Exploration of the potential energy surface for the conformational interconversion of the amyloid $β$ peptide at the fibril end
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| Main Authors: | , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866918020163567616 |
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| author | Oishi, Yasuhiro Kitatani, Motoharu Nakajima, Kichitaro Ogi, Hirotsugu Kusakabe, Koichi |
| author_facet | Oishi, Yasuhiro Kitatani, Motoharu Nakajima, Kichitaro Ogi, Hirotsugu Kusakabe, Koichi |
| contents | The formation of amyloid fibrils comprising amyloid $β$ (A$β$) peptides is associated with the pathology of Alzheimer's disease. In this study, we theoretically investigated the A$β$ structure at the fibril end using the density functional theory calculation. Several twisted conformations were identified as local minima in which a part of the peptide chain bends upward while the rest remains bound to the lower A$β$ monomer. Fibril-to-twisted conformational transition exhibited endothermic behavior, with endothermic energy increasing as more backbone hydrogen bonds were broken. In addition, the loss of van der Waals interaction from the hydrophobic sidechain contributed to endothermicity. The nudged elastic band method was applied to analyze the potential energy surface connecting the fibril and twisted conformations. Comparison of the activation barriers between different twisted conformations revealed that certain twisted conformations returned relatively easily to the fibril conformation, whereas others encountered a higher activation barrier and reverted less readily. Detailed structural analysis revealed that the twisted conformation's propensity to return originates from the local steric hindrance imposed by the sidechain near the torsional axis. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2505_09151 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Exploration of the potential energy surface for the conformational interconversion of the amyloid $β$ peptide at the fibril end Oishi, Yasuhiro Kitatani, Motoharu Nakajima, Kichitaro Ogi, Hirotsugu Kusakabe, Koichi Biological Physics Biomolecules The formation of amyloid fibrils comprising amyloid $β$ (A$β$) peptides is associated with the pathology of Alzheimer's disease. In this study, we theoretically investigated the A$β$ structure at the fibril end using the density functional theory calculation. Several twisted conformations were identified as local minima in which a part of the peptide chain bends upward while the rest remains bound to the lower A$β$ monomer. Fibril-to-twisted conformational transition exhibited endothermic behavior, with endothermic energy increasing as more backbone hydrogen bonds were broken. In addition, the loss of van der Waals interaction from the hydrophobic sidechain contributed to endothermicity. The nudged elastic band method was applied to analyze the potential energy surface connecting the fibril and twisted conformations. Comparison of the activation barriers between different twisted conformations revealed that certain twisted conformations returned relatively easily to the fibril conformation, whereas others encountered a higher activation barrier and reverted less readily. Detailed structural analysis revealed that the twisted conformation's propensity to return originates from the local steric hindrance imposed by the sidechain near the torsional axis. |
| title | Exploration of the potential energy surface for the conformational interconversion of the amyloid $β$ peptide at the fibril end |
| topic | Biological Physics Biomolecules |
| url | https://arxiv.org/abs/2505.09151 |