Leishmania major peroxidase (LmP) is structurally and functionally similar to the well-studied yeast Cytochrome c peroxidase (CCP). A recent Brownian dynamics study showed that L. major Cytochrome c (LmCytc) associates with LmP by forming an initial complex with the N-terminal helix A of LmP， followed by a movement toward the electron transfer (ET) site observed in the LmP-LmCytc crystal structure. Critical to forming the active electron transfer complex is an intermolecular Arg-Asp ion pair at the center of the interface. If the dissociation reaction is effectively the reverse of the association reaction， then rupture of the Asp-Arg ion pair should be followed by movement of LmCytc back toward LmP helix A.... More
Leishmania major peroxidase (LmP) is structurally and functionally similar to the well-studied yeast Cytochrome c peroxidase (CCP). A recent Brownian dynamics study showed that L. major Cytochrome c (LmCytc) associates with LmP by forming an initial complex with the N-terminal helix A of LmP， followed by a movement toward the electron transfer (ET) site observed in the LmP-LmCytc crystal structure. Critical to forming the active electron transfer complex is an intermolecular Arg-Asp ion pair at the center of the interface. If the dissociation reaction is effectively the reverse of the association reaction， then rupture of the Asp-Arg ion pair should be followed by movement of LmCytc back toward LmP helix A. To test this possibility， we have performed multiple molecular dynamics (MD) simulations of the LmP-LmCytc complex. In five separate simulations， LmCytc is observed to indeed move toward helix A， and in two of the simulations， the Asp-Arg ion pair breaks， which frees LmCytc to fully associate with the LmP helix A secondary binding site. These results support the "bind and crawl" or "velcro" mechanism of association， wherein LmCytc forms a nonspecific electrostatic complex with LmP helix A， followed by a "crawl" toward the ET-active site， where the Asp-Arg ion pair holds the LmCytc in position for rapid ET. These simulations also point to Tyr134 as being important in the association/dissociation reactions. Experimentally mutating Tyr134 to Phe was found to decrease K by 3.6-fold， which is consistent with its predicted role in complex formation by MD simulations.
