We characterize the molecular dynamics of a previously described computational de novo designed enzyme optimized to perform a multistep retrol-aldol reaction when engineered into a TIM barrel protein scaffold. The molecular dynamics simulations show that the protein dynamics under physiological conditions of temperature and aqueous environment distorts the designed geometric factors of the substrate-enzyme reaction intermediates, such that catalysis is limited by the primary retrol-aldol step of proton abstraction from the covalently bound substrate and its interactions with a histidine-aspartate dyad. These results emphasize that computational enzyme designs will benefit from considerations of dynamical fluctuations when optimizing active site geometries.
Article
The Influence of Protein Dynamics on the Success of Computational Enzyme Design
Chemistry
Document Type
Article
Publication Date
1-1-2009
Published In
Journal of the American Chemical Society
Pages
14111-14115
DOI
10.1021/ja905396s
Abstract
Disciplines
Citation Information
Jory Z. Ruscio, Jonathan E. Kohn, K. Aurelia Ball, Teresa Head Gordon. The influence of protein dynamics on the success of computational enzyme design. Journal of the American Chemical Society, 2009; 131:14111-14115.