Department of Chemistry

Biochemistry & Chemical Biology

Research ImageGraduate students in biochemistry and chemical biology meld molecular and structural biology with physical, organic and analytical chemistry to understand the molecular basis of biological processes and of human disease. Research in the Biochemistry and Chemical Biology Division focuses on the structure and function of proteins, membranes, DNA, RNA, large macromolecular complexes and viruses, natural product biogenesis, synthetic biology, and genomics.

Students are a constant source of new hypotheses for mechanisms underlying cellular machines like the ribosome and spliceosome, and for the protein and RNA folding problems. Students tackle these problems using biochemical methods, chemical biosensor technologies, protein and nucleic acid crystallography, in vitro and in vivo evolution, multi-dimensional NMR spectroscopy, surface chemistry, atomic force microscopy, fluorescence spectroscopy, and high-resolution mass spectrometry.

Doctoral students in Biochemistry and Chemical Biology leave the Department broadly trained for leadership roles in academia and industry.




Microdomain Occupancy

Presently, there are few estimates of the number of molecules occupying membrane domains. In a collaborative work published in the journal Traffic, researchers in the Thompson Group describe how they, using a total internal reflection fluorescence microscopy (TIRFM) imaging approach, based on comparing the intensities of fluorescently labeled microdomains with those of single fluorophores, measured the occupancy of DC-SIGN, a C-type lectin, in membrane microdomains.

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DC-SIGN or its mutants were labeled with primary monoclonal antibodies (mAbs) in either dendritic cells (DCs) or NIH3T3 cells, or expressed as GFP fusions in NIH3T3 cells. The number of DC-SIGN molecules per microdomain ranges from only a few to over 20, while microdomain dimensions range from the diffraction limit to > 1 µm. The largest fraction of microdomains, appearing at the diffraction limit, in either immature DCs or 3 T3 cells contains only 4–8 molecules of DC-SIGN, consistent with the group's preliminary super-resolution Blink microscopy estimates. The article further discusses how these small assemblies are sufficient to bind and efficiently internalize a small (∼50 nm) pathogen, dengue virus, leading to infection of host cells.


Authentic Cellular Environment

In a collaborative effort initiated by Jillian Tyrrell, a graduate student in the Biological Division, and funded by the National Science Foundation, the groups of Gary Pielak and Kevin Weeks tackled the challenging problem of understanding how the authentic cellular environment affects RNA structure. To date, essentially all biophysical studies performed on RNA have employed highly simplified conditions in dilute solution in vitro. Biologists simply had no idea how RNA structures in cells might be different from that in simple solution.

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The collaborators, as published in Biochemistry, showed that the cytoplasm of healthy living bacterial cells has large effects on the structure of the aptamer domain of a riboswitch RNA and stabilizes, or pre-organizes, a highly structured form of the RNA. Importantly, the in-cell structure cannot be mimicked using simple in vitro conditions.


Representative Publications

RNA Motif Discovery by SHAPE and Mutational Profiling (SHAPE-MaP). Nathan A Siegfried, Steven Busan, Greggory M Rice, Julie A E Nelson & Kevin M Weeks. Nature Methods 11, 959–965 (2014).

Residue Level Quantification of Protein Stability in Living Cells. William B. Monteith and Gary J. Pielak. PNAS July 21, 2014, doi: 10.1073/pnas.1406845111 .

Nitric Oxide-Releasing Quaternary Ammonium-Modified Poly(amidoamine) Dendrimers as Dual Action Antibacterial Agents. Brittany V. Worley , Danielle L. Slomberg , and Mark H. Schoenfisch. Bioconjugate Chem., 2014, 25 (5), pp 918–927.

Protein Crowder Charge and Protein Stability. Mohona Sarkar, Joe Lu, and Gary Pielak. Biochemistry, 2014, 53 (10), pp 1601–1606.

Strategies for Protein NMR in Escherichia coli. Guohua Xu, Yansheng Ye, Xiaoli Liu, Shufen Cao, Qiong Wu, Kai Cheng, Maili Liu, Gary J. Pielak, and Conggang Li. Biochemistry, 2014, 53 (12), pp 1971–1981.

Long-Wavelength Fluorescent Reporters for Monitoring Protein Kinase Activity. Nathan P. Oien, Luong T. Nguyen, Dr. Finith E. Jernigan, Prof. Melanie A. Priestman and Prof. David S. Lawrence. Article first published online: 6 MAR 2014, DOI: 10.1002/anie.201309691.

Low Copy Numbers of DC-SIGN in Cell Membrane Microdomains: Implications for Structure and Function. Ping Liu, Xiang Wang, Michelle S. Itano, Aaron K. Neumann, Aravinda M. de Silva, Ken Jacobson, Nancy L. Thompson. Traffic, Volume 15, Issue 2, pages 179–196, February 2014.

The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure. Jillian Tyrrell, Jennifer L. McGinnis, Kevin M. Weeks, and Gary J. Pielak . Biochemistry, Article ASAP, DOI: 10.1021/bi401207q.

Impact of Reconstituted Cytosol on Protein Stability. Mohona Sarkar, Austin E. Smith, and Gary J. Pielak. Published online before print, November 11, 2013, doi: 10.1073/pnas.1312678110 PNAS November 11, 2013.

Molecular Basis for pH-Dependent Mucosal Dehydration in Cystic Fibrosis Airways. Alaina L. Garlanda, William G. Waltonb, Raymond D. Coakley, Chong D. Tan, Rodney C. Gilmore, Carey A. Hobbs, Ashutosh Tripathy, Lucy A. Clunes, Sompop Bencharit, M. Jackson Stutts, Laurie Betts, Matthew R. Redinbo, and Robert Tarran. PNAS, September 16, 2013, doi: 10.1073/pnas.1311999110.