Felix Autenrieth, Emad Tajkhorshid, Klaus Schulten, and Zaida Luthey-Schulten.
Role of water in transient cytochrome c2 docking.
Journal of Physical Chemistry B, 108:20376-20387, 2004.
AUTE2004
Cytochrome c (cyt c) is a small water-soluble redox protein that facilitates electron
transfer in photosynthesis and respiration by alternately docking to integral membrane
proteins such as the photosynthetic reaction center (RC). Recently, a high resolution X-ray
structure was solved for the RC-cyt complex of Rhodobacter sphaeroides,
revealing important contacts between the RC in its ground state and reduced cyt
mediated by bridging water molecules. In this article we compare the variations in
these contacts and in the interface in general for both redox states of cyt that
resulted from full-atom simulations of the complexes embedded in a membrane with
explicit water molecules. Molecular dynamics simulations of the two redox states of the
RC-cyt system were performed using the CHARMM27 parameters developed for
the oxidized and reduced forms of the heme prosthethic group. In its overall dynamics
the encounter complex was found to be very similar in both redox states, exhibiting at the
interface a stable hydrophobic tunnelling domain and a broad basin of attraction. The
differences between the redox states are subtle and involve the formation of a structured
cluster of water molecules in the reduced cyt system. Fluctuations of water and
residues at the interface increase upon oxidation and probably mediate the undocking
process. The observed differences between the two redox states of the system can only be
attributed to the different electrostatic potentials generated by heme in the interface
region, as no other modifications were introduced. As the time scale of the undocking
process is beyond the time scales reachable by full atomic molecular dynamics simulation
of the system, we employed steered molecular dynamics to investigate and compare the
energetics associated with the unbinding of RC-cyt in the reduced and oxidized
forms.
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