Research Topics
Genomes and Genes | Honggao YanSummaryAffiliation: Michigan State University Country: USA Publications
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Publications
Role of protein conformational dynamics in the catalysis by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinaseHonggao Yan
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
Protein Pept Lett 18:328-35. 2011....- Role of glutamate 64 in the activation of the prodrug 5-fluorocytosine by yeast cytosine deaminaseJifeng Wang
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
Biochemistry 51:475-86. 2012..The results of the experimental and computational studies together indicate that Glu64 plays a critical role in both the binding and the chemical transformation in the conversion of the prodrug 5FC to the anticancer drug 5-fluorouracil... - Hydrogen-bond detection, configuration assignment and rotamer correction of side-chain amides in large proteins by NMR spectroscopy through protium/deuterium isotope effectsAizhuo Liu
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
Chembiochem 9:2860-71. 2008..Rotamer correction by differential isotope effects is not only robust, but also simple and can be applied to large proteins... 
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 studiesYue Li
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
Biochemistry 44:8590-9. 2005..When these results are taken together, they suggest that the critical functional importance of loop 3 is not due to the interactions of the R84 guanidinium group or the W89 indole ring with the substrates...- Mechanism of dihydroneopterin aldolase. NMR, equilibrium and transient kinetic studies of the Staphylococcus aureus and Escherichia coli enzymesYi Wang
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
FEBS J 274:2240-52. 2007..The results show that the two enzymes have significantly different binding and catalytic properties, in accordance with the significant sequence differences between them... - A molecular dynamics study of the ligand release path in yeast cytosine deaminaseLishan Yao
Department of Chemistry, Michigan State University Center for Biological Modeling, East Lansing, Michigan 48824, USA
Biophys J 92:2301-10. 2007.... - Mechanism of dihydroneopterin aldolase: functional roles of the conserved active site glutamate and lysine residuesYi Wang
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
Biochemistry 45:15232-9. 2006..In contrast, E22 and K100 of SaDHNA are important for catalysis, but their roles in substrate binding are minor. On the other hand, E21 and K98 of EcDHNA are important for both substrate binding and catalysis... - A molecular dynamics exploration of the catalytic mechanism of yeast cytosine deaminaseLishan Yao
Department of Chemistry, MSU Center for Biological Modeling, Michigan State University, East Lansing, Michigan 48824, USA
J Phys Chem B 109:7500-10. 2005..The simulations also reveal small motions of the C-terminus and the loop that contains Phe114 that may be important for reactant binding and product release... - TROSY of side-chain amides in large proteinsAizhuo Liu
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
J Magn Reson 186:319-26. 2007..The TROSY effects on the 15N-H(E){D(Z)} isotopomers of side-chain amides are as significant as on backbone amides... - A point mutation converts dihydroneopterin aldolase to a cofactor-independent oxygenaseYi Wang
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, 48824, USA
J Am Chem Soc 128:13216-23. 2006..The conserved tyrosine residue plays only a minor role in the formation of the enol reaction intermediate but a critical role in the protonation of the enol intermediate to form 4... - Mechanism of the conformational transitions in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by NMR spectroscopyGuangyu Li
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
Biochemistry 45:12573-81. 2006.... - Catalytic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: site-directed mutagenesis and biochemical studiesYue Li
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
Biochemistry 42:1581-8. 2003..Both R82 and R92 are important for catalysis, and R92 plays a critical role in the transition state stabilization... - Product release is rate-limiting in the activation of the prodrug 5-fluorocytosine by yeast cytosine deaminaseLishan Yao
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
Biochemistry 44:5940-7. 2005..The transient kinetic and NMR results together suggest that the release of 5FU is rate-limiting in the activation of the prodrug 5FC by yCD and may involve multiple steps... - Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF, hepatitis delta antigen, and stimulatory factor IIChunfen Zhang
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 1319, USA
J Biol Chem 278:50101-11. 2003..In the presence of HDAg and SII, pausing is observed without stimulation of transcript cleavage, indicating that the EC can pause without backtracking beyond the pre-translocated state... - A combined ONIOM quantum chemical-molecular dynamics study of zinc-uracil bond breaking in yeast cytosine deaminaseLishan Yao
Department of Chemistry, and MSU Center for Biological Modeling, Michigan State University, East Lansing, Michigan 48824, USA
J Phys Chem B 110:26320-6. 2006..In the work presented here, the combined ONIOM MD method is used to show that the barrier for bond cleavage is small, approximately 3 kcal/mol, and, consequently, should not be the rate-limiting step in the reaction... 
Dynamics in Thermotoga neapolitana adenylate kinase: 15N relaxation and hydrogen-deuterium exchange studies of a hyperthermophilic enzyme highly active at 30 degrees CHarini Krishnamurthy
Program in Cell and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
Biochemistry 48:2723-39. 2009..Our NMR relaxation and hydrogen-deuterium exchange studies therefore suggest that TNAK maintains high activity at 30 degrees C by localizing flexibility to the hinge regions that are key to facilitating conformational changes...- NMR detection of bifurcated hydrogen bonds in large proteinsAizhuo Liu
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
J Am Chem Soc 130:2428-9. 2008 - Catalytic mechanism of guanine deaminase: an ONIOM and molecular dynamics studyLishan Yao
Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
J Phys Chem B 111:4200-10. 2007..The Zn-O2 bond can be broken without the assistance of water during the release of xanthine... - Mechanism of dihydroneopterin aldolase: a molecular dynamics study of the apo enzyme and its product complexLishan Yao
Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
J Phys Chem B 110:1443-56. 2006..An analysis of the various components that contribute to the exit path energy and entropy provides insight into the energy-entropy compensation for product release... - Catalytic mechanism of yeast cytosine deaminase: an ONIOM computational studyStepan Sklenak
Center for Biological Modeling and Departments of Biochemistry and Chemistry, Michigan State University, East Lansing, MI 48824, USA
J Am Chem Soc 126:14879-89. 2004..The rate determining step in the oxygen exchange is the formation of the gem-diol intermediate, which is also the rate determining step for the overall yCD-catalyzed deamination reaction... - Simultaneous NMR assignment of backbone and side chain amides in large proteins with IS-TROSYAizhuo Liu
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
J Biomol NMR 36:205-14. 2006.... - Bile Acid secreted by male sea lamprey that acts as a sex pheromoneWeiming Li
Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
Science 296:138-41. 2002..Hence, the male of this fish species signals both its reproductive status and location to females by secreting a pheromone that can act over long distances... - Chemical transformation is not rate-limiting in the reaction catalyzed by Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinaseYue Li
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
Biochemistry 41:8777-83. 2002..These results form a thermodynamic and kinetic framework for dissecting the roles of active site residues in the substrate binding and catalysis by HPPK... - NTP-driven translocation by human RNA polymerase IIYuri A Nedialkov
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, Japan
J Biol Chem 278:18303-12. 2003.... - 'Top-down' characterization of site-directed mutagenesis products of Staphylococcus aureus dihydroneopterin aldolase by multistage tandem mass spectrometry in a linear quadrupole ion trapGwynyth Scherperel
Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
Analyst 131:291-302. 2006..This work highlights the need for further studies to characterize the charge state, sequence and structural dependence to the low energy collision induced dissociation reactions of multiply protonated intact protein ions... - Scoring ligand similarity in structure-based virtual screeningMaria I Zavodszky
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 1319, USA
J Mol Recognit 22:280-92. 2009..This was particularly true in the S1 pocket, which was occupied by all the docked compounds... - Thermotoga neapolitana adenylate kinase is highly active at 30 degrees CClaire Vieille
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824, USA
Biochem J 372:577-85. 2003..The unusually high activity of TNAK at 30 degrees C makes it an interesting model to test the role of enzyme flexibility in activity... - Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysisYijun Gu
Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
J Mol Biol 319:779-89. 2002..The crystal structure of MtSK (this work) and that of Erwinia chrysanthemi SK suggest a concerted conformational change of the LID and SB domains upon nucleotide binding... - Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATPRong Yang
Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
Biophys J 89:95-106. 2005..The lessons learned here offer valuable structural insights into the workings of HPPK and should be useful for structure-based drug design... - Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanismJianhua Gan
Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
Biochemistry 46:9513-22. 2007..On the basis of preexisting and novel structural and biochemical data, a catalytic mechanism is proposed... - Conformations of nucleotides bound to wild type and Y78F mutant yeast guanylate kinase: proton two-dimensional transferred NOESY measurementsBruce D Ray
Department of Physics, Indiana University-Purdue University at Indianapolis, 402 North Blackford Street, Indianapolis, Indiana 46202-3273, USA
Biochemistry 44:13762-70. 2005..This difference suggests that an unfavorable torsion may be a large part of the mechanism for significantly weaker GMP binding to reaction complexes of the Y78F mutant... - Essential roles of a dynamic loop in the catalysis of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinaseJaroslaw Blaszczyk
Macromolecular Crystallography Laboratory, National Cancer Institute, P O Box B, Frederick, Maryland 21702, USA
Biochemistry 43:1469-77. 2004..The loop plays an important role in the stabilization of the ternary complex and is critical for catalysis... - Dynamic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: crystallographic studiesJaroslaw Blaszczyk
Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
Biochemistry 42:1573-80. 2003..Two oxidized forms of HP are observed with an occupancy ratio of 0.50:0.50 in the 0.89-A structure. The oxidation of HP has significant impact on its binding to the protein as well as the conformation of nearby residue W89... - Hydrolysis of ATP by aminoglycoside 3'-phosphotransferases: an unexpected cost to bacteria for harboring an antibiotic resistance enzymeChoonkeun Kim
Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
J Biol Chem 281:6964-9. 2006..The implication is that, in the absence of selection, bacteria harboring an enzyme that catalyzes the consumption of key metabolites could experience the loss of the plasmid that encodes for the given enzyme... - Fluorinated aminoglycosides and their mechanistic implication for aminoglycoside 3'-phosphotransferases from Gram-negative bacteriaChoonkeun Kim
Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
Biochemistry 43:2373-83. 2004..These findings collectively argue that the Gram-negative APH(3')s show significant nucleophilic participation in the transition state for the phosphate transfer reaction... - Reaction trajectory of pyrophosphoryl transfer catalyzed by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinaseJaroslaw Blaszczyk
Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
Structure 12:467-75. 2004..AMP.HPPP (ternary complex of HPPK with both product molecules) and HPPK.HPPP (binary complex of HPPK with one product), which we present in this study... - Structure and activity of Yersinia pestis 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as a novel target for the development of antiplague therapeuticsJaroslaw Blaszczyk
Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
Acta Crystallogr D Biol Crystallogr 63:1169-77. 2007..Therefore, these structural and biochemical data are valuable for the design of novel medical countermeasures against plague...
Research Grants
- STRUCTURE/FUNCTION RELATIONSHIPS OF HPPKHonggao Yan; Fiscal Year: 2002..In specific Aim 5, NMR will be used to identify the active-site residues and to determine the structures of HPPK in complex with substrate analogues. ..
- Structure and Mechanism of Folate Biosynthetic EnzymesHonggao Yan; Fiscal Year: 2007..In Specific Aim 5, we will identify residues involved in general acid/base catalysis in DHNA by a combination of site-directed mutagenesis, transient kinetic pH-rate profile analysis, and NMR spectroscopic titration. ..