"Bind and Crawl" Association Mechanism of Leishmania Major Peroxidase and Cytochrome C Revealed by Brownian and Molecular Dynamics Simulations.Fields, J.B., Hollingsworth, S.A., Chreifi, G., Heyden, M., Arce, A.P., Magana-Garcia, H.I., Poulos, T.L., Tobias, D.J.
(2015) Biochemistry 54: 7272
- PubMed: 26598276
- DOI: 10.1021/acs.biochem.5b00569
- PubMed Abstract:
Leishmania major, the parasitic causative agent of leishmaniasis, produces a heme peroxidase (LmP), which catalyzes the peroxidation of mitochondrial cytochrome c (LmCytc) for protection from reactive oxygen species produced by the host. The associat ...
Leishmania major, the parasitic causative agent of leishmaniasis, produces a heme peroxidase (LmP), which catalyzes the peroxidation of mitochondrial cytochrome c (LmCytc) for protection from reactive oxygen species produced by the host. The association of LmP and LmCytc, which is known from kinetics measurements to be very fast (∼10(8) M(-1) s(-1)), does not involve major conformational changes and has been suggested to be dominated by electrostatic interactions. We used Brownian dynamics simulations to investigate the mechanism of formation of the LmP-LmCytc complex. Our simulations confirm the importance of electrostatic interactions involving the negatively charged D211 residue at the LmP active site, and reveal a previously unrecognized role in complex formation for negatively charged residues in helix A of LmP. The crystal structure of the D211N mutant of LmP reported herein is essentially identical to that of wild-type LmP, reinforcing the notion that it is the loss of charge at the active site, and not a change in structure, that reduces the association rate of the D211N variant of LmP. The Brownian dynamics simulations further show that complex formation occurs via a "bind and crawl" mechanism, in which LmCytc first docks to a location on helix A that is far from the active site, forming an initial encounter complex, and then moves along helix A to the active site. An atomistic molecular dynamics simulation confirms the helix A binding site, and steady state activity assays and stopped-flow kinetics measurements confirm the role of helix A charges in the association mechanism.
Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States.