Sodium perchlorate effects on the helical stability of a mainly alanine peptide

Abstract

Sodium perchlorate salt (NaClO(4)) is commonly used as an internal intensity standard in ultraviolet resonance Raman (UVRR) spectroscopy experiments. It is well known that NaClO(4) can have profound effects on peptide stability. The impact of NaClO(4) on protein stability in UVRR experiments has not yet been fully investigated. It is well known from experiment that protein stability is strongly affected by the solution composition (water, salts, osmolytes, etc.). Therefore, it is of the utmost importance to understand the physical basis on which the presence of salts and osmolytes in the solution impact protein structure and stability. The aim of this study is to investigate the effects of NaClO(4), on the helical stability of an alanine peptide in water. Based upon replica-exchange molecular dynamics data, it was found that NaClO(4) solution strongly stabilizes the helical state and that the number of pure helical conformations found at room temperature is greater than in pure water. A thorough investigation of the anion effects on the first and second solvation shells of the peptide, along with the Kirkwood-Buff theory for solutions, allows us to explain the physical mechanisms involved in the observed specific ion effects. A direct mechanism was found in which ClO(4)(-) ions are strongly attracted to the folded backbone.

Figure 1

(A) LR nucleation parameter (v). (B) LR helix propagation (w) as a function of temperature.

Figure 2

Normalized probability of the dihedral angle (Φ,Ψ) values sampled during the simulations at 300 K for (A) AP in TIP3P water and (B) AP in NaClO₄ solution.

Figure 3

(A and B) Helical content per snapshot averaged over the entire trajectory versus temperature for (A) AP in TIP3P water and (B) AP in NaClO₄ solution. (C) Non-PPII states of AP in 0.2 M NaClO₄ compared with non-PPII states in pure water. The temperature-dependent basis spectra of the PPII-like conformations were calculated using the method of Lednev et al. (56). We then digitally smoothed and subtracted the appropriate amount of the PPII-like conformation basis spectra from the measured and smoothed UVRR of AP.

Figure 4

(A and B) Averaged CD spectra for AP in TIP3P explicit water (A) and in NaClO₄ solution (B), shown only at selected temperatures 275 K, 285 K, 300 K, 350 K, 380 K, 410 K, and 505 K, for better clarity. (C) CD spectra for AP in pure water from CD experiments.

Figure 5

Averaged ellipticity, θ₂₂₂, for AP in TIP3P water and in NaClO₄ solution.

Figure 6

RDFs for O-H (A) and O-O (B) in TIP3P solution (black line) and NaClO₄ solution (green line). No significant global changes in the water structure are observed.

Figure 7

Color maps representing the average closest distances between (A) the O atoms at ClO₄⁻ and each backbone C_β and (B) the O atoms at ClO₄⁻ and each NH₂ at each arginine during the simulation at 300 K. The color represents the probability range, from least probable (blue) to most probable (red).

Figure 8

RDFs between the backbone Cα and water molecules for (A) AP in TIP3P and (B) AP in NaClO₄ solution.

Figure 9

RDFs between the backbone Cα and the center of mass of the ClO₄⁻ ions for selected temperatures from 270 K to 505 K.