Functional sites of cytochrome c and other electron carrier proteins: semi-empirical molecular orbital program PM3 applied to the conformational analysis of Cys-X1-X2-Cys peptides.
The semi-empirical molecular orbital program, MOPAC version 6.0, PM3 was applied to estimate the distance between two sulfur atoms of two Cys side chains in optimized conformers of Cys-X1-X2-Cys sequences, as well as the total energy of that conformer relative to the most stable one. Some Cys-X1-X2-Cys tetrapeptides found in cytochrome c were optimized to conformers whose sulfur-sulfur distances were just suitable for binding to heme, whereas some tetrapeptides not found in cytochrome c were unable to be optimized to heme-binding conformers. Similarly, Cys-X1-X2-Cys tetrapeptides found in [4Fe-4S]ferredoxin were optimized to [4Fe-4S]-binding conformers, etc. The tetrapeptides found in the redox site of thioredoxin were optimized to conformers in which the two sulfur atoms were in van der Waals contact, so that a disulfide bond may be formed during the function. The conclusion has been drawn that the combination of X1 and X2 in a Cys-X1-X2-Cys sequence may be determining for that sequence to be a functional redox site in an electron carrier protein.
Shimura
M
M
Department of Chemistry, Shizuoka University, Japan.
Hirota
F
F
Yagi
T
T
D000595:Amino Acid Sequence; D001665:Binding Sites; D003574:Cytochrome c Group / Q000737:chemistry*; D004579:Electron Transport; D007506:Iron-Sulfur Proteins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D012416:Rubredoxins / Q000737:chemistry*; D013329:Structure-Activity Relationship
D003574:Cytochrome c Group; D007506:Iron-Sulfur Proteins; D012416:Rubredoxins