title: Combining MFD and PIE for accurate single-pair Förster resonance energy transfer measurements.
abstract: Single-pair Förster resonance energy transfer (spFRET) experiments using single-molecule burst analysis on a confocal microscope are an ideal tool to measure inter- and intramolecular distances and dynamics on the nanoscale. Different techniques have been developed to maximize the amount of information available in spFRET burst analysis experiments. Multiparameter fluorescence detection (MFD) is used to monitor a variety of fluorescence parameters simultaneously and pulsed interleaved excitation (PIE) employs direct excitation of the acceptor to probe its presence and photoactivity. To calculate accurate FRET efficiencies from spFRET experiments with MFD or PIE, several calibration measurements are usually required. Herein, we demonstrate that by combining MFD with PIE information regarding all calibration factors as well as an accurate determination of spFRET histograms can be performed in a single measurement. In addition, the quality of overlap of the different detection volumes as well as the detection of acceptor photophysics can be investigated with MFD-PIE. Bursts containing acceptor photobleaching can be identified and excluded from further investigation while bursts that contain FRET dynamics are unaffected by this analysis. We have employed MFD-PIE to accurately analyze the effects of nucleotides and substrate on the interdomain separation in DnaK, the major bacterial heat shock protein 70 (Hsp70). The interdomain distance increases from 47 Å in the ATP-bound state to 84 Å in the ADP-bound state and slightly contracts to 77 Å when a substrate is bound. This is in contrast to what was observed for the mitochondrial member of the Hsp70s, Ssc1, supporting the notion of evolutionary specialization of Hsp70s for different cellular functions in different organisms and cell organelles.
authors.affiliation: Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science (CiPSM) and Center for Nanoscience, Ludwig-Maximilians-Universität München, Butenandtstr. 11, Gerhard-Ertl-Building, 81377 Munich, Germany.
authors.forename: Volodymyr
authors.initials: V
authors.lastname: Kudryavtsev
authors.forename: Martin
authors.initials: M
authors.lastname: Sikor
authors.forename: Stanislav
authors.initials: S
authors.lastname: Kalinin
authors.forename: Dejana
authors.initials: D
authors.lastname: Mokranjac
authors.forename: Claus A M
authors.initials: CA
authors.lastname: Seidel
authors.forename: Don C
authors.initials: DC
authors.lastname: Lamb
mesh_terms: D000244:Adenosine Diphosphate / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D005454:Fluorescence Polarization; D031541:Fluorescence Resonance Energy Transfer; D018840:HSP70 Heat-Shock Proteins / Q000737:chemistry* / Q000378:metabolism; D008962:Models, Theoretical; D011485:Protein Binding; D013379:Substrate Specificity
chemical_list: D029968:Escherichia coli Proteins; D018840:HSP70 Heat-Shock Proteins; D000244:Adenosine Diphosphate; C063842:dnaK protein, E coli