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Hall D. Biophysical Reviews' "Meet the Editors Series": a profile of Damien Hall. Biophys Rev 2023; 15:1883-1896. [PMID: 38192343 PMCID: PMC10771549 DOI: 10.1007/s12551-023-01176-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2023] [Indexed: 01/10/2024] Open
Abstract
This piece introduces Damien Hall, Chief Editor of the Biophysical Reviews journal since 2019. Currently working as an Assistant Professor at Kanazawa University, the author describes his association with the journal along with some parts of his family history and academic journey.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164 Japan
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2
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Hall D. MIL-CELL: a tool for multi-scale simulation of yeast replication and prion transmission. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:673-704. [PMID: 37670150 PMCID: PMC10682183 DOI: 10.1007/s00249-023-01679-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 09/07/2023]
Abstract
The single-celled baker's yeast, Saccharomyces cerevisiae, can sustain a number of amyloid-based prions, the three most prominent examples being [URE3], [PSI+], and [PIN+]. In the laboratory, haploid S. cerevisiae cells of a single mating type can acquire an amyloid prion in one of two ways (i) spontaneous nucleation of the prion within the yeast cell, and (ii) receipt via mother-to-daughter transmission during the cell division cycle. Similarly, prions can be lost due to (i) dissolution of the prion amyloid by its breakage into non-amyloid monomeric units, or (ii) preferential donation/retention of prions between the mother and daughter during cell division. Here we present a computational tool (Monitoring Induction and Loss of prions in Cells; MIL-CELL) for modelling these four general processes using a multiscale approach describing both spatial and kinetic aspects of the yeast life cycle and the amyloid-prion behavior. We describe the workings of the model, assumptions upon which it is based and some interesting simulation results pertaining to the wave-like spread of the epigenetic prion elements through the yeast population. MIL-CELL is provided as a stand-alone GUI executable program for free download with the paper. MIL-CELL is equipped with a relational database allowing all simulated properties to be searched, collated and graphed. Its ability to incorporate variation in heritable properties means MIL-CELL is also capable of simulating loss of the isogenic nature of a cell population over time. The capability to monitor both chronological and reproductive age also makes MIL-CELL potentially useful in studies of cell aging.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa, 920-1164, Japan.
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3
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Kumar M, Teakel SL, Swarbrick C, Chowdhury IS, Thorn DC, Sunde M, Carver JA, Forwood JK. Amyloid fibril formation, structure and domain swapping of acyl-coenzyme A thioesterase-7. FEBS J 2023; 290:4057-4073. [PMID: 37042241 DOI: 10.1111/febs.16795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/23/2023] [Accepted: 04/11/2023] [Indexed: 04/13/2023]
Abstract
Acyl-coenzyme A thioesterase (Acot) enzymes are involved in a broad range of essential intracellular roles including cell signalling, lipid metabolism, inflammation and the opening of ion channels. Dysregulation in lipid metabolism has been linked to neuroinflammatory and neurological disorders such as Alzheimer's and Parkinson's diseases. Structurally, Acot enzymes adopt a circularised trimeric arrangement with each monomer containing an N- and a C-terminal hotdog domain. Acot7 spontaneously forms amyloid fibrils in vitro under physiological conditions. The resultant amyloid fibrillar structures were characterised by dye-binding fluorescence assays, far-UV circular dichroism spectroscopy, transmission electron microscopy and X-ray fibre diffraction. Acot7 has an unusual mechanism of aggregation with no lag phase. The initial phase (~ 18 h) of aggregation involves conformational rearrangement within the oligomers to form species of enhanced β-sheet character. The subsequent loss of α-helical structure is accompanied by large-scale amyloid fibril formation. The crystal structure of Acot7 revealed an unexpected arrangement of the two domains within the circularised trimeric structure, which is the basis for a proposed mechanism of amyloid fibril formation involving domain swapping during the initial phase of aggregation. Acot7 formed fibrils in the presence of its substrate arachidonoyl-CoA and its inhibitors and maintained its enzyme activity during fibril assembly. It is proposed that the Acot7 fibrillar form acts as functional amyloid.
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Affiliation(s)
- Manjeet Kumar
- Research School of Chemistry, The Australian National University, Acton, Australia
| | - Sarah L Teakel
- School of Dentistry and Medical Science, Charles Sturt University, Wagga Wagga, Australia
| | - Crystall Swarbrick
- School of Dentistry and Medical Science, Charles Sturt University, Wagga Wagga, Australia
| | - Intifar S Chowdhury
- Research School of Chemistry, The Australian National University, Acton, Australia
| | - David C Thorn
- Research School of Chemistry, The Australian National University, Acton, Australia
| | - Margaret Sunde
- School of Medical Sciences, The University of Sydney, Australia
| | - John A Carver
- Research School of Chemistry, The Australian National University, Acton, Australia
| | - Jade K Forwood
- School of Dentistry and Medical Science, Charles Sturt University, Wagga Wagga, Australia
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4
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A fortunate period of overlap with Prof. Haruki Nakamura. Biophys Rev 2022; 14:1239-1245. [PMID: 36589736 PMCID: PMC9786412 DOI: 10.1007/s12551-022-01033-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The author recounts a period of overlap with Prof. Haruki Nakamura that stretched from 2007 till the present day. Starting as a short-term research fellow in his laboratory, the author has also been a coauthor, academic colleague, and joint journal editorial board member of Prof. Nakamura.
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Chen EHL, Lin KM, Sang JC, Ho MR, Lee CH, Shih O, Su CJ, Yeh YQ, Jeng US, Chen RPY. Condition-dependent structural collapse in the intrinsically disordered N-terminal domain of prion protein. IUBMB Life 2021; 74:780-793. [PMID: 34288372 DOI: 10.1002/iub.2528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 11/06/2022]
Abstract
Prion protein is composed of a structure-unsolved N-terminal domain and a globular C-terminal domain. Under limited trypsin digestion, mouse recombinant prion protein can be cleaved into two parts at residue Lys105. Here, we termed these two fragments as the N-domain (sequence 23-105) and the C-domain (sequence 106-230). In this study, the structural properties of the N-domain, the C-domain, and the full-length protein were explored using small-angle X-ray scattering, analytical ultracentrifugation, circular dichroism spectroscopy, and the 8-anilino-1-naphthalenesulfonic acid binding assay. The conformation and size of the prion protein were found to change sensitively under the solvent conditions. The positive residues in the sequence 23-99 of the N-domain were found to be responsible for the enhanced flexibility with the salt concentration reduced below 5 mM. The C-domain containing a hydrophobic patch tends to unfold and aggregate during a salt-induced structural collapse. The N-domain collapsed together with the C-domain at pH 5.2, whereas it collapsed independently at pH 4.2. The positively charged cluster (sequence 100-105) in the N-domain contributed to protecting the exposed hydrophobic surface of the C-domain.
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Affiliation(s)
- Eric H-L Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kuei-Ming Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Jason C Sang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chih-Hsuan Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Chun-Jen Su
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan.,Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Rita P-Y Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.,Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, Taiwan
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Hall D. A simple method for modeling amyloid kinetics featuring position biased fiber breakage. Biophys Physicobiol 2020; 17:30-35. [PMID: 33110736 PMCID: PMC7550252 DOI: 10.2142/biophysico.bsj-2020003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/12/2020] [Indexed: 12/01/2022] Open
Abstract
A mathematical model of amyloid fiber formation is described that is able to simply specify different rates of fiber breakage at internal versus end regions. This Note presents the derivation of the relevant equations and provides results showing the dramatic effects of position biased fiber breakage on the kinetics of amyloid growth.
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Affiliation(s)
- Damien Hall
- Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bethesda, MD 20892-0830, USA.,Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.,Present address: International Center, Nagoya Institute of Technology, Gokiso, Showa, Nagoya, Aichi 466-8555, Japan
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Masso M, Bansal A, Bansal A, Henderson A. Structure-based functional analysis of BRCA1 RING domain variants: Concordance of computational mutagenesis, experimental assay, and clinical data. Biophys Chem 2020; 266:106442. [PMID: 32916545 DOI: 10.1016/j.bpc.2020.106442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/25/2020] [Accepted: 07/26/2020] [Indexed: 01/16/2023]
Abstract
A significant impediment to the improvement of clinical outcomes in treating breast and ovarian cancers rests with the lack of available interpretations for BRCA1 variants of unknown significance. Two research groups recently implemented large-scale functional assays for quantifying effects of single missense mutations on homology-directed DNA repair activity of BRCA1 variants, which is critical for tumor suppression and strongly correlates with cancer risk, and their results are significantly concordant with each other as well as with known pathogenic and benign variant clinical data. In this work, we implemented an established computational mutagenesis procedure to characterize structural impacts of single residue replacements to the BRCA1 RING domain. The computational data showed similarly strong concordance with known clinical data as well as with experimental data from both functional assays. Predictions made by models trained on our computational data offer a complementary and orthogonal approach for classifying all remaining unexplored BRCA1 RING domain variants.
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Affiliation(s)
- Majid Masso
- School of Systems Biology, College of Science, George Mason University, 10900 University Boulevard MS 5B3, Manassas, VA 20110, USA.
| | - Anirudh Bansal
- School of Systems Biology, College of Science, George Mason University, 10900 University Boulevard MS 5B3, Manassas, VA 20110, USA
| | - Arnav Bansal
- School of Systems Biology, College of Science, George Mason University, 10900 University Boulevard MS 5B3, Manassas, VA 20110, USA
| | - Andrea Henderson
- School of Systems Biology, College of Science, George Mason University, 10900 University Boulevard MS 5B3, Manassas, VA 20110, USA
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Vosoughi A, Sadigh-Eteghad S, Ghorbani M, Shahmorad S, Farhoudi M, Rafi MA, Omidi Y. Mathematical Models to Shed Light on Amyloid-Beta and Tau Protein Dependent Pathologies in Alzheimer's Disease. Neuroscience 2019; 424:45-57. [PMID: 31682825 DOI: 10.1016/j.neuroscience.2019.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 12/11/2022]
Abstract
The number of patients suffering from dementia due to Alzheimer's disease (AD) is constantly rising worldwide. This has accordingly resulted in huge burdens on the health systems and involved families. Lack of profound understanding of neural networking in normal brain and their interruption in AD makes the treatment of this neurodegenerative multifaceted disease a challenging issue. In recent years, mathematical and computational methods have paved the way towards a better understanding of the brain functional connectivity. Thus, much attention has been paid to this matter from both basic science researchers and clinicians with an interdisciplinary approach to determine what is not functioning properly in AD patients and how this malfunctioning can be addressed. In this review, a number of AD-related articles and well-studied pathophysiologic topics (e.g., amyloid-beta, neurofibrillary tangles, Ca2+ dysregulation, and synaptic plasticity alterations) has been literally surveyed from a computational and systems biology point of view. The neural networks were discussed from biological and mathematical point of views and their alterations in recent findings were further highlighted. Application of the graph theoretical analysis in the brain imaging was reviewed, depicting the relations between brain structure and function, without diving into mathematical details. Moreover, differential rate equations were briefly articulated, emphasizing the potential use of these equations in simplifying complex processes in relevance to pathologies of AD. Comprehensive insights were given into the AD progression from neural networks perspective, which may lead us towards potential strategies for early diagnosis and effective treatment of AD.
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Affiliation(s)
- Armin Vosoughi
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Sadigh-Eteghad
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Mehdi Farhoudi
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad A Rafi
- Department of Neurology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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9
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Hall D. On the nature of the optimal form of the holdase-type chaperone stress response. FEBS Lett 2019; 594:43-66. [PMID: 31432502 DOI: 10.1002/1873-3468.13580] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/12/2019] [Accepted: 08/14/2019] [Indexed: 11/08/2022]
Abstract
The holdase paradigm of chaperone action involves preferential binding by the chaperone to the unfolded protein state, thereby preventing it from either, associating with other unstable proteins (to form large dysfunctional aggregates), or being degraded by the proteolytic machinery of the cell/organism. In this paper, we examine the necessary physical constraints imposed upon the holdase chaperone response in a cell-like environment and use these limitations to comment on the likely nature of the optimal form of chaperone response in vivo.
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Affiliation(s)
- Damien Hall
- Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bethesda, MD, USA.,Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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10
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Hirota N, Edskes H, Hall D. Unified theoretical description of the kinetics of protein aggregation. Biophys Rev 2019; 11:191-208. [PMID: 30888575 DOI: 10.1007/s12551-019-00506-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 02/12/2019] [Indexed: 02/07/2023] Open
Abstract
Solution conditions chosen for the production of amyloid can also promote formation of significant extents of amorphous protein aggregate. In one interpretation, the amyloid and amorphous aggregation pathways are considered to be in competition with each other. An alternative conceptualization involves considering amorphous aggregation as an obligatory intermediate process of the amyloid formation pathway. Here, we review recently developed macroscopic-level theories of protein aggregation that unify these two competing models into a single paradigm. Key features of the unified model included (1) a description of the amorphous aggregate as a second liquid phase with the degree of liquid-like character determined by the mobility of the monomer within it, and (2) heterogeneous growth pathways based on nucleation, growth, and fragmentation of amyloid occurring within different phases and at their interfacial boundary. Limiting-case behaviors of the protein aggregation reaction, either singly involving amyloid or amorphous aggregate production, and mixed-case behaviors, involving competitive and/or facilitated growth of amorphous and amyloid species, are presented and reviewed in context. This review principally describes an approach developed by Hirota and Hall 2019 (Hirota, N. and Hall, D. 2019. Protein Aggregation Kinetics: A Unified Theoretical Description. Chapter 7 of 'Protein Solubility and Amorphous Aggregation: From Academic Research to Applications in Drug Discovery and Bioindustry' edited by Y. Kuroda and F. Arisaka. CMC Publishers). Sections of that work are translated from the original Japanese and republished here with the full permission of CMC Publishing Corporation.
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Affiliation(s)
- Nami Hirota
- Do International Trading House, Koshienguchi-1-chome, Nishinomiya, Hyogo, 6113, Japan
| | - Herman Edskes
- Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bld 8, Bethesda, MD, 20892-0830, USA
| | - Damien Hall
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871, Japan.
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11
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Ionic liquids and protein folding-old tricks for new solvents. Biophys Rev 2019; 11:209-225. [PMID: 30888574 DOI: 10.1007/s12551-019-00509-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/15/2019] [Indexed: 01/19/2023] Open
Abstract
One important aspect of the green chemistry revolution has been the use of ionic liquids as the solvent in liquid-phase enzymatic catalysis. An essential requirement for protein enzyme function is the correct folding of the polypeptide chain into its functional "native" state. Quantitative assessment of protein structure may be carried out either empirically, or by using model-based characterization procedures, in which the parameters are defined in terms of a standard reference state. In this short note, we briefly outline the nature of the parameters associated with different empirical and model-based characterization procedures and point out factors which affect their interpretation when using a base solvent different from water. This review principally describes arguments developed by Wakayama et al., Protein Solubility and Amorphous Aggregation: From Academic Research to Applications in Drug Discovery and Bioindustry, 2019, edited by Y. Kuroda and F. Arisaka; CMC Publishing House. Sections of that work are translated from the original Japanese and republished here with the full permission of CMC Publishing Corporation.
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12
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Hall D, Kinjo AR, Goto Y. A new look at an old view of denaturant induced protein unfolding. Anal Biochem 2018; 542:40-57. [DOI: 10.1016/j.ab.2017.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/11/2017] [Accepted: 11/16/2017] [Indexed: 12/15/2022]
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13
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Carver JA, Grosas AB, Ecroyd H, Quinlan RA. The functional roles of the unstructured N- and C-terminal regions in αB-crystallin and other mammalian small heat-shock proteins. Cell Stress Chaperones 2017; 22:627-638. [PMID: 28391594 PMCID: PMC5465038 DOI: 10.1007/s12192-017-0789-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/06/2017] [Accepted: 03/16/2017] [Indexed: 01/18/2023] Open
Abstract
Small heat-shock proteins (sHsps), such as αB-crystallin, are one of the major classes of molecular chaperone proteins. In vivo, under conditions of cellular stress, sHsps are the principal defence proteins that prevent large-scale protein aggregation. Progress in determining the structure of sHsps has been significant recently, particularly in relation to the conserved, central and β-sheet structured α-crystallin domain (ACD). However, an understanding of the structure and functional roles of the N- and C-terminal flanking regions has proved elusive mainly because of their unstructured and dynamic nature. In this paper, we propose functional roles for both flanking regions, based around three properties: (i) they act in a localised crowding manner to regulate interactions with target proteins during chaperone action, (ii) they protect the ACD from deleterious amyloid fibril formation and (iii) the flexibility of these regions, particularly at the extreme C-terminus in mammalian sHsps, provides solubility for sHsps under chaperone and non-chaperone conditions. In the eye lens, these properties are highly relevant as the crystallin proteins, in particular the two sHsps αA- and αB-crystallin, are present at very high concentrations.
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Affiliation(s)
- John A Carver
- Research School of Chemistry, The Australian National University, Acton, ACT, 2601, Australia.
| | - Aidan B Grosas
- Research School of Chemistry, The Australian National University, Acton, ACT, 2601, Australia
| | - Heath Ecroyd
- School of Biological Sciences and the Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Roy A Quinlan
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
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Zhao R, So M, Maat H, Ray NJ, Arisaka F, Goto Y, Carver JA, Hall D. Measurement of amyloid formation by turbidity assay-seeing through the cloud. Biophys Rev 2016; 8:445-471. [PMID: 28003859 PMCID: PMC5135725 DOI: 10.1007/s12551-016-0233-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 10/11/2016] [Indexed: 12/12/2022] Open
Abstract
Detection of amyloid growth is commonly carried out by measurement of solution turbidity, a low-cost assay procedure based on the intrinsic light scattering properties of the protein aggregate. Here, we review the biophysical chemistry associated with the turbidimetric assay methodology, exploring the reviewed literature using a series of pedagogical kinetic simulations. In turn, these simulations are used to interrogate the literature concerned with in vitro drug screening and the assessment of amyloid aggregation mechanisms.
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Affiliation(s)
- Ran Zhao
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia
| | - Masatomo So
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Hendrik Maat
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia
| | - Nicholas J Ray
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia
| | - Fumio Arisaka
- College of Bio-resource Sciences, Nihon University, Chiyoda-ku, Tokyo, 102-8275, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - John A Carver
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia
| | - Damien Hall
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia. .,Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871, Japan.
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15
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Hoshino M. Fibril formation from the amyloid-β peptide is governed by a dynamic equilibrium involving association and dissociation of the monomer. Biophys Rev 2016; 9:9-16. [PMID: 28510040 DOI: 10.1007/s12551-016-0217-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 08/09/2016] [Indexed: 11/28/2022] Open
Abstract
Here I review the molecular mechanisms by which water-soluble monomeric amyloid-β (Aβ) peptides are transformed into well-organized supramolecular complexes called amyloid fibrils. The mechanism of amyloid formation is considered theoretically on the basis of experimental results, and the structural and mechanistic similarities of amyloid fibrils to three-dimensional crystals are highlighted. A number of important results from the literature are described. These include the observation that a correct ratio of monomer association and dissociation rate constants is key for formation of well-organized amyloid fibrils. The dynamic nature of the amyloid-β structure is discussed, along with the possibly obligate requirement of the transient formation of a hairpin-like fold prior to its incorporation into amyloid fibrils. Many rounds of monomer association and dissociation events may be present during an apparently silent lag-period. Amongst these association/dissociation events, interaction between the C-terminal regions of the Aβ peptide seems to be more favored. Such association and dissociation events occurring in a "trial-and-error" fashion may be an important requirement for the formation of well-organized amyloid fibrils.
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Affiliation(s)
- Masaru Hoshino
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi, Sakyo-ku, Kyoto, 606-8501, Japan.
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17
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Hall D, Kardos J, Edskes H, Carver JA, Goto Y. A multi-pathway perspective on protein aggregation: implications for control of the rate and extent of amyloid formation. FEBS Lett 2015; 589:672-9. [PMID: 25647034 PMCID: PMC4349420 DOI: 10.1016/j.febslet.2015.01.032] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/23/2015] [Indexed: 12/29/2022]
Abstract
The nucleation-growth model has been used extensively for characterizing in vitro amyloid fibril formation kinetics and for simulating the relationship between amyloid and disease. In the majority of studies amyloid has been considered as the dominant, or sole, aggregation end product, with the presence of other competing non-amyloid aggregation processes, for example amorphous aggregate formation, being largely ignored. Here, we examine possible regulatory effects that off-pathway processes might exert on the rate and extent of amyloid formation - in particular their potential for providing false positives and negatives in the evaluation of anti-amyloidogenic agents. Furthermore, we investigate how such competing reactions might influence the standard interpretation of amyloid aggregation as a two-state system. We conclude by discussing our findings in terms of the general concepts of supersaturation and system metastability - providing some mechanistic insight as to how these empirical phenomena may manifest themselves in the amyloid arena.
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Affiliation(s)
- Damien Hall
- Research School of Chemistry, Australian National University, Acton, ACT 2601, Australia; Institute for Protein Research, Osaka University, 3-1-Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - József Kardos
- MTA-ELTE NAP B Neuroimmunology Research Group and Department of Biochemistry, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Herman Edskes
- Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bethesda, Bld 8, MD 20892-0830, USA
| | - John A Carver
- Research School of Chemistry, Australian National University, Acton, ACT 2601, Australia
| | - Yuji Goto
- Institute for Protein Research, Osaka University, 3-1-Yamada-oka, Suita, Osaka 565-0871, Japan
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18
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Schreck JS, Yuan JM. A Kinetic Study of Amyloid Formation: Fibril Growth and Length Distributions. J Phys Chem B 2013; 117:6574-83. [DOI: 10.1021/jp401586p] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John S. Schreck
- Department
of Physics, Drexel University, Philadelphia,
Pennsylvania 19104, United States
| | - Jian-Min Yuan
- Department
of Physics, Drexel University, Philadelphia,
Pennsylvania 19104, United States
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Hall D, Edskes H. Computational modeling of the relationship between amyloid and disease. Biophys Rev 2012; 4:205-222. [PMID: 23495357 PMCID: PMC3595053 DOI: 10.1007/s12551-012-0091-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 06/21/2012] [Indexed: 01/29/2023] Open
Abstract
Amyloid is a title conferred upon a special type of linear protein aggregate that exhibits a common set of structural features and dye binding capabilities. The formation of amyloid is associated with over twenty-seven distinct human diseases which are collectively referred to as the amyloidoses. Although there is great diversity amongst the amyloidoses with regard to the polypeptide monomeric precursor, targeted tissues and the nature and time course of disease development, the common underlying link of a structurally similar amyloid aggregate has prompted the search for a unified theory of disease progression in which amyloid production is the central element. Computational modeling has allowed the formulation and testing of scientific hypotheses for exploring this relationship. However, the majority of computational studies on amyloid aggregation are pitched at the atomistic level of description, in simple ideal solution environments, with simulation time scales of the order of microseconds and system sizes limited to a hundred monomers (or less). The experimental reality is that disease related amyloid aggregation processes occur in extremely complex reaction environments (i.e. the human body), over time-scales of months to years with monitoring of the reaction achieved using extremely coarse or indirect experimental markers that yield little or no atomistic insight. Clearly a substantial gap exists between computational and experimental communities with a deficit of 'useful' computational methodology that can be directly related to available markers of disease progression. This Review will place its focus on the development of these latter types of computational models and discuss them in relation to disease onset and progression.
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Affiliation(s)
- Damien Hall
- Institute of Basic Medical Science, University of Tsukuba, Lab 225-B, Building D. 1-1-1 Tennodai, Tsukuba-shi, Ibaraki-ken 305-8577 Japan
| | - Herman Edskes
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830 USA
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On the use of size exclusion chromatography for the resolution of mixed amyloid aggregate distributions: I. Equilibrium partition models. Anal Biochem 2012; 426:69-85. [DOI: 10.1016/j.ab.2012.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/30/2012] [Accepted: 04/01/2012] [Indexed: 11/24/2022]
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Hall D. Semi-automated methods for simulation and measurement of amyloid fiber distributions obtained from transmission electron microscopy experiments. Anal Biochem 2012; 421:262-77. [DOI: 10.1016/j.ab.2011.10.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/04/2011] [Accepted: 10/04/2011] [Indexed: 11/27/2022]
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A model of amyloid's role in disease based on fibril fracture. Biophys Chem 2009; 145:17-28. [PMID: 19735971 DOI: 10.1016/j.bpc.2009.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 08/09/2009] [Accepted: 08/09/2009] [Indexed: 02/04/2023]
Abstract
Although the correlative evidence relating the presence of amyloid fibrils and certain disease states (e.g. Alzheimer's disease and Type 2 Diabetes) is overwhelming, a direct causative role for amyloid has proved harder to establish. Current thinking links a narrow region of the aggregate protein size distribution, the so called 'early aggregate' domain to cellular toxicity. A troubling feature of this theory however is that the nucleated reaction mechanism by which amyloid formation is believed to occur results in a very low number concentration of early aggregates which are rapidly extended to form amyloid fibrils. This situation means that the concentration of early aggregates is very low at the time when they are supposedly at their most toxic. Here we adopt a novel explicit simulation strategy to examine a kinetic regime involving nucleated growth combined with fibril fragmentation under which this situation can be reversed so as to produce a high number concentration of small on-pathway toxic aggregates. Dependent upon the rate of fragmentation, the time scale for generation of toxic early aggregates may be coupled, uncoupled or disassociated from the time scale for the appearance of amyloid fibrils. Furthermore the model presents itself as a biochemical 'switch' transitioning between modes of amyloid induced cell death dependent upon either specific amyloid toxicity or non-specific solid mass induced tissue damage.
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