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Structure resolution

Davis C Woodworth, Langston T Holly, Emeran A Mayer, Noriko Salamon, Benjamin M Ellingson
BACKGROUND: Advanced cervical spondylosis (CS) can cause structural damage to the spinal cord resulting in long-term neurological impairment including neck pain and motor weakness. We hypothesized long-term structural reorganization within the brain in patients with CS. OBJECTIVE: To explore the associations between cortical thickness, subcortical volumes, neurological symptoms, and pain severity in CS patients with or without myelopathy and healthy controls (HCs)...
March 14, 2018: Neurosurgery
Stephen P Muench, Martin van der Laan
In this issue of Molecular Cell, Roh et al. (2018) present a high-resolution cryo-EM structure of the nanodisc-reconstituted yeast Vo proton channel that provides important new insights into subunit arrangements and the proton translocation pathway in V-type ATPases.
March 15, 2018: Molecular Cell
Renata Ferrari, Ezequiel M Marzinelli, Camila Rezende Ayroza, Alan Jordan, Will F Figueira, Maria Byrne, Hamish A Malcolm, Stefan B Williams, Peter D Steinberg
Marine protected areas (MPAs) are designed to reduce threats to biodiversity and ecosystem functioning from anthropogenic activities. Assessment of MPAs effectiveness requires synchronous sampling of protected and non-protected areas at multiple spatial and temporal scales. We used an autonomous underwater vehicle to map benthic communities in replicate 'no-take' and 'general-use' (fishing allowed) zones within three MPAs along 7o of latitude. We recorded 92 taxa and 38 morpho-groups across three large MPAs...
2018: PloS One
Masha M Rosenberg, Alfred G Redfield, Mary Roberts, Lizbeth Hedstrom
The ability of enzymes to modulate the dynamics of bound substrates and cofactors is a critical feature of catalysis, but the role of dynamics has largely been approached from the perspective of the protein. Here we use an underappreciated NMR technique, subtesla high resolution field cycling31 P NMR relaxometry, to interrogate the dynamics of enzyme bound substrates and cofactors in guanosine-5'-monophosphate reductase (GMPR). These experiments reveal distinct binding modes and dynamic profiles associated with the31 P nuclei in the Michaelis complexes for the deamination and hydride transfer steps of the catalytic cycle...
March 16, 2018: Biochemistry
Sophie Meuret, Toon Coenen, Steffi Woo, Yong-Ho Ra, Zetian Mi, Albert Polman
Cathodoluminescence (CL) imaging spectroscopy provides two-dimensional optical excitation images of photonic nanostructures with deep-subwavelength spatial resolution. So far, CL imaging was unable to provide a direct measurement of the excitation and emission probabilities of photonic nanostructures in a spatially resolved manner. Here, we demonstrate that by mapping the cathodoluminescence autocorrelation function g(2) together with the CL spectral distribution the excitation and emission rates can be disentangled at every excitation position...
March 16, 2018: Nano Letters
Sangmoon Yoon, Hyobin Yoo, Seoung-Hun Kang, Miyoung Kim, Young-Kyun Kwon
We report the existence of latent order during core relaxation in the high-angle grain boundaries (GBs) of GaN films using atomic-resolution scanning transmission electron microscopy and ab initio density functional theory calculations. Core structures in the high-angle GBs are characterized by two pairs of Ga-N bonds located next to each other. The core type correlates strongly with the bond angle differences. We identify an order of core relaxation hidden in the high-angle GBs by further classifying the 5/7 atom cores into a stable 5/7 core (5/7(S)) and a metastable 5/7 core (5/7(M))...
March 15, 2018: Scientific Reports
Shuchao Pang, Mehmet A Orgun, Zhezhou Yu
BACKGROUND AND OBJECTIVES: The traditional biomedical image retrieval methods as well as content-based image retrieval (CBIR) methods originally designed for non-biomedical images either only consider using pixel and low-level features to describe an image or use deep features to describe images but still leave a lot of room for improving both accuracy and efficiency. In this work, we propose a new approach, which exploits deep learning technology to extract the high-level and compact features from biomedical images...
May 2018: Computer Methods and Programs in Biomedicine
Oneida Espinosa-Álvarez, Paola A Ortiz, Luciana Lima, André G Costa-Martins, Myrna G Serrano, Stephane Herder, Gregory A Buck, Erney P Camargo, Patrick B Hamilton, Jamie R Stevens, Marta M G Teixeira
Trypanosoma rangeli and Trypanosoma cruzi are generalist trypanosomes sharing a wide range of mammalian hosts; they are transmitted by triatomine bugs, and are the only trypanosomes infecting humans in the Neotropics. Their origins, phylogenetic relationships, and emergence as human parasites have long been subjects of interest. In the present study, taxon-rich analyses (20 trypanosome species from bats and terrestrial mammals) using ssrRNA, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH), heat shock protein-70 (HSP70) and Spliced Leader (SL) RNA sequences, and multilocus phylogenetic analyses using 11 single copy genes from 15 selected trypanosomes, provide increased resolution of relationships between species and clades, strongly supporting two main sister lineages: lineage Schizotrypanum, comprising T...
March 12, 2018: International Journal for Parasitology
Sebastian Hiller, Björn M Burmann
Living cells contain molecular chaperones that are organized in intricate networks to surveil protein homeostasis by avoiding polypeptide misfolding, aggregation, and the generation of toxic species. In addition, cellular chaperones also fulfill a multitude of alternative functionalities: transport of clients towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver clients towards proteolysis machineries. Until recently, the only available source of atomic resolution information for virtually all chaperones were crystal structures of their client-free, apo-forms...
April 2018: Journal of Magnetic Resonance
Zhou Hong, Juan Li, Sangita Biswas, Cheng-Shuai Jiang, Yu Huang, Tao Sun, Yang Niu, Jian-Qiang Yu, Wei-Qi Li, Yao Yao
Tamarix ramosissima is a traditional Chinese herbal medicine used for rheumatoid arthritis (RA) treatment in Northwest China. Chemical investigation of EtOH/H2O extracts of T. ramosissima led to the discovery of a new flavonol, ramosissimin (1), together with the known flavonoids compounds quercetin (2), quercetin-3'4'-dimethylether (3) and kaempferol (4). By means of high resolution electrospray ionization mass spectroscopy (HRESIMS) and 1D and 2D-NMR experiments, and after comparison with literature data, the structures of the compounds were determined...
March 5, 2018: Die Pharmazie
Z A Afonina, V A Shirokov
Polyribosomes in cells usually have a certain structural organization whose significance has not yet been elucidated. The development of cryo electron tomography has provided a new approach to study polyribosome structure. New data confirm or correct observations made earlier by classical techniques of electron microscopy. The existence of circular and linear (zigzag) topology of polyribosomes was confirmed, and their relationship with the frequently observed two-row forms was clarified. Contacts between ribosomes have been identified in densely packed three-dimensional helical polyribosomes...
January 2018: Biochemistry. Biokhimii︠a︡
Bing-You Yang, Zhang-Lin Chen, Yan Liu, Jiang-Tao Guo, Hai-Xue Kuang
A new lignan named schilignan F (1), together with twelve known ones (2-13), were isolated from the rattan stems of Schisandra chinensis. Their chemical structures were elucidated by spectroscopic methods including one and two-dimensional NMR spectra referring to the literatures as well as high-resolution mass spectrometric analysis. All compounds were evaluated for their cytotoxicities against human Hela cancer cell lines in vitro. The results showed that compounds 2, 6 and 8 exhibited weak cytotoxic activity with IC50 values of 30...
March 16, 2018: Natural Product Research
Chao Wang, Zhi-Yi Hu, Heng Zhao, Wenbei Yu, Sijia Wu, Jing Liu, Lihua Chen, Yu Li, Bao-Lian Su
We report three types of conducting polymers (CPs), polyaniline (PANI), polypyrrole (PPY) and poly (3,4-ethylenedioxythiophene) (PEDOT) to modify the surface of the CdS nanorods to probe their photocorrosion inhibition and photocatalytic hydrogen production. Various characterizations, such as high resolution transmission electron microscopy (HRTEM), X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV) and density function theory (DFT) calculations have been conducted to reveal the intrinsic structure of the as-constructed CPs@CdS (@ means CPs at the surface of CdS) core-shell nanorods...
March 6, 2018: Journal of Colloid and Interface Science
Carol Kelly, James D Chalmers, Iain Crossingham, Nicola Relph, Lambert M Felix, David J Evans, Stephen J Milan, Sally Spencer
BACKGROUND: Bronchiectasis is a chronic respiratory disease characterised by abnormal and irreversible dilatation and distortion of the smaller airways. Bacterial colonisation of the damaged airways leads to chronic cough and sputum production, often with breathlessness and further structural damage to the airways. Long-term macrolide antibiotic therapy may suppress bacterial infection and reduce inflammation, leading to fewer exacerbations, fewer symptoms, improved lung function, and improved quality of life...
March 15, 2018: Cochrane Database of Systematic Reviews
Céline Ronin, David Mendes Costa, Joana Tavares, Joana Faria, Fabrice Ciesielski, Paola Ciapetti, Terry K Smith, Jane MacDougall, Anabela Cordeiro-da-Silva, Iain K Pemberton
The de novo crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1 (LiSir2rp1) has been solved at 1.99Å in complex with an acetyl-lysine peptide substrate. The structure is broadly commensurate with Hst2/SIRT2 proteins of yeast and human origin, reproducing many of the structural features common to these sirtuin deacetylases, including the characteristic small zinc-binding domain, and the larger Rossmann-fold domain involved in NAD+-binding interactions. The two domains are linked via a cofactor binding loop ordered in open conformation...
2018: PloS One
Benjamin Stauch, Vadim Cherezov
G protein-coupled receptors (GPCRs) represent a large superfamily of membrane proteins that mediate cell signaling and regulate a variety of physiological processes in the human body. Structure-function studies of this superfamily were enabled a decade ago by multiple breakthroughs in technology that included receptor stabilization, crystallization in a membrane environment, and microcrystallography. The recent emergence of X-ray free-electron lasers (XFELs) has further accelerated structural studies of GPCRs and other challenging proteins by overcoming radiation damage and providing access to high-resolution structures and dynamics using micrometer-sized crystals...
March 15, 2018: Annual Review of Biophysics
Andrea Torchi, Davide Bochicchio, Giovanni M Pavan
The rational design of supramolecular polymers that can adapt or respond in time to specific stimuli in controlled way is interesting for many applications, but this requires understanding the molecular factors that make the material faster or slower in responding to the stimulus. To this end, it is necessary to study the dynamic adaptive properties at submolecular resolution, which is difficult at experimental level. Here we show coarse-grained molecular dynamics simulations (<5Å resolution) demonstrating how the dynamic adaptivity and stimuli responsiveness of a supramolecular polymer is controlled by the intrinsic dynamics of the assembly, which is in turn determined by the structure of the monomers...
March 15, 2018: Journal of Physical Chemistry. B
Qing Li, Biao Yang, Jonas Björk, Qigang Zhong, Huanxin Ju, Junjie Zhang, Nan Cao, Ziliang Shi, Haiming Zhang, Daniel Ebeling, Andre Schirmeisen, Junfa Zhu, Lifeng Chi
Hierarchical control of chemical reactions is being considered as one of the most ambitious and challenging topics in modern organic chemistry. In this study, we have realized the one-by-one scission of the X-H bonds (X=N and C) of aromatic amines in a controlled fashion on the Cu(111) surface. Each dehydrogenation reaction leads to certain metal-organic supramolecular structures, which were monitored in single-bond resolution via scanning tunneling microscopy and non-contact atomic force microscopy. Moreover, the reaction pathways were elucidated from X-ray photoelectron spectroscopy measurements and density functional theory calculations...
March 15, 2018: Journal of the American Chemical Society
Lauriane Lecoq, Shishan Wang, Thomas Wiegand, Stéphane Bressanelli, Michael Nassal, Beat H Meier, Anja Böckmann
The hepatitis B virus (HBV) icosahedral nucleocapsid is assembled from 240 chemically identical core protein molecules and, structurally, comprises four groups of symmetrically nonequivalent subunits. We show here that this asymmetry is reflected in solid-state NMR spectra of the capsids in which peak splitting is observed for a subset of residues. We compare this information to dihedral angle variations from available 3D structures, and also to computational predictions of dynamic domains and molecular hinges...
March 15, 2018: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Dehbia Benkerrou, Matteo Ceccarelli
One of the greatest health threats facing modern medicine is the emergence of new bacterial strains which are increasingly resistant to almost all currently available antibiotics. According to a CDC (Center for Disease Control and Prevention) report published in 2013, 63% of Acinetobacter species have been identified as Multidrug resistant strains. As for other Gram-negative bacteria, the presence of an outer membrane increases the intrinsic resistance of A. baumannii to most antibiotics. The outer membrane of A...
March 15, 2018: Physical Chemistry Chemical Physics: PCCP
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