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.

 

 

 

Quinary Structure Modulates Protein Stability

Protein quinary interactions organize the cellular interior and its metabolism. Although the interactions stabilizing secondary, tertiary, and quaternary protein structure are well defined, details about the protein–matrix contacts that compose quinary structure remain elusive. This gap exists because proteins function in the crowded cellular environment, but are traditionally studied in simple buffered solutions.

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Researchers in the Pielak Group use NMR-detected H/D exchange to quantify quinary interactions between the B1 domain of protein G and the cytosol of Escherichia coli. In their work, published in PNAS, the group demonstrates that a surface mutation in this protein is 10-fold more destabilizing in cells than in buffer, a surprising result that firmly establishes the significance of quinary interactions. Remarkably, the energy involved in these interactions can be as large as the energies that stabilize specific protein complexes. These results will drive the critical task of implementing quinary structure into models for understanding the proteome.

 

Phototherapeutics

Light-activatable drugs offer the promise of controlled release with exquisite temporal and spatial resolution. However, light-sensitive prodrugs are typically converted to their active forms using short-wavelength irradiation, which displays poor tissue penetrance. Researchers in the David Lawrence Group report in Angewandte Chemie, International Edition, on erythrocyte-mediated assembly of long-wavelength-sensitive phototherapeutics.

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The activating wavelength of the constructs is readily preassigned by using fluorophores with the desired excitation wavelength λex. Drug release from the erythrocyte carrier was confirmed by standard analytical tools and by the expected biological consequences of the liberated drugs in cell culture: methotrexate, binding to intracellular dihydrofolate reductase; colchicine, inhibition of microtubule polymerization; dexamethasone, induced nuclear migration of the glucocorticoid receptor.

 

Representative Publications

Local Iontophoretic Administration of Cytotoxic Therapies to Solid Tumors. James D. Byrne, Mohammad N. R. Jajja, Adrian T. O’Neill, Lissett R. Bickford, Amanda W. Keeler, Nabeel Hyder, Kyle Wagner, Allison Deal, Ryan E. Little, Richard A. Moffitt, Colleen Stack, Meredith Nelson, Christopher R. Brooks, William Lee, J. Chris Luft, Mary E. Napier, David Darr, Carey K. Anders, Richard Stack, Joel E. Tepper, Andrew Z. Wang, William C. Zamboni, Jen Jen Yeh, and Joseph M. DeSimone. Sci Transl Med 4 February 2015: Vol. 7, Issue 273, p. 273ra14.

Quinary Structure Modulates Protein Stability in Cells. William B. Monteith, Rachel D. Cohen, Austin E. Smith, Emilio Guzman-Cisneros, and Gary J. Pielak. PNAS, Early Edition, doi 10.1073 pnas.1417415112 .

Cell-Mediated Assembly of Phototherapeutics. Weston J. Smith, Nathan P. Oien, Robert M. Hughes, Christina M. Marvin, Zachary L. Rodgers, Junghyun Lee and David S. Lawrence. Angewandte Chemie International Edition, Volume 53, Issue 41, pages 10945-10948, October 6, 2014.

Optogenetic Engineering: Light-Directed Cell Motility. Robert M. Hughes and David S. Lawrence. Angewandte Chemie International Edition, Volume 53, Issue 41, pages 10904-10907, October 6, 2014.

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.