Structure, lipid scrambling activity and role in autophagosome formation of ATG9A.

De novo formation of the double-membrane compartment autophagosome is seeded by small vesicles carrying membrane protein autophagy-related 9 (ATG9), the function of which remains unknown. Here we find that ATG9A scrambles phospholipids of membranes in vitro. Cryo-EM structures of human ATG9A reveal a trimer with a solvated central pore, which is connected laterally to the cytosol through the cavity within each protomer. Similarities to ABC exporters suggest that ATG9A could be a transporter that uses the central pore to function. Moreover, molecular dynamics simulation suggests that the central pore opens laterally to accommodate lipid headgroups, thereby enabling lipids to flip. Mutations in the pore reduce scrambling activity and yield markedly smaller autophagosomes, indicating that lipid scrambling by ATG9A is essential for membrane expansion. We propose ATG9A acts as a membrane-embedded funnel to facilitate lipid flipping and to redistribute lipids added to the outer leaflet of ATG9 vesicles, thereby enabling growth into autophagosomes.

Adaptive Partitioning QM/MM for Molecular Dynamics Simulations: 6. Proton Transport through a Biological Channel.

Adaptive quantum-mechanics/molecular-mechanics (QM/MM) dynamics simulations feature on-the-fly reclassification of atoms as QM or MM continuously and smoothly as trajectories are propagated. This allows one to use small, mobile QM subsystems, the contents of which are dynamically updated as needed. In this work, we report the first adaptive QM/MM simulations of H+ transfer through a biological channel, in particular, the protein EcCLC, a chloride channel (CLC) Cl-/H+ antiporter derived from E. coli. To this end, the H+ indicator previously formulated for approximating the location of an excess H+ in bulk water was extended to include Cl- ions and carboxyl groups as H+ donors/acceptors. Furthermore, when setting up buffer groups, a new "sushi-roll" scheme was employed to group multiple water molecules, ions, and titratable residues along the one-dimensional channel for adaptive partitions. Our simulations reveal that the H+ relay path, which consists of water molecules in the pore, a bound Cl- ion at the central binding site (Cl-cen) of the protein, and the external gating residue E148, exhibits certain mobility within the channel. A two-stage journey of H+ migration was observed: the H+ moves toward Cl-cen and is then shared between Cl-cen and nearby water molecules in the first stage and departs from Cl-cen via nearly concerted transfer to protonate E148 in the second stage. Most of the simulated trajectories show the bound Cl- ion in the channel to be transiently protonated, a possibility that was previously suggested by experiments and computations. Comparisons with conventional QM/MM simulations revealed that both adaptive and conventional treatments yield similar qualitative pictures. This work demonstrates the feasibility of adaptive QM/MM in the simulations of H+ migration through biological channels.