Computational protocol: Stability of the PHF10 subunit of PBAF signature module is regulated by phosphorylation: role of β-TrCP

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[…] The spatial structure of β-TrCP1 WD-domain was taken from the bank of three-dimensional structures PDB (PDBid - 1P22). Initial optimization and preparation of the receptor structure was carried out using Sybyl8.1 (Tripos L.P.) and AutodockTools software. Using Sybyl8.1 we constructed the following peptides:Peptide1-Normal - DSDGDSDDGEDPeptide1-A- DADGDADDGEDPeptide1-E - DEDGDEDDGEDPeptide1-P- DS(-p)DGDS(-p)DDGED (all highlighted serines are phosphorylated)Peptide2-Normal - DSSSGNVSEGESPPDSPeptide2-A - DSSSGNVAEGEAPPDSPeptide2-E - DSSSGNVEEGEEPPDSPeptide2-P1 - DSSSGNVS(-p)EGESPPDS (only the first highlighted serine is phosphorylated)Peptide2-P2 - DSSSGNVS(-p)EGES(-p)PPDS (all highlighted serines are phosphorylated)As we studied only small parts of the PHF10 protein flexible loop, CH3- caps were placed at the N- and C- terminus of the constructed peptides to eliminate unwanted charges at the ends, that could affect docking results. Docking was performed using Autodock Vina. During molecular docking the receptor molecule remained rigid while the peptides were treated as flexible. All of the obtained peptides conformations were evaluated based on Vina DockScore, RMSD calculations and the interaction energy with the help of Sybyl8.1 software. The binding energy calculations were performed based on the individual free energy values of peptides, receptor molecule (TrCP1) and their complexes. During free energy calculations Tripos force field was used for energy minimization procedures. Partial charges were calculated using the Gasteiger-Huckel method. The final values of binding energies were calculated using the equation:ΔGbindΔGcomplex−(ΔGreceptor+ΔGpeptide). […]

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