Computational protocol: A Molecular Model for the Differential Activation of STAT3 and STAT6 by the Herpesviral Oncoprotein Tip

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Protocol publication

[…] Separate molecular dynamics simulations were performed for each STAT-peptide system with the AMBER9 package and the parm99SB force field , following an established protocol . Acetyl and N-methyl groups were added at the N- and C-termini of the proteins and peptides to reduce terminal charge effects during the simulations. For the phosphorylated tyrosines, we used the parameters developed in our group . All systems were neutralized with an appropriate number of counterions, and solvated with TIP3P water molecules in a box of at least 10 Å between the solute and the borders. The systems were minimized in two-steps, and heated up to 298 K in 1 ns using SHAKE constraints on hydrogens and small restraints on the Cα atoms. For each system, 24 ns of production run were carried out and coordinate snapshots were saved every 1 ps.Salt bridges and hydrogen bonds between the SH2 domain and the peptides were identified using VMD : the cut-off were 3.2 Å between oxygen and nitrogen atoms of the salt bridged residues, 3.0 Å between the heavy atoms involved in hydrogen bonding, and an angle cut-off of 120 degrees. A cutoff of 5.0 Å between the heavy atoms was used to define hydrophobic interactions. The programs RasMol ,VMD , DS Viewer Pro (Version 6.0), and Povray (Version 3.6 for Windows) were used for structural analysis and visualization. The final figures were prepared with Adobe Photoshop CS and CorelDRAW 12. […]

Pipeline specifications

Software tools RasMol, CorelDraw
Applications Drug design, Miscellaneous
Diseases Neoplasms