Abstract
Coarse-grained molecular dynamics simulations of the E. coli outer membrane proteins FhuA, LamB, NanC, OmpA and OmpF in a POPE/POPG (3∶1) bilayer were performed to characterise the diffusive nature of each component of the membrane. At small observation times (<10 ns) particle vibrations dominate phospholipid diffusion elevating the calculated values from the longer time-scale bulk value (>50 ns) of 8.5×10−7 cm2 s−1. The phospholipid diffusion around each protein was found to vary based on distance from protein. An asymmetry in the diffusion of annular lipids in the inner and outer leaflets was observed and correlated with an asymmetry in charged residues in the vicinity of the inner and outer leaflet head-groups. Protein rotational and translational diffusion were also found to vary with observation time and were inversely correlated with the radius of gyration of the protein in the plane of the bilayer. As the concentration of protein within the bilayer was increased, the overall mobility of the membrane decreased reflected in reduced lipid diffusion coefficients for both lipid and protein components. The increase in protein concentration also resulted in a decrease in the anomalous diffusion exponent α of the lipid. Formation of extended clusters and networks of proteins led to compartmentalisation of lipids in extreme cases.
Highlights
Lipid–protein interactions play an important role in the function and organisation of membrane proteins, either through macroscopic bilayer properties or via individual protein–lipid interactions [1,2,3]
Biological membranes are selective barriers which control the entry/exit of molecules to/from the interior of a cell. They are composed of a lipid bilayer in which are embedded many membrane proteins
We use molecular dynamics computer simulations to quantify how mobility within the membrane decreases as the protein concentration increases
Summary
Lipid–protein interactions play an important role in the function and organisation of membrane proteins, either through macroscopic bilayer properties or via individual protein–lipid interactions [1,2,3]. E.g. those involved with the regulation of membrane composition or maintaining an asymmetric leaflet distribution, the necessity of such interactions is evident, whilst for others that depend on lateral pressure or local bilayer deformation for function the interaction may be more subtle [4]. Much discussion as to the nature of cluster formation has centred around the formation of lipid rafts in certain membranes [9], but it should be noted that lateral interactions of crowded membrane proteins are a more general property of cell membranes [10] and are of importance in e.g. bacterial [11,12] as well as mammalian cell membranes
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