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YiLei Zhao Profile Page
YiLei Zhao
YiLei Zhao
Professor. Dr.
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cbb.sjtu.edu.cn/faculty.php#zhao
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Resume

Prof. Yi-Lei Zhao obtained his Ph.D. at Hong Kong University of Science and Technology (1998-2002), M.Sc. at Peking University (1994-1997), and B.S. at University of Science and Technology of China (1989-1994). He conducted his Postdoctoral research at University of California, Los Angeles, USA (2002-2005), and worked at National Institute of Standards and Technology, Maryland, USA (2005-2009) as foreign researcher. He was awarded with the UCLA Excellent Postdoctoral Prize in 2005 and the PM-USA INEST Research Fellowship in 2005-2007. He has then returned China and joined the School of Life Sciences and Biotechnology at SJTU as a full-professor in 2009, and PI of State Key Laboratory of Microbial Metabolism, Shanghai Center for Systems Biomedicine, and Shanghai Center for Bioinformation Technology. In the beginning first ten years of academic life (1989-1998), he was trained as a material scientist to synthesize and characterize inorganic superconductors and metal-organic photosensitive materials, and fabricate micro-cavity device for solar-cell and chemical sensor. Then he dedicated himself to fundamental research of structural properties of natural and non-natural peptides, protein, and nucleic acids from 1998. His Ph. D thesis was titled “Theoretical Studies on Secondary Structures of Peptides” and his postdoctoral research focused on nitric oxide-related protein post-translational modification (PTM). He has published 8 papers in the Journal of American Chemical Society and 1 paper in Accounts of Chemical Research and many in other ACS journals with the first and corresponding authorship about molecular recognition and reaction mechanism. Currently, he is the Associate Head of Department of Bioinformatics and Biostatistics, teaches the courses of “Molecular Modeling” and “Computational Biology”for undergraduate and graduate students, and also serves as members of the National Energy-saving and Emission-reduction Professional Committee, the Jiu-San Society (a Chinese Democratic Party), the Chinese Chemical Society, the American Chemical Society, the American Physical Society. Now he study computational chemical biology; his research is funded by the National High-tech R&D Program 863 #2012AA020403, the NSCF Creative Research Group #30821005, Shanghai Pujiang Talent Program, Shanghai Oriental Professorial Scholarship.

Research

Molecular mechanism for reaction and recognition in chemistry and biochemistry:
1) Molecular mechanism of enzymatic reaction
With experimental kinetics and theoretical computation, probe electronic structure evolution of enzymatic reactions, and develop a fast QM-MM based protocol to calculate activation energy.
2) Influence of NA chemical modification on DNA and RNA structure
By using quantum chemistry and the derivative scoring function, unveil consequence of NA chemical modifications (such as phosphorothioation and isonucleoside doping) on DNA and RNA secondary and tertiary structures.
3) Structural Bioinformatics of NO-related protein post-translational modification
Based on massively proteomic data in literatures, study the site-specificity of NO-related PTMs with the topological-sequential feature selection.

Papers

1) Xu, M.-J.; Liu, X.-J.; Zhao, Y.-L.; Liu, D.; Xu, Z.-H.; Lang, X.-M.; Ao, P.; Lin, W.-H.; Yang, S.-L.; Zhang, Z.-G.; Xu, J. (2012) Identification and Characterization of an Anti-Fibrotic Benzopyran Compound Isolated from Mangrove-Derived Streptomyces xiamenensis. Marine Drugs 10, 639-654.

2). Li, YQ; Du, XL; Lu, ZJ; Wu, DQ; Zhao, YL; Ren, B; Huang, JF; Huang, XQ; Xu, YH; Xu, YQ.(2011) “Regulatory Feedback Loop of Two phz Gene Clusters through 5′-Untranslated Regions in Pseudomonas sp. M18”. PLoS ONE 6(4): e19413.

3). Li, X.-L.; Xu, M.-J.; Zhao, YL; Xu. J. (2010) “A Novel Benzo[f][1,7] Naphthyridine Produced by Streptomyces Albogriseolus from Mangrove Sediments”. Molecules, 15(12), 9298-9307.

4). Schulz, P.; Zangmeister, C. D.; Zhao, YL; Frail, P. R.; Saudari, S. R.; Gonzalez, C. A.; Kagan, C. R.; Wuttig, M.; van Zee, R. D .(2010) “Comparison of the Energy-level Alignment of Thiolate and Carbodithiolate-Bound Self-Assembled Monolayers on Gold”. J. Phys. Chem. C, 114 (48), 20843–20851.

5). Zhao, Y.-L.*; Meot-Ner, M.; Gonzalez, C. (2009) “Ionic Hydrogen Bond Networks and Ion Solvation 1. An Efficient Monte Carlo / Quantum Mechanical Method for Structural Search and Energy Computations: Ammonium/Water”, J. Phys. Chem. A, 113(12), 2967-2974.

6). Zhao, Y.-L.*; Flora, J. W.; Thweatt, W. D.; Garrison, S.L.; Gonzalez, C.; Houk, K.N.; Marquez, M. (2009) “Phosphine Polymerization by Nitric Oxide: Experimental Characterization and Theoretical Predictions of Mechanism”, Inorganic Chemistry, 48(3), 1223-1231.

7). Bartalis, J.; Zhao, YL, Flora, J. W.; Paine, J. B.; Wooten, J. B. (2009) “Carbon-Centered Radicals in Cigarette Smoke: Acyl and Alkylaminocarbonyl Radicals”, Analytical Chemistry, 81(2), 631-641.

8). Penoni, A.; Palmisano, G.; Zhao, YL; Houk, K. N.; Volkman, J.; Nicholas, K. M. (2009) “On the Mechanism of Nitrosoarene-Alkyne Cycloaddition”, J. Am. Soc. Chem. 131(2), 653-661.

9). Wu, Y.-D.; Han, W.; Wang, D.-P.; Gao, Y.; Zhao, YL. (2008) “Theoretical Analysis of Secondary Structures of beta-Peptides”, Accounts of Chemical Research, 41, 1418-1427.

10). Zhao, YL; Laufer, A.H.; Halpern, J.; Fahr, A. (2007) “Hydrogen Migration and Vinylidene Pathway for Formation of Methane in the 193 nm Photodissociation of Propene; CH3CH=CH2 and CD3CD=CD2”, Journal of Physical Chemistry A.111, 8330-8335.

11). DeChancie, J.; Clemente, F. R.; Smith, A. J. T.; Gunaydin, H.; Zhao, Y.-L.; Zhang, X.; Houk, K. N. (2007) “How Similar are Enzyme Active Site Geometries Derived from Quantum Mechanical Theozymes to Crystal Structures of Enzyme-inhibitor Complexes? Implications for Enzyme Design”, Protein Science, 16, 1851-1866.

12). Zhao, Y.-L.*; Garrison, S.L.; Gonzalez, C.; Thweatt, W.D.; Marquez, M. (2007) “N-Nitrosation of Amines by NO2 and NO: a Theoretical Study”, Journal of Physical Chemistry A. 111, 2200-2205.

13). Edwards, N.; Helgeson, R.; Zhao, YL; Houk, K. N. (2006) “Pyridine-based Cavitands for Acid and Carboxylate Recognition”, Molecular Crystals and Liquid Crystals, 456, 175-192.

14). Zhao, Y.-L.; Suhrada, C. P.; Jung, M. E.; Houk, K. N. (2006) “Theoretical Investigation of the Stereoselective Stepwise Cope Rearrangement of a 3-Vinylmethylenecyclobutane” J. Am. Chem. Soc. 128 (34); 11106-11113.

15). Zhao, Y.-L.; Houk, K. N. (2006) “Thionitroxides, RS-NH-O●: The Structure of the SNO Moiety in "S-Nitrosohemoglobin", A Possible NO Reservoir and Transporter”, J. Am. Chem. Soc. 128(5), 1422-1423.

16). Zhao, Y.-L.; Jones, W. H.; Monnat, F., Wudl, F.; Houk, K. N. (2005) “Mechanisms of the Thermal Decomposition of Polysulfone: A DFT and CBS-QB3 study”, Macromolecules, 38(24); 10279-10285.

17). Zhao, YL; McCarren, P.R.; Houk, K. N.; Choi, BY; Toone, E. J. (2005) “Nitrosonium-Catalyzed Decomposition of S-Nitrosothiols in Solution: A Theoretical and Experimental Study.” J. Am. Chem. Soc. 127(31), 10917-10924.

18). Palmer L. C.; Zhao, YL; Houk, K. N. Rebek, J. Jr. (2005) “Diastereoselection of Chiral Acids in a Cylindrical Capsule”, Chem. Comm., 29, 3667-3669.

19). Zhao, YL; Bartberger, M.D.; Goto, K.; Shimada, K.; Kawashima, T; Houk, K. N. (2005) “Theoretical Evidence for Enhanced NO Dimerization in Aromatic Hosts: Implications for the Role of the Electrophile (NO)2 in Nitric Oxide Chemistry”(Communication), JACS, 127(22), 7964-7965.

20). Zhao, YL; Houk, K. N.; Rechavi, D.; Scarso, A.; Rebek, J. Jr. (2004) “Equilibrium Isotope Effects as a Probe of Nonbonding Attractions”(Communication), J. Am. Chem. Soc. 126(37), 11428-11429.

21). Zhao, YL; Houk, K. N.; Olson, L. P. (2004) “Mechanisms of Peroxynitrous Acid and Methyl Peroxynitrite, ROONO (R = H, Me), Rearrangements: A Conformation-Dependent Homolytic Dissociation.”(Article) Journal of Physical Chemistry A, 108(27), 5864-5871.

22). Zhao YL; Wu YD. (2002): “A Theoretical Study on b-Sheet Models: Is the Formation of Hydrogen Bond Network Cooperative?” J. Am. Chem. Soc. 124(8), 1570-1571.

23). Wu, YD; Lin, JQ; Zhao, YL. (2002) “Theoretical study of b-peptide models: intrinsic preferences of helical structures.” Helvetica Chimica Acta, 85(10), 3144-3160.

24). Wu YD.; Zhao YL (2001):“A Theoretical Study on the Origin of Cooperativity in the Formation of 310- and a-Helices”J. Am. Chem. Soc. 123(22), 5313-5319.

25). Zhao YL, Zhou DJ, Huang CH, Gan LB, Ying LM, Zhao XS, Zhang B, Ma Y, Xu M, Wu K (1998): “Langmuir-Blodgett Film of a Europium Complex and Its Application in a Silver Mirror Planar Microcavity”, Langmuir, 14(2), 417-422.

26). Zhao YL, Gan LB, Zhou DJ, Huang CH, Jiang JZ, Liu W (1998): “Photocurrent Generation from a Self-Assembling Guest-Host LB Film of C60(HOOCCHNHCHCOOH) and Octopentyloxy Phthalocyanine,” Solid State Communications, 106(1), 43-48.

27). Huang YY, Zhao YL, Gan LB, Huang CH, Wu NZ. (1998): “Langmuir-Blodgett Film Formation of a Fullerene Dicarboxylic Acid Derivative C60(HOOCCHNHCHCOOH) and its Photocurrent Generation”, J. of Colloid and Interface Science, 204(2), 277-283.

28). Lang AD, Zhai J, Huang CH, Gan LB, Zhao YL, Zhou DJ, Chen ZD. (1998): “Relationship between Structures and Photocurrent Generation Properties in a Series of Hemicyanine Congeners”, J. Phys. Chem. B. 102(8),1424-1429.

29). Huang YY, Gan LB, Huang CH, Zhao YL, Zhai J, Zou YD, Tan J, Zhao XS. (1998): “Studies on the Langmuir Films of the Quinone Compounds with Long Alkyl Side Chains and Their Surface Potential”, Chemical Journal of Chinese Universities, 19, 1323-1325. [in Chinese: 黄岩谊,甘良兵,黄春辉,赵一雷,翟锦,邹永德,谭俊,赵新生 “带有长侧链醌类化合物的Langmuir膜及其表面电势”高等学校化学学报]

30). Zhao YL, Zhou DJ, Yao GQ, Huang CH (1997): “Strong luminescent terbium(III)-pyrazolone complexes and their Langmuir-Blodgett films”, Langmuir, 13(15), 4060-4065.

31). Zhou DJ, Zhao YL, Gan LB, Luo CP, Huang CH, Luo MJ, Pan JQ, Wu Z (1997): “Synthesis of C60-Pyrrolidine Derivatives by 1,3-Dipolar Cycloaddition of Azomethine Ylides to C60”— Chemical Journal of Chinese Universities, 18(5), 665-670. [in Chinese: 周德健,赵一雷,甘良兵,骆初平,黄春辉,吕木坚,潘景岐,武轾 “含氮Ylide对C60的1, 3-偶极环加成反应法合成含吡咯环C60衍生物”高等学校化学学报]

32). Zhao YL, Gan LB, Zhou DJ, Luo CP, Huang CH, Jia GC, Wu T. (1997): “Synthesis of Proline Fullerene Derivative”, Chinese Science Bulletin, 42(16), 1360-1363. [in Chinese: 赵一雷,甘良兵,周德健,骆初平,黄春辉,贾国成,武轾 “1, 3-偶极环加成反应合成脯氨酸C60衍生物”科学通报]

33). Zhang, B, Ma Y, Xu M, Wu K, Huang CH, Zhao YL, Zhuo DJ, Yin LM, Zhao XS (1997) “Planar Organic Microcavity of Eu-Chelate Film with Metal Mirrors”, Solid State Communications, 104(10), 593-596

34). Luo CP, Huang CH, Gan LB, Zhou DJ, Xia WS, Zhuang QK, Zhao YL, Huang YY. (1996): “An Investigation of Photoelectrochemsitry of C60 and Its Derivatives of C60-Pyrrolidine by Monolayer Modified SnO2 Electrodes”J. Phys. Chem., 100(41), 16685-16689.

35). Zhao YL, Gan LB, Huang CH, (1996, review) “C60 Ultro-thin Regulated Film”, Chemistry in Universities, 1996, 11(4), 1-4. [in Chinese: 赵一雷,甘良兵,黄春辉“C60的超薄有序膜”大学化学,11(4),1-4.

36). Li H, Huang CH, Zhao YL, Li TK, Bai J, Zhao XS, Xia XH.(1995): “Langmuir-Blodgett Film and Second Harmonic Generation of a Series of New Nonlinear Optical Rare Earth Complexes”,— Solid State Communications. 94(9), 731-733.

37). Tang KB, Zhao YL, Chen ZY, Qian YT, Chao LZ, Zhang YH. (1994) “Effect of Cd Substitution on Superconductivity of Bi2222 Cuprates”,Physica C., 232,131-135

Achievement

Prof. Zhao has systemically investigated the nitric oxide chemistry and biochemistry, proposing a variety of useful concepts based on quantum chemistry computation in the related publications: 1) conformation-dependent peroxynitrate degradation form deleterious ROS and RNS species, 2) nitrosonium-catalyzed S-nitrosothiol decomposition occurs under normoxia condition, 3) oxidative reactivity of nitric oxide dimer leads to nucleophile phosphine and sulfide oxidation, 4) thionitroxide biological radical involves in hemoglobin S-nitrosylation as a critical intermediate, and etc. The above works were recognized by the UCLA Excellent Postdoctoral Award and the INEST Research Fellowship. He also pioneered the Repetitive-Unit-Z-matrix methodology to study the internal interaction in biomolecular helical and sheet-folding structures, such as polypeptides constructed with --, and -amino acids. He fabricated the first thickness-fully-controlled rare-earth fluorescent micro-cavity with LB technology and thereby awarded with the Peking U. Rare-earth Research Prize. He obtains two software registrations (#2011SR077761, #2012SR005766) and holds one in-application patent (#201110125025.0) from National Copyright Agency, about the GPU-MC computation and fast-QM conformation search.