A Stark Spectroscopic Study of <i>N</i>(3)-Methyl, <i>N</i>(10)-Isobutyl-7,8-Dimethylisoalloxazine in Nonpolar Low-Temperature Glasses:  Experiment and Comparison with Calculations

Stanley, Robert J.; Siddiqui, M. Salim

doi:10.1021/jp011971j

Cited by 27 publications

(53 citation statements)

References 47 publications

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“…Several hybrid exchange-correlation (XC) functionals, which differ in the amount of exact exchange, were investigated. The charge densities for methyl-isoalloxazine with the Becke-Half-and-Half-LYP (BHHLYP) XC functional, which has been described in earlier work, 86 yielded the closest match with the experimental difference dipole moment 89 , 90 between the excited and the ground states of the flavin chromophore (Figure S3 in the Supporting Information ). Therefore, the atomic partial charges (APCs) obtained with BHHLYP were used to calculate the electrochromic shifts.…”

Section: Computational Detailsmentioning

confidence: 65%

Revealing the Functional States in the Active Site of BLUF Photoreceptors from Electrochromic Shift Calculations

2014

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Photoexcitation with blue light of the flavin chromophore in BLUF photoreceptors induces a switch into a metastable signaling state that is characterized by a red-shifted absorption maximum. The red shift is due to a rearrangement in the hydrogen bond pattern around Gln63 located in the immediate proximity of the isoalloxazine ring system of the chromophore. There is a long-lasting controversy between two structural models, named Q63A and Q63J in the literature, on the local conformation of the residues Gln63 and Tyr21 in the dark state of the photoreceptor. As regards the mechanistic details of the light-activation mechanism, rotation of Gln63 is opposed by tautomerism in the Q63A and Q63J models, respectively. We provide a structure-based simulation of electrochromic shifts of the flavin chromophore in the wild type and in various site-directed mutants. The excellent overall agreement between experimental and computed data allows us to evaluate the two structural models. Compelling evidence is obtained that the Q63A model is incorrect, whereas the Q63J is fully consistent with the present computations. Finally, we confirm independently that a keto–enol tautomerization of the glutamine at position 63, which was proposed as molecular mechanism for the transition between the dark and the light-adapted state, explains the measured 10 to 15 nm red shift in flavin absorption between these two states of the protein. We believe that the accurateness of our results provides evidence that the BLUF photoreceptors absorption is fine-tuned through electrostatic interactions between the chromophore and the protein matrix, and finally that the simplicity of our theoretical model is advantageous as regards easy reproducibility and further extensions.

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Section: Computational Detailsmentioning

confidence: 65%

Revealing the Functional States in the Active Site of BLUF Photoreceptors from Electrochromic Shift Calculations

2014

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“…Thus, the local hydrogen-bond network becomes more flexible and also more water molecules can penetrate into or are trapped around the function site, resulting in a larger stabilization energy in 1 ps and suggesting a more polar environment in HQ state. Since the stabilization energy depends on the local polarization and the dipole-moment change (Δ μ⃗ ) between the ground and excited states, and the recent experiments by Stark spectroscopy suggested a similar value of dipole-moment changes in three redox states,46–48 the observed large increase of ΔE 1 (360 cm −1 ) in HQ state must reflect the local environment change and in this case both the local water network and protein structure probably become more flexible. Interestingly, we observed a very similar stabilization energy of ΔE 2 (50–60 cm −1 ) for all the three states, reflecting the same amount of relaxation energy from coupled water-protein fluctuations.…”

Section: Resultsmentioning

confidence: 99%

Mapping Solvation Dynamics at the Function Site of Flavodoxin in Three Redox States

Chang

Guo

et al. 2010

J. Am. Chem. Soc.

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Flavoproteins are unique redox coenzymes and the dynamic solvation at their function sites is critical to the understanding of their electron-transfer properties. Here, we report our complete characterization of the function-site solvation of holoflavodoxin in three redox states and of the binding-site solvation of apoflavodoxin. Using intrinsic flavin cofactor and tryptophan residue as the local optical probes with two site-specific mutations, we observed distinct ultrafast solvation dynamics at the function site in the three states and at the related recognition site of the cofactor, ranging from a few to hundreds of picoseconds. The initial ultrafast motion in 1-2.6 ps reflects the local water-network relaxation around the shallow, solvent-exposed function site. The second relaxation in 20-40 ps results from the coupled local water-protein fluctuation. The third dynamics in hundreds of picoseconds is from the intrinsic fluctuation of the loose loops flanking the cofactor at the function site. These solvation dynamics with different amplitudes well correlate with the redox states from the oxidized form, to the more rigid semiquinone and to the much looser hydroquinone. This observation of the redox control of local protein conformation plasticity and water network flexibility is significant and such an intimate relationship is essential to the biological function of interprotein electron transfer.

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“…As large electric fields may shift the vibrational frequencies of complex molecules (68), it is possible that signals from amino acids near FAD are affected by electric field effects arising from excited or charge-separated states. Such Stark effects would expected to be most prominent in the Q 1 intermediate, with its short-range one-electron charge-separated state, and to a less extent FAD*, where the lowest excited state is known to exhibit a modest dipole change jDmj of 1.5 D with respect to the ground state (69). However, the FAD* and Q 1 SADS reported in Fig.…”

Section: Identification Of Fad* Vibrational Signaturementioning

confidence: 93%

Hydrogen Bond Switching among Flavin and Amino Acid Side Chains in the BLUF Photoreceptor Observed by Ultrafast Infrared Spectroscopy

Bonetti

Mathes

Stokkum

et al. 2008

Biophysical Journal

104

169

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BLUF domains constitute a recently discovered class of photoreceptor proteins found in bacteria and eukaryotic algae. BLUF domains are blue-light sensitive through a FAD cofactor that is involved in an extensive hydrogen-bond network with nearby amino acid side chains, including a highly conserved tyrosine and glutamine. The participation of particular amino acid side chains in the ultrafast hydrogen-bond switching reaction with FAD that underlies photoactivation of BLUF domains is assessed by means of ultrafast infrared spectroscopy. Blue-light absorption by FAD results in formation of FAD(*-) and a bleach of the tyrosine ring vibrational mode on a picosecond timescale, showing that electron transfer from tyrosine to FAD constitutes the primary photochemistry. This interpretation is supported by the absence of a kinetic isotope effect on the fluorescence decay on H/D exchange. Subsequent protonation of FAD(*-) to result in FADH(*) on a picosecond timescale is evidenced by the appearance of a N-H bending mode at the FAD N5 protonation site and of a FADH(*) C=N stretch marker mode, with tyrosine as the likely proton donor. FADH(*) is reoxidized in 67 ps (180 ps in D(2)O) to result in a long-lived hydrogen-bond switched network around FAD. This hydrogen-bond switch shows infrared signatures from the C-OH stretch of tyrosine and the FAD C4=O and C=N stretches, which indicate increased hydrogen-bond strength at all these sites. The results support a previously hypothesized rotation of glutamine by approximately 180 degrees through a light-driven radical-pair mechanism as the determinant of the hydrogen-bond switch.

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A Stark Spectroscopic Study of N(3)-Methyl, N(10)-Isobutyl-7,8-Dimethylisoalloxazine in Nonpolar Low-Temperature Glasses: Experiment and Comparison with Calculations

Cited by 27 publications

References 47 publications

Revealing the Functional States in the Active Site of BLUF Photoreceptors from Electrochromic Shift Calculations

Revealing the Functional States in the Active Site of BLUF Photoreceptors from Electrochromic Shift Calculations

Mapping Solvation Dynamics at the Function Site of Flavodoxin in Three Redox States

Hydrogen Bond Switching among Flavin and Amino Acid Side Chains in the BLUF Photoreceptor Observed by Ultrafast Infrared Spectroscopy

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