Structures of enzyme-substrate complexes of lysozyme

Area of Science:

• Biochemistry
• Structural Biology
• Computational Chemistry

Background:

• Lysozyme (mucopeptide N-acetylmuramoylhydrolase) is a crucial enzyme in bacterial cell wall hydrolysis.
• Understanding oligosaccharide binding to lysozyme is key to elucidating its enzymatic mechanism.

Purpose of the Study:

• To determine the binding structures of N-acetylglucosamine (GlcNAc) oligosaccharides, specifically (GlcNAc)5 and (GlcNAc)6, within the rigid active site of lysozyme.
• To investigate the conformational preferences of added saccharide residues during binding.

Main Methods:

• Conformational energy calculations were employed to model the binding of oligosaccharides.
• Energy minimization was performed on complexes of lysozyme with (GlcNAc)4, (GlcNAc)5, and (GlcNAc)6.
• Calculated structures were compared with existing experimental data.

Main Results:

• The most stable binding conformation for the fifth GlcNAc residue in (GlcNAc)5 was found to be similar to a left-handed helical structure.
• The sixth GlcNAc residue in (GlcNAc)6 also adopted a left-handed helical conformation.
• Stable binding regions for the fifth and sixth residues were identified near arginyl 45 and asparaginyl 46.
• The C site within the lysozyme active site exhibited the lowest binding energy for GlcNAc.

Conclusions:

• The study provides detailed insights into the binding modes of longer oligosaccharides within the lysozyme active site.
• Computational modeling supports experimental observations regarding GlcNAc binding.
• The findings contribute to a deeper understanding of enzyme-substrate interactions in carbohydrate-active enzymes.