N-Terminal Truncation Does Not Affect the Location of a Conserved Tryptophan in the BLUF Domain of AppA from <i>Rhodobacter sphaeroides</i>

Unno, Masashi; Tsukiji, Yuuki; Kubota, Kensuke; Masuda, Shinji

doi:10.1021/jp305873z

Cited by 7 publications

(5 citation statements)

References 46 publications

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“…Model refinement against Quantum Mechanical (QM) and x-ray data supported the 1YRX Gln orientation 35 , but this was also challenged by a subsequent QM assessment 36 . The Trp in conformation is consistent with spectroscopic, NMR and computational studies 37,38 (and see 2 for discussion). However, structures of other BLUF domains (BP-1 (Tll0078); 1XOP and BlrB; 2BYC) and recently that of nearly full-length AppAΔ399 39 have Trp out in the dark state.…”

Section: Bluf Domainssupporting

confidence: 81%

Photochemistry of flavoprotein light sensors

Conrad¹,

Manahan²,

Crane³

2014

Nat Chem Biol

209

234

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Three major classes of flavin photosensors, LOV domains, BLUF proteins and cryptochromes regulate diverse biological activities in response to blue-light. Recent studies of structure, spectroscopy and chemical mechanism have provided unprecedented insight into how each family operates at the molecular level. In general, the photoexcitation of the flavin cofactor leads to changes in redox and protonation states that ultimately remodel protein conformation and molecular interactions. For LOV domains, issues remain regarding early photochemical events, but common themes in conformational propagation have emerged across a diverse family of proteins. For BLUF proteins, photoinduced electron transfer reactions critical to light conversion are defined, but the subsequent rearrangement of hydrogen bonding networks key for signaling remain highly controversial. For cryptochromes, the relevant photocycles are actively debated, but mechanistic and functional studies are converging. Despite these challenges, our current understanding has enabled the engineering of flavoprotein photosensors for control of signaling processes within cells.

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Section: Bluf Domainssupporting

confidence: 81%

Photochemistry of flavoprotein light sensors

Conrad¹,

Manahan²,

Crane³

2014

Nat Chem Biol

209

234

View full text Add to dashboard Cite

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“…Although support for the Met out conformation has been obtained using spectroscopy (Wu and Gardner 2009), crystallography (Barends et al 2009) and computational methods (Sadeghian et al 2008), it is not seen for all BLUF domains, and its relevance to physiological function has been questioned (Khrenova et al 2013). The suggestion that N-terminal truncation of AppA is responsible for an artefactual conformation has been rejected (Unno et al 2012 truncation, and does not explain the structure of BlrP1 models, which also show both Met out and Met in conformations (Barends et al 2009). …”

Section: Structural Modelsmentioning

confidence: 99%

Seeing the light with BLUF proteins

Park

Tame

2017

Biophys Rev

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First described about 15 years ago, BLUF (Blue Light Using Flavin) domains are light-triggered switches that control enzyme activity or gene expression in response to blue light, remaining activated for seconds or even minutes after stimulation. The conserved, ferredoxin-like fold holds a flavin chromophore that captures the light and somehow triggers downstream events. BLUF proteins are found in both prokaryotes and eukaryotes and have a variety of architectures and oligomeric forms, but the BLUF domain itself seems to have a wellpreserved structure and mechanism that have been the focus of intense study for a number of years. Crystallographic and NMR structures of BLUF domains have been solved, but the conflicting models have led to considerable debate about the atomic details of photo-activation. Advanced spectroscopic and computational methods have been used to analyse the early events after photon absorption, but these too have led to widely differing conclusions. New structural models are improving our understanding of the details of the mechanism and may lead to novel tailor-made tools for optogenetics.

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“…The N-terminal ends are generally neglected, as they are very flexible, and hardly resolved in NMR or X-ray structures. Moreover, a recent experimental work reported the BLUF N-terminus to be of minor importance (Unno et al, 2012 ). The C-terminus, however, may differ with regards to the presence of the capping α-helices, which follow the β-sheet motif in the BLUF sequence.…”

Section: Computational Studies On Blufmentioning

confidence: 99%

A proposal for a dipole-generated BLUF domain mechanism

Mathes

Götze

2015

Front. Mol. Biosci.

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The resting and signaling structures of the blue-light sensing using flavin (BLUF) photoreceptor domains are still controversially debated due to differences in the molecular models obtained by crystal and NMR structures. Photocycles for the given preferred structural framework have been established, but a unifying picture combining experiment and theory remains elusive. We summarize present work on the AppA BLUF domain from both experiment and theory. We focus on IR and UV/vis spectra, and to what extent theory was able to reproduce experimental data and predict the structural changes upon formation of the signaling state. We find that the experimental observables can be theoretically reproduced employing any structural model, as long as the orientation of the signaling essential Gln63 and its tautomer state are a choice of the modeler. We also observe that few approaches are comparative, e.g., by considering all structures in the same context. Based on recent experimental findings and a few basic calculations, we suggest the possibility for a BLUF activation mechanism that only relies on electron transfer and its effect on the local electrostatics, not requiring an associated proton transfer. In this regard, we investigate the impact of dispersion correction on the interaction energies arising from weakly bound amino acids.

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N-Terminal Truncation Does Not Affect the Location of a Conserved Tryptophan in the BLUF Domain of AppA from Rhodobacter sphaeroides

Cited by 7 publications

References 46 publications

Photochemistry of flavoprotein light sensors

Photochemistry of flavoprotein light sensors

Seeing the light with BLUF proteins

A proposal for a dipole-generated BLUF domain mechanism

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