Quantitative investigations into the molecular mechanisms of amyloid fibril fragmentation
Lead Research Organisation:
University of Kent
Department Name: Sch of Biosciences
Abstract
Amyloid fibrils are forms of protein that have received much recent attention through their association with numerous devastating human brain diseases. Examples include Alzheimer, Creutzfeldt-Jakob (CJD), Huntington and Parkinson diseases. Furthermore, the unusual physical characteristics of amyloid fibrils mean that they have the potential to become strong and stable engineered nanomaterials. Breaking amyloid fibrils into smaller pieces is a key process that must be fully understood if we are to understand how amyloid fibrils normally function in nature, and how they are involved in diseases so we can develop effective therapies against the amyloid-associated diseases. Nevertheless, the causes and consequences of amyloid fibril fragmentation remain a largely unexplored area of research. The long-term goal of this project is to resolve the molecular and cellular mechanisms of fibril fragmentation.
Amyloid fibrils are assembled from whole or parts of normal proteins and the devastating human diseases associated with amyloid are linked to the way the amyloid fibrils are assembled and deposited in the brain or in other parts of the human body. However, amyloid fibrils have also been recognised as a class of natural protein forms, so-called 'functional amyloids'. Functional amyloids can play a number of important roles in bacteria, yeast and even humans. A sub-class of amyloids can spread between organisms by forming small seeds through the fragmentation of larger fibrils. This sub-class is referred to as prions and they exist in humans where they cause diseases such as CJD. In baker's yeast, they confer special cellular properties on the cells that are passed on from generation to generation; a form of 'protein gene'. To fully understand how prions are formed and transmitted requires that we understand how the prion seeds (which we call propagons) are generated through amyloid fibril fragmentation. Detailed characterisation of amyloid fibrils of different origins has revealed incredibly strong structures that are commonly only tens of nanometres thick but many micrometers long. The fragmentation property of amyloid fibrils is, however, the dominating factor for their stability. Fibril fragmentation is also an important factor in amyloid-associated disease because it influences the size and shape of the disease-associated forms of the fibrils, which are typically large clumps of aggregates. How easy do disease-associated prions spread, how fast are amyloid aggregates assembled and deposited, and how toxic are these aggregates to cells are important disease properties that are influenced by amyloid fibril fragmentation.
To address these points, our goal is to answer the following questions: how are amyloid fibrils fragmented, how fast can they fragment, and how is fragmentation linked to their properties in living cells. Using a combination of experimental, theoretical and computational approaches, the fragmentation properties of three different amyloids will be studied: one that forms a prion in yeast, one that is associated with human disease, and the third is an artificial model system. The insights gained from this project will also be critical for further exploring amyloid fibrils as potential nanomaterial in technological applications, and will provide new insights that will facilitate the future development of therapeutic strategies against amyloid associated disease.
Amyloid fibrils are assembled from whole or parts of normal proteins and the devastating human diseases associated with amyloid are linked to the way the amyloid fibrils are assembled and deposited in the brain or in other parts of the human body. However, amyloid fibrils have also been recognised as a class of natural protein forms, so-called 'functional amyloids'. Functional amyloids can play a number of important roles in bacteria, yeast and even humans. A sub-class of amyloids can spread between organisms by forming small seeds through the fragmentation of larger fibrils. This sub-class is referred to as prions and they exist in humans where they cause diseases such as CJD. In baker's yeast, they confer special cellular properties on the cells that are passed on from generation to generation; a form of 'protein gene'. To fully understand how prions are formed and transmitted requires that we understand how the prion seeds (which we call propagons) are generated through amyloid fibril fragmentation. Detailed characterisation of amyloid fibrils of different origins has revealed incredibly strong structures that are commonly only tens of nanometres thick but many micrometers long. The fragmentation property of amyloid fibrils is, however, the dominating factor for their stability. Fibril fragmentation is also an important factor in amyloid-associated disease because it influences the size and shape of the disease-associated forms of the fibrils, which are typically large clumps of aggregates. How easy do disease-associated prions spread, how fast are amyloid aggregates assembled and deposited, and how toxic are these aggregates to cells are important disease properties that are influenced by amyloid fibril fragmentation.
To address these points, our goal is to answer the following questions: how are amyloid fibrils fragmented, how fast can they fragment, and how is fragmentation linked to their properties in living cells. Using a combination of experimental, theoretical and computational approaches, the fragmentation properties of three different amyloids will be studied: one that forms a prion in yeast, one that is associated with human disease, and the third is an artificial model system. The insights gained from this project will also be critical for further exploring amyloid fibrils as potential nanomaterial in technological applications, and will provide new insights that will facilitate the future development of therapeutic strategies against amyloid associated disease.
Technical Summary
In order to characterise the molecular mechanisms of amyloid fibril fragmentation, to quantify the rates of fibril fragmentation, and to determine the influence of fragmentation on cellular processes, a combination of experimental, theoretical and computational approaches will be employed. The fibril fragmentation properties of three amyloid models: the yeast prion protein Sup35, human alpha-synuclein, and hen egg white lysozyme, representing a functional, a disease-related and an artificial model system, respectively, will be examined. Firstly, their fibril stability towards fragmentation will be characterised using tapping-mode atomic force microscopy. Image data collected during fragmentation facilitated by stirring will be analysed through the application of statistical image analysis methods in order to quantify changes in fibril dimensions. Secondly, models of how fibril fragmentation might occur will be developed and computer simulations of fragmentation processes will be performed in parallel with the experiments. Modelling strategies, through a systems approach with large-scale population balance simulations will be developed to tackle the complexities of heterogeneous mixture of species involved in fibril fragmentation. Potential models will be quantitatively tested against the data using regression and model comparison methods to delineate models that can describe and predict fibril fragmentation. Thirdly, the in vitro measurements of fragmentation properties will be applied to the quantitative characterisation of the biological consequence of Sup35 fibril fragmentation in yeast cells. How changes in the fragmentation properties of Sup35 fibrils affect the resulting [PSI+] prion phenotype in vivo will be accessed using mutants of Sup35. This application of quantitative fibril fragmentation analysis will test the hypothesis that enzyme controlled fibril fragmentation is an integral part of functional amyloid in biology.
Planned Impact
The findings of this proposed project will not only benefit researchers exploring the basic mechanisms of amyloid formation or prion propagation, they will likely have a number of important applications. Using amyloid fibrils in novel bio-nanomaterials, and developing therapies targeting amyloid disease are examples of the many potential applications of the findings of this project. These potential applications will revolutionise a variety of industries in the medical, tele-communication and manufacturing sectors, as well as improve life in general in an aging population. In addition, this project will provide a postdoctoral researcher with an unique training opportunity. The postdoctoral scientist will develop skills to apply mathematics, chemistry and physics methods to solve important biological problems, and learn to communicate ideas across disciplinary boundaries. The findings of this project will be of interest to a wide group of researchers in diverse disciplines through the means of publications in open access multidisciplinary peer-reviewed journals and presentations in international conferences covering topics ranging from biology, physics, chemistry to material science. Any potential commercial applications arising from this proposal will be explored with the help and support from the Kent Innovation and Enterprise business development unit within the University of Kent.
Organisations
People |
ORCID iD |
Wei-Feng Xue (Principal Investigator) |
Publications
Marchante R
(2017)
The physical dimensions of amyloid aggregates control their infective potential as prion particles.
in eLife
Al-Hilaly YK
(2016)
The involvement of dityrosine crosslinking in a-synuclein assembly and deposition in Lewy Bodies in Parkinson's disease.
in Scientific reports
Tournus M
(2021)
Insights into the dynamic trajectories of protein filament division revealed by numerical investigation into the mathematical model of pure fragmentation.
in PLoS computational biology
Tuite MF
(2014)
Dynamic prions revealed by magic.
in Chemistry & biology
Xue W
(2014)
Bio-nanoimaging
Smith RA
(2015)
Analysis of Toxic Amyloid Fibril Interactions at Natively Derived Membranes by Ellipsometry.
in PloS one
Xue WF
(2013)
An imaging and systems modeling approach to fibril breakage enables prediction of amyloid behavior.
in Biophysical journal
Koloteva-Levine N
(2021)
Amyloid particles facilitate surface-catalyzed cross-seeding by acting as promiscuous nanoparticles.
in Proceedings of the National Academy of Sciences of the United States of America
Koloteva-Levine N
(2020)
Amyloid particles facilitate surface-catalyzed cross-seeding by acting as promiscuous nanoparticles
Description | - Developed a robust experimental methodology that produces high quality image and kinetic data on the fragmentation of amyloid fibrils - Developed a generic theory that can explain the division of amyloid particles. - Established the molecular mechanisms and to quantified the rates of fragmentation for three types of amyloid fibril models. - Discovered a relationship between the infectious potential of prions amyloid particles and their length distribution |
Exploitation Route | The experimental approach and the theory and model can be used by research to explain the potential capacity of amyloid and prion propagation, such as in the case of recently reported possible spreading of Alzheimer's Abeta aggregates. |
Sectors | Agriculture, Food and Drink,Chemicals,Education,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology,Other |
Description | Research into amyloid fibril fragmentation has led to a new idea on how to target amyloid associated disease, e.g. stabilising aggregates as a possible way to combat amyloid. This project has also been trans-disciplinary in involving bio-mathematics. The PI has been involved in educational workshops with young researchers from mathematics background together with experimental/bioscience background on educational and research cultures, demonstrating how mathematics can offer a deeper understanding of key biological questions. |
First Year Of Impact | 2019 |
Sector | Education,Healthcare |
Impact Types | Cultural,Societal |
Title | Mathematical model on the dynamical stability of amyloid towards breakage |
Description | The division of amyloid protein fibrils is required for the propagation of the amyloid state, and is an important contributor to their stability, pathogenicity and normal function. Here, we combine kinetic nano-scale imaging experiments with analysis of a mathematical model to resolve and compare the division stability of amyloid fibrils. Our theoretical results show that the division of any type of filament is uniquely described by a set of three characteristic properties, resulting in convergence to self-similar length distributions distinct to each fibril type and conditions applied. By applying these results to profile the dynamical stability towards breakage for four different amyloid types, we reveal particular differences in the division properties of disease-related amyloid formed from alpha-synuclein compared with non-disease associated model amyloid, the former showing lowered intrinsic stability towards breakage and increased likelihood of shedding smaller particles. Our results enable the comparison of protein filaments' intrinsic dynamic stabilities, which are key to unravelling their toxic and infectious potentials. |
Type Of Material | Model of mechanisms or symptoms - in vitro |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | Model published in Beal et al., iScience 23, 101512. The model has been well received by the amyloid research community through conference talks. |
Description | ?Prediction of amyloid behavior? ? through single-particle analysis? of amyloid assembly and disassembly kinetics |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | Invited talk at Biophysical Colloquium, Cambridge, UK. My talk influenced views and provoked discussions in the field. |
Year(s) Of Engagement Activity | 2014 |
Description | ?Prediction of amyloid behavior? ?through analysis of amyloid formation kinetics ? and fibril length quantification by Atomic Force Microscopy |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | Invited talk at Université Pierre et Marie Curie, Paris, France My talk influenced views and provoked discussions in the field. |
Year(s) Of Engagement Activity | 2014 |
Description | ?Prediction of amyloid behavior? through fibril length quantification? by Atomic Force Microscopy |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Type Of Presentation | keynote/invited speaker |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Talk at ADAM2013, 4th Scandinavian Meeting on Amyloid Proteins and Disease, Lund, Sweden My talk influenced views and provoked discussions in the field. |
Year(s) Of Engagement Activity | 2013 |
Description | ?The Mechanism of? Fibril Fragmentation |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Type Of Presentation | keynote/invited speaker |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Talk at Conferences Jacques-Monod - Protein misfolding in disease, Roscoff, France My talk influenced views and provoked discussions in the field. |
Year(s) Of Engagement Activity | 2013 |
Description | A systems approach to fibril fragmentation - Experiments, Models and Predictions |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Type Of Presentation | keynote/invited speaker |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Conference talk (academic audience) at the "Biomolecular Thermodynamics" conference, a two day conference organised by the IOP Biological Physics Group, 26-27 November 2012, Institute of Physics, London, UK My talk influenced views and provoked discussions in the field. |
Year(s) Of Engagement Activity | 2012 |
Description | Amyloid proteins: from Alzheimer's disease, spider silk to evolution of early life |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Undergraduate students |
Results and Impact | BioSoc society Research talk event |
Year(s) Of Engagement Activity | 2015 |
Description | Atomic force microscopy imaging of the dividing amyloid particles |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited talk, Lund OMM Meeting talk, Sweden |
Year(s) Of Engagement Activity | 2015 |
Description | Importance of size and long-range structure in the prediction of the biological behavior of amyloid |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited talk at Wash U, St Louis, MO, USA |
Year(s) Of Engagement Activity | 2015 |
Description | Invited (virtual) talk, Mathematical Methods for the Study of Self-organization in the Biological Sciences, Vienna, Austria (Zoom) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Invited (virtual) talk, Mathematical Methods for the Study of Self-organization in the Biological Sciences, Vienna, Austria (Zoom) |
Year(s) Of Engagement Activity | 2020 |
Description | Invited talk, CENTURI seminar, Marseille, France |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Invited speaker at the multidisciplinary CENTURI seminar, Marseille, France |
Year(s) Of Engagement Activity | 2019 |
Description | Invited talk, Department of Chemistry and Institute for Life Sciences seminar, Southampton, UK |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Other audiences |
Results and Impact | Invited talk at Department of Chemistry and Institute for Life Sciences seminar, Southampton, UK |
Year(s) Of Engagement Activity | 2020 |
Description | Jacques-Louis Lions Laboratory Math-Bio-Health group Seminar, Paris, France (Zoom) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Invited (virtual) talk at Jacques-Louis Lions Laboratory Math-Bio-Health group Seminar, Paris, France (Zoom) |
Year(s) Of Engagement Activity | 2020 |
Description | Modelling amyloid protein self-assembly - Bridging experiments and theory |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited talk, 10th ECMTB and SMB 2016 conference, Nottingham, UK |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.ecmtb2016.org |
Description | Nano-scale Properties of the Amyloid Life-cycle |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited research talk, TU Delft, Delft, Netherlands |
Year(s) Of Engagement Activity | 2016 |
Description | Prediction of disease-associated amyloid properties and behaviour |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | Chemical Biology Club (CBC) seminar, Kingston |
Year(s) Of Engagement Activity | 2015 |
Description | Protein Aggregation - Biophysics and Mathematics Workshop, Vienna, Austria |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Protein Aggregation - Biophysics and Mathematics Workshop, Vienna, Austria |
Year(s) Of Engagement Activity | 2017 |
URL | https://www.wpi.ac.at/event_view.php?id_activity=229 |
Description | QMUL School of Biological and Chemical Sciences research seminar, London, UK |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | Invited seminar talk at QMUL School of Biological and Chemical Sciences research seminar, London, UK |
Year(s) Of Engagement Activity | 2018 |
Description | Quantitative characterization of The Mechanism of Fibril Fragmentation and The Fibril's Stability Toward Breakage |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Type Of Presentation | keynote/invited speaker |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Talk at FASEB - Molecular Mechanisms and Physiological Consequences of Protein Aggregation, Big Sky, MT, USA My talk influenced views and provoked discussions in the field. |
Year(s) Of Engagement Activity | 2013 |
Description | SMB2021, Virtual |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Virtual SMB2021, MMPB-MS17 |
Year(s) Of Engagement Activity | 2021 |
Description | Seeing nanometre sized protein structures associated with neurodegenerative diseases |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | National Science and Engineering Week open lecture at Beaney Institute, Canterbury (non-academic audience) My talk informed the public about my research and generated interest and further discussions. |
Year(s) Of Engagement Activity | 2013 |
Description | Systems modelling of Protein self-assembly in the Amyloid life-cycle |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Invited talk, Centre for Mathematical Medicine and Biology Seminar Series, Nottingham, UK |
Year(s) Of Engagement Activity | 2016 |
Description | Talk at FASEB Protein Aggregation, Steamboat Springs, CO, USA |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Talk at FASEB Protein Aggregation, Steamboat Springs, CO, USA |
Year(s) Of Engagement Activity | 2017 |
Description | Talk at ICSB 2017, Virginia Tech, Blacksburg, VA, USA |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Talk at ICSB 2017, Virginia Tech, Blacksburg, VA, USA |
Year(s) Of Engagement Activity | 2017 |
Description | Talk at Protein folding, binding and assembly mini-symposium, Lund, Sweden |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Protein folding, binding and assembly mini-symposium, Lund, Sweden |
Year(s) Of Engagement Activity | 2019 |
Description | Talk at SLU, Biochemistry Seminar, St Louis, MO, USA |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Invited talk at SLU, Biochemistry Seminar, St Louis, MO, USA |
Year(s) Of Engagement Activity | 2019 |
Description | The division of amyloid particles put under the microscope: Comparing the stability of amyloid fibrils toward breakage |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited talk at FASEB Molecular Mechanisms and Physiological Consequences of Protein Aggregation, West Palm Beach, FL, USA |
Year(s) Of Engagement Activity | 2015 |
Description | The mechanism of amyloid fibril fragmentation and the stability of amyloid fibrils toward breakage |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Type Of Presentation | keynote/invited speaker |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Talk at British Biophysical Society Meeting, Warwick 2014. My talk influenced views and provoked discussions in the field. |
Year(s) Of Engagement Activity | 2014 |
Description | The properties of nano-scale amyloid fibril fragments in vitro and in vivo |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Invited talk, Biophysical Seminar, Cambridge Chemistry Department, Cambridge, UK |
Year(s) Of Engagement Activity | 2016 |
Description | Workshop presentation at Growth and division workshop, UCL, London, UK |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Invited speaker at Growth and division workshop, UCL, London, UK |
Year(s) Of Engagement Activity | 2019 |