-L-alanyl-D-isoglutaminyl]-N 6 -stearoyl-Llysine), a potent muramyl dipeptide (MDP) analogue with increased lipophilicity, has been studied in DMSO-d 6 solution with nmr methods and molecular dynamics (MD) simulations. The proton spectra show the presence of the a-and b-anomers of the pyranosyl ring in the ratio of 3:1. The molecule is in the negative nuclear Overhauser effect (NOE) regime at 25ЊC and 300 MHz, but shows some positive cross peaks in the stearoyl-lysine moiety in the NOE spectroscopy (NOESY) spectra; at 600 MHz only the stearoyl moiety remains in the positive regime. The temperature dependence of the alanyl amide proton chemical shift (02.7 ppb/K) points to its involvement in intramolecular H bonding. An extensive conformational search in vacuo indicates that the preferred conformations contain the b-turn like structure characterized by the intramolecular H-bond N-Acetyl-CO-HN-Ala; it coexists with the type II b-turn characterized by the H-bond Mur-CO-H E N T -iGln only in some high energy structures obtained by the conformational search (relative energy ú 20 kcal/mol). Such an S-shaped conformation was never found in the 0.5 ns simulation involving explicit DMSO solvent molecules where only the Ala amide proton is significantly protected from the solvent; some (short-lived) g- turns in the alanyl-isoglutaminyl backbone are also observed. No conformational preferences of the stearoyl-lysine moiety could be deduced from the NOE data; the increased flexibility of this part of the molecule relative to the muramoyl moiety is in agreement with the shorter local correlation times evident from NOESY spectra. The set of conformations that are most similar to the set of candidates for the bioactive conformation of MDP obtained by the CCLUES procedure [P. Pristovs ˇek et al. (