1
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Louros N, Schymkowitz J, Rousseau F. Mechanisms and pathology of protein misfolding and aggregation. Nat Rev Mol Cell Biol 2023; 24:912-933. [PMID: 37684425 DOI: 10.1038/s41580-023-00647-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 09/10/2023]
Abstract
Despite advances in machine learning-based protein structure prediction, we are still far from fully understanding how proteins fold into their native conformation. The conventional notion that polypeptides fold spontaneously to their biologically active states has gradually been replaced by our understanding that cellular protein folding often requires context-dependent guidance from molecular chaperones in order to avoid misfolding. Misfolded proteins can aggregate into larger structures, such as amyloid fibrils, which perpetuate the misfolding process, creating a self-reinforcing cascade. A surge in amyloid fibril structures has deepened our comprehension of how a single polypeptide sequence can exhibit multiple amyloid conformations, known as polymorphism. The assembly of these polymorphs is not a random process but is influenced by the specific conditions and tissues in which they originate. This observation suggests that, similar to the folding of native proteins, the kinetics of pathological amyloid assembly are modulated by interactions specific to cells and tissues. Here, we review the current understanding of how intrinsic protein conformational propensities are modulated by physiological and pathological interactions in the cell to shape protein misfolding and aggregation pathology.
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Affiliation(s)
- Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
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2
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Szała-Mendyk B, Drajkowska A, Molski A. Modified Smoluchowski Rate Equations for Aggregation and Fragmentation in Finite Systems. J Phys Chem B 2023. [PMID: 37369009 DOI: 10.1021/acs.jpcb.3c02884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Protein self-assembly into supramolecular structures is important for cell biology. Theoretical methods employed to investigate protein aggregation and analogous processes include molecular dynamics simulations, stochastic models, and deterministic rate equations based on the mass-action law. In molecular dynamics simulations, the computation cost limits the system size, simulation length, and number of simulation repeats. Therefore, it is of practical interest to develop new methods for the kinetic analysis of simulations. In this work we consider the Smoluchowski rate equations modified to account for reversible aggregation in finite systems. We present several examples and argue that the modified Smoluchowski equations combined with Monte Carlo simulations of the corresponding master equation provide an effective tool for developing kinetic models of peptide aggregation in molecular dynamics simulations.
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Affiliation(s)
- Beata Szała-Mendyk
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Aleksandra Drajkowska
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Andrzej Molski
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
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3
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The gel mechanism and carrier quality of fibrous and granular whey protein self-assembly. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.108302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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4
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Behera A, Sharma O, Paul D, Sain A. Temperature-dependent Self assembly of biofilaments during red blood cell sickling. J Chem Phys 2022; 157:014105. [DOI: 10.1063/5.0091690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular self-assembly plays vital role in various biological functions. However, when aberrant molecules self-assemble to form large aggregates, it can give rise to various diseases. For example, the sickle cell disease andAlzheimer's disease are caused by self-assembled hemoglobin fibers and amyloid plaques, respectively. Here we studythe assembly kinetics of such fibers using kinetic Monte- Carlo simulation. We focus on the initial lag time of thesehighly stochastic processes, during which self-assembly is very slow. The lag time distributions turn out to be similarfor two very different regimes of polymerization, namely, a) when polymerization is slow and depolymerization is fast,and b) the opposite case, when polymerization is fast and depolymerization is slow. Using temperature dependent on-and off-rates for hemoglobin fiber growth, reported in recent in-vitro experiments, we show that the mean lag time canexhibit non-monotonic behavior with respect to change in temperature.
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Affiliation(s)
| | - Oshin Sharma
- Indian Institute of Technology Bombay Department of Biosciences and Bioengineering, India
| | - Debjani Paul
- Biosciences and Bioengineering, Indian Institute of Technology Bombay, India
| | - Anirban Sain
- Physics, Indian Institute of Technology Bombay Department of Physics, India
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5
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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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6
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Bridstrup J, Schreck JS, Jorgenson JL, Yuan JM. Stochastic Kinetic Treatment of Protein Aggregation and the Effects of Macromolecular Crowding. J Phys Chem B 2021; 125:6068-6079. [PMID: 34080429 DOI: 10.1021/acs.jpcb.1c00959] [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
Investigation of protein self-assembly processes is important for understanding the growth processes of functional proteins as well as disease-causing amyloids. Inside cells, intrinsic molecular fluctuations are so high that they cast doubt on the validity of the deterministic rate-equation approach. Furthermore, the protein environments inside cells are often crowded with other macromolecules, with volume fractions of the crowders as high as 40%. We have developed a stochastic kinetic framework using Gillespie's algorithm for general systems undergoing particle self-assembly, including particularly protein aggregation at the cellular level. The effects of macromolecular crowding are investigated using models built on scaled-particle and transition-state theories. The stochastic kinetic method can be formulated to provide information on the dominating aggregation mechanisms in a method called reaction frequency (or propensity) analysis. This method reveals that the change of scaling laws related to the lag time can be directly related to the change in the frequencies of reaction mechanisms. Further examination of the time evolution of the fibril mass and length quantities unveils that maximal fluctuations occur in the periods of rapid fibril growth and the fluctuations of both quantities can be sensitive functions of rate constants. The presence of crowders often amplifies the roles of primary and secondary nucleation and causes shifting in the relative importance of elongation, shrinking, fragmentation, and coagulation of linear aggregates. We also show a dual effect of changing volume on the halftime of aggregation for ApoC2 which is reduced in the presence of crowders. A comparison of the results of stochastic simulations with those of rate equations gives us information on the convergence relation between them and how the roles of reaction mechanisms change as the system volume is varied.
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Affiliation(s)
- John Bridstrup
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - John S Schreck
- National Center for Atmospheric Research, Boulder, Colorado 80305, United States
| | | | - Jian-Min Yuan
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
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7
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Kinetic analysis reveals that independent nucleation events determine the progression of polyglutamine aggregation in C. elegans. Proc Natl Acad Sci U S A 2021; 118:2021888118. [PMID: 33836595 PMCID: PMC7980373 DOI: 10.1073/pnas.2021888118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Protein aggregation is associated with a wide range of degenerative human diseases with devastating consequences, as exemplified by Alzheimer's, Parkinson's, and Huntington's diseases. In vitro kinetic studies have provided a mechanistic understanding of the aggregation process at the molecular level. However, it has so far remained largely unclear to what extent the biophysical principles of amyloid formation learned in vitro translate to the complex environment of living organisms. Here, we take advantage of the unique properties of a Caenorhabditis elegans model expressing a fluorescently tagged polyglutamine (polyQ) protein, which aggregates into discrete micrometer-sized inclusions that can be directly visualized in real time. We provide a quantitative analysis of protein aggregation in this system and show that the data are described by a molecular model where stochastic nucleation occurs independently in each cell, followed by rapid aggregate growth. Global fitting of the image-based aggregation kinetics reveals a nucleation rate corresponding to 0.01 h-1 per cell at 1 mM intracellular protein concentration, and shows that the intrinsic molecular stochasticity of nucleation accounts for a significant fraction of the observed animal-to-animal variation. Our results highlight how independent, stochastic nucleation events in individual cells control the overall progression of polyQ aggregation in a living animal. The key finding that the biophysical principles associated with protein aggregation in small volumes remain the governing factors, even in the complex environment of a living organism, will be critical for the interpretation of in vivo data from a wide range of protein aggregation diseases.
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8
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Shen JL, Tsai MY, Schafer NP, Wolynes PG. Modeling Protein Aggregation Kinetics: The Method of Second Stochasticization. J Phys Chem B 2021; 125:1118-1133. [PMID: 33476161 DOI: 10.1021/acs.jpcb.0c10331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nucleation of protein aggregates and their growth are important in determining the structure of the cell's membraneless organelles as well as the pathogenesis of many diseases. The large number of molecular types of such aggregates along with the intrinsically stochastic nature of aggregation challenges our theoretical and computational abilities. Kinetic Monte Carlo simulation using the Gillespie algorithm is a powerful tool for modeling stochastic kinetics, but it is computationally demanding when a large number of diverse species is involved. To explore the mechanisms and statistics of aggregation more efficiently, we introduce a new approach to model stochastic aggregation kinetics which introduces noise into already statistically averaged equations obtained using mathematical moment closure schemes. Stochastic moment equations summarize succinctly the dynamics of the large diversity of species with different molecularity involved in aggregation but still take into account the stochastic fluctuations that accompany not only primary and secondary nucleation but also aggregate elongation, dissociation, and fragmentation. This method of "second stochasticization" works well where the fluctuations are modest in magnitude as is often encountered in vivo where the number of protein copies in some computations can be in the hundreds to thousands. Simulations using second stochasticization reveal a scaling law that correlates the size of the fluctuations in aggregate size and number with the total number of monomers. This scaling law is confirmed using experimental data. We believe second stochasticization schemes will prove valuable for bridging the gap between in vivo cell biology and detailed modeling. (The code is released on https://github.com/MYTLab/stoch-agg.).
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Affiliation(s)
- Jia-Liang Shen
- Department of Chemistry, Tamkang University, New Taipei City 251301, Taiwan
| | - Min-Yeh Tsai
- Department of Chemistry, Tamkang University, New Taipei City 251301, Taiwan
| | - Nicholas P Schafer
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
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9
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Martins PM, Navarro S, Silva A, Pinto MF, Sárkány Z, Figueiredo F, Pereira PJB, Pinheiro F, Bednarikova Z, Burdukiewicz M, Galzitskaya OV, Gazova Z, Gomes CM, Pastore A, Serpell LC, Skrabana R, Smirnovas V, Ziaunys M, Otzen DE, Ventura S, Macedo-Ribeiro S. MIRRAGGE - Minimum Information Required for Reproducible AGGregation Experiments. Front Mol Neurosci 2020; 13:582488. [PMID: 33328883 PMCID: PMC7729192 DOI: 10.3389/fnmol.2020.582488] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Reports on phase separation and amyloid formation for multiple proteins and aggregation-prone peptides are recurrently used to explore the molecular mechanisms associated with several human diseases. The information conveyed by these reports can be used directly in translational investigation, e.g., for the design of better drug screening strategies, or be compiled in databases for benchmarking novel aggregation-predicting algorithms. Given that minute protocol variations determine different outcomes of protein aggregation assays, there is a strong urge for standardized descriptions of the different types of aggregates and the detailed methods used in their production. In an attempt to address this need, we assembled the Minimum Information Required for Reproducible Aggregation Experiments (MIRRAGGE) guidelines, considering first-principles and the established literature on protein self-assembly and aggregation. This consensus information aims to cover the major and subtle determinants of experimental reproducibility while avoiding excessive technical details that are of limited practical interest for non-specialized users. The MIRRAGGE table (template available in Supplementary Information) is useful as a guide for the design of new studies and as a checklist during submission of experimental reports for publication. Full disclosure of relevant information also enables other researchers to reproduce results correctly and facilitates systematic data deposition into curated databases.
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Affiliation(s)
- Pedro M Martins
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Susanna Navarro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alexandra Silva
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Maria F Pinto
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Zsuzsa Sárkány
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisco Figueiredo
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.,International Iberian Nanotechnology Laboratory - Department of Atomic Structure - Composition of Materials, Braga, Portugal
| | - Pedro José Barbosa Pereira
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisca Pinheiro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Zuzana Bednarikova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Michał Burdukiewicz
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Zuzana Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Annalisa Pastore
- UK-DRI Centre at King's College London, the Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Rostislav Skrabana
- Department of Neuroimmunology, Axon Neuroscience R&D Services SE, Bratislava, Slovakia.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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10
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Liu RN, Kang YM. Stochastic master equation for early protein aggregation in the transthyretin amyloid disease. Sci Rep 2020; 10:12437. [PMID: 32709875 PMCID: PMC7381670 DOI: 10.1038/s41598-020-69319-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/10/2020] [Indexed: 11/09/2022] Open
Abstract
It is significant to understand the earliest molecular events occurring in the nucleation of the amyloid aggregation cascade for the prevention of amyloid related diseases such as transthyretin amyloid disease. We develop chemical master equation for the aggregation of monomers into oligomers using reaction rate law in chemical kinetics. For this stochastic model, lognormal moment closure method is applied to track the evolution of relevant statistical moments and its high accuracy is confirmed by the results obtained from Gillespie's stochastic simulation algorithm. Our results show that the formation of oligomers is highly dependent on the number of monomers. Furthermore, the misfolding rate also has an important impact on the process of oligomers formation. The quantitative investigation should be helpful for shedding more light on the mechanism of amyloid fibril nucleation.
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Affiliation(s)
- Ruo-Nan Liu
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China
| | - Yan-Mei Kang
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China.
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11
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Gartner FM, Graf IR, Wilke P, Geiger PM, Frey E. Stochastic yield catastrophes and robustness in self-assembly. eLife 2020; 9:51020. [PMID: 32022683 PMCID: PMC7089767 DOI: 10.7554/elife.51020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/04/2020] [Indexed: 12/02/2022] Open
Abstract
A guiding principle in self-assembly is that, for high production yield, nucleation of structures must be significantly slower than their growth. However, details of the mechanism that impedes nucleation are broadly considered irrelevant. Here, we analyze self-assembly into finite-sized target structures employing mathematical modeling. We investigate two key scenarios to delay nucleation: (i) by introducing a slow activation step for the assembling constituents and, (ii) by decreasing the dimerization rate. These scenarios have widely different characteristics. While the dimerization scenario exhibits robust behavior, the activation scenario is highly sensitive to demographic fluctuations. These demographic fluctuations ultimately disfavor growth compared to nucleation and can suppress yield completely. The occurrence of this stochastic yield catastrophe does not depend on model details but is generic as soon as number fluctuations between constituents are taken into account. On a broader perspective, our results reveal that stochasticity is an important limiting factor for self-assembly and that the specific implementation of the nucleation process plays a significant role in determining the yield. The self-assembly of a large biological molecule from small building blocks is like finishing a puzzle of magnetic pieces by shaking the box. Even though each piece of the puzzle is attracted to its correct neighbours, the limited control makes it very hard to finish the puzzle in a short amount of time. The problem becomes even more difficult if several copies of the same puzzle are assembled in one box. If several puzzles start at the same time, the different parts might steal pieces from each other, making it impossible to successfully complete any of the puzzles. This is called a depletion trap. If the box is only shaken and there is no real control over individual pieces, these traps occur at random. Overcoming these random depletion traps is an important challenge when assembling nanostructures and other artificial molecules designed by humans without wasting many, potentially expensive, components. Previous studies have shown that when multiple copies of the same structure are assembled simultaneously, slowing the rate of initiation increases the yield of correctly-made structures. This prevents new structures from stealing pieces from existing structures before they are fully completed. Now, Gartner, Graf, Wilke et al. have used a mathematical model to show that changing the way initiation is delayed leads to different yields. This was especially true for small systems where fluctuations in the availability of the different pieces strongly enhanced the initiation of new structures. In these cases, the self-assembly process terminated undesirably with many incomplete structures. Nanostructures have various applications ranging from drug delivery to robotics. These findings suggest that in order to efficiently assemble biological molecules, the concentrations of the different building blocks need to be tightly controlled. A question for further research is to investigate strategies that reduce fluctuations in the availability of the building blocks to develop more efficient assembly protocols.
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Affiliation(s)
- Florian M Gartner
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, München, Germany
| | - Isabella R Graf
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, München, Germany
| | - Patrick Wilke
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, München, Germany
| | - Philipp M Geiger
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, München, Germany
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, München, Germany
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12
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Amundarain MJ, Herrera MG, Zamarreño F, Viso JF, Costabel MD, Dodero VI. Molecular mechanisms of 33-mer gliadin peptide oligomerisation. Phys Chem Chem Phys 2019; 21:22539-22552. [DOI: 10.1039/c9cp02338k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The 33-mer gliadin peptide oligomerizes driven by its non-ionic polar character, flexible PPII secondary structure and stable glutamine H-bonds.
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Affiliation(s)
- María Julia Amundarain
- Grupo de Biofísica
- Instituto de Física del Sur
- Universidad Nacional del Sur
- Bahía Blanca
- Argentina
| | | | - Fernando Zamarreño
- Grupo de Biofísica
- Instituto de Física del Sur
- Universidad Nacional del Sur
- Bahía Blanca
- Argentina
| | - Juan Francisco Viso
- Grupo de Biofísica
- Instituto de Física del Sur
- Universidad Nacional del Sur
- Bahía Blanca
- Argentina
| | - Marcelo D. Costabel
- Grupo de Biofísica
- Instituto de Física del Sur
- Universidad Nacional del Sur
- Bahía Blanca
- Argentina
| | - Verónica I. Dodero
- Universität Bielefeld
- Fakultät für Chemie
- Organische Chemie
- 33615 Bielefeld
- Germany
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13
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Grigolato F, Arosio P. Sensitivity analysis of the variability of amyloid aggregation profiles. Phys Chem Chem Phys 2019; 21:1435-1442. [DOI: 10.1039/c8cp05904g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The variability of amyloid aggregation profiles is linearly proportional to the duration of the aggregation process, and arises from a perturbation of one or more of the initial conditions.
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Affiliation(s)
- Fulvio Grigolato
- Department of Chemistry and Applied Biosciences
- Swiss Federal Institute of Technology Zurich
- Zurich
- Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences
- Swiss Federal Institute of Technology Zurich
- Zurich
- Switzerland
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14
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Lucas MJ, Keitz BK. Influence of Zeolites on Amyloid-β Aggregation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9789-9797. [PMID: 30060667 DOI: 10.1021/acs.langmuir.8b01496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aggregation of Aβ plays a key role in the progression of Alzheimer's disease. Unfortunately, the Aβ aggregation mechanism is complex, leading to a structurally diverse population of oligomers and amyloid fibrils. Heterogeneous interfaces have been shown to influence the rate of fibrilization and may be useful tools to bias amyloid formation toward specific structures. In order to better understand how exogenous materials influence Aβ aggregation, Aβ1-40 was exposed to zeolite Y containing different metal cations, including Na+, Mg2+, Fe3+, Zn2+, and Cu2+. NaY, MgY, and FeY, all accelerated the kinetics of fibrilization by increasing the primary nucleation rate, while CuY and ZnY inhibited fibrilization. These kinetic effects were supported through binding affinity measurements, in which ZnY and CuY showed higher association constants than the other zeolites. In addition to influencing the kinetics of fibrilization, the zeolites also affected the intermediate structures along the pathway. Western blots confirmed that Aβ1-40 was arrested at the oligomeric stage in the presence of ZnY and CuY, while continuing to the fibrillary state in the presence of other zeolites. Seeding studies showed that NaY and FeY form on-pathway oligomers, while ZnY formed off-pathway oligomers. Overall, our results show that zeolites can impact the aggregation and speciation of amyloids.
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Affiliation(s)
- Michael J Lucas
- McKetta Department of Chemical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Benjamin K Keitz
- McKetta Department of Chemical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
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15
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Herrera MG, Pizzuto M, Lonez C, Rott K, Hütten A, Sewald N, Ruysschaert JM, Dodero VI. Large supramolecular structures of 33-mer gliadin peptide activate toll-like receptors in macrophages. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:1417-1427. [DOI: 10.1016/j.nano.2018.04.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/23/2018] [Accepted: 04/16/2018] [Indexed: 02/08/2023]
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16
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Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ. Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation. Annu Rev Phys Chem 2018; 69:273-298. [PMID: 29490200 DOI: 10.1146/annurev-physchem-050317-021322] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.
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Affiliation(s)
- Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; .,Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Anđela Šarić
- Department of Physics and Astronomy, and Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| | - Johnny Habchi
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Sean Chia
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Georg Meisl
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; .,Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 1HE, United Kingdom; ,
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Abstract
The formation of amyloid fibrils is a central phenomenon in the progressive pathology of many neurodegenerative diseases, as well as in the fabrication of functional materials. Several different molecular processes acting in concert are responsible for the formation of amyloid fibrils from monomeric protein in solution. Here, we describe a method to determine which microscopic processes drive the overall formation of fibrils by using chemical kinetics in combination with systematic experimental datasets analysed in a global manner. We outline general concepts for obtaining suitable kinetic data and detail the key stages of data analysis, from quality control to the verification of a specific mechanism of aggregation.
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Affiliation(s)
- Georg Meisl
- Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - Thomas C T Michaels
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
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Urbic T, Najem S, Dias CL. Thermodynamic properties of amyloid fibrils in equilibrium. Biophys Chem 2017; 231:155-160. [PMID: 28318905 PMCID: PMC5589490 DOI: 10.1016/j.bpc.2017.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/01/2017] [Accepted: 03/02/2017] [Indexed: 11/19/2022]
Abstract
In this manuscript we use a two-dimensional coarse-grained model to study how amyloid fibrils grow towards an equilibrium state where they coexist with proteins dissolved in a solution. Free-energies to dissociate proteins from fibrils are estimated from the residual concentration of dissolved proteins. Consistent with experiments, the concentration of proteins in solution affects the growth rate of fibrils but not their equilibrium state. Also, studies of the temperature dependence of the equilibrium state can be used to estimate thermodynamic quantities, e.g., heat capacity and entropy.
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Affiliation(s)
- Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000, Slovenia.
| | - Sara Najem
- National Center for Remote Sensing, National Council for Scientific Research (CNRS), Riad al Soloh, 1107 2260 Beirut, Lebanon
| | - Cristiano L Dias
- New Jersey Institute of Technology, Physics Department, Newark,NJ 07042-1982,United States
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Shaw M, Bella A, Ryadnov MG. CREIM: Coffee Ring Effect Imaging Model for Monitoring Protein Self-Assembly in Situ. J Phys Chem Lett 2017; 8:4846-4851. [PMID: 28933862 DOI: 10.1021/acs.jpclett.7b02147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Protein self-assembly is fundamental to nanotechnology. Self-assembling structures are produced under static in vitro conditions typically forming over hours. In contrast, hydrodynamic intracellular environments employ far shorter time scales to compartmentalize highly concentrated protein solutions. Herein, we exploit the radial capillary flow within a drying sessile droplet (the coffee ring effect) to emulate dynamic native environments and monitor an archetypal protein assembly in situ using high-speed super-resolution imaging. We demonstrate that the assembly can be empirically driven to completion within minutes to seconds without apparent changes in supramolecular morphology. The model offers a reliable tool for the diagnosis and engineering of self-assembling systems under nonequilibrium conditions.
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Affiliation(s)
- Michael Shaw
- National Physical Laboratory , Hampton Road, Teddington, TW11 0LW, United Kingdom
- Department of Computer Science, University College London , London, WC1 6BT, United Kingdom
| | - Angelo Bella
- National Physical Laboratory , Hampton Road, Teddington, TW11 0LW, United Kingdom
| | - Maxim G Ryadnov
- National Physical Laboratory , Hampton Road, Teddington, TW11 0LW, United Kingdom
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Michaels TCT, Bellaiche MMJ, Hagan MF, Knowles TPJ. Kinetic constraints on self-assembly into closed supramolecular structures. Sci Rep 2017; 7:12295. [PMID: 28947758 PMCID: PMC5613031 DOI: 10.1038/s41598-017-12528-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/04/2017] [Indexed: 11/09/2022] Open
Abstract
Many biological and synthetic systems exploit self-assembly to generate highly intricate closed supramolecular architectures, ranging from self-assembling cages to viral capsids. The fundamental design principles that control the structural determinants of the resulting assemblies are increasingly well-understood, but much less is known about the kinetics of such assembly phenomena and it remains a key challenge to elucidate how these systems can be engineered to assemble in an efficient manner and avoid kinetic trapping. We show here that simple scaling laws emerge from a set of kinetic equations describing the self-assembly of identical building blocks into closed supramolecular structures and that this scaling behavior provides general rules that determine efficient assembly in these systems. Using this framework, we uncover the existence of a narrow range of parameter space that supports efficient self-assembly and reveal that nature capitalizes on this behavior to direct the reliable assembly of viral capsids on biologically relevant timescales.
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Affiliation(s)
- Thomas C T Michaels
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Mathias M J Bellaiche
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Laboratory of Chemical Physics, National Institute of Digestive and Diabetes and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, MA, 02454, USA
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. .,Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 1HE, United Kingdom.
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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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Dear AJ, Michaels TCT, Knowles TPJ. Dynamics of heteromolecular filament formation. J Chem Phys 2016; 145:175101. [DOI: 10.1063/1.4966571] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Michaels TC, Dear AJ, Knowles TP. Scaling and dimensionality in the chemical kinetics of protein filament formation. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1239335] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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