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Herranz-Montoya I, Park S, Djouder N. A comprehensive analysis of prefoldins and their implication in cancer. iScience 2021; 24:103273. [PMID: 34761191 PMCID: PMC8567396 DOI: 10.1016/j.isci.2021.103273] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Prefoldins (PFDNs) are evolutionary conserved co-chaperones, initially discovered in archaea but universally present in eukaryotes. PFDNs are prevalently organized into hetero-hexameric complexes. Although they have been overlooked since their discovery and their functions remain elusive, several reports indicate they act as co-chaperones escorting misfolded or non-native proteins to group II chaperonins. Unlike the eukaryotic PFDNs which interact with cytoskeletal components, the archaeal PFDNs can bind and stabilize a wide range of substrates, possibly due to their great structural diversity. The discovery of the unconventional RPB5 interactor (URI) PFDN-like complex (UPC) suggests that PFDNs have versatile functions and are required for different cellular processes, including an important role in cancer. Here, we summarize their functions across different species. Moreover, a comprehensive analysis of PFDNs genomic alterations across cancer types by using large-scale cancer genomic data indicates that PFDNs are a new class of non-mutated proteins significantly overexpressed in some cancer types.
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Affiliation(s)
- Irene Herranz-Montoya
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Solip Park
- Computational Cancer Genomics Group, Structural Biology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Nabil Djouder
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
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Törner R, Henot F, Awad R, Macek P, Gans P, Boisbouvier J. Backbone and methyl resonances assignment of the 87 kDa prefoldin from Pyrococcus horikoshii. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:351-360. [PMID: 33988824 DOI: 10.1007/s12104-021-10029-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Prefoldin is a heterohexameric protein assembly which acts as a co-chaperonin for the well conserved Hsp60 chaperonin, present in archaebacteria and the eukaryotic cell cytosol. Prefoldin is a holdase, capturing client proteins and subsequently transferring them to the Hsp60 chamber for refolding. The chaperonin family is implicated in the early stages of protein folding and plays an important role in proteostasis in the cytosol. Here, we report the assignment of 1HN, 15N, 13C', 13Cα, 13Cβ, 1Hmethyl, and 13Cmethyl chemical shifts of the 87 kDa prefoldin from the hyperthermophilic archaeon Pyrococcus horikoshii, consisting of two α and four β subunits. 100% of the [13C, 1H]-resonances of Aβ, Iδ1, Iδ2, Tγ2, Vγ2 methyl groups were successfully assigned for both subunits. For the β subunit, showing partial peak doubling, 80% of the backbone resonances were assigned. In the α subunit, large stretches of backbone resonances were not detectable due to slow (μs-ms) time scale dynamics. This conformational exchange limited the backbone sequential assignment of the α subunit to 57% of residues, which corresponds to 84% of visible NMR signals.
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Affiliation(s)
- Ricarda Törner
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71, Avenue des Martyrs, 38044, Grenoble, France.
| | - Faustine Henot
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Rida Awad
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Pavel Macek
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Pierre Gans
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Jerome Boisbouvier
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71, Avenue des Martyrs, 38044, Grenoble, France.
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Zhang K, Tan R, Yao D, Su L, Xia Y, Wu J. Enhanced Production of Soluble Pyrococcus furiosus α-Amylase in Bacillus subtilis through Chaperone Co-Expression, Heat Treatment and Fermentation Optimization. J Microbiol Biotechnol 2021; 31:570-583. [PMID: 33753701 PMCID: PMC9723276 DOI: 10.4014/jmb.2101.01039] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/15/2022]
Abstract
Pyrococcus furiosus α-amylase can hydrolyze α-1,4 linkages in starch and related carbohydrates under hyperthermophilic condition (~ 100°C), showing great potential in a wide range of industrial applications, while its relatively low productivity from heterologous hosts has limited the industrial applications. Bacillus subtilis, a gram-positive bacterium, has been widely used in industrial production for its non-pathogenic and powerful secretory characteristics. This study was conducted to increase production of P. furiosus α-amylase in B. subtilis through three strategies. Initial experiments showed that co-expression of P. furiosus molecular chaperone peptidyl-prolyl cis-trans isomerase through genomic integration mode, using a CRISPR/Cas9 system, increased soluble amylase production. Therefore, considering that native P. furiosus α-amylase is produced within a hyperthermophilic environment and is highly thermostable, heat treatment of intact culture at 90°C for 15 min was performed, thereby greatly increasing soluble amylase production. After optimization of the culture conditions (nitrogen source, carbon source, metal ion, temperature and pH), experiments in a 3-L fermenter yielded a soluble activity of 3,806.7 U/ml, which was 3.3- and 28.2-fold those of a control without heat treatment (1,155.1 U/ml) and an empty expression vector control (135.1 U/ml), respectively. This represents the highest P. furiosus α-amylase production reported to date and should promote innovation in the starch liquefaction process and related industrial productions. Meanwhile, heat treatment, which may promote folding of aggregated P. furiosus α-amylase into a soluble, active form through the transfer of kinetic energy, may be of general benefit when producing proteins from thermophilic archaea.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China
| | - Ruiting Tan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China
| | - Dongbang Yao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China
| | - Yongmei Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P.R. China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, P.R. China,Corresponding author Phone: 86-510-85327802 Fax: 86-510-85326653 E-mail:
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Kumar V, Behl A, Shoaib R, Abid M, Shevtsov M, Singh S. Comparative structural insight into prefoldin subunints of archaea and eukaryotes with special emphasis on unexplored prefoldin of Plasmodium falciparum. J Biomol Struct Dyn 2020; 40:3804-3818. [PMID: 33272134 DOI: 10.1080/07391102.2020.1850527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Prefoldin (PFD) is a heterohexameric molecular chaperone which bind unfolded proteins and subsequently deliver them to a group II chaperonin for correct folding. Although there is structural and functional information available for humans and archaea PFDs, their existence and functions in malaria parasite remains uncharacterized. In the present review, we have collected the available information on prefoldin family members of archaea and humans and attempted to analyze unexplored PFD subunits of Plasmodium falciparum (Pf). Our review enhances the understanding of probable functions, structure and mechanism of substrate binding of Pf prefoldin by comparing with the available information of its homologs in archaea and H. sapiens. Three PfPFD out of six and a Pf prefoldin-like protein are reported to be essential for parasite survival that signifies their importance in malaria parasite biology. Transcriptome analyses suggest that PfPFD subunits are up-regulated at the mRNA level during asexual and sexual stages of parasite life cycle. Our in silico analysis suggested several pivotal proteins like myosin E, cytoskeletal protein (tubulin), merozoite surface protein and ring exported protein 3 as their interacting partners. Based on structural information of archaeal and H. sapiens PFDs, P. falciparum counterparts have been modelled and key interface residues were identified that are critical for oligomerization of PfPFD subunits. We collated information on PFD-substrate binding and PFD-chaperonin interaction in detail to understand the mechanism of substrate delivery in archaea and humans. Overall, our review enables readers to view the PFD family comprehensively. Communicated by Ramaswamy H. SarmaAbbreviations: HSP: Heat shock proteins; CCT: Chaperonin containing TCP-1; PFD: Prefoldin; PFLP: Prefoldin like protein; PfPFD: Plasmodium falciparum prefoldin; Pf: Plasmodium falciparum; H. sapiens: Homo sapiens; M. thermoautotrophicus: Methanobacterium thermoautotrophicus; P. horikoshii: Pyrococcus horikoshii.
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Affiliation(s)
- Vikash Kumar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Ankita Behl
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Rumaisha Shoaib
- Medicinal Chemistry Laboratory, Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Maxim Shevtsov
- Center for Translational Cancer Research Technische, Universität München (TranslaTUM), Radiation Immuno Oncology group, Klinikum rechts der Isar, Munich, Germany.,Institute of Cytology of the Russian Academy of Sciences (RAS), St. Petersburg, Russia.,Department of General Surgery, Pavlov First Saint Petersburg State Medical University, Petersburg, Russia.,Almazov National Medical Research Centre, Polenov Russian Scientific Research Institute of Neurosurgery, St. Petersburg, Russia.,National Center for Neurosurgery, Nur-Sultan, Kazakhstan.,Department of Biomedical Cell Technologies, Far Eastern Federal University, Vladivostok, Russia
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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Mo SJ, Zhao HC, Tian YZ, Zhao HL. The Role of Prefoldin and Its Subunits in Tumors and Their Application Prospects in Nanomedicine. Cancer Manag Res 2020; 12:8847-8856. [PMID: 33061580 PMCID: PMC7520118 DOI: 10.2147/cmar.s270237] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
Prefoldin (PFDN) is a hexameric chaperone complex that is widely found in eukaryotes and archaea and consists of six different subunits (PFDN1-6). Its main function is to transfer actin and tubulin monomers to the eukaryotic cell cytoplasmic chaperone protein (c-CPN) specific binding during the assembly of the cytoskeleton, to stabilize the newly synthesized peptides so that they can be folded correctly. The current study found that each subunit of PFDN has different functions, which are closely related to the occurrence, development and prognosis of tumors. However, the best characteristics of each subunit have not been fully affirmed. The connection between research and tumors can change the understanding of PFDN and further extend its potential prognostic role and structural function to cancer research and clinical practice. This article mainly reviews the role of canonical PFDN and its subunits in tumors and other diseases, and discusses the potential prospects of the unique structure and function of PFDN in nanomedicine.
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Affiliation(s)
- Shao-Jian Mo
- Department of General Surgery, The Affiliated Bethune Hospital of Shanxi Medical University, Taiyuan 030032, People's Republic of China
| | - Hai-Chao Zhao
- Department of General Surgery, The Affiliated Bethune Hospital of Shanxi Medical University, Taiyuan 030032, People's Republic of China
| | - Yan-Zhang Tian
- Department of General Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Taiyuan 030032, People's Republic of China
| | - Hao-Liang Zhao
- Department of General Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Taiyuan 030032, People's Republic of China
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6
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Djohan Y, Azukizawa T, Patmawati, Sakai K, Yano Y, Sato F, Takahashi R, Yohda M, Maeda M, Kamiya N, Zako T. Molecular chaperone prefoldin-assisted biosynthesis of gold nanoparticles with improved size distribution and dispersion. Biomater Sci 2019; 7:1801-1804. [PMID: 30869657 DOI: 10.1039/c8bm01026a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Here we report a novel aspect of molecular chaperone prefoldin (PFD) as a biomaterial in the biocatalytic synthesis of gold nanoparticles (AuNPs) using glycerol dehydrogenase (GLD). We found that PFD could inhibit the aggregation of AuNPs during the biosynthesis, leading to the formation of AuNPs with controlled size distribution.
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Affiliation(s)
- Yovita Djohan
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
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7
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Gestaut D, Roh SH, Ma B, Pintilie G, Joachimiak LA, Leitner A, Walzthoeni T, Aebersold R, Chiu W, Frydman J. The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis. Cell 2019; 177:751-765.e15. [PMID: 30955883 DOI: 10.1016/j.cell.2019.03.012] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 12/03/2018] [Accepted: 03/04/2019] [Indexed: 01/02/2023]
Abstract
Maintaining proteostasis in eukaryotic protein folding involves cooperation of distinct chaperone systems. To understand how the essential ring-shaped chaperonin TRiC/CCT cooperates with the chaperone prefoldin/GIMc (PFD), we integrate cryoelectron microscopy (cryo-EM), crosslinking-mass-spectrometry and biochemical and cellular approaches to elucidate the structural and functional interplay between TRiC/CCT and PFD. We find these hetero-oligomeric chaperones associate in a defined architecture, through a conserved interface of electrostatic contacts that serves as a pivot point for a TRiC-PFD conformational cycle. PFD alternates between an open "latched" conformation and a closed "engaged" conformation that aligns the PFD-TRiC substrate binding chambers. PFD can act after TRiC bound its substrates to enhance the rate and yield of the folding reaction, suppressing non-productive reaction cycles. Disrupting the TRiC-PFD interaction in vivo is strongly deleterious, leading to accumulation of amyloid aggregates. The supra-chaperone assembly formed by PFD and TRiC is essential to prevent toxic conformations and ensure effective cellular proteostasis.
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Affiliation(s)
- Daniel Gestaut
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Soung Hun Roh
- Department of Biological Science, Seoul National University, Seoul, South Korea
| | - Boxue Ma
- Baylor College of Medicine, Houston, TX 77030, USA
| | - Grigore Pintilie
- Department of Biological Science, Seoul National University, Seoul, South Korea
| | - Lukasz A Joachimiak
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, UTSouthwestern, North Campus, Dallas, TX 75390, USA
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Thomas Walzthoeni
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland; PhD Program in Molecular Life Sciences, University of Zurich/ETH Zurich, 8057 Zurich, Switzerland; Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA.
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Kwon OC, Lee EJ, Lee JY, Youn J, Kim TH, Hong S, Lee CK, Yoo B, Robinson WH, Kim YG. Prefoldin 5 and Anti-prefoldin 5 Antibodies as Biomarkers for Uveitis in Ankylosing Spondylitis. Front Immunol 2019; 10:384. [PMID: 30891043 PMCID: PMC6411661 DOI: 10.3389/fimmu.2019.00384] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/14/2019] [Indexed: 01/31/2023] Open
Abstract
Objective: Uveitis is the most common extra-articular manifestation of ankylosing spondylitis (AS), for which no diagnostic biomarkers have been identified. This study was conducted to identify biomarker for uveitis in AS. Methods: To identify autoantibodies associated with uveitis in AS, we performed human protein microarray analysis using sera derived from various autoimmune diseases and ELISA analysis of sera derived from AS and rheumatoid arthritis patients. In the curdlan-induced SKG mice model, ophthalmic examination was performed at week 8 post-immunization and histologic examination of the ocular lesions performed at week 16 post-immunization. Serum levels of target antibodies were assessed at various time-points. To evaluate the functional role of specific autoantibodies, an in vitro apoptosis assay using ARPE-19 cells was performed. Results: Reactivity against prefoldin subunit 5 (PFDN5) was identified in AS with uveitis. Levels of anti-PFDN5 antibodies and PFDN5 in sera from AS with uveitis patients were significantly higher than those in AS without uveitis. At week 8, half of curdlan-treated SKG mice developed anterior uveitis, while all of them developed histologically confirmed uveitis at week 16. The levels of anti-PFDN5 antibodies increased over time in the sera of curdlan-treated SKG mice along with increased expression of PFDN5 and apoptosis in the ocular lesions. Knockdown of PFDN5 in ARPE19 cells resulted in increased apoptosis, suggesting a protective role of PFDN5 against cell death in uveitis. Conclusion: AS patients with uveitis have increased levels of anti-PFDN5 antibodies, and our findings suggest that anti-PFDN5 antibodies could provide a biomarker for uveitis in AS.
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Affiliation(s)
- Oh Chan Kwon
- Division of Rheumatology, Department of Medicine, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, South Korea
| | - Eun-Ju Lee
- Division of Rheumatology, Department of Medicine, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, South Korea.,Asan Institute for Life Science, Asan Medical Center, Seoul, South Korea
| | - Joo Yong Lee
- Department of Ophthalmology, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, South Korea
| | - Jeehee Youn
- Department of Anatomy and Cell Biology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Tae-Hwan Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Seokchan Hong
- Division of Rheumatology, Department of Medicine, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, South Korea
| | - Chang-Keun Lee
- Division of Rheumatology, Department of Medicine, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, South Korea
| | - Bin Yoo
- Division of Rheumatology, Department of Medicine, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, South Korea
| | - William H Robinson
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, United States
| | - Yong-Gil Kim
- Division of Rheumatology, Department of Medicine, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, South Korea
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Abstract
Molecular chaperones promote the correct folding of proteins in aggregation-prone cellular environments by stabilizing nascent polypeptide chains and providing appropriate folding conditions. Prefoldins (PFDs) are molecular chaperones found in archaea and eukaryotes, generally characterized by a unique jellyfish-like hexameric structure consisting of a rigid beta-barrel backbone with protruding flexible coiled-coils. Unlike eukaryotic PFDs that mainly interact with cytoskeletal components, archaeal PFDs can stabilize a wide range of substrates; such versatility reflects PFD's role as a key element in archaeal chaperone systems, which often lack general nascent-chain binding chaperone components such as Hsp70. While archaeal PFDs mainly exist as hexameric complexes, their structural diversity ranges from tetramers to filamentous oligomers. PFDs bind and stabilize nonnative proteins using varying numbers of coiled-coils, and subsequently transfer the substrate to a group II chaperonin (CPN) for refolding. The distinct structure and specific function of archaeal PFDs have been exploited for a broad range of applications in biotechnology; furthermore, a filament-forming variant of PFD has been used to fabricate nanoscale architectures of defined shapes, demonstrating archaeal PFDs' potential applicability in nanotechnology.
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Affiliation(s)
- Samuel Lim
- Department of Chemical and Biological Engineering, University of California, Berkeley, CA, USA
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Douglas S Clark
- Department of Chemical and Biological Engineering, University of California, Berkeley, CA, USA.
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10
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Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly. Sci Rep 2018; 8:13712. [PMID: 30209338 PMCID: PMC6135828 DOI: 10.1038/s41598-018-32009-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/24/2018] [Indexed: 01/27/2023] Open
Abstract
HDAC1 and HDAC2 are components of several corepressor complexes (NuRD, Sin3, CoREST and MiDAC) that regulate transcription by deacetylating histones resulting in a more compact chromatin environment. This limits access of transcriptional machinery to genes and silences transcription. While using an AP-MS approach to map HDAC1/2 protein interaction networks, we noticed that N-terminally tagged versions of HDAC1 and HDAC2 did not assemble into HDAC corepressor complexes as expected, but instead appeared to be stalled with components of the prefoldin-CCT chaperonin pathway. These N-terminally tagged HDACs were also catalytically inactive. In contrast to the N-terminally tagged HDACs, C-terminally tagged HDAC1 and HDAC2 captured complete histone deacetylase complexes and the purified proteins had deacetylation activity that could be inhibited by SAHA (Vorinostat), a Class I/II HDAC inhibitor. This tag-mediated reprogramming of the HDAC1/2 protein interaction network suggests a mechanism whereby HDAC1 is first loaded into the CCT complex by prefoldin to complete folding, and then assembled into active, functional HDAC complexes. Imaging revealed that the prefoldin subunit VBP1 colocalises with nuclear HDAC1, suggesting that delivery of HDAC1 to the CCT complex happens in the nucleus.
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Expression, Functional Characterization, and Preliminary Crystallization of the Cochaperone Prefoldin from the Thermophilic Fungus Chaetomium thermophilum. Int J Mol Sci 2018; 19:ijms19082452. [PMID: 30126249 PMCID: PMC6121465 DOI: 10.3390/ijms19082452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/15/2018] [Accepted: 08/15/2018] [Indexed: 02/07/2023] Open
Abstract
Prefoldin is a hexameric molecular chaperone found in the cytosol of archaea and eukaryotes. Its hexameric complex is built from two related classes of subunits, and has the appearance of a jellyfish: Its body consists of a double β-barrel assembly with six long tentacle-like coiled coils protruding from it. Using the tentacles, prefoldin captures an unfolded protein substrate and transfers it to a group II chaperonin. Based on structural information from archaeal prefoldins, mechanisms of substrate recognition and prefoldin-chaperonin cooperation have been investigated. In contrast, the structure and mechanisms of eukaryotic prefoldins remain unknown. In this study, we succeeded in obtaining recombinant prefoldin from a thermophilic fungus, Chaetomium thermophilum (CtPFD). The recombinant CtPFD could not protect citrate synthase from thermal aggregation. However, CtPFD formed a complex with actin from chicken muscle and tubulin from porcine brain, suggesting substrate specificity. We succeeded in observing the complex formation of CtPFD and the group II chaperonin of C. thermophilum (CtCCT) by atomic force microscopy and electron microscopy. These interaction kinetics were analyzed by surface plasmon resonance using Biacore. Finally, we have shown the transfer of actin from CtPFD to CtCCT. The study of the folding pathway formed by CtPFD and CtCCT should provide important information on mechanisms of the eukaryotic prefoldin–chaperonin system.
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12
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Sahlan M, Zako T, Yohda M. Prefoldin, a jellyfish-like molecular chaperone: functional cooperation with a group II chaperonin and beyond. Biophys Rev 2018; 10:339-345. [PMID: 29427249 DOI: 10.1007/s12551-018-0400-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/23/2018] [Indexed: 01/04/2023] Open
Abstract
Prefoldin is a hexameric molecular chaperone found in the cytosol of archaea and eukaryotes. Its hexameric complex is built from two related classes of subunits and has the appearance of a jellyfish: its body consists of a double beta-barrel assembly with six long tentacle-like coiled coils protruding from it. Using the tentacles, prefoldin captures an unfolded protein substrate and transfers it to a group II chaperonin. The prefoldin-group II chaperonin system is thought to be important for the folding of newly synthesized proteins and for their maintenance, or proteostasis, in the cytosol. Based on structural information of archaeal prefoldins, the mechanisms of substrate recognition and prefoldin-chaperonin cooperation have been investigated. In contrast, the role and mechanism of eukaryotic PFDs remain unknown. Recent studies have shown that prefoldin plays an important role in proteostasis and is involved in various diseases. In this paper, we review a series of studies on the molecular mechanisms of archaeal prefoldins and introduce recent findings about eukaryotic prefoldin.
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Affiliation(s)
- Muhamad Sahlan
- Department of Chemical Engineering, Universitas Indonesia, Depok, Indonesia
- Research Centre for Biomedical Engineering, Faculty of Engineering, Universitas Indonesia, Depok, Indonesia
| | - Tamotsu Zako
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-4-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan.
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Peng S, Chu Z, Lu J, Li D, Wang Y, Yang S, Zhang Y. Heterologous Expression of Chaperones from Hyperthermophilic Archaea Inhibits Aminoglycoside-Induced Protein Misfolding in Escherichia coli. BIOCHEMISTRY (MOSCOW) 2017; 82:1169-1175. [PMID: 29037137 DOI: 10.1134/s0006297917100091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Aminoglycoside antibiotics affect protein translation fidelity and lead to protein aggregation and an increase in intracellular oxidative stress level as well. The overexpression of the chaperonin GroEL/GroES system promotes short-term tolerance to aminoglycosides in Escherichia coli. Here, we demonstrated that the coexpression of prefoldin or Hsp60 originating from the hyperthermophilic archaeon Pyrococcus furiosus in E. coli cells can rescue cell growth and inhibit protein aggregation induced by streptomycin exposure. The results of our study show that hyperthermophilic chaperones endow E. coli with a higher tolerance to streptomycin than the GroEL/GroES system, and that they exert better effects on the reduction of intracellular protein misfolding, indicating that these chaperones have unique features and functions.
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Affiliation(s)
- S Peng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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Zako T, Sahlan M, Fujii S, Yamamoto YY, Tai PT, Sakai K, Maeda M, Yohda M. Contribution of the C-Terminal Region of a Group II Chaperonin to its Interaction with Prefoldin and Substrate Transfer. J Mol Biol 2016; 428:2405-2417. [DOI: 10.1016/j.jmb.2016.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/23/2016] [Accepted: 04/04/2016] [Indexed: 11/28/2022]
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15
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Glover DJ, Clark DS. Oligomeric assembly is required for chaperone activity of the filamentous γ-prefoldin. FEBS J 2015; 282:2985-97. [DOI: 10.1111/febs.13341] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/17/2015] [Accepted: 06/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Dominic J. Glover
- Department of Chemical and Biomolecular Engineering; University of California; Berkeley CA USA
| | - Douglas S. Clark
- Department of Chemical and Biomolecular Engineering; University of California; Berkeley CA USA
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Sahlan M, Kanzaki T, Zako T, Maeda M, Yohda M. Analysis of the interaction mode between hyperthermophilic archaeal group II chaperonin and prefoldin using a platform of chaperonin oligomers of various subunit arrangements. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1804:1810-6. [PMID: 20451672 DOI: 10.1016/j.bbapap.2010.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 04/21/2010] [Accepted: 04/26/2010] [Indexed: 10/19/2022]
Abstract
Prefoldin is a co-chaperone that captures an unfolded protein substrate and transfers it to the group II chaperonin for completion of protein folding. Group II chaperonin of a hyperthermophilic archaeon, Thermococcus strain KS-1, interacts and cooperates with archaeal prefoldins. Although the interaction sites within chaperonin and prefoldin have been analyzed, the binding mode between jellyfish-like hexameric prefoldin and the double octameric ring group II chaperonin remains unclear. As prefoldin binds the chaperonin beta subunit more strongly than the alpha subunit, we analyzed the binding mode between prefoldin and chaperonin in the context of Thermococcus group II chaperonin complexes of various subunit compositions and arrangements. The oligomers exhibited various affinities for prefoldins according to the number and order of subunits. Binding affinity increased with the number of Cpnbeta subunits. Interestingly, chaperonin complexes containing two beta subunits adjacently exhibited stronger affinities than other chaperonin complexes containing the same number of beta subunits. The result suggests that all four beta tentacles of prefoldin interact with the helical protrusions of CPN in the PFD-CPN complex as the previously proposed model that two adjacent PFD beta subunits seem to interact with two CPN adjacent subunits.
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Affiliation(s)
- Muhamad Sahlan
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
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Sahlan M, Zako T, Tai PT, Ohtaki A, Noguchi K, Maeda M, Miyatake H, Dohmae N, Yohda M. Thermodynamic characterization of the interaction between prefoldin and group II chaperonin. J Mol Biol 2010; 399:628-36. [PMID: 20434454 DOI: 10.1016/j.jmb.2010.04.046] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 04/20/2010] [Accepted: 04/23/2010] [Indexed: 11/16/2022]
Abstract
Prefoldin (PFD) is a hexameric chaperone that captures a protein substrate and transfers it to a group II chaperonin (CPN) to complete protein folding. We have studied the interaction between PFD and CPN using those from a hyperthermophilic archaeon, Thermococcus strain KS-1 (T. KS-1). In this study, we determined the crystal structure of the T. KS-1 PFDbeta2 subunit and characterized the interactions between T. KS-1 CPNs (CPNalpha and CPNbeta) and T. KS-1 PFDs (PFDalpha1-beta1 and PFDalpha2-beta2). As predicted from its amino acid sequence, the PFDbeta2 subunit conforms to a structure similar to those of the PFDbeta1 subunit and the Pyrococcus horikoshii OT3 PFDbeta subunit, with the exception of the tip of its coiled-coil domain, which is thought to be the CPN interaction site. The interactions between T. KS-1 CPNs and PFDs (CPNalpha and PFDalpha1-beta1; CPNalpha and PFDalpha2-beta2; CPNbeta and PFDalpha1-beta1; and CPNbeta and PFDalpha2-beta2) were analyzed using the Biacore T100 system at various temperatures ranging from 20 to 45 degrees C. The affinities between PFDs and CPNs increased with an increase in temperature. The thermodynamic parameters calculated from association constants showed that the interaction between PFD and CPN is entropy driven. Among the four combinations of PFD-CPN interactions, the entropy difference in binding between CPNbeta and PFDalpha2-beta2 was the largest, and affinity significantly increased at higher temperatures. Considering that expression of PFDalpha2-beta2 and CPNbeta subunit is induced upon heat shock, our results suggest that PFDalpha1-beta1 is a general PFD for T. KS-1 CPNs, whereas PFDalpha2-beta2 is specific for CPNbeta.
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Affiliation(s)
- Muhamad Sahlan
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
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Abstract
Alzheimer's disease (AD) is an age-related, progressive degenerative disorder that is characterized by synapse and neuron loss in the brain and the accumulation of protein-containing deposits (referred to as 'senile plaques') and neurofibrillary tangles. Insoluble amyloid beta-peptide (Abeta) fibrillar aggregates found in extracellular plaques have long been thought to cause the neurodegenerative cascades of AD. However, accumulating evidence suggests that prefibrillar soluble Abeta oligomers induce AD-related synaptic dysfunction. The size of Abeta oligomers is distributed over a wide molecular weight range (from < 10 kDa to > 100 kDa), with structural polymorphism in Abeta oligomers of similar sizes. Recent studies have demonstrated that Abeta can accumulate in living cells, as well as in extracellular spaces. This review summarizes current research on Abeta oligomers, focusing on their structures and toxicity mechanism. We also discuss possible formation mechanisms of intracellular and extracellular Abeta oligomers.
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Affiliation(s)
- Masafumi Sakono
- Bioengineering Laboratory, RIKEN Institute, Wako, Saitama, Japan
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Zako T, Banba S, Sahlan M, Sakono M, Terada N, Yohda M, Maeda M. Hyperthermophilic archaeal prefoldin shows refolding activity at low temperature. Biochem Biophys Res Commun 2010; 391:467-70. [DOI: 10.1016/j.bbrc.2009.11.081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Accepted: 11/11/2009] [Indexed: 11/15/2022]
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21
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Bando K, Zako T, Sakono M, Maeda M, Wada T, Nishijima M, Fukuhara G, Yang C, Mori T, Pace TCS, Bohne C, Inoue Y. Bio-supramolecular photochirogenesis with molecular chaperone: enantiodifferentiating photocyclodimerization of 2-anthracenecarboxylate mediated by prefoldin. Photochem Photobiol Sci 2010; 9:655-60. [DOI: 10.1039/b9pp00186g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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22
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An exceptionally stable Group II chaperonin from the hyperthermophile Pyrococcus furiosus. Arch Biochem Biophys 2009; 486:12-8. [PMID: 19298788 DOI: 10.1016/j.abb.2009.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 03/04/2009] [Accepted: 03/06/2009] [Indexed: 11/21/2022]
Abstract
The hyperthermophilic archaeon Pyrococcus furiosus (Pf) grows optimally at 100 degrees C and encodes single genes for the Group II chaperonin (Cpn), Pf Cpn and alpha-crystallin homolog, the small Heat shock protein (sHsp). Recombinant Pf Cpn is exceptionally thermostable and remained active in high ionic strength, and up to 3M guanidine hydrochloride (Gdn-HCl). Pf Cpn bound specifically to denatured lysozyme and ATP addition resulted in protection of lysozyme from aggregation and inactivation at 100 degrees C. While complexed to heat inactivated lysozyme, Pf Cpn showed enhanced thermostability and ATPase activity, and increased the optimal temperature for ATPase activity from 90 to 100 degrees C. Protein substrate binding also stabilized the 16-mer oligomer of Pf Cpn in 3M Gdn-HCl and activated ATPase hydrolysis in 3-5M Gdn-HCl. In addition, Pf Cpn recognized and refolded the non-native lysozyme released from Pf sHsp, consistent with the inferred functions of these chaperones as the primary protein folding pathway during cellular heat shock.
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Construction and characterization of the hetero-oligomer of the group II chaperonin from the hyperthermophilic archaeon, Thermococcus sp. strain KS-1. Extremophiles 2009; 13:437-45. [PMID: 19229501 DOI: 10.1007/s00792-009-0229-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 01/27/2009] [Indexed: 01/16/2023]
Abstract
The hyperthermophilic archaeon Thermococcus sp. strain KS-1 (T. KS-1) expresses two different chaperonin subunits, alpha and beta, for the folding of its proteins. The composition of the subunits in the hexadecameric double ring changes with temperature. The content of the beta subunit significantly increases according to the increase in temperature. The homo-oligomer of the beta subunit, Cpn beta, is more thermostable than that of the alpha subunit, Cpn alpha. Since Cpn alpha and Cpn beta also have different protein folding activities and interactions with prefoldin, the hetero-oligomer is thought to exhibit different characteristics according to the content of subunits. The hetero-oligomer of the T. KS-1 chaperonin has not been studied, however, because the alpha and beta subunits form hetero-oligomers of varying compositions when they are expressed simultaneously. In this study, we characterized the T. KS-1 chaperonin hetero-oligomer, Cpn alphabeta, containing both alpha and beta in the alternate order, which was constructed by the expression of alpha and beta subunits in a coordinated fashion and protease digestion. Cpn alphabeta protected citrate synthase from thermal aggregation, promoted the folding of acid-denatured GFP in an ATP-dependent manner, and exhibited an ATP-dependent conformational change. The yield of refolded GFP generated by Cpn alphabeta was almost equivalent to that generated by Cpn beta but lower than that generated by Cpn alpha. In contrast, Cpn alphabeta exhibited almost the same level of thermal stability as Cpn alpha, which was lower than that of Cpn beta. The affinity of Cpn alphabeta to prefoldin was found to be between those of Cpn alpha and Cpn beta, as expected.
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Kida H, Sugano Y, Iizuka R, Fujihashi M, Yohda M, Miki K. Structural and Molecular Characterization of the Prefoldin β Subunit from Thermococcus Strain KS-1. J Mol Biol 2008; 383:465-74. [DOI: 10.1016/j.jmb.2008.08.041] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Revised: 08/12/2008] [Accepted: 08/14/2008] [Indexed: 11/24/2022]
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25
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Sakono M, Zako T, Ueda H, Yohda M, Maeda M. Formation of highly toxic soluble amyloid beta oligomers by the molecular chaperone prefoldin. FEBS J 2008; 275:5982-93. [DOI: 10.1111/j.1742-4658.2008.06727.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Expression Profiles and Physiological Roles of Two Types of Prefoldins from the Hyperthermophilic Archaeon Thermococcus kodakaraensis. J Mol Biol 2008; 382:298-311. [DOI: 10.1016/j.jmb.2008.07.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Revised: 07/11/2008] [Accepted: 07/14/2008] [Indexed: 11/21/2022]
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27
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Iizuka R, Sugano Y, Ide N, Ohtaki A, Yoshida T, Fujiwara S, Imanaka T, Yohda M. Functional Characterization of Recombinant Prefoldin Complexes from a Hyperthermophilic Archaeon, Thermococcus sp. Strain KS-1. J Mol Biol 2008; 377:972-83. [DOI: 10.1016/j.jmb.2008.01.070] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 01/07/2008] [Accepted: 01/22/2008] [Indexed: 11/30/2022]
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28
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Ohtaki A, Kida H, Miyata Y, Ide N, Yonezawa A, Arakawa T, Iizuka R, Noguchi K, Kita A, Odaka M, Miki K, Yohda M. Structure and Molecular Dynamics Simulation of Archaeal Prefoldin: The Molecular Mechanism for Binding and Recognition of Nonnative Substrate Proteins. J Mol Biol 2008; 376:1130-41. [DOI: 10.1016/j.jmb.2007.12.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Revised: 11/28/2007] [Accepted: 12/05/2007] [Indexed: 10/22/2022]
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29
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Effective approaches for the production of heterologous proteins using the Thermococcus kodakaraensis-based translation system. J Biotechnol 2008; 133:177-82. [DOI: 10.1016/j.jbiotec.2007.08.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 08/09/2007] [Accepted: 08/22/2007] [Indexed: 11/17/2022]
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30
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Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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