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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 Protein Stability Analysis of Sse1p Structures.Protein stability changes ΔΔG are computed using a systematic alanine scanning. The protocol involved modification of the protein residues to alanine and computing the effect of each mutation on protein stability using FoldX (A,B) and DUET (C,D) methods respectively. The profiles are annotated using residue numbering in the crystal structure of ATP-Sse1p (pdb id 2QXL) for (A,C) and the crystal structure of ATP-Sse1p in a complex with the NBD of hHsp70 (pdb id 3D2F) for (B,D). The profiles are shown as bars colored according to the adopted scheme as in Fig 6.
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pone.0143752.g007: The Protein Stability Analysis of Sse1p Structures.Protein stability changes ΔΔG are computed using a systematic alanine scanning. The protocol involved modification of the protein residues to alanine and computing the effect of each mutation on protein stability using FoldX (A,B) and DUET (C,D) methods respectively. The profiles are annotated using residue numbering in the crystal structure of ATP-Sse1p (pdb id 2QXL) for (A,C) and the crystal structure of ATP-Sse1p in a complex with the NBD of hHsp70 (pdb id 3D2F) for (B,D). The profiles are shown as bars colored according to the adopted scheme as in Fig 6.

Mentions: Similarly to Dnak, mutations of functional residues in the Hsp110 (Sse1p) produced rather moderate changes in protein stability using both FoldX (Fig 7A and 7B) and DUET methods (Fig 7C and 7D). This is consistent with the experiments in which the CD spectra and thermal melting curves of the Sse1p mutants were similar to the Sse1p-WT in structure and stability [53]. Nonetheless, protein stability residue scanning in the Hsp110 (Sse1p) ATP-bound structures showed noticeably smaller free energy changes for the SBD-β residues as compared to other regions. This energetic analysis reflected the markedly enhanced dynamics of the substrate binding loops in Sse1p and the increased levels of structural rigidity in the SBD-β hydrophobic core residues. Our results also supported previous experimental hypotheses [57, 58], according to which nucleotide-based allosteric communication in Sse1p could be a primary example of entropy-driven cooperativity. This mechanism occurs through redistribution of local conformational ensembles and extensive dynamics exchanges in the SBD-β domain regions, without producing significant structural changes [94].


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 Protein Stability Analysis of Sse1p Structures.Protein stability changes ΔΔG are computed using a systematic alanine scanning. The protocol involved modification of the protein residues to alanine and computing the effect of each mutation on protein stability using FoldX (A,B) and DUET (C,D) methods respectively. The profiles are annotated using residue numbering in the crystal structure of ATP-Sse1p (pdb id 2QXL) for (A,C) and the crystal structure of ATP-Sse1p in a complex with the NBD of hHsp70 (pdb id 3D2F) for (B,D). The profiles are shown as bars colored according to the adopted scheme as in Fig 6.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0143752.g007: The Protein Stability Analysis of Sse1p Structures.Protein stability changes ΔΔG are computed using a systematic alanine scanning. The protocol involved modification of the protein residues to alanine and computing the effect of each mutation on protein stability using FoldX (A,B) and DUET (C,D) methods respectively. The profiles are annotated using residue numbering in the crystal structure of ATP-Sse1p (pdb id 2QXL) for (A,C) and the crystal structure of ATP-Sse1p in a complex with the NBD of hHsp70 (pdb id 3D2F) for (B,D). The profiles are shown as bars colored according to the adopted scheme as in Fig 6.
Mentions: Similarly to Dnak, mutations of functional residues in the Hsp110 (Sse1p) produced rather moderate changes in protein stability using both FoldX (Fig 7A and 7B) and DUET methods (Fig 7C and 7D). This is consistent with the experiments in which the CD spectra and thermal melting curves of the Sse1p mutants were similar to the Sse1p-WT in structure and stability [53]. Nonetheless, protein stability residue scanning in the Hsp110 (Sse1p) ATP-bound structures showed noticeably smaller free energy changes for the SBD-β residues as compared to other regions. This energetic analysis reflected the markedly enhanced dynamics of the substrate binding loops in Sse1p and the increased levels of structural rigidity in the SBD-β hydrophobic core residues. Our results also supported previous experimental hypotheses [57, 58], according to which nucleotide-based allosteric communication in Sse1p could be a primary example of entropy-driven cooperativity. This mechanism occurs through redistribution of local conformational ensembles and extensive dynamics exchanges in the SBD-β domain regions, without producing significant structural changes [94].

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