Volume 74, Issue 1, Pages (January 1998)

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Presentation transcript:

Volume 74, Issue 1, Pages 115-131 (January 1998) Molecular Dynamics Simulations of Individual α-Helices of Bacteriorhodopsin in Dimyristoylphosphatidylcholine. II. Interaction Energy Analysis Thomas B. Woolf Biophysical Journal Volume 74, Issue 1, Pages 115-131 (January 1998) DOI: 10.1016/S0006-3495(98)77773-2 Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 1 Interaction energy distributions between individual DMPC molecules and the full helix for all 10 simulations. The curves are an estimate for the probability of finding a particular number of lipids surrounding the central helix with a particular interaction energy. They have been obtained by computing the interaction energy over the trajectory and binning and normalizing the resulting series of numbers. Biophysical Journal 1998 74, 115-131DOI: (10.1016/S0006-3495(98)77773-2) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 2 Contributions to the total interaction energy from vdW and electrostatic components. The x axis represents the full interaction energy, and the y axis is the value of the vdW or electrostatic interaction energy within the bins. Thus a total interaction energy of −50 kcal/mol might have −25 kcal/mol of electrostatic energy (shown as darker line) and −25 kcal/mol of vdW energy (shown as a thinner‘line). Confidence bars (80%) are computed from five subsets of the full trajectory. Biophysical Journal 1998 74, 115-131DOI: (10.1016/S0006-3495(98)77773-2) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 3 Individual residue interaction energies for all 10 simulations. The interaction energy between a particular amino acid and DMPC was calculated, binned, and normalized. The data points represent the mean value of the distribution, and the lines the rms deviations from the mean. Two y axes are used. The left-hand y axis refers to the filled circles for the noncharged interaction energies. The right-hand y axis refers to the open squares for the charged residue interactions. In each case the residue number is along the x axis. Biophysical Journal 1998 74, 115-131DOI: (10.1016/S0006-3495(98)77773-2) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 4 Individual residue interaction energies for nonpolar amino acids. The range of interaction energies observed for each amino acid is indicated as a function of relative position in the bilayer. The circles are the mean and the lines from the circles an indication of the rms deviation. The number of residues considered and the average over all residues is also shown. The left-hand column is for interactions with DMPC; the right-hand column is for interactions with water. Biophysical Journal 1998 74, 115-131DOI: (10.1016/S0006-3495(98)77773-2) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 5 A plot similar to that in Fig. 4, with the aromatic amino acids. Biophysical Journal 1998 74, 115-131DOI: (10.1016/S0006-3495(98)77773-2) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 6 A plot similar to that in Fig. 4, for the charged amino acids. Biophysical Journal 1998 74, 115-131DOI: (10.1016/S0006-3495(98)77773-2) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 7 A plot similar to that in Fig. 4, for the remaining amino acids. Biophysical Journal 1998 74, 115-131DOI: (10.1016/S0006-3495(98)77773-2) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 8 Illustration of the wedge-shaped selection of atoms for evaluating interactions between a cylindrical stripe and the environment. Biophysical Journal 1998 74, 115-131DOI: (10.1016/S0006-3495(98)77773-2) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 9 Helical stripes of vdW interaction energy determined by selecting atoms within a pie-shaped vertical stripe of each α-helix. The interaction energy between protein and DMPC was determined for all atoms within a region of 45°. The regions were rotated by 5° increments around the full helix. The contour plots were generated by considering the contribution of individual residues to the stripe's interaction. Biophysical Journal 1998 74, 115-131DOI: (10.1016/S0006-3495(98)77773-2) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 10 Similar to Fig. 9, for electostatic interactions. Biophysical Journal 1998 74, 115-131DOI: (10.1016/S0006-3495(98)77773-2) Copyright © 1998 The Biophysical Society Terms and Conditions