NMR structure of entolysin A in micellar DPC solution
1) The polypeptide chain of entolysin A consists of 14 amino acids. 2) The N-terminal amino acid (Leu) is acylated with an (R)-3-hydroxy-decanoic acid (IG8) moeity which is indicated as the first residue. 3) The depsi (ester) bond is established between the ILE15 carboxyl and DSN11 side-chain OH groups.
D-Ser, L-Val, L-Leu, D-Ser, L-Ile amino acids make up a macrocycle within the peptide
The lowest energy NMR structure issued from CNS was refined using unrestrained AMBER molecular dynamics simulations (against the ff14SB force field). Here, we modelled the interaction of a single peptide molecule with an explicit dodecylphosphocholine (DPC) micelle. The representative peptide conformation of the trajectory (=refined structure) was selected using cluster analysis. Solvent model: TIP3P. Occasional too-close contacts present in the NMR structure ensemble (structures #2-#11) are fully removed during the AMBER moleculary dynamics refinement (structure #1).
2.5 mM entolysin A, 150 mM [U-2H] DPC, 90% H2O/10% D2O
Entolysin A was dissolved in the micellar solution of uniformly deuterated dodecylphosphocholine (DPC-d38). Solvent: 10 mM Na2HPO4/NaH2PO4 buffer at pH 7.4.
Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
Brunger, Adams, Clore, Gros, Nilges and Read
Non-ribosomal polypeptide, Cyclic lipodepsipeptide, Antimicrobial peptide, Biosurfactant, SURFACTANT PROTEIN