Yasufumi Umena

Capturing structural intermediates in an animal-like cryptochrome photoreceptor by time-resolved crystallography

Manuel Maestre‐Reyna, Yuhei Hosokawa, Po‐Hsun Wang, Martin Saft et autres

Animal-like cryptochromes are photoreceptors that control circadian rhythm and signaling in many eukaryotes. Transient photoreduction of the cryptochrome flavin chromophore initiated signaling via a poorly understood mechanism. By serial femtosecond crystallography (SFX), we show that the photoreduction mechanism of Chlamydomonas reinhardtii cryptochrome …

tw, jp, de, fr (code pays fourni par la source)

Crystallization and initial X-ray crystallographic analysis of a de novo -designed protein with left-handed βαβ units

Naoki Tomita, Hiroto Murata, Yasufumi Umena, Hiroki Onoda et autres

A newly designed protein featuring a rare left-handed βαβ motif has successfully been crystallized and characterized by preliminary X-ray diffraction. The computational design was conducted using a combination of Rosetta BluePrintBDR , ProteinMPNN and AlphaFold 2, generating eight candidates based on predicted …

jp (code pays fourni par la source)

Electric field-induced volume change in pyro-vanadate-phosphates: Toward an alternative actuator architecture

Kohei Takada, J. Shibutani, Kunio Yagi, Fusao Ikawa et autres

We discovered large electric-field-induced strain in pyro-vanadate-phosphate Cu2−xZnxV1.8P0.2O7. Distinct from conventionally used piezoelectric materials including lead-zirconate-titanate, this material expands almost isotropically at room temperature when an electric field is applied. This volume change, exceeding 1000 ppm under the field of E = …

jp (code pays fourni par la source)

The Blinking of Small-Angle X-ray Scattering Reveals the Degradation Process of Protein Crystals at Microsecond Timescale

Tatsuya Arai, Kazuhiro Mio, Hiroki Onoda, Leonard M. G. Chavas et autres

X-ray crystallography has revolutionized our understanding of biological macromolecules by elucidating their three-dimensional structures. However, the use of X-rays in this technique raises concerns about potential damage to the protein crystals, which results in a quality degradation of the diffraction data even …

jp (code pays fourni par la source)

Biological Advantage of the Arrangements of C-Phycocyanin Chromophores in Phycobilisome from the Electronic Energy Transfer Viewpoint

Kenji Mishima, Mitsuo Shoji, Yasufumi Umena, Yasuteru Shigeta

Abstract In the present study, we report the electronic energy transfer (EET) rate and the EET dynamics in the hexamer of C-phycocyanin (C-PC). The EET rate for the Förster theory was calculated by a quantum chemical method and a master equation was …

jp (code pays fourni par la source)

Observation of energy transfer dynamics in a phycocyanin protein crystal by utilizing femtosecond transient absorption microscopy

Tetsuro Katayama, Shuto Ueda, Yuma Fujita, Yuichiro Akagi et autres

Abstract Energy transfer reactions are important in photosynthetic systems as natural systems and solar cells as artificial systems. Especially in the biological system, the energy transfer reaction from the phycobilisome to the photoreaction system is the essence. Femtosecond transient absorption microscopy was …

jp (code pays fourni par la source)

Development of serial X-ray fluorescence holography for radiation-sensitive protein crystals

Artoni Kevin R. Ang, Yasufumi Umena, Ayana Tomita, Naoya Shibayama et autres

X-ray fluorescence holography (XFH) is a powerful atomic resolution technique capable of directly imaging the local atomic structure around atoms of a target element within a material. Although it is theoretically possible to use XFH to study the local structures of metal …

jp (code pays fourni par la source)

Dynamic interactions in the l-lactate oxidase active site facilitate substrate binding at pH4.5

Naoki Furubayashi, Koji Inaka, Masayuki Kamo, Yasufumi Umena et autres

jp (code pays fourni par la source)

Capturing structural changes of the S 1 to S 2 transition of photosystem II using time-resolved serial femtosecond crystallography

Hongjie Li, Yoshiki Nakajima, Takashi Nomura, Michihiro Sugahara et autres

Photosystem II (PSII) catalyzes light-induced water oxidation through an S i -state cycle, leading to the generation of di-oxygen, protons and electrons. Pump–probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it …

jp (code pays fourni par la source)

Time-Resolved X-ray Crystallography Using Synchrotron Radiation

Ayana Tomita, Yasufumi Umena, Kouhei Ichiyanagi, Ryo Fukaya et autres

‘Softcrystals’ is the name of a group of new functional materials that can cause changes in luminescence properties and crystal phase-transitions by applying relatively weak external fields such as light irradiation, vapor exposure, and mechanical stimuli. The time-scale of these structural transitions …

jp (code pays fourni par la source)

Estimation of the relative contributions to the electronic energy transfer rates based on Förster theory: The case of C-phycocyanin chromophores

Kenji Mishima, Mitsuo Shoji, Yasufumi Umena, Mauro Boero et autres

In the present study, we provide a reformulation of the theory originally proposed by Förster which allows for simple and convenient formulas useful to estimate the relative contributions of transition dipole moments of a donor and acceptor (chemical factors), their orientation factors …

jp, fr (code pays fourni par la source)

放射光X線を用いた時間分解結晶構造解析法

Ayana SATOTOMITA, Yasufumi Umena, Kouhei ICHIYANAGI, Ryo Fukaya et autres