The properties of buried ion pairs are governed by the propensity of proteins to reorganize

Kougentakis, Christos; Skerritt, L.A.; Majumdar, Ananya; Garcia-Moreno, E.B.

doi:10.1101/2020.02.03.932012

Cited by 3 publications

(3 citation statements)

References 64 publications

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“…These data suggest that the hydrophobicity of Leu249 is crucial for the deprotonation of PCB in the Pg state. It is known that the pK a values of charged moieties shift in the direction that favors the neutral state in the hydrophobic protein core (56,57). Therefore, we propose that a "desolvation effect" is the driving force behind the deprotonation of PCB.…”

Section: Discussionmentioning

confidence: 80%

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Nagae

Unno

Koizumi

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Cyanobacteriochromes (CBCRs) are bilin-binding photosensors of the phytochrome superfamily that show remarkable spectral diversity. The green/red CBCR subfamily is important for regulating chromatic acclimation of photosynthetic antenna in cyanobacteria and is applied for optogenetic control of gene expression in synthetic biology. It is suggested that the absorption change of this subfamily is caused by the bilin C15-Z/C15-E photoisomerization and a subsequent change in the bilin protonation state. However, structural information and direct evidence of the bilin protonation state are lacking. Here, we report a high-resolution (1.63Å) crystal structure of the bilin-binding domain of the chromatic acclimation sensor RcaE in the red-absorbing photoproduct state. The bilin is buried within a “bucket” consisting of hydrophobic residues, in which the bilin configuration/conformation is C5-Z,syn/C10-Z,syn/C15-E,syn with the A- through C-rings coplanar and the D-ring tilted. Three pyrrole nitrogens of the A- through C-rings are covered in the α-face with a hydrophobic lid of Leu249 influencing the bilin pKa, whereas they are directly hydrogen bonded in the β-face with the carboxyl group of Glu217. Glu217 is further connected to a cluster of waters forming a hole in the bucket, which are in exchange with solvent waters in molecular dynamics simulation. We propose that the “leaky bucket” structure functions as a proton exit/influx pathway upon photoconversion. NMR analysis demonstrated that the four pyrrole nitrogen atoms are indeed fully protonated in the red-absorbing state, but one of them, most likely the B-ring nitrogen, is deprotonated in the green-absorbing state. These findings deepen our understanding of the diverse spectral tuning mechanisms present in CBCRs.

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Section: Discussionmentioning

confidence: 80%

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Nagae

Unno

Koizumi

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…These data suggest that the hydrophobicity of Leu249 is crucial for the deprotonation of PCB in the Pg state. It is known that the pKa values of charged moieties shift in the direction that favors the neutral state in the hydrophobic protein core (56,57). Therefore, we propose that a "desolvation effect" is the driving force behind the deprotonation of PCB.…”

Section: Discussionmentioning

confidence: 82%

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Nagae

Unno

Koizumi

et al. 2020

Preprint

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Cyanobacteriochromes (CBCRs) are bilin-binding photosensors of the phytochrome superfamily that show remarkable spectral diversity. The green/red CBCR subfamily is important for regulating chromatic acclimation of photosynthetic antenna in cyanobacteria and is applied for optogenetic control of gene expression in synthetic biology. They are suggested to combine the bilin C15-Z/C15-E photoisomerization with a change in the bilin protonation state to drive their absorption changes. However, structural information and direct evidence of the bilin protonation state are lacking. Here we report a high-resolution (1.63Å) crystal structure of the bilin-binding domain of the chromatic acclimation sensor RcaE in the red-absorbing photoproduct state. The bilin is buried within a “pan” consisting of hydrophobic residues, where the bilin configuration/conformation is C5-Z,syn/C10-Z,syn/C15-E,syn with the A–C rings co-planar and the D-ring tilted. Three pyrrole nitrogens of the A–C rings are covered in the α-face with a hydrophobic lid of Leu249 influencing the bilin pKa, whereas they are directly hydrogen-bonded in the β-face with the carboxyl group of Glu217. Glu217 is further connected to a cluster of waters forming a hole in the pan, which are in exchange with solvent waters in molecular dynamics simulation. We propose that the “holey pan” structure functions as a proton-exit/influx pathway upon photoconversion. NMR analysis demonstrated that the four pyrrole nitrogen atoms are indeed fully protonated in the red-absorbing state, but one of them, most likely the B-ring nitrogen, is deprotonated in the green-absorbing state. These findings deepen our understanding of the diverse spectral tuning mechanisms present in CBCRs.Significance StatementGreen/red CBCRs are one of the most important CBCR subfamilies owing to their physiological roles in cyanobacteria phylum and optogenetic applications. They are known to utilize a change in the bilin protonation state to drive the marked change in green/red absorption, but the structural basis of the protochromic green/red photocycle are not well understood. Here, we have determined the crystal structure of the chromatic acclimation sensor RcaE of this subfamily in the photoproduct state, demonstrating a unique conformation of the bilin and its interacting residues. In addition, we provide direct evidence of the protonation state of the bilin via NMR analysis. These findings bring insight to our understanding of the molecular mechanisms underlying the spectral diversity of CBCRs.

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“…This enables the possibility to study the modulation of enzymatic activity due to changes in amino-acid residues of the active sites of enzymes and in the solvent compositions. 81 Another application is the possibility to study the strengthening of stabilising interactions between pairs of residues favouring specific folded states of proteins, 82,83 to withstand extreme environments found in industrial settings.…”

Section: Discussionmentioning

confidence: 99%

Anion–cation contrast of small molecule solvation in salt solutions

Hervø-Hansen

Heyda

Lund

et al. 2022

Phys. Chem. Chem. Phys.

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The properties of buried ion pairs are governed by the propensity of proteins to reorganize

Cited by 3 publications

References 64 publications

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Anion–cation contrast of small molecule solvation in salt solutions

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