Scientific Report 2008
P.G. Schultz, E. Brustad, P. Chen, C.
Dambacher, D. Groff, J. Grünewald, J. Guo, B. Hutchins, S. Kazane, H. Lee,
J.-S. Lee, C. Liu, C. Lyssiotis, C. Melancon, J. Mills, R. Perera, F. Peters,
S. Schiller, M. Sever, L. Supekova, T. Young
are remarkably adept at the synthesis of molecular structure, 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 important proteins involved in such cellular
processes as differentiation, proliferation, and signaling. Indeed, we have identified
molecules that 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 x-ray crystallographic and biochemical studies, together with mRNA
profiling technology and genetic complementation, to characterize the mode of action
of these compounds and to study their effects on cellular processes and in animal
models of regeneration. More recently, we extended such studies to a variety of
genetic and neglected diseases (e.g., malaria, type 1 diabetes, spinal muscular
atrophy, sickle cell anemia). We are also developing and applying modern genomics
tools (e.g., cell-based phenotypic screens of arrayed genomic cDNA and short interfering RNA libraries) and proteomics tools
(mass spectrometric phosphoprotein profiling) to a variety of significant biomedical
problems in cancer biology, neurodegenerative disease, and virology. In addition,
we are investigating the role and regulation of noncoding RNAs.
We have also developed a general biosynthetic
method that makes it possible 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, 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. This approach has been developed for Escherichia coli, yeast,
and mammalian cells, and we are now extending it 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 during translation.
Galkin, A.V., Melnick, J.S., Kim,
S., Hood, T.L., Li, N., Li, L., Xia, G., Steensma, R., Chopiuk, G., Jiang, J., Wan,
Y., Ding, P., Liu, F., Sun, F., Schultz, P.G., Gray, N.S., Warmuth, M. Identification
of NVP-TAE684: a potent, selective. and efficacious inhibitor of NPM-ALK [published
correction appears in Proc. Natl. Acad. Sci. U. S. A. 104:2025, 2007]. Proc. Natl.
Acad. Sci. U. S. A. 104:270, 2007.
Liu, Y., Kern, J.T., Walker, J. R.
Johnson, J., Schultz, P.G., Luesch, H.
A genomic screen for activators of the antioxidant response element. Proc. Natl.
Acad. Sci. U. S. A. 104:5205, 2007.
Gumireddy, K., Sun, F., Klein-Szanto,
A.,J., Gibbins, J.M., Saunders, A., Schultz, P.G., Huang, Q.
In vivo selection for metastasis promoting genes in the mouse. Proc. Natl. Acad.
Sci. U. S. A. 104:6696, 2007.
Liu, W., Alfonta, L., Mack, A.V.,
Schultz, P.G. Structural basis
for the recognition of para-benzoyl-L-phenylalanine by evolved aminoacyl-tRNA
synthetases. Angew. Chem. Int. Ed. 46:6073, 2007.
Xie, J., Supekova, L., Schultz, P.G.
A genetically encoded metabolically
stable analogue of phosphotyrosine in Escherichia coli. ACS Chem. Biol. 2:474,
Wang, J., Schiller, S., Schultz, P.G.
A biosynthetic route to dehydroalanine-containing proteins. Angew. Chem. Int. Ed.
Xie, J., Liu, W., Schultz, P.G.
A genetically encoded bidentate, metal-binding amino acid. Angew. Chem. Int. Ed.
Supekova, L., Supek, F., Lee, J.,
Chen, S., Gray, N., Pezacki, J., Schlapbach, A., Schultz, P.G.
Identification of human kinases involved in hepatitis C virus replication by small
interference RNA library screening. J. Biol. Chem. 283:29, 2008.
Lemke, E.A., Summerer, D., Geierstanger,
B.H., Brittain, S.M., Schultz, P.G.
Control of protein phosphorylation with a genetically encoded photocaged amino acid.
Nat. Chem. Biol. 3:769, 2007.
Guo, J., Wang, J., Anderson, J.C.,
Schultz, P.G. Addition of
acid to the genetic code of bacteria. Angew. Chem. Int. Ed. 47:722, 2008.