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High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin

Nature Nanotechnology volume 5, pages 208–212 (2010)Cite this article

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Abstract

Dynamic changes in protein conformation in response to external stimuli are important in biological processes, but it has proved difficult to directly visualize such structural changes under physiological conditions1,2,3,4,5,6,7,8,9,10. Here, we show that high-speed atomic force microscopy7 can be used to visualize dynamic changes in stimulated proteins. High-resolution movies of a light-driven proton pump, bacteriorhodopsin11,12, reveal that, upon illumination, a cytoplasmic portion of each bacteriorhodopsin monomer is brought into contact with adjacent trimers. The bacteriorhodopsin–bacteriorhodopsin interaction in the transiently formed assembly engenders both positive and negative cooperative effects in the decay kinetics as the initial bacteriorhodopsin recovers and, as a consequence, the turnover rate of the photocycle is maintained constant, on average, irrespective of the light intensity. These results confirm that high-resolution visualization is a powerful approach for studying elaborate biomolecular processes under realistic conditions.

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Figure 1: High-speed AFM images of the cytoplasmic surface of D96N under dark or illuminated conditions.
Figure 2: Displacement of mass centre positions for WT at the cytoplasmic surface.
Figure 3: Cooperative effects on the decay kinetics in D96N.
Figure 4: Decay rate of activated D96N under different light intensities.

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Acknowledgements

This work was supported by Japan Science and Technology Agency for Core Research for Evolutional Science and Technology (T.A.), Grants-in-Aids for Scientific Research from Japan Society for the Promotion of Science (JSPS) (no. 15101005; T.A.) and from the Ministry of Education, Culture, Sports, Science and Technology, Japan (no. 19042009, T.U.; no. 20108014, H.K.), and Research Fellowships of JSPS for Young Scientists (M.S. and H.Y.). The authors thank J.K. Lanyi, S.P. Balashov and L.S. Brown for comments on the draft.

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Authors and Affiliations

  1. Department of Physics, Kanazawa University, Kanazawa, 920-1192, Japan

    Mikihiro Shibata, Hayato Yamashita, Takayuki Uchihashi & Toshio Ando

  2. CREST/JST, Tokyo, 102-0075, Japan

    Takayuki Uchihashi & Toshio Ando

  3. Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, 466-8555, Japan

    Hideki Kandori

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Contributions

T.A., H.K. and M.S. conceived and designed the experiments. T.A. and T.U. developed the high-speed AFM instrument. T.U., M.S. and H.Y. performed the experiments. T.U. and M.S. analysed the data. T.A., T.U. and M.S. co-wrote the paper. All authors discussed the results and commented on the manuscript.

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Correspondence to Toshio Ando.

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The authors declare no competing financial interests.

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Shibata, M., Yamashita, H., Uchihashi, T. et al. High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin. Nature Nanotech 5, 208–212 (2010). https://doi.org/10.1038/nnano.2010.7

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