1
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Axell E, Hu J, Lindberg M, Dear AJ, Ortigosa-Pascual L, Andrzejewska EA, Šneiderienė G, Thacker D, Knowles TPJ, Sparr E, Linse S. The role of shear forces in primary and secondary nucleation of amyloid fibrils. Proc Natl Acad Sci U S A 2024; 121:e2322572121. [PMID: 38875148 PMCID: PMC11194593 DOI: 10.1073/pnas.2322572121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/02/2024] [Indexed: 06/16/2024] Open
Abstract
Shear forces affect self-assembly processes ranging from crystallization to fiber formation. Here, the effect of mild agitation on amyloid fibril formation was explored for four peptides and investigated in detail for A[Formula: see text]42, which is associated with Alzheimer's disease. To gain mechanistic insights into the effect of mild agitation, nonseeded and seeded aggregation reactions were set up at various peptide concentrations with and without an inhibitor. First, an effect on fibril fragmentation was excluded by comparing the monomer-concentration dependence of aggregation kinetics under idle and agitated conditions. Second, using a secondary nucleation inhibitor, Brichos, the agitation effect on primary nucleation was decoupled from secondary nucleation. Third, an effect on secondary nucleation was established in the absence of inhibitor. Fourth, an effect on elongation was excluded by comparing the seeding potency of fibrils formed under idle or agitated conditions. We find that both primary and secondary nucleation steps are accelerated by gentle agitation. The increased shear forces facilitate both the detachment of newly formed aggregates from catalytic surfaces and the rate at which molecules are transported in the bulk solution to encounter nucleation sites on the fibril and other surfaces. Ultrastructural evidence obtained with cryogenic transmission electron microscopy and free-flow electrophoresis in microfluidics devices imply that agitation speeds up the detachment of nucleated species from the fibril surface. Our findings shed light on the aggregation mechanism and the role of detachment for efficient secondary nucleation. The results inform on how to modulate the relative importance of different microscopic steps in drug discovery and investigations.
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Affiliation(s)
- Emil Axell
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Jing Hu
- Division of Physical Chemistry, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Max Lindberg
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Alexander J. Dear
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Lei Ortigosa-Pascual
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Ewa A. Andrzejewska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Greta Šneiderienė
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Dev Thacker
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Tuomas P. J. Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Emma Sparr
- Division of Physical Chemistry, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
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2
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Wei J, Meisl G, Dear A, Oosterhuis M, Melki R, Emanuelsson C, Linse S, Knowles TPJ. Kinetic models reveal the interplay of protein production and aggregation. Chem Sci 2024; 15:8430-8442. [PMID: 38846392 PMCID: PMC11151821 DOI: 10.1039/d4sc00088a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Protein aggregation is a key process in the development of many neurodegenerative disorders, including dementias such as Alzheimer's disease. Significant progress has been made in understanding the molecular mechanisms of aggregate formation in pure buffer systems, much of which was enabled by the development of integrated rate laws that allowed for mechanistic analysis of aggregation kinetics. However, in order to translate these findings into disease-relevant conclusions and to make predictions about the effect of potential alterations to the aggregation reactions by the addition of putative inhibitors, the current models need to be extended to account for the altered situation encountered in living systems. In particular, in vivo, the total protein concentrations typically do not remain constant and aggregation-prone monomers are constantly being produced but also degraded by cells. Here, we build a theoretical model that explicitly takes into account monomer production, derive integrated rate laws and discuss the resulting scaling laws and limiting behaviours. We demonstrate that our models are suited for the aggregation-prone Huntington's disease-associated peptide HttQ45 utilizing a system for continuous in situ monomer production and the aggregation of the tumour suppressor protein P53. The aggregation-prone HttQ45 monomer was produced through enzymatic cleavage of a larger construct in which a fused protein domain served as an internal inhibitor. For P53, only the unfolded monomers form aggregates, making the unfolding a rate-limiting step which constitutes a source of aggregation-prone monomers. The new model opens up possibilities for a quantitative description of aggregation in living systems, allowing for example the modelling of inhibitors of aggregation in a dynamic environment of continuous protein synthesis.
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Affiliation(s)
- Jiapeng Wei
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Georg Meisl
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Alexander Dear
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Department of Biochemistry and Structural Biology, Lund University SE22100 Lund Sweden
| | - Matthijs Oosterhuis
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University Sweden
| | - Ronald Melki
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS 18 Route du Panorama, Fontenay-Aux-Roses cedex 92265 France
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University Sweden
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University Lund Sweden
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Cavendish Laboratory, University of Cambridge J J Thomson Avenue CB3 0HE UK
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3
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Dear A, Thacker D, Wennmalm S, Ortigosa-Pascual L, Andrzejewska EA, Meisl G, Linse S, Knowles TPJ. Aβ Oligomer Dissociation Is Catalyzed by Fibril Surfaces. ACS Chem Neurosci 2024; 15:2296-2307. [PMID: 38785363 PMCID: PMC11157482 DOI: 10.1021/acschemneuro.4c00127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Oligomeric assemblies consisting of only a few protein subunits are key species in the cytotoxicity of neurodegenerative disorders, such as Alzheimer's and Parkinson's diseases. Their lifetime in solution and abundance, governed by the balance of their sources and sinks, are thus important determinants of disease. While significant advances have been made in elucidating the processes that govern oligomer production, the mechanisms behind their dissociation are still poorly understood. Here, we use chemical kinetic modeling to determine the fate of oligomers formed in vitro and discuss the implications for their abundance in vivo. We discover that oligomeric species formed predominantly on fibril surfaces, a broad class which includes the bulk of oligomers formed by the key Alzheimer's disease-associated Aβ peptides, also dissociate overwhelmingly on fibril surfaces, not in solution as had previously been assumed. We monitor this "secondary nucleation in reverse" by measuring the dissociation of Aβ42 oligomers in the presence and absence of fibrils via two distinct experimental methods. Our findings imply that drugs that bind fibril surfaces to inhibit oligomer formation may also inhibit their dissociation, with important implications for rational design of therapeutic strategies for Alzheimer's and other amyloid diseases.
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Affiliation(s)
- Alexander
J. Dear
- Biochemistry
and Structural Biology, Lund University, Lund 221 00, Sweden
- Centre
for Misfolding Diseases Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Dev Thacker
- Biochemistry
and Structural Biology, Lund University, Lund 221 00, Sweden
| | - Stefan Wennmalm
- Department
of Applied Physics, Biophysics Group, SciLifeLab, Royal Institute of Technology-KTH, Solna 171 65, Sweden
| | | | - Ewa A. Andrzejewska
- Centre
for Misfolding Diseases Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Georg Meisl
- Centre
for Misfolding Diseases Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Sara Linse
- Biochemistry
and Structural Biology, Lund University, Lund 221 00, Sweden
| | - Tuomas P. J. Knowles
- Centre
for Misfolding Diseases Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Cavendish
Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, U.K.
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4
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Dear AJ, Teng X, Ball SR, Lewin J, Horne RI, Clow D, Stevenson A, Harper N, Yahya K, Yang X, Brewerton SC, Thomson J, Michaels TCT, Linse S, Knowles TPJ, Habchi J, Meisl G. Molecular mechanism of α-synuclein aggregation on lipid membranes revealed. Chem Sci 2024; 15:7229-7242. [PMID: 38756798 PMCID: PMC11095391 DOI: 10.1039/d3sc05661a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/14/2024] [Indexed: 05/18/2024] Open
Abstract
The central hallmark of Parkinson's disease pathology is the aggregation of the α-synuclein protein, which, in its healthy form, is associated with lipid membranes. Purified monomeric α-synuclein is relatively stable in vitro, but its aggregation can be triggered by the presence of lipid vesicles. Despite this central importance of lipids in the context of α-synuclein aggregation, their detailed mechanistic role in this process has not been established to date. Here, we use chemical kinetics to develop a mechanistic model that is able to globally describe the aggregation behaviour of α-synuclein in the presence of DMPS lipid vesicles, across a range of lipid and protein concentrations. Through the application of our kinetic model to experimental data, we find that the reaction is a co-aggregation process involving both protein and lipids and that lipids promote aggregation as much by enabling fibril elongation as by enabling their initial formation. Moreover, we find that the primary nucleation of lipid-protein co-aggregates takes place not on the surface of lipid vesicles in bulk solution but at the air-water and/or plate interfaces, where lipids and proteins are likely adsorbed. Our model forms the basis for mechanistic insights, also in other lipid-protein co-aggregation systems, which will be crucial in the rational design of drugs that inhibit aggregate formation and act at the key points in the α-synuclein aggregation cascade.
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Affiliation(s)
- Alexander J Dear
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Xiangyu Teng
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Sarah R Ball
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Joshua Lewin
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Robert I Horne
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Daniel Clow
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Alisdair Stevenson
- Department of Biology, Institute of Biochemistry, ETH Zurich Otto Stern Weg 3 8093 Zurich Switzerland
- Bringing Materials to Life Initiative, ETH Zurich Switzerland
| | - Natasha Harper
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Kim Yahya
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Xiaoting Yang
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Suzanne C Brewerton
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - John Thomson
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Thomas C T Michaels
- Department of Biology, Institute of Biochemistry, ETH Zurich Otto Stern Weg 3 8093 Zurich Switzerland
- Bringing Materials to Life Initiative, ETH Zurich Switzerland
| | - Sara Linse
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
- Biochemistry and Structural Biology, Lund University Lund Sweden
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge UK
- Cavendish Laboratory, University of Cambridge Cambridge UK
| | - Johnny Habchi
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Georg Meisl
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
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5
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Yang T, Xue T, Mao J, Chen Y, Tian H, Bartolome A, Xia H, Yao X, Kumar CV, Cheng J, Lin Y. Tailoring Synthetic Polypeptide Design for Directed Fibril Superstructure Formation and Enhanced Hydrogel Properties. J Am Chem Soc 2024; 146:5823-5833. [PMID: 38174701 DOI: 10.1021/jacs.3c10762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The biological significance of self-assembled protein filament networks and their unique mechanical properties have sparked interest in the development of synthetic filament networks that mimic these attributes. Building on the recent advancement of autoaccelerated ring-opening polymerization of amino acid N-carboxyanhydrides (NCAs), this study strategically explores a series of random copolymers comprising multiple amino acids, aiming to elucidate the core principles governing gelation pathways of these purpose-designed copolypeptides. Utilizing glutamate (Glu) as the primary component of copolypeptides, two targeted pathways were pursued: first, achieving a fast fibrillation rate with lower interaction potential using serine (Ser) as a comonomer, facilitating the creation of homogeneous fibril networks; and second, creating more rigid networks of fibril clusters by incorporating alanine (Ala) and valine (Val) as comonomers. The selection of amino acids played a pivotal role in steering both the morphology of fibril superstructures and their assembly kinetics, subsequently determining their potential to form sample-spanning networks. Importantly, the viscoelastic properties of the resulting supramolecular hydrogels can be tailored according to the specific copolypeptide composition through modulations in filament densities and lengths. The findings enhance our understanding of directed self-assembly in high molecular weight synthetic copolypeptides, offering valuable insights for the development of synthetic fibrous networks and biomimetic supramolecular materials with custom-designed properties.
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Affiliation(s)
- Tianjian Yang
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Tianrui Xue
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jianan Mao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Yingying Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huidi Tian
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Arlene Bartolome
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Hongwei Xia
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Challa V Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Jianjun Cheng
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yao Lin
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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6
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Thacker D, Willas A, Dear AJ, Linse S. Role of Hydrophobicity at the N-Terminal Region of Aβ42 in Secondary Nucleation. ACS Chem Neurosci 2022; 13:3477-3487. [PMID: 36411082 PMCID: PMC9732875 DOI: 10.1021/acschemneuro.2c00504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The self-assembly of the amyloid β 42 (Aβ42) peptide is linked to Alzheimer's disease, and oligomeric intermediates are linked to neuronal cell death during the pathology of the disease. These oligomers are produced prolifically during secondary nucleation, by which the aggregation of monomers is catalyzed on fibril surfaces. Significant progress has been made in understanding the aggregation mechanism of Aβ42; still, a detailed molecular-level understanding of secondary nucleation is lacking. Here, we explore the role of four hydrophobic residues on the unstructured N-terminal region of Aβ42 in secondary nucleation. We create eight mutants with single substitutions at one of the four positions─Ala2, Phe4, Tyr10, and Val12─to decrease the hydrophobicity at respective positions (A2T, A2S, F4A, F4S, Y10A, Y10S, V12A, and V12S) and one mutant (Y10F) to remove the polar nature of Tyr10. Kinetic analyses of aggregation data reveal that the hydrophobicity at the N-terminal region of Aβ42, especially at positions 10 and 12, affects the rate of fibril mass generated via secondary nucleation. Cryo-electron micrographs reveal that most of the mutants with lower hydrophobicity form fibrils that are markedly longer than WT Aβ42, in line with the reduced secondary nucleation rates for these peptides. The dominance of secondary nucleation, however, is still retained in the aggregation mechanism of these mutants because the rate of primary nucleation is even more reduced. This highlights that secondary nucleation is a general phenomenon that is not dependent on any one particular feature of the peptide and is rather robust to sequence perturbations.
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Affiliation(s)
- Dev Thacker
- Department
of Biochemistry and Structural Biology, Lund University, Lund22362, Sweden
| | - Amanda Willas
- Department
of Biochemistry and Structural Biology, Lund University, Lund22362, Sweden
| | - Alexander J. Dear
- Department
of Biochemistry and Structural Biology, Lund University, Lund22362, Sweden,Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Sara Linse
- Department
of Biochemistry and Structural Biology, Lund University, Lund22362, Sweden,
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7
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Meisl G, Knowles TPJ, Klenerman D. Mechanistic Models of Protein Aggregation Across Length-Scales and Time-Scales: From the Test Tube to Neurodegenerative Disease. Front Neurosci 2022; 16:909861. [PMID: 35844223 PMCID: PMC9281552 DOI: 10.3389/fnins.2022.909861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022] Open
Abstract
Through advances in the past decades, the central role of aberrant protein aggregation has been established in many neurodegenerative diseases. Crucially, however, the molecular mechanisms that underlie aggregate proliferation in the brains of affected individuals are still only poorly understood. Under controlled in vitro conditions, significant progress has been made in elucidating the molecular mechanisms that take place during the assembly of purified protein molecules, through advances in both experimental methods and the theories used to analyse the resulting data. The determination of the aggregation mechanism for a variety of proteins revealed the importance of intermediate oligomeric species and of the interactions with promotors and inhibitors. Such mechanistic insights, if they can be achieved in a disease-relevant system, provide invaluable information to guide the design of potential cures to these devastating disorders. However, as experimental systems approach the situation present in real disease, their complexity increases substantially. Timescales increase from hours an aggregation reaction takes in vitro, to decades over which the process takes place in disease, and length-scales increase to the dimension of a human brain. Thus, molecular level mechanistic studies, like those that successfully determined mechanisms in vitro, have only been applied in a handful of living systems to date. If their application can be extended to further systems, including patient data, they promise powerful new insights. Here we present a review of the existing strategies to gain mechanistic insights into the molecular steps driving protein aggregation and discuss the obstacles and potential paths to achieving their application in disease. First, we review the experimental approaches and analysis techniques that are used to establish the aggregation mechanisms in vitro and the insights that have been gained from them. We then discuss how these approaches must be modified and adapted to be applicable in vivo and review the existing works that have successfully applied mechanistic analysis of protein aggregation in living systems. Finally, we present a broad mechanistic classification of in vivo systems and discuss what will be required to further our understanding of aggregate formation in living systems.
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Affiliation(s)
- Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- UK Dementia Research Institute, University of Cambridge, Cambridge, United Kingdom
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8
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Michaels TCT, Dear AJ, Cohen SIA, Vendruscolo M, Knowles TPJ. Kinetic profiling of therapeutic strategies for inhibiting the formation of amyloid oligomers. J Chem Phys 2022; 156:164904. [PMID: 35490011 DOI: 10.1063/5.0077609] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein self-assembly into amyloid fibrils underlies several neurodegenerative conditions, including Alzheimer's and Parkinson's diseases. It has become apparent that the small oligomers formed during this process constitute neurotoxic molecular species associated with amyloid aggregation. Targeting the formation of oligomers represents, therefore, a possible therapeutic avenue to combat these diseases. However, it remains challenging to establish which microscopic steps should be targeted to suppress most effectively the generation of oligomeric aggregates. Recently, we have developed a kinetic model of oligomer dynamics during amyloid aggregation. Here, we use this approach to derive explicit scaling relationships that reveal how key features of the time evolution of oligomers, including oligomer peak concentration and lifetime, are controlled by the different rate parameters. We discuss the therapeutic implications of our framework by predicting changes in oligomer concentrations when the rates of the individual microscopic events are varied. Our results identify the kinetic parameters that control most effectively the generation of oligomers, thus opening a new path for the systematic rational design of therapeutic strategies against amyloid-related diseases.
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Affiliation(s)
- Thomas C T Michaels
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Alexander J Dear
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Samuel I A Cohen
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Michele Vendruscolo
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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9
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Makam P, Yamijala SSRKC, Bhadram VS, Shimon LJW, Wong BM, Gazit E. Single amino acid bionanozyme for environmental remediation. Nat Commun 2022; 13:1505. [PMID: 35314678 PMCID: PMC8938493 DOI: 10.1038/s41467-022-28942-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/21/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractEnzymes are extremely complex catalytic structures with immense biological and technological importance. Nevertheless, their widespread environmental implementation faces several challenges, including high production costs, low operational stability, and intricate recovery and reusability. Therefore, the de novo design of minimalistic biomolecular nanomaterials that can efficiently mimic the biocatalytic function (bionanozymes) and overcome the limitations of natural enzymes is a critical goal in biomolecular engineering. Here, we report an exceptionally simple yet highly active and robust single amino acid bionanozyme that can catalyze the rapid oxidation of environmentally toxic phenolic contaminates and serves as an ultrasensitive tool to detect biologically important neurotransmitters similar to the laccase enzyme. While inspired by the laccase catalytic site, the substantially simpler copper-coordinated bionanozyme is ∼5400 times more cost-effective, four orders more efficient, and 36 times more sensitive compared to the natural protein. Furthermore, the designed mimic is stable under extreme conditions (pH, ionic strength, temperature, storage time), markedly reusable for several cycles, and displays broad substrate specificity. These findings hold great promise in developing efficient bionanozymes for analytical chemistry, environmental protection, and biotechnology.
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10
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Blanco MA. Computational models for studying physical instabilities in high concentration biotherapeutic formulations. MAbs 2022; 14:2044744. [PMID: 35282775 PMCID: PMC8928847 DOI: 10.1080/19420862.2022.2044744] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Computational prediction of the behavior of concentrated protein solutions is particularly advantageous in early development stages of biotherapeutics when material availability is limited and a large set of formulation conditions needs to be explored. This review provides an overview of the different computational paradigms that have been successfully used in modeling undesirable physical behaviors of protein solutions with a particular emphasis on high-concentration drug formulations. This includes models ranging from all-atom simulations, coarse-grained representations to macro-scale mathematical descriptions used to study physical instability phenomena of protein solutions such as aggregation, elevated viscosity, and phase separation. These models are compared and summarized in the context of the physical processes and their underlying assumptions and limitations. A detailed analysis is also given for identifying protein interaction processes that are explicitly or implicitly considered in the different modeling approaches and particularly their relations to various formulation parameters. Lastly, many of the shortcomings of existing computational models are discussed, providing perspectives and possible directions toward an efficient computational framework for designing effective protein formulations.
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Affiliation(s)
- Marco A. Blanco
- Materials and Biophysical Characterization, Analytical R & D, Merck & Co., Inc, Kenilworth, NJ USA
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11
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Fu H, Baumgartner R, Song Z, Chen C, Cheng J, Lin Y. Generalized Model of Cooperative Covalent Polymerization: Connecting the Supramolecular Binding Interactions with the Catalytic Behavior. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c02606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hailin Fu
- Department of Chemistry and Polymer Program at the Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ryan Baumgartner
- Department of Materials Science and Engineering and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ziyuan Song
- Department of Materials Science and Engineering and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chongyi Chen
- Department of Materials Science and Engineering and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jianjun Cheng
- Department of Materials Science and Engineering and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yao Lin
- Department of Chemistry and Polymer Program at the Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
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12
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Braun GA, Dear AJ, Sanagavarapu K, Zetterberg H, Linse S. Amyloid-β peptide 37, 38 and 40 individually and cooperatively inhibit amyloid-β 42 aggregation. Chem Sci 2022; 13:2423-2439. [PMID: 35310497 PMCID: PMC8864715 DOI: 10.1039/d1sc02990h] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 01/22/2022] [Indexed: 12/22/2022] Open
Abstract
The pathology of Alzheimer's disease is connected to the aggregation of β-amyloid (Aβ) peptide, which in vivo exists as a number of length-variants. Truncations and extensions are found at both the N- and C-termini, relative to the most commonly studied 40- and 42-residue alloforms. Here, we investigate the aggregation of two physiologically abundant alloforms, Aβ37 and Aβ38, as pure peptides and in mixtures with Aβ40 and Aβ42. A variety of molar ratios were applied in quaternary mixtures to investigate whether a certain ratio is maximally inhibiting of the more toxic alloform Aβ42. Through kinetic analysis, we show that both Aβ37 and Aβ38 self-assemble through an autocatalytic secondary nucleation reaction to form fibrillar β-sheet-rich aggregates, albeit on a longer timescale than Aβ40 or Aβ42. Additionally, we show that the shorter alloforms co-aggregate with Aβ40, affecting both the kinetics of aggregation and the resulting fibrillar ultrastructure. In contrast, neither Aβ37 nor Aβ38 forms co-aggregates with Aβ42; however, both short alloforms reduce the rate of Aβ42 aggregation in a concentration-dependent manner. Finally, we show that the aggregation of Aβ42 is more significantly impeded by a combination of Aβ37, Aβ38, and Aβ40 than by any of these alloforms independently. These results demonstrate that the aggregation of any given Aβ alloform is significantly perturbed by the presence of other alloforms, particularly in heterogeneous mixtures, such as is found in the extracellular fluid of the brain.
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Affiliation(s)
- Gabriel A Braun
- Biochemistry and Structural Biology, Lund University Lund Sweden
| | - Alexander J Dear
- Biochemistry and Structural Biology, Lund University Lund Sweden .,Department of Cell Biology, Harvard Medical School Boston MA USA.,Paulson School of Engineering and Applied Science, Harvard University Cambridge MA USA.,Department of Chemistry, University of Cambridge Cambridge UK
| | | | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg Mölndal Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital Mölndal Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology Queen Square London UK.,UK Dementia Research Institute at UCL London UK
| | - Sara Linse
- Biochemistry and Structural Biology, Lund University Lund Sweden
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13
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Ghosh M, Majkowska A, Mirsa R, Bera S, Rodríguez-Cabello JC, Mata A, Adler-Abramovich L. Disordered Protein Stabilization by Co-Assembly of Short Peptides Enables Formation of Robust Membranes. ACS APPLIED MATERIALS & INTERFACES 2022; 14:464-473. [PMID: 34941264 DOI: 10.1021/acsami.1c22136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecular self-assembly is a spontaneous natural process resulting in highly ordered nano to microarchitectures. We report temperature-independent formation of robust stable membranes obtained by the spontaneous interaction of intrinsically disordered elastin-like polypeptides (ELPs) with short aromatic peptides at temperatures both below and above the conformational transition temperature of the ELPs. The membranes are stable over time and display durability over a wide range of parameters including temperature, pH, and ultrasound energy. The morphology and composition of the membranes were analyzed using microscopy. These robust structures support preosteoblast cell adhesion and proliferation as well as pH-dependent cargo release. Simple noncovalent interactions with short aromatic peptides can overcome conformational restrictions due to the phase transition to facilitate the formation of complex bioactive scaffolds that are stable over a wide range of environmental parameters. This approach offers novel possibilities for controlling the conformational restriction of intrinsically disordered proteins and using them in the design of new materials.
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Affiliation(s)
- Moumita Ghosh
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
- The Centre for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- Department of Chemistry, Techno India University, EM-4, EM Block, Sector V, Bidhannagar, Kolkata, West Bengal 700091, India
| | - Anna Majkowska
- School of Engineering & Materials Science, Queen Mary University of London, London E1 4NS, U.K
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, U.K
| | - Rajkumar Mirsa
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
- The Centre for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Santu Bera
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
- The Centre for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
| | | | - Alvaro Mata
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
- Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
- The Centre for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
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14
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Yang T, Benson K, Fu H, Xue T, Song Z, Duan H, Xia H, Kalluri A, He J, Cheng J, Kumar CV, Lin Y. Modeling and Designing Particle-Regulated Amyloid-like Assembly of Synthetic Polypeptides in Aqueous Solution. Biomacromolecules 2021; 23:196-209. [PMID: 34964619 DOI: 10.1021/acs.biomac.1c01230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In cells, actin and tubulin polymerization is regulated by nucleation factors, which promote the nucleation and subsequent growth of protein filaments in a controlled manner. Mimicking this natural mechanism to control the supramolecular polymerization of macromolecular monomers by artificially created nucleation factors remains a largely unmet challenge. Biological nucleation factors act as molecular scaffolds to boost the local concentrations of protein monomers and facilitate the required conformational changes to accelerate the nucleation and subsequent polymerization. An accelerated assembly of synthetic poly(l-glutamic acid) into amyloid fibrils catalyzed by cationic silica nanoparticle clusters (NPCs) as artificial nucleation factors is demonstrated here and modeled as supramolecular polymerization with a surface-induced heterogeneous nucleation pathway. Kinetic studies of fibril growth coupled with mechanistic analysis demonstrate that the artificial nucleators predictably accelerate the supramolecular polymerization process by orders of magnitude (e.g., shortening the assembly time by more than 10 times) when compared to the uncatalyzed reaction, under otherwise identical conditions. Amyloid-like fibrillation was supported by a variety of standard characterization methods. Nucleation followed a Michaelis-Menten-like scheme for the cationic silica NPCs, while the corresponding anionic or neutral nanoparticles had no effect on fibrillation. This approach shows the effectiveness of charge-charge interactions and surface functionalities in facilitating the conformational change of macromolecular monomers and controlling the rates of nucleation for fibril growth. Molecular design approaches like these inspire the development of novel materials via biomimetic supramolecular polymerizations.
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Affiliation(s)
- Tianjian Yang
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Kyle Benson
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Hailin Fu
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Tianrui Xue
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ziyuan Song
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hanyi Duan
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Hongwei Xia
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ankarao Kalluri
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Jie He
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States.,Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Jianjun Cheng
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Challa V Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Yao Lin
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States.,Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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15
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Zimmermann MR, Bera SC, Meisl G, Dasadhikari S, Ghosh S, Linse S, Garai K, Knowles TPJ. Mechanism of Secondary Nucleation at the Single Fibril Level from Direct Observations of Aβ42 Aggregation. J Am Chem Soc 2021; 143:16621-16629. [PMID: 34582216 DOI: 10.1021/jacs.1c07228] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The formation of amyloid fibrils and oligomers is a hallmark of several neurodegenerative disorders, including Alzheimer's disease (AD), and contributes to the disease pathway. To progress our understanding of these diseases at a molecular level, it is crucial to determine the mechanisms and rates of amyloid formation and replication. In the context of AD, the self-replication of aggregates of the Aβ42 peptide by secondary nucleation, leading to the formation of new aggregates on the surfaces of existing ones, is a major source of both new fibrils and smaller toxic oligomeric species. However, the core mechanistic determinants, including the presence of intermediates, as well as the role of heterogeneities in the fibril population, are challenging to determine from bulk aggregation measurements. Here, we obtain such information by monitoring directly the time evolution of individual fibrils by TIRF microscopy. Crucially, essentially all aggregates have the ability to self-replicate via secondary nucleation, and the amplification of the aggregate concentration cannot be explained by a small fraction of "superspreader" fibrils. We observe that secondary nucleation is a catalytic multistep process involving the attachment of soluble species to the fibril surface, followed by conversion/detachment to yield a new fibril in solution. Furthermore, we find that fibrils formed by secondary nucleation resemble the parent fibril population. This detailed level of mechanistic insights into aggregate self-replication is key in the rational design of potential inhibitors of this process.
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Affiliation(s)
- Manuela R Zimmermann
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Subhas C Bera
- TIFR Centre for Interdisciplinary Sciences, 500046 Hyderabad, India
- Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University, Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Georg Meisl
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | | | - Shamasree Ghosh
- TIFR Centre for Interdisciplinary Sciences, 500046 Hyderabad, India
| | - Sara Linse
- Department of Chemistry, Division for Biochemistry and Structural Biology, Lund University, 221 00 Lund, Sweden
| | - Kanchan Garai
- TIFR Centre for Interdisciplinary Sciences, 500046 Hyderabad, India
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
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16
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Dear AJ, Michaels TCT, Knowles TPJ, Mahadevan L. Feedback control of protein aggregation. J Chem Phys 2021; 155:064102. [PMID: 34391352 DOI: 10.1063/5.0055925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The self-assembly of peptides and proteins into amyloid fibrils plays a causative role in a wide range of increasingly common and currently incurable diseases. The molecular mechanisms underlying this process have recently been discovered, prompting the development of drugs that inhibit specific reaction steps as possible treatments for some of these disorders. A crucial part of treatment design is to determine how much drug to give and when to give it, informed by its efficacy and intrinsic toxicity. Since amyloid formation does not proceed at the same pace in different individuals, it is also important that treatment design is informed by local measurements of the extent of protein aggregation. Here, we use stochastic optimal control theory to determine treatment regimens for inhibitory drugs targeting several key reaction steps in protein aggregation, explicitly taking into account variability in the reaction kinetics. We demonstrate how these regimens may be updated "on the fly" as new measurements of the protein aggregate concentration become available, in principle, enabling treatments to be tailored to the individual. We find that treatment timing, duration, and drug dosage all depend strongly on the particular reaction step being targeted. Moreover, for some kinds of inhibitory drugs, the optimal regimen exhibits high sensitivity to stochastic fluctuations. Feedback controls tailored to the individual may therefore substantially increase the effectiveness of future treatments.
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Affiliation(s)
- Alexander J Dear
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Thomas C T Michaels
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - L Mahadevan
- School of Engineering and Applied Sciences, Department of Physics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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17
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Thompson TB, Meisl G, Knowles TPJ, Goriely A. The role of clearance mechanisms in the kinetics of pathological protein aggregation involved in neurodegenerative diseases. J Chem Phys 2021; 154:125101. [PMID: 33810689 DOI: 10.1063/5.0031650] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The deposition of pathological protein aggregates in the brain plays a central role in cognitive decline and structural damage associated with neurodegenerative diseases. In Alzheimer's disease, the formation of amyloid-β plaques and neurofibrillary tangles of the tau protein is associated with the appearance of symptoms and pathology. Detailed models for the specific mechanisms of aggregate formation, such as nucleation and elongation, exist for aggregation in vitro where the total protein mass is conserved. However, in vivo, an additional class of mechanisms that clear pathological species is present and is believed to play an essential role in limiting the formation of aggregates and preventing or delaying the emergence of disease. A key unanswered question in the field of neuro-degeneration is how these clearance mechanisms can be modeled and how alterations in the processes of clearance or aggregation affect the stability of the system toward aggregation. Here, we generalize classical models of protein aggregation to take into account both production of monomers and the clearance of protein aggregates. We show that, depending on the specifics of the clearance process, a critical clearance value emerges above which accumulation of aggregates does not take place. Our results show that a sudden switch from a healthy to a disease state can be caused by small variations in the efficiency of the clearance process and provide a mathematical framework to explore the detailed effects of different mechanisms of clearance on the accumulation of aggregates.
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Affiliation(s)
- T B Thompson
- Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - G Meisl
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - T P J Knowles
- Department of Chemistry and Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - A Goriely
- Mathematical Institute, University of Oxford, Oxford, United Kingdom
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18
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Morel B, Carrasco-Jiménez MP, Jurado S, Conejero-Lara F. Rapid Conversion of Amyloid-Beta 1-40 Oligomers to Mature Fibrils through a Self-Catalytic Bimolecular Process. Int J Mol Sci 2021; 22:ijms22126370. [PMID: 34198692 PMCID: PMC8232289 DOI: 10.3390/ijms22126370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022] Open
Abstract
The formation of fibrillar aggregates of the amyloid beta peptide (Aβ) in the brain is one of the hallmarks of Alzheimer’s disease (AD). A clear understanding of the different aggregation steps leading to fibrils formation is a keystone in therapeutics discovery. In a recent study, we showed that Aβ40 and Aβ42 form dynamic micellar aggregates above certain critical concentrations, which mediate a fast formation of more stable oligomers, which in the case of Aβ40 are able to evolve towards amyloid fibrils. Here, using different biophysical techniques we investigated the role of different fractions of the Aβ aggregation mixture in the nucleation and fibrillation steps. We show that both processes occur through bimolecular interplay between low molecular weight species (monomer and/or dimer) and larger oligomers. Moreover, we report here a novel self-catalytic mechanism of fibrillation of Aβ40, in which early oligomers generate and deliver low molecular weight amyloid nuclei, which then catalyze the rapid conversion of the oligomers to mature amyloid fibrils. This fibrillation catalytic activity is not present in freshly disaggregated low-molecular weight Aβ40 and is, therefore, a property acquired during the aggregation process. In contrast to Aβ40, we did not observe the same self-catalytic fibrillation in Aβ42 spheroidal oligomers, which could neither be induced to fibrillate by the Aβ40 nuclei. Our results reveal clearly that amyloid fibrillation is a multi-component process, in which dynamic collisions between different interacting species favor the kinetics of amyloid nucleation and growth.
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Affiliation(s)
- Bertrand Morel
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
- Correspondence: (B.M.); (F.C.-L.); Tel.: +34-958-242-371 (F.C.-L.)
| | - María P. Carrasco-Jiménez
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - Samuel Jurado
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
- Correspondence: (B.M.); (F.C.-L.); Tel.: +34-958-242-371 (F.C.-L.)
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19
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Meisl G, Kurt T, Condado-Morales I, Bett C, Sorce S, Nuvolone M, Michaels TCT, Heinzer D, Avar M, Cohen SIA, Hornemann S, Aguzzi A, Dobson CM, Sigurdson CJ, Knowles TPJ. Scaling analysis reveals the mechanism and rates of prion replication in vivo. Nat Struct Mol Biol 2021; 28:365-372. [PMID: 33767451 PMCID: PMC8922999 DOI: 10.1038/s41594-021-00565-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/26/2021] [Indexed: 01/03/2023]
Abstract
Prions consist of pathological aggregates of cellular prion protein and have the ability to replicate, causing neurodegenerative diseases, a phenomenon mirrored in many other diseases connected to protein aggregation, including Alzheimer's and Parkinson's diseases. However, despite their key importance in disease, the individual processes governing this formation of pathogenic aggregates, as well as their rates, have remained challenging to elucidate in vivo. Here we bring together a mathematical framework with kinetics of the accumulation of prions in mice and microfluidic measurements of aggregate size to dissect the overall aggregation reaction into its constituent processes and quantify the reaction rates in mice. Taken together, the data show that multiplication of prions in vivo is slower than in in vitro experiments, but efficient when compared with other amyloid systems, and displays scaling behavior characteristic of aggregate fragmentation. These results provide a framework for the determination of the mechanisms of disease-associated aggregation processes within living organisms.
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Affiliation(s)
- Georg Meisl
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Timothy Kurt
- Department of Pathology, UC San Diego, San Diego, CA, USA
| | - Itzel Condado-Morales
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Cyrus Bett
- Department of Pathology, UC San Diego, San Diego, CA, USA
| | - Silvia Sorce
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Mario Nuvolone
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
- Amyloidosis Research and Treatment Center, Foundation IRCCS Policlinico San Matteo, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Thomas C T Michaels
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Daniel Heinzer
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Merve Avar
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Samuel I A Cohen
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Wren Therapeutics, Cambridge, UK
| | - Simone Hornemann
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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20
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Braun GA, Ary BE, Dear AJ, Rohn MCH, Payson AM, Lee DSM, Parry RC, Friedman C, Knowles TPJ, Linse S, Åkerfeldt KS. On the Mechanism of Self-Assembly by a Hydrogel-Forming Peptide. Biomacromolecules 2020; 21:4781-4794. [PMID: 33170649 DOI: 10.1021/acs.biomac.0c00989] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Self-assembling peptide-based hydrogels are a class of tunable soft materials that have been shown to be highly useful for a number of biomedical applications. The dynamic formation of the supramolecular fibrils that compose these materials has heretofore remained poorly characterized. A better understanding of this process would provide important insights into the behavior of these systems and could aid in the rational design of new peptide hydrogels. Here, we report the determination of the microscopic steps that underpin the self-assembly of a hydrogel-forming peptide, SgI37-49. Using theoretical models of linear polymerization to analyze the kinetic self-assembly data, we show that SgI37-49 fibril formation is driven by fibril-catalyzed secondary nucleation and that all the microscopic processes involved in SgI37-49 self-assembly display an enzyme-like saturation behavior. Moreover, this analysis allows us to quantify the rates of the underlying processes at different peptide concentrations and to calculate the time evolution of these reaction rates over the time course of self-assembly. We demonstrate here a new mechanistic approach for the study of self-assembling hydrogel-forming peptides, which is complementary to commonly used materials science characterization techniques.
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Affiliation(s)
- Gabriel A Braun
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, United States.,Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Lund SE-22100, Sweden
| | - Beatrice E Ary
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, United States
| | - Alexander J Dear
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.,Paulson School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew C H Rohn
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, United States
| | - Abigail M Payson
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, United States
| | - David S M Lee
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, United States
| | - Robert C Parry
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, United States
| | - Connie Friedman
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, United States
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.,Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Lund SE-22100, Sweden
| | - Karin S Åkerfeldt
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, United States
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21
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Koder Hamid M, Rüter A, Kuczera S, Olsson U. Slow Dissolution Kinetics of Model Peptide Fibrils. Int J Mol Sci 2020; 21:ijms21207671. [PMID: 33081320 PMCID: PMC7590008 DOI: 10.3390/ijms21207671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 11/25/2022] Open
Abstract
Understanding the kinetics of peptide self-assembly is important because of the involvement of peptide amyloid fibrils in several neurodegenerative diseases. In this paper, we have studied the dissolution kinetics of self-assembled model peptide fibrils after a dilution quench. Due to the low concentrations involved, the experimental method of choice was isothermal titration calorimetry (ITC). We show that the dissolution is a strikingly slow and reaction-limited process, that can be timescale separated from other rapid processes associated with dilution in the ITC experiment. We argue that the rate-limiting step of dissolution involves the breaking up of inter-peptide β–sheet hydrogen bonds, replacing them with peptide–water hydrogen bonds. Complementary pH experiments revealed that the self-assembly involves partial deprotonation of the peptide molecules.
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22
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The role of fibril structure and surface hydrophobicity in secondary nucleation of amyloid fibrils. Proc Natl Acad Sci U S A 2020; 117:25272-25283. [PMID: 33004626 PMCID: PMC7568274 DOI: 10.1073/pnas.2002956117] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Alzheimer’s disease affects a rapidly growing number of individuals worldwide. Key unresolved questions relate to the onset and propagation of the disease, linked to the self-assembly of amyloid β peptide into fibrillar and smaller aggregates. This study investigates the propagation of aggregates of amyloid β peptide and asks whether hydrophobic molecular features observed on the fibril surface correlate with its ability to catalyze the formation of new aggregates. This question is motivated by the associated formation of intermediate forms that are toxic to neuronal cells. The results imply that surface catalysis is independent of surface details but requires that the monomers that form the new aggregate can adopt the structure of the parent aggregate without steric clashes. Crystals, nanoparticles, and fibrils catalyze the generation of new aggregates on their surface from the same type of monomeric building blocks as the parent assemblies. This secondary nucleation process can be many orders of magnitude faster than primary nucleation. In the case of amyloid fibrils associated with Alzheimer’s disease, this process leads to the multiplication and propagation of aggregates, whereby short-lived oligomeric intermediates cause neurotoxicity. Understanding the catalytic activity is a fundamental goal in elucidating the molecular mechanisms of Alzheimer’s and associated diseases. Here we explore the role of fibril structure and hydrophobicity by asking whether the V18, A21, V40, and A42 side chains which are exposed on the Aβ42 fibril surface as continuous hydrophobic patches play a role in secondary nucleation. Single, double, and quadruple serine substitutions were made. Kinetic analyses of aggregation data at multiple monomer concentrations reveal that all seven mutants retain the dominance of secondary nucleation as the main mechanism of fibril proliferation. This finding highlights the generality of secondary nucleation and its independence of the detailed molecular structure. Cryo-electron micrographs reveal that the V18S substitution causes fibrils to adopt a distinct morphology with longer twist distance than variants lacking this substitution. Self- and cross-seeding data show that surface catalysis is only efficient between peptides of identical morphology, indicating a templating role of secondary nucleation with structural conversion at the fibril surface. Our findings thus provide clear evidence that the propagation of amyloid fibril strains is possible even in systems dominated by secondary nucleation rather than fragmentation.
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Agerschou ED, Borgmann V, Wördehoff MM, Hoyer W. Inhibitor and substrate cooperate to inhibit amyloid fibril elongation of α-synuclein. Chem Sci 2020; 11:11331-11337. [PMID: 34094375 PMCID: PMC8162328 DOI: 10.1039/d0sc04051g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/28/2020] [Indexed: 11/21/2022] Open
Abstract
In amyloid fibril elongation, soluble growth substrate binds to the fibril-end and converts into the fibril conformation. This process is targeted by inhibitors that block fibril-ends. Here, we investigated how the elongation of α-synuclein (αS) fibrils, which are associated with Parkinson's disease and other synucleinopathies, is inhibited by αS variants with a preformed hairpin in the critical N-terminal region comprising residues 36-57. The inhibitory efficiency is strongly dependent on the specific position of the hairpin. We find that the inhibitor and substrate concentration dependencies can be analyzed with models of competitive enzyme inhibition. Remarkably, the growth substrate, i.e., wild-type αS, supports inhibition by stabilizing the elongation-incompetent blocked state. This observation allowed us to create inhibitor-substrate fusions that achieved inhibition at low nanomolar concentration. We conclude that inhibitor-substrate cooperativity can be exploited for the design of fibril growth inhibitors.
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Affiliation(s)
- Emil Dandanell Agerschou
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany
| | - Vera Borgmann
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany
| | - Michael M Wördehoff
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich 52425 Jülich Germany
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