John Z.H. Zhang
Professor of ChemistryB.S. East China Normal University; Ph.D. University of Houston; Postdoctoral Research at University of California, Berkeley
Email:
Phone: 212-998-8412
Office: Silver Center, 100 Washington Square East, Room 1001O
Personal Homepage
Lab Homepage
Areas of Research/Interest
Computational study of protein’s structure and interaction dynamics.
Research Description
Development of original computational methods for accurate and efficient study of biological systems; quantum mechanical methods and their applications to accurately predict protein structure; protein folding; free energy in protein-drug and protein-protein bindings; development of new polarized force field for biomolecular simulation; molecular dynamics simulation and rational drug design.
Publications
L.L. Duan, Y. Mei, Q.G. Zhang, and J.Z.H. Zhang, “Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization”, J. Chem. Phys. 130, 115102 (2009).
Li-Ping Ju, K.L. Han, J. Z.H. Zhang, “Global Dynamics and Transition State Theories: Comparative Study of Reaction Rate Constants for Gas-Phase Chemical Reactions”, J. Comput. Chem. 30, 305-316 (2009).
Y. Tong, C.G. Ji, Y. Mei, J.Z.H. Zhang, “Simulation of NMR Data Reveals that Protein’s local structures Are Stabilized by Electronic Polarization”, J. Am. Chem. Soc. 131, 8636–8641 (2009).
J. Bao, X.Y. Dong, J.Z.H. Zhang, P.S. Arora, “Dynamical Binding of Hydrogen-Bond Surrogate Derived Bak Helices to Antiapoptotic Protein Bcl-x(L)”, J. Phys. Chem. B 113, 3565-3571 (2009).
E.L. Wu, K.L. Han, J.Z.H. Zhang, “Computational Study for Binding of Oscillarin To Human Alpha-Thrombin”, J. Theo. & Comput. Chem. 8, 551-560 (2009).
C.G. Ji and J.Z.H. Zhang, “NMR Scalar Coupling Constant Reveals That Intraprotein Hydrogen Bonds Are Dynamically Stabilized by Electronic Polarization”, J. Phys. Chem. B, 113, 13898-13900 (2009).
C.G. Ji and J.Z.H. Zhang, “Electronic Polarization Is Important in Stabilizing the Native Structures of Proteins”，J. Phys. Chem. B, 113, 16059–16064 (2009).
Y. Mei and J.Z.H. Zhang, “Numerical Stabilities in Fitting Atomic Charges to Electric Field and Electrostatic Potential”, J. Theo. Comput. Chem. 8, 925-942 (2009).
Y.L. Li, L. Han, Y. Mei, and J.Z.J. Zhang, “Time-dependent density functional theory study of absorption spectra of metallocenes”, Chem. Phys. Letts. 482, 217-222 (2009).
Y. Tong, Y. Mei, J.Z.H. Zhang, L.L. Duan, Q.G. Zhang, “Quantum calculation of protein solvation and protein–ligand binding free energy for hiv-1 protease/water complex”, J. Theo. Comput. Chem. 8, 1265-1279 (2009).
H.G. Li, P.L. Huang, D.W. Zhang, Y.T. Sun, H.C. Chen, J. Zhang, P.L. Huang, X.P. Kong, S. Lee-Huang, “A new activity of anti-HIV and anti-tumor protein GAP31: DNA adenosine glycosidase - Structural and modeling insight into its functions”， Biochem. Biophys. Res. Commun., 391, 340-345 (2010).
M. Han and J.Z.H. Zhang, “Class I Phospho-inositide-3-kinases (PI3Ks) Isoform-Specific Inhibition Study by the Combination of Docking and Molecular Dynamics Simulation”, J. Chem. Info. Mod. 50, 136-145 (2010).
Y. Tong, Y. Mei, Y.L. Li, C.G. Ji, J.Z.H. Zhang, “Electrostatic polarization makes substantial contribution to free energy of avidin-biotin binding", J. Am. Chem. Soc. 132, 5137-5142 (2010).
Yunpeng Lu, Y. Mei, J.Z.H. Zhang, Dawei Zhang, “Electron polarization critically stabilizes the Mg2+ complex in the catalytic core domain of HIV-1 integrase”, J. Chem. Phys. (Communications), 132, 131101 (2010).
L.L. Duan, Y. Mei, Y.L. Li, Q.G. Zhang, D.W. Zhang, J.Z.H. Zhang, “Simulation of the thermodynamics of folding and unfolding of the Trp-cage mini-protein TC5b using different combinations of force fields and solvation models”, Science China-Chemistry 53, 196-201 (2010 ).
Li L. Duan,Ye Mei,Dawei Zhang, Qing G. Zhang, and John Z. H. Zhang, “Folding of a Helix at Room Temperature Is Critically Aided by Electrostatic Polarization of Intraprotein Hydrogen Bonds”, J. Am. Chem. Soc. 132, 11159–11164 (2010).
P. Wang and J.Z.H. Zhang, “Selective Binding of Antiinfluenza Drugs and Their Analogues to 'Open' and 'Closed' Conformations of H5N1 Neuraminidase”, J. Phys. Chem. B 114, 12958-12964 (2010).
D.W. Zhang, L.Z. Yu, P.L. Huang, P.L. Huang, S. Lee-Huang, J.Z.H. Zhang, “COMPUTATIONAL DESIGN OF NORBORNANE-BASED HIV-1 PROTEASE INHIBITORS”, J. Theo. Comput. Chem. 9, 471-485 (2010).
Y. Xiang, L.L. Duan, J.Z.H. Zhang, “Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy”, Phys. Chem. Chem. Phys. 12, 15681-15688 (2010).
X. Y. Wang and J.Z.H. Zhang, “Effect of polarization on the stability of a helix dimer”, Chem. Phys. Lett. 501, 508-512 (2011).
Y. Xiang, L.L. Duan, J.Z.H. Zhang, “Protein’s electronic polarization contributes significantly to its catalytic function”, J. Chem. Phys. 134, 205101 (2011).
L.L. Duan, Y. Mei, Q.G. Zhang, and J.Z.H. Zhang, “Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization”, J. Chem. Phys. 130, 115102 (2009).
Li-Ping Ju, K.L. Han, J. Z.H. Zhang, “Global Dynamics and Transition State Theories: Comparative Study of Reaction Rate Constants for Gas-Phase Chemical Reactions”, J. Comput. Chem. 30, 305-316 (2009).
Y. Tong, C.G. Ji, Y. Mei, J.Z.H. Zhang, “Simulation of NMR Data Reveals that Protein’s local structures Are Stabilized by Electronic Polarization”, J. Am. Chem. Soc. 131, 8636–8641 (2009).
J. Bao, X.Y. Dong, J.Z.H. Zhang, P.S. Arora, “Dynamical Binding of Hydrogen-Bond Surrogate Derived Bak Helices to Antiapoptotic Protein Bcl-x(L)”, J. Phys. Chem. B 113, 3565-3571 (2009).
E.L. Wu, K.L. Han, J.Z.H. Zhang, “Computational Study for Binding of Oscillarin To Human Alpha-Thrombin”, J. Theo. & Comput. Chem. 8, 551-560 (2009).
C.G. Ji and J.Z.H. Zhang, “NMR Scalar Coupling Constant Reveals That Intraprotein Hydrogen Bonds Are Dynamically Stabilized by Electronic Polarization”, J. Phys. Chem. B, 113, 13898-13900 (2009).
C.G. Ji and J.Z.H. Zhang, “Electronic Polarization Is Important in Stabilizing the Native Structures of Proteins”，J. Phys. Chem. B, 113, 16059–16064 (2009).
Y. Mei and J.Z.H. Zhang, “Numerical Stabilities in Fitting Atomic Charges to Electric Field and Electrostatic Potential”, J. Theo. Comput. Chem. 8, 925-942 (2009).
Y.L. Li, L. Han, Y. Mei, and J.Z.J. Zhang, “Time-dependent density functional theory study of absorption spectra of metallocenes”, Chem. Phys. Letts. 482, 217-222 (2009).
Y. Tong, Y. Mei, J.Z.H. Zhang, L.L. Duan, Q.G. Zhang, “Quantum calculation of protein solvation and protein–ligand binding free energy for hiv-1 protease/water complex”, J. Theo. Comput. Chem. 8, 1265-1279 (2009).
H.G. Li, P.L. Huang, D.W. Zhang, Y.T. Sun, H.C. Chen, J. Zhang, P.L. Huang, X.P. Kong, S. Lee-Huang, “A new activity of anti-HIV and anti-tumor protein GAP31: DNA adenosine glycosidase - Structural and modeling insight into its functions”， Biochem. Biophys. Res. Commun., 391, 340-345 (2010).
M. Han and J.Z.H. Zhang, “Class I Phospho-inositide-3-kinases (PI3Ks) Isoform-Specific Inhibition Study by the Combination of Docking and Molecular Dynamics Simulation”, J. Chem. Info. Mod. 50, 136-145 (2010).
Y. Tong, Y. Mei, Y.L. Li, C.G. Ji, J.Z.H. Zhang, “Electrostatic polarization makes substantial contribution to free energy of avidin-biotin binding", J. Am. Chem. Soc. 132, 5137-5142 (2010).
Yunpeng Lu, Y. Mei, J.Z.H. Zhang, Dawei Zhang, “Electron polarization critically stabilizes the Mg2+ complex in the catalytic core domain of HIV-1 integrase”, J. Chem. Phys. (Communications), 132, 131101 (2010).
L.L. Duan, Y. Mei, Y.L. Li, Q.G. Zhang, D.W. Zhang, J.Z.H. Zhang, “Simulation of the thermodynamics of folding and unfolding of the Trp-cage mini-protein TC5b using different combinations of force fields and solvation models”, Science China-Chemistry 53, 196-201 (2010 ).
Li L. Duan,Ye Mei,Dawei Zhang, Qing G. Zhang, and John Z. H. Zhang, “Folding of a Helix at Room Temperature Is Critically Aided by Electrostatic Polarization of Intraprotein Hydrogen Bonds”, J. Am. Chem. Soc. 132, 11159–11164 (2010).
P. Wang and J.Z.H. Zhang, “Selective Binding of Antiinfluenza Drugs and Their Analogues to 'Open' and 'Closed' Conformations of H5N1 Neuraminidase”, J. Phys. Chem. B 114, 12958-12964 (2010).
D.W. Zhang, L.Z. Yu, P.L. Huang, P.L. Huang, S. Lee-Huang, J.Z.H. Zhang, “COMPUTATIONAL DESIGN OF NORBORNANE-BASED HIV-1 PROTEASE INHIBITORS”, J. Theo. Comput. Chem. 9, 471-485 (2010).
Y. Xiang, L.L. Duan, J.Z.H. Zhang, “Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy”, Phys. Chem. Chem. Phys. 12, 15681-15688 (2010).
X. Y. Wang and J.Z.H. Zhang, “Effect of polarization on the stability of a helix dimer”, Chem. Phys. Lett. 501, 508-512 (2011).
Y. Xiang, L.L. Duan, J.Z.H. Zhang, “Protein’s electronic polarization contributes significantly to its catalytic function”, J. Chem. Phys. 134, 205101 (2011).
Fellowships/Honors
Camille and Henry Dreyfus New Faculty Award (1990), NSF Presidential Faculty Fellow (1994), Alfred P. Sloan Foundation Research Fellow (1995), Camille Dreyfus Teacher-Scholar (1995)
