Abstract
Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of allostery, we introduced a community-hopping model of allosteric communication. Atomistic reconstruction of signaling pathways in the DnaK structures captured a direction-specific mechanism and molecular details of signal transmission that are fully consistent with the mutagenesis experiments. The results of our study reconciled structural and functional experiments from a network-centric perspective by showing that global properties of the residue interaction networks and coevolutionary signatures may be linked with specificity and diversity of allosteric regulation mechanisms.
Highlights
The evolutionary conserved and versatile 70-kilodalton heat shock proteins Hsp70s play a central role in supervision of various protein folding processes and coordination of a broad range of cellular events–from maintenance of cellular homeostasis to regulation of the heat shock response [1,2,3,4,5,6,7,8]
Structural and biophysical investigations of various E. coli Hsp70 (DnaK) constructs [17,18,19,20,21,22,23,24,25,26] have established that the nucleotidebinding domain (NBD) and substrate-binding domain (SBD) are only loosely coupled in the extended ADPbound and the nucleotide-free states, whereas ATP binding shifts thermodynamic preferences and stabilizes a compact domain-docked DnaK structure, leading to stimulation of the ATPase activity and substrate release (Fig 1)
To discriminate coevolutionary associations driven by functional constraints from those determined by common ancestry, the covariance metric based on mutual information (MI) calculations was adjusted by the average product correction (APC) [104,105,106]
Summary
The evolutionary conserved and versatile 70-kilodalton (kDa) heat shock proteins Hsp70s play a central role in supervision of various protein folding processes and coordination of a broad range of cellular events–from maintenance of cellular homeostasis to regulation of the heat shock response [1,2,3,4,5,6,7,8]. The Hsp biochemical cycle involves a precisely orchestrated succession of nucleotide-induced allosteric structural changes that are executed through complex and adaptive interactions with co-chaperones, J-domain proteins DnaJ and Hsp which accelerate ATP hydrolysis, and nucleotide exchange factors assisting in a timely progression of the ATP-ADP exchange [13,14,15,16]. During this cycle, ATP binding in the nucleotidebinding domain (NBD) accelerates substrate dissociation from the substrate-binding domain (SBD), while substrate binding synchronously stimulates ATPase hydrolysis in the NBD A limited entropydriven allostery could present a dominant “modus operandi” of the Sse biochemical cycle, where ATP hydrolysis is coupled to the substrate release via redistribution of conformational dynamics in the functional regions
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