1
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Wales DJ. Energy Landscapes and Heat Capacity Signatures for Monomers and Dimers of Amyloid-Forming Hexapeptides. Int J Mol Sci 2023; 24:10613. [PMID: 37445791 DOI: 10.3390/ijms241310613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Amyloid formation is a hallmark of various neurodegenerative disorders. In this contribution, energy landscapes are explored for various hexapeptides that are known to form amyloids. Heat capacity (CV) analysis at low temperature for these hexapeptides reveals that the low energy structures contributing to the first heat capacity feature above a threshold temperature exhibit a variety of backbone conformations for amyloid-forming monomers. The corresponding control sequences do not exhibit such structural polymorphism, as diagnosed via end-to-end distance and a dihedral angle defined for the monomer. A similar heat capacity analysis for dimer conformations obtained using basin-hopping global optimisation shows clear features in end-to-end distance versus dihedral correlation plots, where amyloid-forming sequences exhibit a preference for larger end-to-end distances and larger positive dihedrals. These results hold true for sequences taken from tau, amylin, insulin A chain, a de novo designed peptide, and various control sequences. While there is a little overall correlation between the aggregation propensity and the temperature at which the low-temperature CV feature occurs, further analysis suggests that the amyloid-forming sequences exhibit the key CV feature at a lower temperature compared to control sequences derived from the same protein.
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Affiliation(s)
- David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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2
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Skamris T, Vestergaard B, Madsen KL, Langkilde AE, Foderà V. Identifying Biological and Biophysical Features of Different Maturation States of α-Synuclein Amyloid Fibrils. Methods Mol Biol 2023; 2551:321-344. [PMID: 36310213 DOI: 10.1007/978-1-0716-2597-2_22] [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] [Indexed: 06/16/2023]
Abstract
Protein aggregates, hereunder amyloid fibrils, can undergo a maturation process, whereby early formed aggregates undergo a structural and physicochemical transition leading to more mature species. In the case of amyloid-related diseases, such maturation confers distinctive biological properties of the aggregates, which may account for a range of diverse pathological subtypes. Here, we present a protocol for the preparation of α-synuclein amyloid fibrils differing in the level of their maturation. We utilize widely accessible biophysical techniques to characterize the structure and morphology and a simple thermal treatment procedure to test their thermodynamic stability. Their biological properties are probed by means of binding to native plasma membrane sheets originating from mammalian cell lines.
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Affiliation(s)
- Thomas Skamris
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth L Madsen
- Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Annette E Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
| | - Vito Foderà
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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3
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Buell AK. Stability matters, too - the thermodynamics of amyloid fibril formation. Chem Sci 2022; 13:10177-10192. [PMID: 36277637 PMCID: PMC9473512 DOI: 10.1039/d1sc06782f] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/30/2022] [Indexed: 12/26/2022] Open
Abstract
Amyloid fibrils are supramolecular homopolymers of proteins that play important roles in biological functions and disease. These objects have received an exponential increase in attention during the last few decades, due to their role in the aetiology of a range of severe disorders, most notably some of a neurodegenerative nature. While an overwhelming number of experimental studies exist that investigate how, and how fast, amyloid fibrils form and how their formation can be inhibited, a much more limited body of experimental work attempts to answer the question as to why these types of structures form (i.e. the thermodynamic driving force) and how stable they actually are. In this review, I attempt to give an overview of the types of experiments that have been performed to-date to answer these questions, and to summarise our current understanding of amyloid thermodynamics.
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Affiliation(s)
- Alexander K Buell
- Technical University of Denmark, Department of Biotechnology and Biomedicine Søltofts Plads, Building 227 2800 Kgs. Lyngby Denmark
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4
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Breakdown of supersaturation barrier links protein folding to amyloid formation. Commun Biol 2021; 4:120. [PMID: 33500517 PMCID: PMC7838177 DOI: 10.1038/s42003-020-01641-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
The thermodynamic hypothesis of protein folding, known as the "Anfinsen's dogma" states that the native structure of a protein represents a free energy minimum determined by the amino acid sequence. However, inconsistent with the Anfinsen's dogma, globular proteins can misfold to form amyloid fibrils, which are ordered aggregates associated with diseases such as Alzheimer's and Parkinson's diseases. Here, we present a general concept for the link between folding and misfolding. We tested the accessibility of the amyloid state for various proteins upon heating and agitation. Many of them showed Anfinsen-like reversible unfolding upon heating, but formed amyloid fibrils upon agitation at high temperatures. We show that folding and amyloid formation are separated by the supersaturation barrier of a protein. Its breakdown is required to shift the protein to the amyloid pathway. Thus, the breakdown of supersaturation links the Anfinsen's intramolecular folding universe and the intermolecular misfolding universe.
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5
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Hentschel L, Hansen J, Egelhaaf SU, Platten F. The crystallization enthalpy and entropy of protein solutions: microcalorimetry, van't Hoff determination and linearized Poisson–Boltzmann model of tetragonal lysozyme crystals. Phys Chem Chem Phys 2021; 23:2686-2696. [DOI: 10.1039/d0cp06113a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microcalorimetric and van't Hoff determinations as well as a theoretical description provide a consistent picture of the crystallization enthalpy and entropy of protein solutions and their dependence on physicochemical solution parameters.
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Affiliation(s)
- Lorena Hentschel
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
| | - Jan Hansen
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
| | - Stefan U. Egelhaaf
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
| | - Florian Platten
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
- Institute of Biological Information Processing (IBI-4: Biomacromolecular Systems and Processes)
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6
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The growth of amyloid fibrils: rates and mechanisms. Biochem J 2019; 476:2677-2703. [DOI: 10.1042/bcj20160868] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 12/19/2022]
Abstract
AbstractAmyloid fibrils are β-sheet-rich linear protein polymers that can be formed by a large variety of different proteins. These assemblies have received much interest in recent decades, due to their role in a range of human disorders. However, amyloid fibrils are also found in a functional context, whereby their structural, mechanical and thermodynamic properties are exploited by biological systems. Amyloid fibrils form through a nucleated polymerisation mechanism with secondary processes acting in many cases to amplify the number of fibrils. The filamentous nature of amyloid fibrils implies that the fibril growth rate is, by several orders of magnitude, the fastest step of the overall aggregation reaction. This article focusses specifically on in vitro experimental studies of the process of amyloid fibril growth, or elongation, and summarises the state of knowledge of its kinetics and mechanisms. This work attempts to provide the most comprehensive summary, to date, of the available experimental data on amyloid fibril elongation rate constants and the temperature and concentration dependence of amyloid fibril elongation rates. These data are compared with those from other types of protein polymers. This comparison with data from other polymerising proteins is interesting and relevant because many of the basic ideas and concepts discussed here were first introduced for non-amyloid protein polymers, most notably by the Japanese school of Oosawa and co-workers for cytoskeletal filaments.
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7
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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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8
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Gelenter MD, Smith KJ, Liao SY, Mandala VS, Dregni AJ, Lamm MS, Tian Y, Xu W, Pochan DJ, Tucker TJ, Su Y, Hong M. The peptide hormone glucagon forms amyloid fibrils with two coexisting β-strand conformations. Nat Struct Mol Biol 2019; 26:592-598. [PMID: 31235909 PMCID: PMC6609468 DOI: 10.1038/s41594-019-0238-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/29/2019] [Indexed: 12/20/2022]
Abstract
Glucagon and insulin maintain blood glucose homeostasis and are used to treat hypoglycemia and hyperglycemia, respectively, in patients with diabetes. Whereas insulin is stable for weeks in its solution formulation, glucagon fibrillizes rapidly at the acidic pH required for solubility and is therefore formulated as a lyophilized powder that is reconstituted in an acidic solution immediately before use. Here we use solid-state NMR to determine the atomic-resolution structure of fibrils of synthetic human glucagon grown at pharmaceutically relevant low pH. Unexpectedly, two sets of chemical shifts are observed, indicating the coexistence of two β-strand conformations. The two conformations have distinct water accessibilities and intermolecular contacts, indicating that they alternate and hydrogen bond in an antiparallel fashion along the fibril axis. Two antiparallel β-sheets assemble with symmetric homodimer cross sections. This amyloid structure is stabilized by numerous aromatic, cation-π, polar and hydrophobic interactions, suggesting mutagenesis approaches to inhibit fibrillization could improve this important drug.
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Affiliation(s)
- Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Katelyn J Smith
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Shu-Yu Liao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry & Biochemistry, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aurelio J Dregni
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew S Lamm
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Yu Tian
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
- Institute for Molecular Engineering, The University of Chicago, Eckhardt Research Center, Chicago, IL, USA
| | - Wei Xu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | | | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ, USA.
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
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9
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Skamris T, Marasini C, Madsen KL, Foderà V, Vestergaard B. Early Stage Alpha-Synuclein Amyloid Fibrils are Reservoirs of Membrane-Binding Species. Sci Rep 2019; 9:1733. [PMID: 30741994 PMCID: PMC6370759 DOI: 10.1038/s41598-018-38271-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 12/19/2018] [Indexed: 11/16/2022] Open
Abstract
The presence of αSN fibrils indisputably associates with the development of synucleinopathies. However, while certain fibril morphologies have been linked to downstream pathological phenotypes, others appear less harmful, leading to the concept of fibril strains, originally described in relation to prion disease. Indeed, the presence of fibrils does not associate directly with neurotoxicity. Rather, it has been suggested that the toxic compounds are soluble amyloidogenic oligomers, potentially co-existing with fibrils. Here, combining synchrotron radiation circular dichroism, transmission electron microscopy and binding assays on native plasma membrane sheets, we reveal distinct biological and biophysical differences between initial and matured fibrils, transformed within the timespan of few days. Immature fibrils are reservoirs of membrane-binding species, which in response to even gentle experimental changes release into solution in a reversible manner. In contrast, mature fibrils, albeit macroscopically indistinguishable from their less mature counterparts, are structurally robust, shielding the solution from the membrane active soluble species. We thus show that particular biological activity resides transiently with the fibrillating sample, distinct for one, but not the other, spontaneously formed fibril polymorph. These results shed new light on the principles of fibril polymorphism with consequent impact on future design of assays and therapeutic development.
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Affiliation(s)
- Thomas Skamris
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Carlotta Marasini
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Kenneth L Madsen
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, The Panum Institute, Maersk Tower 7.5, 2200, Copenhagen, Denmark
| | - Vito Foderà
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark.
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark.
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10
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Ziehm T, Buell AK, Willbold D. Role of Hydrophobicity and Charge of Amyloid-Beta Oligomer Eliminating d-Peptides in the Interaction with Amyloid-Beta Monomers. ACS Chem Neurosci 2018; 9:2679-2688. [PMID: 29893543 DOI: 10.1021/acschemneuro.8b00132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Inhibition of the self-assembly process of amyloid-beta and even more the removal of already existing toxic amyloid-beta assemblies represent promising therapeutic strategies against Alzheimer's disease. To approach this aim, we selected a d-enantiomeric peptide by phage-display based on the interaction with amyloid-beta monomers. This lead compound was successfully optimized by peptide microarrays with respect to its affinity and specificity to the target resulting in d-peptides with both increased hydrophobicity and net charge. Here, we present a detailed biophysical characterization of the interactions between these optimized d-peptides and amyloid-beta monomers in comparison to the original lead compound in order to obtain a more thorough understanding of the physicochemical determinants of the interactions. Kinetics and apparent stoichiometry of complex formation were studied using surface plasmon resonance. Potential modes of binding to amyloid-beta were identified, and the influences of ionic strength on complex stability, as well as on the inhibitory effect on amyloid-beta aggregation were investigated. The results reveal a very different mode of interaction of the optimized d-peptides based on a combination of electrostatic and hydrophobic interactions as compared to the mostly electrostatically driven interaction of the lead compound. These conclusions were supported by the thermodynamic profiles of the interaction between optimized d-peptides and Aβ monomers, which indicate an increase in binding entropy with respect to the lead compound.
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Affiliation(s)
- Tamar Ziehm
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Alexander K. Buell
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
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11
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Adachi M, Noji M, So M, Sasahara K, Kardos J, Naiki H, Goto Y. Aggregation-phase diagrams of β 2-microglobulin reveal temperature and salt effects on competitive formation of amyloids versus amorphous aggregates. J Biol Chem 2018; 293:14775-14785. [PMID: 30077972 DOI: 10.1074/jbc.ra118.004683] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/28/2018] [Indexed: 11/06/2022] Open
Abstract
Several serious diseases are associated with crystal-like amyloid fibrils or glass-like amorphous aggregates of denatured proteins. However, protein aggregation involving both types of aggregates has not yet been elucidated in much detail. Using a protein associated with dialysis-related amyloidosis, β2-microglobulin (β2m), we previously demonstrated that amyloid fibrils and amorphous aggregates form competitively depending on salt (NaCl) concentration. To examine the generality of the underlying competitive mechanisms, we herein investigated the effects of heat on acid-denatured β2m at pH 2. Using thioflavin fluorescence, CD, and light scattering analysis along with atomic force microscopy imaging, we found that the temperature-dependent aggregation of β2m markedly depends on NaCl concentration. Stepwise transitions from monomers to amyloids and then back to monomers were observed at low NaCl concentrations. Amorphous aggregates formed rapidly at ambient temperatures at high NaCl concentrations, but the transition from amorphous aggregates to amyloids occurred only as the temperature increased. Combining the data from the temperature- and NaCl-dependent transitions, we constructed a unified phase diagram of conformational states, indicating a parabolic solubility curve with a minimum NaCl concentration at ambient temperatures. Although amyloid fibrils formed above this solubility boundary, amorphous aggregates dominated in regions distant from this boundary. Kinetic competition between supersaturation-limited slow amyloid fibrillation and supersaturation-unlimited fast amorphous aggregation deformed the phase diagram, with amyloid regions disappearing with fast titration rates. We conclude that phase diagrams combining thermodynamics and kinetics data provide a comprehensive view of β2m aggregation exhibiting severe hysteresis depending on the heat- or salt-titration rates.
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Affiliation(s)
- Masayuki Adachi
- From the Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Masahiro Noji
- From the Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Masatomo So
- From the Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Kenji Sasahara
- From the Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - József Kardos
- the ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary, and
| | - Hironobu Naiki
- Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Yuji Goto
- From the Institute for Protein Research, Osaka University, Osaka 565-0871, Japan,
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12
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Kinoshita M, Lin Y, Dai I, Okumura M, Markova N, Ladbury JE, Sterpone F, Lee YH. Energy landscape of polymorphic amyloid generation of β2-microglobulin revealed by calorimetry. Chem Commun (Camb) 2018; 54:7995-7998. [DOI: 10.1039/c8cc02718h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ITC-based energy landscape provides a comprehensive understanding of amyloid aggregation in terms of thermodynamics and kinetics.
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Affiliation(s)
| | - Yuxi Lin
- Department of Chemistry
- Sookmyung Women's University
- Seoul
- Korea
| | - Itoh Dai
- Institute for Protein research
- Osaka University
- Suita
- Japan
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences (FRIS)
- Tohoku University
- Sendai 980-8578
- Japan
| | | | - John E. Ladbury
- School of Molecular and Cellular Biology
- University of Leeds
- Leeds
- UK
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- Université Paris Denis Diderot
- Sorbonne Paris Cité
- PSL Research University
| | - Young-Ho Lee
- Institute for Protein research
- Osaka University
- Suita
- Japan
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13
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Urbic T, Najem S, Dias CL. Thermodynamic properties of amyloid fibrils in equilibrium. Biophys Chem 2017; 231:155-160. [PMID: 28318905 PMCID: PMC5589490 DOI: 10.1016/j.bpc.2017.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/01/2017] [Accepted: 03/02/2017] [Indexed: 11/19/2022]
Abstract
In this manuscript we use a two-dimensional coarse-grained model to study how amyloid fibrils grow towards an equilibrium state where they coexist with proteins dissolved in a solution. Free-energies to dissociate proteins from fibrils are estimated from the residual concentration of dissolved proteins. Consistent with experiments, the concentration of proteins in solution affects the growth rate of fibrils but not their equilibrium state. Also, studies of the temperature dependence of the equilibrium state can be used to estimate thermodynamic quantities, e.g., heat capacity and entropy.
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Affiliation(s)
- Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000, Slovenia.
| | - Sara Najem
- National Center for Remote Sensing, National Council for Scientific Research (CNRS), Riad al Soloh, 1107 2260 Beirut, Lebanon
| | - Cristiano L Dias
- New Jersey Institute of Technology, Physics Department, Newark,NJ 07042-1982,United States
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14
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Kinetics and polymorphs of yeast prion Sup35NM amyloidogenesis. Int J Biol Macromol 2017; 102:1241-1249. [PMID: 28476595 DOI: 10.1016/j.ijbiomac.2017.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/14/2017] [Accepted: 05/01/2017] [Indexed: 11/22/2022]
Abstract
Amyloidogenic proteins often form many types of aggregates, which are a critical determinant of cytotoxicity and tissue specificity. However, the molecular mechanisms underlying the generation of distinct amyloids and their influence on cells remain largely unknown. We herein investigated the polymorphic amyloid formation of the yeast prion protein, Sup35NM, an intrinsically disordered N-terminal fragment of Sup35, under various conditions and its potential relationship to cytotoxicity. Sup35NM aggregated to amyloid fibrils with distinct kinetics, structures, morphologies, tinctorial properties, and conformational stabilities depending on the concentration of NaCl, pH, and temperature, indicating the polymorphic amyloidogenesis of Sup35NM. Detailed kinetic analyses of Sup35NM amyloid formation revealed a strong inverse correlation between the lag time and elongation rate without a correlation between kinetic and structural parameters. These results suggest that kinetic polymorphisms due to distinct nucleation and elongation rates result in structural polymorphs of amyloid fibrils, and also that conditions that enhance or inhibit the nucleation of Sup35NM promote or delay fibril growth. The deleterious effects of polymorphic Sup35NM amyloid fibrils on membrane integrity and cell vitality were minimal. We hypothesize that the innocuous polymorphic nature of Sup35NM amyloid fibrils may be beneficial for gaining time for prion infection prior to cell death.
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15
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Rao Jampani S, Mahmoudinobar F, Su Z, Dias CL. Thermodynamics of Aβ16-21 dissociation from a fibril: Enthalpy, entropy, and volumetric properties. Proteins 2015; 83:1963-72. [PMID: 26264694 DOI: 10.1002/prot.24875] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/22/2015] [Accepted: 08/02/2015] [Indexed: 11/10/2022]
Abstract
Here, we provide insights into the thermodynamic properties of A β16-21 dissociation from an amyloid fibril using all-atom molecular dynamics simulations in explicit water. An umbrella sampling protocol is used to compute potentials of mean force (PMF) as a function of the distance ξ between centers-of-mass of the A β16-21 peptide and the preformed fibril at nine temperatures. Changes in the enthalpy and the entropic energy are determined from the temperature dependence of these PMF(s) and the average volume of the simulation box is computed as a function of ξ. We find that the PMF at 310 K is dominated by enthalpy while the entropic energy does not change significantly during dissociation. The volume of the system decreases during dissociation. Moreover, the magnitude of this volume change also decreases with increasing temperature. By defining dock and lock states using the solvent accessible surface area (SASA), we find that the behavior of the electrostatic energy is different in these two states. It increases (unfavorable) and decreases (favorable) during dissociation in lock and dock states, respectively, while the energy due to Lennard-Jones interactions increases continuously in these states. Our simulations also highlight the importance of hydrophobic interactions in accounting for the stability of A β16-21.
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Affiliation(s)
- Srinivasa Rao Jampani
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, 07102-1982
| | - Farbod Mahmoudinobar
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, 07102-1982
| | - Zhaoqian Su
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, 07102-1982
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, 07102-1982
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16
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The physical chemistry of the amyloid phenomenon: thermodynamics and kinetics of filamentous protein aggregation. Essays Biochem 2014; 56:11-39. [DOI: 10.1042/bse0560011] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this chapter, we present an overview of the kinetics and thermodynamics of protein aggregation into amyloid fibrils. The perspective we adopt is largely experimental, but we also discuss recent developments in data analysis and we show that only a combination of well-designed experiments with appropriate theoretical modelling is able to provide detailed mechanistic insight into the complex pathways of amyloid formation. In the first part of the chapter, we describe measurements of the thermodynamic stability of the amyloid state with respect to the soluble state of proteins, as well as the magnitude and origin of this stability. In the second part, we discuss in detail the kinetics of the individual molecular steps in the overall mechanism of the conversion of soluble protein into amyloid fibrils. Finally, we highlight the effects of external factors, such as salt type and concentration, chemical denaturants and molecular chaperones on the kinetics of aggregation.
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Ikenoue T, Lee YH, Kardos J, Saiki M, Yagi H, Kawata Y, Goto Y. Cold denaturation of α-synuclein amyloid fibrils. Angew Chem Int Ed Engl 2014; 53:7799-804. [PMID: 24920162 DOI: 10.1002/anie.201403815] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Indexed: 01/03/2023]
Abstract
Although amyloid fibrils are associated with numerous pathologies, their conformational stability remains largely unclear. Herein, we probe the thermal stability of various amyloid fibrils. α-Synuclein fibrils cold-denatured to monomers at 0-20 °C and heat-denatured at 60-110 °C. Meanwhile, the fibrils of β2-microglobulin, Alzheimer's Aβ1-40/Aβ1-42 peptides, and insulin exhibited only heat denaturation, although they showed a decrease in stability at low temperature. A comparison of structural parameters with positive enthalpy and heat capacity changes which showed opposite signs to protein folding suggested that the burial of charged residues in fibril cores contributed to the cold denaturation of α-synuclein fibrils. We propose that although cold-denaturation is common to both native proteins and misfolded fibrillar states, the main-chain dominated amyloid structures may explain amyloid-specific cold denaturation arising from the unfavorable burial of charged side-chains in fibril cores.
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Affiliation(s)
- Tatsuya Ikenoue
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan)
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18
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Ikenoue T, Lee YH, Kardos J, Saiki M, Yagi H, Kawata Y, Goto Y. Cold Denaturation of α-Synuclein Amyloid Fibrils. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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19
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Ikenoue T, Lee YH, Kardos J, Yagi H, Ikegami T, Naiki H, Goto Y. Heat of supersaturation-limited amyloid burst directly monitored by isothermal titration calorimetry. Proc Natl Acad Sci U S A 2014; 111:6654-9. [PMID: 24753579 PMCID: PMC4020073 DOI: 10.1073/pnas.1322602111] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amyloid fibrils form in supersaturated solutions via a nucleation and growth mechanism. Although the structural features of amyloid fibrils have become increasingly clearer, knowledge on the thermodynamics of fibrillation is limited. Furthermore, protein aggregation is not a target of calorimetry, one of the most powerful approaches used to study proteins. Here, with β2-microglobulin, a protein responsible for dialysis-related amyloidosis, we show direct heat measurements of the formation of amyloid fibrils using isothermal titration calorimetry (ITC). The spontaneous fibrillation after a lag phase was accompanied by exothermic heat. The thermodynamic parameters of fibrillation obtained under various protein concentrations and temperatures were consistent with the main-chain dominated structural model of fibrils, in which overall packing was less than that of the native structures. We also characterized the thermodynamics of amorphous aggregation, enabling the comparison of protein folding, amyloid fibrillation, and amorphous aggregation. These results indicate that ITC will become a promising approach for clarifying comprehensively the thermodynamics of protein folding and misfolding.
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Affiliation(s)
- Tatsuya Ikenoue
- aDivision of Protein Structural Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Young-Ho Lee
- aDivision of Protein Structural Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - József Kardos
- bDepartment of Biochemistry, Eötvös Loránd University, 1117, Budapest, Hungary; and
| | - Hisashi Yagi
- aDivision of Protein Structural Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Takahisa Ikegami
- aDivision of Protein Structural Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Hironobu Naiki
- cFaculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Yuji Goto
- aDivision of Protein Structural Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
- 2To whom correspondence should be addressed. E-mail:
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20
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Schirò G, Vetri V, Andersen C, Natali F, Koza M, Leone M, Cupane A. The Boson Peak of Amyloid Fibrils: Probing the Softness of Protein Aggregates by Inelastic Neutron Scattering. J Phys Chem B 2014; 118:2913-23. [DOI: 10.1021/jp412277y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- G. Schirò
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
| | - V. Vetri
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
| | - C.B. Andersen
- Department
of Diabetes Biophysics, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - F. Natali
- CNR-IOM, c/o Institut Laue Langevin, Grenoble, France
| | - M.M. Koza
- Institut Laue Langevin, Grenoble, France
| | - M. Leone
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
| | - A. Cupane
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
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21
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Doyle CM, Rumfeldt JA, Broom HR, Broom A, Stathopulos PB, Vassall KA, Almey JJ, Meiering EM. Energetics of oligomeric protein folding and association. Arch Biochem Biophys 2012; 531:44-64. [PMID: 23246784 DOI: 10.1016/j.abb.2012.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/29/2012] [Accepted: 12/05/2012] [Indexed: 12/11/2022]
Abstract
In nature, proteins most often exist as complexes, with many of these consisting of identical subunits. Understanding of the energetics governing the folding and misfolding of such homooligomeric proteins is central to understanding their function and misfunction, in disease or biotechnology. Much progress has been made in defining the mechanisms and thermodynamics of homooligomeric protein folding. In this review, we outline models as well as calorimetric and spectroscopic methods for characterizing oligomer folding, and describe extensive results obtained for diverse proteins, ranging from dimers to octamers and higher order aggregates. To our knowledge, this area has not been reviewed comprehensively in years, and the collective progress is impressive. The results provide evolutionary insights into the development of subunit interfaces, mechanisms of oligomer folding, and contributions of oligomerization to protein stability, function and regulation. Thermodynamic analyses have also proven valuable for understanding protein misfolding and aggregation mechanisms, suggesting new therapeutic avenues. Successful recent designs of novel, functional proteins demonstrate increased understanding of oligomer folding. Further rigorous analyses using multiple experimental and computational approaches are still required, however, to achieve consistent and accurate prediction of oligomer folding energetics. Modeling the energetics remains challenging but is a promising avenue for future advances.
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Affiliation(s)
- Colleen M Doyle
- Guelph-Waterloo Centre for Graduate Studies in Chemistry and Biochemistry, and Department of Chemistry, University of Waterloo, 200 University Ave. West, Waterloo, ON, Canada
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22
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Ghai R, Falconer RJ, Collins BM. Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010. J Mol Recognit 2012; 25:32-52. [PMID: 22213449 DOI: 10.1002/jmr.1167] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.
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Affiliation(s)
- Rajesh Ghai
- Institute for Molecular Bioscience (IMB), University of Queensland, St. Lucia, Queensland, 4072, Australia
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23
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Scavenius C, Ghodke S, Otzen DE, Enghild JJ. Hydrogen exchange mass spectrometry as an analytical tool for the analysis of amyloid fibrillogenesis. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 302:167-173. [PMID: 22267952 PMCID: PMC3261750 DOI: 10.1016/j.ijms.2010.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this study, we have used glucagon as a model system for analyzing amyloid fibrillogenesis by hydrogen exchange MALDI mass spectrometry (HXMS). The hydrogen exchange mass spectrometry data correlated well with the traditional method based on Thioflavin T fluorescence and provided quantitative information by measuring the fibrillating molecules directly. The hydrogen exchange mass spectrometry data collected during fibrillogenesis revealed that glucagon fibrillation was a two component system showing an on/off type of interaction where only monomeric and fibrils were present without any substantial amount of intermediate species. This was evident by the extensive deuteration of the monomer and protection of the entire 29 residue glucagon peptide upon fibrillation.. The method complements the traditional procedures and has the potential to provide new information with respect to the nature of transient species, the structure of the growing fibrils and the mechanism of formation.
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Affiliation(s)
| | | | | | - Jan J. Enghild
- Address correspondence to: Jan J. Enghild, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-80 00 Aarhus C, Denmark. Tel. (+45) 8942 5062; Fax: (+45) 8942 5063;
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Pedersen JS, Andersen CB, Otzen DE. Amyloid structure--one but not the same: the many levels of fibrillar polymorphism. FEBS J 2010; 277:4591-601. [PMID: 20977663 DOI: 10.1111/j.1742-4658.2010.07888.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Many proteins and peptides can form amyloid-like structures both in vivo and in vitro. Although strikingly similar fibrillar structures can be observed across a variety of amino acid sequences, the fibrils formed often exhibit a stunning wealth of polymorphisms at the level of electron or atomic force microscopy. This appears to violate the Anfinsen principle seen for globular proteins, where each protein sequence codes for just one well-defined fold. To a large extent, polymorphism reflects variable packing of a single protofilament structure in the mature fibrils. However, we and others have recently demonstrated that polymorphism can also reflect real structural differences in the molecular packing of the polypeptide chains leading to several possible protofilament structures and diverse mature fibrillar structures. Glucagon has been a particularly useful model system for studying the fibrillogenesis mechanisms that lead to the formation of structural polymorphism, thanks to its single tryptophan residue and the availability of large quantities at pharmaceutical-grade quality. Combinations of structural investigations and seed extension experiments have revealed the reproducible formation of at least five different self-propagating fibril types from subtle variations in growth conditions. These reflect the underlying complexity of the peptide conformational landscape and provide a link to natively disordered proteins, where structure is dictated by context in the form of different binding partners. Here we review some of the latest advances in the study of glucagon fibrillar polymorphism and their implications for mechanisms of fibril formation in general.
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Affiliation(s)
- Jesper S Pedersen
- Department of Biochemistry, Molecular Biology, and Cell Biology, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208, USA.
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Abstract
Protein aggregation and formation of amyloid fibrils is a phenomenon usually associated with proteotoxicity and degenerative diseases, such as type 2 diabetes, Alzheimer's disease, and prion diseases. However, several protein and peptide hormones are known to have a high propensity to form amyloid-like fibrils in vitro raising concerns about safety and stability of pharmaceutical protein solutions. Comprehensive understanding of the aggregation mechanisms is an important prerequisite to the design of strategies to prevent fibril formation. Detailed kinetic, spectroscopic, and morphological studies have revealed that glucagon can form several types of fibrils that differ at the level of molecular packing of the peptide. Each type forms through distinct nucleation-dependent aggregation pathways influenced by solution conditions and can be self-propagated by seeding. An increasing number of functional amyloid-like structures have been discovered in nature, and it has recently been proposed that an amyloid-like state of glucagon may be utilized by the pancreatic α-cells as in vivo storage form. This article reviews the current state of our knowledge about the nature of the different types of amyloid-like glucagon fibrils, the mechanisms by which they form, and discusses implications for formulation strategies and the safety of glucagon pharmaceuticals.
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Affiliation(s)
- Jesper Søndergaard Pedersen
- Department of Biochemistry, Molecular Biology, and Cell Biology, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA.
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