The pMMO is a microbial membrane-bound enzyme present in methanotrophs, capable of oxidizing methane into methanol. One of the major obstacles in experimental characterization of pMMO is its activity dependence on the native membrane environment. The mechanisms behind this dependence are poorly understood. Recent cryo-EM structures reveal significant lipid densities in both the central pore and the surrounding periphery of the protein, suggesting lipid interactions stabilize not only the trimeric architecture but also conserved regions proximal to the active site that were disordered in previous crystal structures. However, the exact identity of these lipids is unknown, and they are difficult to identify via standard experimental procedures. We have employed a multiscale computational approach to investigate the pMMO-membrane system, combining coarse-grained and all-atom molecular dynamics (MD) simulations with the LipIDens pipeline. The analysis of the pMMO-lipid interface in a native-like membrane environment reveals that cardiolipin (CDL), a unique anionic phospholipid with four acyl chains and a double-phosphate headgroup, is the most dominant non-annular lipid. CDL occupies specific, high-affinity binding sites within the protein's pore and periphery, including protomer interface regions, suggesting a crucial role in structural stabilization. These interactions are complemented by significant interactions of POPE, POPG, DPPE, and DPPG, highlighting the role of a complex lipid milieu supporting pMMO’s structural stability and activity. These findings can potentially guide the rational design of biomimetic membranes for the efficient capture and conversion of near-ambient methane.
Rao et al. (Sun,) studied this question.