The inhibition mechanism of carp (Cyprinus carpio) stefin to cathepsin B and their tertiary structures

Carp is a major economic species. However, fish or surimi gel will easily soften during processing or storage due to its abundant endogenous protease, which will seriously affect the product quality. Because of the high inhibitory activity to cysteine protease, stefin has great potential as an additive for the improvement of fish softening. In this study, molecular dynamics simulation was used to explore the inhibition mechanism of carp stefin to cathepsin B (CTS B) and their tertiary structures. The results showed that carp stefin is a single domain protein with four stranded beta-sheets and a alpha-helix. CTS B is a typical papain-like fold containing two domains. During the inhibition process, the wedge-shaped structure created by N-terminal trunk and the two hairpin loops of stefin would insert into the groove between two domains of CTS B. Besides, the inhibition can be spontaneous in pure water through hydrogen bonding, VDW and electrostatic interactions. And the Cys3, His83 and Val49 of carp stefin were the critical residues for the inhibition to CTS B. The results may provide a theoretical reference for the application of stefin in the processing and storage of fish products.

Automated summary

This study used molecular dynamics simulation to explore the inhibition mechanism of carp stefin to cathepsin B, revealing the structural features and critical residues involved in the inhibition process. The results may offer theoretical insights for the application of stefin in the processing and storage of fish products.