Modeling of the structure and electronic spectra of green fluorescent protein chromophore

The structure and electronic absorption spectra of a model green fluorescent protein chromophore were studied in the neutral, cationic, and anionic forms in the isolated state. The energies of S ₀-S ₁ vertical transitions were calculated using a new method based on a modified multiconfiguration quasi-degenerate perturbation theory (aug-MCQDPT2). This method was used to obtain quantitative estimates of S ₀-S ₁ vertical transition energies for chromophores in the isolated state, 2.54, 3.12, and 3.11 eV (the experimental values were 2.59, 3.05, and 2.99 eV) for the anionic, cationic, and neutral forms, respectively.     

Gas-phase spectroscopy of protonated 3-OH kynurenine and argpyrimidine. comparison of experimental results to theoretical modeling

The aging process of the human lens is associated with accumulation of chromophores and fluorophores that impair visual function. In the present study, we examined the photodissociation of 3-OH-kynurenine and argpyrimidine. Furthermore, absorption spectra obtained in gas phase using an electrostatic ion storage ring were studied as gas phase absorption have been shown to be more similar to the in vivo condition than absorption spectra obtained in the liquid phase. Experimental results were compared to theoretical modeling using the multistate, multireference perturbation theory approach combined with advanced molecular modeling tools to account for the solvent effects and to provide direct support for band assignments. Absorption maxima were determined both experimentally and theoretically and significant differences between the two chromophores were found. In particular, 3-OH-kynurenine demonstrated a blue-shift of more than 130 nm in the aqueous phase compared to the gas-phase due to the existence of different 3-OH-kynurenine conformers, which are stable under different conditions and originate from the interplay between intra- and intermolecular interactions. Photodissociation of argpyrimidine and 3-OH-kynurenine was observed in vacuum thus confirming the results previously obtained in liquid phase demonstrating that the photodestruction takes place in both media.     

Photodissociation pathways and lifetimes of protonated peptides and their dimers

Photodissociation lifetimes and fragment channels of gas-phase, protonated YA(n) (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of ~200 ns while the protonated dimers show an additional slow dissociation component with a lifetime of ~2 μs. Laser power dependence measurements enabled us to ascribe the fast channel in the monomer and the slow channel in the dimer to a one-photon process, whereas the fast dimer channel is from a two-photon process. The slow (1 photon) dissociation channel in the dimer was found to result in cleavage of the H-bonds after energy transfer through these H-bonds. In general, the dissociation of these protonated peptides is non-prompt and the decay time was found to increase with the size of the peptides. Quantum RRKM calculations of the microcanonical rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both found in space.     

Electrical transport and magnetic ordering in R 2Ti3Ge4 (R=Dy, Ho and Er) compounds

New R ₂Ti₃Ge₄ (R=Dy, Ho and Er) intermetallic compounds have been synthesized and characterized by X-ray diffraction and low temperature ac magnetic susceptibility, electrical resistivity and thermoelectric power measurements were carried out. The compounds crystallize in the parent, Sm₅Ge₄-type orthorhombic structure (space group Pnma) and lanthanide contraction is observed as one moves along the rare-earth series. The changeover from paramagnetic to antiferromagnetic phase happens at low temperatures and the ordering temperature scales with the de Gennes factor. The electrical resistivity is metallic with a negative curvature above 100 K. Thermopower displays a weak maximum at temperatures less than 50 K signifying the possible phonon and magnon drag effects.     

Modeling photoabsorption of the asFP595 chromophore

The fluorescent protein asFP595 is a promising photoswitchable biomarker for studying processes in living cells. We present the results of a high level theoretical study of photoabsorption properties of the model asFP595 chromophore molecule in biologically relevant protonation states: anionic, zwitterionic, and neutral. Ground state equilibrium geometry parameters are optimized in the PBE0/(aug)-cc-pVDZ density functional theory approximation. An augmented version of multiconfigurational quasidegenerate perturbation theory (aug-MCQDPT2) following the state-averaged CASSCF/(aug)-cc-pVDZ calculations is used to estimate the vertical S0-S1 excitation energies for all chromophore species. An accuracy of this approach is validated by comparing the computed estimates of the S0-S1 absorption maximum of the closely related chromophore from the DsRed protein to the known experimental value in the gas phase. An influence of the CASSCF active space on the aug-MCQDPT2 excitation energies is analyzed. The zwitterionic form of the asFP595 chromophore is found to be the most sensitive to a particular choice and amount of active orbitals. This observation is explained by the charge-transfer type of the S0-S1 transition involving the entire conjugated pi-electron system for the zwitterionic protonation state. According to the calculation results, the anionic form in the trans conformation is found to possess the most red-shifted absorption band with the maximum located at 543 nm. The bands of the zwitterionic and neutral forms are considerably blue-shifted compared to those of the anionic form. These conclusions are at variance with the results obtained in the TDDFT approximation for the asFP595 chromophore. The absorption wavelengths computed in the aug-MCQDPT2/CASSCF theory are as follows: 543 (535), 470 (476), and 415 (417) nm for the anionic, zwitterionic, and neutral forms of the trans and cis (in parentheses) isomers of the asFP595 chromophore. These data can be used as a reference for further theoretical studies of the asFP595 chromophore in different media and for modeling photoabsorption properties of the asFP595 fluorescent protein.     

The photophysics of isolated protein chromophores

Gas-phase absorption properties of chromophores of several photoactive proteins have been studied experimentally at the electrostatic heavy-ion storage ring ELISA in Aarhus. The absorption wavelength has been calculated using an augmented effective Hamiltonian technique based on the multiconfigurational quasi-degenerate perturbation theory. The results have been compared to those of widely used state-specific second-order perturbation theory formalisms and their multistate extensions and also to ground-state linear response methods. It would appear that ab initio theory is now at a stage where the intrinsic properties of the chromophore molecules may be predicted with reasonable precision. There is evidence that in terms of absorption there is almost vacuum-like conditions in the hydrophobic interior of some proteins like the green fluorescent protein (GFP). In others, like for example the visual opsins, some significant perturbations are responsible for colour tuning.     

Structures of the Peptide–Water Complexes Studied by the Hybrid Quantum Mechanical—Molecular Mechanical (QM/MM) Technique

Applications of a new approach to the hybrid quantum mechanical and molecular mechanical (QM/MM) theory based on the effective fragment potential technique to calculations of the structures of the peptide—water complexes are described. Our approach assumes that the MM subsystem is viewed as a flexible composition of effective fragments, while fragment–fragment interactions are replaced by MM force fields. In this work, the QM subsystem is composed of water molecules and the MM part refers to peptides. Different isomers of the hydrogen-bonded complex of the dipeptide N-acetyl-L-alanine N-methylamide (AAMA) with four water molecules are considered, and the results of QM/MM calculations are compared to experimental data and to the results of the density functional theory (DFT) treatment. The properties of water chains inside polypeptide tubes, modeling proton wires inside ionic channels, are described.     

UV Excited‐State Photoresponse of Biochromophore Negative Ions

Members of the green fluorescent protein (GFP) family may undergo irreversible phototransformation upon irradiation with UV light. This provides clear evidence for the importance of the higher‐energy photophysics of the chromophore, which remains essentially unexplored. By using time‐resolved action and photoelectron spectroscopy together with high‐level electronic structure theory, we directly probe and identify higher electronically excited singlet states of the isolated para‐ and meta‐chromophore anions of GFP. These molecular resonances are found to serve as a doorway for very efficient electron detachment in the gas phase. Inside the protein, this band is found to be resonant with the quasicontinuum of a solvated electron, thus enhancing electron transfer from the GFP to the solvent. This suggests a photophysical pathway for photoconversion of the protein, where GFP resonant photooxidation in solution triggers radical redox reactions inside these proteins.