Simulation of the conformation of the murein fabric: the oligoglycan, penta-muropeptide, and cross-linked nona-muropeptide.

The structure and conformation of the sacculus of bacteria at a scale much larger than just the component disaccharide penta-muropeptide is not well known and is crucially important for the understanding of bacterial growth and cell wall function. By computer simulations, the minimal energy conformations and the energy needed for stretching the component parts were found. The oligosaccharide chain, modeled as (GlcNAc-MurNAc)8 when under no tension, can assumed a variety of nearly iso-energetic conformations. These included a variety of bends and kinks, with the chain forming an irregular random coil. In the most relaxed and minimal energy state, the D-lactyl groups of the MurNAc (N-acetyl muramic acid) residues protruded at about an angle of 90 degrees relative to the D-lactyl groups of their immediate MurNAc neighbors in the same chain. The cell wall penta-muropeptide precursor is identical for Escherichia coli and Bacillus subtilis; it also adopted many conformations, each of an energy almost equal to the global minimum. The cross-bridged structure of the tail-to-tail linkage of disaccharide nona-muropeptide has a second type of association, in addition to the covalent cross-bridge, which has not been considered before. This is the ionic interaction between the free D-Ala and the free amino group of the m-A2 pm. In vivo, when the cross-bridge is stretched (in the computer to simulate growth), this pairing dissociates. The possible biological significance of this is that it exposes the underlying 'tail-to-tail' peptide bond to autolysis and will expose both the ends of the m-A2 pm and the D-AlaD-Ala groups that may then be able to react with nascent penta-muropeptides to form trimers. This suggests a new model for growth of the bacterial cell wall that depends on changes in the chemical conformation of the cross-bridge structure as it comes to bear stress.