Mechanistic aspects of proton chain transfer in the green fluorescent protein : Part II. A comparison of minimal quantum chemical models

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.

Unraveling the Mechanistic Pathway for the Dual Fluorescence in Green Fluorescent Protein (GFP) Chromophore Analogue: A Detailed Theoretical Investigation

The photophysical properties of the para-sulfonamide (p-TsABDI) analogue of the green fluorescent protein (GFP) chromophore with both proton donating and accepting sites have been exploited in polar solvents to understand the origin of the unusual dual fluorescence nature of the chromophore. In the polar solvents, the compound undergoes structural rearrangement upon photoexcitation, leading to the ultrafast excited-state intermolecular proton transfer (ESIPT) phenomenon at the S₁ surface. In this work, we employed both the static electronic structure calculations and on-the-fly molecular dynamics simulation to unravel the underlying reason for this peculiar behavior of the p-TsABDI analogue in polar solvents. To represent this adequately and provide extensive information on the ESIPT mechanism mediated by the solvent molecules, we considered explicit solvent molecules using the integral equation formalism variant of polarizable continuum (IEFPCM) model. From the static calculation analysis, we can conclude that the dual emissive behavior of the compound is ascribed to the proton transfer (PT) phenomena in the excited-state. However, based on the static calculation exclusively, it is hard to ascertain the mechanistic pathway of the PT phenomena. Hence, to investigate the dynamics and reaction mechanism for the ESIPT process, we performed the on-the-fly dynamics simulation for p-TsABDI in solvent clusters. Dynamics simulation results reveal that, based on the time lag between all the proton transfer processes, the ESIPT mechanism occurs in a stepwise manner from the benzylidene moiety of the chromophore to its imidazolinone moiety. However, the nonexistence of crossings between the S₁- and S₀-states confirms the PT characteristics of the reactions.

The mechanism of oxidation in chromophore maturation of wild-type green fluorescent protein: a theoretical study

DFT calculations suggested that the thermodynamically unfavourable cyclized product was trapped by oxidation.

Electric field effect on the ground state proton transfer in the H-bonded HBDI complex: an implication of the green fluorescent protein

In this paper, first-principles calculations were performed regarding the electric field effect on the ground state proton transfer (GSPT) in the H-bonded p-hydroxybenzylideneimidazolidinone (HBDI) network that represents the active site of the green fluorescent protein (GFP).

Theoretical studies of chromophore maturation in the wild-type green fluorescent protein: ONIOM(DFT:MM) investigation of the mechanism of cyclization

The availability of a gene encoding green fluorescence immediately stimulates interest in the puzzle of autocatalytic formation of the green fluorescent protein (GFP) chromophore. Numerous experimental and theoretical studies have indicated that cyclization is the first and most important step in the maturation process of the GFP. In our previous paper based on cluster models [J. Phys. Chem. B2010, 114, 9698-9705], two possible mechanisms have been investigated with the conclusion that the backbone condensation initiated by deprotonation of the Gly67 amide nitrogen is easier than deprotonation of the Tyr66 α-carbon. However, the impact of the protein environment on the reaction mechanism remains to be explored. In this paper, we investigated the two possible mechanisms with inclusion of protein environmental effects by using molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Our calculations reveal no hydrogen bonding network that would facilitate deprotonation of the amide nitrogen of Gly67, although it is the lower energy pathway in the cluster model system. Contrastingly, there is a hydrogen bonding network between Tyr66 α-carbon and Glu222, which is in good agreement with X-ray data. The ONIOM studies show that proton transfer from Tyr66 α-carbon to Glu222 is a long-distance charge transfer process. The charge distribution of the MM region has a significant perturbation to the wave function for the QM region, with the QM energy for the proton transfer product being increased under the influence of the electrostatic protein environment. The barrier for the rate-limiting step in cyclization is quite high, about 40.0 kcal/mol in the case of ONIOM-EE.

The mechanism of cyclization in chromophore maturation of green fluorescent protein: a theoretical study

An intriguing aspect of the green fluorescent protein (GFP) is the autocatalytic post-translational modification that results in the formation of its chromophore. Numerous experimental and theoretical studies indicate that cyclization is the first and the most important step in the maturation process. In this work, two proposed mechanisms for the cyclization were investigated by using the hybrid density functional theory method B3LYP. Cluster models corresponding to the two mechanisms proposed by Wachter et al. [J. Biol. Chem. 2005, 280, 26248-26255] are constructed on the basis of the X-ray crystal structure (PDB entry 2AWJ) and corresponding reaction path potential energy profiles for the two cyclization mechanisms are presented. Our results suggest that the backbone condensation initiated by deprotonation of the Gly67 amide nitrogen is easier than deprotonation of the Tyr66 alpha-carbon. Moreover, Arg96 fulfills the role of stabilizing the enolate moiety, and Glu222 plays the role of a general base. The formation of the cyclized product is found to be 16.0 and 18.6 kcal/mol endothermic with respect to the two models, which is in agreement with experimental observation.

Structural and Relaxation Effects in Proton Wire Energetics: Model Studies of the Green Fluorescent Protein Photocycle

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.