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Pleckstrin homology (PH) domains are lipid-binding modules present in peripheral membrane proteins which interact with phosphatidyl-inositol phosphates (PIPs) in cell membranes. We use multiscale molecular dynamics simulations to characterize the localization and anomalous dynamics of the DAPP1 PH domain on the surface of a PIP-containing lipid bilayer. Both translational and rotational diffusion of the PH domain on the lipid membrane surface exhibit transient subdiffusion, with an exponent α ≈ 0.5 for times of less than 10 ns. In addition to a PIP3 molecule at the canonical binding site of the PH domain, we observe additional PIP molecules in contact with the protein. Fluctuations in the number of PIPs associated with the PH domain exhibit 1/f noise. We suggest that the anomalous diffusion and long-term correlated interaction of the PH domain with the membrane may contribute to an enhanced probability of encounter with target complexes on cell membrane surfaces.

Original publication

DOI

10.1038/srep18245

Type

Journal article

Journal

Sci Rep

Publication Date

14/12/2015

Volume

5

Keywords

Algorithms, Cell Membrane, Lipid Bilayers, Lipid-Linked Proteins, Models, Molecular, Molecular Conformation, Molecular Dynamics Simulation, Phosphatidylinositol Phosphates, Protein Interaction Domains and Motifs