Jing Li, Zhiyu Zhao, and Emad Tajkhorshid.
Locking two rigid-body bundles in an outward-facing conformation: A
general ion-coupling mechanism in LeuT-fold transporters.
Scientific Reports, 9:19479, 2019.
(PMC: PMC6925253)
LI2019-ET
In secondary active transporters, electrochemical gradient of ions across the
membrane fuels the ``uphill'' translocation of the substrate via the alternating-
access mechanism. Despite recent significant experimental and computational
studies, how driving ions couple to conformational dynamics of the transporters
remains unclear. In the present study, we employ extended molecular dynamics
(MD) simulations to study the impact of + binding on the structure and
dynamics of a LeuT-fold, +-coupled secondary transporter (Mhp1) in its
major conformational states, i.e., the outward-facing (OF) and inward-facing
(IF) states, as well as on the transition between the states. Microseconds
equilibrium MD simulations clearly illustrate that + stabilizes an OF
conformation favorable for substrate association, by binding to a highly
conserved site at the interface between the two helical bundles and restraining
their relative position and motion in the OF state. Furthermore, !
a special-protocol time-dependent biased simulation for state transition
estimates that + binding increases the barrier along the
OF
IF transition. These synergistic + binding effects
allosterically couple the ion and substrate binding sites and modify the kinetics
of state transition, which together increase the lifetime of an OF conformation
with high affinity for substrate binding, thereby facilitating capturing the
substrate efficiently from a low-concentration environment to fulfill the
physiological function of the transporter. Based on the similarity between our
findings for Mhp1 and experimental reports on LeuT, we propose that this model
may represent a general +-coupling mechanism among LeuT-fold
transporters deeply rooted in their common architecture.
IF transition. These synergistic + binding effects
allosterically couple the ion and substrate binding sites and modify the kinetics
of state transition, which together increase the lifetime of an OF conformation
with high affinity for substrate binding, thereby facilitating capturing the
substrate efficiently from a low-concentration environment to fulfill the
physiological function of the transporter. Based on the similarity between our
findings for Mhp1 and experimental reports on LeuT, we propose that this model
may represent a general +-coupling mechanism among LeuT-fold
transporters deeply rooted in their common architecture.
