Table 1.
Non-extensive list of tools usable for atomic/macromolecular-level study of MCSs.
| Technique | Usage | Reference |
|---|---|---|
| In silico | ||
| Hypermatrix | Energy-based calculation of lipid-ligand interactions and 3D arrangements | Deleu et al., 2014; Cacas et al., 2016 |
| IMPALA | Energy-based prediction of the insertion of molecules in lipid bilayers | Basyn et al., 2001; Lins et al., 2001; Cacas et al., 2016 |
| Molecular dynamics | Atomic and coarse grained simulations to study the behavior over time of lipids bilayers and proteins | Deleu et al., 2014; Yamamoto et al., 2016; Duncan et al., 2017; Gronnier et al., 2017 |
| In vitro | ||
| PIP Strips | Determination of protein ability to interact with specific anionic lipids | Pérez-Sancho et al., 2016 |
| Liposome flottation/sedimentation assays | Determination of protein ability to interact with a lipid bilayer | Schapire et al., 2008; Pérez-Sancho et al., 2016; Meca et al., 2018 |
| Tubule formation by optical tweezers on liposome | Study of membrane curvature-induced sorting of proteins | Aimon et al., 2014; Prévost et al., 2015; Chen et al., 2016b |
| In vitro tethering to reconstitute simplified MCS with isolated protein and controlled lipid and ion environment. | Characterization of the ability of a protein to tether two liposomes using dynamic light scattering and the inter-liposome distance by FRET. Visualize the tethering ultrastructure using cryo-electron microscopy | Mesmin et al., 2013; Lin et al., 2014; Diao et al., 2015 |
| Isothermal Titration Calorimetry (ITC) | Determination of the affinity constant and thermodynamics parameters for the interaction between proteins and liposomes. | Ghai et al., 2012 |
| Langmuir Trough | Determination of the kinetics of adsorption and affinity parameters of proteins for lipid monolayers | Eeman et al., 2006; Calvez et al., 2011; Gronnier et al., 2017 |
| Solid state NMR | Study lipid-protein interactions and the deformation of the lipid membrane caused by the interaction at atomic level | Huster, 2014; Gronnier et al., 2017 |
| In situ | ||
| (Cryo) electron tomography | Visualize MCS architecture at macromolecular scale | Collado and Fernández-Busnadiego, 2017; Nicolas et al., 2017 |