Distance distributions and dynamics of a zinc finger peptide from fluorescence resonance energy transfer measurements

Interdependence of free zinc changes and protein complex assembly – insights into zinc signal regulation

Small and local changes in cellular free zinc concentration affect protein assembly.

Effect of Diffusion on Resonance Energy Transfer Rate Distributions: Implications for Distance Measurements

Intrinsically disordered protein regions and many other biopolymers lack the three-dimensional structure that could be determined by X-ray crystallography or NMR, which encourages the application of alternative experimental methods. Time-resolved resonance energy transfer data are often used to measure distances between two fluorophores attached to a flexible biopolymer. This is complicated by the rotational and translational diffusion of the fluorophores and by nonmonoexponential donor decay in the absence of the acceptor. Equation I(DA)(t) = I(D)(t)·F(t) is derived here, which is applicable regardless of whether I(D)(t) is monoexponential. I(D)(t) and I(DA)(t) are the δ-excitation donor emission decays in the absence and in the presence of the acceptor; F(t) contains information about energy transfer, donor-acceptor distance distribution, and diffusion dynamics. It is shown that in the absence of rotational and translational diffusion, F(t) is a continuous distribution of exponentials, whereas in the presence of rotational and translational diffusion, F(t) is a sum of discrete exponentials. For each case it is shown how F(t) is related to the distance distribution. Experimental data obtained with a flexible tetradecapeptide in aqueous solution clearly demonstrate that F(t) is a sum of discrete exponential terms. A partial differential equation describing resonance energy transfer in the presence of both rotational and translational diffusion of the donor and acceptor tethered to the ends of a semiflexible chain is solved in this work using a combination of analytical and numerical methods; the solution is used to fit time-resolved emission of the donor, which makes it possible to determine the model parameters: contour length, persistence length, and the end-to-end translational diffusion coefficient.

Resolution of multiexponential spectral relaxation of Yt-base by global analysis of collisionally quenched samples

We measured the wavelength-dependent intensity decays of 4,9-dihydro-4,6-dimethyl-9-oxo-1H-imidazo-1,2a-purine (Yt-base) in propanol to determine the time-resolved emission spectra and rates of spectral relaxation. We found that resolution of the spectral relaxation times was dramatically improved by global analysis of the frequency-domain data with increasing amounts of the collisional quencher CCl4. Collisional quenching preferentially decreases the longer-lived relaxed component of the emission, thereby increasing the fractional contribution of the incompletely relaxed portion of the emission. The data could not be explained by a single spectral relaxation time, and at least two relaxation times are needed to describe the time-dependent emission center of gravity of Yt-base.

Förster energy transfer from nonexponentially decaying donors

Necessary modifications to the expression for the Förster energy transfer rate are discussed when fluorescence decay of the donor in the absence of acceptor is nonexponential. Discrete and continuous models of the nonexponentiality are taken into account. No general solution of the problem is found. It is, however, suggested that in many of the biochemical problems the most appropriate modification of the transfer rate can be that which is based on the assumption of the same constant value of the radiative decay rate for all donor molecules. The effect of the assumed form of the Förster energy transfer rate on the recovered values of the distance distribution and dynamics parameters of some exemplary bichromophoric systems is examined.