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

Proteins. 2014 Sep;82(9):1985-99. doi: 10.1002/prot.24553. Epub 2014 Apr 18.

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.

Keywords: PA26; PAN-like; adaptively biased molecular dynamics (ABMD); free energy of translocation; hybrid proteasome; proteasome core particle (CP).

MeSH terms

  • Archaea / enzymology
  • Archaeal Proteins / chemistry*
  • Archaeal Proteins / metabolism*
  • Computational Biology
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Proteasome Endopeptidase Complex / metabolism*
  • Protein Transport
  • Proteolysis

Substances

  • Archaeal Proteins
  • Proteasome Endopeptidase Complex