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97 results on '"Tono, K."'

1. TR-SFX MmCPDII-DNA complex: 500 ns time-point collected in SACLA. Includes 500 ns, dark, and extrapolated structure factors

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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2. TR-SFX MmCPDII-DNA complex: 250 ps snapshot. Includes 250 ps, dark, and extrapolated structure factors

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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3. TR-SFX MmCPDII-DNA complex: 2 ns snapshot. Includes 2 ns, dark, and extrapolated structure factors

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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4. TR-SFX MmCPDII-DNA complex: 100 ps snapshot. Includes 100ps, dark, and extrapolated structure factors

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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5. TR-SFX MmCPDII-DNA complex: 10 ns time-point collected in SACLA. Includes 10 ns, dark, and extrapolated structure factors

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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6. TR-SFX MmCPDII-DNA complex: 25 us time-point collected in SACLA. Includes 25 us, dark, and extrapolated structure factors

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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7. TR-SFX MmCPDII-DNA complex: 3.35 ns snapshot. Includes 3.35 ns, dark, and extrapolated structure factors

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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8. TR-SFX MmCPDII-DNA complex: dark state as collected in SACLA

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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9. Dark, fully reduced structure of the MmCPDII-DNA complex as produced at SwissFEL

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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10. DF-SFX MmCPDII-DNA complex: steady state oxidized complex

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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11. TR-SFX MmCPDII-DNA complex: 6 ns snapshot. Includes 6 ns, dark, and extrapolated structure factors

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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12. TR-SFX MmCPDII-DNA complex: 650 ps snapshot. Includes 650ps, dark, and extrapolated structure factors

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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13. TR-SFX MmCPDII-DNA complex: 450 ps snapshot. Includes 450ps, dark, and extrapolated structure factors

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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14. TR-SFX MmCPDII-DNA complex: 10 ns snapshot. Includes 10 ns, dark, and extrapolated structure factors. Collected at SwissFEL

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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15. TR-SFX MmCPDII-DNA complex: 1 ns snapshot. Includes 1 ns, dark, and extrapolated structure factors

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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16. MmCPDII-DNA complex containing low-dosage, light induced repaired DNA.

Author

Maestre-Reyna, M., primary, Wang, P.-H., additional, Nango, E., additional, Hosokawa, Y., additional, Saft, M., additional, Furrer, A., additional, Yang, C.-H., additional, Ngura Putu, E.P.G., additional, Wu, W.-J., additional, Emmerich, H.-J., additional, Engilberge, S., additional, Caramello, N., additional, Wranik, M., additional, Glover, H.L., additional, Franz-Badur, S., additional, Wu, H.-Y., additional, Lee, C.-C., additional, Huang, W.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Liao, J.-H., additional, Weng, J.-H., additional, Gad, W., additional, Chang, C.-W., additional, Pang, A.H., additional, Gashi, D., additional, Beale, E., additional, Ozerov, D., additional, Milne, C., additional, Cirelli, C., additional, Bacellar, C., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Spadaccini, R., additional, Royant, A., additional, Yamamoto, J., additional, Iwata, S., additional, Standfuss, J., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2023
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19. Observing soft x-ray magnetization-induced second harmonic generation at a heterojunction interface

Author

Sumi, T., primary, Horio, M., additional, Senoo, T., additional, Kubota, Y., additional, Yamaguchi, G., additional, Wada, T., additional, Miyamoto, M., additional, Yamaguchi, K., additional, Tsujikawa, Y., additional, Sato, Y., additional, Niibe, M., additional, Hirata, Y., additional, Miyauchi, Y., additional, Oshima, D., additional, Kato, T., additional, Owada, S., additional, Tono, K., additional, Yabashi, M., additional, and Matsuda, I., additional

Published
2023
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20. Corrigendum to ultrafast anisotropic disordering in graphite driven by intense hard X-ray pulses

Author

Hartley, N.J., primary, Grenzer, J., additional, Lu, W., additional, Huang, L.G., additional, Inubushi, Y., additional, Kamimura, N., additional, Katagiri, K., additional, Kodama, R., additional, Kon, A., additional, Lipp, V., additional, Makita, M., additional, Matsuoka, T., additional, Medvedev, N., additional, Nakajima, S., additional, Ozaki, N., additional, Pikuz, T., additional, Rode, A.V., additional, Sagae, D., additional, Schuster, A.K., additional, Tono, K., additional, Voigt, K., additional, Vorberger, J., additional, Yabuuchi, T., additional, and Kraus, D., additional

Published
2023
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21. Erratum: Using Diffuse Scattering to Observe X-Ray-Driven Nonthermal Melting [Phys. Rev. Lett. 126 , 015703 (2021)]

Author

Hartley, N. J., primary, Grenzer, J., additional, Huang, L., additional, Inubushi, Y., additional, Kamimura, N., additional, Katagiri, K., additional, Kodama, R., additional, Kon, A., additional, Lu, W., additional, Makita, M., additional, Matsuoka, T., additional, Nakajima, S., additional, Ozaki, N., additional, Pikuz, T., additional, Rode, A., additional, Sagae, D., additional, Schuster, A. K., additional, Tono, K., additional, Voigt, K., additional, Vorberger, J., additional, Yabuuchi, T., additional, McBride, E. E., additional, and Kraus, D., additional

Published
2022
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22. class II photolyase MmCPDII semiquinone to fully reduced TR-SFX studies (10 ns time-point)

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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23. class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (50 ns time-point)

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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24. class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (250 ns time-point)

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

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2022
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25. class II photolyase MmCPDII semiquinone to fully reduced TR-SFX studies (semiquinone dark structure)

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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26. Dark adapted MmCPDII during oxidized to semiquinone TR-SFX studies

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

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2022
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27. class II photolyase MmCPDII semiquinone to fully reduced TR-SFX studies (5 us time-point)

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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28. class II photolyase MmCPDII semiquinone to fully reduced TR-SFX studies (30 ns time-point)

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

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2022
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29. class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (1 us time-point)

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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30. class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (10 ns time-point)

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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31. SFX structure of archaeal class II CPD photolyase from Methanosarcina mazei in the semiquinone state

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.C., additional, Nango, E., additional, Gusti-Ngurah-Putu, E.-P., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Tanaka, R., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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32. class II photolyase MmCPDII semiquinone to fully reduced TR-SFX studies (1 us time-point)

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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33. Re-refinement of the 2XRY X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.C., additional, Nango, E., additional, Gusti-Ngurah-Putu, E.-P., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Tanaka, R., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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34. class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (400 us time-point)

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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35. class II photolyase MmCPDII semiquinone to fully reduced TR-SFX studies (30 us time-point)

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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36. SFX structure of archaeal class II CPD photolyase from Methanosarcina mazei in the oxidized state

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.C., additional, Nango, E., additional, Gusti-Ngurah-Putu, E.-P., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Tanaka, R., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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37. SFX structure of archaeal class II CPD photolyase from Methanosarcina mazei in the fully reduced state

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.C., additional, Nango, E., additional, Gusti-Ngurah-Putu, E.-P., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Tanaka, R., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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38. class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (1 ms time-point)

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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39. class II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (5 ms time-point)

Author

Maestre-Reyna, M., primary, Yang, C.-H., additional, Huang, W.-C., additional, Nango, E., additional, Ngura Putu, E.P.G., additional, Franz-Badur, S., additional, Wu, W.-J., additional, Wu, H.-Y., additional, Wang, P.-H., additional, Hosokawa, Y., additional, Saft, M., additional, Emmerich, H.-J., additional, Liao, J.-H., additional, Lee, C.-C., additional, Huang, K.-F., additional, Chang, Y.-K., additional, Weng, J.-H., additional, Royant, A., additional, Gad, W., additional, Pang, A.H., additional, Chang, C.-W., additional, Sugahara, M., additional, Owada, S., additional, Joti, Y., additional, Yamashita, A., additional, Tanaka, R., additional, Tanaka, T., additional, Luo, F.J., additional, Tono, K., additional, Kiontke, S., additional, Yamamoto, J., additional, Iwata, S., additional, Essen, L.-O., additional, Bessho, Y., additional, and Tsai, M.-D., additional

Published
2022
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41. SFX structure of dehaloperoxidase B in the ferric form

Author

Moreno Chicano, T., primary, Ebrahim, A.E., additional, Axford, D.A., additional, Sherrell, D.A., additional, Sugimoto, H., additional, Tono, K., additional, Owada, S., additional, Worrall, J.W., additional, Strange, R.W., additional, Owen, R.L., additional, and Hough, M.A., additional

Published
2021
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42. Intersubunit Coupling Enables Fast CO2-Fixation by Reductive Carboxylases

Author

Hasan DeMirci, Yashas Rao, Gabriele M. Stoffel, Bastian Vögeli, Kristina Schell, Aharon Gomez, Alexander Batyuk, Cornelius Gati, Raymond G. Sierra, Mark S. Hunter, E. Han Dao, Halil I. Ciftci, Brandon Hayes, Fredric Poitevin, Po-Nan Li, Manat Kaur, Kensuke Tono, David Adrian Saez, Samuel Deutsch, Yasuo Yoshikuni, Helmut Grubmüller, Tobias J. Erb, Esteban Vöhringer-Martinez, Soichi Wakatsuki, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Rao, Y., Stoffel, G.M., Vögeli, B., Schell, K., Gomez, A., Batyuk, A., Gati, C., Sierra, R.G., Hunter, M.S., Dao, E.H., Ciftci, H.I., Hayes, B., Poitevin, F., Li, P.-N., Kaur, M., Tono, K., Saez, D.A., Deutsch, S., Yoshikuni, Y., Grubmüller, H., Erb, T.J., Vöhringer-Martinez, E., Wakatsuki, S., College of Sciences, and Department of Molecular Biology and Genetics

Subjects
Active state, Dynamic structure, Molecular mechanism, Chemistry, General Chemical Engineering, Chemical Sciences, General Chemistry
Abstract

Enoyl-CoA carboxylases/reductases (ECRs) are some of the most efficient CO2-fixing enzymes described to date. However, the molecular mechanisms underlying the extraordinary catalytic activity of ECRs on the level of the protein assembly remain elusive. Here we used a combination of ambient-temperature X-ray free electron laser (XFEL) and cryogenic synchrotron experiments to study the structural organization of the ECR from Kitasatospora setae. The K. setae ECR is a homotetramer that differentiates into a pair of dimers of open- and dosed-form subunits in the catalytically active state. Using molecular dynamics simulations and structure-based mutagenesis, we show that catalysis is synchronized in the K. setae ECR across the pair of dimers. This conformational coupling of catalytic domains is conferred by individual amino acids to achieve high CO2-fixation rates. Our results provide unprecedented insights into the dynamic organization and synchronized inter- and intrasubunit communications of this remarkably efficient CO2-fixing enzyme during catalysis., NSF Science and Technology Center Grant; Biology with X-ray Lasers, BioXFEL; Scientific and Technological Research Council of Turkey (TÜBİTAK); 2232 International Fellowship for Outstanding Researchers Program; 1001 Scientific and Technological Research Projects Funding Program; U.S. Department of Energy; Office of Science; Office of Basic Energy Sciences; European Union (EU); Horizon 2020 ; European Research Council (ERC); SYBORG; U.S. Department of Energy Joint Genome Institute; DOE Office of Science User Facility; Max Planck Society; a Max-Planck-Partner Group; CONICYT; CONICYT Doctorado Nacional Grant; Fondo Nacional de Desarrollo Científico y Tecnológico (Fondecyt) Postdoctoral Fellowship; DOE Office of Science, Biological Environmental Research; National Institutes of Health; National Science Foundation Major Research Instrument Grant; NIGMS; Stanford PRECOURT Institute

Published
2022

43. Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography.

Author

Maity B, Shoji M, Luo F, Nakane T, Abe S, Owada S, Kang J, Tono K, Tanaka R, Pham TT, Kojima M, Hishikawa Y, Tanaka J, Tian J, Nagama M, Suzuki T, Noya H, Nakasuji Y, Asanuma A, Yao X, Iwata S, Shigeta Y, Nango E, and Ueno T

Subjects
Crystallography, X-Ray, Porosity, Coordination Complexes chemistry, Models, Molecular, Animals, Carbon Monoxide chemistry, Time Factors, Chickens, Muramidase chemistry, Manganese chemistry
Abstract

Determining short-lived intermediate structures in chemical reactions is challenging. Although ultrafast spectroscopic methods can detect the formation of transient intermediates, real-space structures cannot be determined directly from such studies. Time-resolved serial femtosecond crystallography (TR-SFX) has recently proven to be a powerful method for capturing molecular changes in proteins on femtosecond timescales. However, the methodology has been mostly applied to natural proteins/enzymes and limited to reactions promoted by synthetic molecules due to structure determination challenges. This work demonstrates the applicability of TR-SFX for investigations of chemical reaction mechanisms of synthetic metal complexes. We fix a light-induced CO-releasing Mn(CO) 3 reaction center in porous hen egg white lysozyme (HEWL) microcrystals. By controlling light exposure and time, we capture the real-time formation of Mn-carbonyl intermediates during the CO release reaction. The asymmetric protein environment is found to influence the order of CO release. The experimentally-observed reaction path agrees with quantum mechanical calculations. Therefore, our demonstration offers a new approach to visualize atomic-level reactions of small molecules using TR-SFX with real-space structure determination. This advance holds the potential to facilitate design of artificial metalloenzymes with precise mechanisms, empowering design, control and development of innovative reactions., (© 2024. The Author(s).)

Published
2024
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44. Sub-photon accuracy noise reduction of a single shot coherent diffraction pattern with an atomic model trained autoencoder.

Author

Ishikawa T, Takeo Y, Sakurai K, Yoshinaga K, Furuya N, Inubushi Y, Tono K, Joti Y, Yabashi M, Kimura T, and Yoshimi K

Abstract

Single-shot imaging with femtosecond X-ray lasers is a powerful measurement technique that can achieve both high spatial and temporal resolution. However, its accuracy has been severely limited by the difficulty of applying conventional noise-reduction processing. This study uses deep learning to validate noise reduction techniques, with autoencoders serving as the learning model. Focusing on the diffraction patterns of nanoparticles, we simulated a large dataset treating the nanoparticles as composed of many independent atoms. Three neural network architectures are investigated: neural network, convolutional neural network and U-net, with U-net showing superior performance in noise reduction and subphoton reproduction. We also extended our models to apply to diffraction patterns of particle shapes different from those in the simulated data. We then applied the U-net model to a coherent diffractive imaging study, wherein a nanoparticle in a microfluidic device is exposed to a single X-ray free-electron laser pulse. After noise reduction, the reconstructed nanoparticle image improved significantly even though the nanoparticle shape was different from the training data, highlighting the importance of transfer learning.

Published
2024
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45. Comprehensive Application of XFEL Microcrystallography for Challenging Targets in Various Organic Compounds.

Author

Takaba K, Maki-Yonekura S, Inoue I, Tono K, Fukuda Y, Shiratori Y, Peng Y, Morimoto J, Inoue S, Higashino T, Sando S, Hasegawa T, Yabashi M, and Yonekura K

Abstract

There is a growing demand for structure determination from small crystals, and the three-dimensional electron diffraction (3D ED) technique can be employed for this purpose. However, 3D ED has certain limitations related to the crystal thickness and data quality. We here present the application of serial X-ray crystallography (SX) with X-ray free electron lasers (XFELs) to small (a few μm or less) and thin (a few hundred nm or less) crystals of novel compounds dispersed on a substrate. For XFEL exposures, two-dimensional (2D) scanning of the substrate coupled with rotation enables highly efficient data collection. The recorded patterns can be successfully indexed using lattice parameters obtained through 3D ED. This approach is especially effective for challenging targets, including pharmaceuticals and organic materials that form preferentially oriented flat crystals in low-symmetry space groups. Some of these crystals have been difficult to solve or have yielded incomplete solutions using 3D ED. Our extensive analyses confirmed the superior quality of the SX data regardless of crystal orientations. Additionally, 2D scanning with XFEL pulses gives an overall distribution of the samples on the substrate, which can be useful for evaluating the properties of crystal grains and the quality of layered crystals. Therefore, this study demonstrates that XFEL crystallography has become a powerful tool for conducting structure studies of small crystals of organic compounds.

Published
2024
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46. Author Correction: Structural evidence for intermediates during O 2 formation in photosystem II.

Author

Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, and Yachandra VK

Published
2024
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47. Oxygen-evolving photosystem II structures during S 1 -S 2 -S 3 transitions.

Author

Li H, Nakajima Y, Nango E, Owada S, Yamada D, Hashimoto K, Luo F, Tanaka R, Akita F, Kato K, Kang J, Saitoh Y, Kishi S, Yu H, Matsubara N, Fujii H, Sugahara M, Suzuki M, Masuda T, Kimura T, Thao TN, Yonekura S, Yu LJ, Tosha T, Tono K, Joti Y, Hatsui T, Yabashi M, Kubo M, Iwata S, Isobe H, Yamaguchi K, Suga M, and Shen JR

Subjects
Biocatalysis radiation effects, Calcium metabolism, Crystallography, Electron Transport radiation effects, Electrons, Manganese metabolism, Oxidation-Reduction radiation effects, Protons, Time Factors, Tyrosine metabolism, Water chemistry, Water metabolism, Oxygen chemistry, Oxygen metabolism, Photosystem II Protein Complex chemistry, Photosystem II Protein Complex metabolism, Photosystem II Protein Complex radiation effects
Abstract

Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of S i states (i = 0-4) at the Mn 4 CaO 5 cluster 1-3 , during which an extra oxygen (O6) is incorporated at the S 3 state to form a possible dioxygen 4-7 . Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). Y Z , a tyrosine residue that connects the reaction centre P680 and the Mn 4 CaO 5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca 2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O-O bond formation., (© 2024. The Author(s).)

Published
2024
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49. Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase.

Author

Safari C, Ghosh S, Andersson R, Johannesson J, Båth P, Uwangue O, Dahl P, Zoric D, Sandelin E, Vallejos A, Nango E, Tanaka R, Bosman R, Börjesson P, Dunevall E, Hammarin G, Ortolani G, Panman M, Tanaka T, Yamashita A, Arima T, Sugahara M, Suzuki M, Masuda T, Takeda H, Yamagiwa R, Oda K, Fukuda M, Tosha T, Naitow H, Owada S, Tono K, Nureki O, Iwata S, Neutze R, and Brändén G

Subjects
Catalytic Domain, Crystallography, Oxidation-Reduction, Oxygen metabolism, Electron Transport Complex IV metabolism, Carbon Monoxide chemistry
Abstract

Cytochrome c oxidase (C c O) is part of the respiratory chain and contributes to the electrochemical membrane gradient in mitochondria as well as in many bacteria, as it uses the energy released in the reduction of oxygen to pump protons across an energy-transducing biological membrane. Here, we use time-resolved serial femtosecond crystallography to study the structural response of the active site upon flash photolysis of carbon monoxide (CO) from the reduced heme a 3 of ba 3 -type C c O. In contrast with the aa 3 -type enzyme, our data show how CO is stabilized on Cu B through interactions with a transiently ordered water molecule. These results offer a structural explanation for the extended lifetime of the Cu B -CO complex in ba 3 -type C c O and, by extension, the extremely high oxygen affinity of the enzyme.

Published
2023
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50. Visualizing the DNA repair process by a photolyase at atomic resolution.

Author

Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Müller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, and Tsai MD

Subjects
Catalysis, Crystallography methods, DNA chemistry, DNA radiation effects, Protein Conformation, Ultraviolet Rays, Archaeal Proteins chemistry, Deoxyribodipyrimidine Photo-Lyase chemistry, DNA Repair, Methanosarcina enzymology, Pyrimidine Dimers chemistry
Abstract

Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.

Published
2023
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