Multiscale Simulations on Spectral Tuning and the Photoisomerization

Article pubs.acs.org/JCTC

Multiscale Simulations on Spectral Tuning and the Photoisomerization Mechanism in Fluorescent RNA Spinach Xin Li,*,† Lung Wa Chung,*,‡ and Guohui Li*,† †

State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China ‡ Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China

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S Supporting Information *

ABSTRACT: Fluorescent RNA aptamer Spinach can bind and activate a green fluorescent protein (GFP)-like chromophore (an anionic DFHBDI chromophore) displaying green fluorescence. Spectroscopic properties, spectral tuning, and the photoisomerization mechanism in the Spinach-DFHBDI complex have been investigated by high-level QM and hybrid ONIOM(QM:AMBER) methods (QM method: (TD)DFT, SF-BHHLYP, SAC-CI, LT-DF-LCC2, CASSCF, or MSCASPT2), as well as classical molecular dynamics (MD) simulations. First, our benchmark calculations have shown that TD-DFT and spin-flip (SF) TD-DFT (SFBHHLYP) failed to give a satisfactory description of absorption and emission of the anionic DFHBDI chromophore. Comparatively, SAC-CI, LT-DF-LCC2, and MSCASPT2 can give more reliable transition energies and are mainly used to further study the spectra of the anionic DFHBDI chromophore in Spinach. The RNA environmental effects on the spectral tuning and the photoisomerization mechanism have been elucidated. Our simulations show that interactions of the anionic cis-DFHBDI chromophore with two G-quadruplexes as well as a UAU base triple suppress photoisomerization of DFHBDI. In addition, strong hydrogen bonds between the anionic cis-DFHBDI chromophore and nearby nucleotides facilitate its binding to Spinach and further inhibit the cis-trans photoisomerization of DFHBDI. Solvent molecules, ions, and loss of key hydrogen bonds with nearby nucleotides could induce dissociation of the anionic trans-DFHBDI chromophore from the binding site. These results provide new insights into fluorescent RNA Spinach and may help rational design of other fluorescent RNAs.

1. INTRODUCTION Green fluorescent protein (GFP) and its derivatives have widespread applications in various biological systems.1−4 Recently, Spinach, Spinach2, and Broccoli, powerful and novel RNA mimics of GFP, have been developed and designed to selectively bind GFP-like chromophores/ligands (such as the 3′,5′-difluoro-4′-hydroxybenzylidene-2,3-dimethyl-imidazolinone (DFHBDI) anion in Scheme 1a and Chart 1) and induce green fluorescence.5−14 Moreover, the designed DFHBDI is in an anionic form, because two fluorine substituents increase the acidity and reduce the pKa of DFHBDI (pKa = 5.5). Spinach binding to the phenolate form of DFHBDI was found to have an enhanced fluorescence quantum yield (0.72) and brightness.5−9 As a widely used GFP and derivatives, this engineered green fluorescent RNA is very useful in, for example, labeling and imaging of RNAs, where its use makes GFP fusion proteins unnecessary. These studies have attracted the attention of many researchers.1−21,22a,23−26 Fluorescence of the anionic cis-DFHBDI chromophore in Spinach, light-induced photoconversion, and dissociation of the chromophore from Spinach have been reported recently.5−11 For example, the fluorescence decay and fluorescence recovery were found to be dependent on concentration of DFHBDI. The cis-trans photoisomerized product was proposed to quickly © 2016 American Chemical Society

dissociate from Spinach. Then, a new cis-DFHBDI chromophore in solution binds to Spinach to recover fluorescence.11 Crystal structures of Spinach in the presence and in the absence of a DFHBDI chromophore have been obtained recently and have provided important structural information concerning Spinach-DFHBDI complexes (Scheme 1).12,13 In these crystal structures, the DFHBDI chromophore was found to be planar and to interact with surrounding nucleotides via π−π stacking and hydrogen bonding. G-quadruplexes and a few adjacent nucleotides were proposed as essential in the binding site of the chromophore in Spinach, and it was proposed that a miniaturized baby Spinach still retains the level of fluorescence as is present in wild-type Spinach.12,13 By comparing the crystal structures of Spinach in the presence and in the absence of the DFHBDI chromophore, one can find that several nucleotides around the binding site change their positions significantly.12 Especially, a coplanar guanine nucleotide reorientates its base to form hydrogen bonding with the chromophore. In addition, the AAU base triple of Spinach in the absence of DFHBDI is changed to a new UAU base triple in the Spinach-DFHBDI complex. The new base triple Received: June 6, 2016 Published: September 29, 2016 5453

DOI: 10.1021/acs.jctc.6b00578 J. Chem. Theory Comput. 2016, 12, 5453−5464

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Journal of Chemical Theory and Computation

Scheme 1. Models of (a) the cis-DFHBDI Anion, (b) the trans-DFHBDI Anion, (c) a Spinach-DFHBDI Complex (R), (d) a Small Model (Rs) Spinach-DFHBDI Complex, and (e) the DFHBDI Binding Site in Spinach

Spinach12) was adopted in the second small model (Rs). The RNA systems with crystallographic water molecules and ions (Mg2+ and K+) were neutralized by adding K+ ions and were then fully solvated in a cuboid box (127 Å × 99.7 Å × 138 Å and 92.6 Å × 91 Å × 122 Å for the first and second models, respectively) of TIP3P water molecules by the AMBER Leap module.34−36 The AMBER ff99bsc0χOL3 force field was used for Spinach.37−41 RESP charges calculated at the HF/6-31G(d) level and the similar AMBER atom types were applied for DFHBDI.34,42 Molecular mechanics (MM) energy minimizations followed by molecular dynamics (MD) simulations (details given in the Supporting Information) were performed in the AMBER 14 package.34 Water molecules and ions within about 12 and 16 Å of the Spinach-DFHBDI complex and its small model complex, respectively, were extracted for the following ONIOM calculations. Moreover, for the case of a few additional snapshots from MD simulations, water molecules and ions within about 11 Å of the Spinach-DFHBDI complex were kept in the ONIOM calculations. 2.2. QM and ONIOM Calculations. Ground-state (S0) geometries of anionic cis- and trans-DFHBDI in the gas phase were first optimized by density functional theory (DFT: B3LYP or CAM-B3LYP, with 6-31+G(d,p) and 6-311++G(d,p) basis sets) and two-state-average (SA2) and three-state-average (SA3) CASSCF(16e,14o)/6-31G(d) (with all valence πelectrons and orbitals included in the active space, Figures S1 and S2) methods.43−49 The first excited-state (S1) geometry optimizations of the anionic cis- and trans-DFHBDI in the gas phase were carried out by time-dependent density functional theory (TD-DFT: TD-B3LYP or TD-CAM-B3LYP, with 631+G(d,p) and 6-311++G(d,p) basis sets),50,51 SAC-CI/ D95(d),52−54 and SA2-CASSCF(16e,14o)/6-31G(d) 46,47 methods. Then, the vertical absorption and emission energies were evaluated by different QM methods, such as TDDFT,50,51 spin-flip (SF) TD-DFT (SF-BHHLYP/6-311+G(d,p)), 5 5 , 5 6 SAC-CI/D95(d), 5 2 − 5 4 LT-DF-LCC2/ccpVDZ,57,58 and MS-CASPT2//SA3-CASSCF(16e,14o)/6-

Chart 1. Structural Formula of the Anionic Form of HBDI and DFHBDI

and G-quadruplexes give more space for the DFHBDI chromophore. Some nearby nucleotides also change positions of their bases after the chromophore binds to Spinach. Although these interesting and important investigations on Spinach have been reported, there remain some unresolved issues. In this work, multiscale simulations including high-level QM and ONIOM(QM:MM) calculations27−33 and classical molecular dynamics (MD) simulations have been carried out for the first time to examine spectral-tuning and the photoisomerization mechanism in the Spinach-DFHBDI complex. With these highly accurate theoretical methods, this study should help understand and predict the photophysical as well as photochemical properties of this novel fluorescent RNA Spinach.

2. COMPUTATIONAL DETAILS 2.1. Setup of Systems and Classical Simulations. The initial structure of the Spinach-DFHBDI complex was taken from the PDB databank (code: 4KZD, RNA sequence: 5′GDPGACGCGACCGAAAUGGUGAAGGACGGGUCCAGUGCGAAACACGCACUGUUGAGUAGAGUGUGAGCUCCGUAACUGGUCGCGUC3′).12 Two models (Scheme 1) were constructed for our simulations: the sequence 2-84 was chosen for the first model (R); the sequence 16-69 (a truncated Spinach, which was suggested to retain the fluorescence of 5454


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Figure 1. In the gas phase, key bond lengths of the DFHBDI anion in (a) S0 and (b) S1 calculated by different methods. The bond labels are given in Scheme 1a.

31G(d) (with an imaginary level shift of 0.3 au).48,49,59−61 The Gaussian 09,42 Q-Chem,62 Molpro,63,64 and Molcas65 programs were used for these calculations. From classical MM minimization and MD simulations, geometries of Spinach-DFHBDI complexes in S0 and S1 were further optimized by ONIOM(DFT:AMBER) and ONIOM(TD-DFT:AMBER), respectively.19−21,27−33 In the ONIOM optimization for the small model (Scheme 1d), one K+ ion close to the phenolate oxygen of DFHBDI was included in the QM region. Electronic embedding (EE) scheme was applied for all these geometry optimizations, except for one unsuccessful case from the MM minimized structure of the SpinachDFHBDI complex (Scheme 1c). Moreover, the ONIOM(CASSCF:AMBER) method was also employed to optimize geometries of the Spinach-DFHBDI complexes in S0 and S1, where QM energies and gradients were externally computed by the Molpro program.63,64 For these ONIOM(CASSCF:AMBER) optimizations, a mechanical embedding (ME) scheme was used, and the S0 and S1 charges of DFHBDI were updated in each optimization until energy was converged. The ONIOM-EE scheme was utilized to calculate all vertical

absorption and emission energies of DFHBDI in Spinach. In addition, the cis-trans photoisomerization of DFHBDI in Spinach was studied by the ONIOM(CASSCF:AMBER) method. Potential energy curve (PEC) for the cis-trans photoisomerization was obtained from relaxed scan optimization of a key dihedral angle, which has been widely and successfully used in many photobiological systems (e.g., GFP or retinal-type chromophore involving motion of more than one dihedral angle).22 PEC for the photoisomerization of DFHBDI in Spinach was then refined by using MS-CASPT2 as the QM method. Water molecules within about 6 Å (∼8 Å for the small model) of the Spinach-DFHBDI complex were optimized, and the rest of the water molecules were frozen in the ONIOM optimization.19,21,31,32

3. RESULTS AND DISCUSSION Geometrical features, absorption, and emission of DFHBDI in the gas phase are first discussed in section 3.1. Key results and discussion for geometry, absorption, and emission of cisDFHBDI in Spinach are then presented in section 3.2. Furthermore, the photoisomerization mechanism of DFHBDI 5455


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Journal of Chemical Theory and Computation in Spinach is discussed in section 3.3. The trans-DFHBDI in Spinach is then addressed in section 3.4. Finally, a comparison of fluorescence activation in Spinach and GFP is simply summarized in section 3.5. 3.1. Absorption and Emission of DFHBDI in the Gas Phase. The key geometric and spectroscopic properties of the DFHBDI anion in the gas phase were given in Figure 1 and Tables 1 and 2 as well as Tables S1 and S2, respectively.

Table 2. Calculated Emission Energies of Anionic DFHBDI in the Gas Phasea,b cis-DFHBDI emission TD-B3LYP/BS0 TD-CAM-B3LYP/BS0 SF-BHHLYP/BS1//TD-B3LYP/BS0 SF-BHHLYP/BS1//TD-CAM-B3LYP/ BS0 SAC-CI/BS2 SAC-CI/BS2//TD-B3LYP/BS0 SAC-CI/BS2//TD-CAM-B3LYP/BS0 SAC-CI/BS2//CASSCF/BS4 LT-DF-LCC2/BS3//TD-B3LYP/BS0 LT-DF-LCC2/BS3//TD-CAM-B3LYP/ BS0 LT-DF-LCC2/BS3//SAC-CI/BS2 LT-DF-LCC2/BS3//CASSCF/BS4 MS-CASPT2/BS4//TD-B3LYP/BS0 MS-CASPT2/BS4//TD-CAM-B3LYP/ BS0 MS-CASPT2/BS4//SAC-CI/BS2 MS-CASPT2/BS4//CASSCF/BS4

Table 1. Calculated Absorption Energies of Anionic DFHBDI in the Gas Phasea,b cis-DFHBDI absorption TD-B3LYP/BS0//B3LYP/BS0 TD-CAM-B3LYP/BS0//CAM-B3LYP/ BS0 SF-BHHLYP/BS1//B3LYP/BS0 SF-BHHLYP/BS1//CAM-B3LYP/BS0 SAC-CI/BS2//B3LYP/BS0 SAC-CI/BS2//CAM-B3LYP/BS0 SAC-CI/BS2//CASSCF/BS4 LT-DF-LCC2/BS3//B3LYP/BS0 LT-DF-LCC2/BS3//CAM-B3LYP/BS0 LT-DF-LCC2/BS3//CASSCF/BS4 MS-CASPT2/BS4//B3LYP/BS0 MS-CASPT2/BS4//CAM-B3LYP/BS0 MS-CASPT2/BS4//CASSCF/BS4c

trans-DFHBDI

eV

f

eV

f

3.01 3.11

0.96 1.06

3.05 3.15

0.91 0.98

3.07 3.11 2.40 2.46 2.44 2.39 2.43 2.44 2.54 2.58 2.60

NA NA 0.90 0.91 0.90 0.81 0.81 0.81 1.38 1.38 1.39

3.09 3.13 2.36 2.40 2.43 2.41 2.45 2.47 2.53 2.57 2.60

NA NA 0.80 0.80 0.82 0.73 0.74 0.75 1.23 1.24 1.26

trans-DFHBDI

eV

f

eV

f

2.82 2.96 2.88 2.95

0.74 1.00 NA NA

2.90 2.99 2.90 2.96

0.82 0.92 NA NA

2.22 2.10 2.24 2.22 2.19 2.28

0.83 0.76 0.83 0.81 0.70 0.76

2.27 2.16 2.22 2.11 2.24 2.29

0.77 0.74 0.74 0.71 0.68 0.69

2.27 2.24 2.39 2.43

0.76 0.74 1.24 1.31

2.33 2.24 2.37 2.42

0.71 0.67 1.17 1.18

2.44 2.40

1.32 1.28

2.46 2.37

1.20 1.15

a

a

BS0: 6-31+G(d,p); BS1: 6-311+G(d,p); BS2: D95(d); BS3: ccpVDZ; BS4: 6-31G(d). bThe calculated emission values on the basis of geometries optimized by TD-DFT/6-311++G(d,p) (TD-DFT/BSL) are given in Table S2. The effects of small and large basis sets (BS0 and BSL) on the S1 geometry and emission of anionic DFHBDI are not significant.

3.1.1. Key Ground- and Excited-State Geometrical Features. Generally, the optimized key bond lengths of the cis- and trans-DFHBDI in S0 are similar. This structural feature is the same as was found in a GFP-type chromophore, 4′hydroxybenzylidene-imidazolinone (HBI), in our previous study.19 Also, the ground-state geometries of DFHBDI calculated by the B3LYP and CAM-B3LYP methods are similar to those by the CASSCF method, with the maximum deviation of about 0.02 Å for the CN (R1) and CO (R3 and R10) bonds (see Figure 1a). For the DFHBDI anion in S1, the high-level CASSCF and SAC-CI methods give similar geometry (Figure 1b). Compared to the geometry optimized by the CASSCF or SAC-CI method, TD-CAM-B3LYP can give a slightly better result than TDB3LYP. As shown in Figure 1, it is clear that the bridge bonds (R5 and R6) are elongated in S1, relative to those in S0. Comparing cis- and trans-DFHBDI in S1, the difference of bridge bonds are the most obvious (more elongated R5 and shortened R6 bonds in trans-DFHBDI than in cis-DFHBDI). In addition, geometrical features of DFHBDI are comparable to those of HBI19 and 4′-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI, Chart 1) in Figure S3. These results suggest that the difluoro substituent effect on the chromophore geometry is minor. 3.1.2. Vertical Absorption and Emission. In experiment, the measured absorption energy of the cis anionic GFP

chromophore (cis-HBDI) in vacuo is 2.59 eV,66 while there are no measured values of anionic DFHBDI in vacuo. Herein, the vertical absorption energies of the anionic cis- and transDFHBDI chromophores in the gas-phase were computed (Table 1). SAC-CI/D95(d) and LT-DF-LCC2/cc-pVDZ methods give the comparable absorption (∼2.4−2.5 eV), which are slightly lower than the absorption (∼2.5−2.6 eV) calculated by the MS-CASPT2(16e,14o)/6-31G(d) method. Compared to the above high-level calculations, TD-B3LYP, TD-CAM-B3LYP, and SF-BHHLYP methods overestimate the absorption energy (>3.0 eV). Overall, the MS-CASPT2 method should be the most reliable method with which to evaluate the spectroscopic properties of anionic DFHBDI in the gas phase, because the MS-CASPT2 computed absorption energy of the anionic cis-HBDI chromophore in the gas phase (∼2.6 eV in Table S3) agrees well with the measured value (2.59 eV) in vacuo.66 In addition, the vertical emission energies for the cis- and trans-DFHBDI chromophores (optimized by TD-DFT, SACCI, and CASSCF methods) were also evaluated (Table 2). Again, the SAC-CI and LT-DF-LCC2 methods give similar emission values (∼2.1−2.3 eV), which are lower than the emission (∼2.4−2.5 eV) calculated by the MS-CASPT2 method. Nevertheless, TD-B3LYP, TD-CAM-B3LYP, and SFBHHLYP methods give a larger error for the vertical emission energy (>2.8 eV), compared to the high-level methods. In general, different conformations (cis/trans) and geometries optimized by different methods have a minor effect on the calculated absorption and emission energies of anionic DFHBDI in the gas phase. Compared with our MS-CASPT2 computed absorption (∼2.6 eV) and emission (∼2.5 eV) of anionic HBDI in the gas phase, our calculations show that the difluoro substituent effect in DFHBDI leads to a small red shift

BS0: 6-31+G(d,p); BS1: 6-311+G(d,p); BS2: D95(d); BS3: ccpVDZ; BS4: 6-31G(d). bThe calculated absorption values on the basis of geometries optimized by DFT/6-311++G(d,p) (DFT/BSL) are given in Table S1. The effects of small and large basis sets (BS0 and BSL) on the S0 geometry and absorption of anionic DFHBDI are minor. cThe MS-CASPT2 calculated absorption is very similar for the geometry optimized by SA2-CASSCF/BS2 (using the Molpro program) or SA3-CASSCF/BS2 (using the Molcas program).

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Journal of Chemical Theory and Computation of ∼0.04 eV in the absorption and emission energies (Tables 1, 2, and S1−S3). 3.2. Absorption and Emission of DFHBDI in Spinach. 3.2.1. Key Ground-State and Excited-State Geometries. For cis-DFHBDI in Spinach12 (Figure 2 and Scheme 1c-d), one of

CI method (∼2.3 eV), while the LT-DF-LCC2 method gives a slightly better result (∼2.4−2.5 eV in Table 3). Comparatively, Table 3. ONIOM(QM1:AMBER)-EE Calculated Vertical Absorption and Emission Energies of the Anionic cisDFHBDI Chromophore in Spinach, Based on the Optimized S0 and S1 Geometries by ONIOM(QM2/631+G(d,p):AMBER)a,b QM2 methods (geometry)

QM1 methods (energy) SAC-CI/ D95(d) LT-DF-LCC2/ cc-pVDZ MS-CASPT2/ 6-31G(d) SAC-CI/ D95(d) LT-DF-LCC2/ cc-pVDZ MS-CASPT2/ 6-31G(d) exptl

B3LYP

CAM-B3LYP

TD-CAMB3LYP

absorption

absorption

emission

models

eV

f

eV

f

eV

f

R

2.26

0.81

2.30

0.80

2.08

0.73

R

2.41

0.76

2.45

0.76

2.27

0.70

R

2.57

1.35

2.61

1.35

2.45

1.27

Rs

2.47

0.78

2.56

0.77

2.20

0.74

Rs

2.48

0.66

2.54

0.65

2.38

0.70

Rs

2.78

1.20

1.14

2.65

R

5

2.64, 2.66,

2.88 13

2.77

7

2.47,

1.21 13

2.485,7

a ONIOM-ME optimized geometry for the model R. ONIOM-EE optimized geometry with one nearby K+ ion in the QM region for the small model Rs. bTD-DFT cannot give reliable absorption and emission data (Table S4).

the MS-CASPT2-calculated absorption of ∼2.6 eV (Table 3) agrees well with the measured excitation maximum of DFHBDI in Spinach (2.64−2.66 eV)5,13 and Spinach2 (2.77 eV).7 Moreover, the computed absorption energy of DFHBDI in Spinach is about 2.65 eV (Table S5), based on the ONIOM optimized geometry with a large QM region including DFHBDI and G23, G54, and U50 as well as A53 bases. In addition, the calculated vertical absorption energy of the anionic DFHBDI chromophore in the small model Rs is generally higher than that in the model R (Table 3). The vertical emission energy was also calculated by using SAC-CI, LT-DF-LCC2, or MS-CASPT2 as the QM method in ONIOM-EE calculations. As listed in Table 3, the SAC-CI method gives a lower value for the emission energy (∼2.1 eV) of the anionic cis-DFHBDI chromophore in Spinach. The LTDF-LCC2-calculated vertical emission energy (∼2.3 eV) shows a smaller error. Whereas the MS-CASPT2-calculated value (2.45 eV) is in a good agreement with the experimental values (2.47−2.48 eV).5,7,13 Again, the calculated vertical emission energy of the anionic DFHBDI chromophore in the small model Rs is ∼0.2 eV higher than the model R. In addition, the vertical absorption and emission energies of the anionic cis-DFHBDI chromophore in Spinach have also been computed by using MS-CASPT2/6-31G(d) as the QM method in the ONIOM-EE calculations, based on the S0 and S1 geometries optimized by the ONIOM(CASSCF/6-31G(d):AMBER) method. As shown in Table 4, the calculated vertical absorption (2.63 eV) and emission (2.41 eV) of the anionic DFHBDI chromophore in Spinach agree well with the experiments.5,7,13 The K+ ion near the phenolate oxygen of DFHBDI in the small model Rs may play a key effect on the

Figure 2. Computed binding site of the Spinach-DFHBDI complex for (a) R and (b) Rs models. Key distances in Å were obtained from the geometry optimization by ONIOM(B3LYP/6-31+G(d,p):AMBER) (left) and ONIOM(CASSCF/6-31G(d):AMBER) (right).

the K+ ions which were added to neutralize the system moves into the vicinity of the phenolate oxygen of the chromophore in Rs, but not in R, during the MM minimization. Inspection of the ONIOM-optimized Spinach-DFHBDI complex (Figures 2 and S4−S5) revealed several factors that can contribute to the fluorescence of the cis-DFHBDI chromophore in Spinach. The first is the extensive stacking of DFHBDI with its upper Gquadruplex and its lower UAU base pairs, which keep the chromophore planar. The second is a hydrogen bond between the phenolate oxygen of DFHBDI and the 2′-OH of G23, which also forms a hydrogen bond with the 2′-OH of U50. In addition, there are strong hydrogen bonds between DFHBDI and the base of G28 and the 2′-OH of A53. These interactions should constrain the cis-DFHBDI chromophore to the limited cavity in Spinach. Moreover, a single positively charged K+ ion was found to coordinate with the negatively charged phenolate oxygen of DFHBDI in the small model, and this could further stabilize the anionic form of the chromophore. 3.2.2. Vertical Absorption and Emission of the SpinachDFHBDI Complex. The vertical absorption energy of the anionic cis-DFHBDI chromophore in Spinach was calculated by SAC-CI, LT-DF-LCC2, and MS-CASPT2 methods as the QM method, with the ONIOM(QM:MM)-EE scheme. The computed vertical absorption energy of the anionic DFHBDI chromophore in Spinach is slightly underestimated by the SAC5457


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therefore, any moieties which can gain larger electrostatic interaction from the more negatively charged imidazolinone ring and bridge CH part should stabilize S1 more than S0 (a smaller S1−S0 energy gap) and contribute to the red-shifted spectra of DFHBDI in Spinach, whereas any moieties which have weaker electrostatic interaction with the less negatively charged phenolate ring should relatively destabilize S1 (a larger S1−S0 energy gap) and lead to the blue-shifted spectra in Spinach. First, one K+ ion located between two G-quadruplexes was proposed to stabilize G-quadruplex base pairs in experiments.12,13 This K+ is above the bridge CH and imidazolinone oxygen and can stabilize S1 more than S0 of DFHBDI, leading to the red-shifted absorption and emission of DFHBDI by ∼0.1 eV (Scheme 2 and Table 4). Second, additional K+ ions close to DFHBDI observed in a crystal structure were suggested to stabilize the anionic chromophore.13 In Rs, one K+ ion (called K+(sol), near the phenolate ring) can destabilize S1 of DFHBDI, and thus it induces blue-shifted absorption and emission of DFHBDI by at least ∼0.1 eV (Scheme 2 and Table 4). The soluble cations could therefore modulate the spectra of Spinach.9a Third, hydrogen bonds and bases of nucleotides also affect the spectra of DFHBDI in Spinach. For example, the 2′OH of A53 (A53OH) and the base of G28 (G28b) which form hydrogen bonds with the imidazolinone ring contribute to the red-shifted absorption and emission of DFHBDI in Spinach (∼0.02−0.1 eV, Scheme 2 and Table 4), as a result of the increased stabilization in S1 as opposed to S0 of DFHBDI. The effect of G28 base is larger than that of the 2′-OH of A53, due to the stronger hydrogen bonding of DFHBDI with G28 than with A53 (Figure 2). 3.2.3.2. The Dynamic Environment. By inspection of snapshots from the classical MD simulations, several water molecules and K+ ions were seen to approach the phenolate ring and interact with DFHBDI. Hydrogen bonds of G23 and A53 with DFHBDI can sometimes be broken (blue and cyan lines in Figure 3), but hydrogen bonds between G28 and DFHBDI remain intact (orange and pink lines in Figure 3) during the simulation time. This is consistent with the experimental observation that the guanine (G28) plays a key role in the fluorescence activation of DFHBDI in Spinach.12,13

Table 4. MS-CASPT2/6-31G(d) as the QM Method in the ONIOM-EE Calculations of Vertical Absorption and Emission of the Spinach-DFHDBI Complex, Based on the ONIOM(CASSCF/6-31G(d):AMBER) Optimized S0 and S1 Geometries absorption R cis-DFHBDIQM(R)a without charges:b

Rs cis-DFHBDIQM(Rs)a without charges:b

K+ A53OH G28b

K+ K+(sol)

emission

eV

f

eV

f

2.63 2.59 2.73 2.66 2.73 2.74 2.60 2.88 2.65

1.37 1.38 1.32 1.35 1.33 1.35 1.38 1.29 1.41

2.41 2.37 2.52 2.43 2.51 2.53 2.39 2.68 2.47

1.25 1.25 1.19 1.23 1.19 1.23 1.27 1.17 1.29

a

The bare chromophore taken from the optimized Spinach-DFHBDI complex was used to evaluate the absorption and emission energies. b Atomic charges of these parts were excluded in the ONIOM-EE calculations.

blue-shifted absorption (2.74 eV) and emission (2.53 eV) shown in Table 4, which will be discussed in the next section. 3.2.3. The Environmental Effect on Absorption and Emission of DFHBDI in Spinach. 3.2.3.1. The Static Environment. Very similar absorption and emission data were found in the bare DFHBDI chromophore (cis-DFHBDIQM) which was taken from the two models of Spinach (Tables 4 and S6). However, a blue shift in the absorption and emission of the anionic DFHBDI chromophore in Spinach was observed, especially in Rs, and, therefore, the key roles in absorption and emission of the K+ ions, hydrogen bonds, and bases around the binding site were further investigated (Scheme 2 and Tables 4 and S6). As shown in Figure S2 and Scheme 2, intramolecular charge transfer occurs from the phenolate ring to the imidazolinone ring and bridge CH part of the anionic DFHBDI chromophore in the S0 → S1 transition: the phenolate ring becomes less negatively charged, while the imidazolinone ring and bridge CH part become more negatively charged. Upon the excitation, Scheme 2. Schematic Presentation of the DFHBDI Binding Site in Spinach

Figure 3. Key hydrogen-bonding distances in the classical MD simulation. 5458


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Figure 4. Potential energy curves for (a) clockwise (180° → 90°) and (b) counterclockwise (180° → 260°) photoisomerization around the dihedral τ of DFHBDI in Spinach. FC: Franck−Condon. FS: fluorescent state.

3.3. Photoisomerization Mechanism of DFHBDI in Spinach. 3.3.1. Potential Energy Curves. To study the cistrans photoisomerization mechanism, the isomerization around one bridge dihedral τ (see Chart 1) of DFHBDI in S1 was investigated in the gas phase and in Spinach (Figures 4, S6, and S7). For the photoisomerization of anionic DFHBDI in the gas phase (Figure S6), there is a very small barrier (∼1−2 kcal/ mol), which is similar to the GFP-type chromophore.25,26 However, one previous CASPT2//CASSCF study suggested that the fluorescent state (FS) of HBI may not exist in the gas phase.26 Comparatively, by using the ONIOM(MS-CASPT2// CASSCF:AMBER)-EE method, the calculated potential energy profile for the photoisomerization of the anionic DFHBDI chromophore in Spinach was found to be unfavorable (with a barrier of ∼13−17 kcal/mol, see Figure 4), due mainly to the large environmental effect. When excluding the energetic contribution from the RNA environment, a barrier from the

Furthermore, additional ONIOM(QM:MM) optimizations for nine snapshots taken from MD simulations of the SpinachDFHBDI complex were performed, and then the absorption and emission were calculated (Tables S7 and S8). The ground state of the Spinach-DFHBDI complex can be strongly stabilized by water molecules and K+ ions, which come close to the phenolate ring in different conformations. Hence, the calculated absorption/emission of DFHBDI in Spinach obtained from these ONIOM optimized snapshots are largely blue-shifted, compared to that obtained from the energy minimized X-ray crystal structure (Tables 3, S7, and S8). As listed in Table S9, the dynamic environment contributes to the blue-shifted absorption of DFHBDI in Spinach by ∼0.4−0.5 eV. One water molecule and one K+ ion close to the phenolate ring of DFHBDI can contribute to the blue-shifted absorption by ∼0.1 and 0.1−0.2 eV, respectively. Therefore, solvent molecules and soluble cations could modulate the spectra of Spinach.9 5459


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Figure 5. (a) Bridge bond lengths, (b) key dihedrals, and (c) charges of DFHBDI during the photoisomerization.

QM term was found to be ∼2−3 kcal/mol. The difference in the barrier (∼1 kcal/mol) between the QM contribution of DFHBDI in Spinach and the gas phase should attribute to the RNA geometrical effect on the chromophore. The RNA environment further raises the barrier by ∼10−15 kcal/mol. Moreover, the barrier for the clockwise rotation of the chromophore is higher than that for the counterclockwise rotation by ∼4 kcal/mol. Thus, the Spinach RNA environment (e.g., key hydrogen bonds and steric effects from Gquadruplexes and UAU base triple) disfavors the cis-trans photoisomerization of DFHBDI and maintains the planar chromophore, which is the key to the fluorescence. In this respect, some mutations of any layer of G-quadruplexes, G28, or A53 in the base triple were reported to reduce or abolish the fluorescence of DFHBDI in Spinach.12,13 The above-discussed

effect of RNA environment is similar to that observed in the GFP-like proteins.19,20,25,26,67 By inspection of the S0 and S1 energy curves of the clockwise or counterclockwise photoisomerization of DFHBDI in Spinach (Figure 4), the energy gap becomes smaller when the dihedral τ is highly rotated. The mixing of the states (closed-shell and 1(π,π*) states) was found for DFHBDI in Spinach, when the dihedral τ is around 90° or 260°. Moreover, a sloped conical interaction may exist for the photoisomerization of the anionic DFHBDI chromophore in Spinach.26 3.3.2. Geometry and Charge of DFHBDI. Now let us pay attention to changes of the geometry and charge of the DFHBDI chromophore during the photoisomerization in Spinach. When the dihedral τ of DFHBDI is rotated by ∼50−60°, the R5 bond length increases and that of R6 5460


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found to be broken: A53 forms a hydrogen bond with the imidazolinone oxygen of DFHBDI, and G28 shifts toward the phenolate side. Comparatively, hydrogen bonds of DFHBDI with G23 and A53 remain intact for trans″-DFHBDI in Spinach, but G28 shifts slightly. In this connection, it was proposed that the trans isomer of DFHBDI has steric clashes and fewer hydrogen bonds than cis-DFHBDI in Spinach.13 3.4.2. Dissociation of the trans-DFHBDI Chromophore in Spinach. Classical MD simulations were performed starting from the ONIOM-optimized trans′- and trans″-DFHBDI in Spinach (Figures 6 and S8). The trans″-DFHBDI was found to move out of the binding site of Spinach in the MD simulation (Figure S9). Possibly, this is driven by interactions with water molecules and cations close to the DFHBDI anion and weakened or broken hydrogen bonds with nearby nucleotides in Spinach.13 In addition, the gate and cavity formed within the G-quadruplex and the UAU base triple was found to be open during the dissociation of trans″-DFHBDI in Spinach. The base of A58 changes its position and may reconstruct a base triple after trans-DFHBDI moves out of Spinach. Another cisDFHBDI in solution may bind to Spinach by forming favorable interactions. This is consistent with the observed photoconversion and fast dissociation of trans-DFHBDI resulting in the fluorescence decay and the DFHBDI concentration dependent recovery in Spinach.11 3.5. Fluorescence Activation in Spinach and GFP. DFHBDI as a new GFP-like chromophore is in the anionic form, since two fluorine substituents increase its acidity and reduce its pKa. The Spinach-DFHBDI complex has an enhanced fluorescence quantum yield and brightness.5−9 The anionic cis-DFHBDI chromophore can bind to Spinach in a specific binding site within the rigid two-layer G-quadruplexes and the relatively flexible base triple (Schemes 1e and 2). This binding in Spinach involves formation of hydrogen bonds with its nearby nucleotides as well as stacking interactions with Gquadruplex and the base triple. These structural features in Spinach enforce a planar conformation of the anionic DFHBDI chromophore to minimize radiationless decay and suppress cistrans photoisomerization of DFHBDI (with a higher barrier, Figure 4), that thus enhances the green fluorescence of the DFHBDI chromophore. Both Spinach and GFP or GFP-like proteins bind favorably with the cis conformer of the chromophore through hydrogen bonds and stacking interactions to retain the planarity of the chromophore and to enhance fluorescence. However, the anionic DFHBDI chromophore in Spinach may interact with water molecules and cations in solution. In addition, the fluorescence decay and recovery of the Spinach-DFHBDI complex are related to the DFHBDI concentration and its dissociation or association with Spinach. These features are different from GFP and its derivatives. The chromophore in GFP or GFP-like proteins is buried in the β-barrel of the protein and is covalently linked with the protein. Therefore, it is hard for the GFP or GFP-like chromophore to interact directly with water molecules and cations in solution, and dissociation of the GFP or GFP-like chromophore is impossible. Moreover, excited-state proton transfer (ESPT) through the hydrogenbond network is responsible for photoactivation of the neutral GFP or GFP-like chromophore to generate the anionic chromophore. ESPT does not operate in Spinach.

decreases, both to extremes, and the bond orders of these bonds are reversed (Figure 5a). The photoisomerization of DFHBDI proceeds through a hula-twist-like (not one-bondflip) mechanism in the limited Spinach cavity, since the adjacent dihedral angle ϕ (see Chart 1) also rotates together with rotation of the dihedral τ of DFHBDI (Figure 5b) However, one-bond-flip photoisomerization was found for the anionic DFHBDI chromophore in the gas phase, because the adjacent dihedral angle only rotates slightly (Figure S6). When the anionic cis-DFHBDI chromophore in Spinach rotates in a clockwise or counterclockwise direction, the charges in the phenolate ring (C-ring) and the imidazolinone ring (Nring) become more and less negative, respectively (Figure 5c). The charge of the bridge CH increases slightly at the beginning of the rotation but then decreases after the variation of dihedral τ exceeds ∼40°. These results suggest intramolecular electron transfers mainly from the imidazolinone ring to the phenolate ring and bridge CH in the photoisomerization. As a consequence, the hydrogen bonds between the phenolate oxygen of DFHBDI and 2′-OH of G23 as well as water molecules become stronger. In addition, electrostatic interactions between the highly twisted DFHBDI and its nearby cations should be enhanced. The imidazolinone ring with lower negative charge in S1 leads to a weakening of the hydrogen bonds between DFHBDI and G28/A53. The above-discussed features found for the anionic DFHBDI chromophore are qualitatively similar to those found for the wild-type GFP chromophore (HBDI or HBI), which have been reported by several research groups.19,20,25,26,67−69 3.4. The trans-DFHBDI in Spinach. 3.4.1. The Formation of trans-DFHBDI in Spinach. The highly twisted DFHBDI in S1 can regenerate the original cis conformer or further isomerize to form the trans conformer after decaying to S0. Here, the trans′- and trans″-DFHBDI were obtained from the clockwise and counterclockwise rotation around the dihedral τ of cisDFHBDI in Spinach, respectively (Figures 6 and S8 and Table S10), on the assumption that the photoisomerization of DFHBDI occurs only rarely. For trans′-DFHBDI in Spinach, the key hydrogen bonds of DFHBDI with G28 and G23 were

Figure 6. Superimposition of cis-DFHBDI (in green) and (a) trans′DFHBDI (in cyan) as well as (b) trans″-DFHBDI (in pink) from the cis-trans photoisomerization of the DFHBDI chromophore in Spinach. 5461


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(9) (a) You, M.; Jaffrey, S. R. Structure and Mechanism of RNA Mimics of Green Fluorescent Protein. Annu. Rev. Biophys. 2015, 44, 187−206. (b) Laptenok, S. P.; Conyard, J.; Bulman Page, P. C.; Chan, Y.; You, M.; Jaffrey, S. R.; Meech, S. R. Photoacid behaviour in a fluorinated green fluorescent protein chromophore ultrafast formation of anion and zwitterion states. Chem. Sci. 2016, 7, 5747−5752. (10) Wang, P.; Querard, J.; Maurin, S.; Nath, S. S.; Le Saux, T. L.; Gautier, A.; Jullien, L. Photochemical Properties of Spinach and Its Use in Selective Imaging. Chem. Sci. 2013, 4, 2865−2873. (11) Han, K. Y.; Leslie, B. J.; Fei, J.; Zhang, J.; Ha, T. Understanding the Photophysics of the Spinach−DFHBI RNA Aptamer−Fluorogen Complex To Improve Live-Cell RNA Imaging. J. Am. Chem. Soc. 2013, 135, 19033−19038. (12) Huang, H.; Suslov, N. B.; Li, N.-S.; Shelke, S. A.; Evans, M. E.; Koldobskaya, Y.; Rice, P. A.; Piccirilli, J. A. A G-Quadruplex− Containing RNA Activates Fluorescence in a GFP-like Fluorophore. Nat. Chem. Biol. 2014, 10, 686−691. (13) Warner, K. D.; Chen, M. C.; Song, W.; Strack, R. L.; Thorn, A.; Jaffrey, S. R.; Ferré-D’Amaré, A. R. Structural Basis for Activity of Highly Efficient RNA Mimics of Green Fluorescent Protein. Nat. Struct. Mol. Biol. 2014, 21, 658−663. (14) Ketterer, S.; Fuchs, D.; Weber, W.; Meier, M. Systematic Reconstruction of Binding and Stability Landscapes of the Fluorogenic Aptamer Spinach. Nucleic Acids Res. 2015, 43, 9564−9572. (15) Daday, C.; Curutchet, C.; Sinicropi, A.; Mennucci, B.; Filippi, C. Chromophore−Protein Coupling beyond Nonpolarizable Models: Understanding Absorption in Green Fluorescent Protein. J. Chem. Theory Comput. 2015, 11, 4825−4839. (16) Bravaya, K. B.; Grigorenko, B. L.; Nemukhin, A. V.; Krylov, A. I. Quantum Chemistry Behind Bioimaging: Insights from Ab Initio Studies of Fluorescent Proteins and Their Chromophores. Acc. Chem. Res. 2012, 45, 265−275. (17) Cui, G.; Lan, Z.; Thiel, W. Intramolecular Hydrogen Bonding Plays a Crucial Role in the Photophysics and Photochemistry of the GFP Chromophore. J. Am. Chem. Soc. 2012, 134, 1662−1672. (18) Hasegawa, J. Y.; Fujimoto, K. J.; Nakatsuji, H. Color Tuning in Photofunctional Proteins. ChemPhysChem 2011, 12, 3106−3115. (19) Li, X.; Chung, L. W.; Mizuno, H.; Miyawaki, A.; Morokuma, K. A Theoretical Study on the Nature of On- and Off-States of Reversibly Photoswitching Fluorescent Protein Dronpa: Absorption, Emission, Protonation, and Raman. J. Phys. Chem. B 2010, 114, 1114−1126. (20) Li, X.; Chung, L. W.; Mizuno, H.; Miyawaki, A.; Morokuma, K. Primary Events of Photodynamics in Reversible Photoswitching Fluorescent Protein Dronpa. J. Phys. Chem. Lett. 2010, 1, 3328−3333. (21) Li, X.; Chung, L. W.; Mizuno, H.; Miyawaki, A.; Morokuma, K. Competitive Mechanistic Pathways for Green-to-Red Photoconversion in the Fluorescent Protein Kaede: A Computational Study. J. Phys. Chem. B 2010, 114, 16666−16675. (22) (a) Virshup, A. M.; Punwong, C.; Pogorelov, T. V.; Lindquist, B. A.; Ko, C.; Martínez, T. J. Photodynamics in Complex Environments: Ab Initio Multiple Spawning Quantum Mechanical/Molecular Mechanical Dynamics. J. Phys. Chem. B 2009, 113, 3280−3291. (b) Tomasello, G.; Olaso-González, G.; Altoè, P.; Stenta, M.; SerranoAndrés, L.; Merchán, M.; Orlandi, G.; Bottoni, A.; Garavelli, M. Electrostatic Control of the Photoisomerization Efficiency and Optical Properties in Visual Pigments: On the Role of Counterion Quenching. J. Am. Chem. Soc. 2009, 131, 5172−5186. (c) Strambi, A.; Durbeej, B.; Ferré, N.; Olivucci, M. Anabaena Sensory Rhodopsin is A LightDriven Unidirectional Rotor. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 21322−21326. (d) Altoè, P.; Cembran, A.; Olivucci, M.; Garavelli, M. Aborted Double Bicycle-Pedal Isomerization with Hydrogen Bond Breaking is the Primary Event of Bacteriorhodopsin Proton Pumping. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 20172−20177. (23) Hasegawa, J. Y.; Fujimoto, K.; Swerts, B.; Miyahara, T.; Nakatsuji, H. Excited States of GFP Chromophore and Active Site Studied by the SAC-CI Method: Effect of Protein-Environment and Mutations. J. Comput. Chem. 2007, 28, 2443−2452. (24) Vendrell, O.; Gelabert, R.; Moreno, M.; Lluch, J. M. Potential Energy Landscape of the Photoinduced Multiple Proton-Transfer

4. CONCLUSION For the first time, our multiscale simulations have elucidated spectral tuning and the photoisomerization mechanism in the Spinach-DFHBDI complex at the atomic scale. Moieties (e.g., K+, the 2′-OH of A53, and the base of G28) can stabilize S1 more than S0 of DFHBDI and thus induce the red-shifted spectra in the Spinach-DFHBDI complex. Moreover, the steric repulsion from the two layers (G-quadruplex and UAU base triple) and the formation of strong hydrogen bonds with nearby nucleotides suppress the cis-trans photoisomerization of DFHBDI in Spinach. These structural factors result in green fluorescence of the anionic DFHBDI chromophore in Spinach. Furthermore, trans-DFHBDI could dissociate from the binding site in Spinach, since the RNA environment binds to transDFHBDI unfavorably. Obviously, the fluorescence decay and recovery of the Spinach-DFHBDI complex are distinct from GFP or GFP-like proteins.

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ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jctc.6b00578. Simulation details, Figures S1−S9, Tables S1−S10, Cartesian coordinates of DFHBDI in the gas phase, and supplementary citations (PDF)

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AUTHOR INFORMATION

Corresponding Authors

*E-mail: [email protected]. *E-mail: [email protected]. *E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS X.L. thanks DICP for the 100 Talents Support Grant. This work is supported by the NSFC (Grant Nos. 21373203 and 21473086) and the Shenzhen Science and Technology Innovation Committee (KQTD20150717103157174).

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REFERENCES

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