2 research outputs found
Ion Binding and Internal Hydration in the Multidrug Resistance Secondary Active Transporter NorM Investigated by Molecular Dynamics Simulations
Recently, a 3.65 Ã… resolution structure of the transporter
NorM from the multidrug and toxic compound extrusion family has been
determined in the outward-facing conformation. This antiporter uses
electrochemical gradients to drive substrate export of a large class
of antibiotic and toxic compounds in exchange for small monovalent
cations (H<sup>+</sup> and Na<sup>+</sup>), but the molecular details
of this mechanism are still largely unknown. Here we report all-atom
molecular dynamics simulations of NorM, with and without the bound
Na<sup>+</sup> cation and at different ion concentrations. Spontaneous
binding of Na<sup>+</sup> is observed in several independent simulations
with transient ion binding to D36 being necessary to reach the final
binding site for which two competitive binding modes occur. Finally,
the simulations indicate that the extracellular vestibule of the transporter
invariably loses its characteristic V shape indicated by the crystallographic
data, and it is reduced to a narrow permeation pathway lined by polar
residues that can act as a specific pore for the transport of small
cations. This event, together with the available structures of evolutionarily
related transporters of the major facilitator superfamily (MFS), suggests
that differences in the hydrophobic content of the extracellular vestibule
may be characteristic of multidrug resistance transporters in contrast
to substrate-selective members of the MFS
Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle
A combined strategy based on the
computation of absorption energies,
using the ZINDO/S semiempirical method, for a statistically relevant
number of thermally sampled configurations extracted from QM/MM trajectories
is used to establish a one-to-one correspondence between the structures
of the different early intermediates (dark, batho, BSI, lumi) involved
in the initial steps of the rhodopsin photoactivation mechanism and
their optical spectra. A systematic analysis of the results based
on a correlation-based feature selection algorithm shows that the
origin of the color shifts among these intermediates can be mainly
ascribed to alterations in intrinsic properties of the chromophore
structure, which are tuned by several residues located in the protein
binding pocket. In addition to the expected electrostatic and dipolar
effects caused by the charged residues (Glu113, Glu181) and to strong
hydrogen bonding with Glu113, other interactions such as π-stacking
with Ala117 and Thr118 backbone atoms, van der Waals contacts with
Gly114 and Ala292, and CH/Ï€ weak interactions with Tyr268, Ala117,
Thr118, and Ser186 side chains are found to make non-negligible contributions
to the modulation of the color tuning among the different rhodopsin
photointermediates