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John Lute Markley

TitleProfessor Adjoint
InstitutionUniversity of Colorado Denver - Denver Campus
DepartmentCLAS-Chemistry

    Collapse Research 
    Collapse research activities and funding
    R01GM127666     (MARKLEY, JOHN LUTE)Sep 1, 2019 - Aug 31, 2021
    NIH
    Biogenesis of human mitochondrial iron-sulfur proteins
    Role: Principal Investigator
    R01GM109046     (HOCH, JEFFREY C)May 15, 2014 - Mar 31, 2023
    NIH
    The BMRB as an evolving resource for biomolecular structure-function research
    Role: Co-Principal Investigator
    U01GM094622     (MARKLEY, JOHN LUTE)Sep 30, 2010 - Jun 30, 2016
    NIH
    Partnership for High-Throughput Enabled Biology of the Mitochondrial Proteome
    Role: Principal Investigator
    S10RR029220     (MARKLEY, JOHN L)Apr 8, 2010 - Apr 7, 2011
    NIH
    Upgrade of the NMRFAM 750 MHz NMR Spectrometer
    Role: Principal Investigator
    S10RR025062     (MARKLEY, JOHN L)Jul 1, 2008 - Jun 30, 2010
    NIH
    Integrated state-of-the-art LC-MS/NMR system for the University of Wisconsin
    Role: Principal Investigator
    S10RR023438     (MARKLEY, JOHN L)Feb 1, 2008 - Jan 31, 2010
    NIH
    NMR Spectrometer System Optimized for Direct 13C or 15N Detection
    Role: Principal Investigator
    U54GM074901     (MARKLEY, JOHN LUTE)Jul 1, 2005 - Jun 30, 2011
    NIH
    Specialized Center for Eukaryotic Structural Genomics
    Role: Principal Investigator
    R13GM065241     (MARKLEY, JOHN L)Jul 15, 2002 - Jun 30, 2003
    NIH
    CONFERENCE ON MAGNETIC RESONANCE IN BIOLOGICAL SYSTEMS
    Role: Principal Investigator
    P41GM066326     (MARKLEY, JOHN L)Jul 1, 2002 - Jun 30, 2008
    NIH
    900 MHz NMR Spectrometer Biomolecular Investigations
    Role: Principal Investigator
    P50GM064598     (MARKLEY, JOHN L)Sep 28, 2001 - Aug 31, 2006
    NIH
    Center for Eukaryotic Structural Genomics
    Role: Principal Investigator
    S10RR015740     (MARKLEY, JOHN L)Apr 1, 2001 - Mar 31, 2002
    NIH
    900 MHZ NMR SPECTROMETER
    Role: Principal Investigator
    R13CA087730     (MARKLEY, JOHN L)Aug 1, 2000 - Jul 31, 2001
    NIH
    CONFERNCE ON MAGNETIC RESONANCE IN BIOLOGICAL SYSTEMS
    Role: Principal Investigator
    R01GM058667     (MARKLEY, JOHN L)Feb 1, 1999 - Jan 31, 2012
    NIH
    NMR Spectroscopy of Iron-Sulfur Proteins
    Role: Principal Investigator
    R13CA079101     (MARKLEY, JOHN L)Aug 18, 1998 - Aug 17, 1999
    NIH
    CONFERENCE ON MAGNETIC RESONANCE IN BIOLOGICAL SYSTEMS
    Role: Principal Investigator
    P41GM103399     (BUTCHER, SAMUEL E)Mar 1, 1997 - Feb 28, 2021
    NIH
    National Biomedical NMR Resource at Madison
    Role: Co-Principal Investigator
    P41LM005799     (MARKLEY, JOHN LUTE)Sep 1, 1996 - Sep 14, 2014
    NIH
    Biological Magnetic Resonance Data Bank
    Role: Principal Investigator
    S10RR008438     (MARKLEY, JOHN L)Aug 1, 1993 - Jul 31, 1994
    NIH
    CONSOLE UPGRADES FOR NMR FACILITY
    Role: Principal Investigator
    T32GM008293     (JACKSON, MEYER B.)Jul 1, 1989 - Jun 30, 2018
    NIH
    Predoctoral Training in Molecular Biophysics
    Role: Co-Principal Investigator
    R01LM004958     (MARKLEY, JOHN L)Aug 1, 1988 - Jan 31, 1996
    NIH
    CREATION AND ANALYSIS OF ARCHIVAL PROTEIN NMR DATABASE
    Role: Principal Investigator
    S10RR002781     (MARKLEY, JOHN L)Apr 1, 1986 - Mar 31, 1987
    NIH
    WIDE-BORE 9.4 TESLA NMR SPECTROMETER FOR UW-MADISON
    Role: Principal Investigator
    P41RR002301     (MARKLEY, JOHN L)Jul 1, 1985 - Feb 28, 2015
    NIH
    National Biomedical NMR Resource at Madison
    Role: Principal Investigator
    R37GM035976     (MARKLEY, JOHN L)Jun 1, 1985 - May 31, 1999
    NIH
    NMR SPECTROSCOPY IN PROTEIN CHEMISTRY
    Role: Principal Investigator
    R01GM035976     (MARKLEY, JOHN L)Jun 1, 1985 - May 31, 1988
    NIH
    NMR SPECTROSCOPY IN PROTEIN CHEMISTRY
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Manthey I, Tonelli M, Ii LC, Rahimi M, Markley JL, Lee W. POKY software tools encapsulating assignment strategies for solution and solid-state protein NMR data. J Struct Biol X. 2022; 6:100073. PMID: 36081577.
      View in: PubMed
    2. Dwarasala A, Rahimi M, Markley JL, Lee W. ssPINE: Probabilistic Algorithm for Automated Chemical Shift Assignment of Solid-State NMR Data from Complex Protein Systems. Membranes (Basel). 2022 Aug 26; 12(9). PMID: 36135853.
      View in: PubMed
    3. 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. PMID: 32926121.
      View in: PubMed
    4. 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. PMID: 34004411.
      View in: PubMed
    5. 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. PMID: 31930377.
      View in: PubMed
    6. 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. PMID: 31819058.
      View in: PubMed
    7. Lee W, Bahrami A, Dashti HT, Eghbalnia HR, Tonelli M, Westler WM, Markley JL. I-PINE web server: an integrative probabilistic NMR assignment system for proteins. J Biomol NMR. 2019 May; 73(5):213-222. PMID: 31165321.
      View in: PubMed
    8. Frederick RO, Haruta M, Tonelli M, Lee W, Cornilescu G, Cornilescu CC, Sussman MR, Markley JL. Function and solution structure of the Arabidopsis thaliana RALF8 peptide. Protein Sci. 2019 06; 28(6):1115-1126. PMID: 31004454.
      View in: PubMed
    9. Shrestha OK, Sharma R, Tomiczek B, Lee W, Tonelli M, Cornilescu G, Stolarska M, Nierzwicki L, Czub J, Markley JL, Marszalek J, Ciesielski SJ, Craig EA. Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70. PLoS One. 2019; 14(5):e0217098. PMID: 31091298.
      View in: PubMed
    10. Lee W, Tonelli M, Wu C, Aceti DJ, Amarasinghe GK, Markley JL. Backbone resonance assignments and secondary structure of Ebola nucleoprotein 600-739 construct. Biomol NMR Assign. 2019 10; 13(2):315-319. PMID: 31076990.
      View in: PubMed
    11. Lee W, Markley JL. PINE-SPARKY.2 for automated NMR-based protein structure research. Bioinformatics. 2018 05 01; 34(9):1586-1588. PMID: 29281006.
      View in: PubMed
    12. Schilke BA, Ciesielski SJ, Ziegelhoffer T, Kamiya E, Tonelli M, Lee W, Cornilescu G, Hines JK, Markley JL, Craig EA. Broadening the functionality of a J-protein/Hsp70 molecular chaperone system. PLoS Genet. 2017 Oct; 13(10):e1007084. PMID: 29084221.
      View in: PubMed
    13. 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. PMID: 27169728.
      View in: PubMed
    14. 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. PMID: 27023095.
      View in: PubMed
    15. 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. PMID: 26965640.
      View in: PubMed
    16. Dashti H, Tonelli M, Lee W, Westler WM, Cornilescu G, Ulrich EL, Markley JL. Probabilistic validation of protein NMR chemical shift assignments. J Biomol NMR. 2016 Jan; 64(1):17-25. PMID: 26724815.
      View in: PubMed
    17. Dashti H, Tonelli M, Markley JL. ADAPT-NMR 3.0: utilization of BEST-type triple-resonance NMR experiments to accelerate the process of data collection and assignment. J Biomol NMR. 2015 Jul; 62(3):247-52. PMID: 26021595.
      View in: PubMed
    18. Dashti H, Lee W, Tonelli M, Cornilescu CC, Cornilescu G, Assadi-Porter FM, Westler WM, Eghbalnia HR, Markley JL. NMRFAM-SDF: a protein structure determination framework. J Biomol NMR. 2015 Aug; 62(4):481-95. PMID: 25900069.
      View in: PubMed
    19. Lee W, Tonelli M, Markley JL. NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics. 2015 Apr 15; 31(8):1325-7. PMID: 25505092.
      View in: PubMed
    20. Lee W, Stark JL, Markley JL. PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination. J Biomol NMR. 2014 Nov; 60(2-3):73-5. PMID: 25190042.
      View in: PubMed
    21. 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. PMID: 24937088.
      View in: PubMed
    22. Tonelli M, Eller CH, Singarapu KK, Lee W, Bahrami A, Westler WM, Raines RT, Markley JL. Assignments of RNase A by ADAPT-NMR and enhancer. Biomol NMR Assign. 2015 Apr; 9(1):81-8. PMID: 24619609.
      View in: PubMed
    23. Poplawski A, Hu K, Lee W, Natesan S, Peng D, Carlson S, Shi X, Balaz S, Markley JL, Glass KC. Molecular insights into the recognition of N-terminal histone modifications by the BRPF1 bromodomain. J Mol Biol. 2014 Apr 17; 426(8):1661-76. PMID: 24333487.
      View in: PubMed
    24. Lee W, Hu K, Tonelli M, Bahrami A, Neuhardt E, Glass KC, Markley JL. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers. J Magn Reson. 2013 Nov; 236:83-8. PMID: 24091140.
      View in: PubMed
    25. Lee W, Bahrami A, Markley JL. ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy. Bioinformatics. 2013 Feb 15; 29(4):515-7. PMID: 23220573.
      View in: PubMed
    26. Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL. PACSY, a relational database management system for protein structure and chemical shift analysis. J Biomol NMR. 2012 Oct; 54(2):169-79. PMID: 22903636.
      View in: PubMed
    27. Kobayashi N, Harano Y, Tochio N, Nakatani E, Kigawa T, Yokoyama S, Mading S, Ulrich EL, Markley JL, Akutsu H, Fujiwara T. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database. J Biomol NMR. 2012 Aug; 53(4):311-20. PMID: 22689068.
      View in: PubMed
    28. Doreleijers JF, Vranken WF, Schulte C, Markley JL, Ulrich EL, Vriend G, Vuister GW. NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. Nucleic Acids Res. 2012 Jan; 40(Database issue):D519-24. PMID: 22139937.
      View in: PubMed
    29. Lee W, Kim JH, Westler WM, Markley JL. PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination. Bioinformatics. 2011 Jun 15; 27(12):1727-8. PMID: 21511715.
      View in: PubMed
    30. 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. PMID: 21373839.
      View in: PubMed
    31. Takeda M, Hallenga K, Shigezane M, Waelchli M, L?hr 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. PMID: 21316281.
      View in: PubMed
    32. Lee W, Westler WM, Bahrami A, Eghbalnia HR, Markley JL. PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy. Bioinformatics. 2009 Aug 15; 25(16):2085-7. PMID: 19497931.
      View in: PubMed
    33. 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. PMID: 19282963.
      View in: PubMed
    34. 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. PMID: 18259166.
      View in: PubMed
    35. Wang L, Eghbalnia HR, Markley JL. Probabilistic approach to determining unbiased random-coil carbon-13 chemical shift values from the protein chemical shift database. J Biomol NMR. 2006 Jul; 35(3):155-65. PMID: 16799859.
      View in: PubMed
    36. Eghbalnia HR, Wang L, Bahrami A, Assadi A, Markley JL. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements. J Biomol NMR. 2005 May; 32(1):71-81. PMID: 16041485.
      View in: PubMed
    37. 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. PMID: 12932460.
      View in: PubMed
    38. Hemmi H, Studts JM, Chae YK, Markley JL, Fox BG. Assignment of 1H, 13C and 15N NMR signals in the toluene 4-monooxygenase effector protein. J Biomol NMR. 2000 Apr; 16(4):359-60. PMID: 10826893.
      View in: PubMed
    39. 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. PMID: 9878473.
      View in: PubMed
    40. Markley JL, Bax A, Arata Y, Hilbers CW, Kaptein R, Sykes BD, Wright PE, W?thrich K. Recommendations for the presentation of NMR structures of proteins and nucleic acids--IUPAC-IUBMB-IUPAB Inter-Union Task Group on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy. Eur J Biochem. 1998 Aug 15; 256(1):1-15. PMID: 9746340.
      View in: PubMed
    41. Markley JL, Bax A, Arata Y, Hilbers CW, Kaptein R, Sykes BD, Wright PE, W?thrich K. Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. J Biomol NMR. 1998 Jul; 12(1):1-23. PMID: 9729785.
      View in: PubMed
    42. 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. PMID: 9460246.
      View in: PubMed
    43. 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. PMID: 8589602.
      View in: PubMed
    44. 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. PMID: 8019143.
      View in: PubMed
    45. 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. PMID: 1731949.
      View in: PubMed
    46. 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. PMID: 2125478.
      View in: PubMed
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