Probing Mechanisms of Allosteric Regulation in AAA+ ATPases for Microtubule Severing and Protein Disaggregation

An essential class of biological machines, known as AAA+ (ATPases Associated with diverse cellular Activities), play a crucial role in protein remodeling for various essential cellular functions. The operation of these machines relies on intra- and inter-ring allosteric communication to apply mechanical force onto the substrate via protruding loops into the central channel.

This research study aimed to explore the mechanisms behind these allosteric interactions by comparing katanin, a microtubule severing protein with a clade 3 AAA domain, and the double-ring ClpB, a protein disaggregase possessing both clade 3 and clade 5 AAA domains.

Through molecular dynamics simulations, machine learning, and bioinformatic analysis, researchers discovered that both katanin and ClpB exhibit comparable mechanisms involving the clade 3 domain, as well as unique processes involving the clade 5 domain in ClpB. The study found that nucleotide and substrate polypeptide binding restrict the conformational landscape sampled by both katanin and ClpB, resulting in ligand-specific conformations in the case of ClpB.

The investigation further revealed that secondary structure elements contribute significantly to allosteric communication, with regions adjacent to the nucleotide-binding site and the pore loops playing a crucial role. Amino acid-level analysis of the allosteric pathways unveiled that intra-ring cooperativity is responsible for modulating long-distance communication within the AAA+ protomers.