The Shimadzu Encouragement Prize is awarded to researchers who are under the age of 45 and affiliated with research institutes in Japan. The prize recognizes their significant contributions in fundamental and applied/practical research, particularly on scientific measurement. Their research is expected to be further developed and make a valuable impact on science and technology.

Research title:

Development of data processing methods to improve temporal and spatial resolution of structural biology and capture atomic motion

 Structural biology aims to determine three-dimensional structures of biomolecules such as proteins and contributes to the understanding of their mechanisms. It also benefits the design of pharmaceuticals and agrochemicals that modulate their functions. Existing methods of structural biology had limitations in studying membrane proteins, large complexes and/or those with structural or compositional heterogeneities. It was difficult to study dynamic structural transitions. Single Particle Analysis (SPA) with cryo-electron microscopes and Serial Femtosecond Crystallography (SFX) with X-ray free electron lasers are new measurement techniques that overcome these difficulties.

 Dr. Nakane has been working on data processing methods for these new approaches. He is one of the developers of RELION, an open-source software package for SPA, and improved spatial resolution by modeling and correcting lens aberrations, magnification anisotropy and Ewald sphere curvatures, which had been ignored or crudely approximated before. He achieved the true atomic resolution in protein SPA for the first time and resolved hydrogen atoms. He also developed the MultiBody refinement, which can analyze continuous molecular flexibilities. In SFX, he established data processing protocols that can capture weak signals and enabled experimental phasing and time-resolved experiments from fewer crystals in a shorter time than before. He set up a data processing pipeline at SACLA, the Japanese XFEL facility.

 In collaboration with biologists, he processed datasets of many proteins important for biomedicine and clean energy, including photosystem II involved in photosynthesis, bacteriorhodopsin, a light-driven proton pump and the spike protein of the SARS-CoV-2 coronavirus. His programs are distributed under open-source licenses and used by both academic institutes and pharmaceutical companies all over the world.

Message from the prize recipient:

 It is my great pleasure to have my contributions to data processing methods recognized in this award. I would like to thank all my collaborators who have worked with me and/or provided interesting datasets.

 Since joining the Institute for Protein Research, I have been working on MicroED, a new electron-microscopy technique to determine three-dimensional chemical structures, in addition to SFX and SPA. I am also building computer clusters and maintaining raw data repositories dedicated to structure biology and chemistry datasets. I am committed to leveraging the interdisciplinary environment of the IPR, where not only biologists but also chemists and computational scientists collaborate, and strive to advance data processing methods and promote open science.

Related links

https://www.shimadzu.co.jp/ssf/news/2023/news20231206-2.html
(in Japanese)