Hierarchical friction memory leads to subdiffusive configurational dynamics of fast-folding proteins
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| Main Authors: | , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866916807455014912 |
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| author | Klimek, Anton Dalton, Benjamin A. Tepper, Lucas Netz, Roland R. |
| author_facet | Klimek, Anton Dalton, Benjamin A. Tepper, Lucas Netz, Roland R. |
| contents | Proteins often exhibit subdiffusive configurational dynamics. The origins of this subdiffusion are still unresolved. We investigate the impact of non-Markovian friction and the free energy landscape on the dynamics of fast-folding proteins in terms of the mean squared displacement (MSD) and the mean first-passage-time (MFPT) of the folding reaction coordinate. We find the friction memory kernel from published molecular dynamics (MD) simulations to be well-described by a hierarchical multi-exponential function, which gives rise to subdiffusion in the MSD over a finite range of time. We show that friction memory effects in fast-folding proteins dominate the scaling behavior of the MSD compared to effects due to the folding free energy landscape. As a consequence, Markovian models are insufficient for capturing the folding dynamics, as quantified by the MSD and the MFPT, even when including coordinate-dependent friction. Our results demonstrate the importance of memory effects in protein folding and conformational dynamics and explicitly show that subdiffusion in fast-folding protein dynamics originates from memory effects, not from the free energy landscape and not from coordinate-dependent friction. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2506_18823 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Hierarchical friction memory leads to subdiffusive configurational dynamics of fast-folding proteins Klimek, Anton Dalton, Benjamin A. Tepper, Lucas Netz, Roland R. Soft Condensed Matter Biological Physics Proteins often exhibit subdiffusive configurational dynamics. The origins of this subdiffusion are still unresolved. We investigate the impact of non-Markovian friction and the free energy landscape on the dynamics of fast-folding proteins in terms of the mean squared displacement (MSD) and the mean first-passage-time (MFPT) of the folding reaction coordinate. We find the friction memory kernel from published molecular dynamics (MD) simulations to be well-described by a hierarchical multi-exponential function, which gives rise to subdiffusion in the MSD over a finite range of time. We show that friction memory effects in fast-folding proteins dominate the scaling behavior of the MSD compared to effects due to the folding free energy landscape. As a consequence, Markovian models are insufficient for capturing the folding dynamics, as quantified by the MSD and the MFPT, even when including coordinate-dependent friction. Our results demonstrate the importance of memory effects in protein folding and conformational dynamics and explicitly show that subdiffusion in fast-folding protein dynamics originates from memory effects, not from the free energy landscape and not from coordinate-dependent friction. |
| title | Hierarchical friction memory leads to subdiffusive configurational dynamics of fast-folding proteins |
| topic | Soft Condensed Matter Biological Physics |
| url | https://arxiv.org/abs/2506.18823 |