5I4Y

Exploring onset of lysozyme denaturation by urea: soak period 10 hours.

Summary for 5I4Y

• Entry DOI: 10.2210/pdb5i4y/pdb
• Related: 5I4W 5I4X 5I53 5I54
• Descriptor: Lysozyme C, UREA, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: lysozyme, denaturation, urea, hydrolase
• Biological source: Gallus gallus (Chicken)
• Cellular location: Secreted: P00698
• Total number of polymer chains: 1
• Total formula weight: 15627.77

Authors

Hosur, M.V.,Raskar, T.,Khavnekar, S. (deposition date: 2016-02-13, release date: 2017-02-15, Last modification date: 2024-10-23)

Primary citation

Raskar, T.,Khavnekar, S.,Hosur, M.
Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation
Sci Rep, 6:32277-32277, 2016

PubMed Abstract: Temporal binding of urea to lysozyme was examined using X-ray diffraction of single crystals of urea/lysozyme complexes prepared by soaking native lysozyme crystals in solutions containing 9 M urea. Four different soak times of 2, 4, 7 and 10 hours were used. The five crystal structures (including the native lysozyme), refined to 1.6 Å resolution, reveal that as the soaking time increased, more and more first-shell water molecules are replaced by urea. The number of hydrogen bonds between urea and the protein is similar to that between protein and water molecules replaced by urea. However, the number of van der Waals contacts to protein from urea is almost double that between the protein and the replaced water. The hydrogen bonding and van der Waals interactions are initially greater with the backbone and later with side chains of charged residues. Urea altered the water-water hydrogen bond network both by replacing water solvating hydrophobic residues and by shortening the first-shell intra-water hydrogen bonds by 0.2 Å. These interaction data suggest that urea uses both 'direct' and 'indirect' mechanisms to unfold lysozyme. Specific structural changes constitute the first steps in lysozyme unfolding by urea.

PubMed: 27573790
DOI: 10.1038/srep32277

Experimental method

X-RAY DIFFRACTION (1.607 Å)