Varying molecular interactions explain crowder-dependent enzyme function of a viral protease

Biochemical processes in cells, including enzyme-catalyzed reactions, occur in crowded conditions with various background macromolecules occupying up to 40% of cytoplasm’s volume. Viral enzymes in the host cell also encounter such crowded conditions as they often function at the endoplasmic reticulum membranes. We focus on an enzyme encoded by the hepatitis C virus, the NS3/4A protease, which is crucial for viral replication. We have previously found experimentally that synthetic crowders, polyethylene glycol (PEG) and branched polysucrose (Ficoll), differently affect the kinetic parameters of peptide hydrolysis catalyzed by NS3/4A. To gain understanding of the reasons for such behavior, we perform atomistic molecular dynamics simulations of NS3/4A in the presence of either PEG or Ficoll crowders and with and without the peptide substrates. We find that both crowder types make nanosecond long contacts with the protease and slow down its diffusion. However, they also affect the enzyme structural dynamics; crowders induce functionally relevant helical structures in the disordered parts of the protease cofactor, NS4A, with the PEG effect being more pronounced. Overall, PEG interactions with NS3/4A are slightly stronger but Ficoll forms more hydrogen bonds with NS3. The crowders also interact with substrates; we find that the substrate diffusion is reduced much more in the presence of PEG than Ficoll. However, contrary to NS3, the substrate interacts more strongly with Ficoll than with PEG crowders, with the substrate diffusion being similar to crowder diffusion. Importantly, crowders affect also the substrate-enzyme interactions. We observe that both PEG and Ficoll enhance the presence of substrates near the active site, especially near catalytic His57 but Ficoll crowders increase substrate binding more than PEG molecules. The presence of crowders also enhances the stability of Zn2+ ion coordination necessary for structural stability of NS3/4A enabling catalysis. AUTHOR SUMMARY Enzyme-catalyzed reactions in reality occur in the crowded environment of the cell. Therefore, viruses entering the host cells also encounter a crowded surrounding in which the viral enzymes are replicated. One such enzyme is the NS3/4A protease encoded by the hepatitis C virus. This enzyme is crucial for viral replication and is used as the therapeutic target for clinically approved drugs. To gain understanding of this enzyme function and explain our previous experiments on its in vitro activity, we performed atomistic molecular dynamics simulations in the presence of synthetic crowders (polyethylene glycol and polysucrose) mimicking the cellular crowd. Based on these simulations we describe in detail how and why these crowders affect the diffusion and structural dynamics of this enzyme and enzyme-substrate interactions. In fact, crowders enhance substrate binding, which may have vast consequences for its function in the host cell and drug-design.