Asymmetric Conformational Dynamics of the ClpB Disaggregase Nanomachine

The requisite remodeling of the protein structure in the degradation and disaggregation pathway is controlled by powerful AAA+ (ATPases Associated with diverse cellular Activities) motor proteins, which transduce chemical energy to mechanical energy. Repetitive application of mechanical force by these machines assists disassembly of misfolded substrate proteins or aggregates and promotes translocation of the polypeptide chain through a narrow pore. We performed molecular dynamics simulations of the ClpB disaggregation machine, a AAA+ motor with a double ring hexameric structure that contains two nucleotide binding domains per protomer. We probed factors underlying asymmetric ring dynamics of ClpB using both supervised and unsupervised machine learning approaches. Our results indicate that the ClpB hexamer is stabilized by a network of cross-protomer electrostatic interactions located in the central pore. Our community network clustering approach reveals strong collaboration between neighboring protomers. Predicted relaxation times of the pore loops dynamics correspond to tens to hundreds of microseconds on the millisecond experimental timescales, in excellent agreement with the relaxation times obtained using single-molecule FRET experiments.