Photoactivation Intermediates of a G‑Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation

Rhodopsin is a G-protein coupled receptor functioning as a photoreceptor for vision through photoactivation of a covalently bound ligand of a retinal protonated Schiff base chromophore. Despite the availability of structural information on the inactivated and activated forms of the receptor, the transition processes initiated by the photoabsorption have not been well understood. Here we theoretically examined the photoactivation processes by means of molecular dynamics (MD) simulations and <i>ab initio</i> quantum mechanical/molecular mechanical (QM/MM) free energy geometry optimizations which enabled accurate geometry determination of the ligand molecule in ample statistical conformational samples of the protein. Structures of the intermediate states of the activation process, blue-shifted intermediate and Lumi, as well as the dark state first generated by MD simulations and then refined by the QM/MM free energy geometry optimizations were characterized by large displacement of the β-ionone ring of retinal along with change in the hydrogen bond of the protonated Schiff base. The <i>ab initio</i> calculations of vibrational and electronic spectroscopic properties of those states well reproduced the experimental observations and successfully identified the molecular origins underlying the spectroscopic features. The structural evolution in the formation of the intermediates provides a molecular insight into the efficient activation processes of the receptor

Molecular Mechanism of Wide Photoabsorption Spectral Shifts of Color Variants of Human Cellular Retinol Binding Protein II

Color variants of human cellular retinol binding protein II (hCRBPII) created by protein engineering were recently shown to exhibit anomalously wide photoabsorption spectral shifts over ∼200 nm across the visible region. The remarkable phenomenon provides a unique opportunity to gain insight into the molecular basis of the color tuning of retinal binding proteins for understanding of color vision as well as for engineering of novel color variants of retinal binding photoreceptor proteins employed in optogenetics. Here, we report a theoretical investigation of the molecular mechanism underlying the anomalously wide spectral shifts of the color variants of hCRBPII. Computational modeling of the color variants with hybrid molecular simulations of free energy geometry optimization succeeded in reproducing the experimentally observed wide spectral shifts, and revealed that protein flexibility, through which the active site structure of the protein and bound water molecules is altered by remote mutations, plays a significant role in inducing the large spectral shifts

Molecular Mechanism of Wide Photoabsorption Spectral Shifts of Color Variants of Human Cellular Retinol Binding Protein II

Color variants of human cellular retinol binding protein II (hCRBPII) created by protein engineering were recently shown to exhibit anomalously wide photoabsorption spectral shifts over ∼200 nm across the visible region. The remarkable phenomenon provides a unique opportunity to gain insight into the molecular basis of the color tuning of retinal binding proteins for understanding of color vision as well as for engineering of novel color variants of retinal binding photoreceptor proteins employed in optogenetics. Here, we report a theoretical investigation of the molecular mechanism underlying the anomalously wide spectral shifts of the color variants of hCRBPII. Computational modeling of the color variants with hybrid molecular simulations of free energy geometry optimization succeeded in reproducing the experimentally observed wide spectral shifts, and revealed that protein flexibility, through which the active site structure of the protein and bound water molecules is altered by remote mutations, plays a significant role in inducing the large spectral shifts

Facile Catch and Release of Fullerenes Using a Photoresponsive Molecular Tube

A novel M₂L₂ molecular tube capable of binding fullerene C₆₀ was synthesized from bispyridine ligands with embedded anthracene panels and Ag­(I) hinges. Unlike previous molecular cages and capsules, this open-ended tubular host can accommodate a single molecule of various C₆₀ derivatives with large substituents. The fullerene guest can then be released by using the ideal, noninvasive external stimulus, light

Effects of deprotonation of both Glu122 and Glu129 in the ground state.

<p>Structural comparison of the intracellular constrictions between the ATR-E122p-E129p and ATR-E122Δp-E129Δp simulations. (A) Overall structures of snapshots from the last frame of both simulations. Key residues are highlighted in orange and magenta. (B) Magnified view of the intracellular and central constrictions (left and right panels, respectively). Double arrows indicate the possible motions of Glu121-Arg307 (red), Glu122-His173 (cyan), Glu122-Arg307 (green) and Glu129-Asn297 (magenta). (C-F) Distances between (C) Glu121-Arg307, (D) Glu122-His173, (E) Glu122-Arg307, and (F) Glu129-Asn297. (G, H) Distribution of water molecules in the (G) ATR-E122p-E129p and (H) ATR-E122Δp-E129Δp simulations. The distribution maps are contoured at the probability density of 0.0015 molecules Å^-3 ns^-1. The time-averaged structure of the protein over 150 ns is shown.</p

Simulation systems used in this research.

<p>The simulations performed in this research. In this table, “p” and “Δp” refer to protonated and deprotonated glutamate, respectively.</p><p>Simulation systems used in this research.</p

Correlation analysis for the 13-<i>cis</i>R-122Δp-129p simulation.

<p>(A) The matrix of correlation coefficients for the pairs of Cα atoms. (B) Mapping of the correlation coefficients to the structure. The black dashed circle represents the pair of Cα atoms with a correlation coefficient greater than 0.7. The red dashed circle represents the pair of Cα atoms in TM2 and TM7 that has a negative correlation coefficient.</p

Effects of the deprotonation of either Glu122 or Glu129 in the ground state.

<p>(A, B, C) Distances between (A) Glu129-Asn297, (B) Glu122-His273 and (C) Glu122-Arg307 in the ATR-E122p-E129Δp and ATR-E122Δp-E129p simulations. (D, E) Distributions of water molecules in the ATR-E122p-E129Δp and ATR-E122Δp-E129p simulations. The distribution map is contoured at the probability density of 0.0015 molecules Å^-3 ns^-1. The time-averaged structure of the protein over 150 ns is shown.</p

Electrophysiological analysis for C1C2 variants.

<p>(A) The peak amplitudes of the photocurrents, normalized by the cell’s input capacitance. (B) Conforcal images of representative HEK293 cells expressing the C1C2 WT and its mutants. Scale bar represents 30 μm. (C) The expression level of each C1C2 variant measured by the membrane/cytosol ratio of GFP fluorescence. (D-G) The current-voltage (<i>I-V</i>) relation curves for each mutant. (H, I) The kinetic parameters for each mutant, (H) opening rates (τ_on) and (I) closing rates (τ_off). The error bars represent s.e.m. of 3 experiments (n = 5–17 cells). * p < 0.05.</p

The conformational change in Trp262 upon retinal isomerization.

<p>(A) Structural comparison between the snapshots from the ATR-bound (grey) and 13-<i>cis</i>R-bound (green) simulations. (B) Magnified view of retinal and Trp262, from the orange-highlighted region in the left panel. Double arrows indicate the possible motions of Trp262. (C) The RMSD values of the Trp262 atoms, relative to those of the crystal structure. (D) The peak amplitudes of the photocurrents, normalized by the cell’s input capacitance. (E) Conforcal images of representative HEK293 cells expressing the C1C2 WT and W262A mutants. Scale bar represents 30 μm. (F) The expression level of W262A mutant measured by the membrane/cytosol ratio of GFP fluorescence. The error bars represent s.e.m. of 3 experiments (n = 5–17 cells). * <i>p</i> < 0.05.</p