scholarly journals Crystal structure of a far-red–sensing cyanobacteriochrome reveals an atypical bilin conformation and spectral tuning mechanism

2021 ◽  
Vol 118 (12) ◽  
pp. e2025094118
Author(s):  
Sepalika Bandara ◽  
Nathan C. Rockwell ◽  
Xiaoli Zeng ◽  
Zhong Ren ◽  
Cong Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Room Temperature ◽  
Uv Light ◽  
Bathochromic Shift ◽  
Red Light ◽  
Site Directed Mutagenesis ◽  
Tuning Mechanism ◽  
Pi Conjugated ◽  
Adaptive Processes ◽  
Serial Crystallography

Cyanobacteriochromes (CBCRs) are small, linear tetrapyrrole (bilin)-binding photoreceptors in the phytochrome superfamily that regulate diverse light-mediated adaptive processes in cyanobacteria. More spectrally diverse than canonical red/far-red–sensing phytochromes, CBCRs were thought to be restricted to sensing visible and near UV light until recently when several subfamilies with far-red–sensing representatives (frCBCRs) were discovered. Two of these frCBCRs subfamilies have been shown to incorporate bilin precursors with larger pi-conjugated chromophores, while the third frCBCR subfamily uses the same phycocyanobilin precursor found in the bulk of the known CBCRs. To elucidate the molecular basis of far-red light perception by this third frCBCR subfamily, we determined the crystal structure of the far-red–absorbing dark state of one such frCBCR Anacy_2551g3 from Anabaena cylindrica PCC 7122 which exhibits a reversible far-red/orange photocycle. Determined by room temperature serial crystallography and cryocrystallography, the refined 2.7-Å structure reveals an unusual all-Z,syn configuration of the phycocyanobilin (PCB) chromophore that is considerably less extended than those of previously characterized red-light sensors in the phytochrome superfamily. Based on structural and spectroscopic comparisons with other bilin-binding proteins together with site-directed mutagenesis data, our studies reveal protein–chromophore interactions that are critical for the atypical bathochromic shift. Based on these analyses, we propose that far-red absorption in Anacy_2551g3 is the result of the additive effect of two distinct red-shift mechanisms involving cationic bilin lactim tautomers stabilized by a constrained all-Z,syn conformation and specific interactions with a highly conserved anionic residue.

scholarly journals Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome

2009 ◽  
Vol 106 (37) ◽  
pp. 15639-15644 ◽  
Author(s):  
Xiaojing Yang ◽  
Jane Kuk ◽  
Keith Moffat
Keyword(s):  
Crystal Structure ◽  
Pseudomonas Aeruginosa ◽  
Crystal Packing ◽  
Red Light ◽  
Binding Pocket ◽  
Site Directed Mutagenesis ◽  
Light Responses ◽  
Propionate Group ◽  
Core Module ◽  
Absorbing States

Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria by means of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here, we report the crystal structure of the Q188L mutant of Pseudomonas aeruginosa bacteriophytochrome (PaBphP) photosensory core module, which exhibits altered photoconversion behavior and different crystal packing from wild type. We observe two distinct chromophore conformations in the Q188L crystal structure that we identify with the Pfr and Pr states. The Pr/Pfr compositions, varying from crystal to crystal, seem to correlate with light conditions under which the Q188L crystals are cryoprotected. We also compare all known Pr and Pfr structures. Using site-directed mutagenesis, we identify residues that are involved in stabilizing the 15Ea (Pfr) and 15Za (Pr) configurations of the biliverdin chromophore. Specifically, Ser-261 appears to be essential to form a stable Pr state in PaBphP, possibly by means of its interaction with the propionate group of ring C. We propose a “flip-and-rotate” model that summarizes the major conformational differences between the Pr and Pfr states of the chromophore and its binding pocket.

scholarly journals Room temperature synthesis of low-dimensional rubidium copper halide colloidal nanocrystals with near unity photoluminescence quantum yield

Nanoscale ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 59-65
Author(s):  
Parth Vashishtha ◽  
Thomas J. N. Hooper ◽  
Yanan Fang ◽  
Deviana Kathleen ◽  
David Giovanni ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Quantum Yield ◽  
Room Temperature ◽  
Uv Light ◽  
Colloidal Nanocrystals ◽  
Temperature Synthesis ◽  
Copper Halide ◽  
One Dimensional ◽  
Photoluminescence Quantum Yield ◽  
Low Dimensional

Demonstration of Rb2CuX3 (X = Br, Cl) colloidal nanocrystals under UV light with a representation of one-dimensional Rb2CuBr3 crystal structure.

scholarly journals Photosensing and Characterizing of the Pristine and In-, Sn-Doped Bi2Se3 Nanoplatelets Fabricated by Thermal V–S Process

Nanomaterials ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1352
Author(s):  
Chih-Chiang Wang ◽  
Fuh-Sheng Shieu ◽  
Han C. Shih
Keyword(s):  
Crystal Structure ◽  
Uv Light ◽  
Red Light ◽  
Optical Bandgap ◽  
Detection Sensitivity ◽  
Thermal Cvd ◽  
Good Surface ◽  
Photo Detection ◽  
Surface Conduction ◽  
Photocurrent Decay

Pristine, and In-, Sn-, and (In, Sn)-doped Bi2Se3 nanoplatelets synthesized on Al2O3(100) substrate by a vapor–solid mechanism in thermal CVD process via at 600 °C under 2 × 10−2 Torr. XRD and HRTEM reveal that In or Sn dopants had no effect on the crystal structure of the synthesized rhombohedral-Bi2Se3. FPA–FTIR reveals that the optical bandgap of doped Bi2Se3 was 26.3%, 34.1%, and 43.7% lower than pristine Bi2Se3. XRD, FESEM–EDS, Raman spectroscopy, and XPS confirm defects (In3+Bi3+), (In3+V0), (Sn4+Bi3+), (V0Bi3+), and (Sn2+Bi3+). Photocurrent that was generated in (In,Sn)-doped Bi2Se3 under UV(8 W) and red (5 W) light revealed stable photocurrents of 5.20 × 10−10 and 0.35 × 10−10 A and high Iphoto/Idark ratios of 30.7 and 52.2. The rise and fall times of the photocurrent under UV light were 4.1 × 10−2 and 6.6 × 10−2 s. Under UV light, (In,Sn)-dopedBi2Se3 had 15.3% longer photocurrent decay time and 22.6% shorter rise time than pristine Bi2Se3, indicating that (In,Sn)-doped Bi2Se3 exhibited good surface conduction and greater photosensitivity. These results suggest that In, Sn, or both dopants enhance photodetection of pristine Bi2Se3 under UV and red light. The findings also suggest that type of defect is a more important factor than optical bandgap in determining photo-detection sensitivity. (In,Sn)-doped Bi2Se3 has greater potential than undoped Bi2Se3 for use in UV and red-light photodetectors.

scholarly journals 2′-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography

2021 ◽  
Vol 118 (21) ◽  
pp. e2100170118
Author(s):  
Mateusz Wilamowski ◽  
Darren A. Sherrell ◽  
George Minasov ◽  
Youngchang Kim ◽  
Ludmilla Shuvalova ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Untranslated Region ◽  
Drug Target ◽  
Room Temperature ◽  
Fixed Target ◽  
Methyltransferase Activity ◽  
Before And After ◽  
Viral Proliferation ◽  
Serial Crystallography

The genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus has a capping modification at the 5′-untranslated region (UTR) to prevent its degradation by host nucleases. These modifications are performed by the Nsp10/14 and Nsp10/16 heterodimers using S-adenosylmethionine as the methyl donor. Nsp10/16 heterodimer is responsible for the methylation at the ribose 2′-O position of the first nucleotide. To investigate the conformational changes of the complex during 2′-O methyltransferase activity, we used a fixed-target serial synchrotron crystallography method at room temperature. We determined crystal structures of Nsp10/16 with substrates and products that revealed the states before and after methylation, occurring within the crystals during the experiments. Here we report the crystal structure of Nsp10/16 in complex with Cap-1 analog (m7GpppAm2′-O). Inhibition of Nsp16 activity may reduce viral proliferation, making this protein an attractive drug target.

scholarly journals Molecular Basis of Far-red Sensing in Cyanobacteriochrome

2020 ◽  
Author(s):  
Sepalika Bandara ◽  
Nathan Rockwell ◽  
Xiaoli Zeng ◽  
Zhong Ren ◽  
Cong Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Basis ◽  
Binding Proteins ◽  
Red Light ◽  
Adaptive Responses ◽  
Deep Tissue ◽  
Adaptive Processes ◽  
Competition For Light ◽  
Light Capture

AbstractCyanobacteriochromes are small, panchromatic photoreceptors in the phytochrome superfamily that regulate diverse light-mediated adaptive processes in cyanobacteria. The molecular basis of far-red (FR) light perception by cyanobacteriochromes is currently unknown. Here we report the crystal structure of a far-red-sensing cyanobacteriochrome from Anabaena cylindrica PCC 7122, which exhibits a reversible far-red/orange photocycle. The 2.7 Å structure of its FR-absorbing dark state, determined by room temperature serial crystallography and cryo-crystallography, reveals an all-Z,syn configuration of its bound linear tetrapyrrole (bilin) chromophore that is less extended than the bilin chromophores of all known phytochromes. Based on structural comparisons with other bilin-binding proteins and extensive spectral analyses on mutants, we identify key protein-chromophore interactions that enable far-red sensing in bilin-binding proteins. We propose that FR-CBCRs employ two distinct tuning mechanisms, which work together to produce a large batho-chromatic shift. Findings of this work have important implications for development and improvement of photoproteins with far-red absorption and fluorescence.Significance StatementPhytochromes are well known far-red-light sensors found in plants that trigger adaptive responses to facilitate competition for light capture with neighboring plants. Red- and far-red-sensing are critical to cyanobacteria living in the far-red-enriched shade of plants. Here we report the crystal structure of a far-red-sensing cyanobacteriochrome, a distant cyanobacterial relative of phytochrome. These studies shed insight into the poorly understood molecular basis of far-red-sensing by phytobilin-based photoreceptors. Owing to the deep tissue penetration of far-red light, far-red-sensing photoreceptors offer promising protein scaffolds for developing gene-based photoswitches, optoacoustic contrast agents and fluorescent probes for in situ imaging and optogenetic applications.

Single Crystal Growth of High-Pressure Phases of Ice and Salt Hydrate Far Below the Original Melting Point by Mixing Alcohol: Crystal Structure Determination of Magnesium Chloride Heptahydrate

2020 ◽  
Author(s):  
Keishiro Yamashita ◽  
Kazuki Komatsu ◽  
Hiroyuki Kagi
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Crystal Growth ◽  
Single Crystal ◽  
Room Temperature ◽  
Growth Technique ◽  
Salt Hydrate ◽  
X Ray

An crystal-growth technique for single crystal x-ray structure analysis of high-pressure forms of hydrogen-bonded crystals is proposed. We used alcohol mixture (methanol: ethanol = 4:1 in volumetric ratio), which is a widely used pressure transmitting medium, inhibiting the nucleation and growth of unwanted crystals. In this paper, two kinds of single crystals which have not been obtained using a conventional experimental technique were obtained using this technique: ice VI at 1.99 GPa and MgCl<sub>2</sub>·7H<sub>2</sub>O at 2.50 GPa at room temperature. Here we first report the crystal structure of MgCl2·7H2O. This technique simultaneously meets the requirement of hydrostaticity for high-pressure experiments and has feasibility for further in-situ measurements.

scholarly journals Crystal structure of K[Hg(SCN)3] – a redetermination

2014 ◽  
Vol 70 (9) ◽  
pp. i46-i46 ◽  
Author(s):  
Matthias Weil ◽  
Thomas Häusler
Keyword(s):  
Crystal Structure ◽  
Room Temperature ◽  
Three Dimensional ◽  
Lattice Parameters ◽  
Bond Lengths ◽  
Dimensional Network ◽  
Anisotropic Displacement Parameters ◽  
Precision And Accuracy ◽  
Standard Deviations ◽  
Atomic Coordinates

The crystal structure of the room-temperature modification of K[Hg(SCN)3], potassium trithiocyanatomercurate(II), was redetermined based on modern CCD data. In comparison with the previous report [Zhdanov & Sanadze (1952).Zh. Fiz. Khim.26, 469–478], reliability factors, standard deviations of lattice parameters and atomic coordinates, as well as anisotropic displacement parameters, were revealed for all atoms. The higher precision and accuracy of the model is, for example, reflected by the Hg—S bond lengths of 2.3954 (11), 2.4481 (8) and 2.7653 (6) Å in comparison with values of 2.24, 2.43 and 2.77 Å. All atoms in the crystal structure are located on mirror planes. The Hg2+cation is surrounded by four S atoms in a seesaw shape [S—Hg—S angles range from 94.65 (2) to 154.06 (3)°]. The HgS4polyhedra share a common S atom, building up chains extending parallel to [010]. All S atoms of the resulting1∞[HgS2/1S2/2] chains are also part of SCN−anions that link these chains with the K+cations into a three-dimensional network. The K—N bond lengths of the distorted KN7polyhedra lie between 2.926 (2) and 3.051 (3) Å.

scholarly journals Color-tuning of natural variants of heliorhodopsin

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Se-Hwan Kim ◽  
Kimleng Chuon ◽  
Shin-Gyu Cho ◽  
Ahreum Choi ◽  
Seanghun Meas ◽  
...  
Keyword(s):  
3D Structure ◽  
Site Directed Mutagenesis ◽  
Type I ◽  
Transmembrane Helices ◽  
Color Tuning ◽  
Tuning Mechanism ◽  
Spectral Changes ◽  
His Tag ◽  
Natural Variants ◽  
Retinal Chromophore

AbstractMicrobial rhodopsins are distributed through many microorganisms. Heliorhodopsins are newly discovered but have an unclear function. They have seven transmembrane helices similar to type-I and type-II rhodopsins, but they are different in that the N-terminal region of heliorhodopsin is cytoplasmic. We chose 13 representative heliorhodopsins from various microorganisms, expressed and purified with an N-terminal His tag, and measured the absorption spectra. The 13 natural variants had an absorption maximum (λmax) in the range 530–556 nm similar to proteorhodopsin (λmax = 490–525 nm). We selected several candidate residues that influence rhodopsin color-tuning based on sequence alignment and constructed mutants via site-directed mutagenesis to confirm the spectral changes. We found two important residues located near retinal chromophore that influence λmax. We also predict the 3D structure via homology-modeling of Thermoplasmatales heliorhodopsin. The results indicate that the color-tuning mechanism of type-I rhodopsin can be applied to understand the color-tuning of heliorhodopsin.

Synthesis, crystal structure, luminescence, and photocatalytic properties of a 2D Cu(II) metal-organic frameworks based on 3,5-di(1H-benzimidazol-1-yl)pyridine and 4,4′-oxybis(benzoate) ligands

2020 ◽  
Vol 75 (8) ◽  
pp. 727-732
Author(s):  
Chen Zhang ◽  
Jian-Qing Tao
Keyword(s):  
Crystal Structure ◽  
Thermal Analysis ◽  
Uv Light ◽  
Metal Organic Framework ◽  
Metal Organic Frameworks ◽  
X Ray Diffraction ◽  
X Ray ◽  
Uv Light Irradiation ◽  
Photocatalytic Activities ◽  
Metal Organic

AbstractA new Cu(II) metal-organic framework, [Cu(L)(OBA)·H2O]n (1) [H2OBA = 4,4′-oxybis(benzoic acid), L = 3,5-di(1H-benzimidazol-1-yl)pyridine] was hydrothermally synthesized and characterized through IR spectroscopy, elemental and thermal analysis and single-crystal X-ray diffraction. Complex 1 is a four-connected uni-nodal 2D net with a (44·62) topology which shows an emission centered at λ ∼393 nm upon excitation at λ = 245 nm. Moreover, complex 1 possesses high photocatalytic activities for the decomposition of Rhodamine B (RhB) under UV light irradiation.

scholarly journals Exploring the Structural Chemistry of Pyrophosphoramides: N,N′,N″,N‴-Tetraisopropylpyrophosphoramide

Chemistry ◽  
2021 ◽  
Vol 3 (1) ◽  
pp. 149-163
Author(s):  
Duncan Micallef ◽  
Liana Vella-Zarb ◽  
Ulrich Baisch
Keyword(s):  
Crystal Structure ◽  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Hydrogen Bonding ◽  
Nmr Spectroscopy ◽  
Ir Spectroscopy ◽  
Room Temperature ◽  
Intermolecular Hydrogen Bonding ◽  
X Ray Diffraction ◽  
X Ray

N,N′,N″,N‴-Tetraisopropylpyrophosphoramide 1 is a pyrophosphoramide with documented butyrylcholinesterase inhibition, a property shared with the more widely studied octamethylphosphoramide (Schradan). Unlike Schradan, 1 is a solid at room temperature making it one of a few known pyrophosphoramide solids. The crystal structure of 1 was determined by single-crystal X-ray diffraction and compared with that of other previously described solid pyrophosphoramides. The pyrophosphoramide discussed in this study was synthesised by reacting iso-propyl amine with pyrophosphoryl tetrachloride under anhydrous conditions. A unique supramolecular motif was observed when compared with previously published pyrophosphoramide structures having two different intermolecular hydrogen bonding synthons. Furthermore, the potential of a wider variety of supramolecular structures in which similar pyrophosphoramides can crystallise was recognised. Proton (1H) and Phosphorus 31 (31P) Nuclear Magnetic Resonance (NMR) spectroscopy, infrared (IR) spectroscopy, mass spectrometry (MS) were carried out to complete the analysis of the compound.

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