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.
Department of Bioengineering, Graduate Group in Biophysics, University of California, Berkeley, Berkeley, California 94720, USA.
Jory Z
JZ
Ruscio
Jonathan E
JE
Kohn
K Aurelia
KA
Ball
Teresa
T
Head-Gordon
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