Electronic spectra of flavin in different redox and protonation states: a computational perspective on the effect of the electrostatic environment

Kabir, Mohammad Pabel; Orozco‐Gonzalez, Yoelvis; Gozem, Samer

doi:10.1039/c9cp02230a

Cited by 46 publications

(87 citation statements)

References 99 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…44 , here, and also in the accompanying article 56 ). Potentially negatively charged amino acids also do not produce a substantial blue shift, contrary to what might have been expected from the electrostatic tuning maps 42,72 . Evidently, Glu148 and Asp148 either do not interact with FMN, or interact with it in the protonated form (hydrogen-bonded conformation in Figure 4E).…”

Section: Discussioncontrasting

confidence: 65%

Insights into the mechanisms of LOV domain color tuning from a set of high-resolution X-ray structures

Remeeva

Nazarenko

Kovalev

et al. 2021

Preprint

View full text Add to dashboard Cite

Light-oxygen-voltage (LOV) domains are widespread photosensory modules that can be used in fluorescence microscopy, optogenetics and controlled production of reactive oxygen species. All of the currently known LOV domains have absorption maxima in the range of ~440 to ~450 nm, and it is not clear whether they can be shifted significantly using mutations. Here, we have generated a panel of LOV domain variants by mutating the key chromophore-proximal glutamine amino acid of a thermostable flavin based fluorescent protein CagFbFP (Gln148) to asparagine, aspartate, glutamate, histidine, lysine and arginine. Absorption spectra of all of the mutants are blue-shifted, with the maximal shift of 8 nm observed for the Q148H variant. While CagFbFP and its Q148N/D/E variants are not sensitive to pH, Q148H/K/R reveal a moderate red shift induced by acidic pH. To gain further insight, we determined high resolution crystal structures of all of the mutants studied at the resolutions from 1.07 Å for Q148D to 1.63 Å for Q148R. Whereas in some of the variants, the amino acid 148 remains in the vicinity of the flavin, in Q148K, Q148R and partially Q148D, the C-terminus of the protein unlatches and the side chain of the residue 148 is reoriented away from the chromophore. Our results explain the absence of color shifts from replacing Gln148 with charged amino acids and pave the way for rational design of color-shifted flavin based fluorescent proteins.

show abstract

Section: Discussioncontrasting

confidence: 65%

Insights into the mechanisms of LOV domain color tuning from a set of high-resolution X-ray structures

Remeeva

Nazarenko

Kovalev

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…4 A physically more appealing alternative for modeling the band broadening is to take vibronic effects into account by explicitly calculating the coupling between vibrational motion and electronic transitions. [2][3][4][12][13][14][15][16][17][18][19][20][21][22] Since the molecular structure of the excited state differs from the molecular structure of the ground-state, the absorption intensity depends on Franck-Condon factors, 23 which are according to the Franck-Condon principle in the first approximation proportional to the square of the overlap of the vibrational wave functions of the ground and excited electronic states. Since the molecular structures of the two states are different, the normal coordinates of the vibrational modes are also different leading to the Duschinsky effect.…”

Section: Introductionmentioning

confidence: 99%

Calculation of vibrationally resolved absorption spectra of acenes and pyrene

Benkyi

Tapavicza

Fliegl

et al. 2019

Phys. Chem. Chem. Phys.

View full text Add to dashboard Cite

show abstract

“…Both N286A (results not shown) and Q258A‐N286A, for reasons which are obvious in model F of Figure 1, fail to produce the WT LOV spectrum exhibited in Figure 2. A small peak around 415 nm though matches neutral hydroquinone state of flavin in time‐dependent density functional theory calculations, 28 presence of doublet at 360 and 378 nm makes the spectrum difficult to explain. However, the spectral characteristics in the visible region do not completely match with neutral hydroquinone state of protein‐bound flavin 31 .…”

Section: Resultsmentioning

confidence: 96%

“…Such dark‐state contacts are necessary for the depiction of discrete vibronic structures with an absorption maximum at 447 nm. A recent study considered “Electrostatic Spectral Tuning Maps (ESTM)” 28 for simulating UV‐vis spectrum of the flavin chromophore. It is depicted that the nonpolar environment surrounding flavin is primarily responsible for the generation of triple vibronic structures.…”

Section: Resultsmentioning

confidence: 99%

Residue interaction dynamics in Vaucheria aureochrome1 light‐oxygen‐voltage: Bridging theory and experiments

et al. 2020

View full text Add to dashboard Cite

Allosteric communication is the basis of signaling and information transfer. Collective interactions between amino acid residues, which are spatially distributed in the three dimensional structure of a protein molecule, form the basis of allosteric network. While the construction of residue interaction graphs (RIG) is based on static crystal structures of proteins, it is important to extract information on protein dynamics to understand allostery. Therefore, quantitative analysis of RIG based on the framework of differential network (DN), is immensely helpful in identifying key amino acid residue interactions within such communication pathways. While the simultaneous availability of protein structures from two different states is essential for DN, there are additional challenges. Crystallographic artifacts like nonbiological dimeric arrangements within the crystal lattice automatically influence the construction and eventually the interpretation of RIG. Therefore, experimental validation of predictions from the analyses of RIG is naturally scarce in the literature. Herein, we study the photo sensor domain of the signaling photoreceptor transcription factor, aureochrome1, to understand light-driven signaling. We perform direct experiments to verify the predictions from RIG using the machinery of DN. However, the agreement leaves scope for improvement. We then discuss the notion of quaternary structure alignment to obtain a biologically meaningful dimer. Thence, we reconstruct the RIG and reanalyze the modified structure. Results of these reanalyses render far superior agreement with experiments. Therefore, this notion of addressing crystallographic biases provides a fresh yet general approach for reconciliation of theory and experiments. It is applicable beyond the present case to all signaling proteins in general.

show abstract

Electronic spectra of flavin in different redox and protonation states: a computational perspective on the effect of the electrostatic environment

Abstract: This study discusses how UV/vis absorption spectra of flavin in different redox and protonation states are shifted by the nearby electrostatic microenvironment.

Cited by 46 publications

References 99 publications

Insights into the mechanisms of LOV domain color tuning from a set of high-resolution X-ray structures

Insights into the mechanisms of LOV domain color tuning from a set of high-resolution X-ray structures

Calculation of vibrationally resolved absorption spectra of acenes and pyrene

Residue interaction dynamics in Vaucheria aureochrome1 light‐oxygen‐voltage: Bridging theory and experiments

Contact Info

Product

Resources

About