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Center for Nonlinear Studies |
Internal structural motions in proteins are essential to their functions. Early models considered these as simple Brownian motions in the overdamped limit. However, experimental and simulation data from past decades have shown that the protein internal dynamics exhibit clearly non-exponential relaxation and subdiffusive behavior. In this talk, data obtained from an extensive set of molecular dynamics simulations of three very different globular proteins are presented. The results demonstrate that the structural fluctuations observed are highly complex, manifesting in non-ergodic and self-similar subdiffusive dynamics. The characteristic time of the motion observed at a given timescale is dependent on the length of the observation time, indicating an aging effect. By comparing the simulation results to the existing single-molecule fluorescence spectroscopic data on other globular proteins, we found the characteristic relaxation time for a distance fluctuation within the protein, such as inter-domain or inter-residue motions, increase with the length of the observation time in a simple power-law that appears to be universal and protein-independent, spanning over enormous 13 decades in timescales ranging from picoseconds up to hundreds of seconds. The dynamics observed is best described by a subdiffusive continuous time random walk model, which describes a non-ergodic stochastic process, fully consistent with the observed aging behavior. The present results suggest that the structural dynamics of single protein molecules is likely to remain non-ergodic and out of equilibrium on most timescales over which protein functions occur, eventually persists up to typical lifespan of proteins in vivo. Potential origins and implications of the non-ergodic protein dynamics are discussed.
Host: Gnana Gnanakaran