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A three-dimensional movie of structural changes in bacteriorhodopsin
Nango, Eriko,Royant, Antoine,Kubo, Minoru,Nakane, Takanori,Wickstrand, Cecilia,Kimura, Tetsunari,Tanaka, Tomoyuki,Tono, Kensuke,Song, Changyong,Tanaka, Rie,Arima, Toshi,Yamashita, Ayumi,Kobayashi, Jun American Association for the Advancement of Scienc 2016 Science Vol.354 No.6319
<P>Bacteriorhodopsin (bR) is a light-driven proton pump and a model membrane transport protein. We used time-resolved serial femtosecond crystallography at an x-ray free electron laser to visualize conformational changes in bR from nanoseconds to milliseconds following photoactivation. An initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. The resulting cascade of structural changes throughout the protein shows how motions are choreographed as bR transports protons uphill against a transmembrane concentration gradient.</P>
Grease matrix as a versatile carrier of proteins for serial crystallography
Sugahara, Michihiro,Mizohata, Eiichi,Nango, Eriko,Suzuki, Mamoru,Tanaka, Tomoyuki,Masuda, Tetsuya,Tanaka, Rie,Shimamura, Tatsuro,Tanaka, Yoshiki,Suno, Chiyo,Ihara, Kentaro,Pan, Dongqing,Kakinouchi, Ke Nature Publishing Group 2015 NATURE METHODS Vol. No.
Serial femtosecond X-ray crystallography (SFX) has revolutionized atomic-resolution structural investigation by expanding applicability to micrometer-sized protein crystals, even at room temperature, and by enabling dynamics studies. However, reliable crystal-carrying media for SFX are lacking. Here we introduce a grease-matrix carrier for protein microcrystals and obtain the structures of lysozyme, glucose isomerase, thaumatin and fatty acid–binding protein type 3 under ambient conditions at a resolution of or finer than 2 Å.
Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography
Fukuda, Yohta,Tse, Ka Man,Nakane, Takanori,Nakatsu, Toru,Suzuki, Mamoru,Sugahara, Michihiro,Inoue, Shigeyuki,Masuda, Tetsuya,Yumoto, Fumiaki,Matsugaki, Naohiro,Nango, Eriko,Tono, Kensuke,Joti, Yasumas National Academy of Sciences 2016 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.113 No.11
<P>Proton-coupled electron transfer (PCET), a ubiquitous phenomenon in biological systems, plays an essential role in copper nitrite reductase (CuNiR), the key metalloenzyme in microbial denitrification of the global nitrogen cycle. Analyses of the nitrite reduction mechanism in CuNiR with conventional synchrotron radiation crystallography (SRX) have been faced with difficulties, because X-ray photoreduction changes the native structures of metal centers and the enzyme-substrate complex. Using serial femtosecond crystallography (SFX), we determined the intact structures of CuNiR in the resting state and the nitrite complex (NC) state at 2.03- and 1.60-angstrom resolution, respectively. Furthermore, the SRX NC structure representing a transient state in the catalytic cycle was determined at 1.30-angstrom resolution. Comparison between SRX and SFX structures revealed that photoreduction changes the coordination manner of the substrate and that catalytically important His255 can switch hydrogen bond partners between the backbone carbonyl oxygen of nearby Glu279 and the side-chain hydroxyl group of Thr280. These findings, which SRX has failed to uncover, propose a redox-coupled proton switch for PCET. This concept can explain how proton transfer to the substrate is involved in intramolecular electron transfer and why substrate binding accelerates PCET. Our study demonstrates the potential of SFX as a powerful tool to study redox processes in metalloenzymes.</P>