Allosteric fine-tuning of the conformational equilibrium poises the chaperone BiP for post-translational regulation

Wieteska, Łukasz; Shahidi, Saeid; Zhuravleva, Anastasia

doi:10.7554/elife.29430

Cited by 39 publications

(67 citation statements)

References 55 publications

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“…Surprisingly, similar behavior was not observed for ATP-bound DnaK. This might be explained by the insufficient SEC separation of the docked and undocked DnaK molecules, or by a more continuous distribution of DnaK molecules between docked/undocked/ intermediate states in the presence of ATP (11,37,38). To verify whether our purified proteins are conformationally active, we tested their ability to release substrate peptide in the presence of ATP (supplemental Fig.…”

Section: Hsp70 and Hsc70mentioning

confidence: 84%

Human Stress-inducible Hsp70 Has a High Propensity to Form ATP-dependent Antiparallel Dimers That Are Differentially Regulated by Cochaperone Binding*

Trčka

Ďurech

Vaňková

et al. 2019

Molecular & Cellular Proteomics

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In BriefThe oligomerization (and particularly dimerization) of Hsp70 proteins plays an important role in their chaperoning activities.Here, we report that human stress-inducible Hsp70 possesses the highest propensity among analyzed Hsp70 homologs to form dimers in the presence of ATP. ATP-bound Hsp70 assembles in solution as an antiparallel dimer closely resembling the dimeric structures captured in DnaK and BiP crystals. ATP-dependent Hsp70 dimerization is necessary for efficient Hsp40 interaction and is differentially affected by TPR cochaperone binding. Graphical Abstract Highlights• Hsp70 homologs differ in their oligomeric properties in the presence of ATP.• Human inducible Hsp70 forms ATP-dependent anti-parallel dimers with high propensity.• Dimerization of ATP-bound Hsp70 is required for effective Hsp70-Hsp40 interaction.• ATP-dependent interaction with Tomm34 TPR cochaperone disrupts Hsp70 dimer.

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Section: Hsp70 and Hsc70mentioning

confidence: 84%

Human Stress-inducible Hsp70 Has a High Propensity to Form ATP-dependent Antiparallel Dimers That Are Differentially Regulated by Cochaperone Binding*

Trčka

Ďurech

Vaňková

et al. 2019

Molecular & Cellular Proteomics

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“…However, recent single molecule experiments indicate that the frequency of such transitions differs among members of the Hsp70 family 7-9,18,35-37 . Interestingly, eukaryotic Hsp70s such as BiP of the endoplasmic reticulum 8, 36 or Hsp70 and Hsc70 37 of the cytosol, display conformational dynamics markedly different from DnaK and mitochondrial Hsp70. They have D SBD replaced by asparagine, pointing to the importance of the R NBD centered interactions for the allostery of Hsp70s.…”

Section: Discussionmentioning

confidence: 99%

Two-step mechanism of J-domain action in driving Hsp70 function

Tomiczek

Delewski

Nierzwicki

et al. 2020

Preprint

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J-domain proteins (JDPs), obligatory Hsp70 cochaperones, play critical roles in protein homeostasis. They promote key allosteric transitions that stabilize Hsp70 interaction with substrate polypeptides upon hydrolysis of its bound ATP. Although a recent crystal structure revealed the physical mode of interaction between a J-domain and an Hsp70, the structural and dynamic consequences of J-domain action once bound and how Hsp70s discriminate among its multiple JDP partners remain enigmatic. We combined free energy simulations, biochemical assays and evolutionary analyses to address these issues. Our results indicate that the invariant aspartate of the J-domain perturbs a conserved intramolecular Hsp70 network of contacts that crosses domains. This perturbation leads to destabilization of the domain-domain interface -thereby promoting the allosteric transition that triggers ATP hydrolysis. While this mechanistic step is driven by conserved residues, evolutionarily variable residues are key to initial JDP/Hsp70 recognition -via electrostatic interactions between oppositely charged surfaces. We speculate that these variable residues allow an Hsp70 to discriminate amongst JDP partners, as many of them have coevolved. Together, our data points to a two-step mode of J-domain action, a recognition stage followed by a mechanistic stage. are able to discriminate amongst their multiple JDP partners, thus enabling evolution of complex JDP/Hsp70 interaction networks. ResultsStructural model of the Hsc20-Ssq1 complex. To obtain a structural model of the JDP-Hsp70 complex formed by Hsc20 and Ssq1, we combined protein-protein docking with all-atom molecular dynamics (MD) simulations ( Supplementary Fig. S1). This approach revealed a dominant bound state that accounted for 56% of the bound population ( Fig. 1, Supplementary Fig. S2a). No other bound state accounted for more than 6% of the ensemble; these minor states rapidly interconverted and had a clear tendency to converge to the most populated bound state ( Supplementary Fig. S2b). The binding mode in this dominant state closely resembles the recently published X-ray structure of DnaJ's J-domain in complex with DnaK (DnaJ JD -DnaK) 22 . Helices II and III are oriented very similarly in the two complexes -with a backbone root mean square deviation (RMSD) of 4.17 Å ( Supplementary Fig. S3). More specifically, the J-domains bind at the NBD/SBDb,linker interface such that helix II predominantly interacts with the b-sheet region of NBD subdomain IIa and helix III with SBDb (Fig. 1). The HPD residues are positioned nearly identically in the two complexes, towards R167/R207 of NBD subdomain Ia in DnaK/Ssq1 (referred to as R NBD throughout), the arginine that previous analyses of DnaK established as important for allosteric transitions 14,20,21 . D HPD interferes in Hsp70 interdomain interactions by perturbing critical R NBD contacts.To address the question of the mechanism of J-domain action, we employed MD simulations that, unlike most other methods, allow studying of transient r...

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“…Most HSP70 do their work coupling the Mg 2+ -dependent hydrolisis of ATP to large conformational changes, involving movements of its structural domains (SBD and NBD) and the interdomain linker. So, HSP70 protein function rely on a dynamic ATP dependent cycle in which several conformations are visited, with different substrate binding affinities in them [45][46][47]. For example in DnaK, ATP binding favors a compact, domain-docked, and linker-bound conformation, which has low ATPase activity [3,45].…”

Section: Bip Allosteric Mechanismmentioning

confidence: 99%

“…So, HSP70 protein function rely on a dynamic ATP dependent cycle in which several conformations are visited, with different substrate binding affinities in them [45][46][47]. For example in DnaK, ATP binding favors a compact, domain-docked, and linker-bound conformation, which has low ATPase activity [3,45]. Substrate binding to this state stabilizes a transient domain-undocked conformation, with a linker-bound state, that has high ATPase activity and fast substrate binding and release kinetics but low substrate affinity.…”

Section: Bip Allosteric Mechanismmentioning

confidence: 99%

“…Substrate binding to this state stabilizes a transient domain-undocked conformation, with a linker-bound state, that has high ATPase activity and fast substrate binding and release kinetics but low substrate affinity. Then, when ATP is hydrolyzed to ADP, it is favored a domainundocked conformation, linker-unbound state, which has high substrate affinity but very slow substrate binding and release kinetics [45][46][47][48]. Recently, X-ray structures of ATP-bound DnaK [49] and human BiP [44] have shown that both proteins have big structural similarity, but their functional activity (and between different Hsp70s) varies significantly between them [3].…”

Section: Bip Allosteric Mechanismmentioning

confidence: 99%

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Mechanical Properties of Chaperone BiP, the Master Regulator of the Endoplasmic Reticulum

Alfaro-Valdés¹,

Burgos‐Bravo²,

Casanova-Morales³

et al. 2019

Endoplasmic Reticulum

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Immunoglobulin heavy-chain-binding protein (BiP protein) is a 75-kDa Hsp70 monomeric ATPase motor that plays broad and crucial roles maintaining proteostasis inside the cell. Its malfunction has been related with the appearance of many and important health problems such as neurodegenerative diseases, cancer, and heart diseases, among others. In particular, it is involved in many endoplasmic reticulum (ER) processes and functions, such as protein synthesis, folding, and assembly, and also it works in the posttranslational mechanism of protein translocation. However, it is unknown what kind of molecular motor BiP works like, since the mechanochemical mechanism that BiP utilizes to perform its work during posttranslational translocation across the ER is not fully understood. One novel approach to study both structural and catalytic properties of BiP considers that the viscoelastic regime behavior of the enzymes (considering them as a spring) and their mechanical properties are correlated with catalysis and ligand binding. Structurally, BiP is formed by two domains, and to establish a correlation between BiP structure and catalysis and how its conformational and viscoelastic changes are coupled to ligand binding, catalysis, and allosterism (information transmitted between the domains), optical tweezers and nano-rheology techniques have been essential in this regard.

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Allosteric fine-tuning of the conformational equilibrium poises the chaperone BiP for post-translational regulation

Cited by 39 publications

References 55 publications

Human Stress-inducible Hsp70 Has a High Propensity to Form ATP-dependent Antiparallel Dimers That Are Differentially Regulated by Cochaperone Binding*

Human Stress-inducible Hsp70 Has a High Propensity to Form ATP-dependent Antiparallel Dimers That Are Differentially Regulated by Cochaperone Binding*

Two-step mechanism of J-domain action in driving Hsp70 function

Mechanical Properties of Chaperone BiP, the Master Regulator of the Endoplasmic Reticulum

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