51
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Choi SI. A Simple Principle for Understanding the Combined Cellular Protein Folding and Aggregation. Curr Protein Pept Sci 2020; 21:3-21. [DOI: 10.2174/1389203720666190725114550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/27/2022]
Abstract
Proteins can undergo kinetic/thermodynamic partitioning between folding and aggregation. Proper protein folding and thermodynamic stability are crucial for aggregation inhibition. Thus, proteinfolding principles have been widely believed to consistently underlie aggregation as a consequence of conformational change. However, this prevailing view appears to be challenged by the ubiquitous phenomena that the intrinsic and extrinsic factors including cellular macromolecules can prevent aggregation, independently of (even with sacrificing) protein folding rate and stability. This conundrum can be definitely resolved by ‘a simple principle’ based on a rigorous distinction between protein folding and aggregation: aggregation can be controlled by affecting the intermolecular interactions for aggregation, independently of the intramolecular interactions for protein folding. Aggregation is beyond protein folding. A unifying model that can conceptually reconcile and underlie the seemingly contradictory observations is described here. This simple principle highlights, in particular, the importance of intermolecular repulsive forces against aggregation, the magnitude of which can be correlated with the size and surface properties of molecules. The intermolecular repulsive forces generated by the common intrinsic properties of cellular macromolecules including chaperones, such as their large excluded volume and surface charges, can play a key role in preventing the aggregation of their physically connected polypeptides, thus underlying the generic intrinsic chaperone activity of soluble cellular macromolecules. Such intermolecular repulsive forces of bulky cellular macromolecules, distinct from protein conformational change and attractive interactions, could be the puzzle pieces for properly understanding the combined cellular protein folding and aggregation including how proteins can overcome their metastability to amyloid fibrils in vivo.
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Affiliation(s)
- Seong Il Choi
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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52
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Amin-Wetzel N, Neidhardt L, Yan Y, Mayer MP, Ron D. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife 2019; 8:50793. [PMID: 31873072 PMCID: PMC6996924 DOI: 10.7554/elife.50793] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022] Open
Abstract
Coupling of endoplasmic reticulum (ER) stress to dimerisation-dependent activation of the UPR transducer IRE1 is incompletely understood. Whilst the luminal co-chaperone ERdj4 promotes a complex between the Hsp70 BiP and IRE1's stress-sensing luminal domain (IRE1LD) that favours the latter's monomeric inactive state and loss of ERdj4 de-represses IRE1, evidence linking these cellular and in vitro observations is presently lacking. We report that enforced loading of endogenous BiP onto endogenous IRE1α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated BiP-induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent with active destabilisation of the IRE1LD dimer. Together, these observations support a competition model whereby waning ER stress passively partitions ERdj4 and BiP to IRE1LD to initiate active repression of UPR signalling.
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Affiliation(s)
- Niko Amin-Wetzel
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, United Kingdom
| | - Lisa Neidhardt
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, United Kingdom
| | - Yahui Yan
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, United Kingdom
| | - Matthias P Mayer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - David Ron
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, United Kingdom
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53
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Assenza S, Sassi AS, Kellner R, Schuler B, De Los Rios P, Barducci A. Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones. eLife 2019; 8:e48491. [PMID: 31845888 PMCID: PMC7000219 DOI: 10.7554/elife.48491] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 12/17/2019] [Indexed: 11/13/2022] Open
Abstract
Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here, we combine complementary theoretical approaches to elucidate the structural and thermodynamic details of the chaperone-induced expansion of a substrate protein, with a particular emphasis on the critical role played by ATP hydrolysis. We first determine the conformational free-energy cost of the substrate expansion due to the binding of multiple chaperones using coarse-grained molecular simulations. We then exploit this result to implement a non-equilibrium rate model which estimates the degree of expansion as a function of the free energy provided by ATP hydrolysis. Our results are in quantitative agreement with recent single-molecule FRET experiments and highlight the stark non-equilibrium nature of the process, showing that Hsp70s are optimized to effectively convert chemical energy into mechanical work close to physiological conditions.
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Affiliation(s)
- Salvatore Assenza
- Laboratory of Food and Soft MaterialsETH ZürichZürichSwitzerland
- Departmento de Física Teórica de la Materia CondensadaUniversidad Autónoma de MadridMadridSpain
| | - Alberto Stefano Sassi
- Institute of Physics, School of Basic SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- IBM TJ Watson Research CenterYorktown HeightsNew YorkUnited States
| | - Ruth Kellner
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
| | - Benjamin Schuler
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
- Department of PhysicsUniversity of ZurichZurichSwitzerland
| | - Paolo De Los Rios
- Institute of Physics, School of Basic SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Alessandro Barducci
- Centre de Biochimie Structurale (CBS)INSERM, CNRS, Université de MontpellierMontpellierFrance
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54
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Velasco L, Dublang L, Moro F, Muga A. The Complex Phosphorylation Patterns that Regulate the Activity of Hsp70 and Its Cochaperones. Int J Mol Sci 2019; 20:ijms20174122. [PMID: 31450862 PMCID: PMC6747476 DOI: 10.3390/ijms20174122] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022] Open
Abstract
Proteins must fold into their native structure and maintain it during their lifespan to display the desired activity. To ensure proper folding and stability, and avoid generation of misfolded conformations that can be potentially cytotoxic, cells synthesize a wide variety of molecular chaperones that assist folding of other proteins and avoid their aggregation, which unfortunately is unavoidable under acute stress conditions. A protein machinery in metazoa, composed of representatives of the Hsp70, Hsp40, and Hsp110 chaperone families, can reactivate protein aggregates. We revised herein the phosphorylation sites found so far in members of these chaperone families and the functional consequences associated with some of them. We also discuss how phosphorylation might regulate the chaperone activity and the interaction of human Hsp70 with its accessory and client proteins. Finally, we present the information that would be necessary to decrypt the effect that post-translational modifications, and especially phosphorylation, could have on the biological activity of the Hsp70 system, known as the “chaperone code”.
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Affiliation(s)
- Lorea Velasco
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Leire Dublang
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Fernando Moro
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain.
| | - Arturo Muga
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain.
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55
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Wentink A, Nussbaum-Krammer C, Bukau B. Modulation of Amyloid States by Molecular Chaperones. Cold Spring Harb Perspect Biol 2019; 11:a033969. [PMID: 30755450 PMCID: PMC6601462 DOI: 10.1101/cshperspect.a033969] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aberrant protein aggregation is a defining feature of most neurodegenerative diseases. During pathological aggregation, key proteins transition from their native state to alternative conformations, which are prone to oligomerize into highly ordered fibrillar states. As part of the cellular quality control machinery, molecular chaperones can intervene at many stages of the aggregation process to inhibit or reverse aberrant protein aggregation or counteract the toxicity associated with amyloid species. Although the action of chaperones is considered cytoprotective, essential housekeeping functions can be hijacked for the propagation and spreading of protein aggregates, suggesting the cellular protein quality control system constitutes a double-edged sword in neurodegeneration. Here, we discuss the various mechanisms used by chaperones to influence protein aggregation into amyloid fibrils to understand how the interplay of these activities produces specific cellular outcomes and to define mechanisms that may be targeted by pharmacological agents for the treatment of neurodegenerative conditions.
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Affiliation(s)
- Anne Wentink
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Carmen Nussbaum-Krammer
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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56
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Hsp70 molecular chaperones: multifunctional allosteric holding and unfolding machines. Biochem J 2019; 476:1653-1677. [PMID: 31201219 DOI: 10.1042/bcj20170380] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022]
Abstract
The Hsp70 family of chaperones works with its co-chaperones, the nucleotide exchange factors and J-domain proteins, to facilitate a multitude of cellular functions. Central players in protein homeostasis, these jacks-of-many-trades are utilized in a variety of ways because of their ability to bind with selective promiscuity to regions of their client proteins that are exposed when the client is unfolded, either fully or partially, or visits a conformational state that exposes the binding region in a regulated manner. The key to Hsp70 functions is that their substrate binding is transient and allosterically cycles in a nucleotide-dependent fashion between high- and low-affinity states. In the past few years, structural insights into the molecular mechanism of this allosterically regulated binding have emerged and provided deep insight into the deceptively simple Hsp70 molecular machine that is so widely harnessed by nature for diverse cellular functions. In this review, these structural insights are discussed to give a picture of the current understanding of how Hsp70 chaperones work.
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57
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The Physics of Entropic Pulling: A Novel Model for the Hsp70 Motor Mechanism. Int J Mol Sci 2019; 20:ijms20092334. [PMID: 31083504 PMCID: PMC6539501 DOI: 10.3390/ijms20092334] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 01/04/2023] Open
Abstract
Hsp70s use ATP to generate forces that disassemble protein complexes and aggregates, and that translocate proteins into organelles. Entropic pulling has been proposed as a novel mechanism, distinct from the more familiar power-stroke and Brownian ratchet models, for how Hsp70s generate these forces. Experimental evidence supports entropic pulling, but this model may not be well understood among scientists studying these systems. In this review we address persistent misconceptions regarding the dynamics of proteins in solution that contribute to this lack of understanding, and we clarify the basic physics of entropic pulling with some simple analogies. We hope that increased understanding of the entropic pulling mechanism will inform future efforts to characterize how Hsp70s function as motors, and how they coordinate with their regulatory cochaperones in mechanochemical cycles that transduce the energy of ATP hydrolysis into physical changes in their protein substrates.
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58
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Durie CL, Lin J, Scull NW, Mack KL, Jackrel ME, Sweeny EA, Castellano LM, Shorter J, Lucius AL. Hsp104 and Potentiated Variants Can Operate as Distinct Nonprocessive Translocases. Biophys J 2019; 116:1856-1872. [PMID: 31027887 DOI: 10.1016/j.bpj.2019.03.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 03/14/2019] [Accepted: 03/25/2019] [Indexed: 01/09/2023] Open
Abstract
Heat shock protein (Hsp) 104 is a hexameric ATPases associated with diverse cellular activities motor protein that enables cells to survive extreme stress. Hsp104 couples the energy of ATP binding and hydrolysis to solubilize proteins trapped in aggregated structures. The mechanism by which Hsp104 disaggregates proteins is not completely understood but may require Hsp104 to partially or completely translocate polypeptides across its central channel. Here, we apply transient state, single turnover kinetics to investigate the ATP-dependent translocation of soluble polypeptides by Hsp104 and Hsp104A503S, a potentiated variant developed to resolve misfolded conformers implicated in neurodegenerative disease. We establish that Hsp104 and Hsp104A503S can operate as nonprocessive translocases for soluble substrates, indicating a "partial threading" model of translocation. Remarkably, Hsp104A503S exhibits altered coupling of ATP binding to translocation and decelerated dissociation from polypeptide substrate compared to Hsp104. This altered coupling and prolonged substrate interaction likely increases entropic pulling forces, thereby enabling more effective aggregate dissolution by Hsp104A503S.
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Affiliation(s)
- Clarissa L Durie
- University of Alabama at Birmingham, Chemistry Department, Birmingham, Alabama
| | - JiaBei Lin
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nathaniel W Scull
- University of Alabama at Birmingham, Chemistry Department, Birmingham, Alabama
| | - Korrie L Mack
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Meredith E Jackrel
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elizabeth A Sweeny
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Laura M Castellano
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aaron L Lucius
- University of Alabama at Birmingham, Chemistry Department, Birmingham, Alabama.
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59
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Ihara M, Shichijo K, Kudo T, Ohtsuka K. Reactivation of heat-inactivated Ku proteins by heat shock cognate protein HSC73. Int J Hyperthermia 2019; 36:438-443. [PMID: 30922135 DOI: 10.1080/02656736.2019.1587009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
PURPOSE Mouse double-stranded DNA-dependent protein kinase (DNA-PK) activity is heat sensitive. Recovery of heat-inactivated DNA repair activity is a problem after combination therapy with radiation and heat. We investigated the mechanism of recovery of heat-inactivated DNA-PK activity. METHODS Hybrid cells containing a fragment of human chromosome 8 in scid cells (RD13B2) were used. DNA-PK activity was measured by an in vitro assay. Immunoprecipitation of the nuclear extract was performed with an anti-Ku80 antibody. Proteins co-precipitated with Ku80 were separated by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis and detected by Western blotting using anti-heat shock protein (HSP)72 and anti-heat shock cognate protein (HSC)73 antibodies. HSC73 was overexpressed with the pcDNA3.1 vector. Short hairpin (sh)RNA was used to downregulate HSC73 and HSP72. RESULTS The activity of heat-inactivated DNA-PK recovered to about 50% of control during an additional incubation at 37 °C after heat treatment at 44 °C for 15 min in the presence of cycloheximide (which inhibits de novo protein synthesis). Maximal recovery was observed within 3 h of incubation at 37 °C after heat treatment. Constitutively expressed HSC73, which folds newly synthesized proteins, reached maximal levels 3 h after heat treatment using a co-immunoprecipitation assay with the Ku80 protein. Inhibiting HSC73, but not HSP72, expression with shRNA decreased the recovery of DNA-PK activity after heat treatment. CONCLUSIONS These results suggest that de novo protein synthesis is unnecessary for recovery of some heat-inactivated DNA-PK. Rather, it might be reactivated by the molecular chaperone activity of HSC73, but not HSP72.
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Affiliation(s)
- Makoto Ihara
- a Department of Radioisotope Medicine, Atomic Bomb Disease and Hibakusha Medicine Unit, Atomic Bomb Disease Institute , Nagasaki University , Nagasaki , Japan
| | - Kazuko Shichijo
- b Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease and Hibakusha Medicine Unit, Atomic Bomb Disease Institute , Nagasaki University , Nagasaki , Japan
| | - Takashi Kudo
- a Department of Radioisotope Medicine, Atomic Bomb Disease and Hibakusha Medicine Unit, Atomic Bomb Disease Institute , Nagasaki University , Nagasaki , Japan
| | - Kenzo Ohtsuka
- c Laboratory of Cell and Stress Biology, College of Bioscience and Biotechnology , Chubu University , Kasugai , Japan
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60
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Ganesan I, Theg SM. Structural considerations of folded protein import through the chloroplast TOC/TIC translocons. FEBS Lett 2019; 593:565-572. [PMID: 30775779 DOI: 10.1002/1873-3468.13342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 11/11/2022]
Abstract
Protein import into chloroplasts is carried out by the protein translocons at the outer and inner envelope membranes (TOC and TIC). Detailed structures for these translocons are lacking, with only a low-resolution TOC complex structure available. Recently, we showed that the TOC/TIC translocons can import folded proteins, a rather unique feat for a coupled double membrane system. We also determined the maximum functional TOC/TIC pore size to be 30-35 Å. Here, we discuss how such large pores could form and compare the structural dynamics of the pore-forming Toc75 subunit to its bacterial/mitochondrial Omp85 family homologs. We put forward structural models that can be empirically tested and also briefly review the pore dynamics of other protein translocons with known structures.
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Affiliation(s)
- Iniyan Ganesan
- Department of Plant Biology, University of California Davis, CA, USA
| | - Steven M Theg
- Department of Plant Biology, University of California Davis, CA, USA
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61
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Conversion of a soluble protein into a potent chaperone in vivo. Sci Rep 2019; 9:2735. [PMID: 30804538 PMCID: PMC6389997 DOI: 10.1038/s41598-019-39158-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 01/18/2019] [Indexed: 01/31/2023] Open
Abstract
Molecular chaperones play an important role in cellular protein-folding assistance and aggregation inhibition. As a different but complementary model, we previously proposed that, in general, soluble cellular macromolecules with large excluded volume and surface charges exhibit intrinsic chaperone activity to prevent aggregation of their connected polypeptides irrespective of the connection type, thereby contributing to efficient protein folding. As a proof of concept, we here demonstrated that a model recombinant protein with a specific sequence-binding domain robustly exerted chaperone activity toward various proteins harbouring a short recognition tag of 7 residues in Escherichia coli. The chaperone activity of this protein was comparable to that of representative E. coli chaperones in vivo. Furthermore, in vitro refolding experiments confirmed the in vivo results. Our findings reveal that a soluble protein exhibits the intrinsic chaperone activity to prevent off-pathway aggregation of its interacting proteins, leading to more productive folding while allowing them to fold according to their intrinsic folding pathways. This study gives new insights into the plausible chaperoning role of soluble cellular macromolecules in terms of aggregation inhibition and indirect folding assistance.
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62
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Mitochondrial presequence import: Multiple regulatory knobs fine-tune mitochondrial biogenesis and homeostasis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:930-944. [PMID: 30802482 DOI: 10.1016/j.bbamcr.2019.02.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 12/22/2022]
Abstract
Mitochondria are pivotal organelles for cellular signaling and metabolism, and their dysfunction leads to severe cellular stress. About 60-70% of the mitochondrial proteome consists of preproteins synthesized in the cytosol with an amino-terminal cleavable presequence targeting signal. The TIM23 complex transports presequence signals towards the mitochondrial matrix. Ultimately, the mature protein segments are either transported into the matrix or sorted to the inner membrane. To ensure accurate preprotein import into distinct mitochondrial sub-compartments, the TIM23 machinery adopts specific functional conformations and interacts with different partner complexes. Regulatory subunits modulate the translocase dynamics, tailoring the import reaction to the incoming preprotein. The mitochondrial membrane potential and the ATP generated via oxidative phosphorylation are key energy sources in driving the presequence import pathway. Thus, mitochondrial dysfunctions have rapid repercussions on biogenesis. Cellular mechanisms exploit the presequence import pathway to monitor mitochondrial dysfunctions and mount transcriptional and proteostatic responses to restore functionality.
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63
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Ueda E, Tamura Y, Sakaue H, Kawano S, Kakuta C, Matsumoto S, Endo T. Myristoyl group-aided protein import into the mitochondrial intermembrane space. Sci Rep 2019; 9:1185. [PMID: 30718713 PMCID: PMC6362269 DOI: 10.1038/s41598-018-38016-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/12/2018] [Indexed: 12/20/2022] Open
Abstract
The MICOS complex mediates formation of the crista junctions in mitochondria. Here we analyzed the mitochondrial import pathways for the six yeast MICOS subunits as a step toward understanding of the assembly mechanisms of the MICOS complex. Mic10, Mic12, Mic26, Mic27, and Mic60 used the presequence pathway to reach the intermembrane space (IMS). In contrast, Mic19 took the TIM40/MIA pathway, through its CHCH domain, to reach the IMS. Unlike canonical TIM40/MIA substrates, presence of the N-terminal unfolded DUF domain impaired the import efficiency of Mic19, yet N-terminal myristoylation of Mic19 circumvented this effect. The myristoyl group of Mic19 binds to Tom20 of the TOM complex as well as the outer membrane, which may lead to "entropy pushing" of the DUF domain followed by the CHCH domain of Mic19 into the import channel, thereby achieving efficient import.
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Affiliation(s)
- Eri Ueda
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
- Department of Biological Science, Graduate School of Science, Osaka University, 1-1 machikaneyama-cho, Toyonaka, 560-0043, Osaka, Japan
| | - Yasushi Tamura
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, 990-8560, Japan
| | - Haruka Sakaue
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Research Center for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Shin Kawano
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Research Center for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Chika Kakuta
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Shunsuke Matsumoto
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Research Center for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.
- Research Center for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.
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65
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Dahiya V, Buchner J. Functional principles and regulation of molecular chaperones. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:1-60. [PMID: 30635079 DOI: 10.1016/bs.apcsb.2018.10.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To be able to perform their biological function, a protein needs to be correctly folded into its three dimensional structure. The protein folding process is spontaneous and does not require the input of energy. However, in the crowded cellular environment where there is high risk of inter-molecular interactions that may lead to protein molecules sticking to each other, hence forming aggregates, protein folding is assisted. Cells have evolved robust machinery called molecular chaperones to deal with the protein folding problem and to maintain proteins in their functional state. Molecular chaperones promote efficient folding of newly synthesized proteins, prevent their aggregation and ensure protein homeostasis in cells. There are different classes of molecular chaperones functioning in a complex interplay. In this review, we discuss the principal characteristics of different classes of molecular chaperones, their structure-function relationships, their mode of regulation and their involvement in human disorders.
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Affiliation(s)
- Vinay Dahiya
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany.
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66
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Mayer MP, Gierasch LM. Recent advances in the structural and mechanistic aspects of Hsp70 molecular chaperones. J Biol Chem 2018; 294:2085-2097. [PMID: 30455352 DOI: 10.1074/jbc.rev118.002810] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hsp70 chaperones are central hubs of the protein quality control network and collaborate with co-chaperones having a J-domain (an ∼70-residue-long helical hairpin with a flexible loop and a conserved His-Pro-Asp motif required for ATP hydrolysis by Hsp70s) and also with nucleotide exchange factors to facilitate many protein-folding processes that (re)establish protein homeostasis. The Hsp70s are highly dynamic nanomachines that modulate the conformation of their substrate polypeptides by transiently binding to short, mostly hydrophobic stretches. This interaction is regulated by an intricate allosteric mechanism. The J-domain co-chaperones target Hsp70 to their polypeptide substrates, and the nucleotide exchange factors regulate the lifetime of the Hsp70-substrate complexes. Significant advances in recent years are beginning to unravel the molecular mechanism of this chaperone machine and how they treat their substrate proteins.
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Affiliation(s)
- Matthias P Mayer
- From the Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany and
| | - Lila M Gierasch
- the Departments of Biochemistry and Molecular Biology and.,Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
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67
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Uhl M, Seifert U. Force-dependent diffusion coefficient of molecular Brownian ratchets. Phys Rev E 2018; 98:022402. [PMID: 30253613 DOI: 10.1103/physreve.98.022402] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Indexed: 11/07/2022]
Abstract
We study the mean velocity and diffusion constant in three related models of molecular Brownian ratchets. Brownian ratchets can be used to describe translocation of biopolymers like DNA through nanopores in cells in the presence of chaperones on the trans side of the pore. Chaperones can bind to the polymer and prevent it from sliding back through the pore. First, we study a simple model that describes the translocation in terms of an asymmetric random walk. It serves as an introductory example but already captures the main features of a Brownian ratchet. We then provide an analytical expression for the diffusion constant in the classical model of a translocation ratchet that was first proposed by Peskin et al. [C. S. Peskin, G. M. Odell, and G. F. Oster, Cellular motions and thermal fluctuations: The Brownian ratchet, Biophys. J. 65, 316 (1993)BIOJAU0006-349510.1016/S0006-3495(93)81035-X]. This model is based on the assumption that the binding and unbinding of the chaperones are much faster than the diffusion of the DNA strand. To remedy this shortcoming, we propose a modified model that is also applicable if the (un)binding rates are finite. We calculate the force-dependent mean velocity and diffusivity for this model and compare the results to the original one. Our analysis shows that for large pulling forces the predictions of both models can differ strongly even if the (un)binding rates are large in comparison to the diffusion timescale but still finite. Furthermore, implications of the thermodynamic uncertainty relation on the efficiency of Brownian ratchets are discussed.
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Affiliation(s)
- Matthias Uhl
- II. Institut für Theoretische Physik, Universität Stuttgart, 70550 Stuttgart, Germany
| | - Udo Seifert
- II. Institut für Theoretische Physik, Universität Stuttgart, 70550 Stuttgart, Germany
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68
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Knyazev DG, Kuttner R, Zimmermann M, Sobakinskaya E, Pohl P. Driving Forces of Translocation Through Bacterial Translocon SecYEG. J Membr Biol 2018; 251:329-343. [PMID: 29330604 PMCID: PMC6028853 DOI: 10.1007/s00232-017-0012-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 12/22/2017] [Indexed: 11/09/2022]
Abstract
This review focusses on the energetics of protein translocation via the Sec translocation machinery. First we complement structural data about SecYEG's conformational rearrangements by insight obtained from functional assays. These include measurements of SecYEG permeability that allow assessment of channel gating by ligand binding and membrane voltage. Second we will discuss the power stroke and Brownian ratcheting models of substrate translocation and the role that the two models assign to the putative driving forces: (i) ATP (SecA) and GTP (ribosome) hydrolysis, (ii) interaction with accessory proteins, (iii) membrane partitioning and folding, (iv) proton motive force (PMF), and (v) entropic contributions. Our analysis underlines how important energized membranes are for unravelling the translocation mechanism in future experiments.
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Affiliation(s)
- Denis G Knyazev
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria.
| | - Roland Kuttner
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
| | - Mirjam Zimmermann
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
| | | | - Peter Pohl
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
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69
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Kivinen N. The role of autophagy in age-related macular degeneration. Acta Ophthalmol 2018; 96 Suppl A110:1-50. [PMID: 29633521 DOI: 10.1111/aos.13753] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Niko Kivinen
- Department of Ophthalmology; University of Eastern Finland; Kuopio Finland
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70
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Nillegoda NB, Wentink AS, Bukau B. Protein Disaggregation in Multicellular Organisms. Trends Biochem Sci 2018; 43:285-300. [PMID: 29501325 DOI: 10.1016/j.tibs.2018.02.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/29/2018] [Accepted: 02/01/2018] [Indexed: 12/13/2022]
Abstract
Protein aggregates are formed in cells with profoundly perturbed proteostasis, where the generation of misfolded proteins exceeds the cellular refolding and degradative capacity. They are a hallmark of protein conformational disorders and aged and/or environmentally stressed cells. Protein aggregation is a reversible process in vivo, which counteracts proteotoxicities derived from aggregate persistence, but the chaperone machineries involved in protein disaggregation in Metazoa were uncovered only recently. Here we highlight recent advances in the mechanistic understanding of the major protein disaggregation machinery mediated by the Hsp70 chaperone system and discuss emerging alternative disaggregation activities in multicellular organisms.
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Affiliation(s)
- Nadinath B Nillegoda
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Anne S Wentink
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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71
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Perales-Calvo J, Giganti D, Stirnemann G, Garcia-Manyes S. The force-dependent mechanism of DnaK-mediated mechanical folding. SCIENCE ADVANCES 2018; 4:eaaq0243. [PMID: 29487911 PMCID: PMC5817926 DOI: 10.1126/sciadv.aaq0243] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/09/2018] [Indexed: 05/27/2023]
Abstract
It is well established that chaperones modulate the protein folding free-energy landscape. However, the molecular determinants underlying chaperone-mediated mechanical folding remain largely elusive, primarily because the force-extended unfolded conformation fundamentally differs from that characterized in biochemistry experiments. We use single-molecule force-clamp spectroscopy, combined with molecular dynamics simulations, to study the effect that the Hsp70 system has on the mechanical folding of three mechanically stiff model proteins. Our results demonstrate that, when working independently, DnaJ (Hsp40) and DnaK (Hsp70) work as holdases, blocking refolding by binding to distinct substrate conformations. Whereas DnaK binds to molten globule-like forms, DnaJ recognizes a cryptic sequence in the extended state in an unanticipated force-dependent manner. By contrast, the synergetic coupling of the Hsp70 system exhibits a marked foldase behavior. Our results offer unprecedented molecular and kinetic insights into the mechanisms by which mechanical force finely regulates chaperone binding, directly affecting protein elasticity.
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Affiliation(s)
- Judit Perales-Calvo
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King’s College London, WC2R 2LS London, UK
| | - David Giganti
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King’s College London, WC2R 2LS London, UK
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Univ. Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King’s College London, WC2R 2LS London, UK
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72
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Abstract
Efficient movement of proteins across membranes is required for cell health. The translocation process is particularly challenging when the channel in the membrane through which proteins must pass is narrow—such as those in the membranes of the endoplasmic reticulum and mitochondria. Hsp70 molecular chaperones play roles on both sides of these membranes, ensuring efficient translocation of proteins synthesized on cytosolic ribosomes into the interior of these organelles. The “import motor” in the mitochondrial matrix, which is essential for driving the movement of proteins across the mitochondrial inner membrane, is arguably the most complex Hsp70-based system in the cell.
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Affiliation(s)
- Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin - Madison, 433 Babcock Drive, Madison, WI, 53706, USA.
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73
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Backes S, Herrmann JM. Protein Translocation into the Intermembrane Space and Matrix of Mitochondria: Mechanisms and Driving Forces. Front Mol Biosci 2017; 4:83. [PMID: 29270408 PMCID: PMC5725982 DOI: 10.3389/fmolb.2017.00083] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 11/24/2017] [Indexed: 11/17/2022] Open
Abstract
Mitochondria contain two aqueous subcompartments, the matrix and the intermembrane space (IMS). The matrix is enclosed by both the inner and outer mitochondrial membranes, whilst the IMS is sandwiched between the two. Proteins of the matrix are synthesized in the cytosol as preproteins, which contain amino-terminal matrix targeting sequences that mediate their translocation through translocases embedded in the outer and inner membrane. For these proteins, the translocation reaction is driven by the import motor which is part of the inner membrane translocase. The import motor employs matrix Hsp70 molecules and ATP hydrolysis to ratchet proteins into the mitochondrial matrix. Most IMS proteins lack presequences and instead utilize the IMS receptor Mia40, which facilitates their translocation across the outer membrane in a reaction that is coupled to the formation of disulfide bonds within the protein. This process requires neither ATP nor the mitochondrial membrane potential. Mia40 fulfills two roles: First, it acts as a holdase, which is crucial in the import of IMS proteins and second, it functions as a foldase, introducing disulfide bonds into newly imported proteins, which induces and stabilizes their natively folded state. For several Mia40 substrates, oxidative folding is an essential prerequisite for their assembly into oligomeric complexes. Interestingly, recent studies have shown that the two functions of Mia40 can be experimentally separated from each other by the use of specific mutants, hence providing a powerful new way to dissect the different physiological roles of Mia40. In this review we summarize the current knowledge relating to the mitochondrial matrix-targeting and the IMS-targeting/Mia40 pathway. Moreover, we discuss the mechanistic properties by which the mitochondrial import motor on the one hand and Mia40 on the other, drive the translocation of their substrates into the organelle. We propose that the lateral diffusion of Mia40 in the inner membrane and the oxidation-mediated folding of incoming polypeptides supports IMS import.
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Affiliation(s)
- Sandra Backes
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
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74
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De Los Rios P, Goloubinoff P. Hsp70 chaperones use ATP to remodel native protein oligomers and stable aggregates by entropic pulling. Nat Struct Mol Biol 2017; 23:766-9. [PMID: 27605203 DOI: 10.1038/nsmb.3283] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Paolo De Los Rios
- Institute of Physics, School of Basic Sciences and Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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75
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Protein aggregation: From background to inhibition strategies. Int J Biol Macromol 2017; 103:208-219. [DOI: 10.1016/j.ijbiomac.2017.05.048] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 01/01/2023]
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76
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Wruck F, Avellaneda MJ, Koers EJ, Minde DP, Mayer MP, Kramer G, Mashaghi A, Tans SJ. Protein Folding Mediated by Trigger Factor and Hsp70: New Insights from Single-Molecule Approaches. J Mol Biol 2017; 430:438-449. [PMID: 28911846 DOI: 10.1016/j.jmb.2017.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/26/2017] [Accepted: 09/04/2017] [Indexed: 01/01/2023]
Abstract
Chaperones assist in protein folding, but what this common phrase means in concrete terms has remained surprisingly poorly understood. We can readily measure chaperone binding to unfolded proteins, but how they bind and affect proteins along folding trajectories has remained obscure. Here we review recent efforts by our labs and others that are beginning to pry into this issue, with a focus on the chaperones trigger factor and Hsp70. Single-molecule methods are central, as they allow the stepwise process of folding to be followed directly. First results have already revealed contrasts with long-standing paradigms: rather than acting only "early" by stabilizing unfolded chain segments, these chaperones can bind and stabilize partially folded structures as they grow to their native state. The findings suggest a fundamental redefinition of the protein folding problem and a more extensive functional repertoire of chaperones than previously assumed.
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Affiliation(s)
- Florian Wruck
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | | | - Eline J Koers
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | - David P Minde
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | - Matthias P Mayer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Alireza Mashaghi
- Leiden Academic Centre for Drug Research, Faculty of Mathematics and Natural Sciences, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Sander J Tans
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands.
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77
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Sassi AS, Assenza S, De Los Rios P. Shape of a Stretched Polymer. PHYSICAL REVIEW LETTERS 2017; 119:037801. [PMID: 28777625 DOI: 10.1103/physrevlett.119.037801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Indexed: 06/07/2023]
Abstract
The shape of a polymer plays an important role in its interactions with surrounding molecules. We characterize the shape and the orientational properties of a polymer chain under tension in a good solvent, a physical condition that is often realized both in single-molecule experiments and in vivo. Our findings reveal the existence of hitherto unobserved universal laws encompassing polymers with different rigidities and including the possible presence of excluded-volume effects, showing that both shape and orientation are solely determined by the force contribution to the free energy. In doing so, they also provide a simple way to retrieve these quantities from the knowledge of the force-versus-extension curve.
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Affiliation(s)
- Alberto S Sassi
- Laboratoire de Biophysique Statistique, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Salvatore Assenza
- Laboratoire de Biophysique Statistique, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Paolo De Los Rios
- Laboratoire de Biophysique Statistique, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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78
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Malinverni D, Jost Lopez A, De Los Rios P, Hummer G, Barducci A. Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis. eLife 2017; 6. [PMID: 28498104 PMCID: PMC5519331 DOI: 10.7554/elife.23471] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/10/2017] [Indexed: 01/01/2023] Open
Abstract
The interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of the interaction remain elusive and contrasting models have been proposed for the transient Hsp70/Hsp40 complexes. Here we combine molecular simulations based on both coarse-grained and atomistic models with coevolutionary sequence analysis to shed light on this problem by focusing on the bacterial DnaK/DnaJ system. The integration of these complementary approaches resulted in a novel structural model that rationalizes previous experimental observations. We identify an evolutionarily conserved interaction surface formed by helix II of the DnaJ J-domain and a structurally contiguous region of DnaK, involving lobe IIA of the nucleotide binding domain, the inter-domain linker, and the β-basket of the substrate binding domain. DOI:http://dx.doi.org/10.7554/eLife.23471.001
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Affiliation(s)
- Duccio Malinverni
- Laboratoire de Biophysique Statistique, Faculté de Sciences de Base, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Paolo De Los Rios
- Laboratoire de Biophysique Statistique, Faculté de Sciences de Base, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gerhard Hummer
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Institut für Biophysik, Johann Wolfgang Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Alessandro Barducci
- Inserm, U1054, Montpellier, France.,Université de Montpellier, CNRS, UMR 5048, Centre de Biochimie Structurale, Montpellier, France
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79
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Abstract
Mitochondria are essential organelles with numerous functions in cellular metabolism and homeostasis. Most of the >1,000 different mitochondrial proteins are synthesized as precursors in the cytosol and are imported into mitochondria by five transport pathways. The protein import machineries of the mitochondrial membranes and aqueous compartments reveal a remarkable variability of mechanisms for protein recognition, translocation, and sorting. The protein translocases do not operate as separate entities but are connected to each other and to machineries with functions in energetics, membrane organization, and quality control. Here, we discuss the versatility and dynamic organization of the mitochondrial protein import machineries. Elucidating the molecular mechanisms of mitochondrial protein translocation is crucial for understanding the integration of protein translocases into a large network that controls organelle biogenesis, function, and dynamics.
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Affiliation(s)
- Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, and BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany; ,
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, and BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany; ,
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80
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Modular transcriptional repertoire and MicroRNA target analyses characterize genomic dysregulation in the thymus of Down syndrome infants. Oncotarget 2016; 7:7497-533. [PMID: 26848775 PMCID: PMC4884935 DOI: 10.18632/oncotarget.7120] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/23/2016] [Indexed: 12/25/2022] Open
Abstract
Trisomy 21-driven transcriptional alterations in human thymus were characterized through gene coexpression network (GCN) and miRNA-target analyses. We used whole thymic tissue--obtained at heart surgery from Down syndrome (DS) and karyotipically normal subjects (CT)--and a network-based approach for GCN analysis that allows the identification of modular transcriptional repertoires (communities) and the interactions between all the system's constituents through community detection. Changes in the degree of connections observed for hierarchically important hubs/genes in CT and DS networks corresponded to community changes. Distinct communities of highly interconnected genes were topologically identified in these networks. The role of miRNAs in modulating the expression of highly connected genes in CT and DS was revealed through miRNA-target analysis. Trisomy 21 gene dysregulation in thymus may be depicted as the breakdown and altered reorganization of transcriptional modules. Leading networks acting in normal or disease states were identified. CT networks would depict the "canonical" way of thymus functioning. Conversely, DS networks represent a "non-canonical" way, i.e., thymic tissue adaptation under trisomy 21 genomic dysregulation. This adaptation is probably driven by epigenetic mechanisms acting at chromatin level and through the miRNA control of transcriptional programs involving the networks' high-hierarchy genes.
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81
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Becirovic L, Brown IR. Targeting of Heat Shock Protein HSPA6 (HSP70B') to the Periphery of Nuclear Speckles is Disrupted by a Transcription Inhibitor Following Thermal Stress in Human Neuronal Cells. Neurochem Res 2016; 42:406-414. [PMID: 27743288 DOI: 10.1007/s11064-016-2084-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 12/21/2022]
Abstract
Heat shock proteins (Hsps) are a set of highly conserved proteins involved in cellular repair and protective mechanisms. The intracellular localization of inducible members of the HSPA (HSP70) family can be used as an index to identify stress-sensitive sites in differentiated human neuronal cells. Following thermal stress, the little studied HSPA6 (HSP70B') was targeted to the periphery of nuclear speckles (perispeckles) that are sites of transcription factories. Triptolide, a fast-acting transcription inhibitor, knocked down levels of the large subunit of RNA polymerase II, RPB1, during the time-frame when HSPA6 associated with perispeckles. Administration of triptolide to heat shocked human neuronal SH-SY5Y cells, disrupted HSPA6 localization to perispeckles, suggesting the involvement of HSPA6 in transcriptional recovery after stress. The HSPA6 gene is present in the human genome but is not found in the genomes of the mouse and rat. Hence current animal models of neurodegenerative diseases lack a member of the HSPA family that exhibits the feature of stress-induced targeting to perispeckles.
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Affiliation(s)
- Larissa Becirovic
- Department of Biological Sciences, Centre for the Neurobiology of Stress, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Ian R Brown
- Department of Biological Sciences, Centre for the Neurobiology of Stress, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada.
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82
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Hristozova N, Tompa P, Kovacs D. A Novel Method for Assessing the Chaperone Activity of Proteins. PLoS One 2016; 11:e0161970. [PMID: 27564234 PMCID: PMC5001627 DOI: 10.1371/journal.pone.0161970] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/15/2016] [Indexed: 12/02/2022] Open
Abstract
Protein chaperones are molecular machines which function both during homeostasis and stress conditions in all living organisms. Depending on their specific function, molecular chaperones are involved in a plethora of cellular processes by playing key roles in nascent protein chain folding, transport and quality control. Among stress protein families-molecules expressed during adverse conditions, infection, and diseases-chaperones are highly abundant. Their molecular functions range from stabilizing stress-susceptible molecules and membranes to assisting the refolding of stress-damaged proteins, thereby acting as protective barriers against cellular damage. Here we propose a novel technique to test and measure the capability for protective activity of known and putative chaperones in a semi-high throughput manner on a plate reader. The current state of the art does not allow the in vitro measurements of chaperone activity in a highly parallel manner with high accuracy or high reproducibility, thus we believe that the method we report will be of significant benefit in this direction. The use of this method may lead to a considerable increase in the number of experimentally verified proteins with such functions, and may also allow the dissection of their molecular mechanism for a better understanding of their function.
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Affiliation(s)
- Nevena Hristozova
- Structural Biology Department, Flemish Institute of Biotechnology, Brussels, Belgium
- Structural Biology Department, Free University Brussels, Brussels, Belgium
| | - Peter Tompa
- Structural Biology Department, Flemish Institute of Biotechnology, Brussels, Belgium
- Structural Biology Department, Free University Brussels, Brussels, Belgium
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Denes Kovacs
- Structural Biology Department, Flemish Institute of Biotechnology, Brussels, Belgium
- Structural Biology Department, Free University Brussels, Brussels, Belgium
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83
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Fernández-Fernández MR, Sot B, Valpuesta JM. Molecular chaperones: functional mechanisms and nanotechnological applications. NANOTECHNOLOGY 2016; 27:324004. [PMID: 27363314 DOI: 10.1088/0957-4484/27/32/324004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Molecular chaperones are a group of proteins that assist in protein homeostasis. They not only prevent protein misfolding and aggregation, but also target misfolded proteins for degradation. Despite differences in structure, all types of chaperones share a common general feature, a surface that recognizes and interacts with the misfolded protein. This and other, more specialized properties can be adapted for various nanotechnological purposes, by modification of the original biomolecules or by de novo design based on artificial structures.
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Affiliation(s)
- M Rosario Fernández-Fernández
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus de la Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain
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84
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Clathrin-coat disassembly illuminates the mechanisms of Hsp70 force generation. Nat Struct Mol Biol 2016; 23:821-9. [PMID: 27478930 PMCID: PMC5016234 DOI: 10.1038/nsmb.3272] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/06/2016] [Indexed: 01/04/2023]
Abstract
Hsp70s use ATP hydrolysis to disrupt protein:protein associations or move macromolecules. One example is Hsc70-mediated disassembly of clathrin coats that form on vesicles during endocytosis. We exploit the exceptional features of these coats to test three models—Brownian ratchet, power-stroke and entropic pulling—proposed to explain how Hsp70s transform their substrates. Our data rule out the ratchet and power-stroke models, and instead support a collision pressure mechanism whereby collisions between clathrin coat walls and Hsc70s drive coats apart. Collision pressure is the complement to the pulling force described in the entropic pulling model. We also find that self-association can augment collision pressure to allow disassembly of clathrin lattices predicted to resist disassembly. These results illuminate how Hsp70s generate the forces that transform their substrates.
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85
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Celaya G, Fernández-Higuero JA, Martin I, Rivas G, Moro F, Muga A. Crowding Modulates the Conformation, Affinity, and Activity of the Components of the Bacterial Disaggregase Machinery. J Mol Biol 2016; 428:2474-2487. [DOI: 10.1016/j.jmb.2016.04.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 12/13/2022]
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86
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Clare DK, Saibil HR. ATP-driven molecular chaperone machines. Biopolymers 2016; 99:846-59. [PMID: 23877967 PMCID: PMC3814418 DOI: 10.1002/bip.22361] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/08/2013] [Indexed: 01/17/2023]
Abstract
This review is focused on the mechanisms by which ATP binding and hydrolysis drive chaperone machines assisting protein folding and unfolding. A survey of the key, general chaperone systems Hsp70 and Hsp90, and the unfoldase Hsp100 is followed by a focus on the Hsp60 chaperonin machine which is understood in most detail. Cryo-electron microscopy analysis of the E. coli Hsp60 GroEL reveals intermediate conformations in the ATPase cycle and in substrate folding. These structures suggest a mechanism by which GroEL can forcefully unfold and then encapsulate substrates for subsequent folding in isolation from all other binding surfaces.
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Affiliation(s)
- Daniel K Clare
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
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87
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Finka A, Mattoo RUH, Goloubinoff P. Experimental Milestones in the Discovery of Molecular Chaperones as Polypeptide Unfolding Enzymes. Annu Rev Biochem 2016; 85:715-42. [PMID: 27050154 DOI: 10.1146/annurev-biochem-060815-014124] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molecular chaperones control the cellular folding, assembly, unfolding, disassembly, translocation, activation, inactivation, disaggregation, and degradation of proteins. In 1989, groundbreaking experiments demonstrated that a purified chaperone can bind and prevent the aggregation of artificially unfolded polypeptides and use ATP to dissociate and convert them into native proteins. A decade later, other chaperones were shown to use ATP hydrolysis to unfold and solubilize stable protein aggregates, leading to their native refolding. Presently, the main conserved chaperone families Hsp70, Hsp104, Hsp90, Hsp60, and small heat-shock proteins (sHsps) apparently act as unfolding nanomachines capable of converting functional alternatively folded or toxic misfolded polypeptides into harmless protease-degradable or biologically active native proteins. Being unfoldases, the chaperones can proofread three-dimensional protein structures and thus control protein quality in the cell. Understanding the mechanisms of the cellular unfoldases is central to the design of new therapies against aging, degenerative protein conformational diseases, and specific cancers.
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Affiliation(s)
- Andrija Finka
- Laboratory of Biophysical Statistics, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Rayees U H Mattoo
- Department of Structural Biology, Stanford University, Stanford, California 94305;
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland;
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88
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A novel Hsp70 inhibitor prevents cell intoxication with the actin ADP-ribosylating Clostridium perfringens iota toxin. Sci Rep 2016; 6:20301. [PMID: 26839186 PMCID: PMC4738285 DOI: 10.1038/srep20301] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/30/2015] [Indexed: 12/14/2022] Open
Abstract
Hsp70 family proteins are folding helper proteins involved in a wide variety of cellular pathways. Members of this family interact with key factors in signal transduction, transcription, cell-cycle control, and stress response. Here, we developed the first Hsp70 low molecular weight inhibitor specifically targeting the peptide binding site of human Hsp70. After demonstrating that the inhibitor modulates the Hsp70 function in the cell, we used the inhibitor to show for the first time that the stress-inducible chaperone Hsp70 functions as molecular component for entry of a bacterial protein toxin into mammalian cells. Pharmacological inhibition of Hsp70 protected cells from intoxication with the binary actin ADP-ribosylating iota toxin from Clostridium perfringens, the prototype of a family of enterotoxins from pathogenic Clostridia and inhibited translocation of its enzyme component across cell membranes into the cytosol. This finding offers a starting point for novel therapeutic strategies against certain bacterial toxins.
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89
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Suhonen PM, Linna RP. Chaperone-assisted translocation of flexible polymers in three dimensions. Phys Rev E 2016; 93:012406. [PMID: 26871100 DOI: 10.1103/physreve.93.012406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Indexed: 06/05/2023]
Abstract
Polymer translocation through a nanometer-scale pore assisted by chaperones binding to the polymer is a process encountered in vivo for proteins. Studying the relevant models by computer simulations is computationally demanding. Accordingly, previous studies are either for stiff polymers in three dimensions or flexible polymers in two dimensions. Here, we study chaperone-assisted translocation of flexible polymers in three dimensions using Langevin dynamics. We show that differences in binding mechanisms, more specifically, whether a chaperone can bind to a single site or multiple sites on the polymer, lead to substantial differences in translocation dynamics in three dimensions. We show that the single-binding mode leads to dynamics that is very much like that in the constant-force driven translocation and accordingly mainly determined by tension propagation on the cis side. We obtain β≈1.26 for the exponent for the scaling of the translocation time with polymer length. This fairly low value can be explained by the additional friction due to binding particles. The multiple-site binding leads to translocation the dynamics of which is mainly determined by the trans side. For this process we obtain β≈1.36. This value can be explained by our derivation of β=4/3 for constant-bias translocation, where translocated polymer segments form a globule on the trans side. Our results pave the way for understanding and utilizing chaperone-assisted translocation where variations in microscopic details lead to rich variations in the emerging dynamics.
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Affiliation(s)
- P M Suhonen
- Department of Computer Science, Aalto University, Post Office Box 15400, FI-00076 Aalto, Finland
| | - R P Linna
- Department of Computer Science, Aalto University, Post Office Box 15400, FI-00076 Aalto, Finland
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90
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Banerjee R, Gladkova C, Mapa K, Witte G, Mokranjac D. Protein translocation channel of mitochondrial inner membrane and matrix-exposed import motor communicate via two-domain coupling protein. eLife 2015; 4:e11897. [PMID: 26714107 PMCID: PMC4749553 DOI: 10.7554/elife.11897] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 12/28/2015] [Indexed: 12/18/2022] Open
Abstract
The majority of mitochondrial proteins are targeted to mitochondria by N-terminal presequences and use the TIM23 complex for their translocation across the mitochondrial inner membrane. During import, translocation through the channel in the inner membrane is coupled to the ATP-dependent action of an Hsp70-based import motor at the matrix face. How these two processes are coordinated remained unclear. We show here that the two domain structure of Tim44 plays a central role in this process. The N-terminal domain of Tim44 interacts with the components of the import motor, whereas its C-terminal domain interacts with the translocation channel and is in contact with translocating proteins. Our data suggest that the translocation channel and the import motor of the TIM23 complex communicate through rearrangements of the two domains of Tim44 that are stimulated by translocating proteins.
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Affiliation(s)
- Rupa Banerjee
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Christina Gladkova
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Koyeli Mapa
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Gregor Witte
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Dejana Mokranjac
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität, Munich, Germany
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91
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Nillegoda NB, Bukau B. Metazoan Hsp70-based protein disaggregases: emergence and mechanisms. Front Mol Biosci 2015; 2:57. [PMID: 26501065 PMCID: PMC4598581 DOI: 10.3389/fmolb.2015.00057] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/22/2015] [Indexed: 11/13/2022] Open
Abstract
Proteotoxic stresses and aging cause breakdown of cellular protein homeostasis, allowing misfolded proteins to form aggregates, which dedicated molecular machines have evolved to solubilize. In bacteria, fungi, protozoa and plants protein disaggregation involves an Hsp70•J-protein chaperone system, which loads and activates a powerful AAA+ ATPase (Hsp100) disaggregase onto protein aggregate substrates. Metazoans lack cytosolic and nuclear Hsp100 disaggregases but still eliminate protein aggregates. This longstanding puzzle of protein quality control is now resolved. Robust protein disaggregation activity recently shown for the metazoan Hsp70-based disaggregases relies instead on a crucial cooperation between two J-protein classes and interaction with the Hsp110 co-chaperone. An expanding multiplicity of Hsp70 and J-protein family members in metazoan cells facilitates different configurations of this Hsp70-based disaggregase allowing unprecedented versatility and specificity in protein disaggregation. Here we review the architecture, operation, and adaptability of the emerging metazoan disaggregation system and discuss how this evolved.
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Affiliation(s)
- Nadinath B Nillegoda
- Center for Molecular Biology (ZMBH) of the University of Heidelberg and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology (ZMBH) of the University of Heidelberg and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance Heidelberg, Germany
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92
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Nillegoda NB, Bukau B. Metazoan Hsp70-based protein disaggregases: emergence and mechanisms. Front Mol Biosci 2015; 2:57. [PMID: 26501065 DOI: 10.3389/fmolb.2015.00057/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/22/2015] [Indexed: 05/25/2023] Open
Abstract
Proteotoxic stresses and aging cause breakdown of cellular protein homeostasis, allowing misfolded proteins to form aggregates, which dedicated molecular machines have evolved to solubilize. In bacteria, fungi, protozoa and plants protein disaggregation involves an Hsp70•J-protein chaperone system, which loads and activates a powerful AAA+ ATPase (Hsp100) disaggregase onto protein aggregate substrates. Metazoans lack cytosolic and nuclear Hsp100 disaggregases but still eliminate protein aggregates. This longstanding puzzle of protein quality control is now resolved. Robust protein disaggregation activity recently shown for the metazoan Hsp70-based disaggregases relies instead on a crucial cooperation between two J-protein classes and interaction with the Hsp110 co-chaperone. An expanding multiplicity of Hsp70 and J-protein family members in metazoan cells facilitates different configurations of this Hsp70-based disaggregase allowing unprecedented versatility and specificity in protein disaggregation. Here we review the architecture, operation, and adaptability of the emerging metazoan disaggregation system and discuss how this evolved.
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Affiliation(s)
- Nadinath B Nillegoda
- Center for Molecular Biology (ZMBH) of the University of Heidelberg and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology (ZMBH) of the University of Heidelberg and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance Heidelberg, Germany
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93
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Cressiot B, Braselmann E, Oukhaled A, Elcock AH, Pelta J, Clark PL. Dynamics and Energy Contributions for Transport of Unfolded Pertactin through a Protein Nanopore. ACS NANO 2015; 9:9050-61. [PMID: 26302243 PMCID: PMC4835817 DOI: 10.1021/acsnano.5b03053] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To evaluate the physical parameters governing translocation of an unfolded protein across a lipid bilayer, we studied protein transport through aerolysin, a passive protein channel, at the single-molecule level. The protein model used was the passenger domain of pertactin, an autotransporter virulence protein. Transport of pertactin through the aerolysin nanopore was detected as transient partial current blockades as the unfolded protein partially occluded the aerolysin channel. We compared the dynamics of entry and transport for unfolded pertactin and a covalent end-to-end dimer of the same protein. For both the monomer and the dimer, the event frequency of current blockades increased exponentially with the applied voltage, while the duration of each event decreased exponentially as a function of the electrical potential. The blockade time was twice as long for the dimer as for the monomer. The calculated activation free energy includes a main enthalpic component that we attribute to electrostatic interactions between pertactin and the aerolysin nanopore (despite the low Debye length), plus an entropic component due to confinement of the unfolded chain within the narrow pore. Comparing our experimental results to previous studies and theory suggests that unfolded proteins cross the membrane by passing through the nanopore in a somewhat compact conformation according to the "blob" model of Daoud and de Gennes.
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Affiliation(s)
- Benjamin Cressiot
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Esther Braselmann
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | | | - Adrian H. Elcock
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
| | - Juan Pelta
- LAMBE UMR 8587 CNRS, University of Évry-Val-d'Essonne, Évry, France
| | - Patricia L. Clark
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
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94
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Nillegoda NB, Kirstein J, Szlachcic A, Berynskyy M, Stank A, Stengel F, Arnsburg K, Gao X, Scior A, Aebersold R, Guilbride DL, Wade RC, Morimoto RI, Mayer MP, Bukau B. Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation. Nature 2015; 524:247-51. [PMID: 26245380 PMCID: PMC4830470 DOI: 10.1038/nature14884] [Citation(s) in RCA: 258] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 07/08/2015] [Indexed: 01/24/2023]
Abstract
Protein aggregates are the hallmark of stressed and ageing cells, and characterize several pathophysiological states. Healthy metazoan cells effectively eliminate intracellular protein aggregates, indicating that efficient disaggregation and/or degradation mechanisms exist. However, metazoans lack the key heat-shock protein disaggregase HSP100 of non-metazoan HSP70-dependent protein disaggregation systems, and the human HSP70 system alone, even with the crucial HSP110 nucleotide exchange factor, has poor disaggregation activity in vitro. This unresolved conundrum is central to protein quality control biology. Here we show that synergic cooperation between complexed J-protein co-chaperones of classes A and B unleashes highly efficient protein disaggregation activity in human and nematode HSP70 systems. Metazoan mixed-class J-protein complexes are transient, involve complementary charged regions conserved in the J-domains and carboxy-terminal domains of each J-protein class, and are flexible with respect to subunit composition. Complex formation allows J-proteins to initiate transient higher order chaperone structures involving HSP70 and interacting nucleotide exchange factors. A network of cooperative class A and B J-protein interactions therefore provides the metazoan HSP70 machinery with powerful, flexible, and finely regulatable disaggregase activity and a further level of regulation crucial for cellular protein quality control.
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Affiliation(s)
- Nadinath B Nillegoda
- Center for Molecular Biology of the University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Janine Kirstein
- Leibniz-Institute for Molecular Pharmacology (FMP), 13125 Berlin, Germany
| | - Anna Szlachcic
- Center for Molecular Biology of the University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Mykhaylo Berynskyy
- Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany
| | - Antonia Stank
- 1] Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany [2] Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Florian Stengel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Kristin Arnsburg
- Leibniz-Institute for Molecular Pharmacology (FMP), 13125 Berlin, Germany
| | - Xuechao Gao
- Center for Molecular Biology of the University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Annika Scior
- Leibniz-Institute for Molecular Pharmacology (FMP), 13125 Berlin, Germany
| | - Ruedi Aebersold
- 1] Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland [2] Faculty of Science, University of Zurich, 8057 Zurich, Switzerland
| | - D Lys Guilbride
- Center for Molecular Biology of the University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Rebecca C Wade
- 1] Center for Molecular Biology of the University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany [2] Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany [3] Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany
| | - Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Matthias P Mayer
- Center for Molecular Biology of the University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
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95
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Reidy M, Masison DC. Yeast prions help identify and define chaperone interaction networks. Curr Pharm Biotechnol 2015; 15:1008-18. [PMID: 25373385 DOI: 10.2174/1389201015666141103021035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 07/22/2014] [Accepted: 10/05/2014] [Indexed: 11/22/2022]
Abstract
Proteins in the cell experience various stressful conditions that can affect their ability to attain and maintain the structural conformations they need to perform effectively. Protein chaperones are an important part of a cellular protein quality control system that protects the integrity of the proteome in the face of such challenges. Chaperones from different conserved families have multiple members that cooperate to regulate each other's activity and produce machines that perform a variety of tasks. The large numbers of related chaperones with both functionally overlapping and distinct activities allows fine-tuning of the machinery for specific tasks, but presents a daunting degree of complexity. Yeast prions are misfolded forms of cellular proteins whose propagation depends on the action of protein chaperones. Studying how propagation of yeast prions is affected by alterations in functions of various chaperones provides an approach to understanding this complexity.
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Affiliation(s)
| | - Daniel C Masison
- Building 8, Room 225, 8 Center Drive, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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96
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Finka A, Sood V, Quadroni M, Rios PDL, Goloubinoff P. Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs. Cell Stress Chaperones 2015; 20:605-20. [PMID: 25847399 PMCID: PMC4463922 DOI: 10.1007/s12192-015-0583-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 03/08/2015] [Accepted: 03/10/2015] [Indexed: 11/18/2022] Open
Abstract
Classic semiquantitative proteomic methods have shown that all organisms respond to a mild heat shock by an apparent massive accumulation of a small set of proteins, named heat-shock proteins (HSPs) and a concomitant slowing down in the synthesis of the other proteins. Yet unexplained, the increased levels of HSP messenger RNAs (mRNAs) may exceed 100 times the ensuing relative levels of HSP proteins. We used here high-throughput quantitative proteomics and targeted mRNA quantification to estimate in human cell cultures the mass and copy numbers of the most abundant proteins that become significantly accumulated, depleted, or unchanged during and following 4 h at 41 °C, which we define as mild heat shock. This treatment caused a minor across-the-board mass loss in many housekeeping proteins, which was matched by a mass gain in a few HSPs, predominantly cytosolic HSPCs (HSP90s) and HSPA8 (HSC70). As the mRNAs of the heat-depleted proteins were not significantly degraded and less ribosomes were recruited by excess new HSP mRNAs, the mild depletion of the many housekeeping proteins during heat shock was attributed to their slower replenishment. This differential protein expression pattern was reproduced by isothermal treatments with Hsp90 inhibitors. Unexpectedly, heat-treated cells accumulated 55 times more new molecules of HSPA8 (HSC70) than of the acknowledged heat-inducible isoform HSPA1A (HSP70), implying that when expressed as net copy number differences, rather than as mere "fold change" ratios, new biologically relevant information can be extracted from quantitative proteomic data. Raw data are available via ProteomeXchange with identifier PXD001666.
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Affiliation(s)
- Andrija Finka
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
- Laboratoire de Biophysique Statistique, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Vishal Sood
- Laboratoire de Biophysique Statistique, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Manfredo Quadroni
- Department of Biochemistry, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Paolo De Los Rios
- Laboratoire de Biophysique Statistique, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
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97
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Finka A, Sharma SK, Goloubinoff P. Multi-layered molecular mechanisms of polypeptide holding, unfolding and disaggregation by HSP70/HSP110 chaperones. Front Mol Biosci 2015; 2:29. [PMID: 26097841 PMCID: PMC4456865 DOI: 10.3389/fmolb.2015.00029] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/19/2015] [Indexed: 11/24/2022] Open
Abstract
Members of the HSP70/HSP110 family (HSP70s) form a central hub of the chaperone network controlling all aspects of proteostasis in bacteria and the ATP-containing compartments of eukaryotic cells. The heat-inducible form HSP70 (HSPA1A) and its major cognates, cytosolic HSC70 (HSPA8), endoplasmic reticulum BIP (HSPA5), mitochondrial mHSP70 (HSPA9) and related HSP110s (HSPHs), contribute about 3% of the total protein mass of human cells. The HSP70s carry out a plethora of housekeeping cellular functions, such as assisting proper de novo folding, assembly and disassembly of protein complexes, pulling polypeptides out of the ribosome and across membrane pores, activating and inactivating signaling proteins and controlling their degradation. The HSP70s can induce structural changes in alternatively folded protein conformers, such as clathrin cages, hormone receptors and transcription factors, thereby regulating vesicular trafficking, hormone signaling and cell differentiation in development and cancer. To carry so diverse cellular housekeeping and stress-related functions, the HSP70s act as ATP-fuelled unfolding nanomachines capable of switching polypeptides between different folded states. During stress, the HSP70s can bind (hold) and prevent the aggregation of misfolding proteins and thereafter act alone or in collaboration with other unfolding chaperones to solubilize protein aggregates. Here, we discuss the common ATP-dependent mechanisms of holding, unfolding-by-clamping and unfolding-by-entropic pulling, by which the HSP70s can apparently convert various alternatively folded and misfolded polypeptides into differently active conformers. Understanding how HSP70s can prevent the formation of cytotoxic protein aggregates, pull, unfold, and solubilize them into harmless species is central to the design of therapies against protein conformational diseases.
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Affiliation(s)
- Andrija Finka
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne Lausanne, Switzerland ; Laboratoire de Biophysique Statistique, School of Basic Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne Lausanne, Switzerland
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98
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Alzahrani H, Winter J, Boocock D, De Girolamo L, Forsythe SJ. Characterization of outer membrane vesicles from a neonatal meningitic strain of Cronobacter sakazakii. FEMS Microbiol Lett 2015; 362:fnv085. [PMID: 26023200 DOI: 10.1093/femsle/fnv085] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2015] [Indexed: 01/05/2023] Open
Abstract
Cronobacter sakazakii is associated with severe and often fatal cases of infant meningitis and necrotizing enterocolitis. The form of meningitis differs from that due to Neisseria meningitidis and Streptococcus spp., in that it is highly invasive and destructive towards human brain cells. However, there is relatively little understanding of the cytopathogenic interaction of C. sakazakii with host cells which results in stimulation of an inflammatory immune response. The production of Cronobacter outer membrane vesicles (OMV) and their potential pathogenic functions have not yet been elucidated. This study is the first to show that C. sakazakii produce OMV, which may play a role in the activation of cytopathogenic and host cell responses on human intestinal epithelial cells. Cronobacter sakazakii strain 767 was used which had been isolated from a fatal outbreak of neonatal meningitis and necrotizing enterocolitis. Cronobacter sakazakii OMV were internalized by Caco-2 cells, increased cell proliferation and stimulated the host's innate proinflammatory response without inducing overt toxicity. A total of 18 OMV-associated proteins were identified by mass spectrometry and their potential pathogenicity roles were evaluated. Collectively, these data indicate that C. sakazakii OMV could play a role in pathogenesis by delivering bacterial toxins into host epithelial cells, driving proliferative and proinflammatory responses.
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Affiliation(s)
- Hayat Alzahrani
- Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Jody Winter
- Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - David Boocock
- John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Luigi De Girolamo
- Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Stephen J Forsythe
- Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
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99
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Sousa R, Lafer EM. The role of molecular chaperones in clathrin mediated vesicular trafficking. Front Mol Biosci 2015; 2:26. [PMID: 26042225 PMCID: PMC4436892 DOI: 10.3389/fmolb.2015.00026] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/05/2015] [Indexed: 12/04/2022] Open
Abstract
The discovery that the 70 kD “uncoating ATPase,” which removes clathrin coats from vesicles after endocytosis, is the constitutively expressed Hsc70 chaperone was a surprise. Subsequent work, however, revealed that uncoating is an archetypal Hsp70 reaction: the cochaperone auxilin, which contains a clathrin binding domain and an Hsc70 binding J domain, recruits Hsc70*ATP to the coat and, concomitant with ATP hydrolysis, transfers it to a hydrophobic Hsc70-binding element found on a flexible tail at the C-terminus of the clathrin heavy chain. Release of clathrin in association with Hsc70*ADP follows, and the subsequent, persistent association of clathrin with Hsc70 is important to prevent aberrant clathrin polymerization. Thus, the two canonical functions of Hsp70—dissociation of existing protein complexes or aggregates, and binding to a protein to inhibit its inappropriate aggregation—are recapitulated in uncoating. Association of clathrin with Hsc70 in vivo is regulated by Hsp110, an Hsp70 NEF that is itself a member of the Hsp70 family. How Hsp110 activity is itself regulated to make Hsc70-free clathrin available for endocytosis is unclear, though at synapses it's possible that the influx of calcium that accompanies depolarization activates the Ca++/calmodulin dependent calcineurin phosphatase which then dephosphorylates and activates Hsp110 to stimulate ADP/ATP exchange and release clathrin from Hsc70*ADP:clathrin complexes.
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Affiliation(s)
- Rui Sousa
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio San Antonio, TX, USA
| | - Eileen M Lafer
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio San Antonio, TX, USA
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Schulz C, Schendzielorz A, Rehling P. Unlocking the presequence import pathway. Trends Cell Biol 2015; 25:265-75. [DOI: 10.1016/j.tcb.2014.12.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 10/24/2022]
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