Publications

 

57. Burkholder, N.T., Sipe, S.N., Escobar, E.E., Kumar, M., Irani, S., Yang, W., Wu, H., Matthews, W.M., Brodbelt, J.S., and Zhang, Y. (2019).
Mapping RNAPII CTD phosphorylation reveals that the identity and modification of seventh heptad residues direct Tyr1 phosphorylation. ACS Chem Biol. 2019 Sep 25. doi: 10.1021/acschembio.9b00610. [Epub ahead of print] PubMed PMID: 31553563.

 

56. Mayfield, J.E., Irani, S., Escobar, E.E., Zhang, Z., Burkholder, N.T., Robinson, M.R., Mehaffey, M.R., Sipe, S.N.,Yang, W., Prescott, N., Kathuria, K.R., Liu, Z., Brodbelt, J.S. and Zhang, Y.* (2019).
Tyr1 phosphorylation promotes phosphorylation of Ser2 on the C-terminal domain of eukaryotic RNA polymerase II by P-TEFb. eLife 2019 doi:10.7554/eLife.48725

 

55. Naowarojnan, N., Irani, S. (co-first author), Hu, W., Cheng, R., Zhang, L., Li, X., Chen, J.*, Zhang, Y.*, and Liu, P.* (2019). Crystal Structure of the Ergothioneine Sulfoxide Synthase from Candidatus Chloracidobacterium thermophilum
and Structure-Guided Engineering To Modulate Its Substrate Selectivity. ACS Catal. 2019 July 2. doi.org/10.1021/acscatal.9b02054 *co-corresponding author in publication

 

54. Baas, B., Medellin, B.P., LeVieux, J.A., de Ruijter, M., Zhang, Y.J.*, Brown, S.D., Akiva, E., Babbitt, P.C., and Whitman, C.P.* (2019). Structural, Kinetic, and Mechanistic Analysis of an Asymmetric 4-Oxalocrotonate Tautomerase Trimer.
Biochemistry. 2019 May 10.doi: 10.1021/acs.biochem.9b00303 *co-corresponding author in publication

 

53. Irani, S., Sipe, S.N., Yang, W., Burkholder, N. T., Lin, B., Sim, K., Matthews, W. L., Brodbelt, J.S. and Zhang, Y. (2019). Structural determinants for accurate dephosphorylation of RNA polymerase II by its cognate CTD phosphatase during eukaryotic transcription.
Jour. of Biol. Chem. 2019 Apr 10.doi: 10.1074/jbc.RA119.007697 .

 

52. Wang, S. A., Ko, Y., Zeng, J., Geng, Y., Ren, D., Ogasawara, Y., Irani, S., Zhang, Y., Liu, H. W. (2019). 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. 2019 Apr 8. doi: 10.1021/jacs.9b00241. PubMed PMID: 30942582.

 

51.Burkholder, N.T., Mayfield, J.E., Yu, X., Irani, S., Arce, D.K., Jiang, F., Matthews, W.L., Xue, Y., Zhang, Y. J. (2018). Phosphatase activity of Small C-terminal domain phosphatase 1 (SCP1) controls the stability of the key neuronal regulator RE1-silencing transcription factor (REST).
Jour. of Biol. Chem. doi:10.1074/jbc.RA118.004722

 

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. 607; 269-297.
doi:10.1016/bs.mie.2018.04.020

 

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. 57, 25, 3524-3536 doi:10.1021/acs.biochem.8b00532.
*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. 2018 May 17; 25(5): 519-529.e4. doi:10.1016/j.chembiol.2018.02.002

 

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. 57 (6), 1012-1021. 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. 293(7), 2342-2357.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. 2017 Dec 15; 636: 50-56. doi:10.1016/j.abb.2017.10.018

 

44. Lee, C.H., Romain, G., Yan, W., 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. 18(8),889-898. 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. 8,15233. 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. 8,15231. 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. 56(6), 876-885. 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. 12 (1), 153-162. doi:10.1021/acschembio.6b00729 *co-corresponding author

 

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. 23(1), 120-127. 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.T., 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 *co-corresponding author

 

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 *co-corresponding author

 

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 *co-corresponding author

 

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), 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 *co-corresponding author

 

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, R.H., 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. 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, K.P., 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. USA. 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. doi:10.1016/S0968-0896(03)00458-9

 

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. doi:10.1016/S0968-0896(03)00457-7

 

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. doi:10.1016/S0968-0896(03)00456-5

 

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. doi:10.1021/bi020522m

 

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. doi:10.1016/S0968-0896(02)00102-5

 

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. doi:10.1021/bi991711g