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Extracting the Underlying Unique Reaction Scheme from a Single-Molecule Time Series

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Cell Signaling Reactions

Abstract

Single molecule spectroscopy provides us with a new means to look deeply into the question of how an individual molecule behaves when performing biological functions in a thermally fluctuating environment. However, what information one can extract from the observed data is still an open question. We overview our new method which extracts the underlying reaction scheme, a state-space network (SSN), from the time series data of an experimental measurement. We demand that a time series analysis should provide not only an interpretation of the dynamical behavior but also provide new insights into biological functions buried in ensemble-based measurements. Our method is based on the combination of information theory and Wavelet multiresolution decomposition analysis. The resultant reaction scheme does not rely on an a priori ansatz like local equilibrium and detailed balance. It is mathematically assured as unique, minimally complex and stochastic, but best predictive. We demonstrate the potential of this method by applying it to the analysis of an anomalous conformation in Flavin oxidoreductase dependent on the timescale of observation. We also discuss future perspectives concerning its use as a new means for the exploration of single molecule biophysics.

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Acknowledgements

We thank Prof. Haw Yang for his continuous valuable contributions to our project from his experimentalist’s viewpoint. We also thank Profs. Satoshi Takahashi and Mikito Toda for their valuable discussions. We acknowledge financial support from JSPS, JST/CREST, Grant-in-Aid for Research on Priority Areas ‘Systems Genomics,’ ‘Real Molecular Theory’, and ‘Innovative nano-science,’ MEXT.

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Authors and Affiliations

  1. Molecule & Life Nonlinear Sciences Laboratory, Research Institute for Electronic Science, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan

    Chun Biu Li & Tamiki Komatsuzaki

  2. Core Reseach for Evolution Science and Technology(CREST), Japan Science and Technology Agency(IST), Kawaguchi, Saitama, 332–0012, Japan

    Tamiki Komatsuzaki

Authors
  1. Chun Biu Li
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  2. Tamiki Komatsuzaki
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Correspondence to Tamiki Komatsuzaki .

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Editors and Affiliations

  1. , Cellular Informatics Laboratory, RIKEN, Hirosawa 2-1, Wako, 351-0198, Japan

    Yasushi Sako

  2. Graduate School of Frontier Biosciences, Laboratories of Nanobiology, Osaka University, Yamadaoka 1-3, Suita, 565-871, Japan

    Masahiro Ueda

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Li, C.B., Komatsuzaki, T. (2011). Extracting the Underlying Unique Reaction Scheme from a Single-Molecule Time Series. In: Sako, Y., Ueda, M. (eds) Cell Signaling Reactions. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-9864-1_11

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