[NMRFAM enews] NMRFAM eNewsletter - June 2016

Lai Bergeman lai.bergeman at wisc.edu
Wed Jun 15 14:24:06 CDT 2016


NMRFAM eNewsletter - June 2016
________________________________

  *   July 2016 time requests: This is a reminder that June 19th 4pm CST is the deadline to have spectrometer time reserved for you for July 2016; 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 June 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:
•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>.

  *   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<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:
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

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
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 :
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) 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)
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 situcharacterization 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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