The simulations
were based on the crystal structure of the oxidized form of bovine
heart cytochrome c (PDB entry: 2B4Z) using the GROMOS1122 software and the GROMOS 54A723 force field. The crystal structure was modified by removing
the covalent bond between the heme and His 18 and Met 80, while adding
the thioether bridges to the heme vinyl groups through Cys 14 and
Cys 17. The simulations of the reduced form used the same initial
structure but different charge parameters on the heme. The GROMOS++24 package was used for simulation analysis. The
dihedral-based secondary structure classification was based on the
work of Hollingsworth et al.25 (link) The precise
simulation settings are described in theSupporting
Information .
were based on the crystal structure of the oxidized form of bovine
heart cytochrome c (PDB entry: 2B4Z) using the GROMOS1122 software and the GROMOS 54A723 force field. The crystal structure was modified by removing
the covalent bond between the heme and His 18 and Met 80, while adding
the thioether bridges to the heme vinyl groups through Cys 14 and
Cys 17. The simulations of the reduced form used the same initial
structure but different charge parameters on the heme. The GROMOS++24 package was used for simulation analysis. The
dihedral-based secondary structure classification was based on the
work of Hollingsworth et al.25 (link) The precise
simulation settings are described in the
Information
