title: 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 α2u-globulin (α2u). 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 α2u 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 α2u 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 α2u providing an acceptable dissociation constant indicating the binding efficiency of α2u. The obtained results are in corroboration with the data made through computational approach.
authors.affiliation: 1] Centre for Pheromone Technology, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli - 620 024, Tamil Nadu, India [2].
authors.forename: Renganathan
authors.initials: R
authors.lastname: Ilayaraja
authors.affiliation: 1] Institute of Medical Biology, A-STAR, Biopolis Drive, Singapore [2].
authors.forename: Ramalingam
authors.initials: R
authors.lastname: Rajkumar
authors.affiliation: Centre for Pheromone Technology, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli - 620 024, Tamil Nadu, India.
authors.forename: Durairaj
authors.initials: D
authors.lastname: Rajesh
authors.affiliation: Centre for Pheromone Technology, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli - 620 024, Tamil Nadu, India.
authors.forename: Arumugam Ramachandran
authors.initials: AR
authors.lastname: Muralidharan
authors.affiliation: The Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore - 637553.
authors.forename: Parasuraman
authors.initials: P
authors.lastname: Padmanabhan
authors.affiliation: Centre for Pheromone Technology, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli - 620 024, Tamil Nadu, India.
authors.forename: Govindaraju
authors.initials: G
authors.lastname: Archunan
mesh_terms: D000510:Alpha-Globulins / Q000378:metabolism*; D000818:Animals; D002352:Carrier Proteins / Q000378:metabolism*; D002850:Chromatography, Gel; D005204:Farnesol / Q000378:metabolism*; D005434:Flow Cytometry; D005453:Fluorescence; D005455:Fluorescent Antibody Technique; D008297:Male; D062105:Molecular Docking Simulation; D009284:Naphthols / Q000378:metabolism*; D010675:Pheromones / Q000378:metabolism*; D051381:Rats; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D000510:Alpha-Globulins; D002352:Carrier Proteins; D009284:Naphthols; D010675:Pheromones; C013803:alpha 2u globulin; D005204:Farnesol; C028405:2-naphthol