2025/01/15 by Luca Maggi, Maggi, Luca
Biochemistry, Genetics and Molecular Biology · Chemistry · Physics and Astronomy · #Protein Structure and Dynamics #Molecular spectroscopy and chirality #Spectroscopy and Quantum Chemical Studies
paper · pdf · doi:10.48550/arxiv.2501.08754
The study of microscopic protein dynamics has historically presented significant challenges to researchers seeking to develop a comprehensive and detailed description of its diverse and intriguing features. Recent experimental and theoretical studies have proposed the hypothesis that protein dynamics may be non-ergodic. The implications of this finding are of paramount importance from both a practical and theoretical standpoint. In this study, we employ all-atom molecular dynamics simulations to examine these results over a time window spanning from picoseconds to nanoseconds. To this end, we utilize widely used statistical tools. Our findings challenge the conclusions of previous studies, which suggested that proteins exhibit non-ergodic dynamics. Instead, we demonstrate that deviations from ergodic behavior are due to incomplete convergence of the investigated quantities. Additionally, we discuss the implications of findings that suggest a potential breaking of the ergodic hypothesis over larger time windows, which were not directly investigated in this study.