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Dangi A, Qureshi T, Chinnathambi S, Kiran Marelli U. Macrocyclic peptides derived from AcPHF6* and AcPHF6 to selectively modulate the Tau aggregation. Bioorg Chem 2024; 151:107625. [PMID: 39013241 DOI: 10.1016/j.bioorg.2024.107625] [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: 05/30/2024] [Revised: 06/28/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024]
Abstract
Ten macrocyclic peptides, each comprising 14 amino acids, were designed and synthesized based on the Tau aggregation model hexapeptides AcPHF6* and AcPHF6. The design took into account the aggregation tendencies of each residue in AcPHF6* and AcPHF6, their aggregation models, while employing peptide-based structural design principles including N-methylation to promote turns and to block hydrogen bond propagation and elongation of the aggregation chain. NMR analysis supported that all these peptides adopted an antiparallel β-sheet conformation. Self-aggregation studies characterized the aggregation properties of these peptides, identifying two peptides with the highest (P3) and lowest (P8) aggregation tendencies. In cross-aggregation studies with the parent peptides AcPHF6* and AcPHF6, P3 and P8 were found to promote and reduce aggregation, respectively. Furthermore, P3 and P8 demonstrated an enhancement and diminution effect on the aggregation of K18wt, indicating their capacity to modulate aggregation even at the macromolecular level. Thus, the two simple peptides, P3 and P8 selectively exhibit pro- or anti-aggregation effects on PHF peptides and Tau. This study, has thus developed structurally well-defined non-complex peptides, derived from AcPHF6* and AcPHF6, to modulate Tau aggregation as desired, offering applications in Tau model studies and the development of Tau aggregation inhibitors or promoters.
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Affiliation(s)
- Abha Dangi
- Central NMR Facility, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India; Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, UP, 201002, India
| | - Tazeen Qureshi
- Neurobiology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, UP, 201002, India
| | - Subashchandrabose Chinnathambi
- Neurobiology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, UP, 201002, India.
| | - Udaya Kiran Marelli
- Central NMR Facility, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India; Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, UP, 201002, India.
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2
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Shah SJA, Zhang Q, Guo J, Liu H, Liu H, Villà-Freixa J. Identification of Aggregation Mechanism of Acetylated PHF6* and PHF6 Tau Peptides Based on Molecular Dynamics Simulations and Markov State Modeling. ACS Chem Neurosci 2023; 14:3959-3971. [PMID: 37830541 DOI: 10.1021/acschemneuro.3c00578] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
The microtubule-associated protein tau (MAPT) has a critical role in the development and preservation of the nervous system. However, tau's dysfunction and accumulation in the human brain can lead to several neurodegenerative diseases, such as Alzheimer's disease, Down's syndrome, and frontotemporal dementia. The microtubule binding (MTB) domain plays a significant, important role in determining the tau's pathophysiology, as the core of paired helical filaments PHF6* (275VQIINK280) and PHF6 (306VQIVYK311) of R2 and R3 repeat units, respectively, are formed in this region, which promotes tau aggregation. Post-translational modifications, and in particular lysine acetylation at K280 of PHF6* and K311 of PHF6, have been previously established to promote tau misfolding and aggregation. However, the exact aggregation mechanism is not known. In this study, we established an atomic-level nucleation-extension mechanism of the separated aggregation of acetylated PHF6* and PHF6 hexapeptides, respectively, of tau. We show that the acetylation of the lysine residues promotes the formation of β-sheet enriched high-ordered oligomers. The Markov state model analysis of ac-PHF6* and ac-PHF6 aggregation revealed the formation of an antiparallel dimer nucleus which could be extended from both sides in a parallel manner to form mixed-oriented and high-ordered oligomers. Our study describes the detailed mechanism for acetylation-driven tau aggregation, which provides valuable insights into the effect of post-translation modification in altering the pathophysiology of tau hexapeptides.
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Affiliation(s)
| | - Qianqian Zhang
- Faculty of Applied Sciences, Macao Polytechnic University, 999078 Macao, SAR, China
| | - Jingjing Guo
- Faculty of Applied Sciences, Macao Polytechnic University, 999078 Macao, SAR, China
| | - Hongli Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 221004 Xuzhou, Jiangsu, China
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, 999078 Macao, SAR, China
| | - Jordi Villà-Freixa
- Departament de Biociències, Universitat de Vic─Universitat Central de Catalunya, 08500 Vic, Spain
- Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central (IRIS-CC), 08500 Vic, Spain
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Akbari V, Mohammadi S, Mehrabi M, Ghobadi S, Farrokhi A, Khodarahmi R. Investigation of the role of prolines 232/233 in RTPPK motif in tau protein aggregation: An in vitro study. Int J Biol Macromol 2022; 219:1100-1111. [PMID: 36049563 DOI: 10.1016/j.ijbiomac.2022.08.160] [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: 02/17/2022] [Revised: 07/26/2022] [Accepted: 08/23/2022] [Indexed: 11/18/2022]
Abstract
Disease-related tau protein in Alzheimer's disease is hyperphosphorylated and aggregates into neurofibrillary tangles. The cis-proline isomer of the pSer/Thr-Pro sequence has been proposed to act as a precursor of aggregation ('Cistauosis' hypothesis), but this aggregation scheme is not yet entirely accepted. Hence to investigate isomer-specific-aggregation of tau, proline residues at the RTPPK motif were replaced by alanine residues (with permanent trans configuration) employing genetic engineering methods. RTPAK, RTAPK, and RTAAK mutant variants of tau were generated, and their in vitro aggregation propensity was investigated using multi-spectroscopic techniques. Besides, the cell toxicity of oligomers/fibrils was analyzed and compared to those of the wild-type (WT) tau. Analyses of mutant variants have shown to be in agreement (to some degree) to the theory of the 'cistauosis' hypothesis. The results showed that the trans isomer in the 232-rd residue (P232A mutant rather than P233A) had reduced aggregation propensity. However, this study did not illustrate any statistically significant difference between the wild and the mutant protein aggregations concerning cell toxicity.
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Affiliation(s)
- Vali Akbari
- Department of Biology, Faculty of Sciences, Razi University, Kermanshah, Iran; Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences (KUMS), Kermanshah, Iran
| | - Soheila Mohammadi
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Masomeh Mehrabi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences (KUMS), Kermanshah, Iran
| | - Sirous Ghobadi
- Department of Biology, Faculty of Sciences, Razi University, Kermanshah, Iran.
| | - Alireza Farrokhi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences (KUMS), Kermanshah, Iran
| | - Reza Khodarahmi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences (KUMS), Kermanshah, Iran; Department of Pharmacognosy and Biotechnology, Faculty of Pharmacy, Kermanshah University of Medical Sciences (KUMS), Kermanshah, Iran.
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4
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Sakata T, Shiratori R, Kato M. Hydrogel-Coated Gate Field-Effect Transistor for Real-Time and Label-Free Monitoring of β-Amyloid Aggregation and Its Inhibition. Anal Chem 2022; 94:2820-2826. [PMID: 35119275 DOI: 10.1021/acs.analchem.1c04339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper, we propose a hydrogel-coated gate field-effect transistor (FET) for the real-time and label-free monitoring of β-amyloid (Aβ) aggregation and its inhibition. The hydrogel used in this study is composed of poly tetramethoxysilane (TMOS), in which Aβ monomers are entrapped and then aggregate, and coated on the gate insulator; that is, Aβ aggregation is induced in the vicinity of the sensing surface. With the Aβ hydrogel-coated gate FET, the steplike decrease in the surface potential of the Aβ hydrogel-coated gate electrode is electrically monitored in real time, according to the stepwise aggregation of Aβ monomers to form into fibrils through oligomers and so forth in stages. This is because the capacitance of the Aβ-hydrogel membrane decreases depending on the stage of aggregation; that is, the hydrophobicity of the Aβ-hydrogel membrane increases stepwise depending on the amount of Aβ aggregates. The formation of Aβ fibrils is also confirmed in the measurement solution using a fluorescent dye, thioflavin T, which selectively binds to the Aβ fibrils. Moreover, the addition of daunomycin, an inhibitor of Aβ aggregation, to the measurement solution suppresses the stepwise electrical response of the Aβ hydrogel-coated gate FET. Thus, a platform based on the Aβ hydrogel-coated gate FET is suitable for a simple screening system for inhibitors of Aβ aggregation, which may lead the identification of potential therapeutic agents for Alzheimer's disease.
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Affiliation(s)
- Toshiya Sakata
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Reiko Shiratori
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masaru Kato
- Department of Bioanalytical Chemistry, School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
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Nguyen PH, Tufféry P, Derreumaux P. Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations. Methods Mol Biol 2022; 2405:95-113. [PMID: 35298810 DOI: 10.1007/978-1-0716-1855-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Amyloid fibril formation is an intrinsic property of short peptides, non-disease proteins, and proteins associated with neurodegenerative diseases. Aggregates of the Aβ and tau proteins, the α-synuclein protein, and the prion protein are observed in the brain of Alzheimer's, Parkinson's, and prion disease patients, respectively. Due to the transient short-range and long-range interactions of all species and their high aggregation propensities, the conformational ensemble of these devastating proteins, the exception being for the monomeric prion protein, remains elusive by standard structural biology methods in bulk solution and in lipid membranes. To overcome these limitations, an increasing number of simulations using different sampling methods and protein models have been performed. In this chapter, we first review our main contributions to the field of amyloid protein simulations aimed at understanding the early aggregation steps of short linear amyloid peptides, the conformational ensemble of the Aβ40/42 dimers in bulk solution, and the stability of Aβ aggregates in lipid membrane models. Then we focus on our studies on the interactions of amyloid peptides/inhibitors to prevent aggregation, and long amyloid sequences, including new results on a monomeric tau construct.
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Affiliation(s)
- Phuong Hoang Nguyen
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Pierre Tufféry
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, RPBS, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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De SK, Maity A, Chakraborty A. Underlying Mechanisms for the Modulation of Self-Assembly and the Intrinsic Fluorescent Properties of Amino Acid-Functionalized Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5022-5033. [PMID: 33856214 DOI: 10.1021/acs.langmuir.1c00431] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The origin of the blue fluorescence of proteins and peptides in the visible region has been a subject of intense debate despite several efforts. Although aromatic amino acids, namely tryptophan (Trp), tyrosine (Tyr), and phenylalanine (Phe) are responsible for the intrinsic luminescence of proteins and peptides, the underlying mechanism and contributions of these amino acids to the unusual blue fluorescence are still not well resolved. In the present endeavor, we show that the clusterization of both aromatic and aliphatic amino acids on the surface of the gold nanoparticles (Au NPs) leads to clusteroluminescence, which could be linked to the unusual fluorescence properties of the proteins and peptides and have been ignored in the past. The amino acid monomers initially form small aggregates through clusterization, which provides the fundamental building blocks to establish the amyloid structure as well as the luminescence property. Because of the clusterization, these Au NPs/nano-aggregate systems are also found to exhibit remarkable stability against the freeze-thaw cycle and several other external stimuli, which can be useful for biological and biomedical applications.
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Affiliation(s)
- Soumya Kanti De
- Discipline of Chemistry, Indian Institute of Technology Indore, Indore 452020, Madhya Pradesh, India
| | - Avijit Maity
- Discipline of Chemistry, Indian Institute of Technology Indore, Indore 452020, Madhya Pradesh, India
| | - Anjan Chakraborty
- Discipline of Chemistry, Indian Institute of Technology Indore, Indore 452020, Madhya Pradesh, India
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Yang J, Agnihotri MV, Huseby CJ, Kuret J, Singer SJ. A theoretical study of polymorphism in VQIVYK fibrils. Biophys J 2021; 120:1396-1416. [PMID: 33571490 DOI: 10.1016/j.bpj.2021.01.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 02/06/2023] Open
Abstract
The VQIVYK fragment from the Tau protein, also known as PHF6, is essential for aggregation of Tau into neurofibrillary lesions associated with neurodegenerative diseases. VQIVYK itself forms amyloid fibrils composed of paired β-sheets. Therefore, the full Tau protein and VQIVYK fibrils have been intensively investigated. A central issue in these studies is polymorphism, the ability of a protein to fold into more than one structure. Using all-atom molecular simulations, we generate five stable polymorphs of VQIVYK fibrils, establish their relative free energy with umbrella sampling methods, and identify the side chain interactions that provide stability. The two most stable polymorphs, which have nearly equal free energy, are formed by interdigitation of the mostly hydrophobic VIY "face" sides of the β-sheets. Another stable polymorph is formed by interdigitation of the QVK "back" sides. When we turn to examine structures from cryo-electron microscopy experiments on Tau filaments taken from diseased patients or generated in vitro, we find that the pattern of side chain interactions found in the two most stable face-to-face as well as the back-to-back polymorphs are recapitulated in amyloid structures of the full protein. Thus, our studies suggest that the interactions stabilizing PHF6 fibrils explain the amyloidogenicity of the VQIVYK motif within the full Tau protein and provide justification for the use of VQIVYK fibrils as a test bed for the design of molecules that identify or inhibit amyloid structures.
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Affiliation(s)
- Jaehoon Yang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Mithila V Agnihotri
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Carol J Huseby
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Jeff Kuret
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio.
| | - Sherwin J Singer
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio.
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8
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Xiao S, Wu Q, Yao X, Zhang J, Zhong W, Zhao J, Liu Q, Zhang M. Inhibitory Effects of Isobavachalcone on Tau Protein Aggregation, Tau Phosphorylation, and Oligomeric Tau-Induced Apoptosis. ACS Chem Neurosci 2021; 12:123-132. [PMID: 33320518 DOI: 10.1021/acschemneuro.0c00617] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative diseases without any effective medicine treatments. The neurofibrillary tangles containing hyperphosphorylated tau protein are one important pathological characteristic. Thus, one practicable strategy for AD drug design is to discover compounds that could inhibit tau protein aggregation and/or phosphorylation. In this study, isobavachalcone, a natural plant-derived compound, has been shown to inhibit tau protein aggregation and disaggregate tau fibrils in vitro by directly interacting with tau protein at amino acids I278, V309, etc. It is able to reduce tau phosphorylation at four disease-related sites in vivo by regulating the critical kinase and protein phosphatase, GSK3β and PP2A. The compound also exhibits protection against tau oligomers-induced apoptosis through the mitochondria and ER mediated apoptotic pathways. In summary, isobavachalcone is a promising candidate for further evaluation as a potential preventive and therapeutic medicine for AD.
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Affiliation(s)
- Shifeng Xiao
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China
| | - Qiuping Wu
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xuanbao Yao
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Jiahao Zhang
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Weicong Zhong
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Junyi Zhao
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Qiong Liu
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Mohan Zhang
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
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Kim YC, Jeong BH. In Silico Evaluation of Acetylation Mimics in the 27 Lysine Residues of Human Tau Protein. Curr Alzheimer Res 2020; 16:379-387. [PMID: 30907318 DOI: 10.2174/1567205016666190321161032] [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] [Received: 12/18/2018] [Revised: 03/11/2019] [Accepted: 03/17/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND Various neurodegenerative diseases, including Alzheimer's disease (AD), are related to abnormal hyperphosphorylated microtubule-associated protein tau accumulation in brain lesions. Recent studies have focused on toxicity caused by another post-translational modification (PTM), acetylation of the lysine (K) residues of tau protein. Because there are numerous acetylation sites, several studies have introduced mimics of tau acetylation using amino acid substitutions from lysine to glutamine (Q). However, human tau protein contains over 20 acetylation sites; thus, investigation of the effects of an acetylated tau is difficult. OBJECTIVE Here, the authors in silico evaluated acetylation effects using SIFT, PolyPhen-2 and PROVEAN which can estimate the effects of amino acid substitutions based on the sequence homology or protein structure in tau isoforms. In addition, they also investigated 27 acetylation effects on the amyloid formation of tau proteins using Waltz. RESULTS 15 acetylation mimics were estimated to be the most detrimental, which indicates that there may be novel pathogenic acetylation sites in the human tau protein. Interestingly, the deleterious effect of acetylation mimics was different according to the type of isoforms. Furthermore, all acetylation mimics were predicted to be a region of amyloid formation at the codons 274-279 of human tau protein. Notably, acetylation mimic of codon 311 (K311Q) induced the formation of an additional amyloid region located on codons 306-311 of the human tau protein. CONCLUSION To the best of our knowledge, this is the first simultaneous in-silico evaluation of the acetylation state of 27 human tau protein residues.
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Affiliation(s)
- Yong-Chan Kim
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan, Jeonbuk 570-390, Korea.,Department of Bioactive Material Sciences, Chonbuk National University, Jeonju, Jeonbuk 561-756, Korea
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan, Jeonbuk 570-390, Korea.,Department of Bioactive Material Sciences, Chonbuk National University, Jeonju, Jeonbuk 561-756, Korea
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10
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Ojaghi S, Mohammadi S, Amani M, Ghobadi S, Bijari N, Esmaeili S, Khodarahmi R. Sunset yellow degradation product, as an efficient water-soluble inducer, accelerates 1N4R Tau amyloid oligomerization: In vitro preliminary evidence against the food colorant safety in terms of "Triggered Amyloid Aggregation". Bioorg Chem 2020; 103:104123. [PMID: 32781343 DOI: 10.1016/j.bioorg.2020.104123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 12/30/2022]
Abstract
Today, Alzheimer's disease (AD) as the most prevalent type of dementia turns into one of the most severe health problems. Neurofibrillary tangle (NFT), mostly comprised of fibrils formed by Tau, is a hallmark of a class of neurodegenerative diseases. Tau protein promotes assembly and makes stable microtubules that play a role in the appropriate function of neurons. Polyanionic cofactors such as heparin, and azo dyes, can induce aggregation of tau protein in vitro. Sunset Yellow is a food colorant used widely in food industries. In the current work, we introduced degradation product (DP) of Sunset Yellow as an effective inducer of Tau aggregation. Two Tau aggregation inducers were produced, and then the aggregation kinetics and the structure of 1N4R Tau amyloid fibrils were characterized using ThT fluorescence spectroscopy, X-Ray Diffraction (XRD), circular dichroism (CD) and atomic force microscopy (AFM). Also, the toxic effects of the induced aggregates on RBCs and SH-SY5Y cells were demonstrated by hemolysis and LDH assays, respectively. Both inducers efficiently accelerated the formation of the amyloid fibril. Along with the confirmation of the β-sheets structure in Tau aggregates by Far-UV CD spectra, X-ray diffractions revealed the typical cross-β diffraction pattern. The oligomer formation in the presence of DPs was also confirmed by AFM. The possible in vivo effect of artificial azo dyes on Tau aggregation should be considered seriously as a newly opened dimension in food safety and human health.
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Affiliation(s)
- Sara Ojaghi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; Department of Biology, Faculty of Sciences, Razi University, Kermanshah, Iran
| | - Soheila Mohammadi
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mojtaba Amani
- Faculty of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Sirous Ghobadi
- Department of Biology, Faculty of Sciences, Razi University, Kermanshah, Iran
| | - Nooshin Bijari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajjad Esmaeili
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Reza Khodarahmi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; Department of Pharmacognosy and Biotechnology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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11
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Zaguri D, Shaham-Niv S, Chakraborty P, Arnon Z, Makam P, Bera S, Rencus-Lazar S, Stoddart PR, Gazit E, Reynolds NP. Nanomechanical Properties and Phase Behavior of Phenylalanine Amyloid Ribbon Assemblies and Amorphous Self-Healing Hydrogels. ACS APPLIED MATERIALS & INTERFACES 2020; 12:21992-22001. [PMID: 32307977 DOI: 10.1021/acsami.0c01574] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Phenylalanine was the minimalistic and first of numerous nonproteinaceous building blocks to be demonstrated to form amyloid-like fibrils. This unexpected organization of such a simple building block into canonical architecture, which was previously observed only with proteins and peptides, has numerous implications for medicine and supramolecular chemistry. However, the morphology of phenylalanine fibrils and their mechanical properties was never characterized in solutions. Here, using electron and atomic force microscopy, we analyze the morphological and mechanical properties of phenylalanine fibrils in both air and fluids. The fibrils demonstrate an exceptionally high Young's modulus (up to 30 GPa) and are found to be composed of intertwined protofilaments in a helical or twisted ribbon morphology. In addition, X-ray scattering experiments provide convincing evidence of an amyloidal cross-β-like secondary structure within the nanoassemblies. Furthermore, increasing the phenylalanine concentration results in the formation of highly homogenous, noncrystalline, self-healing hydrogels that display storage and loss moduli significantly higher than similar noncovalently cross-linked biomolecular nanofibrillar scaffolds. These remarkably stiff nanofibrillar hydrogels can be harnessed for various technological and biomedical applications, such as self-healing, printable, structural, load-bearing 3D scaffolds. The properties of this simple but quite remarkable hydrogel open a possibility to utilize it in the biomaterial industry.
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Affiliation(s)
- Dor Zaguri
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shira Shaham-Niv
- BLAVATNIK CENTER for Drug Discovery, Metabolite Medicine Division, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Priyadarshi Chakraborty
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Zohar Arnon
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Pandeeswar Makam
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Santu Bera
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sigal Rencus-Lazar
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Paul R Stoddart
- ARC Training Centre in Biodevices, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Ehud Gazit
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- BLAVATNIK CENTER for Drug Discovery, Metabolite Medicine Division, Tel Aviv University, Tel Aviv 6997801, Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Nicholas P Reynolds
- ARC Training Centre in Biodevices, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3083, Australia
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12
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Nagaraj M, Ahmed M, Lyngsø J, Vad BS, Bøggild A, Fillipsen A, Pedersen JS, Otzen DE, Akbey Ü. Predicted Loop Regions Promote Aggregation: A Study of Amyloidogenic Domains in the Functional Amyloid FapC. J Mol Biol 2020; 432:2232-2252. [DOI: 10.1016/j.jmb.2020.01.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/27/2020] [Accepted: 01/27/2020] [Indexed: 02/08/2023]
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13
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Akbari V, Ghobadi S, Mohammadi S, Khodarahmi R. The antidepressant drug; trazodone inhibits Tau amyloidogenesis: Prospects for prophylaxis and treatment of AD. Arch Biochem Biophys 2020; 679:108218. [DOI: 10.1016/j.abb.2019.108218] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 10/25/2022]
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14
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Dangi A, Balmik AA, Ghorpade AK, Gorantla NV, Sonawane SK, Chinnathambi S, Marelli UK. Residue-based propensity of aggregation in the Tau amyloidogenic hexapeptides AcPHF6* and AcPHF6. RSC Adv 2020; 10:27331-27335. [PMID: 35516938 PMCID: PMC9055513 DOI: 10.1039/d0ra03809a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/09/2020] [Indexed: 11/21/2022] Open
Abstract
In Alzheimer's disease and related tauopathies, the aggregation of microtubule-associated protein, Tau, into fibrils occurs via the interaction of two hexapeptide motifs PHF* 275VQIINK280 and PHF 306VQIVYK311 as β-sheets. To understand the role of the constituent amino acids of PHF and PHF* in the aggregation, a set of 12 alanine mutant peptides was synthesized by replacing each amino acid in PHF and PHF* with alanine and they were characterized by nuclear magnetic resonance (NMR) spectroscopy, circular dichroism (CD), transmission electron microscopy (TEM) and ThS/ANS fluorescence assay. Our studies show that while the aggregation was suppressed in most of the alanine mutant peptides, replacement of glutamine by alanine in both PHF and PHF* enhanced the fibrillization. In the alanine mutant peptides of AcPHF6* and AcPHF6, only the peptides with glutamine to alanine substitution show aggregation akin to that of the parent peptides.![]()
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Affiliation(s)
- Abha Dangi
- Central NMR Facility
- CSIR-National Chemical Laboratory
- 411008 Pune
- India
- Division of Organic Chemistry
| | - Abhishek Ankur Balmik
- Academy of Scientific and Innovative Research (AcSIR)
- 110025 New Delhi
- India
- Neurobiology Group
- Division of Biochemical Sciences
| | - Archana Kisan Ghorpade
- Central NMR Facility
- CSIR-National Chemical Laboratory
- 411008 Pune
- India
- Division of Organic Chemistry
| | - Nalini Vijay Gorantla
- Academy of Scientific and Innovative Research (AcSIR)
- 110025 New Delhi
- India
- Neurobiology Group
- Division of Biochemical Sciences
| | - Shweta Kishor Sonawane
- Academy of Scientific and Innovative Research (AcSIR)
- 110025 New Delhi
- India
- Neurobiology Group
- Division of Biochemical Sciences
| | - Subashchandrabose Chinnathambi
- Academy of Scientific and Innovative Research (AcSIR)
- 110025 New Delhi
- India
- Neurobiology Group
- Division of Biochemical Sciences
| | - Udaya Kiran Marelli
- Central NMR Facility
- CSIR-National Chemical Laboratory
- 411008 Pune
- India
- Division of Organic Chemistry
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15
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Pyridine-2,3-dicarboxylate, quinolinic acid, induces 1N4R Tau amyloid aggregation in vitro: Another evidence for the detrimental effect of the inescapable endogenous neurotoxin. Chem Biol Interact 2019; 315:108884. [PMID: 31678113 DOI: 10.1016/j.cbi.2019.108884] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/18/2019] [Accepted: 10/26/2019] [Indexed: 01/19/2023]
Abstract
Quinolinic acid (QA) known as a neuro-active metabolite associated with the kynurenine pathway. At high concentrations, QA is often involved in the initiation and development of several human neurologic diseases, like Alzheimer's disease. Because of the QA action as the NMDA receptor, it is considered as a potent excitotoxin in vivo. Since it is probable that different mechanisms are employed by QA, activation of NMDA receptors cannot fully explain the revealed toxicity and it is even believed that there are multiple unknown mechanisms/targets leading to QA cytotoxicity. Herein we report accelerated amyloid oligomerization of 1N4R Tau under the effect of QA, in vitro, then the molecular structure, morphology and toxicity of the protein aggregate were documented by using various theoretical/experimental approaches. The possible mechanism of action of QA-induced Tau oligomerization has also been explored.
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16
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Shin WS, Di J, Cao Q, Li B, Seidler PM, Murray KA, Bitan G, Jiang L. Amyloid β-protein oligomers promote the uptake of tau fibril seeds potentiating intracellular tau aggregation. Alzheimers Res Ther 2019; 11:86. [PMID: 31627745 PMCID: PMC6800506 DOI: 10.1186/s13195-019-0541-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/22/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND Repeated failure of drug candidates targeting Alzheimer's disease (AD) in clinical trials likely stems from a lack of understanding of the molecular mechanisms underlying AD pathogenesis. Recent research has highlighted synergistic interactions between aggregated amyloid-β (Aβ) and tau proteins in AD, but the molecular details of how these interactions drive AD pathology remain elusive and speculative. METHODS Here, we test the hypothesis that Aβ potentiates intracellular tau aggregation, and show that oligomeric Aβ specifically exacerbates proteopathic seeding by tau. Using tau-biosensor cells, we show that treatment with sub-toxic concentrations of Aβ oligomers, but not monomers or fibrils, "primes" cells, making them more susceptible to tau seeding. The treatment with Aβ oligomers enhances intracellular tau aggregation in a dose-dependent manner when the cells are seeded with either recombinant or brain-derived tau fibrils, whereas little or no aggregation is observed in the absence of Aβ-oligomer priming. RESULTS Priming by Aβ oligomers appears to be specific to tau, as α-synuclein seeding is unaffected by this treatment. Aβ oligomer-enhanced tau seeding also occurs in primary mouse neurons and human neuroblastoma cells. Using fluorescently labeled tau seeds, we find that treatment with Aβ oligomers significantly enhances the cellular uptake of tau seeds, whereas a known tau-uptake inhibitor blocks the effect of Aβ on tau uptake. CONCLUSION The ability of Aβ to promote tau seeding suggests a specific and plausible mechanism by which extracellular Aβ initiates a deleterious cascade that is unique to AD. These data suggest that the Aβ-mediated potentiation of tau uptake into cells should also be taken into account when designing Aβ-targeted therapeutics.
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Affiliation(s)
- Woo Shik Shin
- Department of Neurology, David Geffen School of Medicine, UCLA, 635 Charles E Young Drive South, Los Angeles, CA 90095 USA
| | - Jing Di
- Department of Neurology, David Geffen School of Medicine, UCLA, 635 Charles E Young Drive South, Los Angeles, CA 90095 USA
| | - Qin Cao
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, UCLA, Los Angeles, CA 90095-1570 USA
| | - Binsen Li
- Department of Neurology, David Geffen School of Medicine, UCLA, 635 Charles E Young Drive South, Los Angeles, CA 90095 USA
| | - Paul M. Seidler
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, UCLA, Los Angeles, CA 90095-1570 USA
| | - Kevin A. Murray
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, UCLA, Los Angeles, CA 90095-1570 USA
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, UCLA, 635 Charles E Young Drive South, Los Angeles, CA 90095 USA
- Brain Research Institute, and Molecular Biology Institute, UCLA, Los Angeles, CA 90095 USA
| | - Lin Jiang
- Department of Neurology, David Geffen School of Medicine, UCLA, 635 Charles E Young Drive South, Los Angeles, CA 90095 USA
- Brain Research Institute, and Molecular Biology Institute, UCLA, Los Angeles, CA 90095 USA
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17
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Viswanathan GK, Paul A, Gazit E, Segal D. Naphthoquinone Tryptophan Hybrids: A Promising Small Molecule Scaffold for Mitigating Aggregation of Amyloidogenic Proteins and Peptides. Front Cell Dev Biol 2019; 7:242. [PMID: 31750300 PMCID: PMC6843079 DOI: 10.3389/fcell.2019.00242] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 10/02/2019] [Indexed: 12/22/2022] Open
Abstract
A current challenge faced by researchers is the lack of disease-modifying therapeutics for amyloid formation that is associated with several human diseases. Although the monomeric proteins or peptides involved in various amyloidogenic diseases do not have amino acid sequence homology, there appears to be a structural correlation among the amyloid assemblies, which are responsible for distinct pathological conditions. Here, we review our work on Naphthoquinone Tryptophan (NQTrp) hybrids, a small molecule scaffold that can generically modulate neuronal and non-neuronal amyloid aggregation both in vitro and in vivo. NQTrp reduces the net amyloid load by inhibiting the process of amyloid formation and disassembling the pre-formed fibrils, both in a dose-dependent manner. As a plausible mechanism of action, NQTrp effectively forms hydrogen bonding and hydrophobic interactions, such as π-π stacking, with the vital residues responsible for the initial nucleation of protein/peptide aggregation. This review highlights the effectiveness of the NQTrp hybrid scaffold for developing novel small molecule modulators of amyloid aggregation.
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Affiliation(s)
- Guru KrishnaKumar Viswanathan
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Ashim Paul
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Segal
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel.,Interdisciplinary Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
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18
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Fanni AM, Vander Zanden CM, Majewska PV, Majewski J, Chi EY. Membrane-mediated fibrillation and toxicity of the tau hexapeptide PHF6. J Biol Chem 2019; 294:15304-15317. [PMID: 31439664 DOI: 10.1074/jbc.ra119.010003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/18/2019] [Indexed: 01/29/2023] Open
Abstract
The aggregation of the tau protein into neurofibrillary tangles is believed to correlate with cognitive decline in several neurodegenerative disorders, including Alzheimer's disease. Recent studies suggest that tau's interactions with the cell membrane could serve as a toxicity pathway and also enhance fibrillation into paired helical filaments (PHFs). Conformational changes associated with tau-membrane interactions are poorly understood, and their characterization could improve our understanding of tau pathogenicity. In this study, we investigated the molecular level structural changes associated with the interaction of the tau hexapeptide PHF6 with model lipid membranes and characterized the effects of these interactions on membrane stability and peptide fibrillation. We used two PHF6 forms, the aggregation-prone PHF6 with N-terminal acetylation (Ac-PHF6) and the non-aggregation prone PHF6 with a standard N terminus (NH3 +-PHF6). We found that both PHF6 peptides are neurotoxic and exhibit similar membrane-mediated changes, consisting of: 1) favorable interactions with anionic membranes, 2) membrane destabilization through lipid extraction, and 3) membrane-mediated fibrillation. The rate at which these changes occurred was the main difference between the two peptides. NH3 +-PHF6 displayed slow membrane-mediated fibrillation after 6 days of incubation, whereas Ac-PHF6 adopted a β-sheet conformation at the surface of the membrane within hours. Ac-PHF6 interactions with the membrane were also accompanied by membrane invagination and rapid membrane destabilization. Overall, our results reveal that membrane interactions could play a critical role in tau toxicity and fibrillation, and highlight that unraveling these interactions is important for significantly advancing the development of therapeutic strategies to manage tau-associated neurodegenerative diseases.
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Affiliation(s)
- Adeline M Fanni
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131.,Biomedical Engineering Graduate Program, University of New Mexico, Albuquerque, New Mexico 87131
| | - Crystal M Vander Zanden
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131.,Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131
| | - Paulina V Majewska
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131
| | - Jaroslaw Majewski
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131.,Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545.,Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, Virginia 22314
| | - Eva Y Chi
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131 .,Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131
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19
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Carbamylation promotes amyloidogenesis and induces structural changes in Tau-core hexapeptide fibrils. Biochim Biophys Acta Gen Subj 2018; 1862:2590-2604. [PMID: 30071272 DOI: 10.1016/j.bbagen.2018.07.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/10/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Carbamylation is a non-enzymatic post-translational modification (PTM), which involves the covalent modification of N-terminus of protein or ε-amino group of Lys. The role of carbamylation in several age-related disorders is well documented, however, the relationship between carbamylation and neurodegenerative disorders including Alzheimer's disease remains uncharted. METHODS In the present study, using aggregation-prone tau-core hexapeptide fragments 306VQIVYK311 (PHF6) and 275VQIINK280 (PHF6*) as models, we have elucidated the effect of carbamylation on aggregation kinetics and the changes occurring in the 3-dimensional architecture of fibrils using biophysical assays and molecular dynamics simulations. RESULTS We found that carbamylation aids in amyloid formation and can convert the unstructured off-pathway aggregates into robust amyloids, which were toxic to cells. Electron microscopy images and molecular dynamics simulations of PHF6 fibrils showed that carbamylated peptides can form excess hydrogen bonds and modulate the pitch length and twist of peptides fibrils. We have also compared N-terminal carbamylation to acetylation and further extended our finding to full length tau that exhibits aggregation upon carbamylation even in the absence of any external inducer. CONCLUSION Our in vitro and in silico results together suggest that carbamylation can modulate the aggregation pathway of the amyloidegenic sequences and cause structural changes in fibril assemblies. GENERAL SIGNIFICANCE Carbamylation acts as a switch, which triggers the aggregation in short amyloidogenic peptide fragments and modulate the structural changes in resulting amyloid fibrils.
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20
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Haj E, Losev Y, Guru KrishnaKumar V, Pichinuk E, Engel H, Raveh A, Gazit E, Segal D. Integrating in vitro and in silico approaches to evaluate the "dual functionality" of palmatine chloride in inhibiting and disassembling Tau-derived VQIVYK peptide fibrils. Biochim Biophys Acta Gen Subj 2018; 1862:1565-1575. [PMID: 29634991 DOI: 10.1016/j.bbagen.2018.04.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/20/2018] [Accepted: 04/03/2018] [Indexed: 01/02/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common neurodegenerative disorder which is characterized by the deposits of intra-cellular tau protein and extra-cellular amyloid-β (Aβ) peptides in the human brain. Understanding the mechanism of protein aggregation and finding compounds that are capable of inhibiting its aggregation is considered to be highly important for disease therapy. METHODS We used an in vitro High-Throughput Screening for the identification of potent inhibitors of tau aggregation using a proxy model; a highly aggregation-prone hexapeptide fragment 306VQIVYK311 derived from tau. Using ThS fluorescence assay we screened a library of 2401 FDA approved, bio-active and natural compounds in attempt to find molecules which can efficiently modulate tau aggregation. RESULTS Among the screened compounds, palmatine chloride (PC) alkaloid was able to dramatically reduce the aggregation propensity of PHF6 at sub-molar concentrations. PC was also able to disassemble preformed aggregates of PHF6 and reduce the amyloid content in a dose-dependent manner. Insights obtained from MD simulation showed that PC interacted with the key residues of PHF6 responsible for β-sheet formation, which could likely be the mechanism of inhibition and disassembly. Furthermore, PC could effectively inhibit the aggregation of full-length tau and disassemble preformed aggregates. CONCLUSIONS We found that PC possesses "dual functionality" towards PHF6 and full-length tau, i.e. inhibit their aggregation and disassemble pre-formed fibrils. GENERAL SIGNIFICANCE The "dual functionality" of PC is valuable as a disease modifying strategy for AD, and other tauopathies, by inhibiting their progress and reducing the effect of fibrils already present in the brain.
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Affiliation(s)
- Esraa Haj
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Yelena Losev
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
| | - V Guru KrishnaKumar
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel; Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Edward Pichinuk
- BLAVATNIK CENTER for Drug Discovery, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Hamutal Engel
- BLAVATNIK CENTER for Drug Discovery, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Avi Raveh
- BLAVATNIK CENTER for Drug Discovery, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel; BLAVATNIK CENTER for Drug Discovery, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Daniel Segal
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel; The Interdisciplinary Sagol School of Neurosciences, Tel-Aviv University, Tel Aviv 69978, Israel.
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21
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Jehle F, Fratzl P, Harrington MJ. Metal-Tunable Self-Assembly of Hierarchical Structure in Mussel-Inspired Peptide Films. ACS NANO 2018; 12:2160-2168. [PMID: 29385330 DOI: 10.1021/acsnano.7b07905] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Bottom-up control over structural hierarchy from the nanoscale through the macroscale is a critical aspect of biological materials fabrication and function, which can inspire production of advanced materials. Mussel byssal threads are a prime example of protein-based biofibers in which hierarchical organization of protein building blocks coupled via metal complexation leads to notable mechanical behaviors, such as high toughness and self-healing. Using a natural amino acid sequence from byssal thread proteins, which functions as a pH-triggered self-assembly point, we created free-standing peptide films with complex hierarchical organization across multiple length scales that can be controlled by inclusion of metal ions (Zn2+ and Cu2+) during the assembly process. Additionally, analysis of film mechanical performance indicates that metal coordination bestows up to an order of magnitude increase in material stiffness, providing a paradigm for creating tunable polymeric materials with multiscale organizational structure.
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Affiliation(s)
- Franziska Jehle
- Department of Biomaterials , Max Planck Institute of Colloids and Interfaces , Potsdam 14476 , Germany
| | - Peter Fratzl
- Department of Biomaterials , Max Planck Institute of Colloids and Interfaces , Potsdam 14476 , Germany
| | - Matthew J Harrington
- Department of Biomaterials , Max Planck Institute of Colloids and Interfaces , Potsdam 14476 , Germany
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22
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Affiliation(s)
- I. W. Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
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23
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Jouanne M, Rault S, Voisin-Chiret AS. Tau protein aggregation in Alzheimer's disease: An attractive target for the development of novel therapeutic agents. Eur J Med Chem 2017; 139:153-167. [PMID: 28800454 DOI: 10.1016/j.ejmech.2017.07.070] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 12/28/2022]
Abstract
Alzheimer's Disease (AD) is a neurodegenerative brain disorder in which many biological dysfunctions are involved. Among them, two main types of lesions were discovered and widely studied: the amyloid plaques and the neurofibrillary tangles (NFTs). These two lesions are caused by the dysfunction and the accumulation of two proteins which are, respectively, the beta-amyloid peptide and the tau protein. The process that leads these two proteins to aggregate is complex and is the subject of current studies. After a brief description of the aggregation mechanisms, we will provide an overview of new therapeutic agents targeting the different dysfunctions and toxic species found during aggregation.
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Affiliation(s)
- Marie Jouanne
- Université Caen Normandie, France; UNICAEN, CERMN - EA 4258, FR CNRS 3038 INC3M, SF 4206 ICORE, bd Becquerel, F-14032 Caen, France
| | - Sylvain Rault
- Université Caen Normandie, France; UNICAEN, CERMN - EA 4258, FR CNRS 3038 INC3M, SF 4206 ICORE, bd Becquerel, F-14032 Caen, France
| | - Anne-Sophie Voisin-Chiret
- Université Caen Normandie, France; UNICAEN, CERMN - EA 4258, FR CNRS 3038 INC3M, SF 4206 ICORE, bd Becquerel, F-14032 Caen, France.
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24
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Hierarchical Self-Assembly of Amino Acid Derivatives into Enzyme-Responsive Luminescent Gel. CHEMOSENSORS 2017. [DOI: 10.3390/chemosensors5010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Shaham-Niv S, Rehak P, Vuković L, Adler-Abramovich L, Král P, Gazit E. Formation of Apoptosis-Inducing Amyloid Fibrils by Tryptophan. Isr J Chem 2016. [DOI: 10.1002/ijch.201600076] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shira Shaham-Niv
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Tel Aviv 69978 Israel
| | - Pavel Rehak
- Department of Chemistry; University of Illinois at Chicago; Chicago USA
| | - Lela Vuković
- Department of Chemistry; University of Texas at El Paso; El Paso USA
| | - Lihi Adler-Abramovich
- Department of Oral Biology; The Goldschleger School of Dental Medicine; Tel Aviv University; Tel Aviv 69978 Israel
| | - Petr Král
- Department of Chemistry; University of Illinois at Chicago; Chicago USA
- Department of Physics; University of Illinois at Chicago; Chicago USA
- Department of Biopharmaceutical Sciences; University of Illinois at Chicago; Chicago USA
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Tel Aviv 69978 Israel
- Department of Materials Science and Engineering; Iby and Aladar Fleischman Faculty of Engineering; Tel Aviv University; Tel Aviv 69978 Israel
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26
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Jangholi A, Ashrafi-Kooshk MR, Arab SS, Riazi G, Mokhtari F, Poorebrahim M, Mahdiuni H, Kurganov BI, Moosavi-Movahedi AA, Khodarahmi R. Appraisal of role of the polyanionic inducer length on amyloid formation by 412-residue 1N4R Tau protein: A comparative study. Arch Biochem Biophys 2016; 609:1-19. [DOI: 10.1016/j.abb.2016.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 10/21/2022]
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27
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Utility of Solution X-Ray Scattering for the Development of Antibody Biopharmaceuticals. J Pharm Sci 2016; 105:3278-3289. [DOI: 10.1016/j.xphs.2016.07.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/14/2016] [Accepted: 07/26/2016] [Indexed: 12/31/2022]
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28
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Banik D, Dutta R, Banerjee P, Kundu S, Sarkar N. Inhibition of Fibrillar Assemblies of l-Phenylalanine by Crown Ethers: A Potential Approach toward Phenylketonuria. J Phys Chem B 2016; 120:7662-70. [DOI: 10.1021/acs.jpcb.6b05209] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Debasis Banik
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Rupam Dutta
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Pavel Banerjee
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Sangita Kundu
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Nilmoni Sarkar
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
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29
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Frenkel-Pinter M, Richman M, Belostozky A, Abu-Mokh A, Gazit E, Rahimipour S, Segal D. Selective Inhibition of Aggregation and Toxicity of a Tau-Derived Peptide using Its Glycosylated Analogues. Chemistry 2016; 22:5945-52. [DOI: 10.1002/chem.201504950] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Moran Frenkel-Pinter
- Department Molecular Microbiology and Biotechnology, and the Interdisciplinary Sagol School of Neurosciences; George S. Wise Faculty of Life Sciences; Tel-Aviv University; Tel Aviv 69978 Israel
| | - Michal Richman
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Anna Belostozky
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Amjaad Abu-Mokh
- Department Molecular Microbiology and Biotechnology, and the Interdisciplinary Sagol School of Neurosciences; George S. Wise Faculty of Life Sciences; Tel-Aviv University; Tel Aviv 69978 Israel
| | - Ehud Gazit
- Department Molecular Microbiology and Biotechnology, and the Interdisciplinary Sagol School of Neurosciences; George S. Wise Faculty of Life Sciences; Tel-Aviv University; Tel Aviv 69978 Israel
| | - Shai Rahimipour
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Daniel Segal
- Department Molecular Microbiology and Biotechnology, and the Interdisciplinary Sagol School of Neurosciences; George S. Wise Faculty of Life Sciences; Tel-Aviv University; Tel Aviv 69978 Israel
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30
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Lee M, Baek I, Choi H, Kim JI, Na S. Effects of lysine residues on structural characteristics and stability of tau proteins. Biochem Biophys Res Commun 2015; 466:486-92. [DOI: 10.1016/j.bbrc.2015.09.056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 09/11/2015] [Indexed: 11/26/2022]
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31
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Accardo A, Shalabaeva V, Di Cola E, Burghammer M, Krahne R, Riekel C, Dante S. Superhydrophobic Surfaces Boost Fibril Self-Assembly of Amyloid β Peptides. ACS APPLIED MATERIALS & INTERFACES 2015; 7:20875-20884. [PMID: 26306595 DOI: 10.1021/acsami.5b06219] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Amyloid β (Aβ) peptides are the main constituents of Alzheimer's amyloid plaques in the brain. Here we report how the unique microfluidic flows exerted by droplets sitting on superhydrophobic surfaces can influence the aggregation mechanisms of several Aβ fragments by boosting their fibril self-assembly. Aβ(25-35), Aβ(1-40), and Aβ(12-28) were dried both on flat hydrophilic surfaces (contact angle (CA) = 37.3°) and on nanostructured superhydrophobic ones (CA = 175.8°). By embedding nanoroughened surfaces on top of highly X-ray transparent Si3N4 membranes, it was possible to probe the solid residues by raster-scan synchrotron radiation X-ray microdiffraction (μXRD). As compared to residues obtained on flat Si3N4 membranes, a general enhancement of fibrillar material was detected for all Aβ fragments dried on superhydrophobic surfaces, with a particular emphasis on the shorter ones. Indeed, both Aβ(25-35) and Aβ(12-28) showed a marked crystalline cross-β phase with varying fiber textures. The homogeneous evaporation rate provided by these nanostructured supports, and the possibility to use transparent membranes, can open a wide range of in situ X-ray and spectroscopic characterizations of amyloidal peptides involved in neurodegenerative diseases and for the fabrication of amyloid-based nanodevices.
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Affiliation(s)
- Angelo Accardo
- Istituto Italiano di Tecnologia , Via Morego 30, Genova 16163, Italy
| | | | - Emanuela Di Cola
- The European Synchrotron, CS40220 , 38043 Cedex 9 Grenoble, France
| | - Manfred Burghammer
- The European Synchrotron, CS40220 , 38043 Cedex 9 Grenoble, France
- Department of Analytical Chemistry, Ghent University , Krijgslaan 281, Ghent 9000, Belgium
| | - Roman Krahne
- Istituto Italiano di Tecnologia , Via Morego 30, Genova 16163, Italy
| | - Christian Riekel
- The European Synchrotron, CS40220 , 38043 Cedex 9 Grenoble, France
| | - Silvia Dante
- Istituto Italiano di Tecnologia , Via Morego 30, Genova 16163, Italy
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32
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The effect of Arg on the structure perturbation and chaperone activity of α-crystallin in the presence of the crowding agent, dextran. Appl Biochem Biotechnol 2014; 174:739-50. [PMID: 25091326 DOI: 10.1007/s12010-014-1092-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/21/2014] [Indexed: 10/24/2022]
Abstract
α-Crystallin is a protein that is expressed at high levels in all vertebrate eye lenses. It has a molecular weight of 20 kDa and is composed of two subunits: αA and αB. α-Crystallin is a member of the small heat shock protein (sHsps) family that has been shown to prevent protein aggregation. Small molecules are organic compounds that have low molecular weight (<800 Da). Arginin (Arg) is a small molecule and has been shown to prevent protein aggregation through interaction with partially folded intermediates. In this study, the effect of Arg on the chaperone activity of α-crystallin in the presence of dextran, as a crowding agent, against ordered and disordered aggregation of different target proteins (α-lactalbumin, ovotransferrin, and catalase) has been investigated. The experiments were done using visible absorption spectroscopy, ThT-binding assay, fluorescence spectroscopy, and CD spectroscopy. The results showed that in amorphous aggregation and amyloid fibril formation, both in the presence and absence of dextran, Arg had a positive effect on the chaperone action of α-crystallin. However, in the presence of dextran, the effect of Arg on the chaperone ability of α-crystallin was less than in its absence. Thus, our result suggests that crowding interior media decreases the positive effect of Arg on the chaperone ability of α-crystallin. This is a very important issue, since we are trying to find a mechanism to protect living cells against the toxic effect of protein aggregation.
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33
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Bhattacharya S, Pandey NK, Roy A, Dasgupta S. Effect of (-)-epigallocatechin gallate on the fibrillation of human serum albumin. Int J Biol Macromol 2014; 70:312-9. [PMID: 25017180 DOI: 10.1016/j.ijbiomac.2014.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 07/02/2014] [Accepted: 07/04/2014] [Indexed: 01/05/2023]
Abstract
Human serum albumin (HSA), the most abundant plasma protein in the human body is known to form fibrils under partial denaturing conditions. Natural polyphenols are known to interact with HSA and some polyphenols have been shown to be potent inhibitors of amyloid fibrillation. (-)-Epigallocatechin gallate (EGCG), the major component of green tea is known to inhibit amyloid fibrillation. In this report, we have investigated the effect of EGCG on native HSA as well as on the fibrillation process of HSA from amide III band analysis of their respective visible Raman spectra. The differential role of the tryptophan (Trp214) residue present in domain II of HSA in the absence and presence of EGCG has been pointed out using fluorescence anisotropy and visible Raman spectroscopy.
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Affiliation(s)
| | - Nitin K Pandey
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Anushree Roy
- Department of Physics, Indian Institute of Technology, Kharagpur 721302, India.
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India.
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34
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Bhattacharya S, Ghosh S, Pandey NK, Chaudhury S, Dasgupta S, Roy A. Distribution of protein Ramachandran psi (ψ) angle using non-resonance visible raman scattering measurements. J Phys Chem B 2013; 117:13993-4000. [PMID: 24134469 DOI: 10.1021/jp408009y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Knowing the distribution of Ramachandran angles helps in understanding peptide and protein backbone conformation. Empirical relations are proposed to correlate the spectral profile of the amide III3 band, obtained from ultraviolet resonance Raman measurements (UVRR), with the Ramachandran dihedral psi angle distribution in small peptide and protein molecules, in different environmental conditions (Mikhonin et al. J. Phys. Chem. B 2006, 110, 1928-1943). It has also been used for more complicated structures, like large globular proteins and protein fibrils. In our work here, we use visible Raman spectra and available empirical relations to obtain similar correlations for human serum albumin, hen egg white lysozyme, and human gamma crystallin. We also report the dihedral angle distribution in fibrils and a denatured protein in an ethanol environment using the same spectroscopic technique.
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35
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Muñoz E, Sreelatha A, Garriga R, Baughman RH, Goux WJ. Amyloidogenic Peptide/Single-Walled Carbon Nanotube Composites Based on Tau-Protein-Related Peptides Derived from AcPHF6: Preparation and Dispersive Properties. J Phys Chem B 2013; 117:7593-604. [DOI: 10.1021/jp402057d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Edgar Muñoz
- Instituto de Carboquı́mica ICB-CSIC, Miguel Luesma Castán 4, 50018 Zaragoza,
Spain
| | - Anju Sreelatha
- Department of Molecular
Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Rosa Garriga
- Departamento de Quı́mica
Fı́sica, Universidad de Zaragoza, 50009 Zaragoza, Spain
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36
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Ramachandran G, Udgaonkar JB. Mechanistic studies unravel the complexity inherent in tau aggregation leading to Alzheimer's disease and the tauopathies. Biochemistry 2013; 52:4107-26. [PMID: 23721410 DOI: 10.1021/bi400209z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The aggregation of the protein tau into amyloid fibrils is known to be involved in the causation of the neurodegenerative tauopathies and the progression of cognitive decline in Alzheimer's disease. This review surveys the mechanism of tau aggregation with special emphasis on the information obtained from biochemical and biophysical studies. First, tau is described from a structure-function perspective. Subsequently, the connection of tau to neurodegeneration is explained, and a description of the tau amyloid fibril is provided. Lastly, studies of the mechanism of tau fibril formation are reviewed, and the physiological significance of these studies with reference to how they can clarify many aspects of disease progression is described. The aim of this review is to underscore how mechanistic studies reveal the complexity of the tau fibril formation pathway and the plethora of species populated on or off the pathway of aggregation, and how this information can be beneficial in the design of inhibitors or drugs that ameliorate neurodegeneration.
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Affiliation(s)
- Gayathri Ramachandran
- National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India
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37
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Yao J, Gao X, Sun W, Yao T, Shi S, Ji L. Molecular Hairpin: A Possible Model for Inhibition of Tau Aggregation by Tannic Acid. Biochemistry 2013; 52:1893-902. [DOI: 10.1021/bi400240c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Junliang Yao
- Department of Chemistry, Tongji University, Shanghai 200092, China
| | - Xing Gao
- Department of Chemistry, Tongji University, Shanghai 200092, China
| | - Wenliang Sun
- Department of Chemistry, Tongji University, Shanghai 200092, China
| | - Tianming Yao
- Department of Chemistry, Tongji University, Shanghai 200092, China
| | - Shuo Shi
- Department of Chemistry, Tongji University, Shanghai 200092, China
| | - Liangnian Ji
- MOE Laboratory of Bioinorganic
and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, China
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38
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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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39
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The fuzzy coat of pathological human Tau fibrils is a two-layered polyelectrolyte brush. Proc Natl Acad Sci U S A 2012; 110:E313-21. [PMID: 23269837 DOI: 10.1073/pnas.1212100110] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structure and properties of amyloid-like Tau fibrils accumulating in neurodegenerative diseases have been debated for decades. Although the core of Tau fibrils assembles from short β-strands, the properties of the much longer unstructured Tau domains protruding from the fibril core remain largely obscure. Applying immunogold transmission EM, and force-volume atomic force microscopy (AFM), we imaged human Tau fibrils at high resolution and simultaneously mapped their mechanical and adhesive properties. Tau fibrils showed a ≈ 16-nm-thick fuzzy coat that resembles a two-layered polyelectrolyte brush, which is formed by the unstructured short C-terminal and long N-terminal Tau domains. The mechanical and adhesive properties of the fuzzy coat are modulated by electrolytes and pH, and thus by the cellular environment. These unique properties of the fuzzy coat help in understanding how Tau fibrils disturb cellular interactions and accumulate in neurofibrillary tangles.
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40
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Cheon M, Chang I, Hall CK. Influence of temperature on formation of perfect tau fragment fibrils using PRIME20/DMD simulations. Protein Sci 2012; 21:1514-27. [PMID: 22887126 PMCID: PMC3526993 DOI: 10.1002/pro.2141] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 08/06/2012] [Indexed: 02/06/2023]
Abstract
We investigate the fibrillization process for amyloid tau fragment peptides (VQIVYK) by applying the discontinuous molecular dynamics method to a system of 48 VQIVYK peptides modeled using a new protein model/force field, PRIME20. The aim of the article is to ascertain which factors are most important in determining whether or not a peptide system forms perfect coherent fibrillar structures. Two different directional criteria are used to determine when a hydrogen bond occurs: the original H-bond constraints and a parallel preference H-bond constraint that imparts a slight bias towards the formation of parallel versus antiparallel strands in a β-sheet. Under the original H-bond constraints, the resulting fibrillar structures contain a mixture of parallel and antiparallel pairs of strands within each β-sheet over the whole fibrillization temperature range. Under the parallel preference H-bond constraints, the β-sheets within the fibrillar structures are more likely to be parallel and indeed become perfectly parallel, consistent with X-ray crystallography, at a high temperature slightly below the fibrillization temperature. The high temperature environment encourages the formation of perfect fibril structures by providing enough time and space for peptides to rearrange during the aggregation process. There are two different kinetic mechanisms, template assembly with monomer addition at high temperature and merging/rearrangement without monomer addition at low temperature, which lead to significant differences in the final fibrillar structure. This suggests that the diverse fibril morphologies generally observed in vitro depend more on environmental conditions than has heretofore been appreciated.
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Affiliation(s)
- Mookyung Cheon
- Center for Proteome Biophysics, Department of Physics, Pusan National UniversityBusan 609-735, Korea
| | - Iksoo Chang
- Center for Proteome Biophysics, Department of Physics, Pusan National UniversityBusan 609-735, Korea
| | - Carol K Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State UniversityRaleigh, North Carolina 27695-7905
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41
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Cheng PN, Spencer R, Woods RJ, Glabe CG, Nowick JS. Heterodivalent linked macrocyclic β-sheets with enhanced activity against Aβ aggregation: two sites are better than one. J Am Chem Soc 2012; 134:14179-84. [PMID: 22827298 DOI: 10.1021/ja305416a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This paper reports a series of heterodivalent linked macrocyclic β-sheets 6 that are not only far more active against amyloid-β (Aβ) aggregation than their monovalent components 1a and 1b but also are dramatically more active than their homodivalent counterparts 4 and 5. The macrocyclic β-sheet components 1a and 1b comprise pentapeptides derived from the N- and C-terminal regions of Aβ and molecular template and turn units that enforce a β-sheet structure and block aggregation. Thioflavin T fluorescence assays show that heterodivalent linked macrocyclic β-sheets 6 delay Aβ(1-40) aggregation 6-8-fold at equimolar concentrations and substantially delay aggregation at substoichiometric concentrations, while homodivalent linked macrocyclic β-sheets 4 and 5 and monovalent macrocyclic β-sheets 1a and 1b only exhibit more modest effects at equimolar or greater concentrations. A model to explain these observations is proposed, in which the inhibitors bind to and stabilize the early β-structured Aβ oligomers and thus delay aggregation. In this model, heterodivalent linked macrocyclic β-sheets 6 bind to the β-structured oligomers more strongly, because N-terminal-derived component 1a can bind to the N-terminal-based core of the β-structured oligomers, while the C-terminal-derived component 1b can achieve additional interactions with the C-terminal region of Aβ. The enhanced activity of the heterodivalent compounds suggests that polyvalent inhibitors that can target multiple regions of amyloidogenic peptides and proteins are better than those that only target a single region.
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Affiliation(s)
- Pin-Nan Cheng
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, USA
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42
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Shashilov V, Xu M, Makarava N, Savtchenko R, Baskakov IV, Lednev IK. Dissecting structure of prion amyloid fibrils by hydrogen-deuterium exchange ultraviolet Raman spectroscopy. J Phys Chem B 2012; 116:7926-30. [PMID: 22681559 PMCID: PMC3490051 DOI: 10.1021/jp2122455] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The molecular mechanisms underlying structural diversity of amyloid fibrils or prion strains formed within the same primary structure is considered to be one of the most enigmatic questions in prion biology. We report here on the direct characterization of amyloid structures using a novel spectroscopic technique, hydrogen-deuterium exchange ultraviolet Raman spectroscopy. This method enables us to assess the structural differences within highly ordered cross-β-cores of two amyloid states produced within the same amino acid sequence of full-length mammalian prion protein. We found that while both amyloid states consisted of β-structures, their cross-β-cores exhibited hydrogen bonding of different strengths. Moreover, Raman spectroscopy revealed that both amyloid states displayed equally narrow crystalline-like bands, suggesting uniform structures of cross-β-cores within each state. Taken together, these data suggest that highly polymorphous fibrils can display highly uniform structures of their cross-β-core and belong to the same prion strain.
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Affiliation(s)
- Victor Shashilov
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY, USA 12222
| | - Ming Xu
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY, USA 12222
| | - Natallia Makarava
- Center for Biomedical Engineering and Technology and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA 21201
| | - Regina Savtchenko
- Center for Biomedical Engineering and Technology and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA 21201
| | - Ilia V. Baskakov
- Center for Biomedical Engineering and Technology and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA 21201
| | - Igor K. Lednev
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY, USA 12222
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43
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Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria. Nat Chem Biol 2012; 8:701-6. [DOI: 10.1038/nchembio.1002] [Citation(s) in RCA: 294] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 05/07/2012] [Indexed: 11/08/2022]
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44
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Frydman-Marom A, Convertino M, Pellarin R, Lampel A, Shaltiel-Karyo R, Segal D, Caflisch A, Shalev DE, Gazit E. Structural basis for inhibiting β-amyloid oligomerization by a non-coded β-breaker-substituted endomorphin analogue. ACS Chem Biol 2011; 6:1265-76. [PMID: 21892833 DOI: 10.1021/cb200103h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The distribution of endomorphins (EM) 1 and 2 in the human brain inversely correlates with cerebral neurodegeneration in Alzheimer's disease (AD), implying a protective role. These endogenous opioid peptides incorporate aromatic residues and a β-breaker motif, as seen in several optimized inhibitors of Aβ aggregation. The activity of native endomorphins was studied, as well as the rationally designed analogue Aib-1, which includes a remarkably efficient β-breaker, α-aminoisobutyric acid (Aib). In vitro and GFP fusion protein assays showed that Aib-1 interacted with Aβ and markedly inhibited the formation of toxic oligomer and fibril growth. Moreover, Aib-1 prevented the toxicity of Aβ toward neuronal PC12 cells and markedly rectified reduced longevity of an AD fly model. Atomistic simulations and NMR-derived solution structures revealed that Aib-1 significantly reduced the propensity of Aβ to aggregate due to multimode interactions including aromatic, hydrophobic, and polar contacts. We suggest that hindering the self-assembly process by interfering with the aromatic core of amyloidogenic peptides may pave the way toward developing therapeutic agents to treat amyloid-associated diseases.
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Affiliation(s)
- Anat Frydman-Marom
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Marino Convertino
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Riccardo Pellarin
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Ayala Lampel
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Ronit Shaltiel-Karyo
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Daniel Segal
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Deborah E. Shalev
- Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
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45
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Ramachandran G, Udgaonkar JB. Understanding the kinetic roles of the inducer heparin and of rod-like protofibrils during amyloid fibril formation by Tau protein. J Biol Chem 2011; 286:38948-59. [PMID: 21931162 DOI: 10.1074/jbc.m111.271874] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The aggregation of the natively disordered protein, Tau, to form lesions called neurofibrillary tangles is a characteristic feature of several neurodegenerative tauopathies. The polyanion, heparin, is commonly used as an inducer in studies of Tau aggregation in vitro, but there is surprisingly no comprehensive model describing, quantitatively, all aspects of the heparin-induced aggregation reaction. In this study, rate constants and extents of fibril formation by the four repeat domain of Tau (Tau4RD) have been reproducibly determined over a full range of heparin and protein concentrations. The kinetic role of heparin in the nucleation-dependent fibril formation reaction is shown to be limited to participation in the initial rate-limiting steps; a single heparin molecule binds two Tau4RD molecules, forming an aggregation-competent protein dimer, which then serves as a building block for further fibril growth. Importantly, the minimal kinetic model that is proposed can quantitatively account for the characteristic bell-shaped dependence of the aggregation kinetics on the stoichiometry of protein to heparin. Very importantly, this study also identifies for the first time short and thin, rod-like protofibrils that are populated transiently, early during the time course of fibril formation. The identification of these protofibrils as bona fide off-pathway species has implications for the development of therapies for tauopathies based on driving fibril formation as a means of protecting the cell from smaller, putatively toxic aggregates.
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Affiliation(s)
- Gayathri Ramachandran
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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46
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Frydman-Marom A, Shaltiel-Karyo R, Moshe S, Gazit E. The generic amyloid formation inhibition effect of a designed small aromatic β-breaking peptide. Amyloid 2011; 18:119-27. [PMID: 21651439 DOI: 10.3109/13506129.2011.582902] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The development of generic inhibitors in order to control the formation of amyloid fibrils and early oligomers is still an unmet medical need. As it is hypothesized that amyloid assemblies represent a generic protein supramolecular structure of low free energy, targeting the key molecular recognition and self-assembly events may provide the route for the development of such potential therapeutic agents. We have previously demonstrated the ability of hybrid molecules composed of an aromatic moiety and the α-aminoisobutyric acid β-sheet breaker elements to act as excellent inhibitors of amyloid fibril formation. Specifically, the D-Trp-Aib was shown to be a superb inhibitor of the formation of Alzheimer's disease β-amyloid fibrils and oligomers both in vitro and in vivo. Here, we demonstrate that the rationally designed molecule has the generic ability to inhibit amyloid fibril formation by calcitonin, α-synuclein, and the islet amyloid polypeptide. Moreover, we demonstrate the inability of two modified peptides, D-Ala-Aib and D-Trp-Ala, to inhibit and disassemble amyloid fibril formation, a fact that provides an additional evidence for the suggested structural basis of the inhibitor activity. Taken together, we believe that the use of β-breaker elements combined with aromatic moiety may present a promising approach for the development of fibrillization inhibition drug candidate.
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Affiliation(s)
- Anat Frydman-Marom
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
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47
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Landahl EC, Antipova O, Bongaarts A, Barrea R, Berry R, Binder LI, Irving T, Orgel J, Vana L, Rice SE. X-ray diffraction from intact tau aggregates in human brain tissue. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH. SECTION A, ACCELERATORS, SPECTROMETERS, DETECTORS AND ASSOCIATED EQUIPMENT 2011; 649:184-187. [PMID: 21876609 PMCID: PMC3162212 DOI: 10.1016/j.nima.2011.01.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We describe an instrument to record x-ray diffraction patterns from diseased regions of human brain tissue by combining an in-line visible light fluorescence microscope with an x-ray diffraction microprobe. We use thiazine red fluorescence to specifically label and detect the filamentous tau protein pathology associated with Pick's disease, as several labs have done previously. We demonstrate that thiazine red-enhanced regions within the tissue show periodic structure in x-ray diffraction that is not observed in healthy tissue. One observed periodicity (4.2 Å) is characteristic of cross-beta sheet structure, consistent with previous results from powder diffraction studies performed on purified, dried tau protein.
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Affiliation(s)
- Eric C Landahl
- DePaul University, Department of Physics, 2219 N. Kenmore Ave., Chicago, IL 60614
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48
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Plumley JA, Dannenberg JJ. Comparison of β-sheets of capped polyalanine with those of the tau-amyloid structures VQIVYK and VQIINK. A density functional theory study. J Phys Chem B 2011; 115:10560-6. [PMID: 21797271 DOI: 10.1021/jp205388q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We present ONIOM calculations using B3LYP/d95(d,p) as the high and AM1 as the low level on parallel β-sheets containing from two to ten strands of Ac-VQIVYK-NHMe and Ac-VQIINK-NHMe, as well as both parallel and antiparallel Ac-AAAAAA-NHMe. We find that the first two sequences form more stable sheets due to the additional H-bonding between the Q's in the side chains of both and the N's in the side chain of Ac-VQIINK-NHMe. However, the H-bonds in the amyloid chains are significantly weakened by attractive strain, which prevents all the interstrand H-bonds from achieving their optimal geometries simultaneously and requires high distortion energies for the individual strands in the sheets. The antiparallel Ac-AAAAAA-NHMe's are generally more stable and more cooperative than the parallel sheets, principally due to the higher distortion energies of the latter.
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Affiliation(s)
- Joshua A Plumley
- Department of Chemistry, City University of New York-Hunter College and Graduate School, 695 Park Avenue, New York, New York 10065, United States
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The Effects of Regularly Spaced Glutamine Substitutions on Alpha-Helical Peptide Structures. A DFT/ONIOM Study. Chem Phys Lett 2011; 512:255-257. [PMID: 21927063 DOI: 10.1016/j.cplett.2011.07.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The side-chains of the residues of glutamine (Q) and asparagine (N) contain amide groups. These can H-bond to each other in patterns similar to those of the backbone amides in α-helices. We show that mutating multiple Q's for alanines (A's) in a polyalanine helix stabilizes the helical structure, while similar mutations with multiple N's do not. We suggest that modification of peptides by incorporating Q's in such positions can make more robust helices that can be used to test the effects of secondary structures in biochemical experiments linked to proteins with variable structures such as tau and α-synuclein.
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Zheng J, Liu C, Sawaya MR, Vadla B, Khan S, Woods RJ, Eisenberg D, Goux WJ, Nowick JS. Macrocyclic β-sheet peptides that inhibit the aggregation of a tau-protein-derived hexapeptide. J Am Chem Soc 2011; 133:3144-57. [PMID: 21319744 PMCID: PMC3048834 DOI: 10.1021/ja110545h] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
This paper describes studies of a series of macrocyclic β-sheet peptides 1 that inhibit the aggregation of a tau-protein-derived peptide. The macrocyclic β-sheet peptides comprise a pentapeptide "upper" strand, two δ-linked ornithine turn units, and a "lower" strand comprising two additional residues and the β-sheet peptidomimetic template "Hao". The tau-derived peptide Ac-VQIVYK-NH(2) (AcPHF6) aggregates in solution through β-sheet interactions to form straight and twisted filaments similar to those formed by tau protein in Alzheimer's neurofibrillary tangles. Macrocycles 1 containing the pentapeptide VQIVY in the "upper" strand delay and suppress the onset of aggregation of the AcPHF6 peptide. Inhibition is particularly pronounced in macrocycles 1a, 1d, and 1f, in which the two residues in the "lower" strand provide a pattern of hydrophobicity and hydrophilicity that matches that of the pentapeptide "upper" strand. Inhibition varies strongly with the concentration of these macrocycles, suggesting that it is cooperative. Macrocycle 1b containing the pentapeptide QIVYK shows little inhibition, suggesting the possibility of a preferred direction of growth of AcPHF6 β-sheets. On the basis of these studies, a model is proposed in which the AcPHF6 amyloid grows as a layered pair of β-sheets and in which growth is blocked by a pair of macrocycles that cap the growing paired hydrogen-bonding edges. This model provides a provocative and appealing target for future inhibitor design.
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Affiliation(s)
- Jing Zheng
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, USA
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