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Kuramochi M, Dong Y, Yang Y, Arai T, Okada R, Shinkai Y, Doi M, Aoyama K, Sekiguchi H, Mio K, Tsuda S, Sasaki YC. Dynamic motions of ice-binding proteins in living Caenorhabditis elegans using diffracted X-ray blinking and tracking. Biochem Biophys Rep 2022; 29:101224. [PMID: 35146137 PMCID: PMC8819013 DOI: 10.1016/j.bbrep.2022.101224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 11/15/2022] Open
Affiliation(s)
- Masahiro Kuramochi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, 277-8565, Japan
- Corresponding author. Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511, Japan.
| | - Yige Dong
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Yue Yang
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Tatsuya Arai
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Rio Okada
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Yoichi Shinkai
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Japan
| | - Motomichi Doi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Japan
| | - Kouki Aoyama
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Hiroshi Sekiguchi
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Kazuhiro Mio
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, 277-8565, Japan
| | - Sakae Tsuda
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, 277-8565, Japan
| | - Yuji C. Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, 277-8565, Japan
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
- Corresponding author. Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan.
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Hosoe Y, Sekiguchi H, Sasaki YC, Oda M. Structural dynamics of a DNA-binding protein analyzed using diffracted X-ray tracking. Biophys Chem 2021; 278:106669. [PMID: 34416518 DOI: 10.1016/j.bpc.2021.106669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/27/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022]
Abstract
Diffracted X-ray tracking (DXT) is one of methods for the real-time evaluation of protein structural dynamics by detecting the movement of a gold-nanocrystal attached to a target protein. However, one of the technical concerns is the size of the gold-nanocrystals, which are larger than the protein. In our previous results of mean square angular displacement curves in DXT analysis, dynamical movements of the DNA-binding protein, c-Myb R2R3, were observed in only one population in either DNA-unbound or -bound state, and was found to decrease upon DNA binding. In this study, c-Myb R2R3 dynamical movements were re-evaluated with a low density of the protein immobilized on the DXT substrate, to decrease the possibility that the gold-nanocrystals attached to more than one R2R3 molecule. We observed two dynamical moving populations in the DNA-bound state, which could be classified due to electrostatic attraction and repulsion between the DNA-protein complexes, and determined the apparent angular diffusion constant, which was similar to the value calculated in our previous study. We showed more real movement of the protein could be observed by lowering the immobilization density of the protein.
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Affiliation(s)
- Yuhi Hosoe
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Hiroshi Sekiguchi
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yuji C Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan.
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Tilting and rotational motions of silver halide crystal with diffracted X-ray blinking. Sci Rep 2021; 11:4097. [PMID: 33674698 PMCID: PMC7935957 DOI: 10.1038/s41598-021-83320-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/02/2021] [Indexed: 11/13/2022] Open
Abstract
The dynamic properties of crystalline materials are important for understanding their local environment or individual single-grain motions. A new time-resolved observation method is required for use in many fields of investigation. Here, we developed in situ diffracted X-ray blinking to monitor high-resolution diffraction patterns from single-crystal grains with a 50 ms time resolution. The diffraction spots of single grains of silver halides and silver moved in the θ and χ directions during the photolysis chemical reaction. The movements of the spots represent tilting and rotational motions. The time trajectory of the diffraction intensity reflecting those motions was analysed by using single-pixel autocorrelation function (sp-ACF). Single-pixel ACF analysis revealed significant differences in the distributions of the ACF decay constants between silver halides, suggesting that the motions of single grains are different between them. The rotational diffusion coefficients for silver halides were estimated to be accurate at the level of approximately 0.1 to 0.3 pm2/s. Furthermore, newly formed silver grains on silver halides correlated with their ACF decay constants. Our high-resolution atomic scale measurement—sp-ACF analysis of diffraction patterns of individual grains—is useful for evaluating physical properties that are broadly applicable in physics, chemistry, and materials science.
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