Understanding and improving de novo design of proteins: New insights from molecular dynamics modeling

BIOL 66

Katrin Spiegel, spiegel@cmm.upenn.edu1, Matteo Dal Peraro, matteodp@cmm.upenn.edu2, Jennifer R. Calhoun, jrose2@sas.upenn.edu3, William F DeGrado, wdegrado@mail.med.upenn.edu3, and Michael L. Klein, klein@seas.upenn.edu1. (1) Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Phialdelphia, PA 19104-6323, (2) Center for Molecular Modeling, Chemistry Department, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, (3) Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 1009 Stellar Chance Building, 36th & Hamilton Walk, Philadelphia, PA 19104-6323
There is a need for rapid, accurate force fields that can assist in metallo-protein analysis and design. Recent work in the design of mimics of dimetal proteins highlights the requirements for activity. DF1 and DFsc belong to a class of de novo designed proteins, which mimics the overall fold and active site geometry of a series of diiron and dimanganese proteins. The natural enzymes catalyze different reactions, depending on the nature of the metal coordination sphere. Here, we use a non-bonded model to represent the metal ligand interactions, which implicitly takes into account charge redistribution effects between the metal and its ligands. In a first study, we look at geometric and dynamical differences between DF1 and the natural enzyme Manganese Catalase. Our classical simulations reproduce a conformational change observed in the crystal structure of DF1 and indicate that the active site is too crowded in the synthetic enzyme, preventing the substrate from binding to the active site. Two hypothetical mutants are studied, which could improve the active site accessibility and hence the activity of the protein. Motivated by the fair accuracy of the non-bonded model to reproduce the bimetal active site and global structural transitions, we use the same approach to model the single chain variant DFsc. Mutation experiments on DFsc have shown that subtle changes in the metal pocket can trigger oxidation of iron from the ferrous to the ferric form. Classical simulations help identifying structural rearrangements that occur upon mutation and could favor oxidation.
 

Protein Structure and Folding
4:30 PM-6:30 PM, Sunday, 10 September 2006 Moscone Center -- Hall D, Poster

Division of Biological Chemistry

The 232nd ACS National Meeting, San Francisco, CA, September 10-14, 2006