Abstract
Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here, we combine complementary theoretical approaches to elucidate the structural and thermodynamic details of the chaperone-induced expansion of a substrate protein, with a particular emphasis on the critical role played by ATP hydrolysis. We first determine the conformational free-energy cost of the substrate expansion due to the binding of multiple chaperones using coarse-grained molecular simulations. We then exploit this result to implement a non-equilibrium rate model which estimates the degree of expansion as a function of the free energy provided by ATP hydrolysis. Our results are in quantitative agreement with recent single-molecule FRET experiments and highlight the stark non-equilibrium nature of the process, showing that Hsp70s are optimized to effectively convert chemical energy into mechanical work close to physiological conditions.
Highlights
Even though in vitro most proteins can reach their native structure spontaneously (Anfinsen, 1973), this is not always the case in cellular conditions and proteins can populate misfolded states which can form cytotoxic aggregates (Dobson, 2003)
Hsp70s consist of two domains: the substrate binding domain (SBD) interacts with disparate substrate proteins, whereas the nucleotide binding domain (NBD) is responsible for the binding and hydrolysis of ATP
We relied on a one-bead-per-residue Coarse Grained (CG) force field (Smith et al, 2014), which has been tailored to match experimental Forster resonance energy transfer (FRET) data of intrinsically disordered proteins and satisfactorily reproduces the compactness of unfolded rhodanese in native conditions without any further tuning
Summary
Even though in vitro most proteins can reach their native structure spontaneously (Anfinsen, 1973), this is not always the case in cellular conditions and proteins can populate misfolded states which can form cytotoxic aggregates (Dobson, 2003). In order to counteract misfolding and aggregation, cells employ specialized proteins, called molecular chaperones, which act on non-native protein substrates by processes that stringently depend on ATP hydrolysis for most chaperone families (Hartl, 1996). The ubiquitous 70 kDa heat-shock proteins (Hsp70s) play a special role because they assist a plethora of fundamental cellular processes beyond prevention of aggregation (Clerico et al, 2019; Rosenzweig et al, 2019). Hsp70s consist of two domains: the substrate binding domain (SBD) interacts with disparate substrate proteins, whereas the nucleotide binding domain (NBD) is responsible for the binding and hydrolysis of ATP. The two domains are allosterically coupled, and the nature of the nucleotide bound to the NBD affects the structure of the SBD
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