Publications

Aceti DJ, Bingman CA, Wrobel RL, Frederick RO, Makino SI, Nichols KW, Sahu SC, Bergeman LF, Blommel PG, Cornilescu CC, Gromek KA, Seder KD, Hwang S, Primm JG, Sabat G, Vojtik FC, Volkman BF, Zolnai Z, Phillips GN Jr, Markley JL, Fox BG. (2014) 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.. J Struct Funct Genomics, in press. PMID:25854603 / PMCID Journal - In Process

Alderson TR, Kim JH, Cai K, Frederick RO, Tonelli M, Markley JL (2014) The specialized Hsp70 (HscA) interdomain linker binds to its nucleotide-binding domain and stimulates ATP hydrolysis in both cis and trans configurations. Biochemistry, 53(46):7148-59. PMID:25372495 / PMCID:PMC4245983

Alderson TR, Kim JH, Cai K, Frederick RO, Tonelli M, Markley JL (2014) 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(50):7999. PMID:25495500 / PMCID:PMC4278680

Alderson TR, Markley JL (2013) Biophysical characterization of a-synuclein and its controversial structure. Intrinsically Disordered Proteins 1(1):18-39. PMID:24634806 / PMCID:PMC3908606

Beebe ET, Makino SI, Markley JL, Fox BG (2014) Automated cell-free protein production methods for structural studies. Pharmacol Toxicol 1140:117-35. PMID:24590713 / PMCID - Policy Exempt

Cai K, Frederick RO, Kim JH, Reinen NM, Tonelli M, Markley JL (2013) 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 Sscaffold protein (ISCU). J Biol Chem 288(40):28755-70. PMID:23940031 / PMCID:PMC3789972

Dai Z, Kim JH, Tonelli M, Ali IK, Markley JL (2014) pH-induced conformational change of IscU at low pH correlates with protonation/deprotonation of two conserved histidine residues. Biochemistry 53(32):5290-7. PMID:25055301 / PMCID:PMC4139155

Dai Z, Tonelli M, Markley JL (2012) Metamorphic protein IscU changes conformation by cis-trans isomerizations of two peptidyl-prolyl peptide bonds. Biochemistry 51(48):9595-602. PMID:23110687 / PMCID:PMC3567208

Eletsky A, Jeong MY, Kim H, Lee HW, Xiao R, Pagliarini DJ, Prestegard JH, Winge DR, Montelione GT, Szyperski T (2012) Solution NMR structure of yeast succinate dehydrogenase flavinylation factor Sdh5 reveals a putative Sdh1 binding site. Biochemistry 51(43):8475-7. PMID:23062074 / PMCID:PMC3667956

Hsueh KL, Tonelli M, Cai K, Westler WM, Markley JL (2013) Electron transfer mechanism of the Rieske protein from Thermus thermophiles from solution NMR investigations. Biochemistry 52(17):2862-73. PMID:23480240 / PMCID:PMC3686548

Khadria AS, Mueller BK, Stefely JA, Tan CH, Pagliarini DJ, Senes A (2014) A Gly-zipper motif mediates homodimerization of the transmembrane domain of the mitochondrial kinase ADCK3. J Am Chem Soc 2014 136(40):14068-77. PMID:25216398 / PMCID:PMC4195374

Kim JH, Alderson TR, Frederick RO, Markley JL (2014) Nucleotide-dependent interactions within a specialized Hsp70/Hsp40 complex involved in Fe-S cluster biogenesis. J Am Chem Soc 136(33):11586-9. PMID:25080945 / PMCID:PMC4140450

Kim JH, Bothe JR, Frederick RO, Holder JC, Markley JL (2014) Role of IscX in iron-sulfur cluster biogenesis in Escherichia coli. J Am Chem Soc 136(22):7933-42. PMID:24810328 / PMCID:PMC4063190

Kim JH, Bothe JR, Reid Alderson T, Markley JL (2014) Tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies. Biochim Biophys Acta pii: S0167-4889(14)00418-2. PMID:25450980 / PMCID:PMC4390431

Kim JH, Frederick RO, Reinen MN, Troupis AT, Markley JL (2013) [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. J Am Chem Soc 135(22):8117-20. PMID:23682711 / PMCID:PMC3677232

Kim JH, Tonelli M, Frederick RO, Chow DC, Markley JL (2012) 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). J Biol Chem 287(37):31406-13. PMID:22782893 / PMCID:PMC3438969

Kim JH, Tonelli M, Kim T, Markley JL (2012) Three-dimensional structure and determinants of stability of the iron-sulfur cluster scaffold protein IscU from Escherichia coli. Biochemistry 51(28):5557-63. PMID:22734684 / PMCID:PMC3445271

Kim JH, Tonelli M, Markley JL (2012) Disordered form of the scaffold protein IscU is the substrate for iron-sulfur cluster assembly on cysteine desulfurase. Proc Natl Acad Sci USA 109(2):454-9. PMID:22203963 / PMCID:PMC3258623

Lee W, Watters KE, Troupis AT, Reinen NM, Suchy FP, Moyer KL, Frederick RO, Tonelli M, Aceti DJ, Palmenberg AC, Markley JL (2014) Solution structure of the 2A protease from a common cold agent, human rhinovirus C2, strain W12. PLoS One 9(6):e97198. PMID:24937088 / PMCID:PMC4061012

Lohman DC, Forouhar F, Beebe ET, Stefely MS, Minogue CE, Ulbrich A, Stefely JA, Sukumar S, Luna-Sanchez M, Jochem A, Lew S, Seetharaman J, Xiao R, Wang H, Westphall MS, Wrobel RL, Everett JK, Mitchell JC, Lopez LC, Coon JJ, Tong L, Pagliarini DJ (2014) Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis. Proc Natl Acad Sci USA 111(44):E4697-705. PMID:25339443 / PMCID:PMC4226113

Makino SI, Beebe ET, Markley JL, Fox BG (2014) Cell-free protein synthesis for functional and structural studies. Methods Mol Biol 1091:161-78. PMID:24203331 / PMCID - Policy Exempt

Markley JL, Kim JH, Dai Z, Bothe JR, Cai K, Frederick RO, Tonelli M (2013) Metamorphic protein IscU alternates conformations in the course of its role as the scaffold protein for iron-sulfur cluster biosynthesis and delivery. FEBS Lett 587(8):1172-9. PMID:23333622 / PMCID:PMC3960074

Pagliarini DJ, Rutter J (2013) Hallmarks of a new era in mitochondrial biochemistry. Genes Dev 27(24):2615-27. PMID:24352419 / PMCID:PMC3877752

Ramelot TA, Yang Y, Sahu ID, Lee H-W, Xiao R, Lorigan GA, Montelione GT, Kennedy MA (2013) NMR structure and MD simulations of the AAA protease intermembrane space domain indicates peripheral membrane localization within the hexaoligomer. FEBS Lett S0014-5793(13)00694-7. PMID:24055473 / PMCID:PMC4043124

Stefely JA, Reidenbach AG, Ulbrich A, Oruganty K, Floyd BJ, Jochem A, Saunders JM, Johnson IE, Minogue CE, Wrobel RL, Barber GE, Lee D, Li S, Kannan N, Coon JJ, Bingman CA, Pagliarini DJ (2014) Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthesis. Mol Cell 2014, 57(1):83-94. PMID:25498144 / PMCID:PMC4289473

Still AJ, Floyd BJ, Hebert AS, Bingman CA, Carson JJ, Gunderson DR, Dolan BK, Grimsrud PA, Dittenhafer-Reed KE, Stapleton DS, Keller MP, Westphall MS, Denu JM, Attie AD, Coon JJ, Pagliarini DJ. (2013) Quantification of mitochondrial acetylation dynamics highlights prominent sites of metabolic regulation. J Biol Chem 288(36):26209-19. PMID:23864654 / PMCID:PMC3764825

Takasuka TE, Walker JA, Bergeman LF, Vander Meulen KA, Makino S, Elsen NL, Fox BG (2014) Cell-free translation of biofuel enzymes. Methods Mol Biol 1118:71-95. PMID:24395410 / PMCID - Policy Exempt