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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

Heisler, J., Chavan, A., Chang, Y.-G., LiWang, A. “Real-time in vitro fluorescence anisotropy of the cyanobacterial circadian clock.”, Methods Protoc., 2, 42. (2019)

Kocherzhenko, A. A., Shedge, S. V., Sosa Vazquez, X., Maat, J., Wilmer, J., Tillack, A. F., Johnson, L. E., et al. “Unraveling Excitonic Effects for the First Hyperpolarizabilities of Chromophore Aggregates.”, The Journal of Physical Chemistry C, 123, 13818-13836 (2019)

Zuehlsdorff, T. J., Napoli, J. A., Milanese, J. M., Markland, T. E., & Isborn, C. M. “Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water.”, The Journal of Chemical Physics, 149, 024107. (2018)

Robinson, B., Johnson, L., Elder, D. L., Kocherzhenko, A., Isborn, C., Haffner, C., Heni, W., et al. “Optimization of Plasmonic-Organic Hybrid Electro-Optics.”, Journal of Lightwave Technology, 1-1. (2018)

Shahar Sukenik, Mohammed Salam, Yuhan Wang, and Martin Gruebele, “In-Cell Titration of Small Solutes Controls Protein Stability and Aggregation.”, Journal of the American Chemical Society 140 (33), 10497-10503 (2018)

Swan, J. A., Golden, S. S., LiWang, A., Partch, C. L. “Structure, function, and mechanism of the core circadian clock in cyanobacteria.”, J. Biol. Chem., 293, 5026-5034. (2018)

Welkie, D. G., Rubin, B. E., Chang, Y. -G., Diamond, S., Rifkin, S. A., LiWang, A., Golden, S. S. “Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA.”, Proc. Natl. Acad. Sci. USA, 115, E7174-E7183. (2018)

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)

Yuhan Wang, Shahar Sukenik, Caitlin M. Davis, and Martin Gruebele, “Cell Volume Controls Protein Stability and Compactness of the Unfolded State.”, The Journal of Physical Chemistry B 122 (49), 11762-11770 (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)