Exploring the aggregation of amyloid-β 42 through Monte Carlo simulations

Dey, Priya; Biswas, Parbati

doi:10.1016/j.bpc.2023.107011

Cited by 6 publications

(2 citation statements)

References 66 publications

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“…73 On the other hand, computational simulations are also useful for obtaining the dynamic structural information of AβOs by using Monte Carlo, ab initio or molecular dynamics approaches. 13,74–78 Microsecond molecular dynamics simulations enable the study of the translational and rotational conformational spaces of AβOs in both solution and lipid phases. 76 These findings would provide valuable information for the discovery of druggable sites and the structural design of targeting agents.…”

Section: Amyloid-β Oligomers In Admentioning

confidence: 99%

Recent developments in the chemical biology of amyloid-β oligomer targeting

et al. 2023

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Section: Amyloid-β Oligomers In Admentioning

confidence: 99%

Recent developments in the chemical biology of amyloid-β oligomer targeting

et al. 2023

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“…The focus of our review is on molecular dynamics (MD) simulations as opposed to Monte Carlo simulations, 17 as the former have contributed the most to the field of amyloid aggregation simulations. 13,14,16 This is for several reasons, one of them being the ease of use of MD simulations as one has not to worry about the right choice of Monte Carlo moves.…”

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confidence: 99%

A brief history of amyloid aggregation simulations

Fatafta,

Khaled,

Kav

et al. 2024

WIREs Comput Mol Sci

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Amyloid proteins are characterized by their tendency to aggregate into amyloid fibrils, which are often associated with devastating diseases. Aggregation pathways typically involve unfolding or misfolding of monomeric proteins and formation of transient oligomers and protofibrils before the final aggregation product is formed. The conformational dynamics and polymorphic and volatile nature of these aggregation intermediates make their characterization by experimental techniques alone insufficient and also require computational approaches. Over the past 25 years, the size of simulated amyloid aggregation systems and the length of these simulations have increased significantly. These advances are discussed here. The review includes simulation approaches that model the aggregating peptides or proteins at both the all‐atom and coarse‐grained levels, use molecular dynamics simulations or Monte Carlo sampling to simulate the conformational changes, and present results for various amyloid peptides and proteins ranging from Lys‐Phe‐Phe‐Glu (KFFE) as the smallest system to as an intermediate‐sized peptide to α‐synuclein. The presentation of the history of amyloid aggregation simulations concludes with a discussion of where the future of these simulations may lie.This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods

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