Jianpeng Ma, Ph.D.
Professor, Biochemistry & Molecular Biology
Baylor College of Medicine
Fudan University, B.S.
Boston University, Ph.D
Harvard University, Postdoc
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.
- Chen X, Ni F, Tian X, Kondrashkina E, Wang Q and Ma J. Structural Basis of Actin Filament Nucleation by Tandem W Domains. Cell Rep, S2211-1247(13)00210-6 (2013). PubMed
- Lu M and Ma J. PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment. J Mol Biol, 425(6):1082-98 (2013). PubMed
- Lu M, Ming D and Ma J. fSUB: Normal Mode Analysis with Flexible Substructures. J Phys Chem B, 116(29):8636-45 (2012). PubMed
- Zeng J, Kirk BD, Gou Y, Wang Q and Ma J. Genome-wide polycomb target gene prediction in Drosophilia melanogaster. Nucleic Acid Res, 40(13)5848-63 (2012). PubMed
- Lu M and Ma J. Normal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic models. Arch Biochem Biophys, 508(1):64-71 (2011). PubMed
- Cheng X, Wang Q, Ni F and Ma J. Structure of the full-length Shaker potassium channel Kv1.2 by normal-mode-based X-ray crystallographic refinement. Proc Natl Acad Sci USA, 107(25):11352-7 (2010). PubMed
- Ma J. Explicit orientation dependence in empirical potentials and its significance to side-chain modeling. Acc Chem Res, 42(8):1087-96 (2009). PubMed
For more publications, see listing on PubMed.
Department: Biochemistry and Molecular Biology
Address: Baylor College of Medicine
One Baylor Plaza
Houston, TX 77030
Additional Links: Ma Lab, Biochemistry and Molecular Biology