Computational protocol: The transcriptional co-activator LEDGF/p75 displays a dynamic scan-and-lock mechanism for chromatin tethering

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Protocol publication

[…] To select residues important for the interaction of the PWWP domain of LEDGF/p75 with DNA we used biomolecular modeling. First, we modeled the structure of the PWWP domain of LEDGF/p75 using the latest available version of Modeller (), with the NMR structure (PDB 2B8A) of the HDGF-PWWP as a template (). Second, we predicted putative DNA binding residues using the HotPatch algorithm (). This analysis indicated residues K56 and R74 to be solvent exposed and not required for the stabilization of the tertiary structure of the protein, minimizing the chance of perturbing the PWWP folding. Of concern, these residues in the LEDGF/p75-PWWP are conserved in the HDGF-PWWP sequence and were already shown to be important for DNA binding of the HDGF-PWWP (). […]

Pipeline specifications

Software tools MODELLER, HotPatch
Applications Protein structure analysis, Protein physicochemical analysis
Organisms Human immunodeficiency virus 1