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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
    2019

    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

    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

    Intrinsic cleavage of RNA polymerase II adopts a nucleobase-independent mechanism assisted by transcript phosphate

    Tse, C. K. M., Xu, J., Xu, L., Sheong, F. K., Wang, S., Chow, H. Y., Gao, X., Li, X., Cheung, P. P. H., Wang, D., Zhang, Y. & Huang, X., Mar 1 2019, In : Nature Catalysis. 2, 3, p. 228-235 8 p.

    Research output: Contribution to journalArticle

    RNA Polymerase II
    RNA
    Phosphates
    Oxygen
    Mechanics
    field theory (physics)
    Tensors
    tensors
    Neural networks
    learning

    Two symmetric arginine residues play distinct roles in thermus thermophilus argonaute DNA guide strand-mediated DNA target cleavage

    Lei, J., Sheng, G., Cheung, P. P. H., Wang, S., Li, Y., Gao, X., Zhang, Y., Wang, Y. & Huang, X., Jan 15 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 3, p. 845-853 9 p.

    Research output: Contribution to journalArticle

    R 486
    Thermus thermophilus
    DNA Cleavage
    Arginine
    DNA
    2018

    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

    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
    DNA Repair
    Yeast
    Repair
    Nucleotides
    Yeasts
    Nucleosomes
    DNA Repair
    Repair
    Nucleotides
    Genes
    2017

    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

    Improving scoring-docking-screening powers of protein–ligand scoring functions using random forest

    Wang, C. & Zhang, Y., Jan 30 2017, In : Journal of Computational Chemistry. 38, 3, p. 169-177 9 p.

    Research output: Contribution to journalArticle

    Random Forest
    Docking
    Scoring
    Screening
    Power of Test

    Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[a]pyrene-Derived Lesion

    Fu, I., Cai, Y., Geacintov, N., Zhang, Y. & Broyde, S., Apr 11 2017, In : Biochemistry. 56, 14, p. 1963-1973 11 p.

    Research output: Contribution to journalArticle

    Acetylation
    Nucleosomes
    Benzo(a)pyrene
    Histones
    Lysine
    Benzo(a)pyrene
    DNA Repair
    Repair
    Nucleotides
    DNA

    Targeting Unoccupied Surfaces on Protein-Protein Interfaces

    Rooklin, D., Modell, A. E., Li, H., Berdan, V., Arora, P. & Zhang, Y., Nov 8 2017, In : Journal of the American Chemical Society. 139, 44, p. 15560-15563 4 p.

    Research output: Contribution to journalArticle

    Membrane Proteins
    Peptidomimetics
    Proteins
    Amino Acid Motifs
    Fluorescence Polarization
    2016

    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

    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
    Nucleosomes
    Benzo(a)pyrene
    Molecular Dynamics Simulation
    Transcription
    Epigenomics

    Force field development with density-based energy decomposition analysis

    Zhou, N., Wu, Q. & Zhang, Y., Mar 14 2016, Many-Body Effects and Electrostatics in Biomolecules. Pan Stanford Publishing Pte. Ltd., p. 121-145 25 p.

    Research output: Chapter in Book/Report/Conference proceedingChapter

    field theory (physics)
    Decomposition
    decomposition
    energy

    Resveratrol serves as a protein-substrate interaction stabilizer in human SIRT1 activation

    Hou, X., Rooklin, D., Fang, H. & Zhang, Y., Nov 30 2016, In : Scientific Reports. 6, 38186.

    Research output: Contribution to journalArticle

    Proteins
    Insurance Benefits
    Wine
    Molecular Dynamics Simulation
    NAD
    2015

    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

    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

    Mechanistic insights into a classic wonder drug-aspirin

    Lei, J., Zhou, Y., Xie, D. & Zhang, Y., Jan 14 2015, In : Journal of the American Chemical Society. 137, 1, p. 70-73 4 p.

    Research output: Contribution to journalArticle

    Aspirin
    Enzyme inhibition
    Acetylation
    Pharmaceutical Preparations
    Molecular dynamics
    Pyrimidine Dimers
    DNA Repair
    Repair
    Nucleotides
    DNA

    Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An Ab initio QM/MM molecular dynamics study

    Gong, W., Wu, R. & Zhang, Y., Nov 1 2015, In : Journal of Computational Chemistry. 36, 30, p. 2228-2235 8 p.

    Research output: Contribution to journalArticle

    Histone Deacetylases
    Zinc
    Sulfhydryl Compounds
    Molecular Dynamics
    Molecular dynamics
    2014

    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

    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

    Peptide conformation analysis using an integrated bayesian approach

    Xiao, X., Kallenbach, N. & Zhang, Y., Sep 9 2014, In : Journal of Chemical Theory and Computation. 10, 9, p. 4152-4159 8 p.

    Research output: Contribution to journalArticle

    Peptides
    peptides
    Conformations
    proteins
    Proteins

    Structural and dynamic characterization of polymerase κ's minor groove lesion processing reveals how adduct topology impacts fidelity

    Lior-Hoffmann, L., Ding, S., Geacintov, N. E., Zhang, Y. & Broyde, S., Sep 9 2014, In : Biochemistry. 53, 35, p. 5683-5691 9 p.

    Research output: Contribution to journalArticle

    Topology
    Kerosene
    2-Acetylaminofluorene
    Gasoline
    Molecular modeling
    2013

    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

    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

    Sirtuin deacetylation mechanism and catalytic role of the dynamic cofactor binding loop

    Shi, Y., Zhou, Y., Wang, S. & Zhang, Y., Feb 7 2013, In : Journal of Physical Chemistry Letters. 4, 3, p. 491-495 5 p.

    Research output: Contribution to journalArticle

    Enzymes
    Sirtuins
    Molecular mechanics
    enzymes
    Quantum theory
    2012

    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

    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

    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

    Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion

    Lior-Hoffmann, L., Wang, L., Wang, S., Geacintov, N. E., Broyde, S. & Zhang, Y., Oct 2012, In : Nucleic Acids Research. 40, 18, p. 9193-9205 13 p.

    Research output: Contribution to journalArticle

    DNA-Directed DNA Polymerase
    Mechanics
    Water
    DNA
    Phosphoranes

    QM/MM molecular dynamics study of purine-specific nucleoside hydrolase

    Wu, R., Gong, W., Liu, T., Zhang, Y. & Cao, Z., Feb 16 2012, In : Journal of Physical Chemistry B. 116, 6, p. 1984-1991 8 p.

    Research output: Contribution to journalArticle

    N-Glycosyl Hydrolases
    Hydrolases
    purines
    nucleosides
    hydrolysis

    Revelation of a catalytic calcium-binding site elucidates unusual metal dependence of a human apyrase

    Rooklin, D. W., Lu, M. & Zhang, Y., Sep 19 2012, In : Journal of the American Chemical Society. 134, 37, p. 15595-15603 9 p.

    Research output: Contribution to journalArticle

    Apyrase
    nucleotidase
    Binding sites
    Calcium
    Metals
    2011

    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

    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

    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

    Molecular mechanism for eliminylation, a newly discovered post-translational modification

    Ke, Z., Smith, G. K., Zhang, Y. & Guo, H., Jul 27 2011, In : Journal of the American Chemical Society. 133, 29, p. 11103-11105 3 p.

    Research output: Contribution to journalArticle

    Phosphothreonine
    Cell signaling
    Lyases
    Threonine
    Post Translational Protein Processing

    Serine protease acylation proceeds with a subtle re-orientation of the histidine ring at the tetrahedral intermediate

    Zhou, Y. & Zhang, Y., Feb 7 2011, In : Chemical Communications. 47, 5, p. 1577-1579 3 p.

    Research output: Contribution to journalArticle

    Acylation
    Serine Proteases
    Histidine
    Trypsin
    Free energy

    Zinc chelation with hydroxamate in histone deacetylases modulated by water access to the linker binding channel

    Wu, R., Lu, Z., Cao, Z. & Zhang, Y., Apr 27 2011, In : Journal of the American Chemical Society. 133, 16, p. 6110-6113 4 p.

    Research output: Contribution to journalArticle

    Histone Deacetylases
    Chelation
    Hydroxamic Acids
    Zinc
    Water
    2010

    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

    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

    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

    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

    Reaction mechanism of monoethanolamine with CO2 in aqueous solution from molecular modeling

    Xie, H. B., Zhou, Y., Zhang, Y. & Johnson, J. K., Nov 4 2010, In : Journal of Physical Chemistry A. 114, 43, p. 11844-11852 9 p.

    Research output: Contribution to journalArticle

    monoethanolamine (MEA)
    Ethanolamine
    Molecular modeling
    zwitterions
    Carbamates
    2009

    Ab initio quantum mechanical/molecular mechanical studies of histone modifying enzymes

    Zhang, Y., 2009, Multi-scale quantum models for biocatalysis: Modern techniques and applications. York, D. M. & Lee, T-S. (eds.). New York: Springer Verlag, p. 341-350

    Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

    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