Computational protocol: SMAR1 coordinates HDAC6-induced deacetylation of Ku70 and dictates cell fate upon irradiation

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Protocol publication

[…] To perform protein–protein docking of HDAC6, SMAR1 and Ku70, the structural coordinates of HDAC6 (3C5K) and Ku70 (1JEQ) were obtained from PDB database. Crystal structure of free domain of Ku70, which is not bound to Ku80, was extracted from the Ku70:Ku80 complex. Next, the structure of SMAR1 was built with I-TASSER online server (Michigan, MI, USA). The structural coordinates of all the three systems were optimized in the protein preparation wizard of Maestro. All the missing hydrogen atoms were added and further subjected to energy minimization with OPLS-2005. The interaction models for SMAR1, HDAC6 and Ku70 were obtained with ZDOCK (v.3.0.2; University of Massachusetts, Worchester, MA, USA), which predicts the interacting models by the fast Fourier transform and allows 3D searches of spatial degrees of freedom between the macromolecules. The predicted docked models of HDAC6–SMAR1–Ku70 were further analyzed with the PyMol (Schrodinger). […]

Pipeline specifications

Software tools I-TASSER, ZDOCK, PyMOL
Application Protein interaction analysis