Lipid regulated conformational dynamics of the longin SNARE protein Ykt6 revealed by molecular dynamics simulations

The conformation and subcellular localization of R-SNARE protein Ykt6 are regulated by the lipidation state of its C-terminal CCAIM motif. Biochemical and crystallography studies showed that lipid molecules binding at a hydrophobic pocket at the interface between the longin domain and the SNARE core can lock Ykt6 at a closed conformation and mimic the farnesylated state of Ykt6. In this study, we performed in silico farnesylation of Ykt6 and explored the conformational dynamics of Ykt6 using conventional and steered MD simulations. We found that the farnesylated Ykt6 model structure is stable during the 2 μs simulation and the farnesyl group adopts conformations similar to those of the DPC molecule bound to Ykt6. Both DPC binding and farnesylation were found to reduce the conformational flexibility of Ykt6 and hinder the dissociation of SNARE core from the longin domain. The dissociation of the αF-αG segment is the rate-limiting step during the putative closed-to-open conformational transition of Ykt6, and the key residues involved in this process are consistent with the experimental mutagenesis study.