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https://www.readbyqxmd.com/read/29232406/compatible-topologies-and-parameters-for-nmr-structure-determination-of-carbohydrates-by-simulated-annealing
#1
Yingang Feng
The use of NMR methods to determine the three-dimensional structures of carbohydrates and glycoproteins is still challenging, in part because of the lack of standard protocols. In order to increase the convenience of structure determination, the topology and parameter files for carbohydrates in the program Crystallography & NMR System (CNS) were investigated and new files were developed to be compatible with the standard simulated annealing protocols for proteins and nucleic acids. Recalculating the published structures of protein-carbohydrate complexes and glycosylated proteins demonstrates that the results are comparable to the published structures which employed more complex procedures for structure calculation...
2017: PloS One
https://www.readbyqxmd.com/read/29232109/impact-of-chemical-cross-linking-on-protein-structure-and-function
#2
Daniel Rozbesky, Michal Rosulek, Zdenek Kukacka, Josef Chmelik, Petr Man, Petr Novák
Chemical cross-linking coupled with mass spectrometry is a popular technique for deriving structural information of proteins and protein complexes. Also, cross-linking has become a powerful tool for stabilizing macromolecular complexes for single-particle cryo-electron microscopy. However, an effect of cross-linking on protein structure and function should not be forgotten, and surprisingly it has not been investigated in detail so far. Here, we used kinetic studies, mass spectrometry, and NMR spectroscopy to systematically investigate an impact of cross-linking on structure and function of human carbonic anhydrase and alcohol dehydrogenase 1 from Saccharomyces cerevisiae...
December 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29232017/ph-resistant-monodispersed-polymer-lipid-nanodiscs
#3
Thirupathi Ravula, Nathaniel Z Hardin, Sudheer Ramadugu, Sarah J Cox, Ayyalusamy Ramamoorthy
Polymer lipid nanodiscs have provided an invaluable system for structural and functional studies of membrane proteins in their near-native environment. In spite of the recent advances in the development and usage of polymer lipid nanodisc systems, lack of control over size and poor tolerance to pH and divalent metal ions are major limitations for further applications. Here we report a facile modification of a low molecular weight styrene maleic acid copolymer to form monodispersed lipid bilayer nanodiscs that show ultra-stability towards a pH range of 2...
December 12, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29230599/erratum-to-nitrogen-detected-trosy-at-high-field-yields-high-resolution-and-sensitivity-for-protein-nmr
#4
Koh Takeuchi, Haribabu Arthanari, Ichio Shimada, Gerhard Wagner
The authors regret a mistake appeared in the supplement of this paper.
December 11, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29229527/surface-proteins-and-the-formation-of-biofilms-by-staphylococcus-aureus
#5
Sung Joon Kim, James Chang, Binayak Rimal, Hao Yang, Jacob Schaefer
Staphylococcus aureus biofilms pose a serious clinical threat as reservoirs for persistent infections. Despite this clinical significance, the composition and mechanism of formation of S. aureus biofilms are unknown. To address these problems, we used solid-state NMR to examine S. aureus (SA113), a strong biofilm-forming strain. We labeled whole cells and cell walls of planktonic cells, young biofilms formed for 12-24h after stationary phase, and more mature biofilms formed for up to 60h after stationary phase...
December 8, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29229353/novel-1-4-benzothazines-obliterate-cox-2-mediated-jak-2-stat-3-signals-with-potential-regulation-of-oxidative-and-metabolic-stress-during-colorectal-cancer
#6
Amit Rai, Umesh Kumar, Vinit Raj, Ashok K Singh, Pranesh Kumar, Amit K Keshari, Dinesh Kumar, Biswanath Maity, Arnab De, Amalesh Samanta, Sneha Nath, Anand Prakash, Sunil Babu Gosipatala, Gyan Chand, Sudipta Saha
1,4-benzothiazines have ameliorative effects through inhibition of COX-2 mediated STAT-3 pathways at G-protein couple receptor site. As per this scenario, we recently prepared and tested novel 1,4-benzothiazine derivatives against HT-29 human colon cancer cell line. Two compounds namely AR13 and AR15 showed higher inhibitions among all the synthesized compounds. In the present context, we conducted the in vivo antiproliferative action and identified the molecular mechanism associated to cytotoxic action of AR13 and AR15 in dimethylhydrazine (DMH) induced colorectal carcinoma (CRC) model...
December 8, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/29229300/c-myc-g-quadruplex-binding-by-the-rna-polymerase-i-inhibitor-bmh-21-and-analogues-revealed-by-a-combined-nmr-and-biochemical-approach
#7
Loana Musso, Stefania Mazzini, Anna Rossini, Lorenzo Castagnoli, Leonardo Scaglioni, Roberto Artali, Massimo Di Nicola, Franco Zunino, Sabrina Dallavalle
BACKGROUND: Pyridoquinazolinecarboxamides have been reported as RNA polymerase I inhibitors and represent a novel class of potential antitumor agents. BMH-21, was reported to intercalate with GC-rich rDNA, resulting in nucleolar stress as a primary mechanism of cytotoxicity. METHODS: The interaction of BMH-21 and analogues with DNA G-quadruplex structures was studied by NMR and molecular modelling. The cellular response was investigated in a panel of human tumor cell lines and protein expression was examined by Western Blot analysis...
December 8, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29228719/levels-of-leydig-cell-autophagy-regulate-the-fertility-of-male-naked-mole-rats
#8
Wenjing Yang, Li Li, Xiaofeng Huang, Guanghan Kan, Lifang Lin, Jishuai Cheng, Chen Xu, Wei Sun, Wei Cong, Shanmin Zhao, Shufang Cui
Fertility is abolished in nonbreeding males in colonies of natal naked mole-rats (NMRs). Although spermatogenesis occurs in both breeding and nonbreeding male NMRs, the mechanisms underlying the differences in fertility between breeders and nonbreeders remain unexplored. In this study, a significant decrease in autophagy was observed in Leydig cells of the testis from nonbreeding male NMRs. This alteration was visualised as a significant decrease in the levels of autophagy-related gene 7 (Atg7), Atg5, microtubule-associated protein 1A/B light chain 3 (LC3-II/I) and the number of autophagosomes and an increase in P62 levels using Western blotting analyses...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228582/comparative-study-of-macrophages-in-naked-mole-rats-and-icr-mice
#9
Jishuai Cheng, Zheng Yuan, Wenjing Yang, Chang Xu, Wei Cong, Lifang Lin, Shanmin Zhao, Wei Sun, Xiaosong Bai, Shufang Cui
The domestic and foreign scholars have studied naked mole rats more focused on the respect such as its long life, resistant to low oxygen, little spontaneous tumor, but the study of the immune system is little. In this study, we compared the anatomy and tissue morphology of NMR and ICR mouse spleens and found that the gross appearance of the NNMR spleen differed from ICR. There were more macrophages in NNMR spleens than in ICR spleens. Furthermore, we focused on the differences of macrophages. We compared their phagocytic capabilities and the data showed that NNMR macrophages are more phagocytic than ICR mouse macrophages...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29227646/direct-observation-of-carbohydrate-hydroxyl-protons-in-hydrogen-bonds-with-a-protein
#10
Gustav Nestor, Taigh Anderson, Stefan Oscarson, Angela M Gronenborn
Hydroxyl proton resonances of uniformly 13C-labeled Manα(1-2)Manα(1-2)ManαOMe (Man3) bound to cyanovirin-N (CV-N) were detected at ambient temperature in aqueous solution by NMR spectroscopy. The directions of the hydroxyl groups were determined based on NOEs and a previously unknown hydrogen bonding network between Man3 and CV-N was discovered. This is the first report on detecting hydroxyl protons of a protein-bound carbohydrate in aqueous solution by NMR. Approaches such as presented here may open the door for accurately determining inter-molecular hydrogen bonds in carbohydrate-protein complexes...
December 11, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29224182/stable-and-rigid-dtpa-like-paramagnetic-tags-suitable-for-in-vitro-and-in-situ-protein-nmr-analysis
#11
Jia-Liang Chen, Yu Zhao, Yan-Jun Gong, Bin-Bin Pan, Xiao Wang, Xun-Cheng Su
Organic synthesis of a ligand with high binding affinities for paramagnetic lanthanide ions is an effective way of generating paramagnetic effects on proteins. These paramagnetic effects manifested in high-resolution NMR spectroscopy are valuable dynamic and structural restraints of proteins and protein-ligand complexes. A paramagnetic tag generally contains a metal chelating moiety and a reactive group for protein modification. Herein we report two new DTPA-like tags, 4PS-PyDTTA and 4PS-6M-PyDTTA that can be site-specifically attached to a protein with a stable thioether bond...
December 9, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29223569/isolated-mangiferin-and-naringenin-exert-antidiabetic-effect-via-ppar%C3%AE-glut4-dual-agonistic-action-with-strong-metabolic-regulation
#12
Ashok K Singh, Vinit Raj, Amit K Keshari, Amit Rai, Pranesh Kumar, Atul Rawat, Biswanath Maity, Dinesh Kumar, Anand Prakash, Arnab De, Amalesh Samanta, Bolay Bhattacharya, Sudipta Saha
In this study, we isolated two compounds from the leaves of Salacia oblonga (SA1, mangiferin and SA2, naringenin), and their structures were confirmed by infrared spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, and mass spectrometry. SA1 and SA2 were orally administered to streptozotocin-induced diabetic rats at 50 and 100 mg/kg daily for 15 days. Blood glucose level, serum lipid profile, oxidative stress parameters, histopathology, docking, molecular parameters, and NMR-based metabolic perturbation studies were performed to investigate the pharmacological activities of SA1 and SA2...
December 6, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/29223566/progress-in-proton-detected-solid-state-nmr-ssnmr-super-fast-2d-ssnmr-collection-for-nano-mole-scale-proteins
#13
Yoshitaka Ishii, Ayesha Wickramasinghe, Isamu Matsuda, Yuki Endo, Yuji Ishii, Yusuke Nishiyama, Takahiro Nemoto, Takayuki Kamihara
Proton-detected solid-state NMR (SSNMR) spectroscopy has attracted much attention due to its excellent sensitivity and effectiveness in the analysis of trace amounts of amyloid proteins and other important biological systems. In this perspective article, we present the recent sensitivity limit of 1H-detected SSNMR using "ultra-fast" magic-angle spinning (MAS) at a spinning rate (νR) of 80-100 kHz. It was demonstrated that the high sensitivity of 1H-detected SSNMR at νR of 100 kHz and fast recycling using the paramagnetic-assisted condensed data collection (PACC) approach permitted "super-fast" collection of 1H-detected 2D protein SSNMR...
November 28, 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/29223532/new-insights-into-the-influence-of-monofluorination-on-dimyristoylphosphatidylcholine-membrane-properties-a-solid-state-nmr-study
#14
Marie-Claude Gagnon, Erik Strandberg, Anne S Ulrich, Jean-François Paquin, Michèle Auger
Solid-state 19F NMR spectroscopy is a method of choice to study the interactions between lipid membranes and other molecules such as peptides, proteins or drugs. Numerous fluorine-labeled NMR probes have been developed over the last few years, especially fluorine-labeled peptides. In order to develop a new kind of NMR reporter molecule and a complementary approach to fluorine-labeling of peptides, we synthesized six monofluorinated derivatives of the lipid dimyristoylphosphatidylcholine (F-DMPC), with the fluorine atom located along the acyl chain linked to the central glycerol position...
December 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29223460/investigation-of-anticancer-properties-of-caffeinated-complexes-via-computational-chemistry-methods
#15
Koray Sayin, Ayhan Üngördü
Computational investigations were performed for 1,3,7-trimethylpurine-2,6-dione, 3,7-dimethylpurine-2,6-dione, their Ru(II) and Os(III) complexes. B3LYP/6-311++G(d,p)(LANL2DZ) level was used in numerical calculations. Geometric parameters, IR spectrum, 1H-, 13C and 15N NMR spectrum were examined in detail. Additionally, contour diagram of frontier molecular orbitals (FMOs), molecular electrostatic potential (MEP) maps, MEP contour and some quantum chemical descriptors were used in the determination of reactivity rankings and active sites...
December 6, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29222330/discovery-of-stimulator-binding-to-a-conserved-pocket-in-the-heme-domain-of-soluble-guanylyl-cyclase
#16
Jessica A Wales, Cheng-Yu Chen, Linda Breci, Andrzej Weichsel, Sylvie G Bernier, James E Sheppeck, Robert Solinga, Takashi Nakai, Paul A Renhowe, Joon Jung, William R Montfort
Soluble guanylyl cyclase (sGC) is the receptor for nitric oxide and a highly sought-after therapeutic target for the management of cardiovascular diseases. New compounds that stimulate sGC show clinical promise, but where these stimulator compounds bind and how they function remains unknown. Here, using a photolyzable diazirine derivative of a novel stimulator compound, IWP-051, and MS analysis, we localized drug binding to the β1 heme domain of sGC proteins from the hawkmoth Manduca sexta and from human. Covalent attachments to the stimulator were also identified in bacterial homologs of the sGC heme domain, referred to as H-NOX domains, including those from Nostoc sp...
December 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29221883/anti-neuroinflammatory-effects-of-sesquiterpenoids-isolated-from-nardostachys-jatamansi
#17
Chi-Su Yoon, Kwan-Woo Kim, Sang-Chan Lee, Youn-Chul Kim, Hyuncheol Oh
Two new nardosinone-type sesquiterpenoids, namely kanshone J (1) and kanshone K (2) along with seven known terpenoids (3-9) were isolated from the rhizomes and roots of Nardostachys jatamansi DC (Valerianaceae). The structures of these compounds were determined mainly by analysis of 1D-, 2D-NMR and MS data. In addition, the absolute configuration of compound 1 was assigned by application of the modified Mosher's method. In an initial assay to evaluate their anti-neuroinflammatory effects, compounds 1-5 and 9 exhibited dose-dependent inhibitory effects on lipopolysaccharide (LPS)-induced nitric oxide (NO) production in BV2 cells, with IC50 values ranging from 2...
November 24, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29218635/long-range-paramagnetic-nmr-data-can-provide-a-closer-look-on-metal-coordination-in-metalloproteins
#18
Linda Cerofolini, Tommaso Staderini, Stefano Giuntini, Enrico Ravera, Marco Fragai, Giacomo Parigi, Roberta Pierattelli, Claudio Luchinat
Paramagnetic NMR data can be profitably incorporated in structural refinement protocols of metalloproteins or metal-substituted proteins, mostly as distance or angle restraints. However, they could in principle provide much more information, because the magnetic susceptibility of a paramagnetic metal ion is largely determined by its coordination sphere. This information can in turn be used to evaluate changes occurring in the coordination sphere of the metal when ligands (e.g.: inhibitors) are bound to the protein...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218631/intracellular-metal-binding-and-redox-behavior-of-human-dj-1
#19
Letizia Barbieri, Enrico Luchinat, Lucia Banci
DJ-1 is a conserved, ubiquitous protein associated to a large number of intracellular processes. Human DJ-1 has been linked to several pathologies, including hereditary forms of Parkinson's disease, cancer, and amyotrophic lateral sclerosis. Several cytoprotective functions of DJ-1 have been reported, however, its actual mechanisms of action remain elusive. In vitro, DJ-1 has been shown to bind zinc and copper(II) at its active site, which contains a conserved cysteine (C106), and copper(I) at a different binding site...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218630/differential-reactivity-of-closely-related-zinc-ii-binding-metallothioneins-from-the-plant-arabidopsis-thaliana
#20
Hasan T Imam, Claudia A Blindauer
The dynamics of metal binding to and transfer from metalloproteins involved in metal homeostasis are important for understanding cellular distribution of metal ions. The dicotyledonous plant Arabidopsis thaliana has two type 4 seed-specific metallothionein homologues, MT4a and MT4b, with likely roles in zinc(II) homeostasis. These two metallothioneins are 84% identical, with full conservation of all metal-binding cysteine and histidine residues. Yet, differences in their spatial and temporal expression patterns suggested divergence in their biological roles...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
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