Computer Simulation of Small Molecule Permeation across a Lipid Bilayer: Dependence on Bilayer Properties and Solute Volume, Size, and Cross-Sectional.

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Presentation transcript:

Computer Simulation of Small Molecule Permeation across a Lipid Bilayer: Dependence on Bilayer Properties and Solute Volume, Size, and Cross-Sectional Area D. Bemporad, C. Luttmann, J.W. Essex Biophysical Journal Volume 87, Issue 1, Pages 1-13 (July 2004) DOI: 10.1529/biophysj.103.030601 Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 1 (Top) Relative diffusion coefficients versus free volume percentage; the former are D-values divided by D at 30.5Å from the bilayer center (which is in bulk water). (Bottom) Relative diffusion coefficients versus the inverse of lipid trans/gauche interconversion times. Biophysical Journal 2004 87, 1-13DOI: (10.1529/biophysj.103.030601) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 2 Free volume distribution (percentage) along the bilayer normal. Biophysical Journal 2004 87, 1-13DOI: (10.1529/biophysj.103.030601) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 3 Electron density profile. Biophysical Journal 2004 87, 1-13DOI: (10.1529/biophysj.103.030601) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 4 Time autocorrelation functions for torsional angles along the lipid tails. The shorter the decay time, the closer to the terminal methyl. Biophysical Journal 2004 87, 1-13DOI: (10.1529/biophysj.103.030601) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 5 Log-log plots of diffusion coefficients as a function of solute volume at different z-depths (in Å) in the membrane. Solid lines are linear regression. The s-slopes are also reported. Biophysical Journal 2004 87, 1-13DOI: (10.1529/biophysj.103.030601) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 6 Log-log plots of diffusion coefficients as a function of solute mass at different z-depths (in Å) in the membrane. Solid lines are linear regression. The s-slopes are also reported. Biophysical Journal 2004 87, 1-13DOI: (10.1529/biophysj.103.030601) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 7 Calculation of solute cross-sectional area. The cross-sectional area is calculated as the area observed when looking from the arrows toward the molecules in the plane of the page. Biophysical Journal 2004 87, 1-13DOI: (10.1529/biophysj.103.030601) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 8 Log-log plot of diffusion coefficients as a function of solute cross-sectional areas Sd at different z-depths (in Å) in the membrane. The s-values are slopes of linear regressions. Biophysical Journal 2004 87, 1-13DOI: (10.1529/biophysj.103.030601) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 9 Log-log plots of permeability-partition ratio versus solute mass M, volume Vd, and cross-sectional area Sd. The s-values are slopes of linear regressions. Biophysical Journal 2004 87, 1-13DOI: (10.1529/biophysj.103.030601) Copyright © 2004 The Biophysical Society Terms and Conditions