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Chemical Biology

Experimental, computational and theoretical methods and techniques from chemistry have played crucial roles in the elucidation of the molecular basis of life. Challenges posed by specific biological problems are driving the development of new analytical tools and prompting advances in the physical and chemical sciences. Chemists increasingly take inspiration from and/or directly use biological processes to develop structures and materials with novel chemical functions. A number of our faculty members work at this dynamic interface between chemistry and biology. The Colvin group works on modeling semi-structured biomolecular systems, while the Isborn group models how biological systems, like light harvesting proteins and photoreceptor proteins, interact with light.  Andy LiWang's group is resolving the structural and biochemical basis of rhythmicity of the circadian clock, which is used for time keeping in life cycles. Patti LiWang's group determines the structure of chemokines and how they affect HIV and inflammatory diseases. 

The Noy group studies molecular transport and signal transduction across nanoscale interfaces and develops biomimetic nanostructures that facilitate the creation of bioelectronic devices and circuits. The Sukenik lab develops live-cell microscopy methods, and combines them with spectroscopy and computational modeling to understand the complex interplay between proteins and the cellular environment in health and disease. The Ye group is engaged in the hierarchical self-assembly of nucleic acid nanostructures as well as the development of new tools to analyze single DNA molecules.

Image1: Three proteins of the cyanobacterial circadian clock that form a self-sustained circadian oscillator when combined with ATP, courtesy of Professor Andy LiWang.

Image2: 3D reconstruction of a whole cell and its nucleus before and after exposure to hyperosmotic conditions, courtesy of Professor Shahar Sukenik.


Representative Publications

  • CM Davis, M Gruebele, S Sukenik. How does solvation in the cell affect protein folding and binding? , Current opinion in structural biology., 48, 323-29. (2018)
  • S Sukenik, P Ren, M Gruebele. Weak protein-protein interactions in live cells are quantified by cell-volume modulation , PNAS., 114, 6776-6781. (2017)
  • Tseng, R., Goularte, N. F., Chavan, A., Luu, J., Cohen, S. E., Chang, Y.-G., Heisler, J., Li, S., Michael, A. K., Tripathi, S., Golden, S. S., LiWang, A., Partch, C. L.. Structural basis of the day-night transition in a bacterial circadian clock , Science., 355, 1174-1180. (2017)
  • Li Zhang, Carolina Herrera, Jeannine Coburn, Natalia Olejniczak, Paul Ziprin, David Kaplan, and Patricia J. LiWang. Sustained release and stability to high temperatures of HIV inhibitors by encapsulation in silk fibroin disks, ACS:Biomaterials., 3, 1654-1665 (2017)
  • Chang, Y. -G., Cohen, S. E., Phong, C., Myers, W. K., Kim, Y., -I., Tseng, R., Lin, J., Zhang, L., Boyd, J. S., Lee, Y., Kang, S., Lee, D., Li, S., Britt, R. D., Rust, M., J., Golden, S., S., LiWang, A. A protein fold switch joins the circadian oscillator to clock output in cyanobacteria, Science., 349, 324-328. (2015)
  • Roger, T., Chang, Y. -G., Bravo, I., Latham, R., Chaudhary, A., Kuo, N. -W., LiWang, A. Cooperative KaiA-KaiB-KaiC interactions affect KaiB/SasA competition in the circadian clock of cyanobacteria, J. Mol. Biol., 426, 389-402. (2014)
  • R. Tunuguntla, M. Bangar, K. Kim, P. Stroeve, C.M. Ajo-Franklin, A. Noy, Lipid Bilayer Composition can Influence the Orientation of Proteorhodopsin in Artificial Membranes, Biophys. J., v. 105, p. 1388 (2013)
  • Gary R. Abel, Eric A. Josephs, Norman Luong, and Tao Ye. A switchable surface enables visualization of single DNA hybridization events with atomic force microscopy. J. Am. Chem. Soc., 135, 6399-6402(2013)
  • Eric A. Josephs and Tao Ye. Nanoscale spatial distribution of thiolated DNA on model nucleic acid sensor surfaces. ACS Nano, 7, 3653-3660(2013)
  • C. M. Isborn, A. W. Götz, M. A. Clark, R. C. Walker, and T. J. Martínez. Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. J. Chem. Theory Comput., 8, pp 5092–5106 (2012)
  • Eric Josephs and Tao Ye. A Single-molecule view of conformational switching of DNA tethered to a gold electrode. J. Am. Chem. Soc.,134, 10021–10030 (2012)
  • Lu Zhang, Justin A. Kerszulis, Ronald J. Clark, Tao Ye , Lei Zhu. Catechol boronate formation and its electrochemical oxidation. Chem. Commun. 5491–5495 (2009)