Paper Citing NAMD - Abstract
Kokhan, Oleksandr; Shinkarev, Vladimir P.; Wraight, Colin A.
Binding of Imidazole to the Heme of Cytochrome c(1) and Inhibition of the bc(1) Complex from Rhodobacter sphaeroides I. EQUILIBRIUM AND MODELING STUDIES
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:22513-22521, JUL 16 2010
We have used imidazole (Im) and N-methylimidazole (MeIm) as probes of the heme-binding cavity of membrane-bound cytochrome (cyt) c(1) in detergent-solubilized bc(1) complex from Rhodobacter sphaeroides. Imidazole binding to cyt c1 substantially lowers the midpoint potential of the heme and fully inhibits bc1 complex activity. Temperature dependences showed that binding of Im (K-d approximate to 330 mu M, 25 degrees C, pH 8) is enthalpically driven (Delta H-0 = -56 kJ/mol, Delta S-0 = -121 J/mol/K), whereas binding of MeIm is 30 times weaker (K-d approximate to 9.3 mM) and is entropically driven (Delta H-0 = 47 kJ/mol, Delta S-0 degrees = 197 J/mol/K). The large enthalpic and entropic contributions suggest significant structural and solvation changes in cyt c1 triggered by ligand binding. Comparison of these results with those obtained previously for soluble cyts c and c(2) suggested that Im binding to cyt c(1) is assisted by formation of hydrogen bonds within the heme cleft. This was strongly supported by molecular dynamics simulations of Im adducts of cyts c, c2, and c1, which showed hydrogen bonds formed between the N delta H of Im and the cyt c(1) protein, or with a water molecule sequestered with the ligand in the heme cleft.
