BIOT 429 |
| Computer simulations play an increasingly significant role in understanding the underlying physical principles that dictate protein folding, stability and function, and computational advances in this area have greatly improved protein design predictions. While it is not yet possible to robustly predict structure and function de novo, it is possible to assess the impact of mutations on existing, well-characterized proteins. In this study we are developing and testing a computational framework to systematically transfer a binding site to a protein with known scaffold. In response to these design challenges we put forth a two-level procedure where we first identify where are the most appropriate locations to graft the new binding pocket into the protein structure. This challenge gives rise to a high dimensional search problem which we tackle using combinatorial optimization to identify promising locations to place the new binding site. Once a set of promising grafting sites is identified the next step involves the identification of mutations in the neighboring residues around the grafted binding site such that the geometry of the binding site is preserved upon energy minimization. Detailed atomistic energy calculations are employed to identify what mutations, if any, are needed to ensure that the minimum energy conformation of the binding pocket coincides with the configuration desired for function. This computational framework is benchmarked against the results available in the literature for transferring metal binding site for catalytic antibody and azurin-thioredoxin systems as well as transferring an active site into a protein of known scaffold. |
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Biophysical and Biomolecular Symposium: Protein Engineering
8:00 AM-11:00 AM, Thursday, August 23, 2007 BCEC -- 108, Oral
Division of Biochemical Technology |