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- Woitowich, N. C., et al.
(författare)
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Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome
- 2018
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Ingår i: Iucrj. - : International Union of Crystallography (IUCr). - 2052-2525. ; 5:Part 5, s. 619-634
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Tidskriftsartikel (refereegranskat)abstract
- Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxobacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruitingbody formation of this photomorphogenic bacterium. SaBphP1 lacks a conserved histidine (His) in the chromophore-binding domain that stabilizes the Pr state in the classical BphPs. Instead it contains a threonine (Thr), a feature that is restricted to several myxobacterial phytochromes and is not evolutionarily understood. SaBphP1 structures of the chromophore binding domain (CBD) and the complete photosensory core module (PCM) in wild-type and Thr-to-His mutant forms reveal details of the molecular mechanism of the Pr/Pfr transition associated with the physiological response of this myxobacterium to red light. Specifically, key structural differences in the CBD and PCM between the wild-type and the Thr-to-His mutant involve essential chromophore contacts with proximal amino acids, and point to how the photosignal is transduced through the rest of the protein, impacting the essential enzymatic activity in the photomorphogenic response of this myxobacterium.
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- Edlund, Petra, et al.
(författare)
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The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 angstrom resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 angstrom resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.
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- Nango, E., et al.
(författare)
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A three-dimensional movie of structural changes in bacteriorhodopsin
- 2016
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 354:6319, s. 1552-1557
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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- Kubo, M., et al.
(författare)
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Nanosecond pump-probe device for time-resolved serial femtosecond crystallography developed at SACLA
- 2017
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Ingår i: Journal of Synchrotron Radiation. - : International Union of Crystallography (IUCr). - 1600-5775. ; 24, s. 1086-1091
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Tidskriftsartikel (refereegranskat)abstract
- X-ray free-electron lasers (XFELs) have opened new opportunities for timeresolved X-ray crystallography. Here a nanosecond optical-pump XFEL-probe device developed for time-resolved serial femtosecond crystallography (TRSFX) studies of photo-induced reactions in proteins at the SPring-8 Angstrom Compact free-electron LAser (SACLA) is reported. The optical-fiber-based system is a good choice for a quick setup in a limited beam time and allows pump illumination from two directions to achieve high excitation efficiency of protein microcrystals. Two types of injectors are used: one for extruding highly viscous samples such as lipidic cubic phase (LCP) and the other for pulsed liquid droplets. Under standard sample flow conditions from the viscous-sample injector, delay times from nanoseconds to tens of milliseconds are accessible, typical time scales required to study large protein conformational changes. A first demonstration of a TR-SFX experiment on bacteriorhodopsin in bicelle using a setup with a droplet-type injector is also presented.
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- Han, Y., et al.
(författare)
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Finite element analysis of kinematic behaviour and injuries to pedestrians in vehicle collisions
- 2012
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Ingår i: International Journal of Crashworthiness. - : Informa UK Limited. - 1358-8265 .- 1754-2111. ; 17:2, s. 141-152
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Tidskriftsartikel (refereegranskat)abstract
- In vehicle-to-pedestrian collisions, the characteristics of a vehicle's frontal shape and structural stiffness have a significant influence on the kinematics and injury risk of the pedestrian's body regions. In the present study, the kinematic behaviour and injury risk of the pedestrians were investigated in collisions against vehicles with different frontal shapes. The THUMS (Total HUman Model for Safety) pedestrian finite element (FE) model was used and impacted by three different types of vehicle FE models (passenger car, one-box vehicle and sport-utility vehicle [SUV]) representing the different frontal shapes at 40 km/h. In the simulation with the passenger car-to-pedestrian impact, the pedestrian wrapped around the hood, and the resulting bending moment of the lower extremity and head injury criterion (HIC) value were high. In the simulation with the one-box vehicle-to-pedestrian impact, the pedestrian's upper torso was directly hit by the front end of the vehicle. The pelvis and chest had contact with the stiff vehicle frontal panel, resulting in a high stress being observed on the rib cage. In the simulation with the SUV-to-pedestrian impact, the force of the pelvis was high due to the contact with the vehicle hood's leading edge. The results indicated that the frontal shape of the vehicle has a large effect on the pedestrian kinematic behaviour, including the impact velocity of the pelvis, chest, and head against the vehicle. Moreover, the stiffness of the vehicle structure can affect the deformation mode of the human body segments, such as the lower extremities and the rib cage. The injury predictions for each body region from the FE analyses agreed with observations from pedestrian accidents involving a car, one-box vehicle and SUV, respectively.
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