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Chemical crystallography

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
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
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)...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
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
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 16, 2017: Physical Chemistry Chemical Physics: PCCP
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
Katharina Veith, Maria Martinez Molledo, Yasser Almeida Hernandez, Inokentijs Josts, Julius Nitsche, Christian Löw, Henning Tidow
A crucial bottleneck in membrane protein structural biology is the difficulty in identifying a detergent that can maintain the stability and functionality of integral membrane proteins (IMPs). Detergents are poor membrane mimics and their common use in membrane protein crystallography may be one reason for the challenges in obtaining high-resolution crystal structures of many IMP families. Lipid-like peptides (LLPs) have detergent-like properties and have been proposed as alternatives for the solubilization of GPCRs and other membrane proteins...
June 11, 2017: Chembiochem: a European Journal of Chemical Biology
Akira Naito, Nobuaki Matsumori, Ayyalusamy Ramamoorthy
A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules...
June 6, 2017: Biochimica et Biophysica Acta
Bobo Dang, Sandeep Chhabra, Michael W Pennington, Raymond S Norton, Stephen B H Kent
ShK toxin from the sea anemone Stichodactyla helianthus is a 35-residue protein that binds to the Kv1.3 ion channel with high affinity. Recently we determined the X-ray structure of ShK toxin by racemic crystallography, in the course of which we discovered that D-ShK has a near-background IC50 value ~50,000 times lower than that of the L-ShK toxin. This lack of activity was at odds with previously reported results for an ShK diastereomer designated D-allo-ShK for which significant biological activity had been observed in a similar receptor-blocking assay...
June 8, 2017: Journal of Biological Chemistry
Jing Wu, Shanmugam Thiyagarajan, Célia Fonseca Guerra, Pieter Eduard, Martin Lutz, Bart A J Noordover, Cor E Koning, Daan S van Es
New 2/5 1-carbon extended isohexide building blocks are now synthetically accessible by a convenient, selective base-catalyzed epimerization of the corresponding dinitriles. Kinetic experiments using the strong organic base 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) show that all three possible isohexide dinitrile isomers are in a dynamic equilibrium. An epimerization mechanism is proposed, based on DFT calculations. Structural identification of all three possible isomers is based on NMR analysis as well as single crystal x-ray crystallography...
June 7, 2017: ChemSusChem
Simon D Brandt, Pierce V Kavanagh, Brendan Twamley, Folker Westphal, Simon P Elliott, Jason Wallach, Alexander Stratford, Landon M Klein, John D McCorvy, David E Nichols, Adam L Halberstadt
Lysergic acid diethylamide (LSD) is perhaps one of the best-known psychoactive substances and many structural modifications of this prototypical lysergamide have been investigated. Several lysergamides were recently encountered as "research chemicals" or new psychoactive substances (NPS). Although lysergic acid morpholide (LSM-775) appeared on the NPS market in 2013, there is disagreement in the literature regarding the potency and psychoactive properties of LSM-775 in humans. The present investigation attempts to address the gap of information that exists regarding the analytical profile and pharmacological effects of LSM-775...
June 5, 2017: Drug Testing and Analysis
Qiuchen Zhao, Fengrui Yao, Zequn Wang, Shibin Deng, Lianming Tong, Kaihui Liu, Jin Zhang
Controllable synthesis of carbon nanotubes (CNTs) is of great importance in its further application, which attracts broad attention. As growth and etching are the two sides in the process of material crystallography and the control of the competition between them forms the foundation for modern technology of materials design and manufacture, the understanding on etching process of carbon nanotubes is still very unclear because technically it is of great challenge to characterize the dynamics in such small one-dimensional (1D) scale...
June 6, 2017: Advanced Materials
Stephen K Burley, Helen M Berman, Gerard J Kleywegt, John L Markley, Haruki Nakamura, Sameer Velankar
The Protein Data Bank (PDB)--the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes--was established in 1971, becoming the first open-access digital resource in the biological sciences. The PDB archive currently houses ~130,000 entries (May 2017). It is managed by the Worldwide Protein Data Bank organization (wwPDB;, which includes the RCSB Protein Data Bank (RCSB PDB;, the Protein Data Bank Japan (PDBj;, the Protein Data Bank in Europe (PDBe; pdbe...
2017: Methods in Molecular Biology
Elspeth F Garman, Martin Weik
Radiation damage inflicted on macromolecular crystals during X-ray diffraction experiments remains a limiting factor for structure solution, even when samples are cooled to cryotemperatures (~100 K). Efforts to establish mitigation strategies are ongoing and various approaches, summarized below, have been investigated over the last 15 years, resulting in a deeper understanding of the physical and chemical factors affecting damage rates. The recent advent of X-ray free electron lasers permits "diffraction-before-destruction" by providing highly brilliant and short (a few tens of fs) X-ray pulses...
2017: Methods in Molecular Biology
Marius Schmidt
Time-resolved macromolecular crystallography unifies protein structure determination with chemical kinetics. With the advent of fourth generation X-ray sources the time-resolution can be on the order of 10-40 fs, which opens the ultrafast time scale to structure determination. Fundamental motions and transitions associated with chemical reactions in proteins can now be observed. Moreover, new experimental approaches at synchrotrons allow for the straightforward investigation of all kind of reactions in biological macromolecules...
2017: Methods in Molecular Biology
Abel Moreno
This chapter provides a review of different advanced methods that help to increase the success rate of a crystallization project, by producing larger and higher quality single crystals for determination of macromolecular structures by crystallographic methods. For this purpose, the chapter is divided into three parts. The first part deals with the fundamentals for understanding the crystallization process through different strategies based on physical and chemical approaches. The second part presents new approaches involved in more sophisticated methods not only for growing protein crystals but also for controlling the size and orientation of crystals through utilization of electromagnetic fields and other advanced techniques...
2017: Methods in Molecular Biology
John R Helliwell
Since the Protein Data Bank was founded in 1971 there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database, founded in 1965, there are more than 800,000 'small molecule' crystal structure depositions, and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs...
June 1, 2017: Bioscience Reports
Juan Ramón Avilés-Moreno, Francisco Gámez, Giel Berden, Jos Oomens, Bruno Martínez-Haya
The antibiotic activity of nonactin is sustained by its ability to transport K(+) across lipophilic phases, e.g., the cell membranes. Such a feature can be traced back to a specific ionophoric behavior and to a balanced hydrophobicity modulated by the formation of a cation complex. In this study, the dominant conformations and coordination arrangements in the alkali cation complexes (Na(+), K(+), Cs(+)) of nonactin are characterized by means of action vibrational spectroscopy and quantum chemical computations...
June 14, 2017: Physical Chemistry Chemical Physics: PCCP
Aleksandar Bijelic, Annette Rompel
Protein crystallography represents at present the most productive and most widely used method to obtain structural information on target proteins and protein-ligand complexes within the atomic resolution range. The knowledge obtained in this way is essential for understanding the biology, chemistry, and biochemistry of proteins and their functions but also for the development of compounds of high pharmacological and medicinal interest. Here, we address the very central problem in protein crystallography: the unpredictability of the crystallization process...
May 31, 2017: Accounts of Chemical Research
Stephanie M Barbon, Viktor N Staroverov, Joe B Gilroy
Five new compounds comprised of unprecedented boron-nitrogen heterocycles have been isolated from a single reaction of a potentially tetradentate N₂O₂³¯ formazanate ligand with BF₃.OEt₂ and NEt₃. Optimized yields for each product were obtained through variation of experimental conditions and rationalized in terms of relative Gibbs free energies of the products as determined by electronic structure calculations. Chemical reduction of two of these compounds resulted in the formation of a stable anion, radical anion, and diradical dianion...
May 31, 2017: Angewandte Chemie
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