Essential function of the N‐termini tails of the proteasome for the gating mechanism revealed by molecular dynamics simulations

Proteasome is involved in the degradation of proteins. Proteasome activators bind to the proteasome core particle (CP) and facilitate opening a gate of the CP, where Tyr8 and Asp9 in the N‐termini tails of the CP form the ordered open gate. In a double mutant (Tyr8Gly/Asp9Gly), the N‐termini tails are disordered and the stabilized open‐gate conformation cannot be formed. To understand the gating mechanism of the CP for the translocation of the substrate, four different molecular dynamics simulations were carried out: ordered‐ and Tyr8Gly/Asp9Gly disordered‐gate models of the CP complexed with an ATP‐independent PA26 and ordered‐ and disordered‐gate models of the CP complexed with an ATP‐dependent PAN‐like activator. The free‐energies of the translocation of a polypeptide substrate moving through the gate were estimated. In the ordered‐gate models, the substrate in the activator was more stable than that in the CP. The conformational entropy of the N‐termini tails of the CP was larger when the substrate was in the activator than in the CP. In the disordered‐gate models, the substrate in the activator was more destabilized than in the ordered‐gate models. The mutated N‐termini tails became randomized and their increased conformational entropy could no longer increase further even when the substrate was in the activator, meaning the randomized N‐termini tails had lost the ability to stabilize the substrate in the activator. Thus, it was concluded that the dynamics of the N‐termini tails entropically play a key role in the translocation of the substrate. Proteins 2014; 82:1985–1999. © 2014 Wiley Periodicals, Inc.