FRAP: Automatic Analysis of Protein Data

The simulation depicts a FRAP experiment in which protein fluorescence (the number of blue particles) within the   target circle is plotted automatically every 5 sec.  After 55 sec, an intense flash bleaches all fluorescence within the target, and the recovery of protein fluorescence is plotted periodically thereafter.  In this experiment the amount of fluorescently labeled protein has been increased to obtain statistically reasonable data (a good "signal-to-noise ratio"!) and the lipid is unlabeled (but represented by the pink background).

Note the asymptote of fluorescence recovery never reaches the original, pre-bleach steady-state level?  Why not?

Closer examination of the target indicates some bleached proteins vibrate but don't diffuse within the plane of the membrane while others do; the latter are gradually replaced by unbleached proteins as they diffuse out of the target circle.  Knowing this, you should be able to detect similar differences in all the membrane proteins in the entire field of view: some are free to diffuse while others appear tethered. What might be the cause of such heterogeneous protein organization?

In addition to integral protein, plasma membranes also contain peripheral protein that is linked with their outer and/or inner surfaces.  On th cytoplasmic surface, peripheral membrane components include cytoskeletal elements, enzymes and regulatory proteins, and in many cells a network of peripheral cytoskeletal proteins is anchored in numerous locations to integral proteins.  This network shapes the membrane (and help shape the cell it envelopes).  Not surprisingly, the integral membrane components of this cytoskeletal complex anchor (and are in turn anchored by) the fibrous cytoplasmic elements and thus exhibit very limited ability to diffuse.  To view this network in the simulation above, render the membrane transparent by pressing the "Matrix" button in the top panel.  (Pressing it again makes the membrane opaque.)