Research ArticleBIOPHYSICS

Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity

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Science Advances  20 Jan 2017:
Vol. 3, no. 1, e1601871
DOI: 10.1126/sciadv.1601871
  • Fig. 1 The TAMSDs of 97 trajectories of the PH domain on the membrane surface.

    The measurement time for each trajectory t is 8 μs. The black solid lines are shown for reference.

  • Fig. 2 Anticorrelated motion and non-Gaussianity of the PH domain diffusing on the membrane surface.

    (A) Normalized DAF CΔ(t)/CΔ(0) of the protein for Δ = 0.1 ns (black) and 2 ns (yellow). The inset shows the log-log plot. The solid and dashed cyan lines indicate the theory of FBM. (B) The propagator as a function of the normalized position, defined by Embedded Image, where the SDs σ are 0.1, 0.6, and 5.4 nm for Δ = 10−4, 10−2, and 1 μs, respectively. Each different symbol represents a different lag time Δ. The dashed line is a Gaussian distribution with unit variance. The propagators deviate from Gaussianity for x > 4σ.

  • Fig. 3 Temporally heterogeneous diffusion process of the PH domain.

    (A) Snapshots of the PH domain in a many-PIP–bound state (upper) and a few-PIP–bound state (lower). The PH domain, lipid bilayer, and bound PIP are colored yellow, silver, and cyan/red, respectively. (B) Time series of the short-time diffusivity estimated by our method and the time-averaged number of bound PIPs corresponding to the diffusive state. (C) Correlation between the short-time diffusion coefficient and number of bound PIPs in each state. (D) Lateral trajectory of a PH domain on the membrane surface. Colors of the trajectory correspond to each state in (B). The black triangles indicate the start and end points.

  • Fig. 4 RSD of TAMSDs of the protein (denoted by “• ”).

    The red solid line represents the RSD of TAMSDs of the LEFD model with γ = 0.6, τc = 10 μs, DF = 17 μm2/s, and DS = 14 μm2/s. The black solid line is shown for reference.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/3/1/e1601871/DC1

    fig. S1. Distance between the COM of the protein and the bilayer for the 100 repeat simulations.

    fig. S2. Ergodicity of the diffusion process.

    fig. S3. Short-time diffusivity of the PH domain and number of bound PIP molecules.

    fig. S4. PDF of the diffusion coefficient calculated by Formula for Δ = 0.1 μs and t = 1 μs.

    fig. S5. PDFs of the residence times of many-PIP–bound and few-PIP–bound states.

    fig. S6. Stochastic simulation of the LEFD model.

    fig. S7. PIP molecules around the PH domain.

  • Supplementary Materials

    This PDF file includes:

    • fig. S1. Distance between the COM of the protein and the bilayer for the 100 repeat simulations.
    • fig. S2. Ergodicity of the diffusion process.
    • fig. S3. Short-time diffusivity of the PH domain and number of bound PIP molecules.
    • fig. S4. PDF of the diffusion coefficient calculated by D = δ2 (Δ; t) / 2dΔ for Δ = 0.1 μs and t = 1 μs.
    • fig. S5. PDFs of the residence times of many-PIP–bound and few-PIP–bound states.
    • fig. S6. Stochastic simulation of the LEFD model.
    • fig. S7. PIP molecules around the PH domain.

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