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https://www.readbyqxmd.com/read/28821744/exploring-the-sequence-based-prediction-of-folding-initiation-sites-in-proteins
#1
Daniele Raimondi, Gabriele Orlando, Rita Pancsa, Taushif Khan, Wim F Vranken
Protein folding is a complex process that can lead to disease when it fails. Especially poorly understood are the very early stages of protein folding, which are likely defined by intrinsic local interactions between amino acids close to each other in the protein sequence. We here present EFoldMine, a method that predicts, from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events. The method is based on early folding data from hydrogen deuterium exchange (HDX) data from NMR pulsed labelling experiments, and uses backbone and sidechain dynamics as well as secondary structure propensities as features...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28820912/impact-of-novel-palmitoylated-prolactin-releasing-peptide-analogs-on-metabolic-changes-in-mice-with-diet-induced-obesity
#2
Veronika Pražienková, Martina Holubová, Helena Pelantová, Martina Bugáňová, Zdenko Pirník, Barbora Mikulášková, Andrea Popelová, Miroslava Blechová, Martin Haluzík, Blanka Železná, Marek Kuzma, Jaroslav Kuneš, Lenka Maletínská
Analogs of anorexigenic neuropeptides, such as prolactin-releasing peptide (PrRP), have a potential as new anti-obesity drugs. In our previous study, palmitic acid attached to the N-terminus of PrRP enabled its central anorexigenic effects after peripheral administration. In this study, two linkers, γ-glutamic acid at Lys11 and a short, modified polyethylene glycol at the N-terminal Ser and/or Lys11, were applied for the palmitoylation of PrRP31 to improve its bioavailability. These analogs had a high affinity and activation ability to the PrRP receptor GPR10 and the neuropeptide FF2 receptor, as well as short-term anorexigenic effect similar to PrRP palmitoylated at the N-terminus...
2017: PloS One
https://www.readbyqxmd.com/read/28820582/pathogenic-mutations-induce-partial-structural-changes-in-native-%C3%AE-sheet-structure-of-transthyretin-and-accelerate-aggregation
#3
Kwang Hun Lim, Anvesh K R Dasari, Renze Ma, Ivan Hung, Zhehong Gan, Jeffery W Kelly, Michael C Fitzgerald
Amyloid formation of natively folded proteins involves global and/or local unfolding of the native state to form aggregation-prone intermediates. Here we report solid-state NMR structural studies of amyloid derived from wild-type (WT) and more aggressive mutant forms of transthyretin (TTR) to investigate the structural changes associated with effective TTR aggregation. We employed selective 13C-labeling schemes to investigate structural features of β-structured core regions in amyloid states of WT and two mutant forms (V30M and L55P) of TTR...
August 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28820479/esterification-mechanism-of-bagasse-modified-with-glutaric-anhydride-in-1-allyl-3-methylimidazolium-chloride
#4
Huihui Wang, Wei Chen, Xueqin Zhang, Chuanfu Liu, Runcang Sun
The esterification of bagasse with glutaric anhydride could increase surface adhesion compatibility and the surface of derived polymers has the potential of immobilizing peptides or proteins for biomedical application. Due to its complicated components, the esterification mechanism of bagasse esterified with glutaric anhydride in ionic liquids has not been studied. In this paper, the homogenous esterification of bagasse with glutaric anhydride was comparatively investigated with the isolated cellulose, hemicelluloses, and lignin in 1-allyl-3-methylimidazolium chloride (AmimCl) to reveal the reaction mechanism...
August 18, 2017: Materials
https://www.readbyqxmd.com/read/28820253/bioinorganic-chemistry-of-parkinson-s-disease-affinity-and-structural-features-of-cu-i-binding-to-the-full-length-%C3%AE-synuclein-protein
#5
Marco C Miotto, Mayra D Pavese, Liliana Quintanar, Markus Zweckstetter, Christian Griesinger, Claudio O Fernández
Alterations in the levels of copper in brain tissue and formation of α-synuclein (αS)-copper complexes might play a key role in the amyloid aggregation of αS and the onset of Parkinson's disease (PD). Recently, we demonstrated that formation of the high-affinity Cu(I) complex with the N-terminally acetylated form of the protein αS substantially increases and stabilizes local conformations with α-helical secondary structure and restricted motility. In this work, we performed a detailed NMR-based structural characterization of the Cu(I) complexes with the full-length acetylated form of its homologue β-synuclein (βS), which is colocalized with αS in vivo and can bind copper ions...
August 18, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28819722/carbon-and-amide-detect-backbone-assignment-methods-of-a-novel-repeat-protein-from-the-staphylocoagulase-in-s-aureus
#6
Markus Voehler, Maddur Appajaiah Ashoka, Jens Meiler, Paul E Bock
The C-terminal repeat domain of staphylocoagulase that is secreted by the S. aureus is believed to play an important role interacting with fibrinogen and promotes blood clotting. To study this interaction by NMR, full assignment of each amide residue in the HSQC spectrum was required. Despite of the short sequence of the repeat construct, the HSQC spectrum contained a substantial amount of overlapped and exchange broadened resonances, indicating little secondary or tertiary structure. This caused severe problems while using the conventional, amide based NMR method for the backbone assignment...
August 17, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28819150/the-g%C3%AE-i-giv-binding-interface-is-a-druggable-protein-protein-interaction
#7
Vincent DiGiacomo, Alain Ibáñez de Opakua, Maria P Papakonstantinou, Lien T Nguyen, Nekane Merino, Juan B Blanco-Canosa, Francisco J Blanco, Mikel Garcia-Marcos
Heterotrimeric G proteins are usually activated by the guanine-nucleotide exchange factor (GEF) activity of GPCRs. However, some non-receptor proteins are also GEFs. GIV (a.k.a Girdin) was the first non-receptor protein for which the GEF activity was ascribed to a well-defined protein sequence that directly binds Gαi. GIV expression promotes metastasis and disruption of its binding to Gαi blunts the pro-metastatic behavior of cancer cells. Although this suggests that inhibition of the Gαi-GIV interaction is a promising therapeutic strategy, protein-protein interactions (PPIs) are considered poorly "druggable" targets requiring case-by-case validation...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819146/liquid-liquid-phase-separation-of-the-microtubule-binding-repeats-of-the-alzheimer-related-protein-tau
#8
Susmitha Ambadipudi, Jacek Biernat, Dietmar Riedel, Eckhard Mandelkow, Markus Zweckstetter
The protein Tau aggregates into tangles in the brain of patients with Alzheimer's disease. In solution, however, Tau is intrinsically disordered, highly soluble, and binds to microtubules. It is still unclear what initiates the conversion from an innocuous phase of high solubility and functionality to solid-like neurotoxic deposits. Here, we show that the microtubule-binding repeats of Tau, which are lysine-rich, undergo liquid-liquid phase separation in solution. Liquid-liquid demixing causes molecular crowding of amyloid-promoting elements of Tau and drives electrostatic coacervation...
August 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28818778/potential-effect-of-compounds-isolated-from-coffea-arabica-against-uv-b-induced-skin-damage-by-protecting-fibroblast-cells
#9
Yong-Hun Cho, Ashutosh Bahuguna, Han-Hyuk Kim, Dong-In Kim, Hyeon-Jeong Kim, Jae-Myo Yu, Hyun-Gug Jung, Jae-Yoon Jang, Jae-Hoon Kwak, Geun-Hye Park, O-Jun Kwon, Young Je Cho, Jeong Yeon An, Cheorun Jo, Sun Chul Kang, Bong-Jeun An
Ultraviolet (UV) radiation has adverse effects on extracellular matrix (ECM) proteins, leading to formation of wrinkles a hallmark of premature skin aging. The adverse effects of UV radiation are associated with induction of matrix metalloproteinases (MMPs) expression and degradation of collagen and elastin. The present study investigated anti-wrinkle effects of chlorogenic acid (CGA), pyrocatechol (PC) and 3,4,5-tricaffeoyl quinic acid (TCQ), isolated from beans of Coffea arabica, against UV-B stimulated mouse fibroblast cells (CCRF) by measuring expression levels of MMP-1, 3, 9, and type-I procollagen...
August 9, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28818490/inhibition-of-quorum-sensing-controlled-biofilm-formation-in-pseudomonas-aeruginosa-by-quorum-sensing-inhibitors
#10
Kalaiarasan Ellappan, Kottha Thirumalaswamy, Belgode Narasimha Harish, Gnanasambandam Vasuki, Veeresh Kumar Sali, James John
Antimicrobial therapy against extensively drug-resistant (XDR) P. aeruginosa biofilms is less efficient compared to the treatment of equal bacterial counts of free-floating planktonic cells, which has become a serious threat in hospital environment. P. aeruginosa regulate their cooperative activities and physiological process through a cell to cell chemical communication process called Quorum sensing (QS). This attracted our interest to synthesize, and to chemically characterize two anti-QS compounds, N-(4-{4-fluoroanilno} butanoyl) -L-homoserine lactone (FABHL) and N-(4-{4-chlororoanilno} butanoyl) -L-homoserine lactone (CABHL) to inhibit biofilm formation via disabling the QS circuits...
August 14, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28817602/exploring-the-potential-of-a-structural-alphabet-based-tool-for-mining-multiple-target-conformations-and-target-flexibility-insight
#11
Leslie Regad, Jean-Baptiste Chéron, Dhoha Triki, Caroline Senac, Delphine Flatters, Anne-Claude Camproux
Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC), obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility...
2017: PloS One
https://www.readbyqxmd.com/read/28817073/extended-physicochemical-characterization-of-the-synthetic-anticoagulant-pentasaccharide-fondaparinux-sodium-by-quantitative-nmr-and-single-crystal-x-ray-analysis
#12
William de Wildt, Huub Kooijman, Carel Funke, Bülent Üstün, Afranina Leika, Maarten Lunenburg, Frans Kaspersen, Edwin Kellenbach
Fondaparinux sodium is a synthetic pentasaccharide representing the high affinity antithrombin III binding site in heparin. It is the active pharmaceutical ingredient of the anticoagulant drug Arixtra(®). The single crystal X-ray structure of Fondaparinux sodium is reported, unequivocally confirming both structure and absolute configuration. The iduronic acid adopts a somewhat distorted chair conformation. Due to the presence of many sulfur atoms in the highly sulfated pentasaccharide, anomalous dispersion could be applied to determine the absolute configuration...
August 17, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28816463/signaling-related-mobility-changes-in-bacterial-chemotaxis-receptors-revealed-by-solid-state-nmr
#13
Maryam Kashefi, Lynmarie K Thompson
Bacteria employ remarkable membrane-bound nanoarrays to sense their environment and direct their swimming. Arrays consist of chemotaxis receptor trimers of dimers that are bridged at their membrane-distal tips by rings of two cytoplasmic proteins, a kinase CheA and a coupling protein CheW. It is not clear how ligand binding to the periplasmic domain of the receptor deactivates the CheA kinase bound to the cytoplasmic tip ~300 Å away, but the mechanism is thought to involve changes in dynamics within the cytoplasmic domain...
August 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28816462/-1-h-detected-redor-with-fast-magic-angle-spinning-of-a-deuterated-protein
#14
Manali Ghosh, Chad M Rienstra
Rotational echo double resonance (REDOR) is a highly successful method for heteronuclear distance determination in biological solid-state NMR, and 1H detection methods have emerged in recent years as a powerful approach to improving sensitivity and resolution for small sample quantities by utilizing fast magic-angle spinning (>30 kHz) and deuteration strategies. In theory, involving 1H as one of the spins for measuring REDOR effects can greatly increase the distance measurement range, but few experiments of this type have been reported...
August 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28815423/backbone-and-side-chain-1-h-15-n-and-13-c-resonance-assignments-of-a-novel-staphylococcal-inhibitor-of-myeloperoxidase
#15
Nicoleta T Ploscariu, Alvaro I Herrera, Srinivas Jayanthi, Thallapuranam K Suresh Kumar, Brian V Geisbrecht, Om Prakash
The bacterium Staphylococcus aureus produces an array of anti-inflammatory molecules that prevent the innate immune system from recognizing it as a pathogen and clearing it from the host. In the acute phase of inflammation, our immune system relies on neutrophils to clear invading bacteria. Recently, novel classes of secreted proteins from S. aureus, including the Extracellular Adherence Protein (EAP) family (Stapels et al., Proc Natl Acad Sci USA 111:13187-13192, 2014) and the Staphylococcal Peroxidase Inhibitor (SPIN), (unpublished work) have been identified as highly selective inhibitors acting on Neutrophil Serine Proteases (NSPs) and myeloperoxidase (MPO) respectively...
August 16, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28815397/detecting-and-accounting-for-multiple-sources-of-positional-variance-in-peak-list-registration-analysis-and-spin-system-grouping
#16
Andrey Smelter, Eric C Rouchka, Hunter N B Moseley
Peak lists derived from nuclear magnetic resonance (NMR) spectra are commonly used as input data for a variety of computer assisted and automated analyses. These include automated protein resonance assignment and protein structure calculation software tools. Prior to these analyses, peak lists must be aligned to each other and sets of related peaks must be grouped based on common chemical shift dimensions. Even when programs can perform peak grouping, they require the user to provide uniform match tolerances or use default values...
August 16, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28814948/synthesis-characterization-cytotoxic-activity-and-interactions-with-ct-dna-and-bsa-of-cationic-ruthenium-ii-complexes-containing-dppm-and-quinoline-carboxylates
#17
Edinaldo N da Silva, Paulo A B da Silva, Angélica E Graminha, Pollyanna F de Oliveira, Jaqueline L Damasceno, Denise C Tavares, Alzir A Batista, Gustavo Von Poelhsitz
The complexes cis-[Ru(quin)(dppm)2]PF6 and cis-[Ru(kynu)(dppm)2]PF6 (quin = quinaldate; kynu = kynurenate; dppm = bis(diphenylphosphino)methane) were prepared and characterized by elemental analysis, electronic, FTIR, (1)H, and (31)P{(1)H} NMR spectroscopies. Characterization data were consistent with a cis arrangement for the dppm ligands and a bidentate coordination through carboxylate oxygens of the quin and kynu anions. These complexes were not able to intercalate CT-DNA as shown by circular dichroism spectroscopy...
2017: Bioinorganic Chemistry and Applications
https://www.readbyqxmd.com/read/28813684/mimicking-mechanical-response-of-natural-tissues-strain-hardening-induced-by-transient-reticulation-in-lactose-modified-chitosan-chitlac
#18
Michela Cok, Pasquale Sacco, Davide Porrelli, Andrea Travan, Massimiliano Borgogna, Eleonora Marsich, Sergio Paoletti, Ivan Donati
The effect of transient cross-links has been explored on a lactose-modified chitosan, which previously had shown interesting biological features. The presence of galactose side chains and of the polyol spacer resulted particularly appealing for the reticulation by borate ions. The interaction between chitlac and borax was investigated by means of (11)B-NMR while rheology pointed to a marked non-linear behavior depending on the amount of borax added to the system. The presence of limited amount of cross-linking ion led to dilatant behavior when the steady flow curve was measured...
August 13, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28813018/biophysical-and-computational-studies-of-the-vcci-vmip-ii-complex
#19
Anna F Nguyen, Nai-Wei Kuo, Laura J Showalter, Ricardo Ramos, Cynthia M Dupureur, Michael E Colvin, Patricia J LiWang
Certain viruses have the ability to subvert the mammalian immune response, including interference in the chemokine system. Poxviruses produce the chemokine binding protein vCCI (viral CC chemokine inhibitor; also called 35K), which tightly binds to CC chemokines. To facilitate the study of vCCI, we first provide a protocol to produce folded vCCI from Escherichia coli (E. coli.) It is shown here that vCCI binds with unusually high affinity to viral Macrophage Inflammatory Protein-II (vMIP-II), a chemokine analog produced by the virus, human herpesvirus 8 (HHV-8)...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28813004/lactose-binding-induces-opposing-dynamics-changes-in-human-galectins-revealed-by-nmr-based-hydrogen-deuterium-exchange
#20
Chih-Ta Henry Chien, Meng-Ru Ho, Chung-Hung Lin, Shang-Te Danny Hsu
Galectins are β-galactoside-binding proteins implicated in a myriad of biological functions. Despite their highly conserved carbohydrate binding motifs with essentially identical structures, their affinities for lactose, a common galectin inhibitor, vary significantly. Here, we aimed to examine the molecular basis of differential lactose affinities amongst galectins using solution-based techniques. Consistent dissociation constants of lactose binding were derived from nuclear magnetic resonance (NMR) spectroscopy, intrinsic tryptophan fluorescence, isothermal titration calorimetry and bio-layer interferometry for human galectin-1 (hGal1), galectin-7 (hGal7), and the N-terminal and C-terminal domains of galectin-8 (hGal8(NTD) and hGal8(CTD), respectively)...
August 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
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