Conformational energy refinement of horse-heart ferricytochrome c.

The research study is about the refinement of the X-ray structure of horse-heart ferricytochrome c using conformational energy calculations. The results showed a successful refinement that resembles the X-ray structure closely and exhibits a low conformational energy.

Methodology

The methodology of this research consisted of a three-stage computational procedure for conformational energy calculations:

• Stage I involved the adjustment of atomic positions to meet idealized bond lengths and angles typical of small amino acid derivatives, while maintaining as close proximity as possible to the X-ray coordinates.
• Stage II saw the elimination of atomic overlaps through the adjustment of the backbone and side-chain dihedral angles to minimize the nonbonded energy, hydrogen-bonded energy, and rotational energy contributions.
• In Stage III, the final stage, the researchers accounted for the electrostatic energy and a more accurate hydrogen-bonded energy treatment, in addition to the energy contributions evaluated in stage II. A gradually decreasing “fitting potential” was imposed during stages II and III, aimed to keep the computed structure as similar to the x-ray structure while maintaining a low-energy conformation.

Findings

The result of the computational procedure was a refined computed structure of cytochrome c that exhibited a low conformational energy of -504 kcal/mol. The computed structure closely resembled the X-ray structure, with a Root Mean Square (RMS) deviation of 0.77 Å for all atoms.

Special Treatment

During the process, a special treatment was needed for the phenylalanine-82 component. The initial X-ray structure showed the phenyl ring of this component pointing away from the heme. However, in the final computed structure, the phenyl ring was tucked into the heme crevice. This position is similar to that observed in the reduced form of tuna cytochrome c, in the oxidized form of Rhodospirillum rubrum cytochrome c2, and also in the recently determined structure of oxidized tuna cytochrome c, showing consistent alignment with other related structures.