NMR structure of xantholysin A in micellar DPC solution
1) The polypeptide chain of xantholysin 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 SER8 side-chain OH group.
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)
3.2 mM xantholysin A, 162.9 mM [U-2H] DPC, 90% H2O/10% D2O
Xantholysin 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
Occasional too-close contacts present in the NMR structure ensemble (structures #2-#11) are fully removed during the AMBER moleculary dynamics refinement (structure #1)
Non-ribosomal polypeptide, Cyclic lipodepsipeptide, Antimicrobial peptide, Biosurfactant, SURFACTANT PROTEIN