Paper Citing NAMD - Abstract
Kokhan, Oleksandr; Wraight, Colin A.; Tajkhorshid, Emad
The Binding Interface of Cytochrome c and Cytochrome c(1) in the bc(1) Complex: Rationalizing the Role of Key Residues
BIOPHYSICAL JOURNAL, 99:2647-2656, OCT 20 2010
The interaction of cytochrome c with ubiquinol-cytochrome c oxidoreductase (bc(1) complex) has been studied for >30 years, yet many aspects remain unclear or controversial. We report the first molecular dynamic simulations of the cyt c-bc(1) complex interaction. Contrary to the results of crystallographic studies, our results show that there are multiple dynamic hydrogen bonds and salt bridges in the cyt c-c(1) interface. These include most of the basic cyt c residues previously implicated in chemical modification studies. We suggest that the static nature of x-ray structures can obscure the quantitative significance of electrostatic interactions between highly mobile residues. This provides a clear resolution of the discrepancy between the structural data and functional studies. It also suggests a general need to consider dynamic interactions of charged residues in protein-protein interfaces. In addition, a novel structural change in cyt c is reported, involving residues 21-25, which may be responsible for cyt c destabilization upon binding. We also propose a mechanism of interaction between cyt c(1) monomers responsible for limiting the binding of cyt c to only one molecule per bc(1) dimer by altering the affinity of the cytochrome c binding site on the second cyt c(1) monomer.
