. & Markley, J. L. (2012) Robust, Integrated Computational Control of NMR Experiments to Achieve Optimal Assignment by ADAPT-NMR, PLoS One. 7, 233175. (PMCID: PMC3299752)

    Lee, W., Yu, W., Kim, S. Chang, I., Lee, W. & Markley, J. L. (2012) PACSY, a relational database management system for protein structure and chemical shift analysis, J. Biomol. NMR, 154, 169-79.(PMCID: PMC3542970)

    Chylla, R. A., Hu, K., Ellinger, J. J. & Markley, J. J. (2011) Deconvolution of two-dimensional NMR spectra by fast Maximum Likelihood Reconstruction: application to quantitative metabolomics, Anal. Chem, 83, 4871-80. (PMCID: PMC3114465)

    Lee, W., Kim, J. H., Westler, W. M. & Markley, J. L. (2011) PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination, Bioinformatics 27, 1727-8. (PMCID: PMC3106192)

    Lewis, I. A., Schommer, S. C. & Markley, J. L. (2009) rNMR open source software for identifying and quantifying metabolites in NMR spectra, Magn. Reson. Chem., 47, (S 1), S123-S126. (PMCID: PMC2798074)

    Lee, W., Westler, W. M., Bahrami, A., Eghbalnia, H. & Markley, J. L. (2009) PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy. Boinformatics. 25, 2085-7. (PMCID: PMC2723000)

    Bahrami, A., Assadi, A. H., Markley, J. L. & Eghbalnia, H. R. (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. PLoS Comput Biol., 5(3):e1000307. [PMCID: PMC2645676]

    Cornilescu, G. Bahrami, A. Tonelli, M., Markley, J. L. & Eghbalnia, H. R. (2007) HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections, J Biomol. NMR. 38, 341-51.

    Wang L., Eghbalnia, H. R., Bahrami, A. & Markley, J. L. (2005) Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications. J Biomol. NMR, 32 (1):13-22.

    Eghbalnia, H. R., Wang, L., Bahrami, A. Assadi, A. & Markley, J. L. (2005) Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements., J Biomol. NMR, 32 (1) 71-81.

    Eghbalnia, H. R., Bahrami, A. Tonelli, M., Hallenga, K. & Markley, J. L. (2005) High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection. J Am. Chem. Soc. 127, 12528-36.

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    Biochem 800 – Practical Nuclear Magnetic Resonance Theory

    Biochem 801 – Biochemical Applications of Nuclear Magnetic Resonance

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

    Workshop "Ultrahigh Field NMR and MRI: Science at a Crossroads" November 12-13, NIH

    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: Mark Anderson
    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