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Molecular dynamics simulations are performed to investigate the counteracting effect of trehalose against urea-induced denaturation of S-peptide analogue. The calculations of Cα root-mean-square deviation, radius of gyration, and solvent-accessible surface area reveal that the peptide loses its native structure in aqueous 8 M urea solution at 310 K and that this unfolding process is prevented in the presence of trehalose. Interestingly, the native structure of the peptide in ternary mixed urea/trehalose solution is similar to that in the pure water system. The estimation of helical percentage of peptide residues as well as peptide-peptide intramolecular hydrogen bond number for different systems also support the above findings. Decomposition of protein-urea total interaction energy into electrostatic and van der Waals contributions shows that the presence of trehalose molecules makes the latter contribution unfavorable without affecting the former. These observations are further supported by preferential interaction calculations. Furthermore, the hydrogen bond analyses show that with the addition of urea molecules to the peptide-water system, the formation of peptide-urea hydrogen bonds takes place at the expense of peptide-water hydrogen bonds. In ternary mixed osmolytes system, because of formation of a considerable amount of peptide-trehalose hydrogen bonds, some urea molecules are excluded from the peptide surface. This essentially reduces the interaction between peptide and urea molecules, and because of this, we notice a reduction in the number of peptide-urea hydrogen bonds. Interestingly, the total number of peptide-solution species hydrogen bonds in the pure water system is very similar to that for the mixed osmolytes system. From these observations we infer that in the ternary solution, peptide-solution species hydrogen bonds are shared by water, urea, and trehalose molecules. The presence of trehalose in the mixed osmolyte system causes a significant reduction in the translational dynamics of water molecules. We discuss these results to understand the molecular explanation of trehalose's counteracting ability on urea-induced protein denaturation.

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.

To investigate the underlying mechanism by which trehalose acts as a bioprotectant against thermal denaturation of protein in aqueous solution, we carry out classical molecular dynamics simulations at two different temperatures. Though it is widely accepted that trehalose acts as an antidote against such protein structural destabilization and numerous hypotheses have been proposed in regard to its mechanism of stabilization, there is still no definitive generally accepted answer to this question and it remains a subject of active research. In view of this, in this article we report the thermal denaturation process of a 15-residue S-peptide analogue at 360 K temperature and the counteracting ability of trehalose of varying concentrations at that temperature. In order to verify the conformational stability of the peptide at ambient temperature condition, we also carry out a separate simulation of peptide-water binary system at 300 K temperature. The goal is to provide a molecular level understanding of how trehalose protects protein at elevated temperature. The Cα-rmsd calculation shows that in pure water, the peptide is stable at 300 K temperature and its unfolding is observed at 360 K. However, in peptide-water-trehalose ternary system, the value of Cα-rmsd decreases as trehalose concentration is increased. Remarkably, at the highest trehalose concentration considered in this study, the value of Cα-rmsd at 360 K is similar to that of water-peptide binary system at 300 K temperature. Further, the calculations of radius of gyration of Cα-atoms and helical percentage of the peptide residues support the above observations. The total number of hydrogen bonds formed by the peptide with solution species (trehalose and water) remains constant, though the peptide water hydrogen bond decreases and peptide trehalose hydrogen bond increases with increasing trehalose concentration. This finding suggests replacement of water molecules by trehalose molecules and supports water replacement hypothesis. The calculations of preferential interaction parameter show that at the peptide surface, trehalose molecules are slightly more preferred over water and for the most concentrated solutions, a prominent exclusion of water and enrichment of trehalose molecules is observed. Also observed are (i) trehalose-induced second shell collapse of water structure, (ii) the growth of trehalose cluster as concentration is increased, and (iii) trehalose-induced slowing down of the translational motion of both water and trehalose, the effect being more pronounced for the latter. Implications of these results for counteracting mechanism of trehalose are discussed.

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.

Molecular dynamics simulations were carried out to investigate the influences of aqueous trehalose solution on the hydrophobic interactions between neopentane molecules. In this study, we consider six different trehalose concentrations ranging from 0% to 56%. We observe that with increasing trehalose concentration the dispersion of solute neopentane takes place. The neopentane-neopentane association constant value decreases with addition of trehalose. Our preferential interaction calculations suggest that with increasing trehalose concentration neopentane interacts preferentially with water over trehalose. Site-site neopentane-trehalose rdfs indicate that trehalose molecules are expelled out from the neopentane surface. Also observed are (i) trehalose induced second shell collapse of water network (ii) decrease in average number of water-water and water-trehalose hydrogen bonds with increasing trehalose concentration. We also find that addition of trehalose decreases the translational motion of all the solution species. The decrease in diffusion coefficient value is more pronounced for trehalose. We, further, observe that the ratio of the diffusion coefficient values of water and trehalose increases with increasing trehalose concentration.

We report molecular dynamics simulation results of aqueous solution of NMA both in the presence and absence of trehalose at five different temperatures ranging from 285 K to 345 K at 1 atm pressure. For each temperature, we consider six different trehalose concentrations ranging from 0% to 66%. For a given temperature, we find the accumulation of more than expected water molecules in the first solvation shell of hydrophobic methyl group of NMA when trehalose concentration is very high. Further, our calculations of hydrogen bond properties reveal the formation of more and more trehalose–NMA hydrogen bonds and the breaking of water–NMA hydrogen bonds as trehalose concentration is increased. Interestingly, the breaking of NMA–water hydrogen bonds is well compensated by the formation of NMA–trehalose hydrogen bonds keeping the total number of hydrogen bonds formed by a single NMA molecule to remain unchanged. These observations are in accordance with water replacement hypothesis . Though we observe that temperature induced breaking of water–trehalose hydrogen bonds, remarkably, water–water and trehalose–trehalose hydrogen bonds tend to offset the effect of temperature when trehalose concentration is high. This implies that in a concentrated solution at higher temperature trehalose molecules play a minor role by reducing the number of water molecules available for protein. The calculated site–site distribution functions involving NMA and water molecules show that the former prefers to act as acceptor and not as a donor when it forms hydrogen bonds with water. Further, in consistent with the previously reported results (N. T. Skipper, Chem. Phys. Lett, 207 (1993) 424), we find that temperature induced slight breaking of water structure whereas, a prominent enhancement in the water structure is observed as trehalose concentration increases. The translational motion of different solution species increases with increasing temperature. On the other hand, trehalose induced retardation in the diffusion coefficient values for different solution species with more profound effect for trehalose and NMA molecules are observed. Also observed are: (a) enhancement in the trehalose–trehalose hydrogen bond network as trehalose concentration increases and (b) the presence of NMA molecules in the cluster of trehalose. [ABSTRACT FROM AUTHOR]