Figure 1.
Relative abundance of membrane protein subunits with different number of transmembrane (TM) helices.
The histograms are based on data for synaptic vesicles [21], and the outer membrane (OM) of the Gram-negative bacterium A. baumannii [33]. Proteins with no predicted TM domains were excluded.
Figure 2.
Excluded-area interactions and channel gating.
(A) Gating of a channel (red) crowded by a single crowder (gray) of radius in the constant area ensemble, where the total surface area is fixed by the outer walls (dashed). (B) In the constant tension ensemble with applied tension
, the total area increases as the channel opens, so that the total lipid area is conserved. For disk-shaped particles of finite size, the free area available for each center of mass is limited by the minimum distance between two centers of mass. This effect can be illustrated by exclusion zones of width
around each protein. In the constant tension ensemble, the reduced area for the crowders is due to larger exclusion zone in the open compare to the closed state. In the high density regime (C), the exclusion zones overlap, which complicates the analysis. We use scaled-particle theory to analyze this case.
Table 1.
Entropic surface and line tensions induced by crowders.
Table 2.
Estimated crowding effects on MscL gating.
Table 3.
List of symbols.
Figure 3.
The effect of crowding on the open probability as a function of applied tension
. The graphs illustrate the ideal gas (
) and scaled-particle theory (SPT,
) results of table 2, using the constant tension ensemble as is appropriate for MscL. All non-crowding contributions to the gating free energy are lumped together in the gating tension
.
Figure 4.
Mechanisms for different excluded area for proteins and lipids.
One difference between the hard disk model of membrane proteins (A), and more complex protein structures (B,C) might be thought of in terms of different effective radii and
for steric exclusion of surrounding proteins and lipids respectively. A protein (red) with a large domain outside of the bilayer (B) might exclude surrounding proteins, but not lipids, from approaching the transmembrane domain (dark red). Similarly, proteins with different hydrophobic thickness than the surrounding bilayer (C) generate a local zone of deformed lipid bilayer (gray) that effectively excludes other well-matched proteins. Horizontal lines indicate the surrounding lipid bilayer.