1
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The Link That Binds: The Linker of Hsp70 as a Helm of the Protein's Function. Biomolecules 2019; 9:biom9100543. [PMID: 31569820 PMCID: PMC6843406 DOI: 10.3390/biom9100543] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/13/2019] [Accepted: 09/21/2019] [Indexed: 12/26/2022] Open
Abstract
The heat shock 70 (Hsp70) family of molecular chaperones plays a central role in maintaining cellular proteostasis. Structurally, Hsp70s are composed of an N-terminal nucleotide binding domain (NBD) which exhibits ATPase activity, and a C-terminal substrate binding domain (SBD). The binding of ATP at the NBD and its subsequent hydrolysis influences the substrate binding affinity of the SBD through allostery. Similarly, peptide binding at the C-terminal SBD stimulates ATP hydrolysis by the N-terminal NBD. Interdomain communication between the NBD and SBD is facilitated by a conserved linker segment. Hsp70s form two main subgroups. Canonical Hsp70 members generally suppress protein aggregation and are also capable of refolding misfolded proteins. Hsp110 members are characterized by an extended lid segment and their function tends to be largely restricted to suppression of protein aggregation. In addition, the latter serve as nucleotide exchange factors (NEFs) of canonical Hsp70s. The linker of the Hsp110 family is less conserved compared to that of the canonical Hsp70 group. In addition, the linker plays a crucial role in defining the functional features of these two groups of Hsp70. Generally, the linker of Hsp70 is quite small and varies in size from seven to thirteen residues. Due to its small size, any sequence variation that Hsp70 exhibits in this motif has a major and unique influence on the function of the protein. Based on sequence data, we observed that canonical Hsp70s possess a linker that is distinct from similar segments present in Hsp110 proteins. In addition, Hsp110 linker motifs from various genera are distinct suggesting that their unique features regulate the flexibility with which the NBD and SBD of these proteins communicate via allostery. The Hsp70 linker modulates various structure-function features of Hsp70 such as its global conformation, affinity for peptide substrate and interaction with co-chaperones. The current review discusses how the unique features of the Hsp70 linker accounts for the functional specialization of this group of molecular chaperones.
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2
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English CA, Sherman W, Meng W, Gierasch LM. The Hsp70 interdomain linker is a dynamic switch that enables allosteric communication between two structured domains. J Biol Chem 2017; 292:14765-14774. [PMID: 28754691 DOI: 10.1074/jbc.m117.789313] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/19/2017] [Indexed: 12/20/2022] Open
Abstract
Hsp70 molecular chaperones play key roles in cellular protein homeostasis by binding to exposed hydrophobic regions of incompletely folded or aggregated proteins. This crucial Hsp70 function relies on allosteric communication between two well-structured domains: an N-terminal nucleotide-binding domain (NBD) and a C-terminal substrate-binding domain (SBD), which are tethered by an interdomain linker. ATP or ADP binding to the NBD alters the substrate-binding affinity of the SBD, triggering functionally essential cycles of substrate binding and release. The interdomain linker is a well-structured participant in the interdomain interface in ATP-bound Hsp70s. By contrast, in the ADP-bound state, exemplified by the Escherichia coli Hsp70 DnaK, the interdomain linker is flexible. Hsp70 interdomain linker sequences are highly conserved; moreover, mutations in this region compromise interdomain allostery. To better understand the role of this region in Hsp70 allostery, we used molecular dynamics simulations to explore the conformational landscape of the interdomain linker in ADP-bound DnaK and supported our simulations by strategic experimental data. We found that while the interdomain linker samples many conformations, it behaves as three relatively ordered segments connected by hinges. As a consequence, the distances and orientations between the NBD and SBD are limited. Additionally, the C-terminal region of the linker forms previously unreported, transient interactions with the SBD, and the predominant linker-docking site is available in only one allosteric state, that with high affinity for substrate. This preferential binding implicates the interdomain linker as a dynamic allosteric switch. The linker-binding site on the SBD is a potential target for small molecule modulators of the Hsp70 allosteric cycle.
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Affiliation(s)
| | - Woody Sherman
- From the Departments of Biochemistry and Molecular Biology and.,Schrödinger Inc., Cambridge, Massachusetts 02142.,Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 and
| | - Wenli Meng
- From the Departments of Biochemistry and Molecular Biology and
| | - Lila M Gierasch
- From the Departments of Biochemistry and Molecular Biology and .,Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 and
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3
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Stetz G, Verkhivker GM. Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication. PLoS Comput Biol 2017; 13:e1005299. [PMID: 28095400 PMCID: PMC5240922 DOI: 10.1371/journal.pcbi.1005299] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/06/2016] [Indexed: 12/28/2022] Open
Abstract
Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of allostery, we introduced a community-hopping model of allosteric communication. Atomistic reconstruction of signaling pathways in the DnaK structures captured a direction-specific mechanism and molecular details of signal transmission that are fully consistent with the mutagenesis experiments. The results of our study reconciled structural and functional experiments from a network-centric perspective by showing that global properties of the residue interaction networks and coevolutionary signatures may be linked with specificity and diversity of allosteric regulation mechanisms. The diversity of allosteric mechanisms in the Hsp70 proteins could range from modulation of the inter-domain interactions and conformational dynamics to fine-tuning of the Hsp70 interactions with co-chaperones. The goal of this study is to present a systematic computational analysis of the dynamic and evolutionary factors underlying allosteric structural transformations of the Hsp70 proteins. We investigated the relationship between functional dynamics, residue coevolution, and network organization of residue interactions in the Hsp70 proteins. The results of this study revealed that conformational dynamics of the Hsp70 proteins may be linked with coevolutionary propensities and mutual information dependencies of the protein residues. Modularity and connectivity of allosteric interactions in the Hsp70 chaperones are coordinated by stable functional sites that feature unique coevolutionary signatures and high network centrality. The emergence of the inter-domain communities that are coordinated by functional centers and include highly coevolving residues could facilitate structural transitions through cooperative reorganization of the local interacting modules. We determined that the differences in the modularity of the residue interactions and organization of coevolutionary networks in DnaK may be associated with variations in their allosteric mechanisms. The network signatures of the DnaK structures are characteristic of a population-shift allostery that allows for coordinated structural rearrangements of local communities. A dislocation of mediating centers and insufficient coevolutionary coupling between functional regions may render a reduced cooperativity and promote a limited entropy-driven allostery in the Sse1 chaperone that occurs without structural changes. The results of this study showed that a network-centric framework and a community-hopping model of allosteric communication pathways may provide novel insights into molecular and evolutionary principles of allosteric regulation in the Hsp70 proteins.
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Affiliation(s)
- Gabrielle Stetz
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Chapman University School of Pharmacy, Irvine, California, United States of America
- * E-mail:
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4
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Dantu SC, Khavnekar S, Kale A. Conformational dynamics of Peb4 exhibit “mother’s arms” chain model: a molecular dynamics study. J Biomol Struct Dyn 2016; 35:2186-2196. [DOI: 10.1080/07391102.2016.1209131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Sarath Chandra Dantu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sagar Khavnekar
- UM-DAE Centre for Excellence in Basic Science, University of Mumbai, Vidhyanagari Campus, Mumbai 400098, India
| | - Avinash Kale
- UM-DAE Centre for Excellence in Basic Science, University of Mumbai, Vidhyanagari Campus, Mumbai 400098, India
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5
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Nyakundi DO, Vuko LAM, Bentley SJ, Hoppe H, Blatch GL, Boshoff A. Plasmodium falciparum Hep1 Is Required to Prevent the Self Aggregation of PfHsp70-3. PLoS One 2016; 11:e0156446. [PMID: 27253881 PMCID: PMC4890766 DOI: 10.1371/journal.pone.0156446] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/14/2016] [Indexed: 11/29/2022] Open
Abstract
The majority of mitochondrial proteins are encoded in the nucleus and need to be imported from the cytosol into the mitochondria, and molecular chaperones play a key role in the efficient translocation and proper folding of these proteins in the matrix. One such molecular chaperone is the eukaryotic mitochondrial heat shock protein 70 (Hsp70); however, it is prone to self-aggregation and requires the presence of an essential zinc-finger protein, Hsp70-escort protein 1 (Hep1), to maintain its structure and function. PfHsp70-3, the only Hsp70 predicted to localize in the mitochondria of P. falciparum, may also rely on a Hep1 orthologue to prevent self-aggregation. In this study, we identified a putative Hep1 orthologue in P. falciparum and co-expression of PfHsp70-3 and PfHep1 enhanced the solubility of PfHsp70-3. PfHep1 suppressed the thermally induced aggregation of PfHsp70-3 but not the aggregation of malate dehydrogenase or citrate synthase, thus showing specificity for PfHsp70-3. Zinc ions were indeed essential for maintaining the function of PfHep1, as EDTA chelation abrogated its abilities to suppress the aggregation of PfHsp70-3. Soluble and functional PfHsp70-3, acquired by co-expression with PfHep-1, will facilitate the biochemical characterisation of this particular Hsp70 protein and its evaluation as a drug target for the treatment of malaria.
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Affiliation(s)
- David O. Nyakundi
- Biotechnology Innovation Centre, Rhodes University, Grahamstown 6140, South Africa
| | - Loyiso A. M. Vuko
- Biotechnology Innovation Centre, Rhodes University, Grahamstown 6140, South Africa
| | - Stephen J. Bentley
- Biotechnology Innovation Centre, Rhodes University, Grahamstown 6140, South Africa
| | - Heinrich Hoppe
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Gregory L. Blatch
- Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
- College of Health and Biomedicine, Victoria University, Melbourne, Victoria 8001, Australia
| | - Aileen Boshoff
- Biotechnology Innovation Centre, Rhodes University, Grahamstown 6140, South Africa
- * E-mail:
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6
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Fukuzono T, Pastuhov SI, Fukushima O, Li C, Hattori A, Iemura SI, Natsume T, Shibuya H, Hanafusa H, Matsumoto K, Hisamoto N. Chaperone complex BAG2-HSC70 regulates localization of Caenorhabditis elegans leucine-rich repeat kinase LRK-1 to the Golgi. Genes Cells 2016; 21:311-24. [PMID: 26853528 DOI: 10.1111/gtc.12338] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 01/15/2023]
Abstract
Mutations in LRRK2 are linked to autosomal dominant forms of Parkinson's disease. We identified two human proteins that bind to LRRK2: BAG2 and HSC70, which are known to form a chaperone complex. We characterized the role of their Caenorhabditis elegans homologues, UNC-23 and HSP-1, in the regulation of LRK-1, the sole homologue of human LRRK2. In C. elegans, LRK-1 determines the polarized sorting of synaptic vesicle (SV) proteins to the axons by excluding SV proteins from the dendrite-specific transport machinery in the Golgi. In unc-23 mutants, SV proteins are localized to both presynaptic and dendritic endings in neurons, a phenotype also observed in lrk-1 deletion mutants. Furthermore, we isolated mutations in the hsp-1 gene that can suppress the unc-23, but not the lrk-1 defect. We show that UNC-23 determines LRK-1 localization to the Golgi apparatus in cooperation with HSP-1. These results describe a chaperone-dependent mechanism through which LRK-1 localization is regulated.
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Affiliation(s)
- Takashi Fukuzono
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Strahil Iv Pastuhov
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Okinobu Fukushima
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Chun Li
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Ayuna Hattori
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Shun-ichiro Iemura
- National Institutes of Advanced Industrial Science and Technology, Molecular Profiling Research Center for Drug Discovery (Molprof), Kohtoh-ku, Tokyo, 135-0064, Japan
| | - Tohru Natsume
- National Institutes of Advanced Industrial Science and Technology, Molecular Profiling Research Center for Drug Discovery (Molprof), Kohtoh-ku, Tokyo, 135-0064, Japan
| | - Hiroshi Shibuya
- Department of Molecular Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Hiroshi Hanafusa
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Kunihiro Matsumoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Naoki Hisamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
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7
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Malaga F, Mayberry O, Park DJ, Rodgers ME, Toptygin D, Schleif RF. A genetic and physical study of the interdomain linker of E. Coli
AraC protein-a trans
-subunit communication pathway. Proteins 2016; 84:448-60. [DOI: 10.1002/prot.24990] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/23/2015] [Accepted: 01/12/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Fabiana Malaga
- Biology Department; UPCH; Lima San Martín De Porres Peru
| | - Ory Mayberry
- Department of Biology; Johns Hopkins University; Baltimore Maryland 21218
| | - David J. Park
- Tufts University Medical School; Boston Massachusetts
| | - Michael E. Rodgers
- Department of Biology; Johns Hopkins University; Baltimore Maryland 21218
| | - Dmitri Toptygin
- Department of Biology; Johns Hopkins University; Baltimore Maryland 21218
| | - Robert F. Schleif
- Department of Biology; Johns Hopkins University; Baltimore Maryland 21218
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8
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Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins. PLoS One 2015; 10:e0143752. [PMID: 26619280 PMCID: PMC4664246 DOI: 10.1371/journal.pone.0143752] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/09/2015] [Indexed: 01/04/2023] Open
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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9
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Roy J, Mitra S, Sengupta K, Mandal AK. Hsp70 clears misfolded kinases that partitioned into distinct quality-control compartments. Mol Biol Cell 2015; 26:1583-600. [PMID: 25739454 PMCID: PMC4436772 DOI: 10.1091/mbc.e14-08-1262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 02/26/2015] [Indexed: 01/13/2023] Open
Abstract
Hsp70 facilitates maturation of newly synthesized kinases and assists degradation of kinases under normal and stressed conditions. Hsp70 degrades misfolded kinases that partition into different quality-control compartments by promoting their ubiquitination, thus protecting cells from proteotoxic stress. Hsp70 aids in protein folding and directs misfolded proteins to the cellular degradation machinery. We describe discrete roles of Hsp70,SSA1 as an important quality-control machinery that switches functions to ameliorate the cellular environment. SSA1 facilitates folding/maturation of newly synthesized protein kinases by aiding their phosphorylation process and also stimulates ubiquitylation and degradation of kinases in regular protein turnover or during stress when kinases are denatured or improperly folded. Significantly, while kinases accumulate as insoluble inclusions upon SSA1 inhibition, they form soluble inclusions upon Hsp90 inhibition or stress foci during heat stress. This suggests formation of inclusion-specific quality-control compartments under various stress conditions. Up-regulation of SSA1 results in complete removal of these inclusions by the proteasome. Elevation of the cellular SSA1 level accelerates kinase turnover and protects cells from proteotoxic stress. Upon overexpression, SSA1 targets heat-denatured kinases toward degradation, which could enable them to recover their functional state under physiological conditions. Thus active participation of SSA1 in the degradation of misfolded proteins establishes an essential role of Hsp70 in deciding client fate during stress.
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Affiliation(s)
- Joydeep Roy
- Division of Molecular Medicine, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Sahana Mitra
- Division of Molecular Medicine, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Kaushik Sengupta
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064, India
| | - Atin K Mandal
- Division of Molecular Medicine, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
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10
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Kim JH, Bothe JR, Alderson TR, Markley JL. Tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1416-28. [PMID: 25450980 DOI: 10.1016/j.bbamcr.2014.11.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/18/2014] [Accepted: 11/13/2014] [Indexed: 12/26/2022]
Abstract
Proteins containing iron-sulfur (Fe-S) clusters arose early in evolution and are essential to life. Organisms have evolved machinery consisting of specialized proteins that operate together to assemble Fe-S clusters efficiently so as to minimize cellular exposure to their toxic constituents: iron and sulfide ions. To date, the best studied system is the iron-sulfur cluster (isc) operon of Escherichia coli, and the eight ISC proteins it encodes. Our investigations over the past five years have identified two functional conformational states for the scaffold protein (IscU) and have shown that the other ISC proteins that interact with IscU prefer to bind one conformational state or the other. From analyses of the NMR spectroscopy-derived network of interactions of ISC proteins, small-angle X-ray scattering (SAXS) data, chemical crosslinking experiments, and functional assays, we have constructed working models for Fe-S cluster assembly and delivery. Future work is needed to validate and refine what has been learned about the E. coli system and to extend these findings to the homologous Fe-S cluster biosynthetic machinery of yeast and human mitochondria. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Jin Hae Kim
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jameson R Bothe
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - T Reid Alderson
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John L Markley
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Alderson TR, Kim JH, Cai K, Frederick RO, Tonelli M, Markley JL. The specialized Hsp70 (HscA) interdomain linker binds to its nucleotide-binding domain and stimulates ATP hydrolysis in both cis and trans configurations. Biochemistry 2014; 53:7148-59. [PMID: 25372495 PMCID: PMC4245983 DOI: 10.1021/bi5010552] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
Proteins
from the isc operon of Escherichia
coli constitute the machinery used to synthesize iron–sulfur
(Fe–S) clusters for delivery to recipient apoproteins. Efficient
and rapid [2Fe-2S] cluster transfer from the holo-scaffold protein
IscU depends on ATP hydrolysis in the nucleotide-binding domain (NBD)
of HscA, a specialized Hsp70-type molecular chaperone with low intrinsic
ATPase activity (0.02 min−1 at 25 °C, henceforth
reported in units of min–1). HscB, an Hsp40-type
cochaperone, binds to HscA and stimulates ATP hydrolysis to promote
cluster transfer, yet while the interactions between HscA and HscB
have been investigated, the role of HscA’s interdomain linker
in modulating ATPase activity has not been explored. To address this
issue, we created three variants of the 40 kDa NBD of HscA: NBD alone
(HscA386), NBD with a partial linker (HscA389), and NBD with the full linker (HscA395). We found that
the rate of ATP hydrolysis of HscA395 (0.45 min–1) is nearly 15-fold higher than that of HscA386 (0.035
min–1), although their apparent affinities for ATP
are equivalent. HscA395, which contains the full covalently
linked linker peptide, exhibited intrinsic tryptophan fluorescence
emission and basal thermostability that were higher than those of
HscA386. Furthermore, HscA395 displayed narrower 1HN line widths in its two-dimensional 1H–15N TROSY-HSQC spectrum in comparison to HscA386, indicating that the peptide in the cis configuration binds to and stabilizes the structure of the NBD.
The addition to HscA386 of a synthetic peptide with a sequence
identical to that of the interdomain linker (L387LLDVIPLS395) stimulated its ATPase activity and induced widespread
NMR chemical shift perturbations indicative of a binding interaction
in the trans configuration.
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Affiliation(s)
- T Reid Alderson
- Department of Biochemistry, ‡Mitochondrial Protein Partnership, Center for Eukaryotic Structural Genomics, and §National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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12
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Samaddar M, Goswami AV, Purushotham J, Hegde P, D'Silva P. Role of the loop L4,5 in allosteric regulation in mtHsp70s: in vivo significance of domain communication and its implications in protein translocation. Mol Biol Cell 2014; 25:2129-42. [PMID: 24829379 PMCID: PMC4091826 DOI: 10.1091/mbc.e14-03-0821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The SBD loop L4,5 in mtHsp70s functions synergistically with the linker region to maintain the interdomain interface governing protein translocation and mitochondrial biogenesis. Intragenic suppressors of a communication-impaired L4,5 mutant reveal molecular insights into the allosteric regulation of mtHsp70s at the in vivo level. Mitochondrial Hsp70 (mtHsp70) is essential for a vast repertoire of functions, including protein import, and requires effective interdomain communication for efficient partner-protein interactions. However, the in vivo functional significance of allosteric regulation in eukaryotes is poorly defined. Using integrated biochemical and yeast genetic approaches, we provide compelling evidence that a conserved substrate-binding domain (SBD) loop, L4,5, plays a critical role in allosteric communication governing mtHsp70 chaperone functions across species. In yeast, a temperature-sensitive L4,5 mutation (E467A) disrupts bidirectional domain communication, leading to compromised protein import and mitochondrial function. Loop L4,5 functions synergistically with the linker in modulating the allosteric interface and conformational transitions between SBD and the nucleotide-binding domain (NBD), thus regulating interdomain communication. Second-site intragenic suppressors of E467A isolated within the SBD suppress domain communication defects by conformationally altering the allosteric interface, thereby restoring import and growth phenotypes. Strikingly, the suppressor mutations highlight that restoration of communication from NBD to SBD alone is the minimum essential requirement for effective in vivo function when primed at higher basal ATPase activity, mimicking the J-protein–bound state. Together these findings provide the first mechanistic insights into critical regions within the SBD of mtHsp70s regulating interdomain communication, thus highlighting its importance in protein translocation and mitochondrial biogenesis.
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Affiliation(s)
- Madhuja Samaddar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | | | - Jaya Purushotham
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Pushpa Hegde
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Patrick D'Silva
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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13
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Doyle SM, Genest O, Wickner S. Protein rescue from aggregates by powerful molecular chaperone machines. Nat Rev Mol Cell Biol 2013; 14:617-29. [PMID: 24061228 DOI: 10.1038/nrm3660] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein quality control within the cell requires the interplay of many molecular chaperones and proteases. When this quality control system is disrupted, polypeptides follow pathways leading to misfolding, inactivity and aggregation. Among the repertoire of molecular chaperones are remarkable proteins that forcibly untangle protein aggregates, called disaggregases. Structural and biochemical studies have led to new insights into how these proteins collaborate with co-chaperones and utilize ATP to power protein disaggregation. Understanding how energy-dependent protein disaggregating machines function is universally important and clinically relevant, as protein aggregation is linked to medical conditions such as Alzheimer's disease, Parkinson's disease, amyloidosis and prion diseases.
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Affiliation(s)
- Shannon M Doyle
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bldg. 37, Room 5144, Bethesda, Maryland 20892, USA
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14
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Hatherley R, Blatch GL, Bishop ÖT. Plasmodium falciparumHsp70-x: a heat shock protein at the host–parasite interface. J Biomol Struct Dyn 2013; 32:1766-79. [DOI: 10.1080/07391102.2013.834849] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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15
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Zuiderweg ERP, Bertelsen EB, Rousaki A, Mayer MP, Gestwicki JE, Ahmad A. Allostery in the Hsp70 chaperone proteins. Top Curr Chem (Cham) 2013; 328:99-153. [PMID: 22576356 PMCID: PMC3623542 DOI: 10.1007/128_2012_323] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Heat shock 70-kDa (Hsp70) chaperones are essential to in vivo protein folding, protein transport, and protein re-folding. They carry out these activities using repeated cycles of binding and release of client proteins. This process is under allosteric control of nucleotide binding and hydrolysis. X-ray crystallography, NMR spectroscopy, and other biophysical techniques have contributed much to the understanding of the allosteric mechanism linking these activities and the effect of co-chaperones on this mechanism. In this chapter these findings are critically reviewed. Studies on the allosteric mechanisms of Hsp70 have gained enhanced urgency, as recent studies have implicated this chaperone as a potential drug target in diseases such as Alzheimer's and cancer. Recent approaches to combat these diseases through interference with the Hsp70 allosteric mechanism are discussed.
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Affiliation(s)
- Erik R P Zuiderweg
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA.
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16
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Abstract
Hep1 acts as a specialized chaperone to mediate the de novo folding of yeast mitochondrial Hsp70. Chaperones mediate protein folding and prevent deleterious protein aggregation in the cell. However, little is known about the biogenesis of chaperones themselves. In this study, we report on the biogenesis of the yeast mitochondrial Hsp70 (mtHsp70) chaperone, which is essential for the functionality of mitochondria. We show in vivo and in organello that mtHsp70 rapidly folds after its import into mitochondria, with its ATPase domain and peptide-binding domain (PBD) adopting their structures independently of each other. Importantly, folding of the ATPase domain but not of the PBD was severely affected in the absence of the Hsp70 escort protein, Hep1. We reconstituted the folding of mtHsp70, demonstrating that Hep1 and ATP/ADP were required and sufficient for its de novo folding. Our data show that Hep1 bound to a folding intermediate of mtHsp70. Binding of an adenine nucleotide triggered release of Hep1 and folding of the intermediate into native mtHsp70. Thus, Hep1 acts as a specialized chaperone mediating the de novo folding of an Hsp70 chaperone.
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Affiliation(s)
- Marta Blamowska
- Adolf-Butenandt-Institut, Lehrstuhl für Physiologische Chemie, Ludwig-Maximilians-Universität München, 81377 München, Germany
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17
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Wu CC, Naveen V, Chien CH, Chang YW, Hsiao CD. Crystal structure of DnaK protein complexed with nucleotide exchange factor GrpE in DnaK chaperone system: insight into intermolecular communication. J Biol Chem 2012; 287:21461-70. [PMID: 22544739 PMCID: PMC3375567 DOI: 10.1074/jbc.m112.344358] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The conserved, ATP-dependent bacterial DnaK chaperones process client substrates with the aid of the co-chaperones DnaJ and GrpE. However, in the absence of structural information, how these proteins communicate with each other cannot be fully delineated. For the study reported here, we solved the crystal structure of a full-length Geobacillus kaustophilus HTA426 GrpE homodimer in complex with a nearly full-length G. kaustophilus HTA426 DnaK that contains the interdomain linker (acting as a pseudo-substrate), and the N-terminal nucleotide-binding and C-terminal substrate-binding domains at 4.1-Å resolution. Each complex contains two DnaKs and two GrpEs, which is a stoichiometry that has not been found before. The long N-terminal GrpE α-helices stabilize the linker of DnaK in the complex. Furthermore, interactions between the DnaK substrate-binding domain and the N-terminal disordered region of GrpE may accelerate substrate release from DnaK. These findings provide molecular mechanisms for substrate binding, processing, and release during the Hsp70 chaperone cycle.
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Affiliation(s)
- Ching-Chung Wu
- From the Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan, ,the Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, and
| | - Vankadari Naveen
- the Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, and ,the Molecular Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei 115, Taiwan
| | - Chin-Hsiang Chien
- From the Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan, , To whom correspondence may be addressed. Tel.: 886-2-2826-7121; Fax: 886-2-2826-4843; E-mail:
| | - Yi-Wei Chang
- the Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, and
| | - Chwan-Deng Hsiao
- the Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, and , To whom correspondence may be addressed. Tel.: 886-2-2788-2743; Fax: 886-2-2782-6085; E-mail:
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18
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Sun L, Edelmann FT, Kaiser CJO, Papsdorf K, Gaiser AM, Richter K. The lid domain of Caenorhabditis elegans Hsc70 influences ATP turnover, cofactor binding and protein folding activity. PLoS One 2012; 7:e33980. [PMID: 22479492 PMCID: PMC3315512 DOI: 10.1371/journal.pone.0033980] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 02/20/2012] [Indexed: 12/27/2022] Open
Abstract
Hsc70 is a conserved ATP-dependent molecular chaperone, which utilizes the energy of ATP hydrolysis to alter the folding state of its client proteins. In contrast to the Hsc70 systems of bacteria, yeast and humans, the Hsc70 system of C. elegans (CeHsc70) has not been studied to date. We find that CeHsc70 is characterized by a high ATP turnover rate and limited by post-hydrolysis nucleotide exchange. This rate-limiting step is defined by the helical lid domain at the C-terminus. A certain truncation in this domain (CeHsc70-Δ545) reduces the turnover rate and renders the hydrolysis step rate-limiting. The helical lid domain also affects cofactor affinities as the lidless mutant CeHsc70-Δ512 binds more strongly to DNJ-13, forming large protein complexes in the presence of ATP. Despite preserving the ability to hydrolyze ATP and interact with its cofactors DNJ-13 and BAG-1, the truncation of the helical lid domain leads to the loss of all protein folding activity, highlighting the requirement of this domain for the functionality of the nematode's Hsc70 protein.
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Affiliation(s)
| | | | | | | | | | - Klaus Richter
- Center for Integrated Protein Science Munich (CIPSM) and Department Chemie, Technische Universität München, Garching, Germany
- * E-mail:
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19
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Kumar DP, Vorvis C, Sarbeng EB, Cabra Ledesma VC, Willis JE, Liu Q. The four hydrophobic residues on the Hsp70 inter-domain linker have two distinct roles. J Mol Biol 2011; 411:1099-113. [PMID: 21762702 DOI: 10.1016/j.jmb.2011.07.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/13/2011] [Accepted: 07/01/2011] [Indexed: 12/14/2022]
Abstract
The ubiquitous molecular chaperone 70-kDa heat shock proteins (Hsp70) play key roles in maintaining protein homeostasis. Hsp70s contain two functional domains: a nucleotide binding domain and a substrate binding domain. The two domains are connected by a highly conserved inter-domain linker, and allosteric coupling between the two domains is critical for chaperone function. The auxiliary chaperone 40-kDa heat shock proteins (Hsp40) facilitate all the biological processes associated with Hsp70s by stimulating the ATPase activity of Hsp70s. Although an overall essential role of the inter-domain linker in both allosteric coupling and Hsp40 interaction has been suggested, the molecular mechanisms remain largely unknown. Previously, we reported a crystal structure of a full-length Hsp70 homolog, in which the inter-domain linker forms a well-ordered β strand. Four highly conserved hydrophobic residues reside on the inter-domain linker. In DnaK, a well-studied Hsp70, these residues are V389, L390, L391, and L392. In this study, we biochemically dissected their roles. The inward-facing side chains of V389 and L391 form extensive hydrophobic contacts with the nucleotide binding domain, suggesting their essential roles in coupling the two functional domains, a hypothesis confirmed by mutational analysis. On the other hand, L390 and L392 face outward on the surface. Mutation of either abolishes DnaK's in vivo function, yet intrinsic biochemical properties remain largely intact. In contrast, Hsp40 interaction is severely compromised. Thus, for the first time, we separated the two essential roles of the highly conserved Hsp70 inter-domain linker: coupling the two functional domains through V389 and L391 and mediating the interaction with Hsp40 through L390 and L392.
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Affiliation(s)
- Divya Prasanna Kumar
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
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20
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Chang L, Miyata Y, Ung PMU, Bertelsen EB, McQuade TJ, Carlson HA, Zuiderweg ERP, Gestwicki JE. Chemical screens against a reconstituted multiprotein complex: myricetin blocks DnaJ regulation of DnaK through an allosteric mechanism. ACTA ACUST UNITED AC 2011; 18:210-21. [PMID: 21338918 DOI: 10.1016/j.chembiol.2010.12.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 12/03/2010] [Accepted: 12/06/2010] [Indexed: 12/31/2022]
Abstract
DnaK is a molecular chaperone responsible for multiple aspects of bacterial proteostasis. The intrinsically slow ATPase activity of DnaK is stimulated by its co-chaperone, DnaJ, and these proteins often work in concert. To identify inhibitors we screened plant-derived extracts against a reconstituted mixture of DnaK and DnaJ. This approach resulted in the identification of flavonoids, including myricetin, which inhibited activity by up to 75%. Interestingly, myricetin prevented DnaJ-mediated stimulation of ATPase activity, with minimal impact on either DnaK's intrinsic turnover rate or its stimulation by another co-chaperone, GrpE. Using NMR, we found that myricetin binds DnaK at an unanticipated site between the IB and IIB subdomains and that it allosterically blocked binding of DnaK to DnaJ. Together, these results highlight a "gray box" screening approach, which might facilitate the identification of inhibitors of other protein-protein interactions.
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Affiliation(s)
- Lyra Chang
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
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21
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Schweizer RS, Aponte RA, Zimmermann S, Weber A, Reinstein J. Fine tuning of a biological machine: DnaK gains improved chaperone activity by altered allosteric communication and substrate binding. Chembiochem 2011; 12:1559-73. [PMID: 21656889 DOI: 10.1002/cbic.201000786] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Indexed: 11/09/2022]
Abstract
DnaK is a member of the Hsp70 family of molecular chaperones. This molecular machine couples the binding and hydrolysis of ATP to binding and release of substrate proteins. The switches that are involved in allosteric communication within this multidomain protein are mostly unknown. Previous insights were largely obtained by mutants, which displayed either wild-type activity or reduced folding assistance of substrate proteins. With a directed evolution approach for improved folding assistance we selected a DnaK variant characterized by a glycine to alanine substitution at position 384 (G384A); this resulted in a 2.5-fold higher chaperone activity in an in vitro DnaK-assisted firefly luciferase refolding assay. Quantitative biochemical characterization revealed several changes of key kinetic parameters compared to the wild type. Most pronounced is a 13-fold reduced rate constant for substrate release in the ATP-bound state, which we assume, in conjunction with the resulting increase in substrate affinity, to be related to improved chaperone activity. As the underlying mechanistic reason for this change we propose an altered interface of allosteric communication of mutant G384A, which is notably located at a hinge position between nucleotide and substrate binding domain.
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Affiliation(s)
- Regina S Schweizer
- Department for Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
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22
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Clerico EM, Zhuravleva A, Smock RG, Gierasch LM. Segmental isotopic labeling of the Hsp70 molecular chaperone DnaK using expressed protein ligation. Biopolymers 2011; 94:742-52. [PMID: 20564022 DOI: 10.1002/bip.21426] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Introducing biophysical labels into specific regions of large and dynamic multidomain proteins greatly facilitates mechanistic analysis. Ligation of expressed domains that are labeled in a desired manner before assembly of the intact molecular machine provides such a strategy. We have elaborated an experimental route using expressed protein ligation (EPL) to create an Hsp70 molecular chaperone (the E. coli Hsp70, DnaK) where only one of the two constituent domains was labeled, in this case with NMR active isotopes, allowing visualization of the single domain in the context of the two domain protein. Several technical obstacles were overcome, including choice of site for ligation with retention of function, optimization of ligation yield, and purification from unreacted domains. Ligated semilabeled DnaK was successfully produced with a Cys residue at position 383, and the ligated product harboring the Cys mutation was confirmed to be functional and identical to an expressed Cys-containing two-domain construct. The NMR spectrum of the segmentally labeled protein was considerably simplified, enabling unequivocal assignment and enhanced analysis of dynamics, as a prelude to exploring the energy landscape for allostery in the Hsp70 family.
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Affiliation(s)
- Eugenia M Clerico
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst 01003, MA
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23
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Abstract
Molecular chaperones of the Hsp70 family have diverse functions in cells. They assist the folding of newly synthesized and stress-denatured proteins, as well as the import of proteins into organelles, and the dissociation of aggregated proteins. The well-conserved Hsp70 chaperones are ATP dependent: binding and hydrolysis of ATP regulates their interactions with unfolded polypeptide substrates, and ATPase cycling is necessary for their function. All cellular functions of Hsp70 chaperones use the same mechanism of ATP-driven polypeptide binding and release. The Hsp40 co-chaperones stimulate ATP hydrolysis by Hsp70 and the type 1 Hsp40 proteins are conserved from Escherichia coli to humans. Various nucleotide exchange factors also promote the Hsp70 ATPase cycle. Recent advances have added to our understanding of the Hsp70 mechanism at a molecular level.
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Affiliation(s)
- Jason C Young
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
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24
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Affiliation(s)
- Christopher G. Evans
- Department of Pathology and the Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216
| | - Lyra Chang
- Department of Pathology and the Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216
| | - Jason E. Gestwicki
- Department of Pathology and the Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216
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25
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Taneva SG, Moro F, Velázquez-Campoy A, Muga A. Energetics of nucleotide-induced DnaK conformational states. Biochemistry 2010; 49:1338-45. [PMID: 20078127 DOI: 10.1021/bi901847q] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Hsp70 chaperones are molecular switches that use the free energy of ATP binding and hydrolysis to modulate their affinity for protein substrates and, most likely, to remodel non-native interactions allowing proper substrate folding. By means of isothermal titration calorimetry, we have measured the thermodynamics of ATP and ADP binding to (i) wild-type DnaK, the main bacterial Hsp70; (ii) two single-point mutants, DnaK(T199A), which lacks ATPase activity but maintains conformational changes similar to those observed in the wild-type protein, and DnaK(R151A), defective in interdomain communication; and iii) two deletion mutants, the isolated nucleotide binding domain (K-NBD) and a DeltaLid construct [DnaK(1-507)]. At 25 degrees C, ATP binding to DnaK results in a fast endothermic and a slow exothermic process due to ATP hydrolysis. We demonstrate that the endothermic event is due to the allosteric coupling between ATP binding to the nucleotide binding domain and the conformational rearrangement of the substrate binding domain. The interpretation of our data is compatible with domain docking upon ATP binding and shows that this conformational change carries an energy penalty of ca. 1 kcal/mol. The conformational energy stored in the ATP-bound DnaK state, together with the free energy of ATP hydrolysis, can be used in remodeling bound substrates.
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Affiliation(s)
- Stefka G Taneva
- Unidad de Biofsica (CSIC/UPV-EHU) y Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apartado 644, 48080 Bilbao, Spain
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26
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Aponte RA, Zimmermann S, Reinstein J. Directed evolution of the DnaK chaperone: mutations in the lid domain result in enhanced chaperone activity. J Mol Biol 2010; 399:154-67. [PMID: 20381501 DOI: 10.1016/j.jmb.2010.03.060] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 03/26/2010] [Accepted: 03/30/2010] [Indexed: 11/18/2022]
Abstract
We improved the DnaK molecular chaperone system for increased folding efficiency towards two target proteins, by using a multi-parameter screening procedure. First, we used a folding-deficient C-terminal truncated chloramphenicol acetyl transferase (CAT_Cd9) to obtain tunable selective pressure for enhanced DnaK chaperon function in vivo. Second, we screened selected clones in vitro for CAT_Cd9 activity after growth under selective pressure. We then analyzed how these variants performed as compared to wild type DnaK towards folding assistance of a second target protein; namely, chemically denatured firefly luciferase. A total of 11 single point DnaK mutants and 1 truncated variant were identified using CAT_Cd9 as the protein target, while 4 of the 12 selected variants showed improved luciferase refolding in vitro. This shows that improving the DnaK chaperone by using a certain target substrate protein, does not necessarily result in a loss or reduction in its ability to assist other proteins. Of the 12 identified mutations, half were clustered in the nucleotide binding domain, and half in the lid domain (LD) of DnaK. The truncated variant is characterized by a 35-residue C-terminal truncation (Cd35) and exhibited the highest improvement for luciferase refolding. Cd35 showed a 7-fold increase in initial refolding rate for denatured luciferase and resulted in a 5-fold increase in maximal luminescence as compared to wild type DnaK. Given that the best in vitro performing mutants contained LD substitutions, and that the LD is not involved in ATP binding, ATP hydrolysis or client protein association, but is involved in allosteric regulation of the chaperone cycle, we propose that improved DnaK variants result in changes to allosteric domain communication, ultimately retuning the ATP-dependent chaperone cycle.
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Affiliation(s)
- Raphael A Aponte
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120 Heidelberg, Germany
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27
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Blamowska M, Sichting M, Mapa K, Mokranjac D, Neupert W, Hell K. ATPase domain and interdomain linker play a key role in aggregation of mitochondrial Hsp70 chaperone Ssc1. J Biol Chem 2009; 285:4423-31. [PMID: 20007714 DOI: 10.1074/jbc.m109.061697] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The co-chaperone Hep1 is required to prevent the aggregation of mitochondrial Hsp70 proteins. We have analyzed the interaction of Hep1 with mitochondrial Hsp70 (Ssc1) and the determinants in Ssc1 that make it prone to aggregation. The ATPase and peptide binding domain (PBD) of Hsp70 proteins are connected by a linker segment that mediates interdomain communication between the domains. We show here that the minimal Hep1 binding entity of Ssc1 consists of the ATPase domain and the interdomain linker. In the absence of Hep1, the ATPase domain with the interdomain linker had the tendency to aggregate, in contrast to the ATPase domain with the mutated linker segment or without linker, and in contrast to the PBD. The closest homolog of Ssc1, bacterial DnaK, and a Ssc1 chimera, in which a segment of the ATPase domain of Ssc1 was replaced by the corresponding segment from DnaK, did not aggregate in Delta hep1 mitochondria. The propensity to aggregate appears to be a specific property of the mitochondrial Hsp70 proteins. The ATPase domain in combination with the interdomain linker is crucial for aggregation of Ssc1. In conclusion, our results suggest that interdomain communication makes Ssc1 prone to aggregation. Hep1 counteracts aggregation by binding to this aggregation-prone conformer.
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Affiliation(s)
- Marta Blamowska
- Adolf-Butenandt-Institut für Physiologische Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5, 81377 München, Germany
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28
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Shonhai A, Boshoff A, Blatch GL. The structural and functional diversity of Hsp70 proteins from Plasmodium falciparum. Protein Sci 2007; 16:1803-18. [PMID: 17766381 PMCID: PMC2206976 DOI: 10.1110/ps.072918107] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
It is becoming increasingly apparent that heat shock proteins play an important role in the survival of Plasmodium falciparum against temperature changes associated with its passage from the cold-blooded mosquito vector to the warm-blooded human host. Interest in understanding the possible role of P. falciparum Hsp70s in the life cycle of the parasite has led to the identification of six HSP70 genes. Although most research attention has focused primarily on one of the cytosolic Hsp70s (PfHsp70-1) and its endoplasmic reticulum homolog (PfHsp70-2), further functional insights could be inferred from the structural motifs exhibited by the rest of the Hsp70 family members of P. falciparum. There is increasing evidence that suggests that PfHsp70-1 could play an important role in the life cycle of P. falciparum both as a chaperone and immunogen. In addition, P. falciparum Hsp70s and Hsp40 partners are implicated in the intracellular and extracellular trafficking of proteins. This review summarizes data emerging from studies on the chaperone role of P. falciparum Hsp70s, taking advantage of inferences gleaned from their structures and information on their cellular localization. The possible associations between P. falciparum Hsp70s with their cochaperone partners as well as other chaperones and proteins are discussed.
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Affiliation(s)
- Addmore Shonhai
- Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, Grahamstown 6140, South Africa
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29
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Swain JF, Dinler G, Sivendran R, Montgomery DL, Stotz M, Gierasch LM. Hsp70 chaperone ligands control domain association via an allosteric mechanism mediated by the interdomain linker. Mol Cell 2007; 26:27-39. [PMID: 17434124 PMCID: PMC1894942 DOI: 10.1016/j.molcel.2007.02.020] [Citation(s) in RCA: 237] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 01/24/2007] [Accepted: 02/20/2007] [Indexed: 11/16/2022]
Abstract
Hsp70 chaperones assist in protein folding, disaggregation, and membrane translocation by binding to substrate proteins with an ATP-regulated affinity that relies on allosteric coupling between ATP-binding and substrate-binding domains. We have studied single- and two-domain versions of the E. coli Hsp70, DnaK, to explore the mechanism of interdomain communication. We show that the interdomain linker controls ATPase activity by binding to a hydrophobic cleft between subdomains IA and IIA. Furthermore, the domains of DnaK dock only when ATP binds and behave independently when ADP is bound. Major conformational changes in both domains accompany ATP-induced docking: of particular importance, some regions of the substrate-binding domain are stabilized, while those near the substrate-binding site become destabilized. Thus, the energy of ATP binding is used to form a stable interface between the nucleotide- and substrate-binding domains, which results in destabilization of regions of the latter domain and consequent weaker substrate binding.
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Affiliation(s)
- Joanna F. Swain
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
| | - Gizem Dinler
- Department of Chemistry, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
| | - Renuka Sivendran
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
| | - Diana L. Montgomery
- Department of Chemistry, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
| | - Mathias Stotz
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
| | - Lila M. Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
- Department of Chemistry, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
- *To whom correspondence should be addressed at: , phone: 413-545-6094, fax: 413-545-1289
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30
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Vogel M, Mayer MP, Bukau B. Allosteric Regulation of Hsp70 Chaperones Involves a Conserved Interdomain Linker. J Biol Chem 2006; 281:38705-11. [PMID: 17052976 DOI: 10.1074/jbc.m609020200] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The 70-kDa heat shock proteins (Hsp70) are essential members of the cellular chaperone machinery that assists protein-folding processes. To perform their functions Hsp70 chaperones toggle between two nucleotide-controlled conformational states. ATP binding to the ATPase domain triggers the transition to the low affinity state of the substrate-binding domain, while substrate binding to the substrate-binding domain in synergism with the action of a J-domain-containing cochaperone stimulates ATP hydrolysis and thereby transition to the high affinity state. Thus, ATPase and substrate-binding domains mutually affect each other through an allosteric control mechanism, the basis of which is largely unknown. In this study we identified two positively charged, surface-exposed residues in the ATPase domain and a negatively charged residue in the linker connecting both domains that are important for interdomain communication. Furthermore, we demonstrate that the linker alone is sufficient to stimulate the ATPase activity, an ability that is lost upon amino acid replacement. The linker therefore is most likely the lever that is wielded by the substrate-binding domain and the cochaperone onto the ATPase domain to induce a conformation favorable for ATP hydrolysis. Based on our results we propose a mechanism of interdomain communication.
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Affiliation(s)
- Markus Vogel
- Zentrum für Molekulare Biologie der Universität Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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31
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Nicoll WS, Boshoff A, Ludewig MH, Hennessy F, Jung M, Blatch GL. Approaches to the isolation and characterization of molecular chaperones. Protein Expr Purif 2005; 46:1-15. [PMID: 16199180 DOI: 10.1016/j.pep.2005.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 08/02/2005] [Accepted: 08/04/2005] [Indexed: 10/25/2022]
Abstract
Molecular chaperones are integral components of the cellular machinery involved in ensuring correct protein folding and the continued maintenance of protein structure. An understanding of these ubiquitous molecules is key to finding cures to protein misfolding diseases such as Alzheimer's and Creutzfeldt-Jacob diseases. In addition, further understanding of chaperones will enhance our comprehension of the way the body copes with the environmental stresses that humans encounter daily. Our laboratory and our collaborators specialize in the production and characterization of chaperones from a wide variety of sources in order to gain a fuller understanding of how chaperones function in the cell. In this review, we primarily use the Hsp70/Hsp40 chaperone pair as an example to discuss recent advances in technology and reductions in cost that lend themselves to chaperone purification from both native and recombinant sources. Common assays to assess purified chaperone activity are also discussed.
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Affiliation(s)
- William S Nicoll
- Chaperone Research Group, Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, Grahamstown, South Africa
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Shonhai A, Boshoff A, Blatch GL. Plasmodium falciparum heat shock protein 70 is able to suppress the thermosensitivity of an Escherichia coli DnaK mutant strain. Mol Genet Genomics 2005; 274:70-8. [PMID: 15973516 DOI: 10.1007/s00438-005-1150-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Accepted: 03/23/2005] [Indexed: 10/25/2022]
Abstract
Heat shock protein 70 (Hsp 70) and heat shock protein 40 (Hsp 40) are molecular chaperones that ensure that the proteins of the cell are properly folded and functional under both normal and stressful conditions. The malaria parasite Plasmodium falciparum is known to overproduce a heat shock protein 70 (PfHsp 70) in response to thermal stress; however, the in vivo function of this protein still needs to be explored. Using in vivo complementation assays, we found that PfHsp 70 was able to suppress the thermosensitivity of an Escherichia coli dnaK 756 strain, but not that of the corresponding deletion strain (DeltadnaK 52) or dnaK 103 strain, which produces a truncated DnaK. Constructs were generated that encoded the ATPase domain of PfHsp 70 fused to the substrate-binding domain (SBD) of E. coli DnaK (referred to as PfK), and the ATPase domain of E. coli DnaK coupled to the SBD of PfHsp 70 (KPf). PfK was unable to suppress the thermosensitivity of any of the E. coli strains. In contrast, KPf was able to suppress the thermosensitivity in the E. coli dnaK 756 strain. We also identified two key amino acid residues (V 401 and Q 402) in the linker region between the ATPase domain and SBD that are essential for the in vivo function of PfHsp 70. This is the first example of an Hsp70 from a eukaryotic parasite that can suppress thermosensitivity in a prokaryotic system. In addition, our results also suggest that interdomain communication is critical for the function of the PfHsp 70 and PfHsp 70-DnaK chimeras. We discuss the implications of these data for the mechanism of action of the Hsp70-Hsp 40 chaperone machinery.
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Affiliation(s)
- Addmore Shonhai
- Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, P.O. Box 94, Grahamstown 6140, South Africa
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Abstract
During the past two years, a large amount of biochemical, biophysical and low- to high-resolution structural data have provided mechanistic insights into the machinery of protein folding and unfolding. It has emerged that dual functionality in terms of folding and unfolding might exist for some systems. The majority of folding/unfolding machines adopt oligomeric ring structures in a cooperative fashion and utilise the conformational changes induced by ATP binding/hydrolysis for their specific functions.
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Affiliation(s)
- Xiaodong Zhang
- Centre for Structural Biology, Department of Biological Sciences, Imperial College of Science, Technology and Medicine, Flowers Building, South Kensington, SW7 2AZ, London, UK.
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