uri physics colloquium

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

Dmitri Toptygin, Ph. D
Department of Biology, Johns Hopkins University

Authors: Dmitri Toptygin,* Alexander F. Chin, and Vincent J. Hilser.
Department of Biology, Johns Hopkins University, Baltimore, Maryland

abstract

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 non-monoexponential donor decay in the absence of the acceptor. Equation IDA(t)=ID(t)·F(t) is applicable regardless of whether ID(t) is monoexponential. ID(t) and IDA(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. 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. In each case F(t) is related to the distance distribution, but the relations are different in the absence and in the presence of diffusion. Experimental data obtained with a flexible tetradecapeptide in aqueous solution clearly demonstrate that F(t) is a sum of discrete exponential terms. Assuming that the end-to-end distance distribution is consistent with the semiflexible chain model, the model parameters (contour length and persistence length) and the end-to-end translational diffusion coefficient can be determined from experimental data.