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赵一雷博士介绍(PI)

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课题组长:赵一雷 博士,教授。1989-1994年中国科技大学学士;1994-1997年北京大学硕士;1998-2002年香港科技大学博士;2002-2005年美国加州大学洛杉矶分校博士后;2005-2009年美国国家标准技术研究所研究员;2009至今,上海生物信息技术研究中心PI、上海交通大学博士生导师。主要研究方向为计算化学生物学,采用生物信息学的方法挖掘生物学中的功能蛋白和基因,并从生物大分子的三维结构及电子结构的角度结合实验表征研究其独特的分子机理和潜在的应用性能,特别是开拓计算生物学在医药卫生和生物合成等方面的应用, 包括: 1DNA硫化学修饰和转录后调控等表观遗传性,蛋白质翻译后修饰如巯基亚硝化的分子机制;2)生化反应动力学研究,如酶化学、酶工程、微生物代谢途径分析和改造,特别是生物质能源和环境有机污染物的生物转化,抗生素、抗肿瘤药物的生物合成中的分子设计。上海市“东方学者”特聘教授,教育部新世纪优秀人才,浦江计划人才,计算化学与分子生物信息学实验室负责人,上海交通大学微生物代谢国家重点实验室、系统医学研究院、科学工程计算教育部重点实验室研究员,国家基金委“重要微生物合成代谢与分解代谢的分子机理”创新研究团队骨干成员。

【主要论文】

1. Zhang Y.C., Liang J., Lian P., Han Y.W., Chen Y.F., Bai L.Q., Wang Z.J., Liang J.D., Deng Z.X., Zhao Y.-L.* 2012, Theoretical study on steric effects of DNA phosphorothioation: B-helical destabilization in Rp-phosphorothioated DNA. J. Phys. Chem. B. 116:10639–10648.

2. Liang J., Cheng S.L., Hou J.W., Xu Z.H., Zhao Y.-L.* 2012, Car-Parinello molecular dynamics simulations of thionitroxide and S-nitrosothiol in the gas phase, methanol, and water — A theoretical study of S-nitrosylation. Science China -Chemistry, 55: 2081–2088.3. Xie X.Q., Liang J.D., Pu T.N., Xu F., Yao F., Yang Y., Zhao Y.-L., You D.L., Zhou X.F., Deng Z.X., Wang Z.J. 2012, Phosphorothioate DNA as an antioxidant in bacteria. Nucl. Acids Res. 40:9115–9124.4. 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. 

【申请/获得专利&软件著作权】

1. 徐真昊,赵一雷*《基于快速量子化学计算方法的多分子构象搜索软件》,授权号:2011SR0777612. 贺宇杰,徐真昊,赵一雷* 《基于改进蒙地卡罗算法的染色体粗粒化模拟GPU软件》,授权号:2012SR0057663. 赵一雷*,成尚利,徐真昊 《基于氨基酸拓扑网络的蛋白质特征位点对比分析软件》,授权号:2012SR1072874. 赵一雷*,尹建民,徐真昊 《基于GPU技术与快速量子化学计算方法的多分子构象搜索软件》,授权号:2012SR110566;


【主要论文】
 

Nitric oxide chemistry and biochemistry (一氧化氮的化学与生物化学)

1)      Zhao, YL; 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.

2)      Zhao, YL*; 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.

3)      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.

4)      Zhao, YL*; 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.

5)      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.” Journal of Physical Chemistry A, 108(27), 5864-5871.

6)      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”, J. Am. Chem. Soc., 127(22), 7964-7965. Reaction Mechanism (反应机理)

7)      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.

8)      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.

9)      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.

10)   Zhao, YL; 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.

11)   Zhao, YL; 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. Molecular recognition (分子识别)

12)   Li, Y.; Du, X.; Lu, Z.J.; Wu, D.; Zhao, YL et al. (2011) “Regulatory Feedback Loop of Two phz Gene Clusters through 5’-Untranslated Regions in Pseudomonas sp. M18”. PLoS ONE, 6(4): e19413.

 13)   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.

14)   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.

15)   Zhao, YL*; 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.

16)   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.

17)   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.

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; Houk, K. N.; Rechavi, D.; Scarso, A.; Rebek, J. Jr. (2004) “Equilibrium Isotope Effects as a Probe of Nonbonding Attractions”, J. Am. Chem. Soc. 126(37), 11428-11429.   Peptide and Protein Structures (多肽蛋白质高级结构)

20)   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, 14181427.

21)   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.

22)   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.

23)   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.