个人简介
“计算化学与分子生物信息学”课题组组长 主要从事结构生物信息学和计算化学生物学领域的研究，例如DNA硫修饰的分子结构基础与其抗氧化机制、加氧酶和水解酶的催化机制及其在环保和能源科学应用、ROS相关的氧化还原类型蛋白质翻译后修饰及医学应用。曾在吴云东、黄春辉、钱逸泰、Houk等四位院士直接指导下从事材料化学和理论化学研究，研究成果包括：提出生物高分子重复单元结构（Foldamer）在高级结构中的耦合作用、R手性硫修饰对DNA双螺旋性结构的不稳定效应、生物ROS自由基的形成及对蛋白质的修饰作用。约50篇SCI论文发表在Account Chemical Research、Angew Chem、JACS（8篇）等分子机制研究的旗舰杂志上，总影响因子大约190， 被引用超过600次，H因子15。
教育经历
2002.10-2005.09 美国加州大学洛杉矶分校 博士后访问学者
1999.01-2002.04 香港科技大学 博士
1994.09-1997.06 北京大学 硕士
1989.09-1994.06 中国科技大学 学士
工作经历
2014.03- 上海交通大学生命科学技术学院，院长助理
2011.12- 上海交通大学微生物代谢国家重点实验室，研究员
2010.10- 上海交通大学生物信息学与生物统计学系，副主任
2009.05- 上海交通大学生命科学技术学院，教授 博士生导师
2005.10-2009.04 美国国家标准技术研究所(NIST)，外国研究员
2002.10-2005.09 美国加州大学洛杉矶分校(UCLA)，访问学者
1997.06-1998.12 中国化工信息中心，工程师
荣誉奖励
2014年 九三学社上海交通大学委员会委员、闵行区侨联委员
2013年 上海市生物信息学会第三届理事
2012年 教育部新世纪优秀人才
2010年 上海市浦江人才计划
2010年 《生物医学工程与临床》编委
2009年 上海市“东方学者”特聘教授
2005-07年 美国PMUSA-INEST Fellowship
2005年 UCLA优秀博士后嘉奖（美国）
1. Cheng SL, Shi T, Wang XL, Liang J, Wu H, Xie L, Li YX, Zhao YL*. Features of S-nitrosylation based on statistical analysis and molecular
dynamics simulation: Cysteine acidity, surrounding basicity, steric hindrance and local flexibility. Mol BioSyst, 2014, DOI: 10.1039/C4MB00322E (online ahead).
2. Shi T, Luo Y, Wang XL, Lu S, Zhao YL*, Jian Zhang*. Theoretical studies on the mechanism, enantioselectivity, and axial ligand effect of a Ru(salen)-catalyzed asymmetric cyclopropanation reaction. Organometallics, 2014, dx.doi.org/10.1021/om400956z (online ahead)
3. Qi Y, Zhu J, Sun Y, Du Y, Chu J, Shi T, Zhao YL*, Wang XL*. Theoretical studies of the binding-affinity and reactivity between laccase and phenolic substrates. Chem J Chinese Univ, 2014, 35(4):776-83.
4. Zhang G, Zhang W, Zhang Q, Shi T, Ma L, Zhu Y, Li S, Zhang H, Zhao YL, Shi R, Zhang CS*. Mechanistic insights into polycyclic formation by reductive cyclization in Ikarugamycin biosynthesis. Angew Chem Int Ed, 2014, 53(19): 4840-4
5. Wu G, Chen D, Tang H, Ren Y, Chen Q, Lv Y, Zhang Z, ZhaoYL*, Yao Y, Xu P*. Structural insights into the specific recognition of N-heterocycle biodenitrogenation-derived substrates by microbial amide hydrolases. Mol Microbio, 2014, 91(5), 1009-21.
6. Cheng S, Lian B, Liang J, Shi T, Xie L, Zhao YL*. Site selectivity for protein tyrosine nitration: insights from features of structure and topological network. Mol Biosyst, 2013, 9: 2860-8.
7. Huang Y, Chen Z, Chen Y, Zhang H, Zhang Y, Zhao YL, Yang Z*, Zhang LH*. Effects of conformational alteration induced by D-/L-isonucleoside incorporation in siRNA on their stability in serum and silencing activity. Bioconjugate Chem, 2013, 24:951-9.
8. Lei Y, Zhang F, Chen QH, Lin SJ, Zhao YL, Li ZY*. The role of aromatic L-amino acid decarboxylase in bacillamide C biosynthesis by Bacillus atrophaeus C89. Sci Rep, 2013, 3:1753.
9. Chen D, Tang H, Lv Y, Zhang Z, Shen K, Lin K, Zhao YL, Wu G*, Xu P*. Structural and computational studies of the maleate isomerase from Pseudomonas putida S16 reveal a breathing motion wrapping the substrate inside. Mol Microbio, 2014, 91(5), 1009-21.
10. Zhang Y, Liang J, Lian P, Han Y, Chen Y, Bai L, Wang Z, Liang J, Deng Z, Zhao YL*. Theoretical study on steric effect of DNA phsphorothioation: B-helical destabilization in Rp-phosphorothioated DNA. J Phys Chem B, 2012, 116:10639-48
11. Liang J, Cheng SL, Hou J, Xu ZH, Zhao YL*. Car-Parinello molecular dynamics simulations of thionitroxide and S-nitrosothiol in the gas phase, methanol, and water - A theoretical study of S-nitrosylation. Sci China Chem, 2012, 55(10): 2081-8.
12. Xie X, Liang J, Pu T, Xu F, Yao F, Yang Y, Zhao YL, You D, Zhou X, Deng Z*, Wang Z*. Phosphorothioate DNA as an antioxidant in bacteria. Nuc Acids Res, 2012, 40(18):9115-24.
13. Xu M, Liu X, Zhao YL, Liu D, Xu Z, Lang X, Ao P, Lin W, Yang S, Zhang Z*, Xu J*. Identification and characterization of an anti-fibrotic benzopyran compound isolated from mangrove-derived Streptomyces xiamenensis. Mar Drugs, 2012, 10, 639-54.
14. Li Y, Du X, Lu Z, Wu D, Zhao YL, Ren B, Huang J, Huang X, Xu Y, Xu Y*. Regulatory feedback loop of two phz gene clusters through 5’-untranslated regions in Pseudomonas sp. M18. Plos One, 2011, 6(4):e19413.
15. Li X, Xu M, Zhao YL, Xu J. A novel benzo[f][1,7]-naphthyridine produced by Streptomyces Albogriseolus from mangrove sediments. Molecules, 2010, 15:9298-307.
16. Schulz P, Zangmeister C*, Zhao YL, Frail P, Saudari S, Gonzalez C, Kagan C, Wuttig M, van Zee R. Comparison of the energy-level alignment of thiolate- and carbodithiolate-bound self-assembled monolayers on gold. J Phys Chem C, 2010, 114:20843–51.
17. Zhao YL*, Meot-Ner M, Gonzalez C. 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, 2009, 113:2967–74.
18. Zhao YL*, Flora J, Thweatt W, Garrison S, Gonzalez C, Houk K, Marquez M. Phosphine polymerization by nitric oxide: Experimental characterization and theoretical predictions of mechanism. Inorg Chem, 2009, 48:1223-31.
19. Bartalis J, Zhao YL, Flora J, Paine III J, Wooten J*. Carbon-centered radicals in cigarette smoke: acyl and alkylaminocarbonyl radicals. Anal Chem, 2009, 81:631–41.
20. Penoni A, Palmisano G, Zhao YL, Houk K, Volkman J, Nicholas K. On the mechanism of nitrosoarene-alkyne cycloaddition. JACS, 2009, 131:653-61.
