2023/06/13 by Luca Maggi, Maggi, Luca
Biochemistry, Genetics and Molecular Biology · Chemistry · Physics and Astronomy · #Biological Physics (physics.bio-ph) #FOS: Physical sciences #Molecular spectroscopy and chirality #Protein Structure and Dynamics #Soft Condensed Matter (cond-mat.soft) #Spectroscopy and Quantum Chemical Studies
paper · pdf · doi:10.48550/arxiv.2306.07825
openalex publication_date 2023/06/13 · openalex created_date 2023/06/15 · openalex updated_date 2026/07/28
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.