Conformational free-energy landscapes for a peptide in saline environments

Abstract

The conformations that proteins adopt in solution are a function of both their primary structure and surrounding aqueous environment. Recent experimental and computational work on small peptides, e.g., polyK, polyE, and polyR, have highlighted an interesting and unusual behavior in the presence of aqueous ions such as ClO₄⁻, Na⁺, and K⁺. Notwithstanding the aforementioned studies, as of this writing, the nature of the driving force induced by the presence of ions and its role on the conformational stability of peptides remains only partially understood. Molecular-dynamics simulations have been performed on the heptapeptide AEAAAEA in NaCl and KCl solutions at concentrations of 0.5, 1.0, and 2.0 M. Metadynamics in conjunction with a three-dimensional model reaction coordinate was used to sample the conformational space of the peptide. All simulations were run for 2 μs. Free-energy landscapes were computed over the model reaction coordinate for the peptide in each saline assay as well as in the absence of ions. Circular dichroism spectra were also calculated from each trajectory. In the presence of Na⁺ and K⁺ ions, no increase in helicity is observed with respect to the conformation in pure water.

Figure 1

Free-energy surfaces for Ace-AEAAAEA-Nme in 1.0 M KCl (A), 1.0 M NaCl (B), and water (C) over our defined MRC. The five colored spheres in each plot show the location of five relevant conformations for small peptides: PPII (purple), 2.5₁ helix (red), 3₁₀ helix (blue), α-helix (green), and π-helix (orange). Colored isosurfaces represent specific free energy values (pink, <7 kcal/mol; red-orange, <6 kcal/mol; yellow, <5 kcal/mol; green, <4 kcal/mol; blue, <3 kcal/mol; violet, <2 kcal/mol; and black, <1 kcal/mol). Isosurfaces (white) show the portion of conformational space sampled during a given simulation. Selected conformers observed in respective trajectories are shown around each plot, while their locations on the MRC are also indicated. Ions that were observed to be interacting with a conformer are represented as large, colored spheres: sodium (yellow) and potassium (bronze).

Figure 2

Five conformations of interest for the polypeptide, AEAAAEA. The conformers are the π-helix (A), α-helix (B), 3₁₀ helix (C), PPII (D), and 2.5₁ helix (E). Each conformer is displayed from the side (top row) and looking down on the N-terminus of the peptide (bottom row). The color of each backbone matches the corresponding colored spheres in Figs. 1 and 3. (Green ball-and-stick representation) Glutamic-acid side chains.

Figure 3

Free-energy landscapes for the zwitterionic AEAAAEA peptide in 1.0 M KCl (A), 1.0 M NaCl (B), and water (C) over our defined MRC. The five colored spheres in each plot show the location of five relevant conformations for small peptides: PPII (purple), 2.5₁ helix (red), 3₁₀ helix (blue), α-helix (green), and π-helix (orange). Colored isosurfaces represent specific free energy values (pink, <7 kcal/mol; red-orange, <6 kcal/mol; yellow, <5 kcal/mol; green, <4 kcal/mol; blue, <3 kcal/mol; violet, <2 kcal/mol; and black, <1 kcal/mol). Isosurfaces (white) show the portion of conformational space sampled during a given simulation. Selected conformers observed in respective trajectories are shown around each plot, while their locations on the MRC are also indicated. Ions that were observed to be interacting with a conformer are represented as large, colored spheres (sodium, yellow; potassium, bronze; and chloride, cyan).

Figure 4

(A) Free-energy landscape of Ace-AEAAAEA-Nme illustrating the path used as the model unidimensional reaction coordinate (ξ) to construct the one-dimensional free-energy profiles shown in Fig. 5. (Thick, red line) Path is indicated on the plot, where the initial and final states of ξ are defined as the α-helix (ξ = 0) and a random coil (ξ = 1), respectively. (B) Potential of mean force plots obtained from the computed three-dimensional landscapes for Ace-AEAAAEA-Nme in pure water (black), 1.0 M KCl (blue), and 1.0 M NaCl (red). The reaction coordinate (ξ) is described visually here, as going from the α-helix to a random coil.

Figure 5

Computed circular-dichroism spectra of zwitterionic AEAAAEA (top panel) and Ace-AEAAAEA-Nme (bottom panel) in various aqueous systems.