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https://www.readbyqxmd.com/read/27914049/modeling-binding-affinity-of-pathological-mutations-for-computational-protein-design
#1
Miguel Romero-Durana, Chiara Pallara, Fabian Glaser, Juan Fernández-Recio
An important aspect of protein functionality is the formation of specific complexes with other proteins, which are involved in the majority of biological processes. The functional characterization of such interactions at molecular level is necessary, not only to understand biological and pathological phenomena but also to design improved, or even new interfaces, or to develop new therapeutic approaches. X-ray crystallography and NMR spectroscopy have increased the number of 3D protein complex structures deposited in the Protein Data Bank (PDB)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913182/virtual-screening-and-biophysical-studies-lead-to-hsp90-inhibitors
#2
Renjie Huang, Daniel M Ayine-Tora, M Nasri Muhammad Rosdi, Yu Li, Jóhannes Reynisson, Ivanhoe K H Leung
Heat shock protein 90 (HSP90) is a molecular chaperone that plays important functional roles in cells. The chaperone activity of HSP90 is regulated by the hydrolysis of ATP at the protein's N-terminal domain. HSP90, in particular the N-terminal domain, is a current inhibition target for therapeutic treatments of cancers. This paper describes an application of virtual screening, thermal shift assaying and protein NMR spectroscopy leading to the discovery of HSP90 inhibitors that contain the resorcinol structure...
November 23, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27912907/bioactivity-guided-isolation-of-anti-inflammatory-triterpenoids-from-the-sclerotia-of-poria-cocos-using-lps-stimulated-raw264-7-cells
#3
Seoung Rak Lee, Seulah Lee, Eunjung Moon, Hye-Jin Park, Hyun Bong Park, Ki Hyun Kim
Poria cocos Wolf (Polyporaceae) has been used as a medicinal fungus to treat various diseases since ancient times. This study aimed to investigate the anti-inflammatory chemical constituents of the sclerotia of P. cocos. Based on bioassay-guided fractionation using lipopolysaccharide (LPS)-stimulated Raw264.7 cells, chemical investigation of the EtOH extract of the sclerotia of P. cocos resulted in the isolation and identification of eight compounds including six triterpenoids, namely poricoic acid A (1), 3-O-acetyl-16α-hydroxydehydrotrametenolic acid (2), polyporenic acid C (3), 3β-hydroxylanosta-7,9(11),24-trien-21-oic acid (4), trametenolic acid (5), and dehydroeburicoic acid (6), as well as (-)-pinoresinol (7) and protocatechualdehyde (8)...
November 23, 2016: Bioorganic Chemistry
https://www.readbyqxmd.com/read/27912872/anti-allergic-potential-of-typhonium-blumei-inhibition-of-degranulation-via-suppression-of-pi3k-plc%C3%AE-2-phosphorylation-and-calcium-influx
#4
Michal Korinek, Kuan-Ming Chen, Yu-Han Jiang, Mohamed El-Shazly, Joel Stocker, Chon-Kit Chou, Tsong-Long Hwang, Yang-Chang Wu, Bing-Hung Chen, Fang-Rong Chang
BACKGROUND: Typhonium blumei Nicolson & Sivadasan (Araceae) is a traditional Chinese medicinal herb possessing detumescent, detoxifying, and anti-inflammatory activities. It is used in Taiwan as a folk medicine to treat cancer and inflammatory diseases. Typhonium blumei is usually not distinguished from Typhonium roxburghii Schott and they are commonly used interchangeably. PURPOSE: To evaluate and compare the anti-allergic and anti-inflammatory properties of T...
December 15, 2016: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
https://www.readbyqxmd.com/read/27911811/the-structure-of-the-catechin-binding-site-of-human-sulfotransferase-1a1
#5
Ian Cook, Ting Wang, Mark Girvin, Thomas S Leyh
We are just beginning to understand the allosteric regulation of the human cytosolic sulfotransferase (SULTs) family-13 disease-relevant enzymes that regulate the activities of hundreds, if not thousands, of signaling small molecules. SULT1A1, the predominant isoform in adult liver, harbors two noninteracting allosteric sites, each of which binds a different molecular family: the catechins (naturally occurring flavonols) and nonsteroidal antiinflammatory drugs (NSAIDs). Here, we present the structure of an SULT allosteric binding site-the catechin-binding site of SULT1A1 bound to epigallocatechin gallate (EGCG)...
November 23, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911361/spin-saturation-transfer-difference-nmr-sstd-nmr-a-new-tool-to-obtain-kinetic-parameters-of-chemical-exchange-processes
#6
María Teresa Quirós, Colin Macdonald, Jesús Angulo, María Paz Muñoz
This detailed protocol describes the new Spin Saturation Transfer Difference Nuclear Magnetic Resonance protocol (SSTD NMR), recently developed in our group to study processes of mutual-site chemical exchange that are difficult to analyze by traditional methods. As the name suggests, this method combines the Spin Saturation Transfer method used for small molecules, with the Saturation Transfer Difference (STD) NMR method employed for the study of protein-ligand interactions, by measuring transient spin saturation transfer along increasing saturation times (build-up curves) in small organic and organometallic molecules undergoing chemical exchange...
November 12, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27910948/improved-in-cell-structure-determination-of-proteins-at-near-physiological-concentration
#7
Teppei Ikeya, Tomomi Hanashima, Saori Hosoya, Manato Shimazaki, Shiro Ikeda, Masaki Mishima, Peter Güntert, Yutaka Ito
Investigating three-dimensional (3D) structures of proteins in living cells by in-cell nuclear magnetic resonance (NMR) spectroscopy opens an avenue towards understanding the structural basis of their functions and physical properties under physiological conditions inside cells. In-cell NMR provides data at atomic resolution non-invasively, and has been used to detect protein-protein interactions, thermodynamics of protein stability, the behavior of intrinsically disordered proteins, etc. in cells. However, so far only a single de novo 3D protein structure could be determined based on data derived only from in-cell NMR...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27907876/rational-design-and-synthesis-of-1-5-disubstituted-tetrazoles-as-potent-inhibitors-of-the-mdm2-p53-interaction
#8
Ewa Surmiak, Constantinos G Neochoritis, Bogdan Musielak, Aleksandra Twarda-Clapa, Katarzyna Kurpiewska, Grzegorz Dubin, Carlos Camacho, Tad A Holak, Alexander Dömling
Using the computational pharmacophore-based ANCHOR.QUERY platform a new scaffold was discovered. Potent compounds evolved inhibiting the protein-protein interaction p53-MDM2. An extensive SAR study was performed based on our four-point pharmacophore model, yielding derivatives with affinity to MDM2 in the nanomolar range. Their binding affinity with MDM2 was evaluated using both fluorescence polarization (FP) assay and 2D-NMR-HSQC experiments.
November 16, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27907055/effect-of-glu12-his89-interaction-on-dynamic-structures-in-hiv-1-p17-matrix-protein-elucidated-by-nmr
#9
Yuta Konagaya, Rina Miyakawa, Masumi Sato, Akimasa Matsugami, Satoru Watanabe, Fumiaki Hayashi, Takanori Kigawa, Chiaki Nishimura
To test the existence of the salt bridge and stability of the HIV-1 p17 matrix protein, an E12A (mutated at helix 1) was established to abolish possible electrostatic interactions. The chemical shift perturbation from the comparison between wild type and E12A suggested the existence of an electrostatic interaction in wild type between E12 and H89 (located in helix 4). Unexpectedly, the studies using urea denaturation indicated that the E12A substitution slightly stabilized the protein. The dynamic structure of E12A was examined under physiological conditions by both amide proton exchange and relaxation studies...
2016: PloS One
https://www.readbyqxmd.com/read/27902927/antidiabetic-activity-of-ganoderma-lucidum-polysaccharides-f31-down-regulated-hepatic-glucose-regulatory-enzymes-in-diabetic-mice
#10
Chun Xiao, Qingping Wu, Jumei Zhang, Yizhen Xie, Wen Cai, Jianbin Tan
ETHNOPHARMACOLOGICAL RELEVANCE: Ganoderma lucidum (Lin Zhi) has been used to treat diabetes in Chinese folk for centuries. Our laboratory previously demonstrated that Ganoderma lucidum polysaccharides (GLPs) had hypoglycemic effects in diabetic mice. Our aim was to identify the main bioactives in GLPs and corresponding mechanism of action. MATERIALS AND METHODS: Four polysaccharide-enriched fraction were isolated from GLPs and the antidiabetic activities were evaluated by type 2 diabetic mice...
November 27, 2016: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/27902713/association-of-n-linked-glycoprotein-acetyls-and-colorectal-cancer-incidence-and-mortality
#11
Paulette D Chandler, Akintunde O Akinkuolie, Deirdre K Tobias, Patrick R Lawler, Chungying Li, M Vinayaga Moorthy, Lu Wang, Daniel A Duprez, David R Jacobs, Robert J Glynn, James Otvos, Margery A Connelly, Wendy S Post, Paul M Ridker, JoAnn E Manson, Julie E Buring, I-Min Lee, Samia Mora
BACKGROUND: Acute phase proteins highlight the dynamic interaction between inflammation and oncogenesis. GlycA, a novel nuclear magnetic resonance (NMR) inflammatory marker that identifies primarily circulating N-acetyl glycan groups attached to acute phase proteins, may be a future CRC risk biomarker. METHODS: We examined the association between GlycA and incident CRC and mortality in two prospective cohorts (N = 34,320); Discovery cohort: 27,495 participants from Women's Health Study (WHS); Replication cohort: 6,784 participants from Multi-Ethnic Study of Atherosclerosis (MESA)...
2016: PloS One
https://www.readbyqxmd.com/read/27901101/structural-basis-for-the-dissociation-of-%C3%AE-synuclein-fibrils-triggered-by-pressure-perturbation-of-the-hydrophobic-core
#12
Guilherme A P de Oliveira, Mayra de A Marques, Carolina Cruzeiro-Silva, Yraima Cordeiro, Caroline Schuabb, Adolfo H Moraes, Roland Winter, Hartmut Oschkinat, Debora Foguel, Mônica S Freitas, Jerson L Silva
Parkinson's disease is a neurological disease in which aggregated forms of the α-synuclein (α-syn) protein are found. We used high hydrostatic pressure (HHP) coupled with NMR spectroscopy to study the dissociation of α-syn fibril into monomers and evaluate their structural and dynamic properties. Different dynamic properties in the non-amyloid-β component (NAC), which constitutes the Greek-key hydrophobic core, and in the acidic C-terminal region of the protein were identified by HHP NMR spectroscopy. In addition, solid-state NMR revealed subtle differences in the HHP-disturbed fibril core, providing clues to how these species contribute to seeding α-syn aggregation...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900841/the-role-of-the-prod1-membrane-anchor-in-newt-limb-regeneration
#13
Kaoru Nomura, Yasushi Tanimoto, Fumio Hayashi, Erisa Harada, Xiao-Yuan Shan, Masafumi Shionyu, Atsushi Hijikata, Tsuyoshi Shirai, Kenichi Morigaki, Keiko Shimamoto
Prod1 is a protein that regulates limb regeneration in salamanders by determining the direction of limb growth. Prod1 is attached to the membrane by a glycosylphosphatidylinositol (GPI) anchor, but the role of membrane anchoring in the limb regeneration process is poorly understood. In this study, we investigated the functional role of the anchoring of Prod1 to the membrane by using its synthetic mimics in combination with solid-state NMR spectroscopy and fluorescent microscopy techniques. Anchoring did not affect the three-dimensional structure of Prod1 but did induce aggregation by aligning the molecules and drastically reducing the molecular motion on the two-dimensional membrane surface...
November 30, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27899638/structure-and-folding-of-the-tetrahymena-telomerase-rna-pseudoknot
#14
Darian D Cash, Juli Feigon
Telomerase maintains telomere length at the ends of linear chromosomes using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). An essential part of TER is the template/pseudoknot domain (t/PK) which includes the template, for adding telomeric repeats, template boundary element (TBE), and pseudoknot, enclosed in a circle by stem 1. The Tetrahymena telomerase holoenzyme catalytic core (p65-TER-TERT) was recently modeled in our 9 Å resolution cryo-electron microscopy map by fitting protein and TER domains, including a solution NMR structure of the Tetrahymena pseudoknot...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899179/capillary-methacrylate-based-monoliths-by-grafting-from-to-%C3%AE-ray-polymerization-on-a-tentacle-type-reactive-surface-for-the-liquid-chromatographic-separations-of-small-molecules-and-intact-proteins
#15
Patrizia Simone, Giuseppe Pierri, Donatella Capitani, Alessia Ciogli, Giancarlo Angelini, Ornella Ursini, Gennaro Gentile, Alberto Cavazzini, Claudio Villani, Francesco Gasparrini
Capillary methacrylate-based monoliths were prepared for the high performance liquid chromatography (HPLC) separation of both small molecules and large biomolecules. An efficient grafting from/to synthetic approach was adopted introducing a network of activated sites in the inner wall surface using the new silanization agent (N-trimethoxysilylpropyl)-polyethylenimine. Copolymerization of lauryl methacrylate monomer and 1,6-hexanediol dimethacrylate cross-linker in the presence of porogenic solvents was obtained under continuous γ-ray exposure with high conversion yield...
November 23, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/27897362/unambiguous-determination-of-protein-arginine-ionization-states-in-solution-by-nmr-spectroscopy
#16
Yuichi Yoshimura, Nur Alia Oktaviani, Kento Yonezawa, Hironari Kamikubo, Frans A A Mulder
Because arginine residues in proteins are expected to be in their protonated form almost without exception, reports demonstrating that a protein arginine residue is charge-neutral are rare and potentially controversial. Herein, we present a (13) C-detected NMR experiment for probing individual arginine residues in proteins notwithstanding the presence of chemical and conformational exchange effects. In the experiment, the (15) N(η) and (15) N(ϵ) chemical shifts of an arginine head group are correlated with that of the directly attached (13) C(ζ) ...
November 29, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27897281/platinum-ii-o-s-complexes-as-potential-metallodrugs-against-cisplatin-resistance
#17
Jana Hildebrandt, Norman Häfner, Helmar Görls, Daniel Kritsch, Giarita Ferraro, Matthias Dürst, Ingo B Runnebaum, Antonello Merlino, Wolfgang Weigand
We report on platinum(ii) complexes with different cinnamic acid derivatives as ligands with cytotoxic activity against Cisplatin resistant ovarian cancer cell line subcultures of SKOV3 and A2780. A typical mechanism of action for platinum(ii) complexes as Cisplatin itself is binding to the DNA and inducing double-strand breaks. We examined the biological behavior of these potential drugs with 9-methylguanine using NMR spectroscopic methods and their DNA damage potential including γH2AX-foci analyses. X-ray diffraction methods have been used to elucidate the molecular structures of the platinum(ii) complexes...
November 29, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/27896733/3d-computational-modeling-of-proteins-using-sparse-paramagnetic-nmr-data
#18
Kala Bharath Pilla, Gottfried Otting, Thomas Huber
Computational modeling of proteins using evolutionary or de novo approaches offers rapid structural characterization, but often suffers from low success rates in generating high quality models comparable to the accuracy of structures observed in X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. A computational/experimental hybrid approach incorporating sparse experimental restraints in computational modeling algorithms drastically improves reliability and accuracy of 3D models. This chapter discusses the use of structural information obtained from various paramagnetic NMR measurements and demonstrates computational algorithms implementing pseudocontact shifts as restraints to determine the structure of proteins at atomic resolution...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896020/identification-of-phenolic-secondary-metabolites-from-schotia-brachypetala-sond-fabaceae-and-demonstration-of-their-antioxidant-activities-in-caenorhabditis-elegans
#19
Mansour Sobeh, Esraa ElHawary, Herbenya Peixoto, Rola M Labib, Heba Handoussa, Noha Swilam, Ahmed H El-Khatib, Farukh Sharapov, Tamer Mohamed, Sonja Krstin, Michael W Linscheid, Abdel Nasser Singab, Michael Wink, Nahla Ayoub
BACKGROUND: Schotia brachypetala Sond. (Fabaceae) is an endemic tree of Southern Africa whose phytochemistry and pharmacology were slightly studied. The present work aimed at profiling the major phenolics compounds present in the hydro-alcohol extract from S. brachypetala leaves (SBE) using LC/HRESI/MS/MS and NMR and prove their antioxidant capabilities using novel methods. METHODS: In vitro assays; DPPH, TEAC persulfate decolorizing kinetic and FRAP assays, and in vivo assays: Caenorhabditis elegans strains maintenance, Intracellular ROS in C...
2016: PeerJ
https://www.readbyqxmd.com/read/27894420/structural-basis-for-the-recognition-of-spliceosomal-smn-b-b-proteins-by-the-rbm5-ocre-domain-in-splicing-regulation
#20
André Mourão, Sophie Bonnal, Komal Soni, Lisa Warner, Rémy Bordonné, Juan Valcárcel, Michael Sattler
The multi-domain splicing factor RBM5 regulates the balance between antagonistic isoforms of the apoptosis-control genes FAS/CD95, Caspase-2 and AID. An OCRE (OCtamer REpeat of aromatic residues) domain found in RBM5 is important for alternative splicing regulation and mediates interactions with components of the U4/U6.U5 tri-snRNP. We show that the RBM5 OCRE domain adopts a unique β-sheet fold. NMR and biochemical experiments demonstrate that the OCRE domain directly binds to the proline-rich C-terminal tail of the essential snRNP core proteins SmN/B/B'...
November 29, 2016: ELife
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