In silico prediction of amino acids involved in cCPE۲۹۰-۳۱۹ interaction with claudin ۴

Among the ۲۶ human claudin proteins, the food-poisoning bacterium Clostridium perfringens produces an enterotoxin (~ ۳۵.۰۰ kDa) that specifically targets human claudin ۴, causing diarrhea by fluid accumulation in the intestinal cavity. The Clostridium perfringens enterotoxin (CPE) C-terminal domain (cCPE ~ ۱۵.۰۰ kDa) tightly binds to claudin ۴ and disrupts the tight junction barriers in the intestines. In this study, we aimed to determine the contribution and type of amino acid interactions involved in association between claudin ۴ and the C-terminal CPE. First, the three-dimensional format of claudin ۴ was downloaded from RCSB. Then, during ۶۰.۰۰ nanoseconds (nsec), molecular dynamics simulation was conducted using the GROMACS package on CPE of crystallographic structure. The results indicated that the simulations performed well during the simulation times and there were no noticeable problems or artifacts. We found that Coulombic (glycine ۳۱۷, proline ۳۱۱ and serine ۳۱۳) and Lennard-Jones (tyrosine ۳۱۰, leucine ۳۱۵, serine ۳۱۳ and glycine ۳۱۷) interactions played a significant role in complex stability. This information localized the C-terminal of CPE as a linear sequence sufficient for recognition and binding to the eukaryotic CPE receptor. A detailed description of the dissociation process brings valuable insight into the interaction of the claudin ۴-cCPE۲۹۰-۳۱۹ complexes, which could help in the future to design more potent drugs.

Keywords:

Claudin , Clostridium perfringens , Interaction , Molecular Dynamics Simulation