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Molecular dynamics simulations areperformed to investigate thecounteracting effect of trehalose against urea-induced denaturationof S-peptide analogue. The calculations of Cαroot-mean-square deviation, radius of gyration, andsolvent-accessible surface area reveal that the peptide loses itsnative structure in aqueous 8 M urea solution at 310 K and that thisunfolding process is prevented in the presence of trehalose. Interestingly,the native structure of the peptide in ternary mixed urea/trehalosesolution is similar to that in the pure water system. The estimationof helical percentage of peptide residues as well as peptide–peptideintramolecular hydrogen bond number for different systems also supportthe above findings. Decomposition of protein–urea total interactionenergy into electrostatic and van der Waals contributions shows thatthe presence of trehalose molecules makes the latter contributionunfavorable without affecting the former. These observations are furthersupported by preferential interaction calculations. Furthermore, thehydrogen bond analyses show that with the addition of urea moleculesto the peptide–water system, the formation of peptide–ureahydrogen bonds takes place at the expense of peptide–waterhydrogen bonds. In ternary mixed osmolytes system, because of formationof a considerable amount of peptide–trehalose hydrogen bonds,some urea molecules are excluded from the peptide surface. This essentiallyreduces the interaction between peptide and urea molecules, and becauseof this, we notice a reduction in the number of peptide–ureahydrogen bonds. Interestingly, the total number of peptide–solutionspecies hydrogen bonds in the pure water system is very similar tothat for the mixed osmolytes system. From these observations we inferthat in the ternary solution, peptide–solution species hydrogenbonds are shared by water, urea, and trehalose molecules. The presenceof trehalose in the mixed osmolyte system causes a significant reductionin the translational dynamics of water molecules. We discuss theseresults to understand the molecular explanation of trehalose’scounteracting ability on urea-induced protein denaturation. [ABSTRACT FROM AUTHOR]

Toinvestigate the underlying mechanism by which trehalose actsas a bioprotectant against thermal denaturation of protein in aqueoussolution, we carry out classical molecular dynamics simulations attwo different temperatures. Though it is widely accepted that trehaloseacts as an antidote against such protein structural destabilizationand numerous hypotheses have been proposed in regard to its mechanismof stabilization, there is still no definitive generally acceptedanswer to this question and it remains a subject of active research.In view of this, in this article we report the thermal denaturationprocess of a 15-residue S-peptide analogue at 360 K temperature andthe counteracting ability of trehalose of varying concentrations atthat temperature. In order to verify the conformational stabilityof the peptide at ambient temperature condition, we also carry outa separate simulation of peptide–water binary system at 300K temperature. The goal is to provide a molecular level understandingof how trehalose protects protein at elevated temperature. The Cα-rmsd calculation shows that in pure water, the peptideis stable at 300 K temperature and its unfolding is observed at 360K. However, in peptide–water–trehalose ternary system,the value of Cα-rmsd decreases as trehalose concentrationis increased. Remarkably, at the highest trehalose concentration consideredin this study, the value of Cα-rmsd at 360 K is similarto 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 theabove observations. The total number of hydrogen bonds formed by thepeptide with solution species (trehalose and water) remains constant,though the peptide water hydrogen bond decreases and peptide trehalosehydrogen bond increases with increasing trehalose concentration. Thisfinding suggests replacement of water molecules by trehalose moleculesand supports water replacement hypothesis. The calculations of preferentialinteraction parameter show that at the peptide surface, trehalosemolecules are slightly more preferred over water and for the mostconcentrated solutions, a prominent exclusion of water and enrichmentof trehalose molecules is observed. Also observed are (i) trehalose-inducedsecond shell collapse of water structure, (ii) the growth of trehalosecluster as concentration is increased, and (iii) trehalose-inducedslowing down of the translational motion of both water and trehalose,the effect being more pronounced for the latter. Implications of theseresults for counteracting mechanism of trehalose are discussed. [ABSTRACT FROM AUTHOR]

Wehave carried out molecular dynamics simulation to investigatethe role of trehalose molecules on the change in the structural anddynamical properties of aqueous N-methylacetamide(NMA) solution. In this study, we considered six different trehaloseconcentrations ranging from 0 to 66%. Results are discussed in theframework of hydrophobic interactions between different methyl groupsof NMA, structure of the solutions, and hydrogen bonding interactionsbetween different solution species. We observe that the propensityof hydrophobic association through the methyl groups of NMA is essentiallyinsensitive to trehalose concentration except for higher trehaloseconcentration where the hydrophobic interactions between the hydrophobicmethyl groups are getting reduced. Also observed are (i) trehaloseinduced slight collapse of the second hydration shell of water, (ii)presence of excess water molecules near NMA, and (iii) exclusion oftrehalose from NMA. Our NMA–water radial distribution functionanalyses followed by average number of hydrogen bonds per NMA calculationsreveal that, in the hydration of NMA molecules, its carbonyl groupoxygen (over amide hydrogen) is predominantly involved. As trehaloseis added, we observe, in accordance with the water replacement hypothesis,the replacement of water–NMA hydrogen bonds by NMA–trehalosehydrogen bonds, keeping the average number of hydrogen bonds formedby a single NMA with different solution species essentially unchanged.Our hydrogen bond calculations further reveal that addition of trehalosereplaces water–NMA hydrogen bonds by water–trehalosehydrogen bonds. And as a result, we find that the average number ofhydrogen bonds formed by a water molecule remain unchanged. We alsofind that addition of trehalose decreases the translational motionof all the solution species sharply. [ABSTRACT FROM AUTHOR]

Antisense medications treat diseases that cannot be treated using traditional pharmacological technologies. Nucleotide monomers of bare and phosphorothioate (PS)-modified LNA, N-MeO-amino-BNA, 2',4'-BNA NC [NH], 2',4'-BNA NC [NMe], and N-Me-aminooxy-BNA antisense modifications were considered for a detailed DFT-based quantum chemical study to estimate their molecular-level structural and electronic properties. Oligomer hybrid duplex stability is described by performing an elaborate MD simulation study by incorporating the PS-LNA and PS-BNA antisense modifications onto 14-mer ASO/RNA hybrid gapmer type duplexes targeting protein PTEN mRNA nucleic acid sequence (5'- CTTAGCACTGGCCT -3'/3'-GAAUCGUGACCGGA-5'). Replica sets of MD simulations were performed accounting to two data sets, each set simulated for 1 μs simulation time. Bulk properties of oligomers are regulated by the chemical properties of their monomers. As such, the primary goal of this work focused on establishing an organized connection between the monomeric BNA nucleotide's electronic effects observed in DFT studies and the macroscopic behavior of the BNA antisense oligomers, as observed in MD simulations. The results from this study predicted that spatial orientation of MO-isosurfaces of the BNA nucleotides are concentrated in the nucleobase region. These BNA nucleotides may become less accessible for various electronic interactions when coupled as ASOs forming duplexes with target RNAs and when the ASO/RNA duplexes further bind with the RNase H. Understanding such electronic interactions is crucial to design superior antisense modifications with specific electronic properties. Also, for the particular nucleic acid sequence solvation of the duplexes although were higher compared to the natural oligonucleotides, their binding energies being relatively lower may lead to decreased antisense activity compared to existing analogs such as the LNAs and MOEs. Fine tuning these BNAs to obtain superior binding affinity is thus a necessity.

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.