50. Burkholder, N.T., Medellin, B.P., Irani, S., Matthews, W.L., Showalter, S.A.,and Zhang, Y.J. (2018). Chemical tools for studying the impact of cis/trans prolyl isomerization on RNA polymerase II CTD phosphatase activity and specificity. Methods in Enzymology. In press


49. LeVieux, J.A., Medellin, B. (co-first author), Johnson, W.H. Jr., Erwin, K., Li, W., Johnson, I.A., Zhang, Y.J.*, Whitman, C.P.* (2018).
Structural Characterization of the Hydratase-Aldolases, NahE and PhdJ: Implications for the Specificity, Catalysis, and N-Acetylneuraminate Lyase Subgroup of the Aldolase Superfamily Biochemistry. doi: 10.1021/acs.biochem.8b00532. In press.
*co-corresponding author


48. Irani, S., Naowarojna, N., Tang, Y., Kathuria, K.R., Wang, S., Dhembi, A., Lee, N., Yan, W., Lyu, H., Costello, C.E., Liu, P. and Zhang, Y.J. (2018). Snapshots of C-S cleavage in Egt2 reveals substrate specificity and reaction mechanism. Cell Chemical Biology. In press


47.Stack,T.M.M., Li, W., Johnson, W.H., Zhang, Y.J., Whitman, C.P. (2018). Inactivation of 4-Oxalocrotonate Tautomerase by 5-Halo-2-hydroxy-2,4-pentadienoates. Biochemistry. doi: 10.1021/acs.biochem.7b00899


46. Davidson, R., Baas, B-J., Akiva, E., Holliday, G. L., Polacco, B. J., LeVieux, J. A., Pullara, C. R., Zhang, Y. J., Whitman, C. P., and Babbitt, P. C. (2017). A Global View of Structure-Function Relationships in the Tautomerase Superfamily Jour. of Biol. Chem.doi: 10.1074/jbc.M117.815340.


45. LeVieux, J. A., Baas, B-J., Kaoud, T. S., Davidson, R., Babbitt, P. C., Zhang, Y. J., and Whitman, C. P. (2017). 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.


44. Lee, C. H., Romain, G, Yan, W. P., Watanabe, M., Charab, W., Todorova, B., Lee J., Triplett, K., Donkor, M., Lungu, O. I., Lux, A., Marshall, N., Lindorfer, M. A., Goff, O. R., Balbino, B., Kang, T. H., Tanno, H., Delidaki, G., Alford, C., Taylor, R. P. Nimmerjahn, F., Varadarajan, N., Bruhns, P., Zhang, Y. J. and Georgiou, G. (2017). 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. doi:10.1038/ni.3770


43. Gibbs, E. B., Lu, F., B., Fisher, M. J., Medellin, B. P., Laremore, T. N., Zhang, Y. J., Gilmour, D. S.,and Showalter, S. A. (2017). Phosphorylation Induces Sequence-Specific Conformational Switches in the RNA Polymerase II C-Terminal Domain. Nature Communications. doi:10.1038/ncomms15233


42. Portz, B., Lu, F., Gibbs, E.B., Mayfield, J.E., Mehaffey, M.R., Zhang, Y. J., Brodbelt, J.S., Showalter, S.A., Gilmour, D.S. (2017). Structural heterogeneity in the intrinsically disordered RNA polymerase II C-terminal domain. Nature Communications. doi: 10.1038/ncomms15231


41. Yan, W., Georgiou, G., Stone, E. and Zhang, Y. J. (2017).Structural Snapshots of an Engineered Cystathionine-gamma-lyase Reveal the Critical Role of Electrostatic Interactions in the Active Site. Biochemistry. doi: 10.1021/acs.biochem.6b01172


40. LeVieux, J.A., Johnson, W.H., Erwin, K., Li, W., Zhang, Y. J. and Whitman, C.P. (2016).The baterial catabolism of polycyclic aromatic hydrocarbons: Characterization of three hydratase-aldolase-catalyzed reactions. Perspective in Science. 9, 33-41, doi: 10.1016/j.pisc.2016.03.025


39. Mayfield, J.E., Robinson, M.R., Cotham, V.C., Irani, S., Matthews, W.L., Ram, A., Gilmour, D.S., Cannon, J.R., Zhang, Y. J.*, and Brodbelt, J.S*. (2016). Mapping the phosphorylation pattern of Drosophila RNA polymerase II carboxyl-terminal domain using ultraviolet photodissociation mass spectrometry. ACS Chem Biol. doi:10.1021/acschembio.6b00729


38. Cramer, S., Saha, A., Tadi, S., Tiziani, S., Yan, W., Triplett, K., Lamb, C., Alters, S., Johnson, D., Zhang, Y., DiGiovanni, J., Georgiou, G., and Stone, E. (2016). Systemic depletion of serum L-Cyst(e)ine with an engineered human enzyme induces production of reactive oxygen species and suppresses tumor growth in mice. Nature Medicine. doi:10.1038/nm.4232


37. Irani, S., Yogesha, S. D., Mayfield, J. E., Zhang, M., Zhang, Y., Matthews, W., Nie, G., Prescott, N., Zhang, Y.* (2016). Structure of Saccharomyces cerevisiae Rtr1 reveals an active site for an atypical phosphatase. Sci. Signal. 9(417)doi:10.1126/scisignal.aad4805


36. Mayfield, J. E., Burkholder, N., and Zhang,Y.* (2016). Dephosphorylating eukaryotic RNA polymerase II. BBA Proteins Proteom. 1864 (4) 372-387 doi:10.1016/j.bbapap.2016.01.007


35. Li, W., Irani. S., Crutchfield, A., Hodge, K., Matthews, W., Patel, P., Zhang,Y.*, and Stone, E.* (2016). Intramolecular Cleavage of the hASRGL1 Homodimer Occurs in Two Stages. Biochem.55(6) 960-9 doi:10.1021/acs.biochem.5b01157


34. Yan, W., Song, H., Song, F., Guo, Y., Wu, C.H., Her, A.S., Pu,Y., Wang, S., Naowarojna, N., Weitz, A., Hendrich, M.P., Costello, C.E., Zhang, L.*, Liu, P.,* and Zhang,Y.* (2015). Endoperoxide Formation by an a-Ketoglutarate-dependent Mononuclear Non-heme Iron Enzyme. Nature.527 539-543 doi:10.1038/nature15519


33. Mayfield, J. E., Fan, S., Wei, S., Zhang, M., Li, B., Ellington, A.D., Etzkorn, F.A., and Zhang,Y.* (2015). Chemical tools to decipher regulation of phosphatases by proline isomerization on eukaryotic RNA polymerase II. (cover story) ACS Chem Biol.10(10)2405-14 doi:10.1021/acschembio.5b00296


32. Wei, S., Kozono, S., Kats, L., Nechama, M., Li, W., Guarnerio, J., Luo, M., You, M.H., Yao, Y., Kondo, A., Hu, H., Bozkurt, G., Moerke, N., Cao, S., Reschke, M., Chen, C.H., Rego, E.M., Lo-Coco, F., Cantley, L.C., Lee, T.H., Wu, H., Zhang, Y., Pandolfi, P.P., Zhou, X.Z., Lu, K.P. (2015). Active Pin1 is a key target of all-trans retinoic acid in acute promyelocytic leukemia and breast cancer. Nat Med.21 457-466 doi:10.1038/nm.3839.


31. He, Y., Guo, X., Yu, Z.H., Wu, L., Gunawan, A.M., Zhang, Y., Dixon, J.E., Zhang, Z.Y.(2015). A potent and selective inhibitor for the UBLCP1 proteasome phosphatase. Bioorg. Med. Chem.23(12)2798-2809 doi:10.1016/j.bmc.2015.03.066


30. Chen, C., Li, W., Sultana, R., You, M., Kondo, A., Shahpasand, K., Kim, B., Luo, M., Nechama, M., Lin, Y., Yao, Y., Lee, T., Zhou, X., Swomley, A., Butterfield, D., Zhang, Y.*, Lu, K.(2015). Pin1 cysteine-113 oxidation inhibits its catalytic activity and cellular function in Alzheimer's disease. Neurobiol. Dis.,(76)13-23. doi:10.1016/j.nbd.2014.12.027


29.  O'Brien, J. P., Li, W., Zhang  Y., Brodbelt, J. S. (2014). Characterization of Native Protein Complexes Using Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc., 136 (37), pp 12920-12928 doi: 10.1021/ja505217w


28.  Yogesha S. D. , Mayfield J. E. and Zhang  Y. (2014). Cross-talk of phosphorylation and prolyl isomerization of the C-terminal domain of RNA Polymerase II. Molecules 19(2),1481-1511.doi:10.3390/molecules19021481


27.  Luo, Y., Yogesha, S. D., Cannon, J. R., Yan, W., Ellington, A. D., Brodbelt, J. S., & Zhang, Y. (2013). Novel Modifications on C-terminal Domain of RNA Polymerase II Can Fine-tune the Phosphatase Activity of Ssu72. ACS Chem Biol.8(9),2042-2052. doi:10.1021/cb400229c


26.  Shaw, J. B., Li, W., Holden, D. D., Zhang, Y., Griep-Raming, J., Fellers, R. T., Early, B. P., Thomas, P. M.,  Kelleher, N. L., Brodbelt, J. S. (2013). Complete Protein Characterization Using Top-Down Mass Spectrometry and Ultraviolet Photodissociation. J Am Chem Soc.135(34),12646-12651. doi:10.1021/ja4029654


25. Li, W., Cantor, J. R., Yogesha, S. D., Yang, S., Chantranupong, L., Liu, J. Q., Agnello, G., Georgiou, G., Stone, E. M., Zhang, Y. (2012). Uncoupling intramolecular processing and substrate hydrolysis in the N-terminal nucleophile hydrolase hASRGL1 by circular permutation. ACS Chem Biol, 7(11), 1840-1847. doi:10.1021/cb300232n


24. Zhang, M., Wang, X. J., Chen, X., Bowman, M. E., Luo, Y., Noel, J. P., Ellington, A. D., Etzkorn, F. A.,  Zhang, Y.* (2012). Structural and kinetic analysis of prolyl-isomerization/phosphorylation cross-talk in the CTD code. ACS Chem Biol, 7(8), 1462-1470. doi:10.1021/cb3000887  *co-corresponding author in publication


23.  Tavares, C. D., O'Brien, J. P., Abramczyk, O., Devkota, A. K., Shores, K. S., Ferguson, S. B., Kaoud, T. S., Warthaka, M., Marshall, K. D., Keller, K. M., Zhang, Y., Brodbelt, J. S., Ozpolat, B., Dalby, K. N. (2012). Calcium/calmodulin stimulates the autophosphorylation of elongation factor 2 kinase on Thr-348 and Ser-500 to regulate its activity and calcium dependence. Biochemistry, 51(11), 2232-2245. doi:10.1021/bi201788e


22.  Xu, G. G., Zhang, Y.*, Mercedes-Camacho, A. Y., & Etzkorn, F. A.*(2011). A reduced-amide inhibitor of Pin1 binds in a conformation resembling a twisted-amide transition state. Biochemistry, 50(44), 9545-9550. doi:10.1021/bi201055c

 *co-corresponding author in publication       


21.  Burks, E. A., Yan, W., Johnson, W. H., Jr., Li, W., Schroeder, G. K., Min, C., Gerratana, B., Zhang, Y.*, Whitman, C. P. (2011). Kinetic, crystallographic, and mechanistic characterization of TomN: elucidation of a function for a 4-oxalocrotonate tautomerase homologue in the tomaymycin biosynthetic pathway. Biochemistry, 50(35), 7600-7611. doi:10.1021/bi200947w

 *co-corresponding author in publication


20.  Lee, T. H., Chen, C. H., Suizu, F., Huang, P., Schiene-Fischer, C., Daum, S., Zhang, Y., Goate, A., Chen, RH., Zhou, X. Z., Lu, K. P. (2011). Death-associated protein kinase 1 phosphorylates Pin1 and inhibits its prolyl isomerase activity and cellular function. Mol Cell, 42(2), 147-159. doi: 10.1016/j.molcel.2011.03.005


19.   Zhang, M., Cho, E. J., Burstein, G., Siegel, D., & Zhang, Y. (2011). Selective inactivation of a human neuronal silencing phosphatase by a small molecule inhibitor. ACS Chem Biol, 6(5), 511-519. doi:10.1021/cb100357t

          (Featured cover May 2011, featured story in podcast May 2011)


18. Zhang, Y., Zhang, M., & Zhang, Y. (2011). Crystal structure of Ssu72, an essential eukaryotic phosphatase specific for the C-terminal domain of RNA polymerase II, in complex with a transition state analogue. Biochem J, 434(3), 435-444. doi:10.1042/BJ20101471      


17. Zhang, M., Gill, G. N., & Zhang, Y. (2010). Bio-molecular architects: a scaffold provided by the C-terminal domain of eukaryotic RNA polymerase II. Nano Rev, 1. doi:10.3402/nano.v1i0.5502 (invited review)


16.  Zhang, M., Liu, J., Kim, Y., Dixon, J. E., Pfaff, S. L., Gill, G. N., Noel, J. P., Zhang, Y. (2010). Structural and functional analysis of the phosphoryl transfer reaction mediated by the human small C-terminal domain phosphatase, Scp1. Protein Sci, 19(5), 974-986. doi:10.1002/pro.375




Publications during graduate and postdoctoral training




15.  Zhang, Y., Daum, S., Wildemann, D., Zhou, X. Z., Verdecia, M. A., Bowman, M. E., Lücke, C., Hunter, T., Lu, KP., Fischer, G., Noel, J. P. (2007). Structural basis for high-affinity peptide inhibition of human Pin1. ACS Chem Biol, 2(5), 320-328. doi:10.1021/cb7000044


14.  Zhang, Y., Kim, Y., Genoud, N., Gao, J., Kelly, J. W., Pfaff, S. L., Gill, G. N., Dixon, J. E.,  Noel, J. P. (2006). Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1. Mol Cell, 24(5), 759-770. doi:10.1016/j.molcel.2006.10.027


13.  Jager, M., Zhang, Y., Bieschke, J., Nguyen, H., Dendle, M., Bowman, M. E., Noel, J. P., Gruebele, M., Kelly, J. W. (2006). Structure-function-folding relationship in a WW domain. Proc Natl Acad Sci U S A, 103(28), 10648-10653. doi:10.1073/pnas.0600511103


12.  Cheng, H., Hwang, I., Chong, Y., Tavassoli, A., Webb, M. E., Zhang, Y., Wilson, I. A., Benkovic, S. J., Boger, D. L. (2005). Synthesis and biological evaluation of N-[4-[5-(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)-2-(2,2,2-trifluoroacetyl)pe ntyl]benzoyl]-L-glutamic acid as a potential inhibitor of GAR Tfase and the de novo purine biosynthetic pathway. Bioorg Med Chem, 13(10), 3593-3599. doi:10.1016/j.bmc.2004.11.049


11.  Chong, Y., Hwang, I., Tavassoli, A., Zhang, Y., Wilson, I. A., Benkovic, S. J., & Boger, D. L. (2005). Synthesis and biological evaluation of alpha- and gamma-carboxamide derivatives of 10-CF3CO-DDACTHF. Bioorg Med Chem, 13(10), 3587-3592. doi:10.1016/j.bmc.2004.11.050


10.  Cheng, H., Chong, Y., Hwang, I., Tavassoli, A., Zhang, Y., Wilson, I. A., Benkovic, S. J., Boger, D. L. (2005). Design, synthesis, and biological evaluation of 10-methanesulfonyl-DDACTHF, 10-methanesulfonyl-5-DACTHF, and 10-methylthio-DDACTHF as potent inhibitors of GAR Tfase and the de novo purine biosynthetic pathway. Bioorg Med Chem, 13(10), 3577-3585. doi:10.1016/j.bmc.2004.12.004


9.  Zhang, Y., Wang, L., Schultz, P. G., & Wilson, I. A. (2005). Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine. Protein Sci, 14(5), 1340-1349. doi:10.1110/ps.041239305


8.  Desharnais, J., Hwang, I., Zhang, Y., Tavassoli, A., Baboval, J., Benkovic, S. J., Wilson, I. A., Boger, D. L. (2003). Design, synthesis and biological evaluation of 10-CF3CO-DDACTHF analogues and derivatives as inhibitors of GAR Tfase and the de novo purine biosynthetic pathway. Bioorg Med Chem, 11(20), 4511-4521


7.   Marsilje, T. H., Hedrick, M. P., Desharnais, J., Capps, K., Tavassoli, A., Zhang, Y., Wilson, I. A., Benkovic, S. J., Boger, D. L. (2003). 10-(2-benzoxazolcarbonyl)-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid: a potential inhibitor of GAR transformylase and AICAR transformylase. Bioorg Med Chem, 11(20), 4503-4509


6.  Marsilje, T. H., Hedrick, M. P., Desharnais, J., Tavassoli, A., Zhang, Y., Wilson, I. A., Benkovic, S. J., Boger, D. L. (2003). Design, synthesis, and biological evaluation of simplified alpha-keto heterocycle, trifluoromethyl ketone, and formyl substituted folate analogues as potential inhibitors of GAR transformylase and AICAR transformylase. Bioorg Med Chem, 11(20), 4487-4501.


5.  Zhang, Y., Desharnais, J., Marsilje, T. H., Li, C., Hedrick, M. P., Gooljarsingh, L. T., Tavassoli, A., Benkovic, S. J., Olson, A. J., Boger, C. L., Wilson, I. A. (2003). Rational design, synthesis, evaluation, and crystal structure of a potent inhibitor of human GAR Tfase: 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid. Biochemistry, 42(20), 6043-6056. doi:10.1021/bi034219c


4.  Peters, R. J., Carter, O. A., Zhang, Y., Matthews, B. W., & Croteau, R. B. (2003). Bifunctional abietadiene synthase: mutual structural dependence of the active sites for protonation-initiated and ionization-initiated cyclizations. Biochemistry, 42(9), 2700-2707. doi:10.1021/bi020492n


3.  Zhang, Y., Desharnais, J., Greasley, S. E., Beardsley, G. P., Boger, D. L., & Wilson, I. A. (2002). Crystal structures of human GAR Tfase at low and high pH and with substrate beta-GAR. Biochemistry, 41(48), 14206-14215.


2.  Marsilje, T. H., Labroli, M. A., Hedrick, M. P., Jin, Q., Desharnais, J., Baker, S. J., Gooljarsingh, L. T., Ramcharan, J., Tavassoli, A., Zhang, Y., Wilson, I. A., Beardsley, G. P., Benkovic, S. J., Boger, D. L. (2002). 10-Formyl-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid (10-formyl-DDACTHF): a potent cytotoxic agent acting by selective inhibition of human GAR Tfase and the de novo purine biosynthetic pathway. Bioorg Med Chem, 10(8), 2739-2749.


1.  Lowther, W. T., Zhang, Y., Sampson, P. B., Honek, J. F., & Matthews, B. W. (1999). Insights into the mechanism of Escherichia coli methionine aminopeptidase from the structural analysis of reaction products and phosphorus-based transition-state analogues. Biochemistry, 38(45), 14810-14819.