1
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Bacchella C, Guerriere TB, Monzani E, Dell'Acqua S. Cysteine in the R3 Tau Peptide Modulates Hemin Binding and Reactivity. Inorg Chem 2024. [PMID: 38897979 DOI: 10.1021/acs.inorgchem.4c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Tau is a neuronal protein involved in axonal stabilization; however under pathological conditions, it triggers the deposition of insoluble neurofibrillary tangles, which are one of the biomarkers for Alzheimer's disease. The factors that might influence the fibrillation process are i) two cysteine residues in two pseudorepetitive regions, called R2 and R3, which can modulate protein-protein interaction via disulfide cross-linking; ii) an increase of reactive oxygen species affecting the post-translational modification of tau; and iii) cytotoxic levels of metals, especially ferric-heme (hemin), in hemolytic processes. Herein, we investigated how the cysteine-containing R3 peptide (R3C) and its Cys→Ala mutant (R3A) interact with hemin and how their binding affects the oxidative damage of the protein. The calculated binding constants are remarkably higher for the hemin-R3C complex (LogK1 = 5.90; LogK2 = 5.80) with respect to R3A (LogK1 = 4.44; LogK2 < 2), although NMR and CD investigations excluded the direct binding of cysteine as an iron axial ligand. Both peptides increase the peroxidase-like activity of hemin toward catecholamines and phenols, with a double catalytic efficiency detected for hemin-R3C systems. Moreover, the presence of cysteine significantly alters the susceptibility of R3 toward oxidative modifications, easily resulting in peptide dopamination and formation of cross-linked S-S derivatives.
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Affiliation(s)
- Chiara Bacchella
- Dipartimento di Chimica, Università di Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Teresa Benedetta Guerriere
- Dipartimento di Chimica, Università di Pavia, Via Taramelli 12, Pavia 27100, Italy
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 9, Pavia 27100, Italy
| | - Enrico Monzani
- Dipartimento di Chimica, Università di Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Simone Dell'Acqua
- Dipartimento di Chimica, Università di Pavia, Via Taramelli 12, Pavia 27100, Italy
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2
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Zheng L, Shi S, Sun X, Lu M, Liao Y, Zhu S, Zhang H, Pan Z, Fang P, Zeng Z, Li H, Li Z, Xue W, Zhu F. MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics. Brief Bioinform 2024; 25:bbae006. [PMID: 38305456 PMCID: PMC10835750 DOI: 10.1093/bib/bbae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 02/03/2024] Open
Abstract
Protein structure prediction is a longstanding issue crucial for identifying new drug targets and providing a mechanistic understanding of protein functions. To enhance the progress in this field, a spectrum of computational methodologies has been cultivated. AlphaFold2 has exhibited exceptional precision in predicting wild-type protein structures, with performance exceeding that of other methods. However, predicting the structures of missense mutant proteins using AlphaFold2 remains challenging due to the intricate and substantial structural alterations caused by minor sequence variations in the mutant proteins. Molecular dynamics (MD) has been validated for precisely capturing changes in amino acid interactions attributed to protein mutations. Therefore, for the first time, a strategy entitled 'MoDAFold' was proposed to improve the accuracy and reliability of missense mutant protein structure prediction by combining AlphaFold2 with MD. Multiple case studies have confirmed the superior performance of MoDAFold compared to other methods, particularly AlphaFold2.
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Affiliation(s)
- Lingyan Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
| | - Shuiyang Shi
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xiuna Sun
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
| | - Mingkun Lu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
| | - Yang Liao
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Sisi Zhu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Pan Fang
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhenyu Zeng
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Honglin Li
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhaorong Li
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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3
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Zhong H, Liu H, Liu H. Molecular Mechanism of Tau Misfolding and Aggregation: Insights from Molecular Dynamics Simulation. Curr Med Chem 2024; 31:2855-2871. [PMID: 37031392 DOI: 10.2174/0929867330666230409145247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/01/2023] [Accepted: 02/27/2023] [Indexed: 04/10/2023]
Abstract
Tau dysfunction has a close association with many neurodegenerative diseases, which are collectively referred to as tauopathies. Neurofibrillary tangles (NFTs) formed by misfolding and aggregation of tau are the main pathological process of tauopathy. Therefore, uncovering the misfolding and aggregation mechanism of tau protein will help to reveal the pathogenic mechanism of tauopathies. Molecular dynamics (MD) simulation is well suited for studying the dynamic process of protein structure changes. It provides detailed information on protein structure changes over time at the atomic resolution. At the same time, MD simulation can also simulate various conditions conveniently. Based on these advantages, MD simulations are widely used to study conformational transition problems such as protein misfolding and aggregation. Here, we summarized the structural features of tau, the factors affecting its misfolding and aggregation, and the applications of MD simulations in the study of tau misfolding and aggregation.
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Affiliation(s)
- Haiyang Zhong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hongli Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao, SAR, 999078, China
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4
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Billings JL, Hilton JBW, Liddell JR, Hare DJ, Crouch PJ. Fundamental Neurochemistry Review: Copper availability as a potential therapeutic target in progressive supranuclear palsy: Insight from other neurodegenerative diseases. J Neurochem 2023; 167:337-346. [PMID: 37800457 DOI: 10.1111/jnc.15978] [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: 05/16/2023] [Revised: 08/21/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
Since the first description of Parkinson's disease (PD) over two centuries ago, the recognition of rare types of atypical parkinsonism has introduced a spectrum of related PD-like diseases. Among these is progressive supranuclear palsy (PSP), a neurodegenerative condition that clinically differentiates through the presence of additional symptoms uncommon in PD. As with PD, the initial symptoms of PSP generally present in the sixth decade of life when the underpinning neurodegeneration is already significantly advanced. The causal trigger of neuronal cell loss in PSP is unknown and treatment options are consequently limited. However, converging lines of evidence from the distinct neurodegenerative conditions of PD and amyotrophic lateral sclerosis (ALS) are beginning to provide insights into potential commonalities in PSP pathology and opportunity for novel therapeutic intervention. These include accumulation of the high abundance cuproenzyme superoxide dismutase 1 (SOD1) in an aberrant copper-deficient state, associated evidence for altered availability of the essential micronutrient copper, and evidence for neuroprotection using compounds that can deliver available copper to the central nervous system. Herein, we discuss the existing evidence for SOD1 pathology and copper imbalance in PSP and speculate that treatments able to provide neuroprotection through manipulation of copper availability could be applicable to the treatment of PSP.
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Affiliation(s)
- Jessica L Billings
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - James B W Hilton
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Jeffrey R Liddell
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Dominic J Hare
- School of Mathematical and Physical Sciences, University of Technology Sydney, Broadway, Ultimo, New South Wales, Australia
| | - Peter J Crouch
- Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
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5
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Wang L, Wei Y, Sun Z, Jiang LH, Yin Y, Zheng P, Fu Y, Wang H, Li C, Wang JZ. DpdtpA, A Multi-metal Ion Chelator, Attenuates Tau Phosphorylation and Microglial Inflammatory Response via Regulating the PI3K/AKT/GSK-3β Signal Pathways. Neuroscience 2023; 526:196-203. [PMID: 37419407 DOI: 10.1016/j.neuroscience.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
Tau protein hyperphosphorylation and formation of intracellular neurofibrillary tangles (NFTs) are one of the histopathological hallmarks of Alzheimer's disease (AD) and positively correlated with the severity of AD symptoms. NFTs contain a large number of metal ions that play an important role in regulating tau protein phosphorylation and AD progression. Extracellular tau induces primary phagocytosis of stressed neurons and neuronal loss by activating microglia. Here, we studied the effects of a multi-metal ion chelator, DpdtpA, on tau-induced microglial activation and inflammatory responses and the underlying mechanisms. Treatment with DpdtpA attenuated the increase in the expression of NF-κB and production of inflammatory cytokines, IL-1β, IL-6 and IL-10, in rat microglial cells induced by expression of human tau40 proteins. Treatment with DpdtpA also suppressed tau protein expression and phosphorylation. Moreover, treatment with DpdtpA prevented tau-induced activation of glycogen synthase kinase-3β (GSK-3β) and inhibition of phosphatidylinositol-3-hydroxy kinase (PI3K)/AKT. Collectively, these results show that DpdtpA can attenuate tau phosphorylation and inflammatory responses of microglia by regulating the PI3K/AKT/GSK-3β signal pathways, providing a new option to alleviate neuroinflammation for the treatment of AD.
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Affiliation(s)
- Lu Wang
- Henan Key Laboratory of Neurorestoratology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Department of Physiology and Pathophysiology, Xinxiang Medical University, Xinxiang, China.
| | - Yingjuan Wei
- Department of Physiology and Pathophysiology, Xinxiang Medical University, Xinxiang, China
| | - Zhenzhou Sun
- Department of Physiology and Pathophysiology, Xinxiang Medical University, Xinxiang, China
| | - Lin-Hua Jiang
- Sino-UK Joint Laboratory of Brain Function and Injury of Henan Province, Xinxiang Medical University, Xinxiang, China
| | - Yaling Yin
- Department of Physiology and Pathophysiology, Xinxiang Medical University, Xinxiang, China
| | - Panpan Zheng
- Department of Physiology and Pathophysiology, Xinxiang Medical University, Xinxiang, China
| | - Yun Fu
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
| | - Hongwei Wang
- Department of Physiology and Pathophysiology, Xinxiang Medical University, Xinxiang, China
| | - Changzheng Li
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
| | - Jian-Zhi Wang
- Henan Key Laboratory of Neurorestoratology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Key Laboratory of Ministry of Education of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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6
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Kola A, Nencioni F, Valensin D. Bioinorganic Chemistry of Micronutrients Related to Alzheimer's and Parkinson's Diseases. Molecules 2023; 28:5467. [PMID: 37513339 PMCID: PMC10385134 DOI: 10.3390/molecules28145467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Metal ions are fundamental to guarantee the regular physiological activity of the human organism. Similarly, vitamins play a key role in many biological functions of the metabolism, among which are coenzymes, redox mediators, and antioxidants. Due to their importance in the human organism, both metals and vitamins have been extensively studied for their involvement in neurodegenerative diseases (NDs). However, the full potential of the interaction between vitamins and metal ions has not been fully explored by researchers yet, and further investigation on this topic is needed. The aim of this review is to provide an overview of the scientific literature on the implications of vitamins and selected metal ions in two of the most common neurodegenerative diseases, Alzheimer's and Parkinson's disease. Furthermore, vitamin-metal ion interactions are discussed in detail focusing on their bioinorganic chemistry, with the perspective of arousing more interest in this fascinating bioinorganic field.
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Affiliation(s)
| | | | - Daniela Valensin
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (A.K.); (F.N.)
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7
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Duan H, Li J, Xue J, Qi D. Metal-Enhanced Helical Chirality of Coil Macromolecules: Bioinspired by Metal Coordination-Induced Protein Folding. Biomacromolecules 2023; 24:344-357. [PMID: 36563170 DOI: 10.1021/acs.biomac.2c01165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Although the supramolecular helical structures of biomacromolecules have been studied, the examples of supramolecular systems that are assembled using coils to form helical polymer chains are still limited. Inspired by enhanced helical chirality at the supramolecular level in metal coordination-induced protein folding, a series of alanine-based coil copolymers (poly-(l-co-d)-ala-NH2) carrying (l)- and (d)-alanine pendants were synthesized as a fresh research model to study the cooperative processes between homochirality property and metal coordination. The complexes of poly-(l-co-d)-ala-NH2 and metal ions underwent a coil-to-helix transition and exhibited remarkable nonlinear effects based on the enantiomeric excess of the monomer unit in the copolymers, affording enhanced helical chirality compared to poly-(l-co-d)-ala-NH2. More importantly, the synergistic effect of amplification of asymmetry and metal coordination triggered the formation of a helical molecular orbital on the polymer backbone via the coordination with the d orbital of copper ions. Thus, the helical chirality enhancement degree of poly-(l-co-d)-ala-NH2/Cu2+ complexes (31.4) is approximately 3 times higher than that of poly-(l-co-d)-ala-NH2/Ag+ complexes (9.8). This study not only provides important mechanistic insights into the enhancement of helical chirality for self-assembly but also establishes a new strategy for studying the homochiral amplification of asymmetry in biological supramolecular systems.
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Affiliation(s)
- Huimin Duan
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology, Ministry of Education, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China.,Zhejiang Provincial Engineering Research Center for Green and Low-carbon Dyeing & Finishing, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Jiawei Li
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology, Ministry of Education, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China.,Zhejiang Provincial Engineering Research Center for Green and Low-carbon Dyeing & Finishing, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China.,Zhejiang Provincial Innovation Center of Advanced Textile Technology, Shaoxing 312000, China
| | - Jiadan Xue
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Dongming Qi
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology, Ministry of Education, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China.,Zhejiang Provincial Engineering Research Center for Green and Low-carbon Dyeing & Finishing, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China.,Zhejiang Provincial Innovation Center of Advanced Textile Technology, Shaoxing 312000, China
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8
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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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9
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Bacchella C, Gentili S, Mozzi SI, Monzani E, Casella L, Tegoni M, Dell’Acqua S. Role of the Cysteine in R3 Tau Peptide in Copper Binding and Reactivity. Int J Mol Sci 2022; 23:ijms231810726. [PMID: 36142637 PMCID: PMC9503722 DOI: 10.3390/ijms231810726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/07/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
Tau is a widespread neuroprotein that regulates the cytoskeleton assembly. In some neurological disorders, known as tauopathies, tau is dissociated from the microtubule and forms insoluble neurofibrillary tangles. Tau comprises four pseudorepeats (R1-R4), containing one (R1, R2, R4) or two (R3) histidines, that potentially act as metal binding sites. Moreover, Cys291 and Cys322 in R2 and R3, respectively, might have an important role in protein aggregation, through possible disulfide bond formation, and/or affecting the binding and reactivity of redox-active metal ions, as copper. We, therefore, compare the interaction of copper with octadeca-R3-peptide (R3C) and with the mutant containing an alanine residue (R3A) to assess the role of thiol group. Spectrophotometric titrations allow to calculate the formation constant of the copper(I) complexes, showing a remarkable stronger interaction in the case of R3C (l log Kf = 13.4 and 10.5 for copper(I)-R3C and copper(I)-R3A, respectively). We also evaluate the oxidative reactivity associated to these copper complexes in the presence of dopamine and ascorbate. Both R3A and R3C peptides increase the capability of copper to oxidize catechols, but copper-R3C displays a peculiar mechanism due to the presence of cysteine. HPLC-MS analysis shows that cysteine can form disulfide bonds and dopamine-Cys covalent adducts, with potential implication in tau aggregation process.
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Affiliation(s)
- Chiara Bacchella
- Dipartimento di Chimica, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Silvia Gentili
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Sara Ida Mozzi
- Dipartimento di Chimica, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Enrico Monzani
- Dipartimento di Chimica, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Luigi Casella
- Dipartimento di Chimica, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
- Correspondence:
| | - Matteo Tegoni
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Simone Dell’Acqua
- Dipartimento di Chimica, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
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10
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Dong X, Qi R, Qiao Q, Li X, Li F, Wan J, Zhang Q, Wei G. Heparin remodels the microtubule-binding repeat R3 of Tau protein towards fibril-prone conformations. Phys Chem Chem Phys 2021; 23:20406-20418. [PMID: 34494046 DOI: 10.1039/d1cp02651h] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Abnormal aggregation of proteins into pathological amyloid fibrils is implicated in a wide range of devastating human neurodegenerative diseases. Intracellular fibrillary inclusions formed by Tau protein are characterized as the hallmark of tauopathies, including Alzheimer's disease and frontotemporal dementia. Heparin has been often used to trigger Tau aggregation in in vitro studies. However, the conformational changes induced by heparin and the underlying mechanism of promotion of Tau aggregation by heparin are not well understood. Structural characterization of Tau oligomers in the early stage of fibrillation is of great importance but remains challenging due to their dynamic and heterogeneous nature. R3, the third microtubule-binding repeat of Tau, contains the fibril-nucleating core (PHF6) and is crucial for Tau aggregation. In this study, utilizing extensive all-atom replica-exchange molecular dynamic simulations, we explored the conformational ensembles of R3 monomer/dimer in the absence and presence of heparin. Our results show that without heparin, both monomeric and dimeric R3 preferentially adopt collapsed β-sheet-containing conformations and PHF6 plays an important role in the formation of interchain β-sheet structures, while in the presence of heparin, R3 can populate relatively extended disordered states where chain dimension is similar to that of R3 in Tau filaments. Through electrostatic, hydrogen-bonding and hydrophobic interactions, heparin has a preference for interacting with residues V306/Q307/K317/K321/H329/H330/K331 which distribute throughout the entire sequence of R3, in turn acting as a template to extend R3 conformations. More importantly, heparin alters intramolecular/intermolecular interaction patterns of R3 and increases the intermolecular contact regions. Our results suggest that heparin remodels the conformations of R3 towards fibril-prone structures by increasing chain dimension and intermolecular contact regions, which may shed light on the atomic mechanism of heparin-induced amyloid fibrillization of Tau protein.
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Affiliation(s)
- Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China.
| | - Ruxi Qi
- Cryo-EM Center, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
| | - Qin Qiao
- Digital Medical Research Center, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Fudan University, Shanghai 200032, People's Republic of China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Fangying Li
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China.
| | - Jiaqian Wan
- College of Physical Education and Training, Shanghai University of Sport, Shanghai 200438, People's Republic of China
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, Shanghai 200438, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China.
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