教职员工
兼职教授
讲席教授
杰出人才
其他获奖
马剑鹏
马剑鹏 博士
清华大学生命学院教授,博士生导师,“千人计划”入选者
美国贝勒医学院生物化学和分子生物学系Lodwick T. Bolin讲席教授
美国莱斯大学生物工程系教授
 
教育经历:
1981-1985      就读于复旦大学化学系,获化学学士学位
1990-1996      就读于Boston University,获化学博士学位
 
工作经历:
1996-2000       哈佛大学化学系博士后
2000-2004       贝勒医学院生物化学和分子生物学系及莱斯大学生物工程系助理教授
2004-2008       贝勒医学院生物化学和分子生物学系及莱斯大学生物工程系副教授
2008-2010       贝勒医学院生物化学和分子生物学系及莱斯大学生物工程系教授
2010-present  贝勒医学院生物化学和分子生物学系及莱斯大学生物工程系Lodwick T. Bolin讲席教授
2011-present  清华大学生命学院教授,博士生导师,“千人计划”入选者
 
研究领域:
计算生物学:全力发展新的计算方法来模拟生物体系,改良结构建模,和准确预测蛋白质和核糖核酸结构。
细胞和结构生物学:利用生物化学、分子生物学、细胞生物学、发育生物学和生物信息学等多学科技术手段研究肌球蛋白的信号传递以及表观遗传因子在胚胎干细胞和肿瘤细胞发育中的作用。
 
代表性论文(2004年-至今):
  1. Yinghao Wu and Jianpeng Ma (2004). Refinement of F-actin Model Against Fibre Diffraction Data by Long range Normal Modes. Biophys. J. 86: 116-124.
  2. Jacob Brink, Steven J. Ludtke, Yifei Kong, Salih J. Wakil, Jianpeng Ma and Wah Chiu (2004). Experimental Verification of Conformational Variation of Human Fatty Acid Synthase as Predicted by Normal Mode Analysis. Structure 12:185-191.
  3. Jianpeng Ma (2004). New Advances in Normal Mode Analysis of Supermolecular Complexes and Applications to Structural Refinement. Curr. Prot. Pept. Sci 5:119-123 (Invited review).
  4. Terence C. Flynn and Jianpeng Ma (2004). Theoretical analysis of twist/bend ratio and mechanical moduli of bacterial flagellar hook and filament. Biophys. J. 86: 3204-3210.
  5. Yifei Kong, Xing Zhang, Timothy S. Baker and Jianpeng Ma (2004). A Structural-informatics Approach for Tracing b-sheets: Building Pseudo-Ca-traces for b-strands in Intermediate-Resolution Density Maps. J. Mol. Biol. 339: 117-130.
  6. Arjan van der Vaart, Jianpeng Ma and Martin Karplus (2004). The Unfolding Action of GroEL on A Protein Substrate. Biophys. J. 87:562-573.
  7. Qiang Cui, Guohui Li, Jianpeng Ma and Martin Karplus (2004). A Normal Mode Analysis of Structural Plasticity in the Biomolecular Motor F1-ATPase. J. Mol. Biol. 340:345-372.
  8. Yinghao Wu and Jianpeng Ma (2004). Normal-mode-based Refinement of an F-actin Model Against Fibre Diffraction Data. Fibre Diffraction Review 12: 25-28 (Invited review).
  9. Martin Karplus, Yi Qin Gao, Jianpeng Ma, Arjan van der Vaart, and Wei Yang (2005). Protein Structural Transitions and Their Functional Role. Phil. Trans. R. Soc. A 363: 331-356.
  10. Jianpeng Ma (2005). Usefulness and Limitations of Normal Mode Analysis in Modeling Dynamics of Biomolecular Complexes. Structure 13: 373-380.
  11. Yechun Xu, Jianhua Shen, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Jianpeng Ma and Hualiang Jiang (2005). Conformational Transition of Amyloid beta-peptide. Proc. Natl. Acad. Sci. USA. 102: 5403-5407.
  12. B. K. Muralidhara, Mingzhi Chen, Jianpeng Ma, and Pernilla Wittung-Stafshede (2005). Effect of Inorganic Phosphate on FMN Binding and Loop Flexibility in Desulfovibrio desulfuricans Apo-falvodoxin. J. Mol. Biol. 349:87-97.
  13. Sergei Trakhanov, Nand K. Vyas, Hartmut Luecke, David M. Kristensen, Jianpeng Ma, and Florante A. Quiocho (2005). Ligand-free and -bound Structures of the Binding Protein (LivJ) of the Escherichia coli ABC Leucine/Isoleucine/Valine Transport System: Trajectory and Dynamics of the Interdomain Rotation and Ligand Specificity. Biochemistry. 44:6597-6608.
  14. Yinghao Wu, Mingzhi Chen, Mingyang Lu, Qinghua Wang, and Jianpeng Ma (2005). Determining Protein Topology from Skeletons of Secondary Structures. J. Mol. Biol. 350:571-586.
  15. L. Elchlnger, ...., Jianpeng Ma et al. (2005). The Genome of the Social Amoda Dictyostelium Discoideum. Nature 435:43-57.
  16. Mingyang Lu and Jianpeng Ma (2005). The Role of Shape in Determining Molecular Motions. Biophys. J. 89:2395-2401.
  17. Yinghao Wu, Xia Tian, Mingyang Lu, Mingzhi Chen, Qinghua Wang and Jianpeng Ma (2005). Folding of Small Helical Proteins Assisted by Small Angle X-ray Scattering Profiles. Structure 13:1587-1597.
  18. Michael Perham, Mingzhi Chen, Jianpeng Ma, and Pernilla Wittung-Stafshede (2005). Unfolding of Heptameric Co-chaperonin Protein Follows "Fly Casting" Mechanism: Observation of Transient Nonative Haptamer. J. Am. Chem. Soc. 127:16402-16403.
  19. Yifei Kong, Jianpeng Ma, Martin Karplus, and William N. Lipscomb (2006). The Allosteric Mechanism of Yeast Chorismate Mutase: A Dynamics Analysis. J. Mol. Biol. 356:237-247.
  20. Rajesh R. Singh, Kumaralal Kaluarachchi, Mingzhi Chen, Suresh K. Rayala, Seetharaman Balasenthil, Jianpeng Ma, and Rakesh Kumar (2006). Solution Structure and Antiestrogenic Activity of the Unique C-terminal, NR-box Motif-containing Region of MTA1s. J. Biol. Chem. 281:25612-25621.
  21. Mingyang Lu, Billy Poon, and Jianpeng Ma (2006). A New Method for Coarse-grained Elastic Normal Mode Analysis. J Chem. Comput. Theory. 2:464-471.
  22. Billy K. Poon, Xiaorui Chen, Mingyang Lu, Nand K. Vyas, Florante A. Quiocho, Qinghua Wang and Jianpeng Ma (2007). Normal Mode Refinement of Anisotropic Thermal Parameters for A Supramolecular Complexe at 3.42-Å Crystallographic Resolution. Proc. Natl. Acad. Sci. USA. 104:7869-7874.
  23. Yinghao Wu, Mingyang Lu, Mingzhi Chen, Jialin Li & Jianpeng Ma (2007). OPUS-Ca: A Knowledge-based Potential Function Requiring Only C? Positions. Prot. Sci. 16:1449-1463.
  24. Xiaorui Chen, Billy K. Poon, Athanasios Dousis, Qinghua Wang & Jianpeng Ma (2007). Normal Mode Refinement of Anisotropic Thermal Parameters for Potassium Channel KcsA at 3.2 Å Crystallographic Resolution. Structure 15: 955-962.
  25. Qinghua Wang, Xia Tian, Xiaorui Chen and Jianpeng Ma (2007). Structural Basis for Receptor Specificity of Influenza B Virus Hemagglutinin. Proc. Natl. Acad. Sci. USA. 104:16874-16879.
  26. Cheng Zhang and Jianpeng Ma (2007). Simulation via direct computation of partition functions. Phys Rev E Stat Nonlin Soft Matter Phys. 76:036708.
  27. Feng Cheng, Qinghua Wang, Mingzhi Chen, Florante A. Quiocho & Jianpeng Ma (2007). Molecular Docking Study of the Interactions between the Thioesterase Domain of Human Fatty Acid Synthase and Its Ligands. Proteins: Structure, Function, and Bioinfo. 70:1228-1234.
  28. Mingyang Lu, Athanasios D. Dousis and Jianpeng Ma (2008). OPUS-PSP: An Orientation-dependent Statistical All-atom Potential Derived from Side-chain Packing. J. Mol. Biol. 376: 288-301.
  29. Jingwei Weng, Jianpeng Ma, Kangnian Fan and Wenning Wang (2008). The Conformational Coupling and Translocation Mechanism of Vitamin B12 ATP-Binding Cassette Transporter BtuCD. Biophysical J. 94: 612–621.
  30. Qinghua Wang, Feng Cheng, Mingyang Lu, Xia Tian and Jianpeng Ma (2008). Crystal Structure of Unliganded Influenza B Virus Hemagglutinin. J. Virol. 82:3011-3020.
  31. Mingyang Lu, Athanasios D. Dousis and Jianpeng Ma (2008). OPUS-Rota: a fast and accurate method for side-chain modeling. Protein Sci. 17:1576-85.
  32. Mingyang Lu and Jianpeng Ma (2008). A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography. Proc Natl Acad Sci U S A. 105:15358-63.
  33. Chunying Song, Wenyu Wen, Suresh K. Rayala, Mingzhi Chen, Jianpeng Ma, Mingjie Zhang, and Rakesh Kumar (2008). Serine 88 Phosphorylation of the 8-kDa Dynein Light Chain 1 Is a Molecular Switch for Its Dimerization Status and Functions. J. Biol. Chem. 283: 4004–4013.
  34. Jun Shen, Brian D. Kirk, Jianpeng Ma and Qinghua Wang (2009). Diversifying Selective Pressure on Influenza B Virus Hemagglutinin. J. Med. Virol. 81:114-124.
  35. Yinghao Wu, Athanasios D. Dousis, Mingzhi Chen, Jialin Li, & Jianpeng Ma (2009). OPUS-Dom: Applying the Folding-Based Method VECFOLD to Determine Protein Domain Boundaries. J. Mol. Biol. 385, 1314–1329.
  36. Cheng Zhang & Jianpeng Ma (2009). Counting solutions for the N-queens and Latin-square problems by Monte Carlo simulations. Phys. Rev. E. 79, 016703.
  37. Mingzhi Chen, Athanasios D. Dousis, Yinghao Wu, Pernilla Wittung-Stafshede & Jianpeng Ma (2009). Predicting protein folding cores by empirical potential functions. Archives Biochem. Biophys. 483, 16-22.
  38. Jingwei Weng, Jianpeng Ma, Kangnian Fan, & Wenning Wang (2009). Asymmetric conformational flexibility in the ATP-Binding cassette transporter HI1470/1. Biophys. J. 96, 1918-1930.
  39. Xiaorui Chen, Mingyang Lu, Billy K. Poon, Qinghua Wang and Jianpeng Ma (2009). Structural Improvement of Unliganded Simian Immunodeficiency Virus gp120 Core by Normal-mode-based X-ray Crystallographic Refinement. Acta Cryst. D65. 339-347.
  40. Fengyun Ni, Billy K. Poon, Qinghua Wang and Jianpeng Ma (2009). Application of Normal-mode Refinement to X-ray Crystal Structures at Lower-resolution Limit. Acta Cryst. D65, 633-643.
  41. Cheng Zhang and Jianpeng Ma (2009). Enhanced sampling in generalized ensemble with large gap of sampling parameter: Case study in temperature space random walk. J. Chem. Phys. 130, 194112.
  42. Jianpeng Ma (2009). Explicit Orientation Dependence in Empirical Potentials and Its Significance to Side-Chain Modeling. Accounts of Chemical Research. 42:1087-96.
  43. B. R. Brooks, …., Jianpeng Ma, et al. (2009). CHARMM: The Biomolecular Simulation Program. J. Comput. Chem. 30: 1545-1614.
  44. Jun Shen, Jianpeng Ma and Qinghua Wang (2009). Evolutionary Trends of A(H1N1) Influenza Virus Hemagglutinin Since 1918. PLoS One. 4(11):e7789.
  45. Xiaorui Chen, Qinghua Wang, Fengyun Ni and Jianpeng Ma (2010). Structure of the full-length Shaker potassium channel Kv1.2 by normal-mode-based X-ray crystallographic refinement. Proc Natl Acad Sci U S A. 107:11352-7.
  46. Cheng Zhang and Jianpeng Ma (2010). Enhanced sampling and applications in protein folding in explicit solvent. J. Chem. Phys. 132: 244101.
  47. Mingyang Lu and Jianpeng Ma (2011). Normal mode analysis with molecular geometry restraints: Bridging molecular mechanics and elastic models. Arch Biochem Biophys. 508: 64-71.
荣誉及奖励:
1997-1998   Burroughs Wellcome Fund PMMB 博士后奖学金
1998-2000   National Institutes of Health 博士后奖学金
2003-2005   中国国家自然科学基金会中国海外杰出青年基金B类
2003-2008   美国国家自然科学基金会Faculty Early Career Development (CAREER) Award
2004             美国Welch基金会 Norman Hackerman Award in Chemical Research
2007             入选American Physical Society会士
2008             入选American Association for the Advancement of Science (AAAS)会士
2008             贝勒医学院Michael E. DeBakey Excellence in Research Award
 
联系方式:
北京市清华大学生命科学学院,100084
E-mail: jpma@bcm.edu
 
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