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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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Dear AJ, Meisl G, Michaels TCT, Zimmermann MR, Linse S, Knowles TPJ. The catalytic nature of protein aggregation. J Chem Phys 2020; 152:045101. [PMID: 32007046 PMCID: PMC7377910 DOI: 10.1063/1.5133635] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The formation of amyloid fibrils from soluble peptide is a hallmark of many
neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Characterization
of the microscopic reaction processes that underlie these phenomena have yielded insights
into the progression of such diseases and may inform rational approaches for the design of
drugs to halt them. Experimental evidence suggests that most of these reaction processes
are intrinsically catalytic in nature and may display enzymelike saturation effects under
conditions typical of biological systems, yet a unified modeling framework accounting for
these saturation effects is still lacking. In this paper, we therefore present a universal
kinetic model for biofilament formation in which every fundamental process in the reaction
network can be catalytic. The single closed-form expression derived is capable of
describing with high accuracy a wide range of mechanisms of biofilament formation and
providing the first integrated rate law of a system in which multiple reaction processes
are saturated. Moreover, its unprecedented mathematical simplicity permits us to very
clearly interpret the effects of increasing saturation on the overall kinetics. The
effectiveness of the model is illustrated by fitting it to the data of in
vitro Aβ40 aggregation. Remarkably, we find that primary nucleation becomes
saturated, demonstrating that it must be heterogeneous, occurring at interfaces and not in
solution.
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Affiliation(s)
- Alexander J Dear
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Georg Meisl
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Thomas C T Michaels
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuela R Zimmermann
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, SE22100 Lund, Sweden
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Taylor AIP, Gahan LD, Chakrabarti B, Staniforth RA. A two-step biopolymer nucleation model shows a nonequilibrium critical point. J Chem Phys 2020; 153:025102. [PMID: 32668930 DOI: 10.1063/5.0009394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Biopolymer self-assembly pathways are complicated by the ability of their monomeric subunits to adopt different conformational states. This means nucleation often involves a two-step mechanism where the monomers first condense to form a metastable intermediate, which then converts to a stable polymer by conformational rearrangement of constituent monomers. Nucleation intermediates play a causative role in amyloid diseases such as Alzheimer's and Parkinson's. While existing mathematical models neglect the conversion dynamics, experiments show that conversion events frequently occur on comparable timescales to the condensation of intermediates and growth of mature polymers and thus cannot be ignored. We present a model that explicitly accounts for simultaneous assembly and conversion. To describe conversion, we propose an experimentally motivated initiation-propagation mechanism in which the stable phase arises locally within the intermediate and then spreads by nearest-neighbor interactions, in a manner analogous to one-dimensional Glauber dynamics. Our analysis shows that the competing timescales of assembly and conversion result in a nonequilibrium critical point, separating a regime where intermediates are kinetically unstable from one where conformationally mixed intermediates accumulate. This strongly affects the accumulation rate of the stable biopolymer phase. Our model is uniquely able to explain experimental phenomena such as the formation of mixed intermediates and abrupt changes in the scaling exponent γ, which relates the total monomer concentration to the accumulation rate of the stable phase. This provides a first step toward a general model of two-step biopolymer nucleation, which can quantitatively predict the concentration and composition of biologically crucial intermediates.
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Affiliation(s)
- Alexander I P Taylor
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Lianne D Gahan
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Buddhapriya Chakrabarti
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, United Kingdom
| | - Rosemary A Staniforth
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
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Smith JW, Jiang X, An H, Barclay AM, Licari G, Tajkhorshid E, Moore EG, Rienstra CM, Moore JS, Chen Q. Polymer-Peptide Conjugates Convert Amyloid into Protein Nanobundles through Fragmentation and Lateral Association. ACS APPLIED NANO MATERIALS 2020; 3:937-945. [PMID: 32149271 PMCID: PMC7059651 DOI: 10.1021/acsanm.9b01331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The assembly of proteins into amyloid fibrils has become linked not only with the progression of myriad human diseases, but also important biological functions. Understanding and controlling the formation, structure, and stability of amyloid fibrils is therefore a major scientific goal. Here we utilize electron microscopy-based approaches combined with quantitative statistical analysis to show how recently developed kind of amyloid modulators-multivalent polymer-peptide conjugates (mPPCs)-can be applied to control the structure and stability of amyloid fibrils. In doing so, we demonstrate that mPPCs are able to convert 40-residue amyloid beta fibrils into ordered nanostructures through a combination of fragmentation and bundling. Fragmentation is shown to be consistent with a model where the rate constant of fibril breakage is independent of the fibril length, suggesting a local and specific interaction between fibrils and mPPCs. Subsequent bundling, which was previously not observed, leads to the formation of sheet-like nanostructures which are surprisingly much more uniform than the starting fibrils. These nanostructures have dimensions independent of the molecular weight of the mPPC and retain the molecular-level ordering of the starting amyloid fibrils. Collectively, we reveal quantitative and nanoscopic understanding of how mPPCs can be applied to control amyloid structure and stability, and demonstrate approaches to elucidate nanoscale amyloid phase behavior in the presence of functional macromolecules and other modulators.
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Affiliation(s)
- John W. Smith
- Department of Materials Science and Engineering, University of Illinois, Urbana, Illinois 61801, United States
| | - Xing Jiang
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
| | - Hyosung An
- Department of Materials Science and Engineering, University of Illinois, Urbana, Illinois 61801, United States
- Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801, United States
| | - Alexander M. Barclay
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Giuseppe Licari
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Edwin G. Moore
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Corresponding Authors: , ,
| | - Jeffrey S. Moore
- Department of Materials Science and Engineering, University of Illinois, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Corresponding Authors: , ,
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
- Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Corresponding Authors: , ,
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Carbonell F, Iturria-Medina Y, Evans AC. Mathematical Modeling of Protein Misfolding Mechanisms in Neurological Diseases: A Historical Overview. Front Neurol 2018; 9:37. [PMID: 29456521 PMCID: PMC5801313 DOI: 10.3389/fneur.2018.00037] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/16/2018] [Indexed: 12/12/2022] Open
Abstract
Protein misfolding refers to a process where proteins become structurally abnormal and lose their specific 3-dimensional spatial configuration. The histopathological presence of misfolded protein (MP) aggregates has been associated as the primary evidence of multiple neurological diseases, including Prion diseases, Alzheimer's disease, Parkinson's disease, and Creutzfeldt-Jacob disease. However, the exact mechanisms of MP aggregation and propagation, as well as their impact in the long-term patient's clinical condition are still not well understood. With this aim, a variety of mathematical models has been proposed for a better insight into the kinetic rate laws that govern the microscopic processes of protein aggregation. Complementary, another class of large-scale models rely on modern molecular imaging techniques for describing the phenomenological effects of MP propagation over the whole brain. Unfortunately, those neuroimaging-based studies do not take full advantage of the tremendous capabilities offered by the chemical kinetics modeling approach. Actually, it has been barely acknowledged that the vast majority of large-scale models have foundations on previous mathematical approaches that describe the chemical kinetics of protein replication and propagation. The purpose of the current manuscript is to present a historical review about the development of mathematical models for describing both microscopic processes that occur during the MP aggregation and large-scale events that characterize the progression of neurodegenerative MP-mediated diseases.
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Affiliation(s)
| | - Yasser Iturria-Medina
- Department of Neurology & Neurosurgery, McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, QC, Canada
- Ludmer Centre for NeuroInformatics and Mental Health, Montreal, QC, Canada
| | - Alan C. Evans
- Department of Neurology & Neurosurgery, McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, QC, Canada
- Ludmer Centre for NeuroInformatics and Mental Health, Montreal, QC, Canada
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Xia H, Fu H, Zhang Y, Shih KC, Ren Y, Anuganti M, Nieh MP, Cheng J, Lin Y. Supramolecular Assembly of Comb-like Macromolecules Induced by Chemical Reactions that Modulate the Macromolecular Interactions In Situ. J Am Chem Soc 2017; 139:11106-11116. [DOI: 10.1021/jacs.7b04986] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | - Yanfeng Zhang
- Department
of Materials Science and Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | | | | | | | | | - Jianjun Cheng
- Department
of Materials Science and Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Michaels TCT, Liu LX, Meisl G, Knowles TPJ. Physical principles of filamentous protein self-assembly kinetics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:153002. [PMID: 28170349 DOI: 10.1088/1361-648x/aa5f10] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The polymerization of proteins and peptides into filamentous supramolecular structures is an elementary form of self-organization of key importance to the functioning biological systems, as in the case of actin biofilaments that compose the cellular cytoskeleton. Aberrant filamentous protein self-assembly, however, is associated with undesired effects and severe clinical disorders, such as Alzheimer's and Parkinson's diseases, which, at the molecular level, are associated with the formation of certain forms of filamentous protein aggregates known as amyloids. Moreover, due to their unique physicochemical properties, protein filaments are finding extensive applications as biomaterials for nanotechnology. With all these different factors at play, the field of filamentous protein self-assembly has experienced tremendous activity in recent years. A key question in this area has been to elucidate the microscopic mechanisms through which filamentous aggregates emerge from dispersed proteins with the goal of uncovering the underlying physical principles. With the latest developments in the mathematical modeling of protein aggregation kinetics as well as the improvement of the available experimental techniques it is now possible to tackle many of these complex systems and carry out detailed analyses of the underlying microscopic steps involved in protein filament formation. In this paper, we review some classical and modern kinetic theories of protein filament formation, highlighting their use as a general strategy for quantifying the molecular-level mechanisms and transition states involved in these processes.
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Affiliation(s)
- Thomas C T Michaels
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, United States of America
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