Development of anomalous diffusion among crowding proteins

Abstract

In cell membranes, proteins and lipids diffuse in a highly crowded and heterogeneous landscape, where aggregates and dense domains of proteins or lipids obstruct the path of diffusing molecules. In general, hindered motion gives rise to anomalous transport, though the nature of the onset of this behavior is still under debate and difficult to investigate experimentally. Here, we present a systematic study where proteins bound to supported lipid membranes diffuse freely in two dimensions, but are increasingly hindered by the presence of other like proteins. In our model system, the surface coverage of the protein avidin on the lipid bilayer is well controlled by varying the concentration of biotinylated lipid anchors. Using fluorescence correlation spectroscopy (FCS), we measure the time correlation function over long times and convert it to the mean-square displacement of the diffusing proteins. Our approach allows for high precision data and a clear distinction between anomalous and normal diffusion. It enables us to investigate the onset of anomalous diffusion, which takes place when the area coverage of membrane proteins increases beyond approximately 5%. This transition region exhibits pronounced spatial heterogeneities. Increasing the packing fraction further, transport becomes more and more anomalous, manifested in a decrease of the exponent of subdiffusion.Comment: accepted for publication in Soft Matte

Resolving the kinetics of lipid, protein and peptide diffusion in membranes

“…Molecular motion in these crowded membranes may therefore be restricted by the high protein content. Consistent with this theory, it has been demonstrated that D L decreases linearly with respect to increasing 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 (Ramadurai et al, 2009) and SLBs (Horton et al, 2010). Membrane-embedded proteins that interact with the cytoskeleton naturally display restricted lateral diffusion (Valentine and Haggie, 2011;Haggie et al, 2006).…”

Characterizing anomalous diffusion in crowded polymer solutions and gels over five decades in time with variable-lengthscale fluorescence correlation spectroscopy

“…To further explore the discrepancy in anomalous exponent uncovered between individual ACFs and the diffusion law, we used an ACF inversion method originally proposed by Shusterman et al 39,40 , and later put forward in the context of anomalous diffusion studies 29,41,45 . This method allows extracting a function directly from the ACF, MSD ACF (τ), which corresponds to the mean-squared displacement of the particles as long as their diffusion is governed by a Gaussian propagator (see section 2.1).…”

“…A second type of analysis was performed on the ACF obtained for the protein samples to test the nature of the diffusion, as suggested recently 29,41,45 . After normalization of the experimental ACFs in order to bring the amplitude of the diffusive part to 1, Eq.…”

Simulation of diffusion in a crowded environment

“…Thus, it can be treated as a representative, interesting and challenging problem. 15,16 Experimental studies concerning the motion of proteins and lipids in cells were performed using uorescence correlation spectroscopy, [17][18][19][20] pulsed eld gradient NMR 21 and single particle tracking (SPT). 6,7,[22][23][24][25][26][27] In many cases an anomalous diffusion was detected, i.e.…”