Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK

Bauer, Daniela; Merz, Dale R.; Pelz, Benjamin; Theisen, Kelly E.; Yacyshyn, Gail; Mokranjac, Dejana; Dima, Ruxandra I.; Rief, Matthias

doi:10.1073/pnas.1504625112

Cited by 39 publications

(59 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Several other conserved communities (L324-F356-V331) and (Q343-K270-M346) are shared by the DnaK structures forms and are responsible for structural stability of the subdomain IIA. According to single molecule optical tweezer experiments, nucleotide binding in DnaK is dependent on thermal stability of the subdomain IIA [127] . These studies also showed that stabilization and nucleotide-binding function of the lobe II in DnaK may be associated with structural preservation of residue cluster 330–345 in subdomain IIA.…”

Section: Resultsmentioning

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

Section: Resultsmentioning

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

show abstract

“…Hydrolysis of ATP by the hsp70 NBD keeps the precursor SOD2 protein in an unfolded, import-competent state and increases dissociation of bound SOD2 from hsp70 at the outer mitochondrial membrane, thereby increasing the import and activity of SOD2 (14). Treatment of cultured PAECs with GERAMT-TAT markedly reduced SOD2 localization to the mitochondria at baseline and following ACh stimulation (Fig.…”

Section: ؉mentioning

confidence: 86%

Domain Mapping of Heat Shock Protein 70 Reveals That Glutamic Acid 446 and Arginine 447 Are Critical for Regulating Superoxide Dismutase 2 Function

Afolayan

Alexander

Holme

et al. 2017

Journal of Biological Chemistry

View full text Add to dashboard Cite

Edited by Linda SpremulliStress-inducible heat shock protein 70 (hsp70) interacts with superoxide dismutase 2 (SOD2) in the cytosol after synthesis to transfer the enzyme to the mitochondria for subsequent activation. However, the structural basis for this interaction remains to be defined. To map the SOD2-binding site in hsp70, mutants of hsp70 were made and tested for their ability to bind SOD2. These studies showed that SOD2 binds in the amino acid 393-537 region of the chaperone. To map the hsp70-binding site in SOD2, we used a series of pulldown assays and showed that hsp70 binds to the amino-terminal domain of SOD2. To better define the binding site, we used a series of decoy peptides derived from the primary amino acid sequence in the SOD2-binding site in hsp70. This study shows that SOD2 specifically binds to hsp70 at 445 GERAMT 450 . Small peptides containing GERAMT inhibited the transfer of SOD2 to the mitochondria and decreased SOD2 activity in vitro and in vivo. To determine the amino acid residues in hsp70 that are critical for SOD2 interactions, we substituted each amino acid residue for alanine or more conservative residues, glutamine or asparagine, in the GERAMT-binding site. Substitutions of E446A/Q and R447A/Q inhibited the ability of the GERAMT peptide to bind SOD2 and preserved SOD2 function more than other substitutions. Together, these findings indicate that the GERAMT sequence is critical for hsp70-mediated regulation of SOD2 and that Glu 446 and Arg 447 cooperate with other amino acid residues in the GERAMT-binding site for proper chaperone-dependent regulation of SOD2 antioxidant function.

show abstract

“…The NBD has a deep cleft for binding ATP, while client proteins bind in a β-sandwich region of the SBD (Bertelsen et al, 2009). These two domains are allosterically linked, with nucleotide turnover in the NBD controlling the affinity of SBD-client interactions (Bauer et al, 2015; Clerico et al, 2015; Palleros et al, 1993; Zhuravleva and Gierasch, 2015). In the ATP-bound form, clients bind Hsp70s with fast-on, fast-off kinetics, while hydrolysis to the ADP-bound form stabilizes the SBD-client interaction by slowing the off-rate (Ha and McKay, 1995).…”

Section: Introductionmentioning

confidence: 99%

Stabilizing the Hsp70-Tau Complex Promotes Turnover in Models of Tauopathy

Young

Rauch

Assimon

et al. 2016

Cell Chemical Biology

View full text Add to dashboard Cite

Summary Heat shock protein 70 (Hsp70) is a chaperone that normally scans the proteome and initiates the turnover of some proteins (termed “clients”) by linking them to the degradation pathways. This activity is critical to normal protein homeostasis, yet it appears to fail in diseases associated with abnormal protein accumulation. It is not clear why Hsp70 promotes client degradation under some conditions, while sparing that protein under others. Here, we use a combination of chemical biology and genetics strategies to systematically perturb the affinity of Hsp70 for the model client, tau. This approach revealed that tight complexes between Hsp70 and tau are associated with enhanced turnover while transient interactions favored tau retention. These results suggest that client affinity is one important parameter governing Hsp70-mediated quality control.

show abstract

Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK

Cited by 39 publications

References 42 publications

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

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

Domain Mapping of Heat Shock Protein 70 Reveals That Glutamic Acid 446 and Arginine 447 Are Critical for Regulating Superoxide Dismutase 2 Function

Stabilizing the Hsp70-Tau Complex Promotes Turnover in Models of Tauopathy

Contact Info

Product

Resources

About