1
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Montoya MR, Quanrud GM, Mei L, Moñtano JL, Hong C, Genereux JC. Factors affecting protein recovery during Hsp40 affinity profiling. Anal Bioanal Chem 2024:10.1007/s00216-024-05362-1. [PMID: 38850318 DOI: 10.1007/s00216-024-05362-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 04/30/2024] [Accepted: 05/22/2024] [Indexed: 06/10/2024]
Abstract
The identification and quantification of misfolded proteins from complex mixtures is important for biological characterization and disease diagnosis, but remains a major bioanalytical challenge. We have developed Hsp40 Affinity Profiling as a bioanalytical approach to profile protein stability in response to cellular stress. In this assay, we ectopically introduce the Hsp40 FlagDNAJB8H31Q into cells and use quantitative proteomics to determine how protein affinity for DNAJB8 changes in the presence of cellular stress, without regard for native clients. Herein, we evaluate potential approaches to improve the performance of this bioanalytical assay. We find that although intracellular crosslinking increases recovery of protein interactors, this is not enough to overcome the relative drop in DNAJB8 recovery. While the J-domain promotes Hsp70 association, it does not affect the yield of protein association with DNAJB8 under basal conditions. By contrast, crosslinking and J-domain ablation both substantially increase relative protein interactor recovery with the structurally distinct Class B Hsp40 DNAJB1 but are completely compensated by poorer yield of DNAJB1 itself. Cellular thermal stress promotes increased affinity between DNAJB8H31Q and interacting proteins, as expected for interactions driven by recognition of misfolded proteins. DNAJB8WT does not demonstrate such a property, suggesting that under stress misfolded proteins are handed off to Hsp70. Hence, we find that DNAJB8H31Q is still our most effective recognition element for the recovery of destabilized client proteins following cellular stress.
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Affiliation(s)
- Maureen R Montoya
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA
| | - Guy M Quanrud
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA
| | - Liangyong Mei
- Department of Chemistry, University of North Florida, Jacksonville, FL, USA
| | - José L Moñtano
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA
| | - Caleb Hong
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA
| | - Joseph C Genereux
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA.
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2
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Ryder BD, Ustyantseva E, Boyer DR, Mendoza-Oliva A, Kuska MI, Wydorski PM, Macierzyńska P, Morgan N, Sawaya MR, Diamond MI, Kampinga HH, Joachimiak LA. DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity. Structure 2024; 32:662-678.e8. [PMID: 38508190 PMCID: PMC11162344 DOI: 10.1016/j.str.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 01/17/2024] [Accepted: 02/22/2024] [Indexed: 03/22/2024]
Abstract
J-domain protein (JDP) molecular chaperones have emerged as central players that maintain a healthy proteome. The diverse members of the JDP family function as monomers/dimers and a small subset assemble into micron-sized oligomers. The oligomeric JDP members have eluded structural characterization due to their low-complexity, intrinsically disordered middle domains. This in turn, obscures the biological significance of these larger oligomers in protein folding processes. Here, we identified a short, aromatic motif within DNAJB8 that drives self-assembly through π-π stacking and determined its X-ray structure. We show that mutations in the motif disrupt DNAJB8 oligomerization in vitro and in cells. DNAJB8 variants that are unable to assemble bind to misfolded tau seeds more specifically and retain capacity to reduce protein aggregation in vitro and in cells. We propose a new model for DNAJB8 function in which the sequences in the low-complexity domains play distinct roles in assembly and substrate activity.
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Affiliation(s)
- Bryan D Ryder
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizaveta Ustyantseva
- Department of Biomedical Sciences of Cells & Systems, University Medical Center Groningen, University of Groningen, Groningen 9713 AV, The Netherlands
| | - David R Boyer
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ayde Mendoza-Oliva
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mikołaj I Kuska
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Paweł M Wydorski
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Paulina Macierzyńska
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nabil Morgan
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael R Sawaya
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Harm H Kampinga
- Department of Biomedical Sciences of Cells & Systems, University Medical Center Groningen, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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3
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Desai M, Hemant, Deo A, Naik J, Dhamale P, Kshirsagar A, Bose T, Majumdar A. Mrj is a chaperone of the Hsp40 family that regulates Orb2 oligomerization and long-term memory in Drosophila. PLoS Biol 2024; 22:e3002585. [PMID: 38648719 PMCID: PMC11034981 DOI: 10.1371/journal.pbio.3002585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 03/12/2024] [Indexed: 04/25/2024] Open
Abstract
Orb2 the Drosophila homolog of cytoplasmic polyadenylation element binding (CPEB) protein forms prion-like oligomers. These oligomers consist of Orb2A and Orb2B isoforms and their formation is dependent on the oligomerization of the Orb2A isoform. Drosophila with a mutation diminishing Orb2A's prion-like oligomerization forms long-term memory but fails to maintain it over time. Since this prion-like oligomerization of Orb2A plays a crucial role in the maintenance of memory, here, we aim to find what regulates this oligomerization. In an immunoprecipitation-based screen, we identify interactors of Orb2A in the Hsp40 and Hsp70 families of proteins. Among these, we find an Hsp40 family protein Mrj as a regulator of the conversion of Orb2A to its prion-like form. Mrj interacts with Hsp70 proteins and acts as a chaperone by interfering with the aggregation of pathogenic Huntingtin. Unlike its mammalian homolog, we find Drosophila Mrj is neither an essential gene nor causes any gross neurodevelopmental defect. We observe a loss of Mrj results in a reduction in Orb2 oligomers. Further, Mrj knockout exhibits a deficit in long-term memory and our observations suggest Mrj is needed in mushroom body neurons for the regulation of long-term memory. Our work implicates a chaperone Mrj in mechanisms of memory regulation through controlling the oligomerization of Orb2A and its association with the translating ribosomes.
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Affiliation(s)
- Meghal Desai
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, India
| | - Hemant
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, India
| | - Ankita Deo
- Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Pune, India
| | - Jagyanseni Naik
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, India
| | - Prathamesh Dhamale
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, India
| | - Avinash Kshirsagar
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, India
| | - Tania Bose
- Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Pune, India
| | - Amitabha Majumdar
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, India
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4
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Ryder BD, Ustyantseva E, Boyer DR, Mendoza-Oliva A, Kuska M, Wydorski PM, Macierzynska P, Morgan N, Sawaya MR, Diamond MI, Kampinga HH, Joachimiak L. DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.06.531355. [PMID: 36945632 PMCID: PMC10028812 DOI: 10.1101/2023.03.06.531355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
J-domain protein (JDP) molecular chaperones have emerged as central players that maintain a healthy proteome. The diverse members of the JDP family function as monomers/dimers and a small subset assemble into micron-sized oligomers. The oligomeric JDP members have eluded structural characterization due to their low-complexity, intrinsically disordered middle domains. This in turn, obscures the biological significance of these larger oligomers in protein folding processes. Here, we identified a short, aromatic motif within DNAJB8, that drives self-assembly through pi-pi stacking and determined its X-ray structure. We show that mutations in the motif disrupt DNAJB8 oligomerization in vitro and in cells. DNAJB8 variants that are unable to assemble bind to misfolded tau seeds more specifically and retain capacity to reduce protein aggregation in vitro and in cells. We propose a new model for DNAJB8 function in which the sequences in the low-complexity domains play distinct roles in assembly and substrate activity.
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5
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Chang YL, Yang CC, Huang YY, Chen YA, Yang CW, Liao CY, Li H, Wu CS, Lin CH, Teng SC. The HSP40 family chaperone isoform DNAJB6b prevents neuronal cells from tau aggregation. BMC Biol 2023; 21:293. [PMID: 38110916 PMCID: PMC10729500 DOI: 10.1186/s12915-023-01798-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common neurodegenerative disorder with clinical presentations of progressive cognitive and memory deterioration. The pathologic hallmarks of AD include tau neurofibrillary tangles and amyloid plaque depositions in the hippocampus and associated neocortex. The neuronal aggregated tau observed in AD cells suggests that the protein folding problem is a major cause of AD. J-domain-containing proteins (JDPs) are the largest family of cochaperones, which play a vital role in specifying and directing HSP70 chaperone functions. JDPs bind substrates and deliver them to HSP70. The association of JDP and HSP70 opens the substrate-binding domain of HSP70 to help the loading of the clients. However, in the initial HSP70 cycle, which JDP delivers tau to the HSP70 system in neuronal cells remains unclear. RESULTS We screened the requirement of a diverse panel of JDPs for preventing tau aggregation in the human neuroblastoma cell line SH-SY5Y by a filter retardation method. Interestingly, knockdown of DNAJB6, one of the JDPs, displayed tau aggregation and overexpression of DNAJB6b, one of the isoforms generated from the DNAJB6 gene by alternative splicing, reduced tau aggregation. Further, the tau bimolecular fluorescence complementation assay confirmed the DNAJB6b-dependent tau clearance. The co-immunoprecipitation and the proximity ligation assay demonstrated the protein-protein interaction between tau and the chaperone-cochaperone complex. The J-domain of DNAJB6b was critical for preventing tau aggregation. Moreover, reduced DNAJB6 expression and increased tau aggregation were detected in an age-dependent manner in immunohistochemical analysis of the hippocampus tissues of a mouse model of tau pathology. CONCLUSIONS In summary, downregulation of DNAJB6b increases the insoluble form of tau, while overexpression of DNAJB6b reduces tau aggregation. Moreover, DNAJB6b associates with tau. Therefore, this study reveals that DNAJB6b is a direct sensor for its client tau in the HSP70 folding system in neuronal cells, thus helping to prevent AD.
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Affiliation(s)
- Ya-Lan Chang
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Chan-Chih Yang
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Yun-Yu Huang
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Yi-An Chen
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Chia-Wei Yang
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Chia-Yu Liao
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Hsun Li
- Department of Neurology, National Taiwan University Hospital, No. 7, Chung-Shan South Road, Taipei, 10051, Taiwan
| | - Ching-Shyi Wu
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Chin-Hsien Lin
- Department of Neurology, National Taiwan University Hospital, No. 7, Chung-Shan South Road, Taipei, 10051, Taiwan.
| | - Shu-Chun Teng
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan.
- Center of Precision Medicine, National Taiwan University, Taipei, 10051, Taiwan.
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Abayev-Avraham M, Salzberg Y, Gliksberg D, Oren-Suissa M, Rosenzweig R. DNAJB6 mutants display toxic gain of function through unregulated interaction with Hsp70 chaperones. Nat Commun 2023; 14:7066. [PMID: 37923706 PMCID: PMC10624832 DOI: 10.1038/s41467-023-42735-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Molecular chaperones are essential cellular components that aid in protein folding and preventing the abnormal aggregation of disease-associated proteins. Mutations in one such chaperone, DNAJB6, were identified in patients with LGMDD1, a dominant autosomal disorder characterized by myofibrillar degeneration and accumulations of aggregated protein within myocytes. The molecular mechanisms through which such mutations cause this dysfunction, however, are not well understood. Here we employ a combination of solution NMR and biochemical assays to investigate the structural and functional changes in LGMDD1 mutants of DNAJB6. Surprisingly, we find that DNAJB6 disease mutants show no reduction in their aggregation-prevention activity in vitro, and instead differ structurally from the WT protein, affecting their interaction with Hsp70 chaperones. While WT DNAJB6 contains a helical element regulating its ability to bind and activate Hsp70, in LGMDD1 disease mutants this regulation is disrupted. These variants can thus recruit and hyperactivate Hsp70 chaperones in an unregulated manner, depleting Hsp70 levels in myocytes, and resulting in the disruption of proteostasis. Interfering with DNAJB6-Hsp70 binding, however, reverses the disease phenotype, suggesting future therapeutic avenues for LGMDD1.
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Affiliation(s)
- Meital Abayev-Avraham
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 761000, Israel
| | - Yehuda Salzberg
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 761000, Israel
| | - Dar Gliksberg
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 761000, Israel
| | - Meital Oren-Suissa
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 761000, Israel
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 761000, Israel.
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7
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Österlund N, Frankel R, Carlsson A, Thacker D, Karlsson M, Matus V, Gräslund A, Emanuelsson C, Linse S. The C-terminal domain of the antiamyloid chaperone DNAJB6 binds to amyloid-β peptide fibrils and inhibits secondary nucleation. J Biol Chem 2023; 299:105317. [PMID: 37797698 PMCID: PMC10641233 DOI: 10.1016/j.jbc.2023.105317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
The DNAJB6 chaperone inhibits fibril formation of aggregation-prone client peptides through interaction with aggregated and oligomeric forms of the amyloid peptides. Here, we studied the role of its C-terminal domain (CTD) using constructs comprising either the entire CTD or the first two or all four of the CTD β-strands grafted onto a scaffold protein. Each construct was expressed as WT and as a variant with alanines replacing five highly conserved and functionally important serine and threonine residues in the first β-strand. We investigated the stability, oligomerization, antiamyloid activity, and affinity for amyloid-β (Aβ42) species using optical spectroscopy, native mass spectrometry, chemical crosslinking, and surface plasmon resonance technology. While DNAJB6 forms large and polydisperse oligomers, CTD was found to form only monomers, dimers, and tetramers of low affinity. Kinetic analyses showed a shift in inhibition mechanism. Whereas full-length DNAJB6 activity is dependent on the serine and threonine residues and efficiently inhibits primary and secondary nucleation, all CTD constructs inhibit secondary nucleation only, independently of the serine and threonine residues, although their dimerization and thermal stabilities are reduced by alanine substitution. While the full-length DNAJB6 inhibition of primary nucleation is related to its propensity to form coaggregates with Aβ, the CTD constructs instead bind to Aβ42 fibrils, which affects the nucleation events at the fibril surface. The retardation of secondary nucleation by DNAJB6 can thus be ascribed to the first two β-strands of its CTD, whereas the inhibition of primary nucleation is dependent on the entire protein or regions outside the CTD.
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Affiliation(s)
- Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Rebecca Frankel
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden
| | - Andreas Carlsson
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden
| | - Dev Thacker
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden
| | - Maja Karlsson
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden
| | - Vanessa Matus
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Cecilia Emanuelsson
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden
| | - Sara Linse
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden.
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8
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Shukla VK, Siemons L, Hansen DF. Intrinsic structural dynamics dictate enzymatic activity and inhibition. Proc Natl Acad Sci U S A 2023; 120:e2310910120. [PMID: 37782780 PMCID: PMC10576142 DOI: 10.1073/pnas.2310910120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/14/2023] [Indexed: 10/04/2023] Open
Abstract
Enzymes are known to sample various conformations, many of which are critical for their biological function. However, structural characterizations of enzymes predominantly focus on the most populated conformation. As a result, single-point mutations often produce structures that are similar or essentially identical to those of the wild-type enzyme despite large changes in enzymatic activity. Here, we show for mutants of a histone deacetylase enzyme (HDAC8) that reduced enzymatic activities, reduced inhibitor affinities, and reduced residence times are all captured by the rate constants between intrinsically sampled conformations that, in turn, can be obtained independently by solution NMR spectroscopy. Thus, for the HDAC8 enzyme, the dynamic sampling of conformations dictates both enzymatic activity and inhibitor potency. Our analysis also dissects the functional role of the conformations sampled, where specific conformations distinct from those in available structures are responsible for substrate and inhibitor binding, catalysis, and product dissociation. Precise structures alone often do not adequately explain the effect of missense mutations on enzymatic activity and drug potency. Our findings not only assign functional roles to several conformational states of HDAC8 but they also underscore the paramount role of dynamics, which will have general implications for characterizing missense mutations and designing inhibitors.
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Affiliation(s)
- Vaibhav Kumar Shukla
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Lucas Siemons
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - D. Flemming Hansen
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, LondonWC1E 6BT, United Kingdom
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9
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Carlsson A, Olsson U, Linse S. On the micelle formation of DNAJB6b. QRB DISCOVERY 2023; 4:e6. [PMID: 37593255 PMCID: PMC10427797 DOI: 10.1017/qrd.2023.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/22/2023] [Accepted: 07/11/2023] [Indexed: 08/19/2023] Open
Abstract
The human chaperone DNAJB6b increases the solubility of proteins involved in protein aggregation diseases and suppresses the nucleation of amyloid structures. Due to such favourable properties, DNAJB6b has gained increasing attention over the past decade. The understanding of how DNAJB6b operates on a molecular level may aid the design of inhibitors against amyloid formation. In this work, fundamental aspects of DNAJB6b self-assembly have been examined, providing a basis for future experimental designs and conclusions. The results imply the formation of large chaperone clusters in a concentration-dependent manner. Microfluidic diffusional sizing (MDS) was used to evaluate how DNAJB6b average hydrodynamic radius varies with concentration. We found that, in 20 mM sodium phosphate buffer, 0.2 mM EDTA, at pH 8.0 and room temperature, DNAJB6b displays a micellar behaviour, with a critical micelle concentration (CMC) of around 120 nM. The average hydrodynamic radius appears to be concentration independent between ∼10 μM and 100 μM, with a mean radius of about 12 nm. The CMC found by MDS is supported by native agarose gel electrophoresis and the size distribution appears bimodal in the DNAJB6b concentration range ∼100 nM to 4 μM.
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Affiliation(s)
- Andreas Carlsson
- Biochemistry and Structural Biology, Chemical Centre, Lund University, Lund, Sweden
| | - Ulf Olsson
- Physical Chemistry, Chemical Centre, Lund University, Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Chemical Centre, Lund University, Lund, Sweden
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10
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Chakravarty D, Schafer JW, Porter LL. Distinguishing features of fold-switching proteins. Protein Sci 2023; 32:e4596. [PMID: 36782353 PMCID: PMC9951197 DOI: 10.1002/pro.4596] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Though many folded proteins assume one stable structure that performs one function, a small-but-increasing number remodel their secondary and tertiary structures and change their functions in response to cellular stimuli. These fold-switching proteins regulate biological processes and are associated with autoimmune dysfunction, severe acute respiratory syndrome coronavirus-2 infection, and more. Despite their biological importance, it is difficult to computationally predict fold switching. With the aim of advancing computational prediction and experimental characterization of fold switchers, this review discusses several features that distinguish fold-switching proteins from their single-fold and intrinsically disordered counterparts. First, the isolated structures of fold switchers are less stable and more heterogeneous than single folders but more stable and less heterogeneous than intrinsically disordered proteins (IDPs). Second, the sequences of single fold, fold switching, and intrinsically disordered proteins can evolve at distinct rates. Third, proteins from these three classes are best predicted using different computational techniques. Finally, late-breaking results suggest that single folders, fold switchers, and IDPs have distinct patterns of residue-residue coevolution. The review closes by discussing high-throughput and medium-throughput experimental approaches that might be used to identify new fold-switching proteins.
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Affiliation(s)
- Devlina Chakravarty
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaMarylandUSA
| | - Joseph W. Schafer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaMarylandUSA
| | - Lauren L. Porter
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaMarylandUSA
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaMarylandUSA
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11
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Karamanos TK. Chasing long-range evolutionary couplings in the AlphaFold era. Biopolymers 2023; 114:e23530. [PMID: 36752285 PMCID: PMC10909459 DOI: 10.1002/bip.23530] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/09/2023]
Abstract
Coevolution between protein residues is normally interpreted as direct contact. However, the evolutionary record of a protein sequence contains rich information that may include long-range functional couplings, couplings that report on homo-oligomeric states or even conformational changes. Due to the complexity of the sequence space and the lack of structural information on various members of a protein family, it has been difficult to effectively mine the additional information encoded in a multiple sequence alignment (MSA). Here, taking advantage of the recent release of the AlphaFold (AF) database we attempt to identify coevolutionary couplings that cannot be explained simply by spatial proximity. We propose a simple computational method that performs direct coupling analysis on a MSA and searches for couplings that are not satisfied in any of the AF models of members of the identified protein family. Application of this method on 2012 protein families suggests that ~12% of the total identified coevolving residue pairs are spatially distant and more likely to be disordered than their contacting counterparts. We expect that this analysis will help improve the quality of coevolutionary distance restraints used for structure determination and will be useful in identifying potentially functional/allosteric cross-talk between distant residues.
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12
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Österlund N, Vosselman T, Leppert A, Gräslund A, Jörnvall H, Ilag LL, Marklund EG, Elofsson A, Johansson J, Sahin C, Landreh M. Mass Spectrometry and Machine Learning Reveal Determinants of Client Recognition by Antiamyloid Chaperones. Mol Cell Proteomics 2022; 21:100413. [PMID: 36115577 PMCID: PMC9563204 DOI: 10.1016/j.mcpro.2022.100413] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 01/18/2023] Open
Abstract
The assembly of proteins and peptides into amyloid fibrils is causally linked to serious disorders such as Alzheimer's disease. Multiple proteins have been shown to prevent amyloid formation in vitro and in vivo, ranging from highly specific chaperone-client pairs to completely nonspecific binding of aggregation-prone peptides. The underlying interactions remain elusive. Here, we turn to the machine learning-based structure prediction algorithm AlphaFold2 to obtain models for the nonspecific interactions of β-lactoglobulin, transthyretin, or thioredoxin 80 with the model amyloid peptide amyloid β and the highly specific complex between the BRICHOS chaperone domain of C-terminal region of lung surfactant protein C and its polyvaline target. Using a combination of native mass spectrometry (MS) and ion mobility MS, we show that nonspecific chaperoning is driven predominantly by hydrophobic interactions of amyloid β with hydrophobic surfaces in β-lactoglobulin, transthyretin, and thioredoxin 80, and in part regulated by oligomer stability. For C-terminal region of lung surfactant protein C, native MS and hydrogen-deuterium exchange MS reveal that a disordered region recognizes the polyvaline target by forming a complementary β-strand. Hence, we show that AlphaFold2 and MS can yield atomistic models of hard-to-capture protein interactions that reveal different chaperoning mechanisms based on separate ligand properties and may provide possible clues for specific therapeutic intervention.
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Affiliation(s)
- Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Thibault Vosselman
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Axel Leppert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hans Jörnvall
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Leopold L. Ilag
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Erik G. Marklund
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Arne Elofsson
- Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Huddinge, Sweden
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden,Department of Biology, University of Copenhagen, Denmark,For correspondence: Michael Landreh; Cagla Sahin
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden,For correspondence: Michael Landreh; Cagla Sahin
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13
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J Proteins Counteract Amyloid Propagation and Toxicity in Yeast. BIOLOGY 2022; 11:biology11091292. [PMID: 36138771 PMCID: PMC9495310 DOI: 10.3390/biology11091292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 12/02/2022]
Abstract
Simple Summary Dozens of diseases are associated with misfolded proteins that accumulate in highly ordered fibrous aggregates called amyloids. Protein quality control (PQC) factors keep cells healthy by helping maintain the integrity of the cell’s proteins and physiological processes. Yeast has been used widely for years to study how amyloids cause toxicity to cells and how PQC factors help protect cells from amyloid toxicity. The so-called J-domain proteins (JDPs) are PQC factors that are particularly effective at providing such protection. We discuss how PQC factors protect animals, human cells, and yeast from amyloid toxicity, focusing on yeast and human JDPs. Abstract The accumulation of misfolded proteins as amyloids is associated with pathology in dozens of debilitating human disorders, including diabetes, Alzheimer’s, Parkinson’s, and Huntington’s diseases. Expressing human amyloid-forming proteins in yeast is toxic, and yeast prions that propagate as infectious amyloid forms of cellular proteins are also harmful. The yeast system, which has been useful for studying amyloids and their toxic effects, has provided much insight into how amyloids affect cells and how cells respond to them. Given that an amyloid is a protein folding problem, it is unsurprising that the factors found to counteract the propagation or toxicity of amyloids in yeast involve protein quality control. Here, we discuss such factors with an emphasis on J-domain proteins (JDPs), which are the most highly abundant and diverse regulators of Hsp70 chaperones. The anti-amyloid effects of JDPs can be direct or require interaction with Hsp70.
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14
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Cawood EE, Clore GM, Karamanos TK. Microsecond Backbone Motions Modulate the Oligomerization of the DNAJB6 Chaperone. Angew Chem Int Ed Engl 2022; 61:e202116403. [PMID: 35247211 PMCID: PMC9314120 DOI: 10.1002/anie.202116403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Indexed: 11/12/2022]
Abstract
DNAJB6 is a prime example of an anti‐aggregation chaperone that functions as an oligomer. DNAJB6 oligomers are dynamic and subunit exchange is critical for inhibiting client protein aggregation. The T193A mutation in the C‐terminal domain (CTD) of DNAJB6 reduces both chaperone self‐oligomerization and anti‐aggregation of client proteins, and has recently been linked to Parkinson's disease. Here, we show by NMR, including relaxation‐based methods, that the T193A mutation has minimal effects on the structure of the β‐stranded CTD but increases the population and rate of formation of a partially folded state. The results can be rationalized in terms of β‐strand peptide plane flips that occur on a timescale of ≈100 μs and lead to global changes in the overall pleat/flatness of the CTD, thereby altering its ability to oligomerize. These findings help forge a link between chaperone dynamics, oligomerization and anti‐aggregation activity which may possibly lead to new therapeutic avenues tuned to target specific substrates.
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Affiliation(s)
- Emma E. Cawood
- Astbury Centre for Structural Molecular Biology School of Molecular and Cellular Biology University of Leeds Mount Preston Street Leeds LS2 9JT UK
| | - G. Marius Clore
- Laboratory of Chemical Physics National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health Bethesda MD 20892-0520 USA
| | - Theodoros K. Karamanos
- Astbury Centre for Structural Molecular Biology School of Molecular and Cellular Biology University of Leeds Mount Preston Street Leeds LS2 9JT UK
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15
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Cawood EE, Clore GM, Karamanos TK. Microsecond Backbone Motions Modulate the Oligomerization of the DNAJB6 Chaperone. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202116403. [PMID: 38505697 PMCID: PMC10947091 DOI: 10.1002/ange.202116403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Indexed: 11/09/2022]
Abstract
DNAJB6 is a prime example of an anti-aggregation chaperone that functions as an oligomer. DNAJB6 oligomers are dynamic and subunit exchange is critical for inhibiting client protein aggregation. The T193A mutation in the C-terminal domain (CTD) of DNAJB6 reduces both chaperone self-oligomerization and anti-aggregation of client proteins, and has recently been linked to Parkinson's disease. Here, we show by NMR, including relaxation-based methods, that the T193A mutation has minimal effects on the structure of the β-stranded CTD but increases the population and rate of formation of a partially folded state. The results can be rationalized in terms of β-strand peptide plane flips that occur on a timescale of ≈100 μs and lead to global changes in the overall pleat/flatness of the CTD, thereby altering its ability to oligomerize. These findings help forge a link between chaperone dynamics, oligomerization and anti-aggregation activity which may possibly lead to new therapeutic avenues tuned to target specific substrates.
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Affiliation(s)
- Emma E. Cawood
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsMount Preston StreetLeedsLS2 9JTUK
| | - G. Marius Clore
- Laboratory of Chemical PhysicsNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMD 20892-0520USA
| | - Theodoros K. Karamanos
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsMount Preston StreetLeedsLS2 9JTUK
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16
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Wan Q, Mouton SN, Veenhoff LM, Boersma AJ. A FRET-based method for monitoring structural transitions in protein self-organization. CELL REPORTS METHODS 2022; 2:100184. [PMID: 35475219 PMCID: PMC8960284 DOI: 10.1016/j.crmeth.2022.100184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/12/2021] [Accepted: 02/24/2022] [Indexed: 11/04/2022]
Abstract
Proteins assemble into a variety of dynamic and functional structures. Their structural transitions are often challenging to distinguish inside cells, particularly with a high spatiotemporal resolution. Here, we present a fluorescence resonance energy transfer (FRET)-based method for continuous and high-throughput monitoring of protein self-assemblies to reveal well-resolved transient intermediate states. Intermolecular FRET with both the donor and acceptor proteins at the same target protein provides high sensitivity while retaining the advantage of straightforward ratiometric imaging. We apply this method to monitor self-assembly of three proteins. We show that the mutant Huntingtin exon1 (mHttex1) first forms less-ordered assemblies, which develop into fibril-like aggregates, and demonstrate that the chaperone protein DNAJB6b increases the critical saturation concentration of mHttex1. We also monitor the structural changes in fused in sarcoma (FUS) condensates. This method adds to the toolbox for protein self-assembly structure and kinetics determination, and implementation with native or non-native proteins can inform studies involving protein condensation or aggregation.
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Affiliation(s)
- Qi Wan
- DWI – Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Sara N. Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Liesbeth M. Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnold J. Boersma
- DWI – Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
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17
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Tugarinov V, Ceccon A, Clore GM. NMR methods for exploring 'dark' states in ligand binding and protein-protein interactions. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 128:1-24. [PMID: 35282867 PMCID: PMC8921508 DOI: 10.1016/j.pnmrs.2021.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 05/24/2023]
Abstract
A survey, primarily based on work in the authors' laboratory during the last 10 years, is provided of recent developments in NMR studies of exchange processes involving protein-ligand and protein-protein interactions. We start with a brief overview of the theoretical background of Dark state Exchange Saturation Transfer (DEST) and lifetime line-broadening (ΔR2) NMR methodology. Some limitations of the DEST/ΔR2 methodology in applications to molecular systems with intermediate molecular weights are discussed, along with the means of overcoming these limitations with the help of closely related exchange NMR techniques, such as the measurements of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion, exchange-induced chemical shifts or rapidly-relaxing components of relaxation decays. Some theoretical underpinnings of the quantitative description of global dynamics of proteins on the surface of very high molecular weight particles (nanoparticles) are discussed. Subsequently, several applications of DEST/ΔR2 methodology are described from a methodological perspective with an emphasis on providing examples of how kinetic and relaxation parameters for exchanging systems can be reliably extracted from NMR data for each particular model of exchange. Among exchanging systems that are not associated with high molecular weight species, we describe several exchange NMR-based studies that focus on kinetic modelling of transient pre-nucleation oligomerization of huntingtin peptides that precedes aggregation and fibril formation.
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Affiliation(s)
- Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
| | - Alberto Ceccon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
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18
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Karamanos TK, Clore GM. Large Chaperone Complexes Through the Lens of Nuclear Magnetic Resonance Spectroscopy. Annu Rev Biophys 2022; 51:223-246. [PMID: 35044800 DOI: 10.1146/annurev-biophys-090921-120150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molecular chaperones are the guardians of the proteome inside the cell. Chaperones recognize and bind unfolded or misfolded substrates, thereby preventing further aggregation; promoting correct protein folding; and, in some instances, even disaggregating already formed aggregates. Chaperones perform their function by means of an array of weak protein-protein interactions that take place over a wide range of timescales and are therefore invisible to structural techniques dependent upon the availability of highly homogeneous samples. Nuclear magnetic resonance (NMR) spectroscopy, however, is ideally suited to study dynamic, rapidly interconverting conformational states and protein-protein interactions in solution, even if these involve a high-molecular-weight component. In this review, we give a brief overview of the principles used by chaperones to bind their client proteins and describe NMR methods that have emerged as valuable tools to probe chaperone-substrate and chaperone-chaperone interactions. We then focus on a few systems for which the application of these methods has greatly increased our understanding of the mechanisms underlying chaperone functions. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom;
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA;
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19
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Troussicot L, Burmann BM, Molin M. Structural determinants of multimerization and dissociation in 2-Cys peroxiredoxin chaperone function. Structure 2021; 29:640-654. [PMID: 33945778 DOI: 10.1016/j.str.2021.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/31/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022]
Abstract
Peroxiredoxins (PRDXs) are abundant peroxidases present in all kingdoms of life. Recently, they have been shown to also carry out additional roles as molecular chaperones. To address this emerging supplementary function, this review focuses on structural studies of 2-Cys PRDX systems exhibiting chaperone activity. We provide a detailed understanding of the current knowledge of structural determinants underlying the chaperone function of PRDXs. Specifically, we describe the mechanisms which may modulate their quaternary structure to facilitate interactions with client proteins and how they are coordinated with the functions of other molecular chaperones. Following an overview of PRDX molecular architecture, we outline structural details of the presently best-characterized peroxiredoxins exhibiting chaperone function and highlight common denominators. Finally, we discuss the remarkable structural similarities between 2-Cys PRDXs, small HSPs, and J-domain-independent Hsp40 holdases in terms of their functions and dynamic equilibria between low- and high-molecular-weight oligomers.
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Affiliation(s)
- Laura Troussicot
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Björn M Burmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden.
| | - Mikael Molin
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden; Department of Biology and Biological Engineering, Chalmers University of Technology, 405 30 Göteborg, Sweden.
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20
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Radford SE, Karamanos TK. Finding the sweet spot for chaperone activity. Nat Chem 2021; 13:397-399. [PMID: 33931750 DOI: 10.1038/s41557-021-00691-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.
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21
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Ryder BD, Matlahov I, Bali S, Vaquer-Alicea J, van der Wel PCA, Joachimiak LA. Regulatory inter-domain interactions influence Hsp70 recruitment to the DnaJB8 chaperone. Nat Commun 2021; 12:946. [PMID: 33574241 PMCID: PMC7878476 DOI: 10.1038/s41467-021-21147-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 01/15/2021] [Indexed: 01/18/2023] Open
Abstract
The Hsp40/Hsp70 chaperone families combine versatile folding capacity with high substrate specificity, which is mainly facilitated by Hsp40s. The structure and function of many Hsp40s remain poorly understood, particularly oligomeric Hsp40s that suppress protein aggregation. Here, we used a combination of biochemical and structural approaches to shed light on the domain interactions of the Hsp40 DnaJB8, and how they may influence recruitment of partner Hsp70s. We identify an interaction between the J-Domain (JD) and C-terminal domain (CTD) of DnaJB8 that sequesters the JD surface, preventing Hsp70 interaction. We propose a model for DnaJB8-Hsp70 recruitment, whereby the JD-CTD interaction of DnaJB8 acts as a reversible switch that can control the binding of Hsp70. These findings suggest that the evolutionarily conserved CTD of DnaJB8 is a regulatory element of chaperone activity in the proteostasis network.
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Affiliation(s)
- Bryan D Ryder
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Irina Matlahov
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Sofia Bali
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jaime Vaquer-Alicea
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Neuroscience Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands.
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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