Honggao Yan Recent Publications

Liu A, Lu Z, Wang J, Yao L, Li Y, Yan H. (2008) NMR detection of bifurcated hydrogen bonds in large proteins. J Am Chem Soc. 130(8):2428-9.

Blaszczyk, J., Li, Y., Gan, J., Yan, H.*, and Ji, X.* (2007) Structural basis and catalytic mechanism for the aldolase and epimerase activities of Staphylococcus aureus dihydroneopterin aldolase. J. Mol. Biol. 368, 161-169.

Blaszczyk, J., Li, Y., Cherry, S., Alexandratos, J., Wu, W., Shaw G., Tropea, J. E., Waugh, D. S., Yan, H.*, and Ji, X.* (2007) Structure and activity of Yersinia pestis 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as a novel target for the development of antiplague therapeutics. Acta Crystallogr. D63, in press.

Gan, J., Wu, Y., Prabakaran, P., Gu, Y., Li, Y., Andrykovitch, M., Liu, H., Gong, Y., Yan, H.*, and Ji, X.* (2007) Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism. Biochemistry 46, 9513-9522.

Wang, Y., Li, Y., Wu, Y., and Yan, H. (2007) Mechanism of dihydroneopterin aldolase: NMR, equilibrium and transient kinetic studies of the Staphylococcus aureus and Escherichia coli enzymes. FEBS J. 274, 2240-2252.

Yao, L., Cukier, R. I.*, and Yan, H.* (2007) Catalytic mechanism of guanine deaminase: An ONIOM and molecular dynamics study. J. Phys. Chem. B 111, 4200-4210.

Liu*, A., Yao, L., Li, Y., and Yan, H. (2007) TROSY of side-chain amides in large proteins. J. Magn Reson., in press.

Yao, L., Yan, H.*, and Cukier, R. I.* (2007) A molecular dynamics study of the ligand release path in yeast cytosine deaminase. Biophys. J. 92, 2301-2310.

Wang, Y., Scherperel, G., Roberts, K. D., Jones, A. D., Reid, G. E.*, and Yan, H.* (2006) A point mutation converts dihydroneopterin aldolase to a cofactor-independent oxygenase. J. Am. Chem. Soc. 128, 15232-15239.

Li, G., Felczak, K., Shi, G., and Yan, H. (2006) Mechanism of the conformational transitions in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by NMR spectroscopy. Biochemistry 45, 12573-12581.

Wang, Y., Li, Y., and Yan, H. (2006) Mechanism of dihydroneopterin aldolase: the functional roles of the conserved active site glutamate and lysine residues. Biochemistry 45, 15232-15239.

Liu*, A., Li, Y., Yao, L., and Yan, H. (2006) Simultaneous NMR assignment of backbone and side chain amides in large proteins with IS-TROSY. J. Biomol. NMR 36, 205-214.

Yao, L., Yan, H.*, and Cukier, R. I.* (2006) A combined ONIOM quantum chemical-molecular dynamics study of zinc – uracil bond breaking in yeast cytosine deaminase. J. Phys. Chem. B 110, 26320-26326.

Gan, J., Gu, Y., Li, Y., Yan, H., and Ji, X. (2006) Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimic acid and an ATP analog. Biochemistry 45, 8539-8545.

Kim, C., Cha, J. Y., Yan, H., Vakulenko, S. B., and Mobashery, S. (2006) Hydrolysis of ATP by aminoglycoside 3'-phosphotransferases: An unexpected cost to bacteria for harboring an antibiotic resistance enzyme. J. Biol. Chem. 281, 6964-6969.

Yao, L., Yan, H.*, and Cukier, R. I.* (2006) Mechanism of dihydroneopterin aldolase: a molecular dynamics study of the apo enzyme and its product complex. J. Phys. Chem. B 110, 1443-1456.

Scherperel, G., Yan, H., Wang, Y., and Reid, G. E. (2006) Top-down characterization of site-directed mutagenesis products of Staphylococcus aureus dihydroneopterin aldolase by multistage tandem mass spectrometry in a linear quadrupole ion trap. Analyst 131, 291-302.

Ray, B. D., Jarori, G. K., Raghunathan, V., Yan, H., and Rao, B. D. N. (2005) Conformations of nucleotides bound to wild type and Y78F mutant yeast guanylate kinase: proton two-dimensional transferred NOESY measurements. Biochemistry 44, 13762-13770.

Li, Y., Blaszczyk, J., Yan, W., Shi, G., Ji, X., and Yan, H. (2005) Is the critical role of loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase in catalysis due to loop-3 residues arginine-84 and tryptophan-89? site-directed mutagenesis, biochemical, and crystallographic studies. Biochemistry 44, 8590-8599.

Yang, R, Lee, M. C., Yan, H., and Duan, Y. (2005) Loop conformation and dynamics of the E. coli HPPK apo-enzyme and its binary complex with MgATP. Biophys. J. 89, 95-106.

Yao, L., Li, Y. Wu, Y. Liu, A., and Yan, H. (2005) Product release is rate-limiting in the activation of the prodrug 5-Fluorocytosine by yeast cytosine deaminase. Biochemistry 44, 5940-5947.

Yao, L., Sklenak, S., Yan, H.*, and Cukier, R. I*. (2005) A molecular dynamics exploration of the catalytic mechanism of yeast cytosine deaminase. J. Phys. Chem. B 109, 7500-7510.

Blaszczyk, J., Li, Y., Yan, W., Shi, G., Ji, X., and Yan, H. (2004) Essential roles of a dynamic loop in the catalysis of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Biochemistry 43, 1469-1477.

Sklenak, S., Yao, L., Cukier, R. I., and Yan, H. (2004) Catalytic mechanism of yeast cytosine deaminase. An ONIOM computational study. J. Am. Chem. Soc. 126, 14879-14889.

Blaszczyk, J., Shi, G., Li, Y., Yan, H., and Ji, X. (2004) Reaction trajectory of pyrophosphoryl transfer catalyzed by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Structure 12, 467-475.

Kim, C.; Haddad, J.; Vakulenko, S. B.; Meroueh, S. O.; Wu, Y.; Yan, H.; Mobashery, S. (2004) Fluorinated aminoglycosides and their mechanistic implication for aminoglycoside phosphotransferases from Gram-negative bacteria Biochemistry 43, 2373-2383.

Li, Y., Wu, Y., Blaszczyk, J., Ji, X., and Yan, H. (2003) Catalytic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: site-directed mutagenesis and biochemical studies. Biochemistry 42, 1581-1588.

Blaszczyk, J., Li, Y., Shi, G., Yan, H., and Ji, X. (2003) Dynamic roles of arginine residues 82 and 92 in the catalysis of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: crystallographic studies. Biochemistry 42, 1573-1580.

Zhang, C, Yan, H., and Burton, Z. F. (2003) Combinatorial control of human RNA polymerase II pausing and transcript cleavage by transcription factor IIF, hepatitis delta antigen and TFIIS/SII. J. Biol. Chem. 278, 50101 - 50111.

Nedialkov, Y. A., Gong,X. Q., Hovde, S. L.,Yamaguchi, Y., Handa, H., Geiger, J. H., Yan, H., and Burton, Z. F. (2003) NTP-driven translocation by human RNA polymerase II. J. Biol. Chem. 278, 18303-18312.

Vieille, C., Krishnamurthy, H., Hyun, H.-H, Savchenko, A., Yan, H., and Zeikus, J. G. (2003) Thermotoga neapolitana adenylate kinase is highly active at 30 °C. Biochem. J. 372, 577-585.

Li, W., Scott, A. P., Siefkes, M. J., Yan, H., Liu, Q., Yun, S., and Gage, D. A. (2002) Bile acid secreted by male sea lamprey that acts as a sex pheromone. Science 296, 138-141.

Gu, Y., Reshetnikova, L. Li, Y., Yan, H., Singh, S., and Ji, X. (2002) Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis. J. Mol. Biol. 319, 779-789.

Li, Y., Gong, Y., Shi, G., Blaszczyk, J., Ji, X., and Yan, H. (2002) Chemical transformation is not rate-limiting in the reaction catalyzed by Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Biochemistry 41, 8777-8783.

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