Ground-state proton transfer in the photoswitching reactions of the fluorescent protein Dronpa

Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa

The fluorescent protein Dronpa undergoes reversible photoswitching reactions between the bright "on" and dark "off" states via photoisomerization and proton transfer reactions. We report the room temperature crystal structure of the fast switching Met159Thr mutant of Dronpa at 2.0-Å resolution in the bright on state. Structural differences with the wild type include shifted backbone positions of strand β8 containing Thr159 as well as an altered A-C dimer interface involving strands β7, β8, β10, and β11. The Met159Thr mutation increases the cavity volume for the p-hydroxybenzylidene-imidazolinone chromophore as a result of both the side chain difference and the backbone positional differences.

Photoisomerization and proton transfer in the forward and reverse photoswitching of the fast-switching M159T mutant of the Dronpa fluorescent protein

The fast-switching M159T mutant of the reversibly photoswitchable fluorescent protein Dronpa has an enhanced yield for the on-to-off reaction. The forward and reverse photoreactions proceed via cis-trans and trans-cis photoisomerization, yet protonation and deprotonation of the hydroxyphenyl oxygen of the chromophore is responsible for the majority of the resulting spectroscopic contrast. Ultrafast visible-pump, infrared-probe spectroscopy was used to detect the picosecond, nanosecond, as well as metastable millisecond intermediates. Additionally, static FTIR difference measurements of the Dronpa-M159T mutant correspond very closely to those of the wild type Dronpa, identifying the p-hydroxybenzylidene-imidazolinone chromophore in the cis anion and trans neutral forms in the bright "on" and dark "off" states, respectively. Green excitation of the on state is followed by dominant radiative decay with characteristic time constants of 1.9 ps, 185 ps, and 1.1 ns, and additionally reveals spectral changes belonging to the species decaying with a 1.1 ns time constant, associated with both protein and chromophore modes. A 1 ms measurement of the on state identifies bleach features that correspond to those seen in the static off-minus-on Fourier transform infrared (FTIR) difference spectrum, indicating that thermal protonation of the hydroxyphenyl oxygen proceeds within this time window. Blue excitation of the off state directly resolves the formation of the primary photoproduct with 0.6 and 14 ps time constants, which is stable on the nanosecond time scale. Assignment of the primary photoproduct to the cis neutral chromophore in the electronic ground state is supported by the frequency positions expected relative to those for the nonplanar distorted geometry for the off state. A 1 ms measurement of the off state corresponds closely with the on-minus-off FTIR difference spectrum, indicating thermal deprotonation and rearrangement of the Arg66 side chain to be complete.

Real-time monitoring of chromophore isomerization and deprotonation during the photoactivation of the fluorescent protein Dronpa

Dronpa is a photochromic green fluorescent protein (GFP) homologue used as a probe in super-resolution microscopy. It is known that the photochromic reaction involves cis/trans isomerization of the chromophore and protonation/deprotonation of its phenol group, but the sequence in time of the two steps and their characteristic time scales are still the subject of much debate. We report here a comprehensive UV-visible transient absorption spectroscopy study of the photoactivation mechanism of Dronpa, covering all relevant time scales from ∼100 fs to milliseconds. The Dronpa-2 variant was also studied and showed the same behavior. By carefully controlling the excitation energy to avoid multiphoton processes, we could measure both the spectrum and the anisotropy of the first photoactivation intermediate. We show that the observed few nanometer blue-shift of this intermediate is characteristic for a neutral cis chromophore, and that its anisotropy of ∼0.2 is in good agreement with the reorientation of the transition dipole moment expected upon isomerization. These data constitute the first clear evidence that trans → cis isomerization of the chromophore precedes its deprotonation and occurs on the picosecond time scale, concomitantly to the excited-state decay. We found the deprotonation step to follow in ∼10 μs and lead directly from the neutral cis intermediate to the final state.

Structural basis of photoswitching in fluorescent proteins

Fluorescent proteins have revolutionized life sciences because they allow noninvasive and highly specific labeling of biological samples. The subset of "phototransformable" fluorescent proteins recently attracted a widespread interest, as their fluorescence state can be modified upon excitation at defined wavelengths. The fluorescence emission of Reversibly Switchable Fluorescent Proteins (RSFPs), in particular, can be repeatedly switched on and off. RSFPs enable many new exciting modalities in fluorescence microscopy and biotechnology, including protein tracking, photochromic Förster Resonance Energy Transfer, super-resolution microscopy, optogenetics, and ultra-high-density optical data storage. Photoswitching in RSFPs typically results from chromophore cis-trans isomerization accompanied by a protonation change, but other switching schemes based on, e.g., chromophore hydration/dehydration have also been discovered. In this chapter, we review the main structural features at the basis of photoswitching in RSFPs.

Thermal isomerization of the chromoprotein asFP595 and its kindling mutant A143G: QM/MM molecular dynamics simulations

Chromoprotein asFP595 and its A143G variant called kindling fluorescent protein (KFP) are among the chronologically first species for which trans-cis chromophore isomerization has been proposed as a driving force of photoswitching. In spite of long-lasting efforts to characterize the route between protein conformations referring to the trans and cis forms of the chromophore, the molecular mechanism of this transformation is still under debate. We report the results of computational studies of the trans-cis isomerization of the anionic and neutral chromophore inside the protein matrices in the ground electronic state for both variants, asFP595 and KFP. Corresponding free energy profiles (potentials of mean force) were evaluated by using molecular dynamics simulations with the quantum mechanical-molecular mechanical (QM/MM) forces. The computed free energy barrier for the cis-trans ground state (thermal) isomerization reaction is about 2 kcal/mol higher in KFP than that in asFP595. These results provide interpretation of experimental studies on thermal relaxation from the light-induced activation of fluorescence of these proteins and correctly show that the A143G mutation in asFP595 noticeably increases the lifetime of the fluorescence species.

Protein photochromism observed by ultrafast vibrational spectroscopy

Photochromic proteins, such as Dronpa, are of particular importance in bioimaging and form the basis of ultraresolution fluorescence microscopy. The photochromic reaction involves switching between a weakly emissive neutral trans form of the chromophore (A) and its emissive cis anion (B). Controlling the rates of switching has the potential to significantly enhance the spatial and temporal resolution in microscopy. However, the mechanism of the switching reaction has yet to be established. Here we report a high signal-to-noise ultrafast transient infrared investigation of the photochromic reaction in the mutant Dronpa2, which exhibits facile switching behavior. In these measurements we excite both the A and B forms and observe the evolution in the IR difference spectra over hundreds of picoseconds. Electronic excitation leads to bleaching of the ground electronic state and instantaneous (subpicosecond) changes in the vibrational spectrum of the protein. The chromophore and protein modes evolve with different kinetics. The chromophore ground state recovers in a fast nonsingle-exponential relaxation, while in a competing reaction the protein undergoes a structural change. This results in formation of a metastable form of the protein in its ground electronic state (A'), which subsequently evolves on the time scale of hundreds of picoseconds. The changes in the vibrational spectrum that occur on the subnanosecond time scale do not show unambiguous evidence for either proton transfer or isomerization, suggesting that these low-yield processes occur from the metastable state on a longer time scale and are thus not the primary photoreaction. Formation of A', and further relaxation of this state to the cis anion B, are relatively rare events, thus accounting for the overall low yield of the photochemical reaction.