Molecular mechanism underlying SNARE-mediated membrane fusion enlightened by all-atom molecular dynamics simulations

The SNARE proteins syntaxin-1, SNAP-25 and synaptobrevin mediate
neurotransmitter release by forming tight SNARE complexes that fuse
synaptic vesicles with the plasma membranes in microseconds. Membrane
fusion is generally explained by the action of proteins on macroscopic
membrane properties such as curvature, elastic modulus and tension, and a
widespread model envisions that the SNARE motifs, juxtamembrane linkers
and C-terminal transmembrane regions of synaptobrevin and syntaxin-1 form
continuous helices that act mechanically as semi-rigid rods, squeezing the
membranes together as they assemble (‘zipper’) from the N- to the
C-termini. However, the mechanism underlying fast SNARE-induced membrane
fusion remains unknown. We have used all-atom molecular dynamics
simulations to investigate this mechanism. Our results need to be
interpreted with caution because of the limited number and length of the
simulations, but they suggest a model of membrane fusion that has a
natural physicochemical basis, emphasizes local molecular events over
general membrane properties, and explains extensive experimental data. In
this model, the central event that initiates fast (microsecond scale)
membrane fusion occurs when the SNARE helices zipper into the
juxtamembrane linkers which, together with the adjacent transmembrane
regions, promote encounters of acyl chains from both bilayers at the polar
interface. The resulting hydrophobic nucleus rapidly expands into
stalk-like structures that gradually progress to form a fusion pore, aided
by the SNARE transmembrane regions and without clearly discernible
intermediates. The propensity of polyunsaturated lipids to participate in
encounters that initiate fusion suggests that these lipids may be
important for the high speed of neurotransmitter release.

突触融合蛋白-1（syntaxin-1）、SNAP-25与突触泡蛋白（synaptobrevin）这三类SNARE蛋白（SNARE proteins）可通过形成紧密的SNARE复合物，在微秒级时间内介导突触囊泡与质膜的融合，进而实现神经递质释放。目前膜融合的主流机制阐释多围绕蛋白质对宏观膜特性（如曲率、弹性模量与张力）的调控作用展开，其中被广泛接受的模型认为，突触泡蛋白与突触融合蛋白-1的SNARE基序（SNARE motifs）、膜近端连接区（juxtamembrane linkers）以及C端跨膜结构域会组装形成连续螺旋，在力学上充当半刚性杆，通过从N端到C端的“拉链”过程将双层膜相互拉近并挤压。然而，SNARE蛋白诱导快速膜融合的具体分子机制至今仍未明确。
本研究采用全原子分子动力学模拟（all-atom molecular dynamics simulations）对该机制进行了探究。由于本次模拟的数量与时长均存在局限，研究结果需谨慎解读，但结果提示了一个具备天然物理化学基础的膜融合模型：该模型更侧重局部分子事件而非一般膜的宏观特性，且可解释大量已发表的实验数据。在该模型中，启动快速（微秒级）膜融合的核心事件为：SNARE螺旋拉链至膜近端连接区，后者与相邻的跨膜结构域共同促进双层膜的酰基链在极性界面处发生接触。由此形成的疏水核会迅速扩张为茎状结构，随后在SNARE跨膜结构域的辅助下逐步演化形成融合孔，且整个过程未出现清晰可辨识的中间态。多不饱和脂质参与启动融合的接触过程的特性提示，这类脂质可能对神经递质释放的高速性具有关键作用。