101
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Sousa R. Structural mechanisms of chaperone mediated protein disaggregation. Front Mol Biosci 2014; 1:12. [PMID: 25988153 PMCID: PMC4428496 DOI: 10.3389/fmolb.2014.00012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 08/27/2014] [Indexed: 11/13/2022] Open
Abstract
The ClpB/Hsp104 and Hsp70 classes of molecular chaperones use ATP hydrolysis to dissociate protein aggregates and complexes, and to move proteins through membranes. ClpB/Hsp104 are members of the AAA+ family of proteins which form ring-shaped hexamers. Loops lining the pore in the ring engage substrate proteins as extended polypeptides. Interdomain rotations and conformational changes in these loops coupled to ATP hydrolysis unfold and pull proteins through the pore. This provides a mechanism that progressively disrupts local secondary and tertiary structure in substrates, allowing these chaperones to dissociate stable aggregates such as β-sheet rich prions or coiled coil SNARE complexes. While the ClpB/Hsp104 mechanism appears to embody a true power-stroke in which an ATP powered conformational change in one protein is directly coupled to movement or structural change in another, the mechanism of force generation by Hsp70s is distinct and less well understood. Both active power-stroke and purely passive mechanisms in which Hsp70 captures spontaneous fluctuations in a substrate have been proposed, while a third proposed mechanism-entropic pulling-may be able to generate forces larger than seen in ATP-driven molecular motors without the conformational coupling required for a power-stroke. The disaggregase activity of these chaperones is required for thermotolerance, but unrestrained protein complex/aggregate dissociation is potentially detrimental. Disaggregating chaperones are strongly auto-repressed, and are regulated by co-chaperones which recruit them to protein substrates and activate the disaggregases via mechanisms involving either sequential transfer of substrate from one chaperone to another and/or simultaneous interaction of substrate with multiple chaperones. By effectively subjecting substrates to multiple levels of selection by multiple chaperones, this may insure that these potent disaggregases are only activated in the appropriate context.
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Affiliation(s)
- Rui Sousa
- Department of Biochemistry, University of Texas Health Science Center at San Antonio San Antonio, TX, USA
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102
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Hartmann A, Krainer G, Schlierf M. Different fluorophore labeling strategies and designs affect millisecond kinetics of DNA hairpins. Molecules 2014; 19:13735-54. [PMID: 25255759 PMCID: PMC6271894 DOI: 10.3390/molecules190913735] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 08/21/2014] [Accepted: 08/26/2014] [Indexed: 11/18/2022] Open
Abstract
Changes in molecular conformations are one of the major driving forces of complex biological processes. Many studies based on single-molecule techniques have shed light on conformational dynamics and contributed to a better understanding of living matter. In particular, single-molecule FRET experiments have revealed unprecedented information at various time scales varying from milliseconds to seconds. The choice and the attachment of fluorophores is a pivotal requirement for single-molecule FRET experiments. One particularly well-studied millisecond conformational change is the opening and closing of DNA hairpin structures. In this study, we addressed the influence of base- and terminal-labeled fluorophores as well as the fluorophore DNA interactions on the extracted kinetic information of the DNA hairpin. Gibbs free energies varied from ∆G0 = −3.6 kJ/mol to ∆G0 = −0.2 kJ/mol for the identical DNA hairpin modifying only the labeling scheme and design of the DNA sample. In general, the base-labeled DNA hairpin is significantly destabilized compared to the terminal-labeled DNA hairpin and fluorophore DNA interactions additionally stabilize the closed state of the DNA hairpin. Careful controls and variations of fluorophore attachment chemistry are essential for a mostly undisturbed measurement of the underlying energy landscape of biomolecules.
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Affiliation(s)
- Andreas Hartmann
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany.
| | - Georg Krainer
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany.
| | - Michael Schlierf
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany.
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103
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Otero JH, Lizák B, Feige MJ, Hendershot LM. Dissection of structural and functional requirements that underlie the interaction of ERdj3 protein with substrates in the endoplasmic reticulum. J Biol Chem 2014; 289:27504-12. [PMID: 25143379 DOI: 10.1074/jbc.m114.587147] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
ERdj3, a mammalian endoplasmic reticulum (ER) Hsp40/DnaJ family member, binds unfolded proteins, transfers them to BiP, and concomitantly stimulates BiP ATPase activity. However, the requirements for ERdj3 binding to and release from substrates in cells are not well understood. We found that ERdj3 homodimers that cannot stimulate the ATPase activity of BiP (QPD mutants) bound to unfolded ER proteins under steady state conditions in much greater amounts than wild-type ERdj3. This was due to reduced release from these substrates as opposed to enhanced binding, although in both cases dimerization was strictly required for substrate binding. Conversely, heterodimers consisting of one wild-type and one mutant ERdj3 subunit bound substrates at levels comparable with wild-type ERdj3 homodimers, demonstrating that release requires only one protomer to be functional in stimulating BiP ATPase activity. Co-expressing wild-type ERdj3 and a QPD mutant, which each exclusively formed homodimers, revealed that the release rate of wild-type ERdj3 varied according to the relative half-lives of substrates, suggesting that ERdj3 release is an important step in degradation of unfolded client proteins in the ER. Furthermore, pulse-chase experiments revealed that the binding of QPD mutant homodimers remained constant as opposed to increasing, suggesting that ERdj3 does not normally undergo reiterative binding cycles with substrates.
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Affiliation(s)
- Joel H Otero
- From the Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Beata Lizák
- From the Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Matthias J Feige
- From the Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Linda M Hendershot
- From the Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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104
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Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70. PLoS Comput Biol 2013; 9:e1003379. [PMID: 24348227 PMCID: PMC3861046 DOI: 10.1371/journal.pcbi.1003379] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 10/15/2013] [Indexed: 11/30/2022] Open
Abstract
ATP regulates the function of many proteins in the cell by transducing its binding and hydrolysis energies into protein conformational changes by mechanisms which are challenging to identify at the atomic scale. Based on molecular dynamics (MD) simulations, a method is proposed to analyze the structural changes induced by ATP binding to a protein by computing the effective free-energy landscape (FEL) of a subset of its coordinates along its amino-acid sequence. The method is applied to characterize the mechanism by which the binding of ATP to the nucleotide-binding domain (NBD) of Hsp70 propagates a signal to its substrate-binding domain (SBD). Unbiased MD simulations were performed for Hsp70-DnaK chaperone in nucleotide-free, ADP-bound and ATP-bound states. The simulations revealed that the SBD does not interact with the NBD for DnaK in its nucleotide-free and ADP-bound states whereas the docking of the SBD was found in the ATP-bound state. The docked state induced by ATP binding found in MD is an intermediate state between the initial nucleotide-free and final ATP-bound states of Hsp70. The analysis of the FEL projected along the amino-acid sequence permitted to identify a subset of 27 protein internal coordinates corresponding to a network of 91 key residues involved in the conformational change induced by ATP binding. Among the 91 residues, 26 are identified for the first time, whereas the others were shown relevant for the allosteric communication of Hsp70 s in several experiments and bioinformatics analysis. The FEL analysis revealed also the origin of the ATP-induced structural modifications of the SBD recently measured by Electron Paramagnetic Resonance. The pathway between the nucleotide-free and the intermediate state of DnaK was extracted by applying principal component analysis to the subset of internal coordinates describing the transition. The methodology proposed is general and could be applied to analyze allosteric communication in other proteins. The precise biophysical characterization of the mechanisms of the protein conformational changes controlled by a nucleotide remains a challenge in biology. Molecular dynamics simulations of proteins in different nucleotide-binding states contain information on the nucleotide-dependent conformational dynamics. However, it is difficult to extract relevant information about the conformation-induced mechanism from the raw molecular dynamics data. Herein, we addressed this issue for the major ATP-dependent molecular chaperones Hsp70 s, which contribute to crucial cellular processes and are involved in several neurodegenerative diseases and in cancer. To function, Hsp70 undergoes several conformational changes controlled by the state of its nucleotide-binding domain. We demonstrated that the analysis of the effective free-energy landscape of the protein projected along the amino-acid sequence and computed from the molecular dynamics simulations of Hsp70 in different nucleotide-binding states, holds the key to identify the key residues of the conformational induced pathway. Identification of the key residues involved in the propagation of the structural changes induced by ATP binding offer alternative druggable specific sites other than the ligand binding clefts. The methodology developed for Hsp70 is general and can be adapted to any ligand induced conformational change in proteins.
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105
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Nishimiya D. Proteins improving recombinant antibody production in mammalian cells. Appl Microbiol Biotechnol 2013; 98:1031-42. [PMID: 24327213 DOI: 10.1007/s00253-013-5427-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/20/2013] [Accepted: 11/21/2013] [Indexed: 12/13/2022]
Abstract
Mammalian cells have been successfully used for the industrial manufacture of antibodies due to their ability to synthesize antibodies correctly. Nascent polypeptides must be subjected to protein folding and assembly in the ER and the Golgi to be secreted as mature proteins. If these reactions do not proceed appropriately, unfolded or misfolded proteins are degraded by the ER-associated degradation (ERAD) pathway. The accumulation of unfolded proteins or intracellular antibody crystals accompanied by this failure triggers the unfolded protein response (UPR), which can considerably attenuate the levels of translation, folding, assembly, and secretion, resulting in reduction of antibody productivity. Accumulating studies by omics-based analysis of recombinant mammalian cells suggest that not only protein secretion processes including protein folding and assembly but also translation are likely to be the rate-limiting factors for increasing antibody production. Here, this review describes the mechanism of antibody folding and assembly and recent advantages which could improve recombinant antibody production in mammalian cells by utilizing proteins such as ER chaperones or UPR-related proteins.
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Affiliation(s)
- Daisuke Nishimiya
- New Modality Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan,
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106
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Oaks AW, Sidhu A. Parallel mechanisms for direct and indirect membrane protein trafficking by synucleins. Commun Integr Biol 2013; 6:e26794. [PMID: 24563712 PMCID: PMC3917945 DOI: 10.4161/cib.26794] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 10/11/2013] [Indexed: 12/11/2022] Open
Abstract
More than 2 decades of work have yet to conclusively determine the physiological role of the synuclein proteins, even though these abundant brain constituents are participants in a broad array of cellular processes. Among proposed physiological roles is a functional interaction between the synuclein proteins and monoamine transporters contributing to transporter trafficking through direct protein–protein interactions. Recent work shows that an antagonistic effect of the synuclein proteins on the secretory functions of the endoplasmic reticulum and the Golgi apparatus appears to simultaneously influence trafficking of the dopamine transporter and other membrane proteins. Here, we highlight these new findings in view of the broader literature identifying the role of synucleins in protein trafficking and suggest emerging themes for ongoing and future work in the field of synuclein biology.
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Affiliation(s)
- Adam W Oaks
- Laboratory of Molecular Neurochemistry; Department of Biochemistry and Molecular & Cellular Biology; Georgetown University Medical Center; Washington, DC USA
| | - Anita Sidhu
- Laboratory of Molecular Neurochemistry; Department of Biochemistry and Molecular & Cellular Biology; Georgetown University Medical Center; Washington, DC USA
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107
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Lin CY, Huang JY, Lo LW. Deciphering the catalysis-associated conformational changes of human adenylate kinase 1 with single-molecule spectroscopy. J Phys Chem B 2013; 117:13947-55. [PMID: 24134437 DOI: 10.1021/jp4019537] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human adenylate kinase isoenzyme 1 (AK1) is the key enzyme in maintaining the cellular energy homeostasis. The catalysis-associated conformational changes of AK1 involve large-amplitude rearrangements. To decipher the conformational changes of AK1 at the single-molecule level, we tagged AK1 with two identical fluorophores, one near the substrate-binding site and the other at the boundary of the core domain. We found that magnesium ion binding to AK1 increases the structural heterogeneity of AK1, whereas ADP binding reduces the structural heterogeneity. We exploited the hidden Markov model to extract the underlying catalysis-associated conformational dynamics and determined thermodynamic parameters of the multiple catalytic pathways. The third-order correlation difference calculated from photon fluctuation traces reveals the irreversible nature of the conformational motions, suggesting that single-molecule AK1 is in a nonequilibrium steady state. This discovery offers a fresh viewpoint to look into the molecular mechanisms of cellular biochemistry.
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Affiliation(s)
- Chien Y Lin
- Department of Photonics, Chiao Tung University , Hsinchu, Taiwan
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108
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Wijeyesakere SJ, Rizvi SM, Raghavan M. Glycan-dependent and -independent interactions contribute to cellular substrate recruitment by calreticulin. J Biol Chem 2013; 288:35104-16. [PMID: 24100026 DOI: 10.1074/jbc.m113.507921] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Calreticulin is an endoplasmic reticulum chaperone with specificity for monoglucosylated glycoproteins. Calreticulin also inhibits precipitation of nonglycosylated proteins and thus contains generic protein-binding sites, but their location and contributions to substrate folding are unknown. We show that calreticulin binds glycosylated and nonglycosylated proteins with similar affinities but distinct interaction kinetics. Although both interactions involve the glycan-binding site or its vicinity, the arm-like proline-rich (P-) domain of calreticulin contributes to binding non/deglycosylated proteins. Correspondingly, ensemble FRET spectroscopy measurements indicate that glycosylated and nonglycosylated proteins induce "open" and "closed" P-domain conformations, respectively. The co-chaperone ERp57 influences substrate-binding kinetics and induces a closed P-domain conformation. Together with analysis of the interactions of calreticulin with cellular proteins, these findings indicate that the recruitment of monoglucosylated proteins to calreticulin is kinetically driven, whereas the P-domain and co-chaperone contribute to stable substrate binding. Substrate sequestration in the cleft between the glycan-binding site and P-domain is a likely mechanism for calreticulin-assisted protein folding.
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Affiliation(s)
- Sanjeeva J Wijeyesakere
- From the Department of Microbiology and Immunology, University of Michigan School Medical School, Ann Arbor, Michigan 48109
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109
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Nicolaï A, Delarue P, Senet P. Conformational dynamics of full-length inducible human Hsp70 derived from microsecond molecular dynamics simulations in explicit solvent. J Biomol Struct Dyn 2013; 31:1111-26. [DOI: 10.1080/07391102.2012.726190] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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110
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Mayer MP. Hsp70 chaperone dynamics and molecular mechanism. Trends Biochem Sci 2013; 38:507-14. [PMID: 24012426 DOI: 10.1016/j.tibs.2013.08.001] [Citation(s) in RCA: 300] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/06/2013] [Accepted: 08/06/2013] [Indexed: 01/09/2023]
Abstract
The chaperone functions of heat shock protein (Hsp)70 involve an allosteric control mechanism between the nucleotide-binding domain (NBD) and polypeptide substrate-binding domain (SBD): ATP binding and hydrolysis regulates the affinity for polypeptides, and polypeptide binding accelerates ATP hydrolysis. These data suggest that Hsp70s exist in at least two conformational states. Although structural information on the conformation with high affinity for polypeptides has been available for several years, the conformation with an open polypeptide binding cleft was elucidated only recently. In addition, other biophysical studies have revealed a more dynamic picture of Hsp70s, shedding light on the molecular mechanism by which Hsp70s assist protein folding. In this review recent insights into the structure and mechanism of Hsp70s are discussed.
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Affiliation(s)
- Matthias P Mayer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH-Alliance, Heidelberg, Germany.
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111
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Mashaghi A, Kramer G, Lamb DC, Mayer MP, Tans SJ. Chaperone Action at the Single-Molecule Level. Chem Rev 2013; 114:660-76. [DOI: 10.1021/cr400326k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Alireza Mashaghi
- AMOLF Institute, Science Park
104, 1098 XG Amsterdam, The Netherlands
| | - Günter Kramer
- Zentrum
für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Don C. Lamb
- Physical
Chemistry, Department of Chemistry, Munich Center for Integrated Protein
Science (CiPSM) and Center for Nanoscience, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, Gerhard-Ertl-Building, 81377 Munich, Germany
| | - Matthias P. Mayer
- Zentrum
für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Sander J. Tans
- AMOLF Institute, Science Park
104, 1098 XG Amsterdam, The Netherlands
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112
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Aprile FA, Dhulesia A, Stengel F, Roodveldt C, Benesch JLP, Tortora P, Robinson CV, Salvatella X, Dobson CM, Cremades N. Hsp70 oligomerization is mediated by an interaction between the interdomain linker and the substrate-binding domain. PLoS One 2013; 8:e67961. [PMID: 23840795 PMCID: PMC3696110 DOI: 10.1371/journal.pone.0067961] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 05/24/2013] [Indexed: 12/21/2022] Open
Abstract
Oligomerization in the heat shock protein (Hsp) 70 family has been extensively documented both in vitro and in vivo, although the mechanism, the identity of the specific protein regions involved and the physiological relevance of this process are still unclear. We have studied the oligomeric properties of a series of human Hsp70 variants by means of nanoelectrospray ionization mass spectrometry, optical spectroscopy and quantitative size exclusion chromatography. Our results show that Hsp70 oligomerization takes place through a specific interaction between the interdomain linker of one molecule and the substrate-binding domain of a different molecule, generating dimers and higher-order oligomers. We have found that substrate binding shifts the oligomerization equilibrium towards the accumulation of functional monomeric protein, probably by sequestering the helical lid sub-domain needed to stabilize the chaperone: substrate complex. Taken together, these findings suggest a possible role of chaperone oligomerization as a mechanism for regulating the availability of the active monomeric form of the chaperone and for the control of substrate binding and release.
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Affiliation(s)
- Francesco A. Aprile
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Anne Dhulesia
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Florian Stengel
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Cintia Roodveldt
- CABIMER-Andalusian Center for Molecular Biology and Regenerative Medicine (Consejo Superior de Investigaciones Científicas-University of Seville-UPO-Junta de Andalucia), Seville, Spain
| | - Justin L. P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Paolo Tortora
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Carol V. Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Xavier Salvatella
- Joint BSC-IRB Research Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Nunilo Cremades
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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113
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Tracking the interplay between bound peptide and the lid domain of DnaK, using molecular dynamics. Int J Mol Sci 2013; 14:12675-95. [PMID: 23774839 PMCID: PMC3709807 DOI: 10.3390/ijms140612675] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/10/2013] [Accepted: 06/04/2013] [Indexed: 01/18/2023] Open
Abstract
Hsp70 chaperones consist of two functional domains: the 44 kDa Nucleotide Binding Domain (NBD), that binds and hydrolyses ATP, and the 26 kDa Substrate Binding Domain (SBD), which binds unfolded proteins and reactivates them, utilizing energy obtained from nucleotide hydrolysis. The structure of the SBD of the bacterial Hsp70, DnaK, consists of two sub-domains: A β-sandwich part containing the hydrophobic cavity to which the hepta-peptide NRLLLTG (NR) is bound, and a segment made of 5 α-helices, called the “lid” that caps the top of the β-sandwich domain. In the present study we used the Escherichia coli Hsp70, DnaK, as a model for Hsp70 proteins, focusing on its SBD domain, examining the changes in the lid conformation. We deliberately decoupled the NBD from the SBD, limiting the study to the structure of the SBD section, with an emphasis on the interaction between the charges of the peptide with the residues located in the lid. Molecular dynamics simulations of the complex revealed significant mobility within the lid structure; as the structure was released from the forces operating during the crystallization process, the two terminal helices established a contact with the positive charge at the tip of the peptide. This contact is manifested only in the presence of electrostatic attraction. The observed internal motions within the lid provide a molecular role for the function of this sub-domain during the reaction cycle of Hsp 70 chaperones.
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114
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Qi R, Sarbeng EB, Liu Q, Le KQ, Xu X, Xu H, Yang J, Wong JL, Vorvis C, Hendrickson WA, Zhou L, Liu Q. Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP. Nat Struct Mol Biol 2013; 20:900-7. [PMID: 23708608 DOI: 10.1038/nsmb.2583] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 04/08/2013] [Indexed: 01/29/2023]
Abstract
The 70-kilodalton (kDa) heat-shock proteins (Hsp70s) are ubiquitous molecular chaperones essential for cellular protein folding and proteostasis. Each Hsp70 has two functional domains: a nucleotide-binding domain (NBD), which binds and hydrolyzes ATP, and a substrate-binding domain (SBD), which binds extended polypeptides. NBD and SBD interact little when in the presence of ADP; however, ATP binding allosterically couples the polypeptide- and ATP-binding sites. ATP binding promotes polypeptide release; polypeptide rebinding stimulates ATP hydrolysis. This allosteric coupling is poorly understood. Here we present the crystal structure of an intact ATP-bound Hsp70 from Escherichia coli at 1.96-Å resolution. The ATP-bound NBD adopts a unique conformation, forming extensive interfaces with an SBD that has changed radically, having its α-helical lid displaced and the polypeptide-binding channel of its β-subdomain restructured. These conformational changes, together with our biochemical assays, provide a structural explanation for allosteric coupling in Hsp70 activity.
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Affiliation(s)
- Ruifeng Qi
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
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115
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Real-time observation of the conformational dynamics of mitochondrial Hsp70 by spFRET. EMBO J 2013; 32:1639-49. [PMID: 23624933 DOI: 10.1038/emboj.2013.89] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 03/21/2013] [Indexed: 11/08/2022] Open
Abstract
The numerous functions of the important class of molecular chaperones, heat shock proteins 70 (Hsp70), rely on cycles of intricate conformational changes driven by ATP-hydrolysis and regulated by cochaperones and substrates. Here, we used Förster resonance energy transfer to study the conformational dynamics of individual molecules of Ssc1, a mitochondrial Hsp70, in real time. The intrinsic dynamics of the substrate-binding domain of Ssc1 was observed to be uncoupled from the dynamic interactions between substrate- and nucleotide-binding domains. Analysis of the fluctuations in the interdomain separation revealed frequent transitions to a nucleotide-free state. The nucleotide-exchange factor Mge1 did not induce ADP release, as expected, but rather facilitated binding of ATP. These results indicate that the conformational cycle of Ssc1 is more elaborate than previously thought and provide insight into how the Hsp70s can perform a wide variety of functions.
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116
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Deng Y, Srivastava R, Howell SH. Endoplasmic reticulum (ER) stress response and its physiological roles in plants. Int J Mol Sci 2013; 14:8188-212. [PMID: 23591838 PMCID: PMC3645738 DOI: 10.3390/ijms14048188] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 03/19/2013] [Accepted: 04/01/2013] [Indexed: 01/29/2023] Open
Abstract
The endoplasmic reticulum (ER) stress response is a highly conserved mechanism that results from the accumulation of unfolded or misfolded proteins in the ER. The response plays an important role in allowing plants to sense and respond to adverse environmental conditions, such as heat stress, salt stress and pathogen infection. Since the ER is a well-controlled microenvironment for proper protein synthesis and folding, it is highly susceptible to stress conditions. Accumulation of unfolded or misfolded proteins activates a signaling pathway, called the unfolded protein response (UPR), which acts to relieve ER stress and, if unsuccessful, leads to cell death. Plants have two arms of the UPR signaling pathway, an arm involving the proteolytic processing of membrane-associated basic leucine zipper domain (bZIP) transcription factors and an arm involving RNA splicing factor, IRE1, and its mRNA target. These signaling pathways play an important role in determining the cell's fate in response to stress conditions.
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Affiliation(s)
- Yan Deng
- Plant Sciences Institute and Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; E-Mails: (Y.D.); (R.S.)
| | - Renu Srivastava
- Plant Sciences Institute and Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; E-Mails: (Y.D.); (R.S.)
| | - Stephen H. Howell
- Plant Sciences Institute and Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; E-Mails: (Y.D.); (R.S.)
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117
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Xu LQ, Wu S, Buell AK, Cohen SIA, Chen LJ, Hu WH, Cusack SA, Itzhaki LS, Zhang H, Knowles TPJ, Dobson CM, Welland ME, Jones GW, Perrett S. Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2. Philos Trans R Soc Lond B Biol Sci 2013; 368:20110410. [PMID: 23530260 PMCID: PMC3638396 DOI: 10.1098/rstb.2011.0410] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Ure2p is the protein determinant of the Saccharomyces cerevisiae prion state [URE3]. Constitutive overexpression of the HSP70 family member SSA1 cures cells of [URE3]. Here, we show that Ssa1p increases the lag time of Ure2p fibril formation in vitro in the presence or absence of nucleotide. The presence of the HSP40 co-chaperone Ydj1p has an additive effect on the inhibition of Ure2p fibril formation, whereas the Ydj1p H34Q mutant shows reduced inhibition alone and in combination with Ssa1p. In order to investigate the structural basis of these effects, we constructed and tested an Ssa1p mutant lacking the ATPase domain, as well as a series of C-terminal truncation mutants. The results indicate that Ssa1p can bind to Ure2p and delay fibril formation even in the absence of the ATPase domain, but interaction of Ure2p with the substrate-binding domain is strongly influenced by the C-terminal lid region. Dynamic light scattering, quartz crystal microbalance assays, pull-down assays and kinetic analysis indicate that Ssa1p interacts with both native Ure2p and fibril seeds, and reduces the rate of Ure2p fibril elongation in a concentration-dependent manner. These results provide new insights into the structural and mechanistic basis for inhibition of Ure2p fibril formation by Ssa1p and Ydj1p.
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Affiliation(s)
- Li-Qiong Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, , 15 Datun Road, Chaoyang, Beijing 100101, People's Republic of China
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118
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Abstract
Hsp70 ATP binding induces substrate release, but the transiency of this state has inhibited its characterization. In this issue, Kityk et al. determine the Hsp70(∗)ATP structure utilizing engineered disulfide bonds, providing insights into the workings of this essential molecular machine.
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Affiliation(s)
- Rui Sousa
- Department of Biochemistry, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
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119
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An interdomain energetic tug-of-war creates the allosterically active state in Hsp70 molecular chaperones. Cell 2013; 151:1296-307. [PMID: 23217711 DOI: 10.1016/j.cell.2012.11.002] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 08/10/2012] [Accepted: 10/23/2012] [Indexed: 01/18/2023]
Abstract
The allosteric mechanism of Hsp70 molecular chaperones enables ATP binding to the N-terminal nucleotide-binding domain (NBD) to alter substrate affinity to the C-terminal substrate-binding domain (SBD) and substrate binding to enhance ATP hydrolysis. Cycling between ATP-bound and ADP/substrate-bound states requires Hsp70s to visit a state with high ATPase activity and fast on/off kinetics of substrate binding. We have trapped this "allosterically active" state for the E. coli Hsp70, DnaK, and identified how interactions among the NBD, the β subdomain of the SBD, the SBD α-helical lid, and the conserved hydrophobic interdomain linker enable allosteric signal transmission between ligand-binding sites. Allostery in Hsp70s results from an energetic tug-of-war between domain conformations and formation of two orthogonal interfaces: between the NBD and SBD, and between the helical lid and the β subdomain of the SBD. The resulting energetic tension underlies Hsp70 functional properties and enables them to be modulated by ligands and cochaperones and "tuned" through evolution.
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120
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Abstract
Co-chaperones regulate chaperone activities and are likely to impact a protein-folding environment as much as the chaperone itself. As co-chaperones are expressed substoichiometrically, the ability of co-chaperones to encounter a chaperone is crucial for chaperone activity. ERdj3, an abundant soluble endoplasmic reticulum (ER) co-chaperone of the Hsp70 BiP, stimulates the ATPase activity of BiP to increase BiP's affinity for client (or substrate) proteins. We investigated ERdj3 availability, how ERdj3 levels impact BiP availability, and the significance of J proteins for regulating BiP binding of clients in living cells. FRAP analysis revealed that overexpressed ERdj3-sfGFP dramatically decreases BiP-GFP mobility in a client-dependent manner. By contrast, ERdj3-GFP mobility remains low regardless of client protein levels. Native gels and co-immunoprecipitations established that ERdj3 associates with a large complex including Sec61α. Translocon binding probably ensures rapid encounters between emerging nascent peptides and stimulates BiP activity in the crucial early stages of secretory protein folding. Importantly, mutant BiP exhibited significantly increased mobility when it could not interact with any ERdjs. Thus, ERdjs appear to play the dual roles of increasing BiP affinity for clients and regulating delivery of clients to BiP. Our data suggest that BiP engagement of clients is enhanced in ER subdomains enriched in ERdj proteins.
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Affiliation(s)
- Feng Guo
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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121
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Abstract
Pulsed interleaved excitation (PIE) is the methodology of interleaved or alternating excitation of different fluorophores on the nanosecond timescale, which allows quasi-simultaneous, yet independent measurements to be performed. PIE simplifies quantification of several fluorescence techniques such as FCCS and FRET experiments. Foremost, it allows to specifically filter out spectral emission bleedthrough (crosstalk) and direct excitation without a decrease in the signal-to-noise ratio (SNR) of the experiment. Next, PIE allows determination of the absolute FRET efficiency from FCCS experiments in the case of nonperfect labeling. In recent years, PIE has been utilized in many different advanced FFS techniques. Combining MFD with PIE allows highly accurate and species-specific spFRET analyses to be performed. The combination of scanning FFS techniques with PIE combines the best of both techniques and allows for false-positive free measurements of molecular interactions in vitro and in living cells. In succession, a comprehensive overview of the principle and versatility of the PIE technique is discussed, the theory for analysis with PIE is outlined by comparing CW- and PIE-FCCS and finally, some of the most important applications of the PIE technique in literature are reviewed.
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Affiliation(s)
- Jelle Hendrix
- Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
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122
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Marcinowski M, Rosam M, Seitz C, Elferich J, Behnke J, Bello C, Feige MJ, Becker CFW, Antes I, Buchner J. Conformational selection in substrate recognition by Hsp70 chaperones. J Mol Biol 2012. [PMID: 23207294 DOI: 10.1016/j.jmb.2012.11.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hsp70s are molecular chaperones involved in the folding and assembly of proteins. They recognize hydrophobic amino acid stretches in their substrate binding groove. However, a detailed understanding of substrate specificity is still missing. Here, we use the endoplasmic reticulum-resident Hsp70 BiP to identify binding sites in a natural client protein. Two sites are mutually recognized and form stable Hsp70-substrate complexes. In silico and in vitro analyses revealed an extended substrate conformation as a crucial factor for interaction and show an unexpected plasticity of the substrate binding groove. The basic binding mechanism is conserved among different Hsp70s.
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Affiliation(s)
- Moritz Marcinowski
- Department Chemie, Technische Universität München, 85748 Garching, Germany
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123
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Wiegant F. Hormesis and Cellular Quality Control: A Possible Explanation for the Molecular Mechanisms that Underlie the Benefits of Mild Stress. Dose Response 2012; 11:413-30. [PMID: 23983668 PMCID: PMC3748852 DOI: 10.2203/dose-response.12-030.wiegant] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In contrast to the detrimental action of severe stress conditions, the beneficial effects of mild stress, known as hormesis, is increasingly discussed and studied. A variety of applications for hormesis in risk assessment processes, anti-ageing strategies and clinical therapies have been proposed. The molecular mechanisms underlying the phenomenon of hormesis, however, are not yet fully understood. A possible mechanism that has been proposed for hormesis, the homoeostasis overshoot hypothesis, assumes that an overshoot of repair- and self-recovery mechanisms in response to mild damage can be held responsible for the beneficial effects of hormesis. The present paper proposes 'cellular quality control' as a further explanation of the molecular mechanisms underlying the benefits observed after exposure to mild stress. The most important quality control mechanisms are outlined and their known and hypothesised actions in hormesis are discussed. As an example, different aspects of protein quality control will be described in more detail, which includes the reaction of the cell upon stress-induced protein damage and -aggregation. The regulation of Heat Shock Proteins and components from the ubiquitin proteasome system as part of cellular quality control is described in relation to its beneficial role in hormesis.
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Affiliation(s)
- F.A.C. Wiegant
- University College Utrecht, Science Department, Utrecht University, and Faculty of Science; Department of Biology, Institute of Education, Utrecht University
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124
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Unfolded protein responses with or without unfolded proteins? Cells 2012; 1:926-50. [PMID: 24710536 PMCID: PMC3901143 DOI: 10.3390/cells1040926] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 10/15/2012] [Accepted: 10/22/2012] [Indexed: 01/08/2023] Open
Abstract
The endoplasmic reticulum (ER) is the site of secretory protein biogenesis. The ER quality control (QC) machinery, including chaperones, ensures the correct folding of secretory proteins. Mutant proteins and environmental stresses can overwhelm the available QC machinery. To prevent and resolve accumulation of misfolded secretory proteins in the ER, cells have evolved integral membrane sensors that orchestrate the Unfolded Protein Response (UPR). The sensors, Ire1p in yeast and IRE1, ATF6, and PERK in metazoans, bind the luminal ER chaperone BiP during homeostasis. As unfolded secretory proteins accumulate in the ER lumen, BiP releases, and the sensors activate. The mechanisms of activation and attenuation of the UPR sensors have exhibited unexpected complexity. A growing body of data supports a model in which Ire1p, and potentially IRE1, directly bind unfolded proteins as part of the activation process. However, evidence for an unfolded protein-independent mechanism has recently emerged, suggesting that UPR can be activated by multiple modes. Importantly, dysregulation of the UPR has been linked to human diseases including Type II diabetes, heart disease, and cancer. The existence of alternative regulatory pathways for UPR sensors raises the exciting possibility for the development of new classes of therapeutics for these medically important proteins.
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125
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Kityk R, Kopp J, Sinning I, Mayer MP. Structure and dynamics of the ATP-bound open conformation of Hsp70 chaperones. Mol Cell 2012; 48:863-74. [PMID: 23123194 DOI: 10.1016/j.molcel.2012.09.023] [Citation(s) in RCA: 302] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 08/23/2012] [Accepted: 09/27/2012] [Indexed: 11/18/2022]
Abstract
Central to the chaperone function of Hsp70s is the transition between open and closed conformations of their polypeptide substrate binding domain (SBD), which is regulated through an allosteric mechanism via ATP binding and hydrolysis in their nucleotide binding domain (NBD). Although the structure of the closed conformation of Hsp70s is well studied, the open conformation has remained elusive. Here, we report on the 2.4 Å crystal structure of the ATP-bound open conformation of the Escherichia coli Hsp70 homolog DnaK. In the open DnaK structure, the β sheet and α-helical lid subdomains of the SBD are detached from one another and docked to different faces of the NBD. The contacts between the β sheet subdomain and the NBD reveal the mechanism of allosteric regulation. In addition, we demonstrate that docking of the β sheet and α-helical lid subdomains to the NBD is a sequential process influenced by peptide and protein substrates.
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Affiliation(s)
- Roman Kityk
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
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126
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Juhl C, Kosel D, Beck-Sickinger AG. Two motifs with different function regulate the anterograde transport of the adiponectin receptor 1. Cell Signal 2012; 24:1762-9. [DOI: 10.1016/j.cellsig.2012.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 04/22/2012] [Accepted: 05/05/2012] [Indexed: 01/16/2023]
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127
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Chambers JE, Petrova K, Tomba G, Vendruscolo M, Ron D. ADP ribosylation adapts an ER chaperone response to short-term fluctuations in unfolded protein load. J Cell Biol 2012; 198:371-85. [PMID: 22869598 PMCID: PMC3413365 DOI: 10.1083/jcb.201202005] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 07/09/2012] [Indexed: 12/26/2022] Open
Abstract
Gene expression programs that regulate the abundance of the chaperone BiP adapt the endoplasmic reticulum (ER) to unfolded protein load. However, such programs are slow compared with physiological fluctuations in secreted protein synthesis. While searching for mechanisms that fill this temporal gap in coping with ER stress, we found elevated levels of adenosine diphosphate (ADP)-ribosylated BiP in the inactive pancreas of fasted mice and a rapid decline in this modification in the active fed state. ADP ribosylation mapped to Arg470 and Arg492 in the substrate-binding domain of hamster BiP. Mutations that mimic the negative charge of ADP-ribose destabilized substrate binding and interfered with interdomain allosteric coupling, marking ADP ribosylation as a rapid posttranslational mechanism for reversible inactivation of BiP. A kinetic model showed that buffering fluctuations in unfolded protein load with a recruitable pool of inactive chaperone is an efficient strategy to minimize both aggregation and costly degradation of unfolded proteins.
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Affiliation(s)
- Joseph E. Chambers
- Metabolic Research Laboratories, National Institute for Health Research Cambridge Biomedical Research Centre, and Department of Chemistry, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Kseniya Petrova
- Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, and Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - Giulia Tomba
- Metabolic Research Laboratories, National Institute for Health Research Cambridge Biomedical Research Centre, and Department of Chemistry, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Michele Vendruscolo
- Metabolic Research Laboratories, National Institute for Health Research Cambridge Biomedical Research Centre, and Department of Chemistry, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - David Ron
- Metabolic Research Laboratories, National Institute for Health Research Cambridge Biomedical Research Centre, and Department of Chemistry, University of Cambridge, Cambridge CB2 0QQ, England, UK
- Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, and Department of Medicine, New York University School of Medicine, New York, NY 10016
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128
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Thompson AD, Bernard SM, Skiniotis G, Gestwicki JE. Visualization and functional analysis of the oligomeric states of Escherichia coli heat shock protein 70 (Hsp70/DnaK). Cell Stress Chaperones 2012; 17:313-27. [PMID: 22076723 PMCID: PMC3312962 DOI: 10.1007/s12192-011-0307-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 10/15/2011] [Accepted: 10/17/2011] [Indexed: 01/05/2023] Open
Abstract
The molecular chaperone DnaK binds to exposed hydrophobic segments in proteins, protecting them from aggregation. DnaK interacts with protein substrates via its substrate-binding domain, and the affinity of this interaction is allosterically regulated by its nucleotide-binding domain. In addition to regulating interdomain allostery, the nucleotide state has been found to influence homo-oligomerization of DnaK. However, the architecture of oligomeric DnaK and its potential functional relevance in the chaperone cycle remain undefined. Towards that goal, we examined the structures of DnaK by negative stain electron microscopy. We found that DnaK samples contain an ensemble of monomers, dimers, and other small, defined multimers. To better understand the function of these oligomers, we stabilized them by cross-linking and found that they retained ATPase activity and protected a model substrate from denaturation. However, these oligomers had a greatly reduced ability to refold substrate and did not respond to stimulation by DnaJ. Finally, we observed oligomeric DnaK in Escherichia coli cellular lysates by native gel electrophoresis and found that these structures became noticeably more prevalent in cells exposed to heat shock. Together, these studies suggest that DnaK oligomers are composed of ordered multimers that are functionally distinct from monomeric DnaK. Thus, oligomerization of DnaK might be an important step in chaperone cycling.
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Affiliation(s)
- Andrea D. Thompson
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109 USA
| | - Steffen M. Bernard
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109 USA
| | - Georgios Skiniotis
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 USA
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109 USA
| | - Jason E. Gestwicki
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109 USA
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109 USA
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129
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Sun L, Edelmann FT, Kaiser CJO, Papsdorf K, Gaiser AM, Richter K. The lid domain of Caenorhabditis elegans Hsc70 influences ATP turnover, cofactor binding and protein folding activity. PLoS One 2012; 7:e33980. [PMID: 22479492 PMCID: PMC3315512 DOI: 10.1371/journal.pone.0033980] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 02/20/2012] [Indexed: 12/27/2022] Open
Abstract
Hsc70 is a conserved ATP-dependent molecular chaperone, which utilizes the energy of ATP hydrolysis to alter the folding state of its client proteins. In contrast to the Hsc70 systems of bacteria, yeast and humans, the Hsc70 system of C. elegans (CeHsc70) has not been studied to date. We find that CeHsc70 is characterized by a high ATP turnover rate and limited by post-hydrolysis nucleotide exchange. This rate-limiting step is defined by the helical lid domain at the C-terminus. A certain truncation in this domain (CeHsc70-Δ545) reduces the turnover rate and renders the hydrolysis step rate-limiting. The helical lid domain also affects cofactor affinities as the lidless mutant CeHsc70-Δ512 binds more strongly to DNJ-13, forming large protein complexes in the presence of ATP. Despite preserving the ability to hydrolyze ATP and interact with its cofactors DNJ-13 and BAG-1, the truncation of the helical lid domain leads to the loss of all protein folding activity, highlighting the requirement of this domain for the functionality of the nematode's Hsc70 protein.
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Affiliation(s)
| | | | | | | | | | - Klaus Richter
- Center for Integrated Protein Science Munich (CIPSM) and Department Chemie, Technische Universität München, Garching, Germany
- * E-mail:
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130
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Kudryavtsev V, Sikor M, Kalinin S, Mokranjac D, Seidel CAM, Lamb DC. Combining MFD and PIE for accurate single-pair Förster resonance energy transfer measurements. Chemphyschem 2012; 13:1060-78. [PMID: 22383292 DOI: 10.1002/cphc.201100822] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 12/30/2011] [Indexed: 12/13/2022]
Abstract
Single-pair Förster resonance energy transfer (spFRET) experiments using single-molecule burst analysis on a confocal microscope are an ideal tool to measure inter- and intramolecular distances and dynamics on the nanoscale. Different techniques have been developed to maximize the amount of information available in spFRET burst analysis experiments. Multiparameter fluorescence detection (MFD) is used to monitor a variety of fluorescence parameters simultaneously and pulsed interleaved excitation (PIE) employs direct excitation of the acceptor to probe its presence and photoactivity. To calculate accurate FRET efficiencies from spFRET experiments with MFD or PIE, several calibration measurements are usually required. Herein, we demonstrate that by combining MFD with PIE information regarding all calibration factors as well as an accurate determination of spFRET histograms can be performed in a single measurement. In addition, the quality of overlap of the different detection volumes as well as the detection of acceptor photophysics can be investigated with MFD-PIE. Bursts containing acceptor photobleaching can be identified and excluded from further investigation while bursts that contain FRET dynamics are unaffected by this analysis. We have employed MFD-PIE to accurately analyze the effects of nucleotides and substrate on the interdomain separation in DnaK, the major bacterial heat shock protein 70 (Hsp70). The interdomain distance increases from 47 Å in the ATP-bound state to 84 Å in the ADP-bound state and slightly contracts to 77 Å when a substrate is bound. This is in contrast to what was observed for the mitochondrial member of the Hsp70s, Ssc1, supporting the notion of evolutionary specialization of Hsp70s for different cellular functions in different organisms and cell organelles.
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Affiliation(s)
- Volodymyr Kudryavtsev
- Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science (CiPSM) and Center for Nanoscience, Ludwig-Maximilians-Universität München, Butenandtstr. 11, Gerhard-Ertl-Building, 81377 Munich, Germany
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131
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Lai CW, Otero JH, Hendershot LM, Snapp E. ERdj4 protein is a soluble endoplasmic reticulum (ER) DnaJ family protein that interacts with ER-associated degradation machinery. J Biol Chem 2012; 287:7969-78. [PMID: 22267725 DOI: 10.1074/jbc.m111.311290] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Protein localization within cells regulates accessibility for interactions with co-factors and substrates. The endoplasmic reticulum (ER) BiP co-factor ERdj4 is up-regulated by ER stress and has been implicated in ER-associated degradation (ERAD) of multiple unfolded secretory proteins. Several other ERdj family members tend to interact selectively with nascent proteins, presumably because those ERdj proteins associate with the Sec61 translocon that facilitates entry of nascent proteins into the ER. How ERdj4 selects and targets terminally misfolded proteins for destruction remains poorly understood. In this study, we determined properties of ERdj4 that might aid in this function. ERdj4 was reported to retain its signal sequence and to be resistant to mild detergent extraction, suggesting that it was an integral membrane protein. However, live cell photobleaching analyses of GFP-tagged ERdj4 revealed that the protein exhibits diffusion coefficients uncommonly high for an ER integral membrane protein and more similar to the mobility of a soluble luminal protein. Biochemical characterization established that the ERdj4 signal sequence is cleaved to yield a soluble protein. Importantly, we found that both endogenous and overexpressed ERdj4 associate with the integral membrane protein, Derlin-1. Our findings now directly link ERdj4 to the ERAD machinery and suggest a model in which ERjd4 could help recruit clients from throughout the ER to ERAD sites.
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Affiliation(s)
- Chunwei Walter Lai
- Department of Anatomy & Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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132
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Moro S, Chipman JK, Antczak P, Turan N, Dekant W, Falciani F, Mally A. Identification and Pathway Mapping of Furan Target Proteins Reveal Mitochondrial Energy Production and Redox Regulation as Critical Targets of Furan Toxicity. Toxicol Sci 2012; 126:336-52. [DOI: 10.1093/toxsci/kfs005] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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133
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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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134
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Structural and functional interactions between the cholera toxin A1 subunit and ERdj3/HEDJ, a chaperone of the endoplasmic reticulum. Infect Immun 2011; 79:4739-47. [PMID: 21844235 DOI: 10.1128/iai.05503-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cholera toxin (CT) is endocytosed and transported by vesicle carriers to the endoplasmic reticulum (ER). The catalytic CTA1 subunit then crosses the ER membrane and enters the cytosol, where it interacts with its Gsα target. The CTA1 membrane transversal involves the ER chaperone BiP, but few other host proteins involved with CTA1 translocation are known. BiP function is regulated by ERdj3, an ER-localized Hsp40 chaperone also known as HEDJ. ERdj3 can also influence protein folding and translocation by direct substrate binding. In this work, structural and functional assays were used to examine the putative interaction between ERdj3 and CTA1. Cell-based assays demonstrated that expression of a dominant negative ERdj3 blocks CTA1 translocation into the cytosol and CT intoxication. Binding assays with surface plasmon resonance demonstrated that monomeric ERdj3 interacts directly with CTA1. This interaction involved the A1(2) subdomain of CTA1 and was further dependent upon the overall structure of CTA1: ERdj3 bound to unfolded but not folded conformations of the isolated CTA1 subunit. This was consistent with the chaperone function of ERdj3, as was the ability of ERdj3 to mask the solvent-exposed hydrophobic residues of CTA1. Our data identify ERdj3 as a host protein involved with the CT intoxication process and provide new molecular details regarding CTA1-chaperone interactions.
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135
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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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