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Diffusion of intrinsically disordered proteins within viscoelastic membraneless droplets

Fuga Watanabe, Takuma Akimoto, Robert B. Best, Kresten Lindorff-Larsen, Ralf Metzler, Eiji Yamamoto

TL;DR

The conformation and the instantaneous diffusivity of the proteins significantly vary between the interior and the interface of the droplet, resulting in non-Gaussianity in the displacement distributions.

Abstract

In living cells, intrinsically disordered proteins (IDPs), such as FUS and DDX4, undergo phase separation, forming biomolecular condensates. Using molecular dynamics simulations, we investigate their behavior in their respective homogenous droplets. We find that the proteins exhibit transient subdiffusion due to the viscoelastic nature and confinement effects in the droplets. The conformation and the instantaneous diffusivity of the proteins significantly vary between the interior and the interface of the droplet, resulting in non-Gaussianity in the displacement distributions. This study highlights key aspects of IDP behavior in biomolecular condensates.

Diffusion of intrinsically disordered proteins within viscoelastic membraneless droplets

TL;DR

The conformation and the instantaneous diffusivity of the proteins significantly vary between the interior and the interface of the droplet, resulting in non-Gaussianity in the displacement distributions.

Abstract

In living cells, intrinsically disordered proteins (IDPs), such as FUS and DDX4, undergo phase separation, forming biomolecular condensates. Using molecular dynamics simulations, we investigate their behavior in their respective homogenous droplets. We find that the proteins exhibit transient subdiffusion due to the viscoelastic nature and confinement effects in the droplets. The conformation and the instantaneous diffusivity of the proteins significantly vary between the interior and the interface of the droplet, resulting in non-Gaussianity in the displacement distributions. This study highlights key aspects of IDP behavior in biomolecular condensates.
Paper Structure (1 section, 4 equations, 4 figures)

This paper contains 1 section, 4 equations, 4 figures.

Table of Contents

  1. Acknowledgments

Figures (4)

  • Figure 1: Diffusion of FUS-LCD within a droplet. (A) The snapshot of the droplet, with a radius of approximately $20 \, \mathrm{nm}$, formed by 1,000 molecules of FUS-LCD. Each color in the snapshot represents a different protein. (B) Relative $x$-coordinate of a protein with respect to the droplet's COM. (C) The TAMSDs for the FUS-LCD proteins within the droplet, where different colors represent different proteins.
  • Figure 2: Anticorrelated motion at short times and non-Gaussianity of protein movements within droplets. (A) Normalized DAF of the protein with different lag time $\Delta$. The inset shows the log-log plot for $\Delta = 10^{-4} \, \mathrm{\mu s}$. The black line indicates the theory of FBM. (B) The propagators as a function of the normalized position, defined by $x / \sigma \equiv \chi$, for different lag time $\Delta$, where $\sigma$ is the standard deviation corresponding to each $\Delta$. The black dashed line represents a Gaussian distribution with unit variance.
  • Figure 3: RSD of TAMSDs. The black solid line is a $t^{-0.5}$ scaling, shown for reference.
  • Figure 4: The difference in conformation and diffusivity of proteins at the interior and interface of the droplet. (A) The normalized radial number density of proteins within the droplet. The red and blue regions correspond to the interior and the interface of the droplet, respectively. (B) The PDF of residence times for proteins at the interior and the interface of the droplet. (C) The PDF of $R_g$ and (D) TDC.