John Markley

Summary

Affiliation: University of Wisconsin
Country: USA

Publications

  1. pmc Solution structure of the iron-sulfur cluster cochaperone HscB and its binding surface for the iron-sulfur assembly scaffold protein IscU
    Anna K Füzéry
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Biochemistry 47:9394-404. 2008
  2. pmc The length of the bound fatty acid influences the dynamics of the acyl carrier protein and the stability of the thioester bond
    Gregory A Zornetzer
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin53706, USA
    Biochemistry 49:470-7. 2010
  3. pmc Hyperfine-shifted (13)C and (15)N NMR signals from Clostridium pasteurianum rubredoxin: extensive assignments and quantum chemical verification
    I Jin Lin
    Graduate Program in Biophysics, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    J Am Chem Soc 131:15555-63. 2009
  4. pmc rNMR: open source software for identifying and quantifying metabolites in NMR spectra
    Ian A Lewis
    National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin, Madison, 433 Babcock Drive, Madison, WI 53706 1544, USA
    Magn Reson Chem 47:S123-6. 2009
  5. pmc NMR investigations of the Rieske protein from Thermus thermophilus support a coupled proton and electron transfer mechanism
    Kuang Lung Hsueh
    Graduate Program in Biophysics, 433 Babcock Drive, University of Wisconsin, Madison, Wisconsin 53706, USA
    J Am Chem Soc 132:7908-18. 2010
  6. pmc Simultaneous quantification and identification of individual chemicals in metabolite mixtures by two-dimensional extrapolated time-zero (1)H-(13)C HSQC (HSQC(0))
    Kaifeng Hu
    National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin Madison, Madison, Wisconsin 53706, United States
    J Am Chem Soc 133:1662-5. 2011
  7. pmc Structural characterization of Hsp12, the heat shock protein from Saccharomyces cerevisiae, in aqueous solution where it is intrinsically disordered and in detergent micelles where it is locally α-helical
    Kiran K Singarapu
    National Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, Wisconsin 53705, USA
    J Biol Chem 286:43447-53. 2011
  8. pmc Semiautomated device for batch extraction of metabolites from tissue samples
    James J Ellinger
    National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706 1544, USA
    Anal Chem 84:1809-12. 2012
  9. pmc Robust, integrated computational control of NMR experiments to achieve optimal assignment by ADAPT-NMR
    Arash Bahrami
    National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS ONE 7:e33173. 2012
  10. pmc NMR method for measuring carbon-13 isotopic enrichment of metabolites in complex solutions
    Ian A Lewis
    National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    Anal Chem 82:4558-63. 2010

Research Grants

  1. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John L Markley; Fiscal Year: 2010
  2. NATIONAL BIOMEDICAL NMR RESOURCE AT MADISON
    John Markley; Fiscal Year: 2007
  3. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 1999
  4. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 2007
  5. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John L Markley; Fiscal Year: 2010
  6. 900 MHZ NMR SPECTROMETER
    John Markley; Fiscal Year: 2001
  7. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 2001
  8. Specialized Center for Eukaryotic Structural Genomics
    John Markley; Fiscal Year: 2007
  9. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 2009
  10. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 2000

Detail Information

Publications91

  1. pmc Solution structure of the iron-sulfur cluster cochaperone HscB and its binding surface for the iron-sulfur assembly scaffold protein IscU
    Anna K Füzéry
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Biochemistry 47:9394-404. 2008
    ..IscU.HscB ternary complex. We propose that the conserved patch in the C-domain of HscB is the principal binding site for IscU...
  2. pmc The length of the bound fatty acid influences the dynamics of the acyl carrier protein and the stability of the thioester bond
    Gregory A Zornetzer
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin53706, USA
    Biochemistry 49:470-7. 2010
    ..Thus, acyl-ACP offers an interesting system for future investigations of complex protein motions on the micro- and millisecond time scales...
  3. pmc Hyperfine-shifted (13)C and (15)N NMR signals from Clostridium pasteurianum rubredoxin: extensive assignments and quantum chemical verification
    I Jin Lin
    Graduate Program in Biophysics, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    J Am Chem Soc 131:15555-63. 2009
    ..The methods developed here should be applicable to other proteins that contain a paramagnetic center with high spin and slow electron exchange...
  4. pmc rNMR: open source software for identifying and quantifying metabolites in NMR spectra
    Ian A Lewis
    National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin, Madison, 433 Babcock Drive, Madison, WI 53706 1544, USA
    Magn Reson Chem 47:S123-6. 2009
    ..The rNMR website at http://rnmr.nmrfam.wisc.edu offers downloadable versions of rNMR for Windows, Macintosh, and Linux platforms along with extensive help documentation, instructional videos, and sample data...
  5. pmc NMR investigations of the Rieske protein from Thermus thermophilus support a coupled proton and electron transfer mechanism
    Kuang Lung Hsueh
    Graduate Program in Biophysics, 433 Babcock Drive, University of Wisconsin, Madison, Wisconsin 53706, USA
    J Am Chem Soc 132:7908-18. 2010
    ..Our results are most consistent with a mechanism involving the coupled transfer of an electron and transfer of the proton across the hydrogen bond between the hydroquinone and His154 at the cytochrome b site...
  6. pmc Simultaneous quantification and identification of individual chemicals in metabolite mixtures by two-dimensional extrapolated time-zero (1)H-(13)C HSQC (HSQC(0))
    Kaifeng Hu
    National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin Madison, Madison, Wisconsin 53706, United States
    J Am Chem Soc 133:1662-5. 2011
    ..The concentration measurement for an individual metabolite can be improved by averaging the intensities of multiple, nonoverlapping cross peaks assigned to that metabolite...
  7. pmc Structural characterization of Hsp12, the heat shock protein from Saccharomyces cerevisiae, in aqueous solution where it is intrinsically disordered and in detergent micelles where it is locally α-helical
    Kiran K Singarapu
    National Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, Wisconsin 53705, USA
    J Biol Chem 286:43447-53. 2011
    ..These observations are in agreement with studies suggesting that Hsp12 functions to protect the membrane from desiccation...
  8. pmc Semiautomated device for batch extraction of metabolites from tissue samples
    James J Ellinger
    National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706 1544, USA
    Anal Chem 84:1809-12. 2012
    ..Moreover, we show that aqueous SAMBED-based methods can be completed in less than a quarter of the time required for manual extractions...
  9. pmc Robust, integrated computational control of NMR experiments to achieve optimal assignment by ADAPT-NMR
    Arash Bahrami
    National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS ONE 7:e33173. 2012
    ..We present test cases in which ADAPT-NMR achieved results in two days or less that would have taken two months or more by manual approaches...
  10. pmc NMR method for measuring carbon-13 isotopic enrichment of metabolites in complex solutions
    Ian A Lewis
    National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    Anal Chem 82:4558-63. 2010
    ..34 to 6.2 mM) and can detect molecules at concentrations less than 10 muM. We propose ITOCSY as a practical NMR strategy for metabolic flux analysis, isotope dilution experiments, and other methods that rely on carbon-13 labeling...
  11. pmc Role of aminotransferases in glutamate metabolism of human erythrocytes
    James J Ellinger
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    J Biomol NMR 49:221-9. 2011
    ..We show that up to 89% of the erythrocyte glutamate pool can be derived from ALT and that ALT-derived glutamate is subsequently used for glutathione synthesis...
  12. pmc Two-dimensional concurrent HMQC-COSY as an approach for small molecule chemical shift assignment and compound identification
    Kaifeng Hu
    National Magnetic Resonance Facility at Madison, University of Wisconsin Madison, Madison, WI 53706, USA
    J Biomol NMR 49:291-6. 2011
    ..In addition, we show that the experiment can be used to assign spectra of compounds in a mixture of metabolites in D(2)O...
  13. pmc Three hydrophobic amino acids in Escherichia coli HscB make the greatest contribution to the stability of the HscB-IscU complex
    Anna K Füzéry
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    BMC Biochem 12:3. 2011
    ..However, the individual contribution of each substitution to the observed effect remains to be determined as well as the possible involvement of other residues in the proposed binding site...
  14. pmc BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions
    John L Markley
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706 1544, USA
    J Biomol NMR 40:153-5. 2008
    ..The BMRB now contains an archive of NMR data for metabolites and other small molecules found in biological systems...
  15. pmc The Center for Eukaryotic Structural Genomics
    John L Markley
    Center for Eukaryotic Structural Genomics, Biochemistry Department, University of Wisconsin Madison, Madison, WI 53706, USA
    J Struct Funct Genomics 10:165-79. 2009
    ....
  16. ncbi request reprint Protonation-state dependence of hydrogen bond strengths and exchange rates in a serine protease catalytic triad: bovine chymotrypsinogen A
    J L Markley
    National Magnetic Resonance Facility at Madison, Wisconsin, USA
    Biochemistry 35:11092-7. 1996
    ..mol-1 higher at pH 3.5 than at pH 1 or 9...
  17. pmc Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family
    Robert C Tyler
    Center for Eukaryotic Structural Genomics, Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706 1544, USA
    Biochemistry 45:14325-36. 2006
    ..This work establishes that the domain family COG2388 represents a novel class of acetyltransferase and provides insight into possible mechanistic roles of the conserved Cys76 and His41 residues of this family...
  18. ncbi request reprint Two conformational states of Turkey ovomucoid third domain at low pH: three-dimensional structures, internal dynamics, and interconversion kinetics and thermodynamics
    Jikui Song
    National Magnetic Resonance Facility, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    Biochemistry 42:6380-91. 2003
    ..15)N transverse relaxation results indicate that residues P(6)-Lys(13)-P(3)-Cys(16) in the trans state undergo a dynamic process on the microsecond-millisecond time scale not present in the cis state...
  19. ncbi request reprint NMR solution structure of ATTp, an Arabidopsis thaliana trypsin inhibitor
    Qin Zhao
    Department of Biochemistry, University of Wisconsin Madison, 53706, USA
    Biochemistry 41:12284-96. 2002
    ..The overall fold of ATT(p) is distinct from those of other classes of serine proteinase inhibitors except in the inhibitor loop; therefore, it represents a new inhibitor fold...
  20. ncbi request reprint Solution structure of a ubiquitin-like domain from tubulin-binding cofactor B
    Betsy L Lytle
    Center for Eukaryotic Structural Genomics, Madison, Wisconsin 53706 1549, USA
    J Biol Chem 279:46787-93. 2004
    ....
  21. ncbi request reprint Solution structure of YggX: a prokaryotic protein involved in Fe(II) trafficking
    Qiu Cui
    National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin Madison, 53706, USA
    Proteins 62:578-86. 2006
    ..The finding that iron binds only weakly to YggX, and not to a highly conserved region of the structure, suggests that the role of this protein in iron homeostasis is more complex than previously thought...
  22. ncbi request reprint Cell-free protein production and labeling protocol for NMR-based structural proteomics
    Dmitriy A Vinarov
    Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    Nat Methods 1:149-53. 2004
    ..The three-dimensional (3D) structure of At3g01050.1 shows that this protein is an unusual member of the beta-grasp protein family...
  23. pmc Structural basis for the catalytic mechanism of mammalian 25-kDa thiamine triphosphatase
    Jikui Song
    Center for Eukaryotic Structural Genomics and National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706 1544, USA
    J Biol Chem 283:10939-48. 2008
    ..We propose a mechanism underlying the high substrate specificity of mThTPase and discuss the possible role of water molecules in enzymatic catalysis...
  24. ncbi request reprint BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank
    Jurgen F Doreleijers
    BioMagResBank, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706, U S A
    J Biomol NMR 26:139-46. 2003
    ..The results serve as a model for the development of standards for NMR constraint deposition in computer-readable form. The constraints are updated regularly and are available from the BMRB web site (http://www.bmrb.wisc.edu)...
  25. pmc Structure and dynamics of the iron-sulfur cluster assembly scaffold protein IscU and its interaction with the cochaperone HscB
    Jin Hae Kim
    Biophysics Graduate Program, University of Wisconsin, Madison, Wisconsin 53706, USA
    Biochemistry 48:6062-71. 2009
    ..We conclude that the IscU-HscB complex exists as two (or more) distinct states that interconvert at a rate much faster than the rate of dissociation of the complex and that HscB binds to and stabilizes the ordered state of apo-IscU...
  26. pmc Solution structure of Arabidopsis thaliana protein At5g39720.1, a member of the AIG2-like protein family
    Betsy L Lytle
    Center for Eukaryotic Structural Genomics, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:490-3. 2006
    ..Conservation of residues in a hydrophilic cavity able to bind small ligands in UPF0131 proteins suggests that this may also serve as an active site in AIG2-like proteins...
  27. pmc Solution structure of human sorting nexin 22
    Jikui Song
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706 1544, USA
    Protein Sci 16:807-14. 2007
    ..Because motions in the loops are damped out when dibutanoyl-PtdIns(3)P binds, entropic effects could contribute to the lower affinity of SNX22 for this ligand compared to other PX domains...
  28. ncbi request reprint Protein inhibitors of serine proteinases: role of backbone structure and dynamics in controlling the hydrolysis constant
    Jikui Song
    National Magnetic Resonance Facility, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    Biochemistry 42:5186-94. 2003
    ....
  29. ncbi request reprint 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
    Jikui Song
    National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    Biochemistry 42:2847-56. 2003
    ..Remarkably, in several interacting systems, resonances from different protons within the same residue yielded different pHmid values...
  30. ncbi request reprint Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements
    Hamid R Eghbalnia
    Biochemistry Department, National Magnetic Resonance Facility at Madison, 433 Babcock Drive, Madison, WI 53706, USA
    J Biomol NMR 32:71-81. 2005
    ....
  31. ncbi request reprint Brazzein, a small, sweet protein: effects of mutations on its structure, dynamics and functional properties
    Fariba M Assadi-Porter
    National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin Madison, 433 Babcock Drive, Madison WI 53706, USA
    Chem Senses 30:i90-1. 2005
  32. ncbi request reprint Production in two-liter beverage bottles of proteins for NMR structure determination labeled with either 15N- or 13C-15N
    Qin Zhao
    Center for Eukaryotic Structural Genomics and Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706, USA
    J Struct Funct Genomics 5:87-93. 2004
    ....
  33. ncbi request reprint Solution structure of isoform 1 of Roadblock/LC7, a light chain in the dynein complex
    Jikui Song
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, WI 53706 1544, USA
    J Mol Biol 354:1043-51. 2005
    ..These results provide physical evidence for a symmetrical interaction between dimeric robl1 and the two molecules of IC74-1 in the dynein complex...
  34. ncbi request reprint Comparison of cell-based and cell-free protocols for producing target proteins from the Arabidopsis thaliana genome for structural studies
    Robert C Tyler
    Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, Wisconsin 53706, USA
    Proteins 59:633-43. 2005
    ..coli platform when successful yields more protein, as currently needed for crystallization trials for X-ray structure determination...
  35. pmc Three-dimensional structure determined for a subunit of human tRNA splicing endonuclease (Sen15) reveals a novel dimeric fold
    Jikui Song
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706 1544, USA
    J Mol Biol 366:155-64. 2007
    ..The structural model provides insights into the functional assembly of the human tRNA splicing endonuclease...
  36. ncbi request reprint Stable isotope assisted assignment of elemental compositions for metabolomics
    Adrian D Hegeman
    Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    Anal Chem 79:6912-21. 2007
    ..These results demonstrate that metabolic labeling can be used to provide additional constraints for higher confidence formula assignments over an extended mass range...
  37. ncbi request reprint Probabilistic approach to determining unbiased random-coil carbon-13 chemical shift values from the protein chemical shift database
    Liya Wang
    National Magnetic Resonance Facility at Madison, 433 Babcock Drive, Madison, WI, 53706, USA
    J Biomol NMR 35:155-65. 2006
    ....
  38. pmc Structure of human J-type co-chaperone HscB reveals a tetracysteine metal-binding domain
    Eduard Bitto
    Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, Madison, Wisconsin 53706 1544, USA
    J Biol Chem 283:30184-92. 2008
    ..The normal mode analysis of HscB revealed that this L-shaped protein preferentially undergoes a scissors-like motion that correlates well with the conformational changes of human HscB observed in the crystals...
  39. doi request reprint Wheat germ cell-free expression system for protein production
    Dmitriy A Vinarov
    University of Wisconsin Madison, Madison, Wisconsin, USA
    Curr Protoc Protein Sci . 2006
    ..The methods described in this unit can be used to produce both unlabeled and labeled proteins required for structure-based determinations by NMR spectroscopy or X-ray crystallography...
  40. ncbi request reprint Preparation of isotopically labeled spinach acyl-acyl carrier protein for NMR structural studies
    Gregory A Zornetzer
    Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706 1549, USA
    Protein Expr Purif 46:446-55. 2006
    ....
  41. pmc Solution structure of a late embryogenesis abundant protein (LEA14) from Arabidopsis thaliana, a cellular stress-related protein
    Shanteri Singh
    Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706, USA
    Protein Sci 14:2601-9. 2005
    ....
  42. ncbi request reprint Auto-induction medium for the production of [U-15N]- and [U-13C, U-15N]-labeled proteins for NMR screening and structure determination
    Robert C Tyler
    Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706 1549, USA
    Protein Expr Purif 40:268-78. 2005
    ..1H-15N heteronuclear single quantum correlation spectroscopy as well as 13C; 15N-edited spectroscopy showed that the purified [U-15N]- and [U-13C, U-15N]-labeled proteins were suitable for structure analysis...
  43. ncbi request reprint A graphical approach to tracking and reporting target status in structural genomics
    Xiaokang Pan
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706, USA
    J Struct Funct Genomics 8:209-16. 2007
    ..This software package has facilitated inter-group communication, improved the quality and accuracy of information in our LIMS, and increased the efficiency and accuracy of our reports to PepcDB...
  44. doi request reprint Cell-free protein synthesis technology in NMR high-throughput structure determination
    Shin ichi Makino
    Department of Biochemistry, Center for Eukaryotic Structural Genomics, College of Agricultural and Life Sciences, University of Wisconsin, Madison, WI, USA
    Methods Mol Biol 607:127-47. 2010
    ....
  45. ncbi request reprint Structure of Ala24/Asp61 --> Asp24/Asn61 substituted subunit c of Escherichia coli ATP synthase: implications for the mechanism of proton transport and rotary movement in the F0 complex
    Oleg Y Dmitriev
    Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA
    Biochemistry 41:5537-47. 2002
    ..Based upon the structure, a mechanistic model is discussed that indicates how the wild-type and A24D/D61N subunits could utilize similar helical movements during H(+) transport-coupled rotation of the decameric c ring...
  46. doi request reprint NMR structure of the mengovirus Leader protein zinc-finger domain
    Claudia C Cornilescu
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706 1544, USA
    FEBS Lett 582:896-900. 2008
    ..This structure is divergent from those of other eukaryotic zinc-fingers and instead resembles motifs found in a group of DNA-binding proteins from Archaea...
  47. ncbi request reprint Structural rearrangement of human lymphotactin, a C chemokine, under physiological solution conditions
    E Sonay Kuloğlu
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    J Biol Chem 277:17863-70. 2002
    ..The functional relevance of this structural interconversion remains to be elucidated...
  48. ncbi request reprint Quantum chemical calculations on structural models of the catalytic site of chymotrypsin: comparison of calculated results with experimental data from NMR spectroscopy
    William M Westler
    National Magnetic Resonance Facility at Madison, Department of Biochemistry, and Theoretical Chemistry Institute, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    J Am Chem Soc 124:14373-81. 2002
    ..Models of the transition state that best fit the experimental data are consistent with a "strong" hydrogen bond between His(57) N(delta)(1) and Asp(102) O(delta)(1) but apparently not a "low-barrier" or "very strong" hydrogen bond...
  49. pmc Direct NMR detection of the binding of functional ligands to the human sweet receptor, a heterodimeric family 3 GPCR
    Fariba M Assadi-Porter
    National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    J Am Chem Soc 130:7212-3. 2008
    ..This approach opens new avenues for research on the mechanism of action of the sweet receptor and for the design of new noncalorigenic sweeteners...
  50. pmc Key amino acid residues involved in multi-point binding interactions between brazzein, a sweet protein, and the T1R2-T1R3 human sweet receptor
    Fariba M Assadi-Porter
    National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706, USA
    J Mol Biol 398:584-99. 2010
    ..Results from this study support a multi-point interaction between brazzein and the sweet receptor by some mechanism other than the proposed wedge models...
  51. pmc Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy
    Arash Bahrami
    Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS Comput Biol 5:e1000307. 2009
    ..PINE-NMR achieves robust and consistent results that have been shown to be effective in subsequent steps of NMR structure determination...
  52. pmc Solution structure of a single-domain thiosulfate sulfurtransferase from Arabidopsis thaliana
    Gabriel Cornilescu
    National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin Madison, Madison, Wisconsin 53706 1544, USA
    Protein Sci 15:2836-41. 2006
    ..Versions of this domain that lack the active site cysteine are found in other proteins, such as phosphatases, ubiquitin hydrolases, and sulfuryltransferases...
  53. ncbi request reprint Project management system for structural and functional proteomics: Sesame
    Zsolt Zolnai
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, Madison Wisconsin 53706, USA
    J Struct Funct Genomics 4:11-23. 2003
    ..This software is available to parties interested in using it and assisting to guide its further development...
  54. pmc PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy
    Woonghee Lee
    National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin Madison, Madison, WI 53706, USA
    Bioinformatics 25:2085-7. 2009
    ..Once assignments are fixed, the output files generated by PINE-SPARKY can be used as input to PINE-NMR for further refinements...
  55. pmc Interactions between the human sweet-sensing T1R2-T1R3 receptor and sweeteners detected by saturation transfer difference NMR spectroscopy
    Fariba M Assadi-Porter
    Biochemistry Department and National Magnetic Resonance Facility at Madison, 433 Babcock Drive, Madison WI 53706, USA
    Biochim Biophys Acta 1798:82-6. 2010
    ..Whereas activity assays are unable to distinguish mutations that alter ligand-binding sites from those that alter signal transduction downstream of the binding site, STD NMR now allows us to make this distinction...
  56. pmc One-sample approach to determine the relative orientations of proteins in ternary and binary complexes from residual dipolar coupling measurements
    Marco Tonelli
    National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706 1544, USA
    J Am Chem Soc 131:14138-9. 2009
    ..Because numerous biological processes rely on protein assemblies or transient interactions, this method should be well suited for a wide range of future applications...
  57. ncbi request reprint Correlation of the sweetness of variants of the protein brazzein with patterns of hydrogen bonds detected by NMR spectroscopy
    Fariba M Assadi-Porter
    National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    J Biol Chem 278:31331-9. 2003
    ..Two of the non-sweet variants lack the hydrogen bond connecting the N and C termini. These variants showed greater mobility in the N- and C-terminal regions than wild-type brazzein...
  58. pmc Efficient and rapid protein expression and purification of small high disulfide containing sweet protein brazzein in E. coli
    Fariba M Assadi-Porter
    Biochemistry Department, University of Wisconsin Madison, 171a Biochemistry Addition, 433 Babcock Drive, Madison, WI 53706, USA
    Protein Expr Purif 58:263-8. 2008
    ....
  59. ncbi request reprint High-throughput automated platform for nuclear magnetic resonance-based structural proteomics
    Dmitriy A Vinarov
    Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, WI 53706 1549, USA
    Expert Rev Proteomics 2:49-55. 2005
    ..Utilization of this automated platform technology to screen targets for expression and solubility and to produce stable isotope-labeled samples for nuclear magnetic resonance structure determinations is discussed...
  60. ncbi request reprint High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection
    Hamid R Eghbalnia
    National Magnetic Resonance Facility at Madison, Center for Eukaryotic Structural Genomics, Graduate Program in Biophysics, Biochemistry Department, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    J Am Chem Soc 127:12528-36. 2005
    ..HIFI-NMR required about one-tenth the time for data collection and avoided subsequent data processing and peak-picking. The approach can be implemented on commercial NMR spectrometers and is extensible to higher-dimensional NMR...
  61. ncbi request reprint Dynamics and metal ion binding in the U6 RNA intramolecular stem-loop as analyzed by NMR
    Heike Blad
    NMRFAM, University of Wisconsin Madison, 433 Babcock Dr, Madison, WI 53706, USA
    J Mol Biol 353:540-55. 2005
    ..Addition of Mg2+ shifts the conformational equilibrium toward the high-pH (base-stacked) structure, accompanied by a significant drop in the apparent pK(a) of A79...
  62. ncbi request reprint Wheat germ cell-free platform for eukaryotic protein production
    Dmitriy A Vinarov
    Center for Eukaryotic Structural Genomics, Biochemistry Department, University of Wisconsin Madison, Madison, WI, USA
    FEBS J 273:4160-9. 2006
    ..We present protein yields and costs and compare the wheat germ cell-free approach with alternative methods. Finally, we discuss remaining bottlenecks and approaches to their solution...
  63. ncbi request reprint One-step purification of bacterially expressed recombinant transducin alpha-subunit and isotopically labeled PDE6 gamma-subunit for NMR analysis
    Lian Wang Guo
    Department of Pharmacology, University of Wisconsin, Madison, WI 53706, USA
    Protein Expr Purif 51:187-97. 2007
    ..In addition, our protocol for removing the co-purifying DnaK contaminant may be of general utility in purifying E. coli-expressed recombinant proteins...
  64. ncbi request reprint Probing the sweet determinants of brazzein: wild-type brazzein and a tasteless variant, brazzein-ins(R18a-I18b), exhibit different pH-dependent NMR chemical shifts
    Qin Zhao
    Department of Biochemistry, University of Wisconsin Madison, College of Agricultural and Life Sciences, USA
    Biochem Biophys Res Commun 335:256-63. 2005
    ....
  65. ncbi request reprint Cautionary tail: the presence of an N-terminal tag on dynein light-chain Roadblock/LC7 affects its interaction with a functional partner
    Jikui Song
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, WI 53706 1544, USA
    Protein Pept Lett 14:265-8. 2007
    ..We found that the His-tag introduced a spurious binding site for a second protein, IC74. We propose a molecular mechanism for functional interference by the His-tag...
  66. ncbi request reprint Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO)
    Hamid R Eghbalnia
    Biochemistry Department, National Magnetic Resonance Facility at Madison, 433, Babcock Drive, Madison, WI 53706, USA
    J Biomol NMR 32:219-33. 2005
    ..PISTACHIO represents one component of a comprehensive probabilistic approach we are developing for the collection and analysis of protein NMR data...
  67. ncbi request reprint HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections
    Gabriel Cornilescu
    National Magnetic Resonance Facility at Madison, University of Wisconsin Madison, Madison, WI 53706, USA
    J Biomol NMR 38:341-51. 2007
    ..The statistical measure of reliability, measuring the quality of each RDC value, offers valuable adjunct information even in cases where modest time savings may be realized...
  68. ncbi request reprint Addressing the intrinsic disorder bottleneck in structural proteomics
    Christopher J Oldfield
    Center for Eukaryotic Structural Genomics, Biochemistry Department, University of Wisconsin, Madison, Wisconsin 53706, USA
    Proteins 59:444-53. 2005
    ..Our study indicates that the efficiency of structural proteomics of eukaryotes can be improved significantly by removing targets predicted to be disordered by an algorithm chosen to provide optimal performance...
  69. ncbi request reprint NMR analysis goes nano
    John L Markley
    Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
    Nat Biotechnol 25:750-1. 2007
  70. ncbi request reprint Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics
    George N Phillips
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    J Struct Funct Genomics 8:73-84. 2007
    ..Many times proteins qualify in more than one of these categories. Here we review some of the structures that have connections to human health and disease...
  71. ncbi request reprint Carbonyl carbon label selective (CCLS) 1H-15N HSQC experiment for improved detection of backbone 13C-15N cross peaks in larger proteins
    Marco Tonelli
    Department of Biochemistry, National Magnetic Resonance Facility at Madison, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706, USA
    J Biomol NMR 39:177-85. 2007
    ..This approach will be applicable to families of proteins that have been resistant to NMR structural and dynamic analysis, such as large enzymes, and partially folded or unfolded proteins...
  72. pmc BioMagResBank
    Eldon L Ulrich
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    Nucleic Acids Res 36:D402-8. 2008
    ..protein.osaka-u.ac.jp) and the other at CERM, University of Florence, Florence, Italy (bmrb.postgenomicnmr.net/). The site at Osaka also accepts and processes data depositions...
  73. pmc Small-scale, semi-automated purification of eukaryotic proteins for structure determination
    Ronnie O Frederick
    The University of Wisconsin Center for Eukaryotic Structural Genomics and Department of Biochemistry, University of Wisconsin, Room 141B, 433 Babcock Drive, Madison, WI 53706, USA
    J Struct Funct Genomics 8:153-66. 2007
    ....
  74. ncbi request reprint Macromolecular structure determination by NMR spectroscopy
    John L Markley
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA
    Methods Biochem Anal 44:89-113. 2003
  75. pmc Early formation of a beta hairpin during folding of staphylococcal nuclease H124L as detected by pulsed hydrogen exchange
    William F Walkenhorst
    Department of Chemistry, Loyola University, New Orleans, Louisiana 70118, USA
    Protein Sci 11:82-91. 2002
    ....
  76. ncbi request reprint X-ray structure of Arabidopsis At2g06050, 12-oxophytodienoate reductase isoform 3
    Thomas E Malone
    Molecular and Environmental Toxicology Program, University of Wisconsin Madison, 53706, USA
    Proteins 58:243-5. 2005
  77. pmc Carbon-13 NMR method for the detection of correlated hydrogen exchange at adjacent backbone peptide amides and its application to hydrogen exchange in five antiparallel beta strands within the hydrophobic core of Streptomyces subtilisin inhibitor (SSI)
    Kenichi Uchida
    Graduate School of Science, Tokyo Metropolitan University, 1 1 Minami Ohsawa, Hachioji, Tokyo 192 0397, Japan
    Biochemistry 44:11811-20. 2005
    ..In all cases in which correlated exchange could be measured, the observed sigmoidal pH dependence of X(betagamma) could be replicated roughly from the derived pH-independent rates...
  78. ncbi request reprint (1)H, (13)C and (15)N backbone assignment of a 32 kDa hypothetical protein from Arabidopsis thaliana, At3g16450.1
    Nozomi Sugimori
    J Biomol NMR 30:357-8. 2004
  79. ncbi request reprint Hypothetical protein At2g24940.1 from Arabidopsis thaliana has a cytochrome b5 like fold
    Jikui Song
    J Biomol NMR 30:215-8. 2004
  80. ncbi request reprint Paramagnetic NMR spectroscopy and density functional calculations in the analysis of the geometric and electronic structures of iron-sulfur proteins
    Timothy E Machonkin
    Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA
    Inorg Chem 44:779-97. 2005
    ..The approach described here for iron-sulfur proteins offers new avenues for detailed studies of these and other metalloprotein systems...
  81. ncbi request reprint 1H, 15N and 13C resonance assignments of the putative Bet v 1 family protein At1g24000.1 from Arabidopsis thaliana
    Jikui Song
    J Biomol NMR 32:335. 2005
  82. doi request reprint Metabolite identification via the Madison Metabolomics Consortium Database
    Qiu Cui
    Nat Biotechnol 26:162-4. 2008
  83. pmc Structural dependencies of protein backbone 2JNC' couplings
    Nenad Juranic
    Department of Biochemistry and Molecular Biology, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
    Protein Sci 17:768-76. 2008
    ..Such information, supplemented with the H-bond strengths derived from (h3)J(NC') couplings, provides useful insight into the overall energy profile of the protein backbone in solution...
  84. ncbi request reprint Data management in structural genomics: an overview
    Sabrina Haquin
    Yeast Structural Genomics, IBBMC, Universite Paris Sud, Orsay, France
    Methods Mol Biol 426:49-79. 2008
    ....
  85. ncbi request reprint Backbone 1H, 15N and 13C assignments for the subunit a of the E. coli ATP synthase
    Oleg Y Dmitriev
    J Biomol NMR 29:439-40. 2004
    ..The protein was found to consist of multiple elongated alpha-helical segments. This finding is generally consistent with previous predictions of multiple transmembrane alpha-helices in this polytopic protein...
  86. ncbi request reprint Solution structure of a homodimeric hypothetical protein, At5g22580, a structural genomics target from Arabidopsis thaliana
    Gabriel Cornilescu
    J Biomol NMR 29:387-90. 2004
  87. ncbi request reprint Solution structure of T4moC, the Rieske ferredoxin component of the toluene 4-monooxygenase complex
    Lars Skjeldal
    IKB, Agricultural University of Norway, Box 5040, 1432 NLH, Norway
    J Biol Inorg Chem 9:945-53. 2004
    ..Comparisons are made between the present NMR structure, previous paramagnetic NMR studies of T4moC, and the X-ray structures of other members of the Rieske protein family...
  88. ncbi request reprint 1H, 15N and 13C resonance assignments of a protein involved in the autophagy process, At4g21980.1 from Arabidopsis thaliana
    Young Kee Chae
    J Biomol NMR 32:337. 2005
  89. ncbi request reprint Prevention of aggregation after refolding by balanced stabilization-destabilization: production of the Arabidopsis thaliana protein APG8a (At4g21980) for NMR structure determination
    Young Kee Chae
    Department of Applied Chemistry and Molecular Biology, Sejong University, 98 Gunja Dong, Gwangjin gu, Seoul 143 747, Republic of Korea
    Protein Expr Purif 34:280-3. 2004
    ..This approach of balanced stabilization-destabilization may offer a general approach for structural investigations of proteins that tend to aggregate...
  90. pmc Remediation of the protein data bank archive
    Kim Henrick
    MSD EBI, EMBL Outstation Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 36:D426-33. 2008
    ..The scope and methods used in this project are presented...

Research Grants25

  1. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John L Markley; Fiscal Year: 2010
    ..To achieve these aims, we will make use of state-of-the-art approaches to protein production and isotopic labeling, NMR data collection and analysis, modeling of structures and complexes, and quantum chemical calculations. ..
  2. NATIONAL BIOMEDICAL NMR RESOURCE AT MADISON
    John Markley; Fiscal Year: 2007
    ..Our goal is to develop methods for making these investigations faster and less costly, as well as applicable to larger classes of proteins and nucleic acids of importance in human disease. ..
  3. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 1999
    ....
  4. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 2007
    ..To achieve these aims, we will make use of state-of-the-art approaches to protein production and isotopic labeling, NMR data collection and analysis, modeling of structures and complexes, and quantum chemical calculations. ..
  5. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John L Markley; Fiscal Year: 2010
    ..abstract_text> ..
  6. 900 MHZ NMR SPECTROMETER
    John Markley; Fiscal Year: 2001
    ..abstract_text> ..
  7. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 2001
    ....
  8. Specialized Center for Eukaryotic Structural Genomics
    John Markley; Fiscal Year: 2007
    ..CESG will hold workshops and training programs. Activities of the Center will be monitored and guided by an advisory committee representing both biological and technical expertise. ..
  9. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 2009
    ..To achieve these aims, we will make use of state-of-the-art approaches to protein production and isotopic labeling, NMR data collection and analysis, modeling of structures and complexes, and quantum chemical calculations. ..
  10. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 2000
    ....
  11. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 2007
    ..abstract_text> ..
  12. 900 MHz NMR Spectrometer Biomolecular Investigations
    John Markley; Fiscal Year: 2006
    ..Web-based software will be used to pair users with local collaborator(s), assess specific needs, design and schedule data collection, and share results. ..
  13. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 2006
    ..Effort will also be expended toward developing new methodology for paramagnetic NMR, in particular, for systems that are not amenable to established approaches. ..
  14. Center for Eukaryotic Structural Genomics
    John Markley; Fiscal Year: 2004
    ..thaliana to be funded separately. The methods developed by the Center will be applicable to other eukaryotic genomes, including the human genome. ..
  15. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 2003
    ..Effort will also be expended toward developing new methodology for paramagnetic NMR, in particular, for systems that are not amenable to established approaches. ..
  16. NMR SPECTROSCOPY OF IRON-SULFUR PROTEINS
    John Markley; Fiscal Year: 2002
    ....
  17. CONFERENCE ON MAGNETIC RESONANCE IN BIOLOGICAL SYSTEMS
    John Markley; Fiscal Year: 2002
    ..Those receiving travel support will be selected by a committee composed of the U.S. members of the International Organizing Committee for the meeting. ..