Articles written in Journal of Chemical Sciences

    • In silico studies of the early stages of aggregation of Aβ₄₂ peptides


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      Accumulation of amyloid beta (Aβ) peptide in the brain is responsible for debilitating neurodegenerative disease, namely, Alzheimer’s disease. We have carried out atomistic molecular dynamics simulation to study the early stages of the aggregation process of five full-length Aβ₄₂ peptide monomers with varying secondary structural contents in aqueous solution. Attempts have been made to study the conformational modifications of the Aβ peptide monomers and their dynamical features during the oligomer formation. Inparticular, specific molecular interactions that drive the association process leading to the formation of the stable oligomer have been identified. The calculations revealed that the helix–helix linkage plays an important role forbringing the unstructured regions of the monomers closer for self-assembly. Importantly, it is demonstrated that the contribution originating from the nonpolar interactions between the peptides and the corresponding nonpolarsolvation more than compensates the weakening effect of unfavorable inter-peptide electrostatic interactions, thereby stabilizing the nucleated oligomer.

    • Effect of aggregated Ab protofilaments on intermolecular vibrational spectrum of confined water


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      Alzheimer’s disease, one of most common neurodegenerative diseases, is believed to be caused due to the self-assembly of amyloid beta (Ab) peptides into insoluble fibrils in the brain. Atomistic molecular dynamics simulations have been carried out to probe the effects of non-uniform structural distortions ofaggregated Ab17-42 protofilaments of different sizes, ranging from pentamer to tetradecamer, on the lowfrequency vibrational spectrum of water confined within their amphiphilic nanocores. The calculations revealed increased back scattering of water molecules present either at the exterior surfaces of the protofilaments or confined within their cores, thereby leading to blue shifts of the band corresponding to O ... O ... O bending or restricted transverse motions of water. Due to more restricted environment, the effect is more for the core water molecules. It is observed that the extent of such shifts is sensitive to the degree of confinement within the protofilament cores and the nature of hydrogen bonding. Importantly, the structural crossover of the protofilaments with increased core volume at decamer has been found to be associated with characteristic effect on the low-frequency modes of the water molecules confined within its core.

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