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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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Conformational Dynamics of DnaK and Sse1p Functional States.The computed B-factors obtained from 500 ns MD simulations of the solution structure of an ADP-bound DnaK (pdb id 2KHO) (A); the crystal structure of an ATP-bound DnaK (pdb id 4B9Q) (B); the crystal structure of a Sse1p-ATP (pdb id 2QXL) (C); and the crystal structure of Sse1p in a complex with the NBD of hHsp70 (pdb id 3D2F) (D). The thermal fluctuations are shown only for DnaK and Sse1p residues (B-factors of the hHsp70-NBD counterpart of Sse1p are omitted for clarity and uniformity of presentation). Equilibrium residue fluctuations are annotated and colored according to the adopted coloring scheme of the chaperone subdomains: 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).
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pone.0143752.g003: Conformational Dynamics of DnaK and Sse1p Functional States.The computed B-factors obtained from 500 ns MD simulations of the solution structure of an ADP-bound DnaK (pdb id 2KHO) (A); the crystal structure of an ATP-bound DnaK (pdb id 4B9Q) (B); the crystal structure of a Sse1p-ATP (pdb id 2QXL) (C); and the crystal structure of Sse1p in a complex with the NBD of hHsp70 (pdb id 3D2F) (D). The thermal fluctuations are shown only for DnaK and Sse1p residues (B-factors of the hHsp70-NBD counterpart of Sse1p are omitted for clarity and uniformity of presentation). Equilibrium residue fluctuations are annotated and colored according to the adopted coloring scheme of the chaperone subdomains: 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).

Mentions: All-atom MD simulations of DnaK in the ADP-bound (Fig 2A) and ATP-bound forms (Fig 2B) (500 ns for each system) were combined with the structural stability analysis to quantify conformational changes induced by the nucleotide binding. To provide a direct comparison of conformational ensembles for DnaK and Sse1p chaperones, we also conducted 500 ns MD simulations of the crystal structures of the ATP-bound Sse1p [53] and ATP-bound Sse1p complex with the NBD of human Hsp70 [56]. In simulations of the ADP-DnaK, we observed a significant conformational heterogeneity that was manifested across all subdomains (Fig 3A). Conformational fluctuations were observed in the NBD subdomains, with especially large movements in the subdomain IIB and the SBD-α subdomain (often termed as the α-helical “lid”). Although the SBD-α lid remained stably bound to the SBD-β subdomain during MD simulations of the ADP-DnaK, we detected appreciable, though rather short-lived excursions of the lid, largely involving rigid body motions around the SBD-β (Fig 3A). In these conformations, the SBD-α explored different lid orientations with respect to the SBD-β, probing intermediate states that were previously observed in solution NMR studies [31], electron paramagnetic resonance spectroscopy [40] and single molecule fluorescence spectroscopy [41]. Conformational dynamics of the ADP-DnaK also revealed larger movements of subdomains IIB and SBD-α as evident from the computed B-factors (Fig 3A). In the ATP-bound DnaK, conformational dynamics was characterized by smaller fluctuations of the NBD residues, reflecting structural tightening of the ATP-binding site and the NBD core (Fig 3B).


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)

Conformational Dynamics of DnaK and Sse1p Functional States.The computed B-factors obtained from 500 ns MD simulations of the solution structure of an ADP-bound DnaK (pdb id 2KHO) (A); the crystal structure of an ATP-bound DnaK (pdb id 4B9Q) (B); the crystal structure of a Sse1p-ATP (pdb id 2QXL) (C); and the crystal structure of Sse1p in a complex with the NBD of hHsp70 (pdb id 3D2F) (D). The thermal fluctuations are shown only for DnaK and Sse1p residues (B-factors of the hHsp70-NBD counterpart of Sse1p are omitted for clarity and uniformity of presentation). Equilibrium residue fluctuations are annotated and colored according to the adopted coloring scheme of the chaperone subdomains: 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).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0143752.g003: Conformational Dynamics of DnaK and Sse1p Functional States.The computed B-factors obtained from 500 ns MD simulations of the solution structure of an ADP-bound DnaK (pdb id 2KHO) (A); the crystal structure of an ATP-bound DnaK (pdb id 4B9Q) (B); the crystal structure of a Sse1p-ATP (pdb id 2QXL) (C); and the crystal structure of Sse1p in a complex with the NBD of hHsp70 (pdb id 3D2F) (D). The thermal fluctuations are shown only for DnaK and Sse1p residues (B-factors of the hHsp70-NBD counterpart of Sse1p are omitted for clarity and uniformity of presentation). Equilibrium residue fluctuations are annotated and colored according to the adopted coloring scheme of the chaperone subdomains: 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).
Mentions: All-atom MD simulations of DnaK in the ADP-bound (Fig 2A) and ATP-bound forms (Fig 2B) (500 ns for each system) were combined with the structural stability analysis to quantify conformational changes induced by the nucleotide binding. To provide a direct comparison of conformational ensembles for DnaK and Sse1p chaperones, we also conducted 500 ns MD simulations of the crystal structures of the ATP-bound Sse1p [53] and ATP-bound Sse1p complex with the NBD of human Hsp70 [56]. In simulations of the ADP-DnaK, we observed a significant conformational heterogeneity that was manifested across all subdomains (Fig 3A). Conformational fluctuations were observed in the NBD subdomains, with especially large movements in the subdomain IIB and the SBD-α subdomain (often termed as the α-helical “lid”). Although the SBD-α lid remained stably bound to the SBD-β subdomain during MD simulations of the ADP-DnaK, we detected appreciable, though rather short-lived excursions of the lid, largely involving rigid body motions around the SBD-β (Fig 3A). In these conformations, the SBD-α explored different lid orientations with respect to the SBD-β, probing intermediate states that were previously observed in solution NMR studies [31], electron paramagnetic resonance spectroscopy [40] and single molecule fluorescence spectroscopy [41]. Conformational dynamics of the ADP-DnaK also revealed larger movements of subdomains IIB and SBD-α as evident from the computed B-factors (Fig 3A). In the ATP-bound DnaK, conformational dynamics was characterized by smaller fluctuations of the NBD residues, reflecting structural tightening of the ATP-binding site and the NBD core (Fig 3B).

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