Computational & Experimental
Structural Biology & Cell Biology
Dr. Jianpeng Ma
Baylor College of Medicine & Rice University, Houston, Texas
 
New & Notable
Available Positions
 
Publications
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.
Jingwei Weng, Jianpeng Ma, Kangnian Fan and Wenning Wang (2008). The Conformational Coupling and Translocation Mechanism of Vitamin B12 ATP-Binding Cassette Transporter BtuCD. Biophy. J. 94: 612-621.
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.
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.
Cheng Zhang and Jianpeng Ma (2007). Simulation via direct computation of partition functions. Phys. Rev. E. 76:036708.
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. Featured in Functional Glycomics (13 December 2007).
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 A Crystallographic Resolution. Structure 15:955-962.
Yinghao Wu, Mingyang Lu, Mingzhi Chen, Jialin Li & Jianpeng Ma (2007). OPUS-Ca: A Knowledge-based Potential Function Requiring Only Ca Positions. Prot. Sci. 16:1449-1463.
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.
Chen M, Wilson CJ, Wu Y, Wittung-Stafshede P, Jianpeng Ma (2006). Correlation between Protein Stability Cores and Protein Folding Kinetics: A Case Study on Pseudomonas aeruginosa Apo-Azurin. Structure 14:1401-1410.
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.
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.
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.
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.
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.
Mingyang Lu and Jianpeng Ma (2005). The Role of Shape in Determining Molecular Motions. Biophys. J. 89: 2395-2401.
L. Elchlnger, ...., Jianpeng Ma et al. (2005). The Genome of the Social Amoda Dictyostelium Discoideum. Nature 435:43-57.
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.
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.
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.
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.
Jianpeng Ma (2005). Usefulness and Limitations of Normal Mode Analysis in Modeling Dynamics of Biomolecular Complexes. Structure 13: 373-380.
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.
Arjan van der Vaart, Jianpeng Ma, and Martin Karplus (2004). The Unfolding Action of GroEL on a Protein Substrate. Biophys. J. 87: 562-573.
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.
Yinghao Wu and Jianpeng Ma (2004). Normal-mode-based Refinement of an F-actin Model Against Fiber Diffraction Data. Fiber Diffraction Review 12: 25-28.
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.
Yifei Kong, Xing Zhang, Timothy S. Baker and Jianpeng Ma (2004). A Structural-informatics Approach for Tracing Beta-Sheets: Building Pseudo-C-Alpha Traces for Beta-Strands in Intermediate-resolution Density Maps. J. Mol. Biol. 339: 117-130.
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.
Jianpeng Ma (2004). New Advances in Normal Mode Analysis of Supermolecular Complexes and Applications to Structural Refinement. Curr. Prot. Pept. Sci. 5: 119-123.
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.
Trevor Huyton, Valerie Pye, Louise C. Briggs, Terence C. Flynn, Fabienne Beuron, Hisao Kondo, Jianpeng Ma, Xiaodong Zhang and Paul S. Freemont. (2003). The Crystal Structure of Murine p97/VCP at 3.6 Å. J. Struct. Biol. 144: 337-348.
Terence C. Flynn, Liskin Swint-Kruse, Yifei Kong, Christopher Booth, Kathleen S. Matthews and Jianpeng Ma (2003). Allosteric Transition Pathways in the Lactose Repressor Protein Core Domains: Asymmetric Motions in A Symmetric Homodimer. Prot. Sci. 12: 2523-2541.
Yifei Kong and Jianpeng Ma (2003). A Structural-informatics Approach for Mining Beta-sheets I: Locating Sheets in Intermediate-Resolution Density Maps. J. Mol. Biol. 332: 399-413.
Yifei Kong, Dengming Ming, Yinghao Wu, James K. Stoops, Z. Hong Zhou and Jianpeng Ma (2003). Conformational Flexibility of Pyruvate Dehydrogenase Complexes: A computational Analysis by Quantized Elastic Deformational Model. J. Mol. Biol. 330: 129-135.
Fabienne Beuron, Terence C. Flynn, Jianpeng Ma, Hisao Kondo, Xiaodong Zhang and Paul S. Freemont (2003). Motions and Negative Cooperativity Between p97 Domains Revealed by Cryo-electron Microscopy and Quantized Elastic Deformational Model. J. Mol. Biol. 327: 619-629.
Dengming Ming, Yifei Kong, Yinghao Wu and Jianpeng Ma (2003). Simulation of F-actin Filaments of Several Microns. Biophys. J. 85: 27-35.
Dengming Ming, Yifei Kong, Yinghao Wu and Jianpeng Ma (2003). Substructure Synthesis Method for Simulating Large Molecular Complexes. Proc. Natl. Acad. Sci. USA. 100:104-109.
Dengming Ming, Yifei Kong, Maxime A. Lambert, Zhong Huang and Jianpeng Ma (2002). How to Describe Protein Motion Without Amino-acid Sequence and Atomic Coordinates. Proc. Natl. Acad. Sci. USA. 99: 8620-8625.
Dengming Ming, Yifei Kong, Salih J. Wakil, Jacob Brink and Jianpeng Ma (2002). Domain Movements in Human Fatty Acid Synthase by Quantized Elastic Deformational Model. Proc. Natl. Acad. Sci. USA. 99; 7895-7899.
Michael J. O'Connell, Sergei M. Bachilo, Chad B. Huffman, Valerie C. Moore, Michael S. Strano, Erik H. Haroz, Kristy L. Rialon, Peter J. Boul, William H. Noon, Carter Kittrell, Jianpeng Ma, Robert H. Hauge, R. Bruce Weisman, and Richard E. Smalley (2002). Band-Gap Fluorescence from Individual Single-Walled Carbon Nanotubes. Science 297: 593-596.
William H. Noon, Kevin D. Ausman, Richard E. Smalley and Jianpeng Ma (2002). Helical Ice-sheets Inside Carbon Nanotubes in the Physiological Condition. Chem. Phys. Lett. 335: 445-448.
William H. Noon, Yifei Kong and Jianpeng Ma (2002). Molecular Dynamics Analysis of A Buckyball-antibody Complex. Proc. Natl. Acad. Sci. USA. 99: 6466-6470.
Yifei Kong, Yufeng Shen, Tiffany E. Warth and Jianpeng Ma (2002). Conformational Pathways in the Gating of E.coli Mechanosensitive Channel. Proc. Natl. Acad. Sci. USA. 99: 5999-6004.
Yufeng Shen, Yifei Kong and Jianpeng Ma (2002). Intrinsic Flexibility and Gating Mechanism of the Potassium Channel KcsA. Proc. Natl. Acad. Sci. USA. 99: 1949-1953.
Yifei Kong and Jianpeng Ma (2001). Dynamic Mechanisms of the Membrane Water Channel Aquaporin-1 (AQP-1). Proc. Natl. Acad. Sci. USA. 98: 14345-14349.
Wei Yang, Yi Qin Gao, Qiang Cui, Jianpeng Ma and Martin Karplus. (2003). The Missing Link Between Thermodynamics and Structure in F1-ATPase. Proc. Natl. Acad. Sci. USA. 100: 874-879.
Jianpeng Ma, Terence C. Flynn, Qiang Cui, Andrea Leslie, John E. Walker and Martin Karplus (2002). A Dynamic Analysis of the Rotation Mechanism for Conformational Change in F1-ATPase. Structure 10: 921-931.
Jianpeng Ma, Paul B. Sigler, Zhaohui Xu and Martin Karplus (2000). A Dynamic Model for the Allosteric Mechanism of GroEL. J. Mol. Biol. 302, 303-313.
Christian T. Farrar, Jianpeng Ma, David J. Singel, and Christopher J. Halkides (2000). Structural Changes Induced in p21Ras upon GAP-334 Complexation as Probed by ESEEM Spectroscopy and Molecular-Dynamics Simulation. Structure 8, 1279-1287.
William N. Lipscomb, Gerhard Braus and Jianpeng Ma (1999). Activity, Regulation and Molecular Dynamics in Yeast Chorismate Mutase. Proc. NATO Adv. Study Ins. 302.
Jianpeng Ma and Martin Karplus (1998). The Allosteric Mechanism of the Chaperonin GroEL: A Dynamic Analysis. Proc. Natl. Acad. Sci. USA 95, 8502-8507.
Jianpeng Ma, Xiaofeng Zheng, Georg Schnappauf, Gerhard Braus, Martin Karplus and William N. Lipscomb (1998). Yeast Chorismate Mutase in the R State: Simulations of the Active Site. Proc. Natl. Acad. Sci. USA 95, 14640-14645.
Jianpeng Ma and Martin Karplus (1997). Ligand Induced Conformational Changes in ras p21: A Normal Mode and Energy Minimization Analysis. J. Mol. Biol. 274, 114-131.
Jianpeng Ma and Martin Karplus (1997). Molecular Switch in Signal Transduction: Reaction Paths of the Conformational Changes in ras p21. Proc. Natl. Acad. Sci. USA 94, 11905-11910.
Jianpeng Ma, Shuanghong Huo and John E. Straub (1997). Molecular Dynamics Simulation Study of the B-states of Solvated Carbon Monoxy-myoglobin. J. Am. Chem. Soc. 119, 2541-2551.
Jay Banks, Richard Brower and Jianpeng Ma (1995). Effective Water Model for Monte Carlo Simulations for Protein. Biopolymers 35, 331-341.
John E. Straub, Jianpeng Ma and Patricia Amara. Simulated Annealing Using Coarse Grained Classical Dynamics: Smoluchowski Dynamics in the Gaussian Density Approximation. J. Chem. Phys. 103, 1574-1581 (1995).
Jianpeng Ma, John E. Straub and Eugene I. Shakhnovich. Simulation Study of the Collapse of Linear and Ring Homopolymers. J. Chem. Phys. 103, 2615-2624 (1995).
Jianpeng Ma and John E. Straub (1994). Simulated Annealing Using the Classical Density Distribution. J. Chem. Phys. 101, 533-541.
Jianpeng Ma, David Hsu and John E. Straub (1993). Approximate Solution of the Classical Liouville Equation Using Gaussian Phase Packet Dynamics: Application to Enhanced Equilibrium Averaging and Global Optimization. J. Chem. Phys. 99, 4024-4035.
Zhaonian Cheng, Xuecai Luo, Jianpeng Ma, Jun Shao and Nianyi Chen (1992). Molecular Dynamics Studies of Bond-orientational Order in Molten and Quenched-vitreous State of LiCl. Science in China 35,223.
Zhaonian Cheng, Xuecai Luo, Jianpeng Ma, Jun Shao and Nianyi Chen (1989). Bond-orientational Order in Molten Salt: Molecular Dynamic Simulation. J. Chem. Phys. 91, 4278.
Zhaonian Cheng, Xuecai Luo, Jianpeng Ma, Jun Shao and Nianyi Chen (1989). A Study of Local Structure in Molten Salt by Molecular Dynamic Simulation. Acta Phys. Chim. Sinica 5,264.
Zhaonian Cheng, Xuecai Luo, Jianpeng Ma, Jun Shao and Nianyi Chen (1989). Local Structure in LiCl Quenching Process Simulated by Molecular Dynamics. Acta Phys. Chim. Sinica 5,267.
Jun Shao, Jianpeng Ma, Licheng Yan, Honglin Liu and Nianyi Chen (1988). On the Explanation of the Shift of Raman Frequency of Oxyanions in Molten Salts. Chem. J. Chin. Univ. 9, 864.
Jianpeng Ma, Jun Shao, Licheng Yan, Honglin Liu and Nianyi Chen (1988). A Quantum Chemistry Study of Electronic Spectra of Nitrate Melts. Chin. J. Chem. Phys. 1,164.
 
GroEL
GroEL

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last updated Dec. 10, 2007