De novo design of alpha-helical bundles

University Of Pennsylvania, Philadelphia PA

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Abstract

DESCRIPTION (provided by applicant): The mechanisms by which proteins fold into their well-defined three-dimensional structures, and function is a problem that we are addressing through de novo protein design. In the previous funding period we focused on design and folding of peptides that assemble into three-helix bundles and four-helix diiron proteins. In the coming period, we will design models for a number of redox-active proteins to determine how proteins create environments that define the reactivity and catalytic properties of metal ions and organic cofactors. In addition, we will design a series of peptides that change their aggregation state in response to covalent modification or binding of small molecules. Our specific aims are as follows: Aim 1. Design of proteins that bind diiron cofactors. Diiron proteins use a single di-metal ion cofactor to catalyze a multitude of processes, including reversible oxygen binding, hydrolytic reactions, iron oxidation, organic radical formation, and oxidation of hydrocarbons. How do the structures of these proteins tune the chemical properties of a common diiron center to obtain such a diversity of highly specific catalysts? To address this question, we have designed and structurally characterized several minimal models for diiron proteins. In the coming period we will determine how systematic changes to the solvent-accessibility, electrostatics, and polarity of the dimetal site affect its reactivity and catalytic properties. Aim 2. Computational design of proteins that bind a variety of inorganic and organic cofactors. We will develop novel methods for the design of a variety of helical bundles and b-proteins that encapsulate metal ions, homes, synthetic porphyrins, and linked porphyrin-quinone conjugates. Aim 3. Design of peptides that change their conformations in response to covalent modifications and binding of small molecules. These peptides will be structurally characterized, and used to control non-covalent interactions such as binding to DNA.