Watching a Fine‐tuned Molecular Machine at Work: Structural and Functional Studies of the 26S Proteasome

Abstract

The degradation of ubiquitin‐tagged proteins by the 26S proteasome is a highly complex process with several well‐coordinated sub‐steps, including ubiquitin recognition, deubiquitination, substrate engagement by the AAA+ motor, mechanical unfolding, translocation, and proteolytic cleavage. Our recently developed FRET‐ and fluorescence‐based assays, relying on the labeling of proteasome‐incorporated unnatural amino acids, allow us to dissect the kinetics and coordination of individual processing steps, and study the coupled conformational changes of the proteasome. Single‐molecule measurements provide exciting details about the conformational dynamics of the proteasomal regulatory particle and how ubiquitin binding, substrate engagement by the AAA+ motor, or the presence of certain receptor subunits affect the switching between substrate‐free and substrate‐processing states, which are furthermore controlled through specific interactions between the ATPase hexamer and the proteasomal lid subcomplex.FRET‐based assays reveal how substrates are propelled through the central channel of the proteasome and progress through the various stages of degradation, including a translocation stall during deubiquitination and the backtracking of substrate upon failure to remove ubiquitin chains prior to substrate entry into the AAA+ motor. Our mutational studies thereby provide important new insight into the mechanisms of substrate engagement and the contributions of individual ATPase subunits depending on their position in the vertical spiral‐staircase arrangement of the AAA+ hexamer. By using substrates with various architectures, we also gained a better understanding of how a substrate’s geometry and ubiquitin modifications affect the degradation rate, and how the proteasome may prioritize its substrates in the cell.Support or Funding InformationHoward Hughes Medical Institute; NIH‐NIGMS (R01‐GM094497)