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ABSTRACT: Abstract Recent time resolved lifetime measurements studied the quenching of the fluorescence emitted by a dye covalently bound to the desolvated peptide Dye-Pro4-Arg+-Trp. This peptide sequence was chosen for study since intramolecular interactions constrain all large-scale fluctuations except for those of the interacting dye and Trp sidechain. It was shown that quenching occurred as a result of interaction between the excited dye and tryptophan sidechain. These measurements exhibited a temperature dependence that suggested the quenching mechanism was related to electron transfer. This paper presents a comparison of the experimental quenching rate with the Marcus electron transfer model performed with molecular dynamics (MD) calculations. Taking advantage of the AMOEBA force field that explicitly includes polarizability ensures that the intramolecular electrostatic and polarization interactions in this desolvated peptide ion are treated realistically. MD calculations identify both large-scale fluctuations between conformations as well as small-scale fluctuations within a conformation that are shown to be correlated with torsional dynamics of the Trp sidechain. Trajectories of the Dye-Trp distance identify the occurrence of close separations required for efficient electron transfer. The temperature dependence of the quenching rate closely follows the rate predicted by the Marcus electron transfer model within uncertainties resulting from statistical averages. Estimates of the energy parameters characterizing the Marcus model indicate the electronic coupling matrix element and the reaction free energy derived from the fits are consistent with published values for transfer in polyproline bridged peptides. These calculations help to provide a molecular basis for investigating conformational changes in desolvated biomolecular ions by fluorescence quenching measurements.
The Journal of Physical Chemistry B 01/2013; · 3.70 Impact Factor
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ABSTRACT: The structures, dynamics and energetics of the protonated, derivatized peptide DyeX-(Pro)(4)-Arg(+)-Trp, where "Dye" stands for the BODIPY analog of tetramethyl-rhodamine and X is a (CH(2))(5) linker, have been investigated using a combination of modeling approaches in order to provide a numerical framework to the interpretation of fluorescence quenching data in the gas phase. Molecular dynamics (MD) calculations using the new generation AMOEBA force field were carried out using a representative set of conformations, at eight temperatures ranging from 150 to 500 K. Force field parameters were derived from ab initio calculations for the Dye. Strong electrostatic, polarization and dispersion interactions combine to shape this charged peptide. These effects arise in particular from the electric field generated by the charge of the protonated arginine and from several hydrogen bonds that can be established between the Dye linker and the terminal Trp. This conclusion is based on both the analysis of all structures generated in the MD simulations and on an energy decomposition analysis at classical and quantum mechanical levels. Structural analysis of the simulations at the different temperatures reveals that the relatively rigid polyproline segment allows for the Dye and Trp indole side chain to adopt stacking conformations favorable to electron transfer, yielding support to a model in which it is electron transfer from tryptophan to the dye that drives fluorescence quenching.
The Journal of Physical Chemistry B 01/2013; · 3.70 Impact Factor
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ABSTRACT: The protonated, phosphorylated dipeptide [GpY+H](+) is characterized by mid-infrared multiple-photon dissociation (IRMPD) spectroscopy and quantum-chemical calculations. The ions are generated in an external electrospray source and analyzed in a Fourier transform ion cyclotron resonance mass spectrometer, and their fragmentation is induced by resonant absorption of multiple photons emitted by a tunable free-electron laser. The IRMPD spectra are recorded in the 900-1730 cm(-1) range and compared to the absorption spectra computed for the lowest energy structures. A detailed calibration of computational levels, including B3LYP-D and coupled cluster, is carried out to obtain reliable relative energies of the low-energy conformers. It turns out that a single structure can be invoked to assign the IRMPD spectrum. Protonation at the N terminus leads to the formation of a strong ionic hydrogen bond with the phosphate P=O group in all low-energy structures. This leads to a P=O stretching frequency for [GpY+H](+) that is closer to that of [pS+H](+) than to that of [pY+H](+) and thus demonstrates the sensitivity of this mode to the phosphate environment. The COP phosphate ester stretching mode is confirmed to be an intrinsic diagnostic for identification of which type of amino acid is phosphorylated.
ChemPhysChem 11/2008; 9(17):2564-73. · 3.41 Impact Factor
