Space and Time Evolution of the Electrostatic Potential during the Activation of a Visual Pigment

Animal and microbial retinal proteins employ the Schiff base of retinal as their chromophore. Here, the possible consequences of the charge translocation associated with the light-induced dynamics of the chromophore of a visual opsin are investigated along a representative semiclassical trajectory. We show that the evolution of the electrostatic potential projected by the chromophore onto the surrounding protein displays intense but topographically localized sudden variations in proximity of the decay region. pKa calculations carried out on selected snapshots used as probes, indicate that the only residue which may be sensitive to the electrostatic potential shift is Glu181. Accordingly, our results suggest that the frail Tyr191/268-Glu181-Wat2-Ser186 hydrogen bond network may be perturbed by the transient variations of the electrostatic potential

Unwrapping of Nucleosomal DNA Ends: A Multiscale Molecular Dynamics Study

AbstractTo permit access to DNA-binding proteins involved in the control and expression of the genome, the nucleosome undergoes structural remodeling including unwrapping of nucleosomal DNA segments from the nucleosome core. Here we examine the mechanism of DNA dissociation from the nucleosome using microsecond timescale coarse-grained molecular dynamics simulations. The simulations exhibit short-lived, reversible DNA detachments from the nucleosome and long-lived DNA detachments not reversible on the timescale of the simulation. During the short-lived DNA detachments, 9 bp dissociate at one extremity of the nucleosome core and the H3 tail occupies the space freed by the detached DNA. The long-lived DNA detachments are characterized by structural rearrangements of the H3 tail including the formation of a turn-like structure at the base of the tail that sterically impedes the rewrapping of DNA on the nucleosome surface. Removal of the H3 tails causes the long-lived detachments to disappear. The physical consistency of the CG long-lived open state was verified by mapping a CG structure representative of this state back to atomic resolution and performing molecular dynamics as well as by comparing conformation-dependent free energies. Our results suggest that the H3 tail may stabilize the nucleosome in the open state during the initial stages of the nucleosome remodeling process

Structural rearrangement at the EC/TM domains interface during ion-channel deactivation.

<p>On top, the location of the strictly conserved proline (P268) at the EC/TM interface is shown. The four transmembrane helices and the position of P268 in the active (red) and resting (green) states are indicated. On bottom, the spatial distribution of the center of mass of the five P268 on the plane parallel to the membrane is shown for GluCl active with (red) and without IVM (blue), and GluCl resting (green). The center of the pore is represented by a large black dot.</p

Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics

<div><p>Pentameric ligand-gated ion channels (pLGICs) mediate intercellular communication at synapses through the opening of an ion pore in response to the binding of a neurotransmitter. Despite the increasing availability of high-resolution structures of pLGICs, a detailed understanding of the functional isomerization from closed to open (gating) and back is currently missing. Here, we provide the first atomistic description of the transition from open to closed (un-gating) in the glutamate-gated chloride channel (GluCl) from <i>Caenorhabditis Elegans</i>. Starting with the active-state structure solved in complex with the neurotransmitter L-glutamate and the positive allosteric modulator (PAM) ivermectin, we analyze the spontaneous relaxation of the channel upon removal of ivermectin by explicit solvent/membrane Molecular Dynamics (MD) simulations. The <i>μ</i>s-long trajectories support the conclusion that ion-channel deactivation is mediated by two distinct quaternary transitions, i.e. a global receptor twisting followed by the radial expansion (or blooming) of the extracellular domain. At variance with previous models, we show that pore closing is exclusively regulated by the global twisting, which controls the position of the <i>β</i>1-<i>β</i>2 loop relative to the M2-M3 loop at the EC/TM domain interface. Additional simulations with L-glutamate restrained to the crystallographic binding mode and ivermectin removed indicate that the same twisting isomerization is regulated by agonist binding at the orthosteric site. These results provide a structural model for gating in pLGICs and suggest a plausible mechanism for the pharmacological action of PAMs in this neurotransmitter receptor family. The simulated un-gating converges to the X-ray structure of GluCl resting state both globally and locally, demonstrating the predictive character of state-of-art MD simulations.</p></div

Receptor twisting versus blooming for the four simulations of GluCl.

<p>The simulations of the end points of gating in green (resting) and red (active) sample values of the twisting and blooming reaction coordinates that are consistent with the X-ray structures of GluCl apo (green diamond) and GluCl with IVM bound (red diamond), respectively. When IVM is removed, a striking evolution of both twisting (from 15° to 22°) and blooming (from 8° to 10°) angles is observed. When only L-Glu is bound (orange) the receptor is partially twisted (<i>τ</i> of 17°) and contracted (<i>θ</i>_<i>p</i> of 8°). Isocontour lines on the relaxation of GluCl with IVM removed (blue) are used as visual guidelines to show the existence of a kinetic intermediate sampled in the early stages of the simulation. On the right-hand side, representative structures for the four simulations are shown using the same color code. The structural comparison illustrate the global character of the gating isomerization.</p

Quaternary change of GluCl active upon removal of ivermectin (IVM).

<p>From top to bottom, the time series of the C_<i>α</i>-RMSD of the TMD from the X-ray structure of GluCl apo; the receptor twisting angle; the C_<i>α</i> cross section of the ion pore at the position 9′; and the number of L-Glu bound are shown. All data points correspond to running averages taken over consecutive time windows of 5 ns (i.e. 500 snapshots). To ease the visualization of spontaneous pore-closing only the first 1.5 <i>μ</i>s is shown; full-range analyses are shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005784#pcbi.1005784.s006" target="_blank">S1 Fig</a>. Red and green dashed lines correspond to values obtained from the X-ray structures of GluCl active (PDB code 3RIF) and rest (PDB code 4TNV), respectively.</p

Cartoon representation of GluCl active with L-Glutamate (L-Glu) and ivermectin (IVM) bound; PDB 3RIF.

<p>Two out of the five chains are represented in light and dark grey, respectively. The lipid membrane is materialized by grey lines so as to visualize the structural regions corresponding to the extracellular (ECD) and the transmembrane (TMD) domains. The interfacial loops <i>β</i>1-<i>β</i>2 (ECD) and M2-M3 (TMD) are shown in blue and magenta colors, respectively. The four transmembrane helices per subunit (M1 to M4) are indicated.</p

Ion and water permeability in the four simulations of GluCl.

<p>On top and middle panels, the number of water molecules and chloride ions sitting in the pore region per nanosecond is monitored over time. On bottom, the time series of the water flux through the pore in shown. Strikingly, in the simulation of GluCl with IVM removed (dark and light blue) the number of water molecules inside the pore drops from six to nearly zero in 400 ns in run A, and 800 ns in run B. In sharp contrast, when IVM is bound (red) the average number of water molecules in the pore fluctuates around six.</p