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Chauhan C, Singh P, Muthu SA, Parvez S, Selvapandiyan A, Ahmad B. Plumbagin accelerates serum albumin's amyloid aggregation kinetics and generates fibril polymorphism by inducing non-native β-sheet structures. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141028. [PMID: 38849109 DOI: 10.1016/j.bbapap.2024.141028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
The ligand-induced conformational switch of proteins has great significance in understanding the biophysics and biochemistry of their self-assembly. In this work, we have investigated the ability of plumbagin (PL), a hydroxynaphthoquinone compound found in the root of the medicinal plant Plumbago zeylanica, to modulate aggregation precursor state, aggregation kinetics and generate distinct fibril of human serum albumin (HSA). PL was found to moderately bind (binding constant Ka ∼ 10-4 M-1)) to domain-II of HSA in the stoichiometric ratio of 1:1. We found that PL-HSA complex aggregation was accelerated as compared to that of HSA aggregation and it may be through an independent pathway. We also detected that fibril produced in the presence of PL is wider in diameter, contains a higher amount of β-sheet (∼18%) and disordered (∼46%) structures, and is less stable. We concluded that the acceleration of aggregation reaction and generation of fibril polymorphism was mainly because of the higher extent of unfolding and high content of non-native β-sheet structure in the aggregation precursor state of PL-HSA complex. This study offers opportunities to explore the ability of ligand binding to modulate aggregation reactions and generate polymorphic protein fibrils.
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Affiliation(s)
- Chanchal Chauhan
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India; Department of Molecular Medicine, Jamia Hamdard, New Delhi 10062, India
| | - Poonam Singh
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai 400098, India
| | - Shivani A Muthu
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India; Department of Molecular Medicine, Jamia Hamdard, New Delhi 10062, India
| | - Suhel Parvez
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India
| | | | - Basir Ahmad
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India.
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2
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Fu Z, Crooks EJ, Irizarry BA, Zhu X, Chowdhury S, Van Nostrand WE, Smith SO. An electrostatic cluster guides Aβ40 fibril formation in sporadic and Dutch-type cerebral amyloid angiopathy. J Struct Biol 2024; 216:108092. [PMID: 38615725 PMCID: PMC11162928 DOI: 10.1016/j.jsb.2024.108092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
Cerebral amyloid angiopathy (CAA) is associated with the accumulation of fibrillar Aβ peptides upon and within the cerebral vasculature, which leads to loss of vascular integrity and contributes to disease progression in Alzheimer's disease (AD). We investigate the structure of human-derived Aβ40 fibrils obtained from patients diagnosed with sporadic or familial Dutch-type (E22Q) CAA. Using cryo-EM, two primary structures are identified containing elements that have not been observed in in vitro Aβ40 fibril structures. One population has an ordered N-terminal fold comprised of two β-strands stabilized by electrostatic interactions involving D1, E22, D23 and K28. This charged cluster is disrupted in the second population, which exhibits a disordered N-terminus and is favored in fibrils derived from the familial Dutch-type CAA patient. These results illustrate differences between human-derived CAA and AD fibrils, and how familial CAA mutations can guide fibril formation.
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Affiliation(s)
- Ziao Fu
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, United States; Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, NY 10065, United States
| | - Elliot J Crooks
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, United States
| | - Brandon A Irizarry
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, United States
| | - Xiaoyue Zhu
- George and Anne Ryan Institute for Neuroscience, Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, United States
| | - Saikat Chowdhury
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, United States; CSIR-Centre for Cellular & Molecular Biology, Habsiguda, Uppal Road, Hyderabad 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Kamala Nehru Nagar, Gaziabad 201 002, Uttar Pradesh, India
| | - William E Van Nostrand
- George and Anne Ryan Institute for Neuroscience, Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, United States.
| | - Steven O Smith
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, United States
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3
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Duran-Meza E, Araya-Secchi R, Romero-Hasler P, Soto-Bustamante EA, Castro-Fernandez V, Castillo-Caceres C, Monasterio O, Diaz-Espinoza R. Metal Ions Can Modulate the Self-Assembly and Activity of Catalytic Peptide Amyloids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:6094-6106. [PMID: 38470353 DOI: 10.1021/acs.langmuir.3c02983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Rational design of peptides has become a powerful tool to produce self-assembled nanostructures with the ability to catalyze different chemical reactions, paving the way to develop minimalistic enzyme-like nanomaterials. Catalytic amyloid-like assemblies have emerged among the most versatile and active, but they often require additional factors for activity. Elucidating how these factors influence the structure and activity is key for the design. Here, we showed that biologically relevant metal ions can guide and modulate the self-assembly of a small peptide into diverse amyloid architectures. The morphology and catalytic activity of the resulting fibrils were tuned by the specific metal ion decorating the surface, whereas X-ray structural analysis of the amyloids showed ion-dependent shape sizes. Molecular dynamics simulations showed that the metals can strongly affect the local conformational space, which can trigger major rearrangements of the fibrils. Our results demonstrate that the conformational landscape of catalytic amyloids is broad and tunable by external factors, which can be critical for future design strategies.
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Affiliation(s)
- Eva Duran-Meza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, General Amengual 014, Estación Central, Santiago 9170390, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Raul Araya-Secchi
- Computational Biophysics group, Facultad de Ingenieria, Tecnologia y Diseño, Universidad San Sebastian, Bellavista 7, Recoleta, Santiago 8420524, Chile
- Centro Basal Ciencia & Vida, Universidad San Sebastian, Santiago 8420524, Chile
| | - Patricio Romero-Hasler
- Departamento de Ciencia de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Dr. Carlos Lorca Tobar 964, Independencia, Santiago 81380494, Chile
| | - Eduardo Arturo Soto-Bustamante
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Dr. Carlos Lorca Tobar 964, Independencia, Santiago 81380494, Chile
| | - Victor Castro-Fernandez
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Claudio Castillo-Caceres
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, General Amengual 014, Estación Central, Santiago 9170390, Chile
| | - Octavio Monasterio
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, General Amengual 014, Estación Central, Santiago 9170390, Chile
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4
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Zhou W, O’Neill CL, Ding T, Zhang O, Rudra JS, Lew MD. Resolving the Nanoscale Structure of β-Sheet Peptide Self-Assemblies Using Single-Molecule Orientation-Localization Microscopy. ACS NANO 2024; 18:8798-8810. [PMID: 38478911 PMCID: PMC11025465 DOI: 10.1021/acsnano.3c11771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Synthetic peptides that self-assemble into cross-β fibrils are versatile building blocks for engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarities to amyloid species have been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize by using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize Nile red (NR), an amyloidophilic fluorogenic probe, and single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers KFE8L and KFE8D and the pathological amyloid-beta peptide Aβ42. Importantly, NR SMOLM reveals the helical (bilayer) ribbon structure of both KFE8 and Aβ42 and quantifies the precise tilt of the fibrils' inner and outer backbones in relevant buffer conditions without the need for covalent labeling or sequence mutations. SMOLM also distinguishes polymorphic branched and curved morphologies of KFE8, whose backbones exhibit much more heterogeneity than those of typical straight fibrils. Thus, SMOLM is a powerful tool to interrogate the structural differences and polymorphism between engineered and pathological cross-β-rich fibrils.
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Affiliation(s)
- Weiyan Zhou
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Conor L. O’Neill
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Oumeng Zhang
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Jai S. Rudra
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
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5
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Wittung-Stafshede P. Chemical catalysis by biological amyloids. Biochem Soc Trans 2023; 51:1967-1974. [PMID: 37743793 PMCID: PMC10657172 DOI: 10.1042/bst20230617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
Toxic aggregation of proteins and peptides into amyloid fibers is the basis of several human diseases. In each disease, a particular peptide noncovalently assembles into long thin structures with an overall cross-β fold. Amyloids are not only related to disease: functional amyloids are found in many biological systems and artificial peptide amyloids are developed into novel nanomaterials. Amyloid fibers can act as template for the generation of more amyloids but are considered nonreactive in chemical catalysis. The perception of amyloids as chemically inert species was recently challenged by in vitro work on three human amyloid systems. With the use of model substrates, amyloid-β, α-synuclein and glucagon amyloids were found to catalyze biologically relevant chemical reactions. The detected catalytic activity was much less than that of 'real' enzymes, but like that of designed (synthetic) catalytic amyloids. I here describe the current knowledge around this new activity of natural amyloids and the putative connection to metabolic changes in amyloid diseases. These pioneering studies imply that catalytic activity is an unexplored gain-of-function activity of disease amyloids. In fact, all biological amyloids may harbor intrinsic catalytic activity, tuned by each amyloid's particular fold, that await discovery.
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Huang G, Tang H, Liu Y, Zhang C, Ke PC, Sun Y, Ding F. Direct Observation of Seeded Conformational Conversion of hIAPP In Silico Reveals the Mechanisms for Morphological Dependence and Asymmetry of Fibril Growth. J Chem Inf Model 2023; 63:5863-5873. [PMID: 37651616 PMCID: PMC10529695 DOI: 10.1021/acs.jcim.3c00898] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Rapid growth of amyloid fibrils via a seeded conformational conversion of monomers is a critical step of fibrillization and important for disease transmission and progression. Amyloid fibrils often display diverse morphologies with distinct populations, and yet the molecular mechanisms of fibril elongation and their corresponding morphological dependence remain poorly understood. Here, we computationally investigated the single-molecular growth of two experimentally resolved human islet amyloid polypeptide fibrils of different morphologies. In both cases, the incorporation of monomers into preformed fibrils was observed. The conformational conversion dynamics was characterized by a small number of fibril growth intermediates. Fibril morphology affected monomer binding at fibril elongation and lateral surfaces as well as the seeded conformational conversion dynamics at the fibril ends, resulting in different fibril elongation rates and populations. We also observed an asymmetric fibril growth as in our prior experiments, attributing to differences of two fibril ends in terms of their local surface curvatures and exposed hydrogen-bond donors and acceptors. Together, our mechanistic findings afforded a theoretical basis for delineating different amyloid strains-entailed divergent disease progression.
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Affiliation(s)
- Gangtong Huang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Huayuan Tang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yuying Liu
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Chi Zhang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Pu Chun Ke
- The Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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7
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Zhou W, O’Neill CL, Ding T, Zhang O, Rudra JS, Lew MD. Resolving the nanoscale structure of β-sheet assemblies using single-molecule orientation-localization microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557571. [PMID: 37745382 PMCID: PMC10515885 DOI: 10.1101/2023.09.13.557571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Synthetic peptides that self-assemble into cross-β fibrils have remarkable utility as engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarity to amyloid species has been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers, KFE8L and KFE8D, and the pathological amyloid-beta peptide Aβ42. SMOLM reveals that the orientations of Nile red, as it transiently binds to both KFE8 and Aβ42, are consistent with a helical (bilayer) ribbon structure and convey the precise tilt of the fibrils' inner and outer backbones. SMOLM also finds polymorphic branched and curved morphologies of KFE8 whose backbones exhibit much more heterogeneity than those of more typical straight fibrils. Thus, SMOLM is a powerful tool to interrogate the structural differences and polymorphism between engineered and pathological cross β-rich fibrils.
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Affiliation(s)
- Weiyan Zhou
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Conor L. O’Neill
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Oumeng Zhang
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Jai S. Rudra
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
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8
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Arar S, Haque MA, Kayed R. Protein aggregation and neurodegenerative disease: Structural outlook for the novel therapeutics. Proteins 2023:10.1002/prot.26561. [PMID: 37530227 PMCID: PMC10834863 DOI: 10.1002/prot.26561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
Before the controversial approval of humanized monoclonal antibody lecanemab, which binds to the soluble amyloid-β protofibrils, all the treatments available earlier, for Alzheimer's disease (AD) were symptomatic. The researchers are still struggling to find a breakthrough in AD therapeutic medicine, which is partially attributable to lack in understanding of the structural information associated with the intrinsically disordered proteins and amyloids. One of the major challenges in this area of research is to understand the structural diversity of intrinsically disordered proteins under in vitro conditions. Therefore, in this review, we have summarized the in vitro applications of biophysical methods, which are aimed to shed some light on the heterogeneity, pathogenicity, structures and mechanisms of the intrinsically disordered protein aggregates associated with proteinopathies including AD. This review will also rationalize some of the strategies in modulating disease-relevant pathogenic protein entities by small molecules using structural biology approaches and biophysical characterization. We have also highlighted tools and techniques to simulate the in vivo conditions for native and cytotoxic tau/amyloids assemblies, urge new chemical approaches to replicate tau/amyloids assemblies similar to those in vivo conditions, in addition to designing novel potential drugs.
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Affiliation(s)
- Sharif Arar
- Mitchell Center for Neurodegenerative Diseases
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA
- Department of Chemistry, School of Science, The University of Jordan, Amman 11942, Jordan
| | - Md Anzarul Haque
- Mitchell Center for Neurodegenerative Diseases
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA
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9
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Arnold FJ, Nguyen AD, Bedlack RS, Bennett CL, La Spada AR. Intercellular transmission of pathogenic proteins in ALS: Exploring the pathogenic wave. Neurobiol Dis 2023:106218. [PMID: 37394036 DOI: 10.1016/j.nbd.2023.106218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023] Open
Abstract
In patients with amyotrophic lateral sclerosis (ALS), disease symptoms and pathology typically spread in a predictable spatiotemporal pattern beginning at a focal site of onset and progressing along defined neuroanatomical tracts. Like other neurodegenerative diseases, ALS is characterized by the presence of protein aggregates in postmortem patient tissue. Cytoplasmic, ubiquitin-positive aggregates of TDP-43 are observed in approximately 97% of sporadic and familial ALS patients, while SOD1 inclusions are likely specific to cases of SOD1-ALS. Additionally, the most common subtype of familial ALS, caused by a hexanucleotide repeat expansion in the first intron of the C9orf72 gene (C9-ALS), is further characterized by the presence of aggregated dipeptide repeat proteins (DPRs). As we will describe, cell-to-cell propagation of these pathological proteins tightly correlates with the contiguous spread of disease. While TDP-43 and SOD1 are capable of seeding protein misfolding and aggregation in a prion-like manner, C9orf72 DPRs appear to induce (and transmit) a 'disease state' more generally. Multiple mechanisms of intercellular transport have been described for all of these proteins, including anterograde and retrograde axonal transport, extracellular vesicle secretion, and macropinocytosis. In addition to neuron-to-neuron transmission, transmission of pathological proteins occurs between neurons and glia. Given that the spread of ALS disease pathology corresponds with the spread of symptoms in patients, the various mechanisms by which ALS-associated protein aggregates propagate through the central nervous system should be closely examined.
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Affiliation(s)
- F J Arnold
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - A D Nguyen
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - R S Bedlack
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - C L Bennett
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - A R La Spada
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; Departments of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, University of California, Irvine, Irvine, CA, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA; UCI Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA.
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10
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Björk L, Klingstedt T, Nilsson KPR. Thiophene-Based Ligands: Design, Synthesis and Their Utilization for Optical Assignment of Polymorphic-Disease-Associated Protein Aggregates. Chembiochem 2023; 24:e202300044. [PMID: 36891883 PMCID: PMC10404026 DOI: 10.1002/cbic.202300044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 03/10/2023]
Abstract
The development of ligands for detecting protein aggregates is of great interest, as these aggregated proteinaceous species are the pathological hallmarks of several devastating diseases, including Alzheimer's disease. In this regard, thiophene-based ligands have emerged as powerful tools for fluorescent assessment of these pathological entities. The intrinsic conformationally sensitive photophysical properties of poly- and oligothiophenes have allowed optical assignment of disease-associated protein aggregates in tissue sections, as well as real-time in vivo imaging of protein deposits. Herein, we recount the chemical evolution of different generations of thiophene-based ligands, and exemplify their use for the optical distinction of polymorphic protein aggregates. Furthermore, the chemical determinants for achieving a superior fluorescent thiophene-based ligand, as well as the next generation of thiophene-based ligands targeting distinct aggregated species are described. Finally, the directions for future research into the chemical design of thiophene-based ligands that can aid in resolving the scientific challenges around protein aggregation diseases are discussed.
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Affiliation(s)
- Linnea Björk
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Therése Klingstedt
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - K Peter R Nilsson
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
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11
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Kumar ST, Nazarov S, Porta S, Maharjan N, Cendrowska U, Kabani M, Finamore F, Xu Y, Lee VMY, Lashuel HA. Seeding the aggregation of TDP-43 requires post-fibrillization proteolytic cleavage. Nat Neurosci 2023:10.1038/s41593-023-01341-4. [PMID: 37248338 DOI: 10.1038/s41593-023-01341-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 04/18/2023] [Indexed: 05/31/2023]
Abstract
Despite the strong evidence linking the transactive response DNA-binding protein 43 (TDP-43) aggregation to the pathogenesis of frontotemporal lobar degeneration with TDP-43, amyotrophic lateral sclerosis and several neurodegenerative diseases, our knowledge of the sequence and structural determinants of its aggregation and neurotoxicity remains incomplete. Herein, we present a new method for producing recombinant full-length TDP-43 filaments that exhibit sequence and morphological features similar to those of brain-derived TDP-43 filaments. We show that TDP-43 filaments contain a β-sheet-rich helical amyloid core that is fully buried by the flanking structured domains of the protein. We demonstrate that the proteolytic cleavage of TDP-43 filaments and exposure of this amyloid core are necessary for propagating TDP-43 pathology and enhancing the seeding of brain-derived TDP-43 aggregates. Only TDP-43 filaments with exposed amyloid core efficiently seeded the aggregation of endogenous TDP-43 in cells. These findings suggest that inhibiting the enzymes mediating cleavage of TDP-43 aggregates represents a viable disease-modifying strategy to slow the progression of amyotrophic lateral sclerosis and other TDP-43 proteinopathies.
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Affiliation(s)
- Senthil T Kumar
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Sergey Nazarov
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Sílvia Porta
- Center for Neurodegenerative Disease Research (CNDR), Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Niran Maharjan
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Urszula Cendrowska
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Malek Kabani
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Francesco Finamore
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Yan Xu
- Center for Neurodegenerative Disease Research (CNDR), Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Virginia M-Y Lee
- Center for Neurodegenerative Disease Research (CNDR), Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland.
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12
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Moore K, Sengupta U, Puangmalai N, Bhatt N, Kayed R. Polymorphic Alpha-Synuclein Oligomers: Characterization and Differential Detection with Novel Corresponding Antibodies. Mol Neurobiol 2023; 60:2691-2705. [PMID: 36707462 PMCID: PMC9883140 DOI: 10.1007/s12035-023-03211-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/04/2023] [Indexed: 01/29/2023]
Abstract
The pathological hallmark of many neurodegenerative diseases is the accumulation of characteristic proteinaceous aggregates. Parkinson's disease and dementia with Lewy bodies can be characterized as synucleinopathies due to the abnormal accumulation of the protein alpha-synuclein (α-Syn). Studies have shown amyloidogenic proteins such as α-Syn and tau can exist as polymorphic aggregates, a theory widely studied mostly in their fibrillar morphology. It is now well understood that an intermediate state of aggregates, oligomers, are the most toxic species. We have shown α-Syn, when modified by different physiological inducers, result in distinct oligomeric conformations of α-Syn. Polymorphic α-Syn oligomers exhibit distinct properties such as aggregate size, conformation, and differentially interact with tau. In this study, we confirm α-Syn oligomeric polymorphs furthermore using in-house novel α-Syn toxic conformation monoclonal antibodies (SynTCs). It is unclear the biological relevance of α-Syn oligomeric polymorphisms. Utilizing a combination of biochemical, biophysical, and cell-based assays, we characterize α-Syn oligomeric polymorphs. We found α-Syn oligomeric polymorphs exhibit distinct immunoreactivity and SynTCs exhibit differential selectivity and binding affinity for α-Syn species. Isothermal titration calorimetry experiments suggest distinct α-Syn:SynTC binding enthalpies in a species-specific manner. Additionally, we found SynTCs differentially reduce α-Syn oligomeric polymorph-mediated neurotoxicity and propagation in primary cortical neurons in a polymorph-specific manner. These studies demonstrate the biological significance of polymorphic α-Syn oligomers along with the importance of polymorph-specific antibodies that target toxic α-Syn aggregates. Monoclonal antibodies that can target the conformational heterogeneity of α-Syn oligomeric species and reduce their mediated toxicity have promising immunotherapeutic potential.
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Affiliation(s)
- Kenya Moore
- Mitchell Center for Neurodegenerative Disease, University of Texas Medical Branch, Galveston, TX, USA
- Department of Neurology, Neuroscience and Cell Biology, Medical Research Building Room 10.138C, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1045, USA
| | - Urmi Sengupta
- Mitchell Center for Neurodegenerative Disease, University of Texas Medical Branch, Galveston, TX, USA
- Department of Neurology, Neuroscience and Cell Biology, Medical Research Building Room 10.138C, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1045, USA
| | - Nicha Puangmalai
- Mitchell Center for Neurodegenerative Disease, University of Texas Medical Branch, Galveston, TX, USA
- Department of Neurology, Neuroscience and Cell Biology, Medical Research Building Room 10.138C, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1045, USA
| | - Nemil Bhatt
- Mitchell Center for Neurodegenerative Disease, University of Texas Medical Branch, Galveston, TX, USA
- Department of Neurology, Neuroscience and Cell Biology, Medical Research Building Room 10.138C, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1045, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Disease, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Neurology, Neuroscience and Cell Biology, Medical Research Building Room 10.138C, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1045, USA.
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13
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Obstarczyk P, Pniakowska A, Nonappa, Grzelczak MP, Olesiak-Bańska J. Crown Ether-Capped Gold Nanoclusters as a Multimodal Platform for Bioimaging. ACS OMEGA 2023; 8:11503-11511. [PMID: 37008092 PMCID: PMC10061685 DOI: 10.1021/acsomega.3c00426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/02/2023] [Indexed: 12/01/2023]
Abstract
The distinct polarity of biomolecule surfaces plays a pivotal role in their biochemistry and functions as it is involved in numerous processes, such as folding, aggregation, or denaturation. Therefore, there is a need to image both hydrophilic and hydrophobic bio-interfaces with markers of distinct responses to hydrophobic and hydrophilic environments. In this work, we present a synthesis, characterization, and application of ultrasmall gold nanoclusters capped with a 12-crown-4 ligand. The nanoclusters present an amphiphilic character and can be successfully transferred between aqueous and organic solvents and have their physicochemical integrity retained. They can serve as probes for multimodal bioimaging with light (as they emit near-infrared luminescence) and electron microscopy (due to the high electron density of gold). In this work, we used protein superstructures, namely, amyloid spherulites, as a hydrophobic surface model and individual amyloid fibrils with a mixed hydrophobicity profile. Our nanoclusters spontaneously stained densely packed amyloid spherulites as observed under fluorescence microscopy, which is limited for hydrophilic markers. Moreover, our clusters revealed structural features of individual amyloid fibrils at a nanoscale as observed under a transmission electron microscope. We show the potential of crown ether-capped gold nanoclusters in multimodal structural characterization of bio-interfaces where the amphiphilic character of the supramolecular ligand is required.
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Affiliation(s)
- Patryk Obstarczyk
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Anna Pniakowska
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Nonappa
- Faculty
of Engineering and Natural Sciences, Tampere
University, FI-33720 Tampere, Finland
| | - Marcin P. Grzelczak
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Joanna Olesiak-Bańska
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
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14
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Gold nanomaterials and their potential use as cryo-electron tomography labels. J Struct Biol 2022; 214:107880. [PMID: 35809758 DOI: 10.1016/j.jsb.2022.107880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 12/14/2022]
Abstract
Rapid advances in cryo-electron tomography (cryo-ET) are driving a revolution in cellular structural biology. However, unambiguous identification of specific biomolecules within cellular tomograms remains challenging. Overcoming this obstacle and reliably identifying targets in the crowded cellular environment is of major importance for the understanding of cellular function and is a pre-requisite for high-resolution structural analysis. The use of highly-specific, readily visualised and adjustable labels would help mitigate this issue, improving both data quality and sample throughput. While progress has been made in cryo-CLEM and in the development of cloneable high-density tags, technical issues persist and a robust 'cryo-GFP' remains elusive. Readily-synthesized gold nanomaterials conjugated to small 'affinity modules' may represent a solution. The synthesis of materials including gold nanoclusters (AuNCs) and gold nanoparticles (AuNPs) is increasingly well understood and is now within the capabilities of non-specialist laboratories. The remarkable chemical and photophysical properties of <3nm diameter nanomaterials and their emergence as tools with widespread biomedical application presents significant opportunities to the cryo-microscopy community. In this review, we will outline developments in the synthesis, functionalisation and labelling uses of both AuNPs and AuNCs in cryo-ET, while discussing their potential as multi-modal probes for cryo-CLEM.
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15
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Nazarov S, Chiki A, Boudeffa D, Lashuel HA. Structural Basis of Huntingtin Fibril Polymorphism Revealed by Cryogenic Electron Microscopy of Exon 1 HTT Fibrils. J Am Chem Soc 2022; 144:10723-10735. [PMID: 35679155 DOI: 10.1021/jacs.2c00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The lack of detailed insight into the structure of aggregates formed by the huntingtin protein (HTT) has hampered the efforts to develop therapeutics and diagnostics targeting pathology formation in the brain of patients with Huntington's disease. To address this knowledge gap, we investigated the structural properties of in vitro-generated fibrils from exon1 of the huntingtin protein by cryogenic electron microscopy and single-particle analyses. We show that wildtype and mutant exon1 of the huntingtin protein form nonhelical fibrils with a polyglutamine amyloid core composed of β-hairpins with unique characteristics that have not been previously observed with other amyloid filaments. The stacks of β-hairpins form long planar β-sheets (protofilaments) which combine inter- and intra-molecular interactions, with variable stacking angles and occasional out-of-register states of individual β-hairpins. These features and the propensity of protofilaments to undergo lateral association result in a high degree of fibril polymorphisms, including fibrils composed of varying numbers of protofilaments. Our results allow us to speculate on how the flanking domains are organized around the polyglutamine core of the fibril and provide insight into how they might affect the huntingtin fibril structure and polymorphism. The removal of the first 17 amino acids at the N-terminus resulted in surprising intra-fibril structural heterogeneity and reduced fibril's propensity to lateral associations. Overall, this work provides valuable insights that could help guide future mechanistic studies to elucidate the sequence and structural determinants of huntingtin aggregation, as well as for cryo-EM and structural studies of fibrils derived from huntingtin protein and other disease-associated polyglutamine-containing proteins.
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Affiliation(s)
- Sergey Nazarov
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,BioEM Core Facility and Technology Platform, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Anass Chiki
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Driss Boudeffa
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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16
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Landrieu I, Dupré E, Sinnaeve D, El Hajjar L, Smet-Nocca C. Deciphering the Structure and Formation of Amyloids in Neurodegenerative Diseases With Chemical Biology Tools. Front Chem 2022; 10:886382. [PMID: 35646824 PMCID: PMC9133342 DOI: 10.3389/fchem.2022.886382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022] Open
Abstract
Protein aggregation into highly ordered, regularly repeated cross-β sheet structures called amyloid fibrils is closely associated to human disorders such as neurodegenerative diseases including Alzheimer's and Parkinson's diseases, or systemic diseases like type II diabetes. Yet, in some cases, such as the HET-s prion, amyloids have biological functions. High-resolution structures of amyloids fibrils from cryo-electron microscopy have very recently highlighted their ultrastructural organization and polymorphisms. However, the molecular mechanisms and the role of co-factors (posttranslational modifications, non-proteinaceous components and other proteins) acting on the fibril formation are still poorly understood. Whether amyloid fibrils play a toxic or protective role in the pathogenesis of neurodegenerative diseases remains to be elucidated. Furthermore, such aberrant protein-protein interactions challenge the search of small-molecule drugs or immunotherapy approaches targeting amyloid formation. In this review, we describe how chemical biology tools contribute to new insights on the mode of action of amyloidogenic proteins and peptides, defining their structural signature and aggregation pathways by capturing their molecular details and conformational heterogeneity. Challenging the imagination of scientists, this constantly expanding field provides crucial tools to unravel mechanistic detail of amyloid formation such as semisynthetic proteins and small-molecule sensors of conformational changes and/or aggregation. Protein engineering methods and bioorthogonal chemistry for the introduction of protein chemical modifications are additional fruitful strategies to tackle the challenge of understanding amyloid formation.
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Affiliation(s)
- Isabelle Landrieu
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Elian Dupré
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Davy Sinnaeve
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Léa El Hajjar
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Caroline Smet-Nocca
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
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17
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Li L, Liu J, Li X, Tang Y, Shi C, Zhang X, Cui Y, Wang L, Xu W. Influencing factors and characterization methods of nanoparticles regulating amyloid aggregation. SOFT MATTER 2022; 18:3278-3290. [PMID: 35437550 DOI: 10.1039/d1sm01704g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Human disorders associated with amyloid aggregation, such as Alzheimer's disease and Parkinson's disease, afflict the lives of millions worldwide. When peptides and proteins in the body are converted to amyloids, which have a tendency to aggregate, the toxic oligomers produced during the aggregation process can trigger a range of diseases. Nanoparticles (NPs) have been found to possess surface effects that can modulate the amyloid aggregation process and they have potential application value in the treatment of diseases related to amyloid aggregation and fibrillary tangles. In this review, we discuss recent progress relating to studies of nanoparticles that regulate amyloid aggregation. The review focuses on the factors influencing this regulation, which are important as guidelines for the future design of NPs for the treatment of amyloid aggregation. We describe the characterization methods that have been utilized so far in such studies. This review provides research information and characterization methods for the rational design of NPs, which should result in therapeutic strategies for amyloid diseases.
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Affiliation(s)
- Lingyi Li
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Jianhui Liu
- Yantai Center of Ecology and Environment Monitoring of Shandong Province, Yantai 264025, China
| | - Xinyue Li
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Yuanhan Tang
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Changxin Shi
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Xin Zhang
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Yuming Cui
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Linlin Wang
- State Key Laboratory of Long-Acting and Targeting Drug Delivery System, Shandong Luye Pharmaceutical Co., Ltd, Yantai 264000, China.
| | - Wenlong Xu
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
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18
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Zare I, Yaraki MT, Speranza G, Najafabadi AH, Haghighi AS, Nik AB, Manshian BB, Saraiva C, Soenen SJ, Kogan MJ, Lee JW, Apollo NV, Bernardino L, Araya E, Mayer D, Mao G, Hamblin MR. Gold nanostructures: synthesis, properties, and neurological applications. Chem Soc Rev 2022; 51:2601-2680. [PMID: 35234776 DOI: 10.1039/d1cs01111a] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent advances in technology are expected to increase our current understanding of neuroscience. Nanotechnology and nanomaterials can alter and control neural functionality in both in vitro and in vivo experimental setups. The intersection between neuroscience and nanoscience may generate long-term neural interfaces adapted at the molecular level. Owing to their intrinsic physicochemical characteristics, gold nanostructures (GNSs) have received much attention in neuroscience, especially for combined diagnostic and therapeutic (theragnostic) purposes. GNSs have been successfully employed to stimulate and monitor neurophysiological signals. Hence, GNSs could provide a promising solution for the regeneration and recovery of neural tissue, novel neuroprotective strategies, and integrated implantable materials. This review covers the broad range of neurological applications of GNS-based materials to improve clinical diagnosis and therapy. Sub-topics include neurotoxicity, targeted delivery of therapeutics to the central nervous system (CNS), neurochemical sensing, neuromodulation, neuroimaging, neurotherapy, tissue engineering, and neural regeneration. It focuses on core concepts of GNSs in neurology, to circumvent the limitations and significant obstacles of innovative approaches in neurobiology and neurochemistry, including theragnostics. We will discuss recent advances in the use of GNSs to overcome current bottlenecks and tackle technical and conceptual challenges.
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Affiliation(s)
- Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz 7178795844, Iran
| | | | - Giorgio Speranza
- CMM - FBK, v. Sommarive 18, 38123 Trento, Italy.,IFN - CNR, CSMFO Lab., via alla Cascata 56/C Povo, 38123 Trento, Italy.,Department of Industrial Engineering, University of Trento, v. Sommarive 9, 38123 Trento, Italy
| | - Alireza Hassani Najafabadi
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA.,Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alireza Shourangiz Haghighi
- Department of Mechanical Engineering, Shiraz University of Technology, Modarres Boulevard, 13876-71557, Shiraz, Iran
| | - Amirala Bakhshian Nik
- Department of Biomedical Engineering, Florida International University, Miami, FL 33174, USA
| | - Bella B Manshian
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Herestraat 49, B3000 Leuven, Belgium
| | - Cláudia Saraiva
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362 Esch-sur-Alzette, Luxembourg.,Health Sciences Research Centre (CICS-UBI), University of Beira Interior, Rua Marques d'Avila e Bolama, 6201-001 Covilha, Portugal
| | - Stefaan J Soenen
- NanoHealth and Optical Imaging Group, Department of Imaging and Pathology, KU Leuven, Herestraat 49, B3000 Leuven, Belgium
| | - Marcelo J Kogan
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas, Departamento de Química Farmacológica y Toxicológica, Universidad de Chile, 8380492 Santiago, Chile
| | - Jee Woong Lee
- Department of Medical Sciences, Clinical Neurophysiology, Uppsala University, Uppsala, SE-751 23, Sweden
| | - Nicholas V Apollo
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Liliana Bernardino
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior, Rua Marques d'Avila e Bolama, 6201-001 Covilha, Portugal
| | - Eyleen Araya
- Departamento de Ciencias Quimicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. Republica 275, Santiago, Chile
| | - Dirk Mayer
- Institute of Biological Information Processing, Bioelectronics (IBI-3), Forschungszentrum Jülich GmbH, Germany
| | - Guangzhao Mao
- School of Chemical Engineering, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
| | - Michael R Hamblin
- Laser Research Center, University of Johannesburg, Doorfontein 2028, South Africa.
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19
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Vila-Liarte D, Kotov NA, Liz-Marzán LM. Template-assisted self-assembly of achiral plasmonic nanoparticles into chiral structures. Chem Sci 2022; 13:595-610. [PMID: 35173926 PMCID: PMC8768870 DOI: 10.1039/d1sc03327a] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
The acquisition of strong chiroptical activity has revolutionized the field of plasmonics, granting access to novel light-matter interactions and revitalizing research on both the synthesis and application of nanostructures. Among the different mechanisms for the origin of chiroptical properties in colloidal plasmonic systems, the self-assembly of achiral nanoparticles into optically active materials offers a versatile route to control the structure-optical activity relationships of nanostructures, while simplifying the engineering of their chiral geometries. Such unconventional materials include helical structures with a precisely defined morphology, as well as large scale, deformable substrates that can leverage the potential of periodic patterns. Some promising templates with helical structural motifs like liquid crystal phases or confined block co-polymers still need efficient strategies to direct preferential handedness, whereas other templates such as silica nanohelices can be grown in an enantiomeric form. Both types of chiral structures are reviewed herein as platforms for chiral sensing: patterned substrates can readily incorporate analytes, while helical assemblies can form around structures of interest, like amyloid protein aggregates. Looking ahead, current knowledge and precedents point toward the incorporation of semiconductor emitters into plasmonic systems with chiral effects, which can lead to plasmonic-excitonic effects and the generation of circularly polarized photoluminescence.
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Affiliation(s)
- David Vila-Liarte
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA) Paseo de Miramon 194 20014 Donostia San Sebastián Spain
- Centro de Investigación Biomédica en Red, Biomateriales, Bioingeniería y Nanomedicina (CIBER-BBN) Spain
| | - Nicholas A Kotov
- Department of Chemical Engineering, Materials Science, Department of Biomedical Engineering, University of Michigan Ann Arbor USA
- Biointerfaces Institute, University of Michigan Ann Arbor USA
| | - Luis M Liz-Marzán
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA) Paseo de Miramon 194 20014 Donostia San Sebastián Spain
- Centro de Investigación Biomédica en Red, Biomateriales, Bioingeniería y Nanomedicina (CIBER-BBN) Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
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20
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Obstarczyk P, Lipok M, Żak A, Cwynar P, Olesiak-Banska J. Amyloid fibrils in superstructures – local ordering revealed by polarization analysis of two-photon excited autofluorescence. Biomater Sci 2022; 10:1554-1561. [DOI: 10.1039/d1bm01768c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein misfolding products – amyloids – tend to form distinct fibrillar structures of characteristic fold for a given neurodegenerative disease or pathology. Moreover, amyloids (also in intermediate or distorted state)...
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21
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Chen L, Zhou Z, Zhang Y, Pan J, Wang K, Wang HX. Near-infrared Irradiation Controlled Thermo-Switchable Polymeric Photosensitizer against β-Amyloid Fibrillation. J Mater Chem B 2022; 10:4832-4839. [DOI: 10.1039/d2tb00372d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photothermal therapy (PTT) as an emerging paradigm toward degradation of amyloid-β (Aβ) aggregations has become an effective way of treating Alzheimer’s disease (AD). A promising PTT therapeutic option requires control...
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22
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Shillcock JC, Hastings J, Riguet N, Lashuel HA. Non-monotonic fibril surface occlusion by GFP tags from coarse-grained molecular simulations. Comput Struct Biotechnol J 2021; 20:309-321. [PMID: 35070162 PMCID: PMC8753129 DOI: 10.1016/j.csbj.2021.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 11/23/2022] Open
Abstract
The pathological growth of amyloid fibrils in neurons underlies the progression of neurodegenerative diseases including Alzheimer's and Parkinson's disease. Fibrils form when soluble monomers oligomerise in the cytoplasm. Their subsequent growth occurs via nucleated polymerization mechanisms involving the free ends of the fibrils augmented by secondary nucleation of new oligomers at their surface. Amyloid fibrils possess a complex interactome with diffusing cytoplasmic proteins that regulates many aspects of their growth, seeding capacity, biochemical activity and transition to pathological inclusions in diseased brains. Changes to their surface are also expected to modify their interactome, pathogenicity and spreading in the brain. Many assays visualise fibril formation, growth and inclusion formation by decorating monomeric proteins with fluorescent tags such as GFP. Recent studies from our group suggest that tags with sizes comparable to the fibril radius may modify the fibril surface accessibility and thus their PTM pattern, interactome and ability to form inclusions. Using coarse-grained molecular simulations of a single alpha synuclein fibril tagged with GFP we find that thermal fluctuations of the tags create a non-monotonic, size-dependent sieve around the fibril that perturbs its interactome with diffusing species. Our results indicate that experiments using tagged and untagged monomers to study the growth and interactome of fibrils should be compared with caution, and the confounding effects of the tags are more complex than a reduction in surface accessibility. The prevalence of fluorescent tags in amyloid fibril growth experiments suggests this has implications beyond the specific alpha synuclein fibrils we model here.
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Affiliation(s)
- Julian C. Shillcock
- Blue Brain Project, Ecole polytechnique fédérale de Lausanne, CH-1202 Geneva, Switzerland
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Janna Hastings
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Nathan Riguet
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Hilal A. Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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23
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Richter Ł, Paszkowska K, Cendrowska U, Olgiati F, Silva PJ, Gasbarri M, Guven ZP, Paczesny J, Stellacci F. Broad-spectrum nanoparticles against bacteriophage infections. NANOSCALE 2021; 13:18684-18694. [PMID: 34738613 PMCID: PMC8601202 DOI: 10.1039/d1nr04936d] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Viral infections caused by bacteriophages, i.e., viruses that kill bacteria are one of the most dangerous and common threats for bacteria-based bioreactors. More than 70% of biotechnology companies have admitted to encountering this problem. Despite phage infections being such a dangerous and widespread risk, there are no effective methods to avoid them to date. Herein, we present a novel technology based on nanoparticles that irreversibly deactivates bacteriophages and is safe for bacteria. Our method allows for the unsupervised protection of bacterial processes in the biotechnology industry. Gold nanoparticles coated with a mixture of negatively charged 11-mercapto 1-undecanesulfonic acid (MUS) and hydrophobic 1-octanethiol (OT) ligands are effective at deactivating various types of Escherichia coli-selective phages: T1, T4, and T7. The nanoparticles can lower the titer of phages up to 2 and 5 logs in 6 and 24 h at 50 °C, respectively. A comparative analysis of nanoparticles with different ligand shells illustrates the importance of the combination of negatively charged and hydrophobic ligands that is the key to achieving a good inhibitory concentration (EC50 ≤ 1 μg mL-1) for all tested phages. We show that the nanoparticles are harmless for the commonly used bacteria in industry Escherichia coli and are effective under conditions simulating the environment of bioreactors.
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Affiliation(s)
- Łukasz Richter
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Karolina Paszkowska
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Urszula Cendrowska
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Francesca Olgiati
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Paulo Jacob Silva
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Matteo Gasbarri
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Zekiye Pelin Guven
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Jan Paczesny
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Francesco Stellacci
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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24
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Zhou Z, Gu YQ, Wang HX. Artificial Chiral Interfaces against Amyloid-β Peptide Aggregation: Research Progress and Challenges. ACS Chem Neurosci 2021; 12:4236-4248. [PMID: 34724384 DOI: 10.1021/acschemneuro.1c00544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by an imbalance between the production and clearance of amyloid-β (Aβ) species. AD not only influences the life quality of the patients but also heavily burdens the families and society. Therefore, it is an urgent mission to research and develop some new anti-amyloid aggregation drugs. In recent years, there were research and development of engineered nanostructures as Aβ amyloid inhibitors have attracted extensive attention and become a new frontier in nanomedicine. The effects of nanostructural surface properties (e.g., morphology, charge, hydrophobicity) on inhibition of Aβ aggregation are modulated by adsorbed Aβ peptides. Nevertheless, chirality has been seldom considered in recognition of Aβ species and modulation of Aβ aggregations. Moreover, a more relevant question for chiral inhibitors is little known about the molecular mechanism of how to interface chiral effects Aβ targeting recognition and effective mitigation of amyloidosis at the molecular level. Herein, we review recent experimental and theoretical results acquired in the specific areas of artificial chiral nanostructure inhibitors. This article will be essential to provide a microlevel insight into the effects of chiral nanointerfaces on amyloidosis processes as well as the development of chiral inhibitor drugs against Aβ fibrillation.
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Affiliation(s)
- Zhe Zhou
- Department of Neurology, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - You-Quan Gu
- Department of Neurology, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Hang-Xing Wang
- College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, China
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25
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Matuszyk MM, Garwood CJ, Ferraiuolo L, Simpson JE, Staniforth RA, Wharton SB. Biological and methodological complexities of beta-amyloid peptide: Implications for Alzheimer's disease research. J Neurochem 2021; 160:434-453. [PMID: 34767256 DOI: 10.1111/jnc.15538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 01/01/2023]
Abstract
Although controversial, the amyloid cascade hypothesis remains central to the Alzheimer's disease (AD) field and posits amyloid-beta (Aβ) as the central factor initiating disease onset. In recent years, there has been an increase in emphasis on studying the role of low molecular weight aggregates, such as oligomers, which are suggested to be more neurotoxic than fibrillary Aβ. Other Aβ isoforms, such as truncated Aβ, have also been implicated in disease. However, developing a clear understanding of AD pathogenesis has been hampered by the complexity of Aβ biochemistry in vitro and in vivo. This review explores factors contributing to the lack of consistency in experimental approaches taken to model Aβ aggregation and toxicity and provides an overview of the different techniques available to analyse Aβ, such as electron and atomic force microscopy, nuclear magnetic resonance spectroscopy, dye-based assays, size exclusion chromatography, mass spectrometry and SDS-PAGE. The review also explores how different types of Aβ can influence Aβ aggregation and toxicity, leading to variation in experimental outcomes, further highlighting the need for standardisation in Aβ preparations and methods used in current research.
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Affiliation(s)
- Martyna M Matuszyk
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Claire J Garwood
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Laura Ferraiuolo
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Julie E Simpson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | | | - Stephen B Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
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26
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Singh A, Maharana SK, Shukla R, Kesharwani P. Nanotherapeutics approaches for targeting alpha synuclien protein in the management of Parkinson disease. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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27
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Mehra S, Gadhe L, Bera R, Sawner AS, Maji SK. Structural and Functional Insights into α-Synuclein Fibril Polymorphism. Biomolecules 2021; 11:1419. [PMID: 34680054 PMCID: PMC8533119 DOI: 10.3390/biom11101419] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/21/2022] Open
Abstract
Abnormal accumulation of aggregated α-synuclein (α-Syn) is seen in a variety of neurodegenerative diseases, including Parkinson's disease (PD), multiple system atrophy (MSA), dementia with Lewy body (DLB), Parkinson's disease dementia (PDD), and even subsets of Alzheimer's disease (AD) showing Lewy-body-like pathology. These synucleinopathies exhibit differences in their clinical and pathological representations, reminiscent of prion disorders. Emerging evidence suggests that α-Syn self-assembles and polymerizes into conformationally diverse polymorphs in vitro and in vivo, similar to prions. These α-Syn polymorphs arising from the same precursor protein may exhibit strain-specific biochemical properties and the ability to induce distinct pathological phenotypes upon their inoculation in animal models. In this review, we discuss clinical and pathological variability in synucleinopathies and several aspects of α-Syn fibril polymorphism, including the existence of high-resolution molecular structures and brain-derived strains. The current review sheds light on the recent advances in delineating the structure-pathogenic relationship of α-Syn and how diverse α-Syn molecular polymorphs contribute to the existing clinical heterogeneity in synucleinopathies.
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Affiliation(s)
- Surabhi Mehra
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India; (L.G.); (R.B.); (A.S.S.)
| | | | | | | | - Samir K. Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India; (L.G.); (R.B.); (A.S.S.)
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28
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Capocefalo A, Deckert-Gaudig T, Brasili F, Postorino P, Deckert V. Unveiling the interaction of protein fibrils with gold nanoparticles by plasmon enhanced nano-spectroscopy. NANOSCALE 2021; 13:14469-14479. [PMID: 34473176 DOI: 10.1039/d1nr03190b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The development of various degenerative diseases is suggested to be triggered by the uncontrolled organisation and aggregation of proteins into amyloid fibrils. For this reason, there are ongoing efforts to develop novel agents and approaches, including metal nanoparticle-based colloids, that dissolve amyloid structures and prevent pathogenic protein aggregation. In this contribution, the role of gold nanoparticles (AuNPs) in degrading amyloid fibrils of the model protein lysozyme is investigated. The amino acid composition of fibril surfaces before and after the incubation with AuNPs is determined at the single fibril level by exploiting the high spatial resolution and sensitivity provided by tip-enhanced and surface-enhanced Raman spectroscopies. This combined spectroscopic approach allows to reveal the molecular mechanisms driving the interaction between fibrils and AuNPs. Our results provide an important input for the understanding of amyloid fibrils and could have a potential translational impact on the development of strategies for the prevention and treatment of amyloid-related diseases.
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Affiliation(s)
- Angela Capocefalo
- Dipartimento di Fisica, Sapienza Università di Roma, P. le Aldo Moro 5, Roma, Italy
- CNR-ISC, Istituto dei Sistemi Complessi, c/o Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Roma, Italy
| | - Tanja Deckert-Gaudig
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745 Jena, Germany.
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Jena Helmholtzweg 4, 07743 Jena, Germany
| | - Francesco Brasili
- Dipartimento di Fisica, Sapienza Università di Roma, P. le Aldo Moro 5, Roma, Italy
| | - Paolo Postorino
- Dipartimento di Fisica, Sapienza Università di Roma, P. le Aldo Moro 5, Roma, Italy
| | - Volker Deckert
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745 Jena, Germany.
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Jena Helmholtzweg 4, 07743 Jena, Germany
- Institute of Quantum Science and Engineering, Texas A&M University, College Station, TX 77843-4242, USA
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29
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Zielinski M, Röder C, Schröder GF. Challenges in sample preparation and structure determination of amyloids by cryo-EM. J Biol Chem 2021; 297:100938. [PMID: 34224730 PMCID: PMC8335658 DOI: 10.1016/j.jbc.2021.100938] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/12/2023] Open
Abstract
Amyloids share a common architecture but play disparate biological roles in processes ranging from bacterial defense mechanisms to protein misfolding diseases. Their structures are highly polymorphic, which makes them difficult to study by X-ray diffraction or NMR spectroscopy. Our understanding of amyloid structures is due in large part to recent advances in the field of cryo-EM, which allows for determining the polymorphs separately. In this review, we highlight the main stepping stones leading to the substantial number of high-resolution amyloid fibril structures known today as well as recent developments regarding automation and software in cryo-EM. We discuss that sample preparation should move closer to physiological conditions to understand how amyloid aggregation and disease are linked. We further highlight new approaches to address heterogeneity and polymorphism of amyloid fibrils in EM image processing and give an outlook to the upcoming challenges in researching the structural biology of amyloids.
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Affiliation(s)
- Mara Zielinski
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Christine Röder
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Gunnar F Schröder
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Physics Department, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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30
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Lau HHC, Ingelsson M, Watts JC. The existence of Aβ strains and their potential for driving phenotypic heterogeneity in Alzheimer's disease. Acta Neuropathol 2021; 142:17-39. [PMID: 32743745 DOI: 10.1007/s00401-020-02201-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/17/2022]
Abstract
Reminiscent of the human prion diseases, there is considerable clinical and pathological variability in Alzheimer's disease, the most common human neurodegenerative condition. As in prion disorders, protein misfolding and aggregation is a hallmark feature of Alzheimer's disease, where the initiating event is thought to be the self-assembly of Aβ peptide into aggregates that deposit in the central nervous system. Emerging evidence suggests that Aβ, similar to the prion protein, can polymerize into a conformationally diverse spectrum of aggregate strains both in vitro and within the brain. Moreover, certain types of Aβ aggregates exhibit key hallmarks of prion strains including divergent biochemical attributes and the ability to induce distinct pathological phenotypes when intracerebrally injected into mouse models. In this review, we discuss the evidence demonstrating that Aβ can assemble into distinct strains of aggregates and how such strains may be primary drivers of the phenotypic heterogeneity in Alzheimer's disease.
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31
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Hadi Alijanvand S, Peduzzo A, Buell AK. Secondary Nucleation and the Conservation of Structural Characteristics of Amyloid Fibril Strains. Front Mol Biosci 2021; 8:669994. [PMID: 33937341 PMCID: PMC8085410 DOI: 10.3389/fmolb.2021.669994] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/30/2021] [Indexed: 12/17/2022] Open
Abstract
Amyloid fibrils are ordered protein aggregates and a hallmark of many severe neurodegenerative diseases. Amyloid fibrils form through primary nucleation from monomeric protein, grow through monomer addition and proliferate through fragmentation or through the nucleation of new fibrils on the surface of existing fibrils (secondary nucleation). It is currently still unclear how amyloid fibrils initially form in the brain of affected individuals and how they are amplified. A given amyloid protein can sometimes form fibrils of different structure under different solution conditions in vitro, but often fibrils found in patients are highly homogeneous. These findings suggest that the processes that amplify amyloid fibrils in vivo can in some cases preserve the structural characteristics of the initial seed fibrils. It has been known for many years that fibril growth by monomer addition maintains the structure of the seed fibril, as the latter acts as a template that imposes its fold on the newly added monomer. However, for fibrils that are formed through secondary nucleation it was, until recently, not clear whether the structure of the seed fibril is preserved. Here we review the experimental evidence on this question that has emerged over the last years. The overall picture is that the fibril strain that forms through secondary nucleation is mostly defined by the solution conditions and intrinsic structural preferences, and not by the seed fibril strain.
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Affiliation(s)
- Saeid Hadi Alijanvand
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Alessia Peduzzo
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Lyngby, Denmark
| | - Alexander K. Buell
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Lyngby, Denmark
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32
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Abbas M. Potential Role of Nanoparticles in Treating the Accumulation of Amyloid-Beta Peptide in Alzheimer's Patients. Polymers (Basel) 2021; 13:1051. [PMID: 33801619 PMCID: PMC8036916 DOI: 10.3390/polym13071051] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
The disorder of Alzheimer's is marked by progressive pathophysiological neurodegeneration. The amino acid peptides in the amyloid plaques found in the brains of people with Alzheimer's disease (AD) are known as amyloid-beta (Aβ). Current treatments are not curative, and the effects associated with AD are reduced. Improving treatment results involved the targeting of drugs at optimum therapeutic concentration. Nanotechnology is seen as an unconventional, modern technology that plays a key role in the treatment of Alzheimer's disease. Using nanoparticles, molecular detection, effective drug targeting, and their combination offer high sensitivity. The aim of this review is to shed light on the function and successful role of nanoparticles to resolve Aβ aggregation and thus to help cure Alzheimer's disease. The analysis divides these nanoparticles into three categories: polymer, lipid, and gold nanoparticles. A thorough comparison was then made between the nanoparticles, which are used according to their role, properties, and size in the procedure. The nanoparticles can prevent the accumulation of Aβ during the efficient delivery of the drug to the cells to treat Alzheimer's disease. Furthermore, this comparison demonstrated the ability of these nanoparticles to deal efficiently with Alzheimer's disease. The role of these nanoparticles varied from delivering the drug to brain cells to dealing with the disease-causing peptide.
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Affiliation(s)
- Mohamed Abbas
- Department of Electrical Engineering, College of Engineering, King Khalid University, Abha 61421, Saudi Arabia;
- Department of Computers and Communications, College of Engineering, Delta University for Science and Technology, Gamasa 35712, Egypt
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33
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Pinkerton M, Ruetenik A, Bazylianska V, Nyvltova E, Barrientos A. Salvage NAD+ biosynthetic pathway enzymes moonlight as molecular chaperones to protect against proteotoxicity. Hum Mol Genet 2021; 30:672-686. [PMID: 33749726 DOI: 10.1093/hmg/ddab080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/03/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Human neurodegenerative proteinopathies are disorders associated with abnormal protein depositions in brain neurons. They include polyglutamine (polyQ) conditions such as Huntington's disease (HD) and α-synucleinopathies such as Parkinson's disease (PD). Overexpression of NMNAT/Nma1, an enzyme in the NAD+ biosynthetic salvage pathway, acts as an efficient suppressor of proteotoxicities in yeast, fly and mouse models. Screens in yeast models of HD and PD allowed us to identify three additional enzymes of the same pathway that achieve similar protection against proteotoxic stress: Npt1, Pnc1 and Qns1. The mechanism by which these proteins maintain proteostasis has not been identified. Here, we report that their ability to maintain proteostasis in yeast models of HD and PD is independent of their catalytic activity and does not require cellular protein quality control systems such as the proteasome or autophagy. Furthermore, we show that, under proteotoxic stress, the four proteins are recruited as molecular chaperones with holdase and foldase activities. The NAD+ salvage proteins act by preventing misfolding and, together with the Hsp90 chaperone, promoting the refolding of extended polyQ domains and α-synuclein (α-Syn). Our results illustrate the existence of an evolutionarily conserved strategy of repurposing or moonlighting housekeeping enzymes under stress conditions to maintain proteostasis. We conclude that the entire salvage NAD+ biosynthetic pathway links NAD+ metabolism and proteostasis and emerges as a target for therapeutics to combat age-associated neurodegenerative proteotoxicities.
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Affiliation(s)
- Meredith Pinkerton
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Andrea Ruetenik
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Viktoriia Bazylianska
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,MS in Biochemistry and Molecular Biology, Wayne State University, School of Medicine. Detroit, MI 48201, USA
| | - Eva Nyvltova
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Antoni Barrientos
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine. Miami, FL 33136, USA
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34
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Ragonis-Bachar P, Landau M. Functional and pathological amyloid structures in the eyes of 2020 cryo-EM. Curr Opin Struct Biol 2021; 68:184-193. [PMID: 33631463 DOI: 10.1016/j.sbi.2021.01.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/16/2021] [Accepted: 01/18/2021] [Indexed: 12/18/2022]
Abstract
The amyloid state of protein aggregation is associated with neurodegenerative and systemic diseases but can play physiological roles in many organisms, including as stress granules and virulence determinants. The recent resolution revolution in cryogenic electron microscopy (cryo-EM) has significantly expanded the repertoire of high-resolution amyloid structures, to include, for the first-time, fibrils extracted ex vivo in addition to those formed, or seeded, in vitro. Here, we review recently solved cryo-EM amyloid structures, and compare amino acid prevalence, in efforts to systematically distinguish between pathological and functional amyloids, even though such structural classification is hindered by extensive polymorphism even among fibrils of the same protein, and by dual functioning of some human amyloids in both physiological activities and disease mechanisms. Forthcoming structures of bacterial amyloids may expose specific, evolutionary-designed properties specific to functional fibrils.
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Affiliation(s)
- Peleg Ragonis-Bachar
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; European Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany.
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35
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Hivare P, Panda C, Gupta S, Bhatia D. Programmable DNA Nanodevices for Applications in Neuroscience. ACS Chem Neurosci 2021; 12:363-377. [PMID: 33433192 DOI: 10.1021/acschemneuro.0c00723] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The broad area of neuroscience has witnessed an increasing exploitation of a variety of synthetic biomaterials with controlled nanosized features. Different bionanomaterials offer very peculiar physicochemical and biochemcial properties contributing to the development of novel imaging devices toward imaging the brain, or as smartly functionalized scaffolds, or diverse tools contributing toward a better understanding of nervous tissue and its functions. DNA nanotechnology-based devices and scaffolds have emerged as ideal materials for cellular and tissue engineering due to their very biocompatible properties, robust adaptation with diverse biological systems, and biosafety in terms of reduced immune response triggering. Here we present technologies with respect to DNA nanodevices that are designed to better interact with nervous systems like neural cells, advanced molecular imaging technologies for imaging brain, biomaterials in neural regeneration, neuroprotection, and targeted delivery of drugs and small molecules across the blood-brain barrier. Along with comments regarding the progress of DNA nanotechnology in neuroscience, we also present a perspective on challenges and opportunities for applying DNA nanotechnology in applications pertaining to neurosciences.
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Affiliation(s)
- Pravin Hivare
- Biological Engineering discipline, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
| | - Chinmaya Panda
- Biological Engineering discipline, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
| | - Sharad Gupta
- Biological Engineering discipline, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
| | - Dhiraj Bhatia
- Biological Engineering discipline, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
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36
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Involvement of amyloid proteins in the formation of biofilms in the pathogenic yeast Candida albicans. Res Microbiol 2021; 172:103813. [PMID: 33515679 DOI: 10.1016/j.resmic.2021.103813] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023]
Abstract
Candida species represent a major fungal threat for human health. Within the Candida genus, the yeast Candida albicans is the most frequently incriminated species during episodes of candidiasis or candidemia. Biofilm formation is used by C. albicans to produce a microbial community that is important in an infectious context. The cell wall, the most superficial cellular compartment, is of paramount importance regarding the establishment of biofilms. C. albicans cell wall contains proteins with amyloid properties that are necessary for biofilm formation due to their adhesion properties. This review focuses on these amyloid proteins during biofilm formation in the yeast C. albicans.
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37
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Yilmaz A, Bauersachs J, Bengel F, Büchel R, Kindermann I, Klingel K, Knebel F, Meder B, Morbach C, Nagel E, Schulze-Bahr E, Aus dem Siepen F, Frey N. Diagnosis and treatment of cardiac amyloidosis: position statement of the German Cardiac Society (DGK). Clin Res Cardiol 2021; 110:479-506. [PMID: 33459839 PMCID: PMC8055575 DOI: 10.1007/s00392-020-01799-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022]
Abstract
Systemic forms of amyloidosis affecting the heart are mostly light-chain (AL) and transthyretin (ATTR) amyloidoses. The latter is caused by deposition of misfolded transthyretin, either in wild-type (ATTRwt) or mutant (ATTRv) conformation. For diagnostics, specific serum biomarkers and modern non-invasive imaging techniques, such as cardiovascular magnetic resonance imaging (CMR) and scintigraphic methods, are available today. These imaging techniques do not only complement conventional echocardiography, but also allow for accurate assessment of the extent of cardiac involvement, in addition to diagnosing cardiac amyloidosis. Endomyocardial biopsy still plays a major role in the histopathological diagnosis and subtyping of cardiac amyloidosis. The main objective of the diagnostic algorithm outlined in this position statement is to detect cardiac amyloidosis as reliably and early as possible, to accurately determine its extent, and to reliably identify the underlying subtype of amyloidosis, thereby enabling subsequent targeted treatment.
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Affiliation(s)
- A Yilmaz
- Sektion für Herzbildgebung, Klinik für Kardiologie, Universitätsklinikum Münster, Von-Esmarch-Str. 48, 48149, Münster, Germany.
| | - J Bauersachs
- Klinik für Kardiologie und Angiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - F Bengel
- Klinik für Nuklearmedizin, Medizinische Hochschule Hannover, Hannover, Germany
| | - R Büchel
- Klinik für Nuklearmedizin, Universitätsspital Zürich, Zurich, Switzerland
| | - I Kindermann
- Klinik für Innere Medizin III (Kardiologie, Angiologie und Internistische Intensivmedizin), Universitätsklinikum des Saarlandes und Medizinische Fakultät der Universität des Saarlandes, Homburg, Germany
| | - K Klingel
- Institut für Pathologie und Neuropathologie, Universität Tübingen, Tübingen, Germany
| | - F Knebel
- Medizinische Klinik m.S. Kardiologie und Angiologie, Charite Universitätsmedizin Berlin Campus Mitte, Berlin, Germany
| | - B Meder
- Klinik für Innere Medizin III, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - C Morbach
- Klinik für Innere Medizin III, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - E Nagel
- Interdisziplinäres Amyloidosezentrum Nordbayern, Deutsches Zentrum für Herzinsuffizienz, Medizinische Klinik I der Universität Würzburg, Würzburg, Germany
| | - E Schulze-Bahr
- Institut für Experimentelle und translationale kardiovaskuläre Bildgebung, Universitätsklinikum Frankfurt, Frankfurt, Germany
| | - F Aus dem Siepen
- Institut für Genetik von Herzerkrankungen (IfGH), Universitätsklinikum Münster, Münster, Germany
| | - N Frey
- Klinik für Innere Medizin III, Schwerpunkt Kardiologie und Angiologie, Universitätsklinikum Schleswig-Holstein, Kiel, Germany.,Kommission für Klinische Kardiovaskuläre Medizin, Deutsche Gesellschaft für Kardiologie, Düsseldorf, Germany
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38
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Tavanti F, Pedone A, Menziani MC. Disclosing the Interaction of Gold Nanoparticles with Aβ(1-40) Monomers through Replica Exchange Molecular Dynamics Simulations. Int J Mol Sci 2020; 22:ijms22010026. [PMID: 33375086 PMCID: PMC7792802 DOI: 10.3390/ijms22010026] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022] Open
Abstract
Amyloid-β aggregation is one of the principal causes of amyloidogenic diseases that lead to the loss of neuronal cells and to cognitive impairments. The use of gold nanoparticles treating amyloidogenic diseases is a promising approach, because the chemistry of the gold surface can be tuned in order to have a specific binding, obtaining effective tools to control the aggregation. In this paper, we show, by means of Replica Exchange Solute Tempering Molecular Simulations, how electrostatic interactions drive the absorption of Amyloid-β monomers onto citrates-capped gold nanoparticles. Importantly, upon binding, amyloid monomers show a reduced propensity in forming β-sheets secondary structures that are characteristics of mature amyloid fibrils.
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Affiliation(s)
- Francesco Tavanti
- CNR-NANO Research Center, Via Campi 213/a, 41125 Modena, Italy
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (A.P.); (M.C.M.)
- Correspondence:
| | - Alfonso Pedone
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (A.P.); (M.C.M.)
| | - Maria Cristina Menziani
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (A.P.); (M.C.M.)
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39
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D’Onofrio M, Munari F, Assfalg M. Alpha-Synuclein-Nanoparticle Interactions: Understanding, Controlling and Exploiting Conformational Plasticity. Molecules 2020; 25:E5625. [PMID: 33260436 PMCID: PMC7731430 DOI: 10.3390/molecules25235625] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/29/2022] Open
Abstract
Alpha-synuclein (αS) is an extensively studied protein due to its involvement in a group of neurodegenerative disorders, including Parkinson's disease, and its documented ability to undergo aberrant self-aggregation resulting in the formation of amyloid-like fibrils. In dilute solution, the protein is intrinsically disordered but can adopt multiple alternative conformations under given conditions, such as upon adsorption to nanoscale surfaces. The study of αS-nanoparticle interactions allows us to better understand the behavior of the protein and provides the basis for developing systems capable of mitigating the formation of toxic aggregates as well as for designing hybrid nanomaterials with novel functionalities for applications in various research areas. In this review, we summarize current progress on αS-nanoparticle interactions with an emphasis on the conformational plasticity of the biomolecule.
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Affiliation(s)
| | | | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (M.D.); (F.M.)
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40
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Ostermeier L, de Oliveira GAP, Dzwolak W, Silva JL, Winter R. Exploring the polymorphism, conformational dynamics and function of amyloidogenic peptides and proteins by temperature and pressure modulation. Biophys Chem 2020; 268:106506. [PMID: 33221697 DOI: 10.1016/j.bpc.2020.106506] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 11/15/2022]
Abstract
Our understanding of amyloid structures and the mechanisms by which disease-associated peptides and proteins self-assemble into these fibrillar aggregates, has advanced considerably in recent years. It is also established that amyloid fibrils are generally polymorphic. The molecular structures of the aggregation intermediates and the causes of molecular and structural polymorphism are less understood, however. Such information is mandatory to explain the pathological diversity of amyloid diseases. What is also clear is that not only protein mutations, but also the physiological milieu, i.e. pH, cosolutes, crowding and surface interactions, have an impact on fibril formation. In this minireview, we focus on the effect of the less explored physical parameters temperature and pressure on the fibrillization propensity of proteins and how these variables can be used to reveal additional mechanistic information about intermediate states of fibril formation and molecular and structural polymorphism. Generally, amyloids are very stable and can resist harsh environmental conditions, such as extreme pH, high temperature and high pressure, and can hence serve as valuable functional amyloid. As an example, we discuss the effect of temperature and pressure on the catalytic activity of peptide amyloid fibrils that exhibit enzymatic activity.
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Affiliation(s)
- Lena Ostermeier
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur 1 Str., 02-093 Warsaw, Poland.
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil.
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany.
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41
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Tavanti F, Pedone A, Menziani MC, Alexander-Katz A. Computational Insights into the Binding of Monolayer-Capped Gold Nanoparticles onto Amyloid-β Fibrils. ACS Chem Neurosci 2020; 11:3153-3160. [PMID: 32926781 DOI: 10.1021/acschemneuro.0c00497] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Amyloids-β (Aβ) fibrils are involved in several neurodegenerative diseases. In this study, atomistic molecular dynamics simulations have been used to investigate how monolayer-protected gold nanoparticles interact with Aβ(1-40) and Aβ(1-42) fibrils. Our results show that small gold nanoparticles bind with the external side of amyloid-β fibrils that is involved in the fibrillation process. The binding affinity, studied for both kinds of fibrils as a function of the monolayer composition and the nanoparticle diameter, is modulated by hydrophobic interactions and ligand monolayer conformation. Our findings thus show that monolayer-protected nanoparticles are good candidates to prevent fibril aggregation and secondary nucleation or to deliver drugs to specific fibril regions.
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Affiliation(s)
- Francesco Tavanti
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi, 103, I-41125 Modena, Italy
- CNR-NANO Istituto Nanoscienze, Centro S3, Via Campi 213/A, I-41125 Modena, Italy
| | - Alfonso Pedone
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi, 103, I-41125 Modena, Italy
| | - Maria Cristina Menziani
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi, 103, I-41125 Modena, Italy
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Massachusetts Avenue, 77, Cambridge, Massachusetts 02142, United States
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42
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Feuillie C, Lambert E, Ewald M, Azouz M, Henry S, Marsaudon S, Cullin C, Lecomte S, Molinari M. High Speed AFM and NanoInfrared Spectroscopy Investigation of Aβ 1-42 Peptide Variants and Their Interaction With POPC/SM/Chol/GM1 Model Membranes. Front Mol Biosci 2020; 7:571696. [PMID: 33033718 PMCID: PMC7510551 DOI: 10.3389/fmolb.2020.571696] [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: 06/11/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Due to an aging population, neurodegenerative diseases such as Alzheimer's disease (AD) have become a major health issue. In the case of AD, Aβ1 - 42 peptides have been identified as one of the markers of the disease with the formation of senile plaques via their aggregation, and could play a role in memory impairment and other tragic syndromes associated with the disease. Many studies have shown that not only the morphology and structure of Aβ1 - 42 peptide assembly are playing an important role in the formation of amyloid plaques, but also the interactions between Aβ1 - 42 and the cellular membrane are crucial regarding the aggregation processes and toxicity of the amyloid peptides. Despite the increasing amount of information on AD associated amyloids and their toxicity, the molecular mechanisms involved still remain unclear and require in-depth investigation at the local scale to clearly decipher the role of the sequence of the amyloid peptides, of their secondary structures, of their oligomeric states, and of their interactions with lipid membranes. In this original study, through the use of Atomic Force Microscopy (AFM) related-techniques, high-speed AFM and nanoInfrared AFM, we tried to unravel at the nanoscale the link between aggregation state, structure and interaction with membranes in the amyloid/membrane interaction. Using three mutants of Aβ peptides, L34T, oG37C, and WT Aβ1 - 42 peptides, with differences in morphology, structure and assembly process, as well as model lipidic membranes whose composition and structure allow interactions with the peptides, our AFM study coupling high spatial and temporal resolution and nanoscale structure information clearly evidences a local correlation between the secondary structure of the peptides, their fibrillization kinetics and their interactions with model membranes. Membrane disruption is associated to small transient oligomeric entities in the early stages of aggregation that strongly interact with the membrane, and present an antiparallel β-sheet secondary structure. The strong effect on membrane integrity that exists when these oligomeric Aβ1 - 42 peptides interact with membranes of a particular composition could be a lead for therapeutic studies.
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Affiliation(s)
- Cecile Feuillie
- CBMN, CNRS UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Eleonore Lambert
- LRN EA 4682, Université de Reims Champagne-Ardenne, Reims, France
| | - Maxime Ewald
- LRN EA 4682, Université de Reims Champagne-Ardenne, Reims, France
| | - Mehdi Azouz
- CBMN, CNRS UMR 5248, IPB, Université de Bordeaux, Pessac, France.,Department of Chemistry, Université de Montréal, Montreal, QC, Canada
| | - Sarah Henry
- CBMN, CNRS UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Sophie Marsaudon
- CBMN, CNRS UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | | | - Sophie Lecomte
- CBMN, CNRS UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Michael Molinari
- CBMN, CNRS UMR 5248, IPB, Université de Bordeaux, Pessac, France
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43
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Effects of Airborne Nanoparticles on the Nervous System: Amyloid Protein Aggregation, Neurodegeneration and Neurodegenerative Diseases. NANOMATERIALS 2020; 10:nano10071349. [PMID: 32664217 PMCID: PMC7407104 DOI: 10.3390/nano10071349] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 01/18/2023]
Abstract
How the environment contributes to neurodegenerative diseases such as Alzheimer’s is not well understood. In recent years, science has found augmenting evidence that nano-sized particles generated by transport (e.g., fuel combustion, tire wear and brake wear) may promote Alzheimer’s disease (AD). Individuals residing close to busy roads are at higher risk of developing AD, and nanomaterials that are specifically generated by traffic-related processes have been detected in human brains. Since AD represents a neurodegenerative disease characterized by amyloid protein aggregation, this review summarizes our current knowledge on the amyloid-generating propensity of traffic-related nanomaterials. Certain nanoparticles induce the amyloid aggregation of otherwise soluble proteins in in vitro laboratory settings, cultured neuronal cells and vertebrate or invertebrate animal models. We discuss the challenges for future studies, namely, strategies to connect the wet laboratory with the epidemiological data in order to elucidate the molecular bio-interactions of airborne nanomaterials and their effects on human health.
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44
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Watanabe-Nakayama T, Sahoo BR, Ramamoorthy A, Ono K. High-Speed Atomic Force Microscopy Reveals the Structural Dynamics of the Amyloid-β and Amylin Aggregation Pathways. Int J Mol Sci 2020; 21:E4287. [PMID: 32560229 PMCID: PMC7352471 DOI: 10.3390/ijms21124287] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/09/2020] [Accepted: 06/14/2020] [Indexed: 12/18/2022] Open
Abstract
Individual Alzheimer's disease (AD) patients have been shown to have structurally distinct amyloid-β (Aβ) aggregates, including fibrils, in their brain. These findings suggest the possibility of a relationship between AD progression and Aβ fibril structures. Thus, the characterization of the structural dynamics of Aβ could aid the development of novel therapeutic strategies and diagnosis. Protein structure and dynamics have typically been studied separately. Most of the commonly used biophysical approaches are limited in providing substantial details regarding the combination of both structure and dynamics. On the other hand, high-speed atomic force microscopy (HS-AFM), which simultaneously visualizes an individual protein structure and its dynamics in liquid in real time, can uniquely link the structure and the kinetic details, and it can also unveil novel insights. Although amyloidogenic proteins generate heterogeneously aggregated species, including transient unstable states during the aggregation process, HS-AFM elucidated the structural dynamics of individual aggregates in real time in liquid without purification and isolation. Here, we review and discuss the HS-AFM imaging of amyloid aggregation and strategies to optimize the experiments showing findings from Aβ and amylin, which is associated with type II diabetes, shares some common biological features with Aβ, and is reported to be involved in AD.
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Affiliation(s)
| | - Bikash R. Sahoo
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, and Biomedical Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA;
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA;
| | - Kenjiro Ono
- Division of Neurology, Department of Internal Medicine, School of Medicine, Showa University, Hatanodai, Shinagawa district, Tokyo 142-8666, Japan;
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