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Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.

A Rohrdanz M, Zheng W, Lambeth B, Vreede J, Clementi C - PLoS Comput. Biol. (2014)

Bottom Line: The long transition times render conventional simulation methods ineffective, and yet the short signaling-state lifetime makes experimental data difficult to obtain and interpret.We compare our signaling state prediction with previous computational and more recent experimental results, and the comparison is favorable, which validates the method presented.This approach provides additional insight to understand the PYP photo cycle, and can be applied to other systems for which more direct methods are impractical.

View Article: PubMed Central - PubMed

Affiliation: Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America; Chemistry Department, Rice University, Houston, Texas, United States of America.

ABSTRACT
The nature of the optical cycle of photoactive yellow protein (PYP) makes its elucidation challenging for both experiment and theory. The long transition times render conventional simulation methods ineffective, and yet the short signaling-state lifetime makes experimental data difficult to obtain and interpret. Here, through an innovative combination of computational methods, a prediction and analysis of the biological signaling state of PYP is presented. Coarse-grained modeling and locally scaled diffusion map are first used to obtain a rough bird's-eye view of the free energy landscape of photo-activated PYP. Then all-atom reconstruction, followed by an enhanced sampling scheme; diffusion map-directed-molecular dynamics are used to focus in on the signaling-state region of configuration space and obtain an ensemble of signaling state structures. To the best of our knowledge, this is the first time an all-atom reconstruction from a coarse grained model has been performed in a relatively unexplored region of molecular configuration space. We compare our signaling state prediction with previous computational and more recent experimental results, and the comparison is favorable, which validates the method presented. This approach provides additional insight to understand the PYP photo cycle, and can be applied to other systems for which more direct methods are impractical.

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Configuration from a) pG state (PDB ID: 3PHY), b) experimental signaling state of WT-PYP (PDB ID: 2XK6), c) experimental signaling state of Δ25 (PDB ID: 1XFQ), d) representative configuration from our pB ensemble.In all configurations the chromophore (residue 69) is shown explicitly, with the rest of the protein shown as cartoon. The α3 helix (residues 43–51) is in blue, the chromophore binding cap (residues 98–103) in green, and the first 25 N-terminal residues, when present, in brown.
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pcbi-1003797-g003: Configuration from a) pG state (PDB ID: 3PHY), b) experimental signaling state of WT-PYP (PDB ID: 2XK6), c) experimental signaling state of Δ25 (PDB ID: 1XFQ), d) representative configuration from our pB ensemble.In all configurations the chromophore (residue 69) is shown explicitly, with the rest of the protein shown as cartoon. The α3 helix (residues 43–51) is in blue, the chromophore binding cap (residues 98–103) in green, and the first 25 N-terminal residues, when present, in brown.

Mentions: Figure 3 displays a configuration in the pG state for reference, a configuration from the experimental WT-PYP pB state, a configuration from the experimental signaling state of Δ25, and a configuration from our pB ensemble. In the pG configuration, the chromophore is tucked inside the chromophore binding pocket, the α3 helix (colored in blue) is well formed, and the binding pocket cap (residues 98–103 colored in green) is in place. All three signaling state structures display features known to be associated with the signaling state: the α3 helix is unformed and the chromophore is exposed to the solvent. The pB state is in general less well structured than pG configurations, while some secondary structure elements remain intact. Visually, the secondary structure in the Δ25 configuration looks more well-ordered than the experimental WT-PYP and our pB ensemble. In comparing our result with experimental WT-PYP, the amount of retained secondary structure is similar; however the location of the 25 N-terminal residues differs (discussed more below).


Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.

A Rohrdanz M, Zheng W, Lambeth B, Vreede J, Clementi C - PLoS Comput. Biol. (2014)

Configuration from a) pG state (PDB ID: 3PHY), b) experimental signaling state of WT-PYP (PDB ID: 2XK6), c) experimental signaling state of Δ25 (PDB ID: 1XFQ), d) representative configuration from our pB ensemble.In all configurations the chromophore (residue 69) is shown explicitly, with the rest of the protein shown as cartoon. The α3 helix (residues 43–51) is in blue, the chromophore binding cap (residues 98–103) in green, and the first 25 N-terminal residues, when present, in brown.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4214557&req=5

pcbi-1003797-g003: Configuration from a) pG state (PDB ID: 3PHY), b) experimental signaling state of WT-PYP (PDB ID: 2XK6), c) experimental signaling state of Δ25 (PDB ID: 1XFQ), d) representative configuration from our pB ensemble.In all configurations the chromophore (residue 69) is shown explicitly, with the rest of the protein shown as cartoon. The α3 helix (residues 43–51) is in blue, the chromophore binding cap (residues 98–103) in green, and the first 25 N-terminal residues, when present, in brown.
Mentions: Figure 3 displays a configuration in the pG state for reference, a configuration from the experimental WT-PYP pB state, a configuration from the experimental signaling state of Δ25, and a configuration from our pB ensemble. In the pG configuration, the chromophore is tucked inside the chromophore binding pocket, the α3 helix (colored in blue) is well formed, and the binding pocket cap (residues 98–103 colored in green) is in place. All three signaling state structures display features known to be associated with the signaling state: the α3 helix is unformed and the chromophore is exposed to the solvent. The pB state is in general less well structured than pG configurations, while some secondary structure elements remain intact. Visually, the secondary structure in the Δ25 configuration looks more well-ordered than the experimental WT-PYP and our pB ensemble. In comparing our result with experimental WT-PYP, the amount of retained secondary structure is similar; however the location of the 25 N-terminal residues differs (discussed more below).

Bottom Line: The long transition times render conventional simulation methods ineffective, and yet the short signaling-state lifetime makes experimental data difficult to obtain and interpret.We compare our signaling state prediction with previous computational and more recent experimental results, and the comparison is favorable, which validates the method presented.This approach provides additional insight to understand the PYP photo cycle, and can be applied to other systems for which more direct methods are impractical.

View Article: PubMed Central - PubMed

Affiliation: Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America; Chemistry Department, Rice University, Houston, Texas, United States of America.

ABSTRACT
The nature of the optical cycle of photoactive yellow protein (PYP) makes its elucidation challenging for both experiment and theory. The long transition times render conventional simulation methods ineffective, and yet the short signaling-state lifetime makes experimental data difficult to obtain and interpret. Here, through an innovative combination of computational methods, a prediction and analysis of the biological signaling state of PYP is presented. Coarse-grained modeling and locally scaled diffusion map are first used to obtain a rough bird's-eye view of the free energy landscape of photo-activated PYP. Then all-atom reconstruction, followed by an enhanced sampling scheme; diffusion map-directed-molecular dynamics are used to focus in on the signaling-state region of configuration space and obtain an ensemble of signaling state structures. To the best of our knowledge, this is the first time an all-atom reconstruction from a coarse grained model has been performed in a relatively unexplored region of molecular configuration space. We compare our signaling state prediction with previous computational and more recent experimental results, and the comparison is favorable, which validates the method presented. This approach provides additional insight to understand the PYP photo cycle, and can be applied to other systems for which more direct methods are impractical.

Show MeSH