Membrane Docking of the Synaptotagmin 7 C2A Domain: Computation Reveals Interplay between Electrostatic and Hydrophobic Contributions.
The C2A domain of synaptotagmin 7 (Syt7) is a Ca(2+) and membrane binding module that docks and inserts into cellular membranes in response to elevated intracellular Ca(2+) concentrations. Like other C2 domains, Syt7 C2A binds Ca(2+) and membranes primarily through three loop regions; however, it docks at Ca(2+) 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 Ca(2+) ions in aqueous solution, consistent with prior experimental reports. Upon membrane docking, the outermost Ca(2+) ion interacts directly with lipid headgroups, while the other two Ca(2+) 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° between a more parallel and a more perpendicular orientation, both during and after insertion of the Ca(2+) 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 ( DOI: 10.1021/acs.biochem.5b00421 ). In particular, the strictly conserved residue Phe229 inserted stably ∼4 Å 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.
Department of Chemistry, University of Colorado Denver , Denver, Colorado 80217-3364, United States.
Nara Lee
NL
Chon
Department of Chemistry, University of Colorado Denver , Denver, Colorado 80217-3364, United States.
J Ryan
JR
Osterberg
Department of Chemistry, University of Colorado Denver , Denver, Colorado 80217-3364, United States.
Jack
J
Henderson
Department of Molecular Biology, University of Bergen , 5008 Bergen, Norway.|Computational Biology Unit, Department of Informatics, University of Bergen , 5008 Bergen, Norway.
Hanif M
HM
Khan
Department of Molecular Biology, University of Bergen , 5008 Bergen, Norway.|Computational Biology Unit, Department of Informatics, University of Bergen , 5008 Bergen, Norway.
Nathalie
N
Reuter
Department of Chemistry, University of Colorado Denver , Denver, Colorado 80217-3364, United States.
Jefferson D
JD
Knight
Department of Chemistry, University of Colorado Denver , Denver, Colorado 80217-3364, United States.
Hai
H
Lin
D002118:Calcium / Q000737:chemistry; D057927:Hydrophobic and Hydrophilic Interactions; D008051:Lipid Bilayers / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D055672:Static Electricity; D050857:Synaptotagmins / Q000737:chemistry*
D008051:Lipid Bilayers; D050857:Synaptotagmins; D002118:Calcium