NMRFAM eNewsletter – March 2017


  • April 2017 time requests: This is a reminder that March 19th 4pm CST is the deadline to have spectrometer time reserved for you for April 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 March 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.
  •  2017 NMRFAM Introductory Structure Determination workshop (June 4th- 9th) - http://www.nmrfam.wisc.edu/introductory-workshop.htm
  •  2017 NMRFAM Advanced Structure Determination 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, 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:

            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)

  • 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

(down)

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

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

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:

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

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)

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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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

Telluride School on Biomolecular Structure and Dynamics;Theory and Experiment (July 24-31, 2017) 

AMPERE NMR School (June 25th - July 1, 2017: Zakopane, Poland)

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