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

Basudev Maity (), Mitsuo Shoji (), Fangjia Luo, Takanori Nakane, Satoshi Abe, Shigeki Owada, Jungmin Kang, Kensuke Tono, Rie Tanaka, Thuc Toan Pham, Mariko Kojima, Yuki Hishikawa, Junko Tanaka, Jiaxin Tian, Misaki Nagama, Taiga Suzuki, Hiroki Noya, Yuto Nakasuji, Asuka Asanuma, Xinchen Yao, So Iwata, Yasuteru Shigeta, Eriko Nango () and Takafumi Ueno ()
Additional contact information
Basudev Maity: Tokyo Institute of Technology
Mitsuo Shoji: University of Tsukuba
Fangjia Luo: JASRI
Takanori Nakane: Osaka University
Satoshi Abe: Tokyo Institute of Technology
Shigeki Owada: JASRI
Jungmin Kang: RIKEN SPring-8 Center
Kensuke Tono: JASRI
Rie Tanaka: RIKEN SPring-8 Center
Thuc Toan Pham: Tokyo Institute of Technology
Mariko Kojima: Tokyo Institute of Technology
Yuki Hishikawa: Tokyo Institute of Technology
Junko Tanaka: Tokyo Institute of Technology
Jiaxin Tian: Tokyo Institute of Technology
Misaki Nagama: Tokyo Institute of Technology
Taiga Suzuki: Tokyo Institute of Technology
Hiroki Noya: Tokyo Institute of Technology
Yuto Nakasuji: Tokyo Institute of Technology
Asuka Asanuma: Tokyo Institute of Technology
Xinchen Yao: Tokyo Institute of Technology
So Iwata: RIKEN SPring-8 Center
Yasuteru Shigeta: University of Tsukuba
Eriko Nango: RIKEN SPring-8 Center
Takafumi Ueno: Tokyo Institute of Technology

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-49814-9

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