recent publications
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academic article
- Wang, S. A., Ko, Y., Zeng, J., Geng, Y., Ren, D. A., Ogasawara, Y., Irani, S., Zhang, Y., Liu, H. W. Identification of the Formycin A biosynthetic gene cluster from streptomyces kaniharaensis illustrates the interplay between biological pyrazolopyrimidine formation and de novo purine biosynthesis Journal of the American Chemical Society 2019 141:6127-6131 DOI:10.1021/jacs.9b00241 PMID:30942582 PMCID:PMC6612245
- Burkholder, N. T., Sipe, S. N., Escobar, E. E., Venkatramani, M., Irani, S., Yang, W., Wu, H., Matthews, W. M., Brodbelt, J. S., Zhang, Y. Mapping RNAPII CTD phosphorylation reveals that the identity and modification of seventh heptad residues direct Tyr1 phosphorylation ACS Chemical Biology 2019 14:2264-2275 DOI:10.1021/acschembio.9b00610 PMID:31553563
- Irani, S., Sipe, S. N., Yang, W., Burkholder, N. T., Lin, B., Sim, K., Matthews, W. L., Brodbelt, J. S., Zhang, Y. Structural determinants for accurate dephosphorylation of RNA polymerase II by its cognate C-terminal domain (CTD) phosphatase during eukaryotic transcription Journal of Biological Chemistry 2019 294:8592-8605 DOI:10.1074/jbc.RA119.007697 PMID:30971428 PMCID:PMC6544836
- Baas, B. J., Medellin, B. P., LeVieux, J. A., de Ruijter, M., Zhang, Y. J., Brown, S. D., Akiva, E., Babbitt, P. C., Whitman, C. P. Structural, kinetic, and mechanistic analysis of an asymmetric 4-oxalocrotonate tautomerase trimer Biochemistry 2019 58:2617-2627 DOI:10.1021/acs.biochem.9b00303 PMID:31074977
- 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. A., Kathuria, K. R., Liu, Z., et al. Tyr1 phosphorylation promotes phosphorylation of Ser2 on the C-terminal domain of eukaryotic RNA polymerase II by P-TEFb Elife 2019 8 DOI:10.7554/eLife.48725 PMID:31385803 PMCID:PMC6715403
- 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., Babbitt, P. C. A global view of structure-function relationships in the tautomerase superfamily Journal of Biological Chemistry 2018 293:2342-2357 DOI:10.1074/jbc.M117.815340 PMID:29184004 PMCID:PMC5818174
- Burkholder, N. T., Medellin, B., Irani, S., Matthews, W., Showalter, S. A., Zhang, Y. J. Chemical tools for studying the impact of cis/trans prolyl isomerization on signaling: a case study on RNA polymerase II phosphatase activity and specificity Methods in Enzymology 2018 607:269-297 DOI:10.1016/bs.mie.2018.04.020 PMID:30149861 PMCID:PMC6701646
- Stack, T. M. M., Li, W., Johnson, W. H., Zhang, Y. J., Whitman, C. P. Inactivation of 4-oxalocrotonate tautomerase by 5-Halo-2-hydroxy-2,4-pentadienoates Biochemistry 2018 57:1012-1021 DOI:10.1021/acs.biochem.7600899 PMID:29303557
- Burkholder, N. T., Mayfield, J. E., Yu, X., Irani, S., Arce, D. K., Jiang, F., Matthews, W. L., Xue, Y., Zhang, Y. J. Phosphatase activity of small C-terminal domain phosphatase 1 (SCP1) controls the stability of the key neuronal regulator RE1-silencing transcription factor (REST) Journal of Biological Chemistry 2018 293:16851-16861 DOI:10.1074/jbc.RA118.004722 PMID:30217818 PMCID:PMC6204920
- Irani, S., Naowarojna, N., Tang, Y., Kathuria, K. R., Wang, S., Dhembi, A., Lee, N., Yan, W., Lyu, H., Costello, C. E., Liu, P., Zhang, Y. J. Snapshots of C-S cleavage in Egt2 reveals substrate specificity and reaction mechanism Cell Chemical Biology 2018 25:519-529 DOI:10.1016/j.chembiol.2018.02.002 PMID:29503207 PMCID:PMC5959753
- LeVieux, J. A., Medellin, B., Johnson, W. H., Erwin, K., Li, W., Johnson, I. A., Zhang, Y. J., Whitman, C. P. Structural characterization of the hydratase-aldolases, NahE and PhdJ: implications for the specificity, catalysis, and N-acetylneuraminate lyase subgroup of the aldolase superfamily Biochemistry 2018 57:3524-3536 DOI:10.1021/acs.biochem.8b00532 PMID:29856600
- 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., et al. IgG Fc domains that bind C1q but not effector Fcγ receptors delineate the importance of complement-mediated effector functions Nature Immunology 2017 18:889-+ DOI:10.1038/ni.3770 PMID:28604720 PMCID:PMC6015732
- LeVieux, J. A., Baas, B. J., Kaoud, T. S., Davidson, R., Babbitt, P. C., Zhang, Y. J., Whitman, C. P. 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 Archives of Biochemistry and Biophysics 2017 636:50-56 DOI:10.1016/j.abb.2017.10.018 PMID:29111295 PMCID:PMC5714680
- 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., Brodbelt, J. S. Mapping the phosphorylation pattern of Drosophila melanogaster RNA polymerase II carboxyl-terminal domain using ultraviolet photodissociation mass spectrometry ACS Chemical Biology 2017 12:153-162 DOI:10.1021/acschembio.6b00729 PMID:28103682 PMCID:PMC5376213
- Gibbs, E. B., Lu, F., Portz, B., Fisher, M. J., Medellin, B. P., Laremore, T. N., Zhang, Y. J., Gilmour, D. S., Showalter, S. A. Phosphorylation induces sequence-specific conformational switches in the RNA polymerase II C-terminal domain Nature Communications 2017 8 DOI:10.1038/ncomms15233 PMID:28497798 PMCID:PMC5437310
- 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. Structural heterogeneity in the intrinsically disordered RNA polymerase II C-terminal domain Nature Communications 2017 8 DOI:10.1038/ncomms15231 PMID:28497792 PMCID:PMC5437306
- Yan, W., Stone, E., Zhang, Y. J. Structural snapshots of an engineered cystathionine-γ-lyase reveal the critical role of electrostatic interactions in the active site Biochemistry 2017 56:876-885 DOI:10.1021/acs.biochem.6b01172 PMID:28106980 PMCID:PMC5376214
- Mayfield, J. E., Burkholder, N. T., Zhang, Y. J. Dephosphorylating eukaryotic RNA polymerase II Biochimica Et Biophysica Acta-Proteins and Proteomics 2016 1864:372-387 DOI:10.1016/j.bbapap.2016.01.007 PMID:26779935 PMCID:PMC4761483
- Li, W., Irani, S., Crutchfield, A., Hodge, K., Matthews, W., Patel, P., Zhang, Y. J., Stone, E. Intramolecular cleavage of the hASRGL1 homodimer occurs in two stages Biochemistry 2016 55:960-969 DOI:10.1021/acs.biochem.5b01157 PMID:26780688 PMCID:PMC4809669
- Irani, S., Yogesha, S. D., Mayfield, J., Zhang, M., Zhang, Y., Matthews, W. L., Nie, G., Prescott, N. A., Zhang, Y. J. Structure of Saccharomyces cerevisiae Rtr1 reveals an active site for an atypical phosphatase Science Signaling 2016 9 DOI:10.1126/scisignal.aad4805 PMID:26933063 PMCID:PMC4801511
- Cramer, S. L., Saha, A., Liu, J., Tadi, S., Tiziani, S., Yan, W., Triplett, K., Lamb, C., Alters, S. E., Rowlinson, S., Zhang, Y. J., Keating, M. J., et al. Systemic depletion of L-cyst(e)ine with cyst(e)inase increases reactive oxygen species and suppresses tumor growth Nature Medicine 2016 23:120-127 DOI:10.1038/nm.4232 https://www.nature.com/articles/nm.4232#supplementary-information PMID:27869804 PMCID:PMC5218918
- LeVieux, J. A., Johnson, W. H., Erwin, K., Li, W., Zhang, Y. J., Whitman, C. P. The bacterial catabolism of polycyclic aromatic hydrocarbons: Characterization of three hydratase-aldolase-catalyzed reactions Perspectives in Science 2016 9:33-41 DOI:https://doi.org/10.1016/j.pisc.2016.03.025
- He, Y., Guo, X., Yu, Z. H., Wu, L., Gunawan, A. M., Zhang, Y., Dixon, J. E., Zhang, Z. Y. A potent and selective inhibitor for the UBLCP1 proteasome phosphatase Bioorganic & Medicinal Chemistry 2015 23:2798-2809 DOI:10.1016/j.bmc.2015.03.066 PMID:25907364 PMCID:PMC4451428
- Mayfield, J. E., Fan, S., Wei, S., Zhang, M., Li, B., Ellington, A. D., Etzkorn, F. A., Zhang, Y. J. Chemical tools to decipher regulation of phosphatases by proline isomerization on eukaryotic RNA polymerase II ACS Chemical Biology 2015 10:2405-2414 DOI:10.1021/acschembio.5b00296 PMID:26332362 PMCID:PMC4788383
- Bapat, S. P., Myoung Suh, J., Fang, S., Liu, S., Zhang, Y., Cheng, A., Zhou, C., Liang, Y., LeBlanc, M., Liddle, C., Atkins, A. R., Yu, R. T., et al. Depletion of fat-resident T-reg cells prevents age-associated insulin resistance Nature 2015 528:137-141 DOI:10.1038/nature16151 PMID:26580014 PMCID:PMC4670283
- Yan, W., Song, H., Song, F., Guo, Y., Wu, C. H., Sae Her, A., Pu, Y., Wang, S., Naowarojna, N., Weitz, A., Hendrich, M. P., Costello, C. E., et al. Endoperoxide formation by an α-ketoglutarate-dependent mononuclear non-haem iron enzyme Nature 2015 527:539-543 DOI:10.1038/nature15519 PMID:26524521 PMCID:PMC4804460
- Chen, C. H., Li, W., Sultana, R., You, M. H., Kondo, A., Shahpasand, K., Kim, B. M., Luo, M. L., Nechama, M., Lin, Y. M., Yao, Y., Lee, T. H., et al. Pin1 cysteine-113 oxidation inhibits its catalytic activity and cellular function in Alzheimer's disease Neurobiology of Disease 2015 76:13-23 DOI:10.1016/j.nbd.2014.12.027 PMID:25576397 PMCID:PMC4423621
- O'Brien, J. P., Li, W., Zhang, Y., Brodbelt, J. S. Characterization of native protein complexes using ultraviolet photodissociation mass spectrometry Journal of the American Chemical Society 2014 136:12920-12928 DOI:10.1021/ja505217w PMID:25148649 PMCID:PMC4351866
- Yogesha, S. D., Mayfield, J. E., Zhang, Y. Cross-talk of phosphorylation and prolyl isomerization of the C-terminal domain of RNA Polymerase II Molecules 2014 19:1481-1511 DOI:10.3390/molecules19021481 PMID:24473209 PMCID:PMC4350670
- 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. Complete protein characterization using top-down mass spectrometry and ultraviolet photodissociation Journal of the American Chemical Society 2013 135:12646-12651 DOI:10.1021/ja4029654 PMID:23697802 PMCID:PMC3757099
- Luo, Y., Yogesha, S. D., Cannon, J. R., Yan, W., Ellington, A. D., Brodbelt, J. S., Zhang, Y. Novel modifications on C-terminal domain of RNA polymerase II can fine-tune the phosphatase activity of Ssu72 ACS Chemical Biology 2013 8:2042-2052 DOI:10.1021/cb400229c PMID:23844594
- Zhang, M., Yogesha, S. D., Mayfield, J. E., Gill, G. N., Zhang, Y. Viewing serine/threonine protein phosphatases through the eyes of drug designers FEBS Journal 2013 280:4739-4760 DOI:10.1111/febs.12481 PMID:23937612
- Tavares, C. D. J., 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., et al. Calcium/calmodulin stimulates the autophosphorylation of elongation factor 2 kinase on Thr-348 and Ser-500 to regulate its activity and calcium dependence Biochemistry 2012 51:2232-2245 DOI:10.1021/bi201788e PMID:22329831 PMCID:PMC3401519
- Zhang, M., Wang, X. J., Chen, X., Bowman, M. E., Luo, Y., Noel, J. P., Ellington, A. D., Etzkorn, F. A., Zhang, Y. Structural and kinetic analysis of prolyl-isomerization/phosphorylation cross-talk in the CTD code ACS Chemical Biology 2012 7:1462-1470 DOI:10.1021/cb3000887 PMID:22670809 PMCID:PMC3423551
- Li, W., Cantor, J. R., Yogesha, S. D., Yang, S., Chantranupong, L., Liu, J. Q., Agnello, G., Georgiou, G., Stone, E. M., Zhang, Y. Uncoupling intramolecular processing and substrate hydrolysis in the N-terminal nucleophile hydrolase hASRGL1 by circular permutation ACS Chemical Biology 2012 7:1840-1847 DOI:10.1021/cb300232n PMID:22891768 PMCID:PMC3514461
- Xu, G. G., Zhang, Y., Mercedes-Camacho, A. Y., Etzkorn, F. A. A reduced-amide inhibitor of Pin1 binds in a conformation resembling a twisted-amide transition state Biochemistry 2011 50:9545-9550 DOI:10.1021/bi201055c PMID:21980916 PMCID:PMC3289549
- Zhang, Y., Zhang, M., Zhang, Y. 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 Biochemical Journal 2011 434:435-444 DOI:10.1042/bj20101471 PMID:21204787
- Lee, T. H., Chen, C. H., Suizu, F., Huang, P., Schiene-Fischer, C., Daum, S., Zhang, Y. J., Goate, A., Chen, R. H., Zhou, X. Z., Lu, K. P. Death-associated protein kinase 1 phosphorylates Pin1 and inhibits its prolyl isomerase activity and cellular function Molecular Cell 2011 42:147-159 DOI:10.1016/j.molcel.2011.03.005 PMID:21497122 PMCID:PMC3088080
- Burks, E. A., Yan, W., Johnson Jr., W. H., Li, W., Schroeder, G. K., Min, C., Gerratana, B., Zhang, Y., Whitman, C. P. Kinetic, crystallographic, and mechanistic characterization of TomN: elucidation of a function for a 4-oxalocrotonate tautomerase homologue in the tomaymycin biosynthetic pathway Biochemistry 2011 50:7600-7611 DOI:10.1021/bi200947w PMID:21809870 PMCID:PMC3164527
- Zhang, M., Cho, E. J., Burstein, G., Siegel, D., Zhang, Y. Selective inactivation of a human neuronal silencing phosphatase by a small molecule inhibitor ACS Chemical Biology 2011 6:511-519 DOI:10.1021/cb100357t PMID:21348431
- Zhang, M., Gill, G. N., Zhang, Y. Bio-molecular architects: a scaffold provided by the C-terminal domain of eukaryotic RNA polymerase II Nano Reviews 2010 1 DOI:10.3402/nano.v1i0.5502 PMID:22110856 PMCID:PMC3215212
- Zhang, M., Liu, J., Kim, Y., Dixon, J. E., Pfaff, S. L., Gill, G. N., Noel, J. P., Zhang, Y. Structural and functional analysis of the phosphoryl transfer reaction mediated by the human small C-terminal domain phosphatase, Scp1 Protein Science 2010 19:974-986 DOI:10.1002/pro.375 PMID:20222012 PMCID:PMC2868240
- Zhang, Y., Daum, S., Wildemann, D., Zhou, X. Z., Verdecia, M. A., Bowman, M. E., Lucke, C., Hunter, T., Lu, K. P., Fischer, G., Noel, J. P. Structural basis for high-affinity peptide inhibition of human Pin1 ACS Chemical Biology 2007 2:320-328 DOI:10.1021/cb7000044 PMID:17518432 PMCID:PMC2692202
- Zhang, Y., Ki, Y., Genoud, N., Gao, J. M., Kelly, J. W., Pfaff, S. L., Gill, G. N., Dixon, J. E., Noel, J. P. Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1 Molecular Cell 2006 24:759-770 DOI:10.1016/j.molcel.2006.10.027 PMID:17157258 PMCID:PMC2859291
- Jager, M., Zhang, Y., Bieschke, J., Nguyen, H., Dendle, M., Bowman, M. E., Noel, J. P., Gruebele, M., Kelly, J. W. Structure-function-folding relationship in a WW domain Proceedings of the National Academy of Sciences of the United States of America 2006 103:10648-10653 DOI:10.1073/pnas.0600511103 PMID:16807295 PMCID:PMC1502286
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Zhang, Y., Wang, L., Schultz, P. G., Wilson, I. A.
Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine
Protein Science
2005
14:1340-1349
DOI:10.1110/ps.041239305
PMID:15840835
PMCID:PMC2253270
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Cheng, H., Chong, Y. H., Hwang, I., Tavassoli, A., Zhang, Y., Wilson, I. A., Benkovic, S. J., Boger, D. L.
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
Bioorganic & Medicinal Chemistry
2005
13:3577-3585
DOI:10.1016/j.bmc.2004.12.004
PMID:15848770
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Cheng, H., Hwang, I., Chong, Y. H., Tavassoli, A., Webb, M. E., Zhang, Y., Wilson, I. A., Benkovic, S. J., Boger, D. L.
Synthesis and biological evaluation of N-{4- 5-(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)-2-(2,2,2-trifluoro acetyl)pentyl)benzoyl}-L-glutamic acid as a potential inhibitor of GAR Tfase and the de novo purine biosynthetic pathway
Bioorganic & Medicinal Chemistry
2005
13:3593-3599
DOI:10.1016/j.bme.2004.11.049
PMID:15848772
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Chong, Y., Hwang, I., Tavassoli, A., Zhang, Y., Wilson, I. A., Benkovic, S. J., Boger, D. L.
Synthesis and biological evaluation of α- and γ-carboxamide derivatives of 10-CF3CO-DDACTHF
Bioorganic & Medicinal Chemistry
2005
13:3587-3592
DOI:10.1016/j.bme.2004.11.050
PMID:15848771
- Peters, R. J., Carter, O. A., Zhang, Y., Matthews, B. W., Croteau, R. B. Bifunctional abletadiene synthase: mutual structural dependence of the active sites for protonation-initiated and ionization-initiated cyclizations Biochemistry 2003 42:2700-2707 DOI:10.1021/bi020492n PMID:12614165
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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
Bioorganic & Medicinal Chemistry
2003
11:4503-4509
DOI:10.1016/s0968-0896(03)00457-7
PMID:13129586
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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
Bioorganic & Medicinal Chemistry
2003
11:4511-4521
DOI:10.1016/s0968-0896(03)00458-9
PMID:13129587
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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
Bioorganic & Medicinal Chemistry
2003
11:4487-4501
DOI:10.1016/s0968-0896(03)00456-5
PMID:13129585
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Zhang, Y., Desharnais, J., Marsilje, T. H., Li, C. L., 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
DOI:10.1021/bi034219c
PMID:12755606
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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., et al.
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
Bioorganic & Medicinal Chemistry
2002
10:2739-2749
DOI:10.1016/s0968-0896(02)00102-5
PMID:12057663
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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 β-GAR
Biochemistry
2002
41:14206-14215
DOI:10.1021/bi020522m
PMID:12450384
- Lowther, W. T., Zhang, Y., Sampson, P. B., Honek, J. F., Matthews, B. W. Insights 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 DOI:10.1021/bi991711g PMID:10555963
