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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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Network Analysis of Functional Effects in Sse1p Mutants.Correlations between residue centrality and different functional effects caused by clusters of mutations in Sse1p. (A, B) The relationship between residue centrality in the Sse1p complex with Hsp70 (pdb id 3D2F) and rates of the nucleotide exchange induced by Sse1p mutants. (C, D) The relationship between residue centrality in the Sse1p complex and binding affinities of Sse1p mutants measured in [53]. The clusters of mutations are annotated as in the original experimental study [53]: Sse1-1 (K69M); Sse1-2 (N572Y,E575A); Sse1-3 (A280T,N281A); Sse1-4 (T365V, N367S); Sse1-5 (F392A, F394A); Sse1-6 (D396A); Sse1-7 (L489A, H490A); Sse1-8 (E554A, M557S, L558S); Sse1-9 (L433A, N434P); Sse1-10 (F439L, M441A). To account for clusters of mutations, used in the experiments, we computed the average betweenness value over all residues in a given cluster.
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pone.0143752.g015: Network Analysis of Functional Effects in Sse1p Mutants.Correlations between residue centrality and different functional effects caused by clusters of mutations in Sse1p. (A, B) The relationship between residue centrality in the Sse1p complex with Hsp70 (pdb id 3D2F) and rates of the nucleotide exchange induced by Sse1p mutants. (C, D) The relationship between residue centrality in the Sse1p complex and binding affinities of Sse1p mutants measured in [53]. The clusters of mutations are annotated as in the original experimental study [53]: Sse1-1 (K69M); Sse1-2 (N572Y,E575A); Sse1-3 (A280T,N281A); Sse1-4 (T365V, N367S); Sse1-5 (F392A, F394A); Sse1-6 (D396A); Sse1-7 (L489A, H490A); Sse1-8 (E554A, M557S, L558S); Sse1-9 (L433A, N434P); Sse1-10 (F439L, M441A). To account for clusters of mutations, used in the experiments, we computed the average betweenness value over all residues in a given cluster.

Mentions: To compare force constant and network-based predictions of regulatory residues with the experiments, we utilized a significant body of mutational data obtained for Sse1p-Ssa1 complex analyzed them in different functional assays [56]. These mutations were originally designed to target the nucleotide binding pocket, the inter-domain surface areas and the substrate-binding site. Instead of single substitutions, these experiments probed clusters of mutations in a given region to disrupt the interaction sites. A comprehensive analysis would require conducting independent MD simulations for all studied mutants. We elected to simplify our task and perform a direct mapping of mutational sites onto the residue centrality profile of the Sse1p-hHsp70-NBD complex (Fig 15). These network indices were correlated against various functional measurements [56]. In particular, we analyzed how network properties of functional residues may be related to the nucleotide exchange induced by Sse1p mutant proteins in Ssa1 (Fig 15A and 15B), and binding interactions of Sse1p mutants with Ssa1 (Fig 15C and 15D). Strikingly, it appeared that residue network centrality may be associated with the susceptibility of various Sse1p functions to mutations. For instance, high network centrality was found for residues in the Sse1-2 cluster (N572, E575) and Sse1-8 cluster (E554, M557, L558). Accordingly, mutations of these residues could lead to a pronounced growth defect and impaired nucleotide exchange on Hsp70, which is a central function of Sse1p [56]. A simple mapping of functional changes caused by Sse1p mutations against network properties produced a reasonable correlation and identified functionally important residue clusters. These results indicated that residue centrality may be used as a metric for differentiating functional importance of mutational effects across various chaperone functions.


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)

Network Analysis of Functional Effects in Sse1p Mutants.Correlations between residue centrality and different functional effects caused by clusters of mutations in Sse1p. (A, B) The relationship between residue centrality in the Sse1p complex with Hsp70 (pdb id 3D2F) and rates of the nucleotide exchange induced by Sse1p mutants. (C, D) The relationship between residue centrality in the Sse1p complex and binding affinities of Sse1p mutants measured in [53]. The clusters of mutations are annotated as in the original experimental study [53]: Sse1-1 (K69M); Sse1-2 (N572Y,E575A); Sse1-3 (A280T,N281A); Sse1-4 (T365V, N367S); Sse1-5 (F392A, F394A); Sse1-6 (D396A); Sse1-7 (L489A, H490A); Sse1-8 (E554A, M557S, L558S); Sse1-9 (L433A, N434P); Sse1-10 (F439L, M441A). To account for clusters of mutations, used in the experiments, we computed the average betweenness value over all residues in a given cluster.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0143752.g015: Network Analysis of Functional Effects in Sse1p Mutants.Correlations between residue centrality and different functional effects caused by clusters of mutations in Sse1p. (A, B) The relationship between residue centrality in the Sse1p complex with Hsp70 (pdb id 3D2F) and rates of the nucleotide exchange induced by Sse1p mutants. (C, D) The relationship between residue centrality in the Sse1p complex and binding affinities of Sse1p mutants measured in [53]. The clusters of mutations are annotated as in the original experimental study [53]: Sse1-1 (K69M); Sse1-2 (N572Y,E575A); Sse1-3 (A280T,N281A); Sse1-4 (T365V, N367S); Sse1-5 (F392A, F394A); Sse1-6 (D396A); Sse1-7 (L489A, H490A); Sse1-8 (E554A, M557S, L558S); Sse1-9 (L433A, N434P); Sse1-10 (F439L, M441A). To account for clusters of mutations, used in the experiments, we computed the average betweenness value over all residues in a given cluster.
Mentions: To compare force constant and network-based predictions of regulatory residues with the experiments, we utilized a significant body of mutational data obtained for Sse1p-Ssa1 complex analyzed them in different functional assays [56]. These mutations were originally designed to target the nucleotide binding pocket, the inter-domain surface areas and the substrate-binding site. Instead of single substitutions, these experiments probed clusters of mutations in a given region to disrupt the interaction sites. A comprehensive analysis would require conducting independent MD simulations for all studied mutants. We elected to simplify our task and perform a direct mapping of mutational sites onto the residue centrality profile of the Sse1p-hHsp70-NBD complex (Fig 15). These network indices were correlated against various functional measurements [56]. In particular, we analyzed how network properties of functional residues may be related to the nucleotide exchange induced by Sse1p mutant proteins in Ssa1 (Fig 15A and 15B), and binding interactions of Sse1p mutants with Ssa1 (Fig 15C and 15D). Strikingly, it appeared that residue network centrality may be associated with the susceptibility of various Sse1p functions to mutations. For instance, high network centrality was found for residues in the Sse1-2 cluster (N572, E575) and Sse1-8 cluster (E554, M557, L558). Accordingly, mutations of these residues could lead to a pronounced growth defect and impaired nucleotide exchange on Hsp70, which is a central function of Sse1p [56]. A simple mapping of functional changes caused by Sse1p mutations against network properties produced a reasonable correlation and identified functionally important residue clusters. These results indicated that residue centrality may be used as a metric for differentiating functional importance of mutational effects across various chaperone functions.

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