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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

Analysis of High Centrality Residues in Sse1p Structures.Structural mapping of common peaks in the force constant and network centrality distributions onto Sse1p conformations (A, B). The structures are shown in a ribbon representation and main structural elements, including subdomains and functional residues are annotated and colored according to the adopted scheme. The functional residues of high centrality are shown in spheres and colored according to their respective subdomains. Structural positions of high centrality functional residues are indicated by arrows. The probability distributions of residue centrality in the Sse1p-ATP (C) and Sse1p in a complex with the NBD of hHsp70 (D). These profiles were obtained from MD trajectories by averaging computations of residue centrality over all protein residues in the conformational ensembles.
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pone.0143752.g014: Analysis of High Centrality Residues in Sse1p Structures.Structural mapping of common peaks in the force constant and network centrality distributions onto Sse1p conformations (A, B). The structures are shown in a ribbon representation and main structural elements, including subdomains and functional residues are annotated and colored according to the adopted scheme. The functional residues of high centrality are shown in spheres and colored according to their respective subdomains. Structural positions of high centrality functional residues are indicated by arrows. The probability distributions of residue centrality in the Sse1p-ATP (C) and Sse1p in a complex with the NBD of hHsp70 (D). These profiles were obtained from MD trajectories by averaging computations of residue centrality over all protein residues in the conformational ensembles.

Mentions: Using the results of MD simulations, we also constructed the force constant and residue centrality profiles for ATP-bound Sse1p (Fig 13A and 13B) and Sse1p-hHsp70 complex (Fig 13C and 13D). Despite seemingly similar distributions obtained for DnaK and Sse1p structures, a close inspection revealed subtle but important differences that may be associated with variations of allosteric mechanisms adopted by these chaperones. The central observation of this analysis was the markedly reduced residue centrality and disappearance of hinge sites in the SBD-β subdomain, which reflected the increased conformational flexibility in this region. At the same time, subdomains in the NBD appeared to be increasingly rigid, which may affect global movements in the IA-IIA cleft and rotational motions of subdomain IIB, which are required for nucleotide-dependent allostery. Interestingly, the distribution peaks migrated to residues from subdomain IA, IB and SBD-α (Fig 13). Structural mapping of high centrality residues on Sse1p conformations (Fig 14A and 14B) could illustrate a noticeable shift in the allocation of mediating sites. Among high centrality residues in Sse1p structures were K69, R70 from the nucleotide-binding site (subdomain IB); residues from subdomain IA that are important for catalytic activity (P146, E152, Q153, R154, W148,Y149); A120, F122, I163 (subdomain IA) and a group of SBD-α residues (L747, I557, M558, Q560,D561). These residues are often interconnected through hydrogen bonding and specific interactions. In particular, hydrogen bonding between catalytic residue K69 and Q153 bridges subdomains IA and IB. Some of these residues (R47, I163, and M557) are located at the NBD-SBDα interface. These results supported the notion that the integrity of the NBD-SBDα interface may be vital for Sse1p function as mutations in these positions I163D, M557S, M557D can abolish chaperone activity. [53,56].


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)

Analysis of High Centrality Residues in Sse1p Structures.Structural mapping of common peaks in the force constant and network centrality distributions onto Sse1p conformations (A, B). The structures are shown in a ribbon representation and main structural elements, including subdomains and functional residues are annotated and colored according to the adopted scheme. The functional residues of high centrality are shown in spheres and colored according to their respective subdomains. Structural positions of high centrality functional residues are indicated by arrows. The probability distributions of residue centrality in the Sse1p-ATP (C) and Sse1p in a complex with the NBD of hHsp70 (D). These profiles were obtained from MD trajectories by averaging computations of residue centrality over all protein residues in the conformational ensembles.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0143752.g014: Analysis of High Centrality Residues in Sse1p Structures.Structural mapping of common peaks in the force constant and network centrality distributions onto Sse1p conformations (A, B). The structures are shown in a ribbon representation and main structural elements, including subdomains and functional residues are annotated and colored according to the adopted scheme. The functional residues of high centrality are shown in spheres and colored according to their respective subdomains. Structural positions of high centrality functional residues are indicated by arrows. The probability distributions of residue centrality in the Sse1p-ATP (C) and Sse1p in a complex with the NBD of hHsp70 (D). These profiles were obtained from MD trajectories by averaging computations of residue centrality over all protein residues in the conformational ensembles.
Mentions: Using the results of MD simulations, we also constructed the force constant and residue centrality profiles for ATP-bound Sse1p (Fig 13A and 13B) and Sse1p-hHsp70 complex (Fig 13C and 13D). Despite seemingly similar distributions obtained for DnaK and Sse1p structures, a close inspection revealed subtle but important differences that may be associated with variations of allosteric mechanisms adopted by these chaperones. The central observation of this analysis was the markedly reduced residue centrality and disappearance of hinge sites in the SBD-β subdomain, which reflected the increased conformational flexibility in this region. At the same time, subdomains in the NBD appeared to be increasingly rigid, which may affect global movements in the IA-IIA cleft and rotational motions of subdomain IIB, which are required for nucleotide-dependent allostery. Interestingly, the distribution peaks migrated to residues from subdomain IA, IB and SBD-α (Fig 13). Structural mapping of high centrality residues on Sse1p conformations (Fig 14A and 14B) could illustrate a noticeable shift in the allocation of mediating sites. Among high centrality residues in Sse1p structures were K69, R70 from the nucleotide-binding site (subdomain IB); residues from subdomain IA that are important for catalytic activity (P146, E152, Q153, R154, W148,Y149); A120, F122, I163 (subdomain IA) and a group of SBD-α residues (L747, I557, M558, Q560,D561). These residues are often interconnected through hydrogen bonding and specific interactions. In particular, hydrogen bonding between catalytic residue K69 and Q153 bridges subdomains IA and IB. Some of these residues (R47, I163, and M557) are located at the NBD-SBDα interface. These results supported the notion that the integrity of the NBD-SBDα interface may be vital for Sse1p function as mutations in these positions I163D, M557S, M557D can abolish chaperone activity. [53,56].

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