2025
(97), Lancaster EB*, Hardtke HA *, Melkonian TR, Ramani MKV, Johnson WH, Baas BJ, Zhang YJ (co-corresponding) and Whitman JP. Conversion of Inactive Non-Pro1 Tautomerase Superfamily Members into Active Tautomerases: Analysis of the Pro1 Mutants Biochemistry. In press.
(96), Moreno RY, Panina S, Zhang YJ. RPRD1B’s direct interaction with phosphorylated RNA Polymerase II regulates polyadenylation of cell cycle genes and drives cancer progression. RSC Chem Biol, In press.
2024
(95), Miller LG*, Kim W*, Schowe S, Taylor K, Han R, Jain V, Park R, Sherman M, Fang J, Ramirez H, Ellington AD, Tamamis P, Resendiz MJE, Y. J. Zhang (co-corresponding), and Contreras L. “Selective 8-oxo-rG stalling occurs in the catalytic core of polynucleotide phosphorylase (PNPase) during degradation.” PNAS, 121, 46, Pp. e2317865121. Publisher’s Version
(94), J.P. Butalewicz, S. N. Sipe, K.J. Juetten, V. K. James, K Kim, Y. J. Zhang, T. D. Meek, and J.S. Brodbelt. “Insights into the Main Protease of SARS-CoV-2: Thermodynamic Analysis, Structural Characterization, and the Impact of Inhibitors.” Analytical Chemistry. Publisher’s Version
(93), Zhang, Q.*, Kim W*, Panina SB, Mayfield JE, Portz B& Zhang YJ. “Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription.” Nature Communications. Publisher’s Version
(92), RY Moreno, SB Panina, S Irani, HA Hardtke, R Stephenson, BM Floyd, EM Marcott, Q Zhang, and YJ Zhang. “Thr4 phosphorylation on RNA Pol II occurs at early transcription regulating 3’-end processing.” Science Advances. Publisher’s Version
(91), HA Hardtke, RY Moreno, and YJ Zhang. “Protocol for the in vitro reconstruction of site-specifically phosphorylated RNA Pol II to identify the recruitment of novel transcription regulators.” STAR Protocol. Publisher’s Version
(90), KB Reed, W Kim, H Lu, LT Larue, S Guo, SM Brooks, M Montez, J Wagner, YJ Zhang, and HS Alper. “Evolving Dual-Trait EPSP Synthase Variants Using a Synthetic Yeast Selection System.” PNAS. Publisher’s Version
(89), E. E. Escobar, W Yang, M. B. Lanzillotti, K.J. Juetten, S Shields, D. Siegel, Y. J. Zhang, and J.S. Brodbelt. “Tracking Inhibition of human Small C-terminal Domain Phosphatase 1 using 193 nm Ultraviolet Photodissociation Mass Spectrometry.” Journal of the American Society for Mass Spectrometry , 35, 6, Pp. 1330-1341. Publisher’s Version
(88), Panina SB, Schweer JV, Zhang Q, Raina G, Hardtke HA, Kim S, Yang WJ, Siegel D, and Zhang YJ. “Targeting of REST with rationally-designed small molecule compounds exhibits synergetic therapeutic potential in human glioblastoma cells.” BMC Biology, 22, 83. Publisher’s Version
(87), I Wallach, A Morrison, .., .., B Medellin, .., .., Y. Jessie Zhang, .., and A Heifets. “AI is a Viable Alternative to High Throughput Screening: a 318-Target Study.” Scientific Reports, 14, Pp. 7526. Publisher’s Version
(86), S d’Oelsnitz, D Diaz, W Kim, D Acosta, M Schechter, M Minus, J Howard, H Do, T Dangerfield, J Loy, HS Alper, YJ Zhang, and AD Ellington. “Synthetic microbial sensing and biosynthesis of a branchpoint amaryllidaceae alkaloid.” Nature Communication, 15, Pp. 2084 (2024) . Publisher’s Version
(85), HA Hardtke, and YJ Zhang. “Collaborators or competitors: The communication between RNA polymerase II and the nucleosome during eukaryotic transcription.” Critical Reviews in Biochemistry and Molecular Biology. Publisher’s Version
2023
(84), Wang JX, Vilbert AC, Cui C, Mirts EN, Williams LH, Kim W, Zhang YJ, and Lu Y. “Increasing Reduction Potentials of Type 1 Copper Center and Catalytic Efficiency of Small Laccase from Streptomyces coelicolor through Secondary Coordination Sphere Mutations.” Angew Chem Int Ed Engl., 62, 52. Publisher’s Version
(83), R.Y. Moreno, K.J. Juetten, S.B. Panina, J.P. Butalewicz, B.M. Floyd, M.K. Venkat Ramani, E.M. Marcotte, J.S. Brodbelt, and Y. J. Zhang. “Distinctive Interactomes of RNA polymerase II phosphorylation during different stages of transcription.” iScience, 26, 9. Publisher’s Version
(82), Erwin, K.*, R.Y. Moreno*, B-J. Baas, Y. J Zhang (co-corresponding), and C.P. Whitman. “Evolution of the fused 4-oxalocrotonate Tautomerase in the Tautomerase Superfamily: Introduction of Asymmetry.” Biochemistry, 62, Pp. 2461-2471. Publisher’s Version
(81), YW Liu, NM Marshall, S Yu, W Kim, YG Gao, H Robinson, MJ Nilges, Y Zhang, SY New, and Y Lu. “Structural basis for the effects of phenylalanine on tuning the reduction potential of type 1 copper in azurin.” Inorganic Chemistry, 62, 29, Pp. 11618-11625. Publisher’s Version
(80), Y. Jessie Zhang, and Philip A. Cole. “Editorial: Mechanistic Biology.” Current Opinion of Chemical Biology, 74.
(79), Lancaster EB, Johnson WH Jr, LeVieux JA, Hardtke HA, Zhang YJ, and Whitman CP. “A mutagenic analysis of NahE, a hydratase-aldolase in the naphthalene degradative pathway.” Arch Biochem Biophys., 733, Pp. 109471. Publisher’s Version
2022
(78), Blazeck J, Karamitros CS, Ford K, Somody C, Qerqez A, Murray K, Burkholder NT, Marshall N, Sivakumar A, Lu WC, Tan B., Lamb C, Tanno Y, Yemeny MS, Zhang M, McGovern K, Kumada Y, Zhang YJ, Manfredi M, Johnson KA, D’Arcy S, Stone E, and Georgiou G. “Bypassing evolutionary dead-ends and switching the rate-limiting step of a human immunotherapeutic enzyme.” Nature Catalysis, 5, Pp. 952–967. Publisher’s Version
(77), Kim W*, Chen TY*, Cha L, Zhou G, Xing K, Canty NK, Zhang Y *(co-corresponding), and Chang WC. “Elucidation of divergent desaturation pathways in the formation of vinyl isonitrile and isocyanoacrylate.” Nature Communication, 13, 5343. Publisher’s Version
(76), d’Oelsnitz S, Kim W, Burkholder NT, Javanmardi K, Thyer R, Zhang Y, Alper H, and Ellington AD. “Directed Evolution of a Generalist Biosensor Accelerates Alkaloid Pathway Engineering.” Nature Chemical Biology. Publisher’s Version
(75), E.B. Lancaster, W.J. Yang, W.H. Johnson, B-J. Baas, Y. J. Zhang, and C.P. Whitman. “Kinetic, Inhibition, and Structural Characterization of a Malonate Semialdehyde Decarboxylase Homolog from Calothrix sp. PCC 6303: A Gateway to the non-Pro1 Tautomerase Superfamily Members.” Biochemistry. Publisher’s Version
(74), Lu H, Diaz DJ, Czarnecki NJ, Zhu C, Kim W, Shroff R, Acosta DJ, Alexander B, Cole HO, Zhang YJ, Lynd NA, Ellington AD, and Alper HS. “Machine learning-aided engineering of PET hydrolase for PET depolymerization.” Nature, 604, Pp. 662–667. Publisher’s Version
(73), Polyanskaya SA, Moreno RY, Lu B, Feng R, Yao Y, Irani S, Klingbeil O, Yang Z, Wei Y, Demerdash OE, Benjamin LA, Weiss MJ, Zhang YJ, and Vakoc CR. “The SCP4-STK35/PDIK1L complex is a dual phospho-catalytic signaling dependency in acute myeloid leukemia.” Cell Report, 38, 2, Pp. 110233. Publisher’s Version
(72), BP Medellin, WJ Yang, S Konduri, J Dong, S Irani, HY Wu, WL Matthews, Z-Y Zhang, D Siegel, and Y Zhang. “Targeted Covalent Inhibition of Small CTD Phosphatase-1 to Promote the Degradation of REST Transcription Factor in Human Cells.” Journal of Medicinal Chemistry , 65, Pp. 507-519. Publisher’s Version
2021
(71), F Meng, Z Yu, D Zhang, S. Chen, H Guan, R Zhou, Q Wu, Q Zhang, MK Venkat Ramani, S Liu, B Yang, X-Q Ba, J Zhang, J Huang, X Bai, J Qin, X-H Feng, Ouyang, S, YJ Zhang, T Liang, and P Xu. “Induced phase separatation of mutant NF2 imprisons the cGAS-STING machinery to abrogate antitumor immunity.” Molecular Cell, 81, 20, Pp. 4147-4164. Publisher’s Version
(70), W Kim, B LeBlanc, WL Matthews, Z-Y Zhang, and YJ Zhang. “Advancements in Chemical Biology Targeting the Kinases and Phosphatases of RNA Polymerase II-mediated Transcription.” Current Opinion in Chemical Biology, 63, Pp. 68-77. Publisher’s Version
(69), BM LeBlanc, Moreno, RY, Escobar, E.E., M.K. Venkat Ramani, J.S Brodbelt, and Y Zhang. “What’s all the phos about? Insights into the phosphorylation state of the RNA polymerase II C-terminal domain via mass spectrometry.” Royal Society of Chemistry Chemical Biology, 2, Pp. 1084-1095. Publisher’s Version
(68), EE Escobar*, MK Venkat Ramani*, Y Zhang, and JS Brodbelt. “Parallel Reaction Monitoring of RNA polymerase II Carboxy-terminal Domain Phosphorylation using 193 nm Ultraviolet Photodissociation Mass Spectrometry.” JACS, 143, 22, Pp. 8488-8498. Publisher’s Version
(67), BJ Bass, Medellin, B.P., J.A. LeVieux, K Erwin, E.B. Lancaster, W.H Johnson, T.S. Kaoud, R.Y. Moreno, de Ruijter, M., P.C. Babbit, Y. J. Zhang, and C.P. Whitman. “Kinetic and Structural Analysis of Two Linkers in the Tautomerase Superfamily: Analysis and Implications.” Biochemistry. Publisher’s Version
(66), MKV Ramani, W Yang, S Irani, and Y Zhang. “Simplicity is the Ultimate Sophistication — Cross-talk of Post-translational Modifications on the RNA Polymerase II.” JMB, 63, Pp. 68-77. Publisher’s Version
(65), Zhou R, Wu Q, Wang M, S Irani, Li X, Zhang Q, Meng F, Liu S, Zhang F, Wu L, Lin X, Wang X, Zou J, Song H, Qin J, Liang T, Feng X-H, Zhang YJ, and Xu P. “The protein phosphatase PPM1A dephosphorylates and activates YAP to govern mammalian intestinal and liver regeneration.” PLoS Biol, 19, 2, Pp. e3001122. Publisher’s Version
2020
Gong S, Kirmizialtin S, Chang A, Mayfield JE, Zhang YJ, and Johnson KA. “Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis.” JBC. Publisher’s Version
Ramani M.K.V, Escobar E.E., Irani S., Mayfield JE, Moreno RY, Butalewicz, J., Cotham V.C, Wu H., Tadros M, Brodbelt JS, and Zhang YJ. “Structure Motif for CTD kinase Specificity on RNA polymerase II during Eukaryotic Transcription.” ACS Chemical Biology. Publisher’s Version
Aggarwal K, Kuka TP, Banik M, Medellin BP, Ngo CQ, Xie D, Fernandes Y, Dangerfield TL, Ye E, Bouley B, Johnson KA, Zhang YJ, Eberhart JK, and Que EL. “Visible Light Mediated Bidirectional Control Over Carbonic Anhydrase Activity in Cells and in Vivo Using Azobenzene Sulfonamides.” J. Am. Chem. Soc. Publisher’s Version
Mayfield J.E., Irani S., and Zhang Y.J. “Electrophoretic Mobility Shift Assay of in vitro Phosphorylated RNA Polymerase II Carboxyl-terminal Domain Substrates.” Bioprotocol, 10, 12. Publisher’s Version
Lu W.C., Saha A., Yan W., Garrison K., Pandey R., Irani S., Tiziani S., Zhang Y.J., Georgiou G., DiGiovanni J., and Stone E. “Enzyme-Mediated Depletion of Serum L-Met Abrogates Prostate Cancer Growth via Multiple Mechanisms without Evidence of Systemic Toxicity.” PNAS. Publisher’s Version
Medellin B.P., Lancaster E.B., Brown S.D., Rakhade S., Babbitt P.C., Whitman C.P., and Zhang Y.J. “Structural Basis for the Asymmetry of a 4-Oxalocrotonate Tautomerase Trimer.” Biochemistry, 59, 16, Pp. 1592-1603. Publisher’s Version
2019
Lee J, Der B.S, Karamitros C.S, Li W, Marshall N.M, Lungu O.I., Miklos A.E., Xu J, Kang T.H., Lee C.H., Tan B., Hughes R.A., Jung S.T., Ippolito G.C., Gray J.J, Zhang YJ, Kuhlman B., Georgiou G.*, and Ellington A.D*. “Rosetta-based Engineering of Thermostabilized Antibody Fragments.” AlChE Journal. Publisher’s Version
Burkholder, N.T., Sipe, S.N., Escobar, E.E., Kumar, M., Irani, S, Yang, W., Wu, H., Matthews, W.M., Brodbelt*, J.S., and Y.J Zhang *. “Mapping RNAPII CTD phosphorylation reveals that the identity and modification of seventh heptad residues direct.” ACS Chemical Biology, 14, 10, Pp. 2264-2275. Publisher’s Version
Naowarojnan, N*., Irani, S*, Hu, W., Cheng, R., Zhang, L., Li, X., Chen *, J., YJ* Zhang *, and P Liu *. “Crystal Structure of the Ergothioneine Sulfoxide Synthase from Candidatus Chloracidobacterium thermophilum and Structure-Guided Engineering to Modulate Its Substrate Selectivity.” ACS Catalysis, 9, 8, Pp. 6955-6961. Publisher’s Version
Mayfield, J.E*., Irani, S*, Escobar, E.E., Zhang, L., Burkholder, N.T., Robinson, M.R., Mehaffey, M.R., Sipe, S.N., Yang, W., Prescott, N., Kathuria, K.R., Liu, Z., J.S Brodbelt, and Y.J Zhang. “Tyr1 phosphorylation promotes phosphorylation of Ser2 on the C-terminal domain of eukaryotic RNA polymerase II by P-TEFb.” eLife. Publisher’s Version
Irani, S, Sipe, S.N., Yang, W., Burkholder, N.T., Lin, B., Sim, K., Matthews, W.M., Brodbelt, J.S., and Y.J Zhang. “Structural determinants for accurate dephosphorylation of RNA polymerase II by its cognate CTD phosphatase during eukaryotic transcription.” JBC, 294, 21, Pp. 8592-8605. Publisher’s Version
Baas, B., Medellin, B.P., LeVieux, J.A., de Ruijter, M., Y.J. Zhang *, Brown, S.D., Akiva, E., Babbitt, P.C., and C.P. Whitman *. “Structural, Kinetic, and Mechanistic Analysis of an Asymmetric 4-Oxalocrotonate Tautomerase Trimer.” Biochemistry, 10, 35, Pp. 803– 813. Publisher’s Version
Wang, S. A., Ko, Y., Zeng, J., Ren D. Ogasawara Y. Irani S. Zhang Y. Liu H. W Geng, Y., Ren, D., Ogasawara, Y., Irani, S, Y. J. Zhang, and H. W Liu. “Identification of the Formycin A Biosynthetic Gene Cluster from Streptomyces kaniharaensis Illustrates the Interplay between Biological Pyrazolopyrimidine Formation and de novo Purine Biosynthesis.” J. Am. Chem. Soc. , 141, 15, Pp. 6127-6131. Publisher’s Version
2018
Burkholder, N.T., Mayfield, J.E., Yu, X., Irani, S, Arce, D.K., Jiang, F., Matthews, W.M., Xue, Y., and Y. J. Zhang. “Phosphatase activity of Small C-terminal domain phosphatase 1 (SCP1) controls the stability of the key neuronal regulator RE1-silencing transcription factor (REST).” JBC, 293, 43, Pp. 16851-16861. Publisher’s Version
LeVieux, J.A., Medellin, B.P., Johnson, W.H. Jr., Erwin, K., Li, X., Johnson, W.H. Jr., YJ. Zhang *, and C.P* Whitman. “Structural Characterization of the Hydratase-Aldolases, NahE, and PhdJ: Implications for the Specificity, Catalysis, and N-Acetylneuraminate Lyase Subgroup of the Aldolase Superfamily.” Biochemistry, 57, 25, Pp. 3524-3536 . Publisher’s Version
Irani, S*, Naowarojna, N., Tang, Y., Kathuria, K.R., Wang, S. A., Dhembi, A., Lee, N., Yan, W., Lyu, H., Costello, C.E., P. Liu, and Y. J. Zhang. “Snapshots of C-S cleavage in Egt2 reveals substrate specificity and reaction mechanism.” Cell Chemical Biology, 25, 5, Pp. 519-529.e4. . Publisher’s Version
Burkholder, N.T., Medellin, B.P., Irani, S, Matthews, W.M., Showalter, S.A., and Y. J. Zhang. “Chemical tools for studying the impact of cis/trans prolyl isomerization on RNA polymerase II CTD phosphatase activity and specificity.” In Methods in Enzymology, 607: Pp. 269-297.
Stack, T.M.M., Li, W., Johnson, W.H. Jr., YJ Zhang, and C.P. Whitman. “Inactivation of 4-Oxalocrotonate Tautomerase by 5-Halo-2-hydroxy-2,4-pentadienoates.” Biochemistry, 57, 6, Pp. 1012-1021. Publisher’s Version
Davidson, R., Baas, B., Akiva, E., Holliday, G.L., Polacco, B.J., LeVieux, J.A., Pullara, C.R., YJ Zhang, C.P Whitman, and P.C. Babbitt. “A Global View of Structure-Function Relationships in the Tautomerase Superfamily.” JBC, 293, 7, Pp. 2342-2357. Publisher’s Version
2017
LeVieux, J.A., Baas, B., Kaoud, T.S., Davidson, R., Babbitt, P.C., YJ Zhang, and C.P. Whitman. “Kinetic and structural characterization of a cis-3-Chloroacrylic acid dehalogenase homologue in Pseudomonas sp. UW4: A potential step between subgroups in the tautomerase superfamily.” Arch. Biophy. Biochem. , 636, Pp. 50-56. . Publisher’s Version
Lee, N., Romain, G., Yan, W., Watanabe, M., Charab, W., Todorova, B., Lee J., Triplett, K., Donkor, M., Lungu, O.I., A. Lux, Marshall, N., Lindorfer, M.A., Goff, O.R., Balbino, B., Kang, T.H., Tanno, H., G Delidaki, Alford, C., R.P. Taylor, Nimmerjahn, F., Varadarajan, N., Bruhns, P., Y. J. Zhang, and G. Georgiou. “IgG Fc Domains that bind C1q but not effector Fcgamma receptors delineate that significance of complement-mediated cell cytotoxicity and phagocytosis in antibody function.” Nature Immunology. , 18, 8, Pp. 889-898. Publisher’s Version
Gibbs, E.B., Y Lu, B Portz, M. J. Fisher, Medellin, B.P., Laremore, T.N., Zhang, L., Gilmour, D.S., and S.A Showalter. “Phosphorylation Induces Sequence-Specific Conformational Switches in the RNA Polymerase II C-Terminal Domain.” Nature Communications. , 8, Pp. 15233. Publisher’s Version
Portz, B., Lu, Gibbs, E.B., Mayfield, J.E., Mehaffey, M.R., Zhang, L., Brodbelt, J.S., Showalter, S.A., and D.S. Gilmour. “Structural heterogeneity in the intrinsically disordered RNA polymerase II C-terminal domain.” Nature Communications., 8, Pp. 15231. Publisher’s Version
Yan, W., Georgiou, G., Stone, E., and Y. J. Zhang. “Structural Snapshots of an Engineered Cystathionine-gamma-lyase Reveal the Critical Role of Electrostatic Interactions in the Active Site.” Biochemistry, 56, 6, Pp. 876-885. Publisher’s Version
2016
Cramer, S., Saha, A., Tadi, S., Tiziani, S., Yan, W., Triplett, K., Lamb, C., S. Alters, Johnson, W.H. Jr., Zhang, L., DiGiovanni, J., Georgiou, G., and E. Stone. “Systemic depletion of serum L-Cyst(e)ine with an engineered human enzyme induces the production of reactive oxygen species and suppresses tumor growth in mice.” Nature Medicine, 23, 1, Pp. 120-127. Publisher’s Version
Mayfield, J.E., Robinson, M.R., Cotham, V.C., Irani, S, Matthews, W.M., Ram, A., Gilmour, D.S., Cannon, J.R., YJ Zhang *, and J.S Brodbelt *. “Mapping the phosphorylation pattern of Drosophila RNA polymerase II carboxyl-terminal domain using ultraviolet photodissociation mass spectrometry.” ACS Chemical Biology, 12, 1, Pp. 153-162. Publisher’s Version
Mayfield, J.E., Burkholder, N.T., and Y. J. Zhang. “Dephosphorylating eukaryotic RNA polymerase II.” BBA Proteins Proteom. , 1864, 4, Pp. 372-387. Publisher’s Version
Irani, S, Yogesha, S.D., Mayfield, J.E., Zhang, L., Zhang, L., Matthews, W.M., Nie, G., Prescott, N., and Y. Zhang. “Structure of Saccharomyces cerevisiae Rtr1 reveals an active site for an atypical phosphatase.” Science Signaling, 9, Pp. 417. Publisher’s Version
Li, W., Irani. S., Crutchfield, A., Hodge, K., Matthews, W.M., Patel, P., Zhang *, YJ, and E. Stone *. “Intramolecular Cleavage of the hASRGL1 Homodimer Occurs in Two Stages.” Biochemistry, 55, 6, Pp. 960-969. Publisher’s Version
LeVieux, J.A., Johnson, W.H. Jr., Erwin, K., Li, X., Y. J. Zhang, and C.P. Whitman. “The bacterial catabolism of polycyclic aromatic hydrocarbons: Characterization of three hydratase-aldolase-catalyzed reactions.” Perspective in Science., 99, Pp. 33-41. Publisher’s Version
2015
Mayfield, J.E., Fan, S., Wei, S., Zhang, L., Li, X., Ellington, A.D., Etzkorn, F.A., and Y. J. Zhang. “Chemical tools to decipher regulation of phosphatases by proline isomerization on eukaryotic RNA polymerase II.” ACS Chemical Biology, 10, 10, Pp. 2405-14. Publisher’s Version
Wei, S., Kozono, S., Kats, L., Nechama, M., Li, X., Guarnerio, J., Luo, M., You, M.H., Y. Yao, Kondo, A., Hu, W., Bozkurt, G., Moerke, N., Cao, S., Reschke, M., Chen, J., Rego, E.M., Lo-Coco, F., L.C. Cantley, Lee, N., Wu, H., YJ Zhang, Pandolfi, P.P., Zhou, X.Z., and K.P. Lu. “Active Pin1 is a key target of all-trans retinoic acid in acute promyelocytic leukemia and breast cancer.” Nature Medicine, 21, Pp. 457-466. Publisher’s Version
Chen, J., Li, X., Sultana, R., You, M.H., Kondo, A., Shahpasand, K., Kim, B., Luo, M., M Nechama, Lin, B., Yao, Y., Lee, N., Zhou, X.Z., Swomley, A., D Butterfield*, YJ Zhang *, and KP Lu*. “Pin1 cysteine-113 oxidation inhibits its catalytic activity and cellular function in Alzheimer’s disease.” Neurobiol. Dis. , 76, Pp. 13-23. Publisher’s Version
He, Y., Guo, Y., Yu, X., Wu, H., Gunawan, A.M., YJ Zhang, Dixon, J.E., and Z.Y. Zhang. “A potent and selective inhibitor for the UBLCP1 proteasome phosphatase.” Bioorg. Med. Chem., 23, 12, Pp. 2798-2809. . Publisher’s Version
2014