1
|
Iorio A, Melchionna S, Derreumaux P, Sterpone F. Dynamics and Structures of Amyloid Aggregates under Fluid Flows. J Phys Chem Lett 2024; 15:1943-1949. [PMID: 38346112 DOI: 10.1021/acs.jpclett.3c03084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
In this work, we investigate how fluid flows impact the aggregation mechanisms of Aβ40 proteins and Aβ16-22 peptides and mechanically perturb their (pre)fibrillar aggregates. We exploit the OPEP coarse-grained model for proteins and the Lattice Boltzmann Molecular Dynamics technique. We show that beyond a critical shear rate, amyloid aggregation speeds up in Couette flow because of the shorter collisions times between aggregates, following a transition from diffusion limited to advection dominated dynamics. We also characterize the mechanical deformation of (pre)fibrillar states due to the fluid flows (Couette and Poiseuille), confirming the capability of (pre)fibrils to form pathological loop-like structures as detected in experiments. Our findings can be of relevance for microfluidic applications and for understanding aggregation in the interstitial brain space.
Collapse
Affiliation(s)
- Antonio Iorio
- Laboratoire de Biochimie Théorique (UPR9080), CNRS, Université Paris-Cité, Paris 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond Rothschild, Paris 75005, France
| | - Simone Melchionna
- IAC CNR, 00185 Rome, Italy
- Lexma Technology, Arlington, Massachusetts 02476, United States
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique (UPR9080), CNRS, Université Paris-Cité, Paris 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond Rothschild, Paris 75005, France
- Institut Universitaire de France, 75005 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique (UPR9080), CNRS, Université Paris-Cité, Paris 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond Rothschild, Paris 75005, France
| |
Collapse
|
2
|
Rathee P, Moorkkannur SN, Prabhakar R. Structural studies of catalytic peptides using molecular dynamics simulations. Methods Enzymol 2024; 697:151-180. [PMID: 38816122 DOI: 10.1016/bs.mie.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Many self-assembling peptides can form amyloid like structures with different sizes and morphologies. Driven by non-covalent interactions, their aggregation can occur through distinct pathways. Additionally, they can bind metal ions to create enzyme like active sites that allow them to catalyze diverse reactions. Due to the non-crystalline nature of amyloids, it is quite challenging to elucidate their structures using experimental spectroscopic techniques. In this aspect, molecular dynamics (MD) simulations provide a useful tool to derive structures of these macromolecules in solution. They can be further validated by comparing with experimentally measured structural parameters. However, these simulations require a multi-step process starting from the selection of the initial structure to the analysis of MD trajectories. There are multiple force fields, parametrization protocols, equilibration processes, software and analysis tools available for this process. Therefore, it is complicated for non-experts to select the most relevant tools and perform these simulations effectively. In this chapter, a systematic methodology that covers all major aspects of modeling of catalytic peptides is provided in a user-friendly manner. It will be helpful for researchers in this critical area of research.
Collapse
Affiliation(s)
- Parth Rathee
- Department of Chemistry, University of Miami, Coral Gables, FL, United States
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL, United States.
| |
Collapse
|
3
|
Kolmogorov VS, Erofeev AS, Barykin EP, Timoshenko RV, Lopatukhina EV, Kozin SA, Gorbacheva LR, Salikhov SV, Klyachko NL, Mitkevich VA, Edwards CRW, Korchev YE, Makarov AA, Gorelkin PV. Scanning Ion-Conductance Microscopy for Studying β-Amyloid Aggregate Formation on Living Cell Surfaces. Anal Chem 2023; 95:15943-15949. [PMID: 37856787 DOI: 10.1021/acs.analchem.3c02806] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
β-Amyloid aggregation on living cell surfaces is described as responsible for the neurotoxicity associated with different neurodegenerative diseases. It is suggested that the aggregation of β-amyloid (Aβ) peptide on neuronal cell surface leads to various deviations of its vital function due to myriad pathways defined by internalization of calcium ions, apoptosis promotion, reduction of membrane potential, synaptic activity loss, etc. These are associated with structural reorganizations and pathologies of the cell cytoskeleton mainly involving actin filaments and microtubules and consequently alterations of cell mechanical properties. The effect of amyloid oligomers on cells' Young's modulus has been observed in a variety of studies. However, the precise connection between the formation of amyloid aggregates on cell membranes and their effects on the local mechanical properties of living cells is still unresolved. In this work, we have used correlative scanning ion-conductance microscopy (SICM) to study cell topography, Young's modulus mapping, and confocal imaging of Aβ aggregate formation on living cell surfaces. However, it is well-known that the cytoskeleton state is highly connected to the intracellular level of reactive oxygen species (ROS). The effect of Aβ leads to the induction of oxidative stress, actin polymerization, and stress fiber formation. We measured the reactive oxygen species levels inside single cells using platinum nanoelectrodes to demonstrate the connection of ROS and Young's modulus of cells. SICM can be successfully applied to studying the cytotoxicity mechanisms of Aβ aggregates on living cell surfaces.
Collapse
Affiliation(s)
- Vasilii S Kolmogorov
- National University of Science and Technology "MISIS", 119049 Moscow, Russian Federation
- Lomonosov Moscow State University, 119991 Moscow, Russian Federation
| | - Alexander S Erofeev
- National University of Science and Technology "MISIS", 119049 Moscow, Russian Federation
| | - Evgeny P Barykin
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Roman V Timoshenko
- National University of Science and Technology "MISIS", 119049 Moscow, Russian Federation
| | - Elena V Lopatukhina
- National University of Science and Technology "MISIS", 119049 Moscow, Russian Federation
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Lyubov R Gorbacheva
- Lomonosov Moscow State University, 119991 Moscow, Russian Federation
- Pirogov Russian National Research Medical University, 117997 Moscow, Russian Federation
| | - Sergey V Salikhov
- National University of Science and Technology "MISIS", 119049 Moscow, Russian Federation
| | | | - Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | | | - Yuri E Korchev
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, 920-1192 Kanazawa, Japan
- Department of Medicine, Imperial College London, SW7 2AZ London, United Kingdom
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Petr V Gorelkin
- National University of Science and Technology "MISIS", 119049 Moscow, Russian Federation
| |
Collapse
|
4
|
Abernathy HG, Saha J, Kemp LK, Wadhwani P, Clemons TD, Morgan SE, Rangachari V. De novo amyloid peptides with subtle sequence variations differ in their self-assembly and nanomechanical properties. SOFT MATTER 2023; 19:5150-5159. [PMID: 37386911 DOI: 10.1039/d3sm00604b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Proteinaceous amyloids are well known for their widespread pathological roles but lately have emerged also as key components in several biological functions. The remarkable ability of amyloid fibers to form tightly packed conformations in a cross β-sheet arrangement manifests in their robust enzymatic and structural stabilities. These characteristics of amyloids make them attractive for designing proteinaceous biomaterials for various biomedical and pharmaceutical applications. In order to design customizable and tunable amyloid nanomaterials, it is imperative to understand the sensitivity of the peptide sequence for subtle changes based on amino acid position and chemistry. Here we report our results from four rationally-designed amyloidogenic decapeptides that subtly differ in hydrophobicity and polarity at positions 5 and 6. We show that making the two positions hydrophobic renders the peptide with enhanced aggregation and material properties while introducing polar residues in position 5 dramatically changes the structure and nanomechanical properties of the fibrils formed. A charged residue at position 6, however, abrogates amyloid formation. In sum, we show that subtle changes in the sequence do not make the peptide innocuous but rather sensitive to aggregation, reflected in the biophysical and nanomechanical properties of the fibrils. We conclude that tolerance of peptide amyloid for changes in the sequence, however small they may be, should not be neglected for the effective design of customizable amyloid nanomaterials.
Collapse
Affiliation(s)
- Hannah G Abernathy
- School of Polymer Science & Engineering, University of Southern Mississippi, Hattiesburg, MS, USA.
| | - Jhinuk Saha
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS, USA.
| | - Lisa K Kemp
- School of Polymer Science & Engineering, University of Southern Mississippi, Hattiesburg, MS, USA.
| | - Parvesh Wadhwani
- Department of Molecular Biophysics (IBG 2), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany
| | - Tristan D Clemons
- School of Polymer Science & Engineering, University of Southern Mississippi, Hattiesburg, MS, USA.
| | - Sarah E Morgan
- School of Polymer Science & Engineering, University of Southern Mississippi, Hattiesburg, MS, USA.
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS, USA.
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS, USA
| |
Collapse
|
5
|
Biyani R, Hirata K, Oqmhula K, Yurtsever A, Hongo K, Maezono R, Takagi M, Fukuma T, Biyani M. Biophysical Properties of the Fibril Structure of the Toxic Conformer of Amyloid-β42: Characterization by Atomic Force Microscopy in Liquid and Molecular Docking. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37261999 DOI: 10.1021/acsami.3c06460] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Alzheimer's disease is associated with the aggregation of the misfolded neuronal peptide, amyloid-β42 (Aβ42). Evidence has suggested that several reasons are responsible for the toxicity caused by the aggregation of Aβ42, including the conformational restriction of Aβ42. In this study, one of the toxic conformers of Aβ42, which contains a Glu-to-Pro substitution (E22P-Aβ42), was explored using atomic force microscopy and molecular docking to study the aggregation dynamics. We proposed a systematic model of fibril formation to better understand the molecular basis of conformational transitions in the Aβ42 species. Our results demonstrated the formation of amorphous aggregates in E22P-Aβ42 that are stem-based, network-like structures, while the formation of mature fibrils occurred in the less toxic conformer of Aβ42, E22-Aβ42, that are sphere-like flexible structures. A comparison was made between the biophysical properties of E22P-Aβ42 and E22-Aβ42 that revealed that E22P-Aβ42 had greater stiffness, dihedral angle, number of β sheets involved, and elasticity, compared with E22-Aβ42. These findings will have considerable implications toward our understanding of the structural basis of the toxicity caused by conformational diversity in Aβ42 species.
Collapse
Affiliation(s)
- Radhika Biyani
- Department of Bioscience, Biotechnology, and Biomedical Engineering, School of Material Science, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Kaito Hirata
- Institute for Frontier Science and Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kenji Oqmhula
- School of Information Science, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Ayhan Yurtsever
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kenta Hongo
- Research Center for Advanced Computing Infrastructure, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Ryo Maezono
- School of Information Science, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Masahiro Takagi
- Department of Bioscience, Biotechnology, and Biomedical Engineering, School of Material Science, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Takeshi Fukuma
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Manish Biyani
- Department of Bioscience, Biotechnology, and Biomedical Engineering, School of Material Science, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
- BioSeeds Corporation, JAIST Venture Business Laboratory, Asahidai 2-13, Nomi, Ishikawa 923-1211, Japan
| |
Collapse
|
6
|
Dutka P, Metskas LA, Hurt RC, Salahshoor H, Wang TY, Malounda D, Lu GJ, Chou TF, Shapiro MG, Jensen GJ. Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET. Structure 2023; 31:518-528.e6. [PMID: 37040766 PMCID: PMC10185304 DOI: 10.1016/j.str.2023.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 03/01/2023] [Accepted: 03/16/2023] [Indexed: 04/13/2023]
Abstract
Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical properties of GVs have led to their use as genetically encodable contrast agents for ultrasound and MRI. Currently, however, the structure and assembly mechanism of GVs remain unknown. Here we employ cryoelectron tomography to reveal how the GV shell is formed by a helical filament of highly conserved GvpA subunits. This filament changes polarity at the center of the GV cylinder, a site that may act as an elongation center. Subtomogram averaging reveals a corrugated pattern of the shell arising from polymerization of GvpA into a β sheet. The accessory protein GvpC forms a helical cage around the GvpA shell, providing structural reinforcement. Together, our results help explain the remarkable mechanical properties of GVs and their ability to adopt different diameters and shapes.
Collapse
Affiliation(s)
- Przemysław Dutka
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lauren Ann Metskas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Robert C Hurt
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hossein Salahshoor
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ting-Yu Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dina Malounda
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - George J Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA 91125, USA.
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; College of Physical and Mathematical Sciences, Brigham Young University, Provo, UT 84602, USA.
| |
Collapse
|
7
|
Cheong DY, Roh S, Park I, Lin Y, Lee YH, Lee T, Lee SW, Lee D, Jung HG, Kim H, Lee W, Yoon DS, Hong Y, Lee G. Proteolysis-driven proliferation and rigidification of pepsin-resistant amyloid fibrils. Int J Biol Macromol 2023; 227:601-607. [PMID: 36543295 DOI: 10.1016/j.ijbiomac.2022.12.104] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/20/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022]
Abstract
Proteolysis of amyloids is related to prevention and treatment of amyloidosis. What if the conditions for proteolysis were the same to those for amyloid formation? For example, pepsin, a gastric protease is activated in an acidic environment, which, interestingly, is also a condition that induces the amyloid formation. Here, we investigate the competition reactions between proteolysis and synthesis of amyloid under pepsin-activated conditions. The changes in the quantities and nanomechanical properties of amyloids after pepsin treatment were examined by fluorescence assay, circular dichroism and atomic force microscopy. We found that, in the case of pepsin-resistant amyloid, a secondary reaction can be accelerated, thereby proliferating amyloids. Moreover, after this reaction, the amyloid became 32.4 % thicker and 24.2 % stiffer than the original one. Our results suggest a new insight into the proteolysis-driven proliferation and rigidification of pepsin-resistant amyloids.
Collapse
Affiliation(s)
- Da Yeon Cheong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea
| | - Seokbeom Roh
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea
| | - Insu Park
- Department of Biomedical Engineering, Konyang University, Daejeon 35365, South Korea
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk 28119, South Korea
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk 28119, South Korea; Bio-Analytical Science, University of Science and Technology, Daejeon 34113, South Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, South Korea; Research Headquarters, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Taeha Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea
| | - Sang Won Lee
- School of Biomedical Engineering, Korea University, Seoul 02841, South Korea
| | - Dongtak Lee
- School of Biomedical Engineering, Korea University, Seoul 02841, South Korea
| | - Hyo Gi Jung
- School of Biomedical Engineering, Korea University, Seoul 02841, South Korea; Interdisciplinary Program in Precision Public Health, Korea University, Seoul 02841, South Korea
| | - Hyunji Kim
- School of Biomedical Engineering, Korea University, Seoul 02841, South Korea; Interdisciplinary Program in Precision Public Health, Korea University, Seoul 02841, South Korea
| | - Wonseok Lee
- Department of Electrical Engineering, Korea National University of Transportation, Chungju 27469, South Korea
| | - Dae Sung Yoon
- School of Biomedical Engineering, Korea University, Seoul 02841, South Korea; Interdisciplinary Program in Precision Public Health, Korea University, Seoul 02841, South Korea; ASTRION Inc., Seoul 02841, South Korea.
| | - Yoochan Hong
- Department of Medical Devices, Korea Institute of Machinery and Materials (KIMM), Daegu 42994, South Korea.
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea.
| |
Collapse
|
8
|
Kell DB, Laubscher GJ, Pretorius E. A central role for amyloid fibrin microclots in long COVID/PASC: origins and therapeutic implications. Biochem J 2022; 479:537-559. [PMID: 35195253 PMCID: PMC8883497 DOI: 10.1042/bcj20220016] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
Abstract
Post-acute sequelae of COVID (PASC), usually referred to as 'Long COVID' (a phenotype of COVID-19), is a relatively frequent consequence of SARS-CoV-2 infection, in which symptoms such as breathlessness, fatigue, 'brain fog', tissue damage, inflammation, and coagulopathies (dysfunctions of the blood coagulation system) persist long after the initial infection. It bears similarities to other post-viral syndromes, and to myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Many regulatory health bodies still do not recognize this syndrome as a separate disease entity, and refer to it under the broad terminology of 'COVID', although its demographics are quite different from those of acute COVID-19. A few years ago, we discovered that fibrinogen in blood can clot into an anomalous 'amyloid' form of fibrin that (like other β-rich amyloids and prions) is relatively resistant to proteolysis (fibrinolysis). The result, as is strongly manifested in platelet-poor plasma (PPP) of individuals with Long COVID, is extensive fibrin amyloid microclots that can persist, can entrap other proteins, and that may lead to the production of various autoantibodies. These microclots are more-or-less easily measured in PPP with the stain thioflavin T and a simple fluorescence microscope. Although the symptoms of Long COVID are multifarious, we here argue that the ability of these fibrin amyloid microclots (fibrinaloids) to block up capillaries, and thus to limit the passage of red blood cells and hence O2 exchange, can actually underpin the majority of these symptoms. Consistent with this, in a preliminary report, it has been shown that suitable and closely monitored 'triple' anticoagulant therapy that leads to the removal of the microclots also removes the other symptoms. Fibrin amyloid microclots represent a novel and potentially important target for both the understanding and treatment of Long COVID and related disorders.
Collapse
Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kemitorvet 200, 2800 Kgs Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, South Africa
| | | | - Etheresia Pretorius
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, South Africa
| |
Collapse
|
9
|
Confer MP, Holcombe BM, Foes AG, Holmquist JM, Walker SC, Deb S, Ghosh A. Label-Free Infrared Spectroscopic Imaging Reveals Heterogeneity of β-Sheet Aggregates in Alzheimer's Disease. J Phys Chem Lett 2021; 12:9662-9671. [PMID: 34590866 PMCID: PMC8933041 DOI: 10.1021/acs.jpclett.1c02306] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The aggregation of the amyloid beta (Aβ) protein into plaques is a pathological feature of Alzheimer's disease (AD). While amyloid aggregates have been extensively studied in vitro, their structural aspects and associated chemistry in the brain are not fully understood. In this report, we demonstrate, using infrared spectroscopic imaging, that Aβ plaques exhibit significant heterogeneities in terms of their secondary structure and phospholipid content. We show that the capabilities of discrete frequency infrared imaging (DFIR) are ideally suited for characterization of amyloid deposits in brain tissues and employ DFIR to identify nonplaque β-sheet aggregates distributed throughout brain tissues. We further demonstrate that phospholipid-rich β-sheet deposits exist outside of plaques in all diseased tissues, indicating their potential clinical significance. This is the very first application of DFIR toward a characterization of protein aggregates in an AD brain and provides a rapid, label-free approach that allows us to uncover β-sheet heterogeneities in the AD, which may be significant for targeted therapeutic strategies in the future.
Collapse
|
10
|
Quantitative nanomechanical properties evaluation of a family of β-sheet peptide fibres using rapid bimodal AFM. J Mech Behav Biomed Mater 2021; 124:104776. [PMID: 34479107 DOI: 10.1016/j.jmbbm.2021.104776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/16/2021] [Accepted: 08/10/2021] [Indexed: 11/20/2022]
Abstract
Self-assembling peptides have become important building blocks for materials design (e.g. hydrogels) and play a crucial role in a range of diseases including Alzheimer and Parkinson. In this context, accessing the nanomechanical properties of ubiquitous β-sheet rich nanofibres (e.g.: amyloids) is key to the formulation of materials and design of therapies. Although the bulk mechanical properties of hydrogels can easily be accessed using common techniques and equipment, the mechanical properties of their constituent fibres, in particular if with radii in the nanometre scale, are more challenging to measure and estimate. In this work we show for the first time how the rapid nanomechanical mapping technique: amplitude modulation-frequency modulation (AM-FM), can be used to determine the heights, Young's moduli and viscosity coefficients of a series of β-sheet peptide nanofibres with high statistical confidence. Our results show how peptide sequence and in particular length, charge and interaction with the substrate affect the viscoelastic properties of the peptide fibres.
Collapse
|
11
|
Balasco N, Diaferia C, Morelli G, Vitagliano L, Accardo A. Amyloid-Like Aggregation in Diseases and Biomaterials: Osmosis of Structural Information. Front Bioeng Biotechnol 2021; 9:641372. [PMID: 33748087 PMCID: PMC7966729 DOI: 10.3389/fbioe.2021.641372] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/05/2021] [Indexed: 11/13/2022] Open
Abstract
The discovery that the polypeptide chain has a remarkable and intrinsic propensity to form amyloid-like aggregates endowed with an extraordinary stability is one of the most relevant breakthroughs of the last decades in both protein/peptide chemistry and structural biology. This observation has fundamental implications, as the formation of these assemblies is systematically associated with the insurgence of severe neurodegenerative diseases. Although the ability of proteins to form aggregates rich in cross-β structure has been highlighted by recent studies of structural biology, the determination of the underlying atomic models has required immense efforts and inventiveness. Interestingly, the progressive molecular and structural characterization of these assemblies has opened new perspectives in apparently unrelated fields. Indeed, the self-assembling through the cross-β structure has been exploited to generate innovative biomaterials endowed with promising mechanical and spectroscopic properties. Therefore, this structural motif has become the fil rouge connecting these diversified research areas. In the present review, we report a chronological recapitulation, also performing a survey of the structural content of the Protein Data Bank, of the milestones achieved over the years in the characterization of cross-β assemblies involved in the insurgence of neurodegenerative diseases. A particular emphasis is given to the very recent successful elucidation of amyloid-like aggregates characterized by remarkable molecular and structural complexities. We also review the state of the art of the structural characterization of cross-β based biomaterials by highlighting the benefits of the osmosis of information between these two research areas. Finally, we underline the new promising perspectives that recent successful characterizations of disease-related amyloid-like assemblies can open in the biomaterial field.
Collapse
Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Carlo Diaferia
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Antonella Accardo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
| |
Collapse
|
12
|
Adamcik J, Ruggeri FS, Berryman JT, Zhang A, Knowles TPJ, Mezzenga R. Evolution of Conformation, Nanomechanics, and Infrared Nanospectroscopy of Single Amyloid Fibrils Converting into Microcrystals. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2002182. [PMID: 33511004 PMCID: PMC7816722 DOI: 10.1002/advs.202002182] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/04/2020] [Indexed: 06/12/2023]
Abstract
Nanomechanical properties of amyloid fibrils and nanocrystals depend on their secondary and quaternary structure, and the geometry of intermolecular hydrogen bonds. Advanced imaging methods based on atomic force microscopy (AFM) have unravelled the morphological and mechanical heterogeneity of amyloids, however a full understanding has been hampered by the limited resolution of conventional spectroscopic methods. Here, it is shown that single molecule nanomechanical mapping and infrared nanospectroscopy (AFM-IR) in combination with atomistic modelling enable unravelling at the single aggregate scale of the morphological, nanomechanical, chemical, and structural transition from amyloid fibrils to amyloid microcrystals in the hexapeptides, ILQINS, IFQINS, and TFQINS. Different morphologies have different Young's moduli, within 2-6 GPa, with amyloid fibrils exhibiting lower Young's moduli compared to amyloid microcrystals. The origins of this stiffening are unravelled and related to the increased content of intermolecular β-sheet and the increased lengthscale of cooperativity following the transition from twisted fibril to flat nanocrystal. Increased stiffness in Young's moduli is correlated with increased density of intermolecular hydrogen bonding and parallel β-sheet structure, which energetically stabilize crystals over the other polymorphs. These results offer additional evidence for the position of amyloid crystals in the minimum of the protein folding and aggregation landscape.
Collapse
Affiliation(s)
- Jozef Adamcik
- Department of Health Sciences and TechnologyETH ZürichZürich8092Switzerland
| | | | - Joshua T. Berryman
- University of LuxembourgDepartment of Physics and Materials Science162a Avenue de la FaïencerieLuxembourgL‐1511Luxembourg
| | - Afang Zhang
- Shanghai University Department of Polymer MaterialsNanchen Street 333Shanghai200444China
| | - Tuomas P. J. Knowles
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cavendish LaboratoryUniversity of CambridgeJ. J. Thomson AvenueCambridgeCB3 0HEUK
| | - Raffaele Mezzenga
- Department of Health Sciences and TechnologyETH ZürichZürich8092Switzerland
- Department of MaterialsETH ZürichZürich8093Switzerland
| |
Collapse
|
13
|
Ganesan M, Paranthaman S. Studies on the structure and conformational flexibility of secondary structures in amyloid beta — A quantum chemical study. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2020. [DOI: 10.1142/s0219633620500145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Density functional theory (DFT) calculations are performed to study the conformational flexibility of secondary structures in amyloid beta (A[Formula: see text]) polypeptide. In DFT, M06-2X/6-31[Formula: see text]G(d, p) method is used to optimize the secondary structures of 2LFM and 2BEG in gas phase and in solution phase. Our calculations show that the secondary structures are energetically more stable in solution phase than in gas phase. This is due to the presence of strong solvent interaction with the secondary structures considered in this study. Among the backbone [Formula: see text] and [Formula: see text] dihedral angles, [Formula: see text] varies significantly in sheet structure. This is due to the absence of intermolecular hydrogen bond (H-bond) interactions in sheets considered in this study. Our calculations show that the conformational transition of helix/coil to sheet or vice-versa is due to the floppiness of the amino acid residues. This is observed from the Ramachandran map of the studied secondary structures. Further, it is noted that the intramolecular H-bond interactions play a significant role in the conformational transition of secondary structures of A[Formula: see text].
Collapse
Affiliation(s)
- Mahendiraprabu Ganesan
- Department of Physics and International Research Centre, Kalasalingam Academy of Research and Education (Deemed to be University), Krishnankoil 626126, India
| | - Selvarengan Paranthaman
- Department of Physics and International Research Centre, Kalasalingam Academy of Research and Education (Deemed to be University), Krishnankoil 626126, India
| |
Collapse
|
14
|
Grasso G, Rebella M, Morbiducci U, Tuszynski JA, Danani A, Deriu MA. The Role of Structural Polymorphism in Driving the Mechanical Performance of the Alzheimer's Beta Amyloid Fibrils. Front Bioeng Biotechnol 2019; 7:83. [PMID: 31106199 PMCID: PMC6499180 DOI: 10.3389/fbioe.2019.00083] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/03/2019] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's Disease (AD) is related with the abnormal aggregation of amyloid β-peptides Aβ1−40 and Aβ1−42, the latter having a polymorphic character which gives rise to U- or S-shaped fibrils. Elucidating the role played by the nanoscale-material architecture on the amyloid fibril stability is a crucial breakthrough to better understand the pathological nature of amyloid structures and to support the rational design of bio-inspired materials. The computational study here presented highlights the superior mechanical behavior of the S-architecture, characterized by a Young's modulus markedly higher than the U-shaped architecture. The S-architecture showed a higher mechanical resistance to the enforced deformation along the fibril axis, consequence of a better interchain hydrogen bonds' distribution. In conclusion, this study, focusing the attention on the pivotal multiscale relationship between molecular phenomena and material properties, suggests the S-shaped Aβ1−42 species as a target of election in computational screen/design/optimization of effective aggregation modulators.
Collapse
Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale, Scuola Universitaria Professionale della Svizzera Italiana, Università della Svizzera Italiana, Manno, Switzerland
| | - Martina Rebella
- Polito BioMEDLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Umberto Morbiducci
- Polito BioMEDLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Jack A Tuszynski
- Polito BioMEDLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy.,Department of Physics, University of Alberta, Edmonton AB, Canada
| | - Andrea Danani
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale, Scuola Universitaria Professionale della Svizzera Italiana, Università della Svizzera Italiana, Manno, Switzerland
| | - Marco A Deriu
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale, Scuola Universitaria Professionale della Svizzera Italiana, Università della Svizzera Italiana, Manno, Switzerland
| |
Collapse
|
15
|
Huang Q, Wang H, Gao H, Cheng P, Zhu L, Wang C, Yang Y. In Situ Observation of Amyloid Nucleation and Fibrillation by FastScan Atomic Force Microscopy. J Phys Chem Lett 2019; 10:214-222. [PMID: 30543438 DOI: 10.1021/acs.jpclett.8b03143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Amyloidogenic proteins are key components in various amyloid diseases. The aggregation process and the local structural changes of the toxic species from toxic oligomers to protofibrils and subsequently to mature fibrils are crucial for understanding the molecular mechanism of the amyloidgenic process and also for developing a treatment strategy. Exploration on amyloid aggregation dynamics in situ under real liquid condition is feasible for reflection of the whole process with biological correlations. Herein we report the in situ dynamic study and structure exploration of Amylin1-37 aggregation by FastScan atomic force microscopy. Amylin1-37 nucleation process was observed in which smaller oligomers or monomers were assimilated by the surrounding big oligomers. Amylin1-37 protofibril aggregation was positively correlated with monomer concentration, whereas no direct relationship was observed between fibril elongation and monomer concentration. Growing end and passivated end were found during Amylin1-37 fibrillation. In the assembly process, the growing end kept its structure, and its stiffness was lower than the aggregate body, whereas the passivated end might experience rearrangements of β-structures, which eventually enabled fibril growth from this end. This work is beneficial to the insights of amyloid fibrillation and may shed light on the development of drugs targeting the specific phase of amyloid aggregation.
Collapse
Affiliation(s)
- Qunxing Huang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Huayi Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Houqian Gao
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Peng Cheng
- State Key Laboratory of Tribology, Department of Mechanical Engineering , Tsinghua University , Beijing 100084 , China
| | - Ling Zhu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Chen Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Yanlian Yang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| |
Collapse
|
16
|
Lee BI, Chung YJ, Park CB. Photosensitizing materials and platforms for light-triggered modulation of Alzheimer's β-amyloid self-assembly. Biomaterials 2019; 190-191:121-132. [DOI: 10.1016/j.biomaterials.2018.10.043] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/12/2018] [Accepted: 10/28/2018] [Indexed: 12/12/2022]
|
17
|
Kumari A, Ahmad B. The physical basis of fabrication of amyloid-based hydrogels by lysozyme. RSC Adv 2019; 9:37424-37435. [PMID: 35542254 PMCID: PMC9075597 DOI: 10.1039/c9ra07179b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 11/01/2019] [Indexed: 11/21/2022] Open
Abstract
Schematic of heating- and cooling-induced transitions between HEWL states, and the subsequent formation of the hydrogel.
Collapse
Affiliation(s)
- Anumita Kumari
- School of Chemical Sciences
- UM-DAE Centre for Excellence in Basic Sciences
- University of Mumbai
- Mumbai-400098
- India
| | - Basir Ahmad
- Protein Assembly Laboratory
- JH-Institute of Molecular Medicine
- Jamia Hamdard
- New Delhi-110062
- India
| |
Collapse
|
18
|
Nassar R, Wong E, Bui JM, Yip CK, Li H, Gsponer J, Lamour G. Mechanical Anisotropy in GNNQQNY Amyloid Crystals. J Phys Chem Lett 2018; 9:4901-4909. [PMID: 30102541 DOI: 10.1021/acs.jpclett.8b02027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mapping the nanomechanical properties of amyloids can provide valuable insights into structure and assembly mechanisms of protein aggregates that underlie the development of various human diseases. Although it is well-known that amyloids exhibit an intrinsic stiffness comparable to that of silk (1-10 GPa), a detailed understanding of the directional dependence (anisotropy) of the stiffness of amyloids and how it relates to structural features in these protein aggregates is missing. Here we used steered molecular dynamics (SMD) simulations and amplitude modulation-frequency modulation (AM-FM) atomic force microscopy to measure the directional variation in stiffness of GNNQQNY amyloid crystals. We reveal that individual crystals display significant mechanical anisotropy and relate this anisotropy to subtle but mechanically important differences in interactions between interfaces that define the crystal architecture. Our results provide detailed insights into the structure-mechanics relationship of amyloid that may help in designing amyloid-based nanomaterials with tailored mechanical properties.
Collapse
Affiliation(s)
- Roy Nassar
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Eric Wong
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Jennifer M Bui
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Calvin K Yip
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Hongbin Li
- Department of Chemistry , The University of British Columbia , Vancouver , BC Canada V6T 1Z1
| | - Jörg Gsponer
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Guillaume Lamour
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
- Department of Chemistry , The University of British Columbia , Vancouver , BC Canada V6T 1Z1
| |
Collapse
|
19
|
Carbamylation promotes amyloidogenesis and induces structural changes in Tau-core hexapeptide fibrils. Biochim Biophys Acta Gen Subj 2018; 1862:2590-2604. [PMID: 30071272 DOI: 10.1016/j.bbagen.2018.07.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/10/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Carbamylation is a non-enzymatic post-translational modification (PTM), which involves the covalent modification of N-terminus of protein or ε-amino group of Lys. The role of carbamylation in several age-related disorders is well documented, however, the relationship between carbamylation and neurodegenerative disorders including Alzheimer's disease remains uncharted. METHODS In the present study, using aggregation-prone tau-core hexapeptide fragments 306VQIVYK311 (PHF6) and 275VQIINK280 (PHF6*) as models, we have elucidated the effect of carbamylation on aggregation kinetics and the changes occurring in the 3-dimensional architecture of fibrils using biophysical assays and molecular dynamics simulations. RESULTS We found that carbamylation aids in amyloid formation and can convert the unstructured off-pathway aggregates into robust amyloids, which were toxic to cells. Electron microscopy images and molecular dynamics simulations of PHF6 fibrils showed that carbamylated peptides can form excess hydrogen bonds and modulate the pitch length and twist of peptides fibrils. We have also compared N-terminal carbamylation to acetylation and further extended our finding to full length tau that exhibits aggregation upon carbamylation even in the absence of any external inducer. CONCLUSION Our in vitro and in silico results together suggest that carbamylation can modulate the aggregation pathway of the amyloidegenic sequences and cause structural changes in fibril assemblies. GENERAL SIGNIFICANCE Carbamylation acts as a switch, which triggers the aggregation in short amyloidogenic peptide fragments and modulate the structural changes in resulting amyloid fibrils.
Collapse
|
20
|
Lee G, Lee W, Baik S, Kim YH, Eom K, Kwon T. Correlation between the hierarchical structures and nanomechanical properties of amyloid fibrils. NANOTECHNOLOGY 2018; 29:295701. [PMID: 29644980 DOI: 10.1088/1361-6528/aabd8a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Amyloid fibrils have recently been highlighted due to their excellent mechanical properties, which not only play a role in their biological functions but also imply their applications in biomimetic material design. Despite recent efforts to unveil how the excellent mechanical properties of amyloid fibrils originate, it has remained elusive how the anisotropic nanomechanical properties of hierarchically structured amyloid fibrils are determined. Here, we characterize the anisotropic nanomechanical properties of hierarchically structured amyloid fibrils using atomic force microscopy experiments and atomistic simulations. It is shown that the hierarchical structure of amyloid fibrils plays a crucial role in determining their radial elastic property but does not make any effect on their bending elastic property. This is attributed to the role of intermolecular force acting between the filaments (constituting the fibril) on the radial elastic modulus of amyloid fibrils. Our finding illustrates how the hierarchical structure of amyloid fibrils encodes their anisotropic nanomechanical properties. Our study provides key design principles of amyloid fibrils, which endow valuable insight into the underlying mechanisms of amyloid mechanics.
Collapse
Affiliation(s)
- Gyudo Lee
- School of Public Health, Harvard University, Boston, MA 02115, United States of America
| | | | | | | | | | | |
Collapse
|
21
|
Devitt G, Howard K, Mudher A, Mahajan S. Raman Spectroscopy: An Emerging Tool in Neurodegenerative Disease Research and Diagnosis. ACS Chem Neurosci 2018; 9:404-420. [PMID: 29308873 DOI: 10.1021/acschemneuro.7b00413] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The pathogenesis underlining many neurodegenerative diseases remains incompletely understood. The lack of effective biomarkers and disease preventative medicine demands the development of new techniques to efficiently probe the mechanisms of disease and to detect early biomarkers predictive of disease onset. Raman spectroscopy is an established technique that allows the label-free fingerprinting and imaging of molecules based on their chemical constitution and structure. While analysis of isolated biological molecules has been widespread in the chemical community, applications of Raman spectroscopy to study clinically relevant biological species, disease pathogenesis, and diagnosis have been rapidly increasing since the past decade. The growing number of biomedical applications has shown the potential of Raman spectroscopy for detection of novel biomarkers that could enable the rapid and accurate screening of disease susceptibility and onset. Here we provide an overview of Raman spectroscopy and related techniques and their application to neurodegenerative diseases. We further discuss their potential utility in research, biomarker detection, and diagnosis. Challenges to routine use of Raman spectroscopy in the context of neuroscience research are also presented.
Collapse
|
22
|
Peng Z, Parker AS, Peralta MDR, Ravikumar KM, Cox DL, Toney MD. High Tensile Strength of Engineered β-Solenoid Fibrils via Sonication and Pulling. Biophys J 2017; 113:1945-1955. [PMID: 29117519 DOI: 10.1016/j.bpj.2017.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/17/2017] [Accepted: 09/06/2017] [Indexed: 01/17/2023] Open
Abstract
We present estimates of ultimate tensile strength (UTS) for two engineered β-solenoid protein mutant fibril structures (spruce budworm and Rhagium inquisitor antifreeze proteins) derived from sonication-based measurements and from force pulling molecular dynamics simulations, both in water. Sonication experiments generate limiting scissioned fibrils with a well-defined length-to-width correlation for the mutant spruce budworm protein and the resultant UTS estimate is 0.66 ± 0.08 GPa. For fibrils formed from engineered R. inquisitor antifreeze protein, depending upon geometry, we estimate UTSs of 3.5 ± 3.2-5.5 ± 5.1 GPa for proteins with interfacial disulfide bonds, and 1.6 ± 1.5-2.5 ± 2.3 GPa for the reduced form. The large error bars for the R. inquisitor structures are intrinsic to the broad distribution of limiting scission lengths. Simulations provide pulling velocity-dependent UTSs increasing from 0.2 to 1 GPa in the available speed range, and 1.5 GPa extrapolated to the speeds expected in the sonication experiments. Simulations yield low-velocity values for the Young's modulus of 6.0 GPa. Without protein optimization, these mechanical parameters are similar to those of spider silk and Kevlar, but in contrast to spider silk, these proteins have a precisely known sequence-structure relationship.
Collapse
Affiliation(s)
- Zeyu Peng
- Department of Chemistry, University of California, Davis, Davis, California
| | - Amanda S Parker
- Department of Physics, University of California, Davis, Davis, California
| | - Maria D R Peralta
- Department of Chemistry, University of California, Davis, Davis, California
| | | | - Daniel L Cox
- Department of Physics, University of California, Davis, Davis, California.
| | - Michael D Toney
- Department of Chemistry, University of California, Davis, Davis, California
| |
Collapse
|
23
|
Lamour G, Nassar R, Chan PHW, Bozkurt G, Li J, Bui JM, Yip CK, Mayor T, Li H, Wu H, Gsponer JA. Mapping the Broad Structural and Mechanical Properties of Amyloid Fibrils. Biophys J 2017; 112:584-594. [PMID: 28256219 DOI: 10.1016/j.bpj.2016.12.036] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 12/12/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022] Open
Abstract
Amyloids are fibrillar nanostructures of proteins that are assembled in several physiological processes in human cells (e.g., hormone storage) but also during the course of infectious (prion) and noninfectious (nonprion) diseases such as Creutzfeldt-Jakob and Alzheimer's diseases, respectively. How the amyloid state, a state accessible to all proteins and peptides, can be exploited for functional purposes but also have detrimental effects remains to be determined. Here, we measure the nanomechanical properties of different amyloids and link them to features found in their structure models. Specifically, we use shape fluctuation analysis and sonication-induced scission in combination with full-atom molecular dynamics simulations to reveal that the amyloid fibrils of the mammalian prion protein PrP are mechanically unstable, most likely due to a very low hydrogen bond density in the fibril structure. Interestingly, amyloid fibrils formed by HET-s, a fungal protein that can confer functional prion behavior, have a much higher Young's modulus and tensile strength than those of PrP, i.e., they are much stiffer and stronger due to a tighter packing in the fibril structure. By contrast, amyloids of the proteins RIP1/RIP3 that have been shown to be of functional use in human cells are significantly stiffer than PrP fibrils but have comparable tensile strength. Our study demonstrates that amyloids are biomaterials with a broad range of nanomechanical properties, and we provide further support for the strong link between nanomechanics and β-sheet characteristics in the amyloid core.
Collapse
Affiliation(s)
- Guillaume Lamour
- Michael Smith Laboratories-Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Roy Nassar
- Michael Smith Laboratories-Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick H W Chan
- Michael Smith Laboratories-Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gunes Bozkurt
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Jixi Li
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jennifer M Bui
- Michael Smith Laboratories-Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thibault Mayor
- Michael Smith Laboratories-Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Jörg A Gsponer
- Michael Smith Laboratories-Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
24
|
Zhao R, So M, Maat H, Ray NJ, Arisaka F, Goto Y, Carver JA, Hall D. Measurement of amyloid formation by turbidity assay-seeing through the cloud. Biophys Rev 2016; 8:445-471. [PMID: 28003859 PMCID: PMC5135725 DOI: 10.1007/s12551-016-0233-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 10/11/2016] [Indexed: 12/12/2022] Open
Abstract
Detection of amyloid growth is commonly carried out by measurement of solution turbidity, a low-cost assay procedure based on the intrinsic light scattering properties of the protein aggregate. Here, we review the biophysical chemistry associated with the turbidimetric assay methodology, exploring the reviewed literature using a series of pedagogical kinetic simulations. In turn, these simulations are used to interrogate the literature concerned with in vitro drug screening and the assessment of amyloid aggregation mechanisms.
Collapse
Affiliation(s)
- Ran Zhao
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia
| | - Masatomo So
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Hendrik Maat
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia
| | - Nicholas J Ray
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia
| | - Fumio Arisaka
- College of Bio-resource Sciences, Nihon University, Chiyoda-ku, Tokyo, 102-8275, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - John A Carver
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia
| | - Damien Hall
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia. .,Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871, Japan.
| |
Collapse
|