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atomic structure

Andrew J Doig
The 20 standard amino acids encoded by the Genetic Code were adopted during the RNA World, around 4 billion years ago. This amino acid set could be regarded as a frozen accident, implying that other possible structures could equally well have been chosen to use in proteins. Amino acids were not primarily selected for their ability to support catalysis, since the RNA World already had highly effective cofactors to perform reactions, such as oxidation, reduction and transfer of small molecules. Rather, they were selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets...
December 7, 2016: FEBS Journal
Martin J Fossat, Thuy P Dao, Kelly Jenkins, Mariano Dellarole, Yinshan Yang, Scott A McCallum, Angel E Garcia, Doug Barrick, Christian Roumestand, Catherine A Royer
A complete description of the pathways and mechanisms of protein folding requires a detailed structural and energetic characterization of the conformational ensemble along the entire folding reaction coordinate. Simulations can provide this level of insight for small proteins. In contrast, with the exception of hydrogen exchange, which does not monitor folding directly, experimental studies of protein folding have not yielded such structural and energetic detail. NMR can provide residue specific atomic level structural information, but its implementation in protein folding studies using chemical or temperature perturbation is problematic...
December 6, 2016: Biophysical Journal
Chengwu Yang, Xiaojuan Yu, Stefan Heißler, Alexei Nefedov, Sara Colussi, Jordi Llorca, Alessandro Trovarelli, Yuemin Wang, Christof Wöll
The surface atomic arrangement of metal oxides determines their physical and chemical properties, and the ability to control and optimize structural parameters is of crucial importance for many applications, in particular in heterogeneous catalysis and photocatalysis. Whereas the structures of macroscopic single crystals can be determined with established methods, for nanoparticles (NPs), this is a challenging task. Herein, we describe the use of CO as a probe molecule to determine the structure of the surfaces exposed by rod-shaped ceria NPs...
December 7, 2016: Angewandte Chemie
Dmytro Bykov, Thomas Kjaergaard
We report porting of the Divide-Expand-Consolidate Resolution of the Identity second-order Møller-Plesset perturbation (DEC-RI-MP2) method to the graphic processing units (GPUs) using OpenACC compiler directives. It is shown that the OpenACC compiler directives implementation efficiently accelerates the rate-determining step of the DEC-RI-MP2 method with minor implementation effort. Moreover, the GPU acceleration results in a better load balance and thus in an overall scaling improvement of the DEC algorithm...
December 7, 2016: Journal of Computational Chemistry
Mehdi Bayat, Asieh Sedghi, Leila Ebrahimkhani, Seyyed Javad Sabounchei
N-Heterocyclic carbene and phosphorus ylides are inorganic and organometallic ligands, and their coordination chemistry with transition elements, particularly group 11 metals, would be noticeable. This study seeks to characterize the structure and nature of the C→M bond of group 11 metals (M = Cu(i), Ag(i), Au(i)) in coordination with different monodentate phosphorus ylides {P(Ph)3CHR} and N-heterocyclic carbenes (NHC(R)) (where R = F, Cl, Br, CF3, CH3, H, C(CH3)3, Si(CH3)3, SiH3, Ph). In this regard, DFT calculations with the PBE/def2-TZVP level of theory were applied...
December 7, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Christopher Benndorf, Sebastian Stein, Lukas Heletta, Marcel Kersting, Hellmut Eckert, Rainer Pöttgen
Yttrium-transition metal-magnesium (indium) Heusler phases YPd2Mg, YPd2In, YAg2Mg, YAg2In, YAu2Mg, and YAu2In and their quaternary compounds (solid solutions) Y(Pd0.5Ag0.5)2Mg, Y(Pd0.5Ag0.5)2In, Y(Pd0.5Au0.5)2Mg, Y(Pd0.5Au0.5)2In, Y(Ag0.5Au0.5)2Mg and Y(Ag0.5Au0.5)2In were synthesized from the elements in sealed niobium ampoules in a high-frequency furnace or by arc-melting, respectively. All compounds crystallize with the cubic MnCu2Al type structure (Heusler phase), space group Fm3[combining macron]m. The structure of Y(Ag0...
December 7, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Chengcheng Zhao, Guoqiang Tan, Wei Yang, Chi Xu, Ting Liu, Yuning Su, Huijun Ren, Ao Xia
The novelties in this paper are embodied in the fast interfacial charge transfer in α-Fe2O3-δCδ/FeVO4-x+δCx-δ@C bulk heterojunctions with controllable phase compositions. The carbon source-glucose plays an important role as the connecting bridge between the micelles in the solution, forming interfacial C-O, C-O-Fe and O-Fe-C bonds through dehydration and polymerization reactions. Then the extra VO3(-) around the FeVO4 colloidal particles can react with unstable Fe(OH)3, resulting the phase transformation from α-Fe2O3 (47...
December 7, 2016: Scientific Reports
Tecush Mohammadi, Yousef Ghayeb
Over 100 variants have been designed and studied, using multiple docking methods such as Autodock Vina, ArgusLab, Molegro Virtual Docker (MVD), and Hex-Cuda, to study the effect of alteration in the structure of carbamate based acetylcholyne esterase (AChE) inhibitors. 16 selected systems were then subjected to 14 ns molecular dynamics (MD) simulations. Results from all the docking methods are in agreement. Variants that involved biphenyl substituents possess the most negative binding energies in the -37.64 to -39...
December 7, 2016: Journal of Biomolecular Structure & Dynamics
A R Setoodeh, H Badjian, H Shirzadi Jahromi
Graphene is known for its exceptional mechanical and electrical properties when in the form of a hexagonal monolayer of carbon atoms. In this study, the mechanical properties of hexagonal boron-doped graphene (h-BdGr) sheets with a 2% concentration of boron atoms distributed randomly throughout the layer were investigated. The effects of mono/multi-atomic vacancy defects, with different concentrations and various orientations, as well as temperature, on the tensile behavior of the sheets were examined utilizing molecular dynamic simulations...
January 2017: Journal of Molecular Modeling
Qing Shao, Carol K Hall
The ability of nanoparticles to alter protein structure and dynamics plays an important role in their medical and biological applications. We investigate allosteric effects of gold nanoparticles on human serum albumin protein using molecular simulations. The extent to which bound nanoparticles influence the structure and dynamics of residues distant from the binding site is analyzed. The root mean square deviation, root mean square fluctuation and variation in the secondary structure of individual residues on a human serum albumin protein are calculated for four protein-gold nanoparticle binding complexes...
December 7, 2016: Nanoscale
S Trautmann, J Aizpurua, I Götz, A Undisz, J Dellith, H Schneidewind, M Rettenmayr, V Deckert
Recent experiments have evidenced sub-nanometer resolution in plasmonic-enhanced probe spectroscopy. Such a high resolution cannot be simply explained using the commonly considered radii of metallic nanoparticles on plasmonic probes. In this contribution the effects of defects as small as a single atom found on spherical plasmonic particles acting as probing tips are investigated in connection with the spatial resolution provided. The presence of abundant edge and corner sites with atomic scale dimensions in crystalline metallic nanoparticles is evident from transmission electron microscopy (TEM) images...
December 7, 2016: Nanoscale
Tatsuya Okuno, Koya Kato, Shintaro Minami, Tomoki P Terada, Masaki Sasai, George Chikenji
We discuss methods and ideas of virtual screening (VS) for drug discovery by examining the performance of VS-APPLE, a recently developed VS method, which extensively utilizes the tendency of single binding pockets to bind diversely different ligands, i.e. promiscuity of binding pockets. In VS-APPLE, multiple ligands bound to a pocket are spatially arranged by maximizing structural overlap of the protein while keeping their relative position and orientation with respect to the pocket surface, which are then combined into a multiple-ligand template for screening test compounds...
2016: Biophysics and Physicobiology
Yuka Suzuki, Kei Yura
We investigated the effect of ATP binding to GroEL and elucidated a role of ATP in the conformational change of GroEL. GroEL is a tetradecamer chaperonin that helps protein folding by undergoing a conformational change from a closed state to an open state. This conformational change requires ATP, but does not require the hydrolysis of the ATP. The following three types of conformations are crystalized and the atomic coordinates are available; closed state without ATP, closed state with ATP and open state with ADP...
2016: Biophysics and Physicobiology
Jun Kang, Yeonwon Kim, Hye-Min Kim, Xiulan Hu, Nagahiro Saito, Jae-Hyuk Choi, Myeong-Hoon Lee
C-encapsulated highly pure Ni, Co, and Fe magnetic nanoparticles (MNPs/C) were synthesized by an innovative one-step in-situ plasma in liquid method (solution plasma processing, SPP) without any additional reductants, agents, or treatment. Successful encapsulation of MNPs was demonstrated by using inductively coupled plasma-atomic emission spectrometry and cyclic voltammetry techniques. The obtained X-ray diffraction patterns and transmission electron microscopy images corresponded to MNPs with average diameters of 5 nm and good crystalline structure...
December 6, 2016: Scientific Reports
Deshui Yu, María Martínez Valado, Christoph Hufnagel, Leong Chuan Kwek, Luigi Amico, Rainer Dumke
Hybrids consisting of macroscopic superconducting circuits and microscopic components, such as atoms and spins, have the potential of transmitting an arbitrary state between different quantum species, leading to the prospective of high-speed operation and long-time storage of quantum information. Here we propose a novel hybrid structure, where a neutral-atom qubit directly interfaces with a superconducting charge qubit, to implement the qubit-state transmission. The highly-excited Rydberg atom located inside the gate capacitor strongly affects the behavior of Cooper pairs in the box while the atom in the ground state hardly interferes with the superconducting device...
December 6, 2016: Scientific Reports
Chencheng Xu, Hongchu Du, Alexander J H van der Torren, Jan Aarts, Chun-Lin Jia, Regina Dittmann
We elucidated the formation process for Ruddlesden-Popper-type defects during pulsed laser deposition of Sr rich SrTiO3 thin films by a combined analysis of in-situ atomic force microscopy, low energy electron diffraction and high resolution scanning transmission electron microscopy. At the early growth stage of 1.5 unit cells, the excess Sr results in the formation of SrO on the surface, resulting in a local termination change from TiO2 to SrO, thereby forming a Sr rich (2 × 2) surface reconstruction...
December 6, 2016: Scientific Reports
Paul C Spruijtenburg, Sergey V Amitonov, Filipp Mueller, Wilfred G van der Wiel, Floris A Zwanenburg
In this Report we show the role of charge defects in the context of the formation of electrostatically defined quantum dots. We introduce a barrier array structure to probe defects at multiple locations in a single device. We measure samples both before and after an annealing process which uses an Al2O3 overlayer, grown by atomic layer deposition. After passivation of the majority of charge defects with annealing we can electrostatically define hole quantum dots up to 180 nm in length. Our ambipolar structures reveal amphoteric charge defects that remain after annealing with charging energies of 10 meV in both the positive and negative charge state...
December 6, 2016: Scientific Reports
Nicole Poweleit, Peng Ge, Hong H Nguyen, Rachel R Ogorzalek Loo, Robert P Gunsalus, Z Hong Zhou
Archaea use flagella known as archaella-distinct both in protein composition and structure from bacterial flagella-to drive cell motility, but the structural basis of this function is unknown. Here, we report an atomic model of the archaella, based on the cryo electron microscopy (cryoEM) structure of the Methanospirillum hungatei archaellum at 3.4 Å resolution. Each archaellum contains ∼61,500 archaellin subunits organized into a curved helix with a diameter of 10 nm and average length of 10,000 nm...
December 5, 2016: Nature Microbiology
Li-Kun Yang, Xia-Guang Zhang, Fang-Zu Yang, De-Yin Wu, Zhong-Qun Tian, Xiang-Yang Liu
Density functional theory calculations have been used to elucidate the mechanism of the addition reaction of acetaldehyde to the positively charged hydrogenated silicene (H-silicene). We find that the positively charged H-silicene plane could be partially restructured to form a vacant Si site, enabling a further nucleophilic addition reaction. After acetaldehyde molecule attached to the H-silicene plane, two competing pathways are involved in hydrogen abstraction process: a random reaction mechanism and a chain reaction mechanism...
December 6, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Katarzyna M Psonka-Antonczyk, Per Hammarström, Leif B G Johansson, Mikael Lindgren, Bjørn T Stokke, K Peter R Nilsson, Sofie Nyström
Amyloid plaques composed of fibrillar Amyloid-β (Aβ) are hallmarks of Alzheimer's disease. However, Aβ fibrils are morphologically heterogeneous. Conformation sensitive luminescent conjugated oligothiophenes (LCOs) are versatile tools for monitoring such fibril polymorphism in vivo and in vitro. Biophysical methods applied on in vitro generated Aβ fibrils, stained with LCOs with different binding and fluorescence properties, can be used to characterize the Aβ fibrillation in depth, far beyond that possible for in vivo generated amyloid plaques...
2016: Frontiers in Chemistry
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