Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Mar 30:6:23474.
doi: 10.1038/srep23474.

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

Federica Chiappori  1 , Ivan Merelli  1 , Luciano Milanesi  1 , Giorgio Colombo  2 , Giulia Morra  2
Affiliations

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

Federica Chiappori et al. Sci Rep. .

Abstract

The Hsp70 is an allosterically regulated family of molecular chaperones. They consist of two structural domains, NBD and SBD, connected by a flexible linker. ATP hydrolysis at the NBD modulates substrate recognition at the SBD, while peptide binding at the SBD enhances ATP hydrolysis. In this study we apply Molecular Dynamics (MD) to elucidate the molecular determinants underlying the allosteric communication from the NBD to the SBD and back. We observe that local structural and dynamical modulation can be coupled to large-scale rearrangements, and that different combinations of ligands at NBD and SBD differently affect the SBD domain mobility. Substituting ADP with ATP in the NBD induces specific structural changes involving the linker and the two NBD lobes. Also, a SBD-bound peptide drives the linker docking by increasing the local dynamical coordination of its C-terminal end: a partially docked DnaK structure is achieved by combining ATP in the NBD and peptide in the SBD. We propose that the MD-based analysis of the inter domain dynamics and structure modulation could be used as a tool to computationally predict the allosteric behaviour and functional response of Hsp70 upon introducing mutations or binding small molecules, with potential applications for drug discovery.

PubMed Disclaimer

Figures

Figure 1
Figure 1. Hsp70 conformational cycle.
Open (ATP-bound) (PDB id: 4B9Q) and Closed (ADP-bound) (PDB id: 2KHO) end-points X-ray structure are displayed. NBD lobe I is green, lobe II is blue, linker is violet, βSBD is represented in yellow, and αSBD helices in red. Peptide-substrate bound to the SBD binding cavity of the open conformation induces the ATP hydrolysis and a large structural rearrangement to the closed conformation. This, after nucleotide exchange mediated by Nucleotide Exchange Factors (NEF), undergoes to another conformational transition, with βSBD docked to the NBD and a reduced the affinity for the peptide-substrate.
Figure 2
Figure 2. Contact interface.
Representative conformation of the most populated cluster for each complex is displayed: (a) NBD(ADP)-SBD(free); (b) NBD(ATP)-SBD(free); (c) NBD(ADP)-SBD(NR); (d) NBD(ATP)-SBD(NR); (e) NBD(ADP)-SBD(Api88); (f) NBD(ATP)-SBD(Api88). Regions that correspond to the contacting interfaces between NBD and SBD along the trajectories (see Methods) shown in the colour of the subdomain they belong to (see legend Fig. 1).
Figure 3
Figure 3. Distribution of the SBD centre of mass along the MD trajectories, after aligning the protein to the NBD.
Top, cloud showing the distribution of SBD centre of mass coordinates relative to the starting conformation for ADP bound systems: (A) SBD(free), (B) SBD(NR), (C) SBD(Api88). Bottom, same for ATP bound systems: (E) SBD(free), (F) SBD(NR), (G) SBD(Api88). (D) Distribution of distances from the starting position of the SBD centre of mass for ADP bound systems, obtained after merging the two independent runs for each system (blue: SBD(free), red SBD(NR), black SBD(Api88). (H) Same for ATP bound systems.
Figure 4
Figure 4. Cluster analysis of the linker (370–393).
(a) histogram showing the population of the dominant three clusters according to the nucleotide and ligand state (Top: ADP bound systems, bottom: ATP bound systems. RP indicates the Api88-bound state). (b) Close-up of the representative conformation of the second cluster, showing the arrangement of relevant residues Th383, of Glu213 and Arg167. (c–e) representative conformations of the dominant three clusters (from left to right: first, second, third) showing the terminal C helix in grey cartoon, the NBD in grey surface, the beta and alpha SBD in yellow and red surface, respectively, and highlighting the arrangement of Thr383.
Figure 5
Figure 5. Cluster analysis of the linker-βSBD (393–413).
(a) histogram showing the population of the dominant three clusters broken down according to the nucleotide and ligand state (Top: ADP bound systems, bottom: ATP bound systems. RP indicates the Api88-bound state). (b–d) representative conformations of the dominant three clusters (from left to right: first, second, third) highlighting the analysed region in grey cartoon, the NBD in grey surface and the beta and alpha SBD in yellow and red surface, respectively.
Figure 6
Figure 6. Linker docking.
Plot of distances between linker and loop L6,7 residues in NBD(ATP)-SBD(free) complex on top, and in NBD(ATP)-SBD(NR), in the middle. Screenshots of NBD(ATP)-SBD(NR) complex at the bottom, show the short β-sheet composed by the linker and by loop L6,7.
Figure 7
Figure 7. SBD docking and interactions between linker and loop210.
Plot of the distance between loop210 and linker residues in ATP complexes (a) and in ADP complexes (b). (c) displays residues of loop 210, linker and of the βSBD involved in the interaction necessary for the SBD docking.
Figure 8
Figure 8. Substrate effect βSBD conformation.
(a) histogram showing the population of the dominant three clusters broken down according to the nucleotide and ligand state. (b–d) cartoon representation of cluster centre conformations of first, second and third dominant cluster, respectively.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Mayer M. P. Hsp70 chaperone dynamics and molecular mechanism. Trends Biochem. Sci. 38, 507–514 (2013). - PubMed
    1. Mayer M. P. & Bukau B. Hsp70 chaperones: cellular functions and molecular mechanism. CMLS-Cell Mol. Life S. 62, 670–684 (2005). - PMC - PubMed
    1. Murphy M. E. The HSP70 family and cancer. Carcinogenesis 34, 1181–1188 (2013). - PMC - PubMed
    1. Workman P., Burrows F. J., Neckers L. & Rosen N. Drugging the cancer chaperone Hsp90: combinatorial therapeutic exploitation of oncogene addiction and tumor stress. Ann. N.Y. Acad. Sci. 1113, 202–216 (2007). - PubMed
    1. Whitesell L. & Lindquist S. L. Hsp90 and the chaperoning of cancer. Nat. Rev. Cancer 5, 761–772 (2005). - PubMed

Publication types

MeSH terms

LinkOut - more resources

-