$$\rightleftharpoonup{xx}$$
$$\longleftharp{xx}$$,
$$\longrightharp{xx}$$,
In eukaryotic cells, the dynamin superfamily proteins mediate the remodeling of biological membranes, including membrane tubulation, fission, and fusion1,2,3. Mutations in these proteins lead to a variety of human diseases, such as neurodegenerative diseases. The members of the dynamin superfamily typically contain a GTPase domain, a middle domain consisting of helical bundles, a motif for membrane binding, and a GTPase effector domain (GED). One such dynamin-like GTPase is atlastin (ATL), which catalyzes homotypic membrane fusion of the endoplasmic reticulum (ER) to form a network4,5,6,7,8,9,10. There are three ATLs (ATL1-3) in mammals. The ATL molecule consists of an N-terminal cytosolic region (ATLcyto), including a GTPase domain and a three-helical middle domain (3HB), followed by two transmembrane regions, but lacks the typical GED. Alternatively, ATL contains a C-terminal tail that plays a crucial role in membrane fusion11,12,13.
Efficient membrane fusion has been reported to rely on the GTP hydrolysis-dependent domain rearrangement in ATLcyto14,15,16,17,18,19,20. However, compared to the SNARE complex, which uses folding energy from conformational changes to drive heterotypic membrane fusion21, the homotypic membrane fusion process mediated by ATL and other fusion-specific dynamin-like proteins22 remains elusive. Three crystal structures of human ATL1cyto have been determined in different nucleotide-loading conditions14,15,16,23. In the structures, the two 3HBs in the dimer point in different directions, but a comprehensive model explaining how the conformational dynamics of ATLcyto and its GTPase activity are coupled is still missing.
In the previous model, the monomeric ATL molecules form dimers across different membranes in a GTP-dependent manner to drive membrane fusion. Here, three strategies are described to apply single-molecule Förster resonance energy transfer (smFRET) to directly observe and accurately detect the behavior of individual ATL1cyto molecules. smFRET is a powerful technique extensively utilized to investigate conformational dynamics and interactions of individual biomolecules in real-time, such as GPCR-mediated β-arrestin activation24, chromatin remodeling by Snf225, and domain rearrangements of dynamin-like protein MxA coupled with GTP hydrolysis cycles26. Since smFRET can only effectively detect changes in distance from ~3 nm to ~8 nm, both intermolecular and intramolecular smFRET experiments are required to comprehensively analyze the conformations of ATL1cyto for each nucleotide-loading state. We generated three constructs of ATL1cyto with all native cysteines substituted with alanines and K400 (ATL1cyto-K) or the T51/K400 pair (ATL1cyto-TK) mutated to cysteine for fluorophore labeling. The strategies for immobilizing the ATL1cyto dimer or monomer in a streptavidin-coated microfluidic chamber (Figure 1A) for intermolecular or intramolecular smFRET experiments are shown in Figure 1B-D. This method provides more details on the conformational dynamics of dynamin-like proteins in each step of GTP hydrolysis27.