Extended Data Fig. 4: MD simulation of the docking model of SurE (6KSU) in complex with the branched peptide part of 1 that is tethered on the catalytic Ser63.
From: Non-ribosomal peptide cyclase-directed chemoenzymatic synthesis of lariat lipopeptides
Pseudo-N-terminal residue (l-Ile1′ or d-allo-Ile1′) is set at the N terminus binding site in the initial pose. The branched peptides with the pseudo-N-terminal l-Ile1′ and d-allo-Ile1′ are shown in cyan and pink, respectively. Grey dots indicate the distance between the pseudo-N-terminal Ile1′ nitrogen atom and the C-terminal d-Leu8 carbonyl carbon atom. a. The snapshot of the model with the pseudo-N-terminal l-Ile1′ at 0 ns. b. The snapshot of the model with the pseudo-N-terminal d-allo-Ile1′ at 0 ns. c. The snapshot of the model with the pseudo-N-terminal l-Ile1′ at 10 ns. d. The snapshot of the model with the pseudo-N-terminal d-allo-Ile1′ at 10 ns. e. The snapshot of the model with the pseudo-N-terminal l-Ile1′ at 60 ns. f. The snapshot of the model with the pseudo-N-terminal D-allo-Ile1′ at 60 ns. g. Plot of the distance between the pseudo-N-terminal nitrogen atom (l-Ile1′ N or d-allo-Ile1′ N) and the C-terminal d-Leu8 carbon atom (d-Leu8 C). The initial 10 ns of a production run with distance restraints is shown in grey shading.
