Operation of the Proton Wire in Green Fluorescent Protein. A Quantum Dynamics Simulation (original) (raw)
Related papers
Kinetics of switchable proton escape from a proton-wire within green fluorescence protein
2007
The emission from the acidic form of the green fluorescence protein (GFP) changes with increasing time and temperature from t -1/2 to t -3/2 asymptotics. It is shown that a model of proton diffusion along a one-dimensional hydrogen-bond network within the protein, with a switch (Thr203) allowing for proton escape, explains the data quantitatively. From a comparison of the model with experiment, we obtain the rate parameters for proton dissociation from the chromophore (showing an inVerse temperature effect), the ratio of the proton association constant squared to its diffusion constant (exhibiting no temperature effect), and the time constant for switch opening (with a significant Arrhenius dependence). Thus, proton dissociation has a small negative activation energy (assigned to a complex of the anionic chromophore with H 3 O + ), whereas the switch has a large positive activation energy (assigned to Thr203 side-chain rotation). Proton migration is possibly the outcome of the concerted motion of several protons within GFP.
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.
A concerted mechanism of proton transfer in green fluorescent protein. A theoretical study
Chemical Physics Letters, 2005
In this Letter, the proton transfer in the chromophore site of green fluorescent protein is studied by the B3LYP method with 6-31G(d,p) and 6-31+G(d,p) basis sets. A concerted proton transfer is observed between the chromophore and its neighboring residues (water, His148, Ser205, Glu222). It involves simultaneous motion of three protons. The transition state for hydrogen transfer is located with the transition barrier estimated to be slightly below zero with Zero-Point correction. This is a characteristic feature of low-barrier hydrogen bonds. His148 plays an important stabilizing role on the transition state and thus controls the proton shuttle. Solvation effects based on self-consistent reaction field are found to stabilize the deprotonated form more than its corresponding neutral form.
Australian Journal of Chemistry, 2010
We present the results of a systematic series of constrained minimum energy pathway calculations on ground state potential energy surfaces, for a cluster model of the proton chain transfer that mediates the photocycle of the green fluorescent protein, as well as for a model including the solvated protein environment. The calculations vary in terms of the types of modes that are assumed to be capable of relaxing in concert with the movement of the protons and the results demonstrate that the nature and extent of dynamical relaxation has a substantive impact on the activation energy for the proton transfer. We discuss the implications of this in terms of currently available dynamical models and chemical rate theories that might be brought to bear on the kinetics of this important example of proton chain transfer in a biological system.
Journal of the American Chemical Society, 2006
The green fluorescent protein proton wire operating upon photoexcitation of the internally caged chromophore is investigated by means of classical molecular dynamics and multiconfigurational electronic structure calculations. The structure of the proton wire is studied for the solvated protein, showing that the wire is likely to be found in a configuration ready to operate as soon as the chromophore is photoexcited, and leading to a total of three proton translocations in the vicinity of the chromophore. Multiconfigurational CASSCF and CASPT2 calculations provide a detailed overview of the energy landscape of the proton wire for the ground electronic state S 0, the photoactive 1 ππ* state, and the charge-transfer 1 πσ* state. The results allow discussion of the operation of the wire in terms of the sequence of proton-transfer events and the participation of each electronic state.
Journal of …, 2003
Two ground-state protonation forms causing different absorption peaks of the green fluorescent protein chromophore were investigated by the quantum mechanical SAC/SAC-CI method with regard to the excitation energy, fluorescence energy, and ground-state stability. The environmental effect was taken into account by a continuum spherical cavity model. The first excited state, HOMO-LUMO excitation, has the largest transition moment and thus is thought to be the source of the absorption. The neutral and anionic forms were assigned to the protonation states for the experimental A-and B-forms, respectively. The present results support the previous experimental observations.
Chemical Physics Letters, 2004
The proton transfer from the green fluorescent protein chromophore to a nearby water molecule is studied by means of CASSCF, CASPT2 and TDDFT calculations. A 1 pr* electronic state is found to intersect with the photoactive 1 pp* electronic state along the proton transfer coordinate. This state crossing constitutes a possible non-radiative deactivation pathway of the photoexcited neutral form of the chromophore. A discussion on the performance of the different levels of theory employed is also given, focusing in the ability to correctly describe the 1 pr* electronic state.
Vibrational Spectroscopy, 2012
We present a brief review of the current understanding and analysis of the photocycle of the Green Fluorescent Protein (GFP). GFP is unique to show directed excited state proton transfer (ESPT) in a protein environment, which provides a directional coordinate for the ultrafast proton transfer reactions in contrast with disordered liquids. ESPT proceeds on a picosecond time scale and we consider details of the vibrational response of the chromophore and the protein environment during the course of this reaction. In addition we discuss both experimental and computational methodology and corrections that measure and model vibrational dichroism from polarised pump-probe infrared measurements. For the GFP photocycle, a direct relationship between equilibrium protein side-chain conformation of glutamate 222 and reaction kinetics has been established for the ultrafast ESPT in the fluorescence photocycle. We have resolved the infrared spectral differences between heterogeneous ESPT reaction dynamics that were assigned to the carboxylate of the Glutamate 222 side chain. We additionally discuss photoselection measurements for the molecular interpretation of the vibrational transition dipole moments placed in the X-ray frame as a sensitive probe of the mode character and assess the assignments based on frequency calculations from the analytical second derivative for the isolated chromophore. Dipole gradients can be calculated analytically, or numerically by finite difference. An older software release that displays analytical dipole gradients incorrectly is identified.
Computational and Theoretical Chemistry, 2012
In this paper we perform high level complete active space self-consistent field (CASSCF) and multi-reference configuration interaction (MRCI) calculations to generate three-dimensional potential energy surfaces for the proton chain transfer in the green fluorescent protein (GFP) based on a minimal quantum mechanical cluster model. Both the electronic ground state and the first excited state are considered within an approximate rigid model. We focus on the energetic terms of the proton transfers in this paper, and the exact quantum dynamics simulations for proton transfer on the ground and excited states will be reported later. Our results from MRCI quantum mechanical calculations are contrasted with those of other computational studies using both CASPT2 method and DFT method, and are compared with the experimental findings for GFP in the full protein environment.