The influence of protein dynamics on the success of computational enzyme design.
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.
Ruscio
Jory Z
JZ
Department of Bioengineering, Graduate Group in Biophysics, University of California, Berkeley, Berkeley, California 94720, USA.
Kohn
Jonathan E
JE
Ball
K Aurelia
KA
Head-Gordon
Teresa
T
D002384:Catalysis; D004798:Enzymes / Q000737:chemistry*; D007700:Kinetics; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D011522:Protons; D013379:Substrate Specificity
D004798:Enzymes; D011522:Protons