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Roeselová A, Maslen SL, Shivakumaraswamy S, Pellowe GA, Howell S, Joshi D, Redmond J, Kjær S, Skehel JM, Balchin D. Mechanism of chaperone coordination during cotranslational protein folding in bacteria. Mol Cell 2024; 84:2455-2471.e8. [PMID: 38908370 DOI: 10.1016/j.molcel.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/12/2024] [Accepted: 06/01/2024] [Indexed: 06/24/2024]
Abstract
Protein folding is assisted by molecular chaperones that bind nascent polypeptides during mRNA translation. Several structurally distinct classes of chaperones promote de novo folding, suggesting that their activities are coordinated at the ribosome. We used biochemical reconstitution and structural proteomics to explore the molecular basis for cotranslational chaperone action in bacteria. We found that chaperone binding is disfavored close to the ribosome, allowing folding to precede chaperone recruitment. Trigger factor recognizes compact folding intermediates that expose an extensive unfolded surface, and dictates DnaJ access to nascent chains. DnaJ uses a large surface to bind structurally diverse intermediates and recruits DnaK to sequence-diverse solvent-accessible sites. Neither Trigger factor, DnaJ, nor DnaK destabilize cotranslational folding intermediates. Instead, the chaperones collaborate to protect incipient structure in the nascent polypeptide well beyond the ribosome exit tunnel. Our findings show how the chaperone network selects and modulates cotranslational folding intermediates.
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Affiliation(s)
- Alžběta Roeselová
- Protein Biogenesis Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sarah L Maslen
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | | | - Grant A Pellowe
- Protein Biogenesis Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Steven Howell
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Dhira Joshi
- Chemical Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Joanna Redmond
- Chemical Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - J Mark Skehel
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - David Balchin
- Protein Biogenesis Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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2
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Lindemeier D, Graubner W, Mehner-Breitfeld D, Malešević M, Brüser T. Positive charges promote the recognition of proteins by the chaperone SlyD from Escherichia coli. PLoS One 2024; 19:e0305823. [PMID: 38917203 PMCID: PMC11198818 DOI: 10.1371/journal.pone.0305823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
SlyD is a widely-occurring prokaryotic FKBP-family prolyl isomerase with an additional chaperone domain. Often, such as in Escherichia coli, a third domain is found at its C-terminus that binds nickel and provides it for nickel-enzyme biogenesis. SlyD has been found to bind signal peptides of proteins that are translocated by the Tat pathway, a system for the transport of folded proteins across membranes. Using peptide arrays to analyze these signal peptide interactions, we found that SlyD interacted only with positively charged peptides, with a preference for arginines over lysines, and large hydrophobic residues enhanced binding. Especially a twin-arginine motif was recognized, a pair of highly conserved arginines adjacent to a stretch of hydrophobic residues. Using isothermal titration calorimetry (ITC) with purified SlyD and a signal peptide-containing model Tat substrate, we could show that the wild type twin-arginine signal peptide was bound with higher affinity than an RR>KK mutated variant, confirming that positive charges are recognized by SlyD, with a preference of arginines over lysines. The specific role of negative charges of the chaperone domain surface and of hydrophobic residues in the chaperone active site was further analyzed by ITC of mutated SlyD variants. Our data show that the supposed key hydrophobic residues of the active site are indeed crucial for binding, and that binding is influenced by negative charges on the chaperone domain. Recognition of positive charges is likely achieved by a large negatively charged surface region of the chaperone domain, which is highly conserved although individual positions are variable.
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Affiliation(s)
- Daniel Lindemeier
- Institute of Microbiology, Leibniz Universität Hannover, Hanover, Germany
| | - Wenke Graubner
- Institute of Microbiology, Leibniz Universität Hannover, Hanover, Germany
| | | | - Miroslav Malešević
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Thomas Brüser
- Institute of Microbiology, Leibniz Universität Hannover, Hanover, Germany
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3
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Pan Z, Zhuo L, Wan TY, Chen RY, Li YZ. DnaK duplication and specialization in bacteria correlates with increased proteome complexity. mSystems 2024; 9:e0115423. [PMID: 38530057 PMCID: PMC11019930 DOI: 10.1128/msystems.01154-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 03/10/2024] [Indexed: 03/27/2024] Open
Abstract
The chaperone 70 kDa heat shock protein (Hsp70) is important for cells from bacteria to humans to maintain proteostasis, and all eukaryotes and several prokaryotes encode Hsp70 paralogs. Although the mechanisms of Hsp70 function have been clearly illuminated, the function and evolution of Hsp70 paralogs is not well studied. DnaK is a highly conserved bacterial Hsp70 family. Here, we show that dnaK is present in 98.9% of bacterial genomes, and 6.4% of them possess two or more DnaK paralogs. We found that the duplication of dnaK is positively correlated with an increase in proteomic complexity (proteome size, number of domains). We identified the interactomes of the two DnaK paralogs of Myxococcus xanthus DK1622 (MxDnaKs), which revealed that they are mostly nonoverlapping, although both prefer α and β domain proteins. Consistent with the entire M. xanthus proteome, MxDnaK substrates have both significantly more multi-domain proteins and a higher isoelectric point than that of Escherichia coli, which encodes a single DnaK homolog. MxDnaK1 is transcriptionally upregulated in response to heat shock and prefers to bind cytosolic proteins, while MxDnaK2 is downregulated by heat shock and is more associated with membrane proteins. Using domain swapping, we show that the nucleotide-binding domain and the substrate-binding β domain are responsible for the significant differences in DnaK interactomes, and the nucleotide binding domain also determines the dimerization of MxDnaK2, but not MxDnaK1. Our work suggests that bacterial DnaK has been duplicated in order to deal with a more complex proteome, and that this allows evolution of distinct domains to deal with different subsets of target proteins.IMPORTANCEAll eukaryotic and ~40% of prokaryotic species encode multiple 70 kDa heat shock protein (Hsp70) homologs with similar but diversified functions. Here, we show that duplication of canonical Hsp70 (DnaK in prokaryotes) correlates with increasing proteomic complexity and evolution of particular regions of the protein. Using the Myxococcus xanthus DnaK duplicates as a case, we found that their substrate spectrums are mostly nonoverlapping, and are both consistent to that of Escherichia coli DnaK in structural and molecular characteristics, but show differential enrichment of membrane proteins. Domain/region swapping demonstrated that the nucleotide-binding domain and the β substrate-binding domain (SBDβ), but not the SBDα or disordered C-terminal tail region, are responsible for this functional divergence. This work provides the first direct evidence for regional evolution of DnaK paralogs.
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Affiliation(s)
- Zhuo Pan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Li Zhuo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
- Suzhou Research Institute, Shandong University, Suzhou, China
| | - Tian-yu Wan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Rui-yun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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4
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Zehe M, Kehrein J, Schollmayer C, Plank C, Kovacs H, Merino Asumendi E, Holzgrabe U, Grimm C, Sotriffer C. Combined In-Solution Fragment Screening and Crystallographic Binding-Mode Analysis with a Two-Domain Hsp70 Construct. ACS Chem Biol 2024; 19:392-406. [PMID: 38317495 DOI: 10.1021/acschembio.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Heat shock protein 70 (Hsp70) isoforms are key players in the regulation of protein homeostasis and cell death pathways and are therefore attractive targets in cancer research. Developing nucleotide-competitive inhibitors or allosteric modulators, however, has turned out to be very challenging for this protein family, and no Hsp70-directed therapeutics have so far become available. As the field could profit from alternative starting points for inhibitor development, we present the results of a fragment-based screening approach on a two-domain Hsp70 construct using in-solution NMR methods, together with X-ray-crystallographic investigations and mixed-solvent molecular dynamics simulations. The screening protocol resulted in hits on both domains. In particular, fragment binding in a deeply buried pocket at the substrate-binding domain could be detected. The corresponding site is known to be important for communication between the nucleotide-binding and substrate-binding domains of Hsp70 proteins. The main fragment identified at this position also offers an interesting starting point for the development of a dual Hsp70/Hsp90 inhibitor.
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Affiliation(s)
- Markus Zehe
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
| | - Josef Kehrein
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
| | - Curd Schollmayer
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
| | - Christina Plank
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
- University of Würzburg, Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor-Boveri-Institute, Am Hubland, DE-97074 Würzburg, Germany
| | - Helena Kovacs
- Bruker Switzerland AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland
| | - Eduardo Merino Asumendi
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
| | - Ulrike Holzgrabe
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
| | - Clemens Grimm
- University of Würzburg, Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor-Boveri-Institute, Am Hubland, DE-97074 Würzburg, Germany
| | - Christoph Sotriffer
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
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5
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Dongola TH, Chakafana G, Middlemiss C, Mafethe O, Mokoena F, Zininga T, Shonhai A. Insertion of GGMP repeat residues of Plasmodium falciparum Hsp70-1 in the lid of DnaK adversely impacts client recognition. Int J Biol Macromol 2024; 255:128070. [PMID: 37981279 DOI: 10.1016/j.ijbiomac.2023.128070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 11/21/2023]
Abstract
Although Hsp70 is a conserved molecular chaperone, it exhibits some degree of functional specialisation across species. Features of Hsp70 regulating its functional specialisation remain to be fully established. We previously demonstrated that E. coli Hsp70 (DnaK) exhibits functional features that distinguishes it from PfHsp70-1, a canonical cytosolic Hsp70 of Plasmodium falciparum. One of the defining features of PfHsp70-1 is that it possesses GGMP repeat residues located in its C-terminal lid segment, while DnaK lacks this motif. Previously, we demonstrated that the insertion of GGMP repeat residues of PfHsp70-1 into E. coli DnaK abrogates the chaperone activity of DnaK. However, the role of the GGMP motif in regulating Hsp70 function remains to be fully understood. To explore the function of this motif, we expressed recombinant forms of wild type DnaK and its GGMP insertion motif, DnaK-G and systematically characterised the structure-function features of the two proteins using in silico analysis, biophysical approaches and an in cellulo complementation assay. Our findings demonstrated that the GGMP inserted in DnaK compromised various functional features such as nucleotide binding, allostery, substrate binding affinity and cellular proteome client selectivity. These findings thus, highlight the GGMP motif of Hsp70 as an important functional module.
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Affiliation(s)
| | - Graham Chakafana
- Department of Biochemistry, University of Venda, Thohoyandou 0950, South Africa; Department of Chemistry and Biochemistry, Hampton University, VA 23668-0099, USA
| | - Caitlin Middlemiss
- Department of Chemistry and Biochemistry, Hampton University, VA 23668-0099, USA
| | - Ofentse Mafethe
- Department of Biochemistry, Faculty of Natural and Agricultural Science, North West University, Mmabatho 2790, South Africa
| | - Fortunate Mokoena
- Department of Biochemistry, Faculty of Natural and Agricultural Science, North West University, Mmabatho 2790, South Africa
| | - Tawanda Zininga
- Department of Biochemistry, University of Venda, Thohoyandou 0950, South Africa; Department of Biochemistry, Stellenbosch University, 7602 Matieland, South Africa
| | - Addmore Shonhai
- Department of Biochemistry, University of Venda, Thohoyandou 0950, South Africa.
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6
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Nelson B, Soper N, Lupoli TJ. Bacterial J-Domains with C-Terminal Tags Contact the Substrate Binding Domain of DnaK and Sequester Chaperone Activity. Chembiochem 2023; 24:e202300261. [PMID: 37556312 DOI: 10.1002/cbic.202300261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/11/2023]
Abstract
Functional interactions between the molecular chaperone DnaK and cofactor J-proteins (DnaJs), as well as their homologs, are crucial to the maintenance of proteostasis across cell types. In the bacterial pathogen Mycobacterium tuberculosis, DnaK-DnaJ interactions are essential for cell growth and represent potential targets for antibiotic or adjuvant development. While the N-terminal J-domains of J-proteins are known to form important contacts with DnaK, C-terminal domains have varied roles. Here, we have studied the effect of adding C-terminal tags to N-terminal J-domain truncations of mycobacterial DnaJ1 and DnaJ2 to promote additional interactions with DnaK. We found that His6 tags uniquely promote binding to additional sites in the substrate binding domain at the C-terminus of DnaK. Other C-terminal tags attached to J-domains, even peptides known to interact with DnaK, do not produce the same effects. Expression of C-terminally modified DnaJ1 or DnaJ2 J-domains in mycobacterial cells suppresses chaperone activity following proteotoxic stress, which is exaggerated in the presence of a small-molecule DnaK inhibitor. Hence, this work uncovers genetically encodable J-protein variants that may be used to study chaperone-cofactor interactions in other organisms.
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Affiliation(s)
- Brock Nelson
- Department of Chemistry, New York University, New York, 10003, USA
| | - Nathan Soper
- Department of Chemistry, New York University, New York, 10003, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, New York, 10003, USA
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7
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Richards A, Lupoli TJ. Peptide-based molecules for the disruption of bacterial Hsp70 chaperones. Curr Opin Chem Biol 2023; 76:102373. [PMID: 37516006 PMCID: PMC11217992 DOI: 10.1016/j.cbpa.2023.102373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/31/2023]
Abstract
DnaK is a chaperone that aids in nascent protein folding and the maintenance of proteome stability across bacteria. Due to the importance of DnaK in cellular proteostasis, there have been efforts to generate molecules that modulate its function. In nature, both protein substrates and antimicrobial peptides interact with DnaK. However, many of these ligands interact with other cellular machinery as well. Recent work has sought to modify these peptide scaffolds to create DnaK-selective and species-specific probes. Others have reported protein domain mimics of interaction partners to disrupt cellular DnaK function and high-throughput screening approaches to discover clinically-relevant peptidomimetics that inhibit DnaK. The described work provides a foundation for the design of new assays and molecules to regulate DnaK activity.
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Affiliation(s)
- Aweon Richards
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, New York, NY 10003, USA.
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8
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Singh A, Rief M, Žoldák G. Direct observation of chemo-mechanical coupling in DnaK by single-molecule force experiments. Biophys J 2022; 121:4729-4739. [PMID: 36196054 PMCID: PMC9748191 DOI: 10.1016/j.bpj.2022.09.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/16/2022] [Accepted: 09/29/2022] [Indexed: 12/15/2022] Open
Abstract
Protein allostery requires a communication channel for functional regulation between distal sites within a protein. In the molecular chaperone Hsp70, a two-domain enzyme, the ATP/ADP status of an N-terminal nucleotide-binding domain regulates the substrate affinity of a C-terminal substrate-binding domain. Recently available three-dimensional structures of Hsp70 in ATP/ADP states have provided deep insights into molecular pathways of allosteric signals. However, direct mechanical probing of long-range allosteric coupling between the ATP hydrolysis step and domain states is missing. Using laser optical tweezers, we examined the mechanical properties of a truncated two-domain DnaK(1-552ye) in apo/ADP/ATP- and peptide-bound states. We find that in the apo and ADP states, DnaK domains are mechanically stable and rigid. However, in the ATP state, substrate-binding domain (SBD)∗ye is mechanically destabilized as the result of interdomain docking followed by the unfolding of the α-helical lid. By observing the folding state of the SBD, we could observe the continuous ATP/ADP cycling of the enzyme in real time with a single molecule. The SBD lid closure is strictly coupled to the chemical steps of the ATP hydrolysis cycle even in the presence of peptide substrate.
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Affiliation(s)
- Anubhuti Singh
- Center for Functional Protein Assemblies (CPA), Physik Department, Technische Universität München, Garching, Germany
| | - Matthias Rief
- Center for Functional Protein Assemblies (CPA), Physik Department, Technische Universität München, Garching, Germany.
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University, Košice, Slovakia; Center for Interdisciplinary Biosciences, Cassovia New Industry Cluster (CNIC), Trieda SNP 1, 040 11, Košice, Slovakia.
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9
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Nordquist EB, Clerico EM, Chen J, Gierasch LM. Computationally-Aided Modeling of Hsp70-Client Interactions: Past, Present, and Future. J Phys Chem B 2022; 126:6780-6791. [PMID: 36040440 PMCID: PMC10309085 DOI: 10.1021/acs.jpcb.2c03806] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hsp70 molecular chaperones play central roles in maintaining a healthy cellular proteome. Hsp70s function by binding to short peptide sequences in incompletely folded client proteins, thus preventing them from misfolding and/or aggregating, and in many cases holding them in a state that is competent for subsequent processes like translocation across membranes. There is considerable interest in predicting the sites where Hsp70s may bind their clients, as the ability to do so sheds light on the cellular functions of the chaperone. In addition, the capacity of the Hsp70 chaperone family to bind to a broad array of clients and to identify accessible sequences that enable discrimination of those that are folded from those that are not fully folded, which is essential to their cellular roles, is a fascinating puzzle in molecular recognition. In this article we discuss efforts to harness computational modeling with input from experimental data to develop a predictive understanding of the promiscuous yet selective binding of Hsp70 molecular chaperones to accessible sequences within their client proteins. We trace how an increasing understanding of the complexities of Hsp70-client interactions has led computational modeling to new underlying assumptions and design features. We describe the trend from purely data-driven analysis toward increased reliance on physics-based modeling that deeply integrates structural information and sequence-based functional data with physics-based binding energies. Notably, new experimental insights are adding to our understanding of the molecular origins of "selective promiscuity" in substrate binding by Hsp70 chaperones and challenging the underlying assumptions and design used in earlier predictive models. Taking the new experimental findings together with exciting progress in computational modeling of protein structures leads us to foresee a bright future for a predictive understanding of selective-yet-promiscuous binding exploited by Hsp70 molecular chaperones; the resulting new insights will also apply to substrate binding by other chaperones and by signaling proteins.
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Affiliation(s)
- Erik B. Nordquist
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, 01003, United States
| | - Eugenia M. Clerico
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, 01003, United States
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, 01003, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, 01003, United States
| | - Lila M. Gierasch
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, 01003, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, 01003, United States
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10
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The Role of Hsp90-R2TP in Macromolecular Complex Assembly and Stabilization. Biomolecules 2022; 12:biom12081045. [PMID: 36008939 PMCID: PMC9406135 DOI: 10.3390/biom12081045] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 01/27/2023] Open
Abstract
Hsp90 is a ubiquitous molecular chaperone involved in many cell signaling pathways, and its interactions with specific chaperones and cochaperones determines which client proteins to fold. Hsp90 has been shown to be involved in the promotion and maintenance of proper protein complex assembly either alone or in association with other chaperones such as the R2TP chaperone complex. Hsp90-R2TP acts through several mechanisms, such as by controlling the transcription of protein complex subunits, stabilizing protein subcomplexes before their incorporation into the entire complex, and by recruiting adaptors that facilitate complex assembly. Despite its many roles in protein complex assembly, detailed mechanisms of how Hsp90-R2TP assembles protein complexes have yet to be determined, with most findings restricted to proteomic analyses and in vitro interactions. This review will discuss our current understanding of the function of Hsp90-R2TP in the assembly, stabilization, and activity of the following seven classes of protein complexes: L7Ae snoRNPs, spliceosome snRNPs, RNA polymerases, PIKKs, MRN, TSC, and axonemal dynein arms.
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11
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Johnson OT, Gestwicki JE. Multivalent protein-protein interactions are pivotal regulators of eukaryotic Hsp70 complexes. Cell Stress Chaperones 2022; 27:397-415. [PMID: 35670950 PMCID: PMC9346034 DOI: 10.1007/s12192-022-01281-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022] Open
Abstract
Heat shock protein 70 (Hsp70) is a molecular chaperone and central regulator of protein homeostasis (proteostasis). Paramount to this role is Hsp70's binding to client proteins and co-chaperones to produce distinct complexes, such that understanding the protein-protein interactions (PPIs) of Hsp70 is foundational to describing its function and dysfunction in disease. Mounting evidence suggests that these PPIs include both "canonical" interactions, which are universally conserved, and "non-canonical" (or "secondary") contacts that seem to have emerged in eukaryotes. These two categories of interactions involve discrete binding surfaces, such that some clients and co-chaperones engage Hsp70 with at least two points of contact. While the contributions of canonical interactions to chaperone function are becoming increasingly clear, it can be challenging to deconvolute the roles of secondary interactions. Here, we review what is known about non-canonical contacts and highlight examples where their contributions have been parsed, giving rise to a model in which Hsp70's secondary contacts are not simply sites of additional avidity but are necessary and sufficient to impart unique functions. From this perspective, we propose that further exploration of non-canonical contacts will generate important insights into the evolution of Hsp70 systems and inspire new approaches for developing small molecules that tune Hsp70-mediated proteostasis.
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Affiliation(s)
- Oleta T Johnson
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, 94158, USA.
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12
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Tawde M, Bior A, Feiss M, Teng F, Freimuth P. A polypeptide model for toxic aberrant proteins induced by aminoglycoside antibiotics. PLoS One 2022; 17:e0258794. [PMID: 35486612 PMCID: PMC9053816 DOI: 10.1371/journal.pone.0258794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/01/2022] [Indexed: 11/24/2022] Open
Abstract
Aminoglycoside antibiotics interfere with the selection of cognate tRNAs during translation, resulting in the synthesis of aberrant proteins that are the ultimate cause of cell death. However, the toxic potential of aberrant proteins and how they avoid degradation by the cell’s protein quality control (QC) machinery are not understood. Here we report that levels of the heat shock (HS) transcription factor σ32 increased sharply following exposure of Escherichia coli to the aminoglycoside kanamycin (Kan), suggesting that at least some of the aberrant proteins synthesized in these cells were recognized as substrates by DnaK, a molecular chaperone that regulates the HS response, the major protein QC pathway in bacteria. To further investigate aberrant protein toxic potential and interaction with cell QC factors, we studied an acutely toxic 48-residue polypeptide (ARF48) that is encoded by an alternate reading frame in a plant cDNA. As occurred in cells exposed to Kan, σ32 levels were strongly elevated following ARF48 expression, suggesting that ARF48 was recognized as a substrate by DnaK. Paradoxically, an internal 10-residue region that was tightly bound by DnaK in vitro also was required for the ARF48 toxic effect. Despite the increased levels of σ32, levels of several HS proteins were unchanged following ARF48 expression, suggesting that the HS response had been aborted. Nucleoids were condensed and cell permeability increased rapidly following ARF48 expression, together suggesting that ARF48 disrupts DNA-membrane interactions that could be required for efficient gene expression. Our results are consistent with earlier studies showing that aberrant proteins induced by aminoglycoside antibiotics disrupt cell membrane integrity. Insights into the mechanism for this effect could be gained by further study of the ARF48 model system.
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Affiliation(s)
- Mangala Tawde
- Department of Biological Sciences and Geology, Queensborough Community College, City University of New York, Bayside, New York, United States of America
| | - Abdelaziz Bior
- Department of Natural and Applied Sciences, Cheyney University of Pennsylvania, Cheyney, Pennsylvania, United States of America
| | - Michael Feiss
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, Iowa, United States of America
| | - Feiyue Teng
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Paul Freimuth
- Biology Department, Brookhaven National Laboratory, Upton, New York, United States of America
- * E-mail:
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13
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Hosfelt J, Richards A, Zheng M, Adura C, Nelson B, Yang A, Fay A, Resager W, Ueberheide B, Glickman JF, Lupoli TJ. An allosteric inhibitor of bacterial Hsp70 chaperone potentiates antibiotics and mitigates resistance. Cell Chem Biol 2021; 29:854-869.e9. [PMID: 34818532 DOI: 10.1016/j.chembiol.2021.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 09/20/2021] [Accepted: 11/02/2021] [Indexed: 12/23/2022]
Abstract
DnaK is the bacterial homolog of Hsp70, an ATP-dependent chaperone that helps cofactor proteins to catalyze nascent protein folding and salvage misfolded proteins. In the pathogen Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), DnaK and its cofactors are proposed antimycobacterial targets, yet few small-molecule inhibitors or probes exist for these families of proteins. Here, we describe the repurposing of a drug called telaprevir that is able to allosterically inhibit the ATPase activity of DnaK and to prevent chaperone function by mimicking peptide substrates. In mycobacterial cells, telaprevir disrupts DnaK- and cofactor-mediated cellular proteostasis, resulting in enhanced efficacy of aminoglycoside antibiotics and reduced resistance to the frontline TB drug rifampin. Hence, this work contributes to a small but growing collection of protein chaperone inhibitors, and it demonstrates that these molecules disrupt bacterial mechanisms of survival in the presence of different antibiotic classes.
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Affiliation(s)
- Jordan Hosfelt
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Aweon Richards
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Meng Zheng
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Carolina Adura
- High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brock Nelson
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Amy Yang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Allison Fay
- Immunology Program, Sloan Kettering Insitute, New York, NY 10065, USA
| | - William Resager
- Departments of Biochemistry and Molecular Pharmacology, Neurology and Director Proteomics Lab, Division of Advanced Research Technologies, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Beatrix Ueberheide
- Departments of Biochemistry and Molecular Pharmacology, Neurology and Director Proteomics Lab, Division of Advanced Research Technologies, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - J Fraser Glickman
- High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, New York, NY 10003, USA.
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14
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Li H, Hu L, Cuffee CW, Mohamed M, Li Q, Liu Q, Zhou L, Liu Q. Interdomain interactions dictate the function of the Candida albicans Hsp110 protein Msi3. J Biol Chem 2021; 297:101082. [PMID: 34403698 PMCID: PMC8424595 DOI: 10.1016/j.jbc.2021.101082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/29/2021] [Accepted: 08/13/2021] [Indexed: 01/27/2023] Open
Abstract
Heat shock proteins of 110 kDa (Hsp110s), a unique class of molecular chaperones, are essential for maintaining protein homeostasis. Hsp110s exhibit a strong chaperone activity preventing protein aggregation (the "holdase" activity) and also function as the major nucleotide-exchange factor (NEF) for Hsp70 chaperones. Hsp110s contain two functional domains: a nucleotide-binding domain (NBD) and substrate-binding domain (SBD). ATP binding is essential for Hsp110 function and results in close contacts between the NBD and SBD. However, the molecular mechanism of this ATP-induced allosteric coupling remains poorly defined. In this study, we carried out biochemical analysis on Msi3, the sole Hsp110 in Candida albicans, to dissect the unique allosteric coupling of Hsp110s using three mutations affecting the domain-domain interface. All the mutations abolished both the in vivo and in vitro functions of Msi3. While the ATP-bound state was disrupted in all mutants, only mutation of the NBD-SBDβ interfaces showed significant ATPase activity, suggesting that the full-length Hsp110s have an ATPase that is mainly suppressed by NBD-SBDβ contacts. Moreover, the high-affinity ATP-binding unexpectedly appears to require these NBD-SBD contacts. Remarkably, the "holdase" activity was largely intact for all mutants tested while NEF activity was mostly compromised, although both activities strictly depended on the ATP-bound state, indicating different requirements for these two activities. Stable peptide substrate binding to Msi3 led to dissociation of the NBD-SBD contacts and compromised interactions with Hsp70. Taken together, our data demonstrate that the exceptionally strong NBD-SBD contacts in Hsp110s dictate the unique allosteric coupling and biochemical activities.
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Affiliation(s)
- Hongtao Li
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Liqing Hu
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA,Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Crist William Cuffee
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Mahetab Mohamed
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Qianbin Li
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Qingdai Liu
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, China
| | - Lei Zhou
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Qinglian Liu
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA,For correspondence: Qinglian Liu
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15
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Kohler V, Andréasson C. Hsp70-mediated quality control: should I stay or should I go? Biol Chem 2021; 401:1233-1248. [PMID: 32745066 DOI: 10.1515/hsz-2020-0187] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/11/2020] [Indexed: 12/30/2022]
Abstract
Chaperones of the 70 kDa heat shock protein (Hsp70) superfamily are key components of the cellular proteostasis system. Together with its co-chaperones, Hsp70 forms proteostasis subsystems that antagonize protein damage during physiological and stress conditions. This function stems from highly regulated binding and release cycles of protein substrates, which results in a flow of unfolded, partially folded and misfolded species through the Hsp70 subsystem. Specific factors control how Hsp70 makes decisions regarding folding and degradation fates of the substrate proteins. In this review, we summarize how the flow of Hsp70 substrates is controlled in the cell with special emphasis on recent advances regarding substrate release mechanisms.
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Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
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16
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Hernandez DP, Dittmar G. Peptide array-based interactomics. Anal Bioanal Chem 2021; 413:5561-5566. [PMID: 33942139 PMCID: PMC8092715 DOI: 10.1007/s00216-021-03367-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 01/16/2023]
Abstract
The analysis of protein-protein interactions (PPIs) is essential for the understanding of cellular signaling. Besides probing PPIs with immunoprecipitation-based techniques, peptide pull-downs are an alternative tool specifically useful to study interactome changes induced by post-translational modifications. Peptides for pull-downs can be chemically synthesized and thus offer the possibility to include amino acid exchanges and post-translational modifications (PTMs) in the pull-down reaction. The combination of peptide pull-down and analysis of the binding partners with mass spectrometry offers the direct measurement of interactome changes induced by PTMs or by amino acid exchanges in the interaction site. The possibility of large-scale peptide synthesis on a membrane surface opened the possibility to systematically analyze interactome changes for mutations of many proteins at the same time. Short linear motifs (SLiMs) are amino acid patterns that can mediate protein binding. A significant number of SLiMs are located in regions of proteins, which are lacking a secondary structure, making the interaction motifs readily available for binding reactions. Peptides are particularly well suited to study protein interactions, which are based on SLiM-mediated binding. New technologies using arrayed peptides for interaction studies are able to identify SLIM-based interaction and identify the interaction motifs.
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Affiliation(s)
- Daniel Perez Hernandez
- Proteomics of Cellular Signalling, Department of Infection and Immunity, Luxembourg Institute of Health, 1 A Rue Thomas Edison, 1445, Strassen, Luxembourg
| | - Gunnar Dittmar
- Proteomics of Cellular Signalling, Department of Infection and Immunity, Luxembourg Institute of Health, 1 A Rue Thomas Edison, 1445, Strassen, Luxembourg. .,Department of Life Sciences and Medicine, University of Luxembourg, 4367, Belvaux, Luxembourg.
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17
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Abildgaard AB, Gersing SK, Larsen-Ledet S, Nielsen SV, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome. Biomolecules 2020; 10:E1141. [PMID: 32759676 PMCID: PMC7463752 DOI: 10.3390/biom10081141] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 12/11/2022] Open
Abstract
Protein homeostasis (proteostasis) is essential for the cell and is maintained by a highly conserved protein quality control (PQC) system, which triages newly synthesized, mislocalized and misfolded proteins. The ubiquitin-proteasome system (UPS), molecular chaperones, and co-chaperones are vital PQC elements that work together to facilitate degradation of misfolded and toxic protein species through the 26S proteasome. However, the underlying mechanisms are complex and remain partly unclear. Here, we provide an overview of the current knowledge on the co-chaperones that directly take part in targeting and delivery of PQC substrates for degradation. While J-domain proteins (JDPs) target substrates for the heat shock protein 70 (HSP70) chaperones, nucleotide-exchange factors (NEFs) deliver HSP70-bound substrates to the proteasome. So far, three NEFs have been established in proteasomal delivery: HSP110 and the ubiquitin-like (UBL) domain proteins BAG-1 and BAG-6, the latter acting as a chaperone itself and carrying its substrates directly to the proteasome. A better understanding of the individual delivery pathways will improve our ability to regulate the triage, and thus regulate the fate of aberrant proteins involved in cell stress and disease, examples of which are given throughout the review.
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Affiliation(s)
- Amanda B. Abildgaard
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Sarah K. Gersing
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Sven Larsen-Ledet
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Sofie V. Nielsen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (S.V.N.); (A.S.)
| | - Amelie Stein
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (S.V.N.); (A.S.)
| | - Kresten Lindorff-Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Rasmus Hartmann-Petersen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
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18
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Lebepe CM, Matambanadzo PR, Makhoba XH, Achilonu I, Zininga T, Shonhai A. Comparative Characterization of Plasmodium falciparum Hsp70-1 Relative to E. coli DnaK Reveals the Functional Specificity of the Parasite Chaperone. Biomolecules 2020; 10:biom10060856. [PMID: 32512819 PMCID: PMC7356358 DOI: 10.3390/biom10060856] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/21/2020] [Accepted: 06/01/2020] [Indexed: 12/20/2022] Open
Abstract
Hsp70 is a conserved molecular chaperone. How Hsp70 exhibits specialized functions across species remains to be understood. Plasmodium falciparum Hsp70-1 (PfHsp70-1) and Escherichia coli DnaK are cytosol localized molecular chaperones that are important for the survival of these two organisms. In the current study, we investigated comparative structure-function features of PfHsp70-1 relative to DnaK and a chimeric protein, KPf, constituted by the ATPase domain of DnaK and the substrate binding domain (SBD) of PfHsp70-1. Recombinant forms of the three Hsp70s exhibited similar secondary and tertiary structural folds. However, compared to DnaK, both KPf and PfHsp70-1 were more stable to heat stress and exhibited higher basal ATPase activity. In addition, PfHsp70-1 preferentially bound to asparagine rich peptide substrates, as opposed to DnaK. Recombinant P. falciparum adenosylmethionine decarboxylase (PfAdoMetDC) co-expressed in E. coli with either KPf or PfHsp70-1 was produced as a fully folded product. Co-expression of PfAdoMetDC with heterologous DnaK in E. coli did not promote folding of the former. However, a combination of supplementary GroEL plus DnaK improved folding of PfAdoMetDC. These findings demonstrated that the SBD of PfHsp70-1 regulates several functional features of the protein and that this molecular chaperone is tailored to facilitate folding of plasmodial proteins.
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Affiliation(s)
- Charity Mekgwa Lebepe
- Department of Biochemistry, School of Mathematical & Natural Sciences, University of Venda, Thohoyandou 0950, South Africa; (C.M.L.); (P.R.M.); (T.Z.)
| | - Pearl Rutendo Matambanadzo
- Department of Biochemistry, School of Mathematical & Natural Sciences, University of Venda, Thohoyandou 0950, South Africa; (C.M.L.); (P.R.M.); (T.Z.)
| | - Xolani Henry Makhoba
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa;
| | - Ikechukwu Achilonu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa;
| | - Tawanda Zininga
- Department of Biochemistry, School of Mathematical & Natural Sciences, University of Venda, Thohoyandou 0950, South Africa; (C.M.L.); (P.R.M.); (T.Z.)
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Addmore Shonhai
- Department of Biochemistry, School of Mathematical & Natural Sciences, University of Venda, Thohoyandou 0950, South Africa; (C.M.L.); (P.R.M.); (T.Z.)
- Correspondence:
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19
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The ribosome-associated complex RAC serves in a relay that directs nascent chains to Ssb. Nat Commun 2020; 11:1504. [PMID: 32198371 PMCID: PMC7083937 DOI: 10.1038/s41467-020-15313-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/03/2020] [Indexed: 11/21/2022] Open
Abstract
The conserved ribosome-associated complex (RAC) consisting of Zuo1 (Hsp40) and Ssz1 (non-canonical Hsp70) acts together with the ribosome-bound Hsp70 chaperone Ssb in de novo protein folding at the ribosomal tunnel exit. Current models suggest that the function of Ssz1 is confined to the support of Zuo1, however, it is not known whether RAC by itself serves as a chaperone for nascent chains. Here we show that, via its rudimentary substrate binding domain (SBD), Ssz1 directly binds to emerging nascent chains prior to Ssb. Structural and biochemical analyses identify a conserved LP-motif at the Zuo1 N-terminus forming a polyproline-II helix, which binds to the Ssz1-SBD as a pseudo-substrate. The LP-motif competes with nascent chain binding to the Ssz1-SBD and modulates nascent chain transfer. The combined data indicate that Ssz1 is an active chaperone optimized for transient, low-affinity substrate binding, which ensures the flux of nascent chains through RAC/Ssb. The ribosome-associated complex (RAC), which contains the Hsp40 protein Zuo1 and the non-canonical Hsp70 protein Ssz1 forms a chaperone triad with the fungal-specific Hsp70 protein Ssb. Here the authors combine X-ray crystallography, crosslinking and biochemical experiments and present the structure of the Zuo1 N-terminus bound to Ssz1 and demonstrate that Ssz1 is an active chaperone for nascent chains.
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20
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Li H, Zhu H, Sarbeng EB, Liu Q, Tian X, Yang Y, Lyons C, Zhou L, Liu Q. An unexpected second binding site for polypeptide substrates is essential for Hsp70 chaperone activity. J Biol Chem 2019; 295:584-596. [PMID: 31806707 DOI: 10.1074/jbc.ra119.009686] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/02/2019] [Indexed: 12/14/2022] Open
Abstract
Heat shock proteins of 70 kDa (Hsp70s) are ubiquitous and highly conserved molecular chaperones. They play multiple essential roles in assisting with protein folding and maintaining protein homeostasis. Their chaperone activity has been proposed to require several rounds of binding to and release of polypeptide substrates at the substrate-binding domain (SBD) of Hsp70s. All available structures have revealed a single substrate-binding site in the SBD that binds a single segment of an extended polypeptide of 3-4 residues. However, this well-established single peptide-binding site alone has made it difficult to explain the efficient chaperone activity of Hsp70s. In this study, using purified proteins and site-directed mutagenesis, along with fluorescence polarization and luciferase-refolding assays, we report the unexpected discovery of a second peptide-binding site in Hsp70s. More importantly, the biochemical analyses suggested that this novel binding site, named here P2, is essential for Hsp70 chaperone activity. Furthermore, cross-linking and mutagenesis studies indicated that this second binding site is in the SBD adjacent to the first binding site. Taken together, our results suggest that these two essential binding sites of Hsp70s cooperate in protein folding.
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Affiliation(s)
- Hongtao Li
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Huanyu Zhu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Evans Boateng Sarbeng
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Qingdai Liu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Xueli Tian
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Ying Yang
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Charles Lyons
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Lei Zhou
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Qinglian Liu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298.
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21
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Liu Q, Liang C, Zhou L. Structural and functional analysis of the Hsp70/Hsp40 chaperone system. Protein Sci 2019; 29:378-390. [PMID: 31509306 DOI: 10.1002/pro.3725] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 12/22/2022]
Abstract
As one of the most abundant and highly conserved molecular chaperones, the 70-kDa heat shock proteins (Hsp70s) play a key role in maintaining cellular protein homeostasis (proteostasis), one of the most fundamental tasks for every living organism. In this role, Hsp70s are inextricably linked to many human diseases, most notably cancers and neurodegenerative diseases, and are increasingly recognized as important drug targets for developing novel therapeutics for these diseases. Hsp40s are a class of essential and universal partners for Hsp70s in almost all aspects of proteostasis. Thus, Hsp70s and Hsp40s together constitute one of the most important chaperone systems across all kingdoms of life. In recent years, we have witnessed significant progress in understanding the molecular mechanism of this chaperone system through structural and functional analysis. This review will focus on this recent progress, mainly from a structural perspective.
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Affiliation(s)
- Qinglian Liu
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia
| | - Ce Liang
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia
| | - Lei Zhou
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia
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22
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Sato TK, Kawano S, Endo T. Role of the membrane potential in mitochondrial protein unfolding and import. Sci Rep 2019; 9:7637. [PMID: 31114030 PMCID: PMC6529458 DOI: 10.1038/s41598-019-44152-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/10/2019] [Indexed: 12/02/2022] Open
Abstract
Newly synthesized mitochondrial precursor proteins have to become unfolded to cross the mitochondrial membranes. This unfolding is achieved primarily by mitochondrial Hsp70 (mtHsp70) for presequence-containing precursor proteins. However, the membrane potential across the inner membrane (ΔΨ) could also contribute to unfolding of short-presequence containing mitochondrial precursor proteins. Here we investigated the role of ΔΨ in mitochondrial protein unfolding and import. We found that the effects of mutations in the presequence on import rates are correlated well with the hydrophobicity or ability to interact with import motor components including mtHsp70, but not with ΔΨ (negative inside). A spontaneously unfolded precursor protein with a short presequence is therefore trapped by motor components including mtHsp70, but not ΔΨ, which could cause global unfolding of the precursor protein. Instead, ΔΨ may contribute the precursor unfolding by holding the presequence at the inner membrane for trapping of the unfolded species by the import motor system.
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Affiliation(s)
- Takehiro K Sato
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan.,Spiber Inc. 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Shin Kawano
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan.,Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Toshiya Endo
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan. .,Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan. .,Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.
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23
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Genest O, Wickner S, Doyle SM. Hsp90 and Hsp70 chaperones: Collaborators in protein remodeling. J Biol Chem 2018; 294:2109-2120. [PMID: 30401745 DOI: 10.1074/jbc.rev118.002806] [Citation(s) in RCA: 195] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Heat shock proteins 90 (Hsp90) and 70 (Hsp70) are two families of highly conserved ATP-dependent molecular chaperones that fold and remodel proteins. Both are important components of the cellular machinery involved in protein homeostasis and participate in nearly every cellular process. Although Hsp90 and Hsp70 each carry out some chaperone activities independently, they collaborate in other cellular remodeling reactions. In eukaryotes, both Hsp90 and Hsp70 function with numerous Hsp90 and Hsp70 co-chaperones. In contrast, bacterial Hsp90 and Hsp70 are less complex; Hsp90 acts independently of co-chaperones, and Hsp70 uses two co-chaperones. In this review, we focus on recent progress toward understanding the basic mechanisms of Hsp90-mediated protein remodeling and the collaboration between Hsp90 and Hsp70, with an emphasis on bacterial chaperones. We describe the structure and conformational dynamics of these chaperones and their interactions with each other and with client proteins. The physiological roles of Hsp90 in Escherichia coli and other bacteria are also discussed. We anticipate that the information gained from exploring the mechanism of the bacterial chaperone system will provide the groundwork for understanding the more complex eukaryotic Hsp90 system and its modulation by Hsp90 co-chaperones.
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Affiliation(s)
- Olivier Genest
- From the Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, 13402 Marseille, France and
| | - Sue Wickner
- the Laboratory of Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Shannon M Doyle
- the Laboratory of Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892
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24
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Sugimoto S, Arita-Morioka KI, Terao A, Yamanaka K, Ogura T, Mizunoe Y. Multitasking of Hsp70 chaperone in the biogenesis of bacterial functional amyloids. Commun Biol 2018; 1:52. [PMID: 30271935 PMCID: PMC6123696 DOI: 10.1038/s42003-018-0056-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/19/2018] [Indexed: 11/21/2022] Open
Abstract
Biofilms are intricate communities of microorganisms embedded in a self-produced matrix of extracellular polymer, which provides microbes survival advantages in stressful environments and can cause chronic infections in humans. Curli are functional amyloids that assemble on the extracellular surface of enteric bacteria such as Escherichia coli during biofilm development and colonization. The molecular chaperone DnaK, a bacterial Hsp70 homologue, promotes curli biogenesis via unknown mechanism(s). Here we show that DnaK increases the expression of CsgA and CsgB—the major and minor structural components of curli, respectively—via a quantity and quality control of RpoS, a stationary phase-specific alternative sigma factor regulating bacterial transcription, and CsgD, the master transcriptional regulator of curli formation. DnaK also keeps CsgA and CsgB in a translocation-competent state by binding to their signal peptides prone to aggregation. Our findings suggest that DnaK controls the homoeostasis of curli biogenesis at multiple stages to organize the biofilm matrix. Shinya Sugimoto et al. demonstrate how molecular chaperone DnaK regulates biofilm formation through the production of curli, which anchor enteric bacteria to the biofilm. This finding provides mechanistic insights into the development of anti-biofilm agents as antibiotics.
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Affiliation(s)
- Shinya Sugimoto
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan. .,Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan.
| | - Ken-Ichi Arita-Morioka
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-Ku, Kumamoto, 860-0811, Japan.,Advanced Science Research Center, Fukuoka Dental College, 2-15-1 Tamura, Sawara-Ku, Fukuoka, 814-0193, Japan
| | - Akari Terao
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
| | - Kunitoshi Yamanaka
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-Ku, Kumamoto, 860-0811, Japan
| | - Teru Ogura
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-Ku, Kumamoto, 860-0811, Japan
| | - Yoshimitsu Mizunoe
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan.,Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
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Penke B, Bogár F, Crul T, Sántha M, Tóth ME, Vígh L. Heat Shock Proteins and Autophagy Pathways in Neuroprotection: from Molecular Bases to Pharmacological Interventions. Int J Mol Sci 2018; 19:E325. [PMID: 29361800 PMCID: PMC5796267 DOI: 10.3390/ijms19010325] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/15/2018] [Accepted: 01/18/2018] [Indexed: 02/07/2023] Open
Abstract
Neurodegenerative diseases (NDDs) such as Alzheimer's disease, Parkinson's disease and Huntington's disease (HD), amyotrophic lateral sclerosis, and prion diseases are all characterized by the accumulation of protein aggregates (amyloids) into inclusions and/or plaques. The ubiquitous presence of amyloids in NDDs suggests the involvement of disturbed protein homeostasis (proteostasis) in the underlying pathomechanisms. This review summarizes specific mechanisms that maintain proteostasis, including molecular chaperons, the ubiquitin-proteasome system (UPS), endoplasmic reticulum associated degradation (ERAD), and different autophagic pathways (chaperon mediated-, micro-, and macro-autophagy). The role of heat shock proteins (Hsps) in cellular quality control and degradation of pathogenic proteins is reviewed. Finally, putative therapeutic strategies for efficient removal of cytotoxic proteins from neurons and design of new therapeutic targets against the progression of NDDs are discussed.
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Affiliation(s)
- Botond Penke
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Dóm Square 8, Hungary.
| | - Ferenc Bogár
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Dóm Square 8, Hungary.
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged, H-6720 Szeged, Dóm Square 8, Hungary.
| | - Tim Crul
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62, Hungary.
| | - Miklós Sántha
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62, Hungary.
| | - Melinda E Tóth
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62, Hungary.
| | - László Vígh
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62, Hungary.
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Conformation transitions of the polypeptide-binding pocket support an active substrate release from Hsp70s. Nat Commun 2017; 8:1201. [PMID: 29084938 PMCID: PMC5662698 DOI: 10.1038/s41467-017-01310-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/07/2017] [Indexed: 12/21/2022] Open
Abstract
Cellular protein homeostasis depends on heat shock proteins 70 kDa (Hsp70s), a class of ubiquitous and highly conserved molecular chaperone. Key to the chaperone activity is an ATP-induced allosteric regulation of polypeptide substrate binding and release. To illuminate the molecular mechanism of this allosteric coupling, here we present a novel crystal structure of an intact human BiP, an essential Hsp70 in ER, in an ATP-bound state. Strikingly, the polypeptide-binding pocket is completely closed, seemingly excluding any substrate binding. Our FRET, biochemical and EPR analysis suggests that this fully closed conformation is the major conformation for the ATP-bound state in solution, providing evidence for an active release of bound polypeptide substrates following ATP binding. The Hsp40 co-chaperone converts this fully closed conformation to an open conformation to initiate productive substrate binding. Taken together, this study provided a mechanistic understanding of the dynamic nature of the polypeptide-binding pocket in the Hsp70 chaperone cycle. Hsp70s are highly conserved molecular chaperones that play multiple essential roles in maintaining cellular protein homeostasis. Here, the authors provide structural evidence for active substrate release by Hsp70s upon ATP binding and provide insight into the molecular mechanism of ATP-driven Hsp70 chaperone activity.
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27
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Kishor A, White EJF, Matsangos AE, Yan Z, Tandukar B, Wilson GM. Hsp70's RNA-binding and mRNA-stabilizing activities are independent of its protein chaperone functions. J Biol Chem 2017; 292:14122-14133. [PMID: 28679534 PMCID: PMC5572911 DOI: 10.1074/jbc.m117.785394] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/29/2017] [Indexed: 12/22/2022] Open
Abstract
Hsp70 is a protein chaperone that prevents protein aggregation and aids protein folding by binding to hydrophobic peptide domains through a reversible mechanism directed by an ATPase cycle. However, Hsp70 also binds U-rich RNA including some AU-rich elements (AREs) that regulate the decay kinetics of select mRNAs and has recently been shown to bind and stabilize some ARE-containing transcripts in cells. Previous studies indicated that both the ATP- and peptide-binding domains of Hsp70 contributed to the stability of Hsp70-RNA complexes and that ATP might inhibit RNA recruitment. This suggested the possibility that RNA binding by Hsp70 might mimic features of its peptide-directed chaperone activities. Here, using purified, cofactor-free preparations of recombinant human Hsp70 and quantitative biochemical approaches, we found that high-affinity RNA binding requires at least 30 nucleotides of RNA sequence but is independent of Hsp70's nucleotide-bound status, ATPase activity, or peptide-binding roles. Furthermore, although both the ATP- and peptide-binding domains of Hsp70 could form complexes with an ARE sequence from VEGFA mRNA in vitro, only the peptide-binding domain could recover cellular VEGFA mRNA in ribonucleoprotein immunoprecipitations. Finally, Hsp70-directed stabilization of VEGFA mRNA in cells was mediated exclusively by the protein's peptide-binding domain. Together, these findings indicate that the RNA-binding and mRNA-stabilizing functions of Hsp70 are independent of its protein chaperone cycle but also provide potential mechanical explanations for several well-established and recently discovered cytoprotective and RNA-based Hsp70 functions.
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Affiliation(s)
- Aparna Kishor
- From the Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Elizabeth J F White
- From the Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Aerielle E Matsangos
- From the Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Zisui Yan
- From the Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Bishal Tandukar
- From the Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Gerald M Wilson
- From the Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201.
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28
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Bose D, Chakrabarti A. Substrate specificity in the context of molecular chaperones. IUBMB Life 2017; 69:647-659. [PMID: 28748601 DOI: 10.1002/iub.1656] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/03/2017] [Indexed: 12/23/2022]
Abstract
Molecular chaperones are one of the key players in protein biology and as such their structure and mechanism of action have been extensively studied. However the substrate specificity of molecular chaperones has not been well investigated. This review aims to summarize what is known about the substrate specificity and substrate recognition motifs of chaperones so as to better understand what substrate specificity means in the context of molecular chaperones. Available literature shows that the majority of chaperones have broad substrate range and recognize non-native conformations of proteins depending on recognition of hydrophobic and/or charged patches. Based on these recognition motifs chaperones can select for early, mid or late folding intermediates. Another major contributor to chaperone specificity are the co-chaperones they interact with as well as the sub-cellular location they are expressed in and the inducability of their expression. Some chaperones which have only one or a few known substrates are reported. In their case the mode of recognition seems to be specific structural complementarity between chaperone and substrate. It can be concluded that the vast majority of chaperones do not show a high degree of specificity but recognize elements that signal non-native protein conformation and their substrate range is modulated by the context they function in. However a few chaperones are known that display exquisite specificity of their substrate e.g. mammalian heat shock protein 47 collagen interaction. © 2017 IUBMB Life, 69(9):647-659, 2017.
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Affiliation(s)
- Dipayan Bose
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, India
| | - Abhijit Chakrabarti
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, India
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29
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Nanomechanics of the substrate binding domain of Hsp70 determine its allosteric ATP-induced conformational change. Proc Natl Acad Sci U S A 2017; 114:6040-6045. [PMID: 28533394 DOI: 10.1073/pnas.1619843114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Owing to the cooperativity of protein structures, it is often almost impossible to identify independent subunits, flexible regions, or hinges simply by visual inspection of static snapshots. Here, we use single-molecule force experiments and simulations to apply tension across the substrate binding domain (SBD) of heat shock protein 70 (Hsp70) to pinpoint mechanical units and flexible hinges. The SBD consists of two nanomechanical units matching 3D structural parts, called the α- and β-subdomain. We identified a flexible region within the rigid β-subdomain that gives way under load, thus opening up the α/β interface. In exactly this region, structural changes occur in the ATP-induced opening of Hsp70 to allow substrate exchange. Our results show that the SBD's ability to undergo large conformational changes is already encoded by passive mechanics of the individual elements.
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Liu Q, Li H, Yang Y, Tian X, Su J, Zhou L, Liu Q. A disulfide-bonded DnaK dimer is maintained in an ATP-bound state. Cell Stress Chaperones 2017; 22:201-212. [PMID: 27975204 PMCID: PMC5352592 DOI: 10.1007/s12192-016-0752-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/16/2016] [Accepted: 11/28/2016] [Indexed: 01/16/2023] Open
Abstract
DnaK, a major Hsp70 molecular chaperones in Escherichia coli, is a widely used model for studying Hsp70s. We recently solved a crystal structure of DnaK in complex with ATP and showed that DnaK was packed as a dimer in the crystal structure. Our previous biochemical studies supported the formation of a specific DnaK dimer as observed in the crystal structure in solution in the presence of ATP and suggested an important role of this dimer in efficient interaction with Hsp40 co-chaperones. In this study, we dissected the biochemical properties of this DnaK dimer. To restrict DnaK in this dimer form, we mutated two residues on the dimer interface to cysteine, A303C, and H541C. Upon oxidation, this DnaK-A303C-H541C protein formed a specific dimer linked by disulfide bonds formed between A303C and H541C only in the presence of ATP, consistent with the crystal structure. Intriguingly, this disulfide-bond-linked dimer of DnaK-A303C-H541C has reduced ATPase activity and decreased affinity for peptide substrate. More interestingly, unlike wild-type DnaK, the peptide substrate-binding kinetics of this dimer is drastically accelerated even in the absence of ATP, suggesting this dimer is restricted in an ATP-bound conformation regardless of nucleotide bound, which was further supported by our analysis using tryptophan fluorescence and ATP-induced peptide release. Thus, formation of the dimer restricted DnaK in an ATP-bound state and blocked the progression through the chaperone cycle. Productive progression through the chaperone cycle requires the dissociation of this transient dimer. Surprisingly, a significantly compromised interaction with Hsp40 co-chaperone was observed for this disulfide-bond-linked dimer. Thus, dissociation of this DnaK dimer is equally crucial for efficient Hsp40 interaction. An initial interaction between Hsp70 and Hsp40 requires the formation of DnaK dimer; but a stable Hsp70-Hsp40 interaction may follow the dissociation of the dimer.
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Affiliation(s)
- Qingdai Liu
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, 300457, China.
| | - Hongtao Li
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Ying Yang
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, 300457, China
| | - Xueli Tian
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, 300457, China
| | - Jiayue Su
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, 300457, China
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Lei Zhou
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Qinglian Liu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA.
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31
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Proper Control of Caulobacter crescentus Cell Surface Adhesion Requires the General Protein Chaperone DnaK. J Bacteriol 2016; 198:2631-42. [PMID: 27044628 DOI: 10.1128/jb.00027-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 03/30/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Growth in a surface-attached bacterial community, or biofilm, confers a number of advantages. However, as a biofilm matures, high-density growth imposes stresses on individual cells, and it can become less advantageous for progeny to remain in the community. Thus, bacteria employ a variety of mechanisms to control attachment to and dispersal from surfaces in response to the state of the environment. The freshwater oligotroph Caulobacter crescentus can elaborate a polysaccharide-rich polar organelle, known as the holdfast, which enables permanent surface attachment. Holdfast development is strongly inhibited by the small protein HfiA; mechanisms that control HfiA levels in the cell are not well understood. We have discovered a connection between the essential general protein chaperone, DnaK, and control of C. crescentus holdfast development. C. crescentus mutants partially or completely lacking the C-terminal substrate binding "lid" domain of DnaK exhibit enhanced bulk surface attachment. Partial or complete truncation of the DnaK lid domain increases the probability that any single cell will develop a holdfast by 3- to 10-fold. These results are consistent with the observation that steady-state levels of an HfiA fusion protein are significantly diminished in strains that lack the entire lid domain of DnaK. While dispensable for growth, the lid domain of C. crescentus DnaK is required for proper chaperone function, as evidenced by observed dysregulation of HfiA and holdfast development in strains expressing lidless DnaK mutants. We conclude that DnaK is an important molecular determinant of HfiA stability and surface adhesion control. IMPORTANCE Regulatory control of cell adhesion ensures that bacterial cells can transition between free-living and surface-attached states. We define a role for the essential protein chaperone, DnaK, in the control of Caulobacter crescentus cell adhesion. C. crescentus surface adhesion is mediated by an envelope-attached organelle known as the holdfast. Holdfast development is tightly controlled by HfiA, a small protein inhibitor that directly interacts with a WecG/TagA-family glycosyltransferase required for holdfast biosynthesis. We demonstrate that the C-terminal lid domain of DnaK is not essential for growth but is necessary for proper control of HfiA levels in the cell and for control of holdfast adhesin development.
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32
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Clerico EM, Tilitsky JM, Meng W, Gierasch LM. How hsp70 molecular machines interact with their substrates to mediate diverse physiological functions. J Mol Biol 2015; 427:1575-88. [PMID: 25683596 DOI: 10.1016/j.jmb.2015.02.004] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/06/2015] [Accepted: 02/06/2015] [Indexed: 12/27/2022]
Abstract
Hsp70 molecular chaperones are implicated in a wide variety of cellular processes, including protein biogenesis, protection of the proteome from stress, recovery of proteins from aggregates, facilitation of protein translocation across membranes, and more specialized roles such as disassembly of particular protein complexes. It is a fascinating question to ask how the mechanism of these deceptively simple molecular machines is matched to their roles in these wide-ranging processes. The key is a combination of the nature of the recognition and binding of Hsp70 substrates and the impact of Hsp70 action on their substrates. In many cases, the binding, which relies on interaction with an extended, accessible short hydrophobic sequence, favors more unfolded states of client proteins. The ATP-mediated dissociation of the substrate thus releases it in a relatively less folded state for downstream folding, membrane translocation, or hand-off to another chaperone. There are cases, such as regulation of the heat shock response or disassembly of clathrin coats, however, where binding of a short hydrophobic sequence selects conformational states of clients to favor their productive participation in a subsequent step. This Perspective discusses current understanding of how Hsp70 molecular chaperones recognize and act on their substrates and the relationships between these fundamental processes and the functional roles played by these molecular machines.
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Affiliation(s)
- Eugenia M Clerico
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Life Sciences Laboratory, University of Massachusetts Amherst, 240 Thatcher Way, Amherst, MA 01003, USA
| | - Joseph M Tilitsky
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Life Sciences Laboratory, University of Massachusetts Amherst, 240 Thatcher Way, Amherst, MA 01003, USA
| | - Wenli Meng
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Life Sciences Laboratory, University of Massachusetts Amherst, 240 Thatcher Way, Amherst, MA 01003, USA
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Life Sciences Laboratory, University of Massachusetts Amherst, 240 Thatcher Way, Amherst, MA 01003, USA.
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33
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Podolnikova NP, Podolnikov AV, Haas TA, Lishko VK, Ugarova TP. Ligand recognition specificity of leukocyte integrin αMβ2 (Mac-1, CD11b/CD18) and its functional consequences. Biochemistry 2015; 54:1408-20. [PMID: 25613106 DOI: 10.1021/bi5013782] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The broad recognition specificity exhibited by integrin α(M)β2 (Mac-1, CD11b/CD18) has allowed this adhesion receptor to play innumerable roles in leukocyte biology, yet we know little about how and why α(M)β2 binds its multiple ligands. Within α(M)β2, the α(M)I-domain is responsible for integrin's multiligand binding properties. To identify its recognition motif, we screened peptide libraries spanning sequences of many known protein ligands for α(M)I-domain binding and also selected the α(M)I-domain recognition sequences by phage display. Analyses of >1400 binding and nonbinding peptides derived from peptide libraries showed that a key feature of the α(M)I-domain recognition motif is a small core consisting of basic amino acids flanked by hydrophobic residues. Furthermore, the peptides selected by phage display conformed to a similar pattern. Identification of the recognition motif allowed the construction of an algorithm that reliably predicts the α(M)I-domain binding sites in the α(M)β2 ligands. The recognition specificity of the α(M)I-domain resembles that of some chaperones, which allows it to bind segments exposed in unfolded proteins. The disclosure of the α(M)β2 binding preferences allowed the prediction that cationic host defense peptides, which are strikingly enriched in the α(M)I-domain recognition motifs, represent a new class of α(M)β2 ligands. This prediction has been tested by examining the interaction of α(M)β2 with the human cathelicidin peptide LL-37. LL-37 induced a potent α(M)β2-dependent cell migratory response and caused activation of α(M)β2 on neutrophils. The newly revealed recognition specificity of α(M)β2 toward unfolded protein segments and cationic proteins and peptides suggests that α(M)β2 may serve as a previously proposed "alarmin" receptor with important roles in innate host defense.
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Affiliation(s)
- Nataly P Podolnikova
- Center for Metabolic and Vascular Biology, School of Life Sciences, Arizona State University , Tempe, Arizona 85287, United States
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Chotewutmontri P, Bruce BD. Non-native, N-terminal Hsp70 molecular motor recognition elements in transit peptides support plastid protein translocation. J Biol Chem 2015; 290:7602-21. [PMID: 25645915 DOI: 10.1074/jbc.m114.633586] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Previously, we identified the N-terminal domain of transit peptides (TPs) as a major determinant for the translocation step in plastid protein import. Analysis of Arabidopsis TP dataset revealed that this domain has two overlapping characteristics, highly uncharged and Hsp70-interacting. To investigate these two properties, we replaced the N-terminal domains of the TP of the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and its reverse peptide with a series of unrelated peptides whose affinities to the chloroplast stromal Hsp70 have been determined. Bioinformatic analysis indicated that eight out of nine peptides in this series are not similar to the TP N terminus. Using in vivo and in vitro protein import assays, the majority of the precursors containing Hsp70-binding elements were targeted to plastids, whereas none of the chimeric precursors lacking an N-terminal Hsp70-binding element were targeted to the plastids. Moreover, a pulse-chase assay showed that two chimeric precursors with the most uncharged peptides failed to translocate into the stroma. The ability of multiple unrelated Hsp70-binding elements to support protein import verified that the majority of TPs utilize an N-terminal Hsp70-binding domain during translocation and expand the mechanistic view of the import process. This work also indicates that synthetic biology may be utilized to create de novo TPs that exceed the targeting activity of naturally occurring sequences.
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Affiliation(s)
| | - Barry D Bruce
- From the Graduate School of Genome Science and Technology, Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
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Sarbeng EB, Liu Q, Tian X, Yang J, Li H, Wong JL, Zhou L, Liu Q. A functional DnaK dimer is essential for the efficient interaction with Hsp40 heat shock protein. J Biol Chem 2015; 290:8849-62. [PMID: 25635056 DOI: 10.1074/jbc.m114.596288] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Indexed: 12/28/2022] Open
Abstract
Highly conserved molecular chaperone Hsp70 heat shock proteins play a key role in maintaining protein homeostasis (proteostasis). DnaK, a major Hsp70 in Escherichia coli, has been widely used as a paradigm for studying Hsp70s. In the absence of ATP, purified DnaK forms low-ordered oligomer, whereas ATP binding shifts the equilibrium toward the monomer. Recently, we solved the crystal structure of DnaK in complex with ATP. There are two molecules of DnaK-ATP in the asymmetric unit. Interestingly, the interfaces between the two molecules of DnaK are large with good surface complementarity, suggesting functional importance of this crystallographic dimer. Biochemical analyses of DnaK protein supported the formation of dimer in solution. Furthermore, our cross-linking experiment based on the DnaK-ATP structure confirmed that DnaK forms specific dimer in an ATP-dependent manner. To understand the physiological function of the dimer, we mutated five residues on the dimer interface. Four mutations, R56A, T301A, N537A, and D540A, resulted in loss of chaperone activity and compromised the formation of dimer, indicating the functional importance of the dimer. Surprisingly, neither the intrinsic biochemical activities, the ATP-induced allosteric coupling, nor GrpE co-chaperone interaction is affected appreciably in all of the mutations except for R56A. Unexpectedly, the interaction with co-chaperone Hsp40 is significantly compromised. In summary, this study suggests that DnaK forms a transient dimer upon ATP binding, and this dimer is essential for the efficient interaction of DnaK with Hsp40.
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Affiliation(s)
- Evans Boateng Sarbeng
- From the Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Qingdai Liu
- From the Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Xueli Tian
- From the Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Jiao Yang
- From the Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Hongtao Li
- From the Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Jennifer Li Wong
- From the Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Lei Zhou
- From the Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Qinglian Liu
- From the Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
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Spectroscopic and thermodynamic properties of recombinant heat shock protein A6 from Camelus dromedarius. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 44:17-26. [DOI: 10.1007/s00249-014-0997-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 12/30/2022]
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37
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Purification and biochemical characterization of DnaK and its transcriptional activator RpoH from Neisseria gonorrhoeae. Mol Biol Rep 2014; 41:7945-53. [PMID: 25156536 DOI: 10.1007/s11033-014-3689-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 08/21/2014] [Indexed: 10/24/2022]
Abstract
DnaK plays a central role in stress response in the important human pathogen Neisseria gonorrhoeae. The genes encoding the DnaK chaperone machine (DnaK/DnaJ/GrpE) in N. gonorrhoeae are transcribed from RpoH (σ(32))-dependent promoters. In this study, we cloned, purified and biochemically characterised N. gonorrhoeae DnaK (NgDnaK) and RpoH. The NgDnaK and RpoH sequences are 73 and 50 % identical to the sequences of their respective E. coli counterparts. Similar to EcDnaK, nucleotide-free NgDnaK exists as a mix of monomers, dimers and higher oligomeric species in solution, and dissociates into monomers on addition of ATP. Like E. coli σ(32), RpoH of N. gonorrhoeae is monomeric in solution. Kinetic analysis of the basal ATPase activity of purified NgDnaK revealed a V max of 193 pmol phosphate released per minute per microgram DnaK (which is significantly higher than reported basal ATPase activity of EcDnaK), and the turnover number against ATP was 0.4 min(-1) under our assay conditions. Nucleotide-free NgDnaK bound a short model substrate, NR-peptide, with micromolar affinity close to that reported for EcDnaK. Our analysis showed that interaction between N. gonorrhoeae RpoH and DnaK appears to be ATP-dependent and non-specific, in stark contrast to the E. coli DnaK system where σ(32) and DnaK interact as monomers even in the absence of ATP. Sequence comparison showed that the DnaK-binding site of σ(32) is not conserved in RpoH. Our findings suggest that the mechanism of DnaK/RpoH recognition in N. gonorrhoeae is different from that in E. coli.
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Zhang P, Leu JIJ, Murphy ME, George DL, Marmorstein R. Crystal structure of the stress-inducible human heat shock protein 70 substrate-binding domain in complex with peptide substrate. PLoS One 2014; 9:e103518. [PMID: 25058147 PMCID: PMC4110032 DOI: 10.1371/journal.pone.0103518] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 07/03/2014] [Indexed: 11/18/2022] Open
Abstract
The HSP70 family of molecular chaperones function to maintain protein quality control and homeostasis. The major stress-induced form, HSP70 (also called HSP72 or HSPA1A) is considered an important anti-cancer drug target because it is constitutively overexpressed in a number of human cancers and promotes cancer cell survival. All HSP70 family members contain two functional domains: an N-terminal nucleotide binding domain (NBD) and a C-terminal protein substrate-binding domain (SBD); the latter is subdivided into SBDα and SBDβ subdomains. The NBD and SBD structures of the bacterial ortholog, DnaK, have been characterized, but only the isolated NBD and SBDα segments of eukaryotic HSP70 proteins have been determined. Here we report the crystal structure of the substrate-bound human HSP70-SBD to 2 angstrom resolution. The overall fold of this SBD is similar to the corresponding domain in the substrate-bound DnaK structures, confirming a similar overall architecture of the orthologous bacterial and human HSP70 proteins. However, conformational differences are observed in the peptide-HSP70-SBD complex, particularly in the loop Lα, β that bridges SBDα to SBDβ, and the loop LL,1 that connects the SBD and NBD. The interaction between the SBDα and SBDβ subdomains and the mode of substrate recognition is also different between DnaK and HSP70. This suggests that differences may exist in how different HSP70 proteins recognize their respective substrates. The high-resolution structure of the substrate-bound-HSP70-SBD complex provides a molecular platform for the rational design of small molecule compounds that preferentially target this C-terminal domain, in order to modulate human HSP70 function.
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Affiliation(s)
- Pingfeng Zhang
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry & Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Julia I-Ju Leu
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (JI-JL) (JL); (RM) (RM)
| | - Maureen E. Murphy
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Donna L. George
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ronen Marmorstein
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry & Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (JI-JL) (JL); (RM) (RM)
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Macazo FC, White RJ. Monitoring charge flux to quantify unusual ligand-induced ion channel activity for use in biological nanopore-based sensors. Anal Chem 2014; 86:5519-25. [PMID: 24794413 PMCID: PMC4051251 DOI: 10.1021/ac500832a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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The
utility of biological nanopores for the development of sensors
has become a growing area of interest in analytical chemistry. Their
emerging use in chemical analysis is a result of several ideal characteristics.
First, they provide reproducible control over nanoscale pore sizes
with an atomic level of precision. Second, they are amenable to resistive-pulse
type measurement systems when embedded into an artificial lipid bilayer.
A single binding event causes a change in the flow of millions of
ions across the membrane per second that is readily measured as a
change in current with excellent signal-to-noise ratio. To date, ion
channel-based biosensors have been limited to well-behaved proteins.
Most demonstrations of using ion channels as sensors have been limited
to proteins that remain in the open, conducting state, unless occupied
by an analyte of interest. Furthermore, these proteins are nonspecific,
requiring chemical, biochemical, or genetic manipulations to impart
chemical specificity. Here, we report on the use of the pore-forming
abilities of heat shock cognate 70 (Hsc70) to quantify a specific
analyte. Hsc70 reconstitutes into phospholipid membranes and opens
to form multiple conductance states specifically in the presence of
ATP. We introduce the measurement of “charge flux” to
characterize the ATP-regulated multiconductance nature of Hsc70, which
enables sensitive quantification of ATP (100 μM–4 mM).
We believe that monitoring protein-induced charge flux across a bilayer
membrane represents a universal method for quantitatively monitoring
ion-channel activity. This measurement has the potential to broaden
the library of usable proteins in the development of nanopore-based
biosensors.
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Affiliation(s)
- Florika C Macazo
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County , 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
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Kumar M, Prasanna R, Lone S, Padaria JC, Saxena AK. Cloning and expression of dnaK gene from Bacillus pumilus of hot water spring origin. Appl Transl Genom 2014; 3:14-20. [PMID: 27275408 PMCID: PMC4881820 DOI: 10.1016/j.atg.2013.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/02/2013] [Accepted: 10/01/2013] [Indexed: 06/06/2023]
Abstract
A set of thermotolerant strains isolated from hot springs of Manikaran and Bakreshwar (India) were selected with an aim to isolate dnak gene which encodes DnaK protein. The gene dnaK along with its flanking region was successfully amplified from 5 different strains (4 from Bakreshwar and one from Manikaran). Restriction fragment length polymorphism (RFLP) revealed that amplicons were almost identical in sequence. The dnak gene from one representative, Bacillus pumilus strain B3 isolated from Bakreshwar hot springs was successfully cloned and sequenced. The dnaK gene was flanked by gene grpE on one side. The dnaK gene was 1842 bp in length encoding a polypeptide of 613 amino acid residues. Calculated molecular weight and pI of the protein were 66,128.36 Da and 4.72 respectively. The deduced amino acid sequence of this gene shared high sequence homology with other DnaK proteins and its homologue Hsp 70 from other microorganisms, but possessed 36 substitutions and two insertions, as compared to DnaK protein of Bacillus subtilis. The dnaK gene of B. pumilus was successfully expressed in Escherichia coli BL 21 (DE3) using pET expression systems. Heterologous expression of dnaK of B. pumilus in E. coli BL 21 (DE3) allowed for the growth of E. coli up to 50 °C and survival up to 60 °C for 16 h, suggesting that dnak from B. pumilus imparts tolerance to host cells under high temperature. This novel gene can be an important component for possible utilization in abiotic stress management of plants.
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Affiliation(s)
- Murugan Kumar
- Division of Microbiology, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Radha Prasanna
- Division of Microbiology, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Showkat Lone
- National Research Centre on Plant Biotechnology, New Delhi 110012, India
| | | | - Anil Kumar Saxena
- Division of Microbiology, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
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Liu L, McNeilage RT, Shi LX, Theg SM. ATP requirement for chloroplast protein import is set by the Km for ATP hydrolysis of stromal Hsp70 in Physcomitrella patens. THE PLANT CELL 2014; 26:1246-55. [PMID: 24596240 PMCID: PMC4001381 DOI: 10.1105/tpc.113.121822] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 12/12/2013] [Accepted: 02/09/2014] [Indexed: 05/20/2023]
Abstract
The 70-kD family of heat shock proteins (Hsp70s) is involved in a number of seemingly disparate cellular functions, including folding of nascent proteins, breakup of misfolded protein aggregates, and translocation of proteins across membranes. They act through the binding and release of substrate proteins, accompanied by hydrolysis of ATP. Chloroplast stromal Hsp70 plays a crucial role in the import of proteins into plastids. Mutations of an ATP binding domain Thr were previously reported to result in an increase in the Km for ATP and a decrease in the enzyme's kcat. To ask which chloroplast stromal chaperone, Hsp70 or Hsp93, both of which are ATPases, dominates the energetics of the motor responsible for protein import, we made transgenic moss (Physcomitrella patens) harboring the Km-altering mutation in the essential stromal Hsp70-2 and measured the effect on the amount of ATP required for protein import into chloroplasts. Here, we report that increasing the Km for ATP hydrolysis of Hsp70 translated into an increased Km for ATP usage by chloroplasts for protein import. This thus directly demonstrates that the ATP-derived energy long known to be required for chloroplast protein import is delivered via the Hsp70 chaperones and that the chaperone's ATPase activity dominates the energetics of the reaction.
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Tiroli-Cepeda AO, Lima TB, Balbuena TS, Gozzo FC, Ramos CHI. Structural and functional characterization of the chaperone Hsp70 from sugarcane. Insights into conformational changes during cycling from cross-linking/mass spectrometry assays. J Proteomics 2014; 104:48-56. [PMID: 24530624 DOI: 10.1016/j.jprot.2014.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 01/28/2014] [Accepted: 02/02/2014] [Indexed: 01/20/2023]
Abstract
UNLABELLED Hsp70 cycles from an ATP-bound state, in which the affinity for unfolded polypeptides is low, to an ADP-bound state, in which the affinity for unfolded polypeptides is high, to assist with cell proteostasis. Such cycling also depends on co-chaperones because these proteins control both the Hsp70 ATPase activity and the delivery of unfolded polypeptide chains. Although it is very important, structural information on the entire protein is still scarce. This work describes the first cloning of a cDNA predicted to code for a cytosolic Saccharum spp. (sugarcane) Hsp70, named SsHsp70 here, the purification of the recombinant protein and the characterization of its structural conformation in solution by chemical cross-linking coupled to mass spectrometry. The in vivo expression of SsHsp70 in sugarcane extracts was confirmed by Western blot. Recombinant SsHsp70 was monomeric, both ADP and ATP binding increased its stability and it was efficient in cooperating with co-chaperones: ATPase activity was stimulated by Hsp40s, and it aided the refolding of an unfolded polypeptide delivered by a member of the small Hsp family. The structural conformation results favor a model in which nucleotide-free SsHsp70 is highly dynamic and may fluctuate among different conformations that may resemble those in which nucleotide is bound. BIOLOGICAL SIGNIFICANCE Validation of a sugarcane EST as a true mRNA that encodes a cytosolic Hsp70 (SsHsp70) as confirmed by in vivo expression and characterization of the structure and function of the recombinant protein. SsHsp70 was monomeric, both ADP and ATP binding increased its stability and was efficient in interacting and cooperating with co-chaperones to enhance ATPase activity and refold unfolded proteins. The conformation of nucleotide-free SsHsp70 in solution was much more dynamic than suggested by crystal structures of other Hsp70s. This article is part of a Special Issue entitled: Environmental and structural proteomics.
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Affiliation(s)
- Ana O Tiroli-Cepeda
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagem, Brazil
| | - Tatiani B Lima
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Tiago S Balbuena
- Faculdade de Ciências Agrárias e Veterinárias, UNESP Universidade Estadual Paulista, Campus de Jaboticabal, Jaboticabal, SP 14884-900, Brazil
| | - Fábio C Gozzo
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Carlos H I Ramos
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagem, Brazil.
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Structural studies on the forward and reverse binding modes of peptides to the chaperone DnaK. J Mol Biol 2013; 425:2463-79. [PMID: 23562829 DOI: 10.1016/j.jmb.2013.03.041] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 11/23/2022]
Abstract
Hsp70 chaperones have been implicated in assisting protein folding of newly synthesized polypeptide chains, refolding of misfolded proteins, and protein trafficking. For these functions, the chaperones need to exhibit a significant promiscuity in binding to different sequences of hydrophobic peptide stretches. To characterize the structural basis of sequence specificity and flexibility of the Escherichia coli Hsp70 chaperone DnaK, we have analyzed crystal structures of the substrate binding domain of the protein in complex with artificially designed peptides as well as small proline-rich antimicrobial peptides. The latter peptides from mammals and insects were identified to target DnaK after cell penetration. Interestingly, the complex crystal structures reveal two different peptide binding modes. The peptides can bind either in a forward or in a reverse direction to the conventional substrate binding cleft of DnaK in an extended conformation. Superposition of the two binding modes shows a remarkable similarity in the side chain orientations and hydrogen bonding pattern despite the reversed peptide orientation. The DnaK chaperone has evolved to bind peptides in both orientations in the substrate binding cleft with comparable energy without rearrangements of the protein. Optimal hydrophobic interactions with binding pockets -2 to 0 appear to be the main determinant for the orientation and sequence position of peptide binding.
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44
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Srinivasan SR, Gillies A, Chang L, Thompson AD, Gestwicki JE. Molecular chaperones DnaK and DnaJ share predicted binding sites on most proteins in the E. coli proteome. MOLECULAR BIOSYSTEMS 2012; 8:2323-33. [PMID: 22732719 PMCID: PMC3462289 DOI: 10.1039/c2mb25145k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In Escherichia coli, the molecular chaperones DnaK and DnaJ cooperate to assist the folding of newly synthesized or unfolded polypeptides. DnaK and DnaJ bind to hydrophobic motifs in these proteins and they also bind to each other. Together, this system is thought to be sufficiently versatile to act on the entire proteome, which creates interesting challenges in understanding the interactions between DnaK, DnaJ and their thousands of potential substrates. To address this question, we computationally predicted the number and frequency of DnaK- and DnaJ-binding motifs in the E. coli proteome, guided by free energy-based binding consensus motifs. This analysis revealed that nearly every protein is predicted to contain multiple DnaK- and DnaJ-binding sites, with the DnaJ sites occurring approximately twice as often. Further, we found that an overwhelming majority of the DnaK sites partially or completely overlapped with the DnaJ-binding motifs. It is well known that high concentrations of DnaJ inhibit DnaK-DnaJ-mediated refolding. The observed overlapping binding sites suggest that this phenomenon may be explained by an important balance in the relative stoichiometry of DnaK and DnaJ. To test this idea, we measured the chaperone-assisted folding of two denatured substrates and found that the distribution of predicted DnaK- and DnaJ-binding sites was indeed a good predictor of the optimal stoichiometry required for folding. These studies provide insight into how DnaK and DnaJ might cooperate to maintain global protein homeostasis.
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Affiliation(s)
| | - Anne Gillies
- Chemical Biology Graduate Program, University of Michigan Ann Arbor, MI 48109
| | - Lyra Chang
- Chemical Biology Graduate Program, University of Michigan Ann Arbor, MI 48109
| | - Andrea D. Thompson
- Chemical Biology Graduate Program, University of Michigan Ann Arbor, MI 48109
| | - Jason E. Gestwicki
- Chemical Biology Graduate Program, University of Michigan Ann Arbor, MI 48109
- Department of Pathology and Biological Chemistry and the Life Sciences Institute, University of Michigan Ann Arbor, MI 48109
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Xu X, Sarbeng EB, Vorvis C, Kumar DP, Zhou L, Liu Q. Unique peptide substrate binding properties of 110-kDa heat-shock protein (Hsp110) determine its distinct chaperone activity. J Biol Chem 2011; 287:5661-72. [PMID: 22157767 DOI: 10.1074/jbc.m111.275057] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The molecular chaperone 70-kDa heat-shock proteins (Hsp70s) play essential roles in maintaining protein homeostasis. Hsp110, an Hsp70 homolog, is highly efficient in preventing protein aggregation but lacks the hallmark folding activity seen in Hsp70s. To understand the mechanistic differences between these two chaperones, we first characterized the distinct peptide substrate binding properties of Hsp110s. In contrast to Hsp70s, Hsp110s prefer aromatic residues in their substrates, and the substrate binding and release exhibit remarkably fast kinetics. Sequence and structure comparison revealed significant differences in the two peptide-binding loops: the length and properties are switched. When we swapped these two loops in an Hsp70, the peptide binding properties of this mutant Hsp70 were converted to Hsp110-like, and more impressively, it functionally behaved like an Hsp110. Thus, the peptide substrate binding properties implemented in the peptide-binding loops may determine the chaperone activity differences between Hsp70s and Hsp110s.
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Affiliation(s)
- Xinping Xu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, USA
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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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Liebscher M, Haupt K, Yu C, Jahreis G, Lücke C, Schiene-Fischer C. Rational Design of Novel Peptidic DnaK Ligands. Chembiochem 2010; 11:1727-37. [DOI: 10.1002/cbic.201000166] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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48
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Xing Y, Böcking T, Wolf M, Grigorieff N, Kirchhausen T, Harrison SC. Structure of clathrin coat with bound Hsc70 and auxilin: mechanism of Hsc70-facilitated disassembly. EMBO J 2009; 29:655-65. [PMID: 20033059 PMCID: PMC2830701 DOI: 10.1038/emboj.2009.383] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2009] [Accepted: 11/26/2009] [Indexed: 02/06/2023] Open
Abstract
The chaperone Hsc70 drives the clathrin assembly–disassembly cycle forward by stimulating dissociation of a clathrin lattice. A J-domain containing co-chaperone, auxilin, associates with a freshly budded clathrin-coated vesicle, or with an in vitro assembled clathrin coat, and recruits Hsc70 to its specific heavy-chain-binding site. We have determined by electron cryomicroscopy (cryoEM), at about 11 Å resolution, the structure of a clathrin coat (in the D6-barrel form) with specifically bound Hsc70 and auxilin. The Hsc70 binds a previously analysed site near the C-terminus of the heavy chain, with a stoichiometry of about one per three-fold vertex. Its binding is accompanied by a distortion of the clathrin lattice, detected by a change in the axial ratio of the D6 barrel. We propose that when Hsc70, recruited to a position close to its target by the auxilin J-domain, splits ATP, it clamps firmly onto its heavy-chain site and locks in place a transient fluctuation. Accumulation of the local strain thus imposed at multiple vertices can then lead to disassembly.
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Affiliation(s)
- Yi Xing
- Department of Biological Chemistry and Molecular Pharmacology, Jack and Eileen Connors Structural Biology Laboratory, Harvard Medical School, Boston, MA 02115, USA
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Abstract
Heat shock proteins act as molecular chaperones, facilitating protein folding in cells of living organisms. Their role is particularly important in parasites because environmental changes associated with their life cycles place a strain on protein homoeostasis. Not surprisingly, some heat shock proteins are essential for the survival of the most virulent malaria parasite, Plasmodium falciparum. This justifies the need for a greater understanding of the specific roles and regulation of malarial heat shock proteins. Furthermore, heat shock proteins play a major role during invasion of the host by the parasite and mediate in malaria pathogenesis. The identification and development of inhibitor compounds of heat shock proteins has recently attracted attention. This is important, given the fact that traditional antimalarial drugs are increasingly failing, as a consequence of parasite increasing drug resistance. Heat shock protein 90 (Hsp90), Hsp70/Hsp40 partnerships and small heat shock proteins are major malaria drug targets. This review examines the structural and functional features of these proteins that render them ideal drug targets and the challenges of targeting these proteins towards malaria drug design. The major antimalarial compounds that have been used to inhibit heat shock proteins include the antibiotic, geldanamycin, deoxyspergualin and pyrimidinones. The proposed mechanisms of action of these molecules and the pathways they inhibit are discussed.
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Affiliation(s)
- Addmore Shonhai
- Department of Biochemistry & Microbiology, Zululand University, Kwadlangezwa, South Africa.
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50
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Reyda MR, Fugate CJ, Jarrett JT. A complex between biotin synthase and the iron-sulfur cluster assembly chaperone HscA that enhances in vivo cluster assembly. Biochemistry 2009; 48:10782-92. [PMID: 19821612 DOI: 10.1021/bi901393t] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biotin synthase (BioB) is an iron-sulfur enzyme that catalyzes the last step in biotin biosynthesis, the insertion of sulfur between the C6 and C9 atoms of dethiobiotin to complete the thiophane ring of biotin. Recent in vitro experiments suggest that the sulfur is derived from a [2Fe-2S](2+) cluster within BioB, and that the remnants of this cluster dissociate from the enzyme following each turnover. For BioB to catalyze multiple rounds of biotin synthesis, the [2Fe-2S](2+) cluster in BioB must be reassembled, a process that could be conducted in vivo by the ISC or SUF iron-sulfur cluster assembly systems. The bacterial ISC system includes HscA, an Hsp70 class molecular chaperone, whose yeast homologue has been shown to play an important but nonessential role in assembly of mitochondrial FeS clusters in Saccharomyces cerevisiae. In this work, we show that in Escherichia coli, HscA significantly improves the efficiency of the in vivo assembly of the [2Fe-2S](2+) cluster on BioB under conditions of low to moderate iron. In vitro, we show that HscA binds with increased affinity to BioB missing one or both FeS clusters, with a maximum of two HscA molecules per BioB dimer. BioB binds to HscA in an ATP/ADP-independent manner, and a high-affinity complex is also formed with a truncated form of HscA that lacks the nucleotide binding domain. Further, the BioB-HscA complex binds the FeS cluster scaffold protein IscU in a noncompetitive manner, generating a complex that contains all three proteins. We propose that HscA plays a role in facilitating the transfer of FeS clusters from IscU into the appropriate target apoproteins such as biotin synthase, perhaps by enhancing or prolonging the requisite protein-protein interaction.
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Affiliation(s)
- Michael R Reyda
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
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