Abstract
Docking of a flexible ligand to a rigid protein, followed by molecular dynamics (MD) studies to allow movement of the protein is shown to be a useful method for investigating pharmacologically relevant interactions. Studies of MMB lectins (beta-sheet proteins with shallow binding sites) reveal the importance of dimerisation to the activation of all of the carbohydrate binding sites of these lectins, finalising site III into a shape that can accommodate mannose. Aloe lectin was shown to have the overall fold of a MMB lectin and to be capable of forming a dimeric unit, shown to be stable using MD simulations in a water box. Docking shows that only two binding sites in the aloe dimer are thought to be able to bind mannose, as alterations in the residues vital for binding have occurred, and this is supported by the absence of a cluster of docked conformations in these sites. The presence of many 'sticky' patches on the exterior of aloe lectin are observed, revealing extended binding areas consistent with other members of the family. The motions of the mannose molecules in the binding areas during the molecular dynamics simulations suggest that the hydrogen bonds observed in these protein-carbohydrate complexes are dynamic in nature and can be constantly breaking and reforming. Docking of atropine to the GPCR m1AchR (an alpha-helical transmembrane protein with and enclosed binding site) indicates the presence of two key hydrogen bonds with Ser109 and Asn110. The main influences on docking seem to be shape and size of the ligand rather than charge considerations, although the negatively charged end of the binding pocket orients the molecules in the majority of the dockings in the same direction. Docking studies of atropine and selected analogues to m1AchR and two mutants, Tyr381Phe and Tyr381Ala, produce data which correlate well with experimentally determined pIC50 values and a prediction of pIC50 of previously untested antagonists for this system. Molecular dynamics studies show differential movement in the transmembrane helices for MD studies with acetylcholine, atropine and no ligand bound and rearrangement of some key hydrogen bonds. This leads to a model of inverse agonist functionality for atropine and its analogues involving the prevention of helical movement by the aromatic tail groups of these ligands.