Paper Citing NAMD - Abstract
Tekpinar, Mustafa; Zheng, Wenjun
Unzipping of neuronal snare protein with steered molecular dynamics occurs in three steps
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2381, AUG 2014
Soluble NSF-attachment protein receptors (SNAREs) play a crucial role in membrane fusion. Neuronal SNAREs, a four-helix bundle, help synaptic vesicles fuse with plasma membranes. We applied constant velocity pulling forces in silico to C terminal of synaptobrevin, one of the helices in the bundle, to understand unzipping mechanism of neuronal SNAREs. We observed unzipping of snaptobrevin from the other helices in three steps: linker domain unzipping, C terminal unzipping and N terminal unzipping. Our results have good qualitative agreement with a recent optical tweezer experiment that observes this stepwise unzipping. Since we performed 14 different simulations for two large spring force constants, our results are robust and they reveal atomistic details of these distinct unzipping steps.
