Paper Citing NAMD - Abstract
Chon, Nara Lee; Osterberg, J. Ryan; Henderson, Jack; Khan, Hanif M.; Reuter, Nathalie; Knight, Jefferson D.; Lin, Hai
Membrane Docking of the Synaptotagmin 7 C2A Domain: Computation Reveals Interplay between Electrostatic and Hydrophobic Contributions
BIOCHEMISTRY, 54:5696-5711, SEP 22 2015
The C2A domain of synaptotagmin 7 (Syt7) is a Ca2+ and membrane binding module that docks and inserts into cellular membranes in response to elevated intracellular Ca2+ concentrations. Like other C2 domains, Syt7 C2A binds Ca2+ and membranes primarily through three loop regions; however, it docks at Ca2+ concentrations much lower than those required for other Syt C2A domains. To probe structural components of its unusually strong membrane docking, we conducted atomistic molecular dynamics simulations of Syt7 C2A under three conditions: in aqueous solution, in the proximity of a lipid bilayer membrane, and embedded in the membrane. The simulations of membrane-free protein indicate that Syt7 C2A likely binds three Ca2+ ions in aqueous solution, consistent with prior experimental reports. Upon membrane docking, the outermost Ca2+ ion interacts directly with lipid headgroups, while the other two Ca2+ ions remain chelated by the protein. The membrane-bound domain was observed to exhibit large-amplitude swinging motions relative to the membrane surface, varying by up to 70 degrees between a more parallel and a more perpendicular orientation, both during and after insertion of the Ca2+ binding loops into the membrane. The computed orientation of the membrane-bound protein correlates well with experimental electron paramagnetic resonance measurements presented in the preceding paper (DOT: 10.1021/acs.biochem.5b00421). In particular, the strictly conserved residue Phe229 inserted stably similar to 4 angstrom below the average depth of lipid phosphate groups, providing critical hydrophobic interactions anchoring the domain in the membrane. Overall, the position and orientation of Syt7 C2A with respect to the membrane are consistent with experiments.
