The main role of fractal-like nature of conformational space in subdiffusion in protein

Luca Maggi

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arXiv · 2306.07825

The main role of fractal-like nature of conformational space in subdiffusion in protein

Luca Maggi

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Abstract

Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties exhibited by this dynamic is its subdiffusivity, whose origins are still unknown. Here, by directly comparing all-atom molecular dynamics simulations and theory we show that this behavior mainly arises from the fractal nature of the network of metastable state of conformational state over which protein dynamics, thought as diffusion process, takes place. This process is assumed to be Markovian by the employed theoretical picture. Therefore, to further support its validity, we built a simple Markov state model starting from the simulations outcome and show that it exhibits a subdiffusive behavior, in quantitative agreement with the one associated to the molecular dynamics. Moreover, Molecular dynamics gives direct access to relevant quantities which allowed us to rule out the possibility the Continuous Time Random Walk can explain the protein subdiffusivity.

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Luca Maggi. 2023-06-13. The main role of fractal-like nature of conformational space in subdiffusion in protein. https://arxiv.org/abs/2306.07825

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