Scientific Report 2006

Chemistry

Biological Chemistry

P.G. Schultz, A. Boitano, E. Brustad, M. Bushey, S. Chen, J. Guo, J. Grbic, D. Groff, J. Grünewald, W.Y. Hur, M. Jahnz, T. Kuo, J. Lee, J.-S. Lee, K.-B. Lee, E. Lemke, C. Liu, W. Liu, C. Lyssiotis, J. Mills, M. Mukherji, T. Nom, B. Okram, R. Perera, F. Peters, Y. Ryu, S. Schiller, M. Sever, D. Summerer, L. Supekova, E. Tippmann, M.-L. Tsao, J. Wang, T. Young, Q. Zhang, S. Zhu

Although chemists are remarkably adept at synthesizing molecular structures, they are far less sophisticated in designing and synthesizing molecules with defined biological or chemical functions. Nature, on the other hand, has produced an array of molecules with remarkably complex functions, ranging from photosynthesis and signal transduction to molecular recognition and catalysis. Our aim is to combine the synthetic strategies and biological processes of Nature with the tools and principles of chemistry to create new molecules with novel chemical and biological functions. By studying the properties of the resulting molecules, we can gain new insights into the molecular mechanisms of complex biological and chemical systems.

For example, we have shown that the tremendous combinatorial diversity of the immune response can be chemically reprogrammed to generate selective enzymelike catalysts. We have developed antibodies that catalyze a wide array of chemical and biological reactions, from acyl transfer to redox reactions. Characterization of the structure and mechanisms of these catalytic antibodies has led to important new insights into the mechanisms of biological catalysis. In addition, the detailed characterization of the properties and structures of germ-line and affinity-matured antibodies has revealed fundamental new aspects of the evolution of binding and catalytic function, in particular, the role of structural plasticity in the immune response. Most recently, we have focused on in vitro evolution methods that involve the development of novel chemical screens and selections for identifying metalloantibodies with proteolytic activity.

Our work on catalytic antibodies redirects natural combinatorial diversity to produce new function. We are extending this combinatorial approach to many other problems, including the generation of genetic “microcalorimetes” and yeasts lacking mitochondrial genomes and the ab initio evolution of novel protein domains. We are also generating structure-based combinatorial libraries of small heterocycles that are being used in conjunction with novel cellular and organismal screens to identify important proteins involved in such cellular processes as differentiation, proliferation, and signaling. Indeed, we have identified molecules that control both adult and embryonic stem cell differentiation and self-renewal and that reprogram lineage-committed cells. We are using x-ray crystallographic and biochemical studies, together with genomics technologies, to characterize the mode of action of these compounds and to study their effects on cellular processes. We are also applying genomics tools (cell-based phenotypic screens of arrayed genomic cDNA and small interfering RNA libraries) and proteomics tools (mass spectrometric phosphoprotein profiling) to a variety of important biomedical problems in cancer biology, neurodegenerative and autoimmune diseases, and virology. In addition, we are investigating the role and regulation of noncoding RNAs.

We have also developed a general biosynthetic method that can be used to site specifically incorporate unnatural amino acids into proteins in vitro and in vivo. Using this method, we effectively expanded the genetic codes of both prokaryotic and eukaryotic organisms by adding new components to the biosynthetic machinery of living cells. We have genetically encoded amino acids with novel spectroscopic and chemical properties (e.g., metal-binding, glycosylated, and fluorescent amino acids and photocross-linking and photoisomerizable amino acids) in response to unique 3- and 4-base codons. These amino acids are being used to explore protein structure and function both in vitro and in vivo and to evolve proteins with novel properties. Our results have removed a billion-year constraint imposed by the genetic code on the ability to chemically manipulate the structures of proteins.

Publications

Bose, M., Groff, D., Xie, J., Brustad, E., Schultz, P.G. The incorporation of a photoisomerizable amino acid into proteins in E. coli. J. Am. Chem. Soc. 128:388, 2006.

Chen, S., Do, J., Zhang, Q., Yao, S., Yan, F., Peters, E., Scholer, H., Schultz, P.G., Ding, S. Self-renewal of embryonic stem cells by a small molecule. Proc. Natl. Acad. Sci. U. S. A., in press.

Mukherji, M., Cho, C., Supekova, L., Wang, Y., Batalov, S., Bell, R., Martin, C., Sahasrabuhde, S., Orth, A.P., Chanda, S.K., Schultz, P.G. Functional analysis of human genome for cell-cycle regulators. Proc. Natl. Acad. Sci. U. S. A., in press.

Summerer, D., Chen, S., Wu, N., Deiters, A., Chin, J.W., Schultz, P.G. A genetically encoded fluorescent amino acid. Proc. Natl. Acad. Sci. U. S. A. 103:9785, 2006.

Turner, J.M., Graziano, J., Spraggon, G., Schultz, P.G. Structural characterization of a p-acetylphenylalanyl aminoacyl-tRNA synthetase. J. Am. Chem. Soc. 127:14976, 2005.

Warashina, M., Min, K.H., Kuwabara, T., Huynh, A., Gage, F.H., Schultz, P.G., Ding, S. A synthetic small molecule that induces neuronal differentiation of adult hippocampal neural progenitor cells. Angew. Chem. Int. Ed. 45:591, 2006.

Willingham, A.T., Orth, A.P., Batalov, S., Peters, E.C., Wen, B.G., Aza-Blanc, P., Hogenesch, J.B., Schultz, P.G. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309:1570, 2005.