title: Specificity of Prodan for the self-associating domain of spectrin: a molecular docking study.
abstract: The hydrophobic fluorescent probe Prodan binds to the self-associating domain of spectrin with 1:1 stoichiometry. A model of the self-associating domain was generated based on its homology with other domains of spectrin. Prodan was then docked onto the model, and several sites with low interaction energy were identified. To verify whether the binding of Prodan is specific towards the self-associating domain of spectrin, it was docked on to several other domains of spectrin, having a known three-dimensional structure. Analysis of the docking results suggests that the binding of Prodan to the self-associating domain of spectrin will involve hydrophobic and hydrophilic groups of Prodan. The results clearly indicate the preference of Prodan for a particular binding site of the self-associating domain.
authors.affiliation: Biophysics Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064 India.
authors.forename: Malyasri
authors.initials: M
authors.lastname: Bhattacharya
authors.forename: Chaitali
authors.initials: C
authors.lastname: Mukhopadhyay
authors.forename: Abhijit
authors.initials: A
authors.lastname: Chakrabarti
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002645:Chickens; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013049:Spectrin / Q000737:chemistry* / Q000378:metabolism
chemical_list: D013049:Spectrin