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Yingkai Zhang

Professor of Chemistry

    1993 …2019
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    Research Output 1993 2019

    • 90 Article
    • 2 Chapter (peer-reviewed)
    • 1 Chapter
    • 1 Comment/debate
    Article

    Ab initio QM/MM free-energy studies of arginine deiminase catalysis: The protonation state of the Cys nucleophile

    Ke, Z., Guo, H., Xie, D., Wang, S. & Zhang, Y., Apr 7 2011, In : Journal of Physical Chemistry B. 115, 13, p. 3725-3733 9 p.

    Research output: Contribution to journalArticle

    Arginine
    Nucleophiles
    nucleophiles
    Protonation
    Catalysis

    Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase

    Cisneros, G. A., Liu, H., Zhang, Y. & Yang, W., Aug 27 2003, In : Journal of the American Chemical Society. 125, 34, p. 10384-10393 10 p.

    Research output: Contribution to journalArticle

    Hydrogen
    Carbon
    Acids
    Energy barriers
    Substrates
    Histone-Lysine N-Methyltransferase
    lysine
    Catalysis
    catalysis
    Molecular dynamics
    functionals
    dissociation
    Electrons
    electrons
    interactions

    A Conserved Allosteric Pathway in Tyrosine Kinase Regulation

    Marsiglia, W. M., Katigbak, J., Zheng, S., Mohammadi, M., Zhang, Y. & Traaseth, N. J., Aug 6 2019, In : Structure. 27, 8, p. 1308-1315.e3

    Research output: Contribution to journalArticle

    Isoleucine
    Phenylalanine
    Protein-Tyrosine Kinases
    Phosphotransferases
    Mutation

    Active site cysteine is protonated in the PAD4 michaelis complex: Evidence from born-oppenheimer Ab initio QM/MM molecular dynamics simulations

    Ke, Z., Zhou, Y., Hu, P., Wang, S., Xie, D. & Zhang, Y., Sep 24 2009, In : Journal of Physical Chemistry B. 113, 38, p. 12750-12758 9 p.

    Research output: Contribution to journalArticle

    Arginine
    cysteine
    Cysteine
    Molecular dynamics
    Deprotonation

    Aging mechanism of soman inhibited acetylcholinesterase

    Sirin, G. S., Zhou, Y., Lior-Hoffmann, L., Wang, S. & Zhang, Y., Oct 11 2012, In : Journal of Physical Chemistry B. 116, 40, p. 12199-12207 9 p.

    Research output: Contribution to journalArticle

    Soman
    Acetylcholinesterase
    Aging of materials
    acetylcholine
    Acetylcholine

    AlphaSpace: Fragment-Centric Topographical Mapping to Target Protein-Protein Interaction Interfaces

    Rooklin, D., Wang, C., Katigbak, J., Arora, P. & Zhang, Y., Aug 24 2015, In : Journal of Chemical Information and Modeling. 55, 8, p. 1585-1599 15 p.

    Research output: Contribution to journalArticle

    Proteins
    interaction
    drug
    Membrane Proteins
    Atoms

    Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot Peptides

    Zhou, Y., Xie, D. & Zhang, Y., Apr 21 2016, In : Journal of Physical Chemistry Letters. 7, 7, p. 1138-1142 5 p.

    Research output: Contribution to journalArticle

    Cystines
    Cystine
    Amides
    Peptides
    amides

    An efficient approach for ab initio energy calculation of biopolymers

    Chen, X., Zhang, Y. & Zhang, J., May 8 2005, In : Journal of Chemical Physics. 122, 18, 184105.

    Research output: Contribution to journalArticle

    Biopolymers
    biopolymers
    Fractionation
    caps
    fractionation

    An efficient linear scaling method for ab initio calculation of electron density of proteins

    Gao, A. M., Zhang, D. W., Zhang, J. & Zhang, Y., Aug 21 2004, In : Chemical Physics Letters. 394, 4-6, p. 293-297 5 p.

    Research output: Contribution to journalArticle

    caps
    Carrier concentration
    proteins
    scaling
    Fractionation

    An internal water-retention site in the rhomboid intramembrane protease GlpG ensures catalytic efficiency

    Zhou, Y., Moin, S. M., Urban, S. & Zhang, Y., Jul 3 2012, In : Structure. 20, 7, p. 1255-1263 9 p.

    Research output: Contribution to journalArticle

    Catalytic Domain
    Peptide Hydrolases
    Water
    Catalysis
    Membranes

    Application of the faraday effect in chemistry

    Zhang, Y., Wang, G. & Jiang, Y., 1993, In : Journal of Nanjing University (Natural Science Edition). 29, p. 400-406

    Research output: Contribution to journalArticle

    A proton-shuttle reaction mechanism for histone deacetylase 8 and the catalytic role of metal ions

    Wu, R., Wang, S., Zhou, N., Cao, Z. & Zhang, Y., Jul 14 2010, In : Journal of the American Chemical Society. 132, 27, p. 9471-9479 9 p.

    Research output: Contribution to journalArticle

    Histone Deacetylases
    Metal ions
    Protons
    Metals
    Ions

    A pseudobond approach to combining quantum mechanical and molecular mechanical methods

    Zhang, Y., Lee, T. S. & Yang, W., 1999, In : Journal of Chemical Physics. 110, 1, p. 46-54 9 p.

    Research output: Contribution to journalArticle

    Atoms
    atoms
    Potential energy surfaces
    Molecules
    Covalent bonds

    A transferable nonbonded pairwise force field to model zinc interactions in metalloproteins

    Wu, R., Lu, Z., Cao, Z. & Zhang, Y., Feb 8 2011, In : Journal of Chemical Theory and Computation. 7, 2, p. 433-443 11 p.

    Research output: Contribution to journalArticle

    Metalloproteins
    field theory (physics)
    Zinc
    zinc
    interactions

    A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV

    Wang, L., Yu, X., Hu, P., Broyde, S. & Zhang, Y., Apr 18 2007, In : Journal of the American Chemical Society. 129, 15, p. 4731-4737 7 p.

    Research output: Contribution to journalArticle

    Sulfolobus solfataricus
    DNA Polymerase beta
    DNA
    Water
    Substrates

    Base flipping free energy profiles for damaged and undamaged DNA

    Zheng, H., Cai, Y., Ding, S., Tang, Y., Kropachev, K., Zhou, Y., Wang, L., Wang, S., Geacintov, N., Zhang, Y. & Broyde, S., Dec 20 2010, In : Chemical Research in Toxicology. 23, 12, p. 1868-1870 3 p.

    Research output: Contribution to journalArticle

    DNA Repair
    Free energy
    Repair
    Estuaries
    DNA

    Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions

    Zhou, Y., Wang, S., Li, Y. & Zhang, Y., 2016, In : Methods in Enzymology. 577, p. 105-118 14 p.

    Research output: Contribution to journalArticle

    Molecular Dynamics Simulation
    Molecular dynamics
    Amber
    Computer simulation
    Enzymes

    Born - Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4

    Ke, Z., Wang, S., Xie, D. & Zhang, Y., Dec 31 2009, In : Journal of Physical Chemistry B. 113, 52, p. 16705-16710 6 p.

    Research output: Contribution to journalArticle

    Arginine
    hydrolysis
    Molecular dynamics
    Hydrolysis
    molecular dynamics

    Catalytic mechanism and metal specificity of bacterial peptide deformylase: A density functional theory QM/MM study

    Xiao, C. & Zhang, Y., Jun 7 2007, In : Journal of Physical Chemistry B. 111, 22, p. 6229-6235 7 p.

    Research output: Contribution to journalArticle

    peptide deformylase
    Peptides
    peptides
    Density functional theory
    Metals
    Histone-Lysine N-Methyltransferase
    Molecular Dynamics Simulation
    Histones
    Methylation
    Free energy

    Catalytic reaction mechanism of acetylcholinesterase determined by born-oppenheimer Ab initio QM/MM molecular dynamics simulations

    Zhou, Y., Wang, S. & Zhang, Y., Jul 8 2010, In : Journal of Physical Chemistry B. 114, 26, p. 8817-8825 9 p.

    Research output: Contribution to journalArticle

    Molecular Dynamics Simulation
    Acetylcholinesterase
    Molecular dynamics
    Hydrogen
    Hydrogen bonds

    Computational design of a time-dependent histone deacetylase 2 selective inhibitor

    Zhou, J., Li, M., Chen, N., Wang, S., Luo, H. B., Zhang, Y. & Wu, R., Mar 20 2015, In : ACS Chemical Biology. 10, 3, p. 687-692 6 p.

    Research output: Contribution to journalArticle

    Histone Deacetylase 2
    Protein Isoforms
    Chalcone
    Histone Deacetylase Inhibitors
    Histone Deacetylases

    Computational simulations of zinc enzyme: Challenges and recent advances

    Wu, R., Cao, Z. & Zhang, Y., Jun 2012, In : Progress in Chemistry. 24, 6, p. 1175-1184 10 p.

    Research output: Contribution to journalArticle

    Zinc
    Enzymes
    Molecular dynamics
    Binding Sites
    Computer simulation

    Computational Strategy for Bound State Structure Prediction in Structure-Based Virtual Screening: A Case Study of Protein Tyrosine Phosphatase Receptor Type O Inhibitors

    Hou, X., Rooklin, D., Yang, D., Liang, X., Li, K., Lu, J., Wang, C., Xiao, P., Zhang, Y., Sun, J. P. & Fang, H., Jan 1 2018, (Accepted/In press) In : Journal of Chemical Information and Modeling.

    Research output: Contribution to journalArticle

    Class 3 Receptor-Like Protein Tyrosine Phosphatases
    Phosphatases
    Screening
    Proteins
    Ligands

    Degenerate Ground States and a Fractional Number of Electrons in Density and Reduced Density Matrix Functional Theory

    Yang, W., Zhang, Y. & Ayers, P. W., May 29 2000, In : Physical Review Letters. 84, 22, p. 5172-5175 4 p.

    Research output: Contribution to journalArticle

    ground state
    electrons
    energy
    functionals
    integers
    Electron energy levels
    Charge transfer
    Decomposition
    decomposition
    Dimers

    Density functional study of a weakly hydrogen-bonded benzene-ammonia complex: The importance of the exchange functional

    Enkvist, C., Zhang, Y. & Yang, W., Sep 2000, In : International Journal of Quantum Chemistry. 79, 5, p. 325-329 5 p.

    Research output: Contribution to journalArticle

    Benzene
    Ammonia
    ammonia
    Hydrogen
    benzene

    Describing van der Waals interaction in diatomic molecules with generalized gradient approximations: The role of the exchange functional

    Zhang, Y., Pan, W. & Yang, W., Nov 15 1997, In : Journal of Chemical Physics. 107, 19, p. 7921-7925 5 p.

    Research output: Contribution to journalArticle

    diatomic molecules
    Noble Gases
    Local density approximation
    gradients
    Molecules

    Design, synthesis and biological evaluation of quinoline derivatives as HDAC class I inhibitors

    Chen, C., Hou, X., Wang, G., Pan, W., Yang, X., Zhang, Y. & Fang, H., Jun 16 2017, In : European Journal of Medicinal Chemistry. 133, p. 11-23 13 p.

    Research output: Contribution to journalArticle

    Histone Deacetylase Inhibitors
    Histone Deacetylases
    Derivatives
    Flow cytometry
    Enzyme Assays
    Carbon
    valence
    Atoms
    Electrons
    carbon
    Molecular Dynamics Simulation
    Mechanics
    Free energy
    History
    sampling

    Directional dependence of hydrogen bonds: A density-based energy decomposition analysis and its implications on force field development

    Lu, Z., Zhou, N., Wu, Q. & Zhang, Y., Dec 13 2011, In : Journal of Chemical Theory and Computation. 7, 12, p. 4038-4049 12 p.

    Research output: Contribution to journalArticle

    field theory (physics)
    Hydrogen bonds
    hydrogen bonds
    Decomposition
    decomposition

    DNA cytosine methylation: Structural and thermodynamic characterization of the epigenetic marking mechanism

    Yang, J., Lior-Hoffmann, L., Wang, S., Zhang, Y. & Broyde, S., Apr 23 2013, In : Biochemistry. 52, 16, p. 2828-2838 11 p.

    Research output: Contribution to journalArticle

    Cytosine
    DNA Methylation
    Thermodynamics
    Epigenomics
    Protons
    Nucleosomes
    Benzo(a)pyrene
    Molecular Dynamics Simulation
    Transcription
    Epigenomics

    Flexibility of catalytic zinc coordination in thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM molecular dynamics study

    Wu, R., Hu, P., Wang, S., Cao, Z. & Zhang, Y., Jan 12 2010, In : Journal of Chemical Theory and Computation. 6, 1, p. 337-343 7 p.

    Research output: Contribution to journalArticle

    Thermolysin
    Histone Deacetylases
    Molecular dynamics
    Zinc
    flexibility
    Potential energy surfaces
    Free energy
    enzymes
    potential energy
    free energy

    Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: Energetic and structural relationships to nucleotide excision repair susceptibility

    Cai, Y., Zheng, H., Ding, S., Kropachev, K., Schwaid, A. G., Tang, Y., Mu, H., Wang, S., Geacintov, N. E., Zhang, Y. & Broyde, S., Jul 15 2013, In : Chemical Research in Toxicology. 26, 7, p. 1115-1125 11 p.

    Research output: Contribution to journalArticle

    Benzo(a)pyrene
    Polycyclic Aromatic Hydrocarbons
    DNA Repair
    Free energy
    Repair

    Functional loop dynamics of the S-component of ECF transporter FolT

    Qiu, L., Shen, C., Song, J., Zhang, Y. & Zhang, J., Oct 18 2018, In : Molecular Physics. 116, 19-20, p. 2613-2621 9 p.

    Research output: Contribution to journalArticle

    transporter
    Folic Acid
    Molecular Dynamics Simulation
    molecular dynamics
    Molecular dynamics

    Geometric preferences in iron(II) and zinc(II) model complexes of peptide deformylase

    Karambelkar, V. V., Xiao, C., Zhang, Y., Narducci Sarjeant, A. A. & Goldberg, D. P., Feb 20 2006, In : Inorganic Chemistry. 45, 4, p. 1409-1411 3 p.

    Research output: Contribution to journalArticle

    formic acid
    peptide deformylase
    formates
    peptides
    Metal ions
    Niacinamide
    Molecular Dynamics Simulation
    Molecular dynamics
    Enzymes
    Computer simulation

    How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: A theoretical study

    Cheng, Y., Zhang, Y. & McCammon, J. A., Apr 2006, In : Protein Science. 15, 4, p. 672-683 12 p.

    Research output: Contribution to journalArticle

    Phosphorylation
    Cyclic AMP-Dependent Protein Kinases
    Catalyst activity
    Catalytic Domain
    Theoretical Models

    How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: An ab Initio QM/MM study

    Cheng, Y., Zhang, Y. & McCammon, J. A., Feb 9 2005, In : Journal of the American Chemical Society. 127, 5, p. 1553-1562 10 p.

    Research output: Contribution to journalArticle

    Phosphorylation
    Cyclic AMP-Dependent Protein Kinases
    Protein Kinases
    Catalytic Domain
    Ions
    Histone-Lysine N-Methyltransferase
    Methylation
    Methyltransferases
    Molecular Dynamics Simulation
    Lysine

    How is acetylcholinesterase phosphonylated by Soman? An ab initio QM/MM molecular dynamics study

    Sirin, G. S. & Zhang, Y., Oct 2 2014, In : Journal of Physical Chemistry A. 118, 39, p. 9132-9139 8 p.

    Research output: Contribution to journalArticle

    Soman
    nerves
    Molecular dynamics
    acetylcholine
    molecular dynamics

    How is the active site of enolase organized to catalyze two different reaction steps?

    Liu, H., Zhang, Y. & Yang, W., Jul 19 2000, In : Journal of the American Chemical Society. 122, 28, p. 6560-6570 11 p.

    Research output: Contribution to journalArticle

    Phosphopyruvate Hydratase
    Cations
    Catalytic Domain
    Positive ions
    Metals

    Identification and structure-function analyses of an allosteric inhibitor of the tyrosine phosphatase PTPN22

    Li, K., Hou, X., Li, R., Bi, W., Yang, F., Chen, X., Xiao, P., Liu, T., Lu, T., Zhou, Y., Tian, Z., Shen, Y., Zhang, Y., Wang, J., Fang, H., Sun, J. & Yu, X., Jan 1 2019, In : Journal of Biological Chemistry. 294, 21, p. 8653-8663 11 p.

    Research output: Contribution to journalArticle

    Protein Tyrosine Phosphatases
    Phosphatases
    Phosphoric Monoester Hydrolases
    Tyrosine
    Allosteric Site

    Importance of charge independent effects in readout of the trimethyllysine mark by HP1 chromodomain

    Zhenyu, L., Lai, J. & Zhang, Y., Oct 21 2009, In : Journal of the American Chemical Society. 131, 41, p. 14928-14931 4 p.

    Research output: Contribution to journalArticle

    Histones
    Proteins
    Methylation
    Free energy
    Lysine

    Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis

    Zhou, N., Lu, Z., Wu, Q. & Zhang, Y., Jun 7 2014, In : Journal of Chemical Physics. 140, 21, 214117.

    Research output: Contribution to journalArticle

    Noble Gases
    Parameterization
    parameterization
    Dimers
    rare gases