Research Topics
Species | John MarkleySummaryAffiliation: University of Wisconsin Country: USA Publications
Research Grants
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Detail Information
Publications
Role of aminotransferases in glutamate metabolism of human erythrocytesJames 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...- Two-dimensional concurrent HMQC-COSY as an approach for small molecule chemical shift assignment and compound identificationKaifeng 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... - Three hydrophobic amino acids in Escherichia coli HscB make the greatest contribution to the stability of the HscB-IscU complexAnna 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... 
Protonation-state dependence of hydrogen bond strengths and exchange rates in a serine protease catalytic triad: bovine chymotrypsinogen AJ 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...- BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositionsJohn 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... - The Center for Eukaryotic Structural GenomicsJohn 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.... - Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 familyRobert 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... - NMR solution structure of ATTp, an Arabidopsis thaliana trypsin inhibitorQin 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... - Solution structure of a ubiquitin-like domain from tubulin-binding cofactor BBetsy L Lytle
Center for Eukaryotic Structural Genomics, Madison, Wisconsin 53706 1549, USA
J Biol Chem 279:46787-93. 2004.... - Two conformational states of Turkey ovomucoid third domain at low pH: three-dimensional structures, internal dynamics, and interconversion kinetics and thermodynamicsJikui 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... - Solution structure of YggX: a prokaryotic protein involved in Fe(II) traffickingQiu 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... - Structural basis for the catalytic mechanism of mammalian 25-kDa thiamine triphosphataseJikui 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... - Cell-free protein production and labeling protocol for NMR-based structural proteomicsDmitriy 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... - Solution structure of the iron-sulfur cluster cochaperone HscB and its binding surface for the iron-sulfur assembly scaffold protein IscUAnna 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... - BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data BankJurgen 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)... - Solution structure of isoform 1 of Roadblock/LC7, a light chain in the dynein complexJikui 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... - Solution structure of human sorting nexin 22Jikui 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... - Structure and dynamics of the iron-sulfur cluster assembly scaffold protein IscU and its interaction with the cochaperone HscBJin 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... - Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elementsHamid R Eghbalnia
Biochemistry Department, National Magnetic Resonance Facility at Madison, 433 Babcock Drive, Madison, WI 53706, USA
J Biomol NMR 32:71-81. 2005.... - Comparison of cell-based and cell-free protocols for producing target proteins from the Arabidopsis thaliana genome for structural studiesRobert 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... - Solution structure of Arabidopsis thaliana protein At5g39720.1, a member of the AIG2-like protein familyBetsy 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... - Brazzein, a small, sweet protein: effects of mutations on its structure, dynamics and functional propertiesFariba 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 - Production in two-liter beverage bottles of proteins for NMR structure determination labeled with either 15N- or 13C-15NQin 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.... - Protein inhibitors of serine proteinases: role of backbone structure and dynamics in controlling the hydrolysis constantJikui Song
National Magnetic Resonance Facility, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
Biochemistry 42:5186-94. 2003.... - 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 domainJikui 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... - Preparation of isotopically labeled spinach acyl-acyl carrier protein for NMR structural studiesGregory A Zornetzer
Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1549, USA
Protein Expr Purif 46:446-55. 2006.... - Probabilistic approach to determining unbiased random-coil carbon-13 chemical shift values from the protein chemical shift databaseLiya Wang
National Magnetic Resonance Facility at Madison, 433 Babcock Drive, Madison, WI, 53706, USA
J Biomol NMR 35:155-65. 2006.... - Structure of human J-type co-chaperone HscB reveals a tetracysteine metal-binding domainEduard 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... - Solution structure of a late embryogenesis abundant protein (LEA14) from Arabidopsis thaliana, a cellular stress-related proteinShanteri Singh
Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
Protein Sci 14:2601-9. 2005.... - A graphical approach to tracking and reporting target status in structural genomicsXiaokang 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... - Wheat germ cell-free expression system for protein productionDmitriy 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... - Stable isotope assisted assignment of elemental compositions for metabolomicsAdrian 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... - Auto-induction medium for the production of [U-15N]- and [U-13C, U-15N]-labeled proteins for NMR screening and structure determinationRobert 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... - Three-dimensional structure determined for a subunit of human tRNA splicing endonuclease (Sen15) reveals a novel dimeric foldJikui 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... 
Cell-free protein synthesis technology in NMR high-throughput structure determinationShin 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....- Efficient and rapid protein expression and purification of small high disulfide containing sweet protein brazzein in E. coliFariba 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.... - Carbonyl carbon label selective (CCLS) 1H-15N HSQC experiment for improved detection of backbone 13C-15N cross peaks in larger proteinsMarco 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... - BioMagResBankEldon 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... - Small-scale, semi-automated purification of eukaryotic proteins for structure determinationRonnie 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.... - Solution structure of a single-domain thiosulfate sulfurtransferase from Arabidopsis thalianaGabriel 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... - Structural rearrangement of human lymphotactin, a C chemokine, under physiological solution conditionsE 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... - NMR structure of the mengovirus Leader protein zinc-finger domainClaudia 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... - Direct NMR detection of the binding of functional ligands to the human sweet receptor, a heterodimeric family 3 GPCRFariba 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... - Key amino acid residues involved in multi-point binding interactions between brazzein, a sweet protein, and the T1R2-T1R3 human sweet receptorFariba 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... - The length of the bound fatty acid influences the dynamics of the acyl carrier protein and the stability of the thioester bondGregory 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... - One-sample approach to determine the relative orientations of proteins in ternary and binary complexes from residual dipolar coupling measurementsMarco 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... - PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopyWoonghee Lee
National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin Madison, Madison, WI 53706, USA
Bioinformatics 25:2085-7. 2009..AVAILABILITY: The program, in the form of source code and binary code along with tutorials and reference manuals, is available at http://pine.nmrfam.wisc.edu/PINE-SPARKY... - 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 complexOleg 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... - NMR analysis goes nanoJohn L Markley
Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
Nat Biotechnol 25:750-1. 2007 - Quantum chemical calculations on structural models of the catalytic site of chymotrypsin: comparison of calculated results with experimental data from NMR spectroscopyWilliam 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.... - Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopyArash 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... - Structures of proteins of biomedical interest from the Center for Eukaryotic Structural GenomicsGeorge 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... - Interactions between the human sweet-sensing T1R2-T1R3 receptor and sweeteners detected by saturation transfer difference NMR spectroscopyFariba 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... - Probing the sweet determinants of brazzein: wild-type brazzein and a tasteless variant, brazzein-ins(R18a-I18b), exhibit different pH-dependent NMR chemical shiftsQin Zhao
Department of Biochemistry, University of Wisconsin Madison, College of Agricultural and Life Sciences, USA
Biochem Biophys Res Commun 335:256-63. 2005.... - Addressing the intrinsic disorder bottleneck in structural proteomicsChristopher 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... - High-throughput automated platform for nuclear magnetic resonance-based structural proteomicsDmitriy 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... - Dynamics and metal ion binding in the U6 RNA intramolecular stem-loop as analyzed by NMRHeike 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... - Wheat germ cell-free platform for eukaryotic protein productionDmitriy 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... - High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collectionHamid 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... - One-step purification of bacterially expressed recombinant transducin alpha-subunit and isotopically labeled PDE6 gamma-subunit for NMR analysisLian 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... - Project management system for structural and functional proteomics: SesameZsolt 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... - 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... - Cautionary tail: the presence of an N-terminal tag on dynein light-chain Roadblock/LC7 affects its interaction with a functional partnerJikui 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... - Correlation of the sweetness of variants of the protein brazzein with patterns of hydrogen bonds detected by NMR spectroscopyFariba 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... - HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projectionsGabriel 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... - Macromolecular structure determination by NMR spectroscopyJohn L Markley
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
Methods Biochem Anal 44:89-113. 2003 - Solution structure of T4moC, the Rieske ferredoxin component of the toluene 4-monooxygenase complexLars 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... - Paramagnetic NMR spectroscopy and density functional calculations in the analysis of the geometric and electronic structures of iron-sulfur proteinsTimothy 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... - X-ray structure of Arabidopsis At2g06050, 12-oxophytodienoate reductase isoform 3Thomas E Malone
Molecular and Environmental Toxicology Program, University of Wisconsin-Madison, 53706, USA
Proteins 58:243-5. 2005 - Hypothetical protein At2g24940.1 from Arabidopsis thaliana has a cytochrome b5 like foldJikui Song
J Biomol NMR 30:215-8. 2004 - (1)H, (13)C and (15)N backbone assignment of a 32 kDa hypothetical protein from Arabidopsis thaliana, At3g16450.1Nozomi Sugimori
J Biomol NMR 30:357-8. 2004 - Early formation of a beta hairpin during folding of staphylococcal nuclease H124L as detected by pulsed hydrogen exchangeWilliam F Walkenhorst
Department of Chemistry, Loyola University, New Orleans, Louisiana 70118, USA
Protein Sci 11:82-91. 2002.... - 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... - 1H, 15N and 13C resonance assignments of the putative Bet v 1 family protein At1g24000.1 from Arabidopsis thalianaJikui Song
J Biomol NMR 32:335. 2005 - 1H, 15N and 13C resonance assignments of a protein involved in the autophagy process, At4g21980.1 from Arabidopsis thalianaYoung Kee Chae
J Biomol NMR 32:337. 2005 - Backbone 1H, 15N and 13C assignments for the subunit a of the E. coli ATP synthaseOleg 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... - Solution structure of a homodimeric hypothetical protein, At5g22580, a structural genomics target from Arabidopsis thalianaGabriel Cornilescu
J Biomol NMR 29:387-90. 2004 - Structural dependencies of protein backbone 2JNC' couplingsNenad 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... - Prevention of aggregation after refolding by balanced stabilization-destabilization: production of the Arabidopsis thaliana protein APG8a (At4g21980) for NMR structure determinationYoung 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... - Metabolite identification via the Madison Metabolomics Consortium DatabaseQiu Cui
Nat Biotechnol 26:162-4. 2008 - Remediation of the protein data bank archiveKim 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... - Data management in structural genomics: an overviewSabrina Haquin
Yeast Structural Genomics, IBBMC, Universite Paris Sud, Orsay, France
Methods Mol Biol 426:49-79. 2008....
Research Grants
- NATIONAL BIOMEDICAL NMR RESOURCE AT MADISONJohn 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. ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn 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. ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn Markley; Fiscal Year: 2007..abstract_text> ..
- Specialized Center for Eukaryotic Structural GenomicsJohn 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. ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn 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. ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn 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. ..
- 900 MHz NMR Spectrometer Biomolecular InvestigationsJohn 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. ..
- 900 MHZ NMR SPECTROMETERJohn Markley; Fiscal Year: 2001..abstract_text> ..
- CONFERENCE ON MAGNETIC RESONANCE IN BIOLOGICAL SYSTEMSJohn 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. ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn Markley; Fiscal Year: 2002....
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn 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. ..
- Center for Eukaryotic Structural GenomicsJohn 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. ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn 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. ..
- NMR SPECTROSCOPY OF IRON-SULFUR PROTEINSJohn L Markley; Fiscal Year: 2010..abstract_text> ..