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Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins.

Stetz G, Verkhivker GM - PLoS ONE (2015)

Bottom Line: The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions.We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications.This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones.

View Article: PubMed Central - PubMed

Affiliation: Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America.

ABSTRACT
Hsp70 and Hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. Although many aspects of allosteric regulatory mechanisms in Hsp70 and Hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. In this work, we have combined molecular dynamics simulations and protein stability analysis of the chaperone structures with the network modeling of residue interaction networks to characterize molecular determinants of allosteric mechanisms. We have shown that allosteric mechanisms of Hsp70 and Hsp110 chaperones may be primarily determined by nucleotide-induced redistribution of local conformational ensembles in the inter-domain regions and the substrate binding domain. Conformational dynamics and energetics of the peptide substrate binding with the Hsp70 structures has been analyzed using free energy calculations, revealing allosteric hotspots that control negative cooperativity between regulatory sites. The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions. A smaller allosteric network in Hsp110 structures may elicit an entropy-driven allostery that occurs in the absence of global structural changes. We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications. The network-centric analysis of allosteric interactions has also established that centrality of functional residues could correlate with their sensitivity to mutations across diverse chaperone functions. This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones.

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The Structures and Domain Organization of Functional States in DnaK and Sse1p Chaperones.A solution structure of an ADP-bound DnaK (pdb id 2KHO) (A) and the crystal structure of an ATP-bound DnaK (pdb id 4B9Q) (B). The structures are shown in a ribbon representation and main structural elements are annotated. The NBD subdomains are colored as follows: IA (in blue), IB (in red), IIA (in green), IIB (in cyan), the inter-domain linker (in black), SBD-α (in magenta), and SBD-β (in orange). (C) The crystal structure of the yeast Hsp110 (Sse1p) in a complex with ATP (pdb id 2QXL). (D) The crystal structure of Sse1p in a complex with the NBD of hHsp70 (pdb id 3D2F). The structures are shown in a ribbon representation and main structural elements are annotated and colored as in DnaK. The Sse1p insert in Sse1p-ATP structure is shown in yellow (C) and the NBD of hHsp70 in the Sse1p-Hsp70 complex is shown in pink (D).
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pone.0143752.g002: The Structures and Domain Organization of Functional States in DnaK and Sse1p Chaperones.A solution structure of an ADP-bound DnaK (pdb id 2KHO) (A) and the crystal structure of an ATP-bound DnaK (pdb id 4B9Q) (B). The structures are shown in a ribbon representation and main structural elements are annotated. The NBD subdomains are colored as follows: IA (in blue), IB (in red), IIA (in green), IIB (in cyan), the inter-domain linker (in black), SBD-α (in magenta), and SBD-β (in orange). (C) The crystal structure of the yeast Hsp110 (Sse1p) in a complex with ATP (pdb id 2QXL). (D) The crystal structure of Sse1p in a complex with the NBD of hHsp70 (pdb id 3D2F). The structures are shown in a ribbon representation and main structural elements are annotated and colored as in DnaK. The Sse1p insert in Sse1p-ATP structure is shown in yellow (C) and the NBD of hHsp70 in the Sse1p-Hsp70 complex is shown in pink (D).

Mentions: A significant breakthrough in mechanistic characterization of the Hsp70 chaperone cycle has been made in a series of pioneering structure-functional studies of DnaK that have unveiled for the first time the molecular details of the full-length Hsp70 constructs in the major functional states: nucleotide-free and ADP-bound [31–33], ATP-bound [34,35], and ATP/substrate-bound [36]. The solution NMR structure of the full-length DnaK in the ADP-bound and substrate-bound state (Fig 2A) has confirmed that the NBD, SBD and the inter-domain linker are only weakly bound and move independently, engaging in random collisions on surfaces of the subdomains IA and IIA [31]. NMR studies have also elucidated how ATP binding can facilitate conformational transitions and allosteric communication between radically different functional states. Chemical-shift perturbation patterns for different DnaK states (ligand-bound and apo) and two different inter-domain linker constructs have shown that ATP binding may cause global structural reorganization of the NBD conformation via subtle subdomain motions, bringing the SBD and NBD in a close proximity to enable the inter-domain communication [32]. A solution NMR study of the Hsp70-NBD from Thermus thermophilus, in the ADP and AMP-PNP states has identified similar cooperative rotations of the NBD subdomains upon nucleotide exchange [33]. The crystal structures of a full-length two-domain DnaK in the ATP-bound, domain-docked conformation (Fig 2B) were solved independently using different protein engineering strategies to reduce the intrinsic flexibility of Hsp70 and induce favorable crystallization conditions [34,35]. By introducing a disulfide bridge between the SBD-α and NBD, the crystal structure of the ATP-bound DnaK was obtained, in which the SBD-β and the SBD-α subdomains are docked to the NBD [34]. Another crystal structure of an ATP-bound DnaK has been determined with a shortened L3,4 loop of the SBD-β [35]. Despite these differences in constructs, the underlying molecular details of the ATP-bound DnaK structures are extremely similar (Fig 2B).


Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins.

Stetz G, Verkhivker GM - PLoS ONE (2015)

The Structures and Domain Organization of Functional States in DnaK and Sse1p Chaperones.A solution structure of an ADP-bound DnaK (pdb id 2KHO) (A) and the crystal structure of an ATP-bound DnaK (pdb id 4B9Q) (B). The structures are shown in a ribbon representation and main structural elements are annotated. The NBD subdomains are colored as follows: IA (in blue), IB (in red), IIA (in green), IIB (in cyan), the inter-domain linker (in black), SBD-α (in magenta), and SBD-β (in orange). (C) The crystal structure of the yeast Hsp110 (Sse1p) in a complex with ATP (pdb id 2QXL). (D) The crystal structure of Sse1p in a complex with the NBD of hHsp70 (pdb id 3D2F). The structures are shown in a ribbon representation and main structural elements are annotated and colored as in DnaK. The Sse1p insert in Sse1p-ATP structure is shown in yellow (C) and the NBD of hHsp70 in the Sse1p-Hsp70 complex is shown in pink (D).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4664246&req=5

pone.0143752.g002: The Structures and Domain Organization of Functional States in DnaK and Sse1p Chaperones.A solution structure of an ADP-bound DnaK (pdb id 2KHO) (A) and the crystal structure of an ATP-bound DnaK (pdb id 4B9Q) (B). The structures are shown in a ribbon representation and main structural elements are annotated. The NBD subdomains are colored as follows: IA (in blue), IB (in red), IIA (in green), IIB (in cyan), the inter-domain linker (in black), SBD-α (in magenta), and SBD-β (in orange). (C) The crystal structure of the yeast Hsp110 (Sse1p) in a complex with ATP (pdb id 2QXL). (D) The crystal structure of Sse1p in a complex with the NBD of hHsp70 (pdb id 3D2F). The structures are shown in a ribbon representation and main structural elements are annotated and colored as in DnaK. The Sse1p insert in Sse1p-ATP structure is shown in yellow (C) and the NBD of hHsp70 in the Sse1p-Hsp70 complex is shown in pink (D).
Mentions: A significant breakthrough in mechanistic characterization of the Hsp70 chaperone cycle has been made in a series of pioneering structure-functional studies of DnaK that have unveiled for the first time the molecular details of the full-length Hsp70 constructs in the major functional states: nucleotide-free and ADP-bound [31–33], ATP-bound [34,35], and ATP/substrate-bound [36]. The solution NMR structure of the full-length DnaK in the ADP-bound and substrate-bound state (Fig 2A) has confirmed that the NBD, SBD and the inter-domain linker are only weakly bound and move independently, engaging in random collisions on surfaces of the subdomains IA and IIA [31]. NMR studies have also elucidated how ATP binding can facilitate conformational transitions and allosteric communication between radically different functional states. Chemical-shift perturbation patterns for different DnaK states (ligand-bound and apo) and two different inter-domain linker constructs have shown that ATP binding may cause global structural reorganization of the NBD conformation via subtle subdomain motions, bringing the SBD and NBD in a close proximity to enable the inter-domain communication [32]. A solution NMR study of the Hsp70-NBD from Thermus thermophilus, in the ADP and AMP-PNP states has identified similar cooperative rotations of the NBD subdomains upon nucleotide exchange [33]. The crystal structures of a full-length two-domain DnaK in the ATP-bound, domain-docked conformation (Fig 2B) were solved independently using different protein engineering strategies to reduce the intrinsic flexibility of Hsp70 and induce favorable crystallization conditions [34,35]. By introducing a disulfide bridge between the SBD-α and NBD, the crystal structure of the ATP-bound DnaK was obtained, in which the SBD-β and the SBD-α subdomains are docked to the NBD [34]. Another crystal structure of an ATP-bound DnaK has been determined with a shortened L3,4 loop of the SBD-β [35]. Despite these differences in constructs, the underlying molecular details of the ATP-bound DnaK structures are extremely similar (Fig 2B).

Bottom Line: The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions.We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications.This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones.

View Article: PubMed Central - PubMed

Affiliation: Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America.

ABSTRACT
Hsp70 and Hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. Although many aspects of allosteric regulatory mechanisms in Hsp70 and Hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. In this work, we have combined molecular dynamics simulations and protein stability analysis of the chaperone structures with the network modeling of residue interaction networks to characterize molecular determinants of allosteric mechanisms. We have shown that allosteric mechanisms of Hsp70 and Hsp110 chaperones may be primarily determined by nucleotide-induced redistribution of local conformational ensembles in the inter-domain regions and the substrate binding domain. Conformational dynamics and energetics of the peptide substrate binding with the Hsp70 structures has been analyzed using free energy calculations, revealing allosteric hotspots that control negative cooperativity between regulatory sites. The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions. A smaller allosteric network in Hsp110 structures may elicit an entropy-driven allostery that occurs in the absence of global structural changes. We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications. The network-centric analysis of allosteric interactions has also established that centrality of functional residues could correlate with their sensitivity to mutations across diverse chaperone functions. This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones.

Show MeSH
Related in: MedlinePlus