Luís Pinto da Silva

Computational Studies of the Luciferase Light-Emitting Product: Oxyluciferin.

Firefly luciferase is the most studied bioluminescence system, and its catalyzed reactions have been relatively well characterized. However, the color tuning mechanism that leads to firefly multicolor bioluminescence is still unknown, nor is consensual which is the yellow-green and red emitters. Computational studies have been essential in the study of oxyluciferin (OxyLH2) chemi- and bioluminescence and are responsible for most of our knowledge of this natural phenomenon. The objective of this manuscript is the analysis of the benefits and the conclusions derived from the theoretical studies of the light emitter, OxyLH2, and its applications on bioluminescence research.

Computational Investigation of the Effect of pH on the Color of Firefly Bioluminescence by DFT

In spite of recent advances towards understanding the mechanism of firefly bioluminescence, there is no consensus about which oxyluciferin (OxyLH(2)) species are the red and yellow-green emitters. The crystal structure of Luciola cruciata luciferase (LcLuc) revealed different conformations for the various steps of the bioluminescence reaction, with different degrees of polarity and rigidity of the active-site microenvironment. In this study, these different conformations of luciferase (Luc) are simulated and their effects on the different chemical equilibria of OxyLH(2) are investigated as a function of pH by means of density functional theory with the PBE0 functional. In particular, the thermodynamic properties and the absorption spectra of each species, as well as their relative stabilities in the ground and excited states, were computed in the different conformations of Luc. From the calculations it is possible to derive the acid dissociation and tautomeric constants, and the corresponding distribution diagrams. It is observed that the anionic keto form of OxyLH(2) is both the red and the yellow-green emitter. Consequently, the effect of Luc conformations on the structural and electronic properties of the Keto-(-1) form are studied. Finally, insights into the Luc-catalyzed light-emitting reaction are derived from the calculations. The multicolor bioluminescence can be explained by interactions of the emitter with active-site molecules, the effects of which on light emission are modulated by the internal dielectric constant of the different conformations. These interactions can suffer also from rearrangement due to entry of external solvent and changes in the protonation state of some amino acid residues and adenosine monophosphate (AMP).

Firefly chemiluminescence and bioluminescence: efficient generation of excited states.

Firefly luciferase catalyzes a light-emitting reaction in which an excited-state product is formed. Both experimental and theoretical methodologies are used to study this system, and the reactions catalyzed by luciferase are relatively well characterized. However, the mechanism by which an excited-state product is formed is still unknown. This Minireview deals with the current understanding of firefly bioluminescence and chemiluminescence. Thermal decomposition of simple 1,2-dioxetanes is also discussed, due to their role in formation of the excited-state bioluminophore.

Advances in the knowledge of light emission by firefly luciferin and oxyluciferin.

Firefly luciferase is the most important and studied bioluminescence system. Due to very interesting characteristics, this system has gained numerous biomedical, pharmaceutical and bioanalytical applications, among others. In order to improve the use of this system, various researchers have tried to understand experimentally the colour of bioluminescence, and to create ways of tuning the colour emitted. The objective of this manuscript is to review the experimental studies of firefly luciferin and oxyluciferin, and related analogues, fluorescence and bioluminescence.

Kinetics of inhibition of firefly luciferase by dehydroluciferyl-coenzyme A, dehydroluciferin and L-luciferin.

The inhibition mechanisms of the firefly luciferase (Luc) by three of the most important inhibitors of the reactions catalysed by Luc, dehydroluciferyl-coenzyme A (L-CoA), dehydroluciferin (L) and L-luciferin (L-LH(2)) were investigated. Light production in the presence and absence of these inhibitors (0.5 to 2 μM) has been measured in 50 mM Hepes buffer (pH = 7.5), 10 nM Luc, 250 μM ATP and D-luciferin (D-LH(2), from 3.75 up to 120 μM). Nonlinear regression analysis with the appropriate kinetic models (Henri-Michaelis-Menten and William-Morrison equations) reveals that L-CoA is a non-competitive inhibitor of Luc (K(i) = 0.88 ± 0.03 μM), L is a tight-binding uncompetitive inhibitor (K(i) = 0.00490 ± 0.00009 μM) and L-LH(2) acts as a mixed-type non-competitive-uncompetitive inhibitor (K(i) = 0.68 ± 0.14 μM and αK(i) = 0.34 ± 0.16 μM). The K(m) values obtained for L-CoA, L and L-LH(2) were 16.1 ± 1.0, 16.6 ± 2.3 and 14.4 ± 0.96 μM, respectively. L and L-LH(2) are strong inhibitors of Luc, which may indicate an important role for these compounds in Luc characteristic flash profile. L-CoA K(i) supports the conclusion that CoA can stimulate the light emission reaction by provoking the formation of a weaker inhibitor.

Comparative study of the photoprotolytic reactions of D-luciferin and oxyluciferin.

Optical steady-state and time-resolved spectroscopic methods were used to study the photoprotolytic reaction of oxyluciferin, the active bioluminescence chromophore of the fireflys luciferase-catalyzed reaction. We found that like D-luciferin, the substrate of the firefly bioluminescence reaction, oxyluciferin is a photoacid with pK(a)* value of ∼0.5, whereas the excited-state proton transfer (ESPT) rate coefficient is 2.2 × 10(10) s(-1), which is somewhat slower than that of D-luciferin. The kinetic isotope effect (KIE) on the fluorescence decay of oxyluciferin is 2.5 ± 0.1, the same value as that of D-luciferin. Both chromophores undergo fluorescence quenching in solutions with a pH value below 3.

Theoretical modulation of the color of light emitted by firefly oxyluciferin.

One of the major mysteries regarding firefly bioluminescence is its pH‐dependent multicolor variation. At basic pH, the emission is on the yellow–green region, whereas at acid pH, the light emission is observed on the red region of the visible spectrum. Theoretical calculations using density functional theory, molecular mechanics, and semiempirical methods were made to investigate the effect exerted by intermolecular forces on light emission, and their modulation by polarity, and the differences in the conformation of the active site at basic and acid pH. Red emission is achieved by the weakening of the interactions of the emitter with ionic and hydrophobic molecules, by the polarization of the benzothiazole microenvironment, by ionization of the enzyme‐emitter complex and by changes of the hydrogen bond network. Arg220, Glu346, Ala350, Leu344 and adenosine‐5′‐monophosphate have blue‐shifting effects, while His247, Phe249, Gly341, Thr253, and Ile288 exert a redshifting one.

Study on the Effects of Intermolecular Interactions on Firefly Multicolor Bioluminescence

Firefly luciferase exhibits a color-tuning mechanism based on pH-induced changes in the structure of the active site. These changes increase the polarity of the active site, and thus modulate the intermolecular interactions between the light emitter and active site molecules. In this study, the effects exerted by adenosine monophosphate (AMP), water molecules, and amino acids of Luciola cruciata luciferase active site on the emission wavelength of oxyluciferin were assessed by TD-DFT calculations. The redshift results mainly from decreased interaction of oxyluciferin with AMP and increased interaction of the emitter with a water molecule and Phe249. Breaking of a hydrogen bond between the benzothiazole oxygen atom with formation of a similar bond to the thiazolone oxygen atom is also instrumental.

TD-DFT/molecular mechanics study of the Photinus pyralis bioluminescence system.

This is the first report of a computational study of the bioluminescence of ligand-bound Photinus pyralis luciferase. A time-dependent PBE0/molecular mechanics approach was used to study the interaction between excited-state oxyluciferin (Keto-(-1)) and neighboring active site molecules. The results of these calculations demonstrated that the most important intermolecular interactions are: blue-shifting ionic interactions, red-shifting π-π stacking, and red/blue shifting hydrogen bonding. Subsequent molecular dynamics simulations further supported these conclusions.

Interstate Crossing‐Induced Chemiexcitation as the Reason for the Chemiluminescence of Dioxetanones

The decomposition reaction of dimethyl-1,2-dioxetanone in dichloromethane was studied by using a DFT approach. The low efficiency of triplet and singlet excited-state formation was rationalised. A charge-transfer process was demonstrated to be involved in the chemiluminescence process. Present and previous results allow us to define an interstate crossing-induced chemiexcitation (ICIC) mechanism for the chemiluminescence of dioxetanones. Charge transfer is needed to reach a transition state, in the vicinity of which direct population of excited states is possible. The chemiexcitation process is then governed by singlet/triplet intersystem crossings. Structural modifications then modify the rate of these crossings and the singlet ground and excited-state interaction, thereby modulating the efficiency of this process and the spin of the resulting products.