Common functionally important motions of the nucleotide-binding domain of Hsp70

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication

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.

The diversity of allosteric mechanisms in the Hsp70 proteins could range from modulation of the inter-domain interactions and conformational dynamics to fine-tuning of the Hsp70 interactions with co-chaperones. The goal of this study is to present a systematic computational analysis of the dynamic and evolutionary factors underlying allosteric structural transformations of the Hsp70 proteins. We investigated the relationship between functional dynamics, residue coevolution, and network organization of residue interactions in the Hsp70 proteins. The results of this study revealed that conformational dynamics of the Hsp70 proteins may be linked with coevolutionary propensities and mutual information dependencies of the protein residues. Modularity and connectivity of allosteric interactions in the Hsp70 chaperones are coordinated by stable functional sites that feature unique coevolutionary signatures and high network centrality. The emergence of the inter-domain communities that are coordinated by functional centers and include highly coevolving residues could facilitate structural transitions through cooperative reorganization of the local interacting modules. We determined that the differences in the modularity of the residue interactions and organization of coevolutionary networks in DnaK may be associated with variations in their allosteric mechanisms. The network signatures of the DnaK structures are characteristic of a population-shift allostery that allows for coordinated structural rearrangements of local communities. A dislocation of mediating centers and insufficient coevolutionary coupling between functional regions may render a reduced cooperativity and promote a limited entropy-driven allostery in the Sse1 chaperone that occurs without structural changes. The results of this study showed that a network-centric framework and a community-hopping model of allosteric communication pathways may provide novel insights into molecular and evolutionary principles of allosteric regulation in the Hsp70 proteins.

Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa:d-Lac Ligase VanA

The d-Ala:d-Lac ligase, VanA, plays a critical role in the resistance of vancomycin. Indeed, it is involved in the synthesis of a peptidoglycan precursor, to which vancomycin cannot bind. The reaction catalyzed by VanA requires the opening of the so-called “ω-loop”, so that the substrates can enter the active site. Here, the conformational landscape of VanA is explored by an enhanced sampling approach: the temperature-accelerated molecular dynamics (TAMD). Analysis of the molecular dynamics (MD) and TAMD trajectories recorded on VanA permits a graphical description of the structural and kinetics aspects of the conformational space of VanA, where the internal mobility and various opening modes of the ω-loop play a major role. The other important feature is the correlation of the ω-loop motion with the movements of the opposite domain, defined as containing the residues A149–Q208. Conformational and kinetic clusters have been determined and a path describing the ω-loop opening was extracted from these clusters. The determination of this opening path, as well as the relative importance of hydrogen bonds along the path, permit one to propose some key residue interactions for the kinetics of the ω-loop opening.

Dynamical Structures of Hsp70 and Hsp70-Hsp40 Complexes

Protein misfolding and aggregation are pathological events that place a significant amount of stress on the maintenance of protein homeostasis (proteostasis). For prevention and repair of protein misfolding and aggregation, cells are equipped with robust mechanisms that mainly rely on molecular chaperones. Two classes of molecular chaperones, heat shock protein 70 kDa (Hsp70) and Hsp40, recognize and bind to misfolded proteins, preventing their toxic biomolecular aggregation and enabling refolding or targeted degradation. Here, we review the current state of structural biology of Hsp70 and Hsp40-Hsp70 complexes and examine the link between their structures, dynamics, and functions. We highlight the power of nuclear magnetic resonance spectroscopy to untangle complex relationships behind molecular chaperones and their mechanism(s) of action.