A nano-positioning system for macromolecular structural analysis.
Very often, the positions of flexible domains within macromolecules as well as within macromolecular complexes cannot be determined by standard structural biology methods. To overcome this problem, we developed a method that uses probabilistic data analysis to combine single-molecule measurements with X-ray crystallography data. The method determines not only the most likely position of a fluorescent dye molecule attached to the domain but also the complete three-dimensional probability distribution depicting the experimental uncertainty. With this approach, single-pair fluorescence resonance energy transfer measurements can now be used as a quantitative tool for investigating the position and dynamics of flexible domains within macromolecular complexes. We applied this method to find the position of the 5' end of the nascent RNA exiting transcription elongation complexes of yeast (Saccharomyces cerevisiae) RNA polymerase II and studied the influence of transcription factor IIB on the position of the RNA.
Muschielok
Adam
A
Department of Chemistry and Biochemistry and Center for Integrated Protein Science München, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, 81377 München, Germany.
Andrecka
Joanna
J
Jawhari
Anass
A
Brückner
Florian
F
Cramer
Patrick
P
Michaelis
Jens
J
D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods*; D031541:Fluorescence Resonance Energy Transfer; D008958:Models, Molecular; D008968:Molecular Conformation; D036103:Nanotechnology / Q000295:instrumentation*; D011485:Protein Binding; D012313:RNA / Q000096:biosynthesis / Q000737:chemistry / Q000378:metabolism*; D012319:RNA Polymerase II / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D035581:Transcription Factor TFIIB / Q000737:chemistry / Q000378:metabolism*
D035581:Transcription Factor TFIIB; D012313:RNA; D012319:RNA Polymerase II