Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

Abstract

The thermodynamic properties and phase behavior of water in confined regions can vary significantly from that observed in the bulk. This is particularly true for systems in which the confinement is on the molecular-length scale. In this study, we use molecular dynamics simulations and a powerful solvent analysis technique based on inhomogenous solvation theory to investigate the properties of water molecules that solvate the confined regions of protein active sites. Our simulations and analysis indicate that the solvation of protein active sites that are characterized by hydrophobic enclosure and correlated hydrogen bonds induce atypical entropic and enthalpic penalties of hydration. These penalties apparently stabilize the protein-ligand complex with respect to the independently solvated ligand and protein, which leads to enhanced binding affinities. Our analysis elucidates several challenging cases, including the super affinity of the streptavidin-biotin system.

Fig. 1.

World energies and excess entropies of water molecules in the principal hydration sites of the binding cavities. The world energy is the energy of interaction of the water molecules with the entire system. Shown are data for principle hydration sites that are proximal to hydrophylic protein groups. The points labeled 1, 2, and 3 represent data for hydration sites with unusually high ordering.

Fig. 2.

World energies and excess entropies of water molecules in the principal hydration sites of the binding cavities. The world energy is the energy of interaction of the water molecules with the entire system. Shown are data for principle hydration sites that are proximal to hydrophobic protein groups. The point labeled 4 represents data for a hydration site with unusually high ordering.

Fig. 3.

The binding cavity of streptavidin and a typical solvating water configuration. Also shown is the protein structure that stabilizes the ring. The green lines represent hydrogen bonds. The hydrogen bonds between the ring water molecules and the protein are the correlated hydrogen bonds referred to in the text. The gray scaffolding is the protein that encloses the ring from above.

Fig. 4.

Shown is the same conformation of the water molecules as is shown in Fig. 3 (from a different perspective) with the solvent density averaged over all simulations in green. The hydration sites determined by the clustering of this density are shown in wireframe. Note the near absence of water molecules in the inner part of the five-membered ring and in between the ring sites.

Fig. 5.

A typical configuration for a water molecule in principle hydration site 1 from Fig. 1 in the 1DBJ binding cavity. The molecule is orientationally constrained such that its oxygen atom maintains a hydrogen bond with Asn-35. It is also flanked on three sides (to the left, right, and below) by hydrophobic groups. The two hydrogen bond vectors point toward additional solvent with which the water molecule can hydrogen bond. The purple shading is to the scale of a Van der Waals radius for a water molecule.