微生物代谢国家重点实验室-科研队伍

陈海峰

姓名: 陈海峰

职称: 教授

E-Mail: haifengchen@sjtu.edu.cn

个人主页: http：//cbb.sjtu.edu.cn/

联系电话: 02134204348

个人简历:

个人简介

陈海峰课题组致力于天然无规蛋白精准分子力场的研究，分别发展了基于AMBER与CHARMM的力场参数。参数发表后受到美国加州大学圣地亚哥分校美国科学院院士Andrew McCammon实验室等国内外研究机构的广泛关注。迄今为止已在JACS，NAR, RNA, PNAS等国际著名学术期刊发表了90多篇SCI论文。分获上海市科技进步一等奖及教育部自然科学二等奖。2010年获得上海市浦江人才资助。本课题组热忱欢迎有志于计算生物学的青年学者以博士后或者攻读博士学位身份加盟。

教育经历

2000.09-2003.12: 法国巴黎第七大学计算化学专业博士

1994.09-1997.06: 四川大学化学纤维专业硕士.

1990.09-1994.06: 西安交通大学高分子材料专业学士

工作经历

2018.01-: 上海交通大学微生物代谢国家重点实验室教授，博士生导师

2007.01-2017.12: 上海交通大学生命科学技术学院副教授，博士生导师

2005.01-2006.12: 美国加州大学尔湾分校博士后

1997.07-2004.12: 中科院上海有机化学研究所助理研究员

荣誉奖励

2017年教育部自然科学二等奖

2003年上海市科学技术进步一等奖

学会兼职

2015.01– : Frontiers in Molecular Biosciences副主编
2013.01–: Chemical Biology & Drug Design副主编
1. 天然无规蛋白精准分子力场的研究
2. 天然无规蛋白折叠的分子机制

3. 受体与配体的别构机制研究
1.        D. Song, R. Luo, H.F. Chen^*. The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins. J. Chem. Inf. Model. 2017, 57:1166-1178.

2.        W. Ye, T. Qian,H. Liu,R. Luo, H.F. Chen^*.Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations. J. Chem. Inf. Model. 2017, 57:1153-1165.

3.        X. Guo, J. Han, R. Luo, H.F. Chen^*. Conformation Dynamics of Intrinsically Disordered Protein c-Myb with ff99IDPs Force Field. RSC Advances. 2017, 7:29713 –29721.

4.        PoY. J. Ye, L. Zhou, X. Liu, H. Liu, D. Li, M. Cao, H.F. Chen, L. Xu, J. Zhu, Y. Zhao^*. A novel chemical inhibitor of ABA signaling targets all ABA receptors. Plant Physiol. 2017, 173:2356-2369.

5.        M. A. Hoque, Y. Zhang, L. Chen, G. Yang, M. A. Khatun, H.F. Chen, L. Hao, Y. Feng*. Stepwise Loop Insertion Strategy for Active Site Remodeling to Generate Novel Enzyme Functions. ACS Chem. Biol. 2017, 12:1188–1193.

6.        H. Liu, W. Ye, H.F. Chen*. Positive Cooperative Regulation of Double Binding Sites for Human Acetylcholinesterase. Chem. Biol. Drug Des. 2017, 89:694-704.

7.        D. Song, W. Wang, W. Ye, D. Ji, R. Luo, H.F. Chen^*. ff14IDPs Force Field Improving the Conformation Sampling of Intrinsically Disordered Proteins. Chem. Biol. Drug Des. 2017, 89:5-15.

8.        T. Qian, J. Wo, Y. Zhang, Q. Song, G. Feng, R. Luo, S. Lin, G. Wu, H.F. Chen^*. Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode. Scientific Reports. 2017, 7:40254.

9.        J. Zhang, C. Jiang, W. Ye, R. Luo, H.F. Chen^*. Allosteric Pathways in Tetrahydrofolate Sensing Riboswitch with Dynamics Correlation Network. Mol. BioSyst. 2017, 13:156 -164.

10.    J. Zhang, H. Luo, H. Liu, W. Ye, R. Luo, H.F. Chen^*. Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis. Scientific Reports. 2016, 6: 24587.

11.    W. Wang, C. Jiang, J. Zhang, W. Ye, R. Luo, H.F. Chen^*. Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch. Scientific Reports. 2016, 6: 31005.

12.    J. Yang, H. Liu, X. Liu, C. Gu, R. Luo, H.F. Chen^*. Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis. J. Chem. Inf. Model. 2016, 56: 1184-1192.

13.    M. Rahman,H. Liu, A. Wadood, H.F. Chen^*. Allosteric Mechanism of Cyclopropylindolobenzazepine Inhibitors for HCV NS5B Rdrp via Dynamics Correlation Network Analysis. Mol. BioSyst. 2016, 12:3280-3293.

14.    W. Ye, D. Ji, W. Wang, R. Luo, H.F. Chen^*. Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins. J. Chem. Inf. Model. 2015, 55: 1021-1029.

15.    D. Ji, W. Ye, H.F. Chen^*. Revealing the binding mode between respiratory syncytial virus fusion protein and benzimidazolebased inhibitors. Mol. BioSyst. 2015, 11: 1857-1866.

16.    L. Xu, W. Ye, C. Jiang, J. Yang, J. Zhang, Y. Feng, R. Luo, H.F. Chen^*. Recognition Mechanism between Lac Repressor and DNA with Correlation Network Analysis. J. Phys. Chem. B 2015, 119: 2844-2856.

17.    K. Wu, J. Pang, D. Song, Y. Zhu, C. Wu, T. Shao, H.F. Chen^*. Selectivity Mechanism of ATP-Competitive Inhibitors for PKB and PKA. Chem. Biol. Drug Des. 2015, 86:9-18.

18.    W. Wang, W. Ye, C. Jiang, R. Luo, H.F. Chen^*. New force field on modeling intrinsically disordered proteins. Chem. Biol. Drug Des. 2014, 84: 253-269.

19.    Q. Yu, W. Ye, C. Jiang, R. Luo, H.F. Chen^*. Specific Recognition Mechanism between RNA and KH3 Domain of Nova-2 Protein. J. Phys. Chem. B. 2014. 118: 12426-12434.

20.    Q. Yu, W. Ye, W. Wang, H.F. Chen^*. Global Conformational Selection and Local Induced Fit for the Recognition between Intrinsic Disordered p53 and CBP. PLoS ONE. 2013, 8:e59627.

21.    H. Zhang, Z. Liu, Y. Sun, J. Zhu, S. Lu, X. Liu, Q. Huang,Y. Xie, H. Zhu, S. Dang, H.F. Chen, G. Zheng, Y. Li, Y. Kuang, J. Fei, S. Chen, Z. Chen, Z.G. Wang^*. Rig-I regulates NF-κB activity through binding to Nf-κb13′-UTR mRNA. Proc. Natl. Acad. Sci. U. S. A. 2013, 110:6459-6464.

22.    W. Wang, W. Ye, Q. Yu, C. Jiang, J. Zhang, R. Luo, H.F. Chen^*. Conformational Selection and Induced Fit in Specific Antibody and Antigen Recognition: SPE7 as a Case Study. J. Phys. Chem. B, 2013, 117:4912-4923.

23.    W. Ye, J. Yang, Q. Yu, W. Wang, J. Hancy，R. Luo, H.F. Chen^*. Kink Turn sRNA Folding upon L7Ae Binding with Molecular Dynamics Simulation. Phys. Chem. Chem. Phys. 2013, 15:18510-18522 .

24.    W. Ye, F. Qin, J. Zhang, R. Luo, H.F. Chen*.Atomistic Mechanism of microRNA Translation Upregulation via Molecular Dynamics Simulations. PLoS ONE. 2012, 7: e43788.

25.    W. Ye, Y. Chen, W. Wang, Q. Yu, Y. Li, J. Zhang, H.F. Chen^*. Insight into the Stability of cross-beta Amyloid Fibril from VEALYL Short Peptide with Molecular Dynamics Simulation. PLoS ONE. 2012, 7: e36382.

26. F. Qin, W. Ye, Y. Chen, X. Chen, Y. Li, J. Zhang, H.F. Chen^*. Specific Recognition between Intrinsically Disordered LEF and DNA. Phys. Chem. Chem. Phys. 2012, 14: 538-545.
天然无规蛋白是一类在生理条件下没有稳定三级结构的蛋白质。这类蛋白在真核生物蛋白质组中的含量超过40%，而且天然无规蛋白与肿瘤、心血管疾病、神经退行性疾病以及糖尿病等复杂疾病的发生发展密切相关。与结构蛋白相比，天然无规蛋白具有构象多样性的特点难于采用X-ray、NMR等传统实验方法来研究。分子力场是模拟天然无规蛋白的基础。因而，我们从2013年开始分别矫正了八个无规倾向性的氨基酸、二十种氨基酸、八十种氨基酸环境的CMAP参数，发展了天然无规蛋白的系列精准分子力场。大量的测试结果表明，新力场能重现天然无规蛋白的构象特征，并准确预测天然无规蛋白的化学位移、J-Coupling、NOE等参数。力场参数发表之后，收到大量同行的邮件索要力场参数，其中就包括美国科学院院士Andy McCammon等。这些成果将广泛应用于微生物代谢的分子机制研究。