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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 Functional Cycle of Hsp70 Chaperones.The functional cycle of Hsp70 chaperones. The main steps of the allosteric cycle include the nucleotide exchange in the closed, ADP-bound form (pdb id 2KHO); the formation of partially undocked ATP/substrate-bound intermediate; substrate release and formation of the domain-docked ATP-bound form (pdb id 4B9Q, 4JNE); substrate binding and partial domain undocking in the ATP/substrate-bound state; ATP hydrolysis and stabilization of the domain-undocked, ADP-bound form. The structures are shown in a surface representation and the 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). The inter-domain interfaces NBD/SBD-β, NBD/SBD-α and SBD-β/SBD-α form allosteric hotspots of the Hsp70 functional cycle that are modulated through binding of nucleotides and substrates. The Pymol program was used for rendering protein structures (The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, and LLC).
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pone.0143752.g001: The Functional Cycle of Hsp70 Chaperones.The functional cycle of Hsp70 chaperones. The main steps of the allosteric cycle include the nucleotide exchange in the closed, ADP-bound form (pdb id 2KHO); the formation of partially undocked ATP/substrate-bound intermediate; substrate release and formation of the domain-docked ATP-bound form (pdb id 4B9Q, 4JNE); substrate binding and partial domain undocking in the ATP/substrate-bound state; ATP hydrolysis and stabilization of the domain-undocked, ADP-bound form. The structures are shown in a surface representation and the 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). The inter-domain interfaces NBD/SBD-β, NBD/SBD-α and SBD-β/SBD-α form allosteric hotspots of the Hsp70 functional cycle that are modulated through binding of nucleotides and substrates. The Pymol program was used for rendering protein structures (The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, and LLC).

Mentions: The 70-kilodalton (kDa) Heat shock protein (Hsp70) belongs to a ubiquitous and abundant family of molecular chaperones that play an important role in various cellular processes that involve protein folding, protein quality control and stabilization, trafficking, and turnover [1–7]. Hsp70 proteins occur in all domains of life and are among most conserved proteins found in all organisms. Deregulations of signal transduction pathways are often linked to the Hsp70-regulated processes, and viability of Hsp70 as an attractive and validated drug target has been firmly established [8–12]. Each Hsp70 has two functional domains: a nucleotide-binding domain (NBD), which binds and hydrolyzes ATP, and a substrate-binding domain (SBD), which binds extended polypeptides and client proteins [5–7]. Hsp70 functions are governed by the nucleotide-dependent allosteric cycle between an ATP-bound (open) and ADP-bound (closed) chaperone states, in which ATP binding in the NBD dramatically reduces the affinity for peptide substrates by accelerating binding and release rates in the SBD (Fig 1). ATP hydrolysis can restore Hsp70 to the high-affinity state, but is slow in the absence of substrates and co-chaperone proteins. This biochemical cycle involves a cascade of allosteric conformational changes (Fig 1), in which ATP binding and hydrolysis regulate binding thermodynamics and kinetics of substrate peptides with the SBD [5–7].


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 Functional Cycle of Hsp70 Chaperones.The functional cycle of Hsp70 chaperones. The main steps of the allosteric cycle include the nucleotide exchange in the closed, ADP-bound form (pdb id 2KHO); the formation of partially undocked ATP/substrate-bound intermediate; substrate release and formation of the domain-docked ATP-bound form (pdb id 4B9Q, 4JNE); substrate binding and partial domain undocking in the ATP/substrate-bound state; ATP hydrolysis and stabilization of the domain-undocked, ADP-bound form. The structures are shown in a surface representation and the 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). The inter-domain interfaces NBD/SBD-β, NBD/SBD-α and SBD-β/SBD-α form allosteric hotspots of the Hsp70 functional cycle that are modulated through binding of nucleotides and substrates. The Pymol program was used for rendering protein structures (The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, and LLC).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0143752.g001: The Functional Cycle of Hsp70 Chaperones.The functional cycle of Hsp70 chaperones. The main steps of the allosteric cycle include the nucleotide exchange in the closed, ADP-bound form (pdb id 2KHO); the formation of partially undocked ATP/substrate-bound intermediate; substrate release and formation of the domain-docked ATP-bound form (pdb id 4B9Q, 4JNE); substrate binding and partial domain undocking in the ATP/substrate-bound state; ATP hydrolysis and stabilization of the domain-undocked, ADP-bound form. The structures are shown in a surface representation and the 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). The inter-domain interfaces NBD/SBD-β, NBD/SBD-α and SBD-β/SBD-α form allosteric hotspots of the Hsp70 functional cycle that are modulated through binding of nucleotides and substrates. The Pymol program was used for rendering protein structures (The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, and LLC).
Mentions: The 70-kilodalton (kDa) Heat shock protein (Hsp70) belongs to a ubiquitous and abundant family of molecular chaperones that play an important role in various cellular processes that involve protein folding, protein quality control and stabilization, trafficking, and turnover [1–7]. Hsp70 proteins occur in all domains of life and are among most conserved proteins found in all organisms. Deregulations of signal transduction pathways are often linked to the Hsp70-regulated processes, and viability of Hsp70 as an attractive and validated drug target has been firmly established [8–12]. Each Hsp70 has two functional domains: a nucleotide-binding domain (NBD), which binds and hydrolyzes ATP, and a substrate-binding domain (SBD), which binds extended polypeptides and client proteins [5–7]. Hsp70 functions are governed by the nucleotide-dependent allosteric cycle between an ATP-bound (open) and ADP-bound (closed) chaperone states, in which ATP binding in the NBD dramatically reduces the affinity for peptide substrates by accelerating binding and release rates in the SBD (Fig 1). ATP hydrolysis can restore Hsp70 to the high-affinity state, but is slow in the absence of substrates and co-chaperone proteins. This biochemical cycle involves a cascade of allosteric conformational changes (Fig 1), in which ATP binding and hydrolysis regulate binding thermodynamics and kinetics of substrate peptides with the SBD [5–7].

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