STRUCTURE AND DYNAMICS OF A PEPTIDOGLYCAN MONOMER IN AQUEOUS-SOLUTIONUSING NMR-SPECTROSCOPY AND SIMULATED ANNEALING CALCULATIONS

The conformation of the peptidoglycan monomer (PGM) from Brevibacteriu m divaricatum was determined in aqueous solution using a combined appr oach by 2D NMR spectroscopy, restrained simulated annealing, and molec ular dynamics (MD) calculations. MD simulations in water without exper imental constraints provided insights into the structure and dynamics of this glycopeptide. Hierarchical cluster analyses for conformer clas sifications were performed using a global molecular shape descriptor ( CoMFA steric fields). Principal component analysis was subsequently em ployed to extract orthogonal principal conformational properties. Corr elated dihedral angle mobilities were identified using a dynamic cross correlation map. The calculation of radial distribution functions for all polar protons of the molecule leads to additional information abo ut the solvation of PGM in a protic solvent, while autocorrelation fun ctions for dihedral angle fluctuations were used to monitor dynamic pr ocesses in different regions. From simulated annealing, a set of 11 co nformers was obtained, all characterized by a well-defined extended N- terminal peptide part additionally stabilized by the bound disaccharid e; the C-terminal part, on the other hand, exhibits more conformationa l flexibility in agreement with experimental data and MD simulations. The disaccharide conformation is in agreement with the conformational minimum computed for the model disaccharide 3-O-Me-4-O-beta GlcNAc-alp ha MurNAc using various force fields. Not only the interglycosidic bon d but also the glycopeptide linkage exists in a single, well-defined c onformation, for which no conformational changes can be detected durin g the MD simulations. In contrast, conflicting experimental data for t he N-acetyl group of GlcNAc could be explained using a conformer popul ation analysis based on ROE intensities and coupling constants account ing for a conformational equilibrium with one dominantly populated rot amer.