Steps and Bumps: Precision Extraction of Discrete States of Molecular Machines
We report statistical time-series analysis tools providing improvements in the rapid, precision extraction of discrete state dynamics from time traces of experimental observations of molecular machines. By building physical knowledge and statistical innovations into analysis tools, we provide techni...
| Main Authors: | , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Elsevier
2014
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| Online Access: | http://hdl.handle.net/1721.1/92347 |
| _version_ | 1826195074633957376 |
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| author | Steel, Bradley C. Bai, Fan Sowa, Yoshiyuki Bilyard, Thomas Mueller, David M. Berry, Richard M. Jones, Nick S. Little, Max |
| author2 | Massachusetts Institute of Technology. Media Laboratory |
| author_facet | Massachusetts Institute of Technology. Media Laboratory Steel, Bradley C. Bai, Fan Sowa, Yoshiyuki Bilyard, Thomas Mueller, David M. Berry, Richard M. Jones, Nick S. Little, Max |
| author_sort | Steel, Bradley C. |
| collection | MIT |
| description | We report statistical time-series analysis tools providing improvements in the rapid, precision extraction of discrete state dynamics from time traces of experimental observations of molecular machines. By building physical knowledge and statistical innovations into analysis tools, we provide techniques for estimating discrete state transitions buried in highly correlated molecular noise. We demonstrate the effectiveness of our approach on simulated and real examples of steplike rotation of the bacterial flagellar motor and the F1-ATPase enzyme. We show that our method can clearly identify molecular steps, periodicities and cascaded processes that are too weak for existing algorithms to detect, and can do so much faster than existing algorithms. Our techniques represent a step in the direction toward automated analysis of high-sample-rate, molecular-machine dynamics. Modular, open-source software that implements these techniques is provided. |
| first_indexed | 2024-09-23T10:06:32Z |
| format | Article |
| id | mit-1721.1/92347 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:06:32Z |
| publishDate | 2014 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | mit-1721.1/923472022-09-26T15:46:19Z Steps and Bumps: Precision Extraction of Discrete States of Molecular Machines Steel, Bradley C. Bai, Fan Sowa, Yoshiyuki Bilyard, Thomas Mueller, David M. Berry, Richard M. Jones, Nick S. Little, Max Massachusetts Institute of Technology. Media Laboratory Program in Media Arts and Sciences (Massachusetts Institute of Technology) Little, Max Andrew We report statistical time-series analysis tools providing improvements in the rapid, precision extraction of discrete state dynamics from time traces of experimental observations of molecular machines. By building physical knowledge and statistical innovations into analysis tools, we provide techniques for estimating discrete state transitions buried in highly correlated molecular noise. We demonstrate the effectiveness of our approach on simulated and real examples of steplike rotation of the bacterial flagellar motor and the F1-ATPase enzyme. We show that our method can clearly identify molecular steps, periodicities and cascaded processes that are too weak for existing algorithms to detect, and can do so much faster than existing algorithms. Our techniques represent a step in the direction toward automated analysis of high-sample-rate, molecular-machine dynamics. Modular, open-source software that implements these techniques is provided. Wellcome Trust (London, England) (Massachusetts Institute of Technology. Postdoctoral Fellowship WT090651MF) Biotechnology and Biological Sciences Research Council (Great Britain) (Engineering and Physical Sciences Research Council. Grant BBD0201901) 2014-12-16T20:48:12Z 2014-12-16T20:48:12Z 2011-07 2011-01 Article http://purl.org/eprint/type/JournalArticle 00063495 1542-0086 http://hdl.handle.net/1721.1/92347 Little, Max A., Bradley C. Steel, Fan Bai, Yoshiyuki Sowa, Thomas Bilyard, David M. Mueller, Richard M. Berry, and Nick S. Jones. “Steps and Bumps: Precision Extraction of Discrete States of Molecular Machines.” Biophysical Journal 101, no. 2 (July 2011): 477–485. © 2011 Biophysical Society en_US http://dx.doi.org/10.1016/j.bpj.2011.05.070 Biophysical Journal Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf Elsevier Elsevier |
| spellingShingle | Steel, Bradley C. Bai, Fan Sowa, Yoshiyuki Bilyard, Thomas Mueller, David M. Berry, Richard M. Jones, Nick S. Little, Max Steps and Bumps: Precision Extraction of Discrete States of Molecular Machines |
| title | Steps and Bumps: Precision Extraction of Discrete States of Molecular Machines |
| title_full | Steps and Bumps: Precision Extraction of Discrete States of Molecular Machines |
| title_fullStr | Steps and Bumps: Precision Extraction of Discrete States of Molecular Machines |
| title_full_unstemmed | Steps and Bumps: Precision Extraction of Discrete States of Molecular Machines |
| title_short | Steps and Bumps: Precision Extraction of Discrete States of Molecular Machines |
| title_sort | steps and bumps precision extraction of discrete states of molecular machines |
| url | http://hdl.handle.net/1721.1/92347 |
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