Additional Publications

30. 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

29. Yogesha SD, Mayfield JE and Zhang Y. Cross-Talk of Post-Translational Modifications of the C-terminal Domain of RNA Polymerase II. Molecules. 2014 Jan 19(2):1481-511. ,2 doi:10.3390/molecules19021481.

28. Luo Y, Yogesha SD, Cannon JR, Yan W, Ellington AD, Brodbelt JS and Zhang Y.

Novel Modifications on C-terminal Domain of RNA Polymerase II can Fine-tune the Phosphatase Activity of Ssu72. ACS Chemical Biol. 2013 Sep; 8(9): 2042-52.

27. Shaw JB, Li W, Holden DD, Zhang Y, Griep-Raming J, Fellers RT, Early BP, Thomas PM, Kelleher NL, Brodbelt JS.

Complete Protein Characterization Using Top-Down Mass Spectrometry and Ultraviolet Photodissociation. J Am Chem Soc. 2013. Aug; 135(34): 12646-51.

26. Zhang M, Yogesha SD, Mayfield JE, Gill GN and Zhang Y.

View Serine/Threonine Protein Phosphatases in the Eyes of Drug Designers. FEB J 2013 Oct; 280(19): 4739-60. ,2

25. Li W, Cantor JR, Yogesha SD, Yang S, Chantranupong L, Liu JQ, Agnello G, Georgiou G, Stone EM and Zhang Y.

Uncoupling Intramolecular Processing and Substrate Hydrolysis in the N-terminal Nucleophile Hydrolase hASRGL1 by Circular Permutation. ACS Chemical Biol. 2012 Nov. 7(11): 1840-7.

24. Zhang M, Wang XJ, Chen X, Bowman ME, Luo Y, Noel JP, Ellington AD, Etzkorn EA and Zhang Y.

Structural and Kinetic Analysis of Prolyl-isomerization/ Phosphorylation Cross-Talk in the CTD code. ACS Chemical Biol. 2012 Aug. 7(8):1462-70.

23. Tavares CD, O’Brien JP, Abramczyk O, Devkota AK, Shores KS, Ferguson SB, Kaoud TS, Warthaka M, Marshall KD, Keller KM, Zhang Y, Brodbelt JS, Ozpolat B and Dalby KN. Calcium/Calmodulin Stimulates the Autophosphorylation of Elongation Factor 2 Kinase on Thr348 and Ser500 to Regulate its Activity and Calcium Dependence. Biochemistry. 2012 Mar, 51(11), 2232-2245.

22. Xu, Guoyan; Zhang, Y*; Mercedes-Camacho, Ana; Etzkorn, Felicia*

Reduced-Amide Inhibitor of Pin1 Binds in a Conformation Resembling a Twisted-Amide Transition State. Biochemistry. 2011 Nov 8;50(44):9545-50.*co-corresponding author

21. Burks E.A., Yan W., Johnson Jr.,W H., Li W., Schroeder G.K., Min C., Gerratana B., Zhang Y*., and Whitman C.P*.

  1. Crystallographic, and Mechanistic Characterization of TomN: Elucidation of a Function for a 4-Oxalocrotonate Tautomerase Homologuein the Tomaymycin Biosynthetic Pathway. Biochemistry. Biochemistry. 2011 Sep 6;50(35):7600-11. *co-corresponding author

20. Lee TH, Chen CH, Suizu F, HuangP, Schiene-Fischer C, Daum S, Zhang Y, Goate A, Chen RH, Zhou XZ, Lu KP.

Death-associated protein kinase1 phosphorylates Pin1 and inhibits its prolyl isomerase activity and cellular function. Mol Cell. 2011 Apr22;42(2):147-59.

19. Zhang M, Cho EJ, Burstein G, Siegel D, Zhang Y.

Selective inactivation of a human neuronal silencing phosphatase by a small molecule inhibitor. ACS Chemical Biol.2011 May 20;6(5):511-9.

18. Zhang Y, Zhang M, Zhang Y.

Crystal Structure of Ssu72, an essential eukaryotic phosphatase specific for the C-terminal domain of RNA polymerase II. Biochemical Journal. 2011, 2011 Feb 24;434(3):435-44

17. Zhang M, Gill GN, and Zhang Y.

Biomolecular architects: A scaffold provided by the C-terminal domain of eukaryotic RNA polymerase II. Nano Review2010, 1: 5502 – DOI: 10.3402/nano.v1i0.5502. , 2

16. Zhang M, Liu J, Kim Y, Dixon JE, Pfaff SL, Gill GN, Noel JP, Zhang Y.

Structural and functional analysis of the phosphoryl transfer reaction mediated by the human small C-terminal domain phosphatase, Scp1. Protein Sci. 2010 May;19(5):974-86.

 

15. Zhang Y, Daum S, Wilderman D, Zhou XZ, Verdecia MA, Bowman ME, Hunter T, Lu KP, Fischer G, Noel JP. Structural Basis for High-Affinity Peptide-Based Inhibition of Human Pin1. ACS Chem. Biol. 2007, 2 (5), 320–328.

[Featured as most cited of the year]

14. Zhang Y, Kim Y, Genoud N, Gao J, Kelly JW, Pfaff SL, Gill GN, Dixon JE, and Noel JP.

Preferential dephosphorylation of CTD by Scp1: complex structure of phosphatase Scp1 with CTD of RNA Polymerase II. Mol Cell, 2006; 24 (5): 759-70.

13. Jager M*, Zhang Y*, Nguyen H, Dendle G, Bowman ME, Gruebele M, Kelly JW. Structure-function-folding relationship in a WW domain. Proc Natl Acad Sci U S A.2006;103(28):10648-53.

 

Publications as a graduate student

12. Cheng H, Chong Y, Hwang I, Tavassoli A, Zhang Y, Wilson IA, Benkovic SJ, Boger DL.

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.2005;13(10):3577-85.

11. Chong Y, Hwang I, Tavassoli A, Zhang Y, Wilson IA, Benkovic SJ, Boger DL. Synthesis and biological evaluation of alpha- and gamma-carboxamide derivatives of 10-CF3CO-DDACTHF. Bioorg Med Chem.2005;13(10):3587-92.

10. Cheng H, Hwang I, Chong Y, Tavassoli A, Webb ME, Zhang Y, Wilson IA, Benkovic SJ, Boger DL. Synthesis and biological evaluation of N-{4-[5-(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)-2-(2,2,2-trifluoroacetyl)pentyl]benzoyl}-l-glutamic acid as a potential inhibitor of GAR Tfase and the de novo purine biosynthetic pathway. Bioorg Med Chem. 2005;13(10):3593-9

9. Zhang, Y*., Wang, L.*, Schultz, P.G., Wilson, I.A.

Crystal Structure of apo M. jannashii Tyrosyl-tRNA Synthetase and its O-methyl mutant. Protein Science. 2005;14 (5):1340-9.

8. Desharnais, J., Hwang, I., Zhang, Y., Tavassoli, A., Baboval, J., Benkovic, S.J., Wilson, I.A., Boger, D.L. 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. 2003; 11: 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.

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. 2003;11: 4503-4509.

6. Marsilje, T.H., Hedrick, M.P., Desharnais, J., Tavassoli, A., Zhang, Y., Wilson, I.A., Benkovic, S.J., Boger, D.L.

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. 2003;11: 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, D.L., Wilson, I.A.

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. 2003;42: 6043-6056.

4. Peters, R.J., Carter, O.A., Zhang, Y., Matthews, B.W., Croteau, R.B.., and Chappell, J. Bifunctional abietadiene synthase: mutual structural dependence of the active sites for protonation-initiated and ionization-initiated cyclizations.Biochemistry 2003;42. 2700-2707.

3. Zhang, Y., Desharnais, J., Greasley, S.E., Beardsley, G.P., Boger, D.L., Wilson, I.A.

Crystal structures of human GAR Tfase at low and high pH and with substrate beta-GAR. Biochemistry 2002;41: 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.

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. 2002;10: 2739-2749.

1. Lowther, W.T., Zhang, Y., Smapson, P.B., Honek, J.F., Matthews, B.W.

Insight into the mechanism of Escherichia coli methionine aminopeptidase from the structural analysis of reaction products and phosphorus-based transition-state analogues. Biochemistry 1999; 38: 14810-14819.