Electrostatic Preorganization in Three Distinct Heterogeneous Proteasome β‑Subunits

The origin of the
enzyme’s powerful role in accelerating
chemical reactions is one of the most critical and still widely discussed
questions. It is already accepted that enzymes impose an electrostatic
field onto their substrates by adopting complex three-dimensional
structures; therefore, the preorganization of electric fields inside
protein active sites has been proposed as a crucial contributor to
catalytic mechanisms and rate constant enhancement. In this work,
we focus on three catalytically active β-subunits of 20S proteasomes
with low sequence identity (∼30%) whose active sites, although
situated in an electrostatically miscellaneous environment, catalyze
the same chemical reaction with similar catalytic efficiency. Our
in silico experiments reproduce the experimentally observed equivalent
reactivity of the three sites and show that obliteration of the electrostatic
potential in all active sites would deprive the enzymes of their catalytic
power by slowing down the chemical process by a factor of 1035. To regain enzymatic efficiency, besides catalytic Thr1 and Lys33
residues, the presence of aspartic acid in position 17 and an aqueous
solvent is required, proving that the electrostatic potential generated
by the remaining residues is insignificant for catalysis. Moreover,
it was found that the gradual decay of atomic charges on Asp17 strongly
correlates with the enzyme’s catalytic rate deterioration as
well as with a change in the charge distributions due to introduced
mutations. The computational procedure used and described here may
help identify key residues for catalysis in other biomolecular systems
and consequently may contribute to the process of designing enzyme-like
synthetic catalysts.