	Deqiang (David) Zhang Howard Hughes Medical Institute University of California, San Diego 9500 Gilman Dr., MC 0365 La Jolla, CA 92093-0365 Tel: (858) 822-0255 Fax: (858) 534-4974 Email Address: dzhang@mccammon.ucsd.edu Education California Institute of Technology Pasadena, CA Sept. 1996--Dec. 2002 PhD in Chemistry, with Minor in Computer Science Thesis: Structure-based Design of Mutant Proteins: I. Molecular Docking studies of Amino Acid Binding to Wild-type Aminoacyl-tRNA Synthetases II. Structure-based Design of Mutant Aminoacyl-tRNA Synthetases for Non-natural amino acid Incorporation Advisor: Prof. William A. Goddard III Chinese Academy of Sciences Beijing, China Sept. 1993--June, 1996 MS in Atmospheric Chemistry Thesis: Studies of Reactions for Hydroxyl Radicals with HFC-134a and Some Brominated Compounds and Their Implications in the Atmosphere Advisor: Prof. Jinxian Zhong University of Science & Technology of China Hefei, China Sept. 1988--June, 1993 BS in Chemical Physics, with minor in Economics Thesis: Laser-induced fluorescence spectrum of PH2 radicals cooled in a supersonic free jet Thesis Advisor: Prof. Yang Chen GPA 3.8/4.0, Graduated with the Highest Honor Research Experiences 01/03--resent Research Associate, Howard Hughes Medical Institute, and Dept. of Chem. & Biochem., University of California, San Diego, La Jolla, CA 92093 (With Prof. J. Andrew McCammon ) ¡¤ Investigated the interactions between Nicotinic Acetylcholine Receptor (nAChR) and its ligands using molecular docking and steered molecular dynamics in trying to understand the molecular mechanism involved in the ligand binding and channel gating. ¡¤ Calculated the diffusion rate of acetylcholine to different forms of tetrameric Acetylcholinesterase (AChE) by solving the Smoluchowski equation using finite element method; modeled the oligomeric association of AChE with PRAD using molecular dynamics. ¡¤ Studied the effect of electrostatics of very large molecular assemblies such as the ribosome and virus capsids by solving the Poisson-Boltzmann equation in parallel. ¡¤ Modeled the distribution of viral RNA inside the capsid using the combination of a coarse-grain RNA model and a Monte Carlo approach. ¡¤ Developed methods to improve the scoring function in docking to multiple protein conformation. 9/96--12/02 Research Assistant, Materials and Process Simulation Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125 ¡¤ Developed a Protein Design Method COPÓ (Clash-Opportunity Progressive Design), and used it to design mutant aminoacyl-tRNA synthetases for non-natural amino acid recognition ¡¤ Studied amino acid recognition mechanism by aminoacyl-tRNA synthetases using molecular docking ¡¤ Predicted the structure of tyrosyl-tRNA synthetase from Methanococcus jannaschii using STRUCFAST homology modeling ¡¤ Conducted molecular dynamics simulations on a family of laboratory evolved enzymes with different thermostability and discovered the correlation between low frequency modes and thermostability ¡¤ Unfolding study of the origin of the hyperthermostability of rubredoxin from P. furiosus 9/93--6/96 Research Assistant, Center for Eco-Environmental Research, Chinese Academy of Sciences, Beijing, China ¡¤ Conducted research on the degradation of HFC-134a (a new type of coolant) and a series of brominated compounds in the atmosphere and established their ozone depletion potential (ODP) through modeling ¡¤ Built a simulation system to perform QSAR of trace species in the environment 9/92--6/93 Undergraduate Research Assistant, Dept. of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, China ¡¤ Conducted research on the laser-induced fluorescence spectroscopy of PH₂ radicals Computer and software Skills ¡¤ Minor degree in Computer Science ¡¤ Programming: C (10+ years), C++ (8+ years), Perl (5 years), Java (2 years), C Shell, HTML ¡¤ Operating Systems: Unix (Linux, Solaris, Irix), Windows (95, 98, NT) ¡¤ Computer Algorithms: Familiar with major algorithms (Greedy, Optimization, Computational Geometry, Distributed System Design, etc.) ¡¤ Databases: Familiar with SQL language, mysql, MS Access, RDBMS Design ¡¤ Software Packages: Mathematica, Matlab, Maple ¡¤ Chemistry Software: Cerius2, Insight II, Quanta, Gaussian, Macromodel, Impact, Jaguar, Sybyl, etc. scientific Publications 2. Deqiang Zhang Justin Gullingsrud, & J. Andrew McCammon, 2006, The potentials of mean force for acetylcholine unbinding from the nicotinic acetylcholine receptor ligand binding domain. J. Am. Chem. Soc., in press. 4. `Christopher McClendon, Nagarajan Vaidehi, Victor Kam,` Deqiang Zhang,`& William A. Goddard III, 2006, Fidelity of seryl-tRNA synthetase to binding of natural amino acids from HierDock first principles computations. Protein Engineering, Design & Selection, In press` 5. Robert Konecny, Joanna Trylska, Florence Tama, Deqiang Zhang, Nathan A. Baker, Charles L. Brooks III & J. Andrew McCammon, 2006, Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers, in press. 3. Deqiang Zhang, & J. Andrew McCammon, 2005, The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis. PLoS Comput Biol 1(6): e62 6. Benzhuo Lu, Deqiang Zhang & J. Andrew McCammon, 2005, Computation of electrostatic forces between solvated molecules determined by Poisson-Boltzmann equation using boundary element method. J. Chem. Phys., In press. 7. Deqiang Zhang, Jason Suen, Yongjie Zhang, Yuhua Song, Zoran Radic, Palmer Taylor, Michael Holst, Chandrajit Bajaj, Nathan A. Baker & J. Andrew McCammon, 2005, Tetrameric mouse acetylcholinesterase: Continuum rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophysical J., 88(3), 1659-1665. 8. Deqiang Zhang, Robert Konecny, Nathan A. Baker, & J. Andrew McCammon, 2004, Electrostatic interaction between RNA and protein capsid in CCMV simulated by a Monte Carlo approach. Biopolymers, 75(4), 325-337. 9. Deepshikha Datta, Nagarajan Vaidehi, Deqiang Zhang, & William A. Goddard III, 2004, Selectivity and specificity of ligand binding in methionyl-tRNA synthetase. Protein Science, 13(10), 2693-2705. 10. Patrick L. Wintrode^, Deqiang Zhang^, Nagarajan Vaidehi, Frances H. Arnold & William A. Goddard III, 2003, Molecular Dynamics study of a family of laboratory evolved thermophilic enzymes. J. Mol. Biol. 327(3), 745-757. *Equal authorship 11. Deqiang Zhang, Nagarajan Vaidehi, William A. Goddard III, Joseph Danzer & Derek Debe, 2002, Structure-Based Design of Mutant Methanococcus jannaschii Tyrosyl-tRNA Synthetase for Incorporation of O-Methyl-L-Tyrosine. Proc. Natl. Acad. Sci. 99(10), 6579-6584. 12. Dongping Zhong, Samir Kumar Pal, Deqiang Zhang, Sunney I. Chan & Ahmed H. Zewail, 2002, Femtosecond Dynamics of Rubredoxin: Tryptophan Solvation and Resonance Energy Transfer in the Protein. Proc. Natl. Acad. Sci. 99(1), 13-18. 13. Deqiang Zhang, Jinxian Zhong, & Lianxiong Qiu, 1997, Kinetics of the reaction of hydroxyl radicals with CH2Br2 and its implications in the atmosphere, J. Atmos. Chem., 27(2), 209-215. 14. Deqiang Zhang, Jinxian Zhong, & Lianxiong Qiu, 1997, Rate constants for the reaction of hydroxyl radicals with HFC-134A, J. Environ. Sci., 9(3), 361-365. 15. Deqiang Zhang, & Jinxian Zhong, 1997, The estimation of the ODP values for CH3Br and CH2Br2, Chinese J. Environ. Sci., 17(3). 16. Deqiang Zhang, Jinxian Zhong, & Lianxiong Qiu, 1997, Kinetics for the reaction of hydroxyl radicals with CH₃Br and its implications in the atmosphere, J. Environ. Sci., 9(4), 480-485. 17. Jinxian Zhong & Deqiang Zhang, 1997, Characterization of the photo-oxidization of CH₃Br and CHBr₃ in the presence of H₂O₂, Chinese J. Environ. Sci., 17(2). 18. Deqiang Zhang, Jinxian Zhong, & Lianxiong Qiu, 1997, Rate constants of the reaction of hydroxyl radicals with C₂H₅Br and the tropospheric lifetime of C₂H₅Br, Chinese J. Environ. Sci., 17(4). 19. Yang Chen, Qing Zhang, Deqiang Zhang, Congxiang Chen, Shuqin Yu, & Xingxiao Ma, 1994, Laser-induced fluorescence spectrum of PH2 radicals cooled in a supersonic free jet, Chem. Phys. Lett., 223(1-2), 104-109. 20. Yang Chen, Qing Zhang, Deqiang Zhang, Congxiang Chen & Xingxiao Ma, 1993, The LIF spectrum of PH₂ radicals cooled in a supersonic free jet, Chinese J. Chem. Phys., 6(5), 426-433. Awards and Honors ¡¤ Student Scholarship for Academic Excellence, USTC, 1988-1993 ¡¤ Graduate with the Highest Honor, USTC, 7/1993 ¡¤ College Graduates of the Year, Anhui Provincial Commission of Education, 7/1993 ¡¤ Best Poster Award, MGM Research Conference, San Diego, CA, 3/2004 ¡¤ Best Student Poster Cup, 13th International Meshing Roundtable, Williamburg, VA, USA, 9/2004. Professional Associations and affiliations ¡¤ American Chemical Society (http://www.acs.org) (since 1996) ¡¤ Sigma Xi, the Scientific Research Society (http://www.sigmaxi.org) (since 2002) ¡¤ Biophysical Society, (http://www.biophysics.org) (since 2003) ¡¤ Protein Society, (http://www.proteinsociety.org) (since 2004) ¡¤ NSF Center for the Science & Engineering of Materials at Caltech (http://www.csem.caltech.edu) (2001-2002) ¡¤ NSF Center for Theoretical Biological Physics (http://ctbp.ucsd.edu) (2003-present) Patent The COP Protein Design Tool (US patent pending 60/372074, filed on April 12th, 2003).

Education

California Institute of Technology Pasadena, CA Sept. 1996--Dec. 2002

PhD in Chemistry, with Minor in Computer Science

Thesis: Structure-based Design of Mutant Proteins: I. Molecular Docking studies of Amino Acid Binding to Wild-type Aminoacyl-tRNA Synthetases II. Structure-based Design of Mutant Aminoacyl-tRNA Synthetases for Non-natural amino acid Incorporation

Advisor: Prof. William A. Goddard III

Chinese Academy of Sciences Beijing, China Sept. 1993--June, 1996

MS in Atmospheric Chemistry

Thesis: Studies of Reactions for Hydroxyl Radicals with HFC-134a and Some Brominated Compounds and Their Implications in the Atmosphere

Advisor: Prof. Jinxian Zhong

University of Science & Technology of China Hefei, China Sept. 1988--June, 1993

BS in Chemical Physics, with minor in Economics

Thesis: Laser-induced fluorescence spectrum of PH2 radicals cooled in a supersonic free jet

Thesis Advisor: Prof. Yang Chen

GPA 3.8/4.0, Graduated with the Highest Honor

Research Experiences

01/03--resent Research Associate, Howard Hughes Medical Institute, and Dept. of Chem. & Biochem., University of California, San Diego, La Jolla, CA 92093

(With Prof. J. Andrew McCammon )

¡¤ Investigated the interactions between Nicotinic Acetylcholine Receptor (nAChR) and its ligands using molecular docking and steered molecular dynamics in trying to understand the molecular mechanism involved in the ligand binding and channel gating.

¡¤ Calculated the diffusion rate of acetylcholine to different forms of tetrameric Acetylcholinesterase (AChE) by solving the Smoluchowski equation using finite element method; modeled the oligomeric association of AChE with PRAD using molecular dynamics.

¡¤ Studied the effect of electrostatics of very large molecular assemblies such as the ribosome and virus capsids by solving the Poisson-Boltzmann equation in parallel.

¡¤ Modeled the distribution of viral RNA inside the capsid using the combination of a coarse-grain RNA model and a Monte Carlo approach.

¡¤ Developed methods to improve the scoring function in docking to multiple protein conformation.

9/96--12/02 Research Assistant, Materials and Process Simulation Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125

¡¤ Developed a Protein Design Method COPÓ (Clash-Opportunity Progressive Design), and used it to design mutant aminoacyl-tRNA synthetases for non-natural amino acid recognition

¡¤ Studied amino acid recognition mechanism by aminoacyl-tRNA synthetases using molecular docking

¡¤ Predicted the structure of tyrosyl-tRNA synthetase from Methanococcus jannaschii using STRUCFAST homology modeling

¡¤ Conducted molecular dynamics simulations on a family of laboratory evolved enzymes with different thermostability and discovered the correlation between low frequency modes and thermostability

¡¤ Unfolding study of the origin of the hyperthermostability of rubredoxin from P. furiosus

9/93--6/96 Research Assistant, Center for Eco-Environmental Research, Chinese Academy of Sciences, Beijing, China

¡¤ Conducted research on the degradation of HFC-134a (a new type of coolant) and a series of brominated compounds in the atmosphere and established their ozone depletion potential (ODP) through modeling

¡¤ Built a simulation system to perform QSAR of trace species in the environment

9/92--6/93 Undergraduate Research Assistant, Dept. of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, China

¡¤ Conducted research on the laser-induced fluorescence spectroscopy of PH₂ radicals

Computer and software Skills

¡¤ Minor degree in Computer Science

¡¤ Programming: C (10+ years), C++ (8+ years), Perl (5 years), Java (2 years), C Shell, HTML

¡¤ Operating Systems: Unix (Linux, Solaris, Irix), Windows (95, 98, NT)

¡¤ Computer Algorithms: Familiar with major algorithms (Greedy, Optimization, Computational Geometry, Distributed System Design, etc.)

¡¤ Databases: Familiar with SQL language, mysql, MS Access, RDBMS Design

¡¤ Software Packages: Mathematica, Matlab, Maple

¡¤ Chemistry Software: Cerius2, Insight II, Quanta, Gaussian, Macromodel, Impact, Jaguar, Sybyl, etc.

scientific Publications

2. Deqiang Zhang Justin Gullingsrud, & J. Andrew McCammon, 2006, The potentials of mean force for acetylcholine unbinding from the nicotinic acetylcholine receptor ligand binding domain. J. Am. Chem. Soc., in press.

4. Christopher McClendon, Nagarajan Vaidehi, Victor Kam, Deqiang Zhang,& William A. Goddard III, 2006, Fidelity of seryl-tRNA synthetase to binding of natural amino acids from HierDock first principles computations. Protein Engineering, Design & Selection, In press

5. Robert Konecny, Joanna Trylska, Florence Tama, Deqiang Zhang, Nathan A. Baker, Charles L. Brooks III & J. Andrew McCammon, 2006, Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers, in press. 3. Deqiang Zhang, & J. Andrew McCammon, 2005, The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis. PLoS Comput Biol 1(6): e62 6. Benzhuo Lu, Deqiang Zhang & J. Andrew McCammon, 2005, Computation of electrostatic forces between solvated molecules determined by Poisson-Boltzmann equation using boundary element method. J. Chem. Phys., In press. 7. Deqiang Zhang, Jason Suen, Yongjie Zhang, Yuhua Song, Zoran Radic, Palmer Taylor, Michael Holst, Chandrajit Bajaj, Nathan A. Baker & J. Andrew McCammon, 2005, Tetrameric mouse acetylcholinesterase: Continuum rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophysical J., 88(3), 1659-1665. 8. Deqiang Zhang, Robert Konecny, Nathan A. Baker, & J. Andrew McCammon, 2004, Electrostatic interaction between RNA and protein capsid in CCMV simulated by a Monte Carlo approach. Biopolymers, 75(4), 325-337. 9. Deepshikha Datta, Nagarajan Vaidehi, Deqiang Zhang, & William A. Goddard III, 2004, Selectivity and specificity of ligand binding in methionyl-tRNA synthetase. Protein Science, 13(10), 2693-2705. 10. Patrick L. Wintrode^*, Deqiang Zhang^*, Nagarajan Vaidehi, Frances H. Arnold & William A. Goddard III, 2003, Molecular Dynamics study of a family of laboratory evolved thermophilic enzymes. J. Mol. Biol. 327(3), 745-757. *Equal authorship 11. Deqiang Zhang, Nagarajan Vaidehi, William A. Goddard III, Joseph Danzer & Derek Debe, 2002, Structure-Based Design of Mutant Methanococcus jannaschii Tyrosyl-tRNA Synthetase for Incorporation of O-Methyl-L-Tyrosine. Proc. Natl. Acad. Sci. 99(10), 6579-6584. 12. Dongping Zhong, Samir Kumar Pal, Deqiang Zhang, Sunney I. Chan & Ahmed H. Zewail, 2002, Femtosecond Dynamics of Rubredoxin: Tryptophan Solvation and Resonance Energy Transfer in the Protein. Proc. Natl. Acad. Sci. 99(1), 13-18. 13. Deqiang Zhang, Jinxian Zhong, & Lianxiong Qiu, 1997, Kinetics of the reaction of hydroxyl radicals with CH2Br2 and its implications in the atmosphere, J. Atmos. Chem., 27(2), 209-215. 14. Deqiang Zhang, Jinxian Zhong, & Lianxiong Qiu, 1997, Rate constants for the reaction of hydroxyl radicals with HFC-134A, J. Environ. Sci., 9(3), 361-365. 15. Deqiang Zhang, & Jinxian Zhong, 1997, The estimation of the ODP values for CH3Br and CH2Br2, Chinese J. Environ. Sci., 17(3). 16. Deqiang Zhang, Jinxian Zhong, & Lianxiong Qiu, 1997, Kinetics for the reaction of hydroxyl radicals with CH₃Br and its implications in the atmosphere, J. Environ. Sci., 9(4), 480-485. 17. Jinxian Zhong & Deqiang Zhang, 1997, Characterization of the photo-oxidization of CH₃Br and CHBr₃ in the presence of H₂O₂, Chinese J. Environ. Sci., 17(2). 18. Deqiang Zhang, Jinxian Zhong, & Lianxiong Qiu, 1997, Rate constants of the reaction of hydroxyl radicals with C₂H₅Br and the tropospheric lifetime of C₂H₅Br, Chinese J. Environ. Sci., 17(4). 19. Yang Chen, Qing Zhang, Deqiang Zhang, Congxiang Chen, Shuqin Yu, & Xingxiao Ma, 1994, Laser-induced fluorescence spectrum of PH2 radicals cooled in a supersonic free jet, Chem. Phys. Lett., 223(1-2), 104-109. 20. Yang Chen, Qing Zhang, Deqiang Zhang, Congxiang Chen & Xingxiao Ma, 1993, The LIF spectrum of PH₂ radicals cooled in a supersonic free jet, Chinese J. Chem. Phys., 6(5), 426-433. Awards and Honors ¡¤ Student Scholarship for Academic Excellence, USTC, 1988-1993 ¡¤ Graduate with the Highest Honor, USTC, 7/1993 ¡¤ College Graduates of the Year, Anhui Provincial Commission of Education, 7/1993 ¡¤ Best Poster Award, MGM Research Conference, San Diego, CA, 3/2004 ¡¤ Best Student Poster Cup, 13th International Meshing Roundtable, Williamburg, VA, USA, 9/2004. Professional Associations and affiliations ¡¤ American Chemical Society (http://www.acs.org) (since 1996) ¡¤ Sigma Xi, the Scientific Research Society (http://www.sigmaxi.org) (since 2002) ¡¤ Biophysical Society, (http://www.biophysics.org) (since 2003) ¡¤ Protein Society, (http://www.proteinsociety.org) (since 2004) ¡¤ NSF Center for the Science & Engineering of Materials at Caltech (http://www.csem.caltech.edu) (2001-2002) ¡¤ NSF Center for Theoretical Biological Physics (http://ctbp.ucsd.edu) (2003-present) Patent The COP Protein Design Tool (US patent pending 60/372074, filed on April 12th, 2003).