Jianpeng Ma investigates the relationship between structure and function in biological molecules through computational biophysics, structural biology and the development of mathematical algorithms for computer simulation; supramolecular complexes; computer-aided drug designs; and structural refinement strategies.
Ma is a pioneer in the field of biophysics and leading expert in developing computational methods that have substantially expanded the ability to simulate, model and refine flexible biomolecular systems based on experimental data at low to intermediate resolutions.
To conduct his investigations in computational biophysics and structural biology, Ma develops mathematical algorithms for the computer simulation of supramolecular complexes, computer-aided drug designs, and structural refinement strategies for experimental methods (x-ray crystallography and electron microscopy reconstruction). He is an expert in using x-ray crystallography to decipher the exact 3-D arrangement of atoms.
Ma’s research, which has been supported by the National Institutes of Health, National Science Foundation, and the Welch Foundation, has been published nearly 100 peer-reviewed articles in high-impact journals. His efforts have been honored by the Welch Foundation's Norman Hackerman Award for Chemical Research (2004); NSF CAREER Award (2003); and the Award for Chinese Distinguished Young Scholars Abroad (2003); and the Michael E. DeBakey, M.D., Excellence in Research Award (2008). He is also an elected fellow of the American Physical Society (2007), the American Association for the Advancement of Science (2008), and the American Institute for Medical and Biological Engineering (2011).
The projects in Ma's Laboratory focus at the frontier of modern computational biophysics and structural biology. This includes three major research directions:
Multi-resolution and multi-length scale simulation of supramolecular 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 in modeling the motions of proteins in atomic detail.
These research projects primarily focus on systems that involve coordinated large-domain movements. Recent work on the molecular chaperonin GroEL and F1-ATPase has provided paradigms for this type of research. 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 toward 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.
Ma’s 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.
Ma’s 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 developed in our group. These methods will greatly enhance the ability to obtain meaningful information about protein structure and function from intermediate-resolution data.