Background
Lysozyme is a 147 amino acid protein that can damage bacterial cell walls by destroying the glycosidic bond on the peptidoglycans molecule, particularly in gram-positive bacteria. Its native structure is composed of α and β domains and is cross-linked by four disulfides (Figure 1). Lysozyme can be aggregated by mutation of the lysozyme DNA sequence itself, or from the harsh environment of the cell inside (Figure 2).
Native structure of white hen egg lysozyme (MMDB: 14790 PDB: pdb1E8L1E8L). The amino acid residues are numbered from the terminal α group (N) to the terminal carboxyl group (C). Orange lines indicate the four disulfide bridges. Alpha-helices are visible in the ranges 25 to 35, 90 to 100, and 120 to 125.
Rosetta++ is freely distributed software used to predict all possible protein conformations by calculating the folding energy of the protein sequences. An included docking function is used to simulate a protein binding as homo- and hetero-dimers or trimers structures. This program is used to explore the possible conformations of one protein, which may not be easily found in the traditional approaches, such as NMR and crystallography. From these computer models, we can predict denatured and aggregate forms of proteins.