Effect of Temperature on Excited-State Proton Tunneling in wt-Green Fluorescent Protein

Quantum dynamics of excited state proton transfer in green fluorescent protein

Photoexcitation of green fluorescent protein (GFP) triggers long-range proton transfer along a "wire" of neighboring protein residues, which, in turn, activates its characteristic green fluorescence. The GFP proton wire is one of the simplest, most well-characterized models of biological proton transfer but remains challenging to simulate due to the sensitivity of its energetics to the surrounding protein conformation and the possibility of non-classical behavior associated with the movement of lightweight protons. Using a direct dynamics variational multiconfigurational Gaussian wavepacket method to provide a fully quantum description of both electrons and nuclei, we explore the mechanism of excited state proton transfer in a high-dimensional model of the GFP chromophore cluster over the first two picoseconds following excitation. During our simulation, we observe the sequential starts of two of the three proton transfers along the wire, confirming the predictions of previous studies that the overall process starts from the end of the wire furthest from the fluorescent chromophore and proceeds in a concerted but asynchronous manner. Furthermore, by comparing the full quantum dynamics to a set of classical trajectories, we provide unambiguous evidence that tunneling plays a critical role in facilitating the leading proton transfer.

Proton Wire Dynamics in the Green Fluorescent Protein

Inside proteins, protons move on proton wires (PWs). Starting from the highest resolution X-ray structure available, we conduct a 306 ns molecular dynamics simulation of the (A-state) wild-type (wt) green fluorescent protein (GFP) to study how its PWs change with time. We find that the PW from the chromophore via Ser205 to Glu222, observed in all X-ray structures, undergoes rapid water molecule insertion between Ser205 and Glu222. Sometimes, an alternate Ser205-bypassing PW exists. Side chain rotations of Thr203 and Ser205 play an important role in shaping the PW network in the chromophore region. Thr203, with its bulkier side chain, exhibits slower transitions between its three rotameric states. Ser205 experiences more frequent rotations, slowing down when the Thr203 methyl group is close by. The combined states of both residues affect the PW probabilities. A random walk search for PWs from the chromophore reveals several exit points to the bulk, one being a direct water wire (WW) from the chromophore to the bulk. A longer WW connects the "bottom" of the GFP barrel with a "water pool" (WP1) situated below Glu222. These two WWs were not observed in X-ray structures of wt-GFP, but their analogues have been reported in related fluorescent proteins. Surprisingly, the high-resolution X-ray structure utilized herein shows that Glu222 is protonated at low temperatures. At higher temperatures, we suggest ion pairing between anionic Glu222 and a proton hosted in WP1. Upon photoexcitation, these two recombine, while a second proton dissociates from the chromophore and either exits the protein using the short WW or migrates along the GFP-barrel axis on the long WW. This mechanism reconciles the conflicting experimental and theoretical data on proton motion within GFP.

Time-averaged distributions of solute and solvent motions: exploring proton wires of GFP and PfM2DH

Proton translocation pathways of selected variants of the green fluorescent protein (GFP) and Pseudomonas fluorescens mannitol 2-dehydrogenase (PfM2DH) were investigated via an explicit solvent molecular dynamics-based analysis protocol that allows for direct quantitative relationship between a crystal structure and its time-averaged solute-solvent structure obtained from simulation. Our study of GFP is in good agreement with previous research suggesting that the proton released from the chromophore upon photoexcitation can diffuse through an extended internal hydrogen bonding network that allows for the proton to exit to bulk or be recaptured by the anionic chromophore. Conversely for PfM2DH, we identified the most probable ionization states of key residues along the proton escape channel from the catalytic site to bulk solvent, wherein the solute and high-density solvent crystal structures of binary and ternary complexes were properly reproduced. Furthermore, we proposed a plausible mechanism for this proton translocation process that is consistent with the state-dependent structural shifts observed in our analysis. The time-averaged structures generated from our analyses facilitate validation of MD simulation results and provide a comprehensive profile of the dynamic all-occupancy solvation network within and around a flexible solute, from which detailed hydrogen-bonding networks can be inferred. In this way, potential drawbacks arising from the elucidation of these networks by examination of static crystal structures or via alternate rigid-protein solvation analysis procedures can be overcome. Complementary studies aimed at the effective use of our methodology for alternate implementations (e.g., ligand design) are currently underway.

Coupling of pressure-induced structural shifts to spectral changes in a yellow fluorescent protein

X-ray diffraction analysis of pressure-induced structural changes in the Aequorea yellow fluorescent protein Citrine reveals the structural basis for the continuous fluorescence peak shift from yellow to green that is observed on pressurization. This fluorescence peak shift is caused by a reorientation of the two elements of the Citrine chromophore. This study describes the structural linkages in Citrine that are responsible for the local reorientation of the chromophore. The deformation of the Citrine chromophore is actuated by the differential motion of two clusters of atoms that compose the beta-barrel scaffold of the molecule, resulting in a slight bending of the beta-barrel. The high-pressure structures also show a perturbation of the hydrogen bonding network that stabilizes the excited state of the Citrine chromophore. The perturbation of this network is implicated in the reduction of fluorescence intensity of Citrine. The blue-shift of the Citrine fluorescence spectrum resulting from the bending of the beta-barrel provides structural insight into the transient blue-shifting of isolated yellow fluorescent protein molecules under ambient conditions and suggests mechanisms to alter the time-dependent behavior of Citrine under ambient conditions.

Excited-state proton transfer to solvent from phenol and cyanophenols in water

The excited-state proton transfer (ESPT) to solvent from phenol (PhOH) and cyanophenols (CNOHs) in water was studied by means of time-resolved fluorescence and photoacoustic spectroscopy. A characteristic property of PhOH and CNOHs is that the fluorescence quantum yields of the deprotonated forms are remarkably small (< or = 10(-3)) and the lifetimes are extremely short (< or = 30 ps). Time-resolved fluorescence measurements for PhOH, CNOHs, and their methoxy analogues at 298 K indicate that o- and m-cyanophenols (o- and m-CNOH) undergo rapid ESPT to the solvent water with rate constants of 6.6 x 10(10) and 2.6 x 10(10) s(-1), respectively, whereas the fluorescence properties of PhOH and p-CNOH does not exhibit clear evidence of the ESPT reaction. Photoacoustic measurements show that photoexcitation of o- and m-CNOH in water results in negative volume changes, supporting the occurrence of ESPT to produce a geminate ion pair. In contrast, the volume contractions for the PhOH and p-CNOH solutions are negligibly small, which indicates that, in these compounds, the yields of solvent-separated ion pairs resulting from the ESPT are very small. The volume change per absorbed Einstein (DeltaV(r)) for o-CNOH is obtained to be -5.0 mL Einstein(-1), which is much smaller than the estimated volume contraction per photoconverted mole (DeltaV(R)). This suggests that the geminate recombination between the ejected proton and the cyanophenolate anion occurs after rapid deactivation of the excited ion pair. In the temperature range between 275 and 323 K, the proton dissociation rates of o- and m-CNOH in H(2)O and D(2)O are slower than the solvent relaxation rates evaluated from the Debye dielectric relaxation time, indicating that the overall rate constant is determined mainly by the proton motion along the reaction coordinate.

Proton tunneling: a decay channel of the O-H stretch mode in KTaO3

The vibrational lifetimes of the O-H and O-D stretch modes in the perovskite oxide KTaO3 are measured by pump-probe infrared spectroscopy. Both stretch modes are exceptionally long lived and exhibit a large "reverse" isotope effect, due to a phonon-assisted proton-tunneling process, which involves the O-Ta-O bending motion. The excited-state tunneling rate is found to be 7 orders of magnitude larger than from the ground state in the proton conducting oxide, BaCeO3 [Phys. Rev. B 60, R3713 (1999)].