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Foralosso R, Kopiasz RJ, Alexander C, Mantovani G, Stolnik S. Synthetic macromolecular peptide-mimetics with amino acid substructure residues as protein stabilising excipients. J Mater Chem B 2024; 12:1022-1030. [PMID: 38205916 DOI: 10.1039/d3tb02102e] [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: 01/12/2024]
Abstract
The clinical use of protein and peptide biotherapeutics requires fabrication of stable products. This particularly concerns stability towards aggregation of proteins or peptides. Here, we tested a hypothesis that interactions between a synthetic peptide, which is an aggregation-prone region analogue, and its homologous sequence on a protein of interest, could be exploited to design excipients which stabilise the protein against aggregation. A peptide containing the analogue of lysozyme aggregation-prone region (GILQINSRW) was conjugated to a RAFT agent and used to initiate the polymerisation of N-hydroxyethyl acrylamide, generating a GILQINSRW-HEA90 polymer, which profoundly reduced lysozyme aggregation. Substitution of tryptophan in GILQINSRW with glycine, to form GILQINSRG, revealed that tryptophan is a critical amino acid in the protein stabilisation by GILQINSRW-HEA90. Accordingly, polymeric peptide-mimetics of tryptophan, phenylalanine and isoleucine, which are often present in aggregation-prone regions, were synthesized. These were based on synthetic oligomers of acrylamide derivatives of indole-3 acetic acid (IND), phenylacetic acid (PHEN), or 2-methyl butyric acid (MBA), respectively, conjugated with hydrophilic poly(N-hydroxyethyl acrylamide) blocks to form amphiphilic copolymers denoted as INDm-, PHENm- and MTBm-b-HEAn. These materials were tested as protein stabilisers and it was shown that solution properties and the abilities of these materials to stabilise insulin and the peptide IDR 1018 towards aggregation are dependent on the chemical nature of their side groups. These data suggest a structure-activity relationship, whereby the indole-based INDm-b-HEAn peptide-mimetic displays properties of a potential stabilising excipient for protein formulations.
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Affiliation(s)
| | - Rafał Jerzy Kopiasz
- University of Nottingham, School of Pharmacy, NG7 2RD, UK.
- Warsaw University of Technology, Faculty of Chemistry, Noakowskiego 3 St., 00-664, Warsaw, Poland
| | | | | | - Snow Stolnik
- University of Nottingham, School of Pharmacy, NG7 2RD, UK.
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Hyun Yi J, Cho E, Lee S, Ja Kwon K, Lee S, Lee J, Lee C, Young Shin C, Hyun Kim D, Hee Shim S. Aβ dissociation by pectolinarin may counteract against Aβ-induced synaptic dysfunction and memory impairment. Biochem Pharmacol 2023; 216:115792. [PMID: 37689271 DOI: 10.1016/j.bcp.2023.115792] [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: 07/11/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
Alzheimer's disease (AD) is a degenerative brain disorder characterised by various neurological symptoms, including memory impairment and mood disorders, associated with the abnormal accumulation of amyloid b(Aβ) and tau proteins in the brain. There is still no definitive treatment available for AD, and the Aβ antibody drugs, which are expected to be approved by the FDA, have many limitations. Therefore, there is an urgent need to develop low-molecular-weight therapeutic agents for the management of AD. In this study, we investigated whether pectolinarin, a flavonoid, regulates Aβ aggregation and Aβ-induced toxicity. Pectolinarin demonstrated concentration-dependent inhibition of Aβ aggregation and had the ability to break down pre-formed Aβ aggregates, thereby reducing their neurotoxicity. Furthermore, pectolinarin suppressed Aβ aggregates-induced reduction in long-term potentiation (LTP) in the hippocampus. Oral administration of pectolinarin in experimental animals inhibited memory impairment and LTP deficits induced by Aβ injection in the hippocampus. These results indicate that pectolinarin may reduce toxic Aβ species and Aβ-induced memory impairments and synaptic dysfunction.
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Affiliation(s)
- Jee Hyun Yi
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon 34141, Republic of Korea
| | - Eunbi Cho
- Department of Pharmacology and Department of Advanced Translational Medicine, School of Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Soowon Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyoung Ja Kwon
- Department of Pharmacology and Department of Advanced Translational Medicine, School of Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; Institute of Biomedical Sciences & Technology, Konkuk University, Seoul 05029, Republic of Korea
| | - Seungheon Lee
- Department of Marine Life Sciences, Jeju National University, Jeju 63243, Republic of Korea
| | - Juyong Lee
- Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Arontier Co., Seoul 06735, Republic of Korea
| | - Changyeol Lee
- Herbal Medicine Resources Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea
| | - Chan Young Shin
- Department of Pharmacology and Department of Advanced Translational Medicine, School of Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; Institute of Biomedical Sciences & Technology, Konkuk University, Seoul 05029, Republic of Korea
| | - Dong Hyun Kim
- Department of Pharmacology and Department of Advanced Translational Medicine, School of Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; Institute of Biomedical Sciences & Technology, Konkuk University, Seoul 05029, Republic of Korea.
| | - Sang Hee Shim
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
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Almeida ZL, Brito RMM. Amyloid Disassembly: What Can We Learn from Chaperones? Biomedicines 2022; 10:3276. [PMID: 36552032 PMCID: PMC9776232 DOI: 10.3390/biomedicines10123276] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/26/2022] [Indexed: 12/23/2022] Open
Abstract
Protein aggregation and subsequent accumulation of insoluble amyloid fibrils with cross-β structure is an intrinsic characteristic of amyloid diseases, i.e., amyloidoses. Amyloid formation involves a series of on-pathway and off-pathway protein aggregation events, leading to mature insoluble fibrils that eventually accumulate in multiple tissues. In this cascade of events, soluble oligomeric species are formed, which are among the most cytotoxic molecular entities along the amyloid cascade. The direct or indirect action of these amyloid soluble oligomers and amyloid protofibrils and fibrils in several tissues and organs lead to cell death in some cases and organ disfunction in general. There are dozens of different proteins and peptides causing multiple amyloid pathologies, chief among them Alzheimer's, Parkinson's, Huntington's, and several other neurodegenerative diseases. Amyloid fibril disassembly is among the disease-modifying therapeutic strategies being pursued to overcome amyloid pathologies. The clearance of preformed amyloids and consequently the arresting of the progression of organ deterioration may increase patient survival and quality of life. In this review, we compiled from the literature many examples of chemical and biochemical agents able to disaggregate preformed amyloids, which have been classified as molecular chaperones, chemical chaperones, and pharmacological chaperones. We focused on their mode of action, chemical structure, interactions with the fibrillar structures, morphology and toxicity of the disaggregation products, and the potential use of disaggregation agents as a treatment option in amyloidosis.
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Affiliation(s)
| | - Rui M. M. Brito
- Chemistry Department and Coimbra Chemistry Centre—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
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Jain A, Kassem S, Fisher RS, Wang B, Li TD, Wang T, He Y, Elbaum-Garfinkle S, Ulijn RV. Connected Peptide Modules Enable Controlled Co-Existence of Self-Assembled Fibers Inside Liquid Condensates. J Am Chem Soc 2022; 144:15002-15007. [PMID: 35946870 DOI: 10.1021/jacs.2c05897] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Supramolecular self-assembly of fibrous components and liquid-liquid phase separation are at the extremes of the order-to-disorder spectrum. They collectively play key roles in cellular organization. It is still a major challenge to design systems where both highly ordered nanostructures and liquid-liquid phase-separated domains can coexist. We present a three-component assembly approach that generates fibrous domains that exclusively form inside globally disordered, liquid condensates. This is achieved by creating amphiphilic peptides that combine the features of fibrillar assembly (the amyloid domain LVFFA) and complex coacervation (oligo-arginine and adenosine triphosphate (ATP)) in one peptide, namely, LVFFAR9. When this hybrid peptide is mixed in different ratios with R9 and ATP, we find that conditions can be created where fibrous assembly is exclusively observed inside liquid coacervates. Through fluorescence and atomic force microscopy characterization, we investigate the dynamic evolution of ordered and disordered features over time. It was observed that the fibers nucleate and mature inside the droplets and that these fiber-containing liquid droplets can also undergo fusion, showing that the droplets remain liquid-like. Our work thus generates opportunities for the design of ordered structures within the confined environment of biomolecular condensates, which may be useful to create supramolecular materials in defined compartments and as model systems that can enhance understanding of ordering principles in biology.
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Affiliation(s)
- Ankit Jain
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Salma Kassem
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Rachel S Fisher
- Structural Biology Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Biran Wang
- Molecular Cytology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Tai-De Li
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States.,Department of Physics, City College of New York, City University of New York, New York, New York 10031, United States
| | - Tong Wang
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Ye He
- Neuroscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States.,Division of Science, The City College of New York, New York, New York 10031, United States
| | - Shana Elbaum-Garfinkle
- Structural Biology Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States.,Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Rein V Ulijn
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States.,Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States.,Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
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5
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Molecular Engineering of Peptide–Drug Conjugates for Therapeutics. Pharmaceutics 2022; 14:pharmaceutics14010212. [PMID: 35057106 PMCID: PMC8779610 DOI: 10.3390/pharmaceutics14010212] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 01/28/2023] Open
Abstract
In recent years, hundreds of novel small molecular drugs used for different treatments have been studied in the three phases of clinical trials around the world. However, less than 10% of them are eventually used due to diverse problems. Even some traditional drugs that have been approved by the Food and Drug Administration (FDA) have faced similar dilemmas. For instance, many drugs have poor water solubility, are easily hydrolyzed, or possess undesirable toxicity, while a variety of cancer cells develop drug resistance (DR) or multiple drug resistance (MDR) towards chemotherapeutic agents after long-term therapy. In order to improve the efficacy and efficiency of drugs, research has been directed forward towards the creation of assemblies of peptide–drug conjugates (PDCs) which have proven to possess wide potential for overcoming such complications based on their excellent biocompatibility, controllable biodegradability, site-selective targeting, and comparably low cytotoxicity. In this review, we focus on the recent developments and advances made in the creation of self-assembled nanostructures of PDCs for cancer therapy, on the chemical and physical properties of such drugs and peptides, and how they are arranged together to form diverse supramolecular nanostructures. Additionally, we cover certain mechanisms regarding how peptides or their derivatives enhance the efficiency and efficacy of those selected drugs and provide a brief discussion regarding the perspectives and remaining challenges in this intriguing field.
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An evaluation of the self-assembly enhancing properties of cell-derived hexameric amyloid-β. Sci Rep 2021; 11:11570. [PMID: 34078941 PMCID: PMC8172837 DOI: 10.1038/s41598-021-90680-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/04/2021] [Indexed: 12/17/2022] Open
Abstract
A key hallmark of Alzheimer’s disease is the extracellular deposition of amyloid plaques composed primarily of the amyloidogenic amyloid-β (Aβ) peptide. The Aβ peptide is a product of sequential cleavage of the Amyloid Precursor Protein, the first step of which gives rise to a C-terminal Fragment (C99). Cleavage of C99 by γ-secretase activity releases Aβ of several lengths and the Aβ42 isoform in particular has been identified as being neurotoxic. The misfolding of Aβ leads to subsequent amyloid fibril formation by nucleated polymerisation. This requires an initial and critical nucleus for self-assembly. Here, we identify and characterise the composition and self-assembly properties of cell-derived hexameric Aβ42 and show its assembly enhancing properties which are dependent on the Aβ monomer availability. Identification of nucleating assemblies that contribute to self-assembly in this way may serve as therapeutic targets to prevent the formation of toxic oligomers.
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8
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Residue Interaction Network Analysis Predicts a Val24-Ile31 Interaction May be Involved in Preventing Amyloid-Beta (1-42) Primary Nucleation. Protein J 2021; 40:175-183. [PMID: 33566321 DOI: 10.1007/s10930-021-09965-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2021] [Indexed: 12/15/2022]
Abstract
Alzheimer's disease (AD) patients could benefit from a more effective treatment than the current FDA-approved options. Because amyloid-beta (Aβ) is thought to play a central role in AD pathogenesis, many experimental drugs attempt to reduce Aβ-induced pathology. Preventing amyloid accumulation may be a more effective strategy than clearing Aβ plaques after they form. If preventing Aβ accumulation can treat or prevent AD, then understanding Aβ primary nucleation may aid rational drug design. This study examines Aβ residue interaction networks and reports network and structural observations that may provide insight into primary nucleation. While many studies identify structural features of Aβ that promote aggregation, this study reports features that may resist primary nucleation by examining Aβ42 studies in more and less polar solvents. In Aβ42 in a less polar solvent (PDB ID: 1IYT), Val24 and Ile31 have higher betweenness and residue centrality values. This may be due to a predicted interaction between Val24 and Ile31. Residues in the central hydrophobic cluster (CHC) of Aβ40 and Aβ42 had significantly higher betweenness values compared to the average betweenness of the structures, highlighting the CHC's reported role in oligomerization. The predicted interaction between Val24 and Ile31 may reduce the likelihood of primary nucleation of Aβ.
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9
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Precise magnetic resonance imaging-guided sonodynamic therapy for drug-resistant bacterial deep infection. Biomaterials 2020; 264:120386. [PMID: 32979656 DOI: 10.1016/j.biomaterials.2020.120386] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/04/2020] [Accepted: 09/14/2020] [Indexed: 12/13/2022]
Abstract
The precise treatment of drug-resistant deep bacterial infections remains a huge challenge in clinic. Herein, a polymer-peptide-porphyrin conjugate (PPPC), which can be real-time monitored in infectious site, is developed for accurate and deep sonodynamic therapy (SDT) based on "in vivo self-assembly" strategy. The PPPC contains four moieties, i.e., a hyperbranched polymer backbone, a self-assembled peptide linked with an enzyme-cleavable peptide-poly (ethylene glycol) terminal, a bacterial targeting peptide, and a porphyrin sonosensitizer (MnTCPP) segment. Once PPPC nanoparticles reach the infectious area, the protecting PEG layers are removed due to the over-expressed gelatinase, leading to the secondary assembly into large nanoaggregates and resultant enhanced accumulation of sonosensitizer. The nanoaggregates exhibit enhanced interaction with bacterial membrane and decrease the minimum inhibitory concentration (MIC) significantly. Meanwhile, compared with free MnTCPP, the concentration of which can not be accurately quantified, the accumulation amount of MnTCPP in PPPCs at infectious site can be in situ monitored by magnetic resonance imaging (MRI) using T1 combined with T2. When the concentration of PPPC-1 reaches MIC, the drug-resistant bacterial infection area is exposed to ultrasound irradiation, causing the precise and efficient elimination of bacteria. Therefore, the MRI-guided SDT system shows extraordinary tissue penetration depth, drug concentration monitoring, morphology-transformation induced accumulation and improved treatment capacity toward drug-resistant bacteria.
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Differences in the free energies between the excited states of A β40 and A β42 monomers encode their aggregation propensities. Proc Natl Acad Sci U S A 2020; 117:19926-19937. [PMID: 32732434 DOI: 10.1073/pnas.2002570117] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The early events in the aggregation of the intrinsically disordered peptide, amyloid-β (Aβ), involve transitions from the disordered free energy ground state to assembly-competent states. Are the fingerprints of order found in the amyloid fibrils encoded in the conformations that the monomers access at equilibrium? If so, could the enhanced aggregation rate of Aβ42 compared to Aβ40 be rationalized from the sparsely populated high free energy states of the monomers? Here, we answer these questions in the affirmative using coarse-grained simulations of the self-organized polymer-intrinsically disordered protein (SOP-IDP) model of Aβ40 and Aβ42. Although both the peptides have practically identical ensemble-averaged properties, characteristic of random coils (RCs), the conformational ensembles of the two monomers exhibit sequence-specific heterogeneity. Hierarchical clustering of conformations reveals that both the peptides populate high free energy aggregation-prone ([Formula: see text]) states, which resemble the monomers in the fibril structure. The free energy gap between the ground (RC) and the [Formula: see text] states of Aβ42 peptide is smaller than that for Aβ40. By relating the populations of excited states of the two peptides to the fibril formation time scales using an empirical formula, we explain nearly quantitatively the faster aggregation rate of Aβ42 relative to Aβ40. The [Formula: see text] concept accounts for fibril polymorphs, leading to the prediction that the less stable [Formula: see text] state of Aβ42, encoding for the U-bend fibril, should form earlier than the structure with the S-bend topology, which is in accord with Ostwald's rule rationalizing crystal polymorph formation.
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Zhang K, Yang PP, He PP, Wen SF, Zou XR, Fan Y, Chen ZM, Cao H, Yang Z, Yue K, Zhang X, Zhang H, Wang L, Wang H. Peptide-Based Nanoparticles Mimic Fibrillogenesis of Laminin in Tumor Vessels for Precise Embolization. ACS NANO 2020; 14:7170-7180. [PMID: 32407069 DOI: 10.1021/acsnano.0c02110] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cancer therapeutic strategies based on angiogenesis attract great attention from fundamental and clinical research. Blocking oxygen and nutrition supply to tumor cells could inhibit the growth of tumors based on occlusion of blood vessels in the tumor. Herein, we report a dual-responsive peptide-based nanoparticle, mimicking the laminin fibrillogenesis specifically and highly efficiently in tumor vessels, resulting in the blockage of tumor vessels and the growth inhibition of tumors. The laminin mimic peptide (LMMP) is designed with a fibrillation sequence, a pH-responsive sequence, and a targeting sequence. The LMMP in nanoformulations is delivered to blood vessels in the tumors, where the microenvironment (pH and microthrombus) enable LMMP to process laminin fibrillogenesis, constructing fibrous networks. The laminin-like fibrous networks capture red blood cells etc., forming occlusion specifically in the tumor blood vessels to inhibit the growth of the tumor.
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Affiliation(s)
- Kuo Zhang
- Department of Materials Physics and Chemistry, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, China
| | - Pei-Pei Yang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, China
| | - Ping-Ping He
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, China
| | - Shi-Fang Wen
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, China
| | - Xiao-Ran Zou
- Department of Materials Physics and Chemistry, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, China
| | - Yu Fan
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, China
| | - Zi-Ming Chen
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, China
| | - Hui Cao
- Department of Materials Physics and Chemistry, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Zhou Yang
- Department of Materials Physics and Chemistry, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Kai Yue
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Xinxin Zhang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Hua Zhang
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Lei Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, China
| | - Hao Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- GBA Research Innovation Institute for Nanotechnology, Guangdong 510700, China
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Aggarwal L, Biswas P. Interaction Volume Is a Measure of the Aggregation Propensity of Amyloid-β. J Phys Chem Lett 2020; 11:3993-4000. [PMID: 32352786 DOI: 10.1021/acs.jpclett.0c00922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This study highlights the significance of the partial molar volume of amino acids in predicting the aggregation propensity of an intrinsically disordered protein, amyloid-β (Aβ), and its mutants in aqueous solution. The change in the interaction volume of the protein or mutant is quantitatively correlated with its calculated experimental aggregation propensity. This method also reveals how the interaction volume may be tuned by changing the charge and hydrophobicity of Aβ. While a positive change in the interaction volume and a higher aggregation propensity are observed for mutants with a decrease in the overall charge and/or an increase in hydrophobicity, a reverse trend is observed for the mutants with a decrease in the hydrophobicity and/or an increase in its charge. Hence, the interaction volume may be considered as a key parameter for monitoring protein aggregation that bridges the gap between the experimental aggregation kinetics and solvation thermodynamics.
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Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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Aggarwal L, Biswas P. Effect of Alzheimer’s Disease Causative and Protective Mutations on the Hydration Environment of Amyloid-β. J Phys Chem B 2020; 124:2311-2322. [DOI: 10.1021/acs.jpcb.9b10425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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Pilkington AW, Schupp J, Nyman M, Valentine SJ, Smith DM, Legleiter J. Acetylation of Aβ 40 Alters Aggregation in the Presence and Absence of Lipid Membranes. ACS Chem Neurosci 2020; 11:146-161. [PMID: 31834770 DOI: 10.1021/acschemneuro.9b00483] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A hallmark of Alzheimer's disease (AD) is the formation of senile plaques comprised of the β-amyloid (Aβ) peptide. Aβ fibrillization is a complex nucleation-dependent process involving a variety of metastable intermediate aggregates and features the formation of inter- and intramolecular salt bridges involving lysine residues, K16 and K28. Cationic lysine residues also mediate protein-lipid interactions via association with anionic lipid headgroups. As several toxic mechanisms attributed to Aβ involve membrane interactions, the impact of acetylation on Aβ40 aggregation in the presence and absence of membranes was determined. Using chemical acetylation, varying mixtures of acetylated and nonacetylated Aβ40 were produced. With increasing acetylation, fibril and oligomer formation decreased, eventually completely arresting fibrillization. In the presence of total brain lipid extract (TBLE) vesicles, acetylation reduced the interaction of Aβ40 with membranes; however, fibrils still formed at near complete levels of acetylation. Additionally, the combination of TBLE and acetylated Aβ promoted annular aggregates. Finally, toxicity associated with Aβ40 was reduced with increasing acetylation in a cell culture assay. These results suggest that in the absence of membranes that the cationic character of lysine plays a major role in fibril formation. However, acetylation promotes unique aggregation pathways in the presence of lipid membranes.
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Affiliation(s)
- Albert W. Pilkington
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Jane Schupp
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Morgan Nyman
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Stephen J. Valentine
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - David M. Smith
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States
- Rockefeller Neurosciences Institutes, West Virginia University, 1 Medical Center Drive, P.O. Box 9303, Morgantown, West Virginia 26505, United States
- Department of Neuroscience, West Virginia University, 1 Medical Center Drive, P.O. Box
9303, Morgantown, West Virginia 26505, United States
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
- Rockefeller Neurosciences Institutes, West Virginia University, 1 Medical Center Drive, P.O. Box 9303, Morgantown, West Virginia 26505, United States
- Department of Neuroscience, West Virginia University, 1 Medical Center Drive, P.O. Box
9303, Morgantown, West Virginia 26505, United States
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15
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Mirgorodskaya OA, Kozmin YP, Protasov AD, Toropygin IY, Oleinikov VA. Regulation of Aggregation of Self-Associated Peptides, Including N-Terminal Fragments of the Alzheimer’s β-Amyloid Peptide, by Nitro Derivatives of Azoloazine. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019010096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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He PP, Li XD, Wang L, Wang H. Bispyrene-Based Self-Assembled Nanomaterials: In Vivo Self-Assembly, Transformation, and Biomedical Effects. Acc Chem Res 2019; 52:367-378. [PMID: 30653298 DOI: 10.1021/acs.accounts.8b00398] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Self-assembled nanomaterials show potential high efficiency as theranostic agents for high-performance imaging and therapy. However, superstructures and properties of preassembled nanomaterials are somewhat compromised under complicated physiological conditions. Given the advantages of the dynamic nature and adaptive behavior of self-assembly systems, we propose an "in vivo self-assembly" strategy for in situ construction of nanomaterials in living objects. For the proof-of-concept study of in vivo self-assembly, we developed a bispyrene (BP) molecule as a multifunctional building block. BP molecules show nonfluorescence in the monomeric state. Quantum-chemical calculations indicate that BP forms twisted intramolecular charge transfer states, which are separated into two orthogonal units, preventing the fluorescence emission. Interestingly, the typical excimeric emission of BP is observed with the formation of J-type aggregates, as confirmed by single-crystal X-ray diffraction. Packing of the BP molecules generates parallel pyrene units that interact with adjacent ones in a slipped face-to-face fashion through intermolecular π-π interactions. BP and/or its amphiphilic derivatives are capable of self-aggregating into nanoparticles (NPs) in aqueous solution because of the hydrophobic and π-π interactions of BP. Upon specific biological stimuli, BP NPs can be transformed into variable self-assembled superstructures. Importantly, the self-assembled BP NPs exhibit turn-on fluorescence signals that can be used to monitor the self-assembly/disassembly process in vitro and in vivo. On the basis of the photophysical properties of BP and its aggregates, we synthesized a series of designed BP derivatives as building blocks for in situ construction of functional nanomaterials for bioimaging and/or therapeutics. We observed several new biomedical effects, e.g., (i) the assembly/aggregation-induced retention (AIR) effect, which shows improved accumulation and retention of bioactive nanomaterials in the regions of interests; (ii) the transformation-induced surface adhesion (TISA) effect, which means the BP NPs transform into nanofibers (NFs) on cell surfaces upon binding with specific receptors, which leads to less uptake of BP NPs by cells via traditional endocytosis pathway; and (iii) transformation of the BP NPs into NFs in the tumor microenvironment, showing high accumulation and long-term retention, revealing the transformation-enhanced accumulation and retention (TEAR) effect. In this Account, we summarize the fluorescence property and emission mechanism of BP building blocks upon aggregation in the biological environment. Moreover, BP-derived compounds used for in vivo self-assembly and transformation are introduced involving modulation strategies. Subsequently, unexpected biomedical effects and applications for theranostics of BP based nanomaterials are discussed. We finally conclude with an outlook toward future developments of BP-based self-assembled nanomaterials.
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Affiliation(s)
- Ping-Ping He
- Key Laboratory of Chemistry and Materials Science of the State Ethnic Affairs Commission and Ministry of Education, South-Central University for Nationalities, 182 Minzu Road, Hongshan District, Wuhan, Hubei 430074, China
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Haidian District, Beijing 100190, China
| | - Xiang-Dan Li
- Key Laboratory of Chemistry and Materials Science of the State Ethnic Affairs Commission and Ministry of Education, South-Central University for Nationalities, 182 Minzu Road, Hongshan District, Wuhan, Hubei 430074, China
| | - Lei Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Haidian District, Beijing 100190, China
| | - Hao Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Haidian District, Beijing 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Gera J, Szögi T, Bozsó Z, Fülöp L, Barrera EE, Rodriguez AM, Méndez L, Delpiccolo CM, Mata EG, Cioffi F, Broersen K, Paragi G, Enriz RD. Searching for improved mimetic peptides inhibitors preventing conformational transition of amyloid-β42 monomer. Bioorg Chem 2018; 81:211-221. [DOI: 10.1016/j.bioorg.2018.08.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 01/14/2023]
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18
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An Aβ42 variant that inhibits intra- and extracellular amyloid aggregation and enhances cell viability. Biochem J 2018; 475:3087-3103. [DOI: 10.1042/bcj20180247] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/02/2018] [Accepted: 09/07/2018] [Indexed: 01/06/2023]
Abstract
Aggregation and accumulation of the 42-residue amyloid β peptide (Aβ42) in the extracellular matrix and within neuronal cells is considered a major cause of neuronal cell cytotoxicity and death in Alzheimer's disease (AD) patients. Therefore, molecules that bind to Aβ42 and prevent its aggregation are therapeutically promising as AD treatment. Here, we show that a non-self-aggregating Aβ42 variant carrying two surface mutations, F19S and L34P (Aβ42DM), inhibits wild-type Aβ42 aggregation and significantly reduces Aβ42-mediated cell cytotoxicity. In addition, Aβ42DM inhibits the uptake and internalization of extracellularly added pre-formed Aβ42 aggregates into cells. This was the case in both neuronal and non-neuronal cells co-expressing Aβ42 and Aβ42DM or following pre-treatment of cells with extracellular soluble forms of the two peptides, even at high Aβ42 to Aβ42DM molar ratios. In cells, Aβ42DM associates with Aβ42, while in vitro, the two soluble recombinant peptides exhibit nano-molar binding affinity. Importantly, Aβ42DM potently suppresses Aβ42 amyloid aggregation in vitro, as demonstrated by thioflavin T fluorescence and transmission electron microscopy for detecting amyloid fibrils. Overall, we present a new approach for inhibiting Aβ42 fibril formation both within and outside cells. Accordingly, Aβ42DM should be evaluated in vivo for potential use as a therapeutic lead for treating AD.
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19
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Zhang K, Gao YJ, Yang PP, Qi GB, Zhang JP, Wang L, Wang H. Self-Assembled Fluorescent Organic Nanomaterials for Biomedical Imaging. Adv Healthc Mater 2018; 7:e1800344. [PMID: 30137689 DOI: 10.1002/adhm.201800344] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/21/2018] [Indexed: 11/05/2022]
Abstract
Fluorescent nanomaterials, self-assembled from building blocks through multiple intermolecular interactions show diversified structures and functionalities, and are potential fluorescence contrast agents/probes for high-performance biomedical imaging. Self-assembled nanomaterials exhibit high stability, long circulation time, and targeted biological distribution. This review summarizes recent advances of self-assembled nanomaterials as fluorescence contrast agents/probes for biomedical imaging. The self-assembled nanomaterials are classified into two groups, i.e., ex situ and in situ construction of self-assembled nanomaterials. The advantages of ex situ as well as in situ constructed nanomaterials for biomedical applications are discussed thoroughly. The directions of future developments for self-assembled nanomaterials are provided.
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Affiliation(s)
- Kuo Zhang
- Faculty of Chemistry; Northeast Normal University; Changchun 130024 China
- CAS Center for Excellence Nanoscience; CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety; National Center for Nanoscience and Technology (NCNST); No. 11 Beiyitiao, Zhongguancun Haidian District Beijing 100190 China
| | - Yu-Juan Gao
- CAS Center for Excellence Nanoscience; CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety; National Center for Nanoscience and Technology (NCNST); No. 11 Beiyitiao, Zhongguancun Haidian District Beijing 100190 China
| | - Pei-Pei Yang
- CAS Center for Excellence Nanoscience; CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety; National Center for Nanoscience and Technology (NCNST); No. 11 Beiyitiao, Zhongguancun Haidian District Beijing 100190 China
| | - Guo-Bin Qi
- CAS Center for Excellence Nanoscience; CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety; National Center for Nanoscience and Technology (NCNST); No. 11 Beiyitiao, Zhongguancun Haidian District Beijing 100190 China
| | - Jing-Ping Zhang
- Faculty of Chemistry; Northeast Normal University; Changchun 130024 China
| | - Lei Wang
- CAS Center for Excellence Nanoscience; CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety; National Center for Nanoscience and Technology (NCNST); No. 11 Beiyitiao, Zhongguancun Haidian District Beijing 100190 China
| | - Hao Wang
- CAS Center for Excellence Nanoscience; CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety; National Center for Nanoscience and Technology (NCNST); No. 11 Beiyitiao, Zhongguancun Haidian District Beijing 100190 China
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20
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Sankar K, Krystek SR, Carl SM, Day T, Maier JKX. AggScore: Prediction of aggregation-prone regions in proteins based on the distribution of surface patches. Proteins 2018; 86:1147-1156. [PMID: 30168197 DOI: 10.1002/prot.25594] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 07/12/2018] [Accepted: 08/24/2018] [Indexed: 02/02/2023]
Abstract
Protein aggregation is a phenomenon that has attracted considerable attention within the pharmaceutical industry from both a developability standpoint (to ensure stability of protein formulations) and from a research perspective for neurodegenerative diseases. Experimental identification of aggregation behavior in proteins can be expensive; and hence, the development of accurate computational approaches is crucial. The existing methods for predicting protein aggregation rely mostly on the primary sequence and are typically trained on amyloid-like proteins. However, the training bias toward beta amyloid peptides may worsen prediction accuracy of such models when applied to larger protein systems. Here, we present a novel algorithm to identify aggregation-prone regions in proteins termed "AggScore" that is based entirely on three-dimensional structure input. The method uses the distribution of hydrophobic and electrostatic patches on the surface of the protein, factoring in the intensity and relative orientation of the respective surface patches into an aggregation propensity function that has been trained on a benchmark set of 31 adnectin proteins. AggScore can accurately identify aggregation-prone regions in several well-studied proteins and also reliably predict changes in aggregation behavior upon residue mutation. The method is agnostic to an amyloid-specific aggregation context and thus may be applied to globular proteins, small peptides and antibodies.
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Affiliation(s)
| | - Stanley R Krystek
- Molecular Discovery Technologies, Bristol-Myers Squibb, Princeton, New Jersey
| | - Stephen M Carl
- Discovery Pharmaceutics and Analytical Sciences and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey
| | - Tyler Day
- Schrödinger Inc., New York, New York
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21
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Rosenman DJ, Clemente N, Ali M, García AE, Wang C. High pressure NMR reveals conformational perturbations by disease-causing mutations in amyloid β-peptide. Chem Commun (Camb) 2018; 54:4609-4612. [PMID: 29670961 DOI: 10.1039/c8cc01674g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we present the high pressure NMR characterization of Aβ42 and two Aβ40 variants with Alzheimer-causing mutations E22G and D23N. While chemical shifts only identified localized changes at ambient pressure compared with Aβ40, high pressure NMR revealed a common site with heightened pressure sensitivity at Q15, K16 and L17 in all three variants, which correlates to higher β-propensity at central hydrophobic cluster (CHC) and faster aggregation.
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Affiliation(s)
- David J Rosenman
- Department of Biological Sciences, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, USA.
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22
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Abstract
Previously published experimental studies have suggested that when the 40-residue amyloid beta peptide is encapsulated in a reverse micelle, it folds into a structure that may nucleate amyloid fibril formation (Yeung, P. S.-W.; Axelsen, P. H. J. Am. Chem. Soc. 2012, 134, 6061 ). The factors that induce the formation of this structure have now been identified in a multi-microsecond simulation of the same reverse micelle system that was studied experimentally. Key features of the polypeptide-micelle interaction include the anchoring of a hydrophobic residue cluster into gaps in the reverse micelle surface, the formation of a beta turn at the anchor point that brings N- and C-terminal segments of the polypeptide into proximity, high ionic strength that promotes intramolecular hydrogen bond formation, and deformation of the reverse micelle surface to facilitate interactions with the surface along the entire length of the polypeptide. Together, these features cause the simulation-derived vibrational spectrum to red shift in a manner that reproduces the red-shift previously reported experimentally. On the basis of these findings, a new mechanism is proposed whereby membranes nucleate fibril formation and facilitate the in-register alignment of polypeptide strands that is characteristic of amyloid fibrils.
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Affiliation(s)
- Gözde Eskici
- Department of Biochemistry & Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
| | - Paul H Axelsen
- Departments of Pharmacology, Biochemistry and Biophysics, and Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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23
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Yang PP, Luo Q, Qi GB, Gao YJ, Li BN, Zhang JP, Wang L, Wang H. Host Materials Transformable in Tumor Microenvironment for Homing Theranostics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1605869. [PMID: 28195446 DOI: 10.1002/adma.201605869] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/09/2016] [Indexed: 06/06/2023]
Abstract
A pathology-adaptive nanosystem, in which nest-like hosts are built based on nanofibers that are transformed from i.v. injected nanoparticles under the acidic tumor microenvironment. The solid tumor is artificially modified by nest-like hosts readily and firmly, resulting in highly efficient accumulation and stabilization of guest theranostics. This strategy shows great potential for the theranostics delivery to tumors.
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Affiliation(s)
- Pei-Pei Yang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Qiang Luo
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Faculty of Chemistry, Northeast Normal University, Changchun, 130024, China
| | - Guo-Bin Qi
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Yu-Juan Gao
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Bing-Nan Li
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Faculty of Chemistry, Northeast Normal University, Changchun, 130024, China
| | - Jing-Ping Zhang
- Faculty of Chemistry, Northeast Normal University, Changchun, 130024, China
| | - Lei Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Hao Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
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24
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Chandra B, Korn A, Maity BK, Adler J, Rawat A, Krueger M, Huster D, Maiti S. Stereoisomers Probe Steric Zippers in Amyloid-β. J Phys Chem B 2017; 121:1835-1842. [PMID: 28140589 DOI: 10.1021/acs.jpcb.6b12332] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Shape complementarity between close-packed residues plays a critical role in the amyloid aggregation process. Here, we probe such "steric zipper" interactions in amyloid-β (Aβ40), whose aggregation is linked to Alzheimer's disease, by replacing natural residues by their stereoisomers. Such mutations are expected to specifically destabilize the shape sensitive "packing" interactions, which may potentially increase their solubility and change other properties. We study the stereomutants DF19 and DL34 and also the DA2/DF4/DH6/DS8 mutant of Aβ40. F19-L34 is a critical contact in a tightly packed region of Aβ, while residues 1-9 are known to be disordered. While both DF19 and DL34 slow down the kinetics of aggregation and form amyloid fibrils efficiently, only DL34 increases the final solubility. DF19 gives rise to additional off-pathway aggregation which results in large, kinetically stable aggregates, and has lower net solubility. DA2/DF4/DH6/DS8 does not have an effect on the kinetics or the solubility. Notably, both DF19 and DL34 oligomers have a significantly lower level of interactions with lipid vesicles and live cells. We conclude that stereoisomers can cause complex site dependent changes in amyloid properties, and provide an effective tool to determine the role of individual residues in shaping the packed interiors of amyloid aggregates.
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Affiliation(s)
- Bappaditya Chandra
- Department of Chemical Science, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Alexander Korn
- Institut für Medizinische Physik und Biophysik, Universität Leipzig , Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Barun Kumar Maity
- Department of Chemical Science, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Juliane Adler
- Institut für Medizinische Physik und Biophysik, Universität Leipzig , Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Anoop Rawat
- Department of Chemical Science, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Martin Krueger
- Institut für Medizinische Physik und Biophysik, Universität Leipzig , Härtelstrasse 16-18, D-04107 Leipzig, Germany.,Institut für Anatomie, Universität Leipzig , Liebigstr. 13, D-04103 Leipzig, Germany
| | - Daniel Huster
- Institut für Medizinische Physik und Biophysik, Universität Leipzig , Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Sudipta Maiti
- Department of Chemical Science, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
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25
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Fan HM, Xu Q, Wei DQ. Recent Studies on Mechanisms of New Drug Candidates for Alzheimer’s Disease Interacting with Amyloid-β Protofibrils Using Molecular Dynamics Simulations. TRANSLATIONAL BIOINFORMATICS AND ITS APPLICATION 2017. [DOI: 10.1007/978-94-024-1045-7_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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26
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Hu X, Yang P, He J, Liang R, Niu D, Wang H, Li Y. In vivo self-assembly induced retention of gold nanoparticles for enhanced photothermal tumor treatment. J Mater Chem B 2017; 5:5931-5936. [DOI: 10.1039/c7tb01268c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A simple route to fabricate peptide modified spherical gold nanoparticles with enhanced retention performance in tumor sites for improved photothermal treatment.
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Affiliation(s)
- Xuefeng Hu
- Lab of Low-Dimensional Materials Chemistry
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Peipei Yang
- CAS Center for Excellence in Nanoscience
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety
- National Center for Nanoscience and Technology (NCNST)
- Beijing
- China
| | - Jianping He
- Lab of Low-Dimensional Materials Chemistry
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Ruijie Liang
- Lab of Low-Dimensional Materials Chemistry
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Dechao Niu
- Lab of Low-Dimensional Materials Chemistry
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Hao Wang
- CAS Center for Excellence in Nanoscience
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety
- National Center for Nanoscience and Technology (NCNST)
- Beijing
- China
| | - Yongsheng Li
- Lab of Low-Dimensional Materials Chemistry
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
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27
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Ruiz J, Boehringer R, Grogg M, Raya J, Schirer A, Crucifix C, Hellwig P, Schultz P, Torbeev V. Covalent Tethering and Residues with Bulky Hydrophobic Side Chains Enable Self-Assembly of Distinct Amyloid Structures. Chembiochem 2016; 17:2274-2285. [PMID: 27717158 DOI: 10.1002/cbic.201600440] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Indexed: 11/10/2022]
Abstract
Polymorphism is a common property of amyloid fibers that complicates their detailed structural and functional studies. Here we report experiments illustrating the chemical principles that enable the formation of amyloid polymorphs with distinct stoichiometric composition. Using appropriate covalent tethering we programmed self-assembly of a model peptide corresponding to the [20-41] fragment of human β2-microglobulin into fibers with either trimeric or dimeric amyloid cores. Using a set of biophysical and biochemical methods we demonstrated their distinct structural, morphological, and templating properties. Furthermore, we showed that supramolecular approaches in which the peptide is modified with bulky substituents can also be applied to modulate the formation of different fiber polymorphs. Such strategies, when applied to disease-related peptides and proteins, will greatly help in the evaluation of the biological properties of structurally distinct amyloids.
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Affiliation(s)
- Jérémy Ruiz
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-, UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Régis Boehringer
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-, UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Marcel Grogg
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-, UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Jésus Raya
- Membrane Biophysics and NMR, Institute of Chemistry, University of Strasbourg, CNRS-, UMR 7177, 4 rue Blaise Pascal, 67008, Strasbourg, France
| | - Alicia Schirer
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-, UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Corinne Crucifix
- Department of Integrated Structural Biology, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM-U964, University of Strasbourg, CNRS-, UMR 7104, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Petra Hellwig
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-, UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Patrick Schultz
- Department of Integrated Structural Biology, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM-U964, University of Strasbourg, CNRS-, UMR 7104, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Vladimir Torbeev
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-, UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
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28
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Slyngborg M, Nielsen DA, Fojan P. The Physical Properties and Self-Assembly Potential of the RFFFR Peptide. Chembiochem 2016; 17:2083-2092. [PMID: 27581944 DOI: 10.1002/cbic.201600383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Indexed: 12/22/2022]
Abstract
The self-assembly of fibers from peptides has attracted a tremendous amount of attention due to its many applications, such as in drug-delivery systems, in tissue engineering, and in electronic devices. Recently, the self-assembly potential of the designer peptide RFFFR has been reported. Here it is experimentally verified that the peptide forms fibers that are entangled and form solid spheres without water inside. Upon dilution below the critical fiber concentration, the fibers untangle and become totally separated prior to dissolution. These structures readily bind thioflavin T, resulting in a characteristic change in fluorescent properties consistent with β-sheet-rich amyloid structures with aromatic/hydrophobic grooves. The circular dichroism spectroscopy data are dominated by a π→π* transition, thus indicating that the fibers are stabilized by π-stacking. Contrary to what was expected, the dissolution of the spheres/fibers results in increasing fluorescence anisotropy over time. This is explained in terms of HomoFRET between phenylalanine residues with a T-shaped π-stacking mode, which was determined in another study to be the dominant mode through atomistic simulations and semiempirical calculations. Kelvin probe force microscopy measurements indicate that the spheres and fibers have a conductivity comparable to that of gold. Hence, these self-assembled structures might be applicable in organic solid-state electronic devices. The dissolution properties of the spheres further suggest that they might be used as drug-delivery systems.
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Affiliation(s)
- Morten Slyngborg
- Department of Physics and Nanotechnology, Aalborg University, Skjernvej 4 A, 9220, Aalborg Øst, Denmark
| | - Dennis Achton Nielsen
- Department of Physics and Nanotechnology, Aalborg University, Skjernvej 4 A, 9220, Aalborg Øst, Denmark
| | - Peter Fojan
- Department of Physics and Nanotechnology, Aalborg University, Skjernvej 4 A, 9220, Aalborg Øst, Denmark.
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29
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Truex NL, Wang Y, Nowick JS. Assembly of Peptides Derived from β-Sheet Regions of β-Amyloid. J Am Chem Soc 2016; 138:13882-13890. [PMID: 27642651 PMCID: PMC5089065 DOI: 10.1021/jacs.6b06000] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
In
Alzheimer’s disease, aggregation of the β-amyloid
peptide (Aβ) results in the formation of oligomers and fibrils
that are associated with neurodegeneration. Aggregation of Aβ
occurs through interactions between different regions of the peptide.
This paper and the accompanying paper constitute a two-part investigation
of two key regions of Aβ: the central region and the C-terminal
region. These two regions promote aggregation and adopt β-sheet
structure in the fibrils, and may also do so in the oligomers. In
this paper, we study the assembly of macrocyclic β-sheet peptides
that contain residues 17–23 (LVFFAED) from the central region
and residues 30–36 (AIIGLMV) from the C-terminal region. These
peptides assemble to form tetramers. Each tetramer consists of two
hydrogen-bonded dimers that pack through hydrophobic interactions
in a sandwich-like fashion. Incorporation of a single 15N isotopic label into each peptide provides a spectroscopic probe
with which to elucidate the β-sheet assembly and interaction: 1H,15N HSQC studies facilitate the identification
of the monomers and tetramers; 15N-edited NOESY studies
corroborate the pairing of the dimers within the tetramers. In the
following paper, J. Am. Chem. Soc.2016, DOI: 10.1021/jacs.6b06001, we will extend these studies to elucidate the coassembly of the
peptides to form heterotetramers.
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Affiliation(s)
- Nicholas L Truex
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - Yilin Wang
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
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30
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Turner JP, Chastain SE, Park D, Moss MA, Servoss SL. Modulating amyloid-β aggregation: The effects of peptoid side chain placement and chirality. Bioorg Med Chem 2016; 25:20-26. [PMID: 27776890 DOI: 10.1016/j.bmc.2016.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 10/20/2022]
Abstract
Alzheimer's disease (AD) is characterized by the buildup of insoluble aggregated amyloid-β protein (Aβ) into plaques that accumulate between the neural cells in the brain. AD is the sixth leading cause of death in the United States and is the only cause of death among the top ten that cannot currently be treated or cured (Alzheimer's Association, 2011; Selkoe, 1996). Researchers have focused on developing small molecules and peptides to prevent Aβ aggregation; however, while some compounds appear promising in vitro, the research has not resulted in a viable therapeutic treatment. We previously reported a peptoid-based mimic (JPT1) of the peptide KLVFF (residues 16-20 of Aβ) that modulates Aβ40 aggregation, specifically reducing the total number of fibrillar, β-sheet structured aggregates formed. In this study, we investigate two new variants of JPT1 that probe the importance of aromatic side chain placement (JPT1s) and side chain chirality (JPT1a). Both JPT1s and JPT1a modulate Aβ40 aggregation by reducing total β-sheet aggregates. However, JPT1a also has a pronounced effect on the morphology of fibrillar Aβ40 aggregates. These results suggest that Aβ40 aggregation may follow a different pathway in the presence of peptoids with different secondary structures. A better understanding of the interactions between peptoids and Aβ will allow for improved design of AD treatments.
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Affiliation(s)
- J Phillip Turner
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas, 3202 Bell Engineering Center, Fayetteville, AR 72701, USA
| | - Shelby E Chastain
- Biomedical Engineering Program, University of South Carolina, 1B33 Swearingen Engineering Center, Columbia, SC 29208, USA
| | - Dongwon Park
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas, 3202 Bell Engineering Center, Fayetteville, AR 72701, USA
| | - Melissa A Moss
- Biomedical Engineering Program, University of South Carolina, 1B33 Swearingen Engineering Center, Columbia, SC 29208, USA; Department of Chemical Engineering, University of South Carolina, 2C02 Swearingen Engineering Center, Columbia, SC 29208, USA
| | - Shannon L Servoss
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas, 3202 Bell Engineering Center, Fayetteville, AR 72701, USA.
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31
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Amino acid substitutions [K16A] and [K28A] distinctly affect amyloid β-protein oligomerization. J Biol Phys 2016; 42:453-76. [PMID: 27155979 DOI: 10.1007/s10867-016-9417-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/28/2016] [Indexed: 10/21/2022] Open
Abstract
Amyloid β-protein (A β) assembles into oligomers that play a seminal role in Alzheimer's disease (AD), a leading cause of dementia among the elderly. Despite undisputed importance of A β oligomers, their structure and the basis of their toxicity remain elusive. Previous experimental studies revealed that the [K16A] substitution strongly inhibits toxicity of the two predominant A β alloforms in the brain, A β 40 and A β 42, whereas the [K28A] substitution exerts only a moderate effect. Here, folding and oligomerization of [A16]A β 40, [A28]A β 40, [A16]A β 42, and [A28]A β 42 are examined by discrete molecular dynamics (DMD) combined with a four-bead implicit solvent force field, DMD4B-HYDRA, and compared to A β 40 and A β 42 oligomer formation. Our results show that both substitutions promote A β 40 and A β 42 oligomerization and that structural changes to oligomers are substitution- and alloform-specific. The [K28A] substitution increases solvent-accessible surface area of hydrophobic residues and the intrapeptide N-to-C terminal distance within oligomers more than the [K16A] substitution. The [K16A] substitution decreases the overall β-strand content, whereas the [K28A] substitution exerts only a modest change. Substitution-specific tertiary and quaternary structure changes indicate that the [K16A] substitution induces formation of more compact oligomers than the [K28A] substitution. If the structure-function paradigm applies to A β oligomers, then the observed substitution-specific structural changes in A β 40 and A β 42 oligomers are critical for understanding the structural basis of A β oligomer toxicity and correct identification of therapeutic targets against AD.
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32
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Liang CT, Huang HB, Wang CC, Chen YR, Chang CF, Shiao MS, Chen YC, Lin TH. L17A/F19A Substitutions Augment the α-Helicity of β-Amyloid Peptide Discordant Segment. PLoS One 2016; 11:e0154327. [PMID: 27104649 PMCID: PMC4841593 DOI: 10.1371/journal.pone.0154327] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/12/2016] [Indexed: 11/18/2022] Open
Abstract
β-amyloid peptide (Aβ) aggregation has been thought to be associated with the pathogenesis of Alzheimer’s disease. Recently, we showed that L17A/F19A substitutions may increase the structural stability of wild-type and Arctic-type Aβ40 and decrease the rates of structural conversion and fibril formation. However, the underlying mechanism for the increase of structural stability as a result of the alanine substitutions remained elusive. In this study, we apply nuclear magnetic resonance and circular dichroism spectroscopies to characterize the Aβ40 structure, demonstrating that L17A/F19A substitutions can augment the α-helicity of the residues located in the α/β-discordant segment (resides 15 to 23) of both wild-type and Arctic-type Aβ40. These results provide a structural basis to link the α-helicity of the α/β-discordant segment with the conformational conversion propensity of Aβ.
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Affiliation(s)
- Chu-Ting Liang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Basic Research Division, Medical Research Department, Taipei Veterans General Hospital, Taipei, Taiwan, R.O.C
| | - Hsien-Bin Huang
- Department of Life Science and the Institute of Molecular Biology, National Chung Cheng University, Chiayi, Taiwan, R.O.C
| | - Chih-Ching Wang
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Institute of Biochemistry & Molecular Biology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Yi-Ru Chen
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Department and Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
| | - Ming-Shi Shiao
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - Yi-Cheng Chen
- Department of Medicine, Mackay Medical College, Taipei, Taiwan, R.O.C
- * E-mail: (YCC); (THL)
| | - Ta-Hsien Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Basic Research Division, Medical Research Department, Taipei Veterans General Hospital, Taipei, Taiwan, R.O.C
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Institute of Biochemistry & Molecular Biology, National Yang-Ming University, Taipei, Taiwan, R.O.C
- * E-mail: (YCC); (THL)
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33
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Conformational transition of Aβ 42 inhibited by a mimetic peptide. A molecular modeling study using QM/MM calculations and QTAIM analysis. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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34
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Macdonald B, McCarley S, Noeen S, van Giessen AE. β-Hairpin Crowding Agents Affect α-Helix Stability in Crowded Environments. J Phys Chem B 2016; 120:650-9. [DOI: 10.1021/acs.jpcb.5b10575] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Bryanne Macdonald
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Shannon McCarley
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Sundus Noeen
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Alan E. van Giessen
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
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35
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Yang PP, Zhao XX, Xu AP, Wang L, Wang H. Reorganization of self-assembled supramolecular materials controlled by hydrogen bonding and hydrophilic–lipophilic balance. J Mater Chem B 2016; 4:2662-2668. [DOI: 10.1039/c6tb00097e] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The process of in situ morphology transformation of the polymeric peptide (BKP) from nanoparticles to nanofibers controlled by H-bonds and hydrophobic interactions is explored. Increasing hydrophilic chain length of the molecule accelerates the morphology transformation.
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Affiliation(s)
- Pei-Pei Yang
- CAS Center for Excellence in Nanoscience
- Laboratory for Biological Effects of Nanomaterials and Nanosafety
- National Center for Nanoscience and Technology
- Beijing
- China
| | - Xiao-Xiao Zhao
- CAS Center for Excellence in Nanoscience
- Laboratory for Biological Effects of Nanomaterials and Nanosafety
- National Center for Nanoscience and Technology
- Beijing
- China
| | - An-Ping Xu
- CAS Center for Excellence in Nanoscience
- Laboratory for Biological Effects of Nanomaterials and Nanosafety
- National Center for Nanoscience and Technology
- Beijing
- China
| | - Lei Wang
- CAS Center for Excellence in Nanoscience
- Laboratory for Biological Effects of Nanomaterials and Nanosafety
- National Center for Nanoscience and Technology
- Beijing
- China
| | - Hao Wang
- CAS Center for Excellence in Nanoscience
- Laboratory for Biological Effects of Nanomaterials and Nanosafety
- National Center for Nanoscience and Technology
- Beijing
- China
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36
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Protein N-homocysteinylation: From cellular toxicity to neurodegeneration. Biochim Biophys Acta Gen Subj 2015; 1850:2239-45. [DOI: 10.1016/j.bbagen.2015.08.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/18/2015] [Accepted: 08/24/2015] [Indexed: 12/29/2022]
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37
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Kumar A, Srivastava S, Tripathi S, Singh SK, Srikrishna S, Sharma A. Molecular insight into amyloid oligomer destabilizing mechanism of flavonoid derivative 2-(4' benzyloxyphenyl)-3-hydroxy-chromen-4-one through docking and molecular dynamics simulations. J Biomol Struct Dyn 2015. [PMID: 26208790 DOI: 10.1080/07391102.2015.1074943] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Aggregation of amyloid peptide (Aβ) has been shown to be directly related to progression of Alzheimer's disease (AD). Aβ is neurotoxic and its deposition and aggregation ultimately lead to cell death. In our previous work, we reported flavonoid derivative (compound 1) showing promising result in transgenic AD model of Drosophila. Compound 1 showed prevention of Aβ-induced neurotoxicity and neuroprotective efficacy in Drosophila system. However, mechanism of action of compound 1 and its effect on the amyloid is not known. We therefore performed molecular docking and atomistic, explicit-solvent molecular dynamics simulations to investigate the process of Aβ interaction, inhibition, and destabilizing mechanism. Results showed different preferred binding sites of compound 1 and good affinity toward the target. Through the course of 35 ns molecular dynamics simulation, conformations_5 of compound 1 intercalates into the hydrophobic core near the salt bridge and showed major structural changes as compared to other conformations. Compound 1 showed interference with the salt bridge and thus reducing the inter strand hydrogen bound network. This minimizes the side chain interaction between the chains A-B leading to disorder in oligomer. Contact map analysis of amino acid residues between chains A and B also showed lesser interaction with adjacent amino acids in the presence of compound 1 (conformations_5). The study provides an insight into how compound 1 interferes and disorders the Aβ peptide. These findings will further help to design better inhibitors for aggregation of the amyloid oligomer.
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Affiliation(s)
- Akhil Kumar
- a Biotechnology Division , CSIR-Central Institute of Medicinal and Aromatic Plants , P.O. - CIMAP, Near Kukrail Picnic Spot, Lucknow 226015 , Uttar Pradesh , India
| | - Swati Srivastava
- a Biotechnology Division , CSIR-Central Institute of Medicinal and Aromatic Plants , P.O. - CIMAP, Near Kukrail Picnic Spot, Lucknow 226015 , Uttar Pradesh , India
| | - Shubhandra Tripathi
- a Biotechnology Division , CSIR-Central Institute of Medicinal and Aromatic Plants , P.O. - CIMAP, Near Kukrail Picnic Spot, Lucknow 226015 , Uttar Pradesh , India
| | - Sandeep Kumar Singh
- b Faculty of Science, Department of Biochemistry , Banaras Hindu University , Varanasi 221005 , Uttar Pradesh , India
| | - Saripella Srikrishna
- b Faculty of Science, Department of Biochemistry , Banaras Hindu University , Varanasi 221005 , Uttar Pradesh , India
| | - Ashok Sharma
- a Biotechnology Division , CSIR-Central Institute of Medicinal and Aromatic Plants , P.O. - CIMAP, Near Kukrail Picnic Spot, Lucknow 226015 , Uttar Pradesh , India
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38
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Pietropaolo A, Satriano C, Strano G, La Mendola D, Rizzarelli E. Different zinc(II) complex species and binding modes at Aβ N-terminus drive distinct long range cross-talks in the Aβ monomers. J Inorg Biochem 2015; 153:367-376. [PMID: 26298865 DOI: 10.1016/j.jinorgbio.2015.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 07/24/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
Abstract
The present study addresses the reconstruction of the free-energy landscapes of amyloid-beta1-42 (Aβ42) coordinated respectively with one and two zinc ions, to scrutinize whether different Aβ-zinc complex species, i.e., mononuclear and dinuclear metal complexes, induce different Aβ conformation features. We found a subtle switch of intramolecular interactions, depending both on the zinc coordination environment and on the peptide to zinc stoichiometric ratio. On the one side, hairpin-like structures are predominant in mononuclear complexes, where a salt-bridge that involves Lys28-Glu22 and Lys16-Asp23 is stabilized. On the other side, elongated conformations are instead stabilized in the dinuclear zinc complexes. Experimental studies of atomic force microscopy as well as of zinc-Aβ complex species distribution diagrams provide evidence that the theoretical calculations can be rationalized in terms of the correlation between the increased amount of amorphous aggregates and the Aβ/Zn(2+) ratio.
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Affiliation(s)
- Adriana Pietropaolo
- Dipartimento di Scienze della Salute, Università di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Cristina Satriano
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, viale Andrea Doria, 6, 95125 Catania, Italy
| | - Gaetano Strano
- Fondazione RI.MED, Via Bandiera 11, 90133 Palermo, Italy
| | - Diego La Mendola
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano, 6, 56126 Pisa, Italy
| | - Enrico Rizzarelli
- Istituto di Biostrutture e Bioimagini-Consiglio Nazionale delle Ricerche (IBB-CNR), Via Paolo Gaifami, 18, 95126 Catania, Italy.
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39
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Liu H, Ojha B, Morris C, Jiang M, Wojcikiewicz EP, Rao PPN, Du D. Positively Charged Chitosan and N-Trimethyl Chitosan Inhibit Aβ40 Fibrillogenesis. Biomacromolecules 2015; 16:2363-73. [DOI: 10.1021/acs.biomac.5b00603] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | | | | | | | | | - Praveen P. N. Rao
- School
of Pharmacy, Health Sciences Campus, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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40
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Gao G, Zhang M, Lu P, Guo G, Wang D, Sun T. Chirality-Assisted Ring-Like Aggregation of Aβ(1-40) at Liquid-Solid Interfaces: A Stereoselective Two-Step Assembly Process. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410768] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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41
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Gao G, Zhang M, Lu P, Guo G, Wang D, Sun T. Chirality-assisted ring-like aggregation of aβ(1-40) at liquid-solid interfaces: a stereoselective two-step assembly process. Angew Chem Int Ed Engl 2014; 54:2245-50. [PMID: 25533756 DOI: 10.1002/anie.201410768] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 11/29/2014] [Indexed: 11/07/2022]
Abstract
Molecular chirality is introduced at liquid-solid interfaces. A ring-like aggregation of amyloid Aβ(1-40) on N-isobutyryl-L-cysteine (L-NIBC)-modified gold substrate occurs at low Aβ(1-40) concentration, while D-NIBC modification only results in rod-like aggregation. Utilizing atomic force microscope controlled tip-enhanced Raman scattering, we directly observe the secondary structure information for Aβ(1-40) assembly in situ at the nanoscale. D- or L-NIBC on the surface can guide parallel or nonparallel alignment of β-hairpins through a two-step process based on electrostatic-interaction-enhanced adsorption and subsequent stereoselective recognition. Possible electrostatic interaction sites (R5 and K16) and a chiral recognition site (H14) of Aβ(1-40) are proposed, which may provide insight into the understanding of this effect.
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Affiliation(s)
- Guanbin Gao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070 (PR China)
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42
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Shi H, Kang B, Lee JY. Zn2+ Effect on Structure and Residual Hydrophobicity of Amyloid β-Peptide Monomers. J Phys Chem B 2014; 118:10355-61. [DOI: 10.1021/jp504779m] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hu Shi
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-Ro, Jangan-Gu, Suwon 440-746, South Korea
| | - Baotao Kang
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-Ro, Jangan-Gu, Suwon 440-746, South Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-Ro, Jangan-Gu, Suwon 440-746, South Korea
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43
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Turner JP, Lutz-Rechtin T, Moore KA, Rogers L, Bhave O, Moss MA, Servoss SL. Rationally designed peptoids modulate aggregation of amyloid-beta 40. ACS Chem Neurosci 2014; 5:552-8. [PMID: 24689364 DOI: 10.1021/cn400221u] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia and the sixth leading cause of death in the United States. Plaques composed of aggregated amyloid-beta protein (Aβ) accumulate between the neural cells in the brain and are associated with dementia and cellular death. Many strategies have been investigated to prevent Aβ self-assembly into disease-associated β-sheet amyloid aggregates; however, a promising therapeutic has not yet been identified. In this study, a peptoid-based mimic of the peptide KLVFF (residues 16-20 of Aβ) was tested for its ability to modulate Aβ aggregation. Peptoid JPT1 includes chiral, aromatic side chains to induce formation of a stable helical secondary structure that allows for greater interaction between the aromatic side chains and the cross β-sheet of Aβ. JPT1 was found to modulate Aβ40 aggregation, specifically decreasing lag time to β-sheet aggregate formation as well as the total number of fibrillar, β-sheet structured aggregates formed. These results suggest that peptoids may be able to limit the formation of Aβ aggregates that are associated with AD.
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Affiliation(s)
- J. Phillip Turner
- Department of Chemical Engineering, University of Arkansas, 3202 Bell
Engineering Center, Fayetteville, Arkansas 72701, United States
| | - Tammy Lutz-Rechtin
- Department of Chemical Engineering, University of Arkansas, 3202 Bell
Engineering Center, Fayetteville, Arkansas 72701, United States
| | - Kelly A. Moore
- Department of Chemical Engineering, University of South Carolina, 2C02 Swearingen Engineering Center, Columbia, South Carolina 29208, United States
| | - Lauren Rogers
- Department of Chemical Engineering, University of Arkansas, 3202 Bell
Engineering Center, Fayetteville, Arkansas 72701, United States
| | - Omkar Bhave
- Department of Chemical Engineering, University of Arkansas, 3202 Bell
Engineering Center, Fayetteville, Arkansas 72701, United States
| | - Melissa A. Moss
- Department of Chemical Engineering, University of South Carolina, 2C02 Swearingen Engineering Center, Columbia, South Carolina 29208, United States
| | - Shannon L. Servoss
- Department of Chemical Engineering, University of Arkansas, 3202 Bell
Engineering Center, Fayetteville, Arkansas 72701, United States
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44
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Kannan R, Raju M, Sharma KK. The critical role of the central hydrophobic core (residues 71-77) of amyloid-forming αA66-80 peptide in α-crystallin aggregation: a systematic proline replacement study. Amyloid 2014; 21:103-9. [PMID: 24547912 PMCID: PMC4151328 DOI: 10.3109/13506129.2014.888994] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Age-related cataract formation is marked by the progressive aggregation of lens proteins. The formation of protein aggregates in the aging lens has been shown to correlate with the progressive accumulation of a range of post-translational crystallin modifications, including oxidation, deamidation, racemization, methylation, acetylation, N- and C-terminal truncations and low molecular weight (LMW) crystallin fragments. We found that an αA-crystallin-derived peptide, αA66-80 (1.8 kDa), is a prominent LMW peptide concentrated in water-insoluble fractions of the aging lens. The peptide has amyloid-like properties and preferentially insolubilizes α-crystallin from lens-soluble fractions. It binds at multiple sites and forms a hydrophobically driven non-covalent complex with α-crystallin to induce α-crystallin aggregation. To define the specific role of the αA66-80 peptide in age-related protein aggregation and cataract formation, it is important to understand the mechanisms by which this peptide acts. We used scanning proline mutagenesis to identify which particular sequences of the peptide drive it to form amyloid-like fibrils and induce α-crystallin aggregation. The secondary structure and the aggregate morphology of the peptides were determined using circular dichroism and transmission electron microscopy, respectively. Peptides were also tested for their ability to induce α-crystallin aggregation. We found that proline replacement of any residue in the sequence FVIFLDV, which corresponds to residues 71-77, led to an absence of both fibril formation and α-crystallin aggregation. The apparently critical role of 71-77 residues in αA66-80 explains their significance in the self-assembly processes of the peptide and further provide insights into the mechanism of peptide-induced aggregation. Our findings may have applications in the design of peptide aggregation inhibitors.
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Affiliation(s)
- Rama Kannan
- Department of Biochemistry, University of Missouri , Columbia, MO , USA and
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45
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Jana AK, Sengupta N. Surface induced collapse of Aβ1-42 with the F19A replacement following adsorption on a single walled carbon nanotube. Biophys Chem 2013; 184:108-15. [DOI: 10.1016/j.bpc.2013.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/25/2013] [Accepted: 09/28/2013] [Indexed: 12/12/2022]
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46
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Alzheimer’s disease: A gas model. The NADPH oxidase–Nitric Oxide system as an antibubble biomachinery. Med Hypotheses 2013; 81:976-87. [DOI: 10.1016/j.mehy.2013.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 09/08/2013] [Indexed: 01/01/2023]
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47
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Li G, Pomès R. Binding mechanism of inositol stereoisomers to monomers and aggregates of Aβ(16-22). J Phys Chem B 2013; 117:6603-13. [PMID: 23627280 DOI: 10.1021/jp311350r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Alzheimer's disease (AD) is a severe neurodegenerative disease with no cure. A potential therapeutic approach is to prevent or reverse the amyloid formation of Aβ42, a key pathological hallmark of AD. We examine the molecular basis for stereochemistry-dependent inhibition of the formation of Aβ fibrils in vitro by a polyol, scyllo-inositol. We present molecular dynamics simulations of the monomeric, disordered aggregate, and protofibrillar states of Aβ(16-22), an amyloid-forming peptide fragment of full-length Aβ, successively with and without scyllo-inositol and its inactive stereoisomer chiro-inositol. Both stereoisomers bind monomers and disordered aggregates with similar affinities of 10-120 mM, whereas binding to β-sheet-containing protofibrils yields affinities of 0.2-0.5 mM commensurate with in vitro inhibitory concentrations of scyllo-inositol. Moreover, scyllo-inositol displays a higher binding specificity for phenylalanine-lined grooves on the protofibril surface, suggesting that scyllo-inositol coats the surface of Aβ protofibrils and disrupts their lateral stacking into amyloid fibrils.
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Affiliation(s)
- Grace Li
- Department of Biochemistry, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
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48
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Verma S, Singh A, Mishra A. The effect of fulvic acid on pre‐ and postaggregation state of Aβ17–42: Molecular dynamics simulation studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:24-33. [DOI: 10.1016/j.bbapap.2012.08.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 07/25/2012] [Accepted: 08/20/2012] [Indexed: 11/25/2022]
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49
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Cukalevski R, Boland B, Frohm B, Thulin E, Walsh D, Linse S. Role of aromatic side chains in amyloid β-protein aggregation. ACS Chem Neurosci 2012; 3:1008-16. [PMID: 23259036 PMCID: PMC3526965 DOI: 10.1021/cn300073s] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 09/24/2012] [Indexed: 12/23/2022] Open
Abstract
Aggregation of the amyloid β-protein (Aβ) is believed to be involved in Alzheimer's disease pathogenesis. Here we have investigated the importance of the aromatic rings at positions 19 and 20 for the aggregation rate and mechanism by substituting phenylalanine with leucine. Aggregation kinetics were monitored as a function of time and peptide concentration by thioflavin T (ThT) fluorescence, the aggregation equilibrium by sedimentation assay, structural changes using circular dichroism spectroscopy and the presence of fibrillar material was detected with cryo-transmission electron microscopy. All peptides convert from monomer to amyloid fibrils in a concentration-dependent manner. Substituting F19 with leucine results in a peptide that aggregates significantly slower than the wild type, while substitution of F20 produces a peptide that aggregates faster. The effects of the two substitutions are additive, since simultaneous substitution of F19 and F20 produces a peptide with aggregation kinetics intermediate between F19L and F20L. Our results suggest that the aromatic side-chain of F19 favors nucleation of the aggregation process and may be an important target for therapeutic intervention.
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Affiliation(s)
- Risto Cukalevski
- Chemistry Department and Molecular Protein Science, Lund University, P.O. Box 124, SE221 00 Lund, Sweden
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50
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An effector-reduced anti-β-amyloid (Aβ) antibody with unique aβ binding properties promotes neuroprotection and glial engulfment of Aβ. J Neurosci 2012; 32:9677-89. [PMID: 22787053 DOI: 10.1523/jneurosci.4742-11.2012] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Passive immunization against β-amyloid (Aβ) has become an increasingly desirable strategy as a therapeutic treatment for Alzheimer's disease (AD). However, traditional passive immunization approaches carry the risk of Fcγ receptor-mediated overactivation of microglial cells, which may contribute to an inappropriate proinflammatory response leading to vasogenic edema and cerebral microhemorrhage. Here, we describe the generation of a humanized anti-Aβ monoclonal antibody of an IgG4 isotype, known as MABT5102A (MABT). An IgG4 subclass was selected to reduce the risk of Fcγ receptor-mediated overactivation of microglia. MABT bound with high affinity to multiple forms of Aβ, protected against Aβ1-42 oligomer-induced cytotoxicity, and increased uptake of neurotoxic Aβ oligomers by microglia. Furthermore, MABT-mediated amyloid plaque removal was demonstrated using in vivo live imaging in hAPP((V717I))/PS1 transgenic mice. When compared with a human IgG1 wild-type subclass, containing the same antigen-binding variable domains and with equal binding to Aβ, MABT showed reduced activation of stress-activated p38MAPK (p38 mitogen-activated protein kinase) in microglia and induced less release of the proinflammatory cytokine TNFα. We propose that a humanized IgG4 anti-Aβ antibody that takes advantage of a unique Aβ binding profile, while also possessing reduced effector function, may provide a safer therapeutic alternative for passive immunotherapy for AD. Data from a phase I clinical trial testing MABT is consistent with this hypothesis, showing no signs of vasogenic edema, even in ApoE4 carriers.
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