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Structural and Computational Biology and Molecular Biophysics

Houston, Texas

A BCM research lab.
Structural and Computational Biology & Molecular Biophysics
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Jun Qin, Ph.D.

Jun Qin, Ph.D.

Photograph of Dr. Qin

Department of Biochemistry and Molecular Biology
Department of Molecular and Cellular Biology

Director, Center for Molecular Discovery


  • Ph.D., Life Science, 1996, The Rockefeller University

Network Analysis Proteomics

Our laboratory is interested in understanding several intriguing biological processes, with a special emphasis on the development and application of cutting-edge mass spectrometry-based proteomics toolkits to untangle challenging biological problems.

1. Protein interaction landscape
We have a long standing interest on a concept of "network analysis proteomics." Proteins tend to assemble into multi-subunit protein complexes as the minimal biologically functional units. The execution of biological processes in the cell can be viewed as a network of ordered interactions between different protein complexes. Thus, the understanding of the basic mechanisms of cellular homeostasis relies on our ability to determine the composition of protein complexes and to decipher the interactions between these protein complex modules. Likewise, the understanding of pathogenesis ultimately depends on the knowledge of global perturbations in the protein ‘complexome’, or a cellular network of protein complex interactions during disease development. Specifically, we are analyzing the endogenous protein complexome by immunoprecipitation (IP) with primary antibody and mass spectrometry. We aim at constructing a complete human protein interactome.

2. Method development for biological mass spectrometry
As an important part of our research, we are continuously developing novel MS-based proteomic methods that will enable us to analyze dynamic changes of complex biological processes in a quantitative manner.

3. Proteomic analysis of protein ubiquitination
Protein ubiquitination is one of the major post translational modifications (PTMs) that regulate a very broad spectrum of cellular functions. Deregulation of ubiquitination is associated with many human diseases such as cancer and human neurodegenerative disorders. We are developing novel proteomics strategies to systematically profile ubiquitin proteome, and to study the regulation of such system in the biological contexts.

4. Sister chromatid cohesion in genome maintenance
The cohesin complex plays a central role in genome maintenance by regulating chromosome segregation in mitosis and DNA damage response (DDR) in other phases of the cell cycle. Checkpoint kinas ATM/ATR phosphorylates SMC1 and SMC3, two core components of the cohesin complex. In addition, SMC3 is acetylated at two critical lysine residues and this modification is critical for sister chromatid cohesion and genome instability in both yeast and human. We recently showed that genome-wide binding of SMC1 and SMC3 after ionizing radiation (IR) is enhanced by reinforcing pre-existing cohesin binding sites in human cancer cells. We are now vigorously investigating the functions of sister chromatid cohesion using a combination of mass spectrometry, biochemistry and genetic manipulations.

Selected Publications

  • Krenciute G, Liu S, Yi S, Yucer N, Ortiz P, Liu Q, Kim BJ, Odejimi OA, Leng M, Qing J and Wang Y. Nuclear BAG6-UBL4A-GET4 complex mediates DNA damange signaling and cell death. J Biol Chem, [Epub ahead of print] (2013). PubMed
  • Qin J, Wu SP, Creighton CJ, Dai F, Xie X, Cheng CM, Frolov A, Ayala G, Lin X, Feng XH, Ittmann MM, Tsai SJ, Tsai MJ and Tsai SY. COPU-TFII inhibits TFG-ß-induced growth barrier to promote prostate tumorigenesis. Nature, 493(7431):236-40 (2013). PubMed
  • Ramakrishnan R, Liu H, Donahue H, Malovannaya A, Qin J and Rice AP. Identification of novel CDK9 and Cyclin T1-associated protein (CCAPs) whose siRNA depletion enhances HIV-1 Tat function. Retrovirology, 9:90 (2012). PubMed
  • O'Malley BW, Malovannaya A and Qin J. Minireview: nuclear receptor and coregulator protemics--2012 and beyond. Mol Endocrinol, 26(10):1646-50 (2012). PubMed
  • Chen X, Qin J, Cheng CM, Tsai MJ and Tsai SY. COUP-TFII is a major regulator of cell cycle and Notch signaling pathways. Mol Endocrinol, 26(8):1268-77 (2012). PubMed
  • Han SJ, Hawkins SM, Begum K, Jung SY, Kovanci E, Qin J, Lydon JP, DeMayo FJ and O'Malley BW. A new isoform of steroid receptor coactivator-1 is crucial for pathogenic progression of endometriosis. Nat Med, 18(7):1102-11 (2012). PubMed
  • Long W, Foulds CE, Qin J, Ding C, Lonard DM, Solis LM, Wistuba II, Qin J, Tsai SY, Tsai MJ and O'Malley BW. ERK3 signals through SRC-3 coactivator to promote human lung cancer cell invasion. J Clin Invest, 122(5):1869-80 (2012). PubMed

For more publications, see listing on PubMed

Contact Information:

Department: Biochemistry & Molecular Biology
Address: Baylor College of Medicine
One Baylor Plaza
Room 145E
Houston, TX 77030
Phone: 713-798-1507
Fax: 713-798-1625
Additional Links: Biochemistry and Molecular Biology

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