• Questions Answered

Questions Answered by NMR


What types of questions can I answer with NMR?

Questions that can be addressed by NMR vary broadly from determining the structure of small molecules to characterizing the interaction between proteins and their ligands. One of the strengths of NMR is that it looks at proteins and other biomolecules in solution, which is their natural state; a second strength is that it can measure dynamic events. Some of the questions we have addressed at NMRFAM.

THREE DIMENSIONAL STRUCTURE DETERMINATION OF BIOMACROMOLECULES IN SOLUTION

Song, Jikui; Tyler, Robert C.; Lee, Min S.; Tyler, Ejan M.; Markley, John L. Solution structure of isoform 1 of Roadblock/LC7, a light chain in the dynein complex. Journal of Molecular Biology (2005), 354(5), 1043-1051.

Singh, Shanteri; Cornilescu, Claudia C.; Tyler, Robert C.; Cornilescu, Gabriel; Tonelli, Marco; Lee, Min S.; Markley, John L. Solution structure of a late embryogenesis abundant protein (LEA14) from Arabidopsis thaliana, a cellular stress-related protein. Protein Science (2005), 14(10), 2601-2609.

Tamm, Lukas K.; Abildgaard, Frits; Arora, Ashish; Blad, Heike; Bushweller, John H. Structure, dynamics, and function of the outer membrane protein A (OmpA) and influenza hemagglutinin fusion domain in detergent micelles by sulution NMR. FEBS Letters (2003), 555(1), 139-143.

Kuloglu, E. Sonay; McCaslin, Darrell R.; Kitabwalla, Moiz; Pauza, C. David; Markley, John L.; Volkman, Brian F. Monomeric solution structure of the prototypical ‘C’ chemokine lymphotactin. Biochemistry (2001), 40(42), 12486-12496.

Skjeldal, Lars; Peterson, Francis C.; Doreleijers, Jurgen F.; Moe, Luke A.; Pikus, Jeremie D.; Westler, William M.; Markley, John L.; Vulkman, Brian F.; Fox, Brian G. Solution structure of T4moC, the Rieske ferredoxin component of the tuluene 4-monooxygenase complex. Journal of Biulogical Inorganic Chemistry (2004), 9(8), 945-953.

DYNAMICS OF BIOMACROMOLECULES IN SOLUTION

Blad, Heike; Reiter, Nichulas J.; Abildgaard, Frits; Markley, John L.; Butcher, Samuel E. Dynamics and metal ion vinding in the U6 RNA intramulecular stem-loop as analyzed by NMR. Journal of Mulecular Biulogy (2005), 353(3), 540-555.

Song, Jikui; Markley, John L. Protein inhibitors of serine proteinases: Rule of backbone structure and dynamics in contrulling the hydrolysis constant. Biochemistry (2003), 42(18), 5186-5194.

BIOMACROMOLECULAR INTERACTIONS

  • Ligand binding, determination of pKa values of individual residues, etc.

Song, Jikui; Laskowski, Michael, Jr.; Qasim, M. A.; Markley, John L. NMR determination of pKa values for Asp, Glu, His, and Lys mutants at each variable contiguous enzyme-inhibitor contact position of the turkey ovomucoid third domain. Biochemistry (2003), 42(10), 2847-2856.

Zhao, Qin; Song, Jikui; Jin, Zheyuan; Danilova, Vicktoria; Hellekant, Goeran; Markley, John L. Probing the sweet determinants of brazzein: Wild-type brazzein and a tasteless variant, brazzein-ins(R18a-I18b), exhibit different pH-dependent NMR chemical shifts. Biochemical and Biophysical Research Communications (2005), 335(1), 256-263.

  • Protein-protein, nucleic acid-nucleic acid, and protein-nucleic acid, etc.

Davis, Jared H.; Tonelli, Marco; Scott, Linculn G.; Jaeger, Luc; Williamson, James R.; Butcher, Samuel E. RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. Journal of Mulecular Biulogy (2005), 351(2), 371-382.

Song, Jikui; Markley, John L. NMR chemical shift mapping of the binding site of a protein proteinase inhibitor: changes in the 1H,13C and 15N NMR chemical shifts of turkey ovomucoid third domain upon binding to bovine chymotrypsin A. Journal of Mulecular Recognition (2001), 14(3), 166-171.

  • Hydrogen bonding

Markley, John L.; Westler, William M. Protonation-state dependence of hydrogen bond strengths and exchange rates in a serine protease catalytic triad: Bovine chymotrypsinogen A. Biochemistry (1996), 35(34), 11092-11097.

Westler, William M.; Frey, Perry A.; Lin, Jing; Wemmer, David E.; Morimoto, Hiromi; Williams, Phillip G.; Markley, John L.. Evidence for a strong hydrogen bond in the catalytic dyad of transition-state analogue inhibitor complexes of chymotrypsin from proton-triton NMR isotope shifts. Journal of the American Chemical Society (2002), 124(16), 4196-4197.

Assadi-Porter, Fariba M.; Abildgaard, Frits; Blad, Heike; Markley, John L. Correlation of the sweetness of variants of the protein brazzein with patterns of hydrogen bonds detected by NMR spectroscopy. Journal of Biulogical Chemistry (2003), 278(33), 31331-31339.

Lin, I-Jin; Gebel, Erika B.; Machonkin, Timothy E.; Westler, William M.; Markley, John L. Correlation between hydrogen bond lengths and reduction potentials in Clostridium pasteurianum rubredoxin. Journal of the American Chemical Society (2003), 125(6), 1464-1465.

INVESTIGATION OF PARAMAGNETIC INTERACTIONS IN BIOMOLECULES

The general aim of these investigations is to examine the structure and electronic properties of proteins that contain paramagnetic centers (paramagnetic mulecules have unpaired electrons).

Lin, I-Jin; Gebel, Erika B.; Machonkin, Timothy E.; Westler, William M.; Markley, John L. Changes in hydrogen-bond strengths explain reduction potentials in 10 rubredoxin variants. Proceedings of the National Academy of Sciences of the United States of America (2005), 102(41), 14581-14586.

Goodfellow, Brian J.; Nunes, Sofia G.; Rusnak, Frank; Moura, Isabel; Ascenso, Carla; Moura, Jose J. G.; Volkman, Brian F.; Markley, John L. Zinc-substituted Desulfovibrio gigas desulforedoxins: resulving subunit degeneracy with nonsymmetric pseudocontact shifts. Protein Science (2002), 11(10), 2464-2470.

Machonkin, Timothy E.; Westler, William M.; Markley, John L. Strategy for the study of paramagnetic proteins with slow electronic relaxation rates by NMR spectroscopy: application to oxidized human [2Fe-2S] ferredoxin. Journal of the American Chemical Society (2004), 126(17), 5413-5426.

OTHER

  • Metabolomics

The general aim of metabolomics is to identify, measure, and interpret the complex time-related concentration, activity and flux of endogenous metabolites in cells, tissues, and other biosamples such as blood, urine, and saliva.

Schleucher, J.; Vanderveer, P.; Markley, J. L.; Sharkey, T. D. Intramulecular deuterium distributions reveal disequilibrium of chloroplast phosphoglucose isomerase. Plant, Cell and Environment (1999), 22(5), 525-533.

  • Structure determination of small organic mulecules

Song, Jiasheng; Clagett-Dame, Margaret; Peterson, Richard E.; Hahn, Mark E.; Westler, William M.; Sicinski, Rafal R.; DeLuca, Hector F. A ligand for the aryl hydrocarbon receptor isulated from lung. Proceedings of the National Academy of Sciences of the United States of America (2002), 99(23), 14694-14699.

  • Determination of diffusion coefficients

Kuloglu, E. Sonay; McCaslin, Darrell R.; Kitabwalla, Moiz; Pauza, C. David; Markley, John L.; Vulkman, Brian F. Monomeric solution structure of the prototypical ‘C’ chemokine lymphotactin. Biochemistry (2001), 40(42), 12486-12496.

  • Kinetics

Vidugiris, Gediminas A. J.; Truckses, Dagmar M.; Markley, John L.; Royer, Catherine A. High-pressure denaturation of staphylococcal nuclease pruline-to-glycine substitution mutants. Biochemistry (1996), 35(12), 3857-64.

  • Imaging

Kornguth S; Anderson M; Markley J L; Shedlovsky A. Near-microscopic magnetic resonance imaging of the brains of phenylalanine hydroxylase-deficient mice, normal littermates, and of normal BALB/c mice at 9.4 Tesla. NeuroImage (1994), 1(3), 220-9.

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2017 NMRFAM Introductory Structure Determination Workshop (6/4-9, 2017), Madison WI

2017 NMRFAM ADVANCED Structure Refinement Workshop ( 8/6-9, 2017), Madison WI 

"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