Fig. 2: Ubiquitin promotes an open SPRTN conformation.
From: Allosteric activation of the SPRTN protease by ubiquitin maintains genome stability
a–c Experimental structure of SPRTN’s SprT domain (SPRTNaa28-214), PDB: 6mdx (a), ColabFold predicted structure of SprT (b) and ColabFold predicted structure of a SprT-ubiquitin (Ub1) complex (c). Protease domain is colored in blue, zinc-binding domain (ZBD) in orange and the Ub1 in grey. Zn2+ ions are colored in red. d–f Radius of gyration (Rg) of the indicated structures over 400 ns of molecular dynamics (MD) simulation. Each curve represents an independent MD trajectory (n = 3). Source data are provided as a Source Data file. g–i Main MD-clusters of the indicated structures during MD simulation for 400 ns, generated from three independent trajectories. For SprT (ColabFold predicted) two of three main MD-clusters are depicted. Rg correlating frequencies among all performed simulations are labeled above the structures. j, k Zoom-in to regions i and ii of the SprT-Ub1 complex (i), showing amino acids of ubiquitin (in grey) surrounding residue Leu38 (j) or L99 (k) of SPRTN (in blue) in the wild-type (WT) protein (left) and upon L38S or L99S replacement, respectively (right). l SprT-Ub1 binding energy difference (ΔΔG) between SprT-L38S or -L99S and WT protein obtained from alanine scanning. Bar graphs show the mean ± SD of 301 snapshots from PBSA calculations for the central structure of the largest cluster. Source data are provided as a Source Data file.
