Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

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.

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