Decoding Single Molecule Time Traces with Dynamic Disorder.
Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules, whose dynamic...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2016-12-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC5226833?pdf=render |
| _version_ | 1818947945251209216 |
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| author | Wonseok Hwang Il-Buem Lee Seok-Cheol Hong Changbong Hyeon |
| author_facet | Wonseok Hwang Il-Buem Lee Seok-Cheol Hong Changbong Hyeon |
| author_sort | Wonseok Hwang |
| collection | DOAJ |
| description | Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules, whose dynamic pattern of conformational transitions is affected by slower transition dynamics of internal state hidden in a low dimensional projection. A systematic means to analyze such data is, however, currently not well developed. Here we report a new algorithm-Variational Bayes-double chain Markov model (VB-DCMM)-to analyze single molecule time trajectories that display dynamic disorder. The proposed analysis employing VB-DCMM allows us to detect the presence of dynamic disorder, if any, in each trajectory, identify the number of internal states, and estimate transition rates between the internal states as well as the rates of conformational transition within each internal state. Applying VB-DCMM algorithm to single molecule FRET data of H-DNA in 100 mM-Na+ solution, followed by data clustering, we show that at least 6 kinetic paths linking 4 distinct internal states are required to correctly interpret the duplex-triplex transitions of H-DNA. |
| first_indexed | 2024-12-20T08:38:58Z |
| format | Article |
| id | doaj.art-954f7e81897e4444b8854241a0e76030 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-20T08:38:58Z |
| publishDate | 2016-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-954f7e81897e4444b8854241a0e760302022-12-21T19:46:27ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582016-12-011212e100528610.1371/journal.pcbi.1005286Decoding Single Molecule Time Traces with Dynamic Disorder.Wonseok HwangIl-Buem LeeSeok-Cheol HongChangbong HyeonSingle molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules, whose dynamic pattern of conformational transitions is affected by slower transition dynamics of internal state hidden in a low dimensional projection. A systematic means to analyze such data is, however, currently not well developed. Here we report a new algorithm-Variational Bayes-double chain Markov model (VB-DCMM)-to analyze single molecule time trajectories that display dynamic disorder. The proposed analysis employing VB-DCMM allows us to detect the presence of dynamic disorder, if any, in each trajectory, identify the number of internal states, and estimate transition rates between the internal states as well as the rates of conformational transition within each internal state. Applying VB-DCMM algorithm to single molecule FRET data of H-DNA in 100 mM-Na+ solution, followed by data clustering, we show that at least 6 kinetic paths linking 4 distinct internal states are required to correctly interpret the duplex-triplex transitions of H-DNA.http://europepmc.org/articles/PMC5226833?pdf=render |
| spellingShingle | Wonseok Hwang Il-Buem Lee Seok-Cheol Hong Changbong Hyeon Decoding Single Molecule Time Traces with Dynamic Disorder. PLoS Computational Biology |
| title | Decoding Single Molecule Time Traces with Dynamic Disorder. |
| title_full | Decoding Single Molecule Time Traces with Dynamic Disorder. |
| title_fullStr | Decoding Single Molecule Time Traces with Dynamic Disorder. |
| title_full_unstemmed | Decoding Single Molecule Time Traces with Dynamic Disorder. |
| title_short | Decoding Single Molecule Time Traces with Dynamic Disorder. |
| title_sort | decoding single molecule time traces with dynamic disorder |
| url | http://europepmc.org/articles/PMC5226833?pdf=render |
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