An atomistic view of Hsp70 allosteric crosstalk: from the nucleotide to the substrate binding domain and back

Chiappori, Federica; Merelli, Ivan; Milanesi, Luciano; Colombo, Giorgio; Morra, Giulia

doi:10.1038/srep23474

Cited by 33 publications

(54 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Single-molecule FRET experiments (22) showed that the open SBD form is present (8-11%) under ADP conditions, supporting our results. A weak interaction between the α/β-folded subdomains and physical separation of subdomains was also observed in native-state molecular simulations by using the replica exchange method or following the dynamics of DnaK over tens of nanoseconds of equilibrium molecular dynamics (23,24). As pointed out above, the subdomain interface is easily perturbed allowing the opening of the lid, whereas β7-β8 are still attached to the β-core, which reduces energy costs.…”

Section: Discussion Bifurcating Unfolding Pathways For Sbd and Mechanmentioning

confidence: 87%

Nanomechanics of the substrate binding domain of Hsp70 determine its allosteric ATP-induced conformational change

Mandal

Merz

Buchsteiner

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Owing to the cooperativity of protein structures, it is often almost impossible to identify independent subunits, flexible regions, or hinges simply by visual inspection of static snapshots. Here, we use single-molecule force experiments and simulations to apply tension across the substrate binding domain (SBD) of heat shock protein 70 (Hsp70) to pinpoint mechanical units and flexible hinges. The SBD consists of two nanomechanical units matching 3D structural parts, called the α-and β-subdomain. We identified a flexible region within the rigid β-subdomain that gives way under load, thus opening up the α/β interface. In exactly this region, structural changes occur in the ATP-induced opening of Hsp70 to allow substrate exchange. Our results show that the SBD's ability to undergo large conformational changes is already encoded by passive mechanics of the individual elements.laser trapping | parallel pathways | elasticity | force | protein extension W hen looking at protein structures at atomic resolution, it is often tempting to use macroscopic mechanical analogies to describe their function as molecular machines. However, such analogies are often misleading because boundaries between independently stable subdomains cannot often be determined from structures, owing to the high cooperativity of protein folding and structural transitions. Single-molecule protein nanomechanics have emerged as a tool to force biomolecules through their conformational space and, hence, identify hinges, breaking points, and mechanically stable subdomains (1-3).A prominent example of a protein machine undergoing large conformational change during its functional cycle is the ATP-regulated Hsp70 chaperone DnaK-a central molecular chaperone of the protein quality control network in a cell (4-6). Once ATP is bound to the nucleotide binding domain (NBD, blue-yellow; Fig. 1A) of DnaK, the initially closed substrate binding domain (SBD) opens its binding cleft by engaging the β-subdomain to the NBD. In doing so, it undergoes a dramatic ∼10 Å displacement of its lid subdomain ( Fig. 1A; refs. 7 and 8) to allow exchange of substrates (9). Several crystal structures of the isolated SBD (in which the NBD is absent) have been solved (10-15). In these structures, the absence or presence of peptide clients or nonnatural ligands induce no significant structural changes in the closed conformation. There is no indication in the crystal structures of the huge conformational change of the lid domain of the SBD, seen in the ATP form of the full-length two-domain DnaK. Therefore, the large conformational change of the SBD is only observed in the two-domain DnaK after ATP binding. Thus, although the crystal structures provide us with valuable insights into the 3D arrangement of individual atoms, the thermodynamic and mechanical stability of individual substructures are difficult to predict based on this information alone. Here, we ask how the large ATP-induced changes of the SBD, as seen in the two-domain DnaK, are mirrored in the subdomain integrity and nano...

show abstract

Section: Discussion Bifurcating Unfolding Pathways For Sbd and Mechanmentioning

confidence: 87%

Nanomechanics of the substrate binding domain of Hsp70 determine its allosteric ATP-induced conformational change

Mandal

Merz

Buchsteiner

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…Computational studies have investigated various molecular factors underlying allosteric regulatory mechanisms in the DnaK chaperones by simulating dynamics and energetics of the crystal structures and allosteric pathways [57–68] . Molecular dynamics (MD) simulations and elastic network models have explored evolution and dynamics of the Hsp70 chaperones in binding with client proteins [57] and molecular aspects of nucleotide-induced conformational transitions in these chaperones [58] .…”

Section: Introductionmentioning

confidence: 99%

“…Computational modeling of the residue interactions in combination with in silico alanine scanning of the Hsp70 residues has probed molecular determinants and specific role of functional sites in allosteric signaling and biochemical cycle [67] . MD simulations have elucidated the molecular determinants underlying ligand-induced modulation of conformational dynamics in the DnaK structures, showing that local dynamics changes in response to ligand binding may be coupled to allosteric structural rearrangements [68] . The relationships between protein dynamics and allosteric signaling can be conveniently explored using structural analysis of the residue interaction networks [69–71] .…”

Section: Introductionmentioning

confidence: 99%

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

2017

View full text Add to dashboard Cite

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.

show abstract

“…The same is done with the only available wild-type and fulllength HSPA5 (x-ray crystallography solved structure PDB ID: 5E84 with 2.99 Å resolution) in the open conformation (Yang et al 2015;Yang et al 2017). It is important to use the open conformation of the HSP5A in which the SBDα and SBDβ are apart from each other, and the substrate affinity to SBDβ is higher (Chiappori et al 2016). The available sequences for EBOV GP1 found in the protein database of the National Center for Biotechnology Information (NCBI) are downloaded (ten sequences found in the identical protein group database), and Clustal Omega is utilized to perform multiple sequence alignment (MSA) with the Pep42 sequence CTVALPGGYVRVC (Sievers et al 2011).…”

Section: Methodsmentioning

confidence: 99%

Ebola virus glycoprotein GP1—host cell-surface HSPA5 binding site prediction

Elfiky

2020

Cell Stress and Chaperones

View full text Add to dashboard Cite

Ebola virus (EBOV) infection is a widespread infection that has created a bad memory in Africa. In the 2014 and 2015 outbreak, more than 28,000 infections were reported by the World Health Organization, with about 11,300 deaths in Guinea, Liberia, and Sierra Leone. Heat shock protein A5 (HSPA5), termed also GRP78, is a host cell chaperone protein responsible for the unfolded protein response in the endoplasmic reticulum. Under stress, HSPA5 is upregulated and becomes cell-surface exposed. Recent studies report the association of cell-surface HSPA5 with EBOV glycoproteins GP1 and GP2. In this study, structural and sequence analysis and molecular docking are used to predict the possible binding site between the cell-surface HSPA5 and EBOV GP1. The results show a promising binding site that supports the hypothesis of HSPA5 selectivity for binding to a specific peptide sequence (pep42). This study paves the way to suggest possible inhibitors to stop viral association with cell-surface receptors and subsequently reduce viral infection.

show abstract

An atomistic view of Hsp70 allosteric crosstalk: from the nucleotide to the substrate binding domain and back

Cited by 33 publications

References 36 publications

Nanomechanics of the substrate binding domain of Hsp70 determine its allosteric ATP-induced conformational change

Nanomechanics of the substrate binding domain of Hsp70 determine its allosteric ATP-induced conformational change

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

Ebola virus glycoprotein GP1—host cell-surface HSPA5 binding site prediction

Contact Info

Product

Resources

About