Single-photon smFRET: II. Application to continuous illumination
Here we adapt the Bayesian nonparametrics (BNP) framework presented in the first companion article to analyze kinetics from single-photon, single-molecule Förster resonance energy transfer (smFRET) traces generated under continuous illumination. Using our sampler, BNP-FRET, we learn the escape rates...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-03-01
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| Series: | Biophysical Reports |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667074722000441 |
| _version_ | 1798006006980018176 |
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| author | Ayush Saurabh Matthew Safar Mohamadreza Fazel Ioannis Sgouralis Steve Pressé |
| author_facet | Ayush Saurabh Matthew Safar Mohamadreza Fazel Ioannis Sgouralis Steve Pressé |
| author_sort | Ayush Saurabh |
| collection | DOAJ |
| description | Here we adapt the Bayesian nonparametrics (BNP) framework presented in the first companion article to analyze kinetics from single-photon, single-molecule Förster resonance energy transfer (smFRET) traces generated under continuous illumination. Using our sampler, BNP-FRET, we learn the escape rates and the number of system states given a photon trace. We benchmark our method by analyzing a range of synthetic and experimental data. Particularly, we apply our method to simultaneously learn the number of system states and the corresponding kinetics for intrinsically disordered proteins using two-color FRET under varying chemical conditions. Moreover, using synthetic data, we show that our method can deduce the number of system states even when kinetics occur at timescales of interphoton intervals. |
| first_indexed | 2024-04-11T12:48:04Z |
| format | Article |
| id | doaj.art-fb6150f4728a487481d37b8f7d48aacf |
| institution | Directory Open Access Journal |
| issn | 2667-0747 |
| language | English |
| last_indexed | 2024-04-11T12:48:04Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Biophysical Reports |
| spelling | doaj.art-fb6150f4728a487481d37b8f7d48aacf2022-12-22T04:23:18ZengElsevierBiophysical Reports2667-07472023-03-0131100087Single-photon smFRET: II. Application to continuous illuminationAyush Saurabh0Matthew Safar1Mohamadreza Fazel2Ioannis Sgouralis3Steve Pressé4Center for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, ArizonaCenter for Biological Physics, Arizona State University, Tempe, Arizona; Department of Mathematics and Statistical Science, Arizona State University, Tempe, ArizonaCenter for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, ArizonaDepartment of Mathematics, University of Tennessee Knoxville, Knoxville, TennesseeCenter for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, Arizona; School of Molecular Sciences, Arizona State University, Tempe, Arizona; Corresponding authorHere we adapt the Bayesian nonparametrics (BNP) framework presented in the first companion article to analyze kinetics from single-photon, single-molecule Förster resonance energy transfer (smFRET) traces generated under continuous illumination. Using our sampler, BNP-FRET, we learn the escape rates and the number of system states given a photon trace. We benchmark our method by analyzing a range of synthetic and experimental data. Particularly, we apply our method to simultaneously learn the number of system states and the corresponding kinetics for intrinsically disordered proteins using two-color FRET under varying chemical conditions. Moreover, using synthetic data, we show that our method can deduce the number of system states even when kinetics occur at timescales of interphoton intervals.http://www.sciencedirect.com/science/article/pii/S2667074722000441 |
| spellingShingle | Ayush Saurabh Matthew Safar Mohamadreza Fazel Ioannis Sgouralis Steve Pressé Single-photon smFRET: II. Application to continuous illumination Biophysical Reports |
| title | Single-photon smFRET: II. Application to continuous illumination |
| title_full | Single-photon smFRET: II. Application to continuous illumination |
| title_fullStr | Single-photon smFRET: II. Application to continuous illumination |
| title_full_unstemmed | Single-photon smFRET: II. Application to continuous illumination |
| title_short | Single-photon smFRET: II. Application to continuous illumination |
| title_sort | single photon smfret ii application to continuous illumination |
| url | http://www.sciencedirect.com/science/article/pii/S2667074722000441 |
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