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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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Related in: MedlinePlus

The Residue Depth Profiles in the DnaK States: Structural Mapping and Comparison with the HDX Experiments.The computed RD profiles are compared with the HDX experiments, showing nucleotide-induced protection of functional regions. The effect of nucleotide binding is evaluated using differential plots of the RD profiles between the ATP-DnaK and ADP-DnaK (A). The profiles are shown as bars and colored according to the adopted scheme as in Fig 8. (B) The differential RD values are shown only for the SBD-β subdomain (orange bars) and RD values for residues with the experimentally known HDX peak intensity ratios between ATP-DnaK and ADP- DnaK are highlighted in marron bars. (C) The experimental values of the HDX peak intensity ratios between ATP-DnaK and ADP-DnaK [27]. Residues that are more protected in the ATP-DnaK (HDX peak ratio > 1.1) are shown in blue bars, and residues that are more protected in the ADP-DnaK form (HDX peak intensity ratio < 1.0) are shown in red bars. This annotation is based on the HDX peak assignments as prescribed in [27]. (D). Structural mapping of the ATP-DnaK protected residues depicted in blue spheres and annotated. (E) Structural mapping of the ADP-DnaK protected residues shown in red spheres and annotated. The SBD-β subdomain is shown in orange ribbons. The substrate binding loops L1,2 loop (residues 404–406), L3,4 loop (residues 428–434), and L5,6 loop (residues 458–473) are indicated.
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pone.0143752.g010: The Residue Depth Profiles in the DnaK States: Structural Mapping and Comparison with the HDX Experiments.The computed RD profiles are compared with the HDX experiments, showing nucleotide-induced protection of functional regions. The effect of nucleotide binding is evaluated using differential plots of the RD profiles between the ATP-DnaK and ADP-DnaK (A). The profiles are shown as bars and colored according to the adopted scheme as in Fig 8. (B) The differential RD values are shown only for the SBD-β subdomain (orange bars) and RD values for residues with the experimentally known HDX peak intensity ratios between ATP-DnaK and ADP- DnaK are highlighted in marron bars. (C) The experimental values of the HDX peak intensity ratios between ATP-DnaK and ADP-DnaK [27]. Residues that are more protected in the ATP-DnaK (HDX peak ratio > 1.1) are shown in blue bars, and residues that are more protected in the ADP-DnaK form (HDX peak intensity ratio < 1.0) are shown in red bars. This annotation is based on the HDX peak assignments as prescribed in [27]. (D). Structural mapping of the ATP-DnaK protected residues depicted in blue spheres and annotated. (E) Structural mapping of the ADP-DnaK protected residues shown in red spheres and annotated. The SBD-β subdomain is shown in orange ribbons. The substrate binding loops L1,2 loop (residues 404–406), L3,4 loop (residues 428–434), and L5,6 loop (residues 458–473) are indicated.

Mentions: The RD profiles in DnaK structures (Fig 9A and 9B) showed the larger values and greater protection level for subdomains IA, IB, and IIA, mostly for stable regions near the nucleotide binding site and the inter-domain interfaces. According to this analysis, the average RD values of the SBD-β residues were generally smaller, especially in the domain-docked ATP-DnaK (Fig 9B) reflecting the enhanced dynamics and structural changes of substrate binding loops of the SBD-β. Instructively, the RD values of the hydrophobic core residues I438, V440, L454 and L484 were much larger, indicating that these residues remained structurally stable and protected from solvent exchange. To provide a comparison with the HDX data [27, 28], we analyzed the differential RD profiles that reveal which residues could be more protected in the ATP-bound or ADP-bound forms. The high RD values (greater protection) of the NBD residues and small RD values (low protection) of the substrate binding loops was observed in the ATP-DnaK (Fig 10A). According to the HDX experiments, the SBD fragments 413–437 and 439–457 exchanged amide protons more rapidly in the ATP-bound state as compared with the nucleotide-free DnaK form [28].


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 Residue Depth Profiles in the DnaK States: Structural Mapping and Comparison with the HDX Experiments.The computed RD profiles are compared with the HDX experiments, showing nucleotide-induced protection of functional regions. The effect of nucleotide binding is evaluated using differential plots of the RD profiles between the ATP-DnaK and ADP-DnaK (A). The profiles are shown as bars and colored according to the adopted scheme as in Fig 8. (B) The differential RD values are shown only for the SBD-β subdomain (orange bars) and RD values for residues with the experimentally known HDX peak intensity ratios between ATP-DnaK and ADP- DnaK are highlighted in marron bars. (C) The experimental values of the HDX peak intensity ratios between ATP-DnaK and ADP-DnaK [27]. Residues that are more protected in the ATP-DnaK (HDX peak ratio > 1.1) are shown in blue bars, and residues that are more protected in the ADP-DnaK form (HDX peak intensity ratio < 1.0) are shown in red bars. This annotation is based on the HDX peak assignments as prescribed in [27]. (D). Structural mapping of the ATP-DnaK protected residues depicted in blue spheres and annotated. (E) Structural mapping of the ADP-DnaK protected residues shown in red spheres and annotated. The SBD-β subdomain is shown in orange ribbons. The substrate binding loops L1,2 loop (residues 404–406), L3,4 loop (residues 428–434), and L5,6 loop (residues 458–473) are indicated.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0143752.g010: The Residue Depth Profiles in the DnaK States: Structural Mapping and Comparison with the HDX Experiments.The computed RD profiles are compared with the HDX experiments, showing nucleotide-induced protection of functional regions. The effect of nucleotide binding is evaluated using differential plots of the RD profiles between the ATP-DnaK and ADP-DnaK (A). The profiles are shown as bars and colored according to the adopted scheme as in Fig 8. (B) The differential RD values are shown only for the SBD-β subdomain (orange bars) and RD values for residues with the experimentally known HDX peak intensity ratios between ATP-DnaK and ADP- DnaK are highlighted in marron bars. (C) The experimental values of the HDX peak intensity ratios between ATP-DnaK and ADP-DnaK [27]. Residues that are more protected in the ATP-DnaK (HDX peak ratio > 1.1) are shown in blue bars, and residues that are more protected in the ADP-DnaK form (HDX peak intensity ratio < 1.0) are shown in red bars. This annotation is based on the HDX peak assignments as prescribed in [27]. (D). Structural mapping of the ATP-DnaK protected residues depicted in blue spheres and annotated. (E) Structural mapping of the ADP-DnaK protected residues shown in red spheres and annotated. The SBD-β subdomain is shown in orange ribbons. The substrate binding loops L1,2 loop (residues 404–406), L3,4 loop (residues 428–434), and L5,6 loop (residues 458–473) are indicated.
Mentions: The RD profiles in DnaK structures (Fig 9A and 9B) showed the larger values and greater protection level for subdomains IA, IB, and IIA, mostly for stable regions near the nucleotide binding site and the inter-domain interfaces. According to this analysis, the average RD values of the SBD-β residues were generally smaller, especially in the domain-docked ATP-DnaK (Fig 9B) reflecting the enhanced dynamics and structural changes of substrate binding loops of the SBD-β. Instructively, the RD values of the hydrophobic core residues I438, V440, L454 and L484 were much larger, indicating that these residues remained structurally stable and protected from solvent exchange. To provide a comparison with the HDX data [27, 28], we analyzed the differential RD profiles that reveal which residues could be more protected in the ATP-bound or ADP-bound forms. The high RD values (greater protection) of the NBD residues and small RD values (low protection) of the substrate binding loops was observed in the ATP-DnaK (Fig 10A). According to the HDX experiments, the SBD fragments 413–437 and 439–457 exchanged amide protons more rapidly in the ATP-bound state as compared with the nucleotide-free DnaK form [28].

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