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- Effect of Protein Conformation and AMP Protonation State on Fireflies’ Bioluminescent Emission
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Try out PMC Labs and tell us what you think. Learn More. Controlling the energy of the emitted light i. For instance, in the biomedical field, red emitted light is desirable because of its larger tissue penetration and lower energies. The results show that the emission spectra when considering the protein characterized by a closed conformation are blue-shifted compared to the open conformation.
These findings can be reasoned by the different interactions hydrogen-bonds found between oxyluciferin and the surrounding protein, AMP and water molecules.
This study gets partial insight into the possible origin of the emitted color modulation by changes of the pH or luciferase conformations. The bioluminescence of fireflies is a quite efficient natural process which consists of light emission produced by an enzymatic-chemical reaction. Apart from its outstanding efficiency, this process shows a high substrate specificity. In particular, in a first step the luciferyl-adenylate intermediate is formed, catalyzed by the enzyme reaction 1 in Scheme 1.
Second, the high in energy intermediate dioxetanone is produced by reaction with the dioxygen molecule and release of adenosine monophosphate AMP.
Afterwards, decomposition of dioxetanone leads to the oxidation of luciferin producing the so-called oxyluciferin in the excited state reaction 2 in Scheme 1. Although the mechanism is generally accepted, some crucial aspects such as the chemical nature of the light emitter or the emission color modulation observed when changing the pH, temperature or concentration of divalent metal cations still remain unsolved [ 9 , 10 , 11 ]. Moreover, it has been shown that the color emitted by different beetle luciferase species ranges from yellow-green, to orange or red though the substrate leading to the light emission is the same for all of them [ 12 , 13 ].
Hence, the different luciferase conformations and active sites should explain the different observed colors. To get insight into the role of protein conformation on the color of the emitted light, several mutations of luciferase have been carried out, achieving in most cases a red-shift of the emission [ 14 , 15 , 16 , 17 ]. Focusing on the structure of the enzyme luciferase it consists of two domains, the N-terminal — amino acids and the smaller C-terminal — amino acids , connected by a short flexible hinge region.
These two domains play crucial role in the bioluminescent reaction as the active site is located at the interface between them, around the flexible linker. Luciferase falls within the superfamily of adenylating enzymes, for which two different conformations of the enzyme are adopted for catalyzing two subsequent reactions 1 and 2 in Scheme 1 [ 18 , 19 , 20 ].
For luciferase, only biochemical evidences supported this domain alternation mechanism [ 21 , 22 ] until an engineered luciferase PDB code 4G37 was produced to trap the enzyme in the second catalytic conformation with the C-terminal rotated Figure 1 , compared to the first catalytic conformation PDB code 4G36 [ 23 , 24 ]. It was demonstrated that light was emitted when using the engineered luciferase by providing the luciferyl adenylate intermediate [ 23 ].
Representation of the oxyluciferin chemical forms, protein conformations and AMP protonation states considered in this study. As aforementioned, changes in specific external factors also influence the color emission. In principle, the modification of pH could affect the chemical nature of oxyluciferin or the active site environment. Regarding the active site, different amino acids close to oxyluciferin could be sensitive to pH changes, as well as AMP which lies close to oxyluciferin once it is produced in the second catalytic reaction.
For all these reasons, in this study we propose the analysis of the influence of both the protein conformation and the protonation state of AMP on the emission one of the possible factors sensitive to pH modifications. In particular, MD simulations have been performed to sample the relevant oxyluciferin-surrounding water, protein, AMP interactions.
The phenolate-keto and phenolate-enol chemical forms of oxyluciferin have been selected for this study as they have been postulated to be the most probable light emitters in fireflies [ 28 , 29 , 30 , 31 , 32 ].
In addition, it has been shown that the emission mainly corresponds to that of the phenolate forms as an efficient excited state proton transfer ESPT between the phenol moiety and the surrounding can occur due to the high photoacidity of this hydroxyl group [ 26 , 33 , 34 ].
First, we analyze the effect of the protein conformation on the emission by considering the protein in an open or closed conformation Figure 1. The C-terminal rotation could modify the active site nature, affecting the interactions with oxyluciferin and thus its emission.
Furthermore, we investigate the effect of AMP protonation state on the emitted light as a partial study of the pH effect. The role played by the protonation state of AMP on the emission has already been computationally investigated by using the fragment molecular orbital method [ 35 ].
Although the amino acids and water molecules within a radius of 7. In this section, we analyze the different interactions between the protein, AMP, water and oxyluciferin by performing MD simulations.
In particular, two MD simulations A and B of 10 ns have been performed for each system, starting from the same initial conditions, to ensure an accurate sampling. In particular, two sets of four systems combination of two protein conformations and two protonation states of AMP have been studied, one set for the phenolate-keto form of oxyluciferin and other one for the phenolate-enol form Figure 1. These two oxyluciferin forms have been selected among the six possible chemical forms as they are the most probable forms leading to light emission [ 28 , 29 , 30 , 31 , 32 ].
To check the effect of the protein conformation on the emission spectra, the X-Ray structures of luciferase out of the Protein Data Bank corresponding to the first and second catalytic conformations PDB codes 4G36 and 4G37 respectively have been studied.
The results section is divided in three parts. First, we examine the possible interactions between the oxygen of the phenolate moiety for both keto and enol forms of oxyluciferin with the protein interactions with AMP are not feasible as it is far from this side of oxyluciferin. Second, we analyze the interactions between the oxygen atom of the keto group, for the phenolate-keto form of oxyluciferin, with AMP, water and the protein active site. Finally, we perform a similar study for the enol moiety of the phenolate-enol oxyluciferin.
We start by analyzing the interactions between the oxygen atom of the phenolate moiety O1 in Figure 2 of oxyluciferin and the protein. In this case, the interaction between O1 and AMP is not possible as they are far from each other.
Moreover, we study in this section the keto and enol forms of oxyluciferin, as both share this part of the chromophore in the two protein conformations open and closed. Graphical representation of the two hydrogen-bond patterns found along the simulations keto-4GAMPH as a representative case between the phenolate moiety O1 with a water molecules pattern 1 or b ARG and water molecules pattern 2.
By analyzing the hydrogen-bond interactions between O1 and the protein, mainly two hydrogen-bond patterns have been found along the MD simulations for the eight systems under study.
Pattern 1 is characterized by the interaction of O1 with 2 or 3 water molecules Figure 2 a whereas no interaction with the protein is observed. While, for pattern 2, O1 interacts both with the side chain of ARG and with 1 or 2 water molecules Figure 2 b. As ARG is positively charged and close to O1, their interaction is straightforward, being stable during the simulation time once the hydrogen-bond is formed.
In fact, it has been already shown the crucial role of this arginine in stabilizing a closed conformation of the protein and in creating a positively charged environment around the phenolate moiety of oxyluciferin [ 37 ]. As aforementioned, for each system we perform a set of two MD simulations A and B starting from the same initial conditions.
In some cases, we find the two hydrogen-bond patterns for the same system. For instance, for keto-4GAMP, simulation A is characterized by the interaction of O1 with only water molecules pattern 1 , while during simulation B, ARG is closer to oxyluciferin and interacts with O1 pattern 2.
It is natural to wonder if these different hydrogen-bond patterns lead to distinct emission spectra. To answer this query, we have extracted snapshots from MD simulations A and B, each one characterized by one of the two hydrogen-bond patterns previously described. Then, their corresponding emission spectra have been simulated see Methods section.
By comparing these spectra, we can conclude that the different O1 hydrogen-bond patterns have no influence on the emission, as similar spectra have been obtained for the different sets of simulations Figure 2 c.
In fact, the total number of hydrogen-bond interactions between O1 and the environment either water or ARG is the same for both patterns and this could be the factor that governs the emission wavelength.
In the phenolate-keto chemical form of oxyluciferin, apart from the phenolate moiety it is also possible to have significant interactions between the oxygen atom of the keto group O2 in Figure 3 and the surrounding. In this case, it is crucial to analyze not only the possible interactions between oxyluciferin and water or the protein, but also with AMP as it is quite close to this side of oxyluciferin Figure 3. One possible reason to explain this finding is that less water molecules are inside the protein cavity for the closed protein conformation and so, no interaction between O2 and water is observed.
We can confirm that for the closed conformation 4G37 no water molecules are found close to O2 only for a small fraction of snapshots one water is coming close black histogram in Figure 3 c. However, for the open conformation one water molecule is close to O2 during more than half of the simulation time and for some snapshots even two water molecules can be detected, red histogram in Figure 3 c , leading to a large amount of hydrogen-bond interactions. Hence, we may suspect that the closing of the C-terminal domain could hamper the entrance of water molecules to the active site.
For both, it is again observed that for the closed conformation 4G37 less water molecules are in the protein active site during the simulations Figure S1.
Once identified the different interactions between O2 and the surrounding, inside the open and closed protein conformations, we investigate the influence of the different patterns found on the emission.
In fact, this larger amount of interactions in the thiazolone side could stabilize the LUMO orbital more electron density located in the thiazolone ring compared to the HOMO, Figure S2 , slightly decreasing the emission energy as observed in the simulated spectra. A similar reasoning has been previously followed focused on the interactions between the phenolate part and the environment to explain the emission shift [ 38 ]. Starting with the open protein conformation, we observe that O2 interacts with one water molecule.
Figure 4 a. In detail, the phosphate group rotates leading to stable hydrogen-bond interactions with ARG Figure 4 a. However, a completely different scenario is found for the closed protein conformation.
Figure 4 b. Hence, the phosphate group interacts with the closest residues e. Thereafter, the emission spectra of keto-4GAMP and keto-4GAMP have been simulated to check the effect of the diverse hydrogen-bond patterns found for these systems.
After simulation of the spectra, we can conclude that the emission when considering the closed conformation of the protein is significantly blue shifted 48 nm, 0.
So, the fact that oxyluciferin interacts in a different way with the protein cavity it has moved inside the cavity has a clear effect on the emission. In this section we analyze the interactions between the hydroxyl group i. In contrast to the keto form, in this case the hydrogen atom involved in the hydrogen-bond interactions belongs to oxyluciferin. Hence, it is expected that the hydrogen-bond patterns found along the simulations are different from the ones observed for the keto form of oxyluciferin, described in the previous section.
For the open conformation, mainly two hydrogen-bond patterns have been found. It has to be remarked that for pattern 1 of the open conformation Figure 5 a , the interaction between the enol group and the environment is larger than for pattern 2. Hence, a greater interaction between the enol group and the surrounding is observed for the open than for the closed conformation.
For this reason, we have checked the influence of this finding on the emission spectra. In the case of the phenolate-enol form, the emission of the system with the closed conformation is slightly blue-shifted 11 nm, 0.
Although the energy difference found between the emission maxima is quite small, within the method error, the observed trend can be reasoned by the slightly larger number of interactions found between the enol group and the environment in the open conformation.
Contrary to the keto oxyluciferin form, in this case the phosphate group keeps the same orientation for both protein conformations, phosphate group pointing towards the enol group , due to its strong interaction with oxyluciferin.
The main difference found between the two protein conformations is that more water molecules enter the protein cavity for the open conformation Figure 6 c , as already observed for keto-4GAMPH system. By simulating the emission spectra of these two systems we can conclude that again, the emission of the system with the closed protein conformation is blue-shifted 26 nm, 0.
In the previous section we have presented the effect of the protein conformation and protonation state of AMP on the emission of phenolate-keto and phenolate-enol chemical forms of oxyluciferin, two possible light emitters of fireflies. First, we have analyzed the interactions of the phenolate moiety of oxyluciferin keto and enol chemical forms with the environment. In fact, the X-Ray structure of the part of the active site close to the phenolate moiety of both protein conformations, closed and open, are almost superimposed Figure S3 , in line with the similar interactions found during the MD simulations.
In this case, same emission spectra have been simulated independently of the hydrogen-bond pattern, as both result in a similar stabilization of the HOMO orbital Figure S2. Hence, the key factor responsible of the different simulated emission spectra must therefore lie in another part of the oxyluciferin molecule.
Motivated by finding the origin of the different simulated emission spectra, we have moved to the keto or enol side of oxyluciferin. Regarding the influence of the protein conformation, we can conclude that for all systems under study, the simulated emission spectra for the systems with the closed protein conformation 4G37 are blue-shifted compared to the ones with the open one black vs.
In fact, the most blue-shifted simulated emission has been found for the 4GAMP systems black dotted line in Figure 7 a,b.
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Effect of Protein Conformation and AMP Protonation State on Fireflies’ Bioluminescent Emission
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