Honggao Yan Recent Publications
MI Zavodszky, A Rohatgi, Van JR Voorst, HG Yan, LA Kuhn. (2009) Scoring ligand similarity in structure-based virtual screening. Journal of Molecular Recognition. 22:280-292.
Ray BD, Scott J, Yan H, Rao BD. (2009) Productive versus unproductive nucleotide binding in yeast guanylate kinase mutants: comparison of R41M with K14M by proton two dimensional transferred NOESY. Biochemistry. 48(24):5532-40.
Krishnamurthy H, Munro K, Yan Y, Vieille C. (2009) Dynamics in Thermotoga neapolitana adenylate kinase: N-15 relaxation and hydrogen-deuterium exchange studies of a hyperthermophilic enzyme highly active at 30 degrees C. Biochemistry 48, 2723-2739.
Lescop E, Lu Z, Liu Q, Xu H, Li G, Xia B, Yan H, Jin C. (2009) Dynamics of the conformational transitions in the assembling of the Michaelis Complex of a bisubstrate enzyme: A 15N relaxation study of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Biochemistry 48 (2), 302-312.
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. 63(Pt 11):1169-77.
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.