pH modulates friction memory effects in protein folding
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arXiv
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| Format: | Preprint |
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2024
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| author | Dalton, Benjamin A. Netz, Roland R. |
| author_facet | Dalton, Benjamin A. Netz, Roland R. |
| contents | We study the non-Markovian folding dynamics of the $α$3D protein under low- and neutral-pH conditions. Recently published all-atom simulations of $α$3D by the Shaw group reveal that lowering the pH significantly reduces both native and non-native salt-bridge interactions, which dominate the folding dynamics. Here, we demonstrate that this physiochemical modulation directly perturbs the folding friction, which we evaluate using non-Markovian memory-kernel-extraction techniques. In doing so, we find that the reduction in pH not only decreases the magnitude of the time-dependent friction acting on the protein but also more dramatically shortens the time scale of the friction memory effects. As a result, the folding dynamics in the low pH system are well described by a purely Markovian model. In the neutral pH system, however, the memory time scale is of the same order as the folding time and is accelerated by a factor of 6 compared to a Markovian model prediction. We demonstrate that this memory-induced barrier-crossing speed-up is predicted by non-Markovian reaction-kinetic theories, confirming that non-Markovian models are, in general, necessary for a quantitative description of protein folding dynamics. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2401_12027 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | pH modulates friction memory effects in protein folding Dalton, Benjamin A. Netz, Roland R. Biological Physics We study the non-Markovian folding dynamics of the $α$3D protein under low- and neutral-pH conditions. Recently published all-atom simulations of $α$3D by the Shaw group reveal that lowering the pH significantly reduces both native and non-native salt-bridge interactions, which dominate the folding dynamics. Here, we demonstrate that this physiochemical modulation directly perturbs the folding friction, which we evaluate using non-Markovian memory-kernel-extraction techniques. In doing so, we find that the reduction in pH not only decreases the magnitude of the time-dependent friction acting on the protein but also more dramatically shortens the time scale of the friction memory effects. As a result, the folding dynamics in the low pH system are well described by a purely Markovian model. In the neutral pH system, however, the memory time scale is of the same order as the folding time and is accelerated by a factor of 6 compared to a Markovian model prediction. We demonstrate that this memory-induced barrier-crossing speed-up is predicted by non-Markovian reaction-kinetic theories, confirming that non-Markovian models are, in general, necessary for a quantitative description of protein folding dynamics. |
| title | pH modulates friction memory effects in protein folding |
| topic | Biological Physics |
| url | https://arxiv.org/abs/2401.12027 |