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https://www.readbyqxmd.com/read/28551334/structure-and-dimerization-of-ireb-a-negative-regulator-of-cephalosporin-resistance-in-enterococcus-faecalis
#1
Cherisse L Hall, Betsy L Lytle, Davin Jensen, Jessica S Hoff, Francis C Peterson, Brian F Volkman, Christopher J Kristich
Enterococcus faecalis, a leading cause of hospital-acquired infections, exhibits intrinsic resistance to most cephalosporins, which are antibiotics in the beta-lactam family that target cell-wall biosynthesis. A comprehensive understanding of the underlying genetic and biochemical mechanisms of cephalosporin resistance in E. faecalis is lacking. We previously determined that a transmembrane serine-threonine kinase (IreK) and its cognate phosphatase (IreP) reciprocally regulate cephalosporin resistance in E...
May 24, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28550651/a-new-biphenyl-ether-derivative-produced-by-indonesian-ascidian-derived-penicillium-albobiverticillium
#2
Deiske A Sumilat, Hiroyuki Yamazaki, Kotaro Endo, Henki Rotinsulu, Defny S Wewengkang, Kazuyo Ukai, Michio Namikoshi
A new biphenyl ether derivative, 2-hydroxy-6-(2'-hydroxy-3'-hydroxymethyl-5-methylphenoxy)-benzoic acid (1), was isolated together with the known benzophenone derivative, monodictyphenone (2), from a culture broth of Indonesian ascidian-derived Penicillium albobiverticillium TPU1432 by solvent extraction, ODS column chromatography, and preparative HPLC (ODS). The structure of 1 was elucidated based on NMR experiments. Compound 2 exhibited moderate inhibitory activities against protein tyrosine phosphatase (PTP) 1B, T cell PTP (TCPTP), and CD45 tyrosine phosphatase (CD45), whereas compound 1 modestly inhibited CD45 activity...
May 26, 2017: Journal of Natural Medicines
https://www.readbyqxmd.com/read/28549582/crystal-structure-of-spsb2-in-complex-with-a-rational-designed-rgd-containing-cyclic-peptide-inhibitor-of-spsb2-inos-interaction
#3
Tingting You, Yuhui Wang, Kefa Li, Danting Zhang, Huan Wei, Yanhong Luo, Hua Li, Yongzhi Lu, Xunchen Su, Zhihe Kuang
SPRY domain-containing SOCS box protein 2 (SPSB2) is a negative regulator of inducible nitric oxide synthase (iNOS) that modulates the lifetime of iNOS and thus the levels of nitric oxide (NO) production. Inhibitors that can disrupt the endogenous SPSB2-iNOS interaction and augment NO production have potential as novel antimicrobial and anticancer drugs. In this study, we have designed a cyclic peptide (cR8), containing an RGD motif and the SPSB2 binding motif (DINNNV). ITC and chemical shift perturbation showed that cR8 binds to the iNOS binding site on SPSB2 with a Kd of 671 nM, and saturation transfer difference NMR showed that cR8 binds to αvβ3 integrin-expressing cells...
May 23, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28547869/the-zinc-finger-domain-of-ring-finger-protein-141-reveals-a-unique-ring-fold
#4
Kazuhide Miyamoto, Airi Uechi, Kazuki Saito
Human RING finger protein 141 (RFP141) is a germ cell-specific transcription factor during spermatogenesis. We synthesized a compact construct encoding the C-terminal zinc finger of RFP141 (RFP141C peptide). Herein we determined the solution structure of the RFP141C peptide by nuclear magnetic resonance (NMR). Moreover, NMR data and the chemical modification of cysteine residues demonstrated that the RFP141C peptide binds to two zinc atoms in a cross-brace arrangement. The Simple Modular Architecture Research Tool database predicted the structure of RFP141C as a RING finger...
May 25, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28547731/proline-isomerization-in-the-c-terminal-region-of-hsp27
#5
T Reid Alderson, Justin L P Benesch, Andrew J Baldwin
In mammals, small heat-shock proteins (sHSPs) typically assemble into interconverting, polydisperse oligomers. The dynamic exchange of sHSP oligomers is regulated, at least in part, by molecular interactions between the α-crystallin domain and the C-terminal region (CTR). Here we report solution-state nuclear magnetic resonance (NMR) spectroscopy investigations of the conformation and dynamics of the disordered and flexible CTR of human HSP27, a systemically expressed sHSP. We observed multiple NMR signals for residues in the vicinity of proline 194, and we determined that, while all observed forms are highly disordered, the extra resonances arise from cis-trans peptidyl-prolyl isomerization about the G193-P194 peptide bond...
May 25, 2017: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/28544203/observation-of-ch%C3%A2-%C3%A2-%C3%A2-%C3%AF-interactions-between-methyl-and-carbonyl-groups-in-proteins
#6
Frédéric A Perras, Dominique Marion, Jérôme Boisbouvier, David L Bryce, Michael J Plevin
Protein structure and function is dependent on myriad noncovalent interactions. Direct detection and characterization of these weak interactions in large biomolecules, such as proteins, is experimentally challenging. Herein, we report the first observation and measurement of long-range "through-space" scalar couplings between methyl and backbone carbonyl groups in proteins. These J couplings are indicative of the presence of noncovalent C-H⋅⋅⋅π hydrogen-bond-like interactions involving the amide π network...
May 22, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28543811/the-structural-flexibility-of-the-human-copper-chaperone-atox1-insights-from-combined-pulsed-epr-studies-and-computations
#7
Ariel R Levy, Meital Turgeman, Lada Gevorkyan-Aiapetov, Sharon Ruthstein
Metallochaperones are responsible for shuttling metal ions to target proteins. Thus, a metallochaperone's structure must be sufficiently flexible both to hold onto its ion while traversing the cytoplasm and to transfer the ion to or from a partner protein. Here, we sought to shed light on the structure of Atox1, a metallochaperone involved in the human copper regulation system. Atox1 shuttles copper ions from the main copper transporter, Ctr1, to the ATP7b transporter in the Golgi apparatus. Conventional biophysical tools such as X-ray or NMR cannot always target the various conformational states of metallochaperones, owing to a requirement for crystallography or low sensitivity and resolution...
May 20, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28543298/synthesis-and-preclinical-pharmacokinetic-study-of-dha-10-a-novel-potential-antifungal-pogostone-analogue
#8
Ming Liu, Yanfen Zhou, Jianwei Zhu, Bo Ma, Zheng Fang, Qi Zhang
OBJECTIVES: The emergence of fungal disease calls for the urgency of development of novel drug. In this study, we developed a novel pogostone analogue, DHA-10 and investigated its preclinical pharmacokinetics, tissue distribution, excretion and protein binding rate in rats. METHODS: DHA-10 was synthesized with dehydroacetic acid (DHA) as the starting material and the structure confirmed by NMR and HRMS. The LC-MS/MS was applied to quantitative analysis of DHA-10 concentrations in the biological samples...
May 23, 2017: Journal of Pharmacy and Pharmacology
https://www.readbyqxmd.com/read/28542883/biochemical-characterization-and-dominance-of-different-hydrolases-in-different-types-of-daqu-a-chinese-industrial-fermentation-starter
#9
Jingjing Liu, Jingyu Chen, Yi Fan, Xiaoning Huang, Beizhong Han
BACKGROUND: Daqu is a fermentative saccharification agent that is used to initiate fermentation in the production of Chinese liquor and vinegar. This study investigated the differences of amylase, protease and esterase in dominance of different types of Daqu, which can be useful for quality control and flavor improvement of Daqu production by enzyme technology. RESULTS: Hydrolase activities in different Daqu samples were compared by Principal Component Analysis (PCA)...
May 25, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28541675/prediction-of-bond-vector-autocorrelation-functions-from-larmor-frequency-selective-order-parameter-analysis-of-nmr-relaxation-data
#10
Janet S Anderson, Griselda Hernandez, David M LeMaster
Protein molecular dynamics interpretation of the standard R1, R2 and heteronuclear NOE relaxation measurements has typically been limited to a single S(2) order parameter which is often insufficient to characterize the rich content of these NMR experiments. In the absence of exchange linebroadening, an optimized reduced spectral density analysis of these measurements can yield spectral density values at three distinct frequencies. Surprisingly, these three discrete spectral density values have proven to be sufficient for a Larmor frequency-selective order parameter analysis of the 223 methine and methylene H-C bonds of the B3 domain of Protein G (GB3) to accurately back-calculate the entire curve of the corresponding bond vector autocorrelation functions upon which the NMR relaxation behavior depends...
May 25, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28539640/recalcitrant-carbon-components-in-glomalin-related-soil-protein-facilitate-soil-organic-carbon-preservation-in-tropical-forests
#11
Jing Zhang, Xuli Tang, Siyuan Zhong, Guangcai Yin, Yifei Gao, Xinhua He
Glomalin-related soil protein (GRSP) is known as an important microbial by-product which is crucial for preserving or accumulating soil organic carbon (SOC). However, the underlying mechanisms are not well understood. In this study, we investigated the chemical structures of GRSP and its relationship with SOC using (13)C nuclear magnetic resonance (NMR) in three tropical forests. The three forests, including a planted forest (PF), a secondary forest (MF) and a primary forest (BF), were selected to represent the natural successional process after disturbance in southern China...
May 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28539221/lodopyridones-b-and-c-from-a-marine-sediment-derived-bacterium-saccharomonospora-sp
#12
Tu Cam Le, Chae-Yoon Yim, Songhee Park, Nikita Katila, Inho Yang, Myoung Chong Song, Yeo Joon Yoon, Dong-Young Choi, Hyukjae Choi, Sang-Jip Nam, William Fenical
HPLC-UV guided isolation of the culture broth of a marine bacterium Saccharomonospora sp. CNQ-490 has led to the isolation of two new natural products, lodopyridones B and C (1 and 2) along with the previously reported lodopyridone A (3). Their chemical structures were established from the interpretation of 2D NMR spectroscopic data and the comparison of NMR data with the lodopyridone A (3). Lodopyridones B and C (1 and 2) possess the thiazole, and chloroquinoline groups which are characteristic features of these molecules...
May 12, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28538145/nmr-analysis-of-amide-hydrogen-exchange-rates-in-a-pentapeptide-repeat-protein-from-a-%C3%A2-thaliana
#13
Shenyuan Xu, Shuisong Ni, Michael A Kennedy
At2g44920 from Arabidopsis thaliana is a pentapeptide-repeat protein (PRP) composed of 25 repeats capped by N- and C-terminal α-helices. PRP structures are dominated by four-sided right-handed β-helices typically consisting of mixtures of type II and type IV β-turns. PRPs adopt repeated five-residue (Rfr) folds with an Rfr consensus sequence (STAV)(D/N)(L/F)(S/T/R)(X). Unlike other PRPs, At2g44920 consists exclusively of type II β-turns. At2g44920 is predicted to be located in the thylakoid lumen although its biochemical function remains unknown...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28537726/hot-spotting-with-thermal-scanning-a-ligand-and-structure-independent-assessment-of-target-ligandability
#14
Molly Chilton, Ben Clennell, Fredrik Edfeldt, Stefan Geschwindner
Evaluating the ligandability of a protein target is a key component when defining hit-finding strategies or to prioritize amongst drug targets. Computational as well as biophysical approaches based on nuclear magnetic resonance (NMR) fragment screening are powerful approaches, but suffer from specific constraints that limit their usage. Here, we demonstrate the applicability of high-throughput thermal scanning (HTTS) as a simple and generic biophysical fragment screening method to reproduce assessments from NMR-based screening...
May 24, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28537393/paramagnetic-properties-of-a-crystalline-iron-sulfur-protein-by-magic-angle-spinning-nmr-spectroscopy
#15
Andrea Bertarello, Tobias Schubeis, Carmelo Fuccio, Enrico Ravera, Marco Fragai, Giacomo Parigi, Lyndon Emsley, Guido Pintacuda, Claudio Luchinat
We present the first solid-state NMR study of an iron-sulfur protein. The combined use of very fast (60 kHz) magic-angle spinning and tailored radiofrequency irradiation schemes allows the detection and the assignment of most of the (1)H and (13)C resonances of the oxidized high-potential iron-sulfur protein I from Ectothiorhodospira halophila (EhHiPIP I), including those in residues coordinating the Fe4S4 cluster. For these residues, contact shifts as large as 100 and 400 ppm for (1)H and (13)C resonances, respectively, were observed, which represent the most shifted solid-state NMR signals ever measured in metalloproteins...
May 24, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28537272/fibril-polymorphism-affects-immobilized-non-amyloid-flanking-domains-of-huntingtin-exon1-rather-than-its-polyglutamine-core
#16
Hsiang-Kai Lin, Jennifer C Boatz, Inge E Krabbendam, Ravindra Kodali, Zhipeng Hou, Ronald Wetzel, Amalia M Dolga, Michelle A Poirier, Patrick C A van der Wel
Polyglutamine expansion in the huntingtin protein is the primary genetic cause of Huntington's disease (HD). Fragments coinciding with mutant huntingtin exon1 aggregate in vivo and induce HD-like pathology in mouse models. The resulting aggregates can have different structures that affect their biochemical behaviour and cytotoxic activity. Here we report our studies of the structure and functional characteristics of multiple mutant htt exon1 fibrils by complementary techniques, including infrared and solid-state NMR spectroscopies...
May 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28536266/two-proteins-for-the-price-of-one-structural-studies-of-the-dual-destiny-preproalbumin-with-sunflower-trypsin-inhibitor-1
#17
Bastian Franke, Amy M James, Mehdi Mobli, Michelle L Colgrave, Joshua S Mylne, K Johan Rosengren
Seed storage proteins are both an important source of nutrition for humans and essential for seedling establishment. Interestingly, unusual napin-type 2S seed storage albumin precursors in sunflower contain a sequence that is released as a macrocyclic peptide during post-translational processing. The mechanism by which such peptides emerge from linear precursors proteins has received increased attention, however the structural characterization of intact precursor proteins has been limited. Here we report the 3D NMR structure of the Helianthus annuus PreproAlbumin With Sunflower trypsin inhibitor-1 (PawS1), and provide new insights into the processing of this remarkable dual-destiny protein...
May 23, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28536196/physicochemical-code-for-quinary-protein-interactions-in-escherichia-coli
#18
Xin Mu, Seongil Choi, Lisa Lang, David Mowray, Nikolay V Dokholyan, Jens Danielsson, Mikael Oliveberg
How proteins sense and navigate the cellular interior to find their functional partners remains poorly understood. An intriguing aspect of this search is that it relies on diffusive encounters with the crowded cellular background, made up of protein surfaces that are largely nonconserved. The question is then if/how this protein search is amenable to selection and biological control. To shed light on this issue, we examined the motions of three evolutionary divergent proteins in the Escherichia coli cytoplasm by in-cell NMR...
May 23, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28535993/structural-basis-for-asymmetric-conductance-of-the-influenza-m2-proton-channel-investigated-by-solid-state-nmr-spectroscopy
#19
Venkata S Mandala, Shu Yu Liao, Byungsu Kwon, Mei Hong
The influenza M2 protein forms an acid-activated proton channel that is essential for virus replication. The transmembrane H37 selects for protons under low external pH (pHout) while W41 ensures proton conduction only from the N-terminus to the C-terminus and prevents reverse current under low internal pH (pHin). Here we address the molecular basis for this asymmetric conduction by investigating the structure and dynamics of a mutant channel, W41F, which permits reverse current under low pHin. Solid-state NMR experiments show that W41F M2 retains the pH-dependent α-helical conformations and tetrameric structure of the wild-type channel, but has significantly altered protonation and tautomeric equilibria at H37...
May 20, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28535337/overall-structural-model-of-ns5a-protein-from-hepatitis-c-virus-and-modulation-by-mutations-confering-resistance-of-virus-replication-to-cyclosporin-a
#20
Aurelie Badillo, Veronique Brechot, Stephane Sarrazin, François-Xavier Cantrelle, Frederic Delolme, Marie-Laure Fogeron, Jennifer Molle, Roland Montserret, Anja Bockmann, Ralf Bartenschlager, Volker Lohmann, Guy Lippens, Sylvie Ricard-Blum, Xavier Hanoulle, Francois Penin
Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is a RNA-binding phosphoprotein composed of a N-terminal membrane anchor (AH), a structured domain 1 (D1) and two intrinsically disordered domains (D2 and D3). The knowledge of the functional architecture of this multifunctional protein remains limited. We report here that NS5A-D1D2D3 produced in a wheat germ cell-free system is obtained under a highly phosphorylated state. Its NMR analysis revealed that these phosphorylations do not change the disordered nature of D2 and D3 domains but increase the number of conformers due to partial phosphorylations...
May 23, 2017: Biochemistry
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