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Pipeline publication

[…] versible interaction(s) with binding partners, MSK1 and MKP1., We conducted homology modeling due to the unavailability of crystallographic coordinates of MKP1. The model of active the C-terminus phosphatase domain of MKP1 (172–314 aa) was constructed using PDB ID: 3EZZ as a template. The N-terminal crystal structure of MSK1 is available, but to model the phosphorylated Ser376 residue of the flexible loop near the active site, PDB ID: 3A8X was used as a template for homology modeling of MSK1 with amino acid residues from 42–380. Modeling studies were performed using Swiss Model. The modeled structure of MKP1 and MSK1 were cross-validated using multiple tools such as Procheck, Verify_3D, and Errat using SAVES server ( http://nihserver.mbi.ucla.edu/SAVES/ ). The cross-validated modeled structures of MKP1 and MSK1 are shown as and secondary structures for both are depicted in ., In the crystal structure of histone H3 (PDB ID: 2C1J), acetylation at Lys9 and Lys14 and phosphorylation at Ser10 was generated using Discovery Studio Visualizer version 3.5. A total of seven structures of histone H3 were modeled which encompassed combinations of modifications [Lys9, Ser10, Lys14, Lys9-Ser10, Lys9-Lys14, Ser10-Lys14, and Lys9-Ser10-Lys14] (). The Haddock server was used to score the refinement of PDB ID: 2C1J as native and the modified 14-3-3ζ and histone H3 complex. The Haddock scores of the complexes are tabulated in and ., The full-length (1–21 aa) loop structure of histone H3 was used to build the three PTM-modified structure [Lys9, Lys14, Lys9-Lys14]. The modeled structure of MSK1 was docked with native and the three PTM-modified structure of histone H3 using the Haddock server ( and ). The active site residues (Lys85, Ile88, Val89, Thr95, Arg102, Gln122, and Leu127) of MSK1 and (Lys9, Ser10, and Lys14) of histone H3 were provided as input parameters for targeted docking. The protein-protein interactions, Haddock score, hydrogen bonds, and hydrophobic interactions are tabulated in and ., The molecular interactions of the docked complexes were analyzed using Ligplot for hydrophobic interactions (). Discovery studio visualizer 3.5 was used to identify residues involved in hydrogen bonding between the two proteins and for the diagrammatic illustration of the residues involved in the hydrogen bond formation in the docked complex., The full length (1–21 aa) loop structure of histone H3 from the crystal structure of the Xenopus nucleosome (PDB ID: 1KX5) was used. Histone H3 is 100% conserved between Xenopus and humans. The combination of Lys9, Ser10, and Lys14 modifications was generated by site-specific acetylation and phosphorylation resulting in seven PTM structures of histone H3 [Lys9, Ser10, Lys14, Lys9-Ser10, Lys9-Lys14, Ser10-Lys14, and Lys9-S […]

Pipeline specifications

Software tools ERRAT, HADDOCK, LigPlot+