Recent breakthroughs in protein structure prediction, coupled with continuous progresses in data-intensive experimental characterization of protein complexes (cryo-electron microscopy, mass spectrometry,…) has allowed to investigate large macromolecular protein assemblies with unprecedented accuracy down to the atomistic scale. This conjuncture has opened up incredible possibilities to study the mechanistic details of important cellular machineries with extreme molecular resolution.
However, one open challenge of structural methods is to characterize the presence of protein-bound cofactors, and especially when they bind with low affinity or when they lack a well-defined specific binding site. This is particularly true for non-structural lipid molecules in membrane proteins, as these molecules are often characterized by a dynamical behavior that is hard to characterize with structural approaches.

To this end, we have recently developed new computational assays based on molecular simulations and combined them with various experimental approaches (in situ cryo-ET, fluorescence microscopy, in vitro and in vivo functional assays) to investigate how molecular interactions between proteins and lipids modulate cellular processes. In this contribution, I will show how these developments have allowed us to gain unprecedented molecular insights into key membrane-mediated mechanism, including lipid transport at membrane contact sites, nuclear pore complex formation and intracellular fat accumulation.