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.

 

 

 

Protein Stability

The cell cytoplasm contains a complex array of macromolecules at concentrations exceeding 300 g/L. The natural, most relevant state of a biological macromolecule is thus a "crowded" one. Moving quantitative protein chemistry from dilute solution to the inside of living cells represents a major frontier that will affect not only our fundamental biological knowledge, but also efforts to produce and stabilize protein-based pharmaceuticals.

Research Image

Published in PNAS, researchers in the Pielak Group show that the bacterial cytosol actually destabilizes a test protein, contradicting most theoretical predictions, but in agreement with a novel Escherichia coli model.

 

Cystic Fibrosis Research

In work published in PNAS, the Redinbo Group, in collaboration with the Tarran Group at UNC's Cystic Fibrosis Center, contributed the first crystal structure of SPLUNC1, the most abundantly secreted protein in human lungs. The structure lead the team to make specific electrostatic predictions regarding the surface of the SPLUNC1 protein, which were shown to be correct with respect to how SPLUNC1 controls the proper level of fluid in the lungs.

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Cystic fibrosis, CF, is caused by mutations in the cystic fibrosis transmembrane conductance regulator, CFTR, gene, which codes for a chloride/bicarbonate channel whose absence leads to dehydration and acidification of CF airways. A contributing factor to CF lung disease is dysregulation of the epithelial Na+ channel, ENaC, which exacerbates mucus dehydration.

In the image above, healthy lung cells are on the right. The finger-like cilia point up into the proper fluid level because the blue SPLUNC1 proteins are "plugging" the ENaC channels (orange) which otherwise would remove Na (yellow) along with a lot of water. In CF lungs, left, the pH of the liquid is low, SPLUNC1 cannot bind to ENaC and plug that drain, so the Na and water flow into the cells, and the lungs become dehydrated. This work suggests that future CF therapy be directed toward raising the pH of CF airways.

 

Representative Publications

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.

β-Turn Sequences Promote Stability of Peptide Substrates for Kinases Within the Cytosolic Environment. Shan Yang, Angela Proctor, Lauren L. Cline, Kaiulani M. Houston, Marcey L. Waters and Nancy L. Allbritton. Analyst, 2013,138, 4305-4311.