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 4À ions are strongly attracted to the folded backbone.

Specific Interactions of Sodium Salts with Alanine Dipeptide and Tetrapeptide in Water: Insights from Molecular Dynamics

“…In addition, Dzubiella used oligopeptides containing charged residues. In further work in progress using the AMBER force-field, 64 we were able to show that much longer peptides, comparable to those of Dzubiella, 29,30 or of Asciutto et al, 31 do in fact behave in an opposite way: they show decreased helicity in the presence of electrolytes. Since we believe that this major finding is robust and force-field independent, we have tried to understand its origin by a detailed energy analysis for all possible interactions in our systems.…”

Hofmeister ion effects on the solvation and thermal stability of model proteins lysozyme and myoglobin

“…The ions seem to have multiple effects including ion-specific interactions with proteins, polymers, and solvation waters [4,20]. Multiple studies have shown ion-specific interactions with amino acids, the peptide backbone, and solvation water alter protein structures [21][22][23][24][25][26]. Recently, infrared spectroscopy has been shown to be a useful technique to study differences in peptide and polymer solvation [27].…”

Calculations of shear viscosity, electric conductivity and diffusion coefficients of aqueous sodium perchlorate solutions from molecular dynamics simulations

“…which is the GK relation (9). Since for large t the second integral on the right relaxes to the fixed value more slowly, the diffusion coefficient calculated using MSD and velocity ACF is the same for very long simulation times.…”

“…Although its water solutions are commonly used in many practical applications, e.g. as supporting electrolytes in electrochemical studies, there are only few papers related to NaClO 4 in water [3][4][5][6][7][8][9][10]. In this paper the recent results of shear viscosity, diffusion coefficients and conductivity calculations applying molecular dynamics simulations for different NaClO 4 concentrations in tip3p and tip4p/2005 water models are presented.…”