LC3B-a has a different C-terminal tail conformation and less compact overall structure in solution. A. The initial protein-water system for MD simulation (upper panel) and the homology-modeling structures of LC3B (green) and LC3B-a (orange) for MD simulations (lower panel). Only the backbones are illustrated by cartoon model. B. Superimposition of the simulation snapshots of LC3B or LC3B-a backbone at time t = 3 ns (green), 5ns (blue), 7 ns (yellow), 9 ns (magenta), 11 ns (orange), and 13 ns (cyan). C. The salt bridge between D48 and R70 and the hydrophobic cluster of L44, P45, L47, L71, L73, F79 and Y113 of LC3B are shown. No salt bridge is formed by D48 and R69 of LC3B-a and a weaker hydrophobic contact of L44, F78 and Y112 is presented in LC3B-a. The hydrophobic residues in the C-terminus of LC3B-a are shown as sticks. D. Space-filling model of the simulation snapshot of LC3B and LC3B-a at time t = 13 ns. The figures were generated using the program PyMOL. C’: the C-terminus. E. Far-UV CD spectra of LC3B and LC3B-a in the temperature range of 25°C ~ 75°C. F. Time-dependent trypsin digestion patterns of LC3B and LC3B-a. Small fragments were shown by arrows. Molecular weights (kDa) were shown in the left lane “M”.
Liu et al. BMC Cell Biology 2013 14:27 doi:10.1186/1471-2121-14-27