hide
Free keywords:
-
Abstract:
Single molecule fluorescence resonance energy transfer (smFRET) experiments probe molecular distances
on the nanometer scale. In such experiments, distances are recorded from FRET transfer efficiencies via
the Förster formula, E = 1/(1 + (R/R0)6).
The energy transfer however also depends on the mutual orientation of the two dyes used as
distance reporter. Since this information is typically inaccessible in FRET experiments, one has to rely on
approximations, which reduce the accuracy of these distance measurements. A common approximation
is an isotropic and uncorrelated dye orientation distribution.
To assess the impact of such approximations, we present the algorithms and implementation of a
computational toolkit for the simulation of smFRET on the basis of molecular dynamics (MD) trajectory
ensembles. In this study, the dye orientation dynamics, which are used to determine dynamic FRET
efficiencies, are extracted from MD simulations. In a subsequent step, photons and bursts are generated
using a Monte Carlo algorithm.
The application of the developed toolkit on a poly-proline system demonstrated good agreement
between smFRET simulations and experimental results and therefore confirms our computational
method. Furthermore, it enabled the identification of the structural basis of measured heterogeneity.
The presented computational toolkit is written in Python, available as open-source, applicable to
arbitrary systems and can easily be extended and adapted to further problems.
