Ching-Hsing Yu, Samuel Cukierman, Régis Pomès Biophysical Journal

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Theoretical Study of the Structure and Dynamic Fluctuations of Dioxolane-Linked Gramicidin Channels Ching-Hsing Yu, Samuel Cukierman, Régis Pomès Biophysical Journal Volume 84, Issue 2, Pages 816-831 (February 2003) DOI: 10.1016/S0006-3495(03)74901-7 Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 1 (Top) Dioxolane ring and (bottom) RR-dioxolane flanked by two peptide bonds, RR-[1,3] dioxolane-4,5-dicarboxylic acid bis-methylamide. Heavy atom and torsion definitions are shown. This and subsequent representations of molecular structures were prepared with the program VMD (Humphey et al., 1996). Biophysical Journal 2003 84, 816-831DOI: (10.1016/S0006-3495(03)74901-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 2 Potential energy as a function of torsion θ obtained from (solid) ab initio quantum mechanics and (dashed) molecular mechanics calculations. Biophysical Journal 2003 84, 816-831DOI: (10.1016/S0006-3495(03)74901-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 3 Potential energy surfaces for the conformational isomerization of the dioxolane dipeptide in (θ,δ) torsional space. Angular values are indicated in degrees. Contour spacing is 0.5 kcal/mol. Shading decreases with higher energy. (Top) Ab initio quantum mechanics. (Bottom) Molecular mechanics calculations. Biophysical Journal 2003 84, 816-831DOI: (10.1016/S0006-3495(03)74901-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 4 Potential energy surfaces for the conformational isomerization of the dioxolane dipeptide in (θ,θ′) torsional space. Angular values are indicated in degrees. Contour spacing is 0.5 kcal/mol. Shading decreases with higher energy. (Top) Ab initio quantum mechanics. (Bottom) Molecular mechanics calculations. Biophysical Journal 2003 84, 816-831DOI: (10.1016/S0006-3495(03)74901-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 5 Backbone torsions of the conformations obtained from high-temperature simulated annealing of dioxolane-linked channels shown in (θ,θ′) torsional space. Angular values are indicated in degrees. (Circles) SS-. (Crosses) RR-linked channels. All the SS structures cluster together near (θ, θ′)=(−100°, −100°), whereas the RR structures partition into as many as seven classes centered near (−115°, −15°), (−15°, −115°), (−130°, −120°), (−120°, −130°), (−115°, −115°), (−120°, −165°), and (−120°, −180°), respectively. Biophysical Journal 2003 84, 816-831DOI: (10.1016/S0006-3495(03)74901-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 6 Potential of mean force for the structural fluctuations of the linked channels in (θ,θ′) torsional space. Angular values are indicated in degrees. Contour spacing is 0.5 kcal/mol. Line thickness increases with energy. (Top) SS channel. (Bottom) RR channel. Numbers 1–4 are the labels assigned to each of the conformers of the RR channel. Biophysical Journal 2003 84, 816-831DOI: (10.1016/S0006-3495(03)74901-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 7 Dioxolane chirality and representative conformations of the main chain of dioxolane-linked gramicidin channels, looking from the center of the channel, perpendicularly to the channel axis. Amino acid side chains were omitted for clarity. The hydrogen bonds formed by the two peptide bonds flanking the linker are highlighted. (Left) SS linker. (Right) RR linker. Diagrams illustrating the mode of insertion of the ring are shown at the bottom. Biophysical Journal 2003 84, 816-831DOI: (10.1016/S0006-3495(03)74901-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 8 Middle turn of the SS-linked dimer, looking down the channel axis. Biophysical Journal 2003 84, 816-831DOI: (10.1016/S0006-3495(03)74901-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 9 (Top) Definition of CO tilt angle α controlling the topology of carbonyl O atoms with respect to the channel lumen. (Bottom) Representative backbone conformations of the RR-linked dimer, looking down the channel axis. Conformations 1–4 differ by the topology of the two peptide bonds flanking the dioxolane ring. Biophysical Journal 2003 84, 816-831DOI: (10.1016/S0006-3495(03)74901-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 10 Potential of mean force for the structural fluctuations of native and linked channels in (α,α′) space. Tilt angles are indicated in degrees. Contour spacing is 0.5 kcal/mol. Line thickness increases with energy. (Top) Native gA. (Middle) SS dimer. (Bottom) RR dimer. Biophysical Journal 2003 84, 816-831DOI: (10.1016/S0006-3495(03)74901-7) Copyright © 2003 The Biophysical Society Terms and Conditions