Molecular Dynamics Simulations of Synaptotagmin Binding to Lipid Bilayers

Abstract

Synaptotagmin 1 (Syt1) is a protein associated with synaptic vesicles that serves as a neuronal calcium sensor. In response to an action potential, calcium ions inflow into the nerve terminal, bind Syt1, and trigger fusion of vesicles with the plasma membrane. Although the structure, dynamics, and calcium binding properties of Sy1 have been extensively studied, it is still debated how specifically Syt1 triggers fusion. Syt1 includes a transmembrane region and two cytosolic domains, C2A and C2B, connected by a flexible linker. Both domains have calcium binding loops, and calcium binding is thought to promote the insertion of domain tips into lipid bilayers. To elucidate this mechanism, we performed molecular dynamics (MD) simulations of calcium free and calcium bound forms of Syt1 in water/ion environment and took advantage of periodic boundary conditions to model the dynamics of Syt between bilayer bilayers. We found that calcium binding loops of C2A domain have strong affinity to lipids even in the absence of calcium, and calcium biding strongly promotes their penetration into bilayers. In contrast, C2B binding loops did not interact with lipids in the absence of calcium, and even upon calcium binding only a week interaction of C2B calcium binding loops with lipids was observed. Apparently, this interaction may depend upon lipid composition and may require specific lipids which were not included in our simulations. Calcium binding pockets of C2 domains had a strong preference for facing opposing membranes during the entire length of the simulation. These results suggest a scenario whereby the tip of Syt1 C2A domain preferentially interacts with the vesicle membrane and immerges into lipids upon calcium binding, while C2B domain interacts with the plasma membrane, possibly being anchored by membrane-specific lipids, such as PIP2.