Comparison of the maximum entropy and exponential series methods for the recovery of distributions of lifetimes from fluorescence lifetime data

Siemiarczuk, Aleksander; Wagner, Brian D.; Ware, William R.

doi:10.1021/j100367a080

Cited by 197 publications

(154 citation statements)

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“…4B shows the typical distribution of distances in the LRET sensitized emission intensity decays analyzed by an exponential series method (see "Experimental Procedures") (34,35). This type of analysis can recover lifetime distributions (which can be converted to distance distributions) without assumptions about their shapes, and it can therefore be used to discriminate between continuous distributions and discrete multiexponentials decays (34,35). Clear peaks centered at the distance values obtained from the multiexponential fits confirmed the presence of discrete conformations in MsbA-ND in the apo, ATP-bound, and Vi-inhibited states (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The number of donor-acceptor pairs that contribute to a distance component (percentage MsbA molecules in each conformation) was estimated from the relative intensity of each lifetime component corrected by the rate of energy transfer (k ϭ 1/ DA Ϫ 1/ D ) (18,33). To assess whether LRET intensity decays corresponded to discrete multiexponential decays or a distribution of lifetimes, we analyzed the data by an exponential series method (Felix 32 analysis software; PTI) designed to recover lifetime distributions without any a priori assumptions about their shapes (34,35). We analyzed the decays using a series of 200 exponentials with fixed, logarithmically spaced lifetimes and variable pre-exponentials.…”

Section: Methodsmentioning

confidence: 99%

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The Lipid Bilayer Modulates the Structure and Function of an ATP-binding Cassette Exporter

Zoghbi

Cooper

Altenberg

2016

Journal of Biological Chemistry

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ATP-binding cassette exporters use the energy of ATP hydrolysis to transport substrates across membranes by switching between inward-and outward-facing conformations. Essentially all structural studies of these proteins have been performed with the proteins in detergent micelles, locked in specific conformations and/or at low temperature. Here, we used luminescence resonance energy transfer spectroscopy to study the prototypical ATP-binding cassette exporter MsbA reconstituted in nanodiscs at 37°C while it performs ATP hydrolysis. We found major differences when comparing MsbA in these native-like conditions with double electron-electron resonance data and the crystal structure of MsbA in the open inward-facing conformation. The most striking differences include a significantly smaller separation between the nucleotide-binding domains and a larger fraction of molecules with associated nucleotide-binding domains in the nucleotide-free apo state. These studies stress the importance of studying membrane proteins in an environment that approaches physiological conditions. ATP-binding cassette (ABC)2 transporters constitute one of the largest families of membrane proteins and are found in all domains of life (1-3). They can be either importers (most prokaryote ABC transporters) or exporters (most mammal ABC transporters) (1-3). The core structure of ABC proteins consists of two transmembrane domains that form the translocation pathway and two conserved nucleotide-binding domains (NBDs) that bind and hydrolyze ATP (1-3), a process essential for their function. Binding of ATP promotes the formation of an NBD dimer in a head to tail orientation (4, 5). In the resulting structure two ATP molecules are "sandwiched" at the dimer interface, and residues from both NBDs form each of the two nucleotide-binding sites (1, 4, 5). NBD dimerization is essential for ATP hydrolysis and requires ATP binding to both nucleotide-binding sites (6), whereas dissociation of the dimers occurs following hydrolysis at only one of the two sites (7). This ATP-dependent NBDs dimerization/dissociation process is coupled to rearrangements of the transmembrane helices, switching the transporters from an inward-facing conformation (dissociated NBDs) to an outward-facing conformation (dimeric NBDs), with the concomitant translocation of substrate (1, 3).Two of the most studied ABC exporters are the multidrug resistance protein P-glycoprotein (MDR1 and ABCB1) that plays a role in the resistance to chemotherapy of some forms of cancer (3),and its bacterial homolog, the lipid flippase MsbA (8). MsbA is located in the inner membrane of Gram-negative bacteria, where it transports lipid A from the inner to the outer leaflet (9, 10). MsbA has been crystallized in inward-and outward-facing conformations (11) and has also been extensively studied by different spectroscopic techniques (12-18). Several studies point to large motions between the nucleotide-free "open" inward-facing conformation (NBDs separated by tens of Angstroms) and the ATP-bound "closed" outw...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The Lipid Bilayer Modulates the Structure and Function of an ATP-binding Cassette Exporter

Zoghbi

Cooper

Altenberg

2016

Journal of Biological Chemistry

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“…These time constants are very close to those reported for the corresponding YOYO dyes in DNA. 8,9 The presence of two decay components most probably reflects a distribution of lifetimes due to the heterogeneous base composition of salmon sperm DNA, 25,26 the fluorescence lifetime of YOYO-1 having been shown to depend on the base content. 8 The differences in the fluorescence quantum yields (Table 1) can be well accounted for by different average lifetimes of the dyes, pointing to a very similar radiative rate constant on the order of k rad ) 1.3 × 10 8 s -1 .…”

Section: Resultsmentioning

confidence: 99%

Ultrafast Excited-State Dynamics of Oxazole Yellow DNA Intercalators

Fürstenberg

Vauthey

2007

J. Phys. Chem. B

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The excited-state dynamics of the DNA intercalator YO-PRO-1 and of three derivatives has been investigated in water and in DNA using ultrafast fluorescence spectroscopy. In the free form, the singly charged dyes exist both as monomers and as H-dimers, while the doubly charged dyes exist predominantly as monomers. Both forms are very weakly fluorescent: the monomers because of ultrafast nonradiative deactivation, with a time constant on the order of 3-4 ps, associated with large amplitude motion around the methine bridge, and the H-dimers because of excitonic interaction. Upon intercalation into DNA, large amplitude motion is inhibited, H-dimers are disrupted, and the molecules become highly fluorescent. The early fluorescence dynamics of these dyes in DNA exhibits substantial differences compared with that measured with their homodimeric YOYO analogues, which are ascribed to dissimilarities in their local environment. Finally, the decay of the fluorescence polarization anisotropy reveals ultrafast hopping of the excitation energy between the intercalated dyes. In one case, a marked change of the depolarization dynamics upon increasing the dye concentration is observed and explained in terms of a different binding mode.

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“…40,41 Additionally, a consideration of the intramolecular hydrogen bonding within the macrocycle may yield further insight.…”

Section: ∆G°(ev) ) E°(dmentioning

confidence: 99%

Tuning the Photophysical Behavior of Luminescent Cyclam Derivatives by Cation Binding and Excited State Redox Potential

et al. 2005

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The emission from two photoactive 14-membered macrocyclic ligands, 6-((naphthalen-1-ylmethyl)-amino) trans-6,13-dimethyl-13-amino-1,4,8,11-tetraaza-cyclotetradecane (L 1 ) and 6-((anthracen-9-ylmethyl)-amino)-trans-6, 13-dimethyl-13-amino-1,4,8,11-tetraaza-cyclotetradecane (L 2 ) is strongly quenched by a photoinduced electron transfer (PET) mechanism involving amine lone pairs as electron donors. Time-correlated single photon counting (TCSPC), multiplex transient grating (TG), and fluorescence upconversion (FU) measurements were performed to characterize this quenching mechanism. Upon complexation with the redox inactive metal ion, Zn(II), the emission of the ligands is dramatically altered, with a significant increase in the fluorescence quantum yields due to coordination-induced deactivation of the macrocyclic amine lone pair electron donors. For [ZnL 2 ] 2+ , the substituted exocyclic amine nitrogen, which is not coordinated to the metal ion, does not quench the fluorescence due to an inductive effect of the proximal divalent metal ion that raises the ionization potential. However, for [ZnL 1 ] 2+ , the naphthalene chromophore is a sufficiently strong excited-state oxidant for PET quenching to occur.

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Comparison of the maximum entropy and exponential series methods for the recovery of distributions of lifetimes from fluorescence lifetime data

Cited by 197 publications

References 1 publication

The Lipid Bilayer Modulates the Structure and Function of an ATP-binding Cassette Exporter

The Lipid Bilayer Modulates the Structure and Function of an ATP-binding Cassette Exporter

Ultrafast Excited-State Dynamics of Oxazole Yellow DNA Intercalators

Tuning the Photophysical Behavior of Luminescent Cyclam Derivatives by Cation Binding and Excited State Redox Potential

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