Email

jpma@bcm.edu

Positions

Professor

Biochemistry-Ma Lab
Baylor College of Medicine
Houston, TX, US

Lodwick T. Bolin Professor in Biochemistry

Biochemistry
Baylor College of Medicine and Rice University
Houston, Texas, United States

Member

Dan L Duncan Comprehensive Cancer Center
Baylor College of Medicine
Houston, Texas, United States

Addresses

BCM-Cullen Building (Office)

Room: BCMC-302A
Houston, TX 77030
United States

Education

Advanced Training from Harvard University

01/2000 - Cambridge, MA, United States

Ph.D. from Boston University

01/1996 - Boston, MA, United States

B.S. from Fu-Dan University

01/1985 - Shanghai, China, People's Rep

Honors & Awards

Elected Fellow of the American Institute for Medical Biological Engineering

American Institute for Medical Biological Engineering (01/2013)

2008 Michael E. DeBakey Excellence in Research Award

Baylor College of Medicine (01/2008)

Elected Fellow of the American Association for the Advancement of Science (AAAS)

American Association for the Advancement of Science (AAAS) (01/2008)

Elected Fellow of the American Physical Society (APS)

American Physical Society (APS) (01/2007)

2004 Norman Hackerman Award for Chemical Research

The award is for recognizing his outstanding contributions to biochemistry, biophysics and structural biology. It consists of a $100,000 check, a certificate and a crystal sculpture symbolizing a rising star.

Welch Foundation (01/2004)

Faculty Early Career Development (CAREER) Award

National Science Foundation (01/2003 - 12/2008)

Award for Distinguished Young Scholars Abroad

Chinese National Natural Science Foundation (01/2003 - 12/2005)

Burroughs Wellcome Fund PMMB Postdoctoral Fellow

Burroughs Wellcome Fund (01/1997 - 12/1998)

Advanced Study Institutes Travel Award

National Science Foundation (01/1999)

The Finn Wold Travel Award

Protein Society (01/1998)

Postdoctoral Fellow of the National Institutes of Health (NIH)

National Institutes of Health (NIH) (01/1998 - 12/2000)

Super-computing Grant

Pittsburgh Super-computing Center (PSC) (01/1997)

Free Subscription of J. Phys. Chem. for Cray Super-computing Award

01/1995

Professional Interests

• Viral Pathogens
• Human
• Bioinformatics
• Nano Medicine and Drug Design
• Biophysics and Computational Biology
• Protein Structure-Function and Protein Folding
• Structural Biology and Macromolecular Assemblies
• Signal Transduction
• Stem Cell Biology and Cell Fate Determination
• Gene Expression and Regulation
• Chromosomes, Chromatin, and DNA Biology
• Cancer
• Development and Evoluation
• Genomics, Proteomics, and Metabolomics
• Molecular Basis of Human Disease and Behavior

Professional Statement

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.

Websites

Selected Publications

• Lu M, Dousis AD, Ma J "OPUS-Rota: a fast and accurate method for side-chain modeling.." Protein Sci.. 2008 September ; 17 (9): 1576-85. Pubmed PMID: 18556476
• Lu M, Ma J "A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography.." Proc. Natl. Acad. Sci. U.S.A.. 2008 October 7; 105 (40): 15358-63. Pubmed PMID: 18832168
• Ma J "Explicit orientation dependence in empirical potentials and its significance to side-chain modeling.." Acc. Chem. Res.. 2009 August 18; 42 (8): 1087-96. Pubmed PMID: 19445451
• Chen X, Lu M, Poon BK, Wang Q, Ma J "Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement.." Acta Crystallogr. D Biol. Crystallogr.. 2009 April ; 65 : 339-47. Pubmed PMID: 19307715

Memberships

American Physical Society

Member

American Crystallographic Association

Member

Biomedical Engineering Society

Member

Biophysical Society

Member

American Chemical Society

Member

Protein Society

Member