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

Abstract

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.

Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome

“…(ABMD) method [22] combined with multiple walker method [23] implemented in an in-house molecular dynamics simulation software, SCUBA [16,[24][25][26][27][28] which was initiated to develop by Prof. Go and was named after his hobby. The reaction coordinate d was defined as a distance between two phosphorus atoms of T73 in chains I and J at both DNA ends.…”

Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations

“…Both Lys620Met and Ser668Ala are defective in ATP hydrolysis, resulting in defective MMR). All the conformational analyses of MutS and DNA were carried out using the analysis module in an MD simulation program called SCUBA …”

“…All the conformational analyses of MutS and DNA were carried out using the analysis module in an MD simulation program called SCUBA. [48][49][50][51] Dynamic domains in the complexes analyzed using PCA and Dyndom3D…”

Detection of cave pockets in large molecules: Spaces into which internal probes can enter, but external probes from outside cannot

“…The program GHECOM has been developed for the updated definition of a pocket, and is widely used by many researchers. Ito, J., et al (2012) used it to construct a database for ligand-binding and putative pockets [10], Ishida, H. (2014) employed it in characterizing the cavity regions of conformations of the proteasome sampled by molecular dynamics [11], and Kawabata, T., et al (2017) used it to find putative binding sites for substrate-docking calculations applied to a PET-degrading enzyme [12].…”