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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.


A'α and Jα-crossing angles over the dark-state (dark gray line) and light-state (cyan line) trajectories. The helix angle between the A'α (A,C,E) and Jα helices (B,D,F) between chain A and chain B was calculated with YASARA for each time step by plotting a normal vector along the backbone atoms of the respective residues constituting the helix (A'α: residues 119–133; Jα: residues 3–13). The respective angles were analyzed for all dark- and light-state trajectories as described in the Materials and Methods Section. The panels depict the data derived from the three different simulation runs: 1D, 1L (A,B); 2D, 2L (C,D), and 3D, 3L (E,F).
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Figure 6: A'α and Jα-crossing angles over the dark-state (dark gray line) and light-state (cyan line) trajectories. The helix angle between the A'α (A,C,E) and Jα helices (B,D,F) between chain A and chain B was calculated with YASARA for each time step by plotting a normal vector along the backbone atoms of the respective residues constituting the helix (A'α: residues 119–133; Jα: residues 3–13). The respective angles were analyzed for all dark- and light-state trajectories as described in the Materials and Methods Section. The panels depict the data derived from the three different simulation runs: 1D, 1L (A,B); 2D, 2L (C,D), and 3D, 3L (E,F).

Mentions: The comparison of light- and dark-state simulations reveals different Jα-helix orientations as well as variable Jα mobility between the two states in both the short and the longer trajectories (Figure 6). The depicted helix crossing-angle distribution plots were obtained from the crossing angle of the normal vector as described in the Materials and Methods Section. The light-state conformation seems to be stable with average crossing angles of 38° ± 5° (1L), 41° ± 5° (2L), and 46° ± 6° (3L), respectively (Figures 6B,D,F; cyan line). The corresponding dark-state simulation reveals an increased overall Jα conformational mobility sampling multiple helix angles between 24° and 96° degree over the short trajectories (1D, 2D) (Figures 6B,D, dark gray line). In the longer trajectory a sharper angle distribution, with an average value of 39° ± 6°, is found for the dark-state trajectory (Figure 6F).


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)

A'α and Jα-crossing angles over the dark-state (dark gray line) and light-state (cyan line) trajectories. The helix angle between the A'α (A,C,E) and Jα helices (B,D,F) between chain A and chain B was calculated with YASARA for each time step by plotting a normal vector along the backbone atoms of the respective residues constituting the helix (A'α: residues 119–133; Jα: residues 3–13). The respective angles were analyzed for all dark- and light-state trajectories as described in the Materials and Methods Section. The panels depict the data derived from the three different simulation runs: 1D, 1L (A,B); 2D, 2L (C,D), and 3D, 3L (E,F).
© Copyright Policy
Related In: Results  -  Collection

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Figure 6: A'α and Jα-crossing angles over the dark-state (dark gray line) and light-state (cyan line) trajectories. The helix angle between the A'α (A,C,E) and Jα helices (B,D,F) between chain A and chain B was calculated with YASARA for each time step by plotting a normal vector along the backbone atoms of the respective residues constituting the helix (A'α: residues 119–133; Jα: residues 3–13). The respective angles were analyzed for all dark- and light-state trajectories as described in the Materials and Methods Section. The panels depict the data derived from the three different simulation runs: 1D, 1L (A,B); 2D, 2L (C,D), and 3D, 3L (E,F).
Mentions: The comparison of light- and dark-state simulations reveals different Jα-helix orientations as well as variable Jα mobility between the two states in both the short and the longer trajectories (Figure 6). The depicted helix crossing-angle distribution plots were obtained from the crossing angle of the normal vector as described in the Materials and Methods Section. The light-state conformation seems to be stable with average crossing angles of 38° ± 5° (1L), 41° ± 5° (2L), and 46° ± 6° (3L), respectively (Figures 6B,D,F; cyan line). The corresponding dark-state simulation reveals an increased overall Jα conformational mobility sampling multiple helix angles between 24° and 96° degree over the short trajectories (1D, 2D) (Figures 6B,D, dark gray line). In the longer trajectory a sharper angle distribution, with an average value of 39° ± 6°, is found for the dark-state trajectory (Figure 6F).

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.