Short range photoinduced electron transfer in proteins: QM-MM simulations of tryptophan and flavin fluorescence quenching in proteins

Hybrid quantum mechanical-molecular mechanics (dynamics) were performed on flavin reductase (Fre) and flavodoxin reductase (Fdr), both from Escherichia coli. Each was complexed with riboflavin (Rbf) or flavin mononucleotide (FMN). During 50 ps trajectories, the relative energies of the fluorescing state (S₁) of the isoalloxazine ring and the lowest charge transfer state (CT) were assessed to aid prediction of fluorescence lifetimes that are shortened due to quenching by electron transfer from tyrosine. The simulations for the four cases display a wide range in CT–S₁ energy gap caused by the presence of phosphate, other charged and polar residues, water, and by intermolecular separation between donor and acceptor. This suggests that the Gibbs energy change (ΔG₀) and reorganization energy (λ) for the electron transfer may differ in different flavoproteins.     

Synthesis of proline-modified analogues of the neuroprotective agent glycyl-l-prolyl-glutamic acid (GPE)

The synthesis of ten proline-modified analogues of the neuroprotective tripeptide GPE is described. Five of the analogues incorporate a proline residue with a hydrophobic group at C-2 and two further analogues have this side chain locked into a spirolactam ring system. The pyrrolidine ring was also modified by replacing the γ-CH₂ group with sulfur and/or incorporation of two methyl groups at C-5.     

POLARIZED FLUORESCENCE OF 5-METHYLCYTOSINE SPECIES IN SOLUTION AT ROOM TEMPERATURE

Fluorescence yields (π_f,'s) and polarizations ( P ) are measured for aqueous 5-methylcytosine (˜ 0.1 m M ) at 20°C as a function of pH over the range 2–14. Both properties change abruptly and in parallel at pH's corresponding to the known pK_a values. Polarizations were also obtained for the 5-methylcytosine cation, neutral and anion species in ethylene glycol water glass at ˜180K. The weak fluorescence of the neutral and cation species at 20°C was polarized almost as highly as at low temperature. When the fluorescence lifetimes are assumed to be correctly given by the product of calculated radiative lifetimes and quantum yields, the polarizations are found to be consistent with rotational diffusion rates ˜4 times faster than predicted from Stokes-Einstein models for the neutral and anion species. The cation seemed to rotate about two times more slowly than the neutral and anion species. It was also shown that the properties of the three species are such that a plot of 1/P vs apparent π_f in the pH range 2–11 is fortuitously linear.     

Calorimetric, photometric and lifetime determinations of fluorescence yields of fluorescein dyes

Abstract— The fluorescence yields and lifetimes of fluorescein and nine brominated derivatives in basic ethanol are reported. Calorimetric. photometric, and lifetime methods are used independently to measure the yields. A new and simple calorimetric method is presented for this purpose, and the accuracy of the techniques is assessed. There is good agreement between the calorimetric and photometric results. The importance of parameters such as purity, pH, and fluoresence reabsorption is illustrated. The theoretical determination of the natural radiative lifetime from the absorption spectrum is shown to have inherent ambiguities, so that only calorimetric methods provide a reliable, independent check for photometric yield measurements.     

Ultrafast fluorescence dynamics of tryptophan in the proteins monellin and IIAGlc

The complete time-resolved fluorescence of tryptophan in the proteins monellin and IIA(Glc) has been investigated, using both an upconversion spectrophotofluorometer with 150 fs time resolution and a time-correlated single photon counting apparatus on the 100 ps to 20 ns time scale. In monellin, the fluorescence decay displays multiexponential character with decay times of 1.2 and 16 ps, and 0.6, 2.2, and 4.2 ns. In contrast, IIA(Glc) exhibited no component between 1.2 ps and 0.1 ns. For monellin, surprisingly, the 16 ps fluorescence component was found to have positive amplitude even at longer wavelengths (e.g., 400 nm). In conjunction with quantum mechanical simulation of tryptophan in monellin, the experimental decay associated spectra (DAS) and time-resolved emission spectra (TRES) indicate that this fluorescence decay time should be ascribed to a highly quenched conformer. Recent models (Peon, J.; et al. Proc. Natl.Acad. Sci. U.S.A. 2002, 99, 10964) invoked exchange-coupled relaxation of protein water to explain the fluorescence decay of monellin.     

Dependence of tryptophan emission wavelength on conformation in cyclic hexapeptides

The wavelength of maximum emission of tryptophan depends on the local electrostatic environment of the indole chromophore. The time-resolved emission spectra of seven rigid cyclic hexapeptides containing a single tryptophan residue were measured. The emission maxima of the three decay-associated spectra for the seven peptides ranged from 341 to 359 nm, suggesting that different tryptophan rotamers have different emission maxima even in the case of solvent-exposed tryptophans. This conclusion is supported by quantum mechanical/molecular dynamics simulations of the six canonical side chain rotamers of tryptophan in solvated hexapeptides. The calculated range of emission maxima for the tryptophan rotamers of the seven peptides is 344-365 nm. The precision of the wavelength calculations and the peptide, water, and charged side chain contributions to the spectral shifts are examined. The results indicate that the emission maxima of decay-associated spectra can aid in the assignment of fluorescence lifetimes to tryptophan rotamers.