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Conformational Ensembles from Experimental Data
and Computer Simulations
Poster Abstracts
56
23-POS
Board 23
Fast-NPS - An Analysis Tool to Obtain Structural Information from Single-Molecule
FRET Measurements
Tobias Eilert
, Jens Michaelis.
University of Ulm, Ulm, Baden-Württemberg, Germany.
Fast-Nano-Positioning-System
(Fast-NPS) is an analysis software package that can be used to
analyze
single-molecule FRET
(smFRET) data to obtain quantitative structural information of
macromolecules in their natural environment. In the algorithm a Bayesian model gives rise to a
multivariate probability distribution describing the uncertainty of the structure determination
(Muschielok and Michaelis 2011).
Since Fast-NPS aims to be an easy-to-use general purpose analysis tool for a large variety of
smFRET networks, we established a
Markov Chain Monte Carlo
based sampling engine, that
approximates the target distribution and requires no parameter specification by the user at all.
In previous works this method has already been used to study the position of the exiting RNA
from the eukaryotic RNA polymerase II (Andrecka et al. 2008) and to investigate the influence
of the transcription factor TFIIB on the position of the nascent RNA (Muschielok et al. 2008).
Further, the position of the non-template and upstream DNA in yeast Polymerase II transcription
elongation complexes (Andrecka et al. 2009) and the architecture of a minimal Polymerase II
open promoter complex (Andrecka 2009) were analyzed. Moreover, the NPS was also applied to
shed light on the archaeal initiation complex (Nagy et al. 2015).
Since the molecular surrounding of a dye molecule effects its spatial mobility and thus the
smFRET efficiency, our current developments focus on the specific description of dye models
only driven by data taken from experiments, i.e. time-resolved anisotropy and fluorescence
lifetime measurements.
Further, a recent progress is the Bayesian analysis of the relative orientation of several
macromolecules, i.e. rigid body docking guided by smFRET measurements. After a clustering
step, the uncertainty in structure determination can be visualized by ensembles of rigid bodies in
a static picture or in a video.