Honggao Yan

Summary

Affiliation: Michigan State University
Country: USA

Publications

  1. pmc Role of protein conformational dynamics in the catalysis by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
    Honggao Yan
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
    Protein Pept Lett 18:328-35. 2011
  2. pmc Role of glutamate 64 in the activation of the prodrug 5-fluorocytosine by yeast cytosine deaminase
    Jifeng Wang
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
    Biochemistry 51:475-86. 2012
  3. pmc Hydrogen-bond detection, configuration assignment and rotamer correction of side-chain amides in large proteins by NMR spectroscopy through protium/deuterium isotope effects
    Aizhuo Liu
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
    Chembiochem 9:2860-71. 2008
  4. ncbi request reprint 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
    Yue Li
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
    Biochemistry 44:8590-9. 2005
  5. ncbi request reprint Mechanism of dihydroneopterin aldolase. NMR, equilibrium and transient kinetic studies of the Staphylococcus aureus and Escherichia coli enzymes
    Yi Wang
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
    FEBS J 274:2240-52. 2007
  6. pmc A molecular dynamics study of the ligand release path in yeast cytosine deaminase
    Lishan Yao
    Department of Chemistry, Michigan State University Center for Biological Modeling, East Lansing, Michigan 48824, USA
    Biophys J 92:2301-10. 2007
  7. pmc Mechanism of dihydroneopterin aldolase: functional roles of the conserved active site glutamate and lysine residues
    Yi Wang
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
    Biochemistry 45:15232-9. 2006
  8. ncbi request reprint A molecular dynamics exploration of the catalytic mechanism of yeast cytosine deaminase
    Lishan 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
  9. pmc TROSY of side-chain amides in large proteins
    Aizhuo Liu
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
    J Magn Reson 186:319-26. 2007
  10. ncbi request reprint A point mutation converts dihydroneopterin aldolase to a cofactor-independent oxygenase
    Yi Wang
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, 48824, USA
    J Am Chem Soc 128:13216-23. 2006

Research Grants

Collaborators

Detail Information

Publications38

  1. pmc Role of protein conformational dynamics in the catalysis by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
    Honggao Yan
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
    Protein Pept Lett 18:328-35. 2011
    ....
  2. pmc Role of glutamate 64 in the activation of the prodrug 5-fluorocytosine by yeast cytosine deaminase
    Jifeng 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...
  3. pmc Hydrogen-bond detection, configuration assignment and rotamer correction of side-chain amides in large proteins by NMR spectroscopy through protium/deuterium isotope effects
    Aizhuo 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...
  4. ncbi request reprint 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
    Yue 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...
  5. ncbi request reprint Mechanism of dihydroneopterin aldolase. NMR, equilibrium and transient kinetic studies of the Staphylococcus aureus and Escherichia coli enzymes
    Yi 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...
  6. pmc A molecular dynamics study of the ligand release path in yeast cytosine deaminase
    Lishan Yao
    Department of Chemistry, Michigan State University Center for Biological Modeling, East Lansing, Michigan 48824, USA
    Biophys J 92:2301-10. 2007
    ....
  7. pmc Mechanism of dihydroneopterin aldolase: functional roles of the conserved active site glutamate and lysine residues
    Yi 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...
  8. ncbi request reprint A molecular dynamics exploration of the catalytic mechanism of yeast cytosine deaminase
    Lishan 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...
  9. pmc TROSY of side-chain amides in large proteins
    Aizhuo 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...
  10. ncbi request reprint A point mutation converts dihydroneopterin aldolase to a cofactor-independent oxygenase
    Yi 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...
  11. ncbi request reprint Catalytic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: site-directed mutagenesis and biochemical studies
    Yue 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...
  12. ncbi request reprint Mechanism of the conformational transitions in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by NMR spectroscopy
    Guangyu Li
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
    Biochemistry 45:12573-81. 2006
    ....
  13. ncbi request reprint Product release is rate-limiting in the activation of the prodrug 5-fluorocytosine by yeast cytosine deaminase
    Lishan 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...
  14. ncbi request reprint Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF, hepatitis delta antigen, and stimulatory factor II
    Chunfen 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...
  15. pmc Feedback inhibition of deoxy-D-xylulose-5-phosphate synthase regulates the methylerythritol 4-phosphate pathway
    Aparajita Banerjee
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
    J Biol Chem 288:16926-36. 2013
    ..The feedback inhibition of PtDXS by IDP and DMADP constitutes an important mechanism of metabolic regulation of the MEP pathway and indicates that thiamine pyrophosphate-dependent enzymes may often be affected by IDP and DMADP...
  16. ncbi request reprint A combined ONIOM quantum chemical-molecular dynamics study of zinc-uracil bond breaking in yeast cytosine deaminase
    Lishan 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...
  17. doi request reprint Dynamics in Thermotoga neapolitana adenylate kinase: 15N relaxation and hydrogen-deuterium exchange studies of a hyperthermophilic enzyme highly active at 30 degrees C
    Harini 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...
  18. doi request reprint NMR detection of bifurcated hydrogen bonds in large proteins
    Aizhuo Liu
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
    J Am Chem Soc 130:2428-9. 2008
  19. ncbi request reprint Catalytic mechanism of guanine deaminase: an ONIOM and molecular dynamics study
    Lishan 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...
  20. ncbi request reprint Catalytic mechanism of yeast cytosine deaminase: an ONIOM computational study
    Stepan 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...
  21. ncbi request reprint Mechanism of dihydroneopterin aldolase: a molecular dynamics study of the apo enzyme and its product complex
    Lishan 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...
  22. ncbi request reprint Simultaneous NMR assignment of backbone and side chain amides in large proteins with IS-TROSY
    Aizhuo Liu
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
    J Biomol NMR 36:205-14. 2006
    ....
  23. ncbi request reprint Bile Acid secreted by male sea lamprey that acts as a sex pheromone
    Weiming 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...
  24. ncbi request reprint Chemical transformation is not rate-limiting in the reaction catalyzed by Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
    Yue 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...
  25. ncbi request reprint NTP-driven translocation by human RNA polymerase II
    Yuri A Nedialkov
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 1319, Japan
    J Biol Chem 278:18303-12. 2003
    ....
  26. pmc Thermotoga neapolitana adenylate kinase is highly active at 30 degrees C
    Claire 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...
  27. doi request reprint Scoring ligand similarity in structure-based virtual screening
    Maria 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...
  28. ncbi request reprint 'Top-down' characterization of site-directed mutagenesis products of Staphylococcus aureus dihydroneopterin aldolase by multistage tandem mass spectrometry in a linear quadrupole ion trap
    Gwynyth 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...
  29. pmc Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATP
    Rong 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...
  30. ncbi request reprint Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis
    Yijun 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...
  31. ncbi request reprint Hydrolysis of ATP by aminoglycoside 3'-phosphotransferases: an unexpected cost to bacteria for harboring an antibiotic resistance enzyme
    Choonkeun 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...
  32. ncbi request reprint Dynamic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: crystallographic studies
    Jaroslaw 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...
  33. ncbi request reprint Essential roles of a dynamic loop in the catalysis of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
    Jaroslaw 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...
  34. ncbi request reprint Structure and activity of Yersinia pestis 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as a novel target for the development of antiplague therapeutics
    Jaroslaw 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...
  35. ncbi request reprint Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism
    Jianhua 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...
  36. ncbi request reprint Reaction trajectory of pyrophosphoryl transfer catalyzed by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
    Jaroslaw 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...
  37. ncbi request reprint Fluorinated aminoglycosides and their mechanistic implication for aminoglycoside 3'-phosphotransferases from Gram-negative bacteria
    Choonkeun 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...
  38. ncbi request reprint Conformations of nucleotides bound to wild type and Y78F mutant yeast guanylate kinase: proton two-dimensional transferred NOESY measurements
    Bruce 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...

Research Grants8

  1. STRUCTURE/FUNCTION RELATIONSHIPS OF HPPK
    Honggao 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. ..
  2. Structure and Mechanism of Folate Biosynthetic Enzymes
    Honggao 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. ..