keyword
https://read.qxmd.com/read/38512071/mononuclear-binding-and-catalytic-activity-of-europium-iii-and-gadolinium-iii-at-the-active-site-of-the-model-metalloenzyme-phosphotriesterase
#21
JOURNAL ARTICLE
Callum W Breeze, Yuji Nakano, Eleanor C Campbell, Rebecca L Frkic, David W Lupton, Colin J Jackson
Lanthanide ions have ideal chemical properties for catalysis, such as hard Lewis acidity, fast ligand-exchange kinetics, high coordination-number preferences and low geometric requirements for coordination. As a result, many small-molecule lanthanide catalysts have been described in the literature. Yet, despite the ability of enzymes to catalyse highly stereoselective reactions under gentle conditions, very few lanthanoenzymes have been investigated. In this work, the mononuclear binding of europium(III) and gadolinium(III) to the active site of a mutant of the model enzyme phosphotriesterase are described using X-ray crystallography at 1...
April 1, 2024: Acta Crystallographica. Section D, Structural Biology
https://read.qxmd.com/read/38511968/pressure-induced-structural-optical-and-magnetic-modifications-in-lanthanide-smms
#22
JOURNAL ARTICLE
Fabrice Pointillart, Boris Le Guennic, Olivier Cador
Lanthanide Single-Molecule Magnets are fascinating objects that break magnetic performance records with observable magnetic bistability at the boiling temperature of liquid nitrogen, paving the way for potential applications in high-density data storage. The switching of lanthanide SMM has been successfully achieved using several external stimuli such as redox reaction, pH titration, light irradiation or solvation/desolvation thanks to the high sensitivity of the magnetic anisotropy to any structural change in the lanthanide surrounding...
March 21, 2024: Chemistry: a European Journal
https://read.qxmd.com/read/38511634/n-representable-one-electron-reduced-density-matrix-reconstruction-with-frozen-core-electrons
#23
JOURNAL ARTICLE
Sizhuo Yu, Jean Michel Gillet
Recent advances in quantum crystallography have shown that, beyond conventional charge density refinement, a one-electron reduced density matrix (1-RDM) satisfying N-representability conditions can be reconstructed using jointly experimental X-ray structure factors and directional Compton profiles (DCP) through semidefinite programming. So far, such reconstruction methods for 1-RDM, not constrained to idempotency, have been tested only on a toy model system (CO2 ). In this work, a new method is assessed on crystalline urea [CO(NH2 )2 ] using static (0 K) and dynamic (50 K) artificial experimental data...
May 1, 2024: Acta Crystallographica. Section A, Foundations and Advances
https://read.qxmd.com/read/38511259/a-stable-and-true-blue-emissive-hexacoordinate-si-iv-n-heterocyclic-carbene-complex-and-its-use-in-organic-light-emitting-diodes
#24
JOURNAL ARTICLE
Thibault Thierry, Valerio Giuso, Federico Polo, Pierluigi Mercandelli, Yi-Ting Chen, Chih-Hao Chang, Matteo Mauro, Stéphane Bellemin-Laponnaz
A neutral hexacoordinate Si(IV) complex containing two tridentate N-heterocyclic carbene ligands is synthesised and characterized by X-ray crystallography, optical spectroscopy, electrochemistry and computational methods. The stable compound exhibits remarkable deep-blue photoluminescence particularly in the solid state, which enables its use as an electroluminescent material in organic light-emitting diodes.
March 21, 2024: Dalton Transactions: An International Journal of Inorganic Chemistry
https://read.qxmd.com/read/38510972/phosphopeptide-binding-to-the-n-sh2-domain-of-tyrosine-phosphatase-shp2-correlates-with-the-unzipping-of-its-central-%C3%AE-sheet
#25
JOURNAL ARTICLE
Michelangelo Marasco, John Kirkpatrick, Teresa Carlomagno, Jochen S Hub, Massimiliano Anselmi
SHP2 is a tyrosine phosphatase that plays a regulatory role in multiple intracellular signaling cascades and is known to be oncogenic in certain contexts. In the absence of effectors, SHP2 adopts an autoinhibited conformation with its N-SH2 domain blocking the active site. Given the key role of N-SH2 in regulating SHP2, this domain has been extensively studied, often by X-ray crystallography. Using a combination of structural analyses and molecular dynamics (MD) simulations we show that the crystallographic environment can significantly influence the structure of the isolated N-SH2 domain, resulting in misleading interpretations...
December 2024: Computational and Structural Biotechnology Journal
https://read.qxmd.com/read/38509936/translating-microcalcification-biomarker-information-into-the-laboratory-a-preliminary-assessment-utilizing-core-biopsies-obtained-from-sites-of-mammographic-calcification
#26
JOURNAL ARTICLE
Iain D Lyburn, Robert Scott, Eleanor Cornford, Pascaline Bouzy, Nicholas Stone, Charlene Greenwood, Ihsanne Bouybayoune, Sarah E Pinder, Keith Rogers
RATIONALE AND OBJECTIVES: The potential of breast microcalcification chemistry to provide clinically valuable intelligence is being increasingly studied. However, acquisition of crystallographic details has, to date, been limited to high brightness, synchrotron radiation sources. This study, for the first time, evaluates a laboratory-based system that interrogates histological sections containing microcalcifications. The principal objective was to determine the measurement precision of the laboratory system and assess whether this was sufficient to provide potentially clinical valuable information...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38509117/a-structure-based-designed-small-molecule-depletes-hrpn13-pru-and-a-select-group-of-ken-box-proteins
#27
JOURNAL ARTICLE
Xiuxiu Lu, Monika Chandravanshi, Venkata R Sabbasani, Snehal Gaikwad, V Keith Hughitt, Nana Gyabaah-Kessie, Bradley T Scroggins, Sudipto Das, Wazo Myint, Michelle E Clapp, Charles D Schwieters, Marzena A Dyba, Derek L Bolhuis, Janusz W Koscielniak, Thorkell Andresson, Michael J Emanuele, Nicholas G Brown, Hiroshi Matsuo, Raj Chari, Deborah E Citrin, Beverly A Mock, Rolf E Swenson, Kylie J Walters
Proteasome subunit hRpn13 is partially proteolyzed in certain cancer cell types to generate hRpn13Pru by degradation of its UCHL5/Uch37-binding DEUBAD domain and retention of an intact proteasome- and ubiquitin-binding Pru domain. By using structure-guided virtual screening, we identify an hRpn13 binder (XL44) and solve its structure ligated to hRpn13 Pru by integrated X-ray crystallography and NMR to reveal its targeting mechanism. Surprisingly, hRpn13Pru is depleted in myeloma cells following treatment with XL44...
March 20, 2024: Nature Communications
https://read.qxmd.com/read/38508304/structural-and-functional-characterization-of-a-gene-cluster-responsible-for-deglycosylation-of-c-glucosyl-flavonoids-and-xanthonoids-by-deinococcus-aerius
#28
JOURNAL ARTICLE
Valentina Furlanetto, Dayanand C Kalyani, Anja Kostelac, Jolanta Puc, Dietmar Haltrich, B Martin Hällberg, Christina Divne
Plant C-glycosylated aromatic polyketides are important for plant and animal health. These are specialized metabolites that perform functions both within the plant, and in interaction with soil or intestinal microbes. Despite the importance of these plant compounds, there is still limited knowledge of how they are metabolized. The Gram-positive aerobic soil bacterium Deinococcus aerius strain TR0125 and other Deinococcus species thrive in a wide range of harsh environments. In this work, we identified a C-glycoside deglycosylation gene cluster in the genome of D...
March 18, 2024: Journal of Molecular Biology
https://read.qxmd.com/read/38507258/facile-oxidation-of-ce-iii-to-ce-iv-using-cu-i-salts
#29
JOURNAL ARTICLE
Alexander J Gremillion, Jason Ross, Xiaojuan Yu, Piyuni Ishtaweera, Reiner Anwander, Jochen Autschbach, Gary A Baker, Steven P Kelley, Justin R Walensky
The synthesis, luminescence, and electrochemical properties of the Ce(III) compound, [(C5 Me5 )2 (2,6-i Pr2 C6 H3 O)Ce(THF)], 1 , were investigated. Based on the electrochemical data, treatment of 1 with CuX (X = Cl, Br, I) results in the formation of the corresponding Ce(IV) complexes, [(C5 Me5 )2 (2,6-i Pr2 C6 H3 O)Ce(X)]. Each complex has been characterized using NMR, IR, and UV-vis spectroscopy as well as structurally determined using X-ray crystallography. Additionally, the treatment of [(C5 Me5 )2 (2,6-i Pr2 C6 H3 O)Ce(Br)] with AgF results in the formation of the putative [(C5 Me5 )2 (2,6-i Pr2 C6 H3 O)Ce(F)]...
March 20, 2024: Inorganic Chemistry
https://read.qxmd.com/read/38507205/characterization-of-biological-samples-using-ultra-short-and-ultra-bright-xfel-pulses
#30
JOURNAL ARTICLE
Adam Round, E Jungcheng, Carsten Fortmann-Grote, Klaus Giewekemeyer, Rita Graceffa, Chan Kim, Henry Kirkwood, Grant Mills, Ekaterina Round, Tokushi Sato, Sakura Pascarelli, Adrian Mancuso
The advent of X-ray Free Electron Lasers (XFELs) has ushered in a transformative era in the field of structural biology, materials science, and ultrafast physics. These state-of-the-art facilities generate ultra-bright, femtosecond-long X-ray pulses, allowing researchers to delve into the structure and dynamics of molecular systems with unprecedented temporal and spatial resolutions. The unique properties of XFEL pulses have opened new avenues for scientific exploration that were previously considered unattainable...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507204/x-ray-crystallography-for-macromolecular-complexes
#31
JOURNAL ARTICLE
Francisco J Fernández, Javier Querol-García, Sergio Navas-Yuste, Fabrizio Martino, M Cristina Vega
X-ray crystallography has for most of the last century been the standard technique to determine the high-resolution structure of biological macromolecules, including multi-subunit protein-protein and protein-nucleic acids as large as the ribosome and viruses. As such, the successful application of X-ray crystallography to many biological problems revolutionized biology and biomedicine by solving the structures of small molecules and vitamins, peptides and proteins, DNA and RNA molecules, and many complexes-affording a detailed knowledge of the structures that clarified biological and chemical mechanisms, conformational changes, interactions, catalysis and the biological processes underlying DNA replication, translation, and protein synthesis...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507133/predisposition-in-dynamic-covalent-chemistry-the-role-of-non-covalent-interactions-in-the-assembly-of-tetrahedral-boronate-cages
#32
JOURNAL ARTICLE
Manuel Rondelli, Jorge Pasán, Israel Fernández, Tomás Martín
Directional bonding strategies guide the design of complex molecular architectures, yet challenges arise due to emergent behavior. Rigid structures face geometric constraints and sensitivity to mismatches, hindering the efficient assembly of molecular organic cages (MOCs). Harnessing intramolecular non-covalent interactions offers a promising solution, broadening geometrical possibilities and enhancing adaptability to boost assembly yields. However, identifying these interactions remains challenging, with their full potential sometimes latent until final assembly...
March 20, 2024: Chemistry: a European Journal
https://read.qxmd.com/read/38506716/crystal-structure-of-the-atpase-domain-of-porcine-circovirus-type-2-rep-protein
#33
JOURNAL ARTICLE
Shuaiyin Guan, Zhen Li, Yang Han, Ang Tian, Saisai Zhou, Huanchun Chen, Guiqing Peng, Yunfeng Song
PCV2 belongs to the genus Circovirus in the family Circoviridae , whose genome is replicated by rolling circle replication (RCR). PCV2 Rep is a multifunctional enzyme that performs essential functions at multiple stages of viral replication. Rep is responsible for nicking and ligating single-stranded DNA and unwinding double-stranded DNA (dsDNA). However, the structure and function of the Rep are still poorly understood, which significantly impedes viral replication research. This study successfully resolved the structure of the PCV2 Rep ATPase domain (PRAD) using X-ray crystallography...
March 2024: Journal of General Virology
https://read.qxmd.com/read/38506220/asymmetric-carbene-alkyne-metathesis-mediated-cascade-synthesis-of-benzoxazine-polychiral-polyheterocycles-and-discovery-of-a-novel-pain-blocker
#34
JOURNAL ARTICLE
Shuhao Liu, Haoyi Yang, Jirong Shu, Linna Wu, Yukai Li, Zhijing Zhang, Weijie Guo, Shuxian Cai, Fuyi Li, Wenjiang Liu, Shikun Jia, Song Cai, Taoda Shi, Wenhao Hu
This study introduces a novel approach for synthesizing Benzoxazine-Centered Polychiral Polyheterocycles (BPCPHCs) via an innovative asymmetric carbene-alkyne metathesis-triggered cascade. Overcoming challenges associated with intricate stereochemistry and multiple chiral centers, the catalytic asymmetric Carbene Alkyne Metathesis-mediated Cascade (CAMC) is employed using dirhodium catalyst/Brønsted acid co-catalysis, ensuring precise stereo control as validated by X-ray crystallography. Systematic substrate scope evaluation establishes exceptional diastereo- and enantioselectivities, creating a unique library of BPCPHCs...
March 20, 2024: Angewandte Chemie
https://read.qxmd.com/read/38501509/structural-dynamics-and-functional-cooperativity-of-human-nqo1-by-ambient-temperature-serial-crystallography-and-simulations
#35
JOURNAL ARTICLE
Alice Grieco, Sergio Boneta, José A Gavira, Angel L Pey, Shibom Basu, Julien Orlans, Daniele de Sanctis, Milagros Medina, Jose Manuel Martin-Garcia
The human NQO1 (hNQO1) is a flavin adenine nucleotide (FAD)-dependent oxidoreductase that catalyzes the two-electron reduction of quinones to hydroquinones, being essential for the antioxidant defense system, stabilization of tumor suppressors, and activation of quinone-based chemotherapeutics. Moreover, it is overexpressed in several tumors, which makes it an attractive cancer drug target. To decipher new structural insights into the flavin reductive half-reaction of the catalytic mechanism of hNQO1, we have carried serial crystallography experiments at new ID29 beamline of the ESRF to determine, to the best of our knowledge, the first structure of the hNQO1 in complex with NADH...
April 2024: Protein Science
https://read.qxmd.com/read/38501488/a-cellulosomal-double-dockerin-module-from-clostridium-thermocellum-shows-distinct-structural-and-cohesin-binding-features
#36
JOURNAL ARTICLE
Chao Chen, Hongwu Yang, Sheng Dong, Cai You, Sarah Moraïs, Edward A Bayer, Ya-Jun Liu, Jinsong Xuan, Qiu Cui, Itzhak Mizrahi, Yingang Feng
Cellulosomes are intricate cellulose-degrading multi-enzymatic complexes produced by anaerobic bacteria, which are valuable for bioenergy development and biotechnology. Cellulosome assembly relies on the selective interaction between cohesin modules in structural scaffolding proteins (scaffoldins) and dockerin modules in enzymes. Although the number of tandem cohesins in the scaffoldins is believed to determine the complexity of the cellulosomes, tandem dockerins also exist, albeit very rare, in some cellulosomal components whose assembly and functional roles are currently unclear...
April 2024: Protein Science
https://read.qxmd.com/read/38501175/architecture-of-full-length-type-i-modular-polyketide-synthases-revealed-by-x-ray-crystallography-cryo-electron-microscopy-and-alphafold2
#37
REVIEW
Saket R Bagde, Chu-Young Kim
Covering: up to the end of 2023Type I modular polyketide synthases construct polyketide natural products in an assembly line-like fashion, where the growing polyketide chain attached to an acyl carrier protein is passed from catalytic domain to catalytic domain. These enzymes have immense potential in drug development since they can be engineered to produce non-natural polyketides by strategically adding, exchanging, and deleting individual catalytic domains. In practice, however, this approach frequently results in complete failures or dramatically reduced product yields...
March 19, 2024: Natural Product Reports
https://read.qxmd.com/read/38501110/cryo-electron-microscopy-based-drug-design
#38
REVIEW
Ecenur Cebi, Joohyun Lee, Vinod Kumar Subramani, Nayeon Bak, Changsuk Oh, Kyeong Kyu Kim
Structure-based drug design (SBDD) has gained popularity owing to its ability to develop more potent drugs compared to conventional drug-discovery methods. The success of SBDD relies heavily on obtaining the three-dimensional structures of drug targets. X-ray crystallography is the primary method used for solving structures and aiding the SBDD workflow; however, it is not suitable for all targets. With the resolution revolution, enabling routine high-resolution reconstruction of structures, cryogenic electron microscopy (cryo-EM) has emerged as a promising alternative and has attracted increasing attention in SBDD...
2024: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/38500337/chemical-composition-of%C3%A2-artemisia-scoparia-and-their-bioactivities
#39
JOURNAL ARTICLE
Guziliayi Kuerban, Ablajan Turak, Nurmirza Boymirzayevich Begmatov, Jiangyu Zhao, Haji Akber Aisa
Three undescribed sesquiterpenes (1-3), two enantiomeric pairs of monoterpenes (4a/4b-5a/5b), one alkyne (6), two known alkynes (7-8) and eight known coumarins (9-16) were isolated from the aerial parts extracts of Artemisia scoparia. The structures of these compounds were fully elucidated by their 1D and 2D NMR, HRESIMS spectral data analyses, and comparison with literature. The absolute configurations of compounds were determined by single-crystal X-ray crystallography (1), a comparison of experimental and calculated electronic circular dichroism (ECD) data (2-6)...
March 18, 2024: Chemistry & Biodiversity
https://read.qxmd.com/read/38498884/sulfonamide-incorporated-bis-%C3%AE-aminophosphonates-as-promising-carbonic-anhydrase-inhibitors-design-synthesis-biological-evaluation-and-x-ray-crystallographic-studies
#40
JOURNAL ARTICLE
Marjan Sobati, Morteza Abdoli, Andrea Angeli, Alessandro Bonardi, Marta Ferraroni, Claudiu T Supuran, Raivis Žalubovskis
A novel series of sulfonamide-incorporated bis(α-aminophosphonates) acting as effective carbonic anhydrase (CA, EC 4.2.1.1) inhibitors is reported. The synthesized bivalent ligands were tested against five human (h) isoforms, hCA I, hCA II, hCA VII, hCA IX, and hCA XIII. Such derivatives showed high activity and selectivity against the cancer-related, membrane-bound isoform hCA IX, and among them, compound 5h, tetraisopropyl (1,3-phenylenebis{[(4-sulfamoylphenyl)amino]methylene})bis(phosphonate) showed a KI of 15...
March 18, 2024: Archiv der Pharmazie
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