posted on 2020-06-25, 10:43authored byArjun Saha, Gabriel Oanca, Dibyendu Mondal, Arieh Warshel
The
proteasome is a key protease in the eukaryotic cells which is responsible
for various important cellular processes such as the control of the
cell cycle, immune responses, protein homeostasis, inflammation, apoptosis,
and the response to proteotoxic stress. Acting as a major molecular
machine for protein degradation, proteasome first identifies damaged
or obsolete regulatory proteins by attaching ubiquitin chains and
subsequently utilizes conserved pore loops of the heterohexameric
ring of AAA+ (ATPases associated with diverse cellular activities)
to pull and mechanically unfold and translocate the misfolded protein
to the active site for proteolysis. A detailed knowledge of the reaction
mechanism for this proteasomal proteolysis is of central importance,
both for fundamental understanding and for drug discovery. The present
study investigates the mechanism of the proteolysis by the proteasome
with full consideration of the protein’s flexibility and its
impact on the reaction free energy. Major attention is paid to the
role of the protein electrostatics in determining the activation barriers.
The reaction mechanism is studied by considering a small artificial
fluorogenic peptide substrate (Suc-LLVY-AMC) and evaluating the activation
barriers and reaction free energies for the acylation and deacylation
steps, by using the empirical valence bond method. Our results shed
light on the proteolysis mechanism and thus should be important for
further studies of the proteasome action.