title: A combined atomic force microscopy imaging and docking study to investigate the complex between p53 DNA binding domain and Azurin.
abstract: The tumor suppressor p53 interacts with the redox copper protein Azurin (AZ) forming a complex which is of some relevance in biomedicine and cancer therapy. To obtain information on the spatial organization of this complex when it is immobilized on a substrate, we have used tapping mode-atomic force microscopy (TM-AFM) imaging combined with computational docking. The vertical dimension and the bearing volume of the DNA binding domain (DBD) of p53, anchored to functionalized gold substrate through exposed lysine residues, alone and after deposing AZ, have been measured by TM-AFM. By a computational docking approach, a three-dimensional model for the DBD of p53, before and after addition of AZ, have been predicted. Then we have calculated the possible arrangements of these biomolecular systems on gold substrate by finding a good agreement with the related experimental distribution of the height. The potentiality of the approach combining TM-AFM imaging and computational docking for the study of biomolecular complexes immobilized on substrates is briefly discussed.
authors.affiliation: Biophysics & Nanoscience Centre, CNISM, Facolta' di Scienze, Università della Tuscia, I-01100 Viterbo, Italy. bizzarri@unitus.it
authors.forename: Anna Rita
authors.initials: AR
authors.lastname: Bizzarri
authors.forename: Silvia
authors.initials: S
authors.lastname: Di Agostino
authors.forename: Laura
authors.initials: L
authors.lastname: Andolfi
authors.forename: Salvatore
authors.initials: S
authors.lastname: Cannistraro
mesh_terms: D001400:Azurin / Q000737:chemistry*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D005982:Glutathione Transferase / Q000378:metabolism; D006046:Gold / Q000737:chemistry; D006801:Humans; D007700:Kinetics; D018625:Microscopy, Atomic Force / Q000379:methods*; D008958:Models, Molecular; D008968:Molecular Conformation; D016011:Normal Distribution; D011485:Protein Binding; D012984:Software; D016159:Tumor Suppressor Protein p53 / Q000737:chemistry*
chemical_list: D016159:Tumor Suppressor Protein p53; D001400:Azurin; D006046:Gold; D004247:DNA; D005982:Glutathione Transferase