Accumulation of protein aggregates is lethal to the cell and protein quality control mechanisms such as protein disaggregation and degradation are required to maintain the proper cellular function. These mechanisms are mediated by disaggregation nanomachines, such as ClpB, a heat shock protein of the HSP100 class. ClpB has a double-ring hexameric structure that contains two AAA+ (ATPases Associated with diverse cellular Activities) nucleotide binding domains (NBDs) per protomer. Threading of substrate proteins through the narrow central pore of ClpB is promoted through application of mechanical force by central pore loops (PLs) in repetitive allosteric cycles of ClpB. In this study, we probe factors that determine asymmetric conformational dynamics of ClpB by performing all-atom molecular dynamics simulations for two distinct conformations (ring and spiral states) using apo, nucleotide-, and minimal substrate-bound states. Our simulations indicate that the ClpB hexamer is stabilized by the presence of nucleotides and minimal substrates. Dynamically, NBD rings are stabilized by an extensive network of salt bridges formed by pore loops. Clustering of dynamic motions suggests that PLs of the NBD1 ring work cooperatively whereas those of the NBD2 ring are weakly coupled. The loop relaxation dynamics involves a combination of a single and stretched exponential decay function indicating coupling of local and collective motions. The characteristic relaxation times obtained in nanosecond time scale are in close agreement with single-molecule sm-FRET experiments.

Relaxation dynamics of AAA+ nanomachines involved in protein disaggregation

ACS Spring Meeting 2021

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