John L. Markley - Publications

Affiliations: 
1972-1984 Chemistry Purdue University, West Lafayette, IN, United States 
 1984- Biochemistry University of Wisconsin, Madison, Madison, WI 
Area:
NMR spectroscopy and its biological applications
Website:
http://www.biochem.wisc.edu/faculty/markley/

372 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Markley JL, Dashti H, Wedell JR, Westler WM, Eghbalnia HR. Tools for Enhanced NMR-Based Metabolomics Analysis. Methods in Molecular Biology (Clifton, N.J.). 2037: 413-427. PMID 31463858 DOI: 10.1007/978-1-4939-9690-2_23  1
2019 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. Journal of Biomolecular Nmr. PMID 31165321 DOI: 10.1007/s10858-019-00255-3  1
2019 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, ... ... Markley JL, et al. Author Correction: Mitochondrial metabolism promotes adaptation to proteotoxic stress. Nature Chemical Biology. PMID 31164776 DOI: 10.1038/s41589-019-0315-5  1
2019 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, ... ... Markley JL, et al. Mitochondrial metabolism promotes adaptation to proteotoxic stress. Nature Chemical Biology. PMID 31133756 DOI: 10.1038/s41589-019-0291-9  1
2019 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. 14: e0217098. PMID 31091298 DOI: 10.1371/journal.pone.0217098  1
2019 Lee W, Tonelli M, Wu C, Aceti DJ, Amarasinghe GK, Markley JL. Backbone resonance assignments and secondary structure of Ebola nucleoprotein 600-739 construct. Biomolecular Nmr Assignments. PMID 31076990 DOI: 10.1007/s12104-019-09898-7  1
2019 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 Science : a Publication of the Protein Society. PMID 31004454 DOI: 10.1002/pro.3628  1
2019 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, ... ... Markley JL, et al. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). Acta Crystallographica. Section D, Structural Biology. 75: 451-454. PMID 30988261 DOI: 10.1107/S2059798319004522  1
2019 Dashti H, Wedell JR, Westler WM, Markley JL, Eghbalnia HR. Automated evaluation of consistency within the PubChem Compound database. Scientific Data. 6: 190023. PMID 30778259 DOI: 10.1038/sdata.2019.23  1
2018 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. Journal of Biomolecular Nmr. PMID 30580387 DOI: 10.1007/s10858-018-0220-3  1
2018 Cai K, Markley JL. NMR as a Tool to Investigate the Processes of Mitochondrial and Cytosolic Iron-Sulfur Cluster Biosynthesis. Molecules (Basel, Switzerland). 23. PMID 30200358 DOI: 10.3390/molecules23092213  1
2018 Dashti H, Wedell JR, Westler WM, Tonelli M, Aceti DJ, Amarasinghe GK, Markley JL, Eghbalnia HR. Applications of parameterized NMR spin systems of small molecules. Analytical Chemistry. PMID 30125102 DOI: 10.1021/acs.analchem.8b02660  1
2018 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 (Basel, Switzerland). 23. PMID 30081441 DOI: 10.3390/molecules23081937  1
2018 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 (London, England : 1993). PMID 29983374 DOI: 10.1016/j.str.2018.05.017  1
2018 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, ... ... Markley JL, et al. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Database : the Journal of Biological Databases and Curation. 2018. PMID 29688351 DOI: 10.1093/database/bay002  1
2018 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. Journal of Inorganic Biochemistry. PMID 29576242 DOI: 10.1016/j.jinorgbio.2018.03.007  1
2018 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, et al. Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys. Cell Metabolism. 27: 677-688.e5. PMID 29514073 DOI: 10.1016/j.cmet.2018.01.014  1
2018 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. PMID 29406711 DOI: 10.1021/acs.biochem.7b01234  1
2017 Lee W, Markley JL. PINE-SPARKY.2 for automated NMR-based protein structure research. Bioinformatics (Oxford, England). PMID 29281006 DOI: 10.1093/bioinformatics/btx785  1
2017 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, et al. Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family. Cell Chemical Biology. PMID 29198567 DOI: 10.1016/j.chembiol.2017.11.001  1
2017 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, ... ... Markley JL, et al. Validation of Structures in the Protein Data Bank. Structure (London, England : 1993). 25: 1916-1927. PMID 29174494 DOI: 10.1016/j.str.2017.10.009  1
2017 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. 7. PMID 29144418 DOI: 10.3390/metabo7040061  1
2017 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 Genetics. 13: e1007084. PMID 29084221 DOI: 10.1371/journal.pgen.1007084  1
2017 Dashti H, Westler WM, Tonelli M, Wedell JR, Markley JL, Eghbalnia HR. Spin System Modeling of NMR Spectra for Applications in Metabolomics and Small Molecule Screening. Analytical Chemistry. PMID 29058410 DOI: 10.1021/acs.analchem.7b02884  1
2017 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 (London, England : 1993). 25: 1317-1318. PMID 28877501 DOI: 10.1016/j.str.2017.08.001  1
2017 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, ... ... Markley JL, et al. Chemical Genomics, Structure Elucidation, and In Vivo Studies of the Marine-derived Anticlostridial Ecteinamycin. Acs Chemical Biology. PMID 28708379 DOI: 10.1021/acschembio.7b00388  1
2017 Cornilescu G, Ramos Alvarenga RF, Wyche TP, Bugni TS, Gil RR, Cornilescu CC, Westler WM, Markley JL, Schwieters CD. Progressive Stereo Locking (PSL) - A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and other Small Molecules. Acs Chemical Biology. PMID 28617580 DOI: 10.1021/acschembio.7b00281  1
2017 Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. Methods in Molecular Biology (Clifton, N.J.). 1607: 627-641. PMID 28573592 DOI: 10.1007/978-1-4939-7000-1_26  1
2017 Dashti H, Westler WM, Markley JL, Eghbalnia HR. Unique identifiers for small molecules enable rigorous labeling of their atoms. Scientific Data. 4: 170073. PMID 28534867 DOI: 10.1038/sdata.2017.73  1
2017 Markley JL, Westler WM. Biomolecular NMR: Past and future. Archives of Biochemistry and Biophysics. PMID 28495511 DOI: 10.1016/j.abb.2017.05.003  1
2017 Chae YK, Kim SH, Markley JL. Relationship between recombinant protein expression and host metabolome as determined by two-dimensional NMR spectroscopy. Plos One. 12: e0177233. PMID 28486539 DOI: 10.1371/journal.pone.0177233  1
2017 Cai K, Frederick RO, Tonelli M, Markley JL. Mitochondrial Cysteine Desulfurase and ISD11 Co-expressed in Escherichia coli Yield Complex Containing Acyl Carrier Protein. Acs Chemical Biology. PMID 28233492 DOI: 10.1021/acschembio.6b01005  1
2017 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, ... ... Markley JL, et al. OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. Structure (London, England : 1993). PMID 28190782 DOI: 10.1016/j.str.2017.01.004  1
2016 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. PMID 28001042 DOI: 10.1021/acs.biochem.6b00447  1
2016 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. Journal of Biomedical Semantics. 7: 16. PMID 27927232 DOI: 10.1186/s13326-016-0057-1  1
2016 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 (London, England : 1993). PMID 27818104 DOI: 10.1016/j.str.2016.08.020  1
2016 Eghbalnia HR, Romero PR, Westler WM, Baskaran K, Ulrich EL, Markley JL. Increasing rigor in NMR-based metabolomics through validated and open source tools. Current Opinion in Biotechnology. 43: 56-61. PMID 27643760 DOI: 10.1016/j.copbio.2016.08.005  1
2016 Markley JL, Brüschweiler R, Edison AS, Eghbalnia HR, Powers R, Raftery D, Wishart DS. The future of NMR-based metabolomics. Current Opinion in Biotechnology. 43: 34-40. PMID 27580257 DOI: 10.1016/j.copbio.2016.08.001  1
2016 Berman HM, Burley SK, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. The archiving and dissemination of biological structure data. Current Opinion in Structural Biology. 40: 17-22. PMID 27450113 DOI: 10.1016/j.sbi.2016.06.018  1
2016 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. The Journal of Biological Chemistry. PMID 27382050 DOI: 10.1074/jbc.M116.738781  1
2016 Alderson TR, Kim JH, Markley JL. Dynamical Structures of Hsp70 and Hsp70-Hsp40 Complexes. Structure (London, England : 1993). PMID 27345933 DOI: 10.1016/j.str.2016.05.011  1
2016 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. The Journal of Biological Chemistry. PMID 27281824 DOI: 10.1074/jbc.M115.690651  1
2016 Lee W, Petit CM, Cornilescu G, Stark JL, Markley JL. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data. Journal of Biomolecular Nmr. PMID 27169728 DOI: 10.1007/s10858-016-0036-y  1
2016 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, ... ... Markley JL, et al. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure (London, England : 1993). 24: 502-8. PMID 27050687 DOI: 10.1016/j.str.2016.02.017  1
2016 Lee W, Cornilescu G, Dashti H, Eghbalnia HR, Tonelli M, Westler WM, Butcher SE, Henzler-Wildman KA, Markley JL. Integrative NMR for biomolecular research. Journal of Biomolecular Nmr. PMID 27023095 DOI: 10.1007/s10858-016-0029-x  1
2016 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. Journal of Proteome Research. PMID 26965640 DOI: 10.1021/acs.jproteome.6b00121  1
2016 Markley JL, Maitra S, Hanson PR. Phosphate Tether-Mediated Ring-Closing Metathesis for the Generation of P-Stereogenic, Z-Configured Bicyclo[7.3.1]- and Bicyclo[8.3.1]phosphates. The Journal of Organic Chemistry. PMID 26794367 DOI: 10.1021/acs.joc.5b02473  1
2016 Dashti H, Tonelli M, Lee W, Westler WM, Cornilescu G, Ulrich EL, Markley JL. Probabilistic validation of protein NMR chemical shift assignments. Journal of Biomolecular Nmr. PMID 26724815 DOI: 10.1007/s10858-015-0007-8  1
2016 Assadi-Porter FM, Tonelli M, Maillet EL, Markley JL, Max M. Corrigendum to "Interactions between the human sweet-sensing T1R2-T1R3 receptor and sweeteners detected by saturation transfer difference NMR spectroscopy" [Biochim. Biophys. Acta (1798/2) (2010) 82-86] Biochimica Et Biophysica Acta - Biomembranes. DOI: 10.1016/j.bbamem.2016.01.015  1
2015 Singarapu KK, Tonelli M, Markley JL, Assadi-Porter FM. Structure-function relationships of brazzein variants with altered interactions with the human sweet taste receptor. Protein Science : a Publication of the Protein Society. PMID 26701738 DOI: 10.1002/pro.2870  1
2015 Singarapu KK, Otte MM, Tonelli M, Westler WM, Escalante-Semerena JC, Markley JL. Solution Structural Studies of GTP:Adenosylcobinamide-Phosphateguanylyl Transferase (CobY) from Methanocaldococcus jannaschii. Plos One. 10: e0141297. PMID 26513744 DOI: 10.1371/journal.pone.0141297  1
2015 Eller CH, Chao TY, Singarapu KK, Ouerfelli O, Yang G, Markley JL, Danishefsky SJ, Raines RT. Human Cancer Antigen Globo H Is a Cell-Surface Ligand for Human Ribonuclease 1. Acs Central Science. 1: 181-190. PMID 26405690 DOI: 10.1021/acscentsci.5b00164  1
2015 Bothe JR, Tonelli M, Ali IK, Dai Z, Frederick RO, Westler WM, Markley JL. The Complex Energy Landscape of the Protein IscU. Biophysical Journal. 109: 1019-25. PMID 26331259 DOI: 10.1016/j.bpj.2015.07.045  1
2015 Chen VB, Wedell JR, Wenger RK, Ulrich EL, Markley JL. MolProbity for the masses-of data. Journal of Biomolecular Nmr. 63: 77-83. PMID 26195077 DOI: 10.1007/s10858-015-9969-9  1
2015 Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, et al. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure (London, England : 1993). PMID 26095030 DOI: 10.1016/j.str.2015.05.013  1
2015 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, et al. NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nature Structural & Molecular Biology. 22: 433-4. PMID 26036565 DOI: 10.1038/nsmb.3041  1
2015 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. Journal of Biomolecular Nmr. PMID 26021595 DOI: 10.1007/s10858-015-9950-7  1
2015 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. Journal of Biomolecular Nmr. PMID 25900069 DOI: 10.1007/s10858-015-9933-8  1
2015 Aceti DJ, Bingman CA, Wrobel RL, Frederick RO, Makino S, Nichols KW, Sahu SC, Bergeman LF, Blommel PG, Cornilescu CC, Gromek KA, Seder KD, Hwang S, Primm JG, Sabat G, ... ... Markley JL, et al. Expression platforms for producing eukaryotic proteins: a comparison of E. coli cell-based and wheat germ cell-free synthesis, affinity and solubility tags, and cloning strategies. Journal of Structural and Functional Genomics. 16: 67-80. PMID 25854603 DOI: 10.1007/s10969-015-9198-1  1
2015 Hanson PR, Jayasinghe S, Maitra S, Markley JL. Phosphate tethers in natural product synthesis. Topics in Current Chemistry. 361: 253-71. PMID 25518970 DOI: 10.1007/128_2014_572  1
2015 Lee W, Tonelli M, Markley JL. NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics (Oxford, England). 31: 1325-7. PMID 25505092 DOI: 10.1093/bioinformatics/btu830  1
2015 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. Biochimica Et Biophysica Acta. 1853: 1416-1428. PMID 25450980 DOI: 10.1016/j.bbamcr.2014.11.020  1
2015 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. Biomolecular Nmr Assignments. 9: 81-8. PMID 24619609 DOI: 10.1007/s12104-014-9549-z  1
2014 Alderson TR, Kim JH, Cai K, Frederick RO, Tonelli M, Markley JL. Correction to The Specialized Hsp70 (HscA) Interdomain Linker Binds to Its Nucleotide-Binding Domain and Stimulates ATP Hydrolysis in Both cis and trans Configurations. Biochemistry. 53: 7999. PMID 26653286 DOI: 10.1021/bi501490v  1
2014 Alderson TR, Kim JH, Cai K, Frederick RO, Tonelli M, Markley JL. The specialized Hsp70 (HscA) interdomain linker binds to its nucleotide-binding domain and stimulates ATP hydrolysis in both cis and trans configurations. Biochemistry. 53: 7148-59. PMID 25372495 DOI: 10.1021/bi5010552  1
2014 Berman HM, Burley SK, Kleywegt GJ, Nakamura H, Markley JL. Response to On prompt update of literature references in the Protein Data Bank. Acta Crystallographica. Section D, Biological Crystallography. 70: 2780. PMID 25286863 DOI: 10.1107/S1399004714020513  1
2014 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. The Journal of Biological Chemistry. 289: 32682-93. PMID 25253690 DOI: 10.1074/jbc.M114.580845  1
2014 Lee W, Stark JL, Markley JL. PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination. Journal of Biomolecular Nmr. 60: 73-5. PMID 25190042 DOI: 10.1007/s10858-014-9855-x  1
2014 Kim JH, Alderson TR, Frederick RO, Markley JL. Nucleotide-dependent interactions within a specialized Hsp70/Hsp40 complex involved in Fe-S cluster biogenesis. Journal of the American Chemical Society. 136: 11586-9. PMID 25080945 DOI: 10.1021/ja5055252  1
2014 Berman HM, Kleywegt GJ, Nakamura H, Markley JL. The Protein Data Bank archive as an open data resource. Journal of Computer-Aided Molecular Design. 28: 1009-14. PMID 25062767 DOI: 10.1007/s10822-014-9770-y  1
2014 Dai Z, Kim JH, Tonelli M, Ali IK, Markley JL. pH-induced conformational change of IscU at low pH correlates with protonation/deprotonation of two conserved histidine residues. Biochemistry. 53: 5290-7. PMID 25055301 DOI: 10.1021/bi500313t  1
2014 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. 9: e97198. PMID 24937088 DOI: 10.1371/journal.pone.0097198  1
2014 Kim JH, Bothe JR, Frederick RO, Holder JC, Markley JL. Role of IscX in iron-sulfur cluster biogenesis in Escherichia coli. Journal of the American Chemical Society. 136: 7933-42. PMID 24810328 DOI: 10.1021/ja501260h  1
2014 Whigham LD, Butz DE, Dashti H, Tonelli M, Johnson LK, Cook ME, Porter WP, Eghbalnia HR, Markley JL, Lindheim SR, Schoeller DA, Abbott DH, Assadi-Porter FM. Metabolic Evidence of Diminished Lipid Oxidation in Women With Polycystic Ovary Syndrome. Current Metabolomics. 2: 269-278. PMID 24765590 DOI: 10.2174/2213235X01666131203230512  1
2014 Beebe ET, Makino S, Markley JL, Fox BG. Automated cell-free protein production methods for structural studies. Methods in Molecular Biology (Clifton, N.J.). 1140: 117-35. PMID 24590713 DOI: 10.1007/978-1-4939-0354-2_9  1
2014 Cornilescu CC, Cornilescu G, Burgie ES, Markley JL, Ulijasz AT, Vierstra RD. Dynamic structural changes underpin photoconversion of a blue/green cyanobacteriochrome between its dark and photoactivated states. The Journal of Biological Chemistry. 289: 3055-65. PMID 24337572 DOI: 10.1074/jbc.M113.531053  1
2014 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. Journal of Molecular Biology. 426: 1661-76. PMID 24333487 DOI: 10.1016/j.jmb.2013.12.007  1
2014 Makino S, Beebe ET, Markley JL, Fox BG. Cell-free protein synthesis for functional and structural studies. Methods in Molecular Biology (Clifton, N.J.). 1091: 161-78. PMID 24203331 DOI: 10.1007/978-1-62703-691-7_11  1
2013 Chae YK, Kim SH, Ellinger JE, Markley JL. Dosage Effects of Salt and pH Stresses on Saccharomyces cerevisiae as Monitored via Metabolites by Using Two Dimensional NMR Spectroscopy. Bulletin of the Korean Chemical Society. 34: 3602-3608. PMID 25642011 DOI: 10.5012/bkcs.2013.34.12.3602  1
2013 Alderson TR, Markley JL. Biophysical characterization of α-synuclein and its controversial structure. Intrinsically Disordered Proteins. 1: 18-39. PMID 24634806 DOI: 10.4161/idp.26255  1
2013 Berman H, Kleywegt GJ, Nakamura H, Markley JL. Comment on on the propagation of errors by Jaskolski (2013). Acta Crystallographica. Section D, Biological Crystallography. 69: 2297. PMID 24311571 DOI: 10.1107/S090744491302917X  1
2013 Berman H, Kleywegt GJ, Nakamura H, Markley JL. Comment on timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013). Acta Crystallographica. Section D, Biological Crystallography. 69: 2296. PMID 24311570 DOI: 10.1107/S0907444913029168  1
2013 Ellinger JJ, Chylla RA, Ulrich EL, Markley JL. Databases and Software for NMR-Based Metabolomics. Current Metabolomics. 1. PMID 24260723 DOI: 10.2174/2213235X11301010028  1
2013 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. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 236: 83-8. PMID 24091140 DOI: 10.1016/j.jmr.2013.08.010  1
2013 Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL. Recommendations of the wwPDB NMR Validation Task Force. Structure (London, England : 1993). 21: 1563-70. PMID 24010715 DOI: 10.1016/j.str.2013.07.021  1
2013 Berman HM, Kleywegt GJ, Nakamura H, Markley JL. How community has shaped the Protein Data Bank. Structure (London, England : 1993). 21: 1485-91. PMID 24010707 DOI: 10.1016/j.str.2013.07.010  1
2013 Cai K, Frederick RO, Kim JH, Reinen NM, Tonelli M, Markley JL. Human mitochondrial chaperone (mtHSP70) and cysteine desulfurase (NFS1) bind preferentially to the disordered conformation, whereas co-chaperone (HSC20) binds to the structured conformation of the iron-sulfur cluster scaffold protein (ISCU). The Journal of Biological Chemistry. 288: 28755-70. PMID 23940031 DOI: 10.1074/jbc.M113.482042  1
2013 Kim JH, Frederick RO, Reinen NM, Troupis AT, Markley JL. [2Fe-2S]-ferredoxin binds directly to cysteine desulfurase and supplies an electron for iron-sulfur cluster assembly but is displaced by the scaffold protein or bacterial frataxin. Journal of the American Chemical Society. 135: 8117-20. PMID 23682711 DOI: 10.1021/ja401950a  1
2013 Clos LJ, Jofre MF, Ellinger JJ, Westler WM, Markley JL. NMRbot: Python scripts enable high-throughput data collection on current Bruker BioSpin NMR spectrometers. Metabolomics : Official Journal of the Metabolomic Society. 9: 558-563. PMID 23678341 DOI: 10.1007/s11306-012-0490-9  1
2013 Chylla RA, Van Acker R, Kim H, Azapira A, Mukerjee P, Markley JL, Storme V, Boerjan W, Ralph J. Plant cell wall profiling by fast maximum likelihood reconstruction (FMLR) and region-of-interest (ROI) segmentation of solution-state 2D 1H-13C NMR spectra. Biotechnology For Biofuels. 6: 45. PMID 23622232 DOI: 10.1186/1754-6834-6-45  1
2013 Hsueh KL, Tonelli M, Cai K, Westler WM, Markley JL. Electron transfer mechanism of the Rieske protein from Thermus thermophilus from solution nuclear magnetic resonance investigations. Biochemistry. 52: 2862-73. PMID 23480240 DOI: 10.1021/bi400296c  1
2013 Cornilescu CC, Cornilescu G, Rao H, Porter SF, Tonelli M, DeRider ML, Markley JL, Assadi-Porter FM. Temperature-dependent conformational change affecting Tyr11 and sweetness loops of brazzein. Proteins. 81: 919-25. PMID 23349025 DOI: 10.1002/prot.24259  1
2013 Markley JL, Kim JH, Dai Z, Bothe JR, Cai K, Frederick RO, Tonelli M. Metamorphic protein IscU alternates conformations in the course of its role as the scaffold protein for iron-sulfur cluster biosynthesis and delivery. Febs Letters. 587: 1172-9. PMID 23333622 DOI: 10.1016/j.febslet.2013.01.003  1
2013 Oldfield CJ, Xue B, Van YY, Ulrich EL, Markley JL, Dunker AK, Uversky VN. Utilization of protein intrinsic disorder knowledge in structural proteomics. Biochimica Et Biophysica Acta. 1834: 487-98. PMID 23232152 DOI: 10.1016/j.bbapap.2012.12.003  1
2013 Lee W, Bahrami A, Markley JL. ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy. Bioinformatics (Oxford, England). 29: 515-7. PMID 23220573 DOI: 10.1093/bioinformatics/bts692  1
2013 Berman HM, Kleywegt GJ, Nakamura H, Markley JL. The future of the protein data bank. Biopolymers. 99: 218-22. PMID 23023942 DOI: 10.1002/bip.22132  1
2012 Chae YK, Kim SH, Ellinger JJ, Markley JL. Tracing Metabolite Footsteps of Escherichia coli Along the Time Course of Recombinant Protein Expression by Two-Dimensional NMR Spectroscopy. Bulletin of the Korean Chemical Society. 33: 4041-4046. PMID 23794775 DOI: 10.5012/bkcs.2012.33.12.4041  1
2012 Dai Z, Tonelli M, Markley JL. Metamorphic protein IscU changes conformation by cis-trans isomerizations of two peptidyl-prolyl peptide bonds. Biochemistry. 51: 9595-602. PMID 23110687 DOI: 10.1021/bi301413y  1
2012 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 in Molecular Biology (Clifton, N.J.). 914: 47-63. PMID 22976022 DOI: 10.1007/978-1-62703-023-6_4  1
2012 Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, et al. In support of the BMRB. Nature Structural & Molecular Biology. 19: 854-60. PMID 22955930 DOI: 10.1038/nsmb.2371  1
2012 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. Journal of Biomolecular Nmr. 54: 169-79. PMID 22903636 DOI: 10.1007/s10858-012-9660-3  1
2012 Kim JH, Tonelli M, Frederick RO, Chow DC, Markley JL. Specialized Hsp70 chaperone (HscA) binds preferentially to the disordered form, whereas J-protein (HscB) binds preferentially to the structured form of the iron-sulfur cluster scaffold protein (IscU). The Journal of Biological Chemistry. 287: 31406-13. PMID 22782893 DOI: 10.1074/jbc.M112.352617  1
2012 Zhu J, Rao H, Tonelli M, Westler WM, Singarapu KK, Markley JL, DeLuca HF, Assadi-Porter FM. Efficient stable isotope labeling and purification of vitamin D receptor from inclusion bodies. Protein Expression and Purification. 85: 25-31. PMID 22750673 DOI: 10.1016/j.pep.2012.06.012  1
2012 Kim JH, Tonelli M, Kim T, Markley JL. Three-dimensional structure and determinants of stability of the iron-sulfur cluster scaffold protein IscU from Escherichia coli. Biochemistry. 51: 5557-63. PMID 22734684 DOI: 10.1021/bi300579p  1
2012 Chae YK, Tonneli M, Markley JL. Recombinant production, isotope labeling and purification of ENOD40B: a plant peptide hormone. Protein and Peptide Letters. 19: 808-11. PMID 22702897 DOI: 10.2174/092986612801619624  1
2012 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. Journal of Biomolecular Nmr. 53: 311-20. PMID 22689068 DOI: 10.1007/s10858-012-9641-6  1
2012 Fleischhacker AS, Stubna A, Hsueh KL, Guo Y, Teter SJ, Rose JC, Brunold TC, Markley JL, Münck E, Kiley PJ. Characterization of the [2Fe-2S] cluster of Escherichia coli transcription factor IscR. Biochemistry. 51: 4453-62. PMID 22583201 DOI: 10.1021/bi3003204  1
2012 Bahrami A, Tonelli M, Sahu SC, Singarapu KK, Eghbalnia HR, Markley JL. Robust, integrated computational control of NMR experiments to achieve optimal assignment by ADAPT-NMR. Plos One. 7: e33173. PMID 22427982 DOI: 10.1371/journal.pone.0033173  1
2012 Berman HM, Kleywegt GJ, Nakamura H, Markley JL. The Protein Data Bank at 40: reflecting on the past to prepare for the future. Structure (London, England : 1993). 20: 391-6. PMID 22404998 DOI: 10.1016/j.str.2012.01.010  1
2012 Pal A, Fontanilla D, Gopalakrishnan A, Chae YK, Markley JL, Ruoho AE. The sigma-1 receptor protects against cellular oxidative stress and activates antioxidant response elements. European Journal of Pharmacology. 682: 12-20. PMID 22381068 DOI: 10.1016/j.ejphar.2012.01.030  1
2012 Bahrami A, Clos LJ, Markley JL, Butcher SE, Eghbalnia HR. RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts. Journal of Biomolecular Nmr. 52: 289-302. PMID 22359049 DOI: 10.1007/s10858-012-9603-z  1
2012 Hansen DF, Westler WM, Kunze MB, Markley JL, Weinhold F, Led JJ. Accurate structure and dynamics of the metal-site of paramagnetic metalloproteins from NMR parameters using natural bond orbitals. Journal of the American Chemical Society. 134: 4670-82. PMID 22329704 DOI: 10.1021/ja209348p  1
2012 Ellinger JJ, Miller DC, Lewis IA, Markley JL. Semiautomated device for batch extraction of metabolites from tissue samples. Analytical Chemistry. 84: 1809-12. PMID 22292466 DOI: 10.1021/ac203390v  1
2012 Kim JH, Tonelli M, Markley JL. Disordered form of the scaffold protein IscU is the substrate for iron-sulfur cluster assembly on cysteine desulfurase. Proceedings of the National Academy of Sciences of the United States of America. 109: 454-9. PMID 22203963 DOI: 10.1073/pnas.1114372109  1
2012 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 Research. 40: D519-24. PMID 22139937 DOI: 10.1093/nar/gkr1134  1
2012 Rajbhandari P, Finn G, Solodin NM, Singarapu KK, Sahu SC, Markley JL, Kadunc KJ, Ellison-Zelski SJ, Kariagina A, Haslam SZ, Lu KP, Alarid ET. Regulation of estrogen receptor α N-terminus conformation and function by peptidyl prolyl isomerase Pin1. Molecular and Cellular Biology. 32: 445-57. PMID 22064478 DOI: 10.1128/MCB.06073-11  1
2012 Lee W, Markley JL. PACSY database, a relational database management system for Protein structure and nuclear Magnetic Resonance chemical shift analysis Proceedings - 2012 Ieee International Conference On Bioinformatics and Biomedicine Workshops, Bibmw 2012. 930-932. DOI: 10.1109/BIBMW.2012.6470267  1
2012 Lewis IA, Shortreed MR, Hegeman AD, Markley JL. Novel NMR and MS approaches to metabolomics Methods in Pharmacology and Toxicology. 17: 199-230. DOI: 10.1007/978-1-61779-618-0_7  1
2011 Chae YK, Singarapu K, Westler WM, Markley JL. Recombinant Expression, Isotope Labeling and Purification of the Vitamin D Receptor Binding Peptide. Bulletin of the Korean Chemical Society. 32: 4337-4340. PMID 23626398 DOI: 10.5012/bkcs.2011.32.12.4337  1
2011 Singarapu KK, Zhu J, Tonelli M, Rao H, Assadi-Porter FM, Westler WM, DeLuca HF, Markley JL. Ligand-specific structural changes in the vitamin D receptor in solution. Biochemistry. 50: 11025-33. PMID 22112050 DOI: 10.1021/bi201637p  1
2011 Hu K, Ellinger JJ, Chylla RA, Markley JL. Measurement of absolute concentrations of individual compounds in metabolite mixtures by gradient-selective time-zero 1H-13C HSQC with two concentration references and fast maximum likelihood reconstruction analysis. Analytical Chemistry. 83: 9352-60. PMID 22029275 DOI: 10.1021/ac201948f  1
2011 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 α-helical. The Journal of Biological Chemistry. 286: 43447-53. PMID 21998307 DOI: 10.1074/jbc.M111.306464  1
2011 Tonelli M, Singarapu KK, Makino S, Sahu SC, Matsubara Y, Endo Y, Kainosho M, Markley JL. Hydrogen exchange during cell-free incorporation of deuterated amino acids and an approach to its inhibition. Journal of Biomolecular Nmr. 51: 467-76. PMID 21984356 DOI: 10.1007/s10858-011-9575-4  1
2011 Hu K, Wyche TP, Bugni TS, Markley JL. Selective quantification by 2D HSQC0 spectroscopy of thiocoraline in an extract from a sponge-derived Verrucosispora sp. Journal of Natural Products. 74: 2295-8. PMID 21923106 DOI: 10.1021/np200503c  1
2011 Dittli SM, Rao H, Tonelli M, Quijada J, Markley JL, Max M, Assadi-Porter F, Maillet E. Structural role of the terminal disulfide bond in the sweetness of brazzein. Chemical Senses. 36: 821-30. PMID 21765060 DOI: 10.1093/chemse/bjr057  1
2011 Chylla RA, Hu K, Ellinger JJ, Markley JL. Deconvolution of two-dimensional NMR spectra by fast maximum likelihood reconstruction: application to quantitative metabolomics. Analytical Chemistry. 83: 4871-80. PMID 21526800 DOI: 10.1021/ac200536b  1
2011 Lee W, Kim JH, Westler WM, Markley JL. PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination. Bioinformatics (Oxford, England). 27: 1727-8. PMID 21511715 DOI: 10.1093/bioinformatics/btr200  1
2011 Ellinger JJ, Lewis IA, Markley JL. Role of aminotransferases in glutamate metabolism of human erythrocytes. Journal of Biomolecular Nmr. 49: 221-9. PMID 21380856 DOI: 10.1007/s10858-011-9481-9  1
2011 Hu K, Westler WM, Markley JL. Two-dimensional concurrent HMQC-COSY as an approach for small molecule chemical shift assignment and compound identification. Journal of Biomolecular Nmr. 49: 291-6. PMID 21373839 DOI: 10.1007/s10858-011-9494-4  1
2011 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. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 209: 167-73. PMID 21316281 DOI: 10.1016/j.jmr.2011.01.005  1
2011 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 Biochemistry. 12: 3. PMID 21269500 DOI: 10.1186/1471-2091-12-3  1
2011 Hallows WC, Yu W, Smith BC, Devries MK, Devires MK, Ellinger JJ, Someya S, Shortreed MR, Prolla T, Markley JL, Smith LM, Zhao S, Guan KL, Denu JM. Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction. Molecular Cell. 41: 139-49. PMID 21255725 DOI: 10.1016/j.molcel.2011.01.002  1
2011 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)). Journal of the American Chemical Society. 133: 1662-5. PMID 21247157 DOI: 10.1021/ja1095304  1
2011 Westler WM, Lin IJ, Perczel A, Weinhold F, Markley JL. Hyperfine-shifted 13C resonance assignments in an iron-sulfur protein with quantum chemical verification: aliphatic C-H···S 3-center-4-electron interactions. Journal of the American Chemical Society. 133: 1310-6. PMID 21207994 DOI: 10.1021/ja1049059  1
2010 Neerathilingam M, Markley JL. Auto-induction medium containing glyphosate for high-level incorporation of unusual aromatic amino acids into proteins. Biotechniques. 49: 659-61. PMID 20854268 DOI: 10.2144/000113491  1
2010 Qasim MA, Song J, Markley JL, Laskowski M. Cleavage of peptide bonds bearing ionizable amino acids at P(1) by serine proteases with hydrophobic S(1) pocket. Biochemical and Biophysical Research Communications. 400: 507-10. PMID 20800580 DOI: 10.1016/j.bbrc.2010.08.078  1
2010 Hsueh KL, Westler WM, Markley JL. NMR investigations of the Rieske protein from Thermus thermophilus support a coupled proton and electron transfer mechanism. Journal of the American Chemical Society. 132: 7908-18. PMID 20496909 DOI: 10.1021/ja1026387  1
2010 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. Analytical Chemistry. 82: 4558-63. PMID 20459129 DOI: 10.1021/ac100565b  1
2010 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). The Journal of Biological Chemistry. 285: 17046-53. PMID 20356842 DOI: 10.1074/jbc.M110.101154  1
2010 Assadi-Porter FM, Maillet EL, Radek JT, Quijada J, Markley JL, Max M. Key amino acid residues involved in multi-point binding interactions between brazzein, a sweet protein, and the T1R2-T1R3 human sweet receptor. Journal of Molecular Biology. 398: 584-99. PMID 20302879 DOI: 10.1016/j.jmb.2010.03.017  1
2010 Makino S, Goren MA, Fox BG, Markley JL. Cell-free protein synthesis technology in NMR high-throughput structure determination. Methods in Molecular Biology (Clifton, N.J.). 607: 127-47. PMID 20204854 DOI: 10.1007/978-1-60327-331-2_12  1
2010 Berman HM, Kleywegt GJ, Nakamura H, Markley JL, Burley SK. Safeguarding the integrity of protein archive. Nature. 463: 425. PMID 20110969 DOI: 10.1038/463425c  1
2010 Ulijasz AT, Cornilescu G, Cornilescu CC, Zhang J, Rivera M, Markley JL, Vierstra RD. Structural basis for the photoconversion of a phytochrome to the activated Pfr form. Nature. 463: 250-4. PMID 20075921 DOI: 10.1038/nature08671  1
2010 Zornetzer GA, Tanem J, Fox BG, Markley JL. The length of the bound fatty acid influences the dynamics of the acyl carrier protein and the stability of the thioester bond. Biochemistry. 49: 470-7. PMID 20014832 DOI: 10.1021/bi9014659  1
2010 Goodfellow BJ, Duarte IC, Macedo AL, Volkman BF, Nunes SG, Moura I, Markley JL, Moura JJ. An NMR structural study of nickel-substituted rubredoxin. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 15: 409-20. PMID 19997764 DOI: 10.1007/s00775-009-0613-6  1
2010 Assadi-Porter FM, Tonelli M, Maillet EL, Markley JL, Max M. Interactions between the human sweet-sensing T1R2-T1R3 receptor and sweeteners detected by saturation transfer difference NMR spectroscopy. Biochimica Et Biophysica Acta. 1798: 82-6. PMID 19664591 DOI: 10.1016/j.bbamem.2009.07.021  1
2009 Lewis IA, Campanella ME, Markley JL, Low PS. Role of band 3 in regulating metabolic flux of red blood cells. Proceedings of the National Academy of Sciences of the United States of America. 106: 18515-20. PMID 19846781 DOI: 10.1073/pnas.0905999106  1
2009 Lewis IA, Schommer SC, Markley JL. rNMR: open source software for identifying and quantifying metabolites in NMR spectra. Magnetic Resonance in Chemistry : Mrc. 47: S123-6. PMID 19821464 DOI: 10.1002/mrc.2526  1
2009 Doreleijers JF, Vranken WF, Schulte C, Lin J, Wedell JR, Penkett CJ, Vuister GW, Vriend G, Markley JL, Ulrich EL. The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries. Journal of Biomolecular Nmr. 45: 389-96. PMID 19809795 DOI: 10.1007/s10858-009-9378-z  1
2009 Lin IJ, Xia B, King DS, Machonkin TE, Westler WM, Markley JL. Hyperfine-shifted (13)C and (15)N NMR signals from Clostridium pasteurianum rubredoxin: extensive assignments and quantum chemical verification. Journal of the American Chemical Society. 131: 15555-63. PMID 19799419 DOI: 10.1021/ja905928x  1
2009 Tonelli M, Masterson LR, Cornilescu G, Markley JL, Veglia G. One-sample approach to determine the relative orientations of proteins in ternary and binary complexes from residual dipolar coupling measurements. Journal of the American Chemical Society. 131: 14138-9. PMID 19764746 DOI: 10.1021/ja904766g  1
2009 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 (Oxford, England). 25: 2085-7. PMID 19497931 DOI: 10.1093/bioinformatics/btp345  1
2009 Kim JH, Füzéry AK, Tonelli M, Ta DT, Westler WM, Vickery LE, Markley JL. Structure and dynamics of the iron-sulfur cluster assembly scaffold protein IscU and its interaction with the cochaperone HscB. Biochemistry. 48: 6062-71. PMID 19492851 DOI: 10.1021/bi9002277  1
2009 Wang L, Markley JL. Empirical correlation between protein backbone 15N and 13C secondary chemical shifts and its application to nitrogen chemical shift re-referencing. Journal of Biomolecular Nmr. 44: 95-9. PMID 19436955 DOI: 10.1007/s10858-009-9324-0  1
2009 Montelione GT, Arrowsmith C, Girvin ME, Kennedy MA, Markley JL, Powers R, Prestegard JH, Szyperski T. Unique opportunities for NMR methods in structural genomics. Journal of Structural and Functional Genomics. 10: 101-6. PMID 19288278 DOI: 10.1007/s10969-009-9064-0  1
2009 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 Computational Biology. 5: e1000307. PMID 19282963 DOI: 10.1371/journal.pcbi.1000307  1
2009 Markley JL, Aceti DJ, Bingman CA, Fox BG, Frederick RO, Makino S, Nichols KW, Phillips GN, Primm JG, Sahu SC, Vojtik FC, Volkman BF, Wrobel RL, Zolnai Z. The Center for Eukaryotic Structural Genomics. Journal of Structural and Functional Genomics. 10: 165-79. PMID 19130299 DOI: 10.1007/s10969-008-9057-4  1
2008 Takeda M, Sugimori N, Torizawa T, Terauchi T, Ono AM, Yagi H, Yamaguchi Y, Kato K, Ikeya T, Jee J, Güntert P, Aceti DJ, Markley JL, Kainosho M. Structure of the putative 32 kDa myrosinase-binding protein from Arabidopsis (At3g16450.1) determined by SAIL-NMR. The Febs Journal. 275: 5873-84. PMID 19021763 DOI: 10.1111/j.1742-4658.2008.06717.x  1
2008 Song J, McGivern JV, Nichols KW, Markley JL, Sheets MD. Structural basis for RNA recognition by a type II poly(A)-binding protein. Proceedings of the National Academy of Sciences of the United States of America. 105: 15317-22. PMID 18824697 DOI: 10.1073/pnas.0801274105  1
2008 Cornilescu G, Ulijasz AT, Cornilescu CC, Markley JL, Vierstra RD. Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state. Journal of Molecular Biology. 383: 403-13. PMID 18762196 DOI: 10.1016/j.jmb.2008.08.034  1
2008 Bitto E, Bingman CA, Bittova L, Kondrashov DA, Bannen RM, Fox BG, Markley JL, Phillips GN. Structure of human J-type co-chaperone HscB reveals a tetracysteine metal-binding domain. The Journal of Biological Chemistry. 283: 30184-92. PMID 18713742 DOI: 10.1074/jbc.M804746200  1
2008 Füzéry AK, Tonelli M, Ta DT, Cornilescu G, Vickery LE, Markley JL. Solution structure of the iron-sulfur cluster cochaperone HscB and its binding surface for the iron-sulfur assembly scaffold protein IscU. Biochemistry. 47: 9394-404. PMID 18702525 DOI: 10.1021/bi800502r  1
2008 Haquin S, Oeuillet E, Pajon A, Harris M, Jones AT, van Tilbeurgh H, Markley JL, Zolnai Z, Poupon A. Data management in structural genomics: an overview. Methods in Molecular Biology (Clifton, N.J.). 426: 49-79. PMID 18542857 DOI: 10.1007/978-1-60327-058-8_4  1
2008 Masterson LR, Tonelli M, Markley JL, Veglia G. Simultaneous detection and deconvolution of congested NMR spectra containing three isotopically labeled species. Journal of the American Chemical Society. 130: 7818-9. PMID 18512910 DOI: 10.1021/ja802701w  1
2008 Assadi-Porter FM, Tonelli M, Maillet E, Hallenga K, Benard O, Max M, Markley JL. Direct NMR detection of the binding of functional ligands to the human sweet receptor, a heterodimeric family 3 GPCR. Journal of the American Chemical Society. 130: 7212-3. PMID 18481853 DOI: 10.1021/ja8016939  1
2008 Aceti DJ, Bitto E, Yakunin AF, Proudfoot M, Bingman CA, Frederick RO, Sreenath HK, Vojtik FC, Wrobel RL, Fox BG, Markley JL, Phillips GN. Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000. Proteins. 73: 241-53. PMID 18433060 DOI: 10.1002/prot.22041  1
2008 Juranić N, Dannenberg JJ, Cornilescu G, Salvador P, Atanasova E, Ahn HC, Macura S, Markley JL, Prendergast FG. Structural dependencies of protein backbone 2JNC' couplings. Protein Science : a Publication of the Protein Society. 17: 768-76. PMID 18305196 DOI: 10.1110/ps.073331608  1
2008 Cornilescu CC, Porter FW, Zhao KQ, Palmenberg AC, Markley JL. NMR structure of the mengovirus Leader protein zinc-finger domain. Febs Letters. 582: 896-900. PMID 18291103 DOI: 10.1016/j.febslet.2008.02.023  1
2008 Markley JL, Ulrich EL, Berman HM, Henrick K, Nakamura H, Akutsu H. BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): New policies affecting biomolecular NMR depositions Journal of Biomolecular Nmr. 40: 153-155. PMID 18288446 DOI: 10.1007/s10858-008-9221-y  1
2008 Song J, Bettendorff L, Tonelli M, Markley JL. Structural basis for the catalytic mechanism of mammalian 25-kDa thiamine triphosphatase. The Journal of Biological Chemistry. 283: 10939-48. PMID 18276586 DOI: 10.1074/jbc.M709675200  1
2008 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. Nature Biotechnology. 26: 162-4. PMID 18259166 DOI: 10.1038/nbt0208-162  1
2008 Song J, Guo LW, Muradov H, Artemyev NO, Ruoho AE, Markley JL. Intrinsically disordered gamma-subunit of cGMP phosphodiesterase encodes functionally relevant transient secondary and tertiary structure. Proceedings of the National Academy of Sciences of the United States of America. 105: 1505-10. PMID 18230733 DOI: 10.1073/pnas.0709558105  1
2008 Assadi-Porter FM, Patry S, Markley JL. Efficient and rapid protein expression and purification of small high disulfide containing sweet protein brazzein in E. coli. Protein Expression and Purification. 58: 263-8. PMID 18221889 DOI: 10.1016/j.pep.2007.11.009  1
2008 Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, et al. Remediation of the protein data bank archive. Nucleic Acids Research. 36: D426-33. PMID 18073189 DOI: 10.1093/nar/gkm937  1
2008 Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, ... Markley JL, et al. BioMagResBank. Nucleic Acids Research. 36: D402-8. PMID 17984079 DOI: 10.1093/nar/gkm957  1
2008 Assadi-Porter F, Tonelli M, Radek JT, Cornilescu CC, Markley JL. How sweet it is: Detailed molecular and functional studies of Brazzein, a sweet protein and its analogs Acs Symposium Series. 979: 560-572. DOI: 10.1021/bk-2008-0979.ch036  1
2008 Džakula Z, Westler WM, Markley JL. Corrigendum to "Continuous probability distribution (CUPID) analysis of potentials for internal rotations" [J. Magn. Res. B 111 (1996) 109-126] (DOI:10.1006/jmrb.1996.0070) Journal of Magnetic Resonance. 191: 169. DOI: 10.1016/j.jmr.2008.01.005  1
2007 Pan X, Wesenberg GE, Markley JL, Fox BG, Phillips GN, Bingman CA. A graphical approach to tracking and reporting target status in structural genomics. Journal of Structural and Functional Genomics. 8: 209-16. PMID 18236171 DOI: 10.1007/s10969-007-9037-0  1
2007 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. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 157-68. PMID 17990489  1
2007 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. Analytical Chemistry. 79: 9385-90. PMID 17985927 DOI: 10.1021/ac071583z  1
2007 Frederick RO, Bergeman L, Blommel PG, Bailey LJ, McCoy JG, Song J, Meske L, Bingman CA, Riters M, Dillon NA, Kunert J, Yoon JW, Lim A, Cassidy M, Bunge J, ... ... Markley JL, et al. Small-scale, semi-automated purification of eukaryotic proteins for structure determination. Journal of Structural and Functional Genomics. 8: 153-66. PMID 17985212 DOI: 10.1007/s10969-007-9032-5  1
2007 Cornilescu G, Hadley EB, Woll MG, Markley JL, Gellman SH, Cornilescu CC. Solution structure of a small protein containing a fluorinated side chain in the core. Protein Science : a Publication of the Protein Society. 16: 2089. PMID 17915350 DOI: 10.1110/ps.062557707  1
2007 Wang L, Eghbalnia HR, Markley JL. Nearest-neighbor effects on backbone alpha and beta carbon chemical shifts in proteins. Journal of Biomolecular Nmr. 39: 247-57. PMID 17899393 DOI: 10.1007/s10858-007-9193-3  1
2007 Tonelli M, Masterson LR, Hallenga K, Veglia G, Markley JL. Carbonyl carbon label selective (CCLS) 1H-15N HSQC experiment for improved detection of backbone 13C-15N cross peaks in larger proteins. Journal of Biomolecular Nmr. 39: 177-85. PMID 17828465 DOI: 10.1007/s10858-007-9185-3  1
2007 Phillips GN, Fox BG, Markley JL, Volkman BF, Bae E, Bitto E, Bingman CA, Frederick RO, McCoy JG, Lytle BL, Pierce BS, Song J, Twigger SN. Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics. Journal of Structural and Functional Genomics. 8: 73-84. PMID 17786587 DOI: 10.1007/s10969-007-9023-6  1
2007 Hegeman AD, Schulte CF, Cui Q, Lewis IA, Huttlin EL, Eghbalnia H, Harms AC, Ulrich EL, Markley JL, Sussman MR. Stable isotope assisted assignment of elemental compositions for metabolomics. Analytical Chemistry. 79: 6912-21. PMID 17708672 DOI: 10.1021/ac070346t  1
2007 Markley JL. NMR analysis goes nano. Nature Biotechnology. 25: 750-1. PMID 17621301 DOI: 10.1038/nbt0707-750  1
2007 Cornilescu G, Bahrami A, Tonelli M, Markley JL, Eghbalnia HR. HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections. Journal of Biomolecular Nmr. 38: 341-51. PMID 17610130 DOI: 10.1007/s10858-007-9173-7  1
2007 Song J, Zhao KQ, Newman CL, Vinarov DA, Markley JL. Solution structure of human sorting nexin 22. Protein Science : a Publication of the Protein Society. 16: 807-14. PMID 17400918 DOI: 10.1110/ps.072752407  1
2007 Song J, Markley JL. Cautionary tail: the presence of an N-terminal tag on dynein light-chain Roadblock/LC7 affects its interaction with a functional partner. Protein and Peptide Letters. 14: 265-8. PMID 17346231 DOI: 10.2174/092986607780090801  1
2007 Song J, Markley JL. Three-dimensional structure determined for a subunit of human tRNA splicing endonuclease (Sen15) reveals a novel dimeric fold. Journal of Molecular Biology. 366: 155-64. PMID 17166513 DOI: 10.1016/j.jmb.2006.11.024  1
2007 Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Research. 35: D301-3. PMID 17142228 DOI: 10.1093/nar/gkl971  1
2007 Cornilescu G, Hadley EB, Woll MG, Markley JL, Gellman SH, Cornilescu CC. Solution structure of a small protein containing a fluorinated side chain in the core. Protein Science : a Publication of the Protein Society. 16: 14-9. PMID 17123960 DOI: 10.1110/ps.062557707  1
2007 Guo LW, Assadi-Porter FM, Grant JE, Wu H, Markley JL, Ruoho AE. One-step purification of bacterially expressed recombinant transducin alpha-subunit and isotopically labeled PDE6 gamma-subunit for NMR analysis. Protein Expression and Purification. 51: 187-97. PMID 16938469 DOI: 10.1016/j.pep.2006.07.012  1
2007 Wrobel RL, Bingman CA, Jeon WB, Song J, Vinarov DA, Frederick RO, Aceti DJ, Sreenath HK, Zolnai Z, Vojtik FC, Bitto E, Fox BG, Phillips GN, Markley JL. Structural Proteomics Plant Proteomics. 99-128. DOI: 10.1002/9780470988879.ch5  1
2006 Vinarov DA, Newman CL, Tyler EM, Markley JL, Shahan MN. Wheat germ cell-free expression system for protein production. Current Protocols in Protein Science / Editorial Board, John E. Coligan ... [Et Al.]. Unit 5.18. PMID 18429309 DOI: 10.1002/0471140864.ps0518s44  1
2006 Song J, Lee MS, Carlberg I, Vener AV, Markley JL. Micelle-induced folding of spinach thylakoid soluble phosphoprotein of 9 kDa and its functional implications. Biochemistry. 45: 15633-43. PMID 17176085 DOI: 10.1021/bi062148m  1
2006 Singh S, Hager MH, Zhang C, Griffith BR, Lee MS, Hallenga K, Markley JL, Thorson JS. Structural insight into the self-sacrifice mechanism of enediyne resistance. Acs Chemical Biology. 1: 451-60. PMID 17168523 DOI: 10.1021/cb6002898  1
2006 Tyler RC, Bitto E, Berndsen CE, Bingman CA, Singh S, Lee MS, Wesenberg GE, Denu JM, Phillips GN, Markley JL. Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family. Biochemistry. 45: 14325-36. PMID 17128971 DOI: 10.1021/bi0612059  1
2006 Cornilescu G, Vinarov DA, Tyler EM, Markley JL, Cornilescu CC. Solution structure of a single-domain thiosulfate sulfurtransferase from Arabidopsis thaliana. Protein Science : a Publication of the Protein Society. 15: 2836-41. PMID 17088324 DOI: 10.1110/ps.062395206  1
2006 Ahn HC, Le YT, Nagchowdhuri PS, Derose EF, Putnam-Evans C, London RE, Markley JL, Lim KH. NMR characterizations of an amyloidogenic conformational ensemble of the PI3K SH3 domain. Protein Science : a Publication of the Protein Society. 15: 2552-7. PMID 17001038 DOI: 10.1110/ps.062154306  1
2006 Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL, Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, Heymann B, Jones D, ... Markley JL, et al. Outcome of a Workshop on Archiving Structural Models of Biological Macromolecules Structure. 14: 1211-1217. PMID 16955948 DOI: 10.1016/j.str.2006.06.005  1
2006 Vinarov DA, Loushin Newman CL, Markley JL. Wheat germ cell-free platform for eukaryotic protein production. The Febs Journal. 273: 4160-9. PMID 16930128 DOI: 10.1111/j.1742-4658.2006.05434.x  1
2006 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. Journal of the American Chemical Society. 128: 10672-3. PMID 16910649 DOI: 10.1021/ja0627388  1
2006 Wang L, Eghbalnia HR, Markley JL. Probabilistic approach to determining unbiased random-coil carbon-13 chemical shift values from the protein chemical shift database. Journal of Biomolecular Nmr. 35: 155-65. PMID 16799859 DOI: 10.1007/s10858-006-9022-0  1
2006 Lytle BL, Peterson FC, Tyler EM, Newman CL, Vinarov DA, Markley JL, Volkman BF. Solution structure of Arabidopsis thaliana protein At5g39720.1, a member of the AIG2-like protein family. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 62: 490-3. PMID 16754964 DOI: 10.1107/S1744309106015946  1
2006 Zornetzer GA, Fox BG, Markley JL. Solution structures of spinach acyl carrier protein with decanoate and stearate. Biochemistry. 45: 5217-27. PMID 16618110 DOI: 10.1021/bi052062d  1
2006 Ahn HC, Juranić N, Macura S, Markley JL. Three-dimensional structure of the water-insoluble protein crambin in dodecylphosphocholine micelles and its minimal solvent-exposed surface. Journal of the American Chemical Society. 128: 4398-404. PMID 16569017 DOI: 10.1021/ja057773d  1
2006 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. Proceedings of the National Academy of Sciences of the United States of America. 103: 5302-7. PMID 16567646 DOI: 10.1073/pnas.0507416103  1
2006 Cui Q, Thorgersen MP, Westler WM, Markley JL, Downs DM. Solution structure of YggX: a prokaryotic protein involved in Fe(II) trafficking. Proteins. 62: 578-86. PMID 16329120 DOI: 10.1002/prot.20781  1
2006 Zornetzer GA, White RD, Markley JL, Fox BG. Preparation of isotopically labeled spinach acyl-acyl carrier protein for NMR structural studies. Protein Expression and Purification. 46: 446-55. PMID 16325425 DOI: 10.1016/j.pep.2005.10.015  1
2005 Bitto E, Bingman CA, Allard ST, Wesenberg GE, Aceti DJ, Wrobel RL, Frederick RO, Sreenath H, Vojtik FC, Jeon WB, Newman CS, Primm J, Sussman MR, Fox BG, Markley JL, et al. The structure at 2.4 A resolution of the protein from gene locus At3g21360, a putative Fe(II)/2-oxoglutarate-dependent enzyme from Arabidopsis thaliana. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 61: 469-72. PMID 16511070 DOI: 10.1107/S1744309105011565  1
2005 Song J, Tyler RC, Lee MS, Tyler EM, Markley JL. Solution structure of isoform 1 of Roadblock/LC7, a light chain in the dynein complex. Journal of Molecular Biology. 354: 1043-51. PMID 16289575 DOI: 10.1016/j.jmb.2005.10.017  1
2005 Chae YK, Lee K, Markley JL. 1H, 15N and 13C resonance assignments of a protein involved in the autophagy process, At4g21980.1 from Arabidopsis thaliana. Journal of Biomolecular Nmr. 32: 337. PMID 16211491 DOI: 10.1007/s10858-005-0058-3  1
2005 Song J, Zhao Q, Lee MS, Markley JL. 1H, 15N and 13C resonance assignments of the putative Bet v 1 family protein At1g24000.1 from Arabidopsis thaliana. Journal of Biomolecular Nmr. 32: 335. PMID 16211487 DOI: 10.1007/s10858-005-8205-4  1
2005 Lin IJ, Gebel EB, Machonkin TE, Westler WM, Markley JL. Changes in hydrogen-bond strengths explain reduction potentials in 10 rubredoxin variants. Proceedings of the National Academy of Sciences of the United States of America. 102: 14581-6. PMID 16199518 DOI: 10.1073/pnas.0505521102  1
2005 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. Journal of Molecular Biology. 353: 540-55. PMID 16181635 DOI: 10.1016/j.jmb.2005.08.030  1
2005 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 Science : a Publication of the Protein Society. 14: 2601-9. PMID 16155204 DOI: 10.1110/ps.051579205  1
2005 Andjus RK, Dzakula Z, Markley JL, Macura S. Brain energetics and tolerance to anoxia in deep hypothermia. Annals of the New York Academy of Sciences. 1048: 10-35. PMID 16154918 DOI: 10.1196/annals.1342.003  1
2005 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. Journal of the American Chemical Society. 127: 12528-36. PMID 16144400 DOI: 10.1021/ja052120i  1
2005 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). Journal of Biomolecular Nmr. 32: 219-33. PMID 16132822 DOI: 10.1007/s10858-005-7944-6  1
2005 Uchida K, Markley JL, Kainosho M. 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). Biochemistry. 44: 11811-20. PMID 16128582 DOI: 10.1021/bi050467s  1
2005 Zhao Q, Song J, Jin Z, Danilova V, Hellekant G, Markley JL. Probing the sweet determinants of brazzein: wild-type brazzein and a tasteless variant, brazzein-ins(R18a-I18b), exhibit different pH-dependent NMR chemical shifts. Biochemical and Biophysical Research Communications. 335: 256-63. PMID 16105551 DOI: 10.1016/j.bbrc.2005.07.049  1
2005 Fox BG, Malone TE, Johnson KA, Madson SE, Aceti D, Bingman CA, Blommel PG, Buchan B, Burns B, Cao J, Cornilescu C, Doreleijers J, Ellefson J, Frederick R, Geetha H, ... ... Markley JL, et al. X-ray structure of Arabidopsis At1g77680, 12-oxophytodienoate reductase isoform 1. Proteins. 61: 206-8. PMID 16080145 DOI: 10.1002/prot.20533  1
2005 Singh S, Tonelli M, Tyler RC, Bahrami A, Lee MS, Markley JL. Three-dimensional structure of the AAH26994.1 protein from Mus musculus, a putative eukaryotic Urm1. Protein Science : a Publication of the Protein Society. 14: 2095-102. PMID 16046629 DOI: 10.1110/ps.051577605  1
2005 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. Journal of Biomolecular Nmr. 32: 71-81. PMID 16041485 DOI: 10.1007/s10858-005-5705-1  1
2005 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. Journal of Biomolecular Nmr. 32: 13-22. PMID 16041479 DOI: 10.1007/s10858-005-1717-0  1
2005 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. Journal of Biomolecular Nmr. 32: 1-12. PMID 16041478 DOI: 10.1007/s10858-005-2195-0  1
2005 Peterson FC, Lytle BL, Sampath S, Vinarov D, Tyler E, Shahan M, Markley JL, Volkman BF. Solution structure of thioredoxin h1 from Arabidopsis thaliana. Protein Science : a Publication of the Protein Society. 14: 2195-200. PMID 15987893 DOI: 10.1110/ps.051477905  1
2005 Vinarov DA, Markley JL. High-throughput automated platform for nuclear magnetic resonance-based structural proteomics. Expert Review of Proteomics. 2: 49-55. PMID 15966852 DOI: 10.1586/14789450.2.1.49  1
2005 Machonkin TE, Westler WM, Markley JL. Paramagnetic NMR spectroscopy and density functional calculations in the analysis of the geometric and electronic structures of iron-sulfur proteins. Inorganic Chemistry. 44: 779-97. PMID 15859246 DOI: 10.1021/ic048624j  1
2005 Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CA, Nabuurs SB, Güntert P, Livny M, Markley JL, Nilges M, Ulrich EL, Kaptein R, Bonvin AM. RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins. 59: 662-72. PMID 15822098 DOI: 10.1002/prot.20408  1
2005 Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED. The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins. 59: 687-96. PMID 15815974 DOI: 10.1002/prot.20449  1
2005 Oldfield CJ, Ulrich EL, Cheng Y, Dunker AK, Markley JL. Addressing the intrinsic disorder bottleneck in structural proteomics. Proteins. 59: 444-53. PMID 15789434 DOI: 10.1002/prot.20446  1
2005 Tyler RC, Aceti DJ, Bingman CA, Cornilescu CC, Fox BG, Frederick RO, Jeon WB, Lee MS, Newman CS, Peterson FC, Phillips GN, Shahan MN, Singh S, Song J, Sreenath HK, ... ... Markley JL, et al. Comparison of cell-based and cell-free protocols for producing target proteins from the Arabidopsis thaliana genome for structural studies. Proteins. 59: 633-43. PMID 15789406 DOI: 10.1002/prot.20436  1
2005 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 Expression and Purification. 40: 268-78. PMID 15766868 DOI: 10.1016/j.pep.2004.12.024  1
2005 Stolc V, Samanta MP, Tongprasit W, Sethi H, Liang S, Nelson DC, Hegeman A, Nelson C, Rancour D, Bednarek S, Ulrich EL, Zhao Q, Wrobel RL, Newman CS, Fox BG, ... ... Markley JL, et al. Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proceedings of the National Academy of Sciences of the United States of America. 102: 4453-8. PMID 15755812 DOI: 10.1073/pnas.0408203102  1
2005 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 Science : a Publication of the Protein Society. 14: 1059-63. PMID 15741346 DOI: 10.1110/ps.041246805  1
2005 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. Chemical Senses. 30: i90-1. PMID 15738211 DOI: 10.1093/chemse/bjh128  1
2005 Malone TE, Madson SE, Wrobel RL, Jeon WB, Rosenberg NS, Johnson KA, Bingman CA, Smith DW, Phillips GN, Markley JL, Fox BG. X-ray structure of Arabidopsis At2g06050, 12-oxophytodienoate reductase isoform 3. Proteins. 58: 243-5. PMID 15468319 DOI: 10.1002/prot.20162  1
2005 Markley JL. Vision: Protein solution structure in three days or less?. Emerging methods will accelerate NMR structure determination of small proteins Scientist. 19: 36-37.  1
2004 Vinarov DA, Lytle BL, Peterson FC, Tyler EM, Volkman BF, Markley JL. Cell-free protein production and labeling protocol for NMR-based structural proteomics. Nature Methods. 1: 149-53. PMID 15782178 DOI: 10.1038/nmeth716  1
2004 Sugimori N, Torizawa T, Aceti DJ, Thao S, Markley JL, Kainosho M. (1)H, (13)C and (15)N backbone assignment of a 32 kDa hypothetical protein from Arabidopsis thaliana, At3g16450.1. Journal of Biomolecular Nmr. 30: 357-8. PMID 15756462 DOI: 10.1007/s10858-005-2324-9  1
2004 Song J, Vinarov D, Tyler EM, Shahan MN, Tyler RC, Markley JL. Hypothetical protein At2g24940.1 from Arabidopsis thaliana has a cytochrome b5 like fold. Journal of Biomolecular Nmr. 30: 215-8. PMID 15702529  1
2004 Song J, Zhao Q, Thao S, Frederick RO, Markley JL. Solution structure of a calmodulin-like calcium-binding domain from Arabidopsis thaliana. Journal of Biomolecular Nmr. 30: 451-6. PMID 15630565 DOI: 10.1007/s10858-004-5356-7  1
2004 Skjeldal L, Peterson FC, Doreleijers JF, Moe LA, Pikus JD, Westler WM, Markley JL, Volkman BF, Fox BG. Solution structure of T4moC, the Rieske ferredoxin component of the toluene 4-monooxygenase complex. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 9: 945-53. PMID 15452777 DOI: 10.1007/s00775-004-0594-4  1
2004 Park IY, Eidsness MK, Lin IJ, Gebel EB, Youn B, Harley JL, Machonkin TE, Frederick RO, Markley JL, Smith ET, Ichiye T, Kang C. Crystallographic studies of V44 mutants of Clostridium pasteurianum rubredoxin: effects of side-chain size on reduction potential. Proteins. 57: 618-25. PMID 15382226 DOI: 10.1002/prot.20243  1
2004 Lytle BL, Peterson FC, Qiu SH, Luo M, Zhao Q, Markley JL, Volkman BF. Solution structure of a ubiquitin-like domain from tubulin-binding cofactor B. The Journal of Biological Chemistry. 279: 46787-93. PMID 15364906 DOI: 10.1074/jbc.M409422200  1
2004 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, et al. Crystal structure of the protein from gene At3g17210 of Arabidopsis thaliana. Proteins. 57: 218-20. PMID 15326607 DOI: 10.1002/prot.20215  1
2004 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, ... ... Markley JL, et al. Crystal structure of At2g03760, a putative steroid sulfotransferase from Arabidopsis thaliana. Proteins. 57: 854-7. PMID 15317023 DOI: 10.1002/prot.20258  1
2004 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. Journal of Structural and Functional Genomics. 5: 87-93. PMID 15263847 DOI: 10.1023/B:JSFG.0000029205.65813.42  1
2004 Dmitriev OY, Abildgaard F, Markley JL, Fillingame RH. Backbone 1H, 15N and 13C assignments for the subunit a of the E. coli ATP synthase. Journal of Biomolecular Nmr. 29: 439-40. PMID 15213458 DOI: 10.1023/B:JNMR.0000032519.14221.20  1
2004 Cornilescu G, Cornilescu CC, Zhao Q, Frederick RO, Peterson FC, Thao S, Markley JL. Solution structure of a homodimeric hypothetical protein, At5g22580, a structural genomics target from Arabidopsis thaliana. Journal of Biomolecular Nmr. 29: 387-90. PMID 15213437 DOI: 10.1023/B:JNMR.0000032525.70677.16  1
2004 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. Journal of the American Chemical Society. 126: 5413-26. PMID 15113213 DOI: 10.1021/ja037077i  1
2004 Chae YK, Im H, Zhao Q, Doelling JH, Vierstra RD, Markley JL. Prevention of aggregation after refolding by balanced stabilization-destabilization: production of the Arabidopsis thaliana protein APG8a (At4g21980) for NMR structure determination. Protein Expression and Purification. 34: 280-3. PMID 15003262 DOI: 10.1016/j.pep.2003.11.007  1
2003 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. Journal of Structural and Functional Genomics. 4: 11-23. PMID 12943363 DOI: 10.1023/A:1024684404761  1
2003 Wu WJ, Vidugiris G, Mooberry ES, Westler WM, Markley JL. Mixing apparatus for preparing NMR samples under pressure. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 164: 84-91. PMID 12932460  1
2003 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. 42: 6380-91. PMID 12767219 DOI: 10.1021/bi034053f  1
2003 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. The Journal of Biological Chemistry. 278: 31331-9. PMID 12732626 DOI: 10.1074/jbc.M302663200  1
2003 Song J, Markley JL. Protein inhibitors of serine proteinases: role of backbone structure and dynamics in controlling the hydrolysis constant. Biochemistry. 42: 5186-94. PMID 12731859 DOI: 10.1021/bi034041u  1
2003 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. 42: 2847-56. PMID 12627950 DOI: 10.1021/bi0269512  1
2003 Lin IJ, Gebel EB, Machonkin TE, Westler WM, Markley JL. Correlation between hydrogen bond lengths and reduction potentials in Clostridium pasteurianum rubredoxin. Journal of the American Chemical Society. 125: 1464-5. PMID 12568591 DOI: 10.1021/ja028710n  1
2002 Zhao Q, Chae YK, Markley JL. NMR solution structure of ATTp, an Arabidopsis thaliana trypsin inhibitor. Biochemistry. 41: 12284-96. PMID 12369816 DOI: 10.1021/bi025702a  1
2002 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. Journal of the American Chemical Society. 124: 2497-505. PMID 11890798 DOI: 10.1021/ja0166904  1
2002 Kuloğlu ES, McCaslin DR, Markley JL, Volkman BF. Structural rearrangement of human lymphotactin, a C chemokine, under physiological solution conditions. The Journal of Biological Chemistry. 277: 17863-70. PMID 11889129 DOI: 10.1074/jbc.M200402200  1
2002 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. Journal of the American Chemical Society. 124: 1190-1. PMID 11841286 DOI: 10.1021/ja017169c  1
2002 Walkenhorst WF, Edwards JA, Markley JL, Roder H. Early formation of a beta hairpin during folding of staphylococcal nuclease H124L as detected by pulsed hydrogen exchange. Protein Science : a Publication of the Protein Society. 11: 82-91. PMID 11742125 DOI: 10.1110/ps.28202  1
2001 Wilkens SJ, Westler WM, Markley JL, Weinhold F. Natural J-coupling analysis: interpretation of scalar J-couplings in terms of natural bond orbitals. Journal of the American Chemical Society. 123: 12026-36. PMID 11724611 DOI: 10.1021/ja016284k  1
2001 Kuloglu ES, McCaslin DR, Kitabwalla M, Pauza CD, Markley JL, Volkman BF. Monomeric solution structure of the prototypical 'C' chemokine lymphotactin. Biochemistry. 40: 12486-96. PMID 11601972 DOI: 10.1021/bi011106p  1
2001 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). Journal of Molecular Recognition : Jmr. 14: 166-71. PMID 11391787 DOI: 10.1002/jmr.530  1
2001 Chen D, Zangl AL, Zhao Q, Markley JL, Zheng J, Bird IM, Magness RR. Ovine caveolin-1: cDNA cloning, E. coli expression, and association with endothelial nitric oxide synthase. Molecular and Cellular Endocrinology. 175: 41-56. PMID 11325515 DOI: 10.1016/S0303-7207(01)00403-8  1
2001 Hemmi H, Studts JM, Chae YK, Song J, Markley JL, Fox BG. Solution structure of the toluene 4-monooxygenase effector protein (T4moD). Biochemistry. 40: 3512-24. PMID 11297417 DOI: 10.1021/bi0013703  1
2000 Chae YK, Markley JL. Functional recombinant rabbit muscle phosphoglucomutase from Escherichia coli. Protein Expression and Purification. 20: 124-7. PMID 11035960 DOI: 10.1006/prep.2000.1288  1
2000 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. Journal of Biomolecular Nmr. 16: 359-60. PMID 10826893 DOI: 10.1023/A:1008333115661  1
2000 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. Archives of Biochemistry and Biophysics. 373: 328-34. PMID 10620356 DOI: 10.1006/abbi.1999.1576  1
1999 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. Archives of Biochemistry and Biophysics. 371: 35-40. PMID 10525287 DOI: 10.1006/abbi.1999.1394  1
1999 Qasim MA, Lu SM, Ding J, Bateman KS, James MN, Anderson S, Song J, Markley JL, Ganz PJ, Saunders CW, Laskowski M. Thermodynamic criterion for the conformation of P1 residues of substrates and of inhibitors in complexes with serine proteinases. Biochemistry. 38: 7142-50. PMID 10353824 DOI: 10.1021/bi990265u  1
1999 Xia B, Pikus JD, Xia W, McClay K, Steffan RJ, Chae YK, Westler WM, Markley JL, Fox BG. Detection and classification of hyperfine-shifted 1H, 2H, and 15N resonances of the Rieske ferredoxin component of toluene 4-monooxygenase. Biochemistry. 38: 727-39. PMID 9888813 DOI: 10.1021/bi981851a  1
1998 Dzakula Z, Juranić, DeRider ML, Westler WM, Macura S, Markley JL. Analysis of error propagation from NMR-derived internuclear distances into molecular structure of cyclo-pro-gly. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 135: 454-65. PMID 9878473  1
1998 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. The Journal of Biological Chemistry. 273: 25659-63. PMID 9748232 DOI: 10.1074/jbc.273.40.25659  1
1998 Wang L, Li Y, Abildgaard F, Markley JL, Yan H. NMR solution structure of type II human cellular retinoic acid binding protein: implications for ligand binding. Biochemistry. 37: 12727-36. PMID 9737849 DOI: 10.1021/bi9808924  1
1998 Choe S, Dzakula Z, Kuloglu ES, Markley JL. Assignment of 1H, 13C, and 15N signals of turkey ovomucoid third domain at pH 2.0. Journal of Biomolecular Nmr. 12: 193-5. PMID 9729798  1
1998 Caldwell JE, Abildgaard F, Ming D, Hellekant G, Markley JL. Complete 1H and partial 13C resonance assignments at 37 and 22 degrees C for brazzein, an intensely sweet protein. Journal of Biomolecular Nmr. 11: 231-2. PMID 9679299  1
1998 Weber-Main AM, Hurley JK, Cheng H, Xia B, Chae YK, Markley JL, Martinez-Júlvez M, Gomez-Moreno C, Stankovich MT, Tollin G. An electrochemical, kinetic, and spectroscopic characterization of [2Fe-2S] vegetative and heterocyst ferredoxins from Anabaena 7120 with mutations in the cluster binding loop. Archives of Biochemistry and Biophysics. 355: 181-8. PMID 9675025 DOI: 10.1006/abbi.1998.0743  1
1998 Caldwell JE, Abildgaard F, Dzakula Z, Ming D, Hellekant G, Markley JL. Solution structure of the thermostable sweet-tasting protein brazzein. Nature Structural Biology. 5: 427-31. PMID 9628478 DOI: 10.1038/nsb0698-427  1
1998 Prehoda KE, Mooberry ES, Markley JL. Pressure denaturation of proteins: evaluation of compressibility effects. Biochemistry. 37: 5785-90. PMID 9558311 DOI: 10.1021/bi980384u  1
1998 Xia B, Volkman BF, Markley JL. Evidence for oxidation-state-dependent conformational changes in human ferredoxin from multinuclear, multidimensional NMR spectroscopy. Biochemistry. 37: 3965-73. PMID 9521718 DOI: 10.1021/bi972722h  1
1998 Hirasawa M, Hurley JK, Salamon Z, Tollin G, Markley JL, Cheng H, Xia B, Knaff DB. The role of aromatic and acidic amino acids in the electron transfer reaction catalyzed by spinach ferredoxin-dependent glutamate synthase. Biochimica Et Biophysica Acta. 1363: 134-46. PMID 9507092 DOI: 10.1016/S0005-2728(97)00098-4  1
1997 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. Journal of Biomolecular Nmr. 10: 411-2. PMID 9460246  1
1997 Volkman BF, Prantner AM, Wilkens SJ, Xia B, Markley JL. Assignment of 1H, 13C, and 15N signals of oxidized Clostridium pasteurianum rubredoxin. Journal of Biomolecular Nmr. 10: 409-10. PMID 9460245  1
1997 Hurley JK, Weber-Main AM, Hodges AE, Stankovich MT, Benning MM, Holden HM, Cheng H, Xia B, Markley JL, Genzor C, Gomez-Moreno C, Hafezi R, Tollin G. Iron-sulfur cluster cysteine-to-serine mutants of Anabaena -2Fe-2S- ferredoxin exhibit unexpected redox properties and are competent in electron transfer to ferredoxin:NADP+ reductase. Biochemistry. 36: 15109-17. PMID 9398238 DOI: 10.1021/bi972001i  1
1997 Chivers PT, Prehoda KE, Volkman BF, Kim BM, Markley JL, Raines RT. Microscopic pKa values of Escherichia coli thioredoxin. Biochemistry. 36: 14985-91. PMID 9398223 DOI: 10.1021/bi970071j  1
1997 Wang J, Truckses DM, Abildgaard F, Dzakula Z, Zolnai Z, Markley JL. Solution structures of staphylococcal nuclease from multidimensional, multinuclear NMR: nuclease-H124L and its ternary complex with Ca2+ and thymidine-3',5'-bisphosphate. Journal of Biomolecular Nmr. 10: 143-64. PMID 9369015  1
1997 Hurley JK, Weber-Main AM, Stankovich MT, Benning MM, Thoden JB, Vanhooke JL, Holden HM, Chae YK, Xia B, Cheng H, Markley JL, Martinez-Júlvez M, Gómez-Moreno C, Schmeits JL, Tollin G. Structure-function relationships in Anabaena ferredoxin: correlations between X-ray crystal structures, reduction potentials, and rate constants of electron transfer to ferredoxin:NADP+ reductase for site-specific ferredoxin mutants. Biochemistry. 36: 11100-17. PMID 9287153 DOI: 10.1021/bi9709001  1
1997 Rémigy H, Jaquinod M, Pétillot Y, Gagnon J, Cheng H, Xia B, Markley JL, Hurley JK, Tollin G, Forest E. Probing the influence of mutations on the stability of a ferredoxin by mass spectrometry. Journal of Protein Chemistry. 16: 527-32. PMID 9246639  1
1997 An Z, Zhao Q, McEvoy J, Yuan WM, Markleys JL, Leong SA. The second finger of Urbs1 is required for iron-mediated repression of sid1 in Ustilago maydis Proceedings of the National Academy of Sciences of the United States of America. 94: 5882-5887. PMID 9159169 DOI: 10.1073/pnas.94.11.5882  1
1996 Truckses DM, Somoza JR, Prehoda KE, Miller SC, Markley JL. Coupling between trans/cis proline isomerization and protein stability in staphylococcal nuclease. Protein Science : a Publication of the Protein Society. 5: 1907-16. PMID 8880915 DOI: 10.1002/pro.5560050917  1
1996 Hinck AP, Truckses DM, Markley JL. Engineered disulfide bonds in staphylococcal nuclease: effects on the stability and conformation of the folded protein. Biochemistry. 35: 10328-38. PMID 8756688 DOI: 10.1021/bi960309o  1
1996 Xia B, Cheng H, Bandarian V, Reed GH, Markley JL. Human ferredoxin: overproduction in Escherichia coli, reconstitution in vitro, and spectroscopic studies of iron-sulfur cluster ligand cysteine-to-serine mutants. Biochemistry. 35: 9488-95. PMID 8755728 DOI: 10.1021/bi960467f  1
1996 Hoogstraten CG, Markley JL. Effects of experimentally achievable improvements in the quality of NMR distance constraints on the accuracy of calculated protein structures. Journal of Molecular Biology. 258: 334-48. PMID 8627630 DOI: 10.1006/jmbi.1996.0254  1
1996 Vidugiris GJ, Truckses DM, Markley JL, Royer CA. High-pressure denaturation of staphylococcal nuclease proline-to-glycine substitution mutants. Biochemistry. 35: 3857-64. PMID 8620010 DOI: 10.1021/bi952012g  0.96
1995 Edison AS, Markley JL, Weinhold F. Calculations of one-, two- and three-bond nuclear spin-spin couplings in a model peptide and correlations with experimental data. Journal of Biomolecular Nmr. 5: 332. PMID 22911507 DOI: 10.1007/BF00211763  1
1995 Pinkerton TC, Howe WJ, Ulrich EL, Comiskey JP, Haginaka J, Murashima T, Walkenhorst WF, Westler WM, Markley JL. Protein binding chiral discrimination of HPLC stationary phases made with whole, fragmented, and third domain turkey ovomucoid. Analytical Chemistry. 67: 2354-67. PMID 8686875  1
1995 Hoogstraten CG, Westler WM, Mooberry ES, Macura S, Markley JL. Analysis of transverse cross relaxation in proteins within a simplified relaxation submatrix: BD-ROESY. Journal of Magnetic Resonance. Series B. 109: 76-9. PMID 8581311 DOI: 10.1006/jmrb.1995.1149  1
1995 Hoogstraten CG, Choe S, Westler WM, Markley JL. Comparison of the accuracy of protein solution structures derived from conventional and network-edited NOESY data. Protein Science : a Publication of the Protein Society. 4: 2289-99. PMID 8563625 DOI: 10.1002/pro.5560041106  1
1995 Cheng H, Westler WM, Xia B, Oh BH, Markley JL. Protein expression, selective isotopic labeling, and analysis of hyperfine-shifted NMR signals of Anabaena 7120 vegetative [2Fe-2S]ferredoxin. Archives of Biochemistry and Biophysics. 316: 619-34. PMID 7840674 DOI: 10.1006/abbi.1995.1082  1
1995 Chae YK, Markley JL. Analysis of the hyperfine-shifted nitrogen-15 resonances of the oxidized form of Anabaena 7120 heterocyst ferredoxin. Biochemistry. 34: 188-93. PMID 7819195  1
1995 Xia B, Cheng H, Skjeldal L, Coghlan VM, Vickery LE, Markley JL. Multinuclear magnetic resonance and mutagenesis studies of the histidine residues of human mitochondrial ferredoxin. Biochemistry. 34: 180-7. PMID 7819194  1
1995 Hurley JK, Caffrey MS, Markley JL, Cheng H, Xia B, Chae YK, Holden HM, Tollin G. Mutations of surface residues in Anabaena vegetative and heterocyst ferredoxin that affect thermodynamic stability as determined by guanidine hydrochloride denaturation. Protein Science : a Publication of the Protein Society. 4: 58-64. PMID 7773177 DOI: 10.1002/pro.5560040108  1
1994 Loh SN, Markley JL. Hydrogen bonding in proteins as studied by amide hydrogen D/H fractionation factors: application to staphylococcal nuclease. Biochemistry. 33: 1029-36. PMID 8305430  1
1994 Chae YK, Abildgaard F, Mooberry ES, Markley JL. Multinuclear, multidimensional NMR studies of Anabaena 7120 heterocyst ferredoxin. Sequence-specific resonance assignments and secondary structure of the oxidized form in solution. Biochemistry. 33: 3287-95. PMID 8136364  1
1994 Cheng H, Xia B, Reed GH, Markley JL. Optical, EPR, and 1H NMR spectroscopy of serine-ligated [2Fe-2S] ferredoxins produced by site-directed mutagenesis of cysteine residues in recombinant Anabaena 7120 vegetative ferredoxin. Biochemistry. 33: 3155-64. PMID 8136349  1
1994 Walkenhorst WF, Krezel AM, Rhyu GI, Markley JL. Solution structure of reactive-site hydrolyzed turkey ovomucoid third domain by nuclear magnetic resonance and distance geometry methods. Journal of Molecular Biology. 242: 215-30. PMID 8089843 DOI: 10.1006/jmbi.1994.1574  1
1994 Krezel AM, Darba P, Robertson AD, Fejzo J, Macura S, Markley JL. Solution structure of turkey ovomucoid third domain as determined from nuclear magnetic resonance data. Journal of Molecular Biology. 242: 203-14. PMID 8089842 DOI: 10.1006/jmbi.1994.1573  1
1994 Edison AS, Weinhold F, Westler WM, Markley JL. Estimates of phi and psi torsion angles in proteins from one-, two- and three-bond nuclear spin-spin couplings: application to staphylococcal nuclease. Journal of Biomolecular Nmr. 4: 543-51. PMID 8075540 DOI: 10.1007/BF00156619  1
1994 Edison AS, Markley JL, Weinhold F. Calculations of one-, two- and three-bond nuclear spin-spin couplings in a model peptide and correlations with experimental data. Journal of Biomolecular Nmr. 4: 519-42. PMID 8075539 DOI: 10.1007/BF00156618  1
1994 Holden HM, Jacobson BL, Hurley JK, Tollin G, Oh BH, Skjeldal L, Chae YK, Cheng H, Xia B, Markley JL. Structure-function studies of [2Fe-2S] ferredoxins. Journal of Bioenergetics and Biomembranes. 26: 67-88. PMID 8027024 DOI: 10.1007/BF00763220  1
1994 Edison AS, Abildgaard F, Westler WM, Mooberry ES, Markley JL. Practical introduction to theory and implementation of multinuclear, multidimensional nuclear magnetic resonance experiments. Methods in Enzymology. 239: 3-79. PMID 7830587 DOI: 10.1016/S0076-6879(94)39003-7  1
1994 Gómez-Moreno C, Medina M, Hurley JK, Cusanovich MA, Markley JL, Cheng H, Xia B, Chae YK, Tollin G. Protein engineering for the elucidation of the mechanism of electron transfer in redox proteins. Biochemical Society Transactions. 22: 796-800. PMID 7821688  1
1993 Royer CA, Hinck AP, Loh SN, Prehoda KE, Peng X, Jonas J, Markley JL. Effects of amino acid substitutions on the pressure denaturation of staphylococcal nuclease as monitored by fluorescence and nuclear magnetic resonance spectroscopy. Biochemistry. 32: 5222-32. PMID 8494899  1
1993 Hinck AP, Walkenhorst WF, Westler WM, Choe S, Markley JL. Overexpression and purification of avian ovomucoid third domains in Escherichia coli. Protein Engineering. 6: 221-7. PMID 8475048 DOI: 10.1093/protein/6.2.221  1
1993 Hurley JK, Salamon Z, Meyer TE, Fitch JC, Cusanovich MA, Markley JL, Cheng H, Xia B, Chae YK, Medina M. Amino acid residues in Anabaena ferredoxin crucial to interaction with ferredoxin-NADP+ reductase: site-directed mutagenesis and laser flash photolysis. Biochemistry. 32: 9346-54. PMID 8369305  1
1993 Jacobson BL, Chae YK, Markley JL, Rayment I, Holden HM. Molecular structure of the oxidized, recombinant, heterocyst [2Fe-2S] ferredoxin from Anabaena 7120 determined to 1.7-A resolution. Biochemistry. 32: 6788-93. PMID 8329401  1
1993 Byeon IJ, Yan H, Edison AS, Mooberry ES, Abildgaard F, Markley JL, Tsai MD. Mechanism of adenylate kinase. 1H, 13C, and 15N NMR assignments, secondary structures, and substrate binding sites. Biochemistry. 32: 12508-21. PMID 8241142  1
1993 Hinck AP, Eberhardt ES, Markley JL. NMR strategy for determining Xaa-Pro peptide bond configurations in proteins: mutants of staphylococcal nuclease with altered configuration at proline-117. Biochemistry. 32: 11810-8. PMID 8218252  1
1993 Loh SN, Prehoda KE, Wang J, Markley JL. Hydrogen exchange in unligated and ligated staphylococcal nuclease. Biochemistry. 32: 11022-8. PMID 8218167 DOI: 10.1021/bi00092a011  1
1992 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. 31: 921-36. PMID 1731949  1
1992 Wang JF, Mooberry ES, Walkenhorst WF, Markley JL. Solution studies of staphylococcal nuclease H124L. 1. Backbone 1H and 15N resonances and secondary structure of the unligated enzyme as identified by three-dimensional NMR spectroscopy. Biochemistry. 31: 911-20. PMID 1731948  1
1992 Jacobson BL, Chae YK, Böhme H, Markley JL, Holden HM. Crystallization and preliminary analysis of oxidized, recombinant, heterocyst [2Fe-2S] ferredoxin from Anabaena 7120. Archives of Biochemistry and Biophysics. 294: 279-81. PMID 1550351 DOI: 10.1016/0003-9861(92)90169-W  1
1992 Houseman AL, Oh BH, Kennedy MC, Fan C, Werst MM, Beinert H, Markley JL, Hoffman BM. 14,15N, 13C, 57Fe, and 1,2H Q-band ENDOR study of Fe-S proteins with clusters that have endogenous sulfur ligands. Biochemistry. 31: 2073-80. PMID 1311203 DOI: 10.1021/bi00122a026  1
1992 Rao ST, Shaffie F, Yu C, Satyshur KA, Stockman BJ, Markley JL, Sundarlingam M. Structure of the oxidized long-chain flavodoxin from Anabaena 7120 at 2 A resolution. Protein Science : a Publication of the Protein Society. 1: 1413-27. PMID 1303762 DOI: 10.1002/pro.5560011103  1
1991 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. 30: 7363-8. PMID 1906741  1
1991 Rypniewski WR, Breiter DR, Benning MM, Wesenberg G, Oh BH, Markley JL, Rayment I, Holden HM. Crystallization and structure determination to 2.5-A resolution of the oxidized [2Fe-2S] ferredoxin isolated from Anabaena 7120. Biochemistry. 30: 4126-31. PMID 1902376  0.76
1991 Fejzo J, Krezel AM, Westler WM, Macura S, Markley JL. Refinement of the NMR solution structure of a protein to remove distortions arising from neglect of internal motion. Biochemistry. 30: 3807-11. PMID 1850288  1
1990 Alexandrescu AT, Hinck AP, Markley JL. Coupling between local structure and global stability of a protein: mutants of staphylococcal nuclease. Biochemistry. 29: 4516-25. PMID 2372535  0.92
1990 Wang JF, Hinck AP, Loh SN, Markley JL. Two-dimensional NMR studies of staphylococcal nuclease: evidence for conformational heterogeneity from hydrogen-1, carbon-13, and nitrogen-15 spin system assignments of the aromatic amino acids in the nuclease H124L-thymidine 3',5'-bisphosphate-Ca2+ ternary complex. Biochemistry. 29: 4242-53. PMID 2361141  1
1990 Oh BH, Markley JL. Multinuclear magnetic resonance studies of the 2Fe.2S* ferredoxin from Anabaena species strain PCC 7120. 3. Detection and characterization of hyperfine-shifted nitrogen-15 and hydrogen-1 resonances of the oxidized form. Biochemistry. 29: 4012-7. PMID 2354173  1
1990 Oh BH, Mooberry ES, Markley JL. Multinuclear magnetic resonance studies of the 2Fe.2S* ferredoxin from Anabaena species strain PCC 7120. 2. Sequence-specific carbon-13 and nitrogen-15 resonance assignments of the oxidized form. Biochemistry. 29: 4004-11. PMID 2354172 DOI: 10.1021/bi00468a030  1
1990 Oh BH, Markley JL. Multinuclear magnetic resonance studies of the 2Fe.2S* ferredoxin from Anabaena species strain PCC 7120. 1. Sequence-specific hydrogen-1 resonance assignments and secondary structure in solution of the oxidized form. Biochemistry. 29: 3993-4004. PMID 2354171  1
1990 Robertson AD, Rhyu GI, Westler WM, Markley JL. Assignment of the 13C-NMR spectra of virgin and reactive-site modified turkey ovomucoid third domain. Biopolymers. 29: 461-7. PMID 2331509 DOI: 10.1002/bip.360290216  1
1990 Wang JF, Hinck AP, Loh SN, Markley JL. Two-dimensional NMR studies of staphylococcal nuclease. 2. Sequence-specific assignments of carbon-13 and nitrogen-15 signals from the nuclease H124L-thymidine 3',5'-bisphosphate-Ca2+ ternary complex. Biochemistry. 29: 102-13. PMID 2322533  1
1990 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. 29: 9600-9. PMID 2125478  1
1990 Paulsen KE, Stankovich MT, Stockman BJ, Markley JL. Redox and spectral properties of flavodoxin from Anabaena 7120. Archives of Biochemistry and Biophysics. 280: 68-73. PMID 2112901 DOI: 10.1016/0003-9861(90)90519-5  1
1989 Alexandrescu AT, Ulrich EL, Markley JL. Hydrogen-1 NMR evidence for three interconverting forms of staphylococcal nuclease: effects of mutations and solution conditions on their distribution. Biochemistry. 28: 204-11. PMID 2706243  1
1989 Grissom CB, Markley JL. Staphylococcal nuclease active-site amino acids: pH dependence of tyrosines and arginines by 13C NMR and correlation with kinetic studies. Biochemistry. 28: 2116-24. PMID 2655703  1
1989 Oh BH, Markley JL. Complete 13C resonance assignments of tryptophan in L-lysyl-L-tryptophyl-L-lysine by single-bond and multiple-bond correlated 1H-13C two-dimensional NMR. Biopolymers. 28: 1833-7. PMID 2597735 DOI: 10.1002/bip.360281015  1
1989 Stockman BJ, Reily MD, Westler WM, Ulrich EL, Markley JL. Concerted two-dimensional NMR approaches to hydrogen-1, carbon-13, and nitrogen-15 resonance assignments in proteins. Biochemistry. 28: 230-6. PMID 2539856  1
1988 Westler WM, Stockman BJ, Hosoya Y, Miyake Y, Kainosho M, Markley JL. Correlation of carbon-13 and nitrogen-15 chemical shifts in selectively and uniformly labeled proteins by heteronuclear two-dimensional NMR spectroscopy. Journal of the American Chemical Society. 110: 6256-8. PMID 22148817 DOI: 10.1021/ja00226a057  1
1988 Rhyu GI, Markley JL. Two-dimensional NMR studies of Kazal proteinase inhibitors. 2. Sequence-specific assignments and secondary structure of reactive site modified turkey ovomucoid third domain. Biochemistry. 27: 2529-39. PMID 3382637  1
1988 Alexandrescu AT, Mills DA, Ulrich EL, Chinami M, Markley JL. NMR assignments of the four histidines of staphylococcal nuclease in native and denatured states. Biochemistry. 27: 2158-65. PMID 3288282  1
1988 Robertson AD, Westler WM, Markley JL. Two-dimensional NMR studies of Kazal proteinase inhibitors. 1. Sequence-specific assignments and secondary structure of turkey ovomucoid third domain. Biochemistry. 27: 2519-29. PMID 3164216  1
1988 Oh BH, Westler WM, Darba P, Markley JL. Protein carbon-13 spin systems by a single two-dimensional nuclear magnetic resonance experiment. Science (New York, N.Y.). 240: 908-11. PMID 3129784  1
1988 Stockman BJ, Westler WM, Mooberry ES, Markley JL. Flavodoxin from Anabaena 7120: uniform nitrogen-15 enrichment and hydrogen-1, nitrogen-15, and phosphorus-31 NMR investigations of the flavin mononucleotide binding site in the reduced and oxidized states. Biochemistry. 27: 136-42. PMID 3126808  1
1986 Markley JL, Croll DH, Krishnamoorthi R, Ortiz-Polo G, Westler WM, Bogard WC, Laskowski M. One- and two-dimensional NMR spectral analysis of the consequences of single amino acid replacements in proteins. Journal of Cellular Biochemistry. 30: 291-309. PMID 3711152 DOI: 10.1002/jcb.240300403  1
1985 Rhyu GI, Ray WJ, Markley JL. Multinuclear magnetic resonance studies of metal ion binding sites of phosphoglucomutase. Biochemistry. 24: 2536-41. PMID 2990531  1
1985 Rhyu GI, Ray WJ, Markley JL. Active-site serine phosphate and histidine residues of phosphoglucomutase: pH titration studies monitored by 1H and 31P NMR spectroscopy. Biochemistry. 24: 4746-53. PMID 2934085  1
1984 Markley JL, Westler WM, Chan TM, Kojiro CL, Ulrich EL. Two-dimensional NMR approaches to the study of protein structure and function. Federation Proceedings. 43: 2648-56. PMID 6430721  1
1984 Rhyu GI, Ray WJ, Markley JL. Enzyme-bound intermediates in the conversion of glucose 1-phosphate to glucose 6-phosphate by phosphoglucomutase. Phosphorus NMR studies. Biochemistry. 23: 252-60. PMID 6230103  1
1982 Ogino T, Croll DH, Kato I, Markley JL. Properties of conserved amino acid residues in tandem homologous protein domains. Hydrogen-1 nuclear magnetic resonance studies of the histidines of chicken ovomucoid. Biochemistry. 21: 3452-60. PMID 7115679  1
1979 Porubcan MA, Westler WM, Ibañez IB, Markley JL. (Diisopropylphosphoryl)serine proteinases. Proton and phosphorus-31 nuclear magnetic resonance-pH titration studies. Biochemistry. 18: 4108-16. PMID 39591  1
1978 Porubcan MA, Neves DE, Rausch SK, Markley JL. Active site in zymogens. Proton magnetic resonance pH titration curves of histidine-57 in porcine and bovine trypsinogens and in their complexes with bovine pancreatic trypsin inhibitor (Kunitz). Biochemistry. 17: 4640-7. PMID 31899  0.96
1978 Markley JL, Ibañez IB. Zymogen activation in serine proteinases. Proton magnetic resonance pH titration studies of the two histidines of bovine chymotrypsinogen A and chymotrypsin Aalpha. Biochemistry. 17: 4627-40. PMID 31898  1
1976 Markley JL, Porubcan MA. The charge-relay system of serine proteinases: proton magnetic resonance titration studies of the four histidines of porcine trypsin. Journal of Molecular Biology. 102: 487-509. PMID 5610 DOI: 10.1016/0022-2836(76)90330-2  1
1972 Jardetzky O, Thielmann H, Arata Y, Markley JL, Williams MN. Tentative sequential model for the unfolding and refolding of staphylococcal nuclease at high pH. Cold Spring Harbor Symposia On Quantitative Biology. 36: 257-61. PMID 4343718  1
1970 Jardetzky O, Markley JL. Nuclear magnetic resonance studies on selectively deuterated staphylococcal nuclease. Il Farmaco; Edizione Scientifica. 25: 894-7. PMID 5497436  1
1970 Markley JL, Jardetzky O. Nuclear magnetic resonance studies of the structure and binding sites of enzymes. XIV. Inhibitor binding to staphylococcal nuclease. Journal of Molecular Biology. 50: 223-33. PMID 5476914 DOI: 10.1016/0022-2836(70)90189-0  1
1970 Markley JL, Williams MN, Jardetzky O. Nuclear magnetic resonance studies of the structure and binding sites of enzymes. XII. A conformational equilibrium in staphylococcal nuclease involving a histidine residue. Proceedings of the National Academy of Sciences of the United States of America. 65: 645-51. PMID 5267145  1
1970 Putter I, Markley JL, Jardetzky O. Nuclear magnetic resonance studies of the structure and binding sites of enzymes. XI. Characterization of selectively deuterated analogs of staphylococcal nuclease. Proceedings of the National Academy of Sciences of the United States of America. 65: 395-401. PMID 4984238  1
1969 Putter I, Barreto A, Markley JL, Jardetzky O. Nuclear magnetic resonance studies of the structure and binding sites of enzymes. X. Preparation of selectively deuterated analogs of staphylococcal nuclease. Proceedings of the National Academy of Sciences of the United States of America. 64: 1396-403. PMID 5271760  1
1968 Markley JL, Putter I, Jardetzky O. High-resolution nuclear magnetic resonance spectra of selectively deuterated staphylococcal nuclease. Science (New York, N.Y.). 161: 1249-51. PMID 5673435  1
1967 Markley JL, Meadows DH, Jardetzky O. Nuclear magnetic resonance studies of helix-coil transitions in polyamino acids. Journal of Molecular Biology. 27: 25-40. PMID 6033611  1
1967 Meadows DH, Markley JL, Cohen JS, Jardetzky O. Nuclear magnetic resonance studies of the structure and binding sites of enzymes. I. Histidine residues. Proceedings of the National Academy of Sciences of the United States of America. 58: 1307-13. PMID 5237865  1
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