The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The structures reveal a twist of the D-ring, which lead to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signalling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the water dissociation is key to the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light.

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The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

eLife ◽

10.7554/elife.53514 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 13

Author(s):

Elin Claesson ◽

Weixiao Yuan Wahlgren ◽

Heikki Takala ◽

Suraj Pandey ◽

Leticia Castillon ◽

...

Keyword(s):

Signal Transduction ◽

Structural Changes ◽

Red Light ◽

Crystallographic Data ◽

X Ray ◽

Binding Domains ◽

Delay Times

Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light.

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Structural Insights of SARS-CoV-2 Spike Protein from Delta and Omicron Variants

10.1101/2021.12.08.471777 ◽

2021 ◽

Author(s):

Ali Sadek ◽

David Zaha ◽

Mahmoud Salama Ahmed

Keyword(s):

Viral Entry ◽

Structural Changes ◽

Structural Basis ◽

S Protein ◽

Angiotensin Converting Enzyme 2 ◽

X Ray ◽

X Ray Crystallography ◽

Binding Domains ◽

Structural Insights ◽

Sheer Number

Given the continuing heavy toll of the COVID-19 pandemic and the emergence of the Delta (B.1.617.2) and Omicron (B.1.1.529) variants, the WHO declared both as variants of concern (VOC). There are valid concerns that the latest Omicron variant might have increased infectivity and pathogenicity. In addition, the sheer number of S protein mutations in the Omicron variant raise concerns of potential immune evasion and resistance to therapeutics such as monoclonal antibodies. However, structural insights that underpin the potential increased pathogenicity are unknown. Here we adopted an artificial intelligence (AI)-based approach to predict the structural changes induced by mutations of the Delta and Omicron variants in the spike (S) protein using Alphafold. This was followed by docking the human angiotensin-converting enzyme 2 (ACE2) with the predicted S proteins for Wuhan-Hu-1, Delta, and Omicron variants. Our in-silico structural analysis indicates that S protein for Omicron variant has a higher binding affinity to ACE-2 receptor, compared to Wuhan-Hu-1 and Delta variants. In addition, the recognition sites of the receptor binding domains for Delta and Omicron variants showed lower electronegativity compared to Wuhan-Hu-1. Importantly, further molecular insights revealed significant changes induced at fusion protein (FP) site, which may mediate enhanced viral entry. These results represent the first computational analysis of structural changes associated with Omicron variant using Alphafold, Collectively, our results highlight potential structural basis for enhanced pathogenicity of the Omicron variant, however further validation using X-ray crystallography and cryo-EM are warranted.

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Structural Changes during the Growth of Atomically Precise Metal Oxido Nanoclusters from Combined Pair Distribution Function and Small‐Angle X‐ray Scattering Analysis

Angewandte Chemie International Edition ◽

10.1002/anie.202107902 ◽

2021 ◽

Author(s):

Andy S. Anker ◽

Troels Lindahl Christiansen ◽

Marcus Weber ◽

Martin Schmiele ◽

Erik Brok ◽

...

Keyword(s):

Distribution Function ◽

Small Angle ◽

Pair Distribution Function ◽

Structural Changes ◽

X Ray ◽

X Ray Scattering ◽

Ray Scattering

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Preliminary X-ray crystallographic data on mouse submaxillary gland renin and renin-inhibitor complexes.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)90804-5 ◽

1984 ◽

Vol 259 (20) ◽

pp. 12714-12717

Author(s):

M A Navia ◽

J P Springer ◽

M Poe ◽

J Boger ◽

K Hoogsteen

Keyword(s):

Submaxillary Gland ◽

Crystallographic Data ◽

Renin Inhibitor ◽

X Ray ◽

Mouse Submaxillary Gland

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Pore Modification and Phosphorus Doping Effect on Phosphoric Acid-Activated Fe-N-C for Alkaline Oxygen Reduction Reaction

Nanomaterials ◽

10.3390/nano11061519 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1519

Author(s):

Jong Gyeong Kim ◽

Sunghoon Han ◽

Chanho Pak

Keyword(s):

Phosphoric Acid ◽

Photoelectron Spectroscopy ◽

Structural Changes ◽

Electronic States ◽

Nitrogen Adsorption ◽

Reduction Reaction ◽

Phosphorus Doping ◽

X Ray ◽

Precious Metal Catalysts ◽

Adsorption Desorption

The price and scarcity of platinum has driven up the demand for non-precious metal catalysts such as Fe-N-C. In this study, the effects of phosphoric acid (PA) activation and phosphorus doping were investigated using Fe-N-C catalysts prepared using SBA-15 as a sacrificial template. The physical and structural changes caused by the addition of PA were analyzed by nitrogen adsorption/desorption and X-ray diffraction. Analysis of the electronic states of Fe, N, and P were conducted by X-ray photoelectron spectroscopy. The amount and size of micropores varied depending on the PA content, with changes in pore structure observed using 0.066 g of PA. The electronic states of Fe and N did not change significantly after treatment with PA, and P was mainly found in states bonded to oxygen or carbon. When 0.135 g of PA was introduced per 1 g of silica, a catalytic activity which was increased slightly by 10 mV at −3 mA/cm2 was observed. A change in Fe-N-C stability was also observed through the introduction of PA.

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X-ray computed tomography characterization of soil and rock mixture under cyclic triaxial testing: the effects of confining pressure on meso-structural changes

Environmental Earth Sciences ◽

10.1007/s12665-019-8161-z ◽

2019 ◽

Vol 78 (6) ◽

Author(s):

Y. Wang ◽

D. Zhang ◽

Y. Z. Hu

Keyword(s):

Computed Tomography ◽

Structural Changes ◽

Confining Pressure ◽

Triaxial Testing ◽

Cyclic Triaxial ◽

X Ray ◽

X Ray Computed

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Structural Changes in French VF Treatment Wetland Porous Media during the Rest Period: An Ex Situ Study Using X-ray Tomography

Water ◽

10.3390/w13030389 ◽

2021 ◽

Vol 13 (3) ◽

pp. 389

Author(s):

German Dario Martinez-Carvajal ◽

Laurent Oxarango ◽

Jérôme Adrien ◽

Pascal Molle ◽

Nicolas Forquet

Keyword(s):

Porous Media ◽

Structural Changes ◽

Rest Period ◽

Treatment Wetlands ◽

Ex Situ ◽

Initial Value ◽

Treatment Wetland ◽

X Ray ◽

The Impact ◽

Deposit Layer

Clogging constitutes a major operational issue for treatment wetlands. The rest period is a key feature of French Vertical Flow (VF) treatment wetlands and serves to mitigate clogging. An ex-situ drying experiment was performed to mimic the rest period and record structural changes in the porous media using X-ray Computed Tomography (CT). Samples containing the deposit and gravel layers of a first stage French VF treatment wetland were extracted and left to dry in a control environment. Based on CT scans, three phases were identified (voids, biosolids, and gravels). The impact of the rest period was assessed by means of different pore-scale variables. Ultimately, the volume of biosolids had reduced to 58% of its initial value, the deposit layer thickness dropped to 68% of its initial value, and the void/biosolid specific surface area ratio increased from a minimum value of 1.1 to a maximum of 4.2. Cracks greater than 3 mm developed at the uppermost part of the deposit layer, while, in the gravel layer, the rise in void volume corresponds to pores smaller than 2 mm in diameter. Lastly, the air-filled microporosity is estimated to have increased by 0.11 v/v.

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