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The Skaggs Institute
for Chemical Biology

Scientific Report 2006

Synthetic Protein Engineering

P.E. Dawson, F. Brunel, M. Churchill, A. Dirksen, F.G. Hansen, N. Metanis, S. Shekhter, C. Schroeder, T. Tiefenbrunn

We use synthetic chemistry to synthesize and chemically modify biological macromolecules. Much of our work centers on proteins and the development of efficient methods to assemble large polypeptides in aqueous solution without the use of protecting groups. Using these chemoselective ligation techniques, we are able to chemically synthesize not only fully functional natural proteins but also proteins with elements of structure and function that do not occur naturally. This powerful synthetic access to proteins facilitates the fine-tuning of amino acid side chains
to achieve proteins with greater conformational stability or proteins with altered or improved binding specificity and catalytic activity.

In several of our projects, we focus directly on therapy for human diseases. For example, we are collaborating with D.R. Burton, Scripps Research, and I.A. Wilson, the Skaggs Institute, to develop potential HIV vaccines based on the membrane proximal region of the gp41 glycoprotein. In addition, we hope to use synthetic protein chemistry to engineer stabilized protein-based HIV microbicides to prevent infection. Similarly, we are developing the methods necessary to use traditional medicinal chemistry techniques to develop more efficient protein therapeutics for the treatment of cancer. Finally, we are using our insights into the chemistry of thioester functional groups to better understand protein palmitoylation, which is critical for the development of therapeutic approaches for infantile Batten disease.

Synthetic protein chemistry also enables us to make the specific, subtle changes to the structure of a protein required to address basic questions about how proteins function. For example, we have used a simple amide-to-ester replacement in the polypeptide backbone of proteins to study the thermodynamics and kinetics of protein folding. We are using such backbone-modified proteins to address the role of hydrogen bonding and secondary structure formation in proteins such as chymotrypsin inhibitor 2, IgG-binding proteins, and acylphosphatase. In collaboration with F.E. Romesberg, Scripps Research, we are using synthetic chemistry to incorporate deuterium at specific sites to enable direct observation of protein vibrations by infrared spectroscopy. These approaches are also being used to probe the molecular basis of enzymatic activity. For example, we have probed the role of electrostatic interactions in 4-oxaloacetate tautomerase and the effects of selenocysteine in the oxidoreductase glutaredoxin. In future studies, we will probe the role of dynamics in the catalytic activity of these enzymes.


Brunel, F.M., Zwick, M.B., Cardoso, R.M., Nelson, J.D., Wilson, I.A., Burton, D.R., Dawson, P.E. Structure-function analysis of the epitope for 4E10, a broadly neutralizing human immunodeficiency virus type 1 antibody. J. Virol. 80:1680, 2006.

Cremeens, M.E., Fujisaki, H., Zhang, Y., Zimmermann, J., Sagle, L.B., Matsuda, S., Dawson, P.E., Straub, J.E., Romesberg, F.E. Efforts toward developing direct probes of protein dynamics. J. Am. Chem. Soc. 128:6028, 2006.

Delehanty, J.B., Medintz, I.L., Pons, T., Brunel, F.M., Dawson, P.E., Mattoussi, H. Self-assembled quantum dot-peptide bioconjugates for selective intracellular delivery. Bioconjug. Chem. 17:920, 2006.

Medintz, I.L., Clapp, A.R., Brunel, F.M., Tiefenbrunn, T., Uyeda, H.T., Chang, E.L., Deschamps, J.R., Dawson, P.E., Mattoussi, H. Proteolytic activity monitored by fluorescence resonance energy transfer through quantum-dot-peptide conjugates. Nat. Mater. 5:581, 2006.

Sagle, L.B., Zimmermann, J., Matsuda, S., Dawson, P.E., Romesberg, F.E. Redox-coupled dynamics and folding in cytochrome c. J. Am. Chem. Soc. 128:7909. 2006.


Philip Dawson, Ph.D.
Associate Professor

Dawson Web Site