Hossein Fazelinia, Patrick C. Cirino, Costas D. Maranas
Graduate Student, Chemical Engineering
Despite the plethora of functionalities and exquisite specialization, many biotechnological tasks require proteins to operate under conditions that were not selected for in nature, such as enhanced thermostability, altered substrate specificity, different cofactor dependence, nonaqueous environments and, often, combinations of the above. One of the most challenging tasks of protein design is the introduction of a completely new function into an existing protein scaffold by grafting a new binding and/or active site onto it. In this study, we introduce a new computational algorithm for placing a new binding and/or active site onto a protein structure so as its geometry is minimally perturbed. In response to this design challenge 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 fold by minimizing the departure from a set of geometric restraints. This challenge gives rise to a high dimensional search problem which we tackle using mixed-integer linear optimization. Upon identifying the suitable locations that can accommodate the new binding pocket we subsequently identify whether mutations in the neighboring residues are needed to preserve the conformation of the grafted binding pocket and reduce any steric hindrances. 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 conserves the desired geometry. 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 Zinc binding pocket into catalytic antibody.