1
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Ghosh D, Biswas A, Radhakrishna M. Advanced computational approaches to understand protein aggregation. BIOPHYSICS REVIEWS 2024; 5:021302. [PMID: 38681860 PMCID: PMC11045254 DOI: 10.1063/5.0180691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/18/2024] [Indexed: 05/01/2024]
Abstract
Protein aggregation is a widespread phenomenon implicated in debilitating diseases like Alzheimer's, Parkinson's, and cataracts, presenting complex hurdles for the field of molecular biology. In this review, we explore the evolving realm of computational methods and bioinformatics tools that have revolutionized our comprehension of protein aggregation. Beginning with a discussion of the multifaceted challenges associated with understanding this process and emphasizing the critical need for precise predictive tools, we highlight how computational techniques have become indispensable for understanding protein aggregation. We focus on molecular simulations, notably molecular dynamics (MD) simulations, spanning from atomistic to coarse-grained levels, which have emerged as pivotal tools in unraveling the complex dynamics governing protein aggregation in diseases such as cataracts, Alzheimer's, and Parkinson's. MD simulations provide microscopic insights into protein interactions and the subtleties of aggregation pathways, with advanced techniques like replica exchange molecular dynamics, Metadynamics (MetaD), and umbrella sampling enhancing our understanding by probing intricate energy landscapes and transition states. We delve into specific applications of MD simulations, elucidating the chaperone mechanism underlying cataract formation using Markov state modeling and the intricate pathways and interactions driving the toxic aggregate formation in Alzheimer's and Parkinson's disease. Transitioning we highlight how computational techniques, including bioinformatics, sequence analysis, structural data, machine learning algorithms, and artificial intelligence have become indispensable for predicting protein aggregation propensity and locating aggregation-prone regions within protein sequences. Throughout our exploration, we underscore the symbiotic relationship between computational approaches and empirical data, which has paved the way for potential therapeutic strategies against protein aggregation-related diseases. In conclusion, this review offers a comprehensive overview of advanced computational methodologies and bioinformatics tools that have catalyzed breakthroughs in unraveling the molecular basis of protein aggregation, with significant implications for clinical interventions, standing at the intersection of computational biology and experimental research.
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Affiliation(s)
- Deepshikha Ghosh
- Department of Biological Sciences and Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | - Anushka Biswas
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
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2
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Ghosh D, Agarwal M, Radhakrishna M. Molecular Insights into the Inhibitory Role of α-Crystallin against γD-Crystallin Aggregation. J Chem Theory Comput 2024; 20:1740-1752. [PMID: 38078935 DOI: 10.1021/acs.jctc.3c00774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Cataracts, a major cause of global blindness, contribute significantly to the overall prevalence of blindness. The opacification of the lens, resulting in cataract formation, primarily occurs due to the aggregation of crystallin proteins within the eye lens. Despite the high concentration of these crystallins, they remarkably maintain the lens transparency and refractive index. α-Crystallins (α-crys), acting as chaperones, play a crucial role in preventing crystallin aggregation, although the exact molecular mechanism remains uncertain. In this study, we employed a combination of molecular docking, all-atom molecular dynamics simulations, and advanced free energy calculations to investigate the interaction between γD-crystallin (γD-crys), a major structural protein of the eye lens, and α-crystallin proteins. Our findings demonstrate that α-crys exhibits an enhanced affinity for the NTD2 and CTD4 regions of γD-crys. The NTD2 and CTD4 regions form the interface between the N-terminal domain (NTD) and the C-terminal domain (CTD) of the γD-crys protein. By binding to the interface region between the NTD and CTD of the protein, α-crys effectively inhibits the formation of domain-swapped aggregates and mitigates protein aggregation. Analysis of the Markov state models using molecular dynamics trajectories confirms that minimum free energy conformations correspond to the binding of the α-crystallin domain (ACD) of α-crys to NTD2 and CTD4 that form the interdomain interface.
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Affiliation(s)
- Deepshikha Ghosh
- Department of Biological Sciences and Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | - Manish Agarwal
- Computer Services Centre, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, Delhi 110016, India
| | - Mithun Radhakrishna
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
- Center for Biomedical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
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3
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Jain M, Sahoo A, Matysiak S. Modulation of Aβ 16-22 aggregation by glucose. Phys Chem Chem Phys 2024; 26:5038-5044. [PMID: 38258497 DOI: 10.1039/d3cp04494g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The self-assembly of amyloid-beta (Aβ) peptides into fibrillar structures in the brain is a signature of Alzheimer's disease. Recent studies have reported correlations between Alzheimer's disease and type-2 diabetes. Structurally, hyperglycemia induces covalent protein crosslinkings by advanced glycation end products (AGE), which can affect the stability of Aβ oligomers. In this work, we leverage physics-based coarse-grained molecular simulations to probe alternate thermodynamic pathways that affect peptide aggregation propensities at varying concentrations of glucose molecules. Similar to previous experimental reports, our simulations show a glucose concentration-dependent increase in Aβ aggregation rates, without changes in the overall secondary structure content. We discovered that glucose molecules prefer partitioning onto the aggregate-water interface at a specific orientation, resulting in a loss of molecular rotational entropy. This effectively hastens the aggregation rates, as peptide self-assembly can reduce the available surface area for peptide-glucose interactions. This work introduces a new thermodynamic-driven pathway, beyond chemical cross-linking, that can modulate Aβ aggregation.
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Affiliation(s)
- Meenal Jain
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Abhilash Sahoo
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Center for Computational Mathematics, Flatiron Institute, New York, NY, USA
| | - Silvina Matysiak
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, MD, USA.
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
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4
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Ge WY, Deng X, Shi WP, Lin WJ, Chen LL, Liang H, Wang XT, Zhang TD, Zhao FZ, Guo WH, Yin DC. Amyloid Protein Cross-Seeding Provides a New Perspective on Multiple Diseases In Vivo. Biomacromolecules 2023; 24:1-18. [PMID: 36507729 DOI: 10.1021/acs.biomac.2c01233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Amyloid protein cross-seeding is a peculiar phenomenon of cross-spreading among different diseases. Unlike traditional infectious ones, diseases caused by amyloid protein cross-seeding are spread by misfolded proteins instead of pathogens. As a consequence of the interactions among misfolded heterologous proteins or polypeptides, amyloid protein cross-seeding is considered to be the crucial cause of overlapping pathological transmission between various protein misfolding disorders (PMDs) in multiple tissues and cells. Here, we briefly review the phenomenon of cross-seeding among amyloid proteins. As an interesting example worth mentioning, the potential links between the novel coronavirus pneumonia (COVID-19) and some neurodegenerative diseases might be related to the amyloid protein cross-seeding, thus may cause an undesirable trend in the incidence of PMDs around the world. We then summarize the theoretical models as well as the experimental techniques for studying amyloid protein cross-seeding. Finally, we conclude with an outlook on the challenges and opportunities for basic research in this field. Cross-seeding of amyloid opens up a new perspective in our understanding of the process of amyloidogenesis, which is crucial for the development of new treatments for diseases. It is therefore valuable but still challenging to explore the cross-seeding system of amyloid protein as well as to reveal the structural basis and the intricate processes.
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Affiliation(s)
- Wan-Yi Ge
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xudong Deng
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Wen-Pu Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Wen-Juan Lin
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Liang-Liang Chen
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Huan Liang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xue-Ting Wang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tuo-Di Zhang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Feng-Zhu Zhao
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China.,Non-commissioned Officer School, Army Medical University, Shijiazhuang 050081, China
| | - Wei-Hong Guo
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Da-Chuan Yin
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
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5
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Xu Z, Gong Y, Zou Y, Wan J, Tang J, Zhan C, Wei G, Zhang Q. Dissecting the Inhibitory Mechanism of the αB-Crystallin Domain against Aβ 42 Aggregation and Its Effect on Aβ 42 Protofibrils: A Molecular Dynamics Simulation Study. ACS Chem Neurosci 2022; 13:2842-2851. [PMID: 36153964 DOI: 10.1021/acschemneuro.2c00224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Alzheimer's disease (AD) is related to the misfolding and aggregation of amyloid-β (Aβ) protein, and its major pathological hallmark is fibrillary β-amyloid plaques. Impeding the formation of Aβ β-structure-rich aggregates and dissociating Aβ fibrils are considered potent strategies to suppress the onset and progression of AD. As a molecular chaperone, human αB-crystallin has received extensive attention in the inhibition of protein aggregation. Previous experiments reported that the structured core region of αB-crystallin (αBC) exhibits a better preventive effect on Aβ aggregation and toxicity than the full-length protein. However, the molecular mechanism behind the effect of inhibition remains mostly unknown. Herein, we carried out six 500 ns molecular dynamics (MD) simulations to investigate the inhibitory mechanism of αBC on Aβ42 aggregation. Our simulations show that αBC greatly impedes the formation of β-structure contents. We find that the binding of αBC to the Aβ42 monomer is driven by polar, hydrophobic, and H-bonding interactions. To explore whether αBC could destabilize Aβ42 protofibrils, we also carried out MD simulations of Aβ42 protofibrils with and without αBC. The results show that αBC interacts with three binding sites of the Aβ42 protofibril, and the binding is mainly driven by polar and H-bonding interactions. The binding of αBC at these three sites has a preferred dissociation effect on the β-structure content, kink angle, and K28-A42 salt bridges. Overall, this study not only discloses the molecular mechanism of αBC against Aβ42 aggregation but also demonstrates the disruption effects of αBC on Aβ42 protofibrils, which yields an avenue for designing anti-AD drug candidates.
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Affiliation(s)
- Zhengdong Xu
- School of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China
| | - Yehong Gong
- School of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China.,School of Sports Science and Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, People's Republic of China
| | - Yu Zou
- Department Sport and Exercise Science, College of Education, Zhejiang University, 148 Tianmenshan Road, Hangzhou 310007, Zhejiang, People's Republic of China
| | - Jiaqian Wan
- School of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China
| | - Jiaxing Tang
- School of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China
| | - Chendi Zhan
- 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
| | - 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
| | - Qingwen Zhang
- School of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China
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6
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Sprague-Piercy MA, Rocha MA, Kwok AO, Martin RW. α-Crystallins in the Vertebrate Eye Lens: Complex Oligomers and Molecular Chaperones. Annu Rev Phys Chem 2021; 72:143-163. [PMID: 33321054 PMCID: PMC8062273 DOI: 10.1146/annurev-physchem-090419-121428] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
α-Crystallins are small heat-shock proteins that act as holdase chaperones. In humans, αA-crystallin is expressed only in the eye lens, while αB-crystallin is found in many tissues. α-Crystallins have a central domain flanked by flexible extensions and form dynamic, heterogeneous oligomers. Structural models show that both the C- and N-terminal extensions are important for controlling oligomerization through domain swapping. α-Crystallin prevents aggregation of damaged β- and γ-crystallins by binding to the client protein using a variety of binding modes. α-Crystallin chaperone activity can be compromised by mutation or posttranslational modifications, leading to protein aggregation and cataract. Because of their high solubility and their ability to form large, functional oligomers, α-crystallins are particularly amenable to structure determination by solid-state nuclear magnetic resonance (NMR) and solution NMR, as well as cryo-electron microscopy.
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Affiliation(s)
- Marc A Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA;
| | - Megan A Rocha
- Department of Chemistry, University of California, Irvine, California 92697, USA
| | - Ashley O Kwok
- Department of Chemistry, University of California, Irvine, California 92697, USA
| | - Rachel W Martin
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA;
- Department of Chemistry, University of California, Irvine, California 92697, USA
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7
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Cao Y, He Z, Gao Y, Xin Y, Luo L, Meng F. Boosting the Photodynamic Degradation of Islet Amyloid Polypeptide Aggregates Via a "Bait-Hook-Devastate" Strategy. ACS APPLIED MATERIALS & INTERFACES 2021; 13:14911-14919. [PMID: 33764749 DOI: 10.1021/acsami.1c00082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Photosensitizers that can generate reactive oxygen species (ROS) upon irradiation have emerged as promising agents for photodynamic degradation of toxic amyloid aggregates that are linked to many amyloidogenic diseases. However, due to the ultrastable β-sheet structure in amyloid aggregates and inefficient utilization of the generated ROS, it usually requires high stoichiometric concentration of the photosensitizer and/or intensive light irradiation to fully dissociate aggregates. In this work, we have developed a "bait-hook-devastate" strategy to boost the efficiency of the photodynamic degradation of amyloid aggregates. This strategy employs anionic polyacrylic acid as a bait to accumulate cationic human islet amyloid polypeptide (IAPP) aggregates and positively charged photosensitizer TPCI in a confined area through electronic interactions. Multiple characterization studies proved that the utilization rate of ROS generated by TPCI was remarkably improved via this strategy, which amplified the ability of TPCI to dissociate IAPP aggregates. Rapid and complete degradation of IAPP aggregates could be achieved by irradiating the system under very mild conditions for less than 30 min, and the IAPP-mediated cytotoxicity was also largely alleviated, providing a new paradigm to accelerate photodynamic degradation of amyloid aggregates for further practical applications.
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Affiliation(s)
- Yujuan Cao
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhenyan He
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yuting Gao
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yanru Xin
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Liang Luo
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fanling Meng
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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8
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Muvva C, Murugan NA, Subramanian V. Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations. Int J Mol Sci 2021; 22:ijms22063244. [PMID: 33806726 PMCID: PMC8005029 DOI: 10.3390/ijms22063244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 01/25/2023] Open
Abstract
A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer's disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.
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Affiliation(s)
- Charuvaka Muvva
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden;
- Inorganic & Physical Chemistry Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600020, India;
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Natarajan Arul Murugan
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden;
- Correspondence:
| | - Venkatesan Subramanian
- Inorganic & Physical Chemistry Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600020, India;
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Centre for High Computing, CSIR-CLRI, Adyar, Chennai 600020, India
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9
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Kanchi PK, Dasmahapatra AK. Destabilization of the Alzheimer's amyloid-β protofibrils by THC: A molecular dynamics simulation study. J Mol Graph Model 2021; 105:107889. [PMID: 33725642 DOI: 10.1016/j.jmgm.2021.107889] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/28/2021] [Accepted: 03/01/2021] [Indexed: 10/22/2022]
Abstract
Alzheimer's disease is a leading cause of dementia in the elderly population for which there is no cure at present. Deposits of neurotoxic plaques are found in the brains of patients which are composed of fibrils of the amyloid-β peptide. Molecules which can disrupt these fibrils have gained attention as potential therapeutic agents. Δ-tetrahydrocannabidiol (THC) is a cannabinoid, which can bind to the receptors in the brain, and has shown promise in reducing the fibril content in many experimental studies. In our present study, by employing all atom molecular dynamics simulations, we have investigated the mechanism of the interaction of the THC molecules with the amyloid-β protofibrils. Our results show that the THC molecules disrupt the protofibril structure by binding strongly to them. The driving force for the binding was the hydrophobic interactions with the hydrophobic residues in the fibrils. As a result of these interactions, the tight packing of the hydrophobic core of the protofibrils was made loose, and salt bridges, which were important for stability were disrupted. Hydrogen bonds between the chains of the protofibrils which are important for stability were disrupted, as a result of which the β-sheet content was reduced. The destabilization of the protofibrils by the THC molecules leads to the conclusion that THC molecules may be considered for the therapy in treating Alzheimer's disease.
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Affiliation(s)
- Pavan Krishna Kanchi
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Ashok Kumar Dasmahapatra
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India; Center for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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10
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Ma C, Hunt JB, Selenica MLB, Sanneh A, Sandusky-Beltran LA, Watler M, Daas R, Kovalenko A, Liang H, Placides D, Cao C, Lin X, Orr MB, Zhang B, Gensel JC, Feola DJ, Gordon MN, Morgan D, Bickford PC, Lee DC. Arginase 1 Insufficiency Precipitates Amyloid- β Deposition and Hastens Behavioral Impairment in a Mouse Model of Amyloidosis. Front Immunol 2021; 11:582998. [PMID: 33519806 PMCID: PMC7840571 DOI: 10.3389/fimmu.2020.582998] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/23/2020] [Indexed: 12/17/2022] Open
Abstract
Alzheimer’s disease (AD) includes several hallmarks comprised of amyloid-β (Aβ) deposition, tau neuropathology, inflammation, and memory impairment. Brain metabolism becomes uncoupled due to aging and other AD risk factors, which ultimately lead to impaired protein clearance and aggregation. Increasing evidence indicates a role of arginine metabolism in AD, where arginases are key enzymes in neurons and glia capable of depleting arginine and producing ornithine and polyamines. However, currently, it remains unknown if the reduction of arginase 1 (Arg1) in myeloid cell impacts amyloidosis. Herein, we produced haploinsufficiency of Arg1 by the hemizygous deletion in myeloid cells using Arg1fl/fl and LysMcreTg/+ mice crossed with APP Tg2576 mice. Our data indicated that Arg1 haploinsufficiency promoted Aβ deposition, exacerbated some behavioral impairment, and decreased components of Ragulator-Rag complex involved in mechanistic target of rapamycin complex 1 (mTORC1) signaling and autophagy. Additionally, Arg1 repression and arginine supplementation both impaired microglial phagocytosis in vitro. These data suggest that proper function of Arg1 and arginine metabolism in myeloid cells remains essential to restrict amyloidosis.
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Affiliation(s)
- Chao Ma
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.,Sanders-Brown Center on Aging, Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Jerry B Hunt
- Sanders-Brown Center on Aging, Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, United States.,Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Maj-Linda B Selenica
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States.,Sanders-Brown Center on Aging, Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Awa Sanneh
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Leslie A Sandusky-Beltran
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Mallory Watler
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Rana Daas
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Andrii Kovalenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Huimin Liang
- Sanders-Brown Center on Aging, Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, United States.,Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Devon Placides
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Chuanhai Cao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Xiaoyang Lin
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Michael B Orr
- Spinal Cord and Brain Injury Research Center, Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Bei Zhang
- Spinal Cord and Brain Injury Research Center, Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States.,Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - John C Gensel
- Spinal Cord and Brain Injury Research Center, Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - David J Feola
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Kentucky, Lexington, KY, United States
| | - Marcia N Gordon
- Department of Translational Neuroscience, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Dave Morgan
- Department of Translational Neuroscience, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Paula C Bickford
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.,Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.,Research Service, James A. Haley Veterans Affairs Hospital, Tampa, FL, United States
| | - Daniel C Lee
- Sanders-Brown Center on Aging, Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, United States.,Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
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11
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Jahan I, Nayeem SM. Destabilization of Alzheimer's Aβ 42 protofibrils with acyclovir, carmustine, curcumin, and tetracycline: insights from molecular dynamics simulations. NEW J CHEM 2021. [DOI: 10.1039/d1nj04453b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Among the neurodegenerative diseases, one of the most common dementia is Alzheimer's disease (AD).
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Affiliation(s)
- Ishrat Jahan
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Shahid M. Nayeem
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, UP, India
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12
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Nie RZ, Huo YQ, Yu B, Liu CJ, Zhou R, Bao HH, Tang SW. Molecular insights into the inhibitory mechanisms of gallate moiety on the Aβ 1-40 amyloid aggregation: A molecular dynamics simulation study. Int J Biol Macromol 2020; 156:40-50. [PMID: 32275992 DOI: 10.1016/j.ijbiomac.2020.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/17/2022]
Abstract
Alzheimer's disease is the most common form of neurodegenerative disease and the formation of Aβ amyloid aggregates has been widely demonstrated to be the principal cause of Alzheimer's disease. Our previous study and other studies suggested that the gallate moiety played an obligatory role in the inhibition process of naturally occurring polyphenols on Aβ amyloid fibrils formation. However, the detailed mechanisms were still unknown. Thus, in the present study, the gallic acid (GA) was specially selected and the molecular recognition mechanisms between GA molecules and Aβ1-40 monomer were examined and analyzed by molecular dynamics simulation. The in silico experiments revealed that GA significantly prevented the conformational changes of Aβ1-40 monomer with no β-sheet structure during the whole 100 ns. By analyzing the binding sites of GA molecules to Aβ1-40 monomer, we found that both hydrophilic and hydrophobic amino acid residues were participated in the binding of GA molecules to Aβ1-40 monomer. Moreover, results from the binding free energy analysis further demonstrated that the strength of polar interactions was significantly stronger than that of nonpolar interactions. We believed that our results could help to elucidate the underlying mechanisms of gallate moiety on the anti-amyloidogenic effects of polyphenols at the atomic level.
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Affiliation(s)
- Rong-Zu Nie
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Yin-Qiang Huo
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Bo Yu
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Chuan-Ju Liu
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Rui Zhou
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Hong-Hui Bao
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Shang-Wen Tang
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China.
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13
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Subramaniam J, Yang P, McCarthy MJ, Cunha SR. Identification and characterization of self-association domains on small ankyrin 1 isoforms. J Mol Cell Cardiol 2020; 139:225-237. [PMID: 32035138 PMCID: PMC11042479 DOI: 10.1016/j.yjmcc.2020.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 01/13/2020] [Accepted: 02/03/2020] [Indexed: 10/25/2022]
Abstract
In striated muscles, the large scaffolding protein obscurin and a small SR-integral membrane protein sAnk1.5 control the retention of longitudinal SR across the sarcomere. How a complex of these proteins facilitates localization of longitudinal SR has yet to be resolved, but we hypothesize that obscurin interacts with a complex of sAnk1.5 proteins. To begin to address this hypothesis, we demonstrate that sAnk1.5 interacts with itself and identify two domains mediating self-association. Specifically, we show by co-precipitation and FLIM-FRET analysis that sAnk1.5 and another small AnkR isoform (sAnk1.6) interact with themselves and each other. We demonstrate that obscurin interacts with a complex of sAnk1.5 proteins and that this complex formation is enhanced by obscurin-binding. Using FLIM-FRET analysis, we show that obscurin interacts with sAnk1.5 alone and with sAnk1.6 in the presence of sAnk1.5. We find that sAnk1.5 self-association is disrupted by mutagenesis of residues Arg64-Arg69, residues previously associated with obscurin-binding. Molecular modeling of two interacting sAnk1.5 monomers facilitated the identification of Gly31-Val36 as an additional site of interaction, which was subsequently corroborated by co-precipitation and FLIM-FRET analysis. In closing, these results support a model in which sAnk1.5 forms large oligomers that interact with obscurin to facilitate the retention of longitudinal SR throughout skeletal and cardiac myocytes.
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Affiliation(s)
- Janani Subramaniam
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States of America
| | - Pu Yang
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States of America
| | - Michael J McCarthy
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States of America
| | - Shane R Cunha
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States of America.
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14
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Li X, Wang W, Dong X, Sun Y. Conjugation of RTHLVFFARK to human lysozyme creates a potent multifunctional modulator for Cu2+-mediated amyloid β-protein aggregation and cytotoxicity. J Mater Chem B 2020; 8:2256-2268. [DOI: 10.1039/c9tb02397f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conjugation of alkaline decapeptide (RTHLVFFARK) to lysozyme creates a potent multifunctional modulator (R-hLys) for Cu2+-mediated amyloid β-protein aggregation and cytotoxicity.
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Affiliation(s)
- Xi Li
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300354
- China
| | - Wenjuan Wang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300354
- China
| | - Xiaoyan Dong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300354
- China
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300354
- China
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15
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Ghorbani M, Soleymani H, Allahverdi A, Shojaeilangari S, Naderi-Manesh H. Effects of natural compounds on conformational properties and hairpin formation of amyloid-β 42 monomer: docking and molecular dynamics simulation study. J Biomol Struct Dyn 2019; 38:3371-3383. [PMID: 31496378 DOI: 10.1080/07391102.2019.1664934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The β42 amyloid peptides (Aβ) are identified as a candidate target for Alzheimer's drugs. Phenolic compounds can bind to the Aβ and inhibit amyloid formation. However, the inhibitory mechanism of phenolic compounds remains unclear. In this study, the molecular dynamic simulation and docking program were used to characterize the molecular details of inhibitory mechanism of the phenolic compounds. Our Results show that the phenolic compounds can bind to hydrophobic region in Aβ42 monomer and alter hydrophobic interactions network at Aβ42 which play a key role in β-sheet formation. The cluster analysis and interactions network analysis were used to probe conformational changes in Aβ42. In most populated clusters of Aβ42-phenolic compounds complexes, the sheet structures were not observed or reduced. It seems that the binding of phenolic compounds can induce larger conformational diversity for amyloid peptide and changes conformational properties of amyloid peptide. The phenolic compounds can deform β-Hairpin structure of Aβ by destabilizing salt bridges E22-K28 and D23-K28 which can alter the conformation of Aβ42 in aqueous solution. These findings are in accordance with experimental results, to some extent give a molecular level interpretation for the inhibitory mechanism of phenolic compounds .In addition, this study may add important new details to the inhibitory mechanism of Alzheimer's drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Ghorbani
- Faculty of Biological Sciences, Biophysics Department, Tarbiat Modares University, Tehran, Iran
| | - Hossein Soleymani
- Faculty of Biological Sciences, Biophysics Department, Tarbiat Modares University, Tehran, Iran
| | - Abdollah Allahverdi
- Faculty of Biological Sciences, Biophysics Department, Tarbiat Modares University, Tehran, Iran
| | | | - Hossein Naderi-Manesh
- Faculty of Biological Sciences, Biophysics Department, Tarbiat Modares University, Tehran, Iran.,School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
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16
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An analog derived from phenylpropanoids ameliorates Alzheimer's disease–like pathology and protects mitochondrial function. Neurobiol Aging 2019; 80:187-195. [DOI: 10.1016/j.neurobiolaging.2019.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 04/23/2019] [Accepted: 05/01/2019] [Indexed: 01/14/2023]
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17
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Wang W, Dong X, Sun Y. Modification of Serum Albumin by High Conversion of Carboxyl to Amino Groups Creates a Potent Inhibitor of Amyloid β-Protein Fibrillogenesis. Bioconjug Chem 2019; 30:1477-1488. [PMID: 30964649 DOI: 10.1021/acs.bioconjchem.9b00209] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Fibrillogenesis of amyloid β-protein (Aβ) has been thought to be implicated in the progression of Alzheimer's disease (AD). Therefore, development of high-efficiency inhibitors is one of the strategies for the prevention and treatment of AD. Serum albumin has been found to capture Aβ monomers through its hydrophobic groove and suppress amyloid formation, but the inhibition efficiency is limited. Inspired by the strong inhibition potency of a basic protein, human lysozyme, we have herein proposed to develop a basified serum albumin by converting carboxyl groups into amino groups with ethylenediamine conjugated on the protein surface. The idea was verified with both bovine and human serum albumins (BSA/HSA). Four basified BSA (BSA-B) preparations with amino modification degrees (MDs) from 8.0 to 41.5 were first synthesized. Extensive biophysical and biological analyses revealed that the inhibition potency significantly increased with increasing amino MD. BSA-B of the highest MD (41.5), BSA-B4, which had an isoelectric point of 9.7, presented strong inhibition on Aβ42 fibrillation at a concentration as low as 0.5 μM, at which it functioned similarly with 25 μM native BSA to impede 25 μM Aβ fibrillation. Cell viability assays also confirmed that the detoxification of 5 μM BSA-B4 was superior over 25 μM native BSA by increasing cell viability from 60.6% to 96.0%. Fluorescence quenching study unveiled the decrease of the binding affinity between Aβ42 and the hydrophobic pocket region of BSA-B4, while quartz crystal microbalance experiments demonstrated that the binding constant of BSA-B4 to Aβ42 increased nearly 5 times. Therefore, the increase of electrostatic interactions between BSA-B4 and Aβ42 was the main reason for its high potency. Hence, aminated BSA achieved a conversion of binding way to Aβ from a mainly single-site hydrophobic binding to multiregional electrostatic interactions. Similar results were obtained with basified HSA preparations on inhibiting the amyloid formation and cytotoxicity. This work has thus provided new insights into the development of more efficient protein-based inhibitors against Aβ fibrillogenesis.
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Affiliation(s)
- Wenjuan Wang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
| | - Xiaoyan Dong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
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18
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Liu Y, Jovcevski B, Pukala TL. C-Phycocyanin from Spirulina Inhibits α-Synuclein and Amyloid-β Fibril Formation but Not Amorphous Aggregation. JOURNAL OF NATURAL PRODUCTS 2019; 82:66-73. [PMID: 30620188 DOI: 10.1021/acs.jnatprod.8b00610] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Proteinopathies including cataracts and neurodegenerative diseases, such as Alzheimer's and Parkinson's disease, are characterized by a series of aberrant protein folding events, resulting in amorphous aggregate or amyloid fibril formation. In the latter case, research has heavily focused on the development of small-molecule inhibitors with limited success during clinical trials. However, very few studies have focused on utilizing exogenous proteins as potential aggregation inhibitors. C-Phycocyanin, derived from Spirulina sp., has been known to exert anti-inflammatory properties; however, the ability of C-phycocyanin to inhibit protein aggregation has yet to be investigated. We have demonstrated that C-phycocyanin is an effective inhibitor of A53Tα-synuclein at extremely low substoichiometric ratios (200-fold excess of α-synuclein) and Aβ40/42 fibril formation. However, C-phycocyanin is relatively ineffective in inhibiting the reduction-induced amorphous aggregation of ADH and heat-induced aggregation of catalase. In addition, 2D NMR, ion mobility-mass spectrometry, and analytical-SEC demonstrate that the interaction between C-phycocyanin and α-synuclein is through nonstable interactions, indicating that transient interactions are likely to be responsible for preventing fibril formation. Overall, this work highlights how biomolecules from natural sources could be used to aid in the development of therapeutics to combat protein misfolding diseases.
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Affiliation(s)
- Yanqin Liu
- The School of Technology , Hebei Agricultural University , Cangzhou , Hebei 061100 , People's Republic of China
- The School of Physical Sciences , The University of Adelaide , Adelaide , South Australia 5005 , Australia
| | - Blagojce Jovcevski
- The School of Physical Sciences , The University of Adelaide , Adelaide , South Australia 5005 , Australia
| | - Tara L Pukala
- The School of Physical Sciences , The University of Adelaide , Adelaide , South Australia 5005 , Australia
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19
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Grigolato F, Arosio P. Sensitivity analysis of the variability of amyloid aggregation profiles. Phys Chem Chem Phys 2019; 21:1435-1442. [DOI: 10.1039/c8cp05904g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The variability of amyloid aggregation profiles is linearly proportional to the duration of the aggregation process, and arises from a perturbation of one or more of the initial conditions.
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Affiliation(s)
- Fulvio Grigolato
- Department of Chemistry and Applied Biosciences
- Swiss Federal Institute of Technology Zurich
- Zurich
- Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences
- Swiss Federal Institute of Technology Zurich
- Zurich
- Switzerland
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20
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Saini RK, Shuaib S, Goyal D, Goyal B. Insights into the inhibitory mechanism of a resveratrol and clioquinol hybrid against Aβ42 aggregation and protofibril destabilization: A molecular dynamics simulation study. J Biomol Struct Dyn 2018; 37:3183-3197. [DOI: 10.1080/07391102.2018.1511475] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, India
| | - Suniba Shuaib
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, India
| | - Bhupesh Goyal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, India
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21
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Li X, Xie B, Sun Y. Basified Human Lysozyme: A Potent Inhibitor against Amyloid β-Protein Fibrillogenesis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15569-15577. [PMID: 30407837 DOI: 10.1021/acs.langmuir.8b03278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The aggregation of amyloid β-proteins (Aβ) has been recognized as a key process in the pathogenesis of Alzheimer's disease (AD), so inhibiting Aβ aggregation is an important strategy to prevent the onset and treatment of AD. Our recent work indicated that decreasing the positive charges (or introducing negative charges) on human lysozyme (hLys) was unfavorable in keeping the inhibiting capability of hLys on Aβ aggregation. Therefore, we have herein proposed to basify hLys by conversion of the carboxyl groups into amino groups by modification with ethylene diamine. Basified hLys (Lys-B) preparations of three modification degrees (MDs), denoted as hLys-B1 (MD, 1.5), hLys-B2 (MD, 3.3), and hLys-B3 (MD, 4.4), were synthesized for modulating Aβ fibrillogenesis. The hLys-B preparations kept the stability and biocompatibility as native hLys did, whereas the inhibitory potency of hLys-B on Aβ fibrillogenesis increased with increasing MD. Cytotoxicity analysis showed that cell viability with 2.5 μM hLys-B3 increased from 62.5% (with 25 μM Aβ only) to 76.1%, similar to the case with 12.5 μM hLys (75.5%); cell viability with 6.25 μM hLys-B3 increased to 82.0%, similar to the case with 25 μM hLys (80.9%). The results indicate about four- to fivefold increase in the inhibition efficiency of hLys by the amino modification. Mechanistic analysis suggests that such a superior inhibitory capability of hLys-B was attributed to its more widely distributed positive charges, which promoted broad electrostatic interactions between Aβ and hLys-B. Thus, hLys-B suppressed the conformational transition of Aβ to β-sheet structures at low concentrations (e.g., 2.5 μM hLys-B3), leading to changes in the aggregation pathway and the formation of Aβ species with less cytotoxicity. The findings provided new insights into the development of more potent protein-based inhibitors against Aβ fibrillogenesis.
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Affiliation(s)
- Xi Li
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300354 , China
| | - Baolong Xie
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300354 , China
- Institute of Tianjin Seawater Desalination and Multipurpose Utilization, State Oceanic Administration (SOA) , Tianjin 300192 , China
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300354 , China
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22
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Das P, Matysiak S, Mittal J. Looking at the Disordered Proteins through the Computational Microscope. ACS CENTRAL SCIENCE 2018; 4:534-542. [PMID: 29805999 PMCID: PMC5968442 DOI: 10.1021/acscentsci.7b00626] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Indexed: 05/04/2023]
Abstract
Intrinsically disordered proteins (IDPs) have attracted wide interest over the past decade due to their surprising prevalence in the proteome and versatile roles in cell physiology and pathology. A large selection of IDPs has been identified as potential targets for therapeutic intervention. Characterizing the structure-function relationship of disordered proteins is therefore an essential but daunting task, as these proteins can adapt transient structure, necessitating a new paradigm for connecting structural disorder to function. Molecular simulation has emerged as a natural complement to experiments for atomic-level characterizations and mechanistic investigations of this intriguing class of proteins. The diverse range of length and time scales involved in IDP function requires performing simulations at multiple levels of resolution. In this Outlook, we focus on summarizing available simulation methods, along with a few interesting example applications. We also provide an outlook on how these simulation methods can be further improved in order to provide a more accurate description of IDP structure, binding, and assembly.
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Affiliation(s)
- Payel Das
- IBM Thomas J.
Watson Research Center, Yorktown Heights, New York 10598, United States
- E-mail:
| | - Silvina Matysiak
- Fischell
Department of Bioengineering, University
of Maryland, College Park, Maryland 20742, United States
| | - Jeetain Mittal
- Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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23
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Li X, Xie B, Dong X, Sun Y. Bifunctionality of Iminodiacetic Acid-Modified Lysozyme on Inhibiting Zn 2+-Mediated Amyloid β-Protein Aggregation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5106-5115. [PMID: 29631401 DOI: 10.1021/acs.langmuir.8b00254] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aggregation of amyloid β-proteins (Aβ) mediated by metal ions such as Zn2+ has been suggested to be implicated in the progression of Alzheimer's disease (AD). Hence, development of bifunctional agents capable of inhibiting Aβ aggregation and modulating metal-Aβ species is an effective strategy for the treatment of AD. In this work, we modified iminodiacetic acid (IDA) onto human lysozyme (hLys) surface to create an inhibitor of Zn2+-mediated Aβ aggregation and cytotoxicity. The IDA-modified hLys (IDA-hLys) retained the stability and biocompatibility of native hLys. Extensive biophysical and biological analyses indicated that IDA-hLys significantly attenuated Zn2+-mediated Aβ aggregation and cytotoxicity due to its strong binding affinity for Zn2+, whereas native hLys showed little effect. Stopped-flow fluorescence spectroscopy showed that IDA-hLys could protect Aβ from Zn2+-induced aggregation and rapidly depolymerize Zn2+-Aβ aggregates. The research indicates that IDA-hLys is a bifunctional agent capable of inhibiting Aβ fibrillization and modulating Zn2+-mediated Aβ aggregation and cytotoxicity as a strong Zn2+ chelator.
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Affiliation(s)
- Xi Li
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300354 , China
| | - Baolong Xie
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300354 , China
- Institute of Tianjin Seawater Desalination and Multipurpose Utilization , State Oceanic Administration (SOA) , Tianjin 300192 , China
| | - Xiaoyan Dong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300354 , China
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300354 , China
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24
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Abstract
β- N-Methylamino-l-alanine (BMAA) is a neurotoxic agent implicated in ALS as well as Parkinson's and Alzheimer's diseases. It is produced by blue-green algae and could find its way via fish and seafood into the human food supply. Isolation from biological samples yields the compound in monomeric and protein-bound form. It has been suggested that the protein-bound fraction may result from genetic misincorporation into proteins in place of serine. Concomitant misfolding of the mutated proteins may be responsible for the neurological diseases. Recent reports that contradict the misincorporation theory leave unresolved the nature of the protein-bound form of BMAA. We have found from quantum mechanical calculations on model systems that it is possible to bind BMAA with high affinity in a noncovalent fashion to proteins. Because of our interest in Alzheimer's disease, molecular dynamics simulations were applied to search for such binding between BMAA and the β-amyloid peptide and to discover whether replacement of either of its two serine residues could affect its aggregation into neurotoxic oligomers. No stable noncovalently bound complex was found, and it was concluded that incorporation of BMAA in place of serine would not alter the conformational dynamics of the β-amyloid peptide.
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Affiliation(s)
- Arvi Rauk
- Department of Chemistry , University of Calgary , 2500 University Dr. NW , Calgary , Alberta , Canada T2N 1N4
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25
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Patel CN, Georrge JJ, Modi KM, Narechania MB, Patel DP, Gonzalez FJ, Pandya HA. Pharmacophore-based virtual screening of catechol-o-methyltransferase (COMT) inhibitors to combat Alzheimer's disease. J Biomol Struct Dyn 2017; 36:3938-3957. [PMID: 29281938 DOI: 10.1080/07391102.2017.1404931] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Alzheimer's disease (AD) is one of the most significant neurodegenerative disorders and its symptoms mostly appear in aged people. Catechol-o-methyltransferase (COMT) is one of the known target enzymes responsible for AD. With the use of 23 known inhibitors of COMT, a query has been generated and validated by screening against the database of 1500 decoys to obtain the GH score and enrichment value. The crucial features of the known inhibitors were evaluated by the online ZINC Pharmer to identify new leads from a ZINC database. Five hundred hits were retrieved from ZINC Pharmer and by ADMET (absorption, distribution, metabolism, excretion, and toxicity) filtering by using FAF-Drug-3 and 36 molecules were considered for molecular docking. From the COMT inhibitors, opicapone, fenoldopam, and quercetin were selected, while ZINC63625100_413 ZINC39411941_412, ZINC63234426_254, ZINC63637968_451, and ZINC64019452_303 were chosen for the molecular dynamics simulation analysis having high binding affinity and structural recognition. This study identified the potential COMT inhibitors through pharmacophore-based inhibitor screening leading to a more complete understanding of molecular-level interactions.
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Affiliation(s)
- Chirag N Patel
- a Department of Botany, Bioinformatics and Climate Change Impacts Management , University School of Sciences, Gujarat University , Ahmedabad 380 009 , Gujarat , India
| | - John J Georrge
- b Department of Bioinformatics , Christ College , Rajkot 360 005 , Gujarat , India
| | - Krunal M Modi
- c J. Heyrovský Institute of Physical Chemistry , Academy of Sciences of the Czech Republic , Dolejškova 2155/3, 182 23, Prague 8 , Czech Republic
| | - Moksha B Narechania
- d Human Genetics Division, Department of Zoology, BMTC and HG , University School of Sciences (USSC), Gujarat University , Ahmedabad 380009 , Gujarat , India
| | - Daxesh P Patel
- e Laboratory of Metabolism, Center for Cancer Research , National Cancer Institute, National Institutes of Health , Rockville , MD , USA
| | - Frank J Gonzalez
- e Laboratory of Metabolism, Center for Cancer Research , National Cancer Institute, National Institutes of Health , Rockville , MD , USA
| | - Himanshu A Pandya
- a Department of Botany, Bioinformatics and Climate Change Impacts Management , University School of Sciences, Gujarat University , Ahmedabad 380 009 , Gujarat , India
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26
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Weber OC, Uversky VN. How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β 42 in water. INTRINSICALLY DISORDERED PROTEINS 2017; 5:e1377813. [PMID: 30250773 DOI: 10.1080/21690707.2017.1377813] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/04/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022]
Abstract
Amyloid-β42 (Aβ42) is an intrinsically disordered peptide intimately related to the pathogenesis of several neurodegenerative diseases. Molecular dynamics (MD) simulations are extensively utilized in the characterization of the structures and conformational dynamics of intrinsically disordered proteins (IDPs) including Aβ42, with AMBER and CHARMM parameters being commonly used in these studies. Recently, comparison of the effects of force field parameters on the Aβ42 structures has started to gain significant attention. In this study, the structures of Aβ42 are simulated using AMBER FF99SB and CHARMM22/CMAP parameters via replica exchange MD simulations utilizing a widely used clustering algorithm. These analyses show that the structural properties (extent and positioning of the elements of secondary and tertiary structure), radius of gyration values, number and position of salt bridges are extremely dependent on the chosen force field parameters notably with the usage of clustering algorithms. For example, predicted secondary structure elements, which are of the great importance for better understanding of the molecular mechanisms of neurodegenerative diseases, deviate enormously in models generated using currently available force field parameters for proteins. Based on the derived models, chemical shift values are calculated and compared to the experimentally determined data. This comparison revealed that although both force field parameters yield results in agreement with experiments, the obtained structural properties were rather different using a clustering algorithm. In other words, these results show that the predicted structures depend heavily on the force field parameters. Importantly, since none of the force field parameters currently utilized in MD studies were developed specifically taking into account the disordered nature of IDPs, these findings clearly indicate that new force field parameters have to be developed for IDPs considering their rapid flexibility and dynamics with high amplitude. Furthermore, molecular simulations of IDPs are typically conducted using one water volume. We show that the confined aqueous volume impacts the predicted structural properties of Aβ42 in water. Although up to date, confined aqueous volume effects have been ignored in the MD simulations of IDPs in water, our data indicate that these effects have to be taken into account in predicting the structural and thermodynamic properties of disordered proteins in solution.
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Affiliation(s)
- Orkid Coskuner Weber
- Department of Chemistry and Neurosciences Institute, The University of Texas at San Antonio, San Antonio, TX, USA.,Institut für Physikalische Chemie, Universität zu Köln, Köln, Germany.,Molecular Biotechnology Division, Turkisch-Deutsche Universität, Istanbul Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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27
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Chakraborty S, Das P. Emergence of Alternative Structures in Amyloid Beta 1-42 Monomeric Landscape by N-terminal Hexapeptide Amyloid Inhibitors. Sci Rep 2017; 7:9941. [PMID: 28855598 PMCID: PMC5577341 DOI: 10.1038/s41598-017-10212-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/04/2017] [Indexed: 02/01/2023] Open
Abstract
Alzheimer’s disease (AD) is characterized by deposition of amyloid beta (Aβ) peptides into senile plaques in the brain. While most familial mutations are associated with early-onset AD, recent studies report the AD-protective nature of two genetic human Aβ variants, i.e. A2T and A2V, in the heterozygous state. The mixture of A2V Aβ1-6 (Aβ6) hexapeptide and WT Aβ1–42 (Αβ42) is also found neuroprotective. Motivated by these findings, in this study we investigate the effects of WT, A2V, and A2T Aβ6 hexapeptide binding on the monomeric WT Aβ42 landscape. For this purpose, we have performed extensive atomistic Replica Exchange Molecular Dynamics simulations, elucidating preferential binding of Aβ42 with the A2V and A2T hexapeptides compared to WT Aβ6. A notable reorganization of the Aβ42 landscape is revealed due to hexapeptide association, as manifested by lowering of transient interactions between the central and C-terminal hydrophobic patches. Concurrently, Aβ6-bound Aβ42 monomer exhibits alternative structural features that are strongly dependent on the hexapeptide sequence. For example, a central helix is more frequently populated within the A2T-bound monomer, while A2V-bound Aβ42 is often enhanced in overall disorder. Taken together, the present simulations offer novel molecular insights onto the effect of the N-terminal hexapeptide binding on the Aβ42 monomer structure, which might help in explaining their reported amyloid inhibition properties.
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Affiliation(s)
| | - Payel Das
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA.
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28
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Saini RK, Shuaib S, Goyal B. Molecular insights into Aβ42protofibril destabilization with a fluorinated compound D744: A molecular dynamics simulation study. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2656] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
| | - Suniba Shuaib
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
| | - Bhupesh Goyal
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
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29
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Sandin L, Bergkvist L, Nath S, Kielkopf C, Janefjord C, Helmfors L, Zetterberg H, Blennow K, Li H, Nilsberth C, Garner B, Brorsson AC, Kågedal K. Beneficial effects of increased lysozyme levels in Alzheimer's disease modelled in Drosophila melanogaster. FEBS J 2017; 283:3508-3522. [PMID: 27562772 PMCID: PMC5132093 DOI: 10.1111/febs.13830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 06/18/2016] [Accepted: 08/03/2016] [Indexed: 01/23/2023]
Abstract
Genetic polymorphisms of immune genes that associate with higher risk to develop Alzheimer's disease (AD) have led to an increased research interest on the involvement of the immune system in AD pathogenesis. A link between amyloid pathology and immune gene expression was suggested in a genome‐wide gene expression study of transgenic amyloid mouse models. In this study, the gene expression of lysozyme, a major player in the innate immune system, was found to be increased in a comparable pattern as the amyloid pathology developed in transgenic mouse models of AD. A similar pattern was seen at protein levels of lysozyme in human AD brain and CSF, but this lysozyme pattern was not seen in a tau transgenic mouse model. Lysozyme was demonstrated to be beneficial for different Drosophila melanogaster models of AD. In flies that expressed Aβ1‐42 or AβPP together with BACE1 in the eyes, the rough eye phenotype indicative of toxicity was completely rescued by coexpression of lysozyme. In Drosophila flies bearing the Aβ1‐42 variant with the Arctic gene mutation, lysozyme increased the fly survival and decreased locomotor dysfunction dose dependently. An interaction between lysozyme and Aβ1‐42 in the Drosophila eye was discovered. We propose that the increased levels of lysozyme, seen in mouse models of AD and in human AD cases, were triggered by Aβ1‐42 and caused a beneficial effect by binding of lysozyme to toxic species of Aβ1‐42, which prevented these from exerting their toxic effects. These results emphasize the possibility of lysozyme as biomarker and therapeutic target for AD.
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Affiliation(s)
- Linnea Sandin
- Division of Cell Biology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, Sweden
| | - Liza Bergkvist
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, Sweden
| | - Sangeeta Nath
- Division of Cell Biology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, Sweden
| | - Claudia Kielkopf
- Division of Cell Biology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, Sweden
| | - Camilla Janefjord
- Division of Cell Biology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, Sweden
| | - Linda Helmfors
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, Sweden
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, Sahlgrenska University Hospital, Mölndal, Sweden.,UCL Institute of Neurology, London, UK
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Hongyun Li
- Illawarra Health and Medical Research Institute, University of Wollongong, Australia
| | - Camilla Nilsberth
- Department of Acute Internal Medicine and Geriatrics and Department of Clinical and Experimental Medicine, Linköping University, Sweden
| | - Brett Garner
- Illawarra Health and Medical Research Institute, University of Wollongong, Australia.,School of Biological Sciences, University of Wollongong, Australia
| | - Ann-Christin Brorsson
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, Sweden.
| | - Katarina Kågedal
- Division of Cell Biology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, Sweden.
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30
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Das P, Chacko AR, Belfort G. Alzheimer's Protective Cross-Interaction between Wild-Type and A2T Variants Alters Aβ 42 Dimer Structure. ACS Chem Neurosci 2017; 8:606-618. [PMID: 28292185 DOI: 10.1021/acschemneuro.6b00357] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Whole genome sequencing has recently revealed the protective effect of a single A2T mutation in heterozygous carriers against Alzheimer's disease (AD) and age-related cognitive decline. The impact of the protective cross-interaction between the wild-type (WT) and A2T variants on the dimer structure is therefore of high interest, as the Aβ dimers are the smallest known neurotoxic species. Toward this goal, extensive atomistic replica exchange molecular dynamics simulations of the solvated WT homo- and A2T hetero- Aβ1-42 dimers have been performed, resulting into a total of 51 μs of sampling for each system. Weakening of a set of transient, intrachain contacts formed between the central and C-terminal hydrophobic residues is observed in the heterodimeric system. The majority of the heterodimers with reduced interaction between central and C-terminal regions lack any significant secondary structure and display a weak interchain interface. Interestingly, the A2T N-terminus, particularly residue F4, is frequently engaged in tertiary and quaternary interactions with central and C-terminal hydrophobic residues in those distinct structures, leading to hydrophobic burial. This atypical involvement of the N-terminus within A2T heterodimer revealed in our simulations implies possible interference on Aβ42 aggregation and toxic oligomer formation, which is consistent with experiments. In conclusion, the present study provides detailed structural insights onto A2T Aβ42 heterodimer, which might provide molecular insights onto the AD protective effect of the A2T mutation in the heterozygous state.
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Affiliation(s)
- Payel Das
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Anita R. Chacko
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Georges Belfort
- Howard
P. Isermann Department of Chemical and Biological Engineering, and
Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180-3590, United States
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31
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Han SH, Park JC, Mook-Jung I. Amyloid β-interacting partners in Alzheimer's disease: From accomplices to possible therapeutic targets. Prog Neurobiol 2016; 137:17-38. [DOI: 10.1016/j.pneurobio.2015.12.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 12/02/2015] [Accepted: 12/09/2015] [Indexed: 12/20/2022]
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32
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Somavarapu AK, Kepp KP. Direct Correlation of Cell Toxicity to Conformational Ensembles of Genetic Aβ Variants. ACS Chem Neurosci 2015; 6:1990-6. [PMID: 26447342 DOI: 10.1021/acschemneuro.5b00238] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We report a systematic analysis of conformational ensembles generated from multiseed molecular dynamics simulations of all 15 known genetic variants of Aβ42. We show that experimentally determined variant toxicities are largely explained by random coil content of the amyloid ensembles (correlation with smaller EC50 values; R(2) = 0.54, p = 0.01), and to some extent the helix character (more helix-character is less toxic, R(2) = 0.32, p = 0.07) and hydrophobic surface (R(2) = 0.37, p = 0.04). Our findings suggest that qualitative structural features of the amyloids, rather than the quantitative levels, are fundamentally related to neurodegeneration. The data provide molecular explanations for the high toxicity of E22 variants and for the protective features of the recently characterized A2T variant. The identified conformational features, for example, the local helix-coil-strand transitions of the C-terminals of the peptides, are of likely interest in the direct targeting of amyloids by rational drug design.
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Affiliation(s)
- Arun Kumar Somavarapu
- DTU Chemistry, Technical University of Denmark, Kemiorvet 206, DK-2800 Kongens Lyngby, Denmark
| | - Kasper P. Kepp
- DTU Chemistry, Technical University of Denmark, Kemiorvet 206, DK-2800 Kongens Lyngby, Denmark
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33
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Das P, Murray B, Belfort G. Alzheimer's protective A2T mutation changes the conformational landscape of the Aβ₁₋₄₂ monomer differently than does the A2V mutation. Biophys J 2015; 108:738-47. [PMID: 25650940 DOI: 10.1016/j.bpj.2014.12.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/01/2014] [Accepted: 12/04/2014] [Indexed: 12/20/2022] Open
Abstract
The aggregation of amyloid-β (Aβ) peptides plays a crucial role in the etiology of Alzheimer's disease (AD). Recently, it has been reported that an A2T mutation in Aβ can protect against AD. Interestingly, a nonpolar A2V mutation also has been found to offer protection against AD in the heterozygous state, although it causes early-onset AD in homozygous carriers. Since the conformational landscape of the Aβ monomer is known to directly contribute to the early-stage aggregation mechanism, it is important to characterize the effects of the A2T and A2V mutations on Aβ₁₋₄₂ monomer structure. Here, we have performed extensive atomistic replica-exchange molecular dynamics simulations of the solvated wild-type (WT), A2V, and A2T Aβ₁₋₄₂ monomers. Our simulations reveal that although all three variants remain as collapsed coils in solution, there exist significant structural differences among them at shorter timescales. A2V exhibits an enhanced double-hairpin population in comparison to the WT, similar to those reported in toxic WT Aβ₁₋₄₂ oligomers. Such double-hairpin formation is caused by hydrophobic clustering between the N-terminus and the central and C-terminal hydrophobic patches. In contrast, the A2T mutation causes the N-terminus to engage in unusual electrostatic interactions with distant residues, such as K16 and E22, resulting in a unique population comprising only the C-terminal hairpin. These findings imply that a single A2X (where X = V or T) mutation in the primarily disordered N-terminus of the Aβ₁₋₄₂ monomer can dramatically alter the β-hairpin population and switch the equilibrium toward alternative structures. The atomistically detailed, comparative view of the structural landscapes of A2V and A2T variant monomers obtained in this study can enhance our understanding of the mechanistic differences in their early-stage aggregation.
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Affiliation(s)
- Payel Das
- Soft Matter Theory and Simulations Group, Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York.
| | - Brian Murray
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
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34
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Anbarasu K, Sivakumar J. Multidimensional significance of crystallin protein-protein interactions and their implications in various human diseases. Biochim Biophys Acta Gen Subj 2015; 1860:222-33. [PMID: 26365509 DOI: 10.1016/j.bbagen.2015.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 08/28/2015] [Accepted: 09/08/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND Crystallins are the important structural and functional proteins in the eye lens responsible for refractive index. Post-translational modifications (PTMs) and mutations are major causative factors that affect crystallin structural conformation and functional characteristics thus playing a vital role in the etiology of cataractogenesis. SCOPE OF REVIEW The significance of crystallin protein-protein interactions (PPIs) in the lens and non-lenticular tissues is summarized. MAJOR CONCLUSIONS Aberrancy of PPIs between crystallin, its associated protein and metal ions has been accomplished in various human diseases including cataract. A detailed account on multidimensional structural and functional significance of crystallin PPI in humans must be brought into limelight, in order to understand the biochemical and molecular basis augmenting the aberrancies of such interaction. In this scenario, the present review is focused to shed light on studies which will aid to expand our present understanding on disease pathogenesis related to loss of PPI thereby paving the way for putative future therapeutic targets to curb such diseases. GENERAL SIGNIFICANCE The interactions with α-crystallins always aid to protect their structural and functional characteristics. The up-regulation of αB-crystallin in the non-lenticular tissues always decodes as biomarker for various stress related disorders. For better understanding and treatment of various diseases, PPI studies provide overall outline about the structural and functional characteristics of the proteins. This information not only helps to find out the route of cataractogenesis but also aid to identify potential molecules to inhibit/prevent the further development of such complicated phenomenon. This article is part of a Special Issue entitled Crystallin Biochemistry in Health and Disease.
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Affiliation(s)
- Kumarasamy Anbarasu
- Department of Marine Biotechnology, Bharathidasan University, Tiruchirapalli 620024, Tamil Nadu, India.
| | - Jeyarajan Sivakumar
- Department of Marine Biotechnology, Bharathidasan University, Tiruchirapalli 620024, Tamil Nadu, India
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35
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Helmfors L, Boman A, Civitelli L, Nath S, Sandin L, Janefjord C, McCann H, Zetterberg H, Blennow K, Halliday G, Brorsson AC, Kågedal K. Protective properties of lysozyme on β-amyloid pathology: implications for Alzheimer disease. Neurobiol Dis 2015; 83:122-33. [PMID: 26334479 DOI: 10.1016/j.nbd.2015.08.024] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 08/03/2015] [Accepted: 08/21/2015] [Indexed: 01/24/2023] Open
Abstract
The hallmarks of Alzheimer disease are amyloid-β plaques and neurofibrillary tangles accompanied by signs of neuroinflammation. Lysozyme is a major player in the innate immune system and has recently been shown to prevent the aggregation of amyloid-β1-40 in vitro. In this study we found that patients with Alzheimer disease have increased lysozyme levels in the cerebrospinal fluid and lysozyme co-localized with amyloid-β in plaques. In Drosophila neuronal co-expression of lysozyme and amyloid-β1-42 reduced the formation of soluble and insoluble amyloid-β species, prolonged survival and improved the activity of amyloid-β1-42 transgenic flies. This suggests that lysozyme levels rise in Alzheimer disease as a compensatory response to amyloid-β increases and aggregation. In support of this, in vitro aggregation assays revealed that lysozyme associates with amyloid-β1-42 and alters its aggregation pathway to counteract the formation of toxic amyloid-β species. Overall, these studies establish a protective role for lysozyme against amyloid-β associated toxicities and identify increased lysozyme in patients with Alzheimer disease. Therefore, lysozyme has potential as a new biomarker as well as a therapeutic target for Alzheimer disease.
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Affiliation(s)
- Linda Helmfors
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Andrea Boman
- Experimental Pathology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Livia Civitelli
- Experimental Pathology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Sangeeta Nath
- Experimental Pathology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Linnea Sandin
- Experimental Pathology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Camilla Janefjord
- Experimental Pathology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Heather McCann
- Neuroscience Research Australia and University of New South Wales, Randwick New South Wales 2031, Australia
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, Sahlgrenska University Hospital, 431 30 Mölndal, Sweden; UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, Sahlgrenska University Hospital, 431 30 Mölndal, Sweden
| | - Glenda Halliday
- Neuroscience Research Australia and University of New South Wales, Randwick New South Wales 2031, Australia
| | - Ann-Christin Brorsson
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden.
| | - Katarina Kågedal
- Experimental Pathology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, 581 85 Linköping, Sweden.
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36
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Somavarapu AK, Kepp KP. The Dependence of Amyloid-β Dynamics on Protein Force Fields and Water Models. Chemphyschem 2015; 16:3278-89. [PMID: 26256268 DOI: 10.1002/cphc.201500415] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Indexed: 01/10/2023]
Abstract
We studied the dynamics of Aβ40 , involved in Alzheimer's disease, by using 21 methods combined from Amber03, Amber99sb-ILDN, Charmm27, Charmm22*, OPLS-2001, OPLS-2006, OPLS-2008, Gromos96-43a1, Gromos96-53a6, Gromos96-54a7, and the water models SPC, TIP3P, TIP4P. Major differences in the structural ensembles were systematized: Amber03, Charmm27, and Gromos96-54a7 stabilize the helices; Gromos96-43a1 and Gromos53a6 favor the β-strands (with Charmm22* and Amber99sb-ILDN in between), and OPLS produces unstructured ensembles. The accuracy of the NMR chemical shifts was in the order: Charmm22*>Amber99sb-ILDN>OPLS-2008≈Gromos96-43a1>Gromos96-54a7≈OPLS-2001>OPLS-2006>Gromos96-53a6>Charmm27>Amber03. The computed (3) JHNHα -coupling constants were sensitive to experiment type and Karplus parameterization. Overall, the ensembles of Charmm22* and Amber99sb-ILDN provided the best agreement with experimental NMR and circular dichroism data, providing a model for the real Aβ monomer ensemble. Also, the polar water model TIP3P significantly favored helix and compact conformations.
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Affiliation(s)
| | - Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, DK-2800, Kongens Lyngby, Denmark.
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37
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Biswas A, Karmakar S, Chowdhury A, Das KP. Interaction of α-crystallin with some small molecules and its effect on its structure and function. Biochim Biophys Acta Gen Subj 2015; 1860:211-21. [PMID: 26073614 DOI: 10.1016/j.bbagen.2015.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/23/2015] [Accepted: 06/09/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND α-Crystallin acts like a molecular chaperone by interacting with its substrate proteins and thus prevents their aggregation. It also interacts with various kinds of small molecules that affect its structure and function. SCOPE OF REVIEW In this article we will present a review of work done with respect to the interaction of ATP, peptide generated from lens crystallin and other proteins and some bivalent metal ions with α-crystallin and discuss the role of these interactions on its structure and function and cataract formation. We will also discuss the interaction of some hydrophobic fluorescence probes and surface active agents with α-crystallin. MAJOR CONCLUSIONS Small molecule interaction controls the structure and function of α-crystallin. ATP and Zn+2 stabilize its structure and enhance chaperone function. Therefore the depletion of these small molecules can be detrimental to maintenance of lens transparency. However, the accumulation of small peptides due to protease activity in the lens can also be harmful as the interaction of these peptides with α-crystallin and other crystallin proteins in the lens promotes aggregation and loss of lens transparency. The use of hydrophobic probe has led to a wealth of information regarding the location of substrate binding site and nature of chaperone-substrate interaction. Interaction of surface active agents with α-crystallin has helped us to understand the structural stability and oligomeric dissociation in α-crystallin. GENERAL SIGNIFICANCE These interactions are very helpful in understanding the mechanistic details of the structural changes and chaperone function of α-crystallin. This article is part of a Special Issue entitled Crystallin Biochemistry in Health and Disease.
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Affiliation(s)
- A Biswas
- Protein Chemistry Laboratory, Department of Chemistry, Bose Institute, 93/1 A.P.C. Road, Kolkata 700 009, India.
| | - S Karmakar
- Protein Chemistry Laboratory, Department of Chemistry, Bose Institute, 93/1 A.P.C. Road, Kolkata 700 009, India.
| | - A Chowdhury
- Protein Chemistry Laboratory, Department of Chemistry, Bose Institute, 93/1 A.P.C. Road, Kolkata 700 009, India.
| | - K P Das
- Protein Chemistry Laboratory, Department of Chemistry, Bose Institute, 93/1 A.P.C. Road, Kolkata 700 009, India.
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