Sonolysis of High Macroviscosity Systems: Hen Albumen Hydrogel

Abstract

To understand molecular effects of ultrasound on protein gels (cross-linked, hydrated macromolecular systems of immeasurably high macroviscosity, but low microviscosity), the thick fraction of hen albumen was sonicated. The immeasurably high viscosity of the intact thick fraction decreased to 2.5-4.0 mPa·s (depending on the sample) after a 12 min sonication (0.14 mM of radicals were produced and 19 J g(-1) of thermal energy absorbed) indicating that the 3D protein network was degraded. SDS-PAGE analysis indicated the breaking of intermolecular S-S bridges holding together the protein network rather than the primary structure of constituent proteins. Despite the relatively large concentration of OH radical produced in the sonication time range applied, no protein cross-linking was observed which can be attributed to the high degree of protein glycosylation and protein immobility. Differential scanning calorimetry (DSC) showed that both the amount of bound water and the enthalpy of denaturation of the constituent proteins are not affected by sonication, which is consistent with the SDS-PAGE results. A small increase in sample turbidity can be attributed to the small extent of thermal denaturation occurring in the vicinity of cavitation sites.

CDR-H3 loop ensemble in solution – conformational selection upon antibody binding

“…These structural changes can be understood in terms of conformational selection because, even without the antigen present, the conformation involved in the binding process can frequently be accessed. 22,23 Additionally, the CDR-L3 loop shows fewer clusters by using a smaller distance cut-off compared to the CDR-H3 loop, indicating a higher flexibility. Figure 1 (bottom) emphasizes the structural diversity and the high flexibility of the CDR-H3 loop.…”

“…This paradigm follows the idea of an ensemble of pre-existing conformations with different probabilities from which the binding-competent state is selected. 21,22 Transitions between different states in this preexisting conformational space can occur on different timescales, and therefore calculations of the thermodynamics and kinetics are essential for better understanding and characterization of their conformational diversity. 23 In this study, we applied metadynamics in combination with classical molecular dynamics (MD) simulations as a reliable tool to capture the structural and the dynamic properties of proteinbinding, peptide-binding and hapten-binding antibody CDR-H3 loops.…”