Local Xenon–Protein Interaction Produces Global Conformational Change and Allosteric Inhibition in Lysozyme

Abstract

Noble gases have well-established biological effects, yet their molecular mechanisms remain poorly understood. Here, we investigated, both experimentally and computationally, the molecular modes of xenon (Xe) action in bacteriophage T4 lysozyme (T4L). By combining indirect gassing methods with a colorimetric lysozyme activity assay, a reversible, Xe-specific (20 ± 3)% inhibition effect was observed. Accelerated molecular dynamic simulations revealed that Xe exerts allosteric inhibition on the protein by expanding a C-terminal hydrophobic cavity. Xe-induced cavity expansion results in global conformational changes, with long-range transduction distorting the active site where peptidoglycan binds. Interestingly, the peptide substrate binding site that enables lysozyme specificity does not change conformation. Two T4L mutants designed to reshape the C-terminal Xe cavity established a correlation between cavity expansion and enzyme inhibition. This work also highlights the use of Xe flooding simulations to identify new cryptic binding pockets. These results enrich our understanding of Xe–protein interactions at the molecular level and inspire further biochemical investigations with noble gases.

What is allosteric regulation? Exploring the exceptions that prove the rule!

“…(The exception is when sampling rates and magnitudes of the amplitudes of change are directly opposed so that changes in dynamics do not alter the average conformation ( 58 ).) As examples, when comparing the free enzyme E to the EA complex in Figure 1 C , changes in the average conformation may arise because of changes in positions of side chains and secondary structures, in internal protein motions, in localized folding and unfolding events ( e.g ., biotin protein ligase) ( 59 , 60 , 61 , 62 , 63 , 64 , 65 ), in internal protein cavities ( e.g ., phosphofructokinase) ( 66 , 67 ) and in ordered waters ( e.g ., hemoglobin) ( 68 , 69 , 70 ). However, rather than equating allosteric regulation with ligand binding (which is the comparison of only two enzyme complexes as exemplified in the E and EA comparison), the energy cycle approach defines allosteric regulation of a K-type system as a change in the binding of A caused by the presence of bound X.…”