Insights into the activity and specificity of Trypanosoma cruzi trans-sialidase from molecular dynamics simulations.

Trypanosoma cruzitrans-sialidase (TcTS), which catalyzes the transfer or hydrolysis of terminal sialic acid residues, is crucial to the development and proliferation of the T. cruzi parasite and thus has emerged as a potential drug target for the treatment of Chagas disease. We here probe the origin of the observed preference for the transfer reaction over hydrolysis where the substrate for TcTS is the natural sialyl donor (represented in this work by sialyllactose). Thus, acceptor lactose preferentially attacks the sialyl-enyzme intermediate rather than water. We compare this with the weaker preference for such transfer shown by a synthetic donor substrate, 4-methylumbelliferyl α-d-acetylneuraminide. For this reason, we conducted molecular dynamics simulations of TcTS following its sialylation by the substrate to examine the behavior of the asialyl leaving group by the protein. These simulations indicate that, where lactose is released, this leaving group samples well-defined interactions in the acceptor site, some of which are mediated by localized water molecules; also, the extent of the opening of the acceptor site to solvent is reduced as compared with those of unliganded forms of TcTS. However, where there is release of 4-methylumbelliferone, this leaving group explores a range of transient poses; surrounding active site water is also more disordered. The acceptor site explores more open conformations, similar to the case in which the 4-methylumbelliferone is absent. Thus, the predicted solvent accessibility of sialylated TcTS is increased when 4-methylumbelliferyl α-d-acetylneuraminide is the substrate compared to sialyllactose; this in turn is likely to contribute to a greater propensity for hydrolysis of the covalent intermediate. These computational simulations, which suggest that protein flexibility has a role in the transferase/sialidase activity of TcTS, have the potential to aid in the design of anti-Chagas inhibitors effective against this neglected tropical disease.

An evaluation of the GLYCAM06 and MM3 force fields, and the PM3-D* molecular orbital method for modelling prototype carbohydrate-aromatic interactions.

The structures and interaction energies of 21 binary complexes of fucose and glucose with toluene, 3-methylindole or p-hydroxytoluene, evaluated at the DFT-D level, are used to judge the accuracy of the GLYCAM06 and MM3 force fields, and the PM3-D* molecular orbital method for modelling carbohydrate-arene interactions. The accuracy of the DFT-D method is substantiated by comparison with high level CCSD(T) calculations on a small number of representative complexes. It is found that a correct description of the intermolecular dispersive interactions is essential. Both the PM3-D* method and the GYLCAM06 force field yield interaction energies within 1 kcal mol⁻¹ of the DFT-D values, whilst those from the MM3 force field are in error by more than 2 kcal mol⁻¹.

Binding of pollutant aromatics on carbon nanotubes and graphite.

The semiempirical PM3 method with dispersive corrections (PM3-D) is used to predict the interaction energy of a number of aromatic pollutants with a graphene surface and with carbon nanotubes. It is found that the dispersive interactions are dominant in determining the magnitude of the interaction and that electron transfer between the adsorbate and the surface is small. Good agreement is found between the calculated interaction energies and the experimental affinities measured in an aqueous environment.

Carbohydrate-aromatic pi interactions: a test of density functionals and the DFT-D method.

The performance of a number of computational approaches based upon density functional theory (DFT) for the accurate description of carbohydrate-pi interactions is described. A database containing interaction energies of a small number of representative complexes, computed at a high ab initio level, is described, and is used to judge 18 different density functionals including the M05 and M06 families as well as the DFT method augmented with empirical dispersive corrections (DFT-D). The DFT-D method and the M06 functionals are found to perform particularly well, whilst traditional functionals such as B3LYP perform poorly. The interaction energies for 23 sugar-aromatic complexes calculated by the DFT-D method are compared with the values from the 18 functionals. Again, the M06 class of functional is found to be superior.

Carbohydrate-protein recognition probed by density functional theory and ab initio calculations including dispersive interactions.

Carbohydrate-protein recognition has been studied by electronic structure calculations of complexes of fucose and glucose with toluene, p-hydroxytoluene and 3-methylindole, the latter aromatic molecules being analogues of phenylalanine, tyrosine and tryptophan, respectively. We use mainly a density functional theory model with empirical corrections for the dispersion interactions (DFT-D), this method being validated by comparison with a limited number of high level ab initio calculations. We have calculated both binding energies of the complexes as well as their harmonic vibrational frequencies and proton NMR chemical shifts. We find a range of minimum energy structures in which the aromatic group can bind to either of the two faces of the carbohydrate, the binding being dominated by a combination of OH-pi and CH-pi dispersive interactions. For the fucose-toluene and alpha-methyl glucose-toluene complexes, the most stable structures involve OH-pi interactions, which are reflected in a red shift of the corresponding O-H stretching frequency, in good quantitative agreement with experimental data. For those structures where CH-pi interactions are found we predict a corresponding blue shift in the C-H frequency, which parallels the predicted proton NMR shift. We find that the interactions involving 3-methylindole are somewhat greater than those for toluene and p-hydroxytoluene.