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Chemical crystallography

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https://www.readbyqxmd.com/read/28705433/recent-advances-in-racemic-protein-crystallography
#1
REVIEW
Bingjia Yan, Linzhi Ye, Weiliang Xu, Lei Liu
Solution of the three-dimensional structures of proteins is a critical step in deciphering the molecular mechanisms of their bioactivities. Among the many approaches for obtaining protein crystals, racemic protein crystallography has been developed as a unique method to solve the structures of an increasing number of proteins. Exploiting unnatural protein enantiomers in crystallization and resolution, racemic protein crystallography manifests two major advantages that are 1) to increase the success rate of protein crystallization, and 2) to obviate the phase problem in X-ray diffraction...
May 10, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28703597/natural-and-semisynthetic-tigliane-diterpenoids-with-new-carbon-skeletons-from-euphorbia-dracunculoides-as-a-wnt-signaling-pathway-inhibitor
#2
Li Wang, Jing Yang, Ling-Mei Kong, Jun Deng, Zijun Xiong, Jianping Huang, Jianying Luo, Yijun Yan, Yikao Hu, Xiao-Nian Li, Yan Li, Yong Zhao, Sheng-Xiong Huang
Euphordraculoates A (1) and B (2), featuring tigliane diterpenoids with two new carbon skeletons, were characterized as metabolites of Euphorbia dracunculoides and semisynthetic products, respectively. Their structures were determined by spectroscopic analyses and X-ray crystallography. The respective biosynthetic and chemical formation mechanisms for 1 and 2 from a known tigliane 3 was proposed. The detailed decarbonization mechanism from 3 to 2 was further explored by (18)O-labeling experiment. Compound 2 could inhibit Wnt pathway in a dose- and time-dependent manner...
July 13, 2017: Organic Letters
https://www.readbyqxmd.com/read/28695248/divergent-effects-of-anesthetics-on-lipid-bilayer-properties-and-sodium-channel-function
#3
REVIEW
Karl F Herold, Olaf S Andersen, Hugh C Hemmings
General anesthetics revolutionized medicine by allowing surgeons to perform more complex and much longer procedures. This widely used class of drugs is essential to patient care, yet their exact molecular mechanism(s) are incompletely understood. One early hypothesis over a century ago proposed that nonspecific interactions of anesthetics with the lipid bilayer lead to changes in neuronal function via effects on membrane properties. This model was supported by the Meyer-Overton correlation between anesthetic potency and lipid solubility and despite more recent evidence for specific protein targets, in particular ion-channels, lipid bilayer-mediated effects of anesthetics is still under debate...
July 10, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28694484/self-assembled-%C3%AE-tocopherol-transfer-protein-nanoparticles-promote-vitamin-e-delivery-across-an-endothelial-barrier
#4
Walter Aeschimann, Stefanie Staats, Stephan Kammer, Natacha Olieric, Jean-Marc Jeckelmann, Dimitrios Fotiadis, Thomas Netscher, Gerald Rimbach, Michele Cascella, Achim Stocker
Vitamin E is one of the most important natural antioxidants, protecting polyunsaturated fatty acids in the membranes of cells. Among different chemical isoforms assimilated from dietary regimes, RRR-α-tocopherol is the only one retained in higher animals. This is possible thanks to α-Tocopherol Transfer Protein (α-TTP), which extracts α-tocopherol from endosomal compartments in liver cells, facilitating its distribution into the body. Here we show that, upon binding to its substrate, α-TTP acquires tendency to aggregation into thermodynamically stable high molecular weight oligomers...
July 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28693671/100-years-of-x-ray-crystallography
#5
Terence J Kemp, W Alcock
The developments in crystallography, since it was first covered in Science Progress in 1917, following the formulation of the Bragg equation, are described. The advances in instrumentation and data analysis, coupled with the application of computational methods to data analysis, have enabled the solution of molecular structures from the simplest binary systems to the most complex of biological structures. These developments are shown to have had major impacts in the development of chemical bonding theory and in offering an increasing understanding of enzyme-substrate interactions...
March 1, 2017: Science Progress
https://www.readbyqxmd.com/read/28692285/raman-optical-activity-reveals-carotenoid-photoactivation-events-in-the-orange-carotenoid-protein-in-solution
#6
Tomotsumi Fujisawa, Ryan L Leverenz, Momoka Nagamine, Cheryl A Kerfeld, Masashi Unno
The orange carotenoid protein (OCP) plays an important role in photoprotection in cyanobacteria, which is achieved by the photoconversion from the orange dark state (OCPO) to the red active state (OCPR). Using Raman optical activity (ROA), we studied the conformations of the carotenoid chromophore in the active sites of OCPO and OCPR. This ROA measurement directly observed the chromophore conformation of native OCP in solution, and the measurement of OCPR first demonstrated the ROA spectroscopy for the transient species...
July 10, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28686035/nanoscale-chemical-processes-affecting-storage-capacities-and-seals-during-geologic-co2-sequestration
#7
Young-Shin Jun, Lijie Zhang, Yujia Min, Qingyun Li
Geologic CO2 sequestration (GCS) is a promising strategy to mitigate anthropogenic CO2 emission to the atmosphere. Suitable geologic storage sites should have a porous reservoir rock zone where injected CO2 can displace brine and be stored in pores, and an impermeable zone on top of reservoir rocks to hinder upward movement of buoyant CO2. The injection wells (steel casings encased in concrete) pass through these geologic zones and lead CO2 to the desired zones. In subsurface environments, CO2 is reactive as both a supercritical (sc) phase and aqueous (aq) species...
July 7, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28681606/identification-of-two-secondary-ligand-binding-sites-in-14-3-3-proteins-using-fragment-screening
#8
Eline Sijbesma, Lukasz Skora, Seppe Leysen, Luc Brunsveld, Uwe Koch, Peter Nussbaumer, Wolfgang Jahnke, Christian Ottmann
Proteins typically interact with multiple binding partners and often different parts of their surfaces are employed for establishing these protein-protein interactions (PPIs). The class of 14-3-3 adapter proteins bind to several hundred other proteins in the cell. Multiple small molecules for the modulation of 14-3-3 PPIs have been disclosed, but they all target the conserved phosphopeptide-binding channel so that selectivity is difficult to achieve. Here we report on the discovery of two individual secondary binding sites that have been identified by combining NMR-based fragment screening and X-ray crystallography...
July 6, 2017: Biochemistry
https://www.readbyqxmd.com/read/28677601/a-novel-tubular-hydrogen-bond-pattern-in-a-new-diazaphosphole-oxide-a-combination-of-x-ray-crystallography-and-theoretical-study-of-hydrogen-bonds
#9
Fahimeh Sabbaghi, Mehrdad Pourayoubi, Abolghasem Farhadipour, Nazila Ghorbanian, Pavel V Andreev
In the structure of 2-(4-chloroanilino)-1,3,2λ(4)-diazaphosphol-2-one, C12H11ClN3OP, each molecule is connected with four neighbouring molecules through (N-H)2...O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R(3)3(12) and R4(3)(14) hydrogen-bond ring motifs, combined with a C(4) chain motif. The hole constructed in the tubular architecture includes a 12-atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other...
July 1, 2017: Acta Crystallographica. Section C, Structural Chemistry
https://www.readbyqxmd.com/read/28668125/detection-of-reaction-intermediates-in-mg-2-dependent-dna-synthesis-and-rna-degradation-by-time-resolved-x-ray-crystallography
#10
Nadine L Samara, Yang Gao, Jinjun Wu, Wei Yang
Structures of enzyme-substrate/product complexes have been studied for over four decades but have been limited to either before or after a chemical reaction. Recently using in crystallo catalysis combined with X-ray diffraction, we have discovered that many enzymatic reactions in nucleic acid metabolism require additional metal ion cofactors that are not present in the substrate or product state. By controlling metal ions essential for catalysis, the in crystallo approach has revealed unprecedented details of reaction intermediates...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28666766/toxicogenomic-responses-of-human-alveolar-epithelial-cells-to-tungsten-boride-nanoparticles
#11
Hasan Türkez, Mehmet Enes Arslan, Erdal Sönmez, Abdulgani Tatar, Metin Açikyildiz, Fatime Geyikoğlu
During the recent years, microarray analysis of gene expression has become an inevitable tool for exploring toxicity of drugs and other chemicals on biological systems. Therefore, toxicogenomics is considered as a fruitful area for searching cellular pathways and mechanisms including cancer, immunological diseases, environmental responses, gene-gene interactions and chemical toxicity. In this work, we examined toxic effects of Tungsten Borides NPs on gene expression profiling of the human lung alveolar epithelial cells (HPAEpiC)...
June 27, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28652025/multiple-functionalities-of-reduced-flavin-in-the-non-redox-reaction-catalyzed-by-udp-galactopyranose-mutase
#12
REVIEW
Pablo Sobrado, John J Tanner
Flavin cofactors are widely used by enzymes to catalyze a broad range of chemical reactions. Traditionally, flavins in enzymes are regarded as redox centers, which enable enzymes to catalyze the oxidation or reduction of substrates. However, a new class of flavoenzyme has emerged over the past quarter century in which the flavin functions as a catalytic center in a non-redox reaction. Here we introduce the unifying concept of flavin hot spots to understand and categorize the mechanisms and reactivities of both traditional and noncanonical flavoenzymes...
June 24, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28649740/human-vs-robots-in-the-discovery-and-crystallization-of-gigantic-polyoxometalates
#13
Lee Cronin, Vasilios Duros, Jonathan Grizou, Weimin Xuan, Zied Hosni, De-Liang Long, Haralampos Miras
The discovery of new gigantic molecules formed by self-assembly using single crystal X-ray crystallography is a challenging endeavor as it combines two contingent events; first is the formation of a new molecule, and second its crystallization. Herein, we constructed a workflow that can be followed manually or by a robot to probe the envelope of both events and employed it in the chemical space of a new polyoxometalate cluster, namely Na6[Mo120Ce6O366H12(H2O)78]·200H2O (1) which has a trigonal-ring type architecture (yield 4...
June 25, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28646173/transmembrane-interactions-of-full-length-mammalian-bitopic-cytochrome-p450-cytochrome-b5-complex-in-lipid-bilayers-revealed-by-sensitivity-enhanced-dynamic-nuclear-polarization-solid-state-nmr-spectroscopy
#14
Kazutoshi Yamamoto, Marc A Caporini, Sang-Choul Im, Lucy Waskell, Ayyalusamy Ramamoorthy
The dynamic protein-protein and protein-ligand interactions of integral bitopic membrane proteins with a single membrane-spanning helix play a plethora of vital roles in the cellular processes associated with human health and diseases, including signaling and enzymatic catalysis. While an increasing number of high-resolution structural studies of membrane proteins have successfully manifested an in-depth understanding of their biological functions, intact membrane-bound bitopic protein-protein complexes pose tremendous challenges for structural studies by crystallography or solution NMR spectroscopy...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28636761/molecular-tools-for-facilitative-carbohydrate-transporters
#15
Marina Tanasova, Joseph R Fedie
Facilitative carbohydrate transporters - Gluts - have received a wide attention over decades due to their essential role in the nutrient uptake and links with various metabolic disorders, including diabetes, obesity, and cancer. Endeavors into understanding mechanisms of Glut-mediated nutrient uptake have resulted in the multidisciplinary research field, branching protein chemistry, chemical biology, organic synthesis, crystallography, and biomolecular modeling. Gluts became attractive targets for cancer research and medicinal chemistry, leading to the development of new approaches to cancer diagnostics and providing avenues for cancer-targeting therapeutics...
June 21, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28636340/three-dimensional-modeling-of-quasicrystal-structures-from-x-ray-diffraction-an-icosahedral-al-cu-fe-alloy
#16
Seung-Tae Hong
Quasicrystals (QCs) are well-ordered but aperiodic crystals with classically forbidden symmetries (such as 5-fold). High-dimensional (HD) crystallography is a standard method to locate atom positions explicitly. However, in practice, it is still challenging because of its complexity. Here, we report a new simple approach to three-dimensional (3D) atomic modeling derived from X-ray diffraction data, and apply it to the icosahedral QC Al0.63Cu0.25Fe0.12. Electron density maps were calculated directly from 3D diffraction data indexed with noninteger (fractional) numbers as measured, with proper phases; each of 2(5) = 32 possible phase assignments for the five strongest reflections was used for Fourier synthesis...
June 21, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28630286/efficient-switching-of-mcherry-fluorescence-using-chemical-caging
#17
Bas M C Cloin, Elke De Zitter, Desiree Salas, Vincent Gielen, Gert E Folkers, Marina Mikhaylova, Maike Bergeler, Bartosz Krajnik, Jeremy Harvey, Casper C Hoogenraad, Luc Van Meervelt, Peter Dedecker, Lukas C Kapitein
Fluorophores with dynamic or controllable fluorescence emission have become essential tools for advanced imaging, such as superresolution imaging. These applications have driven the continuing development of photoactivatable or photoconvertible labels, including genetically encoded fluorescent proteins. These new probes work well but require the introduction of new labels that may interfere with the proper functioning of existing constructs and therefore require extensive functional characterization. In this work we show that the widely used red fluorescent protein mCherry can be brought to a purely chemically induced blue-fluorescent state by incubation with β-mercaptoethanol (βME)...
July 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28626553/stepwise-crystallographic-visualization-of-dynamic-guest-binding-in-a-nanoporous-framework
#18
Gabriel Brunet, Damir A Safin, Mohammad Z Aghaji, Koen Robeyns, Ilia Korobkov, Tom K Woo, Muralee Murugesu
Binding sites are at the heart of all host-guest systems, whether biological or chemical. When considering binding sites that form covalent bonds with the guest, we generally envision a single, highly specific binding motif. Through single-crystal X-ray crystallography, the dynamic binding of a guest that displays a variety of covalent binding motifs in a single site of adsorption is directly observed for the first time. The stepwise crystallographic visualization of the incorporation of I2 within a porous MOF is presented, wherein the preferred binding motifs throughout the uptake process are identified...
April 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28621371/does-z-equal-1-or-2-enhanced-powder-nmr-crystallography-verification-of-a-disordered-room-temperature-crystal-structure-of-a-p38-inhibitor-for-chronic-obstructive-pulmonary-disease
#19
Cory M Widdifield, Sten O Nilsson Lill, Anders Broo, Maria Lindkvist, Anna Pettersen, Anna Svensk Ankarberg, Peter Aldred, Staffan Schantz, Lyndon Emsley
The crystal structure of the Form A polymorph of N-cyclopropyl-3-fluoro-4-methyl-5-[3-[[1-[2-[2-(methylamino)ethoxy]phenyl]cyclopropyl]amino]-2-oxo-pyrazin-1-yl]benzamide (i.e., AZD7624), determined using single-crystal X-ray diffraction (scXRD) at 100 K, contains two molecules in the asymmetric unit (Z' = 2) and has regions of local static disorder. This substance has been in phase IIa drug development trials for the treatment of chronic obstructive pulmonary disease, a disease which affects over 300 million people and contributes to nearly 3 million deaths annually...
June 28, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28608673/organic-donor-acceptor-complexes-as-novel-organic-semiconductors
#20
Jing Zhang, Wei Xu, Peng Sheng, Guangyao Zhao, Daoben Zhu
Organic donor-acceptor (DA) complexes have attracted wide attention in recent decades, resulting in the rapid development of organic binary system electronics. The design and synthesis of organic DA complexes with a variety of component structures have mainly focused on metallicity (or even superconductivity), emission, or ferroelectricity studies. Further efforts have been made in high-performance electronic investigations. The chemical versatility of organic semiconductors provides DA complexes with a great number of possibilities for semiconducting applications...
June 13, 2017: Accounts of Chemical Research
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