Crowder-specific modulation of hepatitis C virus NS3/4A protease activity and local structural dynamics

Macromolecular crowding modulates enzyme behavior in crowder- and protein-specific ways, yet its impact on viral proteases, which are often key therapeutic targets, remains unclear. Here, we investigated the hepatitis C virus NS3/4A protease under increasing concentrations of polyethylene glycols (PEGs), ficoll, dextran, and lysozyme using fluorescence-based assays to examine enzyme kinetics, local Trp environments, thermal stability, and rotational restriction of the fluorescent probe in the surrounding medium. PEGs reduced catalytic activity while leaving substrate binding either unaffected or slightly enhanced. These effects were accompanied by a moderate tryptophan fluorescence spectral narrowing, consistent with reduced heterogeneity in local conformational environments. In contrast, ficoll enhanced catalytic efficiency despite stronger fluorescence quenching, indicating local structural changes that favored catalysis. Dextran and lysozyme inhibited protease activity through distinct kinetic patterns, likely reflecting differences in their size, shape, and chemical properties. Thermal analysis revealed crowder-specific local structural changes in NS3/4A without global unfolding up to 65°C, with differences in local stability and flexibility corroborating the observed kinetic effects. Changes in the rotational restriction of the fluorescent probe further indicated that generalized restriction of molecular motion alone could not explain the effects of crowding on NS3/4A. These findings demonstrate that macromolecular crowding modulates NS3/4A catalysis through crowder-specific effects on local structure.