Volume 85, Issue 2, Pages (August 2003)

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Volume 85, Issue 2, Pages 864-875 (August 2003) A Computer Simulation Study of the Hydrated Proton in a Synthetic Proton Channel Yujie Wu, Gregory A. Voth Biophysical Journal Volume 85, Issue 2, Pages 864-875 (August 2003) DOI: 10.1016/S0006-3495(03)74526-3 Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 1 The structures of the composite and reduced LS2 systems. (A) A snapshot of the composite system. The water molecules are displayed in space-fill mode, whereas lipid molecules are shown in stick mode between the two water layers. The protein embedded in the lipid bilayer is represented by its backbone shown in tube mode. (B) A snapshot of the reduced system. The water molecules are displayed in space-fill mode, whereas the protein, which surrounds a thin water column, is shown in stick mode, with its backbone emphasized by thicker sticks. Lipid molecules are not included in the reduced system. Biophysical Journal 2003 85, 864-875DOI: (10.1016/S0006-3495(03)74526-3) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 2 The evolution of the box size (A) and the total potential energy (B) of the simulation of the composite system. Biophysical Journal 2003 85, 864-875DOI: (10.1016/S0006-3495(03)74526-3) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 3 The structural change of the LS2 channel during the simulation of the composite system. (A) The RMSD of the backbone atoms. (B) The distances between each pair of the COMs of the α-helices. (C) The cross angles between two neighboring α-helices. (D) The tilt angles of the helices with respect to the membrane normal. Biophysical Journal 2003 85, 864-875DOI: (10.1016/S0006-3495(03)74526-3) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 4 The change of the number of pore water molecules during the simulation of the composite system. Biophysical Journal 2003 85, 864-875DOI: (10.1016/S0006-3495(03)74526-3) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 5 Comparisons between the composite and reduced systems. (A) The RMSF of the backbone atoms. (B) The pore radii as functions of the channel axis (see text for details). (C) The spatial distribution of the oxygen atoms of the Ser side chains along the z-axis. (D) The functions of the mean squared displacement in the z-direction for pore water molecules. (E) The dipole orientational correlation functions for pore water molecules. Biophysical Journal 2003 85, 864-875DOI: (10.1016/S0006-3495(03)74526-3) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 6 The probability distributions of c12 when the CEC is restrained to different points on the channel axis. A is for different narrow channel regions; B is for different wide channel regions. See text for details. Biophysical Journal 2003 85, 864-875DOI: (10.1016/S0006-3495(03)74526-3) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 7 The free energies of c12 when the CEC is restrained to different points on the channel axis. A is for different narrow channel regions; B is for different wide channel regions. See text for details. Biophysical Journal 2003 85, 864-875DOI: (10.1016/S0006-3495(03)74526-3) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 8 The relative free energy difference between the Zundel and Eigen hydration structures when the CEC is restrained to different points on the channel axis. The pore radius profile for the reduced system with a hydronium in the channel is also shown. Biophysical Journal 2003 85, 864-875DOI: (10.1016/S0006-3495(03)74526-3) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 9 Simulation snapshots showing two representative hydration structures of the excess proton in the LS2 channel. The bulk water molecules are represented in space-fill mode, whereas pore waters are displayed in stick mode. The protein is represented by its backbone displayed in tube mode. The Ser side chains involved in the proton solvation structure are shown in ball-and-stick mode. The transferring hydrogen is shown as a small green ball. The dashed lines show the hydrogen bonds. (A) A stereo view of the snapshot taken from the simulation with the CEC restrained at −3.5Å at 884ps. (B) A stereo view of the snapshot taken from the simulation with the CEC restrained at 1.5Å at 808ps. Biophysical Journal 2003 85, 864-875DOI: (10.1016/S0006-3495(03)74526-3) Copyright © 2003 The Biophysical Society Terms and Conditions