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Ma Y, Wang G, Chen H, Tsai M. Exploring Abeta42 monomer diffusion dynamics on fibril surfaces through molecular simulations. Protein Sci 2025; 34:e70131. [PMID: 40371804 PMCID: PMC12079388 DOI: 10.1002/pro.70131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Revised: 03/14/2025] [Accepted: 04/07/2025] [Indexed: 05/16/2025]
Abstract
This study provides critical insights into the role of surface-mediated processes in Alzheimer's disease, with implications for the aggregation of Abeta42 peptides. Employing coarse-grained molecular dynamics simulations, we focus on elucidating the molecular intricacies of these processes beyond primary nucleation. Central to our investigation is the analysis of a freely diffusing Abeta42 monomer on preformed fibril structures. We conduct detailed calculations of the monomer's diffusion coefficient on fibril surfaces (as a one-dimensional case), along with various monomer orientations. Our findings reveal a strong and consistent correlation between the monomer's diffusion coefficient and its orientation on the surface. Further analysis differentiates the effects of parallel and perpendicular alignments with respect to the fibril axis. Additionally, we explore how different fibril surfaces influence monomer dynamics by comparing the C-terminal and N-terminal surfaces. We find that the monomer exhibits faster diffusion coefficients on the C-terminal surface. Differences in surface roughness (SR), quantified using root-mean-square distances, significantly affect monomer dynamics, thereby influencing its diffusion on the surface. Importantly, this study underscores that fibril twisting acts as a regulatory niche, selectively influencing these orientations and their diffusion properties necessary for facilitating fibril growth within biologically relevant time scales. This discovery opens new avenues for targeted therapeutic strategies aimed at manipulating fibril dynamics to mitigate the progression of Alzheimer's disease.
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Affiliation(s)
- Yuan‐Wei Ma
- Institute of Bioinformatics and Structural BiologyNational Tsing‐Hua UniversityHsinchuTaiwan
- Department of Chemistry and BiochemistryNational Chung Cheng UniversityChiayiTaiwan
| | - Guan‐Fang Wang
- Department of Chemistry and BiochemistryNational Chung Cheng UniversityChiayiTaiwan
| | - Hong‐Yi Chen
- Department of Chemistry and BiochemistryNational Chung Cheng UniversityChiayiTaiwan
| | - Min‐Yeh Tsai
- Department of Chemistry and BiochemistryNational Chung Cheng UniversityChiayiTaiwan
- Center for Nano Bio‐DetectionNational Chung Cheng UniversityChiayiTaiwan
- Division of Physics, National Center for Theoretical SciencesNational Taiwan UniversityTaipeiTaiwan
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Ghosh P, Kundu A, Ganguly D. From experimental studies to computational approaches: recent trends in designing novel therapeutics for amyloidogenesis. J Mater Chem B 2025; 13:858-881. [PMID: 39664012 DOI: 10.1039/d4tb01890g] [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: 12/13/2024]
Abstract
Amyloidosis is a condition marked by misfolded proteins that build up in tissues and eventually destroy organs. It has been connected to a number of fatal illnesses, including non-neuropathic and neurodegenerative conditions, which in turn have a significant influence on the worldwide health sector. The inability to identify the underlying etiology of amyloidosis has hampered efforts to find a treatment for the condition. Despite the identification of a multitude of putative pathogenic variables that may operate independently or in combination, the molecular mechanisms responsible for the development and progression of the disease remain unclear. A thorough investigation into protein aggregation and the impacts of toxic aggregated species will help to clarify the cytotoxicity of aggregation-mediated cellular apoptosis and lay the groundwork for future studies aimed at creating effective treatments and medications. This review article provides a thorough summary of the combination of various experimental and computational approaches to modulate amyloid aggregation. Further, an overview of the latest developments of novel therapeutic agents is given, along with a discussion of the possible obstacles and viewpoints on this developing field. We believe that the information provided by this review will help scientists create innovative treatment strategies that affect the way proteins aggregate.
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Affiliation(s)
- Pooja Ghosh
- Centre for Interdisciplinary Sciences, JIS Institute of Advanced Studies & Research (JISIASR) Kolkata, JIS University, GP Block, Sector-5, Salt Lake, Kolkata 700091, West Bengal, India.
| | - Agnibin Kundu
- Department of Medicine, District Hospital Howrah, 10, Biplabi Haren Ghosh Sarani Lane, Howrah 711101, West Bengal, India
| | - Debabani Ganguly
- Centre for Health Science & Technology, JIS Institute of Advanced Studies & Research (JISIASR) Kolkata, JIS University, GP Block, Sector-5, Salt Lake, Kolkata 700091, West Bengal, India.
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Nirmalraj PN, Bhattacharya S, Thompson D. Accelerated Alzheimer's Aβ-42 secondary nucleation chronologically visualized on fibril surfaces. SCIENCE ADVANCES 2024; 10:eadp5059. [PMID: 39454002 PMCID: PMC11506133 DOI: 10.1126/sciadv.adp5059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 09/23/2024] [Indexed: 10/27/2024]
Abstract
Protein fibril surfaces tend to generate toxic oligomers catalytically. To date, efforts to study the accelerated aggregation steps involved with Alzheimer's disease-linked amyloid-β (Aβ)-42 proteins on fibril surfaces have mainly relied on fluorophore-based analytics. Here, we visualize rare secondary nucleation events on the surface of Aβ-42 fibrils from embryonic to endpoint stages using liquid-based atomic force microscopy. Nanoscale imaging supported by atomic-scale molecular simulations tracked the adsorption and proliferation of oligomeric assemblies at nonperiodically spaced catalytic sites on the fibril surface. Upon confirming that fibril edges are preferential binding sites for oligomers during embryonic stages, the secondary fibrillar size changes were quantified during the growth stages. Notably, a small population of fibrils that displayed higher surface catalytic activity was identified as superspreaders. Profiling secondary fibrils during endpoint stages revealed a nearly threefold increase in their surface corrugation, a parameter we exploit to classify fibril subpopulations.
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Affiliation(s)
- Peter Niraj Nirmalraj
- Transport at Nanoscale Interfaces Laboratory, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, CH-8600, Switzerland
| | - Shayon Bhattacharya
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94T9PX, Ireland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94T9PX, Ireland
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Li C, Wei TY, Cheung MS, Tsai MY. Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin's Regulation on Actin Filaments. J Phys Chem B 2024; 128:4590-4601. [PMID: 38701111 PMCID: PMC11104348 DOI: 10.1021/acs.jpcb.3c07938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/20/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024]
Abstract
Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experiments suggest that cofilin forms functionally distinct oligomers via thiol post-translational modifications (PTMs) that promote actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Utilizing a biasing scheme in simulations, we focus on analyzing dimer conformations conducive to disulfide bond formation. Additionally, we explore potential PTMs arising from the examined conformational ensemble. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. We also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol PTM of cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.
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Affiliation(s)
- Chengxuan Li
- Department
of Physics, University of Washington, Seattle, Washington 98195, United States
- Center
for Theoretical Biological Physics, Rice
University, Houston, Texas 77005, United States
| | - Ting-Yi Wei
- Department
of Chemistry and Biochemistry, National
Chung Cheng University, Minhsiung, Chiayi 621301, Taiwan
| | - Margaret S. Cheung
- Department
of Physics, University of Washington, Seattle, Washington 98195, United States
- Center
for Theoretical Biological Physics, Rice
University, Houston, Texas 77005, United States
- Pacific
Northwest National Laboratory, Seattle, Washington 98109, United States
| | - Min-Yeh Tsai
- Department
of Chemistry and Biochemistry, National
Chung Cheng University, Minhsiung, Chiayi 621301, Taiwan
- Division
of Physics, National Center for Theoretical Sciences, National Taiwan University, Taipei 106319, Taiwan
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Zhang R, Jalali S, Dias CL, Haataja MP. Growth kinetics of amyloid-like fibrils: An integrated atomistic simulation and continuum theory approach. PNAS NEXUS 2024; 3:pgae045. [PMID: 38725528 PMCID: PMC11079572 DOI: 10.1093/pnasnexus/pgae045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/19/2024] [Indexed: 05/12/2024]
Abstract
Amyloid fibrils have long been associated with many neurodegenerative diseases. The conventional picture of the formation and proliferation of fibrils from unfolded proteins comprises primary and secondary nucleation of oligomers followed by elongation and fragmentation thereof. In this work, we first employ extensive all-atom molecular dynamics (MD) simulations of short peptides to investigate the governing processes of fibril growth at the molecular scale. We observe that the peptides in the bulk solution can bind onto and subsequently diffuse along the fibril surface, which leads to fibril elongation via either bulk- or surface-mediated docking mechanisms. Then, to guide the quantitative interpretation of these observations and to provide a more comprehensive picture of the growth kinetics of single fibrils, a continuum model which incorporates the key processes observed in the MD simulations is formulated. The model is employed to investigate how relevant physical parameters affect the kinetics of fibril growth and identify distinct growth regimes. In particular, it is shown that fibrils which strongly bind peptides may undergo a transient exponential growth phase in which the entire fibril surface effectively acts as a sink for peptides. We also demonstrate how the relevant model parameters can be estimated from the MD trajectories. Our results provide compelling evidence that the overall fibril growth rates are determined by both bulk and surface peptide fluxes, thereby contributing to a more fundamental understanding of the growth kinetics of amyloid-like fibrils.
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Affiliation(s)
- Ruoyao Zhang
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Cristiano Luis Dias
- Department of Physics, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Mikko P Haataja
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
- Princeton Materials Institute, Princeton University, Princeton, NJ 08544, USA
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Yagi-Utsumi M, Itoh SG, Okumura H, Yanagisawa K, Kato K, Nishimura K. The Double-Layered Structure of Amyloid-β Assemblage on GM1-Containing Membranes Catalytically Promotes Fibrillization. ACS Chem Neurosci 2023; 14:2648-2657. [PMID: 37482658 PMCID: PMC10401643 DOI: 10.1021/acschemneuro.3c00192] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023] Open
Abstract
Alzheimer's disease (AD) is associated with progressive accumulation of amyloid-β (Aβ) cross-β fibrils in the brain. Aβ species tightly associated with GM1 ganglioside, a glycosphingolipid abundant in neuronal membranes, promote amyloid fibril formation; therefore, they could be attractive clinical targets. However, the active conformational state of Aβ in GM1-containing lipid membranes is still unknown. The present solid-state nuclear magnetic resonance study revealed a nonfibrillar Aβ assemblage characterized by a double-layered antiparallel β-structure specifically formed on GM1 ganglioside clusters. Our data show that this unique assemblage was not transformed into fibrils on GM1-containing membranes but could promote conversion of monomeric Aβ into fibrils, suggesting that a solvent-exposed hydrophobic layer provides a catalytic surface evoking Aβ fibril formation. Our findings offer structural clues for designing drugs targeting catalytically active Aβ conformational species for the development of anti-AD therapeutics.
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Affiliation(s)
- Maho Yagi-Utsumi
- Exploratory
Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Institute
for Molecular Science (IMS), National Institutes
of Natural Sciences, Okazaki, Aichi 444-8585, Japan
- Graduate
School of Pharmaceutical Sciences, Nagoya
City University, Nagoya, Aichi 467-8603, Japan
| | - Satoru G. Itoh
- Exploratory
Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Institute
for Molecular Science (IMS), National Institutes
of Natural Sciences, Okazaki, Aichi 444-8585, Japan
| | - Hisashi Okumura
- Exploratory
Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Institute
for Molecular Science (IMS), National Institutes
of Natural Sciences, Okazaki, Aichi 444-8585, Japan
| | - Katsuhiko Yanagisawa
- Research
and Development Center for Precision Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8550, Japan
- Research
Institute, National Center for Geriatrics
and Gerontology, Obu, Aichi 474-8511, Japan
| | - Koichi Kato
- Exploratory
Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Institute
for Molecular Science (IMS), National Institutes
of Natural Sciences, Okazaki, Aichi 444-8585, Japan
- Graduate
School of Pharmaceutical Sciences, Nagoya
City University, Nagoya, Aichi 467-8603, Japan
| | - Katsuyuki Nishimura
- Institute
for Molecular Science (IMS), National Institutes
of Natural Sciences, Okazaki, Aichi 444-8585, Japan
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