Chemical and Biological Switches

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Complex living systems, such as a developing multicellular organism, remain a barely charted frontier in our molecular understanding of the natural world. One cannot achieve a molecular understanding of such systems solely by studying their isolated components; to capture their essence one must devise methods to study them intact. Optical methods for manipulating molecular structure and function offer the potential to unravel some of the complexity of living systems. They can be used to target individual molecular species at specific sites with very precise timing inside living animals. The power of this approach has been recognized widely ("Method of the Year" in Nature Methods 2010) but there is still a long way to go to make optical control of molecules in vivo generally practical. We propose to create broadly applicable tools to photo-control protein function in living systems. We will take two complementary approaches: (I) We will design and synthesize derivatives of azobenzene that absorb light at visible wavelengths and undergo large conformational changes. Concurrently we will develop a set of rules for how to attach such molecules to proteins so that the azobenzene isomerization drives a functional change in the protein. (II) We will adapt a naturally light-sensitive protein found in bacteria (photoactive yellow protein) for use as a genetically encoded photoswitch. Using a structure-guided protein engineering approach we will make a circular permutant of photoactive yellow protein that can be used to photo-control a diverse array of target proteins. The fundamental development of these optical tools for manipulating proteins will enhance our ability to understand complex living systems.