Simulations of a protein translocation pore: SecY.
SecY is the central channel protein of the SecYEbeta translocon, the structure of which has been determined by X-ray diffraction. Extended (15 ns) MD simulations of the isolated SecY protein in a phospholipid bilayer have been performed to explore the relationship between protein flexibility and the mechanisms of channel gating. In particular, principal components analysis of the simulation trajectory has been used to probe the intrinsic flexibility of the isolated SecY protein in the absence of the gamma-subunit (SecE) clamp. Analysis and visualization of the principal eigenvectors support a "plug and clamshell" model of SecY channel gating. The simulation results also indicate that hydrophobic gating at the central pore ring prevents leakage of water and ions through the channel in the absence of a translocating peptide.