1
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Wu M, Cheng Y, Zhang R, Han W, Jiang H, Bi C, Zhang Z, Ye M, Lin X, Liu Z. Molecular mechanism and therapeutic strategy of bile acids in Alzheimer's disease from the emerging perspective of the microbiota-gut-brain axis. Biomed Pharmacother 2024; 178:117228. [PMID: 39088965 DOI: 10.1016/j.biopha.2024.117228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/19/2024] [Accepted: 07/28/2024] [Indexed: 08/03/2024] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the accumulation of amyloid-β outside neurons and Tau protein inside neurons. Various pathological mechanisms are implicated in AD, including brain insulin resistance, neuroinflammation, and endocrinal dysregulation of adrenal corticosteroids. These factors collectively contribute to neuronal damage and destruction. Recently, bile acids (BAs), which are metabolites of cholesterol, have shown neuroprotective potential against AD by targeting the above pathological changes. BAs can enter the systematic circulation and cross the blood-brain barrier, subsequently exerting neuroprotective effects by targeting several endogenous receptors. Additionally, BAs interact with the microbiota-gut-brain (MGB) axis to improve immune and neuroendocrine function during AD episodes. Gut microbes impact BA signaling in the brain through their involvement in BA biotransformation. In this review, we summarize the role and molecular mechanisms of BAs in AD while considering the MGB axis and propose novel strategies for preventing the onset and progression of AD.
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Affiliation(s)
- Menglu Wu
- Clinical Laboratory, Shaoxing Seventh People's Hospital (Affiliated Mental Health Center, Medical College of Shaoxing University), Shaoxing, Zhejiang, China; Department of Behavioral Neurosciences, Science Research Center of Medical School, Shaoxing University, Shaoxing, Zhejiang, China
| | - Yongyi Cheng
- Department of Behavioral Neurosciences, Science Research Center of Medical School, Shaoxing University, Shaoxing, Zhejiang, China
| | - Ruolin Zhang
- Department of Behavioral Neurosciences, Science Research Center of Medical School, Shaoxing University, Shaoxing, Zhejiang, China
| | - Wenwen Han
- Department of Behavioral Neurosciences, Science Research Center of Medical School, Shaoxing University, Shaoxing, Zhejiang, China
| | - Hanqi Jiang
- Department of Behavioral Neurosciences, Science Research Center of Medical School, Shaoxing University, Shaoxing, Zhejiang, China
| | - Chenchen Bi
- Department of Behavioral Neurosciences, Science Research Center of Medical School, Shaoxing University, Shaoxing, Zhejiang, China
| | - Ziyi Zhang
- Department of Behavioral Neurosciences, Science Research Center of Medical School, Shaoxing University, Shaoxing, Zhejiang, China
| | - Mengfei Ye
- Department of Psychiatry, Shaoxing Seventh People's Hospital (Affiliated Mental Health Center, Medical College of Shaoxing University), Shaoxing, Zhejiang, China
| | - Xiuqin Lin
- Clinical Laboratory, Shaoxing Seventh People's Hospital (Affiliated Mental Health Center, Medical College of Shaoxing University), Shaoxing, Zhejiang, China.
| | - Zheng Liu
- Department of Behavioral Neurosciences, Science Research Center of Medical School, Shaoxing University, Shaoxing, Zhejiang, China; Department of Pharmacology, School of Medicine, Shaoxing University, Shaoxing, Zhejiang, China.
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2
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Johansson L, Sandberg A, Nyström S, Hammarström P, Hallbeck M. Amyloid beta 1-40 and 1-42 fibril ratios and maturation level cause conformational differences with minimal impact on autophagy and cytotoxicity. J Neurochem 2024. [PMID: 39133499 DOI: 10.1111/jnc.16201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/02/2024] [Accepted: 07/25/2024] [Indexed: 08/13/2024]
Abstract
The amyloid β (Aβ) peptide has a central role in Alzheimer's disease (AD) pathology. The peptide length can vary between 37 and 49 amino acids, with Aβ1-42 being considered the most disease-related length. However, Aβ1-40 is also found in Aβ plaques and has shown to form intertwined fibrils with Aβ1-42. The peptides have previously also shown to form different fibril conformations, proposed to be related to disease phenotype. To conduct more representative in vitro experiments, it is vital to uncover the impact of different fibril conformations on neurons. Hence, we fibrillized different Aβ1-40:42 ratios in concentrations of 100:0, 90:10, 75:25, 50:50, 25:75, 10:90 and 0:100 for either 24 h (early fibrils) or 7 days (aged fibrils). These were then characterized based on fibril width, LCO-staining and antibody-staining. We further challenged differentiated neuronal-like SH-SY5Y human cells with the different fibrils and measured Aβ content, cytotoxicity and autophagy function at three different time-points: 3, 24, and 72 h. Our results revealed that both Aβ1-40:42 ratio and fibril maturation affect conformation of fibrils. We further show the impact of these conformation changes on the affinity to commonly used Aβ antibodies, primarily affecting Aβ1-40 rich aggregates. In addition, we demonstrate uptake of the aggregates by neuronally differentiated human cells, where aggregates with higher Aβ1-42 ratios generally caused higher cellular levels of Aβ. These differences in Aβ abundance did not cause changes in cytotoxicity nor in autophagy activation. Our results show the importance to consider conformational differences of Aβ fibrils, as this can have fundamental impact on Aβ antibody detection. Overall, these insights underline the need for further exploration of the impact of conformationally different fibrils and the need to reliably produce disease relevant Aβ aggregates.
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Affiliation(s)
- Lovisa Johansson
- Department of Biomedical and Clinical Sciences and Department of Clinical Pathology, Linköping University, Linköping, Sweden
| | - Alexander Sandberg
- Department of Biomedical and Clinical Sciences and Department of Clinical Pathology, Linköping University, Linköping, Sweden
| | - Sofie Nyström
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Per Hammarström
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Martin Hallbeck
- Department of Biomedical and Clinical Sciences and Department of Clinical Pathology, Linköping University, Linköping, Sweden
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3
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Dey P, Biswas P. Effect of caffeine on the aggregation of amyloid-β-A 3D RISM study. J Chem Phys 2024; 160:125101. [PMID: 38516974 DOI: 10.1063/5.0202636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024] Open
Abstract
Alzheimer's disease is a detrimental neurological disorder caused by the formation of amyloid fibrils due to the aggregation of amyloid-β peptide. The primary therapeutic approaches for treating Alzheimer's disease are targeted to prevent this amyloid fibril formation using potential inhibitor molecules. The discovery of such inhibitor molecules poses a formidable challenge to the design of anti-amyloid drugs. This study investigates the effect of caffeine on dimer formation of the full-length amyloid-β using a combined approach of all-atom, explicit water molecular dynamics simulations and the three-dimensional reference interaction site model theory. The change in the hydration free energy of amyloid-β dimer, with and without the inhibitor molecules, is calculated with respect to the monomeric amyloid-β, where the hydration free energy is decomposed into energetic and entropic components, respectively. Dimerization is accompanied by a positive change in the partial molar volume. Dimer formation is spontaneous, which implies a decrease in the hydration free energy. However, a reverse trend is observed for the dimer with inhibitor molecules. It is observed that the negatively charged residues primarily contribute for the formation of the amyloid-β dimer. A residue-wise decomposition reveals that hydration/dehydration of the side-chain atoms of the charged amino acid residues primarily contribute to dimerization.
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Affiliation(s)
- Priya Dey
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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4
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Sanchis I, Spinelli R, Siano A. Acetylcholine hydrolytic activity of fibrillated β-amyloid (1-40) peptide. Amino Acids 2023; 55:1991-1997. [PMID: 37904049 DOI: 10.1007/s00726-023-03349-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/10/2023] [Indexed: 11/01/2023]
Abstract
Alzheimer's disease is characterized by the presence of senile plaques composed of β-amyloid peptide (Aβ) aggregates with toxic effects that are still not fully understood. Recently, it was discovered that Aβ(1-42) fibrils possess catalytic activity on acetylcholine hydrolysis. Catalytic amyloids are an emerging and exciting field of research. In this study, we examined the catalytic activity of the fibrils formed by Aβ(1-40), the most abundant Aβ variant, on acetylcholine hydrolysis. Our findings reveal that Aβ(1-40) fibrils exhibit moderate enzymatic activity, indicating that natural peptide aggregates could serve as biocatalysts and provide new insights into the potential role of Aβ in neurological disorders.
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Affiliation(s)
- Ivan Sanchis
- Laboratory of Bioactive Peptides, Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- Ministry of Science, Technology and Innovation, National Scientific and Technical Research Council (CONICET), Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
| | - Roque Spinelli
- Laboratory of Bioactive Peptides, Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- Ministry of Science, Technology and Innovation, National Scientific and Technical Research Council (CONICET), Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
| | - Alvaro Siano
- Laboratory of Bioactive Peptides, Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina.
- Ministry of Science, Technology and Innovation, National Scientific and Technical Research Council (CONICET), Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina.
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5
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Zheng G, Hu S, Qin D, Nong C, Yang L, Deng B. Aggregation-induced electrochemiluminescence enhancement of Ag-MOG for amyloid β 42 sensing. Anal Chim Acta 2023; 1281:341898. [PMID: 38783738 DOI: 10.1016/j.aca.2023.341898] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 05/25/2024]
Abstract
This study aimed to introduce an immunosensor for measuring amyloid β 42 (Aβ42) levels by aggregation-induced enhanced electrochemiluminescence (ECL). Metal-organic gels (MOGs) are novel soft materials with advantages such as high gel stability, good light-emitting properties, and easy preparation. This study used silver nanoparticle metal-organic gel (Ag-MOG) as a substrate to connect Aβ42-Ab2 and the cathodoluminescent probe. Potassium persulfate was used as a co-reactant that could emit a high ECL signal. CuS@Au had the benefits of a relatively large surface area with excellent carrier function; therefore, it was used as a substrate to load a large amount of Aβ42-Ab1, significantly improving the immunosensor sensitivity. The ECL intensity of Aβ42 was linear in the range of 0.01 pg/mL to 250 ng/mL with a detection limit of 2.2 fg/mL (S/N = 3) under optimized detection conditions. This ECL immunosensor has been successfully applied to detect Aβ42 in human serum with the advantages of excellent stability and high selectivity. This method not only expands the potential applications of ECL immunosensors based on biological testing and clinical diagnosis but also provides a viable approach to basic clinical testing.
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Affiliation(s)
- Guiyue Zheng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Shenglan Hu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Dongmiao Qin
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Chunlian Nong
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Lijuan Yang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Biyang Deng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China.
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6
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Wu KY, Doan D, Medrano M, Chang CEA. Modeling structural interconversion in Alzheimers' amyloid beta peptide with classical and intrinsically disordered protein force fields. J Biomol Struct Dyn 2022; 40:10005-10022. [PMID: 34152264 DOI: 10.1080/07391102.2021.1939163] [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: 12/16/2022]
Abstract
A comprehensive understanding of the aggregation mechanism in amyloid beta 42 (Aβ42) peptide is imperative for developing therapeutic drugs to prevent or treat Alzheimer's disease. Because of the high flexibility and lack of native tertiary structures of Aβ42, molecular dynamics (MD) simulations may help elucidate the peptide's dynamics with atomic details and collectively improve ensembles not seen in experiments. We applied microsecond-timescale MD simulations to investigate the dynamics and conformational changes of Aβ42 by using a newly developed Amber force field (ff14IDPSFF). We compared the ff14IDPSFF and the regular ff14SB force field by examining the conformational changes of two distinct Aβ42 monomers in explicit solvent. Conformational ensembles obtained by simulations depend on the force field and initial structure, Aβ42α-helix or Aβ42β-strand. The ff14IDPSFF sampled a high ratio of disordered structures and diverse β-strand secondary structures; in contrast, ff14SB favored helicity during the Aβ42α-helix simulations. The conformations obtained from Aβ42β-strand simulations maintained a balanced content in the disordered and helical structures when simulated by ff14SB, but the conformers clearly favored disordered and β-sheet structures simulated by ff14IDPSFF. The results obtained with ff14IDPSFF qualitatively reproduced the NMR chemical shifts well. In-depth peptide and cluster analysis revealed some characteristic features that may be linked to early onset of the fibril-like structure. The C-terminal region (mainly M35-V40) featured in-registered anti-parallel β-strand (β-hairpin) conformations with tested systems. Our work should expand the knowledge of force field and structure dependency in MD simulations and reveals the underlying structural mechanism-function relationship in Aβ42 peptides. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kingsley Y Wu
- Department of Chemistry, University of California, Riverside, CA, USA
| | - David Doan
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Marco Medrano
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, CA, USA
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7
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Saha D, Jana B. Identifying the Template for Oligomer to Fibril Conversion for Amyloid-β (1-42) Oligomers using Hamiltonian Replica Exchange Molecular Dynamics. Chemphyschem 2022; 23:e202200393. [PMID: 36052514 DOI: 10.1002/cphc.202200393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/26/2022] [Indexed: 01/04/2023]
Abstract
The toxicity of amyloid-β (Aβ) oligomers has been known to be higher compared to mature fibrils. Yet the presence of plaques in Alzheimer's disease patients indicates the significance of oligomer to fibril conversion for Aβ aggregates. In this study, we investigate Aβ13-42 oligomers having two to five peptide chains using extensive all-atom molecular dynamics simulations to identify the on- or off-pathway intermediates in fibril formation pathway. Hamiltonian replica exchange method through solute tempering (REST2) has been employed to explore the different structures attained by these aggregates. Using intra-chain and inter-chain contacts as reaction coordinates, we obtain the free energy surface for the Aβ13-42 oligomers. Consequently, their stable conformations and structural features have been identified. The found conformations belonging to most probable structures possess both parallel and anti-parallel β-sheets, characteristic of on- and off-pathway intermediates, respectively. Further, we have measured the tendency to form fibril like interactions among the β-sheet forming residues. Our analysis finds that residues 30-36 possess higher tendency to form fibril like contacts among all the residues. While we find stronger interaction among residues 30-36, these amino acids are also found to be more shielded from water compared to others. With previous experimental studies finding these residues to be more crucial for the stability of Aβ42 oligomers, we propose that interactions within this patch could trigger seed formation that leads to conversion of on-pathway oligomers into disease relevant fibrils.
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Affiliation(s)
- Debasis Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, Jadavpur, Kolkata, 700032, West Bengal, India
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8
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Hu X, Liu C, Wang K, Zhao L, Qiu Y, Chen H, Hu J, Xu J. Multifunctional Anti-Alzheimer’s Disease Effects of Natural Xanthone Derivatives: A Primary Structure-Activity Evaluation. Front Chem 2022; 10:842208. [PMID: 35646819 PMCID: PMC9130743 DOI: 10.3389/fchem.2022.842208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/26/2022] [Indexed: 12/15/2022] Open
Abstract
Background: A series of α-Mangostin (α-M) derivatives were designed and synthesized. α-M and four analogues were evaluated for their multifunctional anti-Alzheimer’s disease (anti-AD) effects on fibrillogenesis, microglial uptake, microglial degradation, and anti-neurotoxicity of Aβ, as well as LPS-induced neuroinflammation. The differences in bioactivities were analyzed to understand the structure-activity relationship for further modifications. Purpose: This study aims to investigate the anti-AD effects of α-M and elucidate its structure-activity relationship by comparing difference between α-M and several analogues. Methods: Aβ fibrillogenesis was detected by Thioflavin T fluorometric assay. The levels of Aβ1-42 and inflammatory cytokines were evaluated by enzyme-linked immunosorbent assay. Neuron viability was examined by the CCK-8 assay. The morphology of ZO-1 of bEnd.3 cultured in BV-2-conditioned medium was evaluated by immunofluorescence staining. Results: Aβ fibrillogenesis was significantly inhibited by co-incubation with α-M, Zcbd-2 or Zcbd-3. α-M, Zcbd-2, Zcbd-3, and Zcbd-4 decreased the levels of Aβ1-42 and inflammatory cytokines, and promoted Aβ uptake, degradation and anti-inflammation effects inflammation in microglia. α-M and Zcbd-3 protected neuron viability from Aβ-induced neurotoxicity, and preserved tight junction integrity of bEnd.3 against LPS-induced neuroinflammation. Conclusion: Zcbd-3 acted as α-M almost in all effects. The structure-activity analysis indicated that the 3-methyl-2-butenyl group at C-8 is essential for the bioactivity of α-M, while modifying the double hydroxylation at the C-2 position may improve the multifunctional anti-AD effects.
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Affiliation(s)
- Xiaoyu Hu
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chan Liu
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Joint International Research Laboratory of Ethnomedicine of Ministry of Education and Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Kaichun Wang
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lanxue Zhao
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Qiu
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongzhuan Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jiangmiao Hu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- *Correspondence: Jiangmiao Hu, ; Jianrong Xu,
| | - Jianrong Xu
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Jiangmiao Hu, ; Jianrong Xu,
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9
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Strazdaite S, Roeters SJ, Sakalauskas A, Sneideris T, Kirschner J, Pedersen KB, Schiøtt B, Jensen F, Weidner T, Smirnovas V, Niaura G. Interaction of Amyloid-β-(1-42) Peptide and Its Aggregates with Lipid/Water Interfaces Probed by Vibrational Sum-Frequency Generation Spectroscopy. J Phys Chem B 2021; 125:11208-11218. [PMID: 34597059 DOI: 10.1021/acs.jpcb.1c04882] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we use surface-sensitive vibrational sum-frequency generation (VSFG) spectroscopy to investigate the interaction between model lipid monolayers and Aβ(1-42) in its monomeric and aggregated states. Combining VSFG with atomic force microscopy (AFM) and thioflavin T (ThT) fluorescence measurements, we found that only small aggregates with probably a β-hairpin-like structure adsorbed to the zwitterionic lipid monolayer (DOPC). In contrast, larger aggregates with an extended β-sheet structure adsorbed to a negatively charged lipid monolayer (DOPG). The adsorption of small, initially formed aggregates strongly destabilized both monolayers, but only the DOPC monolayer was completely disrupted. We showed that the intensity of the amide-II' band in achiral (SSP) and chiral (SPP) polarization combinations increased in time when Aβ(1-42) aggregates accumulated at the DOPG monolayer. Nevertheless, almost no adsorption of preformed mature fibrils to DOPG monolayers was detected. By performing spectral VSFG calculations, we revealed a clear correlation between the amide-II' signal and the degree of amyloid aggregates (e.g., oligomers or (proto)fibrils) of various Aβ(1-42) structures. The calculations showed that only structures with a significant amyloid β-sheet content have a strong amide-II' intensity, in line with previous Raman studies. The combination of the presented results substantiates the amide-II(') band as a legitimate amyloid marker.
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Affiliation(s)
- S Strazdaite
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Sauletekio Ave. 3, Vilnius LT-10257, Lithuania
| | - S J Roeters
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - A Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257 Vilnius, Lithuania
| | - T Sneideris
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257 Vilnius, Lithuania
| | - J Kirschner
- Institute of Solid State Physics, TU Wien, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
| | - K B Pedersen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - B Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - F Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - T Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - V Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257 Vilnius, Lithuania
| | - G Niaura
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Sauletekio Ave. 3, Vilnius LT-10257, Lithuania
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10
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Chatterjee P, Cho MK, Bui HTD, Ham S. Atomic Level Investigations of Early Aggregation of Tau43 in Water
II
.
Tau43‐Aβ42
vs.
Tau43‐
Tau43
Dimerizations. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Prathit Chatterjee
- Department of Chemistry, The Research Institute of Natural Sciences Sookmyung Women's University Seoul 04310 Korea
| | - Myung Keun Cho
- Department of Chemistry, The Research Institute of Natural Sciences Sookmyung Women's University Seoul 04310 Korea
- Department of Chemistry, College of Natural Sciences Seoul National University, Gwanak‐ro 1, Gwanak‐ku Seoul 08826 Korea
| | - Huong T. D. Bui
- Department of Chemistry, The Research Institute of Natural Sciences Sookmyung Women's University Seoul 04310 Korea
| | - Sihyun Ham
- Department of Chemistry, The Research Institute of Natural Sciences Sookmyung Women's University Seoul 04310 Korea
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11
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Chatterjee P, Le T, Bui HTD, Cho MK, Ham S. Atomic Level Investigations of Early Aggregation of Tau43 in Water I. Conformational Propensity of Monomeric Tau43. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Prathit Chatterjee
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
| | - Thi‐Diem Le
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
| | - Huong T. D. Bui
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
| | - Myung Keun Cho
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
- Department of Chemistry College of Natural Sciences, Seoul National University, Gwanak‐ro 1, Gwanak‐ku Seoul 08826 Korea
| | - Sihyun Ham
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
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12
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Abedin F, Tatulian SA. Mutual structural effects of unmodified and pyroglutamylated amyloid β peptides during aggregation. J Pept Sci 2021; 27:e3312. [PMID: 33631839 DOI: 10.1002/psc.3312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/05/2021] [Accepted: 02/16/2021] [Indexed: 11/09/2022]
Abstract
Amyloid β (Aβ) peptide aggregates are linked to Alzheimer's disease (AD). Posttranslationally pyroglutamylated Aβ (pEAβ) occurs in AD brains in significant quantities and is hypertoxic, but the underlying structural and aggregation properties remain poorly understood. Here, the structure and aggregation of Aβ1-40 and pEAβ3-40 are analyzed separately and in equimolar combination. Circular dichroism data show that Aβ1-40 , pEAβ3-40 , and their combination assume α-helical structure in dry state and transition to unordered structure in aqueous buffer. Aβ1-40 and the 1:1 combination gradually acquire β-sheet structure while pEAβ3-40 adopts an α-helix/β-sheet conformation. Thioflavin-T fluorescence studies suggest that the two peptides mutually inhibit fibrillogenesis. Fourier transform infrared (FTIR) spectroscopy identifies the presence of β-turn and α-helical structures in addition to β-sheet structure in peptides in aqueous buffer. The kinetics of transitions from the initial α-helical structure to β-sheet structure were resolved by slow hydration of dry peptides by D2 O vapor, coupled with isotope-edited FTIR. These data confirmed the mutual suppression of β-sheet formation by the two peptides. Remarkably, pEAβ3-40 maintained a significant fraction of α-helical structure in the combined sample, implying a reduced β-sheet propensity of pEAβ3-40 . Altogether, the data imply that the combination of unmodified and pyroglutamylated Aβ peptides resists fibrillogenesis and favors the prefibrillar state, which may underlie hypertoxicity of pEAβ.
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Affiliation(s)
- Faisal Abedin
- Physics Graduate Program, University of Central Florida, Orlando, Florida, USA
| | - Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, Florida, USA
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13
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Neurodegeneration-related beta-amyloid as autocatabolism-attenuator in a micro-in vivo system. IBRO Rep 2020; 9:319-323. [PMID: 33336107 PMCID: PMC7733039 DOI: 10.1016/j.ibror.2020.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/02/2020] [Indexed: 11/24/2022] Open
Abstract
Bdelloids are adaptive models for studying aggregate-metabolism interactions. Starvation causes reversible organ shrinkage in bdelloids. The organ shrinkage is in connection with autocatabolic processes. Beta-amyloid attenuates the starvation-induced germovitellaria shrinkage. Human-type amyloid-aggregates are metabolism-regulators in two bdelloid species.
Investigation of human neurodegeneration-related aggregates of beta-amyloid 1–42 (Aβ42) on bdelloid rotifers is a novel interdisciplinary approach in life sciences. We reapplied an organ size-based in vivo monitoring system, exploring the autocatabolism-related alterations evoked by Aβ42, in a glucose-supplemented starvation model. The experientially easy-to-follow size reduction of the bilateral reproductive organ (germovitellaria) in fasted rotifers was rescued by Aβ42, serving as a nutrient source- and peptide sequence-specific attenuator of the organ shrinkage phase and enhancer of the regenerative one including egg reproduction. Recovery of the germovitellaria was significant in comparison with the greatly shrunken form. In contrast to the well-known neurotoxic Aβ42 (except the bdelloids) with specific regulatory roles, the artificially designed scrambled version (random order of amino acids) was inefficient in autocatabolism attenuation, behaving as negative control. This native Aβ42-related modulation of the ‘functionally reversible organ shrinkage’ can be a potential experiential and supramolecular marker of autocatabolism in vivo.
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Key Words
- AO, acridine orange
- AVOs, acidic vesicular organelles
- Acridine orange (PubChem CID: 62344)
- Autocatabolism
- Aβ, beta-amyloid
- Bdelloid rotifer
- Beta-amyloid
- BisANS (PubChem CID: 16213473)
- BisANS, 4,4′-dianilino-1,1′-binaphthyl-5,5′-disulfonic acid dipotassium salt
- ConA, Concanamycin A
- Concanamycin A (PubChem CID: 6438151)
- D0, Day 0
- D20, Day 20
- D25, Day 25
- FROS, functionally reversible organ shrinkage
- FROSi, FROS index
- Invertebrate
- Metabolism
- NFI%, percentage of normalized fluorescence intensity
- NaOH (PubChem CID: 14798)
- Neutral red (PubChem CID: 11105)
- Organ shrinkage
- PI, propidium-iodide
- Propidium-iodide (PubChem CID: 104981)
- S-Aβ42, scrambled isoform of Aβ
- SEM, standard error of the mean
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14
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Kaur A, Kaur A, Goyal D, Goyal B. How Does the Mono-Triazole Derivative Modulate Aβ 42 Aggregation and Disrupt a Protofibril Structure: Insights from Molecular Dynamics Simulations. ACS OMEGA 2020; 5:15606-15619. [PMID: 32637837 PMCID: PMC7331201 DOI: 10.1021/acsomega.0c01825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/08/2020] [Indexed: 05/31/2023]
Abstract
Clinical studies have identified that abnormal self-assembly of amyloid-β (Aβ) peptide into toxic fibrillar aggregates is associated with the pathology of Alzheimer's disease (AD). The most acceptable therapeutic approach to stop the progression of AD is to inhibit the formation of β-sheet-rich structures. Recently, we designed and evaluated a series of novel mono-triazole derivatives 4(a-x), where compound 4v was identified as the most potent inhibitor of Aβ42 aggregation and disaggregates preformed Aβ42 fibrils significantly. Moreover, 4v strongly averts the Cu2+-induced Aβ42 aggregation and disaggregates the preformed Cu2+-induced Aβ42 fibrils, halts the generation of reactive oxygen species, and shows neuroprotective effects in SH-SY5Y cells. However, the underlying molecular mechanism of inhibition of Aβ42 aggregation by 4v and disaggregation of preformed Aβ42 fibrils remains obscure. In this work, molecular dynamics (MD) simulations have been performed to explore the conformational ensemble of the Aβ42 monomer and a pentameric protofibril structure of Aβ42 in the presence of 4v. The MD simulations highlighted that 4v binds preferentially at the central hydrophobic core region of the Aβ42 monomer and chains D and E of the Aβ42 protofibril. The dictionary of secondary structure of proteins analysis indicated that 4v retards the conformational conversion of the helix-rich structure of the Aβ42 monomer into the aggregation-prone β-sheet conformation. The binding free energy calculated by the molecular mechanics Poisson-Boltzmann surface area method revealed an energetically favorable process with ΔG binding = -44.9 ± 3.3 kcal/mol for the Aβ42 monomer-4v complex. The free energy landscape analysis highlighted that the Aβ42 monomer-4v complex sampled conformations with significantly higher helical contents (35 and 49%) as compared to the Aβ42 monomer alone (17%). Compound 4v displayed hydrogen bonding with Gly37 (chain E) and π-π interactions with Phe19 (chain D) of the Aβ42 protofibril. Further, the per-residue binding free energy analysis also highlighted that Phe19 (chain D) and Gly37 (chain E) of the Aβ42 protofibril showed the maximum contribution in the binding free energy. The decreased binding affinity and residue-residue contacts between chains D and E of the Aβ42 protofibril in the presence of 4v indicate destabilization of the Aβ42 protofibril structure. Overall, the structural information obtained through MD simulations indicated that 4v stabilizes the native helical conformation of the Aβ42 monomer and persuades a destabilization in the protofibril structure of Aβ42. The results of the study will be useful in the rational design of potent inhibitors against amyloid aggregation.
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Affiliation(s)
- Amandeep Kaur
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Anupamjeet Kaur
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Deepti Goyal
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Bhupesh Goyal
- School
of Chemistry & Biochemistry, Thapar
Institute of Engineering & Technology, Patiala 147004, Punjab, India
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15
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Boopathi S, Dinh Quoc Huy P, Gonzalez W, Theodorakis PE, Li MS. Zinc binding promotes greater hydrophobicity inAlzheimer's Aβ42peptide than copper binding: Molecular dynamics and solvation thermodynamics studies. Proteins 2020; 88:1285-1302. [DOI: 10.1002/prot.25901] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/04/2020] [Accepted: 05/13/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Subramanian Boopathi
- Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de IngenieríaUniversidad de Talca Talca Chile
| | | | - Wendy Gonzalez
- Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de IngenieríaUniversidad de Talca Talca Chile
- Millennium Nucleus of Ion Channels‐Associated Diseases (MiNICAD)Universidad de Talca Talca Chile
| | | | - Mai Suan Li
- Institute of PhysicsPolish Academy of Sciences Warsaw Poland
- Institute for Computational Science and Technology, Quang Trung Software City Tan Chanh Hiep Ward Ho Chi Minh City Vietnam
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16
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Saranya V, Mary PV, Vijayakumar S, Shankar R. The hazardous effects of the environmental toxic gases on amyloid beta-peptide aggregation: A theoretical perspective. Biophys Chem 2020; 263:106394. [PMID: 32480019 DOI: 10.1016/j.bpc.2020.106394] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is one of the leading causes of dementia in elderly people. It has been well documented that the exposure to environmental toxins such as CO, CO2, SO2 and NO2 that are present in the air is considered as a hallmark for the progression of Alzheimer's disease. However, their actual mechanism by which environmental toxin triggers the aggregation of Aβ42 peptide at the molecular and atomic levels remain unknown. In this study, molecular dynamics simulation was carried out to study the aggregation mechanism of the Aβ42 peptide due to its interaction of toxic gas (CO, CO2, SO2 and NO2). During the 400 ns simulation, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes have smaller Root Mean Square Deviation values when compared to the Aβ42 peptide, which shows that the interaction of toxic gases (CO, CO2, SO2, and NO2) would increase the Aβ42 peptide structural stability. The radius of gyration analysis also supports that Aβ42 interacted CO2 and SO2 complexes have the minimum value in the range of 0.95 nm and 1.5 nm. It is accounted that the Aβ42 interacted CO2 and SO2 complexes have a greater compact structure in comparison to Aβ42 interacted CO and NO2 complexes. Furthermore, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes exhibited an enhanced secondary structural probability for coil and turn regions with a reduced α-helix probability, which indicates that the interaction of toxic gases may enhance the toxicity and aggregation of Aβ42.
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Affiliation(s)
- Vasudevan Saranya
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India
| | - Pitchumani Violet Mary
- Department of Physics, Sri Shakthi Institute of Engineering and Technology, Coimbatore 641 062, India
| | | | - Ramasamy Shankar
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India.
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17
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Kaur A, Shuaib S, Goyal D, Goyal B. Interactions of a multifunctional di-triazole derivative with Alzheimer's Aβ42monomer and Aβ42protofibril: a systematic molecular dynamics study. Phys Chem Chem Phys 2020; 22:1543-1556. [DOI: 10.1039/c9cp04775a] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The molecular dynamics simulations results highlighted that the multi-target-directed ligand6nstabilizes the native α-helix conformation of the Aβ42monomer and induces a sizable destabilization in the Aβ42protofibril structure.
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Affiliation(s)
- Anupamjeet Kaur
- Department of Chemistry
- Faculty of Basic and Applied Sciences
- Sri Guru Granth Sahib World University
- Fatehgarh Sahib-140406
- India
| | - Suniba Shuaib
- Department of Chemistry
- Faculty of Basic and Applied Sciences
- Sri Guru Granth Sahib World University
- Fatehgarh Sahib-140406
- India
| | - Deepti Goyal
- Department of Chemistry
- Faculty of Basic and Applied Sciences
- Sri Guru Granth Sahib World University
- Fatehgarh Sahib-140406
- India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry
- Thapar Institute of Engineering & Technology
- Patiala-147004
- India
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18
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Maruyama Y, Takano H, Mitsutake A. Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory. Biophys Physicobiol 2019; 16:407-429. [PMID: 31984194 PMCID: PMC6975981 DOI: 10.2142/biophysico.16.0_407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/29/2019] [Indexed: 01/03/2023] Open
Abstract
Molecular dynamics simulation is a fruitful tool for investigating the structural stability, dynamics, and functions of biopolymers at an atomic level. In recent years, simulations can be performed on time scales of the order of milliseconds using special purpose systems. Since the most stable structure, as well as meta-stable structures and intermediate structures, is included in trajectories in long simulations, it is necessary to develop analysis methods for extracting them from trajectories of simulations. For these structures, methods for evaluating the stabilities, including the solvent effect, are also needed. We have developed relaxation mode analysis to investigate dynamics and kinetics of simulations based on statistical mechanics. We have also applied the three-dimensional reference interaction site model theory to investigate stabilities with solvent effects. In this paper, we review the results for designing amino-acid substitution of the 10-residue peptide, chignolin, to stabilize the misfolded structure using these developed analysis methods.
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Affiliation(s)
- Yutaka Maruyama
- Architecture Development Team, FLAGSHIP 2020 Project, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Hiroshi Takano
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Ayori Mitsutake
- Department of Physics, School of Science and Technology, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
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