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Light-induced structural changes in a short light, oxygen, voltage (LOV) protein revealed by molecular dynamics simulations-implications for the understanding of LOV photoactivation.

Bocola M, Schwaneberg U, Jaeger KE, Krauss U - Front Mol Biosci (2015)

Bottom Line: These changes coincide with a displacement of the Iβ and Hβ strands relative to the light-state structure and result in a correlated rotation of both LOV core domains in the dimer.This local Q116-FMN reorientation impacts on an inter-subunit salt-bridge (K117-E96), which is stabilized in the light state, hence accounting for the observed decreased mobility.The proposed mechanism is discussed in light of universal applicability and its implications for the understanding of LOV-based optogenetic tools.

View Article: PubMed Central - PubMed

Affiliation: Lehrstuhl für Biotechnologie, RWTH Aachen University Aachen, Germany.

ABSTRACT
The modularity of light, oxygen, voltage (LOV) blue-light photoreceptors has recently been exploited for the design of LOV-based optogenetic tools, which allow the light-dependent control of biological functions. For the understanding of LOV sensory function and hence the optimal design of LOV-based optogentic tools it is essential to gain an in depth atomic-level understanding of the underlying photoactivation and intramolecular signal-relay mechanisms. To address this question we performed molecular dynamics simulations on both the dark- and light-adapted state of PpSB1-LOV, a short dimeric bacterial LOV-photoreceptor protein, recently crystallized under constant illumination. While LOV dimers remained globally stable during the light-state simulation with regard to the Jα coiled-coil, distinct conformational changes for a glutamine in the vicinity of the FMN chromophore are observed. In contrast, multiple Jα-helix conformations are sampled in the dark-state. These changes coincide with a displacement of the Iβ and Hβ strands relative to the light-state structure and result in a correlated rotation of both LOV core domains in the dimer. These global changes are most likely initiated by the reorientation of the conserved glutamine Q116, whose side chain flips between the Aβ (dark state) and Hβ strand (light state), while maintaining two potential hydrogen bonds to FMN-N5 and FMN-O4, respectively. This local Q116-FMN reorientation impacts on an inter-subunit salt-bridge (K117-E96), which is stabilized in the light state, hence accounting for the observed decreased mobility. Based on these findings we propose an alternative mechanism for dimeric LOV photoactivation and intramolecular signal-relay, assigning a distinct structural role for the conserved "flipping" glutamine. The proposed mechanism is discussed in light of universal applicability and its implications for the understanding of LOV-based optogenetic tools.

No MeSH data available.


Superimposition of 10 snapshots (Δt = 5 ns) of representative (2D, 2L) dark-state (A) and light-state trajectories (B). The snapshots were superimposed with VMD over all backbone atoms of chain A, colored in gray (dark-state) and cyan (light state). In both panels chain B is color coded by simulation time (t = 0: dark red; t = 45 ns: dark blue). The FMN cofactor is shown in stick representation in both subunits. (C) Per residue RMSD of the backbone atoms derived for chain B of the dark-state (dark gray) and the light-state (cyan) trajectories. The red line depicts light-dark RMSD values, with negative values indicating larger changes in the dark state. (D) Residue-resolved RMSF values for the dark-state (dark gray) and light-state (cyan) trajectories. Above the graph, LOV domain secondary structure elements are shown with α-helices in red and β-strands in green.
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Figure 2: Superimposition of 10 snapshots (Δt = 5 ns) of representative (2D, 2L) dark-state (A) and light-state trajectories (B). The snapshots were superimposed with VMD over all backbone atoms of chain A, colored in gray (dark-state) and cyan (light state). In both panels chain B is color coded by simulation time (t = 0: dark red; t = 45 ns: dark blue). The FMN cofactor is shown in stick representation in both subunits. (C) Per residue RMSD of the backbone atoms derived for chain B of the dark-state (dark gray) and the light-state (cyan) trajectories. The red line depicts light-dark RMSD values, with negative values indicating larger changes in the dark state. (D) Residue-resolved RMSF values for the dark-state (dark gray) and light-state (cyan) trajectories. Above the graph, LOV domain secondary structure elements are shown with α-helices in red and β-strands in green.

Mentions: When the resulting trajectories are superimposed globally over the backbone atoms of the dimer, an average RMSD over the backbone atoms of 1.84 Å (dark) 1.66 Å (light) can be calculated, suggesting that larger structural changes do occur during the dark-state simulation compared to the light-state simulation. In order to better visualize potential inter-domain movements, the dark- and light-state trajectories were superimposed over all backbone atoms of chain A (Figures 2A,B). Potential domain rearrangements become then more apparent for chain B of the dimer. Especially, the N- and C-terminal A'α and Jα helices show increased RMSDs in the dark-state simulation. The corresponding RMSD values for the Jα helix (residues 120–132) are 2.75 Å (dark state) and 2.18 (light state). Likewise, for the A'α helix higher RMSD values are observed (dark state: 2.38, light state: 1.82). A residue-resolved RMSD plot (Figure 2C), as well as the corresponding heatmaps (Supplementary Figures 1, 2) pinpoint regions showing increased structural changes in the dark-state (Figure 2C; negative values in the light-dark plot). Those regions are (i) the N-terminal A'α helix, (ii) the Aβ-Bβ loop, (iii) parts of the Fα helix and the adjacent Gβ strand as well as the C-terminal Jα-helix. In the corresponding RMSF plot (Figure 2D) the N- and C-terminal A'α and Jα helices, Aβ-Bβ loop as well as the Hβ-Iβ loop show increased fluctuations. The Hβ-Iβ loop shows similar fluctuations in both the dark- and light-state simulations (Figure 2D).


Light-induced structural changes in a short light, oxygen, voltage (LOV) protein revealed by molecular dynamics simulations-implications for the understanding of LOV photoactivation.

Bocola M, Schwaneberg U, Jaeger KE, Krauss U - Front Mol Biosci (2015)

Superimposition of 10 snapshots (Δt = 5 ns) of representative (2D, 2L) dark-state (A) and light-state trajectories (B). The snapshots were superimposed with VMD over all backbone atoms of chain A, colored in gray (dark-state) and cyan (light state). In both panels chain B is color coded by simulation time (t = 0: dark red; t = 45 ns: dark blue). The FMN cofactor is shown in stick representation in both subunits. (C) Per residue RMSD of the backbone atoms derived for chain B of the dark-state (dark gray) and the light-state (cyan) trajectories. The red line depicts light-dark RMSD values, with negative values indicating larger changes in the dark state. (D) Residue-resolved RMSF values for the dark-state (dark gray) and light-state (cyan) trajectories. Above the graph, LOV domain secondary structure elements are shown with α-helices in red and β-strands in green.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4589677&req=5

Figure 2: Superimposition of 10 snapshots (Δt = 5 ns) of representative (2D, 2L) dark-state (A) and light-state trajectories (B). The snapshots were superimposed with VMD over all backbone atoms of chain A, colored in gray (dark-state) and cyan (light state). In both panels chain B is color coded by simulation time (t = 0: dark red; t = 45 ns: dark blue). The FMN cofactor is shown in stick representation in both subunits. (C) Per residue RMSD of the backbone atoms derived for chain B of the dark-state (dark gray) and the light-state (cyan) trajectories. The red line depicts light-dark RMSD values, with negative values indicating larger changes in the dark state. (D) Residue-resolved RMSF values for the dark-state (dark gray) and light-state (cyan) trajectories. Above the graph, LOV domain secondary structure elements are shown with α-helices in red and β-strands in green.
Mentions: When the resulting trajectories are superimposed globally over the backbone atoms of the dimer, an average RMSD over the backbone atoms of 1.84 Å (dark) 1.66 Å (light) can be calculated, suggesting that larger structural changes do occur during the dark-state simulation compared to the light-state simulation. In order to better visualize potential inter-domain movements, the dark- and light-state trajectories were superimposed over all backbone atoms of chain A (Figures 2A,B). Potential domain rearrangements become then more apparent for chain B of the dimer. Especially, the N- and C-terminal A'α and Jα helices show increased RMSDs in the dark-state simulation. The corresponding RMSD values for the Jα helix (residues 120–132) are 2.75 Å (dark state) and 2.18 (light state). Likewise, for the A'α helix higher RMSD values are observed (dark state: 2.38, light state: 1.82). A residue-resolved RMSD plot (Figure 2C), as well as the corresponding heatmaps (Supplementary Figures 1, 2) pinpoint regions showing increased structural changes in the dark-state (Figure 2C; negative values in the light-dark plot). Those regions are (i) the N-terminal A'α helix, (ii) the Aβ-Bβ loop, (iii) parts of the Fα helix and the adjacent Gβ strand as well as the C-terminal Jα-helix. In the corresponding RMSF plot (Figure 2D) the N- and C-terminal A'α and Jα helices, Aβ-Bβ loop as well as the Hβ-Iβ loop show increased fluctuations. The Hβ-Iβ loop shows similar fluctuations in both the dark- and light-state simulations (Figure 2D).

Bottom Line: These changes coincide with a displacement of the Iβ and Hβ strands relative to the light-state structure and result in a correlated rotation of both LOV core domains in the dimer.This local Q116-FMN reorientation impacts on an inter-subunit salt-bridge (K117-E96), which is stabilized in the light state, hence accounting for the observed decreased mobility.The proposed mechanism is discussed in light of universal applicability and its implications for the understanding of LOV-based optogenetic tools.

View Article: PubMed Central - PubMed

Affiliation: Lehrstuhl für Biotechnologie, RWTH Aachen University Aachen, Germany.

ABSTRACT
The modularity of light, oxygen, voltage (LOV) blue-light photoreceptors has recently been exploited for the design of LOV-based optogenetic tools, which allow the light-dependent control of biological functions. For the understanding of LOV sensory function and hence the optimal design of LOV-based optogentic tools it is essential to gain an in depth atomic-level understanding of the underlying photoactivation and intramolecular signal-relay mechanisms. To address this question we performed molecular dynamics simulations on both the dark- and light-adapted state of PpSB1-LOV, a short dimeric bacterial LOV-photoreceptor protein, recently crystallized under constant illumination. While LOV dimers remained globally stable during the light-state simulation with regard to the Jα coiled-coil, distinct conformational changes for a glutamine in the vicinity of the FMN chromophore are observed. In contrast, multiple Jα-helix conformations are sampled in the dark-state. These changes coincide with a displacement of the Iβ and Hβ strands relative to the light-state structure and result in a correlated rotation of both LOV core domains in the dimer. These global changes are most likely initiated by the reorientation of the conserved glutamine Q116, whose side chain flips between the Aβ (dark state) and Hβ strand (light state), while maintaining two potential hydrogen bonds to FMN-N5 and FMN-O4, respectively. This local Q116-FMN reorientation impacts on an inter-subunit salt-bridge (K117-E96), which is stabilized in the light state, hence accounting for the observed decreased mobility. Based on these findings we propose an alternative mechanism for dimeric LOV photoactivation and intramolecular signal-relay, assigning a distinct structural role for the conserved "flipping" glutamine. The proposed mechanism is discussed in light of universal applicability and its implications for the understanding of LOV-based optogenetic tools.

No MeSH data available.