1
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Lau Y, Oamen HP, Grogg M, Parfenova I, Saarikangas J, Hannay R, Nichols RA, Hilvert D, Barral Y, Caudron F. Whi3 mnemon association with endoplasmic reticulum membranes confines the memory of deceptive courtship to the yeast mother cell. Curr Biol 2022; 32:963-974.e7. [PMID: 35085498 PMCID: PMC8938615 DOI: 10.1016/j.cub.2022.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/19/2021] [Accepted: 01/04/2022] [Indexed: 12/17/2022]
Abstract
Prion-like proteins are involved in many aspects of cellular physiology, including cellular memory. In response to deceptive courtship, budding yeast escapes pheromone-induced cell-cycle arrest through the coalescence of the G1/S inhibitor Whi3 into a dominant, inactive super-assembly. Whi3 is a mnemon (Whi3mnem), a protein that conformational change maintains as a trait in the mother cell but is not inherited by the daughter cells. How the maintenance and asymmetric inheritance of Whi3mnem are achieved is unknown. Here, we report that Whi3mnem is closely associated with endoplasmic reticulum (ER) membranes and is retained in the mother cell by the lateral diffusion barriers present at the bud neck. Strikingly, barrier defects made Whi3mnem propagate in a mitotically stable, prion-like manner. The amyloid-forming glutamine-rich domain of Whi3 was required for both mnemon and prion-like behaviors. Thus, we propose that Whi3mnem is in a self-templating state, lending temporal maintenance of memory, whereas its association with the compartmentalized membranes of the ER prevents infectious propagation to the daughter cells. These results suggest that confined self-templating super-assembly is a powerful mechanism for the long-term encoding of information in a spatially defined manner. Yeast courtship may provide insights on how individual synapses become potentiated in neuronal memory.
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Affiliation(s)
- Yasmin Lau
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Henry Patrick Oamen
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Marcel Grogg
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg, 8093 Zürich, Switzerland
| | - Iuliia Parfenova
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg, 8093 Zürich, Switzerland
| | - Juha Saarikangas
- Helsinki Institute of Life Science HiLIFE, Viikinkaari 5, 00790 Helsinki, Finland; Faculty of Biological and Environmental Sciences, Viikinkaari 5, 00790 Helsinki, Finland; Neuroscience Center, University of Helsinki, Viikinkaari 5, 00790 Helsinki, Finland
| | - Robin Hannay
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Richard Alan Nichols
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg, 8093 Zürich, Switzerland
| | - Yves Barral
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg, 8093 Zürich, Switzerland
| | - Fabrice Caudron
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; IGMM, Univ Montpellier, CNRS, Route de Mende, 34293 Montpellier, France.
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2
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Reselammal DS, Pinhero F, Sharma R, Oliyantakath Hassan MS, Srinivasula SM, Vijayan V. Mapping the Fibril Core of the Prion Subdomain of the Mammalian CPEB3 that is Involved in Long Term Memory Retention. J Mol Biol 2021; 433:167084. [PMID: 34081983 DOI: 10.1016/j.jmb.2021.167084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 11/15/2022]
Abstract
Long-term memory storage is modulated by the prion nature of CPEB3 forming the molecular basis for the maintenance of synaptic facilitation. Here we report that the first prion sub-domain PRD1 of mouse CPEB3 can autonomously form amyloid fibrils in vitro and punctate-like structures in vivo. A ninety-four amino acid sequence within the PRD1 domain, PRD1-core, displays high propensity towards aggregation and associated amyloid characteristics. PRD1-core is characterized using electron microscopy, X-ray diffraction, and solution-state NMR deuterium exchange experiments. Secondary structure elements deduced from solid-state NMR reveal a β-rich core comprising of forty amino acids at the N-terminus of PRD1-core. The synthesized twenty-three amino acid long peptide containing the longest rigid segment (E124-H145) of the PRD1-core rapidly self-aggregates and forms fibrils, indicating a limited aggregation-prone region that could potentially activate the aggregation of the full-length protein. This study provides the first step in identifying the structural trigger for the CPEB3 aggregation process.
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Affiliation(s)
- Dhanya S Reselammal
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Faina Pinhero
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Rahul Sharma
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | | | - Srinivasa M Srinivasula
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Vinesh Vijayan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India.
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3
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Muta H, So M, Sakurai K, Kardos J, Naiki H, Goto Y. Amyloid Formation under Complicated Conditions in Which β 2-Microglobulin Coexists with Its Proteolytic Fragments. Biochemistry 2019; 58:4925-4934. [PMID: 31724398 DOI: 10.1021/acs.biochem.9b00917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloid formation in vivo occurs under complicated conditions in which various amyloidogenic and non-amyloidogenic components coexist, often under crowding. Controversy surrounds the role of additional components under complicated conditions. They have been suggested to accelerate amyloid formation because molecular crowding or interactions with additives increase effective concentrations and, thus, break the supersaturation of amyloidogenic proteins. On the other hand, cellular crowding conditions with various heterogeneous components may retard or prevent amyloid formation because they impede homologous amyloidogenic associations. To elucidate the roles of these additional components, we examined the amyloid formation of β2-microglobulin (β2m), a protein responsible for dialysis-related amyloidosis, with a simplified model system in which intact β2m and its proteolytic peptides coexist. Among the nine proteolytic peptides of β2m produced in vitro with lysyl endopeptidase, the 22-residue K3 peptide is highly amyloidogenic. The amyloid formation of the K3 peptide, which occurred with a lag time of 1 h at pH 2 and 37 °C, was significantly retarded by the coexistence of β2m or a mixture of the proteolytic digests. To identify the sites of inhibitory interactions, we performed paramagnetic relaxation enhancement measurements using spin-labeled K3 and uniformly 15N-labeled β2m with nuclear magnetic resonance detection. The results revealed that K3 interacted weakly with a broad cluster of the hydrophobic residues of β2m, which accommodated the residues located in some distant sequence, leading to competitive inhibition. The results showed that relatively weak and broad interactions formed a nonproductive complex, implying a role for heterogeneous interactions under complicated conditions.
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Affiliation(s)
- Hiroya Muta
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
| | - Masatomo So
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
| | - Kazumasa Sakurai
- Institute of Advanced Technology , Kindai University , Wakayama 649-6493 , Japan
| | - Jozsef Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry , Eötvös Loránd University , Pázmány P. sétány 1/C , Budapest 1117 , Hungary
| | - Hironobu Naiki
- Faculty of Medical Sciences , University of Fukui , Fukui 910-1193 , Japan
| | - Yuji Goto
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
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4
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Narang SS, Shuaib S, Goyal D, Goyal B. In silico-guided identification of potential inhibitors against β2m aggregation in dialysis-related amyloidosis. J Biomol Struct Dyn 2019; 38:3927-3941. [DOI: 10.1080/07391102.2019.1668852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Suniba Shuaib
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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5
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Noji M, Sasahara K, Yamaguchi K, So M, Sakurai K, Kardos J, Naiki H, Goto Y. Heating during agitation of β 2-microglobulin reveals that supersaturation breakdown is required for amyloid fibril formation at neutral pH. J Biol Chem 2019; 294:15826-15835. [PMID: 31495783 DOI: 10.1074/jbc.ra119.009971] [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: 06/27/2019] [Revised: 08/19/2019] [Indexed: 12/27/2022] Open
Abstract
Amyloidosis-associated amyloid fibrils are formed by denatured proteins when supersaturation of denatured proteins is broken. β2-Microglobulin (β2m) forms amyloid fibrils and causes dialysis-related amyloidosis in patients receiving long-term hemodialysis. Although amyloid fibrils of β2m in patients are observed at neutral pH, formation of β2m amyloids in vitro has been difficult to discern at neutral pH because of the amyloid-resistant native structure. Here, to further understand the mechanism underlying in vivo amyloid formation, we investigated the relationship between protein folding/unfolding and misfolding leading to amyloid formation. Using thioflavin T assays, CD spectroscopy, and transmission EM analyses, we found that β2m efficiently forms amyloid fibrils even at neutral pH by heating with agitation at high-salt conditions. We constructed temperature- and NaCl concentration-dependent conformational phase diagrams in the presence or absence of agitation, revealing how amyloid formation under neutral pH conditions is related to thermal unfolding and breakdown of supersaturation. Of note, after supersaturation breakdown and following the law of mass action, the β2m monomer equilibrium shifted to the unfolded state, destabilizing the native state and thereby enabling amyloid formation even under physiological conditions with a low amount of unfolded precursor. The amyloid fibrils depolymerized at both lower and higher temperatures, resembling cold- or heat-induced denaturation of globular proteins. Our results suggest an important role for heating in the onset of dialysis-related amyloidosis and related amyloidoses.
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Affiliation(s)
- Masahiro Noji
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Kenji Sasahara
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Keiichi Yamaguchi
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Kazumasa Sakurai
- Institute of Advanced Technology, Kindai University, Wakayama 649-6493, Japan
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány P. Sétány 1/C, Budapest, 1117, Hungary
| | - Hironobu Naiki
- Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
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6
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Khan MV, Zaman M, Chandel TI, Siddiqui MK, Ajmal MR, Abdelhameed AS, Khan RH. Cationic surfactant mediated fibrillogenesis in bovine liver catalase: a biophysical approach. J Biomol Struct Dyn 2017; 36:2543-2557. [DOI: 10.1080/07391102.2017.1363085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mohsin Vahid Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Masihuz Zaman
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Tajalli Ilm Chandel
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Khursheed Siddiqui
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Mohd. Rehan Ajmal
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Ali Saber Abdelhameed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Rizwan Hasan Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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7
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Ruiz J, Boehringer R, Grogg M, Raya J, Schirer A, Crucifix C, Hellwig P, Schultz P, Torbeev V. Covalent Tethering and Residues with Bulky Hydrophobic Side Chains Enable Self-Assembly of Distinct Amyloid Structures. Chembiochem 2016; 17:2274-2285. [PMID: 27717158 DOI: 10.1002/cbic.201600440] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Indexed: 11/10/2022]
Abstract
Polymorphism is a common property of amyloid fibers that complicates their detailed structural and functional studies. Here we report experiments illustrating the chemical principles that enable the formation of amyloid polymorphs with distinct stoichiometric composition. Using appropriate covalent tethering we programmed self-assembly of a model peptide corresponding to the [20-41] fragment of human β2-microglobulin into fibers with either trimeric or dimeric amyloid cores. Using a set of biophysical and biochemical methods we demonstrated their distinct structural, morphological, and templating properties. Furthermore, we showed that supramolecular approaches in which the peptide is modified with bulky substituents can also be applied to modulate the formation of different fiber polymorphs. Such strategies, when applied to disease-related peptides and proteins, will greatly help in the evaluation of the biological properties of structurally distinct amyloids.
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Affiliation(s)
- Jérémy Ruiz
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-, UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Régis Boehringer
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-, UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Marcel Grogg
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-, UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Jésus Raya
- Membrane Biophysics and NMR, Institute of Chemistry, University of Strasbourg, CNRS-, UMR 7177, 4 rue Blaise Pascal, 67008, Strasbourg, France
| | - Alicia Schirer
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-, UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Corinne Crucifix
- Department of Integrated Structural Biology, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM-U964, University of Strasbourg, CNRS-, UMR 7104, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Petra Hellwig
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-, UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Patrick Schultz
- Department of Integrated Structural Biology, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM-U964, University of Strasbourg, CNRS-, UMR 7104, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Vladimir Torbeev
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-, UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
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8
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Torbeev V, Grogg M, Ruiz J, Boehringer R, Schirer A, Hellwig P, Jeschke G, Hilvert D. Chiral recognition in amyloid fiber growth. J Pept Sci 2016; 22:290-304. [DOI: 10.1002/psc.2861] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/05/2016] [Accepted: 01/11/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires; International Center for Frontier Research in Chemistry, UMR 7006, Université de Strasbourg; 8 allée Gaspard Monge 67000 Strasbourg France
| | - Marcel Grogg
- Laboratory of Organic Chemistry, ETH Zurich; Vladimir-Prelog-Weg 1-5/10; Zürich CH-8093 Switzerland
| | - Jérémy Ruiz
- Institut de Science et d'Ingénierie Supramoléculaires; International Center for Frontier Research in Chemistry, UMR 7006, Université de Strasbourg; 8 allée Gaspard Monge 67000 Strasbourg France
| | - Régis Boehringer
- Institut de Science et d'Ingénierie Supramoléculaires; International Center for Frontier Research in Chemistry, UMR 7006, Université de Strasbourg; 8 allée Gaspard Monge 67000 Strasbourg France
| | - Alicia Schirer
- Laboratoire de Bioélectrochimie et Spectroscopie; Chimie de la Matière Complexe, UMR 7140, Université de Strasbourg-CNRS; 1 rue Blaise Pascal 67070 Strasbourg France
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie; Chimie de la Matière Complexe, UMR 7140, Université de Strasbourg-CNRS; 1 rue Blaise Pascal 67070 Strasbourg France
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry; ETH Zurich, Vladimir-Prelog-Weg 1-5/10; Zürich CH-8093 Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich; Vladimir-Prelog-Weg 1-5/10; Zürich CH-8093 Switzerland
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9
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Hiramatsu H, Ochiai H, Komuro T. Effects of N-Methylated Amyloid-β30-40Peptides on the Fibrillation of Amyloid-β1-40. Chem Biol Drug Des 2015; 87:425-33. [DOI: 10.1111/cbdd.12674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 09/27/2015] [Accepted: 10/14/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Hirotsugu Hiramatsu
- Graduate School of Pharmaceutical Sciences; Tohoku University; Sendai 980-8578 Japan
| | - Hironori Ochiai
- Graduate School of Pharmaceutical Sciences; Tohoku University; Sendai 980-8578 Japan
| | - Tomoyuki Komuro
- Graduate School of Pharmaceutical Sciences; Tohoku University; Sendai 980-8578 Japan
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10
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C-terminal sequence of amyloid-resistant type F apolipoprotein A-II inhibits amyloid fibril formation of apolipoprotein A-II in mice. Proc Natl Acad Sci U S A 2015; 112:E836-45. [PMID: 25675489 DOI: 10.1073/pnas.1416363112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In murine senile amyloidosis, misfolded serum apolipoprotein (apo) A-II deposits as amyloid fibrils (AApoAII) in a process associated with aging. Mouse strains carrying type C apoA-II (APOA2C) protein exhibit a high incidence of severe systemic amyloidosis. Previously, we showed that N- and C-terminal sequences of apoA-II protein are critical for polymerization into amyloid fibrils in vitro. Here, we demonstrate that congenic mouse strains carrying type F apoA-II (APOA2F) protein, which contains four amino acid substitutions in the amyloidogenic regions of APOA2C, were absolutely resistant to amyloidosis, even after induction of amyloidosis by injection of AApoAII. In vitro fibril formation tests showed that N- and C-terminal APOA2F peptides did not polymerize into amyloid fibrils. Moreover, a C-terminal APOA2F peptide was a strong inhibitor of nucleation and extension of amyloid fibrils during polymerization. Importantly, after the induction of amyloidosis, we succeeded in suppressing amyloid deposition in senile amyloidosis-susceptible mice by treatment with the C-terminal APOA2F peptide. We suggest that the C-terminal APOA2F peptide might inhibit further extension of amyloid fibrils by blocking the active ends of nuclei (seeds). We present a previously unidentified model system for investigating inhibitory mechanisms against amyloidosis in vivo and in vitro and believe that this system will be useful for the development of novel therapies.
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11
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Nakano M, Kamino K. Amyloid-like conformation and interaction for the self-assembly in barnacle underwater cement. Biochemistry 2015; 54:826-35. [PMID: 25537316 DOI: 10.1021/bi500965f] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Barnacles are unique marine sessile crustaceans and permanently attach to various foreign surfaces during most of their lifespan. The protein complex secreted from their body and used to attach their calcareous shell to almost all surfaces in water has long fascinated us because we have limited technology with which to attach materials in water. Unraveling the mechanism of underwater attachment by barnacles is thus important for interface science, for the understanding of the biology and physiology of barnacles, and for the development of technology to prevent fouling. Previous studies have indicated that the intermolecular interactions optimized by conformations of the adhesive proteins are crucial in the self-assembly and/or curing of the adhesive. This study aimed to identify the possible structural determinants responsible for the self-assembly. Thioflavin T binding screening of peptides designed on the basis of the primary structure of a bulk 52 kDa cement protein indicated the presence of some amyloidogenic motifs in the protein. The conformation of the peptide was transformed to a β-sheet by an increase in either pH or ionic strength, resulting in its self-assembly. Thioflavin T binding was inhibited by small polyphenolic molecules, suggesting the contribution of aromatic interactions during self-assembly. The occurrence of amyloid-like units in the protein implies that the protein conformation is an important factor contributing to the self-assembly of the cement, the first event of the curing, as the adhesive material is secreted into the seawater out of the animal's body.
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Affiliation(s)
- Masahiro Nakano
- Marine Biotechnology Institute , Kamaishi, Iwate 026-0001, Japan
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12
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Computational Approaches to Identification of Aggregation Sites and the Mechanism of Amyloid Growth. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:213-39. [DOI: 10.1007/978-3-319-17344-3_9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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13
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Ono K, Fujimoto E, Fujimoto N, Akiyama M, Satoh T, Maeda H, Fujii N, Tajima S. In vitro amyloidogenic peptides of galectin-7: possible mechanism of amyloidogenesis of primary localized cutaneous amyloidosis. J Biol Chem 2014; 289:29195-207. [PMID: 25172508 DOI: 10.1074/jbc.m114.592998] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Pathogenesis of primary localized cutaneous amyloidosis (PLCA) is unclear, but pathogenic relationship to keratinocyte apoptosis has been implicated. We have previously identified galectin-7, actin, and cytokeratins as the major constituents of PLCA. Determination of the amyloidogenetic potential of these proteins by thioflavin T (ThT) method demonstrated that galectin-7 molecule incubated at pH 2.0 was capable of binding to the dye, but failed to form amyloid fibrils. When a series of galectin-7 fragments containing β-strand peptides were prepared to compare their amyloidogenesis, Ser(31)-Gln(67) and Arg(120)-Phe(136) were aggregated to form amyloid fibrils at pH 2.0. The rates of aggregation of Ser(31)-Gln(67) and Arg(120)-Phe(136) were dose-dependent with maximal ThT levels after 3 and 48 h, respectively. Their synthetic analogs, Phe(33)-Lys(65) and Leu(121)-Arg(134), which are both putative tryptic peptides, showed comparable amyloidogenesis. The addition of sonicated fibrous form of Ser(31)-Gln(67) or Phe(33)-Lys(65) to monomeric Ser(31)-Gln(67) or Phe(33)-Lys(65) solution, respectively, resulted in an increased rate of aggregation and extension of amyloid fibrils. Amyloidogenic potentials of Ser(31)-Gln(67) and Phe(33)-Lys(65) were inhibited by actin and cytokeratin fragments, whereas those of Arg(120)-Phe(136) and Leu(121)-Arg(134) were enhanced in the presence of Gly(84)-Arg(113), a putative tryptic peptide of galectin-7. Degraded fragments of the galectin-7 molecule produced by limited trypsin digestion, formed amyloid fibrils after incubation at pH 2.0. These results suggest that the tryptic peptides of galectin-7 released at neutral pH, may lead to amyloid fibril formation of PLCA in the intracellular acidified conditions during keratinocyte apoptosis via regulation by the galectin-7 peptide as well as actin and cytokeratins.
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Affiliation(s)
- Koji Ono
- From the Department of Dermatology, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan and
| | - Eita Fujimoto
- From the Department of Dermatology, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan and
| | - Norihiro Fujimoto
- From the Department of Dermatology, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan and
| | - Minoru Akiyama
- From the Department of Dermatology, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan and
| | - Takahiro Satoh
- From the Department of Dermatology, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan and
| | - Hiroki Maeda
- Research Reactor Institute, Kyoto University, Kumatori, Sennan, Osaka 590-0494, Japan
| | - Noriko Fujii
- Research Reactor Institute, Kyoto University, Kumatori, Sennan, Osaka 590-0494, Japan
| | - Shingo Tajima
- From the Department of Dermatology, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan and
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14
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Matsuo K, Hiramatsu H, Gekko K, Namatame H, Taniguchi M, Woody RW. Characterization of intermolecular structure of β(2)-microglobulin core fragments in amyloid fibrils by vacuum-ultraviolet circular dichroism spectroscopy and circular dichroism theory. J Phys Chem B 2014; 118:2785-95. [PMID: 24512563 DOI: 10.1021/jp409630u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Intermolecular structures are important factors for understanding the conformational properties of amyloid fibrils. In this study, vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy and circular dichroism (CD) theory were used for characterizing the intermolecular structures of β2-microglobulin (β2m) core fragments in the amyloid fibrils. The VUVCD spectra of β2m20-41, β2m21-31, and β2m21-29 fragments in the amyloid fibrils exhibited characteristic features, but they were affected not only by the backbone conformations but also by the aromatic side-chain conformations. To estimate the contributions of aromatic side-chains to the spectra, the theoretical spectra were calculated from the simulated structures of β2m21-29 amyloid fibrils with various types of β-sheet stacking (parallel or antiparallel) using CD theory. We found that the experimental spectrum of β2m21-29 fibrils is largely affected by aromatic-backbone couplings, which are induced by the interaction between transitions within the aromatic and backbone chromophores, and these couplings are sensitive to the type of stacking among the β-sheets of the fibrils. Further theoretical analyses of simulated structures incorporating mutated aromatic residues suggested that the β2m21-29 fibrils are composed of amyloid accumulations in which the parallel β-sheets stack in an antiparallel manner and that the characteristic Phe-Tyr interactions among the β-sheet stacks affect the aromatic-backbone coupling. These findings indicate that the coupling components, which depend on the characteristic intermolecular structures, induce the spectral differences among three fragments in the amyloid fibrils. These advanced spectral analyses using CD theory provide a useful method for characterizing the intermolecular structures of protein and peptide fragment complexes.
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Affiliation(s)
- Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University , Higashi-Hiroshima 739-0046, Japan
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15
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Lee YH, Goto Y. Kinetic intermediates of amyloid fibrillation studied by hydrogen exchange methods with nuclear magnetic resonance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1307-23. [DOI: 10.1016/j.bbapap.2012.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 07/24/2012] [Accepted: 07/26/2012] [Indexed: 01/28/2023]
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16
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Uji Y, Motomiya Y, Ando Y. Effect of Heparin on Conformation of the β2-Microglobulin Molecule. Ther Apher Dial 2012; 16:159-62. [DOI: 10.1111/j.1744-9987.2011.01039.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Chaudhary N, Singh S, Nagaraj R. Aggregation properties of a short peptide that mediates amyloid fibril formation in model proteins unrelated to disease. J Biosci 2011; 36:679-89. [DOI: 10.1007/s12038-011-9104-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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18
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Maltsev AV, Bystryak S, Galzitskaya OV. The role of β-amyloid peptide in neurodegenerative diseases. Ageing Res Rev 2011; 10:440-52. [PMID: 21406255 DOI: 10.1016/j.arr.2011.03.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 03/03/2011] [Accepted: 03/07/2011] [Indexed: 12/27/2022]
Abstract
Studies of neurodegenerative disorders (NDDs) are drawing more attention of researchers worldwide due to the high incidence of Alzheimer's disease (AD). The pathophysiology of such disorders is, in part, characterized by the transition of a wild-type peptide from its native conformation into a very stable pathological isoform. Subsequently, these abnormal proteins form aggregates of amyloid fibrils that continuously increase in size. Changes in the metabolic processes of neurons (e.g. oxidative stress, hyperphosphorylation of the tau protein, and resulting secondary changes in the cell metabolism) ultimately lead to cell death. We hypothesize that extracellular deposition of β-amyloid peptide fibrils and neurofibrillary tangles represents the body's adaptation mechanism, aimed at preservation of autonomic functioning; while the cognitive decline is severe, the rest of the organ systems remain unaffected and continue to function. This hypothesis is supported by the fact that destruction of pathological plaques, fibrils, and tangles and the use of vaccines targeting β-amyloid result in undesirable side effects. To gain a better understanding of the pathophysiology of Alzheimer's disease and to develop novel therapies, continued studies of the sporadic form of disease and the mechanisms triggering conformational changes in β-amyloid peptide fragments are essential. This review is focused on studies investigating the formation of amyloid fibrils and their role in the pathogenesis of neurodegenerative diseases. In addition, we discuss a related disorder--amyloidosis--where formation of fibrils, tangles, and plaques leads to neuronal death which may occur as a result of a failed adaptation process. Further in-depth investigation and comprehensive analysis of alterations in the metabolism of APP, β-amyloid, and tau protein, which have a pathological effect on cell membrane, alter phosphate exchange, and impair other key metabolic functions of the cell long before the characteristic amyloid deposition takes place, is warranted. A better understanding of intraneuronal processes is crucial in identifying specific inhibitors of pathologic neuronal processes and, consequently, will allow for targeted therapy, thus maximizing efficacy of selected therapeutic regimens.
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Affiliation(s)
- A V Maltsev
- Russian Gerontological Research Clinical Center, Russian Ministry of Health Care, Moscow, Russia.
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19
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Yanagi K, Ashizaki M, Yagi H, Sakurai K, Lee YH, Goto Y. Hexafluoroisopropanol induces amyloid fibrils of islet amyloid polypeptide by enhancing both hydrophobic and electrostatic interactions. J Biol Chem 2011; 286:23959-66. [PMID: 21566116 PMCID: PMC3129177 DOI: 10.1074/jbc.m111.226688] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 04/28/2011] [Indexed: 12/31/2022] Open
Abstract
Although amyloid fibrils deposit with various proteins, the comprehensive mechanism by which they form remains unclear. We studied the formation of fibrils of human islet amyloid polypeptide associated with type II diabetes in the presence of various concentrations of 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) under acidic and neutral pH conditions using CD, amyloid-specific thioflavin T fluorescence, fluorescence imaging with thioflavin T, and atomic force microscopy. At low pH, the formation of fibrils was promoted by HFIP with an optimum at 5% (v/v). At neutral pH in the absence of HFIP, significant amounts of amorphous aggregates formed in addition to the fibrils. The addition of HFIP suppressed the formation of amorphous aggregates, leading to a predominance of fibrils with an optimum effect at 25% (v/v). Under both conditions, higher concentrations of HFIP dissolved the fibrils and stabilized the α-helical structure. The results indicate that fibrils and amorphous aggregates are different types of precipitates formed by exclusion from water-HFIP mixtures. The exclusion occurs through the combined effects of hydrophobic interactions and electrostatic interactions, both of which are strengthened by low concentrations of HFIP, and a subtle balance between the two types of interactions determines whether the fibrils or amorphous aggregates dominate. We suggest a general view of how the structure of precipitates varies dramatically from single crystals to amyloid fibrils and amorphous aggregates.
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Affiliation(s)
- Kotaro Yanagi
- From the Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Mizue Ashizaki
- From the Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Hisashi Yagi
- From the Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Kazumasa Sakurai
- From the Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Young-Ho Lee
- From the Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Yuji Goto
- From the Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
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20
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Galzitskaya OV. Regions which are Responsible for Swapping are also Responsible for Folding and Misfolding. Open Biochem J 2011; 5:27-36. [PMID: 21769300 PMCID: PMC3134983 DOI: 10.2174/1874091x01105010027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 05/17/2011] [Accepted: 05/28/2011] [Indexed: 12/01/2022] Open
Abstract
Domain swapping is a term used to describe a process when two or more protein chains exchange identical structural elements. Some cases of amyloid formation can be explained through a domain swapping mechanism therefore this deserves theoretical consideration and studying. It has been demonstrated that diverse proteins in sequence and structure are able to oligomerize via domain swapping. This allows us to suggest that the exchangeable regions are important in folding and misfolding processes of proteins, i.e. the residues from the swapping regions are typically incorporated into the native structure early during its formation. The modeling of folding of the proteins with swapped domains demonstrates that the regions exchanged in the oligomeric form in most cases are also responsible for folding and misfolding. For 11 out of 17 proteins, swapping regions intersect with the predicted amyloidogenic regions. Moreover, for 10 out of 17 proteins, high Φ-values (>0.5) belong to residues from the swapping regions. Our data confirm that the exchangeable regions are important in folding, misfolding, and domain swapping processes of the proteins, therefore the suggestion that domain swapping can serve as a mechanism for functional interconversion between monomers and oligomers is likely to be correct.
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Affiliation(s)
- Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya str. 4, Pushchino, Moscow Region, 142290, Russia
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21
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Paulite M, Fakhraai Z, Li ITS, Gunari N, Tanur AE, Walker GC. Imaging secondary structure of individual amyloid fibrils of a β2-microglobulin fragment using near-field infrared spectroscopy. J Am Chem Soc 2011; 133:7376-83. [PMID: 21524071 DOI: 10.1021/ja109316p] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid fibril diseases are characterized by the abnormal production of aggregated proteins and are associated with many types of neuro- and physically degenerative diseases. X-ray diffraction techniques, solid-state magic-angle spinning NMR spectroscopy, circular dichroism (CD) spectroscopy, and transmission electron microscopy studies have been utilized to detect and examine the chemical, electronic, material, and structural properties of amyloid fibrils at up to angstrom spatial resolution. However, X-ray diffraction studies require crystals of the fibril to be analyzed, while other techniques can only probe the bulk solution or solid samples. In the work reported here, apertureless near-field scanning infrared microscopy (ANSIM) was used to probe the secondary structure of individual amyloid fibrils made from an in vitro solution. Simultaneous topographic and infrared images of individual amyloid fibrils synthesized from the #21-31 peptide fragment of β(2)-microglobulin were acquired. Using this technique, IR spectra of the amyloid fibrils were obtained with a spatial resolution of less than 30 nm. It is observed that the experimental scattered field spectrum correlates strongly with that calculated using the far-field absorption spectrum. The near-field images of the amyloid fibrils exhibit much lower scattering of the IR radiation at approximately 1630 cm(-1). In addition, the near-field images also indicate that composition and/or structural variations among individual amyloid fibrils were present.
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Affiliation(s)
- Melissa Paulite
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
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22
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Kang S, Yang JE, Kim J, Ahn M, Koo HJ, Kim M, Lee YS, Paik SR. Removal of intact β2-microglobulin at neutral ph by using seed-conjugated polymer beads prepared with β2-microglobulin-derived peptide (58-67). Biotechnol Prog 2011; 27:521-9. [DOI: 10.1002/btpr.562] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 12/30/2010] [Indexed: 12/19/2022]
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23
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Fogolari F, Corazza A, Varini N, Rotter M, Gumral D, Codutti L, Rennella E, Viglino P, Bellotti V, Esposito G. Molecular dynamics simulation of β₂-microglobulin in denaturing and stabilizing conditions. Proteins 2010; 79:986-1001. [PMID: 21287627 DOI: 10.1002/prot.22940] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 10/22/2010] [Accepted: 11/02/2010] [Indexed: 11/11/2022]
Abstract
β₂-Microglobulin has been a model system for the study of fibril formation for 20 years. The experimental study of β₂-microglobulin structure, dynamics, and thermodynamics in solution, at atomic detail, along the pathway leading to fibril formation is difficult because the onset of disorder and aggregation prevents signal resolution in Nuclear Magnetic Resonance experiments. Moreover, it is difficult to characterize conformers in exchange equilibrium. To gain insight (at atomic level) on processes for which experimental information is available at molecular or supramolecular level, molecular dynamics simulations have been widely used in the last decade. Here, we use molecular dynamics to address three key aspects of β₂-microglobulin, which are known to be relevant to amyloid formation: (1) 60 ns molecular dynamics simulations of β₂-microglobulin in trifluoroethanol and in conditions mimicking low pH are used to study the behavior of the protein in environmental conditions that are able to trigger amyloid formation; (2) adaptive biasing force molecular dynamics simulation is used to force cis-trans isomerization at Proline 32 and to calculate the relative free energy in the folded and unfolded state. The native-like trans-conformer (known as intermediate 2 and determining the slow phase of refolding), is simulated for 10 ns, detailing the possible link between cis-trans isomerization and conformational disorder; (3) molecular dynamics simulation of highly concentrated doxycycline (a molecule able to suppress fibril formation) in the presence of β₂-microglobulin provides details of the binding modes of the drug and a rationale for its effect.
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Affiliation(s)
- Federico Fogolari
- Dipartimento di Scienze e Tecnologie Biomediche, Universita' di Udine, Piazzale Kolbe 4, 33100 Udine, Italy.
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24
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Miller Y, Ma B, Nussinov R. Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev 2010; 110:4820-38. [PMID: 20402519 PMCID: PMC2920034 DOI: 10.1021/cr900377t] [Citation(s) in RCA: 234] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Indexed: 01/13/2023]
Affiliation(s)
| | | | - Ruth Nussinov
- To whom correspondence should be addressed. Tel.: (301) 846-5579. Fax: (301) 846-5598. E-mail:
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25
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Skora L, Becker S, Zweckstetter M. Molten Globule Precursor States Are Conformationally Correlated to Amyloid Fibrils of Human β-2-Microglobulin. J Am Chem Soc 2010; 132:9223-5. [DOI: 10.1021/ja100453e] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lukasz Skora
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany, and DFG Center for the Molecular Physiology of the Brain, 37073 Goettingen, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany, and DFG Center for the Molecular Physiology of the Brain, 37073 Goettingen, Germany
| | - Markus Zweckstetter
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany, and DFG Center for the Molecular Physiology of the Brain, 37073 Goettingen, Germany
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26
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Capone R, Mustata M, Jang H, Arce FT, Nussinov R, Lal R. Antimicrobial protegrin-1 forms ion channels: molecular dynamic simulation, atomic force microscopy, and electrical conductance studies. Biophys J 2010; 98:2644-52. [PMID: 20513409 PMCID: PMC2877344 DOI: 10.1016/j.bpj.2010.02.024] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 01/27/2010] [Accepted: 02/03/2010] [Indexed: 10/19/2022] Open
Abstract
Antimicrobial peptides (AMPs) are an emerging class of antibiotics for controlling health effects of antibiotic-resistant microbial strains. Protegrin-1 (PG-1) is a model antibiotic among beta-sheet AMPs. Antibiotic activity of AMPs involves cell membrane damage, yet their membrane interactions, their 3D membrane-associated structures and the mechanism underlying their ability to disrupt cell membrane are poorly understood. Using complementary approaches, including molecular dynamics simulations, atomic force microscopy (AFM) imaging, and planar lipid bilayer reconstitution, we provide computational and experimental evidence that PG-1, a beta-hairpin peptide, forms ion channels. Simulations indicate that PG-1 forms channel-like structures with loosely attached subunits when reconstituted in anionic lipid bilayers. AFM images show the presence of channel-like structures when PG-1 is reconstituted in dioleoylphosphatidylserine/palmitoyloleoyl phosphatidylethanolamine bilayers or added to preformed bilayers. Planar lipid bilayer electrical recordings show multiple single channel conductances that are consistent with the heterogeneous oligomeric channel structures seen in AFM images. PG-1 channel formation seems to be lipid-dependent: PG-1 does not easily show ion channel electrical activity in phosphatidylcholine membranes, but readily shows channel activity in membranes rich in phosphatidylethanolamine or phosphatidylserine. The combined results support a model wherein the beta-hairpin PG-1 peptide acts as an antibiotic by altering cell ionic homeostasis through ion channel formation in cell membranes.
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Affiliation(s)
- Ricardo Capone
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois
| | - Mirela Mustata
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois
| | - Hyunbum Jang
- Center for Cancer Research Nanobiology Program, NCI-Frederick, SAIC-Frederick, Inc., Frederick, Maryland
| | - Fernando Teran Arce
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, NCI-Frederick, SAIC-Frederick, Inc., Frederick, Maryland
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ratnesh Lal
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois
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27
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Hiramatsu H, Lu M, Goto Y, Kitagawa T. The β-Sheet Structure pH Dependence of the Core Fragments of β2-Microglobulin Amyloid Fibrils. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2010. [DOI: 10.1246/bcsj.20090317] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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28
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Ladner CL, Chen M, Smith DP, Platt GW, Radford SE, Langen R. Stacked sets of parallel, in-register beta-strands of beta2-microglobulin in amyloid fibrils revealed by site-directed spin labeling and chemical labeling. J Biol Chem 2010; 285:17137-47. [PMID: 20335170 PMCID: PMC2878032 DOI: 10.1074/jbc.m110.117234] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
β2-microglobulin (β2m) is a 99-residue protein with an immunoglobulin fold that forms β-sheet-rich amyloid fibrils in dialysis-related amyloidosis. Here the environment and accessibility of side chains within amyloid fibrils formed in vitro from β2m with a long straight morphology are probed by site-directed spin labeling and accessibility to modification with N-ethyl maleimide using 19 site-specific cysteine variants. Continuous wave electron paramagnetic resonance spectroscopy of these fibrils reveals a core predominantly organized in a parallel, in-register arrangement, by contrast with other β2m aggregates. A continuous array of parallel, in-register β-strands involving most of the polypeptide sequence is inconsistent with the cryoelectron microscopy structure, which reveals an architecture based on subunit repeats. To reconcile these data, the number of spins in close proximity required to give rise to spin exchange was determined. Systematic studies of a model protein system indicated that juxtaposition of four spin labels is sufficient to generate exchange narrowing. Combined with information about side-chain mobility and accessibility, we propose that the amyloid fibrils of β2m consist of about six β2m monomers organized in stacks with a parallel, in-register array. The results suggest an organization more complex than the accordion-like β-sandwich structure commonly proposed for amyloid fibrils.
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Affiliation(s)
- Carol L Ladner
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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29
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Hiramatsu H, Lu M, Matsuo K, Gekko K, Goto Y, Kitagawa T. Differences in the molecular structure of beta(2)-microglobulin between two morphologically different amyloid fibrils. Biochemistry 2010; 49:742-51. [PMID: 20028123 DOI: 10.1021/bi901536j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Differences in the molecular structures of beta(2)-microglobulin between the two morphologically different amyloid fibrils having a needlelike [long-straight (LS)] and flexible [wormlike (WL)] character were investigated by infrared, Raman, and vacuum-ultraviolet circular dichroism spectroscopy. It turned out that although the beta-sheet content was comparable between the two kinds of fibrils (53 +/- 6% for the LS fibril and 47 +/- 6% for the WL fibril), the protonation states of the carboxyl side chains were distinctly different; the deprotonated (COO(-)) and protonated (COOH) forms were dominant in the LS and WL fibrils at pH 2.5, respectively, meaning that the pK(a) is specifically lowered in the LS fibril. Such a difference was not observed for the fibrils of the core fragments. Since site-specific interactions generally cause variation in the pK(a) of carboxyl side chains in proteins, these results suggest that "hook"-like interactions generated by hydrogen bonding and the formation of a salt bridge are present in the LS fibril, providing enthalpic stabilization. Presumably, the carboxyl groups fix the spatial arrangement of beta-strands and beta-sheets, bringing about the needlelike morphology. The absence of this regulation would result in the flexible morphology of the WL fibril, providing entropic stabilization.
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Affiliation(s)
- Hirotsugu Hiramatsu
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
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30
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Mustata M, Capone R, Jang H, Arce FT, Ramachandran S, Lal R, Nussinov R. K3 fragment of amyloidogenic beta(2)-microglobulin forms ion channels: implication for dialysis related amyloidosis. J Am Chem Soc 2010; 131:14938-45. [PMID: 19824733 DOI: 10.1021/ja9049299] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Beta(2)-microglobulin (beta(2)m) amyloid deposits are linked to dialysis-related amyloidosis (DRA) in hemodialysis patients. The mechanism by which beta(2)m causes DRA is not understood. It is also unclear whether only the full-length beta(2)m induces pathophysiology or if proteolytic fragments are sufficient for inducing this effect. Ser20-Lys41 (K3) is a digestion fragment of full-length beta(2)m. Solid state NMR (ssNMR) combined with X-ray diffraction and atomic force microscopy (AFM) revealed the characteristic oligomeric amyloid conformation of the U-turn beta-strand-turn-beta-strand motif stacked in parallel and stabilized by intermolecular interactions also shown by Abeta(9-40)/Abeta(17-42) and the CA150 WW domain. Here we use the K3 U-turn atomic coordinates and molecular dynamic (MD) simulations to model K3 channels in the membrane. Consistent with previous AFM imaging of other amyloids that show channel-like structures in the membrane, in the simulations K3 also forms ion channels with 3-6 loosely attached mobile subunits. We carry out AFM, single channel electrical recording, and fluorescence imaging experiments. AFM images display 3D ion channel topography with shapes, morphologies, and dimensions consistent with the theoretical model. Electrical conductance measurements indicate multiple single channel conductances, suggesting that various K3 oligomer sizes can constitute the channel structure. Fluorescence measurements in kidney cells show channel-mediated cell calcium uptake. These results suggest that the beta(2)m-induced DRA can be mediated by ion channels formed by its K3 fragment. Because the beta-strand-turn-beta-strand motif appears to be a universal amyloid feature, its ability to form ion channels further suggests that the motif may play a generic role in toxicity.
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Affiliation(s)
- Mirela Mustata
- Center for Nanomedicine and Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
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31
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Garbuzynskiy SO, Lobanov MY, Galzitskaya OV. FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence. Bioinformatics 2009; 26:326-32. [DOI: 10.1093/bioinformatics/btp691] [Citation(s) in RCA: 271] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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32
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Kameda A, Morita EH, Sakurai K, Naiki H, Goto Y. NMR-based characterization of a refolding intermediate of beta2-microglobulin labeled using a wheat germ cell-free system. Protein Sci 2009; 18:1592-601. [PMID: 19606503 DOI: 10.1002/pro.179] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In patients with dialysis-related amyloidosis, beta2-microglobulin (beta2-m) is a major structural component of amyloid fibrils. It has been suggested that the partial unfolding of beta2-m is a prerequisite to the formation of amyloid fibrils, and that the folding intermediate trapped by the non-native trans-Pro32 isomer leads to the formation of amyloid fibrils. Although clarifying the structure of this refolding intermediate by high resolution NMR spectroscopy is important, this has been made difficult by the limited lifetime of the intermediate. Here, we studied the structure of the refolding intermediate using a combination of amino acid selective labeling with wheat germ cell-free protein synthesis and NMR techniques. The HSQC spectra of beta2-ms labeled selectively at either phenylalanine, leucine, or valine enabled us to monitor the structures of the refolding intermediate. The results suggested that the refolding intermediate has an overall fold and cores similar to the native structure, but contains disordered structures around Pro32. The fluctuation of the beta-sheet regions especially the last half of the betaB strand and the first half of the betaE strand, both suggested to be important for amyloidogenicity, may transform beta2-m into an amyloidogenic structure.
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Affiliation(s)
- Atsushi Kameda
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
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33
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Amyloid fibrils formed by selective N-, C-terminal sequences of mouse apolipoprotein A-II. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1517-29. [DOI: 10.1016/j.bbapap.2009.06.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 06/02/2009] [Accepted: 06/26/2009] [Indexed: 11/19/2022]
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Castillo V, Ventura S. Amyloidogenic regions and interaction surfaces overlap in globular proteins related to conformational diseases. PLoS Comput Biol 2009; 5:e1000476. [PMID: 19696882 PMCID: PMC2719061 DOI: 10.1371/journal.pcbi.1000476] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 07/20/2009] [Indexed: 11/26/2022] Open
Abstract
Protein aggregation underlies a wide range of human disorders. The polypeptides involved in these pathologies might be intrinsically unstructured or display a defined 3D-structure. Little is known about how globular proteins aggregate into toxic assemblies under physiological conditions, where they display an initially folded conformation. Protein aggregation is, however, always initiated by the establishment of anomalous protein-protein interactions. Therefore, in the present work, we have explored the extent to which protein interaction surfaces and aggregation-prone regions overlap in globular proteins associated with conformational diseases. Computational analysis of the native complexes formed by these proteins shows that aggregation-prone regions do frequently overlap with protein interfaces. The spatial coincidence of interaction sites and aggregating regions suggests that the formation of functional complexes and the aggregation of their individual subunits might compete in the cell. Accordingly, single mutations affecting complex interface or stability usually result in the formation of toxic aggregates. It is suggested that the stabilization of existing interfaces in multimeric proteins or the formation of new complexes in monomeric polypeptides might become effective strategies to prevent disease-linked aggregation of globular proteins. The aggregation of proteins in tissues is associated with the pathogenesis of more than 40 human diseases. The polypeptides underlying disorders such as Alzheimer's and Parkinson's are devoid of any regular structure, whereas the polypeptides causing familial amyotrophic lateral sclerosis or nonneuropathic systemic amyloidosis correspond to globular proteins. Little is known about the mechanism by which globular proteins under physiological conditions aggregate from their initially folded and soluble conformations. Interestingly, several of these pathogenic proteins display quaternary structure or are bound to other proteins in their physiological context. In the present work, we show that protein-protein interaction surfaces and regions with high aggregation propensity significantly overlap in these polypeptides. This suggests that the formation of native complexes and self-aggregation reactions probably compete in the cell, explaining why point mutations affecting the interface or the stability of the protein complex lead in many cases to the formation of toxic aggregates. This study proposes general strategies to fight against diseases associated with the deposition of globular polypeptides.
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Affiliation(s)
- Virginia Castillo
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- * E-mail:
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35
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Fang PS, Zhao JH, Liu HL, Liu KT, Chen JT, Tsai WB, Lin HY, Fang HW, Ho Y. Molecular dynamics simulations to investigate the relationship between the structural stability and amyloidogenesis of the wild-type and N-terminal hexapeptide deletion ΔN6 β2-microglobulin. MOLECULAR SIMULATION 2009. [DOI: 10.1080/08927020902818005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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Platt GW, Radford SE. Glimpses of the molecular mechanisms of beta2-microglobulin fibril formation in vitro: aggregation on a complex energy landscape. FEBS Lett 2009; 583:2623-9. [PMID: 19433089 PMCID: PMC2734061 DOI: 10.1016/j.febslet.2009.05.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Revised: 05/01/2009] [Accepted: 05/05/2009] [Indexed: 12/29/2022]
Abstract
Beta(2)-microglobulin (beta(2)m) is a 99-residue protein that aggregates to form amyloid fibrils in dialysis-related amyloidosis. The protein provides a powerful model for exploration of the structural molecular mechanisms of fibril formation from a full-length protein in vitro. Fibrils have been assembled from beta(2)m under both low pH conditions, where the precursor is disordered, and at neutral pH where the protein is initially natively folded. Here we discuss the roles of sequence and structure in amyloid formation, the current understanding of the structural mechanisms of the early stages of aggregation of beta(2)m at both low and neutral pH, and the common and distinct features of these assembly pathways.
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Affiliation(s)
- Geoffrey W Platt
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
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37
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Morinaga A, Ono K, Yamada M. New therapeutic strategy for amyloidosis. FUTURE NEUROLOGY 2009. [DOI: 10.2217/fnl.09.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Evaluation of: Ozawa D, Yagi H, Ban T et al.: Destruction of amyloid fibrils of a β2-microglobulin fragment by laser beam irradiation. J. Biol. Chem. 284(2), 1009–1017 (2009). In this study, the authors discovered that laser beam irradiation with thioflavin T could stop the extension of β2-microglobulin fibrils and even degrade preformed amyloid fibrils. These reactions require both thioflavin T and a laser beam at 442 nm; active oxygen plays an important role. This approach may be a new therapeutic strategy for destroying fibrils in dialysis-related amyloidosis as well as other types of amyloidosis or related disorders, including Alzheimer’s disease, familial amyloid polyneuropathy, Parkinson’s disease and Huntington’s disease.
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Affiliation(s)
- Akiyoshi Morinaga
- Department of Neurology & Neurobiology of Aging, Kanazawa University Graduate School of Medical Science, Kanazawa, 920-8640, Japan
| | - Kenjiro Ono
- Department of Neurology & Neurobiology of Aging, Kanazawa University Graduate School of Medical Science, Kanazawa, 920-8640, Japan and, Department of Neurology, David Geffen School of Medicine & Molecular Biology Institute & Brain Research Institute, University of California, Los Angeles, CA 90095, USA
| | - Masahito Yamada
- Department of Neurology & Neurobiology of Aging, Kanazawa University Graduate School of Medical Science, Kanazawa 920-8640, Japan
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38
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Routledge KE, Tartaglia GG, Platt GW, Vendruscolo M, Radford SE. Competition between intramolecular and intermolecular interactions in an amyloid-forming protein. J Mol Biol 2009; 389:776-86. [PMID: 19393661 PMCID: PMC2722902 DOI: 10.1016/j.jmb.2009.04.042] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 04/09/2009] [Accepted: 04/20/2009] [Indexed: 11/30/2022]
Abstract
Despite much progress in understanding the folding and the aggregation processes of proteins, the rules defining their interplay have yet to be fully defined. This problem is of particular importance since many diseases are initiated by protein unfolding and hence the propensity to aggregate competes with intramolecular collapse and other folding events. Here, we describe the roles of intramolecular and intermolecular interactions in defining the length of the lag time and the apparent rate of elongation of the 100-residue protein human β2-microglobulin at pH 2.5, commencing from an acid-denatured state that lacks persistent structure but contains significant non-random hydrophobic interactions. Using a combination of site-directed mutagenesis, quantitative kinetic analysis and computational methods, we show that only a single region of about 10 residues in length, determines the rate of fibril formation, despite the fact that other regions exhibit a significant intrinsic propensity for aggregation. We rationalise these results by analysing the effect of incorporating the conformational properties of acid-unfolded β2-microglobulin and its variants at pH 2.5 as measured by NMR spectroscopy into the Zyggregator aggregation prediction algorithm. These results demonstrate that residual structure in the precursor state modulates the intrinsic propensity of the polypeptide chain to aggregate and that the algorithm developed here allows the key regions for aggregation to be more clearly identified and the rates of their self-association to be predicted. Given the common propensity of unfolded chains to form non-random intramolecular interactions as monomers and to self-assemble subsequently into amyloid fibrils, the approach developed should find widespread utility for the prediction of regions important in amyloid formation and their rates of self-assembly.
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Affiliation(s)
- Katy E. Routledge
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | | | - Geoffrey W. Platt
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Corresponding authors.
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
- Corresponding authors.
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39
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Fang PS, Zhao JH, Liu HL, Liu KT, Chen JT, Lin HY, Huang CH, Fang HW. Molecular Dynamics Simulations to Gain Insights into the Stability and Morphologies of K3 Oligomers from β2-microglobulin. J Biomol Struct Dyn 2009; 26:549-59. [DOI: 10.1080/07391102.2009.10507270] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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40
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Galzitskaya OV. Are the same or different amino acid residues responsible for correct and incorrect protein folding? BIOCHEMISTRY (MOSCOW) 2009; 74:186-93. [DOI: 10.1134/s0006297909020096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Hamada D, Tanaka T, Tartaglia GG, Pawar A, Vendruscolo M, Kawamura M, Tamura A, Tanaka N, Dobson CM. Competition between Folding, Native-State Dimerisation and Amyloid Aggregation in β-Lactoglobulin. J Mol Biol 2009; 386:878-90. [DOI: 10.1016/j.jmb.2008.12.038] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 12/10/2008] [Accepted: 12/15/2008] [Indexed: 11/15/2022]
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42
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Ozawa D, Yagi H, Ban T, Kameda A, Kawakami T, Naiki H, Goto Y. Destruction of Amyloid Fibrils of a β2-Microglobulin Fragment by Laser Beam Irradiation. J Biol Chem 2009; 284:1009-17. [DOI: 10.1074/jbc.m805118200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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43
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Abstract
beta(2)-microglobulin (beta(2)m) is capable of forming amyloid in osteoarticular structures in kidney failure patients that undergo chronic hemodialysis treatment. Although sophisticated analytical methods have yielded comprehensive data about the conformation of the native protein both as a monomer and as the light chain of the type I major histocompatibility complex, the cause and mechanisms leading to the transformation of beta(2)m into amyloid deposits in patients with dialysis-related amyloidosis are unsettled. The impact on conformational stability of various truncations, cleavages, amino acid substitutions, and divalent cations, especially Cu(2+), however, are highly relevant for understanding beta(2)m unfolding pathways leading to amyloid formation. This review describes the current knowledge about such conformationally destabilizing and amyloidogenic factors and links these to the structure and function of beta(2)m in normal physiology and pathology. Tables listing modifications of beta(2)m found in amyloid from patients and a systematic overview of laboratory conditions conducive to beta(2)m-fibrillogenesis are also included.
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44
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Esposito G, Ricagno S, Corazza A, Rennella E, Gümral D, Mimmi MC, Betto E, Pucillo CE, Fogolari F, Viglino P, Raimondi S, Giorgetti S, Bolognesi B, Merlini G, Stoppini M, Bolognesi M, Bellotti V. The Controlling Roles of Trp60 and Trp95 in β2-Microglobulin Function, Folding and Amyloid Aggregation Properties. J Mol Biol 2008; 378:887-97. [DOI: 10.1016/j.jmb.2008.03.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2007] [Revised: 02/28/2008] [Accepted: 03/02/2008] [Indexed: 10/22/2022]
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45
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The beta-strand-loop-beta-strand conformation is marginally populated in beta2-microglobulin (20-41) peptide in solution as revealed by replica exchange molecular dynamics simulations. Biophys J 2008; 95:510-7. [PMID: 18408040 DOI: 10.1529/biophysj.107.125054] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Solid-state NMR study shows that the 22-residue K3 peptide (Ser(20)-Lys(41)) from beta(2)-microglobulin (beta(2)m) adopts a beta-strand-loop-beta-strand conformation in its fibril state. Residue Pro(32) has a trans conformation in the fibril state of the peptide, while it adopts a cis conformation in the native state of full-length beta(2)m. To get insights into the structural properties of the K3 peptide, and determine whether the strand-loop-strand conformation is encoded at the monomeric level, we run all-atom explicit solvent replica exchange molecular dynamics on both the cis and trans variants. Our simulations show that the conformational space of the trans- and cis-K3 peptides is very different, with 1% of the sampled conformations in common at room temperature. In addition, both variants display only 0.3-0.5% of the conformations with beta-strand-loop-beta-strand character. This finding, compared to results on the Alzheimer's Abeta peptide, suggests that the biases toward aggregation leading to the beta-strand-loop-beta-strand conformation in fibrils are peptide-dependent.
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46
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Platt GW, Routledge KE, Homans SW, Radford SE. Fibril growth kinetics reveal a region of beta2-microglobulin important for nucleation and elongation of aggregation. J Mol Biol 2008; 378:251-63. [PMID: 18342332 PMCID: PMC2627305 DOI: 10.1016/j.jmb.2008.01.092] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 01/22/2008] [Accepted: 01/31/2008] [Indexed: 12/31/2022]
Abstract
Amyloid is a highly ordered form of aggregate comprising long, straight and unbranched proteinaceous fibrils that are formed with characteristic nucleation-dependent kinetics in vitro. Currently, the structural molecular mechanism of fibril nucleation and elongation is poorly understood. Here, we investigate the role of the sequence and structure of the initial monomeric precursor in determining the rates of nucleation and elongation of human β2-microglobulin (β2m). We describe the kinetics of seeded and spontaneous (unseeded) fibril growth of wild-type β2m and 12 variants at pH 2.5, targeting specifically an aromatic-rich region of the polypeptide chain (residues 62–70) that has been predicted to be highly amyloidogenic. The results reveal the importance of aromatic residues in this part of the β2m sequence in fibril formation under the conditions explored and show that this region of the polypeptide chain is involved in both the nucleation and the elongation phases of fibril formation. Structural analysis of the conformational properties of the unfolded monomer for each variant using NMR relaxation methods revealed that all variants contain significant non-random structure involving two hydrophobic clusters comprising regions 29–51 and 58–79, the extent of which is critically dependent on the sequence. No direct correlation was observed, however, between the extent of non-random structure in the unfolded state and the rates of fibril nucleation and elongation, suggesting that the early stages of aggregation involve significant conformational changes from the initial unfolded state. Together, the data suggest a model for β2m amyloid formation in which structurally specific interactions involving the highly hydrophobic and aromatic-rich region comprising residues 62–70 provide a complementary interface that is key to the generation of amyloid fibrils for this protein at acidic pH.
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Affiliation(s)
| | | | | | - Sheena E. Radford
- Corresponding author. Tel.: +44 113 343 3170; fax: +44 113 343 7486.
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47
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Yamamoto K, Yagi H, Ozawa D, Sasahara K, Naiki H, Goto Y. Thiol Compounds Inhibit the Formation of Amyloid Fibrils by β2-Microglobulin at Neutral pH. J Mol Biol 2008; 376:258-68. [DOI: 10.1016/j.jmb.2007.12.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2007] [Revised: 11/23/2007] [Accepted: 12/01/2007] [Indexed: 11/28/2022]
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48
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Liang C, Derreumaux P, Wei G. Structure and aggregation mechanism of beta(2)-microglobulin (83-99) peptides studied by molecular dynamics simulations. Biophys J 2007; 93:3353-62. [PMID: 17693474 PMCID: PMC2072067 DOI: 10.1529/biophysj.107.105585] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many human neurodegenerative diseases are associated with amyloid fibril formation. The human 99-residue beta(2)-microglobulin (beta2m) is one of the most intensively studied amyloid-forming proteins. Recent studies show that the C-terminal fragments 72-99, 83-89, and 91-96 form by themselves amyloid fibrils in vitro and play a significant role in fibrillization of the full-length beta2m protein under acidic pH conditions. In this work, we have studied the equilibrium structures of the 17-residue fragment 83-99 in solution, and investigated its dimerization process by multiple molecular dynamics simulations. We find that an intertwined dimer, with the positions of the beta-strands consistent with the results for the monomer, is a possible structure for two beta2m(83-89) peptides. Based on our molecular-dynamics-generated dimeric structure, a protofibril model is proposed for the full-length beta2m protein.
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Affiliation(s)
- Chungwen Liang
- National Key Surface Physics Laboratory and Department of Physics, Fudan University, Shanghai, China
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49
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Zhang Z, Chen H, Lai L. Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential. Bioinformatics 2007; 23:2218-25. [PMID: 17599928 DOI: 10.1093/bioinformatics/btm325] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
MOTIVATION Experimental evidence suggests that certain short protein segments have stronger amyloidogenic propensities than others. Identification of the fibril-forming segments of proteins is crucial for understanding diseases associated with protein misfolding and for finding favorable targets for therapeutic strategies. RESULT In this study, we used the microcrystal structure of the NNQQNY peptide from yeast prion protein and residue-based statistical potentials to establish an algorithm to identify the amyloid fibril-forming segment of proteins. Using the same sets of sequences, a comparable prediction performance was obtained from this study to that from 3D profile method based on the physical atomic-level potential ROSETTADESIGN. The predicted results are consistent with experiments for several representative proteins associated with amyloidosis, and also agree with the idea that peptides that can form fibrils may have strong sequence signatures. Application of the residue-based statistical potentials is computationally more efficient than using atomic-level potentials and can be applied in whole proteome analysis to investigate the evolutionary pressure effect or forecast other latent diseases related to amyloid deposits. AVAILABILITY The fibril prediction program is available at ftp://mdl.ipc.pku.edu.cn/pub/software/pre-amyl/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhuqing Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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50
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Adachi R, Yamaguchi KI, Yagi H, Sakurai K, Naiki H, Goto Y. Flow-induced alignment of amyloid protofilaments revealed by linear dichroism. J Biol Chem 2007; 282:8978-83. [PMID: 17264078 DOI: 10.1074/jbc.m611738200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Amyloid fibrils underlying various serious amyloidoses including Alzheimer and prion diseases form characteristic deposits in which linear fibrils with an unbranched and rigid morphology associate laterally or radially, e.g. radial senile amyloid plaques of amyloid beta. To clarify the formation of these high order amyloid deposits, studying the rheology is important. A 22-residue K3 peptide fragment of beta2-microglobulin, a protein responsible for dialysis-related amyloidosis, forms long and homogeneous protofilament-like fibrils in 20% (v/v) 2,2,2-trifluoroethanol and 10 mM HCl (pH approximately 2). Here, using circular dichroism and linear dichroism, we observed the flow-induced alignment of fibrils. Analysis of far- and near-UV linear dichroism spectra suggested that both the net pi-pi* transition moment of the backbone carbonyl group and L(b) transition moment of the Tyr(26) side chain are oriented in parallel to the fibril axis, revealing the structural details of amyloid protofilaments. Moreover, the intensities of flow-induced circular dichroism or linear dichroism signals depended critically on the length and type of fibrils, suggesting that they are useful for detecting and characterizing amyloid fibrils.
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Affiliation(s)
- Rumi Adachi
- Institute for Protein Research, Osaka University and CREST, Japan Science and Technology Agency, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
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