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Zhang J, Luo WC, Zhang Y, Li X, Jiang M, Huang K, Yu X, Xu L. Red emissive fluorescent carbon dots based on ternary carbon source for imaging α-synuclein fibrils. J Colloid Interface Sci 2024; 670:576-584. [PMID: 38776692 DOI: 10.1016/j.jcis.2024.05.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/30/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
The misfolding and aggregation of α-synuclein monomers usually cause the occurrence and development of Parkinson's disease (PD). It is important to develop effective methods for detection of α-synuclein aggregates. Carbon dots (CDs) could be the potential fluorescence probe for this purpose owing to their appreciated optical properties. However, undefined structure of CDs and complicated three-dimensional structure of protein severely hindered the design of fluorescence probe towards protein aggregates. Herein, a red emissive fluorescent amphiphilic CD, named as CL-9, was designed with a high sensitivity to α-synuclein fibrils by a one-step heating process, using the ternary carbon source, including Congo red, l-tryptophan and urea. The CL-9 exhibited turn-on red emissive fluorescence towards α-synuclein fibril, but remained no change towards its monomer. Compared with the original Congo red dye, CL-9 exhibited stronger turn-on red fluorescence towards α-synuclein fibrils with better anti-photobleaching resistance, biocompatibility and signal-to-noise ratio. The CL-9 was successful as a fluorescent probe to image α-synuclein fibrils in NL-5901 C. elegans. The present study provided a feasible approach using the multiple carbon sources to construct the CDs based fluorescence probe targeting amyloid proteins.
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Affiliation(s)
- Jintao Zhang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wan-Chun Luo
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yu Zhang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xi Li
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ming Jiang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kun Huang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Xu Yu
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Li Xu
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China.
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2
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Fan X, Zhang X, Yan J, Xu H, Zhao W, Ding F, Huang F, Sun Y. Computational Investigation of Coaggregation and Cross-Seeding between Aβ and hIAPP Underpinning the Cross-Talk in Alzheimer's Disease and Type 2 Diabetes. J Chem Inf Model 2024; 64:5303-5316. [PMID: 38921060 DOI: 10.1021/acs.jcim.4c00859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
The coexistence of amyloid-β (Aβ) and human islet amyloid polypeptide (hIAPP) in the brain and pancreas is associated with an increased risk of Alzheimer's disease (AD) and type 2 diabetes (T2D) due to their coaggregation and cross-seeding. Despite this, the molecular mechanisms underlying their interaction remain elusive. Here, we systematically investigated the cross-talk between Aβ and hIAPP using atomistic discrete molecular dynamics (DMD) simulations. Our results revealed that the amyloidogenic core regions of both Aβ (Aβ10-21 and Aβ30-41) and hIAPP (hIAPP8-20 and hIAPP22-29), driving their self-aggregation, also exhibited a strong tendency for cross-interaction. This propensity led to the formation of β-sheet-rich heterocomplexes, including potentially toxic β-barrel oligomers. The formation of Aβ and hIAPP heteroaggregates did not impede the recruitment of additional peptides to grow into larger aggregates. Our cross-seeding simulations demonstrated that both Aβ and hIAPP fibrils could mutually act as seeds, assisting each other's monomers in converting into β-sheets at the exposed fibril elongation ends. The amyloidogenic core regions of Aβ and hIAPP, in both oligomeric and fibrillar states, exhibited the ability to recruit isolated peptides, thereby extending the β-sheet edges, with limited sensitivity to the amino acid sequence. These findings suggest that targeting these regions by capping them with amyloid-resistant peptide drugs may hold potential as a therapeutic approach for addressing AD, T2D, and their copathologies.
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Affiliation(s)
- Xinjie Fan
- School of Physical Science and Technology, Ningbo University, Ningbo315211, China
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo315211, China
| | - Xiaohan Zhang
- School of Physical Science and Technology, Ningbo University, Ningbo315211, China
| | - Jiajia Yan
- School of Physical Science and Technology, Ningbo University, Ningbo315211, China
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo315211, China
| | - Huan Xu
- School of Physical Science and Technology, Ningbo University, Ningbo315211, China
| | - Wenhui Zhao
- School of Physical Science and Technology, Ningbo University, Ningbo315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina29634, United States
| | - Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo315211, China
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina29634, United States
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3
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Camargo LC, Gering I, Mastalipour M, Kraemer-Schulien V, Bujnicki T, Willbold D, Coronado MA, Eberle RJ. A Snake Venom Peptide and Its Derivatives Prevent Aβ 42 Aggregation and Eliminate Toxic Aβ 42 Aggregates In Vitro. ACS Chem Neurosci 2024. [PMID: 38957957 DOI: 10.1021/acschemneuro.4c00089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024] Open
Abstract
Over a century has passed since Alois Alzheimer first described Alzheimer's disease (AD), and since then, researchers have made significant strides in understanding its pathology. One key feature of AD is the presence of amyloid-β (Aβ) peptides, which form amyloid plaques, and therefore, it is a primary target for treatment studies. Naturally occurring peptides have garnered attention for their potential pharmacological benefits, particularly in the central nervous system. In this study, nine peptide derivatives of Crotamine, a polypeptide from Crotalus durissus terrificus Rattlesnake venom, as well as one d-enantiomer, were evaluated for their ability to modulate Aβ42 aggregation through various assays such as ThT, QIAD, SPR, and sFIDA. All tested peptides were able to decrease Aβ42 aggregation and eliminate Aβ42 aggregates. Additionally, all of the peptides showed an affinity for Aβ42. This study is the first to describe the potential of crotamine derivative peptides against Aβ42 aggregation and to identify a promising d-peptide that could be used as an effective pharmacological tool against AD in the future.
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Affiliation(s)
- Luana Cristina Camargo
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
- Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Ian Gering
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
| | - Mohammadamin Mastalipour
- Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Victoria Kraemer-Schulien
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
| | - Tuyen Bujnicki
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
- Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Mônika A Coronado
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
- Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Raphael J Eberle
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
- Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
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4
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Suri K, Ramesh M, Bhandari M, Gupta V, Kumar V, Govindaraju T, Murugan NA. Role of Amyloidogenic and Non-Amyloidogenic Protein Spaces in Neurodegenerative Diseases and their Mitigation Using Theranostic Agents. Chembiochem 2024; 25:e202400224. [PMID: 38668376 DOI: 10.1002/cbic.202400224] [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: 03/11/2024] [Revised: 04/23/2024] [Indexed: 06/15/2024]
Abstract
Neurodegenerative diseases (NDDs) refer to a complex heterogeneous group of diseases which are associated with the accumulation of amyloid fibrils or plaques in the brain leading to progressive loss of neuronal functions. Alzheimer's disease is one of the major NDD responsible for 60-80 % of all dementia cases. Currently, there are no curative or disease-reversing/modifying molecules for many of the NDDs except a few such as donepezil, rivastigmine, galantamine, carbidopa and levodopa which treat the disease-associated symptoms. Similarly, there are very few FDA-approved tracers such as flortaucipir (Tauvid) for tau fibril imaging and florbetaben (Neuraceq), flutemetamol (Vizamyl), and florbetapir (Amyvid) for amyloid imaging available for diagnosis. Recent advances in the cryogenic electron microscopy reported distinctly different microstructures for tau fibrils associated with different tauopathies highlighting the possibility to develop tauopathy-specific imaging agents and therapeutics. In addition, it is important to identify the proteins that are associated with disease development and progression to know about their 3D structure to develop various diagnostics, therapeutics and theranostic agents. The current article discusses in detail the disease-associated amyloid and non-amyloid proteins along with their structural insights. We comprehensively discussed various novel proteins associated with NDDs and their implications in disease pathology. In addition, we document various emerging chemical compounds developed for diagnosis and therapy of different NDDs with special emphasis on theranostic agents for better management of NDDs.
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Affiliation(s)
- Kapali Suri
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Madhu Ramesh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur P.O., Bengaluru, 560064, Karnataka, India
| | - Mansi Bhandari
- Department of computer science and engineering, Jamia Hamdard University, Hamdard Nagar, New Delhi, Delhi, 110062
| | - Vishakha Gupta
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Virendra Kumar
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur P.O., Bengaluru, 560064, Karnataka, India
| | - N Arul Murugan
- Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT-Delhi) Okhla, Phase III, New Delhi, 110020, India
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5
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Wagner WJ, Gross ML. Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta. MASS SPECTROMETRY REVIEWS 2024; 43:782-825. [PMID: 36224716 PMCID: PMC10090239 DOI: 10.1002/mas.21814] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.
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Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
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6
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Yin X, Zhou H, Cao T, Yang X, Meng F, Dai X, Wang Y, Li S, Zhai W, Yang Z, Chen N, Zhou R. Rational Design of Dual-Functionalized Gd@C 82 Nanoparticles to Relieve Neuronal Cytotoxicity in Alzheimer's Disease via Inhibition of Aβ Aggregation. ACS NANO 2024; 18:15416-15431. [PMID: 38840269 DOI: 10.1021/acsnano.3c08823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
The accumulation of amyloid-β (Aβ) peptides is a major hallmark of Alzheimer's disease (AD) and plays a crucial role in its pathogenesis. Particularly, the structured oligomeric species rich in β-sheet formations were implicated in neuronal organelle damage. Addressing this formidable challenge requires identifying candidates capable of inhibiting peptide aggregation or disaggregating preformed oligomers for effective antiaggregation-based AD therapy. Here, we present a dual-functional nanoinhibitor meticulously designed to target the aggregation driving force and amyloid fibril spatial structure. Leveraging the exceptional structural stability and facile tailoring capability of endohedral metallofullerene Gd@C82, we introduce desired hydrogen-binding sites and charged groups, which are abundant on its surface for specific designs. Impressively, these designs endow the resultant functionalized-Gd@C82 nanoparticles (f-Gd@C82 NPs) with high capability of redirecting peptide self-assembly toward disordered, off-pathway species, obstructing the early growth of protofibrils, and disaggregating the preformed well-ordered protofibrils or even mature Aβ fibrils. This results in considerable alleviation of Aβ peptide-induced neuronal cytotoxicity, rescuing neuronal death and synaptic loss in primary neuron models. Notably, these modifications significantly improved the dispersibility of f-Gd@C82 NPs, thus substantially enhancing its bioavailability. Moreover, f-Gd@C82 NPs demonstrate excellent cytocompatibility with various cell lines and possess the ability to penetrate the blood-brain barrier in mice. Large-scale molecular dynamics simulations illuminate the inhibition and disaggregation mechanisms. Our design successfully overcomes the limitations of other nanocandidates, which often overly rely on hydrophobic interactions or photothermal conversion properties, and offers a viable direction for developing anti-AD agents through the inhibition and even reversal of Aβ aggregation.
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Affiliation(s)
- Xiuhua Yin
- Institute of Quantitative Biology, Shanghai Institute for Advanced Study, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, China
| | - Hong Zhou
- Institute of Quantitative Biology, Shanghai Institute for Advanced Study, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Tiantian Cao
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
- Suzhou Institute of Trade and Commerce, Suzhou 215009, China
| | - Xiner Yang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, China
| | - Fei Meng
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, China
| | - Xing Dai
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, China
| | - Yifan Wang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, China
| | - Sijie Li
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, China
| | - Wangsong Zhai
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, China
| | - Zaixing Yang
- Institute of Quantitative Biology, Shanghai Institute for Advanced Study, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, China
| | - Ning Chen
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, Shanghai Institute for Advanced Study, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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7
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Monteiro C, Gomes MC, Bharmoria P, Freire MG, Coutinho JA, Custódio CA, Mano JF. Human Platelet Lysate-Derived Nanofibrils as Building Blocks to Produce Free-Standing Membranes for Cell Self-Aggregation. ACS NANO 2024; 18:15815-15830. [PMID: 38833572 PMCID: PMC11191744 DOI: 10.1021/acsnano.4c02790] [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] [Received: 02/28/2024] [Revised: 05/12/2024] [Accepted: 05/22/2024] [Indexed: 06/06/2024]
Abstract
Amyloid-like fibrils are garnering keen interest in biotechnology as supramolecular nanofunctional units to be used as biomimetic platforms to control cell behavior. Recent insights into fibril functionality have highlighted their importance in tissue structure, mechanical properties, and improved cell adhesion, emphasizing the need for scalable and high-kinetics fibril synthesis. In this study, we present the instantaneous and bulk formation of amyloid-like nanofibrils from human platelet lysate (PL) using the ionic liquid cholinium tosylate as a fibrillating agent. The instant fibrillation of PL proteins upon supramolecular protein-ionic liquid interactions was confirmed from the protein conformational transition toward cross-β-sheet-rich structures. These nanofibrils were utilized as building blocks for the formation of thin and flexible free-standing membranes via solvent casting to support cell self-aggregation. These PL-derived fibril membranes reveal a nanotopographically rough surface and high stability over 14 days under cell culture conditions. The culture of mesenchymal stem cells or tumor cells on the top of the membrane demonstrated that cells are able to adhere and self-organize in a three-dimensional (3D) spheroid-like microtissue while tightly folding the fibril membrane. Results suggest that nanofibril membrane incorporation in cell aggregates can improve cell viability and metabolic activity, recreating native tissues' organization. Altogether, these PL-derived nanofibril membranes are suitable bioactive platforms to generate 3D cell-guided microtissues, which can be explored as bottom-up strategies to faithfully emulate native tissues in a fully human microenvironment.
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Affiliation(s)
- Cátia
F. Monteiro
- CICECO − Aveiro Institute
of Materials, Department of Chemistry, University
of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
| | - Maria C. Gomes
- CICECO − Aveiro Institute
of Materials, Department of Chemistry, University
of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
| | | | - Mara G. Freire
- CICECO − Aveiro Institute
of Materials, Department of Chemistry, University
of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
| | - João A.
P. Coutinho
- CICECO − Aveiro Institute
of Materials, Department of Chemistry, University
of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
| | - Catarina A. Custódio
- CICECO − Aveiro Institute
of Materials, Department of Chemistry, University
of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
| | - João F. Mano
- CICECO − Aveiro Institute
of Materials, Department of Chemistry, University
of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
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Ren H, Chen H, Kang Y, Liu W, Liu Y, Tao F, Miao S, Zhang Y, Liu Q, Dong M, Liu Y, Liu B, Yang P. Non-fibril amyloid aggregation at the air/water interface: self-adaptive pathway resulting in a 2D Janus nanofilm. Chem Sci 2024; 15:8946-8958. [PMID: 38873054 PMCID: PMC11168098 DOI: 10.1039/d4sc00560k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/27/2024] [Indexed: 06/15/2024] Open
Abstract
The amyloid states of proteins are implicated in several neurodegenerative diseases and bioadhesion processes. However, the classical amyloid fibrillization mechanism fails to adequately explain the formation of polymorphic aggregates and their adhesion to various surfaces. Herein, we report a non-fibril amyloid aggregation pathway, with disulfide-bond-reduced lysozyme (R-Lyz) as a model protein under quasi-physiological conditions. Very different from classical fibrillization, this pathway begins with the air-water interface (AWI) accelerated oligomerization of unfolded full-length protein, resulting in unique plate-like oligomers with self-adaptive ability, which can adjust their conformations to match various interfaces such as the asymmetric AWI and amyloid-protein film surface. The pathway enables a stepwise packing of the plate-like oligomers into a 2D Janus nanofilm, exhibiting a divergent distribution of hydrophilic/hydrophobic residues on opposite sides of the nanofilm. The resulting Janus nanofilm possesses a top-level Young's modulus (8.3 ± 0.6 GPa) among amyloid-based materials and exhibits adhesive strength two times higher (145 ± 81 kPa) than that of barnacle cement. Furthermore, we found that such an interface-directed pathway exists in several amyloidogenic proteins with a similar self-adaptive 2D-aggregation process, including bovine serum albumin, insulin, fibrinogen, hemoglobin, lactoferrin, and ovalbumin. Thus, our findings on the non-fibril self-adaptive mechanism for amyloid aggregation may shed light on polymorphic amyloid assembly and their adhesions through an alternative pathway.
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Affiliation(s)
- Hao Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Huan Chen
- First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University Xi'an 710061 China
| | - Yu Kang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 China
| | - Wei Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Yongchun Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Fei Tao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Shuting Miao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Yingying Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Qian Liu
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Aarhus C Denmark
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Aarhus C Denmark
| | - Yonggang Liu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 China
| | - Bing Liu
- First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University Xi'an 710061 China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
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9
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Kaur G, Mankoo OK, Kaur A, Goyal D, Goyal B. Insights into the baicalein-induced destabilization of LS-shaped Aβ 42 protofibrils using computer simulations. Phys Chem Chem Phys 2024; 26:16674-16686. [PMID: 38809059 DOI: 10.1039/d3cp06006c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Amyloid-β (Aβ) peptides aggregate spontaneously into various aggregating species comprising oligomers, protofibrils, and mature fibrils in Alzheimer's disease (AD). Disrupting β-sheet rich neurotoxic smaller soluble Aβ42 oligomers formed at early stages is considered a potent strategy to interfere with AD pathology. Previous experiments have demonstrated the inhibition of the early stages of Aβ aggregation by baicalein; however, the molecular mechanism behind inhibition remains largely unknown. Thus, in this work, molecular dynamics (MD) simulations have been employed to illuminate the molecular mechanism of baicalein-induced destabilization of preformed Aβ42 protofibrils. Baicalein binds to chain A of the Aβ42 protofibril through hydrogen bonds, π-π interactions, and hydrophobic contacts with the central hydrophobic core (CHC) residues of the Aβ42 protofibril. The binding of baicalein to the CHC region of the Aβ42 protofibril resulted in the elongation of the kink angle and disruption of K28-A42 salt bridges, which resulted in the distortion of the protofibril structure. Importantly, the β-sheet content was notably reduced in Aβ42 protofibrils upon incorporation of baicalein with a concomitant increase in the coil content, which is consistent with ThT fluorescence and AFM images depicting disaggregation of pre-existing Aβ42 fibrils on the incorporation of baicalein. Remarkably, the interchain binding affinity in Aβ42 protofibrils was notably reduced in the presence of baicalein leading to distortion in the overall structure, which agrees with the structural stability analyses and conformational snapshots. This work sheds light on the molecular mechanism of baicalein in disrupting the Aβ42 protofibril structure, which will be beneficial to the design of therapeutic candidates against disrupting β-sheet rich neurotoxic Aβ42 oligomers in AD.
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Affiliation(s)
- Gagandeep Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Opinder Kaur Mankoo
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Anupamjeet Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, DAV College, Sector 10, Chandigarh-160011, India.
| | - Bhupesh Goyal
- Department of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala-147004, Punjab, India.
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10
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Zhang W, Smith N, Zhou Y, McGee CM, Bartoli M, Fu S, Chen J, Domena JB, Joji A, Burr H, Lv G, Cilingir EK, Bedendo S, Claure ML, Tagliaferro A, Eliezer D, Veliz EA, Zhang F, Wang C, Leblanc RM. Carbon dots as dual inhibitors of tau and amyloid-beta aggregation for the treatment of Alzheimer's disease. Acta Biomater 2024:S1742-7061(24)00306-4. [PMID: 38849023 DOI: 10.1016/j.actbio.2024.06.001] [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: 02/10/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Alzheimer's disease (AD) is the most common form of senile dementia, presenting a significant challenge for the development of effective treatments. AD is characterized by extracellular amyloid plaques and intraneuronal neurofibrillary tangles. Therefore, targeting both hallmarks through inhibition of amyloid beta (Aβ) and tau aggregation presents a promising approach for drug development. Carbon dots (CD), with their high biocompatibility, minimal cytotoxicity, and blood-brain barrier (BBB) permeability, have emerged as promising drug nanocarriers. Congo red, an azo dye, has gathered significant attention for inhibiting amyloid-beta and tau aggregation. However, Congo red's inability to cross the BBB limits its potential to be used as a drug candidate for central nervous system (CNS) diseases. Furthermore, current studies only focus on using Congo red to target single disease hallmarks, without investigating dual inhibition capabilities. In this study, we synthesized Congo red-derived CD (CRCD) by using Congo red and citric acid as precursors, resulting in three variants, CRCD1, CRCD2 and CRCD3, based on different mass ratios of precursors. CRCD2 and CRCD3 exhibited sustained low cytotoxicity, and CRCD3 demonstrated the ability to traverse the BBB in a zebrafish model. Moreover, thioflavin T (ThT) aggregation assays and AFM imaging revealed CRCD as potent inhibitors against both tau and Aβ aggregation. Notably, CRCD1 emerged as the most robust inhibitor, displaying IC50 values of 0.2 ± 0.1 and 2.1 ± 0.5 µg/mL against tau and Aβ aggregation, respectively. Our findings underscore the dual inhibitory role of CRCD against tau and Aβ aggregation, showcasing effective BBB penetration and positioning CRCD as potential nanodrugs and nanocarriers for the CNS. Hence, CRCD-based compounds represent a promising candidate in the realm of multi-functional AD therapeutics, offering an innovative formulation component for future developments in this area. STATEMENT OF SIGNIFICANCE: This article reports Congo red-derived carbon dots (CRCD) as dual inhibitors of tau and amyloid-beta (Aβ) aggregation for the treatment of Alzheimer's disease (AD). The CRCD are biocompatible and show strong fluorescence, high stability, the ability to cross the blood-brain barrier, and the function of addressing two major pathological features of AD.
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Affiliation(s)
- Wei Zhang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Nathan Smith
- Department of Biological Sciences, Rensselaer Polytechnic Institute, NY 12180, USA
| | - Yiqun Zhou
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA; Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | - Caitlin M McGee
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Mattia Bartoli
- Department of Applied Science and Technology, Politecnico di Torino, Italy; Center for Sustainable Future Technologies (CSFT), Istituto Italiano di Technologia (IIT), Via Livorno 60, 10144 Turin, Italy
| | - Shiwei Fu
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Jiuyan Chen
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Justin B Domena
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Annu Joji
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Hannah Burr
- Department of Biological Sciences, Rensselaer Polytechnic Institute, NY 12180, USA
| | - Guohua Lv
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Emel K Cilingir
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Susanna Bedendo
- Department of Applied Science and Technology, Politecnico di Torino, Italy
| | - Matteo L Claure
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | | | - David Eliezer
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Eduardo A Veliz
- Department of Natural Sciences, Miami Dade Collage, Miami, FL 33132, USA
| | - Fuwu Zhang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Chunyu Wang
- Department of Biological Sciences, Rensselaer Polytechnic Institute, NY 12180, USA.
| | - Roger M Leblanc
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
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11
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Nagashima K, Watanabe H, Akasaka T, Ono M. Development of Triphenylmethane Dyes for In Vivo Fluorescence Imaging of Aβ Oligomers. ACS Chem Neurosci 2024; 15:2233-2242. [PMID: 38753435 DOI: 10.1021/acschemneuro.4c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
Detection of amyloid β (Aβ) oligomers, regarded as the most toxic aggregated forms of Aβ, can contribute to the diagnosis and treatment of Alzheimer's disease (AD). Thus, the development of imaging probes for in vivo visualization of Aβ oligomers is crucial. However, the structural uncertainty regarding Aβ oligomers makes it difficult to design imaging probes with high sensitivity to Aβ oligomers against highly aggregated Aβ fibrils. In this study, we developed Aβ oligomer-selective fluorescent probes based on triphenylmethane dyes through screening of commercially available compounds followed by structure-activity relationship (SAR) studies on cyclic or acyclic 4-dialkylamino groups. We synthesized 11 triarylmethane-based Aβ oligomer probe (TAMAOP) derivatives. In vitro evaluation of fluorescence properties, TAMAOP-9, which had bulky 4-diisobutylamino groups introduced into three benzenes of a twisted triphenylmethane backbone, showed marked fluorescence enhancement in the presence of Aβ oligomers and demonstrated high selectivity for Aβ oligomers against Aβ fibrils. In docking studies using the Aβ trimer model, TAMAOP-9 bound to the hydrophobic surface and interacted with the side chain of Phe20. In vitro section staining revealed that TAMAOP-9 could visualize Aβ oligomers in the brains of AD model mice. An in vivo fluorescence imaging study using TAMAOP-9 showed significantly higher fluorescence signals from the brains of AD model mice than those of age-matched wild-type mice, confirmed by ex vivo section observation. These results suggest that TAMAOP-9 is a promising Aβ oligomer-targeting fluorescent probe applicable to in vivo imaging.
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Affiliation(s)
- Kotaro Nagashima
- Department of Patho-Functional Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroyuki Watanabe
- Department of Patho-Functional Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takahiro Akasaka
- Department of Patho-Functional Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiro Ono
- Department of Patho-Functional Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
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12
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Suladze S, Sarkar R, Rodina N, Bokvist K, Krewinkel M, Scheps D, Nagel N, Bardiaux B, Reif B. Atomic resolution structure of full-length human insulin fibrils. Proc Natl Acad Sci U S A 2024; 121:e2401458121. [PMID: 38809711 PMCID: PMC11161806 DOI: 10.1073/pnas.2401458121] [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: 02/07/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
Patients with type 1 diabetes mellitus who are dependent on an external supply of insulin develop insulin-derived amyloidosis at the sites of insulin injection. A major component of these plaques is identified as full-length insulin consisting of the two chains A and B. While there have been several reports that characterize insulin misfolding and the biophysical properties of the fibrils, atomic-level information on the insulin fibril architecture remains elusive. We present here an atomic resolution structure of a monomorphic insulin amyloid fibril that has been determined using magic angle spinning solid-state NMR spectroscopy. The structure of the insulin monomer yields a U-shaped fold in which the two chains A and B are arranged in parallel to each other and are oriented perpendicular to the fibril axis. Each chain contains two β-strands. We identify two hydrophobic clusters that together with the three preserved disulfide bridges define the amyloid core structure. The surface of the monomeric amyloid unit cell is hydrophobic implicating a potential dimerization and oligomerization interface for the assembly of several protofilaments in the mature fibril. The structure provides a starting point for the development of drugs that bind to the fibril surface and disrupt secondary nucleation as well as for other therapeutic approaches to attenuate insulin aggregation.
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Affiliation(s)
- Saba Suladze
- Bavarian Nuclear Magnetic Resonance Center at the Department of Biosciences, School of Natural Sciences, Technische Universität München, Garching85747, Germany
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology, Neuherberg85764, Germany
| | - Riddhiman Sarkar
- Bavarian Nuclear Magnetic Resonance Center at the Department of Biosciences, School of Natural Sciences, Technische Universität München, Garching85747, Germany
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology, Neuherberg85764, Germany
| | - Natalia Rodina
- Bavarian Nuclear Magnetic Resonance Center at the Department of Biosciences, School of Natural Sciences, Technische Universität München, Garching85747, Germany
| | - Krister Bokvist
- Sanofi-Aventis Deutschland GmbH, Diabetes Research, Industriepark Höchst, Frankfurt65926, Germany
| | - Manuel Krewinkel
- Sanofi-Aventis Deutschland GmbH, Manufacturing Science and Technology, Industriepark Höchst, Frankfurt65926, Germany
| | - Daniel Scheps
- Chemistry Manufacturing & Controls Microbial Platform, Sanofi-Aventis Deutschland GmbH, Microbial Platform, Industriepark Höchst, Frankfurt65926, Germany
| | - Norbert Nagel
- Sanofi-Aventis Deutschland GmbH, Tides Platform, Industriepark Höchst, Frankfurt65926, Germany
| | - Benjamin Bardiaux
- Institut Pasteur, Department of Structural Biology and Chemistry, Structural Bioinformatics Unit, CNRS UMR 3528, Université Paris Cité, Paris75015, France
- Institut Pasteur, Department of Structural Biology and Chemistry, Bacterial Transmembrane Systems Unit, CNRS UMR 3528, Université Paris Cité, Paris75015, France
| | - Bernd Reif
- Bavarian Nuclear Magnetic Resonance Center at the Department of Biosciences, School of Natural Sciences, Technische Universität München, Garching85747, Germany
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology, Neuherberg85764, Germany
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13
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Im D, Choi TS. Distinctive contribution of two additional residues in protein aggregation of Aβ42 and Aβ40 isoforms. BMB Rep 2024; 57:263-272. [PMID: 38835114 PMCID: PMC11214890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/16/2024] [Accepted: 04/26/2024] [Indexed: 06/06/2024] Open
Abstract
Amyloid-β (Aβ) is one of the amyloidogenic intrinsically disordered proteins (IDPs) that self-assemble to protein aggregates, incurring cell malfunction and cytotoxicity. While Aβ has been known to regulate multiple physiological functions, such as enhancing synaptic functions, aiding in the recovery of the blood-brain barrier/brain injury, and exhibiting tumor suppression/antimicrobial activities, the hydrophobicity of the primary structure promotes pathological aggregations that are closely associated with the onset of Alzheimer's disease (AD). Aβ proteins consist of multiple isoforms with 37-43 amino acid residues that are produced by the cleavage of amyloid-β precursor protein (APP). The hydrolytic products of APP are secreted to the extracellular regions of neuronal cells. Aβ 1-42 (Aβ42) and Aβ 1-40 (Aβ40) are dominant isoforms whose significance in AD pathogenesis has been highlighted in numerous studies to understand the molecular mechanism and develop AD diagnosis and therapeutic strategies. In this review, we focus on the differences between Aβ42 and Aβ40 in the molecular mechanism of amyloid aggregations mediated by the two additional residues (Ile41 and Ala42) of Aβ42. The current comprehension of Aβ42 and Aβ40 in AD progression is outlined, together with the structural features of Aβ42/Aβ40 amyloid fibrils, and the aggregation mechanisms of Aβ42/Aβ40. Furthermore, the impact of the heterogeneous distribution of Aβ isoforms during amyloid aggregations is discussed in the system mimicking the coexistence of Aβ42 and Aβ40 in human cerebrospinal fluid (CSF) and plasma. [BMB Reports 2024; 57(6): 263-272].
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Affiliation(s)
- Dongjoon Im
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Tae Su Choi
- Department of Life Sciences, Korea University, Seoul 02841, Korea
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14
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Rejc L, Knez D, Molina-Aguirre G, Espargaró A, Kladnik J, Meden A, Blinc L, Lozinšek M, Jansen-van Vuuren RD, Rogan M, Martek BA, Mlakar J, Dremelj A, Petrič A, Gobec S, Sabaté R, Bresjanac M, Pinter B, Košmrlj J. Probing Alzheimer's pathology: Exploring the next generation of FDDNP analogues for amyloid β detection. Biomed Pharmacother 2024; 175:116616. [PMID: 38723516 DOI: 10.1016/j.biopha.2024.116616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 06/03/2024] Open
Abstract
Fluorescent probes are a powerful tool for imaging amyloid β (Aβ) plaques, the hallmark of Alzheimer's disease (AD). Herein, we report the synthesis and comprehensive characterization of 21 novel probes as well as their optical properties and binding affinities to Aβ fibrils. One of these dyes, 1Ae, exhibited several improvements over FDDNP, an established biomarker for Aβ- and Tau-aggregates. First, 1Ae had large Stokes shifts (138-213 nm) in various solvents, thereby reducing self-absorption. With a high quantum yield ratio (φ(dichloromethane/methanol) = 104), 1Ae also ensures minimal background emission in aqueous environments and high sensitivity. In addition, compound 1Ae exhibited low micromolar binding affinity to Aβ fibrils in vitro (Kd = 1.603 µM), while increasing fluorescence emission (106-fold) compared to emission in buffer alone. Importantly, the selective binding of 1Ae to Aβ1-42 fibrils was confirmed by an in cellulo assay, supported by ex vivo fluorescence microscopy of 1Ae on postmortem AD brain sections, allowing unequivocal identification of Aβ plaques. The intermolecular interactions of fluorophores with Aβ were elucidated by docking studies and molecular dynamics simulations. Density functional theory calculations revealed the unique photophysics of these rod-shaped fluorophores, with a twisted intramolecular charge transfer (TICT) excited state. These results provide valuable insights into the future application of such probes as potential diagnostic tools for AD in vitro and ex vivo such as determination of Aβ1-42 in cerebrospinal fluid or blood.
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Affiliation(s)
- Luka Rejc
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana SI-1000, Slovenia
| | - Damijan Knez
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana SI-1000, Slovenia
| | | | - Alba Espargaró
- Faculty of Pharmacy, Department of Pharmacy, Pharmaceutical Technology and Physical-Chemistry, Section of Physical-Chemistry, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona 08028, Spain
| | - Jerneja Kladnik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana SI-1000, Slovenia
| | - Anže Meden
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana SI-1000, Slovenia
| | - Lana Blinc
- Laboratory of Neural Plasticity and Regeneration (LNPR), Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, Ljubljana SI-1000, Slovenia
| | - Matic Lozinšek
- Jožef Stefan Institute, Jamova cesta 39, Ljubljana SI-1000, Slovenia
| | - Ross D Jansen-van Vuuren
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana SI-1000, Slovenia
| | - Matic Rogan
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana SI-1000, Slovenia
| | - Bruno Aleksander Martek
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana SI-1000, Slovenia
| | - Jernej Mlakar
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, Korytkova 2, Ljubljana SI-1000, Slovenia
| | - Ana Dremelj
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana SI-1000, Slovenia
| | - Andrej Petrič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana SI-1000, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana SI-1000, Slovenia.
| | - Raimon Sabaté
- Faculty of Pharmacy, Department of Pharmacy, Pharmaceutical Technology and Physical-Chemistry, Section of Physical-Chemistry, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona 08028, Spain.
| | - Mara Bresjanac
- Laboratory of Neural Plasticity and Regeneration (LNPR), Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, Ljubljana SI-1000, Slovenia.
| | - Balazs Pinter
- The University of Texas at El Paso, 500 West University Avenue, El Paso, TX 79968, USA.
| | - Janez Košmrlj
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana SI-1000, Slovenia.
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15
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Gómez-Castro CZ, Quintanar L, Vela A. An N-terminal acidic β-sheet domain is responsible for the metal-accumulation properties of amyloid-β protofibrils: a molecular dynamics study. J Biol Inorg Chem 2024; 29:407-425. [PMID: 38811408 PMCID: PMC11186886 DOI: 10.1007/s00775-024-02061-1] [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: 12/20/2023] [Accepted: 04/10/2024] [Indexed: 05/31/2024]
Abstract
The influence of metal ions on the structure of amyloid- β (Aβ) protofibril models was studied through molecular dynamics to explore the molecular mechanisms underlying metal-induced Aβ aggregation relevant in Alzheimer's disease (AD). The models included 36-, 48-, and 188-mers of the Aβ42 sequence and two disease-modifying variants. Primary structural effects were observed at the N-terminal domain, as it became susceptible to the presence of cations. Specially when β-sheets predominate, this motif orients N-terminal acidic residues toward one single face of the β-sheet, resulting in the formation of an acidic region that attracts cations from the media and promotes the folding of the N-terminal region, with implications in amyloid aggregation. The molecular phenotype of the protofibril models based on Aβ variants shows that the AD-causative D7N mutation promotes the formation of N-terminal β-sheets and accumulates more Zn2+, in contrast to the non-amyloidogenic rodent sequence that hinders the β-sheets and is more selective for Na+ over Zn2+ cations. It is proposed that forming an acidic β-sheet domain and accumulating cations is a plausible molecular mechanism connecting the elevated affinity and concentration of metals in Aβ fibrils to their high content of β-sheet structure at the N-terminal sequence.
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Affiliation(s)
- Carlos Z Gómez-Castro
- Conahcyt-Universidad Autónoma del Estado de Hidalgo, Km 4.5 Carr. Pachuca-Tulancingo, Mineral de La Reforma, 42184, Hidalgo, Mexico.
| | - Liliana Quintanar
- Department of Chemistry, Cinvestav, Av. Instituto Politécnico Nacional 2508, CDMX, San Pedro Zacatenco, 07360, Gustavo A. Madero, Mexico.
| | - Alberto Vela
- Department of Chemistry, Cinvestav, Av. Instituto Politécnico Nacional 2508, CDMX, San Pedro Zacatenco, 07360, Gustavo A. Madero, Mexico.
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16
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Zhao X, Li Y, Li Z, Hu D, Zhang R, Li M, Liu Y, Xiu X, Jia H, Wang H, Liu Y, Yang H, Cheng M. Design and synthesis of hemicyanine-based NIRF probe for detecting Aβ aggregates in Alzheimer's disease. Bioorg Chem 2024; 150:107514. [PMID: 38870704 DOI: 10.1016/j.bioorg.2024.107514] [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: 04/01/2024] [Revised: 05/10/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024]
Abstract
Alzheimer's disease (AD), a progressive neurodegenerative disorder, has garnered increased attention due to its substantial economic burden and the escalating global aging phenomenon. Amyloid-β deposition is a key pathogenic marker observed in the brains of Alzheimer's sufferers. Based on real-time, safe, low-cost, and commonly used, near-infrared fluorescence (NIRF) imaging technology have become an essential technique for the detection of AD in recent years. In this work, NIRF probes with hemicyanine structure were designed, synthesized and evaluated for imaging Aβ aggregates in the brain. We use the hemicyanine structure as the parent nucleus to enhance the probe's optical properties. The introduction of PEG chain is to improve the probe's brain dynamice properties, and the alkyl chain on the N atom is to enhance the fluorescence intensity of the probe after binding to the Aβ aggregates as much as possible. Among these probes, Z2, Z3, Z6, X3, X6 and T1 showed excellent optical properties and high affinity to Aβ aggregates (Kd = 24.31 ∼ 59.60 nM). In vitro brain section staining and in vivo NIRF imaging demonstrated that X6 exhibited superior discrimination between Tg mice and WT mice, and X6 has the best brain clearance rate. As a result, X6 was identified as the optimal probe. Furthermore, the docking theory calculation results aided in describing X6's binding behavior with Aβ aggregates. As a high-affinity, high-selectivity, safe and effective probe of targeting Aβ aggregates, X6 is a promising NIRF probe for in vivo detection of Aβ aggregates in the AD brain.
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Affiliation(s)
- Xueqi Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Yingbo Li
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Zhenli Li
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Dexiang Hu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Ruiwen Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Mengzhen Li
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Yaoyang Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Xiaomeng Xiu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Hongwei Jia
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China
| | - Yang Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China.
| | - Huali Yang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China.
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning, Shenyang 110016, China.
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17
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Todd TW, Islam NN, Cook CN, Caulfield TR, Petrucelli L. Cryo-EM structures of pathogenic fibrils and their impact on neurodegenerative disease research. Neuron 2024:S0896-6273(24)00359-3. [PMID: 38834068 DOI: 10.1016/j.neuron.2024.05.012] [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: 08/22/2023] [Revised: 03/13/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024]
Abstract
Neurodegenerative diseases are commonly associated with the formation of aberrant protein aggregates within the brain, and ultrastructural analyses have revealed that the proteins within these inclusions often assemble into amyloid filaments. Cryoelectron microscopy (cryo-EM) has emerged as an effective method for determining the near-atomic structure of these disease-associated filamentous proteins, and the resulting structures have revolutionized the way we think about aberrant protein aggregation and propagation during disease progression. These structures have also revealed that individual fibril conformations may dictate different disease conditions, and this newfound knowledge has improved disease modeling in the lab and advanced the ongoing pursuit of clinical tools capable of distinguishing and targeting different pathogenic entities within living patients. In this review, we summarize some of the recently developed cryo-EM structures of ex vivo α-synuclein, tau, β-amyloid (Aβ), TAR DNA-binding protein 43 (TDP-43), and transmembrane protein 106B (TMEM106B) fibrils and discuss how these structures are being leveraged toward mechanistic research and therapeutic development.
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Affiliation(s)
- Tiffany W Todd
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Naeyma N Islam
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Casey N Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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18
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Golota NC, Michael B, Saliba EP, Linse S, Griffin RG. Structural characterization of E22G Aβ 1-42 fibrils via1H detected MAS NMR. Phys Chem Chem Phys 2024; 26:14664-14674. [PMID: 38715538 PMCID: PMC11110645 DOI: 10.1039/d4cp00553h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
Amyloid fibrils have been implicated in the pathogenesis of several neurodegenerative diseases, the most prevalent example being Alzheimer's disease (AD). Despite the prevalence of AD, relatively little is known about the structure of the associated amyloid fibrils. This has motivated our studies of fibril structures, extended here to the familial Arctic mutant of Aβ1-42, E22G-Aβ1-42. We found E22G-AβM0,1-42 is toxic to Escherichia coli, thus we expressed E22G-Aβ1-42 fused to the self-cleavable tag NPro in the form of its EDDIE mutant. Since the high surface activity of E22G-Aβ1-42 makes it difficult to obtain more than sparse quantities of fibrils, we employed 1H detected magic angle spinning (MAS) nuclear magnetic resonance (NMR) experiments to characterize the protein. The 1H detected 13C-13C methods were first validated by application to fully protonated amyloidogenic nanocrystals of GNNQQNY, and then applied to fibrils of the Arctic mutant of Aβ, E22G-Aβ1-42. The MAS NMR spectra indicate that the biosynthetic samples of E22G-Aβ1-42 fibrils comprise a single conformation with 13C chemical shifts extracted from hCH, hNH, and hCCH spectra that are very similar to those of wild type Aβ1-42 fibrils. These results suggest that E22G-Aβ1-42 fibrils have a structure similar to that of wild type Aβ1-42.
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Affiliation(s)
- Natalie C Golota
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Brian Michael
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Edward P Saliba
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sara Linse
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, SE 22100, Sweden
| | - Robert G Griffin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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19
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Cereghetti G, Kissling VM, Koch LM, Arm A, Schmidt CC, Thüringer Y, Zamboni N, Afanasyev P, Linsenmeier M, Eichmann C, Kroschwald S, Zhou J, Cao Y, Pfizenmaier DM, Wiegand T, Cadalbert R, Gupta G, Boehringer D, Knowles TPJ, Mezzenga R, Arosio P, Riek R, Peter M. An evolutionarily conserved mechanism controls reversible amyloids of pyruvate kinase via pH-sensing regions. Dev Cell 2024:S1534-5807(24)00271-5. [PMID: 38788715 DOI: 10.1016/j.devcel.2024.04.018] [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: 06/01/2022] [Revised: 10/15/2023] [Accepted: 04/26/2024] [Indexed: 05/26/2024]
Abstract
Amyloids are known as irreversible aggregates associated with neurodegenerative diseases. However, recent evidence shows that a subset of amyloids can form reversibly and fulfill essential cellular functions. Yet, the molecular mechanisms regulating functional amyloids and distinguishing them from pathological aggregates remain unclear. Here, we investigate the conserved principles of amyloid reversibility by studying the essential metabolic enzyme pyruvate kinase (PK) in yeast and human cells. We demonstrate that yeast PK (Cdc19) and human PK (PKM2) form reversible amyloids through a pH-sensitive amyloid core. Stress-induced cytosolic acidification promotes aggregation via protonation of specific glutamate (yeast) or histidine (human) residues within the amyloid core. Mutations mimicking protonation cause constitutive PK aggregation, while non-protonatable PK mutants remain soluble even upon stress. Physiological PK aggregation is coupled to metabolic rewiring and glycolysis arrest, causing severe growth defects when misregulated. Our work thus identifies an evolutionarily conserved, potentially widespread mechanism regulating functional amyloids during stress.
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Affiliation(s)
- Gea Cereghetti
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland; Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK.
| | - Vera M Kissling
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland; Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Empa, 9014 St. Gallen, Switzerland
| | - Lisa M Koch
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Alexandra Arm
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Claudia C Schmidt
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Yannik Thüringer
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub (CEMK), ETH Zurich, 8093 Zürich, Switzerland
| | - Miriam Linsenmeier
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Cédric Eichmann
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Sonja Kroschwald
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Jiangtao Zhou
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Yiping Cao
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Dorota M Pfizenmaier
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Thomas Wiegand
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland; Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Govind Gupta
- Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Empa, 9014 St. Gallen, Switzerland
| | | | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Raffaele Mezzenga
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Paolo Arosio
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
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20
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Parvin F, Haglund S, Wegenast-Braun B, Jucker M, Saito T, Saido TC, Nilsson KPR, Nilsson P, Nyström S, Hammarström P. Divergent Age-Dependent Conformational Rearrangement within Aβ Amyloid Deposits in APP23, APPPS1, and AppNL-F Mice. ACS Chem Neurosci 2024; 15:2058-2069. [PMID: 38652895 PMCID: PMC11099915 DOI: 10.1021/acschemneuro.4c00104] [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: 02/14/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Amyloid plaques composed of fibrils of misfolded Aβ peptides are pathological hallmarks of Alzheimer's disease (AD). Aβ fibrils are polymorphic in their tertiary and quaternary molecular structures. This structural polymorphism may carry different pathologic potencies and can putatively contribute to clinical phenotypes of AD. Therefore, mapping of structural polymorphism of Aβ fibrils and structural evolution over time is valuable to understanding disease mechanisms. Here, we investigated how Aβ fibril structures in situ differ in Aβ plaque of different mouse models expressing familial mutations in the AβPP gene. We imaged frozen brains with a combination of conformation-sensitive luminescent conjugated oligothiophene (LCO) ligands and Aβ-specific antibodies. LCO fluorescence mapping revealed that mouse models APP23, APPPS1, and AppNL-F have different fibril structures within Aβ-amyloid plaques depending on the AβPP-processing genotype. Co-staining with Aβ-specific antibodies showed that individual plaques from APP23 mice expressing AβPP Swedish mutation have two distinct fibril polymorph regions of core and corona. The plaque core is predominantly composed of compact Aβ40 fibrils, and the corona region is dominated by diffusely packed Aβ40 fibrils. Conversely, the AβPP knock-in mouse AppNL-F, expressing the AβPP Iberian mutation along with Swedish mutation has tiny, cored plaques consisting mainly of compact Aβ42 fibrils, vastly different from APP23 even at elevated age up to 21 months. Age-dependent polymorph rearrangement of plaque cores observed for APP23 and APPPS1 mice >12 months, appears strongly promoted by Aβ40 and was hence minuscule in AppNL-F. These structural studies of amyloid plaques in situ can map disease-relevant fibril polymorph distributions to guide the design of diagnostic and therapeutic molecules.
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Affiliation(s)
- Farjana Parvin
- Department
of Physics, Chemistry and Biology (IFM), Linköping University, 58183 Linköping, Sweden
| | - Samuel Haglund
- Department
of Physics, Chemistry and Biology (IFM), Linköping University, 58183 Linköping, Sweden
| | - Bettina Wegenast-Braun
- German
Center for Neurodegenerative Diseases (DZNE), University of Tübingen, 72076 Tübingen, Germany
- Hertie
Institute for Clinical Brain Research, University
of Tübingen, 72076 Tübingen, Germany
| | - Mathias Jucker
- German
Center for Neurodegenerative Diseases (DZNE), University of Tübingen, 72076 Tübingen, Germany
- Hertie
Institute for Clinical Brain Research, University
of Tübingen, 72076 Tübingen, Germany
| | - Takashi Saito
- Laboratory
for Proteolytic Neuroscience, RIKEN Center
for Brain Science, Wako 351-0198, Saitama, Japan
- Department
of Neurocognitive Science, Nagoya City University
Graduate School of Medical Sciences, Nagoya 467-8601, Aichi, Japan
| | - Takaomi C. Saido
- Laboratory
for Proteolytic Neuroscience, RIKEN Center
for Brain Science, Wako 351-0198, Saitama, Japan
| | - K. Peter R. Nilsson
- Department
of Physics, Chemistry and Biology (IFM), Linköping University, 58183 Linköping, Sweden
| | - Per Nilsson
- Department
of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 17177 Solna, Sweden
| | - Sofie Nyström
- Department
of Physics, Chemistry and Biology (IFM), Linköping University, 58183 Linköping, Sweden
| | - Per Hammarström
- Department
of Physics, Chemistry and Biology (IFM), Linköping University, 58183 Linköping, Sweden
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21
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Dong Q, Cui Z, Wu X, Li L, Lu F, Liu F. Natural flavonoid hesperetin blocks amyloid β-protein fibrillogenesis, depolymerizes preformed fibrils and alleviates cytotoxicity caused by amyloids. Food Funct 2024; 15:4233-4245. [PMID: 38517352 DOI: 10.1039/d3fo05566c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
The aggregation of β-amyloid (Aβ) peptides to form amyloid plaques is one of the primary hallmarks for Alzheimer's disease (AD). Dietary flavonoid supplements containing hesperetin have an ability to decline the risk of developing AD, but the molecular mechanism is still unclear. In this work, hesperetin, a flavanone abundant in citrus fruits, has been proven to prevent the formation of Aβ aggregates and depolymerized preformed fibrils in a concentration-dependent fashion. Hesperetin inhibited the conformational conversion from the natural structure to a β-sheet-rich conformation. It was found that hesperetin significantly reduced the cytotoxicity and relieved oxidative stress eventuated by Aβ aggregates in a concentration-dependent manner. Additionally, the beneficial effects of hesperetin were confirmed in Caenorhabditis elegans, including the inhibition of the formation and deposition of Aβ aggregates and extension of their lifespan. Finally, the results of molecular dynamics simulations showed that hesperetin directly interacted with an Aβ42 pentamer mainly through strong non-polar and electrostatic interactions, which destroyed the structural stability of the preformed pentamer. To summarize, hesperetin exhibits great potential as a prospective dietary supplement for preventing and improving AD.
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Affiliation(s)
- Qinchen Dong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
| | - Zhan Cui
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
| | - Xinming Wu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
| | - Li Li
- College of Sciences, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
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22
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Bu F, Dee DR, Liu B. Structural insight into Escherichia coli CsgA amyloid fibril assembly. mBio 2024; 15:e0041924. [PMID: 38501920 PMCID: PMC11005368 DOI: 10.1128/mbio.00419-24] [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: 02/09/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
The discovery of functional amyloids in bacteria dates back several decades, and our understanding of the Escherichia coli curli biogenesis system has gradually expanded over time. However, due to its high aggregation propensity and intrinsically disordered nature, CsgA, the main structural component of curli fibrils, has eluded comprehensive structural characterization. Recent advancements in cryo-electron microscopy (cryo-EM) offer a promising tool to achieve high-resolution structural insights into E. coli CsgA fibrils. In this study, we outline an approach to addressing the colloidal instability challenges associated with CsgA, achieved through engineering and electrostatic repulsion. Then, we present the cryo-EM structure of CsgA fibrils at 3.62 Å resolution. This structure provides new insights into the cross-β structure of E. coli CsgA. Additionally, our study identifies two distinct spatial arrangements within several CsgA fibrils, a 2-CsgA-fibril pair and a 3-CsgA-fibril bundle, shedding light on the intricate hierarchy of the biofilm extracellular matrix and laying the foundation for precise manipulation of CsgA-derived biomaterials.IMPORTANCEThe visualization of the architecture of Escherichia coli CsgA amyloid fibril has been a longstanding research question, for which a high-resolution structure is still unavailable. CsgA serves as a major subunit of curli, the primary component of the extracellular matrix generated by bacteria. The support provided by this extracellular matrix enables bacterial biofilms to resist antibiotic treatment, significantly impacting human health. CsgA has been identified in members of Enterobacteriaceae, with pathogenic E. coli being the most well-known model system. Our novel insights into the structure of E. coli CsgA protofilaments form the basis for drug design targeting diseases associated with biofilms. Additionally, CsgA is widely researched in biomaterials due to its self-assembly characteristics. The resolved spatial arrangements of CsgA amyloids revealed in our study will further enhance the precision design of functional biomaterials. Therefore, our study uniquely contributes to the understanding of CsgA amyloids for both microbiology and material science.
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Affiliation(s)
- Fan Bu
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Derek R. Dee
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Bin Liu
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
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23
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Baghel D, de Oliveira AP, Satyarthy S, Chase WE, Banerjee S, Ghosh A. Structural characterization of amyloid aggregates with spatially resolved infrared spectroscopy. Methods Enzymol 2024; 697:113-150. [PMID: 38816120 PMCID: PMC11147165 DOI: 10.1016/bs.mie.2024.02.013] [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] [Indexed: 06/01/2024]
Abstract
The self-assembly of proteins and peptides into ordered structures called amyloid fibrils is a hallmark of numerous diseases, impacting the brain, heart, and other organs. The structure of amyloid aggregates is central to their function and thus has been extensively studied. However, the structural heterogeneities between aggregates as they evolve throughout the aggregation pathway are still not well understood. Conventional biophysical spectroscopic methods are bulk techniques and only report on the average structural parameters. Understanding the structure of individual aggregate species in a heterogeneous ensemble necessitates spatial resolution on the length scale of the aggregates. Recent technological advances have led to augmentation of infrared (IR) spectroscopy with imaging modalities, wherein the photothermal response of the sample upon vibrational excitation is leveraged to provide spatial resolution beyond the diffraction limit. These combined approaches are ideally suited to map out the structural heterogeneity of amyloid ensembles. AFM-IR, which integrates IR spectroscopy with atomic force microscopy enables identification of the structural facets the oligomers and fibrils at individual aggregate level with nanoscale resolution. These capabilities can be extended to chemical mapping in diseased tissue specimens with submicron resolution using optical photothermal microscopy, which combines IR spectroscopy with optical imaging. This book chapter provides the basic premise of these novel techniques and provides the typical methodology for using these approaches for amyloid structure determination. Detailed procedures pertaining to sample preparation and data acquisition and analysis are discussed and the aggregation of the amyloid β peptide is provided as a case study to provide the reader the experimental parameters necessary to use these techniques to complement their research efforts.
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Affiliation(s)
- Divya Baghel
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - Ana Pacheco de Oliveira
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - Saumya Satyarthy
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - William E Chase
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - Siddhartha Banerjee
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - Ayanjeet Ghosh
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States.
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24
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Klingstedt T, Lantz L, Shirani H, Ge J, Hanrieder J, Vidal R, Ghetti B, Nilsson KPR. Thiophene-Based Ligands for Specific Assignment of Distinct Aβ Pathologies in Alzheimer's Disease. ACS Chem Neurosci 2024; 15:1581-1595. [PMID: 38523263 PMCID: PMC10995944 DOI: 10.1021/acschemneuro.4c00021] [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: 01/11/2024] [Revised: 02/12/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024] Open
Abstract
Aggregated species of amyloid-β (Aβ) are one of the pathological hallmarks in Alzheimer's disease (AD), and ligands that selectively target different Aβ deposits are of great interest. In this study, fluorescent thiophene-based ligands have been used to illustrate the features of different types of Aβ deposits found in AD brain tissue. A dual-staining protocol based on two ligands, HS-276 and LL-1, with different photophysical and binding properties, was developed and applied on brain tissue sections from patients affected by sporadic AD or familial AD associated with the PSEN1 A431E mutation. When binding to Aβ deposits, the ligands could easily be distinguished for their different fluorescence, and distinct staining patterns were revealed for these two types of AD. In sporadic AD, HS-276 consistently labeled all immunopositive Aβ plaques, whereas LL-1 mainly stained cored and neuritic Aβ deposits. In the PSEN1 A431E cases, each ligand was binding to specific types of Aβ plaques. The ligand-labeled Aβ deposits were localized in distinct cortical layers, and a laminar staining pattern could be seen. Biochemical characterization of the Aβ aggregates in the individual layers also showed that the variation of ligand binding properties was associated with certain Aβ peptide signatures. For the PSEN1 A431E cases, it was concluded that LL-1 was binding to cotton wool plaques, whereas HS-276 mainly stained diffuse Aβ deposits. Overall, our findings showed that a combination of ligands was essential to identify distinct aggregated Aβ species associated with different forms of AD.
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Affiliation(s)
- Therése Klingstedt
- Department
of Physics, Chemistry and Biology, Linköping
University, Linköping 581 83, Sweden
| | - Linda Lantz
- Department
of Physics, Chemistry and Biology, Linköping
University, Linköping 581 83, Sweden
| | - Hamid Shirani
- Department
of Physics, Chemistry and Biology, Linköping
University, Linköping 581 83, Sweden
| | - Junyue Ge
- Department
of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology,
The Sahlgrenska Academy, University of Gothenburg,
Mölndal Hospital, Mölndal 431 80, Sweden
| | - Jörg Hanrieder
- Department
of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology,
The Sahlgrenska Academy, University of Gothenburg,
Mölndal Hospital, Mölndal 431 80, Sweden
- Department
of Neurodegenerative Diseases, University
College London Institute of Neurology, Queen Square, London WC1N 3BG, United
Kingdom
| | - Ruben Vidal
- Department
of Pathology and Laboratory Medicine, Indiana
University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Bernardino Ghetti
- Department
of Pathology and Laboratory Medicine, Indiana
University School of Medicine, Indianapolis, Indiana 46202, United States
| | - K. Peter R. Nilsson
- Department
of Physics, Chemistry and Biology, Linköping
University, Linköping 581 83, Sweden
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25
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Agha MM, Uversky VN. Morphological features and types of aggregated structures. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:85-109. [PMID: 38811090 DOI: 10.1016/bs.pmbts.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
In vivo, protein aggregation arises due to incorrect folding or misfolding. The aggregation of proteins into amyloid fibrils is the characteristic feature of various misfolding diseases known as amyloidosis, such as Alzheimer's and Parkinson's disease. The heterogeneous nature of these fibrils restricts the extent to which their structure may be characterized. Advancements in techniques, such as X-ray diffraction, cryo-electron microscopy, and solid-state NMR have yielded intricate insights into structures of different amyloid fibrils. These studies have unveiled a diverse range of polymorphic structures that typically conform to the cross-β amyloid pattern. This chapter provides a concise overview of the information acquired in the field of protein aggregation, with particular focus on amyloids.
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Affiliation(s)
- Mansoureh Mirza Agha
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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26
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Balczon R, Lin MT, Voth S, Nelson AR, Schupp JC, Wagener BM, Pittet JF, Stevens T. Lung endothelium, tau, and amyloids in health and disease. Physiol Rev 2024; 104:533-587. [PMID: 37561137 DOI: 10.1152/physrev.00006.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/26/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023] Open
Abstract
Lung endothelia in the arteries, capillaries, and veins are heterogeneous in structure and function. Lung capillaries in particular represent a unique vascular niche, with a thin yet highly restrictive alveolar-capillary barrier that optimizes gas exchange. Capillary endothelium surveys the blood while simultaneously interpreting cues initiated within the alveolus and communicated via immediately adjacent type I and type II epithelial cells, fibroblasts, and pericytes. This cell-cell communication is necessary to coordinate the immune response to lower respiratory tract infection. Recent discoveries identify an important role for the microtubule-associated protein tau that is expressed in lung capillary endothelia in the host-pathogen interaction. This endothelial tau stabilizes microtubules necessary for barrier integrity, yet infection drives production of cytotoxic tau variants that are released into the airways and circulation, where they contribute to end-organ dysfunction. Similarly, beta-amyloid is produced during infection. Beta-amyloid has antimicrobial activity, but during infection it can acquire cytotoxic activity that is deleterious to the host. The production and function of these cytotoxic tau and amyloid variants are the subject of this review. Lung-derived cytotoxic tau and amyloid variants are a recently discovered mechanism of end-organ dysfunction, including neurocognitive dysfunction, during and in the aftermath of infection.
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Affiliation(s)
- Ron Balczon
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, United States
- Center for Lung Biology, University of South Alabama, Mobile, Alabama, United States
| | - Mike T Lin
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama, United States
- Center for Lung Biology, University of South Alabama, Mobile, Alabama, United States
| | - Sarah Voth
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine, Monroe, Louisiana, United States
| | - Amy R Nelson
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama, United States
- Center for Lung Biology, University of South Alabama, Mobile, Alabama, United States
| | - Jonas C Schupp
- Pulmonary and Critical Care Medicine, Department of Internal Medicine, Yale University, New Haven, Connecticut, United States
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
- German Center for Lung Research (DZL), Hannover, Germany
| | - Brant M Wagener
- Department of Anesthesiology and Perioperative Medicine, University of Alabama-Birmingham, Birmingham, Alabama, United States
| | - Jean-Francois Pittet
- Department of Anesthesiology and Perioperative Medicine, University of Alabama-Birmingham, Birmingham, Alabama, United States
| | - Troy Stevens
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama, United States
- Department of Internal Medicine, University of South Alabama, Mobile, Alabama, United States
- Center for Lung Biology, University of South Alabama, Mobile, Alabama, United States
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27
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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28
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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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29
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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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30
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Sahtoe DD, Andrzejewska EA, Han HL, Rennella E, Schneider MM, Meisl G, Ahlrichs M, Decarreau J, Nguyen H, Kang A, Levine P, Lamb M, Li X, Bera AK, Kay LE, Knowles TPJ, Baker D. Design of amyloidogenic peptide traps. Nat Chem Biol 2024:10.1038/s41589-024-01578-5. [PMID: 38503834 DOI: 10.1038/s41589-024-01578-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 02/09/2024] [Indexed: 03/21/2024]
Abstract
Segments of proteins with high β-strand propensity can self-associate to form amyloid fibrils implicated in many diseases. We describe a general approach to bind such segments in β-strand and β-hairpin conformations using de novo designed scaffolds that contain deep peptide-binding clefts. The designs bind their cognate peptides in vitro with nanomolar affinities. The crystal structure of a designed protein-peptide complex is close to the design model, and NMR characterization reveals how the peptide-binding cleft is protected in the apo state. We use the approach to design binders to the amyloid-forming proteins transthyretin, tau, serum amyloid A1 and amyloid β1-42 (Aβ42). The Aβ binders block the assembly of Aβ fibrils as effectively as the most potent of the clinically tested antibodies to date and protect cells from toxic Aβ42 species.
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Affiliation(s)
- Danny D Sahtoe
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- HHMI, University of Washington, Seattle, WA, USA.
- Hubrecht Institute, Utrecht, the Netherlands.
| | - Ewa A Andrzejewska
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannah L Han
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Enrico Rennella
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Maggie Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Paul Levine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- HHMI, University of Washington, Seattle, WA, USA.
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31
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Banerjee S, Baghel D, Edmonds HO, Ghosh A. Heterotypic Seeding Generates Mixed Amyloid Polymorphs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585264. [PMID: 38559069 PMCID: PMC10980072 DOI: 10.1101/2024.03.15.585264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Aggregation of the amyloid β (Aβ) peptide into fibrils represents one of the major biochemical pathways underlying the development of Alzheimer's disease (AD). Extensive studies have been carried out to understand the role of fibrillar seeds on the overall kinetics of amyloid aggregation. However, the precise effect of seeds that are structurally or sequentially different from Aβ on the structure of the resulting amyloid aggregates is yet to be fully understood. In this work, we use nanoscale infrared spectroscopy to probe the spectral facets of individual aggregates formed by aggregating Aβ42 with antiparallel fibrillar seeds of Aβ (16-22) and E22Q Aβ (1-40) Dutch mutant and demonstrate that Aβ can form heterotypic or mixed polymorphs that deviate significantly from its expected parallel cross β structure. We further show that formation of heterotypic aggregates is not limited to coaggregation of Aβ and its isomers, and that the former can form heterotypic fibrils with alpha synuclein and brain protein lysates. These findings highlight the complexity of Aβ aggregation in AD and underscore the need to explore how Aβ interacts with other brain components, which is crucial for developing better therapeutic strategies for AD.
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Affiliation(s)
- S. Banerjee
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - D. Baghel
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - H. O. Edmonds
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Ayanjeet Ghosh
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
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32
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Shi Y, Sun Y, Li C, Wang S, Wang J, Shi H. Edge Substitution Effects of Histidine Tautomerization Behaviors on the Structural Properties and Aggregation Properties of Aβ(1-42) Mature Fibril. ACS Chem Neurosci 2024; 15:1055-1062. [PMID: 38379141 DOI: 10.1021/acschemneuro.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Histidine behaviors play critical roles in folding and misfolding processes due to the changes in net charge and the various N/N-H orientations on imidazole rings. However, the effect of histidine tautomerization (HIE (Nε-H, ε) and HID (Nδ-H, δ) states) behaviors on the edge chain of Aβ mature fibrils remains inadequately understood, which is critical for finding a strategy to disturb fibril elongation and growth. In the current study, eight independent molecular dynamics simulations were conducted to investigate such impacts on the structural and aggregation properties. Our results from three different binding models revealed that the binding contributions of edge substitution effects are primarily located between chains 1 and 2. Histidine states significantly influence the secondary structure of each domain. Further analysis confirmed that the C1_H6//C1_E11 intrachain interaction is essential in maintaining the internal stability of chain 1, while the C1_H13//C2_H13 and C1_H14//C2_H13 interchain interactions are critical in maintaining the interchain stability of the fibril structure. Our subsequent analysis revealed that the current edge substitution leads to the loss of the C1_H13//C1_E11 intrachain and C1_H13//C2_H14 interchain interactions. The N-terminal regularity was significantly directly influenced by histidine states, particularly by the residue of C1_H13. Our study provides valuable insights into the effect of histidine behaviors on the edge chain of Aβ mature fibril, advancing our understanding of the histidine behavior hypothesis in misfolding diseases.
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Affiliation(s)
- Yaru Shi
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Yue Sun
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Changgui Li
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Shuo Wang
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Jinping Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan 250022, Shandong, China
| | - Hu Shi
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
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33
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Ali A, Dou T, Holman AP, Hung A, Osborne L, Pickett D, Rodriguez A, Zhaliazka K, Kurouski D. The influence of zwitterionic and anionic phospholipids on protein aggregation. Biophys Chem 2024; 306:107174. [PMID: 38211368 DOI: 10.1016/j.bpc.2024.107174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
The progressive aggregation of misfolded proteins is the underlying molecular cause of numerous pathologies including Parkinson's disease and injection and transthyretin amyloidosis. A growing body of evidence indicates that protein deposits detected in organs and tissues of patients diagnosed with such pathologies contain fragments of lipid membranes. In vitro experiments also showed that lipid membranes could strongly change the aggregation rate of amyloidogenic proteins, as well as alter the secondary structure and toxicity of oligomers and fibrils formed in their presence. In this review, the effect of large unilamellar vesicles (LUVs) composed of zwitterionic and anionic phospholipids on the aggregation rate of insulin, lysozyme, transthyretin (TTR) and α- synuclein (α-syn) will be discussed. The manuscript will also critically review the most recent findings on the lipid-induced changes in the secondary structure of protein oligomers and fibrils, as well as reveal the extent to which lipids could alter the toxicity of protein aggregates formed in their presence.
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Affiliation(s)
- Abid Ali
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Tianyi Dou
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Aidan P Holman
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States; Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Andrew Hung
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Luke Osborne
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Davis Pickett
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Axell Rodriguez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Kiryl Zhaliazka
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States; Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, United States.
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34
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Meisl G. The thermodynamics of neurodegenerative disease. BIOPHYSICS REVIEWS 2024; 5:011303. [PMID: 38525484 PMCID: PMC10957229 DOI: 10.1063/5.0180899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024]
Abstract
The formation of protein aggregates in the brain is a central aspect of the pathology of many neurodegenerative diseases. This self-assembly of specific proteins into filamentous aggregates, or fibrils, is a fundamental biophysical process that can easily be reproduced in the test tube. However, it has been difficult to obtain a clear picture of how the biophysical insights thus obtained can be applied to the complex, multi-factorial diseases and what this means for therapeutic strategies. While new, disease-modifying therapies are now emerging, for the most devastating disorders, such as Alzheimer's and Parkinson's disease, they still fall well short of offering a cure, and few drug design approaches fully exploit the wealth of mechanistic insights that has been obtained in biophysical studies. Here, I attempt to provide a new perspective on the role of protein aggregation in disease, by phrasing the problem in terms of a system that, under constant energy consumption, attempts to maintain a healthy, aggregate-free state against the thermodynamic driving forces that inexorably push it toward pathological aggregation.
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Affiliation(s)
- Georg Meisl
- WaveBreak Therapeutics Ltd., Chemistry of Health, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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35
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Nam Y, Prajapati R, Kim S, Shin SJ, Cheong DY, Park YH, Park HH, Lim D, Yoon Y, Lee G, Jung HA, Park I, Kim DH, Choi JS, Moon M. Dual regulatory effects of neferine on amyloid-β and tau aggregation studied by in silico, in vitro, and lab-on-a-chip technology. Biomed Pharmacother 2024; 172:116226. [PMID: 38301421 DOI: 10.1016/j.biopha.2024.116226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/15/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024] Open
Abstract
Alzheimer's disease (AD) is characterized by the presence of two critical pathogenic factors: amyloid-β (Aβ) and tau. Aβ and tau become neurotoxic aggregates via self-assembly, and these aggregates contribute to the pathogenesis of AD. Therefore, there has been growing interest in therapeutic strategies that simultaneously target Aβ and tau aggregates. Although neferine has attracted attention as a suitable candidate agent for alleviating AD pathology, there has been no study investigating whether neferine affects the modulation of Aβ or tau aggregation/dissociation. Herein, we investigated the dual regulatory effects of neferine on Aβ and tau aggregation/dissociation. We predicted the binding characteristics of neferine to Aβ and tau using molecular docking simulations. Next, thioflavin T and atomic force microscope analyses were used to evaluate the effects of neferine on the aggregation or dissociation of Aβ42 and tau K18. We verified the effect of neferine on Aβ fibril degradation using a microfluidic device. In addition, molecular dynamics simulation was used to predict a conformational change in the Aβ42-neferine complex. Moreover, we examined the neuroprotective effect of neferine against neurotoxicity induced by Aβ and tau and their fibrils in HT22 cells. Finally, we foresaw the pharmacokinetic properties of neferine. These results demonstrated that neferine, which has attracted attention as a potential treatment for AD, can directly affect Aβ and tau pathology.
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Affiliation(s)
- Yunkwon Nam
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Ritu Prajapati
- Department of Food and Life Science, Pukyong National University, Busan 48513, Republic of Korea
| | - Sujin Kim
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea; Research Institute for Dementia Science, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Soo Jung Shin
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Da Yeon Cheong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea
| | - Yong Ho Park
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Hyun Ha Park
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Danyou Lim
- Department of Biomedical Engineering, Konyang University, Daejeon 35365, Republic of Korea
| | - Yoojeong Yoon
- Department of Biomedical Engineering, Konyang University, Daejeon 35365, Republic of Korea
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea
| | - Hyun Ah Jung
- Department of Food Science and Human Nutrition, Chonbuk National University, Jeonju 54896, Republic of Korea
| | - Insu Park
- Department of Biomedical Engineering, Konyang University, Daejeon 35365, Republic of Korea.
| | - Dong-Hyun Kim
- Departments of Pharmacology and Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea.
| | - Jae Sue Choi
- Department of Food and Life Science, Pukyong National University, Busan 48513, Republic of Korea.
| | - Minho Moon
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea; Research Institute for Dementia Science, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea.
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36
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Steger G, Riesner D, Prusiner SB. Viroids, Satellite RNAs and Prions: Folding of Nucleic Acids and Misfolding of Proteins. Viruses 2024; 16:360. [PMID: 38543726 PMCID: PMC10975798 DOI: 10.3390/v16030360] [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: 01/20/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 05/23/2024] Open
Abstract
Theodor ("Ted") Otto Diener (* 28 February 1921 in Zürich, Switzerland; † 28 March 2023 in Beltsville, MD, USA) pioneered research on viroids while working at the Plant Virology Laboratory, Agricultural Research Service, USDA, in Beltsville. He coined the name viroid and defined viroids' important features like the infectivity of naked single-stranded RNA without protein-coding capacity. During scientific meetings in the 1970s and 1980s, viroids were often discussed at conferences together with other "subviral pathogens". This term includes what are now called satellite RNAs and prions. Satellite RNAs depend on a helper virus and have linear or, in the case of virusoids, circular RNA genomes. Prions, proteinaceous infectious particles, are the agents of scrapie, kuru and some other diseases. Many satellite RNAs, like viroids, are non-coding and exert their function by thermodynamically or kinetically controlled folding, while prions are solely host-encoded proteins that cause disease by misfolding, aggregation and transmission of their conformations into infectious prion isoforms. In this memorial, we will recall the work of Ted Diener on subviral pathogens.
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Affiliation(s)
- Gerhard Steger
- Institut für Physikalische Biologie, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany;
| | - Detlev Riesner
- Institut für Physikalische Biologie, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany;
| | - Stanley B. Prusiner
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA;
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
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37
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Andrikopoulos N, Tang H, Wang Y, Liang X, Li Y, Davis TP, Ke PC. Exploring Peptido-Nanocomposites in the Context of Amyloid Diseases. Angew Chem Int Ed Engl 2024; 63:e202309958. [PMID: 37943171 DOI: 10.1002/anie.202309958] [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: 07/12/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/10/2023]
Abstract
Therapeutic peptides are a major class of pharmaceutical drugs owing to their target-binding specificity as well as their versatility in inhibiting aberrant protein-protein interactions associated with human pathologies. Within the realm of amyloid diseases, the use of peptides and peptidomimetics tailor-designed to overcome amyloidogenesis has been an active research endeavor since the late 90s. In more recent years, incorporating nanoparticles for enhancing the biocirculation and delivery of peptide drugs has emerged as a frontier in nanomedicine, and nanoparticles have further demonstrated a potency against amyloid aggregation and cellular inflammation to rival strategies employing small molecules, peptides, and antibodies. Despite these efforts, however, a fundamental understanding of the chemistry, characteristics and function of peptido-nanocomposites is lacking, and a systematic analysis of such strategy for combating a range of amyloid pathogeneses is missing. Here we review the history, principles and evolving chemistry of constructing peptido-nanocomposites from bottom up and discuss their future application against amyloid diseases that debilitate a significant portion of the global population.
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Affiliation(s)
- Nicholas Andrikopoulos
- 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
| | - Huayuan Tang
- College of Mechanics and Materials, Hohai University, Nanjing, 211100, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Yue Wang
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou 510006, China
| | - Xiufang Liang
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou 510006, China
| | - Yuhuan Li
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, China
| | - Thomas P Davis
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Pu Chun Ke
- 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
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
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38
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Tian Y, Shang Q, Liang R, Viles JH. Copper(II) Can Kinetically Trap Arctic and Italian Amyloid-β 40 as Toxic Oligomers, Mimicking Cu(II) Binding to Wild-Type Amyloid-β 42: Implications for Familial Alzheimer's Disease. JACS AU 2024; 4:578-591. [PMID: 38425915 PMCID: PMC10900208 DOI: 10.1021/jacsau.3c00687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 03/02/2024]
Abstract
The self-association of amyloid-β (Aβ) peptide into neurotoxic oligomers is believed to be central to Alzheimer's disease (AD). Copper is known to impact Aβ assembly, while disrupted copper homeostasis impacts phenotype in Alzheimer's models. Here we show the presence of substoichiometric Cu(II) has very different impacts on the assembly of Aβ40 and Aβ42 isoforms. Globally fitting microscopic rate constants for fibril assembly indicates copper will accelerate fibril formation of Aβ40 by increasing primary nucleation, while seeding experiments confirm that elongation and secondary nucleation rates are unaffected by Cu(II). In marked contrast, Cu(II) traps Aβ42 as prefibrillar oligomers and curvilinear protofibrils. Remarkably, the Cu(II) addition to preformed Aβ42 fibrils causes the disassembly of fibrils back to protofibrils and oligomers. The very different behaviors of the two Aβ isoforms are centered around differences in their fibril structures, as highlighted by studies of C-terminally amidated Aβ42. Arctic and Italian familiar mutations also support a key role for fibril structure in the interplay of Cu(II) with Aβ40/42 isoforms. The Cu(II) dependent switch in behavior between nonpathogenic Aβ40 wild-type and Aβ40 Arctic or Italian mutants suggests heightened neurotoxicity may be linked to the impact of physiological Cu(II), which traps these familial mutants as oligomers and curvilinear protofibrils, which cause membrane permeability and Ca(II) cellular influx.
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Affiliation(s)
- Yao Tian
- School of Biological and Behavioral
Sciences, Queen Mary University of London, London E1 4NS, U.K.
| | - Qi Shang
- School of Biological and Behavioral
Sciences, Queen Mary University of London, London E1 4NS, U.K.
| | - Ruina Liang
- School of Biological and Behavioral
Sciences, Queen Mary University of London, London E1 4NS, U.K.
| | - John H. Viles
- School of Biological and Behavioral
Sciences, Queen Mary University of London, London E1 4NS, U.K.
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39
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Scheidt HA, Korn A, Schwarze B, Krueger M, Huster D. Conformation of Pyroglutamated Amyloid β (3-40) and (11-40) Fibrils - Extended or Hairpin? J Phys Chem B 2024; 128:1647-1655. [PMID: 38334278 PMCID: PMC10895672 DOI: 10.1021/acs.jpcb.3c07285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/04/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Amyloid β (Aβ) is a hallmark protein of Alzheimer's disease. One physiologically important Aβ variant is formed by initial N-terminal truncation at a glutamic acid position (either E3 or E11), which is subsequently cyclized to a pyroglutamate (either pE3 or pE11). Both forms have been found in high concentrations in the core of amyloid plaques and are likely of high importance in the pathology of Alzheimer's disease. However, the molecular structure of the fibrils of these variants is not entirely clear. Solid-state NMR spectroscopy studies have reported a molecular contact between Gly25 and Ile31, which would disagree with the conventional hairpin model of wildtype (WT-)Aβ1-40 fibrils, most often described in the literature. We investigated the conformation of the monomeric unit of pE3-Aβ3-40 and pE11-Aβ11-40 (and for comparison also wildtype (WT)-Aβ1-40) fibrils to find out whether the hairpin or a newly suggested extended structure dominates the structure of the Aβ monomers in these fibrils. To this end, solid-state NMR spectroscopy was applied probing the inter-residual contacts between Phe19/Leu34, Ala21/Leu34, and especially Gly25/Ile31 using suitable isotopic labeling schemes. In the second part, the flexible turn of the Aβ40 peptides was replaced by a (3-(3-aminomethyl)phenylazo)phenylacetic acid (AMPP)-based photoswitch, which can predefine the peptide conformation to either an extended (trans) or hairpin (cis) conformation. This enables simultaneous spectroscopic assessment of the conformation of the AMPP-photoswitch, allowing in situ structural investigations during fibrillation in contrast to structural techniques such as NMR spectroscopy or cryo-EM, which can only be applied to stable conformers. Both methods confirm an extended structure for the peptidic monomers in fibrils of all investigated Aβ variants. Especially the Gly25/Ile31 contact is a decisive indicator for the extended structure along with the characteristic absorption spectra of trans-AMPP-Aβ.
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Affiliation(s)
- Holger A. Scheidt
- Institute
for Medical Physics and Biophysics, Leipzig
University Härtelstr. 16/18, D-04107 Leipzig, Germany
| | - Alexander Korn
- Institute
for Medical Physics and Biophysics, Leipzig
University Härtelstr. 16/18, D-04107 Leipzig, Germany
| | - Benedikt Schwarze
- Institute
for Medical Physics and Biophysics, Leipzig
University Härtelstr. 16/18, D-04107 Leipzig, Germany
| | - Martin Krueger
- Institute
of Anatomy, Leipzig University, Liebigstr. 13, 04103 Leipzig, Germany
| | - Daniel Huster
- Institute
for Medical Physics and Biophysics, Leipzig
University Härtelstr. 16/18, D-04107 Leipzig, Germany
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40
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Thurber KR, Yau WM, Tycko R. Structure of Amyloid Peptide Ribbons Characterized by Electron Microscopy, Atomic Force Microscopy, and Solid-State Nuclear Magnetic Resonance. J Phys Chem B 2024; 128:1711-1723. [PMID: 38348474 DOI: 10.1021/acs.jpcb.3c07867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Polypeptides often self-assemble to form amyloid fibrils, which contain cross-β structural motifs and are typically 5-15 nm in width and micrometers in length. In many cases, short segments of longer amyloid-forming protein or peptide sequences also form cross-β assemblies but with distinctive ribbon-like morphologies that are characterized by a well-defined thickness (on the order of 5 nm) in one lateral dimension and a variable width (typically 10-100 nm) in the other. Here, we use a novel combination of data from solid-state nuclear magnetic resonance (ssNMR), dark-field transmission electron microscopy (TEM), atomic force microscopy (AFM), and cryogenic electron microscopy (cryoEM) to investigate the structures within amyloid ribbons formed by residues 14-23 and residues 11-25 of the Alzheimer's disease-associated amyloid-β peptide (Aβ14-23 and Aβ11-25). The ssNMR data indicate antiparallel β-sheets with specific registries of intermolecular hydrogen bonds. Mass-per-area values are derived from dark-field TEM data. The ribbon thickness is determined from AFM images. For Aβ14-23 ribbons, averaged cryoEM images show a periodic spacing of β-sheets. The combined data support structures in which the amyloid ribbon growth direction is the direction of intermolecular hydrogen bonds between β-strands, the ribbon thickness corresponds to the width of one β-sheet (i.e., approximately the length of one molecule), and the variable ribbon width is a variable multiple of the thickness of one β-sheet (i.e., a multiple of the repeat distance in a stack of β-sheets). This architecture for a cross-β assembly may generally exist within amyloid ribbons.
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Affiliation(s)
- Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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41
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [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: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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42
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Gardon L, Becker N, Gremer L, Heise H. Structural Impact of N-terminal Pyroglutamate in an Amyloid-β(3-42) Fibril Probed by Solid-State NMR Spectroscopy. Chemistry 2024; 30:e202303007. [PMID: 38100216 DOI: 10.1002/chem.202303007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Indexed: 12/31/2023]
Abstract
Extracellular amyloid-β (Aβ) plaques, primarily formed by Aβ(1-40) and Aβ(1-42) fibrils, are a hallmark of Alzheimer's disease. The Aβ peptide can undergo a high variety of different post-translational modifications including formation of a pyroglutamate (pGlu, pE) at N-terminal Glu3 or Glu11 of truncated Aβ(3-x) or Aβ(11-x), respectively. Here we studied structural similarities and differences between pEAβ(3-42) and LS-shaped Aβ(1-42) fibrils grown under identical conditions (pH 2) using solid-state NMR spectroscopy. We show that the central region of pEAβ(3-42) fibrils including the turn region around V24 is almost identical to Aβ(1-42) showing similar β-strands also at the N-terminus. The missing N-terminal residues D1-A2 along with pE3 formation in pEAβ(3-42) preclude a salt bridge between K28-D1' as in Aβ(1-42) fibrils. G37 and G38 act as highly sensitive internal sensors for the modified N-terminus, which remains rigid over ~five pH units.
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Affiliation(s)
- Luis Gardon
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf, Germany
| | - Nina Becker
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf, Germany
| | - Lothar Gremer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf, Germany
| | - Henrike Heise
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf, Germany
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43
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Frieg B, Han M, Giller K, Dienemann C, Riedel D, Becker S, Andreas LB, Griesinger C, Schröder GF. Cryo-EM structures of lipidic fibrils of amyloid-β (1-40). Nat Commun 2024; 15:1297. [PMID: 38351005 PMCID: PMC10864299 DOI: 10.1038/s41467-023-43822-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/21/2023] [Indexed: 02/16/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive and incurable neurodegenerative disease characterized by the extracellular deposition of amyloid plaques. Investigation into the composition of these plaques revealed a high amount of amyloid-β (Aβ) fibrils and a high concentration of lipids, suggesting that fibril-lipid interactions may also be relevant for the pathogenesis of AD. Therefore, we grew Aβ40 fibrils in the presence of lipid vesicles and determined their structure by cryo-electron microscopy (cryo-EM) to high resolution. The fold of the major polymorph is similar to the structure of brain-seeded fibrils reported previously. The majority of the lipids are bound to the fibrils, as we show by cryo-EM and NMR spectroscopy. This apparent lipid extraction from vesicles observed here in vitro provides structural insights into potentially disease-relevant fibril-lipid interactions.
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Affiliation(s)
- Benedikt Frieg
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Mookyoung Han
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Dietmar Riedel
- Laboratory of Electron Microscopy, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Loren B Andreas
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - Gunnar F Schröder
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany.
- Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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44
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An J, Kim K, Lim HJ, Kim HY, Shin J, Park I, Cho I, Kim HY, Kim S, McLean C, Choi KY, Kim Y, Lee KH, Kim JS. Early onset diagnosis in Alzheimer's disease patients via amyloid-β oligomers-sensing probe in cerebrospinal fluid. Nat Commun 2024; 15:1004. [PMID: 38307843 PMCID: PMC10837422 DOI: 10.1038/s41467-024-44818-x] [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: 03/20/2023] [Accepted: 01/05/2024] [Indexed: 02/04/2024] Open
Abstract
Amyloid-β (Aβ) oligomers are implicated in the onset of Alzheimer's disease (AD). Herein, quinoline-derived half-curcumin-dioxaborine (Q-OB) fluorescent probe was designed for detecting Aβ oligomers by finely tailoring the hydrophobicity of the biannulate donor motifs in donor-π-acceptor structure. Q-OB shows a great sensing potency in dynamically monitoring oligomerization of Aβ during amyloid fibrillogenesis in vitro. In addition, we applied this strategy to fluorometrically analyze Aβ self-assembly kinetics in the cerebrospinal fluids (CSF) of AD patients. The fluorescence intensity of Q-OB in AD patients' CSF revealed a marked change of log (I/I0) value of 0.34 ± 0.13 (cognitive normal), 0.15 ± 0.12 (mild cognitive impairment), and 0.14 ± 0.10 (AD dementia), guiding to distinguish a state of AD continuum for early diagnosis of AD. These studies demonstrate the potential of our approach can expand the currently available preclinical diagnostic platform for the early stages of AD, aiding in the disruption of pathological progression and the development of appropriate treatment strategies.
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Affiliation(s)
- Jusung An
- Department of Chemistry, Korea University, Seoul, 02841, Korea
| | - Kyeonghwan Kim
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon, 21983, Korea
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, 21983, Korea
| | - Ho Jae Lim
- Department of Biomedical Science, Chosun University, Gwangju, 61452, Korea
| | - Hye Yun Kim
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon, 21983, Korea
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, 21983, Korea
| | - Jinwoo Shin
- Department of Chemistry, Korea University, Seoul, 02841, Korea
| | - InWook Park
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon, 21983, Korea
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, 21983, Korea
| | - Illhwan Cho
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon, 21983, Korea
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, 21983, Korea
| | - Hyeong Yun Kim
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon, 21983, Korea
| | - Sunghoon Kim
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon, 21983, Korea
- Medicinal Bioconvergence Research Center, Institute for Artificial Intelligence and Biomedical Research, Gangnam Severance Hospital, Yonsei University, Incheon, 21983, Korea
- College of Pharmacy, College of Medicine, Interdisciplinary Biomedical Center, Gangnam Severance Hospital, Yonsei University, Incheon, 21983, Korea
| | - Catriona McLean
- Department of Pathology, The Alfred Hospital, Melbourne, 3004, Australia
| | - Kyu Yeong Choi
- Gwangju Alzheimer's & Related Dementia Cohort Research Center, Chosun University, Gwangju, 61452, Korea
| | - YoungSoo Kim
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon, 21983, Korea.
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, 21983, Korea.
| | - Kun Ho Lee
- Department of Biomedical Science, Chosun University, Gwangju, 61452, Korea.
- Gwangju Alzheimer's & Related Dementia Cohort Research Center, Chosun University, Gwangju, 61452, Korea.
- Department of Neural Development and Disease, Korea Brain Research Institute, Daegu, 41062, Korea.
| | - Jong Seung Kim
- Department of Chemistry, Korea University, Seoul, 02841, Korea.
- TheranoChem Incorporation, Seongbuk-gu, Seoul, 02856, Korea.
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45
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Zhang Y, Borch LA, Fischer NH, Meldal M. Hydrodynamic Control of Alzheimer Aβ Fibrillation with Glucosaminic Acid Containing Click-Cyclized β-Bodies. J Am Chem Soc 2024; 146:2654-2662. [PMID: 38126710 DOI: 10.1021/jacs.3c12118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
It is well established that the dynamic hydration shell plays a vital role in macromolecular functions such as protein-ligand, protein-protein, protein-DNA, and protein-lipid interactions. Here we investigate how the water modality affects conformational changes, solubility, and motion of fibrillar proteins. The hypothesis is that the introduction of a poly hydroxyl amino acid would increase solvation of the fibril forming peptides, preventing their misfolding and aggregation. For the amyloid β (Aβ) peptide, which is considered to be connected with nervous system diseases, including dementia and cognitive decline in Alzheimer's disease, the formation of β-sheet fibrils always occurs with a conformational change and a decrease in the dynamic hydration shell around Aβ(1-42). We present novel cyclic d-amino acid peptides that effectively inhibit fibrillation through affecting the dynamic hydration shell of Aβ(1-42) in vitro. Using de novo design within the software Molecular Operating Environment (MOE), five different peptides that recognize Alzheimer's fibrils were designed and synthesized. Three of them were cyclic all-d-amino acid peptides incorporating the same polyhydroxy building block derived from d-glucosaminic acid (GA). One peptide was the parent cyclic all d-amino acid inhibitor with no GA incorporated, and another was an all l-amino acid linear fibrillation inhibitor. The GA-containing peptides were found to show significantly improved inhibition of Aβ(1-42) aggregation. The inhibition was dramatically improved by the synergistic application of two GA peptides targeting each end of the growing fibril. The present study may facilitate future developments of intervention strategies for Alzheimer's disease and similar neurodegenerative diseases.
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Affiliation(s)
- Yuan Zhang
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Line A Borch
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Niklas H Fischer
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Morten Meldal
- Center for Evolutionary Chemical Biology, Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
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46
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Martins IM, Lima A, de Graaff W, Cristóvão JS, Brosens N, Aronica E, Kluskens LD, Gomes CM, Azeredo J, Kessels HW. M13 phage grafted with peptide motifs as a tool to detect amyloid-β oligomers in brain tissue. Commun Biol 2024; 7:134. [PMID: 38280942 PMCID: PMC10821927 DOI: 10.1038/s42003-024-05806-5] [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: 03/27/2023] [Accepted: 01/11/2024] [Indexed: 01/29/2024] Open
Abstract
Oligomeric clusters of amyloid-β (Aβ) are one of the major biomarkers for Alzheimer's disease (AD). However, proficient methods to detect Aβ-oligomers in brain tissue are lacking. Here we show that synthetic M13 bacteriophages displaying Aβ-derived peptides on their surface preferentially interact with Aβ-oligomers. When exposed to brain tissue isolated from APP/PS1-transgenic mice, these bacteriophages detect small-sized Aβ-aggregates in hippocampus at an early age, prior to the occurrence of Aβ-plaques. Similarly, the bacteriophages reveal the presence of such small Aβ-aggregates in post-mortem hippocampus tissue of AD-patients. These results advocate bacteriophages displaying Aβ-peptides as a convenient and low-cost tool to identify Aβ-oligomers in post-mortem brain tissue of AD-model mice and AD-patients.
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Affiliation(s)
- Ivone M Martins
- CEB- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
- Netherlands Institute for Neuroscience, Amsterdam, the Netherlands.
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands.
| | - Alexandre Lima
- CEB- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Wim de Graaff
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Joana S Cristóvão
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Niek Brosens
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Eleonora Aronica
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Leon D Kluskens
- CEB- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Cláudio M Gomes
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Joana Azeredo
- CEB- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Helmut W Kessels
- Netherlands Institute for Neuroscience, Amsterdam, the Netherlands.
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands.
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47
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Kreutzer AG, Parrocha CMT, Haerianardakani S, Guaglianone G, Nguyen JT, Diab MN, Yong W, Perez-Rosendahl M, Head E, Nowick JS. Antibodies Raised Against an Aβ Oligomer Mimic Recognize Pathological Features in Alzheimer's Disease and Associated Amyloid-Disease Brain Tissue. ACS CENTRAL SCIENCE 2024; 10:104-121. [PMID: 38292607 PMCID: PMC10823522 DOI: 10.1021/acscentsci.3c00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 02/01/2024]
Abstract
Antibodies that target the β-amyloid peptide (Aβ) and its associated assemblies are important tools in Alzheimer's disease research and have emerged as promising Alzheimer's disease therapies. This paper reports the creation and characterization of a triangular Aβ trimer mimic composed of Aβ17-36 β-hairpins and the generation and study of polyclonal antibodies raised against the Aβ trimer mimic. The Aβ trimer mimic is covalently stabilized by three disulfide bonds at the corners of the triangular trimer to create a homogeneous oligomer. Structural, biophysical, and cell-based studies demonstrate that the Aβ trimer mimic shares characteristics with oligomers of full-length Aβ. X-ray crystallography elucidates the structure of the trimer and reveals that four copies of the trimer assemble to form a dodecamer. SDS-PAGE, size exclusion chromatography, and dynamic light scattering reveal that the trimer also forms higher-order assemblies in solution. Cell-based toxicity assays show that the trimer elicits LDH release, decreases ATP levels, and activates caspase-3/7 mediated apoptosis. Immunostaining studies on brain slices from people who lived with Alzheimer's disease and people who lived with Down syndrome reveal that the polyclonal antibodies raised against the Aβ trimer mimic recognize pathological features including different types of Aβ plaques and cerebral amyloid angiopathy.
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Affiliation(s)
- Adam G. Kreutzer
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Chelsea Marie T. Parrocha
- Department
of Pharmaceutical Sciences, University of
California Irvine, Irvine, California 92697, United States
| | - Sepehr Haerianardakani
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Gretchen Guaglianone
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Jennifer T. Nguyen
- Department
of Pharmaceutical Sciences, University of
California Irvine, Irvine, California 92697, United States
| | - Michelle N. Diab
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - William Yong
- Department
of Pathology and Laboratory Medicine, University
of California Irvine, Irvine, California 92697, United States
| | - Mari Perez-Rosendahl
- Department
of Pathology and Laboratory Medicine, University
of California Irvine, Irvine, California 92697, United States
| | - Elizabeth Head
- Department
of Pathology and Laboratory Medicine, University
of California Irvine, Irvine, California 92697, United States
| | - James S. Nowick
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States
- Department
of Pharmaceutical Sciences, University of
California Irvine, Irvine, California 92697, United States
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48
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Yokoyama K, Barbour E, Hirschkind R, Martinez Hernandez B, Hausrath K, Lam T. Protein Corona Formation and Aggregation of Amyloid β 1-40-Coated Gold Nanocolloids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1728-1746. [PMID: 38194428 DOI: 10.1021/acs.langmuir.3c02923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Amyloid fibrillogenesis is a pathogenic protein aggregation process that occurs through a highly ordered process of protein-protein interactions. To better understand the protein-protein interactions involved in amyloid fibril formation, we formed nanogold colloid aggregates by stepwise additions of ∼2 nmol of amyloid β 1-40 peptide (Aβ1-40) at pH ∼3.7 and ∼25 °C. The processes of protein corona formation and building of gold colloid [diameters (d) of 20 and 80 nm] aggregates were confirmed by a red-shift of the surface plasmon resonance (SPR) band, λpeak, as the number of Aβ1-40 peptides [N(Aβ1-40)] increased. The normalized red-shift of λpeak, Δλ, was correlated with the degree of protein aggregation, and this process was approximated as the adsorption isotherm explained by the Langmuir-Freundlich model. As the coverage fraction (θ) was analyzed as a function of ϕ, which is the N(Aβ1-40) per total surface area of nanogold colloids available for adsorption, the parameters for explaining the Langmuir-Freundlich model were in good agreement for both 20 and 80 nm gold, indicating that ϕ could define the stage of the aggregation process. Surface-enhanced Raman scattering (SERS) imaging was conducted at designated values of ϕ and suggested that a protein-gold surface interaction during the initial adsorption stage may be dependent on the nanosize. The 20 nm gold case seems to prefer a relatively smaller contacting section, such as a -C-N or C═C bond, but a plane of the benzene ring may play a significant role for 80 nm gold. Regardless of the size of the particles, the β-sheet and random coil conformations were considered to be used to form gold colloid aggregates. The methodology developed in this study allows for new insights into protein-protein interactions at distinct stages of aggregation.
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Affiliation(s)
- Kazushige Yokoyama
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Eli Barbour
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Rachel Hirschkind
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Bryan Martinez Hernandez
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Kaylee Hausrath
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Theresa Lam
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
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49
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Huang F, Fan X, Wang Y, Zou Y, Lian J, Wang C, Ding F, Sun Y. Computational insights into the cross-talk between medin and Aβ: implications for age-related vascular risk factors in Alzheimer's disease. Brief Bioinform 2024; 25:bbad526. [PMID: 38271485 PMCID: PMC10810335 DOI: 10.1093/bib/bbad526] [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: 11/08/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
The aggregation of medin forming aortic medial amyloid is linked to arterial wall degeneration and cerebrovascular dysfunction. Elevated levels of arteriolar medin are correlated with an increased presence of vascular amyloid-β (Aβ) aggregates, a hallmark of Alzheimer's disease (AD) and vascular dementia. The cross-interaction between medin and Aβ results in the formation of heterologous fibrils through co-aggregation and cross-seeding processes both in vitro and in vivo. However, a comprehensive molecular understanding of the cross-interaction between medin and Aβ-two intrinsically disordered proteins-is critically lacking. Here, we employed atomistic discrete molecular dynamics simulations to systematically investigate the self-association, co-aggregation and also the phenomenon of cross-seeding between these two proteins. Our results demonstrated that both Aβ and medin were aggregation prone and their mixture tended to form β-sheet-rich hetero-aggregates. The formation of Aβ-medin hetero-aggregates did not hinder Aβ and medin from recruiting additional Aβ and medin peptides to grow into larger β-sheet-rich aggregates. The β-barrel oligomer intermediates observed in the self-aggregations of Aβ and medin were also present during their co-aggregation. In cross-seeding simulations, preformed Aβ fibrils could recruit isolated medin monomers to form elongated β-sheets. Overall, our comprehensive simulations suggested that the cross-interaction between Aβ and medin may contribute to their pathological aggregation, given the inherent amyloidogenic tendencies of both medin and Aβ. Targeting medin, therefore, could offer a novel therapeutic approach to preserving brain function during aging and AD by improving vascular health.
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Affiliation(s)
- Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
| | - Xinjie Fan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Ying Wang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yu Zou
- Department of Sport and Exercise Science, Zhejiang University, Hangzhou 310058, China
| | - Jiangfang Lian
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
| | - Chuang Wang
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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50
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Li Y, Ni N, Lee M, Wei W, Andrikopoulos N, Kakinen A, Davis TP, Song Y, Ding F, Leong DT, Ke PC. Endothelial leakiness elicited by amyloid protein aggregation. Nat Commun 2024; 15:613. [PMID: 38242873 PMCID: PMC10798980 DOI: 10.1038/s41467-024-44814-1] [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: 04/18/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024] Open
Abstract
Alzheimer's disease (AD) is a major cause of dementia debilitating the global ageing population. Current understanding of the AD pathophysiology implicates the aggregation of amyloid beta (Aβ) as causative to neurodegeneration, with tauopathies, apolipoprotein E and neuroinflammation considered as other major culprits. Curiously, vascular endothelial barrier dysfunction is strongly associated with Aβ deposition and 80-90% AD subjects also experience cerebral amyloid angiopathy. Here we show amyloid protein-induced endothelial leakiness (APEL) in human microvascular endothelial monolayers as well as in mouse cerebral vasculature. Using signaling pathway assays and discrete molecular dynamics, we revealed that the angiopathy first arose from a disruption to vascular endothelial (VE)-cadherin junctions exposed to the nanoparticulates of Aβ oligomers and seeds, preceding the earlier implicated proinflammatory and pro-oxidative stressors to endothelial leakiness. These findings were analogous to nanomaterials-induced endothelial leakiness (NanoEL), a major phenomenon in nanomedicine depicting the paracellular transport of anionic inorganic nanoparticles in the vasculature. As APEL also occurred in vitro with the oligomers and seeds of alpha synuclein, this study proposes a paradigm for elucidating the vascular permeation, systemic spread, and cross-seeding of amyloid proteins that underlie the pathogeneses of AD and Parkinson's disease.
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Affiliation(s)
- Yuhuan Li
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, China
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Nengyi Ni
- National University of Singapore, Department of Chemical and Biomolecular Engineering, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Myeongsang Lee
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Wei Wei
- College of Veterinary Medicine, Southwest University, Chongqing, 402460, China
| | - Nicholas Andrikopoulos
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
- The Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Thomas P Davis
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yang Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.
| | - David Tai Leong
- National University of Singapore, Department of Chemical and Biomolecular Engineering, 4 Engineering Drive 4, Singapore, 117585, Singapore.
| | - Pu Chun Ke
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
- The Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China.
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