Evaluating the binding efficiency of pheromone binding protein with its natural ligand using molecular docking and fluorescence analysis.

ABSTRACT: Chemosignals play a crucial role in social and sexual communication among inter- and intra-species. Chemical cues are bound with protein that is present in the pheromones irrespective of sex are commonly called as pheromone binding protein (PBP). In rats, the pheromone compounds are bound with low molecular lipocalin protein ?2u-globulin (?2u). We reported farnesol is a natural endogenous ligand (compound) present in rat preputial gland as a bound volatile compound. In the present study, an attempt has been made through computational method to evaluating the binding efficiency of ?2u with the natural ligand (farnesol) and standard fluorescent molecule (2-naphthol). The docking analysis revealed that the binding energy of farnesol and 2-naphthol was almost equal and likely to share some binding pocket of protein. Further, to extrapolate the results generated through computational approach, the ?2u protein was purified and subjected to fluorescence titration and binding assay. The results showed that the farnesol is replaced by 2-naphthol with high hydrophobicity of TYR120 in binding sites of ?2u providing an acceptable dissociation constant indicating the binding efficiency of ?2u. The obtained results are in corroboration with the data made through computational approach.

SUBMITTER: Ilayaraja R 

PROVIDER: S-EPMC4047529 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature