Jianpeng Ma, Ph.D.
Professor, Biochemistry & Molecular Biology, Pharmacology
Education and Awards
- Ph.D., Boston University, 1996
- Postdoctoral, Harvard University, 1996 - 2000
- NIH Postdoctoral Fellow
- Bouroughs Wellcome PMMB Postdoctoral Fellow
- Chinese Overseas Outstanding Young Faculty Award
- Norman Hackerman Award
Multi-resolution and Multi-length Scale 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 F1-ATPase 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, cryo-EM and Fiber Diffraction
In recent history, molecular dynamics simulation has been successfully employed to significantly improve the structure refinement in X-ray crystallography. However, as structural biology moves towards meeting the new challenges imposed by the study of more complex and more dynamic biological systems, more advanced computational methods are urgently needed to effectively deal with molecular motions in structure refinement. Our group is committed to improving structure refinement in X-ray crystallography, electron cryomicroscopy (cryo-EM) and fiber diffraction. Quantized elastic deformational model (QEDM) has been demonstrated highly effective in assisting cryo-EM single-particle reconstruction of intrinsically flexible biological systems. Substructure synthesis method (SSM) is extremely powerful for enhancing the structure refinement against fiber diffraction data. Moreover, important progress of improving X-ray structure refinement has been recently achieved. These lines of research will undoubtedly provide powerful tools for structure refinement in the wider fields of structural biology.
Structure Modeling and Prediction
With the advance of cryo-EM single-particle reconstruction, more and more intermediate-resolution structures are available. It would be extremely useful if protein secondary structures and protein topology can be determined from intermediate-resolution data. Our group has recently developed sheetminer and sheettracer that are capable of accurately locating beta-sheets and building beta-strands in intermediate-resolution density maps. Once protein secondary structures are in place, protein topology can be determined using approaches recently developed in our group. These methods will greatly enhance one's ability to obtain meaningful information about protein structure and function from intermediate-resolution data.