Molecular modeling of full-length OxyR from Shewanella oneidensis MR-1 and molecular dynamics studies of the activation domain

OxyR is a transcriptional factor, which activates transcription of antioxidant genes. In this study, we constructed a structural model for the full-length OxyR from Shewanella oneidensis MR-1 using threading and comparative modeling techniques. To further study the conformational changes, we also performed molecular dynamics simulations on the activation domain of OxyR. Molecular dynamics simulations were performed using GROMACS force field under periodic boundary conditions. The particle mesh Ewald (PME) method was used to treat long-range electrostatic interactions. The simulation results show that the oxidized form is very stable while the reduced form is quite flexible. Our results suggest that the reduced form provides structural flexibility for disulfide bond formation and which in turn regulates its function.