Molecular Dynamics Group, University of Queensland
Molecular Dynamics Group, University of Groningen

MD

Tutorial

Hen Egg White Lysozyme



The exersise will use the protein lysozyme as an example. Lysozyme is an enzyme which functions to hydrolyze the β(1-4) glycosidic bond between residues of N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) in certain polysaccharides. Substrates of lysozyme include:

For these exercises the protein lysozyme will be used. Lysozyme acts to hydrolyze the β(1-4) glycosidic bonds between residues of N-acetylmuramic acid (NAM) and/or N-acetylglucosamine (NAG) in certain polysaccharides. The substrates of this enzyme include chitin, which is a NAG-polymer found in crustacean shell tissue and the polysaccharide component of the cell walls of certain bacteria.

The principle function of lysozyme is bactericidal. By disrupting the cell wall, the bacteria looses it's integrity and dies. The polysaccharide found in bacterial cell walls is composed of alternating residues of NAG and NAM. Only the glycosidic bonds between the C1 of NAM and the C4 of NAG are hydrolyzed. The diagram below shows the backbone structure of a bacterial cell wall polysaccharide. Oligopeptide side chains may be bonded to the sugar residues.

The structure



Lysozyme consists of a single polypeptide chain of 129 residues. It has an alpha+beta fold, consisting of five to seven alpha helices (depending on the species) and a three-stranded antiparallel beta sheet. The enzyme is approximately ellipsoidal in shape, with a large cleft in one side forming the active site. A model is displayed below:

The principal catalytic residues involved in the hydrolysis are glutamate 35 and asparagine 52. More information on this protein can be found in:

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