Structure and Inhibition of the SARS Coronavirus Envelope Protein Ion Channel

Pervushin, Konstantin; Tan, Edward; Parthasarathy, Krupakar; Lin, Xin; Jiang, Feng Li; Yu, Dejie; Vararattanavech, Ardcharaporn; Soong, Tuck Wah; Liu, Ding Xiang; Torres, Jaume

The energy minimization and all the restrained MD simulations were performed using GROMACS [64] at an atomistic level of detail, using the OPLS-AA [65] force field. Atomic charges were assigned on the basis of the default atomic charge values specified in the OPLS-AA force field. The Van der Waals interactions were modeled using a cut-off distance of 9.0 Ã… . In the simulation, the cell temperature was maintained at 298.15 K using the Berendsen temperature coupling algorithm. The Berendsen pressure coupling algorithm was applied to maintain the pressure of 1.0 bar. With backbone positions restrained, each inter-helical distance constraint includes a 500 ps simulation, enough for the side chains to move into a conformation that is constraint allowed. The lumenal dimensions for the pentameric model were calculated using HOLE [66] and were visualized using VMD [67] .