Jianpeng Ma, Ph.D.
Professor, Biochemistry and MolecBiology
Ph.D.: Boston University
Postdoctoral training: Harvard University
The projects in our research group aim at the frontier of modern computational biophysics and structural biology. There are three major research directions:
Molecular Dynamics (MD) Simulation of Supermolecular Complexes
Large-scale conformational transitions in protein structures play an important role in a variety of cellular processes. Understanding such transitions is one of the central tasks of modern biophysics and structural biology. Among all the available structural and biophysical methods, computer simulation is a powerful method that allows one to model the motions of proteins in atomic details.
The research projects primarily focus on systems that involve coordinated large domain movements. Our recent work on the molecular chaperonin GroEL and on the F1-ATP synthase provided paradigms for this type of research, and it also demonstrates that molecular dynamics simulation has come into an age of realistically modeling very large protein complexes.
Structural Refinement for X-ray Crystallography and EM Reconstruction
In recent history, application of molecular dynamics simulation has significantly improved the structural refinement in x-ray crystallography. However, as structural biology moves towards new challenges from systems such as motors in which parts of the structures are inherently mobile, it is increasingly important to employ more advanced computational methods to model such motions in structure refinement.
Another important trend in structural biology is the fast development of Electron Microscopy (EM) reconstruction, which is now able to deliver 6-7 ?resolution for systems that are difficult to handle by conventional NMR and x-ray crystallography. A combination of EM reconstruction and computational modeling harbors the hope for future realization of atomic resolution measurement. Our goal is to use and develop the state-of-the-art simulation methods to meet the demand of frontier experimental measurement.
As a part of bioinformatics, computer-aided drug design has been an exploding field in recent years.
The research of our group will use both the structure-based approaches and ligand-based approaches such as QSAR (Quantitative Structure-Function Relationship) methods. Several important systems are being targeted.
Kong, Y. and Ma, J. (2003). A structural-informatics approach for mining b-sheets: locating sheets in intermediate-resolution density maps. J. Mol. Biol. 332: 399-413.
Ming, D., Kong, Y., Wu, Y. and Ma, J. (2003). Substructure synthesis method for simulating large molecular complexes. Proc. Natl. Acad. Sci. USA. 100: 104-109.
Noon, W.H., Kong, Y. and Ma, J. (2002). Molecular Dynamics Analysis of A Buckyball-antibody Complex. Proc. Natl. Acad. Sci. USA. 99: 6466-6470.
Kong, Y., Shen, Y., Warth, T.E. and Ma, J. (2002). Conformational Pathways in the Gating of E.coli. Mechanosensitive Channel. Proc. Natl. Acad. Sci. USA 99: 5999-6004.
Noon, W.H., Ausman, K.D., Smalley, R.E. and Ma, J.(2002). Helical ice-sheets inside carbon nanotubes in the physiological condition. Chem. Phys. Lett. 355: 445-448.
Ming, D., Kong, Y., Lambert, M.A., Huang, Z. and Ma, J. (2002). How to describe protein motion without qmino-acid sequence and atomic coordinates. Proc. Natl. Acad. Sci. USA 99: 8620-8625.
Kong, Y. and Ma, J. (2001). Dynamic Mechanisms of the Membrane Water Channel Aquaporin-1 (AQP-1). Proc. Natl. Acad. Sci. USA. 98: 14345-14349.
Ma, J., Sigler, P.B., Xu, Z. and Karplus, M. (2000). A Dynamic Model for the Allosteric Mechanism of GroEL. J. Mol. Biol. 320: 303.
Ma, J., Zheng, X., Schnappauf, G., Braus, G., Karplus, M. and Lipscomb, W.N. (1998). Yeast Chorismate Mutase in the R State: Simulations of the Active Site. Proc. Natl. Acad. Sci. USA 95: 14640.
Ma, J., Huo, S. and Straub, J.E. (1997). Molecular Dynamics Simulation Study of the B-states of Solvated Carbon Monoxy-myoglobin. J. Am. Chem. Soc. 119: 2541.
For more publications, see listing on PubMed.