Characterizing Multiple Molecular States in Single-Molecule Multiparameter Fluorescence Detection by Probability Distribution Analysis

2008 ◽  
Vol 112 (28) ◽  
pp. 8361-8374 ◽  
Author(s):  
Stanislav Kalinin ◽  
Suren Felekyan ◽  
Alessandro Valeri ◽  
Claus A. M. Seidel
Keyword(s):  
Probability Distribution ◽  
Fluorescence Detection ◽  
Single Molecule ◽  
Distribution Analysis

scholarly journals Camera-based single-molecule FRET detection with improved time resolution

2015 ◽  
Vol 17 (41) ◽  
pp. 27862-27872 ◽  
Author(s):  
Shazia Farooq ◽  
Johannes Hohlbein
Keyword(s):  
Probability Distribution ◽  
Single Molecule ◽  
Time Resolution ◽  
Laser Excitation ◽  
Single Molecule Detection ◽  
Distribution Analysis ◽  
Single Molecule Fret ◽  
Alternating Laser Excitation

Here the authors report on significant improvements in time-resolution and throughput in camera-based single-molecule detection by combining stroboscopic alternating-laser excitation with dynamic probability distribution analysis.

Characterizing Single-Molecule FRET Dynamics with Probability Distribution Analysis

ChemPhysChem ◽  
2010 ◽  
Vol 11 (10) ◽  
pp. 2209-2219 ◽  
Author(s):  
Yusdi Santoso ◽  
Joseph P. Torella ◽  
Achillefs N. Kapanidis
Keyword(s):  
Probability Distribution ◽  
Single Molecule ◽  
Distribution Analysis ◽  
Single Molecule Fret

scholarly journals Blinking statistics and molecular counting in direct stochastic reconstruction microscopy (dSTORM)

2021 ◽  
Author(s):  
Lekha Patel ◽  
David Williamson ◽  
Dylan M Owen ◽  
Edward A K Cohen
Keyword(s):  
Probability Distribution ◽  
Single Molecule ◽  
Immunological Synapse ◽  
Training Data ◽  
Supplementary Information ◽  
Cellular Structures ◽  
Exact Probability ◽  
Stochastic Optical Reconstruction Microscopy ◽  
Exact Probability Distribution ◽  
Optical Reconstruction

Abstract Motivation Many recent advancements in single-molecule localization microscopy exploit the stochastic photoswitching of fluorophores to reveal complex cellular structures beyond the classical diffraction limit. However, this same stochasticity makes counting the number of molecules to high precision extremely challenging, preventing key insight into the cellular structures and processes under observation. Results Modelling the photoswitching behaviour of a fluorophore as an unobserved continuous time Markov process transitioning between a single fluorescent and multiple dark states, and fully mitigating for missed blinks and false positives, we present a method for computing the exact probability distribution for the number of observed localizations from a single photoswitching fluorophore. This is then extended to provide the probability distribution for the number of localizations in a direct stochastic optical reconstruction microscopy experiment involving an arbitrary number of molecules. We demonstrate that when training data are available to estimate photoswitching rates, the unknown number of molecules can be accurately recovered from the posterior mode of the number of molecules given the number of localizations. Finally, we demonstrate the method on experimental data by quantifying the number of adapter protein linker for activation of T cells on the cell surface of the T-cell immunological synapse. Availability and implementation Software and data available at https://github.com/lp1611/mol_count_dstorm. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Single-Molecule Fluorescence Detection of a Synthetic Heparan Sulfate Disaccharide

ChemPhysChem ◽  
2016 ◽  
Vol 17 (21) ◽  
pp. 3442-3446 ◽  
Author(s):  
Charlotte E. Dalton ◽  
Steven D. Quinn ◽  
Aidan Rafferty ◽  
Michael J. Morten ◽  
John M. Gardiner ◽  
...  
Keyword(s):  
Heparan Sulfate ◽  
Fluorescence Detection ◽  
Single Molecule ◽  
Single Molecule Fluorescence

scholarly journals Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single-molecule three-color FRET

2021 ◽  
Vol 118 (33) ◽  
pp. e2025578118
Author(s):  
Lena Voith von Voithenberg ◽  
Anders Barth ◽  
Vanessa Trauschke ◽  
Benjamin Demarco ◽  
Swati Tyagi ◽  
...  
Keyword(s):  
Single Molecule ◽  
Structural Changes ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Conformational Space ◽  
Distribution Analysis ◽  
Nucleotide Exchange ◽  
Nucleotide Analogs ◽  
Recognition Mechanism ◽  
Substrate Peptide

Cellular function depends on the correct folding of proteins inside the cell. Heat-shock proteins 70 (Hsp70s), being among the first molecular chaperones binding to nascently translated proteins, aid in protein folding and transport. They undergo large, coordinated intra- and interdomain structural rearrangements mediated by allosteric interactions. Here, we applied a three-color single-molecule Förster resonance energy transfer (FRET) combined with three-color photon distribution analysis to compare the conformational cycle of the Hsp70 chaperones DnaK, Ssc1, and BiP. By capturing three distances simultaneously, we can identify coordinated structural changes during the functional cycle. Besides the known conformations of the Hsp70s with docked domains and open lid and undocked domains with closed lid, we observed additional intermediate conformations and distance broadening, suggesting flexibility of the Hsp70s in adopting the states in a coordinated fashion. Interestingly, the difference of this distance broadening varied between DnaK, Ssc1, and BiP. Study of their conformational cycle in the presence of substrate peptide and nucleotide exchange factors strengthened the observation of additional conformational intermediates, with BiP showing coordinated changes more clearly compared to DnaK and Ssc1. Additionally, DnaK and BiP were found to differ in their selectivity for nucleotide analogs, suggesting variability in the recognition mechanism of their nucleotide-binding domains for the different nucleotides. By using three-color FRET, we overcome the limitations of the usual single-distance approach in single-molecule FRET, allowing us to characterize the conformational space of proteins in higher detail.

Risk Planning with Discrete Distribution Analysis Applied to Petroleum Spills

2013 ◽  
Vol 2 (4) ◽  
pp. 61-78 ◽  
Author(s):  
Roy L. Nersesian ◽  
Kenneth David Strang
Keyword(s):  
Probability Distribution ◽  
Probability Distributions ◽  
Low Cost ◽  
Discrete Distribution ◽  
Distribution Model ◽  
Distribution Analysis ◽  
Distribution Models ◽  
Discrete Probability ◽  
Nonparametric Statistical ◽  
Spreadsheet Software

This study discussed the theoretical literature related to developing and probability distributions for estimating uncertainty. A theoretically selected ten-year empirical sample was collected and evaluated for the Albany NY area (N=942). A discrete probability distribution model was developed and applied for part of the sample, to illustrate the likelihood of petroleum spills by industry and day of week. The benefit of this paper for the community of practice was to demonstrate how to select, develop, test and apply a probability distribution to analyze the patterns in disaster events, using inferential parametric and nonparametric statistical techniques. The method, not the model, was intended to be generalized to other researchers and populations. An interesting side benefit from this study was that it revealed significant findings about where and when most of the human-attributed petroleum leaks had occurred in the Albany NY area over the last ten years (ending in 2013). The researchers demonstrated how to develop and apply distribution models in low cost spreadsheet software (Excel).

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