Integral membrane proteins are localised and functionally regulated by lipids present in the surrounding bilayer. Whilst bacteria such as E. coli have a relatively simple membrane when compared to eukaryotic cells, there is ample evidence that multiple proteins bind, and have their function regulated by, specific lipid interactions. There are a number of ways of identifying protein-lipid interactions in membrane proteins, including through molecular simulation. Here, we highlight the capabilities of this technique by running lipid-binding simulations of 42 different E. coli inner membrane proteins. Our data reveals a strong cross-membrane asymmetry in the nature of protein-lipid interactions, with a marked increase of anionic lipid binding to the inner leaflet regions of membrane proteins. This appears to be driven by an increase in basic residues, suggesting a structural basis for the positive inside rule. We have identified ca. 700 independent cardiolipin binding sites from our data, allowing us dissect the molecular basis of a prototypical cardiolipin headgroup binding site. Applying free energy calculations quantifies the relative contributions of each residue type to cardiolipin binding. These findings demonstrate the potential for large-scale simulations to reveal pertinent underlying biological information applying to a number of systems, and paves the way for future analyses of more complex protein-lipid interactions.
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