Involvement of Water in Carbohydrate−Protein Binding

Abstract

The interactions of trimannosides 1 and 2 with Con A were studied to reveal the effects of displacement of well-ordered water molecules on the thermodynamic parameters of protein-ligand complexation. Trisaccharide 2 is a derivative of 1, in which the hydroxyl at C-2 of the central mannose unit is replaced by a hydroxyethyl moiety. Upon binding, this moiety displaces a conserved water molecule present in the Con A binding site. Structural studies by NMR spectroscopy and MD simulations showed that the two compounds have very similar solution conformational properties. MD simulations of the complexes of Con A with 1 and 2 demonstrated that the hydroxyethyl side chain of 2 can establish the same hydrogen bonds in a low energy conformation with the protein binding site as those mediated by the water molecule in the complex of 1 with Con A. Isothermal titration microcalorimetry (ITC) measurements showed that 2 has a more favorable entropy of binding compared to 1. This term, which was expected, arises from the return of the highly ordered water molecule to bulk solution. The favorable entropy term was, however, offset by a relatively large unfavorable enthalpy term. This observation was rationalized by comparing the extent of hydrogen bond and solvation changes during binding. It is proposed that an indirect interaction through a water molecule will provide a larger number of hydrogen bonds in the complex that have higher occupancies than in bulk solution, thereby stabilizing the complex.

The Structure of Clostridium perfringens NanI Sialidase and Its Catalytic Intermediates

“…In the covalent complex, the relaxed conformation of the ring places the C-1 carboxylate group into the equatorial position, and this now hydrogen bonds to two of these waters. Several studies have indicated that water rearrangement plays an important role in carbohydrate-protein interactions (41,42). The ordering of five extra water molecules in the covalent complex would be expected to decrease the entropy, and subsequently increase the free energy of the system.…”

On the Role of Water Models in Quantifying the Binding Free Energy of Highly Conserved Water Molecules in Proteins: The Case of Concanavalin A

“…In 3HET, a hydroxyethyl group replaces the hydroxyl group at the C2 position of the central mannosyl residue. ITC data 24 showed a more favorable entropy contribution for the binding of 3HET to Con A, relative to 3MAN, which was initially interpreted as indicating the displacement of the conserved water. A subsequent crystallographic and computational study 25 showed that the water was not displaced, although its position was slightly distorted relative to that in the Con AÀ3MAN complex (Figure 1).…”

Is it the shape of the cavity, or the shape of the water in the cavity?

“…Despite the dismissal (on the grounds of correlated errors) of linear correlations between changes in ΔH°b ind and -TΔS°b ind that have been claimed empirically for protein-ligand association (and numerous other chemical processes), [19][20][21][22][23][24] it is clear that, often, changes in the structure of a ligand leads to large changes in enthalpy and entropy of binding, but that these changes compensate in a way that results in small changes in ΔG°b ind . [14,[25][26][27][28][29] There is, however, no unequivocal, molecular-level explanation for entropy-enthalpy compensation, and its origin-even at a conceptual level-remains a controversial subject, [30] despite the qualitative rationalizations for this phenomenon advanced by Dunitz, Williams, and others. [25,31,32] Although these suggestions "make intuitive sense," [32,33] at some level, there is so much in the hydrophobic effect that is nonintuitive (or perhaps intuitive at some level, but still very complicated), that we are currently suspicious of simple, intuitive rationalizations of the even more difficult subject of entropy-enthalpy compensation.…”

“…[14,[25][26][27][28][29] There is, however, no unequivocal, molecular-level explanation for entropy-enthalpy compensation, and its origin-even at a conceptual level-remains a controversial subject, [30] despite the qualitative rationalizations for this phenomenon advanced by Dunitz, Williams, and others. [25,31,32] Although these suggestions "make intuitive sense," [32,33] at some level, there is so much in the hydrophobic effect that is nonintuitive (or perhaps intuitive at some level, but still very complicated), that we are currently suspicious of simple, intuitive rationalizations of the even more difficult subject of entropy-enthalpy compensation.…”