title: Effect of Diffusion on Resonance Energy Transfer Rate Distributions: Implications for Distance Measurements.
abstract: 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.
authors.affiliation: Department of Biology, Johns Hopkins University , Baltimore, Maryland 21218, United States.
authors.forename: Dmitri
authors.initials: D
authors.lastname: Toptygin
authors.affiliation: Department of Biology, Johns Hopkins University , Baltimore, Maryland 21218, United States.
authors.forename: Alexander F
authors.initials: AF
authors.lastname: Chin
authors.affiliation: Department of Biology, Johns Hopkins University , Baltimore, Maryland 21218, United States.
authors.forename: Vincent J
authors.initials: VJ
authors.lastname: Hilser
mesh_terms: D018360:Crystallography, X-Ray; D004058:Diffusion; D004735:Energy Transfer