1 research outputs found
Unraveling the Conformational Landscape of Ligand Binding to Glucose/Galactose-Binding Protein by Paramagnetic NMR and MD Simulations
Protein dynamics
related to function can nowadays be structurally
well characterized (i.e., instances obtained by high resolution structures),
but they are still ill-defined energetically, and the energy landscapes
are only accessible computationally. This is the case for glucoseāgalactose
binding protein (GGBP), where the crystal structures of the apo and
holo states provide structural information for the domain rearrangement
upon ligand binding, while the time scale and the energetic determinants
for such concerted dynamics have been so far elusive. Here, we use
GGBP as a paradigm to define a functional conformational landscape,
both structurally and energetically, by using an innovative combination
of paramagnetic NMR experiments and MD simulations. Anisotropic NMR
parameters induced by self-alignment of paramagnetic metal ions was
used to characterize the ensemble of conformations adopted by the
protein in solution while the rate of interconversion between conformations
was elucidated by long molecular dynamics simulation on two states
of GGBP, the closed-liganded (<i>holo_cl</i>) and open-unloaded
(<i>apo_op</i>) states. Our results demonstrate that, in
its apo state, the protein coexists between open-like (68%) and closed-like
(32%) conformations, with an exchange rate around 25 ns. Despite such
conformational heterogeneity, the presence of the ligand is the ultimate
driving force to unbalance the equilibrium toward the <i>holo_cl</i> form, in a mechanism largely governed by a conformational selection
mechanism