1
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Na D, Lim DH, Hong JS, Lee HM, Cho D, Yu MS, Shaker B, Ren J, Lee B, Song JG, Oh Y, Lee K, Oh KS, Lee MY, Choi MS, Choi HS, Kim YH, Bui JM, Lee K, Kim HW, Lee YS, Gsponer J. A multi-layered network model identifies Akt1 as a common modulator of neurodegeneration. Mol Syst Biol 2023; 19:e11801. [PMID: 37984409 DOI: 10.15252/msb.202311801] [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: 06/05/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023] Open
Abstract
The accumulation of misfolded and aggregated proteins is a hallmark of neurodegenerative proteinopathies. Although multiple genetic loci have been associated with specific neurodegenerative diseases (NDs), molecular mechanisms that may have a broader relevance for most or all proteinopathies remain poorly resolved. In this study, we developed a multi-layered network expansion (MLnet) model to predict protein modifiers that are common to a group of diseases and, therefore, may have broader pathophysiological relevance for that group. When applied to the four NDs Alzheimer's disease (AD), Huntington's disease, and spinocerebellar ataxia types 1 and 3, we predicted multiple members of the insulin pathway, including PDK1, Akt1, InR, and sgg (GSK-3β), as common modifiers. We validated these modifiers with the help of four Drosophila ND models. Further evaluation of Akt1 in human cell-based ND models revealed that activation of Akt1 signaling by the small molecule SC79 increased cell viability in all models. Moreover, treatment of AD model mice with SC79 enhanced their long-term memory and ameliorated dysregulated anxiety levels, which are commonly affected in AD patients. These findings validate MLnet as a valuable tool to uncover molecular pathways and proteins involved in the pathophysiology of entire disease groups and identify potential therapeutic targets that have relevance across disease boundaries. MLnet can be used for any group of diseases and is available as a web tool at http://ssbio.cau.ac.kr/software/mlnet.
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Affiliation(s)
- Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Do-Hwan Lim
- College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
- School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea
| | - Jae-Sang Hong
- College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Daeahn Cho
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Myeong-Sang Yu
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Bilal Shaker
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Jun Ren
- Department of Biomedical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Bomi Lee
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Jae Gwang Song
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Yuna Oh
- Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Kyungeun Lee
- Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Kwang-Seok Oh
- Information-based Drug Research Center, Korea Research Institute of Chemical Technology, Deajeon, Republic of Korea
| | - Mi Young Lee
- Information-based Drug Research Center, Korea Research Institute of Chemical Technology, Deajeon, Republic of Korea
| | - Min-Seok Choi
- College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Han Saem Choi
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Yang-Hee Kim
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Jennifer M Bui
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hyung Wook Kim
- College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Young Sik Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
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2
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Tripathi A, Del Galdo S, Chandramouli B, Kumar N. Distinct dynamical features of plasmodial and human HSP70-HSP110 highlight the divergence in their chaperone-assisted protein folding. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140942. [PMID: 37516289 DOI: 10.1016/j.bbapap.2023.140942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
HSP70 and its evolutionarily diverged co-chaperone HSP110, forms an important node in protein folding cascade. How these proteins maintain the aggregation-prone proteome of malaria parasite in functional state remains underexplored, in contrast to its human orthologs. In this study, we have probed into conformational dynamics of plasmodial HSP70 and HSP110 through multiple μs MD-simulations (ATP-state) and compared with their respective human counterparts. Simulations covered sampling of 3.4 and 2.8 μs for HSP70 and HSP110, respectively, for parasite and human orthologs. We provide a comprehensive description of the dynamic behaviors that characterize the systems and also introduce a parameter for quantifying protein rigidity. For HSP70, the interspecies comparison reveals enhanced flexibility in IA and IB subdomain within the conserved NBD, lesser solvent accessibility of the interdomain linker and distinct dynamics of the SBDβ of Pf HSP70 in comparison to Hs HSP70. In the case of HSP110, notable contrast in the dynamics of NBD, SBDβ and SBDα was observed between parasite and human ortholog. Although HSP70 and HSP110 are members of the same superfamily, we identified specific differences in the subdomain contacts in NBD, linker properties and interdomain movements in their human and parasite orthologs. Our study suggests that differences in conformational dynamics may translate into species-specific differences in the chaperoning activities of HSP70-HSP110 in the parasite and human, respectively. Dynamical features of Pf HSP70-HSP110 may contribute to the maintenance of proteostasis in the parasite during its intracellular survival in the host.
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Affiliation(s)
- Aradhya Tripathi
- Department of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram Extension, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sara Del Galdo
- Science Department, University of Roma Tre, Via della Vasca Navale 84, Rome, Italy
| | | | - Niti Kumar
- Department of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram Extension, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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3
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Hu L, Sun C, Kidd JM, Han J, Fang X, Li H, Liu Q, May AE, Li Q, Zhou L, Liu Q. A first-in-class inhibitor of Hsp110 molecular chaperones of pathogenic fungi. Nat Commun 2023; 14:2745. [PMID: 37173314 PMCID: PMC10182041 DOI: 10.1038/s41467-023-38220-2] [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: 03/05/2022] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Proteins of the Hsp110 family are molecular chaperones that play important roles in protein homeostasis in eukaryotes. The pathogenic fungus Candida albicans, which causes infections in humans, has a single Hsp110, termed Msi3. Here, we provide proof-of-principle evidence supporting fungal Hsp110s as targets for the development of new antifungal drugs. We identify a pyrazolo[3,4-b] pyridine derivative, termed HLQ2H (or 2H), that inhibits the biochemical and chaperone activities of Msi3, as well as the growth and viability of C. albicans. Moreover, the fungicidal activity of 2H correlates with its inhibition of in vivo protein folding. We propose 2H and related compounds as promising leads for development of new antifungals and as pharmacological tools for the study of the molecular mechanisms and functions of Hsp110s.
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Affiliation(s)
- Liqing Hu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, Department of Pharmacy, School of Medicine, Hunan Normal University, Changsha, Hunan, China
| | - Cancan Sun
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Justin M Kidd
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Jizhong Han
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, 518107, Guangdong, China
| | - Xianjun Fang
- Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Hongtao Li
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Qingdai Liu
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Aaron E May
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Qianbin Li
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Lei Zhou
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, 518107, Guangdong, China.
| | - Qinglian Liu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA.
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4
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Lazarev VF, Dutysheva EA, Kanunikov IE, Guzhova IV, Margulis BA. Protein Interactome of Amyloid-β as a Therapeutic Target. Pharmaceuticals (Basel) 2023; 16:312. [PMID: 37259455 PMCID: PMC9965366 DOI: 10.3390/ph16020312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 02/08/2023] [Indexed: 04/12/2024] Open
Abstract
The amyloid concept of Alzheimer's disease (AD) assumes the β-amyloid peptide (Aβ) as the main pathogenic factor, which injures neural and other brain cells, causing their malfunction and death. Although Aβ has been documented to exert its cytotoxic effect in a solitary manner, there is much evidence to claim that its toxicity can be modulated by other proteins. The list of such Aβ co-factors or interactors includes tau, APOE, transthyretin, and others. These molecules interact with the peptide and affect the ability of Aβ to form oligomers or aggregates, modulating its toxicity. Thus, the list of potential substances able to reduce the harmful effects of the peptide should include ones that can prevent the pathogenic interactions by specifically binding Aβ and/or its partners. In the present review, we discuss the data on Aβ-based complexes in AD pathogenesis and on the compounds directly targeting Aβ or the destructors of its complexes with other polypeptides.
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Affiliation(s)
- Vladimir F. Lazarev
- Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
| | - Elizaveta A. Dutysheva
- Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
| | - Igor E. Kanunikov
- Biological Faculty, St. Petersburg State University, 199034 Saint Petersburg, Russia
| | - Irina V. Guzhova
- Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
| | - Boris A. Margulis
- Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
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5
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Karakulak T, Szklarczyk D, Saylan CC, Moch H, von Mering C, Kahraman A. CanIsoNet: a database to study the functional impact of isoform switching events in diseases. BIOINFORMATICS ADVANCES 2023; 3:vbad050. [PMID: 37123454 PMCID: PMC10133402 DOI: 10.1093/bioadv/vbad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/30/2023] [Accepted: 04/13/2023] [Indexed: 05/02/2023]
Abstract
Motivation Alternative splicing, as an essential regulatory mechanism in normal mammalian cells, is frequently disturbed in cancer and other diseases. Switches in the expression of most dominant alternative isoforms can alter protein interaction networks of associated genes giving rise to disease and disease progression. Here, we present CanIsoNet, a database to view, browse and search isoform switching events in diseases. CanIsoNet is the first webserver that incorporates isoform expression data with STRING interaction networks and ClinVar annotations to predict the pathogenic impact of isoform switching events in various diseases. Results Data in CanIsoNet can be browsed by disease or searched by genes or isoforms in annotation-rich data tables. Various annotations for 11 811 isoforms and 14 357 unique isoform switching events across 31 different disease types are available. The network density score for each disease-specific isoform, PFAM domain IDs of disrupted interactions, domain structure visualization of transcripts and expression data of switched isoforms for each sample is given. Additionally, the genes annotated in ClinVar are highlighted in interactive interaction networks. Availability and implementation CanIsoNet is freely available at https://www.caniso.net. The source codes can be found under a Creative Common License at https://github.com/kahramanlab/CanIsoNet_Web. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Tülay Karakulak
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, Zurich, 8091, Switzerland
- Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Damian Szklarczyk
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
- Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Cemil Can Saylan
- Computational Science and Engineering Department, Informatics Institute, Istanbul Technical University, Reşitpaşa, İTÜ Ayazağa Kampüsü, Istanbul, 34467, Türkiye
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, Zurich, 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, 8006, Switzerland
| | - Christian von Mering
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
- Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
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6
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Bracher A, Verghese J. Nucleotide Exchange Factors for Hsp70 Molecular Chaperones: GrpE, Hsp110/Grp170, HspBP1/Sil1, and BAG Domain Proteins. Subcell Biochem 2023; 101:1-39. [PMID: 36520302 DOI: 10.1007/978-3-031-14740-1_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Molecular chaperones of the Hsp70 family are key components of the cellular protein-folding machinery. Substrate folding is accomplished by iterative cycles of ATP binding, hydrolysis, and release. The ATPase activity of Hsp70 is regulated by two main classes of cochaperones: J-domain proteins stimulate ATPase hydrolysis by Hsp70, while nucleotide exchange factors (NEFs) facilitate the conversion from the ADP-bound to the ATP-bound state, thus closing the chaperone folding cycle. NEF function can additionally be antagonized by ADP dissociation inhibitors. Beginning with the discovery of the prototypical bacterial NEF, GrpE, a large diversity of nucleotide exchange factors for Hsp70 have been identified, connecting it to a multitude of cellular processes in the eukaryotic cell. Here we review recent advances toward structure and function of nucleotide exchange factors from the Hsp110/Grp170, HspBP1/Sil1, and BAG domain protein families and discuss how these cochaperones connect protein folding with cellular quality control and degradation pathways.
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Affiliation(s)
- Andreas Bracher
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany.
| | - Jacob Verghese
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
- Trophic Communications GmbH, Munich, Germany
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7
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Intrinsically Disordered Proteins: An Overview. Int J Mol Sci 2022; 23:ijms232214050. [PMID: 36430530 PMCID: PMC9693201 DOI: 10.3390/ijms232214050] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions. This review focuses on different aspects of disordered proteins and disordered protein regions, which form the basis of the so-called "Disorder-function paradigm" of proteins. Additionally, various experimental approaches and computational tools used for characterizing disordered regions in proteins are discussed. Finally, the role of disordered proteins in diseases and their utility as potential drug targets are explored.
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8
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Ahmad A, Mishra R. Polyol and sugar osmolytes stabilize the molten globule state of α-lactalbumin and inhibit amyloid fibril formation. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140853. [PMID: 36096464 DOI: 10.1016/j.bbapap.2022.140853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Protein misfolding and aggregation are associated with several human diseases such as Alzheimer's, Parkinson's, prion related disorders, type-II diabetes, etc. Different strategies using molecular chaperones, synthetic and naturally occurring small molecules, osmolytes, etc. have been used to prevent protein aggregation and amyloid fibril formation. In this study, we have used bovine α-lactalbumin at pH 1.6, 37 °C, and shaking conditions to promote amyloid fibril formation. Polyol and sugar osmolytes like glycerol, sorbitol, and trehalose have been used to inhibit the fibrillation of a number of proteins. In the present work, amyloid fibril formation of α-lactalbumin has been shown by ThT assay and AFM, while changes in the secondary structure during fibrillation has been followed by circular dichroism spectroscopy. Our results show that glycerol, sorbitol, and trehalose affect amyloid fibril formation of α-lactalbumin in a concentration-dependent manner. There is a delay in the lag phase of amyloid fibril formation in sorbitol and trehalose and complete inhibition in 6 M glycerol. Our results indicate that delay in the lag phase and inhibition of amyloid fibril formation are due to the stabilization of molten globule state by these osmolytes. At pH 1.6, the molten globule as well as the amyloid fibrils bind to ANS. However, when pH was shifted from 1.6 to 7, only the oligomeric and the fibrillar species bind to ANS due to refolding of molten globule state. The outcome of this study might be useful in designing small molecules which may stabilize the intermediate states, thus preventing amyloid fibril formation.
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Affiliation(s)
- Aziz Ahmad
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajesh Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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9
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Cabrera Y, Bernardo-Seisdedos G, Dublang L, Albesa-Jové D, Orozco N, Rosa Viguera A, Millet O, Muga A, Moro F. Fine-tuning of the Hsc70-based human protein disaggregase machinery by the distinctive C-terminal extension of Apg2. J Mol Biol 2022; 434:167841. [PMID: 36167183 DOI: 10.1016/j.jmb.2022.167841] [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: 05/26/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 10/31/2022]
Abstract
Apg2, one of the three cytosolic Hsp110 chaperones in humans, supports reactivation of unordered and ordered protein aggregates by Hsc70 (HspA8). Together with DnaJB1, Apg2 serves to nucleate Hsc70 molecules into sites where productive entropic pulling forces can be developed. During aggregate reactivation, Apg2 performs as a specialized nucleotide exchange factor, but the origin of its specialization is poorly defined. Here we report on the role of the distinctive C-terminal extension present in Apg2 and other metazoan homologs. We found that the first part of this Apg2 subdomain with propensity to adopt α-helical structure interacts with the nucleotide binding domain of Hsc70 in a nucleotide-dependent manner, contributing significantly to the stability of the Hsc70:Apg2 complex. Moreover, the second intrinsically disordered segment of Apg2 C-terminal extension plays an important role as a downregulator of nucleotide exchange. An NMR analysis showed that the interaction with Hsc70 nucleotide binding domain modifies the chemical environment of residues located in important functional sites such as the interface between lobe I and II and the nucleotide binding site. Our data indicate that Apg2 C-terminal extension is a fine-tuner of human Hsc70 activity that optimizes the substrate remodeling ability of the chaperone system.
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Affiliation(s)
- Yovana Cabrera
- Instituto Biofisika (UPV/EHU, CSIC) y Dpto. de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena S/N, 48490 Leioa, Spain; Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390 Gothenburg, Sweden
| | | | - Leire Dublang
- Instituto Biofisika (UPV/EHU, CSIC) y Dpto. de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena S/N, 48490 Leioa, Spain
| | - David Albesa-Jové
- Instituto Biofisika (UPV/EHU, CSIC) y Dpto. de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena S/N, 48490 Leioa, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Natalia Orozco
- Fundación Biofísica Bizkaia, Barrio Sarriena S/N, 48940 Leioa, Spain
| | - Ana Rosa Viguera
- Instituto Biofisika (UPV/EHU, CSIC) y Dpto. de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena S/N, 48490 Leioa, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Lab, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Arturo Muga
- Instituto Biofisika (UPV/EHU, CSIC) y Dpto. de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena S/N, 48490 Leioa, Spain
| | - Fernando Moro
- Instituto Biofisika (UPV/EHU, CSIC) y Dpto. de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena S/N, 48490 Leioa, Spain.
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Picone P, Sanfilippo T, Vasto S, Baldassano S, Guggino R, Nuzzo D, Bulone D, San Biagio PL, Muscolino E, Monastero R, Dispenza C, Giacomazza D. From Small Peptides to Large Proteins against Alzheimer’sDisease. Biomolecules 2022; 12:biom12101344. [PMID: 36291553 PMCID: PMC9599460 DOI: 10.3390/biom12101344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common neurodegenerative disorder in the elderly. The two cardinal neuropathological hallmarks of AD are the senile plaques, which are extracellular deposits mainly constituted by beta-amyloids, and neurofibrillary tangles formed by abnormally phosphorylated Tau (p-Tau) located in the cytoplasm of neurons. Although the research has made relevant progress in the management of the disease, the treatment is still lacking. Only symptomatic medications exist for the disease, and, in the meantime, laboratories worldwide are investigating disease-modifying treatments for AD. In the present review, results centered on the use of peptides of different sizes involved in AD are presented.
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Affiliation(s)
- Pasquale Picone
- Istituto per la Ricerca e l’Innovazione Biomedica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
- Dipartmento of Scienze Biologiche, Chimiche, Farmaceutiche e Tecnologiche (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Tiziana Sanfilippo
- Ambulatorio di Nutrizione Clinica ASP Palermo, Via G. Cusmano 24, 90141 Palermo, Italy
- Anestesia e Rianimazione, Presidio Ospedaliero “S. Cimino”, 90141 Termini Imerese, Italy
| | - Sonya Vasto
- Dipartmento of Scienze Biologiche, Chimiche, Farmaceutiche e Tecnologiche (STEBICEF), University of Palermo, 90128 Palermo, Italy
- Istituti Euro-Mediterranei di Scienza e Tecnologia (IEMEST), Via M. Miraglia 20, 90139 Palermo, Italy
| | - Sara Baldassano
- Dipartmento of Scienze Biologiche, Chimiche, Farmaceutiche e Tecnologiche (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Rossella Guggino
- Ambulatorio di Nutrizione Clinica ASP Palermo, Via G. Cusmano 24, 90141 Palermo, Italy
- Anestesia e Rianimazione, Presidio Ospedaliero “S. Cimino”, 90141 Termini Imerese, Italy
| | - Domenico Nuzzo
- Istituto per la Ricerca e l’Innovazione Biomedica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
- Dipartmento of Scienze Biologiche, Chimiche, Farmaceutiche e Tecnologiche (STEBICEF), University of Palermo, 90128 Palermo, Italy
- Correspondence: (D.N.); (D.G.)
| | - Donatella Bulone
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
| | - Pier Luigi San Biagio
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
| | - Emanuela Muscolino
- Dipartimento di Ingegneria, Università degli Studi di Palermo, Viale delle Scienze, Bldg 6, 90128 Palermo, Italy
| | - Roberto Monastero
- Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università degli Studi di Palermo, Via del Vespro 129, 90127 Palermo, Italy
| | - Clelia Dispenza
- Dipartimento di Ingegneria, Università degli Studi di Palermo, Viale delle Scienze, Bldg 6, 90128 Palermo, Italy
| | - Daniela Giacomazza
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via U. La Malfa 153, 90146 Palermo, Italy
- Correspondence: (D.N.); (D.G.)
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Bhadra AK, Rau MJ, Daw JA, Fitzpatrick JAJ, Weihl CC, True HL. Disease-associated mutations within the yeast DNAJB6 homolog Sis1 slow conformer-specific substrate processing and can be corrected by the modulation of nucleotide exchange factors. Nat Commun 2022; 13:4570. [PMID: 35931773 PMCID: PMC9355953 DOI: 10.1038/s41467-022-32318-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Molecular chaperones, or heat shock proteins (HSPs), protect against the toxic misfolding and aggregation of proteins. As such, mutations or deficiencies within the chaperone network can lead to disease. Dominant mutations within DNAJB6 (Hsp40)—an Hsp70 co-chaperone—lead to a protein aggregation-linked myopathy termed Limb-Girdle Muscular Dystrophy Type D1 (LGMDD1). Here, we used the yeast prion model client in conjunction with in vitro chaperone activity assays to gain mechanistic insights into the molecular basis of LGMDD1. Here, we show how mutations analogous to those found in LGMDD1 affect Sis1 (a functional homolog of human DNAJB6) function by altering the structure of client protein aggregates, interfering with the Hsp70 ATPase cycle, dimerization and substrate processing; poisoning the function of wild-type protein. These results uncover the mechanisms through which LGMDD1-associated mutations alter chaperone activity, and provide insights relevant to potential therapeutic interventions. Here the authors describe mechanisms through which analogous LGMDD1 (Limb-Girdle Muscular Dystrophy Type D1) mutations affect Sis1 (a yeast functional homolog of human DNAJB6) chaperone activity and poison the function of wild-type protein; potentially uncovering a new therapeutic route to explore.
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Affiliation(s)
- Ankan K Bhadra
- Department of Cell Biology and Physiology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA
| | - Michael J Rau
- Washington University Center for Cellular Imaging (WUCCI), Washington University School of Medicine, St. Louis, MO, USA
| | - Jil A Daw
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - James A J Fitzpatrick
- Department of Cell Biology and Physiology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA.,Washington University Center for Cellular Imaging (WUCCI), Washington University School of Medicine, St. Louis, MO, USA.,Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Conrad C Weihl
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Heather L True
- Department of Cell Biology and Physiology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8228, St. Louis, MO, 63110, USA.
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12
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Thackray AM, Lam B, McNulty EE, Nalls AV, Mathiason CK, Magadi SS, Jackson WS, Andréoletti O, Marrero-Winkens C, Schätzl H, Bujdoso R. Clearance of variant Creutzfeldt-Jakob disease prions in vivo by the Hsp70 disaggregase system. Brain 2022; 145:3236-3249. [PMID: 35446941 PMCID: PMC9473358 DOI: 10.1093/brain/awac144] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/10/2022] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
The metazoan Hsp70 disaggregase protects neurons from proteotoxicity that arises from the accumulation of misfolded protein aggregates. Hsp70 and its co-chaperones disassemble and extract polypeptides from protein aggregates for refolding or degradation. The effectiveness of the chaperone system decreases with age and leads to accumulation rather than removal of neurotoxic protein aggregates. Therapeutic enhancement of the Hsp70 protein disassembly machinery is proposed to counter late-onset protein misfolding neurodegenerative disease that may arise. In the context of prion disease, it is not known whether stimulation of protein aggregate disassembly paradoxically leads to enhanced formation of seeding competent species of disease-specific proteins and acceleration of neurodegenerative disease. Here we have tested the hypothesis that modulation of Hsp70 disaggregase activity perturbs mammalian prion-induced neurotoxicity and prion seeding activity. To do so we used prion protein (PrP) transgenic Drosophila that authentically replicate mammalian prions. RNASeq identified that Hsp70, DnaJ-1 and Hsp110 gene expression was downregulated in prion-exposed PrP Drosophila. We demonstrated that RNAi knockdown of Hsp110 or DnaJ-1 gene expression in variant Creutzfeldt–Jakob disease prion-exposed human PrP Drosophila enhanced neurotoxicity, whereas overexpression mitigated toxicity. Strikingly, prion seeding activity in variant Creutzfeldt–Jakob disease prion-exposed human PrP Drosophila was ablated or reduced by Hsp110 or DnaJ-1 overexpression, respectively. Similar effects were seen in scrapie prion-exposed ovine PrP Drosophila with modified Hsp110 or DnaJ-1 gene expression. These unique observations show that the metazoan Hsp70 disaggregase facilitates the clearance of mammalian prions and that its enhanced activity is a potential therapeutic strategy for human prion disease.
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Affiliation(s)
- Alana M Thackray
- University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge, CB3 0ES, UK
| | - Brian Lam
- Medical Research Council Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Erin E McNulty
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Amy V Nalls
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Candace K Mathiason
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Srivathsa Subramanya Magadi
- Wallenberg Center for Molecular Medicine, Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Walker S Jackson
- Wallenberg Center for Molecular Medicine, Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Olivier Andréoletti
- UMR INRA ENVT 1225 -Hôtes-Agents Pathogènes, Ecole Nationale Vétérinaire de Toulouse, 23 Chemin des Capelles, 31076 Toulouse, France
| | - Cristóbal Marrero-Winkens
- Calgary Prion Research Unit, Faculty of Veterinary Medicine, University of Calgary TRW 2D10, 3280 Hospital Drive NW, Calgary, AB, Canada T2N 4Z6
| | - Hermann Schätzl
- Calgary Prion Research Unit, Faculty of Veterinary Medicine, University of Calgary TRW 2D10, 3280 Hospital Drive NW, Calgary, AB, Canada T2N 4Z6
| | - Raymond Bujdoso
- University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge, CB3 0ES, UK
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13
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Arhar T, Shkedi A, Nadel CM, Gestwicki JE. The interactions of molecular chaperones with client proteins: why are they so weak? J Biol Chem 2021; 297:101282. [PMID: 34624315 PMCID: PMC8567204 DOI: 10.1016/j.jbc.2021.101282] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 12/30/2022] Open
Abstract
The major classes of molecular chaperones have highly variable sequences, sizes, and shapes, yet they all bind to unfolded proteins, limit their aggregation, and assist in their folding. Despite the central importance of this process to protein homeostasis, it has not been clear exactly how chaperones guide this process or whether the diverse families of chaperones use similar mechanisms. For the first time, recent advances in NMR spectroscopy have enabled detailed studies of how unfolded, "client" proteins interact with both ATP-dependent and ATP-independent classes of chaperones. Here, we review examples from four distinct chaperones, Spy, Trigger Factor, DnaK, and HscA-HscB, highlighting the similarities and differences between their mechanisms. One striking similarity is that the chaperones all bind weakly to their clients, such that the chaperone-client interactions are readily outcompeted by stronger, intra- and intermolecular contacts in the folded state. Thus, the relatively weak affinity of these interactions seems to provide directionality to the folding process. However, there are also key differences, especially in the details of how the chaperones release clients and how ATP cycling impacts that process. For example, Spy releases clients in a largely folded state, while clients seem to be unfolded upon release from Trigger Factor or DnaK. Together, these studies are beginning to uncover the similarities and differences in how chaperones use weak interactions to guide protein folding.
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Affiliation(s)
- Taylor Arhar
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Arielle Shkedi
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Cory M Nadel
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA.
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14
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Li H, Hu L, Cuffee CW, Mohamed M, Li Q, Liu Q, Zhou L, Liu Q. Interdomain interactions dictate the function of the Candida albicans Hsp110 protein Msi3. J Biol Chem 2021; 297:101082. [PMID: 34403698 PMCID: PMC8424595 DOI: 10.1016/j.jbc.2021.101082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/29/2021] [Accepted: 08/13/2021] [Indexed: 01/27/2023] Open
Abstract
Heat shock proteins of 110 kDa (Hsp110s), a unique class of molecular chaperones, are essential for maintaining protein homeostasis. Hsp110s exhibit a strong chaperone activity preventing protein aggregation (the "holdase" activity) and also function as the major nucleotide-exchange factor (NEF) for Hsp70 chaperones. Hsp110s contain two functional domains: a nucleotide-binding domain (NBD) and substrate-binding domain (SBD). ATP binding is essential for Hsp110 function and results in close contacts between the NBD and SBD. However, the molecular mechanism of this ATP-induced allosteric coupling remains poorly defined. In this study, we carried out biochemical analysis on Msi3, the sole Hsp110 in Candida albicans, to dissect the unique allosteric coupling of Hsp110s using three mutations affecting the domain-domain interface. All the mutations abolished both the in vivo and in vitro functions of Msi3. While the ATP-bound state was disrupted in all mutants, only mutation of the NBD-SBDβ interfaces showed significant ATPase activity, suggesting that the full-length Hsp110s have an ATPase that is mainly suppressed by NBD-SBDβ contacts. Moreover, the high-affinity ATP-binding unexpectedly appears to require these NBD-SBD contacts. Remarkably, the "holdase" activity was largely intact for all mutants tested while NEF activity was mostly compromised, although both activities strictly depended on the ATP-bound state, indicating different requirements for these two activities. Stable peptide substrate binding to Msi3 led to dissociation of the NBD-SBD contacts and compromised interactions with Hsp70. Taken together, our data demonstrate that the exceptionally strong NBD-SBD contacts in Hsp110s dictate the unique allosteric coupling and biochemical activities.
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Affiliation(s)
- Hongtao Li
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Liqing Hu
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA,Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Crist William Cuffee
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Mahetab Mohamed
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Qianbin Li
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Qingdai Liu
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, China
| | - Lei Zhou
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Qinglian Liu
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA,For correspondence: Qinglian Liu
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