Wednesday, January 19, 2011

Single Particle Tracking (SPT) in vivo: interpretation of trajectories

Using a single particle tracking approaches it is possible to approach diffusion trajectories with millisecond time resolution. Analyzing these and figuring out what exactly is happening in the cell is a rather complex undertaking. Here are two papers discussing analysis of particle diffusion in vivo:

1. van den Wildenberg et al. Biopolimers 2011 PIMD 21240922

Use of tensors for describing asymmetry of diffusion in the cell (i.e. along the long axis we have less confinement than along the short axis, thus mean square displacement (MSD) plateau is different). Modeling of different confinement geometries (tube, cube, sector) + adding repulsive or attractive potentials describing interactions between the particle and environment.

2. Hall and Hoshino Biophys Rev 2010 PIMD 21088688

Focuses on protein diffusion in the bacterial membrane, comparing experimental data for TatA diffusion with modeling. Again, confinement effects are discussed - SPT data are 2D projection of the 3D diffusion. They model random walk on the surface of bacterial cell was in the same way as Deich at al. PNAS 2004 PIMD 15522969.

Geometric constraints and 2D-to-3D projection affect MSD and CPD (cumulative probability distributions), but not enough to explain thir experimental data.

In order to account for the experimental deviations unexplainable by geometry effects they assume existence of slow and fast particles and add an estimate of the localization precision, and now they get a nice agreement with the experimental data. Roughly 50 / 50 slow and fast.

Effect of localization precision on SPT was earlier discussed in Martin et al. Biophys J. 2002 PIMD 12324428 story: "Apparent subdiffusion inherent to single particle tracking".

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