In the degradation pathway, protein unfolding is commonly a requisite step in the sequence of events leading to the fragmentation of the polypeptide chain. The unfolding process is mediated by ring-shaped AAA+ (ATPases associated with various cellular activities) nanomachines, such as Clps (Caseinolytic proteases), which couple chemical energy to mechanical forces applied onto substrate proteins (SPs). These forces are mediated by allosteric motions of flexible loops that protrude within the narrow Clp central channel and grip the SP. To elucidate conformational changes of the polypeptide chain associated with Clp-mediated SP unfolding and translocation, we perform simulations of implicit solvent and coarse-grained models of titin I27. In open pore configurations, unfolding of unrestrained SPs occurs via an unzipping mechanism, which involves force application along a weak mechanical direction. In the partially closed pore, unfolding occurs via a shearing mechanism, with force application along a strong mechanical direction. We also probe SP unfolding of tandems comprising two or four I27 domains which involve branched pathways and slower time scales. These distinct mechanisms are attributed to slower rotational diffusion of multidomain SPs that hinders access to the soft mechanical direction.

Multiscale modeling of protein unfolding and translocation in the degradation pathway

2019 Fall National Meeting

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