Full time faculty

Adjunct professor

Chair professor

Administration

Jianpeng Ma

Jianpeng Ma, Ph.D.
Professor, School of Life Sciences, Tsinghua University, Beijing, China
Lodwick T. Bolin Professor in Biochemistry, Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
Professor, Department of Bioengineering, Rice University, Houston, Texas, USA
 
Education:
1981£­1985, B.Sc. in Chemistry, Fudan University
1990£­1996, Ph.D. in Chemistry, Boston University
 
Employment:
1996-2000, Postdoctoral Fellow, Harvard University, Cambridge, MA
2000-2004, Assistant Professor, Baylor College of Medicine and Rice University, Houston, TX
2004-2008, Associate Professor, Baylor College of Medicine and Rice University, Houston, TX
2008-2010, Professor, Baylor College of Medicine and Rice University, Houston, TX
2010-present, Lodwick T. Bolin Professor in Biochemistry, Baylor College of Medicine and Rice University, Houston, TX
2011-present, Professor, School of Life Sciences, Tsinghua University, Beijing, China
 
Research Interest:
Computational Biology: To develop new and powerful computational methods for simulating, modeling and refining supramolecular complexes and high-accuracy prediction of protein and RNA structures.
Cell and Structural Biology: Combining techniques of biochemistry, molecular biology, cell biology, developmental biology and bioinformatics to study actin-mediated signal transduction and the mechanisms of epigenetic regulations in embryonic stem cells and cancer cells.
 
Selected Publications (2004-present):
  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. Biophys483, 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 Signi?cance 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.
 
Honors:
1997-1998        Burroughs Wellcome Fund PMMB Postdoctoral Fellow
1998-2000        National Institutes of Health (NIH) Postdoctoral Fellow
2003-2005       Award for Distinguished Young Scholars Abroad, Chinese National Natural Science Foundation
2003-2008       Faculty Early Career Development (CAREER) Award, National Science Foundation
2004                Norman Hackerman Award in Chemical Research, The Welch Foundation
2007                Elected Fellow of American Physical Society (APS)
2008                Elected Fellow of the American Association for the Advancement of Science (AAAS)
2008                Michael E. DeBakey Excellence in Research Award, Baylor College of Medicine
 
Contact Informaton:
School of Life Sciences, Tsinghua University, Beijing, China£¬100084
 


Tsinghua University,Beijing,China,100084
Tel:+86-10-62772269  Fax:+86-10-62788604  Email:swxrs@tsinghua.edu.cn