Fig. 5: The H3K36 and ssK36 peptides unfold upon binding into the active site of SETD2. | Communications Chemistry

Fig. 5: The H3K36 and ssK36 peptides unfold upon binding into the active site of SETD2.

From: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide

Fig. 5

a RMSD between the peptide conformation in the MD simulation and the extended peptide conformation in the crystal structure (dark grey and dark blue lines) and end-to-end distance of the peptides (light grey and light blue lines) in the sMD simulations without repulsive force which resulted in a TS-like structure. The RMSD was calculated using the crystal structures of complexed peptides in SETD2 as references for the extended conformation after positional optimisation by rigid body movement (PDB: 5V21 for H3K36, PDB: 6VDB for ssK36). The N-C distance was calculated as the distance between the backbone nitrogen atoms of A29 and P43. The RMSD and N-C distance were tracked until the minimum RMSD position was reached. Shown are representative replicates from H3K36 and ssK36 sMD simulations. Additional examples are shown in Supplementary Fig. 8. b, c Representative structures from sMD simulations with an RMSD of ~0.5 Å overlayed with crystal structures (PDB 6VDB or 5V21).

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