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, Toshio; Yamashita, A.; Kobayashi, Jun; Hosaka, Toshiaki; Mizohata, Eiichi; Nogly, Przemyslaw; Sugahara, Michihiro; Nam, Daewoong; Nomura, Takashi; Shimamura, Tatsuro; Im, Dohyun; Fujiwara, Takaaki; Yamanaka, Y.; Jeon, Byeonghyun; Nishizawa, Takashi; Oda, Kazumasa; Fukuda, Masahiro; Andersson, Rebecka; Båth, Petra; Dods, Robert; Davidsson, Jan; Matsuoka, Shigeru; Kawatake, Satoshi; Murata, Michio; Nureki, Osamu; Owada, Shigeki; Kameshima, Takashi; Hatsui, Takaki; Joti, Yasumasa; Schertler, Gebhard F. X.; Yabashi, Makina; Bondar, Ana‐Nicoleta; Standfuss, Jörg; Neutze, Richard; Iwata, So

doi:10.1126/science.aah3497

Cited by 366 publications

(404 citation statements)

References 76 publications

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“…Using positive displacement extrusion, a variety of high viscosity materials including the lipidic cubic phase (LCP) matrix used in membrane protein crystallization (Figure 7(d)), 27,141,147,161,163,[171][172][173][174] a grease matrix, [175][176][177] agarose, 178 and hyaluronic acid have been used as carrier materials for serial crystallography. 179 In these methods, the aqueous slurry of crystals is mixed with the higher viscosity component.…”

Section: Viscous Media Extrusionmentioning

confidence: 99%

“…Examples include photolysis-induced dissociation of CO from myoglobin 207,208 and the photocycles of photoactive yellow protein (PYP), 19,199,200,[209][210][211][212][213][214][215] photosystem II, 22,165-167 and bacteriorhodopsin. 174 It is also possible to use laser triggering to initiate a reaction through the photorelease of a caged compound. 202,216 However, many caged compounds suffer from poor solubility, and the resulting rate of initiation is limited by the rate of diffusion.…”

Section: A Laser Triggeringmentioning

confidence: 99%

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Microfluidics: From crystallization to serial time-resolved crystallography

Sui

Perry

2017

Structural Dynamics

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Capturing protein structural dynamics in real-time has tremendous potential in elucidating biological functions and providing information for structure-based drug design. While time-resolved structure determination has long been considered inaccessible for a vast majority of protein targets, serial methods for crystallography have remarkable potential in facilitating such analyses. Here, we review the impact of microfluidic technologies on protein crystal growth and X-ray diffraction analysis. In particular, we focus on applications of microfluidics for use in serial crystallography experiments for the time-resolved determination of protein structural dynamics.

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Section: Viscous Media Extrusionmentioning

confidence: 99%

Section: A Laser Triggeringmentioning

confidence: 99%

Microfluidics: From crystallization to serial time-resolved crystallography

Sui

Perry

2017

Structural Dynamics

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“…The TR-SFX method was also used to determine conformational changes in bacteriorhodopsin (bR), a light-driven proton pump, and a model membrane transport protein, at 13 time points in a scale ranging from nanoseconds to milliseconds following photo activation [12]. The resulting molecular movie elucidated a fundamental mechanism for directional proton transport in bR.…”

Section: Recent Scientific Highlights and New Instrumentsmentioning

confidence: 99%

“…To enable this, we employed unique accelerator technologies: a low emittance injector with a thermionic electron gun (e-gun) and a velocity bunching system; a high-gradient normal-conducting C-band linac; and a short-period in-vacuum undulator [4]. Combining these devices with state-of-the-art X-ray optics [5,6], we have steadily generated XFEL light for users more than 4000 h in FY2016, allowing researchers to produce a number of important scientific results in the fields of biology [7][8][9][10][11][12], chemistry [13][14][15][16], materials science [17][18][19][20], high-energy density science [21], and non-linear X-ray optics [22][23][24][25][26]. The success of SACLA has promoted the development of similar compact XFEL facilities, such as SwissFEL at Paul Scherrer Institut in Switzerland [27].…”

Section: Introductionmentioning

confidence: 99%

Status of the SACLA Facility

et al. 2017

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Abstract:This article reports the current status of SACLA, SPring-8 Angstrom Compact free electron LAser, which has been producing stable X-ray Free Electron Laser (XFEL) light since 2012. A unique injector system and a short-period in-vacuum undulator enable the generation of ultra-short coherent X-ray pulses with a wavelength shorter than 0.1 nm. Continuous development of accelerator technologies has steadily improved XFEL performance, not only for normal operations but also for fast switching operation of the two beamlines. After upgrading the broadband spontaneous-radiation beamline to produce soft X-ray FEL with a dedicated electron beam driver, it is now possible to operate three FEL beamlines simultaneously. Beamline/end-station instruments and data acquisition/analyzation systems have also been upgraded to allow advanced experiments. These efforts have led to the production of novel results and will offer exciting new opportunities for users from many fields of science.

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“…However, the structural information acquired with these three structural methods is limited to static snapshots of proteins. An X-ray-free electron laser can break this limitation and reveal the time-resolved atomic structure of proteins (Nango et al 2016), but it is only applicable to limited targets.…”

Section: Introductionmentioning

confidence: 99%

Directly watching biomolecules in action by high-speed atomic force microscopy

Ando

2017

Biophys Rev

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Proteins are dynamic in nature and work at the single molecule level. Therefore, directly watching protein molecules in dynamic action at high spatiotemporal resolution must be the most straightforward approach to understanding how they function. To make this observation possible, highspeed atomic force microscopy (HS-AFM) has been developed. Its current performance allows us to film biological molecules at 10-16 frames/s, without disturbing their function. In fact, dynamic structures and processes of various proteins have been successfully visualized, including bacteriorhodopsin responding to light, myosin V walking on actin filaments, and even intrinsically disordered proteins undergoing order/disorder transitions. The molecular movies have provided insights that could not have been reached in other ways. Moreover, the cantilever tip can be used to manipulate molecules during successive imaging. This capability allows us to observe changes in molecules resulting from dissection or perturbation. This mode of imaging has been successfully applied to myosin V, peroxiredoxin and doublet microtubules, leading to new discoveries. Since HS-AFM can be combined with other techniques, such as super-resolution optical microscopy and optical tweezers, the usefulness of HS-AFM will be further expanded in the near future.

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A three-dimensional movie of structural changes in bacteriorhodopsin

Cited by 366 publications

References 76 publications

Microfluidics: From crystallization to serial time-resolved crystallography

Microfluidics: From crystallization to serial time-resolved crystallography

Status of the SACLA Facility

Directly watching biomolecules in action by high-speed atomic force microscopy

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