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Theoretical Characterization of Kinetically Stable Proteins

Additional Project Aspects

We will also study the correlation between protein dynamics, multimer formation, and protein sequence evolution. We will employ Hidden Markov Models to identify high entropy mutations (in the information theory sense), with protein structure and dynamics. We will identify correlated amino acids that may be involved in the kinetic stabilization of protein.

A final aspect of this project may be described as follows: Select a fast folding protein and design the TSE such that the protein becomes kinetically trapped. The strategy will be to identify the TSE structures of the protein. Use the method of Verduscolo and Dobson (sp) to construct the TSE by using a phi value constraint. Once the TSE is identified, assuming that small number of mutations will only cause small changes in the TSE, perform optimizations such that the energetics of the TSE and folded state are maximized, without affecting the folding rate. The designed protein will be produced and the resistance to unfolding will be tested by Colon’s laboratory. Candidates for these studies are SH3, Protein L, protein G, or CI2.

The models developed will be relevant to understanding the kinetic stability of certain proteins, and will be used to elucidate the connection between protein structure and kinetic stability.

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