Fig. 2: Investigating the molecular mechanism by which RDW23166.1 specifically recognizes free lysine.
From: Engineering unnatural cells with a 21st amino acid as a living epigenetic sensor
a RDW23166.1 structure (blue) predicted by AlphaFold2. Lysine (Lys, green) was docked into the structure using AutoDock Vina, and zoomed-in views highlight the residues (orange and cyan) surrounding Lys. b Root mean square deviation (RMSD) analysis of the RDW23166.1 backbone and lysine was performed over 100 ns molecular dynamics simulations of the complex systems at 303 K. c Radius of gyration of the backbone was analyzed over 100 ns molecular dynamics simulations of the complex systems at 303 K. d Ligand binding pocket of Tetrahymena GCN5 (PDB: 1QSN) identified by D3Pockets server. e Ligand binding pocket of RDW23166.1 identified by D3Pockets server. f Contact maps of Tetrahymena GCN5 (PDB: 1QSN), human HAT1 (PDB: 2P0W) and RDW23166. g Binding affinity energy of Tetrahymena GCN5, human HAT1, and RDW23166.1 toward different ligands predicted by docking. Histone H3 peptide: KSTGGKAPRKQ; Histone H4 peptide: KGGKGLGKGGAKRHR. h The activity of single mutations in RDW23166.1 was demonstrated through fluorescence experiments. Data are presented as mean values ± SEM from n = 3 independent biological replicates. i The top 12 residues identified for contributing to the residue-level energy of RDW23166.1 docked with Lys. arb. units, arbitrary units. Source data are provided as a Source Data file.
