The active site of hen egg-white lysozyme: flexibility and chemical bonding

Abstract

Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM;Bader (1994), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254-1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337-351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C-HÁ Á ÁO hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.

In-depth understanding of a nano-bio interface between lysozyme and Au NP-immobilized N-doped reduced graphene oxide 2-D scaffolds

“…The enzyme Lys contains two domains, the a-domain and b-domain, 61 and its active site exists inside a deep ssure, where a proton is donated by the side chain of Glu35 present in the a-helical domain to the glycosidic oxygen of the anomeric carbon in the sugar of the bacterium cell wall. 65,66 During hydrolysis, Asp52 plays a crucial role by stabilizing the intermediate formed in the process. [65][66][67] The loading of Lys on Au(0)-NrGO led to a decline in its activity at all concentrations of Au(0)-NrGO.…”

Purification of Egg White Lysozyme from Indonesian Kampung Chicken and Ducks

“…EWL is mostly active against Gram-positive bacteria, while Gramnegative bacteria are relatively resistant as the peptidoglycan layer of Gram-negative bacteria is protected by outer membrane compartment (Turner et al, 2013). The mechanism by which EWL hydrolyzes the β(1-4) glycosidic linkages from NAM to NAG is well studied (Wohlkonig et al, 2010;Held & Smaalen, 2014). The reaction is likely proceeds via a covalent intermediate mechanism, in which Glu35 and Asp52 act as acid and covalent catalysts, respectively.…”

Alginate as a support ligand for enhanced colloidal liquid aphron immobilization of proteins and drug delivery

“…Lysozyme's active site is created by an acidic cleft comprised of aspartic and glutamic acids. As explained by Held and van Smaalen () and Sun, Liao, and Remington (), the active site is stabilized and interacts with substrates via ionic interactions. Due to the nature of the enzyme, it is quite possible that the active site was destabilized as a result of electrostatic interactions induced by alginate.…”