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Tools for Enhanced NMR-Based Metabolomics Analysis.

Markley JL, Dashti H, Wedell JR, Westler WM, Eghbalnia HR.

Methods Mol Biol. 2019;2037:413-427. doi: 10.1007/978-1-4939-9690-2_23.


I-PINE web server: an integrative probabilistic NMR assignment system for proteins.

Lee W, Bahrami A, Dashti HT, Eghbalnia HR, Tonelli M, Westler WM, Markley JL.

J Biomol NMR. 2019 May;73(5):213-222. doi: 10.1007/s10858-019-00255-3. Epub 2019 Jun 4.


Author Correction: Mitochondrial metabolism promotes adaptation to proteotoxic stress.

Tsvetkov P, Detappe A, Cai K, Keys HR, Brune Z, Ying W, Thiru P, Reidy M, Kugener G, Rossen J, Kocak M, Kory N, Tsherniak A, Santagata S, Whitesell L, Ghobrial IM, Markley JL, Lindquist S, Golub TR.

Nat Chem Biol. 2019 Jul;15(7):757. doi: 10.1038/s41589-019-0315-5.


Mitochondrial metabolism promotes adaptation to proteotoxic stress.

Tsvetkov P, Detappe A, Cai K, Keys HR, Brune Z, Ying W, Thiru P, Reidy M, Kugener G, Rossen J, Kocak M, Kory N, Tsherniak A, Santagata S, Whitesell L, Ghobrial IM, Markley JL, Lindquist S, Golub TR.

Nat Chem Biol. 2019 Jul;15(7):681-689. doi: 10.1038/s41589-019-0291-9. Epub 2019 May 27. Erratum in: Nat Chem Biol. 2019 Jun 4;:.


Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70.

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.

PLoS One. 2019 May 15;14(5):e0217098. doi: 10.1371/journal.pone.0217098. eCollection 2019.


Backbone resonance assignments and secondary structure of Ebola nucleoprotein 600-739 construct.

Lee W, Tonelli M, Wu C, Aceti DJ, Amarasinghe GK, Markley JL.

Biomol NMR Assign. 2019 Oct;13(2):315-319. doi: 10.1007/s12104-019-09898-7. Epub 2019 May 10.


Function and solution structure of the Arabidopsis thaliana RALF8 peptide.

Frederick RO, Haruta M, Tonelli M, Lee W, Cornilescu G, Cornilescu CC, Sussman MR, Markley JL.

Protein Sci. 2019 Jun;28(6):1115-1126. doi: 10.1002/pro.3628.


Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB).

Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY.

Acta Crystallogr D Struct Biol. 2019 Apr 1;75(Pt 4):451-454. doi: 10.1107/S2059798319004522. Epub 2019 Apr 8. No abstract available.


Semisynthetic Analogues of Anhydrotetracycline as Inhibitors of Tetracycline Destructase Enzymes.

Markley JL, Fang L, Gasparrini AJ, Symister CT, Kumar H, Tolia NH, Dantas G, Wencewicz TA.

ACS Infect Dis. 2019 Apr 12;5(4):618-633. doi: 10.1021/acsinfecdis.8b00349. Epub 2019 Mar 5.


Automated evaluation of consistency within the PubChem Compound database.

Dashti H, Wedell JR, Westler WM, Markley JL, Eghbalnia HR.

Sci Data. 2019 Feb 19;6:190023. doi: 10.1038/sdata.2019.23.


Current Solution NMR Techniques for Structure-Function Studies of Proteins and RNA Molecules.

Markley JL.

Adv Exp Med Biol. 2018;1105:43-58. doi: 10.1007/978-981-13-2200-6_5. Review.


View from Nuclear Magnetic Resonance Spectroscopy.

Markley JL.

Adv Exp Med Biol. 2018;1105:19-22. doi: 10.1007/978-981-13-2200-6_3. Review.


NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments.

Ulrich EL, Baskaran K, Dashti H, Ioannidis YE, Livny M, Romero PR, Maziuk D, Wedell JR, Yao H, Eghbalnia HR, Hoch JC, Markley JL.

J Biomol NMR. 2019 Feb;73(1-2):5-9. doi: 10.1007/s10858-018-0220-3. Epub 2018 Dec 22. Review.


NMR as a Tool to Investigate the Processes of Mitochondrial and Cytosolic Iron-Sulfur Cluster Biosynthesis.

Cai K, Markley JL.

Molecules. 2018 Aug 31;23(9). pii: E2213. doi: 10.3390/molecules23092213. Review.


Applications of Parametrized NMR Spin Systems of Small Molecules.

Dashti H, Wedell JR, Westler WM, Tonelli M, Aceti D, Amarasinghe GK, Markley JL, Eghbalnia HR.

Anal Chem. 2018 Sep 18;90(18):10646-10649. doi: 10.1021/acs.analchem.8b02660. Epub 2018 Aug 24.


Probing Protein-Protein Interactions Using Asymmetric Labeling and Carbonyl-Carbon Selective Heteronuclear NMR Spectroscopy.

Larsen EK, Olivieri C, Walker C, V S M, Gao J, Bernlohr DA, Tonelli M, Markley JL, Veglia G.

Molecules. 2018 Aug 3;23(8). pii: E1937. doi: 10.3390/molecules23081937. Review.


Architectural Features of Human Mitochondrial Cysteine Desulfurase Complexes from Crosslinking Mass Spectrometry and Small-Angle X-Ray Scattering.

Cai K, Frederick RO, Dashti H, Markley JL.

Structure. 2018 Aug 7;26(8):1127-1136.e4. doi: 10.1016/j.str.2018.05.017. Epub 2018 Jul 5.


Tetracycline-Inactivating Enzymes.

Markley JL, Wencewicz TA.

Front Microbiol. 2018 May 30;9:1058. doi: 10.3389/fmicb.2018.01058. eCollection 2018. Review.


Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

Young JY, Westbrook JD, Feng Z, Peisach E, Persikova I, Sala R, Sen S, Berrisford JM, Swaminathan GJ, Oldfield TJ, Gutmanas A, Igarashi R, Armstrong DR, Baskaran K, Chen L, Chen M, Clark AR, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Ikegawa Y, Kengaku Y, Lawson CL, Liang Y, Mak L, Mukhopadhyay A, Narayanan B, Nishiyama K, Patwardhan A, Sahni G, Sanz-García E, Sato J, Sekharan MR, Shao C, Smart OS, Tan L, van Ginkel G, Yang H, Zhuravleva MA, Markley JL, Nakamura H, Kurisu G, Kleywegt GJ, Velankar S, Berman HM, Burley SK.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay002.


Interactions of iron-bound frataxin with ISCU and ferredoxin on the cysteine desulfurase complex leading to Fe-S cluster assembly.

Cai K, Frederick RO, Tonelli M, Markley JL.

J Inorg Biochem. 2018 Jun;183:107-116. doi: 10.1016/j.jinorgbio.2018.03.007. Epub 2018 Mar 15.


Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys.

Rhoads TW, Burhans MS, Chen VB, Hutchins PD, Rush MJP, Clark JP, Stark JL, McIlwain SJ, Eghbalnia HR, Pavelec DM, Ong IM, Denu JM, Markley JL, Coon JJ, Colman RJ, Anderson RM.

Cell Metab. 2018 Mar 6;27(3):677-688.e5. doi: 10.1016/j.cmet.2018.01.014.


ISCU(M108I) and ISCU(D39V) Differ from Wild-Type ISCU in Their Failure To Form Cysteine Desulfurase Complexes Containing Both Frataxin and Ferredoxin.

Cai K, Frederick RO, Tonelli M, Markley JL.

Biochemistry. 2018 Mar 6;57(9):1491-1500. doi: 10.1021/acs.biochem.7b01234. Epub 2018 Feb 14.


PINE-SPARKY.2 for automated NMR-based protein structure research.

Lee W, Markley JL.

Bioinformatics. 2018 May 1;34(9):1586-1588. doi: 10.1093/bioinformatics/btx785.


Lactobacillus demonstrate thiol-independent metabolism of methylglyoxal: Implications toward browning prevention in Parmesan cheese.

Gandhi NN, Cobra PF, Steele JL, Markley JL, Rankin SA.

J Dairy Sci. 2018 Feb;101(2):968-978. doi: 10.3168/jds.2017-13577. Epub 2017 Dec 21.


Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family.

Reidenbach AG, Kemmerer ZA, Aydin D, Jochem A, McDevitt MT, Hutchins PD, Stark JL, Stefely JA, Reddy T, Hebert AS, Wilkerson EM, Johnson IE, Bingman CA, Markley JL, Coon JJ, Dal Peraro M, Pagliarini DJ.

Cell Chem Biol. 2018 Feb 15;25(2):154-165.e11. doi: 10.1016/j.chembiol.2017.11.001. Epub 2017 Nov 30.


Validation of Structures in the Protein Data Bank.

Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ.

Structure. 2017 Dec 5;25(12):1916-1927. doi: 10.1016/j.str.2017.10.009. Epub 2017 Nov 22.


NMR-Based Identification of Metabolites in Polar and Non-Polar Extracts of Avian Liver.

Fathi F, Brun A, Rott KH, Falco Cobra P, Tonelli M, Eghbalnia HR, Caviedes-Vidal E, Karasov WH, Markley JL.

Metabolites. 2017 Nov 16;7(4). pii: E61. doi: 10.3390/metabo7040061.


Broadening the functionality of a J-protein/Hsp70 molecular chaperone system.

Schilke BA, Ciesielski SJ, Ziegelhoffer T, Kamiya E, Tonelli M, Lee W, Cornilescu G, Hines JK, Markley JL, Craig EA.

PLoS Genet. 2017 Oct 30;13(10):e1007084. doi: 10.1371/journal.pgen.1007084. eCollection 2017 Oct.


Spin System Modeling of Nuclear Magnetic Resonance Spectra for Applications in Metabolomics and Small Molecule Screening.

Dashti H, Westler WM, Tonelli M, Wedell JR, Markley JL, Eghbalnia HR.

Anal Chem. 2017 Nov 21;89(22):12201-12208. doi: 10.1021/acs.analchem.7b02884. Epub 2017 Nov 7.


PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models.

Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J.

Structure. 2017 Sep 5;25(9):1317-1318. doi: 10.1016/j.str.2017.08.001.


Chemical Genomics, Structure Elucidation, and in Vivo Studies of the Marine-Derived Anticlostridial Ecteinamycin.

Wyche TP, Alvarenga RFR, Piotrowski JS, Duster MN, Warrack SR, Cornilescu G, De Wolfe TJ, Hou Y, Braun DR, Ellis GA, Simpkins SW, Nelson J, Myers CL, Steele J, Mori H, Safdar N, Markley JL, Rajski SR, Bugni TS.

ACS Chem Biol. 2017 Sep 15;12(9):2287-2295. doi: 10.1021/acschembio.7b00388. Epub 2017 Jul 26.


Progressive Stereo Locking (PSL): A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and Other Small Molecules.

Cornilescu G, Ramos Alvarenga RF, Wyche TP, Bugni TS, Gil RR, Cornilescu CC, Westler WM, Markley JL, Schwieters CD.

ACS Chem Biol. 2017 Aug 18;12(8):2157-2163. doi: 10.1021/acschembio.7b00281. Epub 2017 Jul 12.


Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.

Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S.

Methods Mol Biol. 2017;1607:627-641. doi: 10.1007/978-1-4939-7000-1_26. Review.


Unique identifiers for small molecules enable rigorous labeling of their atoms.

Dashti H, Westler WM, Markley JL, Eghbalnia HR.

Sci Data. 2017 May 23;4:170073. doi: 10.1038/sdata.2017.73.


Biomolecular NMR: Past and future.

Markley JL, Westler WM.

Arch Biochem Biophys. 2017 Aug 15;628:3-16. doi: 10.1016/ Epub 2017 May 8.


Relationship between recombinant protein expression and host metabolome as determined by two-dimensional NMR spectroscopy.

Chae YK, Kim SH, Markley JL.

PLoS One. 2017 May 9;12(5):e0177233. doi: 10.1371/journal.pone.0177233. eCollection 2017.


P-Stereogenic Bicyclo[4.3.1]phosphite Boranes: Synthesis and Utility of Tunable P-Tether Systems for the Desymmetrization of C2-Symmetric 1,3-anti-Diols.

Markley JL, Hanson PR.

Org Lett. 2017 May 19;19(10):2552-2555. doi: 10.1021/acs.orglett.7b00851. Epub 2017 May 4.


Mitochondrial Cysteine Desulfurase and ISD11 Coexpressed in Escherichia coli Yield Complex Containing Acyl Carrier Protein.

Cai K, Frederick RO, Tonelli M, Markley JL.

ACS Chem Biol. 2017 Apr 21;12(4):918-921. doi: 10.1021/acschembio.6b01005. Epub 2017 Mar 2.


OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK.

Structure. 2017 Mar 7;25(3):536-545. doi: 10.1016/j.str.2017.01.004. Epub 2017 Feb 9.


Human Mitochondrial Ferredoxin 1 (FDX1) and Ferredoxin 2 (FDX2) Both Bind Cysteine Desulfurase and Donate Electrons for Iron-Sulfur Cluster Biosynthesis.

Cai K, Tonelli M, Frederick RO, Markley JL.

Biochemistry. 2017 Jan 24;56(3):487-499. doi: 10.1021/acs.biochem.6b00447. Epub 2017 Jan 11.


Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.

Yokochi M, Kobayashi N, Ulrich EL, Kinjo AR, Iwata T, Ioannidis YE, Livny M, Markley JL, Nakamura H, Kojima C, Fujiwara T.

J Biomed Semantics. 2016 May 5;7(1):16.


Structural/Functional Properties of Human NFU1, an Intermediate [4Fe-4S] Carrier in Human Mitochondrial Iron-Sulfur Cluster Biogenesis.

Cai K, Liu G, Frederick RO, Xiao R, Montelione GT, Markley JL.

Structure. 2016 Dec 6;24(12):2080-2091. doi: 10.1016/j.str.2016.08.020. Epub 2016 Nov 3.


Increasing rigor in NMR-based metabolomics through validated and open source tools.

Eghbalnia HR, Romero PR, Westler WM, Baskaran K, Ulrich EL, Markley JL.

Curr Opin Biotechnol. 2017 Feb;43:56-61. doi: 10.1016/j.copbio.2016.08.005. Epub 2016 Sep 16. Review.


The future of NMR-based metabolomics.

Markley JL, Brüschweiler R, Edison AS, Eghbalnia HR, Powers R, Raftery D, Wishart DS.

Curr Opin Biotechnol. 2017 Feb;43:34-40. doi: 10.1016/j.copbio.2016.08.001. Epub 2016 Aug 28. Review.


The archiving and dissemination of biological structure data.

Berman HM, Burley SK, Kleywegt GJ, Markley JL, Nakamura H, Velankar S.

Curr Opin Struct Biol. 2016 Oct;40:17-22. doi: 10.1016/ Epub 2016 Jul 21. Review.


Structure and Function of the PriC DNA Replication Restart Protein.

Wessel SR, Cornilescu CC, Cornilescu G, Metz A, Leroux M, Hu K, Sandler SJ, Markley JL, Keck JL.

J Biol Chem. 2016 Aug 26;291(35):18384-96. doi: 10.1074/jbc.M116.738781. Epub 2016 Jul 5.


Dynamical Structures of Hsp70 and Hsp70-Hsp40 Complexes.

Alderson TR, Kim JH, Markley JL.

Structure. 2016 Jul 6;24(7):1014-30. doi: 10.1016/j.str.2016.05.011. Epub 2016 Jun 23. Review.


Mechanism of Histone H3K4me3 Recognition by the Plant Homeodomain of Inhibitor of Growth 3.

Kim S, Natesan S, Cornilescu G, Carlson S, Tonelli M, McClurg UL, Binda O, Robson CN, Markley JL, Balaz S, Glass KC.

J Biol Chem. 2016 Aug 26;291(35):18326-41. doi: 10.1074/jbc.M115.690651. Epub 2016 Jun 8.


The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data.

Lee W, Petit CM, Cornilescu G, Stark JL, Markley JL.

J Biomol NMR. 2016 Jun;65(2):51-7. doi: 10.1007/s10858-016-0036-y. Epub 2016 May 12.

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