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Dissolved electrolytes interact with peptides and proteins in aqueous solution. Herein, we study small amide compounds in aqueous electrolyte solutions and link their salting-in and salting-out propensities to molecular-level structural details obtained with molecular simulations. Aqueous solutions of NaF, NaCl, NaBr, NaI, NaNO(3), and NaClO(4) with N-isopropylacrylamide (NiPAM) and N-methylacetamide (NMA) have been investigated. Our results show that NiPAM is salted-in by NaI, mediated through iodide interactions with nonpolar groups, while being salted-out by the other salts. Hydrogen-bonding interactions of anions with the amide group of NiPAM could not be identified, while in the systems with NMA all Hofmeister anions formed stable hydrogen bonds with the amide group. These results indicate that the immediate chemical environment of the backbone amide groups should be considered in studies of protein destabilization by dissolved electrolytes. We furthermore report that all salts but NaI provoke a hydrophobic collapse transition of poly(N-isopropylacrylamide) in water at 300 K, in qualitative agreement with experimentally measured salt effects on the lower critical solution temperature of this system.
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PMID:Hofmeister ion interactions with model amide compounds. 2201 81

We have carried out molecular dynamics simulation to investigate the role of trehalose molecules on the change in the structural and dynamical properties of aqueous N-methylacetamide (NMA) solution. In this study, we considered six different trehalose concentrations ranging from 0 to 66%. Results are discussed in the framework of hydrophobic interactions between different methyl groups of NMA, structure of the solutions, and hydrogen bonding interactions between different solution species. We observe that the propensity of hydrophobic association through the methyl groups of NMA is essentially insensitive to trehalose concentration except for higher trehalose concentration where the hydrophobic interactions between the hydrophobic methyl groups are getting reduced. Also observed are (i) trehalose induced slight collapse of the second hydration shell of water, (ii) presence of excess water molecules near NMA, and (iii) exclusion of trehalose from NMA. Our NMA-water radial distribution function analyses followed by average number of hydrogen bonds per NMA calculations reveal that, in the hydration of NMA molecules, its carbonyl group oxygen (over amide hydrogen) is predominantly involved. As trehalose is added, we observe, in accordance with the water replacement hypothesis, the replacement of water-NMA hydrogen bonds by NMA-trehalose hydrogen bonds, keeping the average number of hydrogen bonds formed by a single NMA with different solution species essentially unchanged. Our hydrogen bond calculations further reveal that addition of trehalose replaces water-NMA hydrogen bonds by water-trehalose hydrogen bonds. And as a result, we find that the average number of hydrogen bonds formed by a water molecule remain unchanged. We also find that addition of trehalose decreases the translational motion of all the solution species sharply.
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PMID:Trehalose induced modifications in the solvation pattern of N-methylacetamide. 2442 2

To provide the underlying mechanism of the inhibiting effect of trehalose on the urea denatured protein, we perform classical molecular dynamics simulations of N-methylacetamide (NMA) in aqueous urea and/or trehalose solution. The site-site radial distribution functions and hydrogen bond properties indicate in binary urea solution the replacement of NMA-water hydrogen bonds by NMA-urea hydrogen bonds. On the other hand, in ternary urea and trehalose solution, trehalose does not replace the NMA-urea hydrogen bonds significantly; rather, it forms hydrogen bonds with the NMA molecule. The calculation of a preferential interaction parameter shows that, at the NMA surface, trehalose molecules are preferred and the preference for urea decreases slightly in ternary solution with respect to the binary solution. The exclusion of urea molecules in the ternary urea-NMA-trehalose system causes alleviation in van der Waals interaction energy between urea and NMA molecules. Our findings also reveal the following: (a) trehalose and urea induced second shell collapse of water structure, (b) a reduction in the mean trehalose cluster size in ternary solution, and (c) slowing down of translational motion of solution species in the presence of osmolytes. Implications of these results for the molecular explanations of the counteracting mechanism of trehalose on urea induced protein denaturation are discussed.
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PMID:Exploring the Counteracting Mechanism of Trehalose on Urea Conferred Protein Denaturation: A Molecular Dynamics Simulation Study. 2611 43

Aqueous N-methylacetamide solutions were investigated by polarization-resolved pump-probe and 2D infrared spectroscopy (2D IR), using the amide I mode as a reporter. The 2D IR results are compared with molecular dynamics simulations and spectral calculations to gain insight into the molecular structures in the mixture. N-Methylacetamide and water molecules tend to form clusters with "frozen" amide I dynamics. This is driven by a hydrophobic collapse as the methyl groups of the N-methylacetamide molecules cluster in the presence of water. Since the studied system can be considered as a simplified model for the backbone of proteins, the present study forms a convenient basis for understanding the structural and vibrational dynamics in proteins. It is particularly interesting to find out that a hydrophobic collapse as the one driving protein folding is observed in such a simple system.
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PMID:Hydrophobic Collapse in N-Methylacetamide-Water Mixtures. 2942 50