Abstract
The spatiotemporal organisation of membranes is often characterised by the formation of large protein clusters. In Escherichia coli, outer membrane protein (OMP) clustering leads to OMP islands, the formation of which underpins OMP turnover and drives organisation across the cell envelope. Modelling how OMP islands form in order to understand their origin and outer membrane behaviour has been confounded by the inherent difficulties of simulating large numbers of OMPs over meaningful timescales. Here, we overcome these problems by training a mesoscale model incorporating thousands of OMPs on coarse-grained molecular dynamics simulations. We achieve simulations over timescales that allow direct comparison to experimental data of OMP behaviour. We show that specific interaction surfaces between OMPs are key to the formation of OMP clusters, that OMP clusters present a mesh of moving barriers that confine newly inserted proteins within islands, and that mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs.
Highlights
The spatiotemporal organisation of membranes is often characterised by the formation of large protein clusters
Total LPS has been estimated by radio-labelling methods[26,27] while total outer membrane protein (OMP) composition has been estimated by proteomics[28]. These previous studies suggest that there are insufficient LPS molecules to encircle every OMP
OMPs at densities mimicking those found in the outer membrane (OM) of E. coli, and incorporated into polymer supported membranes (PSM) composed solely of PE:PG, display diffusion coefficients and levels of restriction almost identical to those observed for OMPs in E. coli[8]
Summary
The spatiotemporal organisation of membranes is often characterised by the formation of large protein clusters. E.g. high-speed AFM enables imaging of the dynamic organisation of OMPs in bacterial membranes in vitro[2], and stimulated emission depletion (STED) can reveal the nanoscale dynamics of lipids in the membranes of living cells[19] Taken together, these approaches provide descriptions of emergent complexities of the dynamic organisation of membranes at meso and micro scales. It is possible to undertake such simulations of membranes on length and timescales, which begin to approach those observed experimentally[22] whilst preserving aspects of the crowding and compositional complexity of cellular membranes[23] This provides an opportunity to use simulations to more fully understand the molecular basis of mesoscale membrane organisation. By successfully bridging the gap between molecular level simulations and experiments, we obtain a mechanistic molecular interpretation of single molecule tracking data, revealing how dynamic clustering of OMPs results in the formation of mesoscale OM islands, which modulate the diffusional mobility of OMPs
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