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Sun X, Ferguson JA, Leach BI, Stanfield RL, Dyson HJ, Wright PE. Probing the Dissociation Pathway of a Kinetically Labile Transthyretin Mutant. J Am Chem Soc 2024; 146:532-542. [PMID: 38134439 PMCID: PMC10926950 DOI: 10.1021/jacs.3c10083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Aggregation of transthyretin (TTR) is associated with devastating amyloid diseases. Amyloidosis begins with the dissociation of the native homotetramer (a dimer of dimers) to form a monomeric intermediate that assembles into pathogenic aggregates. This process is accelerated in vitro at low pH, but the process by which TTR dissociates and reassembles at neutral pH remains poorly characterized due to the low population of intermediates. Here, we use 19F-nuclear magnetic resonance (NMR) and a highly sensitive trifluoromethyl probe to determine the relative populations of the species formed by the dissociation of a destabilized variant, A25T. The A25T mutation perturbs both the strong dimer and weak dimer-dimer interfaces. A tetramer ⇌ dimer ⇌ monomer (TDM) equilibrium model is proposed to account for concentration- and temperature-dependent population changes. Thermodynamic and kinetic parameters and activation energetics for dissociation of the native A25T tetramer, as well as a destabilized alternative tetramer (T*) with a mispacked F87 side chain, were extracted by van't Hoff and 19F-NMR line shape analysis, saturation transfer, and transition state theory. Chemical shifts for the dimer and T* species are degenerate for 19F and methyl probes close to the strong dimer interface, implicating interfacial perturbation as a common structural feature of these destabilized species. All-atom molecular dynamics simulations further suggest more frequent F87 ring flipping on the nanosecond time scale in the A25T dimer than in the native A25T tetramer. Our integrated approach offers quantitative insights into the energy landscape of the dissociation pathway of TTR at neutral pH.
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Affiliation(s)
- Xun Sun
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - James A Ferguson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Benjamin I Leach
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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2
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Ghosh S, Villacorta-Martin C, Lindstrom-Vautrin J, Kenney D, Golden CS, Edwards CV, Sanchorawala V, Connors LH, Giadone RM, Murphy GJ. Mapping cellular response to destabilized transthyretin reveals cell- and amyloidogenic protein-specific signatures. Amyloid 2023; 30:379-393. [PMID: 37439769 DOI: 10.1080/13506129.2023.2224494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/04/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND In ATTR amyloidosis, transthyretin (TTR) protein is secreted from the liver and deposited as toxic aggregates at downstream target tissues. Despite recent advancements in treatments for ATTR amyloidosis, the mechanisms underlying misfolded TTR-mediated cellular damage remain elusive. METHODS In an effort to define early events of TTR-associated stress, we exposed neuronal (SH-SY5Y) and cardiac (AC16) cells to wild-type and destabilized TTR variants (TTRV122I (p.V142I) and TTRL55P (p.L70P)) and performed transcriptional (RNAseq) and epigenetic (ATACseq) profiling. We subsequently compared TTR-responsive signatures to cells exposed to destabilized antibody light chain protein associated with AL amyloidosis as well as ER stressors (thapsigargin, heat shock). RESULTS In doing so, we observed overlapping, yet distinct cell type- and amyloidogenic protein-specific signatures, suggesting unique responses to each amyloidogenic variant. Moreover, we identified chromatin level changes in AC16 cells exposed to mutant TTR that resolved upon pre-incubation with kinetic stabilizer tafamidis. CONCLUSIONS Collectively, these data provide insight into the mechanisms underlying destabilized protein-mediated cellular damage and provide a robust resource representing cellular responses to aggregation-prone proteins and ER stress.
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Affiliation(s)
- Sabrina Ghosh
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
| | | | | | - Devin Kenney
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Carly S Golden
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Camille V Edwards
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
- Amyloidosis Center, Alan and Sandra Gerry Amyloid Research Laboratory, Boston University School of Medicine, Boston, MA, USA
| | - Vaishali Sanchorawala
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
- Amyloidosis Center, Alan and Sandra Gerry Amyloid Research Laboratory, Boston University School of Medicine, Boston, MA, USA
| | - Lawreen H Connors
- Amyloidosis Center, Alan and Sandra Gerry Amyloid Research Laboratory, Boston University School of Medicine, Boston, MA, USA
| | - Richard M Giadone
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
| | - George J Murphy
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
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3
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Sakono M, Nakamura M, Ohshima T, Miyakoshi A, Arai R, Minamihata K, Kamiya N. One-pot synthesis of fibrillar-shaped functional nanomaterial using microbial transglutaminase. J Biosci Bioeng 2023; 135:440-446. [PMID: 37088672 DOI: 10.1016/j.jbiosc.2023.03.015] [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: 06/16/2022] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/25/2023]
Abstract
Recently, functional nanowire production using amyloids as a scaffold for protein immobilization has attracted attention. However, protein immobilization on amyloid fibrils often caused protein inactivation. In this study, we investigated protein immobilization using enzymatic peptide ligation to suppress protein inactivation during immobilization. We attempted to immobilize functional molecules such as green fluorescent protein (GFP) and Nanoluc to a transthyretin (TTR) amyloid using microbial transglutaminase (MTG), which links the glutamine side chain to the primary amine. Linkage between amyloid fibrils and functional molecules was achieved through the MTG substrate sequence, and the functional molecules-loaded nanowires were successfully fabricated. We also found that the synthetic process from amyloidization to functional molecules immobilization could be achieved in a single-step procedure.All rights reserved.
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Affiliation(s)
- Masafumi Sakono
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama 930-8555, Japan.
| | - Mitsuki Nakamura
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama 930-8555, Japan
| | - Tatsuki Ohshima
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama 930-8555, Japan
| | - Ayano Miyakoshi
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama 930-8555, Japan
| | - Ryoichi Arai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda, Nagano 386-8567, Japan; Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Kosuke Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan; Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Mootoka, Nishi-Ku, Fukuoka 819-0395, Japan
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4
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Wang Y, Huang C, Liou G, Hsueh H, Liang C, Tseng H, Huang S, Chao C, Hsieh S, Tzeng S. A molecular basis for tetramer destabilization and aggregation of transthyretin Ala97Ser. Protein Sci 2023; 32:e4610. [PMID: 36851846 PMCID: PMC10037696 DOI: 10.1002/pro.4610] [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: 08/22/2022] [Revised: 02/02/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
Transthyretin (TTR)-related amyloidosis (ATTR) is a syndrome of diseases characterized by the extracellular deposition of fibrillar materials containing TTR variants. Ala97Ser (A97S) is the major mutation reported in Taiwanese ATTR patients. Here, we combine atomic resolution structural information together with the biochemical data to demonstrate that substitution of polar Ser for a small hydrophobic side chain of Ala at residue 97 of TTR largely influences the local packing density of the FG-loop, thus leading to the conformational instability of native tetramer, the increased monomeric species, and thus the enhanced amyloidogenicity of apo-A97S. Based on calorimetric studies, the tetramer destabilization of A97S can be substantially altered by interacting with native stabilizers via similarly energetic patterns compared to that of wild-type (WT) TTR; however, stabilizer binding partially rearranges the networks of hydrogen bonding in TTR variants while FG-loops of tetrameric A97S still remain relatively flexible. Moreover, TTR in complexed with holo-retinol binding protein 4 is slightly influenced by the structural and dynamic changes of FG-loop caused by A97S substitution with an approximately five-fold difference in binding affinity. Collectively, our findings suggest that the amyloidogenic A97S mutation destabilizes TTR by increasing the flexibility of the FG-loop in the monomer, thus modulating the rate of amyloid fibrillization.
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Affiliation(s)
- Yi‐Shiang Wang
- Institute of Biochemistry and Molecular BiologyCollege of Medicine, National Taiwan UniversityTaipeiTaiwan
| | - Chun‐Hsiang Huang
- Protein diffraction group, Experimental instrumentation divisionNational Synchrotron Radiation Research CenterHsinchuTaiwan
| | - Gunn‐Guang Liou
- Office of Research and Development, College of MedicineNational Taiwan UniversityTaipeiTaiwan
| | - Hsueh‐Wen Hsueh
- Department of Anatomy and Cell Biology, College of MedicineNational Taiwan UniversityTaipeiTaiwan
| | - Chi‐Ting Liang
- Institute of Biochemistry and Molecular BiologyCollege of Medicine, National Taiwan UniversityTaipeiTaiwan
| | - Hsi‐Ching Tseng
- Instrumentation CenterNational Taiwan UniversityTaipeiTaiwan
| | | | - Chi‐Chao Chao
- Department of NeurologyNational Taiwan University HospitalTaipeiTaiwan
| | - Sung‐Tsang Hsieh
- Graduate Institute of Brain and Mind SciencesTaipeiTaiwan
- Graduate Institute of Clinical MedicineTaipeiTaiwan
- Center of Precision MedicineNational Taiwan University College of MedicineTaipeiTaiwan
| | - Shiou‐Ru Tzeng
- Institute of Biochemistry and Molecular BiologyCollege of Medicine, National Taiwan UniversityTaipeiTaiwan
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5
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Lee SB, Yu J, Kim H, Kim KW, Jeong JW, Kim YL, Park SJ, Koo TS, Lee C, Hong KB, Choi S. Novel Strategy To Inhibit Transthyretin Amyloidosis via the Synergetic Effect of Chemoselective Acylation and Noncovalent Inhibitor Release. J Med Chem 2023; 66:2893-2903. [PMID: 36749109 DOI: 10.1021/acs.jmedchem.2c01926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Strategies for developing targeted covalent inhibitors (TCIs), which have the advantages of a prolonged duration of action and selectivity toward a drug target, have attracted great interest in drug discovery. Herein, we report chemoselective covalent inhibitors that specifically target lysine ε-amine groups that conjugate with an endogenous protein to prevent disease-causing protein misfolding and aggregation. These TCIs are unique because the benzoyl group is preferentially conjugated to Lys15 at the top of the T4 binding site within transthyretin (TTR) while simultaneously releasing a potent noncovalent TTR kinetic stabilizer. The potency of these covalent inhibitors is superior to tafamidis, the only FDA-approved drug for the treatment of hereditary TTR amyloidosis. In addition to investigations into the covalent modification of TTR via reverse-phase high-performance liquid chromatography, direct methods are performed to confirm and visualize the presumed covalent interaction via mass spectrometry and X-ray crystallography.
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Affiliation(s)
- Seok Beom Lee
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Jaeni Yu
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Hyunwoo Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kun Woo Kim
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Jong Woo Jeong
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Yun Lan Kim
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Sung Jean Park
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, Republic of Korea
| | - Tae-Sung Koo
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Changwook Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ki Bum Hong
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, Republic of Korea
| | - Sungwook Choi
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
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6
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Duan G, Li Y, Ye M, Liu H, Wang N, Luo S. The Regulatory Mechanism of Transthyretin Irreversible Aggregation through Liquid-to-Solid Phase Transition. Int J Mol Sci 2023; 24:ijms24043729. [PMID: 36835140 PMCID: PMC9960511 DOI: 10.3390/ijms24043729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
Transthyretin (TTR) aggregation and amyloid formation are associated with several ATTR diseases, such as senile systemic amyloidosis (SSA) and familial amyloid polyneuropathy (FAP). However, the mechanism that triggers the initial pathologic aggregation process of TTR remains largely elusive. Lately, increasing evidence has suggested that many proteins associated with neurodegenerative diseases undergo liquid-liquid phase separation (LLPS) and subsequent liquid-to-solid phase transition before the formation of amyloid fibrils. Here, we demonstrate that electrostatic interactions mediate LLPS of TTR, followed by a liquid-solid phase transition, and eventually the formation of amyloid fibrils under a mildly acidic pH in vitro. Furthermore, pathogenic mutations (V30M, R34T, and K35T) of TTR and heparin promote the process of phase transition and facilitate the formation of fibrillar aggregates. In addition, S-cysteinylation, which is a kind of post-translational modification of TTR, reduces the kinetic stability of TTR and increases the propensity for aggregation, while another modification, S-sulfonation, stabilizes the TTR tetramer and reduces the aggregation rate. Once TTR was S-cysteinylated or S-sulfonated, they dramatically underwent the process of phase transition, providing a foundation for post-translational modifications that could modulate TTR LLPS in the context of pathological interactions. These novel findings reveal molecular insights into the mechanism of TTR from initial LLPS and subsequent liquid-to-solid phase transition to amyloid fibrils, providing a new dimension for ATTR therapy.
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7
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Mizuguchi M, Nakagawa Y, Inui K, Katayama W, Sawai Y, Shimane A, Kitakami R, Okada T, Nabeshima Y, Yokoyama T, Kanamitsu K, Nakagawa S, Toyooka N. Chlorinated Naringenin Analogues as Potential Inhibitors of Transthyretin Amyloidogenesis. J Med Chem 2022; 65:16218-16233. [PMID: 36472374 DOI: 10.1021/acs.jmedchem.2c00511] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Misfolding and aggregation of transthyretin are implicated in the fatal systemic disease known as transthyretin amyloidosis. Here, we report the development of a naringenin derivative bearing two chlorine atoms that will be efficacious for preventing aggregation of transthyretin in the eye. The amyloid inhibitory activity of the naringenin derivative was as strong as that of tafamidis, which is the first therapeutic agent targeting transthyretin in the plasma. X-ray crystal structures of the compounds in complex with transthyretin demonstrated that the naringenin derivative with one chlorine bound to the thyroxine-binding site of transthyretin in the forward mode and that the derivative with two chlorines bound to it in the reverse mode. An ex vivo competitive binding assay showed that naringenin derivatives exhibited more potent binding than tafamidis in the plasma. Furthermore, an in vivo pharmacokinetic study demonstrated that the dichlorinated derivative was significantly delivered to the eye.
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Affiliation(s)
- Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Yusuke Nakagawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Japan
| | - Kishin Inui
- Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Wakana Katayama
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Yurika Sawai
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Ayaka Shimane
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Ryota Kitakami
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Takuya Okada
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Kayoko Kanamitsu
- Drug Discovery Initiative, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shinsaku Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Naoki Toyooka
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan
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8
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Dasari AKR, Yi S, Coats MF, Wi S, Lim KH. Toxic Misfolded Transthyretin Oligomers with Different Molecular Conformations Formed through Distinct Oligomerization Pathways. Biochemistry 2022; 61:2358-2365. [PMID: 36219173 PMCID: PMC9665167 DOI: 10.1021/acs.biochem.2c00390] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein aggregation is initiated by structural changes from native polypeptides to cytotoxic oligomers, which form cross-β structured amyloid. Identification and characterization of oligomeric intermediates are critically important for understanding not only the molecular mechanism of aggregation but also the cytotoxic nature of amyloid oligomers. Preparation of misfolded oligomers for structural characterization is, however, challenging because of their transient, heterogeneous nature. Here, we report two distinct misfolded transthyretin (TTR) oligomers formed through different oligomerization pathways. A pathogenic TTR variant with a strong aggregation propensity (L55P) was used to prepare misfolded oligomers at physiological pH. Our mechanistic studies showed that the full-length TTR initially forms small oligomers, which self-assemble into short protofibrils at later stages. Enzymatic cleavage of the CD loop was also used to induce the formation of N-terminally truncated oligomers, which was detected in ex vivo cardiac TTR aggregates extracted from the tissues of patients. Structural characterization of the oligomers using solid-state nuclear magnetic resonance and circular dichroism revealed that the two TTR misfolded oligomers have distinct molecular conformations. In addition, the proteolytically cleaved TTR oligomers exhibit a higher surface hydrophobicity, suggesting the presence of distinct oligomerization pathways for TTR oligomer formation. Cytotoxicity assays also revealed that the cytotoxicity of cleaved oligomers is stronger than that of the full-length TTR oligomers, indicating that hydrophobicity might be an important property of toxic oligomers. These comparative biophysical analyses suggest that the toxic cleaved TTR oligomers formed through a different misfoling pathway may adopt distinct structural features that produce higher surface hydrophobicity, leading to the stronger cytotoxic activities.
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Affiliation(s)
- Anvesh K. R. Dasari
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Sujung Yi
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Matthew F. Coats
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Sungsool Wi
- Interdisciplinary Magnetic Resonance (CIMAR), National High Magnetic Field Laboratory (NHMFL), 1800 East, Paul Dirac Dr., Tallahassee, FL 32310, USA
| | - Kwang Hun Lim
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
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9
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Chu X, Wang M, Tang R, Huang Y, Yu J, Cao Y, Zheng Y, Xie Z, Deng J, Wang Z, Ma W, Song W, Wu Y, Lv H, Zhang W, Wang Z, Yuan Y, Liu Y, Meng L. Clinical and biochemical characterization of hereditary transthyretin amyloidosis caused by E61K mutation. Front Mol Neurosci 2022; 15:1003303. [PMID: 36311011 PMCID: PMC9596982 DOI: 10.3389/fnmol.2022.1003303] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
Objects: This study was intended to find out more about the clinical characterizations of patients carrying transthyretin (TTR) E61K (p.Glu81Lys) gene mutation and the biochemical characterization of this mutant protein. Materials and methods: Five patients who had been diagnosed with hereditary transthyretin amyloidosis and two asymptomatic carriers carrying TTR E61K gene mutation were reported. Biochemical and biophysical tests were conducted to observe the thermodynamic and kinetic stability. Fibril formation tests measured by turbidity assay were performed to explore the pathogenicity of this mutation. Kinetic stabilizer responsiveness was measured to determine the inhibitory effect on protein aggregation. Results: The average age of onset for the five patients was 62 years, and the course of the disease ranged from 2 to 10 years. Cardiac disease was prominent in this group of patients. Nerve pathology revealed a mildly to moderately reduced myelinated fiber density and muscle pathology showed predominant neurogenic impairment accompanied by possible myogenic impairment. E61K-TTR was characterized as a kinetically destabilized protein compared to WT-TTR but its thermodynamic stability was not compromised. In addition, the subunit exchange of E61K with WT-TTR further destabilized the heterozygous tetramer. Meanwhile, the E61K:WT heterozygous tetramer exhibited a poor response to kinetic stabilizers in the fibril formation assay. Finally, the serum TTR tetramer concentration was low in E61K-TTR symptomatic patients and in one asymptomatic gene carrier. Vyndamax (Tafamidis) could increase the TTR tetramer concentration. Conclusions: Patients with E61K mutation tended to be late-onset. The concentration of TTR tetramer in the serum might serve as a biomarker to monitor disease progress, therapeutic window time, and therapeutic response to TTR kinetic stabilizer drugs.
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Affiliation(s)
- Xujun Chu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ran Tang
- Dong’e County People’s Hospital, Liaocheng, China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China
| | - Jiaxi Yu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yunfeng Cao
- Shanghai Institute for Biomedical and Pharmaceutical Technologies, NHC Key Laboratory of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drug and Devices, Shanghai, China
| | - Yilei Zheng
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhiying Xie
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Zhi Wang
- Department of Cardiology, Peking University First Hospital, Beijing, China
| | - Wei Ma
- Department of Cardiology, Peking University First Hospital, Beijing, China
| | - Wenjing Song
- Department of Ophthalmology, Peking University First Hospital, Beijing, China
| | - Yuan Wu
- Department of Ophthalmology, Peking University First Hospital, Beijing, China
| | - He Lv
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China
- *Correspondence: Lingchao Meng Yu Liu orcid.org/0000-0002-0779-1488
| | - Lingchao Meng
- Department of Neurology, Peking University First Hospital, Beijing, China
- *Correspondence: Lingchao Meng Yu Liu orcid.org/0000-0002-0779-1488
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10
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The hydrophobic residue Leu73 is crucial for the high stability and low aggregation properties of murine transthyretin. Biochem J 2022; 479:1999-2011. [PMID: 36098398 DOI: 10.1042/bcj20220203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022]
Abstract
Destabilization of human transthyretin leads to its aggregation into amyloid fibrils, which causes a rare, progressive and fatal systemic disorder called ATTR amyloidosis. By contrast, murine transthyretin is known to be very stable and therefore does not aggregate into amyloid fibrils in vivo or in vitro. We examined the hydrophobic residues responsible for the high-stability and low-aggregation properties of murine transthyretin using site-directed mutagenesis. Urea-induced unfolding and thioflavin T fluorescence aggregation assay revealed that Leu73 of murine transthyretin largely contributes to its high stability and low aggregation properties: the I73L mutation stabilized human transthyretin, while the L73I mutation destabilized murine transthyretin. In addition, the I26V/I73L mutation stabilized the amyloidogenic V30M mutant of human transthyretin to the same degree as the suppressor mutation T119M, which protects transthyretin against amyloid fibril aggregation. The I73L mutation resulted in no significant differences in the overall structure of the transthyretin tetramer or the contacts of side-chains in the hydrophobic core of the monomer. We also found that Leu73 of murine transthyretin is conserved in many mammals, while Ile73 of human transthyretin is conserved in monkeys and cats. These studies will provide new insights into the stability and aggregation properties of transthyretin from various mammals.
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11
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Gao L, Xie X, Liu P, Jin J. High-avidity binding drives nucleation of amyloidogenic transthyretin monomer. JCI Insight 2022; 7:150131. [PMID: 35393947 PMCID: PMC9057628 DOI: 10.1172/jci.insight.150131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 02/23/2022] [Indexed: 11/17/2022] Open
Abstract
Amyloidosis involves stepwise growth of fibrils assembled from soluble precursors. Transthyretin (TTR) naturally folds into a stable tetramer, whereas conditions and mutations that foster aberrant monomer formations facilitate TTR oligomeric aggregation and subsequent fibril extension. We investigated the early assembly of oligomers by WT TTR compared with its V30M and V122I variants. We monitored time-dependent redistribution among monomer, dimer, tetramer, and oligomer contents in the presence and absence of multimeric TTR seeds. The seeds were artificially constructed recombinant multimers that contained 20–40 TTR subunits via engineered biotin-streptavidin (SA) interactions. As expected, these multimer seeds rapidly nucleated TTR monomers into larger complexes, while having less effect on dimers and tetramers. In vivo, SA-induced multimers formed TTR-like deposits in the heart and the kidney following i.v. injection in mice. While all 3 variants prominently deposited glomerulus in the kidney, only V30M resulted in extensive deposition in the heart. The cardiac TTR deposits varied in size and shape and were localized in the intermyofibrillar space along the capillaries. These results are consistent with the notion of monomeric TTR engaging in high-avidity interactions with tissue amyloids. Our multimeric induction approach provides a model for studying the initiation of TTR deposition in the heart.
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Affiliation(s)
- Li Gao
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.,Department of Cardiology, and
| | - Xinfang Xie
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.,Department of Nephrology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Pan Liu
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jing Jin
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
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12
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Reum Han A, Hee Jeon E, Woo Kim K, Ki Lee S, Ohn CY, Jean Park S, Sook Kang N, Koo TS, Bum Hong K, Choi S. Synthesis and biological evaluation of quinolone derivatives as transthyretin amyloidogenesis inhibitors and fluorescence sensors. Bioorg Med Chem 2022; 53:116550. [PMID: 34890995 DOI: 10.1016/j.bmc.2021.116550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 11/17/2022]
Abstract
Under certain conditions, numerous soluble proteins possess an inherent tendency to convert into insoluble amyloid aggregates, which are associated with several sporadic and genetic human diseases. Transthyretin (TTR) is one of the more than 30 human amyloidogenic proteins involved in conditions such as senile systemic amyloidosis, familial amyloid polyneuropathy, and familial amyloid cardiomyopathy. Considerable effort has been focused on identifying the native tetrameric TTR stabilizers to inhibit rate-limiting tetramer dissociation and, consequently, ameliorate TTR amyloidogenesis. Here, we describe the design and synthesis of quinolin-2(1H)-one derivatives that could be structurally complementary to the thyroxine-binding site within tetrameric TTR. Among these quinolin-2(1H)-one derivatives, compound 7a allowed 16.7% of V30M-TTR (3.6 μM) fibril formation at the same concentration and 49.6% at a concentration of 1.8 μM. Compound 7a exhibited much greater potency in complex biological samples like human plasma than that observed with tafamidis, the drug approved for the treatment of TTR amyloid cardiomyopathy for wild-type or hereditary TTR-mediated amyloidosis. Furthermore, the unique spectral properties of compound 7a demonstrated its high potential for TTR quantification, imaging sensors, and fluorescent tools to study the mechanism of TTR amyloidogenesis.
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Affiliation(s)
- Ah Reum Han
- Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejon 305-764, Republic of Korea
| | - Eun Hee Jeon
- Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejon 305-764, Republic of Korea
| | - Kun Woo Kim
- Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejon 305-764, Republic of Korea
| | - Seul Ki Lee
- Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejon 305-764, Republic of Korea
| | - Chan-Yeong Ohn
- Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejon 305-764, Republic of Korea
| | - Sung Jean Park
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, 534-2 Yeonsu 3-dong, Yeonsu-gu, Incheon 406-799, Republic of Korea
| | - Nam Sook Kang
- Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejon 305-764, Republic of Korea
| | - Tae-Sung Koo
- Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejon 305-764, Republic of Korea
| | - Ki Bum Hong
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 80 Cheombok-ro, Dong-gu, Daegu 701-310, Republic of Korea.
| | - Sungwook Choi
- Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejon 305-764, Republic of Korea.
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13
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Pacini L, Lesieur C. A computational methodology to diagnose sequence-variant dynamic perturbations by comparing atomic protein structures. Bioinformatics 2021; 38:703-709. [PMID: 34694373 PMCID: PMC8574318 DOI: 10.1093/bioinformatics/btab736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 09/29/2021] [Accepted: 10/21/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION The objective is to diagnose dynamics perturbations caused by amino-acid mutations as prerequisite to assess protein functional health or drug failure, simply using network models of protein X-ray structures. RESULTS We find that the differences in the allocation of the atomic interactions of each amino acid to 1D, 2D, 3D, 4D structural levels between variants structurally robust, recover experimental dynamic perturbations. The allocation measure validated on two B-pentamers variants of AB5 toxins having 17 mutations, also distinguishes dynamic perturbations of pathogenic and non-pathogenic Transthyretin single-mutants. Finally, the main proteases of the coronaviruses SARS-CoV and SARS-CoV-2 exhibit changes in the allocation measure, raising the possibility of drug failure despite the main proteases structural similarity. AVAILABILITY AND IMPLEMENTATION The Python code used for the production of the results is available at github.com/lorpac/protein_partitioning_atomic_contacts. The authors will run the analysis on any PDB structures of protein variants upon request. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lorenza Pacini
- AMPERE, CNRS, Université de Lyon, Lyon, 69622, France,Institut Rhônalpin des systèmes complexes (IXXI), École Normale Supérieure de Lyon, Lyon, 69007, France
| | - Claire Lesieur
- AMPERE, CNRS, Université de Lyon, Lyon, 69622, France,Institut Rhônalpin des systèmes complexes (IXXI), École Normale Supérieure de Lyon, Lyon, 69007, France,To whom correspondence should be addressed. E-mail:
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14
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Ghadie M, Xia Y. Mutation Edgotype Drives Fitness Effect in Human. FRONTIERS IN BIOINFORMATICS 2021; 1:690769. [PMID: 36303776 PMCID: PMC9581054 DOI: 10.3389/fbinf.2021.690769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 08/18/2021] [Indexed: 11/24/2022] Open
Abstract
Missense mutations are known to perturb protein-protein interaction networks (known as interactome networks) in different ways. However, it remains unknown how different interactome perturbation patterns (“edgotypes”) impact organismal fitness. Here, we estimate the fitness effect of missense mutations with different interactome perturbation patterns in human, by calculating the fractions of neutral and deleterious mutations that do not disrupt PPIs (“quasi-wild-type”), or disrupt PPIs either by disrupting the binding interface (“edgetic”) or by disrupting overall protein stability (“quasi-null”). We first map pathogenic mutations and common non-pathogenic mutations onto homology-based three-dimensional structural models of proteins and protein-protein interactions in human. Next, we perform structure-based calculations to classify each mutation as either quasi-wild-type, edgetic, or quasi-null. Using our predicted as well as experimentally determined interactome perturbation patterns, we estimate that >∼40% of quasi-wild-type mutations are effectively neutral and the remaining are mostly mildly deleterious, that >∼75% of edgetic mutations are only mildly deleterious, and that up to ∼75% of quasi-null mutations may be strongly detrimental. These estimates are the first such estimates of fitness effect for different network perturbation patterns in any interactome. Our results suggest that while mutations that do not disrupt the interactome tend to be effectively neutral, the majority of human PPIs are under strong purifying selection and the stability of most human proteins is essential to human life.
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15
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Esperante SA, Varejāo N, Pinheiro F, Sant'Anna R, Luque-Ortega JR, Alfonso C, Sora V, Papaleo E, Rivas G, Reverter D, Ventura S. Disease-associated mutations impacting BC-loop flexibility trigger long-range transthyretin tetramer destabilization and aggregation. J Biol Chem 2021; 297:101039. [PMID: 34343569 PMCID: PMC8406001 DOI: 10.1016/j.jbc.2021.101039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/30/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Hereditary transthyretin amyloidosis (ATTR) is an autosomal dominant disease characterized by the extracellular deposition of the transport protein transthyretin (TTR) as amyloid fibrils. Despite the progress achieved in recent years, understanding why different TTR residue substitutions lead to different clinical manifestations remains elusive. Here, we studied the molecular basis of disease-causing missense mutations affecting residues R34 and K35. R34G and K35T variants cause vitreous amyloidosis, whereas R34T and K35N mutations result in amyloid polyneuropathy and restrictive cardiomyopathy. All variants are more sensitive to pH-induced dissociation and amyloid formation than the wild-type (WT)-TTR counterpart, specifically in the variants deposited in the eyes amyloid formation occurs close to physiological pHs. Chemical denaturation experiments indicate that all the mutants are less stable than WT-TTR, with the vitreous amyloidosis variants, R34G and K35T, being highly destabilized. Sequence-induced stabilization of the dimer–dimer interface with T119M rendered tetramers containing R34G or K35T mutations resistant to pH-induced aggregation. Because R34 and K35 are among the residues more distant to the TTR interface, their impact in this region is therefore theorized to occur at long range. The crystal structures of double mutants, R34G/T119M and K35T/T119M, together with molecular dynamics simulations indicate that their strong destabilizing effect is initiated locally at the BC loop, increasing its flexibility in a mutation-dependent manner. Overall, the present findings help us to understand the sequence-dynamic-structural mechanistic details of TTR amyloid aggregation triggered by R34 and K35 variants and to link the degree of mutation-induced conformational flexibility to protein aggregation propensity.
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Affiliation(s)
- Sebastián A Esperante
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
| | - Nathalia Varejāo
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Francisca Pinheiro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Ricardo Sant'Anna
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Juan Román Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Carlos Alfonso
- Systems Biochemistry of Bacterial Division Laboratory, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Valentina Sora
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark; Cancer Systems Biology, Health and Technology Department, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark; Cancer Systems Biology, Health and Technology Department, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Germán Rivas
- Systems Biochemistry of Bacterial Division Laboratory, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
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16
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Bourgeat L, Pacini L, Serghei A, Lesieur C. Experimental diagnostic of sequence-variant dynamic perturbations revealed by broadband dielectric spectroscopy. Structure 2021; 29:1419-1429.e3. [PMID: 34051139 DOI: 10.1016/j.str.2021.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/23/2021] [Accepted: 05/07/2021] [Indexed: 02/08/2023]
Abstract
Genetic diversity leads to protein robustness, adaptability, and failure. Some sequence variants are structurally robust but functionally disturbed because mutations bring the protein onto unfolding/refolding routes resulting in misfolding diseases (e.g., Parkinson). We assume dynamic perturbations introduced by mutations foster the alternative unfolding routes and test this possibility by comparing the unfolding dynamics of the heat-labile enterotoxin B pentamers and the cholera toxin B pentamers, two pentamers structurally and functionally related and robust to 17 sequence variations. The B-subunit thermal unfolding dynamics are monitored by broadband dielectric spectroscopy in nanoconfined and weakly hydrated conditions. Distinct dielectric signals reveal the different B-subunits unfolding dynamics. Combined with network analyses, the experiments pinpoint the role of three mutations A1T, E7D, and E102A, in diverting LTB5 to alternative unfolding routes that protect LTB5 from dissociation. Altogether, the methodology diagnoses dynamics faults that may underlie functional disorder, drug resistance, or higher virulence of sequence variants.
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Affiliation(s)
- Laëtitia Bourgeat
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69622 Villeurbanne, France; Univ Lyon, CNRS, IMP, 69622, Villeurbanne, France
| | - Lorenza Pacini
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69622 Villeurbanne, France; Institut Rhônalpin des systèmes complexes, IXXI-ENS-Lyon, 69007, Lyon, France
| | | | - Claire Lesieur
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69622 Villeurbanne, France; Institut Rhônalpin des systèmes complexes, IXXI-ENS-Lyon, 69007, Lyon, France.
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17
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Protofibril–Fibril Interactions Inhibit Amyloid Fibril Assembly by Obstructing Secondary Nucleation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Hasecke F, Niyangoda C, Borjas G, Pan J, Matthews G, Muschol M, Hoyer W. Protofibril-Fibril Interactions Inhibit Amyloid Fibril Assembly by Obstructing Secondary Nucleation. Angew Chem Int Ed Engl 2021; 60:3016-3021. [PMID: 33095508 PMCID: PMC7898819 DOI: 10.1002/anie.202010098] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/16/2020] [Indexed: 12/29/2022]
Abstract
Amyloid-β peptides (Aβ) assemble into both rigid amyloid fibrils and metastable oligomers termed AβO or protofibrils. In Alzheimer's disease, Aβ fibrils constitute the core of senile plaques, but Aβ protofibrils may represent the main toxic species. Aβ protofibrils accumulate at the exterior of senile plaques, yet the protofibril-fibril interplay is not well understood. Applying chemical kinetics and atomic force microscopy to the assembly of Aβ and lysozyme, protofibrils are observed to bind to the lateral surfaces of amyloid fibrils. When utilizing Aβ variants with different critical oligomer concentrations, the interaction inhibits the autocatalytic proliferation of amyloid fibrils by secondary nucleation on the fibril surface. Thus, metastable oligomers antagonize their replacement by amyloid fibrils both by competing for monomers and blocking secondary nucleation sites. The protofibril-fibril interaction governs their temporal evolution and potential to exert specific toxic activities.
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Affiliation(s)
- Filip Hasecke
- Institut für Physikalische BiologieHeinrich-Heine-Universität Düsseldorf40204DüsseldorfGermany
| | | | - Gustavo Borjas
- Department of PhysicsUniversity of South FloridaTampaFL33620USA
| | - Jianjun Pan
- Department of PhysicsUniversity of South FloridaTampaFL33620USA
| | | | - Martin Muschol
- Department of PhysicsUniversity of South FloridaTampaFL33620USA
| | - Wolfgang Hoyer
- Institut für Physikalische BiologieHeinrich-Heine-Universität Düsseldorf40204DüsseldorfGermany
- Strukturbiochemie (IBI-7)Forschungszentrum Jülich52425JülichGermany
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19
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Ulamec SM, Brockwell DJ, Radford SE. Looking Beyond the Core: The Role of Flanking Regions in the Aggregation of Amyloidogenic Peptides and Proteins. Front Neurosci 2020; 14:611285. [PMID: 33335475 PMCID: PMC7736610 DOI: 10.3389/fnins.2020.611285] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/02/2020] [Indexed: 12/14/2022] Open
Abstract
Amyloid proteins are involved in many neurodegenerative disorders such as Alzheimer’s disease [Tau, Amyloid β (Aβ)], Parkinson’s disease [alpha-synuclein (αSyn)], and amyotrophic lateral sclerosis (TDP-43). Driven by the early observation of the presence of ordered structure within amyloid fibrils and the potential to develop inhibitors of their formation, a major goal of the amyloid field has been to elucidate the structure of the amyloid fold at atomic resolution. This has now been achieved for a wide variety of sequences using solid-state NMR, microcrystallography, X-ray fiber diffraction and cryo-electron microscopy. These studies, together with in silico methods able to predict aggregation-prone regions (APRs) in protein sequences, have provided a wealth of information about the ordered fibril cores that comprise the amyloid fold. Structural and kinetic analyses have also shown that amyloidogenic proteins often contain less well-ordered sequences outside of the amyloid core (termed here as flanking regions) that modulate function, toxicity and/or aggregation rates. These flanking regions, which often form a dynamically disordered “fuzzy coat” around the fibril core, have been shown to play key parts in the physiological roles of functional amyloids, including the binding of RNA and in phase separation. They are also the mediators of chaperone binding and membrane binding/disruption in toxic amyloid assemblies. Here, we review the role of flanking regions in different proteins spanning both functional amyloid and amyloid in disease, in the context of their role in aggregation, toxicity and cellular (dys)function. Understanding the properties of these regions could provide new opportunities to target disease-related aggregation without disturbing critical biological functions.
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Affiliation(s)
- Sabine M Ulamec
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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20
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Martins PM, Navarro S, Silva A, Pinto MF, Sárkány Z, Figueiredo F, Pereira PJB, Pinheiro F, Bednarikova Z, Burdukiewicz M, Galzitskaya OV, Gazova Z, Gomes CM, Pastore A, Serpell LC, Skrabana R, Smirnovas V, Ziaunys M, Otzen DE, Ventura S, Macedo-Ribeiro S. MIRRAGGE - Minimum Information Required for Reproducible AGGregation Experiments. Front Mol Neurosci 2020; 13:582488. [PMID: 33328883 PMCID: PMC7729192 DOI: 10.3389/fnmol.2020.582488] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Reports on phase separation and amyloid formation for multiple proteins and aggregation-prone peptides are recurrently used to explore the molecular mechanisms associated with several human diseases. The information conveyed by these reports can be used directly in translational investigation, e.g., for the design of better drug screening strategies, or be compiled in databases for benchmarking novel aggregation-predicting algorithms. Given that minute protocol variations determine different outcomes of protein aggregation assays, there is a strong urge for standardized descriptions of the different types of aggregates and the detailed methods used in their production. In an attempt to address this need, we assembled the Minimum Information Required for Reproducible Aggregation Experiments (MIRRAGGE) guidelines, considering first-principles and the established literature on protein self-assembly and aggregation. This consensus information aims to cover the major and subtle determinants of experimental reproducibility while avoiding excessive technical details that are of limited practical interest for non-specialized users. The MIRRAGGE table (template available in Supplementary Information) is useful as a guide for the design of new studies and as a checklist during submission of experimental reports for publication. Full disclosure of relevant information also enables other researchers to reproduce results correctly and facilitates systematic data deposition into curated databases.
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Affiliation(s)
- Pedro M Martins
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Susanna Navarro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alexandra Silva
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Maria F Pinto
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Zsuzsa Sárkány
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisco Figueiredo
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.,International Iberian Nanotechnology Laboratory - Department of Atomic Structure - Composition of Materials, Braga, Portugal
| | - Pedro José Barbosa Pereira
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisca Pinheiro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Zuzana Bednarikova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Michał Burdukiewicz
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Zuzana Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Annalisa Pastore
- UK-DRI Centre at King's College London, the Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Rostislav Skrabana
- Department of Neuroimmunology, Axon Neuroscience R&D Services SE, Bratislava, Slovakia.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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21
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Giadone RM, Liberti DC, Matte TM, Rosarda JD, Torres-Arancivia C, Ghosh S, Diedrich JK, Pankow S, Skvir N, Jean JC, Yates JR, Wilson AA, Connors LH, Kotton DN, Wiseman RL, Murphy GJ. Expression of Amyloidogenic Transthyretin Drives Hepatic Proteostasis Remodeling in an Induced Pluripotent Stem Cell Model of Systemic Amyloid Disease. Stem Cell Reports 2020; 15:515-528. [PMID: 32735824 PMCID: PMC7419739 DOI: 10.1016/j.stemcr.2020.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 01/15/2023] Open
Abstract
The systemic amyloidoses are diverse disorders in which misfolded proteins are secreted by effector organs and deposited as proteotoxic aggregates at downstream tissues. Although well described clinically, the contribution of synthesizing organs to amyloid disease pathogenesis is unknown. Here, we utilize hereditary transthyretin amyloidosis (ATTR amyloidosis) induced pluripotent stem cells (iPSCs) to define the contribution of hepatocyte-like cells (HLCs) to the proteotoxicity of secreted transthyretin (TTR). To this end, we generated isogenic, patient-specific iPSCs expressing either amyloidogenic or wild-type TTR. We combined this tool with single-cell RNA sequencing to identify hepatic proteostasis factors correlating with destabilized TTR production in iPSC-derived HLCs. By generating an ATF6 inducible patient-specific iPSC line, we demonstrated that enhancing hepatic ER proteostasis preferentially reduces the secretion of amyloidogenic TTR. These data highlight the liver's capacity to chaperone misfolded TTR prior to deposition, and moreover suggest the potential for unfolded protein response modulating therapeutics in the treatment of diverse systemic amyloidoses.
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Affiliation(s)
- Richard M Giadone
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, 2nd Floor, Boston, MA 02118, USA
| | - Derek C Liberti
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, 2nd Floor, Boston, MA 02118, USA
| | - Taylor M Matte
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, 2nd Floor, Boston, MA 02118, USA
| | - Jessica D Rosarda
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Celia Torres-Arancivia
- Alan and Sandra Gerry Amyloid Research Laboratory, Amyloidosis Center, Boston University School of Medicine, Boston, MA, USA
| | - Sabrina Ghosh
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, 2nd Floor, Boston, MA 02118, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Sandra Pankow
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Nicholas Skvir
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, 2nd Floor, Boston, MA 02118, USA
| | - J C Jean
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, 2nd Floor, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, 2nd Floor, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Lawreen H Connors
- Alan and Sandra Gerry Amyloid Research Laboratory, Amyloidosis Center, Boston University School of Medicine, Boston, MA, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, 2nd Floor, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - George J Murphy
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, 2nd Floor, Boston, MA 02118, USA; Section of Hematology and Oncology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
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22
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Srinivasan E, Natarajan N, Rajasekaran R. TTRMDB: A database for structural and functional analysis on the impact of SNPs over transthyretin (TTR) using bioinformatic tools. Comput Biol Chem 2020; 87:107290. [PMID: 32512488 DOI: 10.1016/j.compbiolchem.2020.107290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 12/21/2022]
Abstract
Hereditary Transthyretin-associated amyloidosis (ATTR) is an autosomal dominant protein-folding disorder with adult-onset caused by mutation of transthyretin (TTR). TTR is characterized by extracellular deposition of amyloid, leading to loss of autonomy and finally, death. More than 100 distinct mutations in TTR gene have been reported from variable age of onset, clinical expression and penetrance data. Besides, the cure for the disease remains still obscure. Further, the prioritizing of mutations concerning the characteristic features governing the stability and pathogenicity of TTR mutant proteins remains unanswered, to date and thus, a complex state of study for researchers. Herein, we provide a full report encompassing the effects of every reported mutant model of TTR protein about the stability, functionality and pathogenicity using various computational tools. In addition, the results obtained from our study were used to create TTRMDB (Transthyretin mutant database), which could be easy access to researchers at http://vit.ac.in/ttrmdb.
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Affiliation(s)
- E Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore 632014, Tamil Nadu, India
| | - Nandhini Natarajan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore 632014, Tamil Nadu, India
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore 632014, Tamil Nadu, India.
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23
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Guo X, Liu Z, Zheng Y, Li Y, Li L, Liu H, Chen Z, Wu L. Review on the Structures and Activities of Transthyretin Amyloidogenesis Inhibitors. DRUG DESIGN DEVELOPMENT AND THERAPY 2020; 14:1057-1081. [PMID: 32210536 PMCID: PMC7071892 DOI: 10.2147/dddt.s237252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/24/2020] [Indexed: 12/26/2022]
Abstract
Transthyretin (TTR) is a tetrameric protein, and its dissociation, aggregation, deposition, and misfolding are linked to several human amyloid diseases. As the main transporter for thyroxine (T4) in plasma and cerebrospinal fluid, TTR contains two T4-binding sites, which are docked with T4 and subsequently maintain the structural stability of TTR homotetramer. Affected by genetic disorders and detrimental environmental factors, TTR degrades to monomer and/or form amyloid fibrils. Reasonably, stabilization of TTR might be an efficient strategy for the treatment of TTR-related amyloidosis. However, only 10-25% of T4 in the plasma is bound to TTR under physiological conditions. Expectedly, T4 analogs with different structures aiming to bind to T4 pockets may displace the functions of T4. So far, a number of compounds including both natural and synthetic origin have been reported. In this paper, we summarized the potent inhibitors, including bisaryl structure-based compounds, flavonoids, crown ethers, and carboranes, for treating TTR-related amyloid diseases and the combination modes of some compounds binding to TTR protein.
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Affiliation(s)
- Xiaohua Guo
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, People's Republic of China
| | - Zhaowen Liu
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, People's Republic of China
| | - Yizhou Zheng
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, People's Republic of China
| | - Yamei Li
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, People's Republic of China
| | - Linfu Li
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, People's Republic of China
| | - Hai Liu
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, People's Republic of China
| | - Zhixi Chen
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, People's Republic of China
| | - Longhuo Wu
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, People's Republic of China
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24
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Uversky VN, Finkelstein AV. Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions. Biomolecules 2019; 9:E842. [PMID: 31817975 PMCID: PMC6995567 DOI: 10.3390/biom9120842] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Proteins, these evolutionarily-edited biological polymers, are able to undergo intramolecular and intermolecular phase transitions. Spontaneous intramolecular phase transitions define the folding of globular proteins, whereas binding-induced, intra- and inter- molecular phase transitions play a crucial role in the functionality of many intrinsically-disordered proteins. On the other hand, intermolecular phase transitions are the behind-the-scenes players in a diverse set of macrosystemic phenomena taking place in protein solutions, such as new phase nucleation in bulk, on the interface, and on the impurities, protein crystallization, protein aggregation, the formation of amyloid fibrils, and intermolecular liquid-liquid or liquid-gel phase transitions associated with the biogenesis of membraneless organelles in the cells. This review is dedicated to the systematic analysis of the phase behavior of protein molecules and their ensembles, and provides a description of the major physical principles governing intramolecular and intermolecular phase transitions in protein solutions.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow, Russia
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow, Russia
- Biology Department, Lomonosov Moscow State University, 119192 Moscow, Russia
- Bioltechnogy Department, Lomonosov Moscow State University, 142290 Pushchino, Moscow, Russia
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25
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Guillaume YC, Lethier L, Claire A. Thermodynamics of the association of transthyretin and its nanovectorized form with heparan sulfate proteoglycan HPLC stationary phase and correlation with tetramer stability and amyloidogenicity. J LIQ CHROMATOGR R T 2019. [DOI: 10.1080/10826076.2018.1489283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Yves Claude Guillaume
- Univ Franche - Comté, Besançon, France
- EA481 Neurosciences Intégratives et Cliniques/Pôle Chimie Analytique Bioanalytique et Physique (PCABP), Besançon, France
- CHRU Besançon, Pôle Pharmaceutique, Besançon, France
| | - Lydie Lethier
- Univ Franche - Comté, Besançon, France
- EA481 Neurosciences Intégratives et Cliniques/Pôle Chimie Analytique Bioanalytique et Physique (PCABP), Besançon, France
| | - André Claire
- Univ Franche - Comté, Besançon, France
- EA481 Neurosciences Intégratives et Cliniques/Pôle Chimie Analytique Bioanalytique et Physique (PCABP), Besançon, France
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26
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Liu YT, Yen YJ, Ricardo F, Chang Y, Wu PH, Huang SJ, Lin KP, Yu TY. Biophysical characterization and modulation of Transthyretin Ala97Ser. Ann Clin Transl Neurol 2019; 6:1961-1970. [PMID: 31502419 PMCID: PMC6801203 DOI: 10.1002/acn3.50887] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/10/2019] [Accepted: 08/14/2019] [Indexed: 12/19/2022] Open
Abstract
Objective Ala97Ser (A97S) is the major transthyretin (TTR) mutation in Taiwanese patients of familial amyloid polyneuropathy (FAP), characterized by a late‐onset but rapidly deteriorated neuropathy. Tafamidis can restore the stability of some mutant TTR tetramers and slow down the progression of TTR‐FAP. However, there is little understanding of the biophysical features of A97S‐TTR mutant and the pharmacological modulation effect of tafamidis on it. This study aims to delineate the biophysical characteristics of A97S‐TTR and the pharmacological modulation effect of tafamidis on this mutant. Method The stability of TTR tetramers was assessed by urea denaturation and differential scanning calorimetry. Isothermal titration calorimetry (ITC) was used to measure the binding constant of tafamidis to TTR. Nuclear magnetic resonance spectroscopy (NMR) titration experiment was used to map out the tafamidis binding site. Results Chemical and thermal denaturation confirmed the destabilization effect of A97S. Consistent with other the amyloidogenic mutant, A97S‐TTR has slightly lower conformational stability. NMR revealed the binding site of A97S‐TTR with tafamidis is at the thyroxine binding pocket. The ITC experiments documented the high affinity of the binding which can effectively stabilize the A97S‐TTR tetramer. Interpretation This study confirmed the structural modulation effect of tafamidis on A97S‐TTR and implied the potential therapeutic benefit of tafamidis for A97S TTR‐FAP. This approach can be applied to investigate the modulation effect of tafamidis on other rare TTR variants and help to make individualized choices of available treatments for FAP patients.
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Affiliation(s)
- Yo-Tsen Liu
- Division of Epilepsy, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,National Yang-Ming University School of Medicine, Taipei, Taiwan.,Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Yueh-Jung Yen
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Frans Ricardo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Yu Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Pei-Hao Wu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Shing-Jong Huang
- Instrumentation Center, National Taiwan University, Taipei, Taiwan
| | - Kon-Ping Lin
- National Yang-Ming University School of Medicine, Taipei, Taiwan.,Division of Peripheral Nervous System Disorders, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Tsyr-Yan Yu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan.,International Graduate Program of Molecular Science and Technology, National Taiwan University, Taipei, Taiwan
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27
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Estimating dispensable content in the human interactome. Nat Commun 2019; 10:3205. [PMID: 31324802 PMCID: PMC6642175 DOI: 10.1038/s41467-019-11180-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 06/21/2019] [Indexed: 11/21/2022] Open
Abstract
Protein-protein interaction (PPI) networks (interactome networks) have successfully advanced our knowledge of molecular function, disease and evolution. While much progress has been made in quantifying errors and biases in experimental PPI datasets, it remains unknown what fraction of the error-free PPIs in the cell are completely dispensable, i.e., effectively neutral upon disruption. Here, we estimate dispensable content in the human interactome by calculating the fractions of PPIs disrupted by neutral and non-neutral mutations. Starting with the human reference interactome determined by experiments, we construct a human structural interactome by building homology-based three-dimensional structural models for PPIs. Next, we map common mutations from healthy individuals as well as Mendelian disease-causing mutations onto the human structural interactome, and perform structure-based calculations of how these mutations perturb the interactome. Using our predicted as well as experimentally-determined interactome perturbation patterns by common and disease mutations, we estimate that <~20% of the human interactome is completely dispensable. The fraction of protein-protein interactions (PPIs) that can be disrupted without fitness effect is unknown. Here, the authors model how disease-causing mutations and common mutations carried by healthy people perturb the interactome, and estimate that <20% of human PPIs are completely dispensable.
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28
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Structural Stabilization of Human Transthyretin by Centella asiatica (L.) Urban Extract: Implications for TTR Amyloidosis. Biomolecules 2019; 9:biom9040128. [PMID: 30934952 PMCID: PMC6523946 DOI: 10.3390/biom9040128] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 02/07/2023] Open
Abstract
Transthyretin is responsible for a series of highly progressive, degenerative, debilitating, and incurable protein misfolding disorders known as transthyretin (TTR) amyloidosis. Since dissociation of the homotetrameric protein to its monomers is crucial in its amyloidogenesis, stabilizing the native tetramer from dissociating using small-molecule ligands has proven a viable therapeutic strategy. The objective of this study was to determine the potential role of the medicinal herb Centella asiatica on human transthyretin (huTTR) amyloidogenesis. Thus, we investigated the stability of huTTR with or without a hydrophilic fraction of C. asiatica (CAB) against acid/urea-mediated denaturation. We also determined the influence of CAB on huTTR fibrillation using transmission electron microscopy. The potential binding interactions between CAB and huTTR was ascertained by nitroblue tetrazolium redox-cycling and 8-anilino-1-naphthalene sulfonic acid displacement assays. Additionally, the chemical profile of CAB was determined by liquid chromatography quadruple time-of-flight mass spectrometry (HPLC-QTOF-MS). Our results strongly suggest that CAB bound to and preserved the quaternary structure of huTTR in vitro. CAB also prevented transthyretin fibrillation, although aggregate formation was unmitigated. These effects could be attributable to the presence of phenolics and terpenoids in CAB. Our findings suggest that C. asiatica contains pharmaceutically relevant bioactive compounds which could be exploited for therapeutic development against TTR amyloidosis.
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29
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Sharma M, Khan S, Rahman S, Singh LR. The Extracellular Protein, Transthyretin Is an Oxidative Stress Biomarker. Front Physiol 2019; 10:5. [PMID: 30733681 PMCID: PMC6353848 DOI: 10.3389/fphys.2019.00005] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 01/07/2019] [Indexed: 12/02/2022] Open
Abstract
The extracellular protein, transthyretin is responsible for the transport of thyroxin and retinol binding protein complex to the various parts of the body. In addition to this transport function, transthyretin has also been involved in cardiovascular malfunctions, polyneuropathy, psychological disorders, obesity and diabetes, etc. Recent developments have evidenced that transthyretin has been associated with many other biological functions that are directly or indirectly associated with the oxidative stress, the common hallmark for many human diseases. In this review, we have attempted to address that transthyretin is associated with oxidative stress and could be an important biomarker. Potential future perspectives have also been discussed.
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Affiliation(s)
- Meesha Sharma
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
| | - Sheeza Khan
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
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30
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Dasari AKR, Hung I, Gan Z, Lim KH. Two distinct aggregation pathways in transthyretin misfolding and amyloid formation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:344-349. [PMID: 30366153 DOI: 10.1016/j.bbapap.2018.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/17/2018] [Accepted: 10/22/2018] [Indexed: 01/17/2023]
Abstract
Misfolding and amyloid formation of transthyretin (TTR) is implicated in numerous degenerative diseases. TTR misfolding is greatly accelerated under acidic conditions, and thus most of the mechanistic studies of TTR amyloid formation have been conducted at various acidic pH values (2-5). In this study, we report the effect of pH on TTR misfolding pathways and amyloid structures. Our combined solution and solid-state NMR studies revealed that TTR amyloid formation can proceed via at least two distinct misfolding pathways depending on the acidic conditions. Under mildly acidic conditions (pH 4.4), tetrameric native TTR appears to dissociate to monomers that maintain most of the native-like β-sheet structures. The amyloidogenic protein undergoes a conformational transition to largely unfolded states at more acidic conditions (pH 2.4), leading to amyloid with distinct molecular structures. Aggregation kinetics is also highly dependent upon the acidic conditions. TTR quickly forms moderately ordered amyloids at pH 4.4, while the aggregation kinetics is dramatically reduced at a lower pH of 2.4. The effect of the pathogenic mutations on aggregation kinetics is also markedly different under the two different acidic conditions. Pathogenic TTR variants (V30M and L55P) aggregate more aggressively than WT TTR at pH 4.4. In contrast, the single-point mutations do not affect the aggregation kinetics at the more acidic condition of pH 2.4. Given that the pathogenic mutations lead to more aggressive forms of TTR amyloidoses, the mildly acidic condition might be more suitable for mechanistic studies of TTR misfolding and aggregation.
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Affiliation(s)
- Anvesh K R Dasari
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Ivan Hung
- Center of Interdisciplinary Magnetic Resonance (CIMAR), National High Magnetic Field Laboratory (NHMFL), 1800 East, Paul Dirac Dr., Tallahassee, FL 32310, USA
| | - Zhehong Gan
- Center of Interdisciplinary Magnetic Resonance (CIMAR), National High Magnetic Field Laboratory (NHMFL), 1800 East, Paul Dirac Dr., Tallahassee, FL 32310, USA
| | - Kwang Hun Lim
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA.
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31
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Poltash ML, McCabe JW, Shirzadeh M, Laganowsky A, Clowers BH, Russell DH. Fourier Transform-Ion Mobility-Orbitrap Mass Spectrometer: A Next-Generation Instrument for Native Mass Spectrometry. Anal Chem 2018; 90:10472-10478. [PMID: 30091588 PMCID: PMC6464636 DOI: 10.1021/acs.analchem.8b02463] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new instrument configuration for native ion mobility-mass spectrometry (IM-MS) is described. Macromolecule ions are generated by using a static ESI source coupled to an RF ion funnel, and these ions are then mobility and mass analyzed using a periodic focusing drift tube IM analyzer and an Orbitrap mass spectrometer. The instrument design retains the capabilities for first-principles determination of rotationally averaged ion-neutral collision cross sections and high-resolution measurements in both mobility and mass analysis modes for intact protein complexes. Operation in the IM mode utilizes FT-IMS modes (originally described by Knorr ( Knorr , F. J. Anal. Chem . 1985 , 57 ( 2 ), 402 - 406 )), which provides a means to overcome the inherent duty cycle mismatch for drift tube (DT)-IM and Orbitrap mass analysis. The performance of the native ESI-FT-DT-IM-Orbitrap MS instrument was evaluated using the protein complexes Gln K (MW 44 kDa) and streptavidin (MW 53 kDa) bound to small molecules (ADP and biotin, respectively) and transthyretin (MW 56 kDa) bound to thyroxine and zinc.
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Affiliation(s)
- Michael L. Poltash
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jacob W. McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Brian H. Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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32
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Giadone RM, Rosarda JD, Akepati PR, Thomas AC, Boldbaatar B, James MF, Wilson AA, Sanchorawala V, Connors LH, Berk JL, Wiseman RL, Murphy GJ. A library of ATTR amyloidosis patient-specific induced pluripotent stem cells for disease modelling and in vitro testing of novel therapeutics. Amyloid 2018; 25:148-155. [PMID: 30032658 PMCID: PMC6319917 DOI: 10.1080/13506129.2018.1489228] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hereditary transthyretin amyloidosis (ATTR amyloidosis) is an autosomal dominant protein-folding disorder caused by over 100 distinct mutations in the transthyretin (TTR) gene. In ATTR amyloidosis, protein secreted from the liver aggregates and forms amyloid fibrils in downstream target organs, chiefly the heart and peripheral nervous system. Few animal models of ATTR amyloidosis exist and none recapitulate the multisystem complexity and clinical variability associated with disease pathogenesis in patients. Induced pluripotent stem cells (iPSCs) stand to revolutionize the way we study human development, model disease, and perhaps treat patients afflicted with highly variable multisystem diseases such as ATTR amyloidosis. Here, we fully characterize six representative iPSC lines from a library of previously reprogrammed iPSC lines and reprogrammable blood samples derived from ATTR amyloidosis patients. This unique resource, described herein, can be harnessed to study diverse disorder.
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Affiliation(s)
- Richard M Giadone
- a Center for Regenerative Medicine , Boston University School of Medicine , Boston , MA , USA
| | - Jessica D Rosarda
- b Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - Prithvi Reddy Akepati
- a Center for Regenerative Medicine , Boston University School of Medicine , Boston , MA , USA
| | - Arianne C Thomas
- a Center for Regenerative Medicine , Boston University School of Medicine , Boston , MA , USA
| | - Batbold Boldbaatar
- c Alan and Sandra Gerry Amyloid Research Laboratory, Amyloidosis Center , Boston University School of Medicine , Boston , MA , USA
| | - Marianne F James
- a Center for Regenerative Medicine , Boston University School of Medicine , Boston , MA , USA
| | - Andrew A Wilson
- a Center for Regenerative Medicine , Boston University School of Medicine , Boston , MA , USA
| | - Vaishali Sanchorawala
- d Amyloidosis Center , Boston University School of Medicine , Boston , MA , USA.,e Section of Hematology and Oncology, Department of Medicine , Boston University School of Medicine , Boston , MA , USA
| | - Lawreen H Connors
- c Alan and Sandra Gerry Amyloid Research Laboratory, Amyloidosis Center , Boston University School of Medicine , Boston , MA , USA
| | - John L Berk
- d Amyloidosis Center , Boston University School of Medicine , Boston , MA , USA
| | - R Luke Wiseman
- b Department of Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
| | - George J Murphy
- a Center for Regenerative Medicine , Boston University School of Medicine , Boston , MA , USA.,e Section of Hematology and Oncology, Department of Medicine , Boston University School of Medicine , Boston , MA , USA
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33
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Hasecke F, Miti T, Perez C, Barton J, Schölzel D, Gremer L, Grüning CSR, Matthews G, Meisl G, Knowles TPJ, Willbold D, Neudecker P, Heise H, Ullah G, Hoyer W, Muschol M. Origin of metastable oligomers and their effects on amyloid fibril self-assembly. Chem Sci 2018; 9:5937-5948. [PMID: 30079208 PMCID: PMC6050532 DOI: 10.1039/c8sc01479e] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 06/12/2018] [Indexed: 01/05/2023] Open
Abstract
Assembly of rigid amyloid fibrils with their characteristic cross-β sheet structure is a molecular signature of numerous neurodegenerative and non-neuropathic disorders. Frequently large populations of small globular amyloid oligomers (gOs) and curvilinear fibrils (CFs) precede the formation of late-stage rigid fibrils (RFs), and have been implicated in amyloid toxicity. Yet our understanding of the origin of these metastable oligomers, their role as on-pathway precursors or off-pathway competitors, and their effects on the self-assembly of amyloid fibrils remains incomplete. Using two unrelated amyloid proteins, amyloid-β and lysozyme, we find that gO/CF formation, analogous to micelle formation by surfactants, is delineated by a "critical oligomer concentration" (COC). Below this COC, fibril assembly replicates the sigmoidal kinetics of nucleated polymerization. Upon crossing the COC, assembly kinetics becomes biphasic with gO/CF formation responsible for the lag-free initial phase, followed by a second upswing dominated by RF nucleation and growth. RF lag periods below the COC, as expected, decrease as a power law in monomer concentration. Surprisingly, the build-up of gO/CFs above the COC causes a progressive increase in RF lag periods. Our results suggest that metastable gO/CFs are off-pathway from RF formation, confined by a condition-dependent COC that is distinct from RF solubility, underlie a transition from sigmoidal to biphasic assembly kinetics and, most importantly, not only compete with RFs for the shared monomeric growth substrate but actively inhibit their nucleation and growth.
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Affiliation(s)
- Filip Hasecke
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
| | - Tatiana Miti
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Carlos Perez
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Jeremy Barton
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Daniel Schölzel
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Lothar Gremer
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Clara S R Grüning
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
| | - Garrett Matthews
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
| | - Dieter Willbold
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Philipp Neudecker
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Henrike Heise
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Ghanim Ullah
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Martin Muschol
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
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34
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Schonhoft JD, Monteiro C, Plate L, Eisele YS, Kelly JM, Boland D, Parker CG, Cravatt BF, Teruya S, Helmke S, Maurer M, Berk J, Sekijima Y, Novais M, Coelho T, Powers ET, Kelly JW. Peptide probes detect misfolded transthyretin oligomers in plasma of hereditary amyloidosis patients. Sci Transl Med 2018; 9:9/407/eaam7621. [PMID: 28904227 DOI: 10.1126/scitranslmed.aam7621] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/29/2017] [Accepted: 07/21/2017] [Indexed: 12/12/2022]
Abstract
Increasing evidence supports the hypothesis that soluble misfolded protein assemblies contribute to the degeneration of postmitotic tissue in amyloid diseases. However, there is a dearth of reliable nonantibody-based probes for selectively detecting oligomeric aggregate structures circulating in plasma or deposited in tissues, making it difficult to scrutinize this hypothesis in patients. Hence, understanding the structure-proteotoxicity relationships driving amyloid diseases remains challenging, hampering the development of early diagnostic and novel treatment strategies. We report peptide-based probes that selectively label misfolded transthyretin (TTR) oligomers circulating in the plasma of TTR hereditary amyloidosis patients exhibiting a predominant neuropathic phenotype. These probes revealed that there are much fewer misfolded TTR oligomers in healthy controls, in asymptomatic carriers of mutations linked to amyloid polyneuropathy, and in patients with TTR-associated cardiomyopathies. The absence of misfolded TTR oligomers in the plasma of cardiomyopathy patients suggests that the tissue tropism observed in the TTR amyloidoses is structure-based. Misfolded oligomers decrease in TTR amyloid polyneuropathy patients treated with disease-modifying therapies (tafamidis or liver transplant-mediated gene therapy). In a subset of TTR amyloid polyneuropathy patients, the probes also detected a circulating TTR fragment that disappeared after tafamidis treatment. Proteomic analysis of the isolated TTR oligomers revealed a specific patient-associated signature composed of proteins that likely associate with the circulating TTR oligomers. Quantification of plasma oligomer concentrations using peptide probes could become an early diagnostic strategy, a response-to-therapy biomarker, and a useful tool for understanding structure-proteotoxicity relationships in the TTR amyloidoses.
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Affiliation(s)
- Joseph D Schonhoft
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Cecilia Monteiro
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lars Plate
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yvonne S Eisele
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John M Kelly
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel Boland
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergio Teruya
- Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Stephen Helmke
- Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Mathew Maurer
- Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - John Berk
- Boston University School of Medicine, Boston, MA 02118, USA
| | - Yoshiki Sekijima
- Department of Medicine (Neurology and Rheumatology), Shinshu University School of Medicine, Matsumoto, Japan
| | - Marta Novais
- Unidade Corino de Andrade, Department of Neurosciences, Hospital de Santo António, 4099-001 Porto, Portugal
| | - Teresa Coelho
- Unidade Corino de Andrade, Department of Neurosciences, Hospital de Santo António, 4099-001 Porto, Portugal
| | - Evan T Powers
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jeffery W Kelly
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. .,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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35
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Fändrich M, Nyström S, Nilsson KPR, Böckmann A, LeVine H, Hammarström P. Amyloid fibril polymorphism: a challenge for molecular imaging and therapy. J Intern Med 2018; 283:218-237. [PMID: 29360284 PMCID: PMC5820168 DOI: 10.1111/joim.12732] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The accumulation of misfolded proteins (MPs), both unique and common, for different diseases is central for many chronic degenerative diseases. In certain patients, MP accumulation is systemic (e.g. TTR amyloid), and in others, this is localized to a specific cell type (e.g. Alzheimer's disease). In neurodegenerative diseases, NDs, it is noticeable that the accumulation of MP progressively spreads throughout the nervous system. Our main hypothesis of this article is that MPs are not only markers but also active carriers of pathogenicity. Here, we discuss studies from comprehensive molecular approaches aimed at understanding MP conformational variations (polymorphism) and their bearing on spreading of MPs, MP toxicity, as well as MP targeting in imaging and therapy. Neurodegenerative disease (ND) represents a major and growing societal challenge, with millions of people worldwide suffering from Alzheimer's or Parkinson's diseases alone. For all NDs, current treatment is palliative without addressing the primary cause and is not curative. Over recent years, particularly the shape-shifting properties of misfolded proteins and their spreading pathways have been intensively researched. The difficulty in addressing ND has prompted most major pharma companies to severely downsize their nervous system disorder research. Increased academic research is pivotal for filling this void and to translate basic research into tools for medical professionals. Recent discoveries of targeting drug design against MPs and improved model systems to study structure, pathology spreading and toxicity strongly encourage future studies along these lines to provide an opportunity for selective imaging, prognostic diagnosis and therapy.
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Affiliation(s)
- Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
| | - Sofie Nyström
- Department of Physics, Chemistry and Biology, division of Chemistry, Linköping University, Linköping, Sweden
| | - K. Peter R. Nilsson
- Department of Physics, Chemistry and Biology, division of Chemistry, Linköping University, Linköping, Sweden
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Harry LeVine
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA; Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Per Hammarström
- Department of Physics, Chemistry and Biology, division of Chemistry, Linköping University, Linköping, Sweden
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36
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Computational On-Chip Imaging of Nanoparticles and Biomolecules using Ultraviolet Light. Sci Rep 2017; 7:44157. [PMID: 28276489 PMCID: PMC5343455 DOI: 10.1038/srep44157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/02/2017] [Indexed: 12/28/2022] Open
Abstract
Significant progress in characterization of nanoparticles and biomolecules was enabled by the development of advanced imaging equipment with extreme spatial-resolution and sensitivity. To perform some of these analyses outside of well-resourced laboratories, it is necessary to create robust and cost-effective alternatives to existing high-end laboratory-bound imaging and sensing equipment. Towards this aim, we have designed a holographic on-chip microscope operating at an ultraviolet illumination wavelength (UV) of 266 nm. The increased forward scattering from nanoscale objects at this short wavelength has enabled us to detect individual sub-30 nm nanoparticles over a large field-of-view of >16 mm2 using an on-chip imaging platform, where the sample is placed at ≤0.5 mm away from the active area of an opto-electronic sensor-array, without any lenses in between. The strong absorption of this UV wavelength by biomolecules including nucleic acids and proteins has further enabled high-contrast imaging of nanoscopic aggregates of biomolecules, e.g., of enzyme Cu/Zn-superoxide dismutase, abnormal aggregation of which is linked to amyotrophic lateral sclerosis (ALS) - a fatal neurodegenerative disease. This UV-based wide-field computational imaging platform could be valuable for numerous applications in biomedical sciences and environmental monitoring, including disease diagnostics, viral load measurements as well as air- and water-quality assessment.
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37
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Uversky VN. Under-folded proteins: Conformational ensembles and their roles in protein folding, function, and pathogenesis. Biopolymers 2016; 99:870-87. [PMID: 23754493 PMCID: PMC7161862 DOI: 10.1002/bip.22298] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 05/21/2013] [Accepted: 05/30/2013] [Indexed: 11/16/2022]
Abstract
For decades, protein function was intimately linked to the presence of a unique, aperiodic crystal‐like structure in a functional protein. The two only places for conformational ensembles of under‐folded (or partially folded) protein forms in this picture were either the end points of the protein denaturation processes or transiently populated folding intermediates. Recent years witnessed dramatic change in this perception and conformational ensembles, which the under‐folded proteins are, have moved from the shadow. Accumulated to date data suggest that a protein can exist in at least three global forms–functional and folded, functional and intrinsically disordered (nonfolded), and nonfunctional and misfolded/aggregated. Under‐folded protein states are crucial for each of these forms, serving as important folding intermediates of ordered proteins, or as functional states of intrinsically disordered proteins (IDPs) and IDP regions (IDPRs), or as pathology triggers of misfolded proteins. Based on these observations, conformational ensembles of under‐folded proteins can be classified as transient (folding and misfolding intermediates) and permanent (IDPs and stable misfolded proteins). Permanently under‐folded proteins can further be split into intentionally designed (IDPs and IDPRs) and unintentionally designed (misfolded proteins). Although intrinsic flexibility, dynamics, and pliability are crucial for all under‐folded proteins, the different categories of under‐foldedness are differently encoded in protein amino acid sequences. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 870–887, 2013.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142292, Moscow Region, Russia
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38
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Repositioning tolcapone as a potent inhibitor of transthyretin amyloidogenesis and associated cellular toxicity. Nat Commun 2016; 7:10787. [PMID: 26902880 PMCID: PMC4766415 DOI: 10.1038/ncomms10787] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 01/20/2016] [Indexed: 02/05/2023] Open
Abstract
Transthyretin (TTR) is a plasma homotetrameric protein implicated in fatal systemic amyloidoses. TTR tetramer dissociation precedes pathological TTR aggregation. Native state stabilizers are promising drugs to treat TTR amyloidoses. Here we repurpose tolcapone, an FDA-approved molecule for Parkinson's disease, as a potent TTR aggregation inhibitor. Tolcapone binds specifically to TTR in human plasma, stabilizes the native tetramer in vivo in mice and humans and inhibits TTR cytotoxicity. Crystal structures of tolcapone bound to wild-type TTR and to the V122I cardiomyopathy-associated variant show that it docks better into the TTR T4 pocket than tafamidis, so far the only drug on the market to treat TTR amyloidoses. These data indicate that tolcapone, already in clinical trials for familial amyloid polyneuropathy, is a strong candidate for therapeutic intervention in these diseases, including those affecting the central nervous system, for which no small-molecule therapy exists.
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39
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Baranczak A, Kelly JW. A current pharmacologic agent versus the promise of next generation therapeutics to ameliorate protein misfolding and/or aggregation diseases. Curr Opin Chem Biol 2016; 32:10-21. [PMID: 26859714 DOI: 10.1016/j.cbpa.2016.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/14/2016] [Accepted: 01/14/2016] [Indexed: 12/18/2022]
Abstract
The list of protein aggregation-associated degenerative diseases is long and growing, while the portfolio of disease-modifying strategies is very small. In this review and perspective, we assess what has worked to slow the progression of an aggregation-associated degenerative disease, covering the underlying mechanism of pharmacologic action and what we have learned about the etiology of the transthyretin amyloid diseases and likely amyloidoses in general. Next, we introduce emerging therapies that should apply more generally to protein misfolding and/or aggregation diseases, approaches that rely on adapting the protein homeostasis or proteostasis network for disease amelioration.
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Affiliation(s)
- Aleksandra Baranczak
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, CA 92037, USA; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Jeffery W Kelly
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, CA 92037, USA; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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40
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Eisele YS, Monteiro C, Fearns C, Encalada SE, Wiseman RL, Powers ET, Kelly JW. Targeting protein aggregation for the treatment of degenerative diseases. Nat Rev Drug Discov 2015; 14:759-80. [PMID: 26338154 PMCID: PMC4628595 DOI: 10.1038/nrd4593] [Citation(s) in RCA: 294] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The aggregation of specific proteins is hypothesized to underlie several degenerative diseases, which are collectively known as amyloid disorders. However, the mechanistic connection between the process of protein aggregation and tissue degeneration is not yet fully understood. Here, we review current and emerging strategies to ameliorate aggregation-associated degenerative disorders, with a focus on disease-modifying strategies that prevent the formation of and/or eliminate protein aggregates. Persuasive pharmacological and genetic evidence now supports protein aggregation as the cause of postmitotic tissue dysfunction or loss. However, a more detailed understanding of the factors that trigger and sustain aggregate formation and of the structure-activity relationships underlying proteotoxicity is needed to develop future disease-modifying therapies.
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Affiliation(s)
- Yvonne S. Eisele
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Cecilia Monteiro
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Colleen Fearns
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Sandra E. Encalada
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, California 92037, USA
| | - R. Luke Wiseman
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Evan T. Powers
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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41
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Yokoyama T, Kosaka Y, Mizuguchi M. Inhibitory Activities of Propolis and Its Promising Component, Caffeic Acid Phenethyl Ester, against Amyloidogenesis of Human Transthyretin. J Med Chem 2014; 57:8928-35. [DOI: 10.1021/jm500997m] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical
Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Yuto Kosaka
- Faculty of Pharmaceutical
Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical
Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
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42
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Sant'Anna R, Braga C, Varejão N, Pimenta KM, Graña-Montes R, Alves A, Cortines J, Cordeiro Y, Ventura S, Foguel D. The importance of a gatekeeper residue on the aggregation of transthyretin: implications for transthyretin-related amyloidoses. J Biol Chem 2014; 289:28324-37. [PMID: 25086037 PMCID: PMC4192486 DOI: 10.1074/jbc.m114.563981] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Protein aggregation into β-sheet-enriched amyloid fibrils is associated with an increasing number of human disorders. The adoption of such amyloid conformations seems to constitute a generic property of polypeptide chains. Therefore, during evolution, proteins have adopted negative design strategies to diminish their intrinsic propensity to aggregate, including enrichment of gatekeeper charged residues at the flanks of hydrophobic aggregation-prone segments. Wild type transthyretin (TTR) is responsible for senile systemic amyloidosis, and more than 100 mutations in the TTR gene are involved in familial amyloid polyneuropathy. The TTR 26–57 segment bears many of these aggressive amyloidogenic mutations as well as the binding site for heparin. We demonstrate here that Lys-35 acts as a gatekeeper residue in TTR, strongly decreasing its amyloidogenic potential. This protective effect is sequence-specific because Lys-48 does not affect TTR aggregation. Lys-35 is part of the TTR basic heparin-binding motif. This glycosaminoglycan blocks the protective effect of Lys-35, probably by neutralization of its side chain positive charge. A K35L mutation emulates this effect and results in the rapid self-assembly of the TTR 26–57 region into amyloid fibrils. This mutation does not affect the tetrameric protein stability, but it strongly increases its aggregation propensity. Overall, we illustrate how TTR is yet another amyloidogenic protein exploiting negative design to prevent its massive aggregation, and we show how blockage of conserved protective features by endogenous factors or mutations might result in increased disease susceptibility.
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Affiliation(s)
- Ricardo Sant'Anna
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Carolina Braga
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Nathalia Varejão
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Karinne M Pimenta
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Ricardo Graña-Montes
- the Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Aline Alves
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Juliana Cortines
- the Instituto de Microbiologia Professor Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro CEP 21941-590, Brazil and
| | | | - Salvador Ventura
- the Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Debora Foguel
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural,
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43
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Rappley I, Monteiro C, Novais M, Baranczak A, Solis G, Wiseman RL, Helmke S, Maurer MS, Coelho T, Powers ET, Kelly JW. Quantification of transthyretin kinetic stability in human plasma using subunit exchange. Biochemistry 2014; 53:1993-2006. [PMID: 24661308 PMCID: PMC3977577 DOI: 10.1021/bi500171j] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The transthyretin (TTR) amyloidoses are a group of degenerative diseases caused by TTR aggregation, requiring rate-limiting tetramer dissociation. Kinetic stabilization of TTR, by preferential binding of a drug to the native tetramer over the dissociative transition state, dramatically slows the progression of familial amyloid polyneuropathy. An established method for quantifying the kinetic stability of recombinant TTR tetramers in buffer is subunit exchange, in which tagged TTR homotetramers are added to untagged homotetramers at equal concentrations to measure the rate at which the subunits exchange. Herein, we report a subunit exchange method for quantifying the kinetic stability of endogenous TTR in human plasma. The subunit exchange reaction is initiated by the addition of a substoichiometric quantity of FLAG-tagged TTR homotetramers to endogenous TTR in plasma. Aliquots of the subunit exchange reaction, taken as a function of time, are then added to an excess of a fluorogenic small molecule, which immediately arrests further subunit exchange. After binding, the small molecule reacts with the TTR tetramers, rendering them fluorescent and detectable in human plasma after subsequent ion exchange chromatography. The ability to report on the extent of TTR kinetic stabilization resulting from treatment with oral tafamidis is important, especially for selection of the appropriate dose for patients carrying rare mutations. This method could also serve as a surrogate biomarker for the prediction of the clinical outcome. Subunit exchange was used to quantify the stabilization of WT TTR from senile systemic amyloidosis patients currently being treated with tafamidis (20 mg orally, once daily). TTR kinetic stability correlated with the tafamidis plasma concentration.
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Affiliation(s)
- Irit Rappley
- Department of Chemistry, ‡The Skaggs Institute for Chemical Biology, §Department of Molecular and Experimental Medicine, and ∥Department of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92037, United States
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44
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Gasperini RJ, Klaver DW, Hou X, Aguilar MI, Small DH. Mechanisms of transthyretin aggregation and toxicity. Subcell Biochem 2014; 65:211-24. [PMID: 23225005 DOI: 10.1007/978-94-007-5416-4_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Amyloidoses are characterised by the deposition of insoluble protein that occurs in the extracellular compartment of various tissues. One form of amyloidosis is caused by transthyretin (TTR) misfolding and deposition in target tissues. It is clear that many amyloidoses share common features of fibrillogenesis and toxicity. This chapter examines the mechanisms of TTR aggregation with a view to understanding the possible therapeutic interventions in amyloid disease.
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Affiliation(s)
- Robert J Gasperini
- Menzies Research Institute, University of Tasmania, Liverpool Street, 7001, Hobart, TAS, Australia,
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45
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Yokoyama T, Mizuguchi M, Nabeshima Y, Kusaka K, Yamada T, Hosoya T, Ohhara T, Kurihara K, Tanaka I, Niimura N. Hydrogen-bond network and pH sensitivity in human transthyretin. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:834-7. [PMID: 24121323 PMCID: PMC3795539 DOI: 10.1107/s090904951302075x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/25/2013] [Indexed: 05/20/2023]
Abstract
Transthyretin (TTR) is a tetrameric protein. TTR misfolding and aggregation are associated with human amyloid diseases. Dissociation of the TTR tetramer is believed to be the rate-limiting step in the amyloid fibril formation cascade. Low pH is known to promote dissociation into monomer and the formation of amyloid fibrils. In order to reveal the molecular mechanisms underlying pH sensitivity and structural stabilities of TTR, neutron diffraction studies were conducted using the IBARAKI Biological Crystal Diffractometer with the time-of-flight method. Crystals for the neutron diffraction experiments were grown up to 2.5 mm(3) for four months. The neutron crystal structure solved at 2.0 Å revealed the protonation states of His88 and the detailed hydrogen-bond network depending on the protonation states of His88. This hydrogen-bond network is involved in monomer-monomer and dimer-dimer interactions, suggesting that the double protonation of His88 by acidification breaks the hydrogen-bond network and causes the destabilization of the TTR tetramer. Structural comparison with the X-ray crystal structure at acidic pH identified the three amino acid residues responsible for the pH sensitivity of TTR. Our neutron model provides insights into the molecular stability related to amyloidosis.
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Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taro Yamada
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takaaki Hosoya
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
- College of Engineering, Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Takashi Ohhara
- Research Center for Neutron Science and Technology, Comprehensive Research Organization for Science and Society, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Kazuo Kurihara
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
- College of Engineering, Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
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46
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Leung A, Nah S, Reid W, Ebata A, Koch C, Monti S, Genereux J, Wiseman R, Wolozin B, Connors L, Berk J, Seldin D, Mostoslavsky G, Kotton D, Murphy G. Induced pluripotent stem cell modeling of multisystemic, hereditary transthyretin amyloidosis. Stem Cell Reports 2013; 1:451-63. [PMID: 24286032 PMCID: PMC3841264 DOI: 10.1016/j.stemcr.2013.10.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 10/04/2013] [Accepted: 10/07/2013] [Indexed: 11/24/2022] Open
Abstract
Familial transthyretin amyloidosis (ATTR) is an autosomal-dominant protein-folding disorder caused by over 100 distinct mutations in the transthyretin (TTR) gene. In ATTR, protein secreted from the liver aggregates and forms fibrils in target organs, chiefly the heart and peripheral nervous system, highlighting the need for a model capable of recapitulating the multisystem complexity of this clinically variable disease. Here, we describe the directed differentiation of ATTR patient-specific iPSCs into hepatocytes that produce mutant TTR, and the cardiomyocytes and neurons normally targeted in the disease. We demonstrate that iPSC-derived neuronal and cardiac cells display oxidative stress and an increased level of cell death when exposed to mutant TTR produced by the patient-matched iPSC-derived hepatocytes, recapitulating essential aspects of the disease in vitro. Furthermore, small molecule stabilizers of TTR show efficacy in this model, validating this iPSC-based, patient-specific in vitro system as a platform for testing therapeutic strategies.
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Affiliation(s)
- Amy Leung
- Sections of Hematology-Oncology and Computational Biomedicine, Departments of Medicine, Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- Center for Regenerative Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA
| | - Shirley K. Nah
- Sections of Hematology-Oncology and Computational Biomedicine, Departments of Medicine, Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- Center for Regenerative Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA
| | - Whitney Reid
- Sections of Hematology-Oncology and Computational Biomedicine, Departments of Medicine, Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- Center for Regenerative Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA
| | - Atsushi Ebata
- Departments of Pharmacology and Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Clarissa M. Koch
- The Amyloidosis Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Stefano Monti
- Sections of Hematology-Oncology and Computational Biomedicine, Departments of Medicine, Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Joseph C. Genereux
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - R. Luke Wiseman
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Benjamin Wolozin
- Departments of Pharmacology and Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Lawreen H. Connors
- The Amyloidosis Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - John L. Berk
- The Amyloidosis Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - David C. Seldin
- Sections of Hematology-Oncology and Computational Biomedicine, Departments of Medicine, Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- The Amyloidosis Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Gustavo Mostoslavsky
- Center for Regenerative Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA
| | - George J. Murphy
- Sections of Hematology-Oncology and Computational Biomedicine, Departments of Medicine, Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- Center for Regenerative Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA
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47
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Statistical mechanical treatments of protein amyloid formation. Int J Mol Sci 2013; 14:17420-52. [PMID: 23979423 PMCID: PMC3794734 DOI: 10.3390/ijms140917420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/05/2013] [Accepted: 08/09/2013] [Indexed: 11/16/2022] Open
Abstract
Protein aggregation is an important field of investigation because it is closely related to the problem of neurodegenerative diseases, to the development of biomaterials, and to the growth of cellular structures such as cyto-skeleton. Self-aggregation of protein amyloids, for example, is a complicated process involving many species and levels of structures. This complexity, however, can be dealt with using statistical mechanical tools, such as free energies, partition functions, and transfer matrices. In this article, we review general strategies for studying protein aggregation using statistical mechanical approaches and show that canonical and grand canonical ensembles can be used in such approaches. The grand canonical approach is particularly convenient since competing pathways of assembly and dis-assembly can be considered simultaneously. Another advantage of using statistical mechanics is that numerically exact solutions can be obtained for all of the thermodynamic properties of fibrils, such as the amount of fibrils formed, as a function of initial protein concentration. Furthermore, statistical mechanics models can be used to fit experimental data when they are available for comparison.
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48
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Yates CM, Sternberg MJE. The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions. J Mol Biol 2013; 425:3949-63. [PMID: 23867278 DOI: 10.1016/j.jmb.2013.07.012] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Revised: 07/02/2013] [Accepted: 07/09/2013] [Indexed: 12/23/2022]
Abstract
Non-synonymous single nucleotide polymorphisms (nsSNPs) are single base changes leading to a change to the amino acid sequence of the encoded protein. Many of these variants are associated with disease, so nsSNPs have been well studied, with studies looking at the effects of nsSNPs on individual proteins, for example, on stability and enzyme active sites. In recent years, the impact of nsSNPs upon protein-protein interactions has also been investigated, giving a greater insight into the mechanisms by which nsSNPs can lead to disease. In this review, we summarize these studies, looking at the various mechanisms by which nsSNPs can affect protein-protein interactions. We focus on structural changes that can impair interaction, changes to disorder, gain of interaction, and post-translational modifications before looking at some examples of nsSNPs at human-pathogen protein-protein interfaces and the analysis of nsSNPs from a network perspective.
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Affiliation(s)
- Christopher M Yates
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, South Kensington, SW7 2AZ, UK.
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49
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Grimster NP, Connelly S, Baranczak A, Dong J, Krasnova LB, Sharpless KB, Powers ET, Wilson IA, Kelly JW. Aromatic sulfonyl fluorides covalently kinetically stabilize transthyretin to prevent amyloidogenesis while affording a fluorescent conjugate. J Am Chem Soc 2013; 135:5656-68. [PMID: 23350654 PMCID: PMC3630275 DOI: 10.1021/ja311729d] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Molecules that bind selectively to a given protein and then undergo a rapid chemoselective reaction to form a covalent conjugate have utility in drug development. Herein a library of 1,3,4-oxadiazoles substituted at the 2 position with an aryl sulfonyl fluoride and at the 5 position with a substituted aryl known to have high affinity for the inner thyroxine binding subsite of transthyretin (TTR) was conceived of by structure-based design principles and was chemically synthesized. When bound in the thyroxine binding site, most of the aryl sulfonyl fluorides react rapidly and chemoselectively with the pKa-perturbed K15 residue, kinetically stabilizing TTR and thus preventing amyloid fibril formation, known to cause polyneuropathy. Conjugation t50s range from 1 to 4 min, ~1400 times faster than the hydrolysis reaction outside the thyroxine binding site. X-ray crystallography confirms the anticipated binding orientation and sheds light on the sulfonyl fluoride activation leading to the sulfonamide linkage to TTR. A few of the aryl sulfonyl fluorides efficiently form conjugates with TTR in plasma. Eleven of the TTR covalent kinetic stabilizers synthesized exhibit fluorescence upon conjugation and therefore could have imaging applications as a consequence of the environment sensitive fluorescence of the chromophore.
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Affiliation(s)
- Neil P Grimster
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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50
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Lim KH, Dyson HJ, Kelly JW, Wright PE. Localized structural fluctuations promote amyloidogenic conformations in transthyretin. J Mol Biol 2013; 425:977-88. [PMID: 23318953 DOI: 10.1016/j.jmb.2013.01.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 12/21/2012] [Accepted: 01/07/2013] [Indexed: 11/24/2022]
Abstract
The process of transthyretin (TTR) misfolding and aggregation, including amyloid formation, appears to cause a number of degenerative diseases. During amyloid formation, the native protein undergoes a tetramer-to-folded monomer transition, followed by local unfolding of the monomer to an assembly-competent amyloidogenic intermediate. Here we use NMR relaxation dispersion to probe conformational exchange at physiological pH between native monomeric TTR (the F87M/L110M variant) and a small population of a transiently formed amyloidogenic intermediate. The dispersion experiments show that a majority of the residues in the β-sheet containing β-strands D, A, G, and H undergo conformational fluctuations on microsecond-to-millisecond timescales. Exchange broadening is greatest for residues in the outer β-strand H, which hydrogen bonds to β-strand H' of a neighboring subunit in the tetramer, but the associated structural fluctuations propagate across the entire β-sheet. Fluctuations in the other β-sheet are limited to the outer β-strand F, which packs against strand F' in the tetramer, while the B, C, and E β-strands of this sheet remain stable. The structural changes were also investigated under more forcing amyloidogenic conditions (pH6.4-3.7), where β-strand D and regions of the D-E and E-F loops were additionally destabilized, increasing the population of the amyloidogenic intermediate and accelerating amyloid formation. Strands B, C, and E appear to maintain native-like conformations in the partially unfolded, amyloidogenic state of wild-type TTR. In the case of the protective mutant T119M, the conformational fluctuations are suppressed under both physiological and mildly acidic conditions, indicating that the dynamic properties of TTR correlate well with its aggregation propensity.
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Affiliation(s)
- Kwang Hun Lim
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA.
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