[NMRFAM enews] NMRFAM eNewsletter_January 2017

Lai Bergeman lai.bergeman at wisc.edu
Tue Jan 10 11:16:41 CST 2017

NMRFAM eNewsletter – January 2017

  *   Happy New Year from NMRFAM!

  *   February 2017 time requests: This is a reminder that January 19th 4pm CST is the deadline to have spectrometer time reserved for you for February 2017; 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 end-of-day on January 20th, by logging into Sundial<http://www.nmrfam.wisc.edu/howt-to-request-time.htm> and following the requests process.

  *   Contact Lai Bergeman<mailto:lai.bergeman at wisc.edu> by e-mail or at 608-262-3173 for general assistance. For scientific questions/discussions contact Milo Westler<mailto:milo at nmrfam.wisc.edu>.

  *   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<mailto:djaceti at wisc.edu>, 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<mailto:Mark%20Anderson%20%28wombats at nmrfam.wisc.edu%29>.

  *   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.
     *   400 MHz spectrometer (Pisa) was decommissioned in December 2016.

  *   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:

  *   NMRFAM Spectrometers availability (Live Schedule) for current and upcoming month can be view at http://www.nmrfam.wisc.edu/546.htm

  *   NMRFAM instrumentation
Spectrometer status:


Cow name

Shortcut name



Bruker AV-HD 900




OK - cold 1H and13C preamps

Agilent VNS 800




OK - cold probe

Bruker AV III 750




OK - cold probe

Bruker AV III 600


600 I


OK - SampleJet

Agilent VNS 600


600 II


OK - cold probe

Bruker AV III 600


600 III


OK - cold probe

Bruker AV III 600


600 IV


OK - SampleJet (cooled)

Bruker AV III 500


500 I


OK-all cold preamp; SampleJet

Bruker AV III 500


500 II


OK - cold probe





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:
2 - NMRbot
5 - PINE
6 - PINE-Sparky
8 - ADAPT-NMR Enhancer
9 - Newton
10 - PACSY
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 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

·         Eghbalnia H.R., Romero P.R, Westler W.M, Baskaran K., Ulrich E.L, Markley J.L, Increasing rigor in NMR-based metabolomics through validated and open source tools. Curr Opin Biotechnol. 2016. PMID: 27643760

·         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 C.C., 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. 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) fromMethanococcus 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)
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Lai Bergeman
NMRFAM Administrator
RM 171, 433 Babcock Dr.
University of Wisconsin – Madison,
Madison WI 53706
lai.bergeman at wisc.edu
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