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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
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Article
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

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

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

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
Electron energy levels
Charge transfer
Decomposition
decomposition
Dimers