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Pyrococcus furiosus Prolyl Oligopeptidase: A Dynamic Supramolecular Host for Peptidase and Dirhodium Catalysis

preprint
submitted on 06.09.2018 and posted on 07.09.2018 by Ken Ellis-Guardiola, Huan Rui, Ryan Beckner, Poonam Srivastava, Narayanasami Sukumar, Benoît Roux, Jared C. Lewis
Supramolecular catalysis involves the design and characterization of synthetic macromolecules that catalyze chemical reactions. While enzymes are often cited as the inspiration for such catalysts, enzymes can also serve as hosts for non-native catalytic components. Protein-based hosts can be readily produced in E. coli and rapidly evolved for particular applications. Moreover, inherent properties of these systems, including their conformational dynamics, can be exploited for non-native transformations that occur within their interior. Studies on the peptidase activity of a prolyl oligopeptidase from Pyrococcus furiosus (Pfu POP) suggest that its unique two-domain architecture regulates substrate access and specificity. We have established that Pfu POP also serves as an efficient host for asymmetric cyclopropanation upon active-site modification with a dirhodium cofactor. To understand how Pfu POP controls both peptidase and dirhodium catalysis, we determined the crystal structures of this enzyme and its S477C mutant and used these structures as starting points for MD simulations of both the apo structures and systems containing a covalently linked peptidase inhibitor or a dirhodium catalyst. Pfu POP was crystalized in an open conformation, and MD simulations reveal spontaneous transitions between open and closed states, in addition to a number of smaller scale conformational changes, suggesting facile inter-domain movement. Importantly, key aspects of previously reported peptidase kinetics and cyclopropanation selectivity can be rationalized in the context of this inter-domain opening and closing. This finding constitutes a remarkable example in which the conformational dynamics of a supramolecular host affect two different catalytic activities and suggests that Pfu POP could serve as a host for a wide range of non-native catalysts.

Funding

W911NF-14-1-0334, 66796-LS-RIP, W911NF-18-1-0200, CHE-1351991

History

Email Address of Submitting Author

jcl3@iu.edu

Institution

Indiana University

Country

United States

ORCID For Submitting Author

0000-0003-2800-8330

Declaration of Conflict of Interest

no conflict of interest

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