Comparative Simulations
of the Ground State and the
M-Intermediate State of the Sensory Rhodopsin II–Transducer
Complex with a HAMP Domain Model
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Abstract
The complex of sensory rhodopsin II (SRII) and its cognate
transducer
HtrII (2:2 SRII–HtrII complex) consists of a photoreceptor
and its signal transducer, respectively, associated with negative
phototaxis in extreme halophiles. In this study to investigate how
photoexcitation in SRII affects the structures of the complex, we
conducted two series of molecular dynamics simulations of the complex
of SRII and truncated HtrII (residues 1–136) of <i>Natronomonas
pharaonis</i> linked with a modeled HAMP domain in the lipid
bilayer using the two crystal structures of the ground state and the
M-intermediate state as the starting structures. The simulation results
showed significant enhancements of the structural differences observed
between the two crystal structures. Helix F of SRII showed an outward
motion, and the C-terminal end of transmembrane domain 2 (TM2) in
HtrII rotated by ∼10°. The most significant structural
changes were observed in the overall orientations of the two SRII
molecules, closed in the ground state and open in the M-state. This
change was attributed to substantial differences in the structure
of the four-helix bundle of the HtrII dimer causing the apparent rotation
of TM2. These simulation results established the structural basis
for the various experimental observations explaining the structural
differences between the ground state and the M-intermediate state