[NMRFAM enews] NMRFAM eNewsletter_February 2017

Lai Bergeman lai.bergeman at wisc.edu
Thu Feb 16 15:42:32 CST 2017

NMRFAM eNewsletter – February 2017

  *   March 2017 time requests: This is a reminder that February 19th 4pm CST is the deadline to have spectrometer time reserved for you for March 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 February 20th, by logging into Sundial 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>.

  *   2017 NMRFAM Introductory Structure Determination workshop (June 4th- 9th) - http://www.nmrfam.wisc.edu/introductory-workshop.htm<-%20http:/www.nmrfam.wisc.edu/introductory-workshop.htm>

  *   2017 NMRFAM Advanced Structure Refinement Workshop (August 6th -9th) – http://www.nmrfam.wisc.edu/advanced-workshop.htm

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:
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 (Vorges)
·         3.2mm Efree CPMAS probe and 1.3mm ultrafast CPMAS probe- 900 MHz (Fleckvieh)

v  LC/MS micrOTOF Q II is now available for collaboration.
v  Bruker Nanostar SAXS (small angle X-ray scattering) 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 re-tuned 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<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/Spectrometer-Live-Calendar.htm

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

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, 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

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)
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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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