Research Protein Engineering

Protein Engineering: A Lesson from Nucleic Acids

Protein-protein interaction is the most fundamental form of cell signaling, and understanding how the network is wired is essential to understanding the functional role of each individual protein. Protein uses surface morphology as a recognition element for binding (through a multitude of H-bonding, van der Waals, electrostatics, and covalent interactions). Although the kinetic and thermodynamic parameters governing the binding properties of some of these proteins have been fairly understood, it is still problematic to design proteins that would fold and assemble in a prescribed manner. This is largely due to our incomplete understanding of protein folding, and thus, our inability to accurately predict the tertiary structures of proteins based on sequence information, and vice versa. The ability to tailored-design proteins with simple recognition code is essential to deciphering the cellular network, in which any protein can be directed to bind to protein target of interest. Our group is interested in developing methodologies for incorporating nucleic acid-like recognition code into proteins and utilizing this simple (“dial in”) code to redirect the natural protein-protein binding. Based on this concept, we are also working to develop artificial enzymes (transcription factors for regulating gene expression, restriction enzymes for modifying ds-DNA, and so forth), enzymes with novel properties, enzymes with multiple functions, and intricate protein assemblies not accessible by current recombinant techniques (bio-architectural engineering).

Unnatural Signal Transductions, Artificial Enzymes, and Novel Protein Assemblies

References
1. T. C. Bruice and S. J. Benkovic., Chemistry, 39, 6267 (2000).
2. Y. Murakami et al., Chem. Rev., 96, 721 (1996) and references therein.
3. J. W. Bryson et al., Science, 270, 935 (1995). D. A. Wah et al., Nature, 388, 97 (1997). C. A. Orego et al., Curr. Opin. Struct. Biol., 9, 374 (1999) and references therein. P. E. Wright and H. J. Dyson, J. Mol. Biol., 293, 321 (1999) and references therein.
4. J. K. Allerman et al., Nature, 365, 530 (1993). E. Schulze et al., Eur. J. Biochem., 211, 591 (1993). E. Quemeneur et al., Nature, 391, 301 (1998).
5. P. E. Nielsen et al., Science, 254, 1497 (1991).
6. G. Aldrian-Herrada et al., Nuc. Acid. Res., 26, 4910 (1998).
7. M. Egholm et al., Nature, 365, 568 (1993).
8. S. K. Kim et al., J. Am. Chem. Soc., 115, 6477 (1993).
9. S. Scarfi et al., Biochem. Biophys. Res. Com., 236, 323 (1997).
10. L. E. Canne et al., J. Am. Chem. Soc., 121, 8720 (8720).
11. Y-G. Kim et al., Proc. Natl. Acad. Sci. USA., 93, 1156 (1996). M. P. Fitzsimons and J. K. Barton, J. Am. Chem. Soc., 119, 3379 (1997), and references therein.