Scientific Report 2007

Chemistry

Biological Chemistry

P.G. Schultz, A. Boitano, E. Brustad, M. Bushey, C. Dambacher, J. Grbic, D. Groff, J. Grünewald, J. Guo, B. Hutchins, M. Jahnz, H. Lee, J. Lee, J.-S. Lee, K.-B. Lee, C. Liu, W. Liu, C. Lyssiotis, J. Mills, M. Mukherji, R. Perera, F. Peters, Y. Ryu, S. Schiller, M. Sever, V. Smider, L. Supekova, M.-L. Tsao, J. Wang, T. Young

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.

In addition, we are extending this combinatorial approach to many other problems, including the generation of novel cellular reporters, the ab initio evolution of novel protein domains, and the synthesis of structure-based combinatorial libraries of small heterocycles. The libraries of small heterocycles are being used in conjunction with novel cellular and organismal screens to identify molecules that modulate the activity of key proteins involved in cellular processes such as differentiation, proliferation, and apoptosis. Indeed, we have identified molecules that both control adult and embryonic stem cell differentiation and stem cell self-renewal and that reprogram lineage committed cells to alternative cell fates. We are using biochemical and genomics experiments (e.g., mRNA profiling technology, affinity chromatography, genetic complementation) to characterize the mode of action of these compounds and to study their effects in vitro and in animal models of regeneration. We have extended this approach to a variety of genetic and neglected diseases (e.g., malaria, type 1 diabetes, spinal muscular atrophy, childhood cancers). We are also developing and applying modern genomics tools (e.g., 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 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 code of living organisms by adding new components to the existing biosynthetic machinery. We have genetically encoded amino acids with novel spectroscopic and chemical properties (e.g., metal-binding, sulfated, fluorescent, chemically reactive, photocross-linking, and photoisomerizable) 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, create novel therapeutic agents and biomaterials, and evolve proteins with novel properties. Recently, we have extended this approach to yeast and mammalian cells, and we are attempting to adapt this approach to multicellular organisms. Our results have removed a billion-year constraint imposed by the genetic code on the ability to chemically manipulate the structures of proteins.

Publications

Chen, S., Do, J.T., Zhang, Q., Yao, S., Yan, F., Peters, E.C., Schöler, H.R., Schultz, P.G., Ding, S. Self-renewal of embryonic stem cells by a small molecule. Proc. Natl. Acad. Sci. U. S. A. 103:17266, 2006.

Chen, S., Takanashi, S., Zhang, Q., Xiong, W., Peters, E.C., Ding, S., Schultz, P.G. Reversine increases the plasticity of lineage-committed mammalian cells. Proc. Natl. Acad. Sci. U. S. A. 104:10482, 2007.

Deiters, A., Groff, D., Ryu, Y., Xie, J., Schultz, P.G. A genetically encoded photocaged tyrosine. Angew. Chem. Int. Ed. 45:2728, 2006.

Liu, C., Schultz, P.G. Recombinant expression of selectively sulfated proteins in Escherichia coli. Nat. Biotechnol. 24:1436, 2006.

Liu, W., Brock, A., Chen, S., Chen, S., Schultz, P.G. Genetic incorporation of unnatural amino acids into proteins in mammalian cells. Nat. Methods 4:239, 2007.

Luesch, H., Chanda, S.K., Raya, R.M., DeJesus, P.D., Orth, A.P., Walker, J.R., Izpisúa Belmonte, J.C., Schultz, P.G. A functional genomics approach to the mode of action of apratoxin A. Nat. Chem. Biol. 2:158, 2006.

Mukherji, M., Bell, R., Supekova, L., Wang, Y., Orth, A.P., Batalov, S., Miraglia, L., Huesken, D., Lange, J., Martin, C., Sahasrabudhe, S., Reinhardt, M., Natt, F., Hall, J., Mickanin, C., Labow, M., Chanda, S.K., Cho, C.Y., Schultz, P.G. Genome-wide functional analysis of human cell-cycle regulators. Proc. Natl. Acad. Sci. U. S. A. 103:14819, 2006.

Turner, J.M., Graziano, J., Spraggon, G., Schultz, P.G. Structural plasticity of an aminoacyl-tRNA synthetase active site. Proc. Natl. Acad. Sci. U. S. A. 103:6483, 2006.

Wang, J., Xie, J., Schultz, P.G. A genetically encoded fluorescent amino acid. J. Am. Chem. Soc. 128:8738, 2006.

Xie, J., Liu, W., Schultz, P.G. A genetically encoded bidentate, metal-binding amino acid. Angew. Chem. Int. Ed., in press.

Xie, J., Schultz, P.G. A chemical toolkit for proteins: an expanded genetic code. Nat. Rev. Mol. Cell Biol. 7:775, 2006.

Zhang, Q., Major, M., Takanashi, S., Camp, N.D., Peters, E.C., Ginsberg, M.H., Jian, X., Randazzo, P.A., Schultz, P.G., Moon, R.T., Ding, S. Small-molecule synergist of the Wnt/β-catenin signaling pathway. Proc. Natl. Acad. Sci. U. S. A. 104:7444, 2007.