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Connection

John Markley to Magnetic Resonance Spectroscopy

This is a "connection" page, showing publications John Markley has written about Magnetic Resonance Spectroscopy.

 
Connection Strength
  
 
 
7.463
  
  1. Cai K, Markley JL. NMR as a Tool to Investigate the Processes of Mitochondrial and Cytosolic Iron-Sulfur Cluster Biosynthesis. Molecules. 2018 Aug 31; 23(9).
    View in: PubMed
    Score: 0.485
  2. Eghbalnia HR, Romero PR, Westler WM, Baskaran K, Ulrich EL, Markley JL. Increasing rigor in NMR-based metabolomics through validated and open source tools. Curr Opin Biotechnol. 2017 02; 43:56-61.
    View in: PubMed
    Score: 0.423
  3. Markley JL, Brüschweiler R, Edison AS, Eghbalnia HR, Powers R, Raftery D, Wishart DS. The future of NMR-based metabolomics. Curr Opin Biotechnol. 2017 02; 43:34-40.
    View in: PubMed
    Score: 0.422
  4. Lee W, Petit CM, Cornilescu G, Stark JL, Markley JL. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data. J Biomol NMR. 2016 06; 65(2):51-7.
    View in: PubMed
    Score: 0.413
  5. 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 04; 64(4):307-32.
    View in: PubMed
    Score: 0.410
  6. Kim JH, Bothe JR, Alderson TR, Markley JL. 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. 2015 Jun; 1853(6):1416-28.
    View in: PubMed
    Score: 0.373
  7. Chylla RA, Hu K, Ellinger JJ, Markley JL. Deconvolution of two-dimensional NMR spectra by fast maximum likelihood reconstruction: application to quantitative metabolomics. Anal Chem. 2011 Jun 15; 83(12):4871-80.
    View in: PubMed
    Score: 0.293
  8. Hu K, Westler WM, Markley JL. Two-dimensional concurrent HMQC-COSY as an approach for small molecule chemical shift assignment and compound identification. J Biomol NMR. 2011 Apr; 49(3-4):291-6.
    View in: PubMed
    Score: 0.288
  9. Hu K, Westler WM, Markley JL. Simultaneous quantification and identification of individual chemicals in metabolite mixtures by two-dimensional extrapolated time-zero (1)H-(13)C HSQC (HSQC(0)). J Am Chem Soc. 2011 Feb 16; 133(6):1662-5.
    View in: PubMed
    Score: 0.286
  10. Lewis IA, Karsten RH, Norton ME, Tonelli M, Westler WM, Markley JL. NMR method for measuring carbon-13 isotopic enrichment of metabolites in complex solutions. Anal Chem. 2010 Jun 01; 82(11):4558-63.
    View in: PubMed
    Score: 0.274
  11. Lewis IA, Schommer SC, Hodis B, Robb KA, Tonelli M, Westler WM, Sussman MR, Markley JL. Method for determining molar concentrations of metabolites in complex solutions from two-dimensional 1H-13C NMR spectra. Anal Chem. 2007 Dec 15; 79(24):9385-90.
    View in: PubMed
    Score: 0.229
  12. Markley JL. NMR analysis goes nano. Nat Biotechnol. 2007 Jul; 25(7):750-1.
    View in: PubMed
    Score: 0.224
  13. Eghbalnia HR, Bahrami A, Tonelli M, Hallenga K, Markley JL. High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection. J Am Chem Soc. 2005 Sep 14; 127(36):12528-36.
    View in: PubMed
    Score: 0.197
  14. Eghbalnia HR, Bahrami A, Wang L, Assadi A, Markley JL. Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO). J Biomol NMR. 2005 Jul; 32(3):219-33.
    View in: PubMed
    Score: 0.195
  15. Wu WJ, Vidugiris G, Mooberry ES, Westler WM, Markley JL. Mixing apparatus for preparing NMR samples under pressure. J Magn Reson. 2003 Sep; 164(1):84-91.
    View in: PubMed
    Score: 0.171
  16. Cai K, Frederick RO, Markley JL. ISCU interacts with NFU1, and ISCU[4Fe-4S] transfers its Fe-S cluster to NFU1 leading to the production of holo-NFU1. J Struct Biol. 2020 05 01; 210(2):107491.
    View in: PubMed
    Score: 0.135
  17. Dzakula Z, DeRider ML, Westler WM, Macura S, Markley JL. Analysis of error propagation from NMR-derived internuclear distances into molecular structure of cyclo-pro-gly. J Magn Reson. 1998 Dec; 135(2):454-65.
    View in: PubMed
    Score: 0.123
  18. Chylla RA, Volkman BF, Markley JL. Practical model fitting approaches to the direct extraction of NMR parameters simultaneously from all dimensions of multidimensional NMR spectra. J Biomol NMR. 1998 Aug; 12(2):277-97.
    View in: PubMed
    Score: 0.121
  19. Cai K, Frederick RO, Tonelli M, Markley JL. Interactions of iron-bound frataxin with ISCU and ferredoxin on the cysteine desulfurase complex leading to Fe-S cluster assembly. J Inorg Biochem. 2018 06; 183:107-116.
    View in: PubMed
    Score: 0.117
  20. Dashti H, Westler WM, Tonelli M, Wedell JR, Markley JL, Eghbalnia HR. Spin System Modeling of Nuclear Magnetic Resonance Spectra for Applications in Metabolomics and Small Molecule Screening. Anal Chem. 2017 11 21; 89(22):12201-12208.
    View in: PubMed
    Score: 0.115
  21. 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 01; 15(4):1360-8.
    View in: PubMed
    Score: 0.102
  22. Chen VB, Wedell JR, Wenger RK, Ulrich EL, Markley JL. MolProbity for the masses-of data. J Biomol NMR. 2015 Sep; 63(1):77-83.
    View in: PubMed
    Score: 0.098
  23. Gutmanas A, Adams PD, Bardiaux B, Berman HM, Case DA, Fogh RH, Güntert P, Hendrickx PM, Herrmann T, Kleywegt GJ, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, Ragan TJ, Schwieters CD, Tejero R, Ulrich EL, Velankar S, Vranken WF, Wedell JR, Westbrook J, Wishart DS, Vuister GW. NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol. 2015 Jun; 22(6):433-4.
    View in: PubMed
    Score: 0.097
  24. Lee W, Watters KE, Troupis AT, Reinen NM, Suchy FP, Moyer KL, Frederick RO, Tonelli M, Aceti DJ, Palmenberg AC, Markley JL. Solution structure of the 2A protease from a common cold agent, human rhinovirus C2, strain W12. PLoS One. 2014; 9(6):e97198.
    View in: PubMed
    Score: 0.091
  25. Olson JB, Markley JL. Evaluation of an algorithm for the automated sequential assignment of protein backbone resonances: a demonstration of the connectivity tracing assignment tools (CONTRAST) software package. J Biomol NMR. 1994 May; 4(3):385-410.
    View in: PubMed
    Score: 0.090
  26. Ellinger JJ, Miller DC, Lewis IA, Markley JL. Semiautomated device for batch extraction of metabolites from tissue samples. Anal Chem. 2012 Feb 21; 84(4):1809-12.
    View in: PubMed
    Score: 0.077
  27. Venkitakrishnan RP, Benard O, Max M, Markley JL, Assadi-Porter FM. Use of NMR saturation transfer difference spectroscopy to study ligand binding to membrane proteins. Methods Mol Biol. 2012; 914:47-63.
    View in: PubMed
    Score: 0.076
  28. Kim JH, Tonelli M, Markley JL. Disordered form of the scaffold protein IscU is the substrate for iron-sulfur cluster assembly on cysteine desulfurase. Proc Natl Acad Sci U S A. 2012 Jan 10; 109(2):454-9.
    View in: PubMed
    Score: 0.076
  29. Singarapu KK, Tonelli M, Chow DC, Frederick RO, Westler WM, Markley JL. 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 a-helical. J Biol Chem. 2011 Dec 16; 286(50):43447-53.
    View in: PubMed
    Score: 0.075
  30. Ellinger JJ, Lewis IA, Markley JL. Role of aminotransferases in glutamate metabolism of human erythrocytes. J Biomol NMR. 2011 Apr; 49(3-4):221-9.
    View in: PubMed
    Score: 0.072
  31. Füzéry AK, Oh JJ, Ta DT, Vickery LE, Markley JL. Three hydrophobic amino acids in Escherichia coli HscB make the greatest contribution to the stability of the HscB-IscU complex. BMC Biochem. 2011 Jan 26; 12:3.
    View in: PubMed
    Score: 0.072
  32. Takeda M, Hallenga K, Shigezane M, Waelchli M, Löhr F, Markley JL, Kainosho M. Construction and performance of an NMR tube with a sample cavity formed within magnetic susceptibility-matched glass. J Magn Reson. 2011 Apr; 209(2):167-73.
    View in: PubMed
    Score: 0.071
  33. Lewis IA, Schommer SC, Markley JL. rNMR: open source software for identifying and quantifying metabolites in NMR spectra. Magn Reson Chem. 2009 Dec; 47 Suppl 1:S123-6.
    View in: PubMed
    Score: 0.066
  34. Bahrami A, Assadi AH, Markley JL, Eghbalnia HR. Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. PLoS Comput Biol. 2009 Mar; 5(3):e1000307.
    View in: PubMed
    Score: 0.063
  35. Song J, Bettendorff L, Tonelli M, Markley JL. Structural basis for the catalytic mechanism of mammalian 25-kDa thiamine triphosphatase. J Biol Chem. 2008 Apr 18; 283(16):10939-48.
    View in: PubMed
    Score: 0.058
  36. Cui Q, Lewis IA, Hegeman AD, Anderson ME, Li J, Schulte CF, Westler WM, Eghbalnia HR, Sussman MR, Markley JL. Metabolite identification via the Madison Metabolomics Consortium Database. Nat Biotechnol. 2008 Feb; 26(2):162-4.
    View in: PubMed
    Score: 0.058
  37. Markley JL, Anderson ME, Cui Q, Eghbalnia HR, Lewis IA, Hegeman AD, Li J, Schulte CF, Sussman MR, Westler WM, Ulrich EL, Zolnai Z. New bioinformatics resources for metabolomics. Pac Symp Biocomput. 2007; 157-68.
    View in: PubMed
    Score: 0.054
  38. Song J, Markley JL. Three-dimensional structure determined for a subunit of human tRNA splicing endonuclease (Sen15) reveals a novel dimeric fold. J Mol Biol. 2007 Feb 09; 366(1):155-64.
    View in: PubMed
    Score: 0.053
  39. Assadi-Porter FM, Abildgaard F, Blad H, Cornilescu CC, Markley JL. Brazzein, a small, sweet protein: effects of mutations on its structure, dynamics and functional properties. Chem Senses. 2005 Jan; 30 Suppl 1:i90-1.
    View in: PubMed
    Score: 0.047
  40. Machonkin TE, Westler WM, Markley JL. Strategy for the study of paramagnetic proteins with slow electronic relaxation rates by nmr spectroscopy: application to oxidized human [2Fe-2S] ferredoxin. J Am Chem Soc. 2004 May 05; 126(17):5413-26.
    View in: PubMed
    Score: 0.045
  41. Song J, Laskowski M, Qasim MA, Markley JL. Two conformational states of Turkey ovomucoid third domain at low pH: three-dimensional structures, internal dynamics, and interconversion kinetics and thermodynamics. Biochemistry. 2003 Jun 03; 42(21):6380-91.
    View in: PubMed
    Score: 0.042
  42. Song J, Markley JL. Protein inhibitors of serine proteinases: role of backbone structure and dynamics in controlling the hydrolysis constant. Biochemistry. 2003 May 13; 42(18):5186-94.
    View in: PubMed
    Score: 0.042
  43. Wilkens SJ, Westler WM, Markley JL, Weinhold F. Natural J-coupling analysis: interpretation of scalar J-couplings in terms of natural bond orbitals. J Am Chem Soc. 2001 Dec 05; 123(48):12026-36.
    View in: PubMed
    Score: 0.038
  44. Shao H, Boulton S, Olivieri C, Mohamed H, Akimoto M, Subrahmanian MV, Veglia G, Markley JL, Melacini G, Lee W. CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery. Bioinformatics. 2021 05 23; 37(8):1176-1177.
    View in: PubMed
    Score: 0.037
  45. Rahimi M, Lee Y, Markley JL, Lee W. iPick: Multiprocessing software for integrated NMR signal detection and validation. J Magn Reson. 2021 07; 328:106995.
    View in: PubMed
    Score: 0.036
  46. Song J, Markley JL. NMR chemical shift mapping of the binding site of a protein proteinase inhibitor: changes in the (1)H, (13)C and (15)N NMR chemical shifts of turkey ovomucoid third domain upon binding to bovine chymotrypsin A(alpha). J Mol Recognit. 2001 May-Jun; 14(3):166-71.
    View in: PubMed
    Score: 0.036
  47. Weber DK, Wang S, Markley JL, Veglia G, Lee W. PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins. Bioinformatics. 2020 05 01; 36(9):2915-2916.
    View in: PubMed
    Score: 0.034
  48. Assadi-Porter FM, Aceti DJ, Cheng H, Markley JL. Efficient production of recombinant brazzein, a small, heat-stable, sweet-tasting protein of plant origin. Arch Biochem Biophys. 2000 Apr 15; 376(2):252-8.
    View in: PubMed
    Score: 0.034
  49. Assadi-Porter FM, Aceti DJ, Markley JL. Sweetness determinant sites of brazzein, a small, heat-stable, sweet-tasting protein. Arch Biochem Biophys. 2000 Apr 15; 376(2):259-65.
    View in: PubMed
    Score: 0.034
  50. Xia B, Jenk D, LeMaster DM, Westler WM, Markley JL. Electron-nuclear interactions in two prototypical [2Fe-2S] proteins: selective (chiral) deuteration and analysis of (1)H and (2)H NMR signals from the alpha and beta hydrogens of cysteinyl residues that ligate the iron in the active sites of human ferredoxin and Anabaena 7120 vegetative ferredoxin. Arch Biochem Biophys. 2000 Jan 15; 373(2):328-34.
    View in: PubMed
    Score: 0.033
  51. Bortnov V, Tonelli M, Lee W, Lin Z, Annis DS, Demerdash ON, Bateman A, Mitchell JC, Ge Y, Markley JL, Mosher DF. Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum. Nat Commun. 2019 12 09; 10(1):5612.
    View in: PubMed
    Score: 0.033
  52. Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure. 2019 12 03; 27(12):1745-1759.
    View in: PubMed
    Score: 0.033
  53. Volkman BF, Anderson ME, Clark KD, Hayakawa Y, Strand MR, Markley JL. Structure of the insect cytokine peptide plasmatocyte-spreading peptide 1 from Pseudoplusia includens. J Biol Chem. 1999 Feb 19; 274(8):4493-6.
    View in: PubMed
    Score: 0.031
  54. Chae YK, Abildgaard F, Chapman ER, Markley JL. Lipid binding ridge on loops 2 and 3 of the C2A domain of synaptotagmin I as revealed by NMR spectroscopy. J Biol Chem. 1998 Oct 02; 273(40):25659-63.
    View in: PubMed
    Score: 0.030
  55. Markley JL, Bax A, Arata Y, Hilbers CW, Kaptein R, Sykes BD, Wright PE, Wüthrich K. Recommendations for the presentation of NMR structures of proteins and nucleic acids. J Mol Biol. 1998 Jul 31; 280(5):933-52.
    View in: PubMed
    Score: 0.030
  56. Prantner AM, Volkman BF, Wilkens SJ, Xia B, Markley JL. Assignment of 1H, 13C, and 15N signals of reduced Clostridium pasteurianum rubredoxin: oxidation state-dependent changes in chemical shifts and relaxation rates. J Biomol NMR. 1997 Dec; 10(4):411-2.
    View in: PubMed
    Score: 0.029
  57. Markley JL, Westler WM. Protonation-state dependence of hydrogen bond strengths and exchange rates in a serine protease catalytic triad: bovine chymotrypsinogen A. Biochemistry. 1996 Aug 27; 35(34):11092-7.
    View in: PubMed
    Score: 0.026
  58. Wishart DS, Bigam CG, Yao J, Abildgaard F, Dyson HJ, Oldfield E, Markley JL, Sykes BD. 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J Biomol NMR. 1995 Sep; 6(2):135-40.
    View in: PubMed
    Score: 0.025
  59. Huang Y, Nokhrin S, Hassanzadeh-Ghassabeh G, Yu CH, Yang H, Barry AN, Tonelli M, Markley JL, Muyldermans S, Dmitriev OY, Lutsenko S. Interactions between metal-binding domains modulate intracellular targeting of Cu(I)-ATPase ATP7B, as revealed by nanobody binding. J Biol Chem. 2014 Nov 21; 289(47):32682-93.
    View in: PubMed
    Score: 0.023
  60. Wang JF, Hinck AP, Loh SN, LeMaster DM, Markley JL. Solution studies of staphylococcal nuclease H124L. 2. 1H, 13C, and 15N chemical shift assignments for the unligated enzyme and analysis of chemical shift changes that accompany formation of the nuclease-thymidine 3',5'-bisphosphate-calcium ternary complex. Biochemistry. 1992 Jan 28; 31(3):921-36.
    View in: PubMed
    Score: 0.019
  61. Skjeldal L, Westler WM, Oh BH, Krezel AM, Holden HM, Jacobson BL, Rayment I, Markley JL. Two-dimensional magnetization exchange spectroscopy of Anabaena 7120 ferredoxin. Nuclear Overhauser effect and electron self-exchange cross peaks from amino acid residues surrounding the 2Fe-2S* cluster. Biochemistry. 1991 Jul 30; 30(30):7363-8.
    View in: PubMed
    Score: 0.019
  62. Singarapu KK, Radek JT, Tonelli M, Markley JL, Lan Q. Differences in the structure and dynamics of the apo- and palmitate-ligated forms of Aedes aegypti sterol carrier protein 2 (AeSCP-2). J Biol Chem. 2010 May 28; 285(22):17046-53.
    View in: PubMed
    Score: 0.017
  63. Lewis IA, Campanella ME, Markley JL, Low PS. Role of band 3 in regulating metabolic flux of red blood cells. Proc Natl Acad Sci U S A. 2009 Nov 03; 106(44):18515-20.
    View in: PubMed
    Score: 0.016
  64. Cui Q, Thorgersen MP, Westler WM, Markley JL, Downs DM. Solution structure of YggX: a prokaryotic protein involved in Fe(II) trafficking. Proteins. 2006 Mar 15; 62(3):578-86.
    View in: PubMed
    Score: 0.013
  65. Kuloglu ES, McCaslin DR, Markley JL, Volkman BF. Structural rearrangement of human lymphotactin, a C chemokine, under physiological solution conditions. J Biol Chem. 2002 May 17; 277(20):17863-70.
    View in: PubMed
    Score: 0.010
  66. Stockman BJ, Krezel AM, Markley JL, Leonhardt KG, Straus NA. Hydrogen-1, carbon-13, and nitrogen-15 NMR spectroscopy of Anabaena 7120 flavodoxin: assignment of beta-sheet and flavin binding site resonances and analysis of protein-flavin interactions. Biochemistry. 1990 Oct 16; 29(41):9600-9.
    View in: PubMed
    Score: 0.004
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