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https://www.readbyqxmd.com/read/28654715/a-secondary-structure-element-present-in-a-wide-range-of-fucosylated-glycoepitopes
#1
Mario Schubert, Thomas Aeschbacher, Mirko Zierke, Martin Smieško, Mayeul Collot, Jean-Maurice Mallet, Beat Ernst, Frédéric H-T Allain
The increasing understanding of the essential role of carbohydrates in development, and in a wide range of diseases fuels a rapidly growing interest in the basic principles governing carbohydrate-protein interactions. A still heavily debated issue regarding the recognition process is the degree of flexibility or rigidity of oligosaccharides. Combining NMR structure determination based on extensive experimental data with density functional theory (DFT) and database searches, we have identified a set of trisaccharide motifs with a similar conformation that is characterized by a non-conventional C-H⋅⋅⋅O hydrogen bond...
June 27, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28654636/human-cyclophilin-40-unravels-neurotoxic-amyloids
#2
Jeremy D Baker, Lindsey B Shelton, Dali Zheng, Filippo Favretto, Bryce A Nordhues, April Darling, Leia E Sullivan, Zheying Sun, Parth K Solanki, Mackenzie D Martin, Amirthaa Suntharalingam, Jonathan J Sabbagh, Stefan Becker, Eckhard Mandelkow, Vladimir N Uversky, Markus Zweckstetter, Chad A Dickey, John Koren, Laura J Blair
The accumulation of amyloidogenic proteins is a pathological hallmark of neurodegenerative disorders. The aberrant accumulation of the microtubule associating protein tau (MAPT, tau) into toxic oligomers and amyloid deposits is a primary pathology in tauopathies, the most common of which is Alzheimer's disease (AD). Intrinsically disordered proteins, like tau, are enriched with proline residues that regulate both secondary structure and aggregation propensity. The orientation of proline residues is regulated by cis/trans peptidyl-prolyl isomerases (PPIases)...
June 2017: PLoS Biology
https://www.readbyqxmd.com/read/28653216/nmr-characterization-of-htpg-the-e-coli-hsp90-using-sparse-labeling-with-13-c-methyl-alanine
#3
Kari Pederson, Gordon R Chalmers, Qi Gao, Daniel Elnatan, Theresa A Ramelot, Li-Chung Ma, Gaetano T Montelione, Michael A Kennedy, David A Agard, James H Prestegard
A strategy for acquiring structural information from sparsely isotopically labeled large proteins is illustrated with an application to the E. coli heat-shock protein, HtpG (high temperature protein G), a 145 kDa dimer. It uses (13)C-alanine methyl labeling in a perdeuterated background to take advantage of the sensitivity and resolution of Methyl-TROSY spectra, as well as the backbone-centered structural information from (1)H-(13)C residual dipolar couplings (RDCs) of alanine methyl groups. In all, 40 of the 47 expected crosspeaks were resolved and 36 gave RDC data...
June 26, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28652408/the-extreme-c-terminal-region-of-kindlin-2-is-critical-to-its-regulation-of-integrin-activation
#4
Jamila Hirbawi, Katarzyna Bialkowska, Kamila M Bledzka, Jianmin Liu, Koichi Fukuda, Jun Qin, Edward F Plow
Kindlin-2 (K2), a 4.1R-ezrin-radixin-moesin (FERM) domain adaptor protein, mediates numerous cellular responses, including integrin activation. The C-terminal 15 amino acid sequence of K2 is remarkably conserved across species but is absent in canonical FERM proteins including talin. In CHO cells expressing integrin αIIbβ3, co-expression of K2 with talin head (talin-H) domain resulted in robust integrin activation, but this co-activation was lost after deletion of as few as seven amino acids from the K2 C-terminus...
June 26, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28652206/membrane-solid-state-nmr-in-canada-a-historical-perspective
#5
REVIEW
Michèle Auger
This manuscript presents an overview of more than 40years of membrane solid-state nuclear magnetic resonance (NMR) research in Canada. This technique is a method of choice for the study of the structure and dynamics of lipid bilayers; bilayer interactions with a variety of molecules such as membrane peptides, membrane proteins and drugs; and to investigate membrane peptide and protein structure, dynamics, and topology. Canada has a long tradition in this field of research, starting with pioneering work on natural and model membranes in the 1970s in a context of emergence of biophysics in the country...
June 23, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28652006/3d-nus-a-web-server-for-automated-modeling-and-visualization-of-non-canonical-3-dimensional-nucleic-acid-structures
#6
L Ponoop Prasad Patro, Abhishek Kumar, Narendar Kolimi, Thenmalarchelvi Rathinavelan
The inherent conformational flexibility of nucleic acids facilitate the formation of a range of conformations such as duplex, triplex, quadruplex etc. that play crucial roles in biological processes. Elucidation about the influence of non-canonical base pair mismatches on DNA/RNA structures at different sequence contexts to understand mismatch repair and misregulation of alternative splicing mechanisms as well as the sequence dependent effect of RNA-DNA hybrid in relevance to antisense strategy demand their three-dimensional structural information...
June 23, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28650487/engineering-thiophene-based-nanoparticles-to-induce-phototransduction-in-live-cells-under-illumination
#7
M Zangoli, F Di Maria, E Zucchetti, C Bossio, M R Antognazza, G Lanzani, R Mazzaro, F Corticelli, M Baroncini, G Barbarella
We report that nanoparticles prepared from appropriately functionalized polythiophenes once administered to live cells can acquire phototransduction properties under illumination, becoming photoactive sites able to absorb visible light and convert it to an electrical signal through cell membrane polarization. Amine-reactive fluorescent nanoparticles with pendant N-succinimidyl-ester groups (NPs-NHS) are prepared from polythiophenes alternating unsubstituted and 3-(2,5-dioxopyrrolidin-1-yl-8-octanoate)-substituted thiophenes by a nanoprecipitation method...
June 26, 2017: Nanoscale
https://www.readbyqxmd.com/read/28650111/photochromic-dopamine-receptor-ligands-based-on-dithienylethenes-and-fulgides
#8
Daniel Lachmann, Carolin Studte, Barbara Männel, Harald Huebner, Peter Gmeiner, Burkhard König
We describe the incorporation of the well-investigated class of photochromic dithienylethenes (DTEs) and fulgides into known dopamine receptor ligands like 1,4-disubstituted aromatic and hydroxybenzoxazinone piperazines as well as aminoindanes. Subtype and functional selective photochromic ligands were obtained and characterized by NMR and UV-VIS spectroscopic measurements. The photophysical properties of the DTE based dopamine ligands revealed a high fatigue resistance for the diarylmaleimides, but the ringclosure could not be accomplished in polar solvents due to a known twisted intramolecular charge transfer (TICT)...
June 26, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28649731/protein-glycan-quinary-interactions-in-crowding-environment-unveiled-by-nmr-spectroscopy
#9
Ana Diniz, Jorge S Dias, Jesús Jiménez-Barbero, Filipa Marcelo, Eurico J Cabrita
Protein-glycan interactions as modulators for quinary structure in crowding environments were explored. The interaction between human galectin 3 (Gal-3) and distinct macromolecular crowders, such as bovine and human serum albumin (BSA and HSA), Ficoll 70 and PEG3350, was scrutinized. The molecular recognition event of the specific ligand, lactose, by Gal-3 in crowding conditions was evaluated. Gal-3 interactions were monitored by NMR analysing chemical shift perturbation (CSP) and line broadening of 1H15N-HSQC signals...
June 25, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28649017/chiral-alkylated-aniline-as-a-noninvasive-fluorescence-sensor-spectroscopic-and-molecular-modeling-studies
#10
Bidisha Sengupta, Chirantan Sen Mukherjee, Sandipan Chakraborty, Maria Jones Muhammad, William Gladney, George Armstrong
Aniline, heterocyclic aromatic amines, and arylamines are known carcinogens. Recently aniline mustard has come into prominence as a novel anticancer agent. In this project, microwave irradiation has been used to synthesize an optically active alkylated aniline namely 2,6-dimethyl-4-(1-(p-tolyl)ethyl)aniline (abbreviated DMPA). The presence of quartet and doublet peaks in NMR and a single chromatogram in HPLC verified that the final product DMPA, prepared from the synthesis reactions, had no major impurities...
June 7, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28648524/molecular-modelling-of-biomolecules-by-paramagnetic-nmr-and-computational-hybrid-methods
#11
REVIEW
Kala Bharath Pilla, Kari Gaalswyk, Justin L MacCallum
The 3D atomic structures of biomolecules and their complexes are key to our understanding of biomolecular function, recognition, and mechanism. However, it is often difficult to obtain structures, particularly for systems that are complex, dynamic, disordered, or exist in environments like cell membranes. In such cases sparse data from a variety of paramagnetic NMR experiments offers one possible source of structural information. These restraints can be incorporated in computer modelling algorithms that can accurately translate the sparse experimental data into full 3D atomic structures...
June 22, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28648056/anamorsin-ndor1-complex-reduces-2fe-2s-mitoneet-via-a-transient-protein-protein-interaction
#12
Francesca Camponeschi, Simone Ciofi-Baffoni, Lucia Banci
Human mitoNEET is a homodimeric protein anchored to the outer mitochondrial membrane and with a C-terminal [2Fe-2S] binding domain located in the cytosol. Recently, human mitoNEET has been shown to be implicated in Fe/S cluster repair of the cytosolic iron regulatory protein 1 (IRP1), a key regulator of cellular iron homeostasis in mammalian cells. The Fe/S cluster repairing function of mitoNEET is based on a Fe/S redox switch mechanism: under normal cellular conditions, reduced [2Fe-2S](+) mitoNEET is present and is inactive as Fe/S cluster transfer protein; under conditions of oxidative cellular stress, the clusters of mitoNEET become oxidized and the formed [2Fe-2S](2+) mitoNEET species reacts promptly to initiate Fe/S cluster transfer to IRP1 recycling the cytosolic apo-IRP1 into holo-aconitase...
June 25, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28646429/decoupled-side-chain-and-backbone-dynamics-for-proton-translocation-m2-of-influenza-a
#13
Monoj Mon Kalita, Wolfgang B Fischer
The 97 amino acid bitopic membrane protein M2 of influenza A forms a tetrameric bundle in which two of the monomers are covalently linked via a cysteine bridge. In its tetrameric assembly the protein conducts protons across the viral envelope and within intracellular compartments during the infectivity cycle of the virus. A key residue in the translocation of the protons is His-37 which forms a planar tetrad in the configuration of the bundle accepting and translocating the incoming protons from the N terminal side, exterior of the virus, to the C terminal side, inside the virus...
July 2017: Journal of Molecular Modeling
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/28645916/structures-and-dynamics-of-hibernating-ribosomes-from-staphylococcus-aureus-mediated-by-intermolecular-interactions-of-hpf
#15
Iskander Khusainov, Quentin Vicens, Rustam Ayupov, Konstantin Usachev, Alexander Myasnikov, Angelita Simonetti, Shamil Validov, Bruno Kieffer, Gulnara Yusupova, Marat Yusupov, Yaser Hashem
In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structures of hibernating ribosomes from human pathogen Staphylococcus aureus containing a long variant of the hibernation-promoting factor (SaHPF) that we solved using cryo-electron microscopy. Our reconstructions reveal that the N-terminal domain (NTD) of SaHPF binds to the 30S subunit as observed for shorter variants of HPF in other species...
June 23, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28645492/advances-in-stable-isotope-assisted-labeling-strategies-with-information-science
#16
Takanori Kigawa
Stable-isotope (SI) labeling of proteins is an essential technique to investigate their structures, interactions or dynamics by nuclear magnetic resonance (NMR) spectroscopy. The assignment of the main-chain signals, which is the fundamental first step in these analyses, is usually achieved by a sequential assignment method based on triple resonance experiments. Independently of the triple resonance experiment-based sequential assignment, amino acid-selective SI labeling is beneficial for discriminating the amino acid type of each signal; therefore, it is especially useful for the signal assignment of difficult targets...
June 20, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28645072/association-of-the-serum-myeloperoxidase-high-density-lipoprotein-particle-ratio-and-incident-cardiovascular-events-in-a-multi-ethnic-population-observations-from-the-dallas-heart-study
#17
Htet W Khine, John F Teiber, Robert W Haley, Amit Khera, Colby R Ayers, Anand Rohatgi
BACKGROUND AND AIMS: Myeloperoxidase (MPO), a product of systemic inflammation, promotes oxidation of lipoproteins; whereas, high-density lipoprotein (HDL) exerts anti-oxidative effects in part via paraoxonase-1 (PON1). MPO induces dysfunctional HDL particles; however, the interaction of circulating levels of these measures in cardiovascular disease (CVD) has not been studied in humans. We tested whether serum levels of MPO indexed to HDL particle concentration (MPO/HDLp) are associated with increased CVD risk in a large multiethnic population sample, free of CVD at baseline...
June 3, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28644630/expanding-the-therapeutic-potential-of-the-iron-chelator-deferasirox-in-the-development-of-aqueous-stable-ti-iv-anticancer-complexes
#18
Sergio A Loza-Rosas, Alexandra M Vázquez-Salgado, Kennett I Rivero, Lenny J Negrón, Yamixa Delgado, Josué A Benjamín-Rivera, Angel L Vázquez-Maldonado, Timothy B Parks, Charlene Munet-Colón, Arthur D Tinoco
The recent X-ray structure of titanium(IV)-bound human serum transferrin (STf) exhibiting citrate as a synergistic anion reveals a difference in Ti(IV) coordination versus iron(III), the metal endogenously delivered by the protein to cells. This finding enriches our bioinspired drug design strategy for Ti(IV)-based anticancer therapeutics, which applies a family of Fe(III) chelators termed chemical transferrin mimetic (cTfm) ligands to inhibit Fe bioavailability in cancer cells. Deferasirox, a drug used for iron overload disease, is a cTfm ligand that models STf coordination to Fe(III), favoring Fe(III) binding versus Ti(IV)...
June 23, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28644609/galnac-tyrosine-is-a-ligand-of-plant-lectins-antibodies-and-human-and-murine-macrophage-galactose-type-lectins
#19
Ruslan Gibadullin, David Wayne Farnsworth, Joseph J Barchi, Jeffrey C Gildersleeve
In 2011, a new type of protein O-glycosylation was discovered in which N-acetylgalactosamine is attached to the side chain of tyrosine (GalNAc-Tyr). While present on dozens of proteins, the biological roles of GalNAc-Tyr are unknown. To gain insight into this new type of modification, we synthesized a group of GalNAc-Tyr glycopeptides, constructed microarrays, and evaluated potential recognition of GalNAc-Tyr by a series of glycan-binding proteins. Through a series of >150 microarray experiments, we assessed binding properties of a variety of plant lectins, monoclonal antibodies, and endogenous lectins...
June 23, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28644511/bacteriophage-tail-tube-assembly-studied-by-proton-detected-4d-solid-state-nmr
#20
Maximilian Zinke, Pascal Fricke, Camille Samson, Songhwan Hwang, Joseph Wall, Sascha Lange, Sophie Zinn-Justin, Adam Lange
Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2%)...
June 23, 2017: Angewandte Chemie
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