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protein NMR

Ziye Zhang, Joe M Regenstein, Peng Zhou, Yuling Yang
The effects of high intensity ultrasound (HIU) modification (power: 200, 400, 600, 800 and 1000W, corresponding to intensities of: 88, 117, 150, 173 and 193Wcm(-2)) on the physicochemical properties of myofibrillar protein (MP) and water in MP gel were studied. As the HIU power increased, the solubility, surface hydrophobicity and absolute value of the zeta potential increased, while turbidity and total sulfhydryl (SH) group content decreased. The G' and G″ of MP during thermal gelation decreased as ultrasound intensity increased due to greater protein denaturation...
January 2017: Ultrasonics Sonochemistry
Dmitry M Korzhnev, Dante Neculai, Sirano Dhe-Paganon, Cheryl H Arrowsmith, Irina Bezsonova
HLTF is a SWI2/SNF2-family ATP-dependent chromatin remodeling enzyme that acts in the error-free branch of DNA damage tolerance (DDT), a cellular mechanism that enables replication of damaged DNA while leaving damage repair for a later time. Human HLTF and a closely related protein SHPRH, as well as their yeast homologue Rad5, are multi-functional enzymes that share E3 ubiquitin-ligase activity required for activation of the error-free DDT. HLTF and Rad5 also function as ATP-dependent dsDNA translocases and possess replication fork reversal activities...
October 22, 2016: Journal of Biomolecular NMR
Davide Sala, Andrea Giachetti, Claudio Luchinat, Antonio Rosato
The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions...
October 22, 2016: Journal of Biomolecular NMR
Dennis W Piehl, Luis M Blancas-Mejía, Marina Ramirez-Alvarado, Chad M Rienstra
Light chain (AL) amyloidosis is a systemic disease characterized by the formation of immunoglobulin light-chain fibrils in critical organs of the body. The light-chain protein AL-09 presents one severe case of cardiac AL amyloidosis, which contains seven mutations in the variable domain (VL) relative to its germline counterpart, κI O18/O8 VL. Three of these mutations are non-conservative-Y87H, N34I, and K42Q-and previous work has shown that they are responsible for significantly reducing the protein's thermodynamic stability, allowing fibril formation to occur with fast kinetics and across a wide-range of pH conditions...
October 22, 2016: Biomolecular NMR Assignments
Bin Tang, Yanmei Huang, Hongqin Yang, Peixiao Tang, Hui Li
As a natural dietary polyphenol, 3,4,5-tri-O-caffeoylquinic acid (3,4,5-triCQA) exhibits numerous stronger pharmacological activities than that of its analogues. Studies on interaction between 3,4,5-triCQA and protein are very helpful for understanding the mechanism of these enhanced biological functions. In this study, (1)H saturation transfer difference NMR ((1)H STD-NMR) combined with multi-spectroscopy were used to probe the interaction of 3,4,5-triCQA with human serum albumin (HSA). Both qualitative and quantitative (1)H STD-NMR indicated that 3,4,5-triCQA can specifically bind to HSA at the favored Sudlow's site II with caffeoyl groups as the main recognizable moiety...
October 17, 2016: Journal of Photochemistry and Photobiology. B, Biology
Svetlana V Fedorenko, Svetlana L Grechkina, Asiya R Mustafina, Kirill V Kholin, Alexey S Stepanov, Irek R Nizameev, Ildus E Ismaev, Marsil K Kadirov, Rustem R Zairov, Alfia N Fattakhova, Rustem R Amirov, Svetlana E Soloveva
The present work introduces deliberate synthesis of Gd(III)-doped silica nanoparticles with high relaxivity at magnetic field strengths below 1.5T. Modified microemulsion water-in-oil procedure was used in order to achieve superficial localization of Gd(III) complexes within 40-55nm sized silica spheres. The relaxivities of the prepared nanoparticles were measured at 0.47, 1.41 and 1.5T with the use of both NMR analyzer and whole body NMR scanner. Longitudinal relaxivities of the obtained silica nanoparticles reveal significant dependence on the confinement mode, changing from 4...
October 14, 2016: Colloids and Surfaces. B, Biointerfaces
Meng Wang, Ian Tietjen, Min Chen, David E Williams, Julie Daoust, Mark A Brockman, Raymond J Andersen
Eight new sesterterpenoids, alotaketals D (8) and E (9), ansellones D (10), E (11), F (12), and G (13), anvilones A (14), and B (15), have been isolated from extracts of the marine sponge Phorbas sp. collected in Howe Sound British Columbia and their structures have been elucidated by analysis of NMR and MS data. Ansellone F (12) contains a rare 1,2-3,4 bis epoxy decalin substructure. Anvilones A (14) and B (15) have the unprecedented tetracylic anvilane terpenoid carbon skeleton. Using a cell culture model of latent HIV-1 infection, ansellone A (3), alotaketal D (8), and anvilone A (14) were found to induce HIV proviral gene expression similar to a control compound prostratin (1), while the known sesterterpenoid alotaketal C (2), isolated from the same extract, was more potent and gave a stronger response than prostratin (1)...
October 21, 2016: Journal of Organic Chemistry
Hong Zhang, Zheng Dan, Zhi-Jie Ding, Yuan-Zhi Lao, Hong-Sheng Tan, Hong-Xi Xu
A UPLC-PDA-QTOFMS-guided isolation strategy was employed to screen and track potentially new compounds from Garcinia oblongifolia. As a result, two new prenylated xanthones, oblongixanthones D and E (1-2), six new prenylated benzoylphloroglucinol derivatives, oblongifolins V-Z (3-7) and oblongifolin AA (8), as well as a known compound oblongifolin L (9), were isolated from the EtOAc-soluble fraction of an acetone extract of the leaves of Garcinia oblongifolia guided by UPLC-PDA-QTOFMS analysis. The structures of the new compounds were elucidated by 1D- and 2D-NMR spectroscopic analysis and mass spectrometry...
October 21, 2016: Scientific Reports
Hongwei Yao, Myungwoon Lee, Shu Y Liao, Mei Hong
The fusion peptide (FP) and transmembrane domain (TMD) of viral fusion proteins play important roles during virus-cell membrane fusion, by inducing membrane curvature and transient dehydration. The structure of the water-soluble ectodomain of viral fusion proteins has been extensively studied crystallographically, but the structures of the FP and TMD bound to phospholipid membranes are not well understood. We recently investigated the conformations and lipid interactions of the separate FP and TMD peptides of the parainfluenza virus 5 (PIV5) fusion protein F using solid-state NMR...
October 21, 2016: Biochemistry
Flavia A Mercurio, Daniela Marasco, Concetta Di Natale, Luciano Pirone, Susan Costantini, Emilia M Pedone, Marilisa Leone
The EphA2 receptor controls diverse physiological and pathological conditions and its levels are often upregulated in cancer. Targeting receptor overexpression, through modulation of endocytosis and consequent degradation, appears to be an appealing strategy for attacking tumor malignancy. In this scenario, the Sam domain of EphA2 plays a pivotal role because it is the site where protein regulators of endocytosis and stability are recruited by means of heterotypic Sam-Sam interactions. Because EphA2-Sam heterotypic complexes are largely based on electrostatic contacts, we have investigated the possibility of attacking these interactions with helical peptides enriched in charged residues...
October 20, 2016: Chembiochem: a European Journal of Chemical Biology
Christoph Göbl, Moritz Resch, Madeleine Strickland, Christoph Hartlmüller, Martin Viertler, Nico Tjandra, Tobias Madl
The study of intrinsically disordered proteins (IDPs) by NMR often suffers from highly overlapped resonances that prevent unambiguous chemical-shift assignments, and data analysis that relies on well-separated resonances. We present a covalent paramagnetic lanthanide-binding tag (LBT) for increasing the chemical-shift dispersion and facilitating the chemical-shift assignment of challenging, repeat-containing IDPs. Linkage of the DOTA-based LBT to a cysteine residue induces pseudo-contact shifts (PCS) for resonances more than 20 residues from the spin-labeling site...
October 20, 2016: Angewandte Chemie
Krystal A Morales, Yuan Yang, Taylor R Cole, Tatyana I Igumenova
Ca(2+)-dependent conserved-region 2 (C2) domains target their host signaling proteins to anionic membranes. The Ca(2+)-binding event is a prerequisite for membrane association. Here, we investigate multiscale metal-ion-dependent dynamics of the C2 domain of protein kinase Cα (C2α) using NMR spectroscopy. Interactions with metal ions attenuate microsecond-timescale motions of the loop regions, indicating that preorganization of the metal-binding loops occurs before membrane insertion. Binding of a full complement of Ca(2+) ions has a profound effect on the millisecond-timescale dynamics of the N- and C-terminal regions of C2α...
October 18, 2016: Biophysical Journal
Valeria Lanza, Alessio Travaglia, Gaetano Malgieri, Roberto Fattorusso, Giuseppe Grasso, Giuseppe Di Natale, Valeria Zito, Giuseppe Arena, Danilo Milardi, Enrico Rizzarelli
Many biochemical pathways involving nerve growth factor (NGF), a neurotrophin with copper(II) binding abilities, are regulated by the ubiquitin (Ub) proteasome system. However, whether NGF binds Ub and the role played by copper(II) ions in modulating their interactions have not yet been investigated. Herein NMR spectroscopy, circular dichroism, ESI-MS, and titration calorimetry are employed to characterize the interactions of NGF with Ub. NGF1-14 , which is a short model peptide encompassing the first 14 N-terminal residues of NGF, binds the copper-binding regions of Ub (KD =8...
October 19, 2016: Chemistry: a European Journal
Aleksandar Antanasijevic, Nicholas J Hafeman, Smanla Tundup, Carolyn Kingsley, Rama K Mishra, Lijun Rong, Balaji Manicassamy, Duncan Wardrop, Michael Caffrey
The viral envelope protein hemagglutinin (HA) plays a critical role in influenza entry and thus is an attractive target for novel therapeutics. The small molecule tert-butylhydroquinone (TBHQ) has previously been shown to bind to HA and inhibit HA-mediated entry with low micromolar potency. However, enthusiasm for the use of TBHQ has diminished due to the compound's antioxidant properties. In this work we show that the antioxidant properties of TBHQ are not responsible for the inhibition of HA-mediated entry...
September 9, 2016: ACS Infectious Diseases
Laura Bouché, Maria Panico, Paul Hitchen, Daniel Binet, Federico Sastre, Alexandra Faulds-Pain, Esmeralda Valiente, Evgeny Vinogradov, Annie Aubry, Kelly Fulton, Susan Twine, Susan M Logan, Brendan W Wren, Anne Dell, Howard R Morris
Glycosylation of flagellins is a well recognized property of many bacterial species. In this study we describe the structural characterization of novel flagellar glycans from a number of hypervirulent strains of C. difficile. We used mass spectrometry (nano LC- MS and MS/MS analysis) to identify a number of putative glycopeptides which carried a variety of glycoform substitutions each of which was linked through an initial HexNAc residue to Ser or Thr. Detailed analysis of a LLDGSSTEIR glycopeptide released by tryptic digestion, which carried two variant structures, revealed that the glycopeptide contained, in addition to carbohydrate moieties, a novel structural entity...
October 7, 2016: Journal of Biological Chemistry
Yoshiaki Manse, Kiyofumi Ninomiya, Ryosuke Nishi, Iyori Kamei, Yushi Katsuyama, Takahito Imagawa, Saowanee Chaipech, Osamu Muraoka, Toshio Morikawa
An aqueous acetone extract from the fruit of Alpinia galanga (Zingiberaceae) demonstrated inhibitory effects on melanogenesis in theophylline-stimulated murine B16 melanoma 4A5 cells (IC50=7.3μg/mL). Through bioassay-guided separation of the extract, a new 7-O-9'-linked neolignan, named galanganol D diacetate (1), was isolated along with 16 known compounds including 14 phenylpropanoids (2-15). The structure of 1, including its absolute stereochemistry in the C-7 position, was elucidated by means of extensive NMR analysis and total synthesis...
October 6, 2016: Bioorganic & Medicinal Chemistry
Joseph R Sachleben, Aashish N Adhikari, Grzegorz Gawlak, Robert J Hoey, Gaohua Liu, Andrzej Joachimiak, Gaetano T Montelione, Tobin R Sosnick, Shohei Koide
We determined the NMR structure of a highly aromatic (13%) protein of unknown function, Aq1974 from Aquifex aeolicus. The unusual sequence of this protein has a tryptophan content 5 times the normal (six tryptophan residues of 114 or 5.2% while the average tryptophan content is 1.0%) with the tryptophans occurring in a WXW motif. It has no detectable sequence homology with known protein structures. Although its NMR spectrum suggested that the protein was rich in β-sheet, upon resonance assignment and solution structure determination, the protein was found to be primarily α-helical with a small two-stranded β-sheet with a novel fold that we have termed an Aromatic Claw...
October 17, 2016: Protein Science: a Publication of the Protein Society
Joanna J Hoppins, David R Gruber, Heather L Miears, Alexey S Kiryutin, Rustem D Kasymov, Darya V Petrova, Anton V Endutkin, Alexander V Popov, Alexandra V Yurkovskaya, Stanislav O Fedechkin, Jacob A Brockerman, Dmitry O Zharkov, Serge L Smirnov
8-oxoguanine is one of the most abundant and impactful oxidative DNA lesions. However, the reasons underlying its effects, especially those not directly explained by the altered base pairing ability, are poorly understood. We report the effect of the lesion on the action of EcoRI, a widely used restriction endonuclease. Introduction of 8-oxoguanine inside, or adjacent to, the GAATTC recognition site embedded within the Drew-Dickerson dodecamer sequence notably reduced the EcoRI activity. Solution NMR revealed that 8-oxoguanine in the DNA duplex causes substantial alterations in the sugar-phosphate backbone conformation, inducing a BI→BII transition...
2016: PloS One
John Lee
The molecular mechanisms of the bioluminescence systems of the firefly, bacteria, and those utilizing imidazopyrazinone luciferins such as coelenterazine, are gradually being uncovered using modern biophysical methods such as dynamic (ns-ps) fluorescence spectroscopy, NMR, X-ray crystallography, and computational chemistry. The chemical structures of all reactants are well defined and the spatial structures of the luciferases are providing important insight into interactions within the active cavity. It is generally accepted that the firefly and coelenterazine systems, although proceeding by different chemistries, both generate a dioxetanone high energy species that undergoes decarboxylation to form directly the product in its S1 state, the bioluminescence emitter...
October 17, 2016: Photochemistry and Photobiology
Alessandro Piai, Qingshan Fu, Jyoti Dev, James Jeiwen Chou
Structural characterization of transmembrane proteins in isotropic bicelles has become an increasingly popular application of solution NMR spectroscopy, as the fast-tumbling bicelles are membrane-like yet can often yield spectral quality comparable to those of detergent micelles. While larger bicelles are closer to the true lipid bilayer, it remains unclear how large the bicelles need to be to allow accurate assessment of protein transmembrane partition in lipid bilayer. Here, we address the above question from the perspective of protein residing in the bicelles, through systematic measurement of protein chemical shift and transmembrane partition at different lipid:detergent ratios (q), ranging from 0...
October 17, 2016: Chemistry: a European Journal
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