Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
Keywords
Last Name
Institution

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. Evans CM, Phillips M, Malone KL, Tonelli M, Cornilescu G, Cornilescu C, Holton SJ, Gorjánácz M, Wang L, Carlson S, Gay JC, Nix JC, Demeler B, Markley JL, Glass KC. Coordination of Di-Acetylated Histone Ligands by the ATAD2 Bromodomain. Int J Mol Sci. 2021 Aug 24; 22(17). PMID: 34502039.
      View in: PubMed
    4. 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
    5. 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
    6. Velankar S, Burley SK, Kurisu G, Hoch JC, Markley JL. The Protein Data Bank Archive. Methods Mol Biol. 2021; 2305:3-21. PMID: 33950382.
      View in: PubMed
    7. Lloyd JT, McLaughlin K, Lubula MY, Gay JC, Dest A, Gao C, Phillips M, Tonelli M, Cornilescu G, Marunde MR, Evans CM, Boyson SP, Carlson S, Keogh MC, Markley JL, Frietze S, Glass KC. Structural Insights into the Recognition of Mono- and Diacetylated Histones by the ATAD2B Bromodomain. J Med Chem. 2020 11 12; 63(21):12799-12813. PMID: 33084328.
      View in: PubMed
    8. Van QN, López CA, Tonelli M, Taylor T, Niu B, Stanley CB, Bhowmik D, Tran TH, Frank PH, Messing S, Alexander P, Scott D, Ye X, Drew M, Chertov O, Lösche M, Ramanathan A, Gross ML, Hengartner NW, Westler WM, Markley JL, Simanshu DK, Nissley DV, Gillette WK, Esposito D, McCormick F, Gnanakaran S, Heinrich F, Stephen AG. Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane. Proc Natl Acad Sci U S A. 2020 09 29; 117(39):24258-24268. PMID: 32913056.
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    9. Dashti H, Westler WM, Wedell JR, Demler OV, Eghbalnia HR, Markley JL, Mora S. Probabilistic identification of saccharide moieties in biomolecules and their protein complexes. Sci Data. 2020 07 03; 7(1):210. PMID: 32620933.
      View in: PubMed
    10. Aceti DJ, Ahmed H, Westler WM, Wu C, Dashti H, Tonelli M, Eghbalnia H, Amarasinghe GK, Markley JL. Fragment screening targeting Ebola virus nucleoprotein C-terminal domain identifies lead candidates. Antiviral Res. 2020 08; 180:104822. PMID: 32446802.
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    11. Obi JO, Lubula MY, Cornilescu G, Henrickson A, McGuire K, Evans CM, Phillips M, Boyson SP, Demeler B, Markley JL, Glass KC. The BRPF1 bromodomain is a molecular reader of di-acetyllysine. Curr Res Struct Biol. 2020; 2:104-115. PMID: 33554132.
      View in: PubMed
    12. 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
    13. 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. PMID: 32151725.
      View in: PubMed
    14. Barnett BR, Fathi F, Falco Cobra P, Yi SY, Anderson JM, Eghbalnia HR, Markley JL, Yu JJ. Metabolic Changes in Synaptosomes in an Animal Model of Schizophrenia Revealed by 1H and 1H,13C NMR Spectroscopy. Metabolites. 2020 Feb 23; 10(2). PMID: 32102223.
      View in: PubMed
    15. Romero PR, Kobayashi N, Wedell JR, Baskaran K, Iwata T, Yokochi M, Maziuk D, Yao H, Fujiwara T, Kurusu G, Ulrich EL, Hoch JC, Markley JL. BioMagResBank (BMRB) as a Resource for Structural Biology. Methods Mol Biol. 2020; 2112:187-218. PMID: 32006287.
      View in: PubMed
    16. 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.
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    17. 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. PMID: 31780431.
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    18. Tsvetkov P, Detappe A, Cai K, Keys HR, Brune Z, Ying W, Thiru P, Reidy M, Kugener G, Rossen J, Kocak M, Kory N, Tsherniak A, Santagata S, Whitesell L, Ghobrial IM, Markley JL, Lindquist S, Golub TR. Author Correction: Mitochondrial metabolism promotes adaptation to proteotoxic stress. Nat Chem Biol. 2019 Jul; 15(7):757. PMID: 31164776.
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    19. 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
    20. 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.
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    21. Tsvetkov P, Detappe A, Cai K, Keys HR, Brune Z, Ying W, Thiru P, Reidy M, Kugener G, Rossen J, Kocak M, Kory N, Tsherniak A, Santagata S, Whitesell L, Ghobrial IM, Markley JL, Lindquist S, Golub TR. Mitochondrial metabolism promotes adaptation to proteotoxic stress. Nat Chem Biol. 2019 07; 15(7):681-689. PMID: 31133756.
      View in: PubMed
    22. 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
    23. 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
    24. Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). Acta Crystallogr D Struct Biol. 2019 Apr 01; 75(Pt 4):451-454. PMID: 30988261.
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    25. Dashti H, Wedell JR, Westler WM, Markley JL, Eghbalnia HR. Automated evaluation of consistency within the PubChem Compound database. Sci Data. 2019 02 19; 6:190023. PMID: 30778259.
      View in: PubMed
    26. Ulrich EL, Baskaran K, Dashti H, Ioannidis YE, Livny M, Romero PR, Maziuk D, Wedell JR, Yao H, Eghbalnia HR, Hoch JC, Markley JL. NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments. J Biomol NMR. 2019 Feb; 73(1-2):5-9. PMID: 30580387.
      View in: PubMed
    27. 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). PMID: 30200358.
      View in: PubMed
    28. Larsen EK, Olivieri C, Walker C, V S M, Gao J, Bernlohr DA, Tonelli M, Markley JL, Veglia G. Probing Protein-Protein Interactions Using Asymmetric Labeling and Carbonyl-Carbon Selective Heteronuclear NMR Spectroscopy. Molecules. 2018 Aug 03; 23(8). PMID: 30081441.
      View in: PubMed
    29. Cai K, Frederick RO, Dashti H, Markley JL. Architectural Features of Human Mitochondrial Cysteine Desulfurase Complexes from Crosslinking Mass Spectrometry and Small-Angle X-Ray Scattering. Structure. 2018 08 07; 26(8):1127-1136.e4. PMID: 29983374.
      View in: PubMed
    30. 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
    31. 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. PMID: 29576242.
      View in: PubMed
    32. Rhoads TW, Burhans MS, Chen VB, Hutchins PD, Rush MJP, Clark JP, Stark JL, McIlwain SJ, Eghbalnia HR, Pavelec DM, Ong IM, Denu JM, Markley JL, Coon JJ, Colman RJ, Anderson RM. Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys. Cell Metab. 2018 03 06; 27(3):677-688.e5. PMID: 29514073.
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    33. Cai K, Frederick RO, Tonelli M, Markley JL. ISCU(M108I) and ISCU(D39V) Differ from Wild-Type ISCU in Their Failure To Form Cysteine Desulfurase Complexes Containing Both Frataxin and Ferredoxin. Biochemistry. 2018 03 06; 57(9):1491-1500. PMID: 29406711.
      View in: PubMed
    34. Young JY, Westbrook JD, Feng Z, Peisach E, Persikova I, Sala R, Sen S, Berrisford JM, Swaminathan GJ, Oldfield TJ, Gutmanas A, Igarashi R, Armstrong DR, Baskaran K, Chen L, Chen M, Clark AR, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Ikegawa Y, Kengaku Y, Lawson CL, Liang Y, Mak L, Mukhopadhyay A, Narayanan B, Nishiyama K, Patwardhan A, Sahni G, Sanz-García E, Sato J, Sekharan MR, Shao C, Smart OS, Tan L, van Ginkel G, Yang H, Zhuravleva MA, Markley JL, Nakamura H, Kurisu G, Kleywegt GJ, Velankar S, Berman HM, Burley SK. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Database (Oxford). 2018 01 01; 2018. PMID: 29688351.
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    35. Markley JL. View from Nuclear Magnetic Resonance Spectroscopy. Adv Exp Med Biol. 2018; 1105:19-22. PMID: 30617821.
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    36. Markley JL. Current Solution NMR Techniques for Structure-Function Studies of Proteins and RNA Molecules. Adv Exp Med Biol. 2018; 1105:43-58. PMID: 30617823.
      View in: PubMed
    37. Gandhi NN, Cobra PF, Steele JL, Markley JL, Rankin SA. Lactobacillus demonstrate thiol-independent metabolism of methylglyoxal: Implications toward browning prevention in Parmesan cheese. J Dairy Sci. 2018 Feb; 101(2):968-978. PMID: 29274980.
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    38. Reidenbach AG, Kemmerer ZA, Aydin D, Jochem A, McDevitt MT, Hutchins PD, Stark JL, Stefely JA, Reddy T, Hebert AS, Wilkerson EM, Johnson IE, Bingman CA, Markley JL, Coon JJ, Dal Peraro M, Pagliarini DJ. Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family. Cell Chem Biol. 2018 02 15; 25(2):154-165.e11. PMID: 29198567.
      View in: PubMed
    39. Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ. Validation of Structures in the Protein Data Bank. Structure. 2017 12 05; 25(12):1916-1927. PMID: 29174494.
      View in: PubMed
    40. Fathi F, Brun A, Rott KH, Falco Cobra P, Tonelli M, Eghbalnia HR, Caviedes-Vidal E, Karasov WH, Markley JL. NMR-Based Identification of Metabolites in Polar and Non-Polar Extracts of Avian Liver. Metabolites. 2017 Nov 16; 7(4). PMID: 29144418.
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    41. 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. PMID: 29058410.
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    42. 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.
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    43. Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J. PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models. Structure. 2017 09 05; 25(9):1317-1318. PMID: 28877501.
      View in: PubMed
    44. Wyche TP, Alvarenga RFR, Piotrowski JS, Duster MN, Warrack SR, Cornilescu G, De Wolfe TJ, Hou Y, Braun DR, Ellis GA, Simpkins SW, Nelson J, Myers CL, Steele J, Mori H, Safdar N, Markley JL, Rajski SR, Bugni TS. Chemical Genomics, Structure Elucidation, and in Vivo Studies of the Marine-Derived Anticlostridial Ecteinamycin. ACS Chem Biol. 2017 09 15; 12(9):2287-2295. PMID: 28708379.
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    45. Dashti H, Westler WM, Markley JL, Eghbalnia HR. Unique identifiers for small molecules enable rigorous labeling of their atoms. Sci Data. 2017 05 23; 4:170073. PMID: 28534867.
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    46. Markley JL, Westler WM. Biomolecular NMR: Past and future. Arch Biochem Biophys. 2017 08 15; 628:3-16. PMID: 28495511.
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    47. Cai K, Frederick RO, Tonelli M, Markley JL. Mitochondrial Cysteine Desulfurase and ISD11 Coexpressed in Escherichia coli Yield Complex Containing Acyl Carrier Protein. ACS Chem Biol. 2017 04 21; 12(4):918-921. PMID: 28233492.
      View in: PubMed
    48. Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK. OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. Structure. 2017 03 07; 25(3):536-545. PMID: 28190782.
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    49. Cai K, Tonelli M, Frederick RO, Markley JL. Human Mitochondrial Ferredoxin 1 (FDX1) and Ferredoxin 2 (FDX2) Both Bind Cysteine Desulfurase and Donate Electrons for Iron-Sulfur Cluster Biosynthesis. Biochemistry. 2017 01 24; 56(3):487-499. PMID: 28001042.
      View in: PubMed
    50. Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. Methods Mol Biol. 2017; 1607:627-641. PMID: 28573592.
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    51. Cai K, Liu G, Frederick RO, Xiao R, Montelione GT, Markley JL. Structural/Functional Properties of Human NFU1, an Intermediate [4Fe-4S] Carrier in Human Mitochondrial Iron-Sulfur Cluster Biogenesis. Structure. 2016 12 06; 24(12):2080-2091. PMID: 27818104.
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    52. 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. PMID: 27643760.
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    53. 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. PMID: 27580257.
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    54. Berman HM, Burley SK, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. The archiving and dissemination of biological structure data. Curr Opin Struct Biol. 2016 10; 40:17-22. PMID: 27450113.
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    55. Wessel SR, Cornilescu CC, Cornilescu G, Metz A, Leroux M, Hu K, Sandler SJ, Markley JL, Keck JL. Structure and Function of the PriC DNA Replication Restart Protein. J Biol Chem. 2016 08 26; 291(35):18384-96. PMID: 27382050.
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    56. Alderson TR, Kim JH, Markley JL. Dynamical Structures of Hsp70 and Hsp70-Hsp40 Complexes. Structure. 2016 07 06; 24(7):1014-30. PMID: 27345933.
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    57. Kim S, Natesan S, Cornilescu G, Carlson S, Tonelli M, McClurg UL, Binda O, Robson CN, Markley JL, Balaz S, Glass KC. Mechanism of Histone H3K4me3 Recognition by the Plant Homeodomain of Inhibitor of Growth 3. J Biol Chem. 2016 08 26; 291(35):18326-41. PMID: 27281824.
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    58. 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.
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    59. Yokochi M, Kobayashi N, Ulrich EL, Kinjo AR, Iwata T, Ioannidis YE, Livny M, Markley JL, Nakamura H, Kojima C, Fujiwara T. Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. J Biomed Semantics. 2016 05 05; 7(1):16. PMID: 27927232.
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    60. Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure. 2016 Apr 05; 24(4):502-508. PMID: 27050687.
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    61. 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.
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    155. Lin IJ, Chen Y, Fee JA, Song J, Westler WM, Markley JL. Rieske protein from Thermus thermophilus: 15N NMR titration study demonstrates the role of iron-ligated histidines in the pH dependence of the reduction potential. J Am Chem Soc. 2006 Aug 23; 128(33):10672-3. PMID: 16910649.
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    156. 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.
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    157. Ahn HC, Juranic N, Macura S, Markley JL. Three-dimensional structure of the water-insoluble protein crambin in dodecylphosphocholine micelles and its minimal solvent-exposed surface. J Am Chem Soc. 2006 Apr 05; 128(13):4398-404. PMID: 16569017.
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    158. Dmitriev O, Tsivkovskii R, Abildgaard F, Morgan CT, Markley JL, Lutsenko S. Solution structure of the N-domain of Wilson disease protein: distinct nucleotide-binding environment and effects of disease mutations. Proc Natl Acad Sci U S A. 2006 Apr 04; 103(14):5302-7. PMID: 16567646.
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    159. 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. PMID: 16329120.
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    160. Zornetzer GA, White RD, Markley JL, Fox BG. Preparation of isotopically labeled spinach acyl-acyl carrier protein for NMR structural studies. Protein Expr Purif. 2006 Apr; 46(2):446-55. PMID: 16325425.
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    161. Lin IJ, Gebel EB, Machonkin TE, Westler WM, Markley JL. Changes in hydrogen-bond strengths explain reduction potentials in 10 rubredoxin variants. Proc Natl Acad Sci U S A. 2005 Oct 11; 102(41):14581-6. PMID: 16199518.
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    162. 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. PMID: 16144400.
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    163. Singh S, Cornilescu CC, Tyler RC, Cornilescu G, Tonelli M, Lee MS, Markley JL. Solution structure of a late embryogenesis abundant protein (LEA14) from Arabidopsis thaliana, a cellular stress-related protein. Protein Sci. 2005 Oct; 14(10):2601-9. PMID: 16155204.
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    164. Blad H, Reiter NJ, Abildgaard F, Markley JL, Butcher SE. Dynamics and metal ion binding in the U6 RNA intramolecular stem-loop as analyzed by NMR. J Mol Biol. 2005 Oct 28; 353(3):540-55. PMID: 16181635.
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    165. 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. PMID: 16132822.
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    166. 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.
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    167. Doreleijers JF, Nederveen AJ, Vranken W, Lin J, Bonvin AM, Kaptein R, Markley JL, Ulrich EL. BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J Biomol NMR. 2005 May; 32(1):1-12. PMID: 16041478.
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    168. Wang L, Eghbalnia HR, Bahrami A, Markley JL. Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications. J Biomol NMR. 2005 May; 32(1):13-22. PMID: 16041479.
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    169. Tyler RC, Sreenath HK, Singh S, Aceti DJ, Bingman CA, Markley JL, Fox BG. Auto-induction medium for the production of [U-15N]- and [U-13C, U-15N]-labeled proteins for NMR screening and structure determination. Protein Expr Purif. 2005 Apr; 40(2):268-78. PMID: 15766868.
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    170. Song J, Tyler RC, Wrobel RL, Frederick RO, Vojtek FC, Jeon WB, Lee MS, Markley JL. Solution structure of At3g04780.1-des15, an Arabidopsis thaliana ortholog of the C-terminal domain of human thioredoxin-like protein. Protein Sci. 2005 Apr; 14(4):1059-63. PMID: 15741346.
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    171. 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. PMID: 15738211.
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    172. Smith DW, Johnson KA, Bingman CA, Aceti DJ, Blommel PG, Wrobel RL, Frederick RO, Zhao Q, Sreenath H, Fox BG, Volkman BF, Jeon WB, Newman CS, Ulrich EL, Hegeman AD, Kimball T, Thao S, Sussman MR, Markley JL, Phillips GN. Crystal structure of At2g03760, a putative steroid sulfotransferase from Arabidopsis thaliana. Proteins. 2004 Dec 01; 57(4):854-7. PMID: 15317023.
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    173. Bingman CA, Johnson KA, Peterson FC, Frederick RO, Zhao Q, Thao S, Fox BG, Volkman BF, Jeon WB, Smith DW, Newman CS, Ulrich EL, Hegeman A, Sussman MR, Markley JL, Phillips GN. Crystal structure of the protein from gene At3g17210 of Arabidopsis thaliana. Proteins. 2004 Oct 01; 57(1):218-20. PMID: 15326607.
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    174. 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. PMID: 15113213.
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    175. Zhao Q, Frederick R, Seder K, Thao S, Sreenath H, Peterson F, Volkman BF, Markley JL, Fox BG. Production in two-liter beverage bottles of proteins for NMR structure determination labeled with either 15N- or 13C-15N. J Struct Funct Genomics. 2004; 5(1-2):87-93. PMID: 15263847.
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    176. 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.
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    177. Jin Z, Danilova V, Assadi-Porter FM, Markley JL, Hellekant G. Monkey electrophysiological and human psychophysical responses to mutants of the sweet protein brazzein: delineating brazzein sweetness. Chem Senses. 2003 Jul; 28(6):491-8. PMID: 12907586.
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    178. 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. PMID: 12767219.
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    179. Doreleijers JF, Mading S, Maziuk D, Sojourner K, Yin L, Zhu J, Markley JL, Ulrich EL. BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank. J Biomol NMR. 2003 Jun; 26(2):139-46. PMID: 12766409.
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    180. 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. PMID: 12731859.
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    181. Assadi-Porter FM, Abildgaard F, Blad H, Markley JL. Correlation of the sweetness of variants of the protein brazzein with patterns of hydrogen bonds detected by NMR spectroscopy. J Biol Chem. 2003 Aug 15; 278(33):31331-9. PMID: 12732626.
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    182. Song J, Laskowski M, Qasim MA, Markley JL. NMR determination of pKa values for Asp, Glu, His, and Lys mutants at each variable contiguous enzyme-inhibitor contact position of the turkey ovomucoid third domain. Biochemistry. 2003 Mar 18; 42(10):2847-56. PMID: 12627950.
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    183. Lin IJ, Gebel EB, Machonkin TE, Westler WM, Markley JL. Correlation between hydrogen bond lengths and reduction potentials in Clostridium pasteurianum rubredoxin. J Am Chem Soc. 2003 Feb 12; 125(6):1464-5. PMID: 12568591.
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    184. Zolnai Z, Lee PT, Li J, Chapman MR, Newman CS, Phillips GN, Rayment I, Ulrich EL, Volkman BF, Markley JL. Project management system for structural and functional proteomics: Sesame. J Struct Funct Genomics. 2003; 4(1):11-23. PMID: 12943363.
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    185. Markley JL, Ulrich EL, Westler WM, Volkman BF. Macromolecular structure determination by NMR spectroscopy. Methods Biochem Anal. 2003; 44:89-113. PMID: 12647383.
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    186. Westler WM, Weinhold F, Markley JL. Quantum chemical calculations on structural models of the catalytic site of chymotrypsin: comparison of calculated results with experimental data from NMR spectroscopy. J Am Chem Soc. 2002 Dec 04; 124(48):14373-81. PMID: 12452711.
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    187. Westler WM, Frey PA, Lin J, Wemmer DE, Morimoto H, Williams PG, Markley JL. Evidence for a strong hydrogen bond in the catalytic dyad of transition-state analogue inhibitor complexes of chymotrypsin from proton-triton NMR isotope shifts. J Am Chem Soc. 2002 Apr 24; 124(16):4196-7. PMID: 11960433.
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    188. Machonkin TE, Westler WM, Markley JL. (13)C[(13)C] 2D NMR: a novel strategy for the study of paramagnetic proteins with slow electronic relaxation rates. J Am Chem Soc. 2002 Apr 03; 124(13):3204-5. PMID: 11916393.
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    189. DeRider ML, Wilkens SJ, Waddell MJ, Bretscher LE, Weinhold F, Raines RT, Markley JL. Collagen stability: insights from NMR spectroscopic and hybrid density functional computational investigations of the effect of electronegative substituents on prolyl ring conformations. J Am Chem Soc. 2002 Mar 20; 124(11):2497-505. PMID: 11890798.
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    190. 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. PMID: 11889129.
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    191. Wilkens SJ, Westler WM, Weinhold F, Markley JL. Trans-hydrogen-bond (h2)J(NN) and (h1)J(NH) couplings in the DNA A-T base pair: natural bond orbital analysis. J Am Chem Soc. 2002 Feb 20; 124(7):1190-1. PMID: 11841286.
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    192. 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. PMID: 11724611.
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    193. Kuloglu ES, McCaslin DR, Kitabwalla M, Pauza CD, Markley JL, Volkman BF. Monomeric solution structure of the prototypical 'C' chemokine lymphotactin. Biochemistry. 2001 Oct 23; 40(42):12486-96. PMID: 11601972.
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    194. Luo W, Moe LA, Skjeldal L, Pikus JD, Markley JL, Fox BG. Assignment of 1H, 13C and 15N NMR signals from toluene 4-monooxygenase Rieske ferredoxin in its oxidized state. J Biomol NMR. 2001 Sep; 21(1):73-4. PMID: 11693573.
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    195. 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. PMID: 11391787.
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    196. Hemmi H, Studts JM, Chae YK, Song J, Markley JL, Fox BG. Solution structure of the toluene 4-monooxygenase effector protein (T4moD). Biochemistry. 2001 Mar 27; 40(12):3512-24. PMID: 11297417.
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    197. Chae YK, Markley JL. Functional recombinant rabbit muscle phosphoglucomutase from Escherichia coli. Protein Expr Purif. 2000 Oct; 20(1):124-7. PMID: 11035960.
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    198. 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. PMID: 10775410.
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    199. 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. PMID: 10775411.
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    200. 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.
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    201. 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. PMID: 10620356.
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    202. Chae YK, Abildgaard F, Royer CA, Markley JL. Oligomerization of the EK18 mutant of the trp repressor of Escherichia coli as observed by NMR spectroscopy. Arch Biochem Biophys. 1999 Nov 01; 371(1):35-40. PMID: 10525287.
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    203. 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. PMID: 9988679.
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    204. Kaslik G, Westler WM, Gráf L, Markley JL. Properties of the His57-Asp102 dyad of rat trypsin D189S in the zymogen, activated enzyme, and alpha1-proteinase inhibitor complexed forms. Arch Biochem Biophys. 1999 Feb 15; 362(2):254-64. PMID: 9989934.
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    205. 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.
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    206. 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. PMID: 9748232.
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    207. 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--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.
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    208. Volkman BF, Alam SL, Satterlee JD, Markley JL. Solution structure and backbone dynamics of component IV Glycera dibranchiata monomeric hemoglobin-CO. Biochemistry. 1998 Aug 04; 37(31):10906-19. PMID: 9692983.
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    209. 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. PMID: 9751999.
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    210. 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. PMID: 9671561.
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    211. 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. 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.
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    212. 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.
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    213. An Z, Zhao Q, McEvoy J, Yuan WM, Markley JL, Leong SA. The second finger of Urbs1 is required for iron-mediated repression of sid1 in Ustilago maydis. Proc Natl Acad Sci U S A. 1997 May 27; 94(11):5882-7. PMID: 9159169.
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    214. 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. PMID: 8780512.
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    215. 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.
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    216. 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.
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    217. 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.
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    218. 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. PMID: 1906741.
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    219. 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.
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