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protein NMR

Lauren Bottorf, Indra D Sahu, Robert M McCarrick, Gary A Lorigan
Electron spin echo envelope modulation (ESEEM) spectroscopy in combination with site-directed spin labeling (SDSL) has been established as a valuable biophysical technique to provide site-specific local secondary structure of membrane proteins. This pulsed electron paramagnetic resonance (EPR) method can successfully distinguish between α-helices, β-sheets, and 310 -helices by strategically using 2 H-labeled amino acids and SDSL. In this study, we have explored the use of 13 C-labeled residues as the NMR active nuclei for this approach for the first time...
April 22, 2018: Biochimica et Biophysica Acta
Quoc Dat Pham, Amanuel Wolde-Kidan, Anirudh Gupta, Alexander Schlaich, Emanuel Schneck, Roland R Netz, Emma Sparr
Most land-living organisms regularly experience dehydration. In nature, one commonly applied strategy to protect against this osmotic stress is to introduce small polar molecules with low vapor pressure, commonly called osmolytes. Two examples of naturally occurring small polar compounds are urea and trimethylamine N-oxide (TMAO), which are known to have counteracting effects on protein stability. In this work, we investigate the effects of urea and TMAO on lipid self-assembly at varying water contents, focusing on dehydrated conditions...
April 25, 2018: Journal of Physical Chemistry. B
Mauro Pascolutti, Larissa Dirr, Patrice Guillon, Annelies Van Den Bergh, Thomas Ve, Robin J Thomson, Mark von Itzstein
A novel approach to human parainfluenza virus type-3 (hPIV-3) inhibitor design has been evaluated by targeting an unexplored pocket within the active site region of the virus' haemagglutinin-neuraminidase (HN) that is normally occluded upon ligand engagement. To explore this opportunity, we developed a highly efficient route to introduce nitrogen-based functionalities at the naturally unsubstituted C-3 position on the neuraminidase inhibitor template N-acyl-2,3-dehydro-2-deoxy-neuraminic acid (N-acyl-Neu2en), via a regioselective 2,3-bromoazidation...
April 25, 2018: ACS Chemical Biology
Pham Thi-Anh, Imran Shair Mohammad, Vu Van-Tuan, Hu Xiao-Long, Chaurasiya Birendra, Aftab Ulah, Guo Cui, Lv Xian-Yu, Ye Wen-Cai, Wang Hao
A new phloroglucinol derivative, named Eucalyptin B (1), along with five related known compounds (2-6), was isolated from the fruits of Eucalyptus globulus. Their structures were elucidated by means of 1D and 2D NMR spectroscopy, with the absolute configuration of 1 determined by electronic circular dichroism (ECD) calculations. All isolated compounds (1-6) were evaluated for their cytotoxic activities against lung (A549), breast (4T1), and skin (B16F10) cancer cell lines. On the basis of cytoxicity the antitumor activity of Eucalyptin B (1) was further confirmed by apoptosis assay...
April 24, 2018: Chemistry & Biodiversity
Shruthi Venugopal, Chieh Kao, Ritu Chandna, Konerirajapuram N Sulochana, Vivekanandan Subramanian, Mo Chen, R Manjunatha Kini, Ruowen Ge
Anti-angiogenesis therapy is an established therapeutic strategy for cancer. The endogenous angiogenic inhibitor angiostatin contains the first 3-4 kringle domains of plasminogen and inhibits both angiogenesis and vascular permeability. We present here a 10-residue peptide, Angio-3, derived from plasminogen kringle 3, which retains the functions of angiostatin in inhibiting both angiogenesis and vascular permeability. NMR studies indicate that Angio-3 holds a solution structure similar to the corresponding region of kringle 3...
April 24, 2018: Angiogenesis
Kim Potvin-Fournier, Geneviève Valois-Paillard, Marie-Claude Gagnon, Thierry Lefèvre, Pierre Audet, Line Cantin, Jean-François Paquin, Christian Salesse, Michèle Auger
Recoverin is a protein involved in the phototransduction cascade by regulating the activity of rhodopsin kinase through a calcium-dependent binding process at the surface of rod outer segment disk membranes. We have investigated the interaction of recoverin with zwitterionic phosphatidylcholine bilayers, the major lipid component of the rod outer segment disk membranes, using both 31 P and 19 F solid-state nuclear magnetic resonance (NMR) and infrared spectroscopy. In particular, several novel approaches have been used, such as the centerband-only detection of exchange (CODEX) technique to investigate lipid lateral diffusion and 19 F NMR to probe the environment of the recoverin myristoyl group...
April 24, 2018: European Biophysics Journal: EBJ
Pan Chen, Camilla Terenzi, Istvan Furo, Lars A Berglund, Jakob Wohlert
Macromolecular dynamics in biological systems, which play a crucial role for biomolecular function and activity at ambient temperature, depend strongly on hydration. Yet, a generally accepted quantitative model of hydration-dependent phenomena based on local relaxation and diffusive dynamics of both polymer and its hydration water is still missing. In this work, atomistic-scale spatial distributions of motional modes are calculated using molecular dynamics (MD) simulations of hydrated xyloglucan (XG). These are shown to reproduce experimental hydration-dependent 13C NMR longitudinal relaxation times (T1) at room temperature, and relevant features of their broad distributions, which are indicative of locally heterogeneous polymer reorientational dynamics...
April 24, 2018: Biomacromolecules
Robin Rajan, Yu Suzuki, Kazuaki Matsumura
The synthesis of a zwitterionic polymer, poly-sulfobetaine (poly-SPB), which shows remarkable efficiency in the suppression of insulin aggregation is described. Hydrophobic modification of the polymer results in almost complete inhibition at very low polymer concentrations. Further studies reveal that these polymers facilitate the complete retention of insulin's secondary structure, which is otherwise lost after incubation. Refolding studies show that addition of polymers to preaggregated insulin sample leads to the refolding of denatured insulin, indicating their potential to facilitate the refolding of the denatured proteins...
April 24, 2018: Macromolecular Bioscience
Rahul Mishra, Xing Yu, Chandan Kishor, Gavan Holloway, Kam Lau, Mark von Itzstein, Barbara S Coulson, Helen Blanchard
The outer capsid spike protein VP4 of rotaviruses is a major determinant of infectivity and serotype specificity. Proteolytic cleavage of VP4 into 2 domains, VP8* and VP5*, enhances rotaviral infectivity. Interactions between the VP4 carbohydrate-binding domain (VP8*) and cell surface glycoconjugates facilitate initial virus-cell attachment and subsequent cell entry. Our saturation transfer difference nuclear magnetic resonance (STD NMR) and isothermal titration calorimetry (ITC) studies demonstrated that VP8*64-224 of canine rotavirus strain K9 interacts with N-acetylneuraminic and N-glycolylneuraminic acid derivatives, exhibiting comparable binding epitopes to VP8* from other neuraminidase-sensitive animal rotaviruses from pigs (CRW-8), cattle (bovine Nebraska calf diarrhoea virus, NCDV), and Rhesus monkeys (Simian rhesus rotavirus, RRV)...
April 23, 2018: Journal of Molecular Recognition: JMR
Bastian Franke, Christian Opitz, Shin Isogai, Anne Grahl, Leonildo Delgado, Alvar D Gossert, Stephan Grzesiek
Baculovirus-infected insect cells have become a powerful tool to express recombinant proteins for structural and functional studies by NMR spectroscopy. This article provides an introduction into the insect cell/baculovirus expression system and its use for the production of recombinant isotope-labeled proteins. We discuss recent advances in inexpensive isotope-labeling methods using labeled algal or yeast extracts as the amino acid source and give examples of advanced NMR applications for proteins, which have become accessible by this eukaryotic expression host...
April 23, 2018: Journal of Biomolecular NMR
Miriam Kaltenbach, Jason R Burke, Mirco Dindo, Anna Pabis, Fabian S Munsberg, Avigayel Rabin, Shina C L Kamerlin, Joseph P Noel, Dan S Tawfik
The emergence of catalysis in a noncatalytic protein scaffold is a rare, unexplored event. Chalcone isomerase (CHI), a key enzyme in plant flavonoid biosynthesis, is presumed to have evolved from a nonenzymatic ancestor related to the widely distributed fatty-acid binding proteins (FAPs) and a plant protein family with no isomerase activity (CHILs). Ancestral inference supported the evolution of CHI from a protein lacking isomerase activity. Further, we identified four alternative founder mutations, i.e., mutations that individually instated activity, including a mutation that is not phylogenetically traceable...
April 23, 2018: Nature Chemical Biology
Bunta Watanabe, Hiroaki Kirikae, Takao Koeduka, Yoshinori Takeuchi, Tomoki Asai, Yoshiyuki Naito, Hideya Tokuoka, Shinri Horoiwa, Yoshiaki Nakagawa, Bun-Ichi Shimizu, Masaharu Mizutani, Jun Hiratake
4-Coumaroyl-CoA ligase (4CL) is ubiquitous in the plant kingdom, and plays a central role in the biosynthesis of phenylpropanoids such as lignins, flavonoids, and coumarins. 4CL catalyzes the formation of the coenzyme A thioester of cinnamates such as 4-coumaric, caffeic, and ferulic acids, and the regulatory position of 4CL in the phenylpropanoid pathway renders the enzyme an attractive target that controls the composition of phenylpropanoids in plants. In this study, we designed and synthesized mechanism-based inhibitors for 4CL in order to develop useful tools for the investigation of physiological functions of 4CL and chemical agents that modulate plant growth with the ultimate goal to produce plant biomass that exhibits features that are beneficial to humans...
April 4, 2018: Bioorganic & Medicinal Chemistry
Hong Giang T Ly, Guangxia Fu, Aleksandar Kondinski, Bart Bueken, Dirk De Vos, Tatjana N Parac-Vogt
MOF-808, a Zr(IV)-based metal-organic framework, has been proven to be a very effective heterogeneous catalyst for the hydrolysis of the peptide bond in a wide range of peptides and in hen egg white lysozyme protein. The kinetic experiments with a series of Gly-X dipeptides with varying nature of amino acid side chain have shown that MOF-808 exhibits selectivity depending on the size and chemical nature of the X side chain. Dipeptides with smaller or hydrophilic residues were hydrolyzed faster than those with bulky and hydrophobic residues that lack electron rich functionalities which could engage in favourable intermolecular interactions with the btc linkers...
April 23, 2018: Journal of the American Chemical Society
Carolyn Vargas, Christian Schönbeck, Ina Heimann, Sandro Keller
Cyclodextrin (CD) complexation is a convenient method to sequester surfactants in a controllable way, for example, during membrane-protein reconstitution. Interestingly, the equilibrium stability of CD/surfactant inclusion complexes increases with the length of the nonpolar surfactant chain even beyond the point where all hydrophobic contacts within the canonical CD cavity are saturated. To rationalize this observation, we have dissected the inclusion complexation equilibria of a structurally well-defined CD, that is, heptakis(2,6-di-O methyl)-CD (DIMEB), and a homologous series of surfactants, namely, n alkyl-N,N dimethyl-3 ammonio-1 propanesulfonates (SB3 x) with chain lengths ranging from x = 8 to 14...
April 23, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Abbas Kabir, Kalpana Tilekar, Neha Upadhyay, C S Ramaa
Background - Cancer being a complex disease, single targeting agents remains unsuccessful. This calls for "multiple targeting", wherein a single drug is so designed that it will modulate the activity of multiple protein targets. Topoisomerase 2 (Top2) helps in removing DNA tangles and super-coiling during cellular replication, Casein Kinase 2 (CK2) is involved in the phosphorylation of multitude of protein targets. Thus, in the present work, we have tried to develop dual inhibitors of Top2 and CK2...
April 22, 2018: Anti-cancer Agents in Medicinal Chemistry
Swetlana Gautam, Atul K Rawat, Shreesh R Sammi, Subhadeep Roy, Manjari Singh, Uma Devi, Rajnish K Yadav, Lakhveer Singh, Jitendra K Rawat, Mohd N Ansari, Abdulaziz S Saeedan, Dinesh Kumar, Rakesh Pandey, Gaurav Kaithwas
The present study is a pursuit to define implications of dual cyclooxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX) (DuCLOX-2/5) inhibition on various aspects of cancer augmentation and chemoprevention. The monotherapy and combination therapy of zaltoprofen (COX-2 inhibitor) and zileuton (5-LOX inhibitor) were validated for their effect against methyl nitrosourea (MNU) induced mammary gland carcinoma in albino wistar rats. The combination therapy demarcated significant effect upon the cellular proliferation as evidenced through decreased in alveolar bud count and restoration of the histopathological architecture when compared to toxic control...
2018: Frontiers in Pharmacology
Darryl Aucoin, Yongjie Xia, Theint Theint, Philippe S Nadaud, Krystyna Surewicz, Witold K Surewicz, Christopher P Jaroniec
The C-terminally truncated Y145Stop variant of prion protein (PrP23-144), which is associated with heritable PrP cerebral amyloid angiopathy in humans and also capable of triggering a transmissible prion disease in mice, serves as a useful in vitro model for investigating the molecular and structural basis of amyloid strains and cross-seeding specificities. Here, we determine the protein-solvent interfaces in human PrP23-144 amyloid fibrils generated from recombinant 13 C,15 N-enriched protein and incubated in aqueous solution containing paramagnetic Cu(II)-EDTA, by measuring residue-specific 15 N longitudinal paramagnetic relaxation enhancements using two-dimensional magic-angle spinning solid-state NMR spectroscopy...
April 18, 2018: Journal of Structural Biology
Hiroyuki Yamazaki, Kenta Takahashi, Natsuki Iwakura, Tatsuki Abe, Masanari Akaishi, Satomi Chiba, Michio Namikoshi, Ryuji Uchida
A new polyenyl-α-pyrone polyketide, aspopyrone A (1), was isolated from a culture broth of Okinawan plant-associated Aspergillus sp. TMPU1623 by solvent extraction, ODS column chromatography, and preparative HPLC (ODS). The structure of 1 was assigned based on NMR experiments. Compound 1 exhibited protein tyrosine phosphatase (PTP) 1B and T-cell PTP (TCPTP) inhibitory activities with IC50 values of 6.7 and 6.0 μM, respectively.
April 20, 2018: Journal of Antibiotics
Jong-Woon Ha, Hea Jung Park, Junhoo Park, Inwon Lee, Hyun Park, Hoyoul Kong, Jong Mok Park, Do-Hoon Hwang
A series of polystyrene (PS) copolymers containing 2,3,4,5,6-pentafluorostyrene units with different monomer ratios were prepared for antifouling applications. PS, poly(styrene-co-pentafluorostyrene) (poly(S-co-FS)), and poly(pentafluorostyrene) (PFS) were synthesized by free-radical polymerization and characterized by 1H NMR, Fourier-transform infrared spectroscopy, and gel permeation chromatography. The surface energy of the polymer films decreased with increasing content of fluorinated styrene. Protein adsorption experiments were carried out on the synthesized polymer films using fluorescein isothiocyanate-labeled bovine serum albumin as a fluorescent protein...
September 1, 2018: Journal of Nanoscience and Nanotechnology
Takuya Yoshizawa, Rustam Ali, Jenny Jiou, Ho Yee Joyce Fung, Kathleen A Burke, Seung Joong Kim, Yuan Lin, William B Peeples, Daniel Saltzberg, Michael Soniat, Jordan M Baumhardt, Rudolf Oldenbourg, Andrej Sali, Nicolas L Fawzi, Michael K Rosen, Yuh Min Chook
Liquid-liquid phase separation (LLPS) is believed to underlie formation of biomolecular condensates, cellular compartments that concentrate macromolecules without surrounding membranes. Physical mechanisms that control condensate formation/dissolution are poorly understood. The RNA-binding protein fused in sarcoma (FUS) undergoes LLPS in vitro and associates with condensates in cells. We show that the importin karyopherin-β2/transportin-1 inhibits LLPS of FUS. This activity depends on tight binding of karyopherin-β2 to the C-terminal proline-tyrosine nuclear localization signal (PY-NLS) of FUS...
April 19, 2018: Cell
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