Protein-peptide docking using residue restraints
We will drive you through the magical world of macromolecular docking using residue restraints. We will make use of the awesome Google Colab online tool.
1.1. Docking the LMP1 binding peptide onto the TNFR-associated factor 2
Tumor necrosis receptor-associated factors (TRAFs) can turn on numerous genes involved in inflammatory and immune responses and sustain proliferation during tumorigenesis. TRAFs are constitutively recruited by binding an apparent wide spectrum of peptidic sequences, such as the oncoprotein LMP1, for which the crystal structure was solved over 20 years ago (PDB code: 1czy).
For this demonstration, we will assume prior knowledge of two interfacial residues on the receptor, we will select
A.466 as residue restraints.