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https://www.readbyqxmd.com/read/28432945/exploring-isoxsuprine-hydrochloride-binding-with-human-serum-albumin-in-the-presence-of-folic-acid-and-ascorbic-acid-using-multispectroscopic-and-molecular-modeling-methods
#1
Fereshteh Shiri, Somaye Shahraki, Amin Shahriyar, Mostafa Heidari Majd
Isoxsuprine hydrochloride (vasodilator drug), folic acid and ascorbic acid are medicines which can be utilized alone or simultaneously by pregnant women. In the present work the competitive binding of isoxsuprine hydrochloride (ISO) with human serum albumin (HSA) in the absence and presence of folic acid (FOL) and ascorbic acid (AS) was investigated using different spectroscopic probes and molecular docking studies. The results of fluorescence suggested that isoxsuprine alone or in the presence of ascorbic acid can bind to HSA and quench the fluorescence of HSA with static mechanism but For HSA-folic acid-isoxsuprine system, dynamic type of quenching mechanisms is involved...
April 11, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28432925/structure-of-the-s1-subunit-c-terminal-domain-from-bat-derived-coronavirus-hku5-spike-protein
#2
Xue Han, Jianxun Qi, Hao Song, Qihui Wang, Yanfang Zhang, Ying Wu, Guangwen Lu, Kwok-Yung Yuen, Yi Shi, George F Gao
Accumulating evidence indicates that MERS-CoV originated from bat coronaviruses (BatCoVs). Previously, we demonstrated that both MERS-CoV and BatCoV HKU4 use CD26 as a receptor, but how the BatCoVs evolved to bind CD26 is an intriguing question. Here, we solved the crystal structure of the S1 subunit C-terminal domain of HKU5 (HKU5-CTD), another BatCoV that is phylogenetically related to MERS-CoV but cannot bind to CD26. We observed that the conserved core subdomain and those of other betacoronaviruses (betaCoVs) have a similar topology of the external subdomain, indicating the same ancestor of lineage C betaCoVs...
April 19, 2017: Virology
https://www.readbyqxmd.com/read/28432857/on-the-importance-of-intramolecular-hydrogen-bond-cooperativity-in-d-glucose-an-nmr-and-qtaim-approach
#3
John S Lomas, Laurent Joubert
The idea that hydrogen bond cooperativity is responsible for the structure and reactivity of carbohydrates is examined. Density functional theory and gauge-including atomic orbital calculations on the known conformers of the α and β anomers of D-glucopyranose in the gas phase are used to compute proton NMR chemical shifts and interatomic distances, which are taken as criteria for probing intramolecular interactions. Atom-atom interaction energies are calculated by the interacting quantum atoms approach in the framework of the quantum theory of atoms in molecules...
April 22, 2017: Magnetic Resonance in Chemistry: MRC
https://www.readbyqxmd.com/read/28432789/probing-protein-flexibility-reveals-a-mechanism-for-selective-promiscuity
#4
Nicolas A Pabon, Carlos J Camacho
Many eukaryotic regulatory proteins adopt distinct bound and unbound conformations, and use this structural flexibility to bind specifically to multiple partners. However, we lack an understanding of how an interface can select some ligands, but not others. Here, we present a molecular dynamics approach to identify and quantitatively evaluate the interactions responsible for this selective promiscuity. We apply this approach to the anti-cancer target PD-1 and its ligands PD-L1 and PD-L2. We discover that while unbound PD-1 exhibits a hard-to-drug hydrophilic interface, conserved specific triggers encoded in the cognate ligands activate a promiscuous binding pathway that reveals a flexible hydrophobic binding cavity...
April 22, 2017: ELife
https://www.readbyqxmd.com/read/28432760/determination-of-ochratoxin-a-in-black-and-white-pepper-nutmeg-spice-mix-cocoa-and-drinking-chocolate-by-high-performance-liquid-chromatography-coupled-with-fluorescence-detection-collaborative-study
#5
Elena Cubero-Leon, Katrien Bouten, Hamide Senyuva, Joerg Stroka
A method validation study for the determination of ochratoxin A in black and white pepper (Piper spp.), nutmeg (Myristica fragrans), spice mix (blend of ginger, turmeric, pepper, nutmeg, and chili), cocoa powder, and drinking chocolate was conducted according to the International Harmonized Protocol of the International Union of Pure and Applied Chemistry. The method is based on the extraction of samples with aqueous methanol, followed by a cleanup of the extract with an immunoaffinity column. The determination is carried out by reversed-phase LC coupled with a fluorescence detector...
April 22, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28432632/tryptophan-fluorescence-yields-and-lifetimes-as-a-probe-of-conformational-changes-in-human-glucokinase
#6
Bogumil Zelent, Chris Bialas, Ignacy Gryczynski, Pan Chen, Rahul Chib, Karina Lewerissa, Maria G Corradini, Richard D Ludescher, Jane M Vanderkooi, Franz M Matschinsky
Five variants of glucokinase (ATP-D-hexose-6-phosphotransferase, EC 2.7.1.1) including wild type and single Trp mutants with the Trp residue at positions 65, 99, 167 and 257 were prepared. The fluorescence of Trp in all locations studied showed intensity changes when glucose bound, indicating that conformational change occurs globally over the entire protein. While the fluorescence quantum yield changes upon glucose binding, the enzyme's absorption spectra, emission spectra and fluorescence lifetimes change very little...
April 22, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28432453/the-influence-of-oxo-bridged-binuclear-gold-iii-complexes-on-na-k-atpase-activity-a-joint-experimental-and-theoretical-approach
#7
Aleksandra M Bondžić, Mirjana B Čolović, Goran V Janjić, Božidarka Zarić, Sandra Petrović, Danijela Z Krstić, Tiziano Marzo, Luigi Messori, Vesna M Vasić
The in vitro effects of oxo-bridged binuclear gold(III) complexes, i.e., [(bipy2Me)2Au2(μ-O)2][PF6]2 (Auoxo6), Au2[(bipydmb-H)2(μ-O)][PF6] (Au2bipyC) and [Au2(phen(2Me))2(μ-O)2](PF6)2 (Au2phen) on Na/K-ATPase, purified from the porcine cerebral cortex, were investigated. All three studied gold complexes inhibited the enzyme activity in a concentration-dependent manner achieving IC50 values in the low micromolar range. Kinetic analysis suggested an uncompetitive mode of inhibition for Auoxo6 and Au2bipyC, and a mixed type one for Au2phen...
April 21, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/28432424/variations-of-isovaline-structure-related-to-activity-in-the-formalin-foot-assay-in-mice
#8
Timothy Fung, Yahya I Asiri, Richard Wall, Stephan K W Schwarz, Ernest Puil, Bernard A MacLeod
Current centrally acting analgesics such as opioids are associated with adverse effects that limit their use and threaten patient safety. Isovaline is a novel prototype analgesic that produces peripheral antinociception in several pain models with little or no effect on the central nervous system. The aim of this study was to establish a preliminary structure-activity relationship for isovaline derivatives by assaying efficacy in the formalin foot assay and central adverse effect profile in mice. Selected compounds were tested using the formalin foot assay to determine efficacy in reducing formalin-induced behaviors...
April 21, 2017: Amino Acids
https://www.readbyqxmd.com/read/28432364/rrm-domain-of-als-ftd-causing-fus-characteristic-of-irreversible-unfolding-spontaneously-self-assembles-into-amyloid-fibrils
#9
Yimei Lu, Liangzhong Lim, Jianxing Song
526-residue FUS functions to self-assemble into reversible droplets/hydrogels, which could be further solidified into pathological fibrils. FUS is intrinsically prone to aggregation, composed of N-terminal low-sequence complexity (LC); RNA-recognition motif (RRM) and C-terminal LC domains. Intriguingly, previous in vivo studies revealed that its RRM is required for manifesting FUS cytotoxicity but the underlying mechanism remains unknown. Here, we characterized solution conformations of FUS and its five differentially dissected fragments, followed by detailed investigations on thermal unfolding, NMR dynamics and self-assembly of RRM...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432363/joint-based-description-of-protein-structure-its-application-to-the-geometric-characterization-of-membrane-proteins
#10
Jayaraman Thangappan, Sangwook Wu, Sun-Gu Lee
A macroscopic description of a protein structure allows an understanding of the protein conformations in a more simplistic manner. Here, a new macroscopic approach that utilizes the joints of the protein secondary structures as a basic descriptor for the protein structure is proposed and applied to study the arrangement of secondary structures in helical membrane proteins. Two types of dihedral angle, Ω and λ, were defined based on the joint points of the transmembrane (TM) helices and loops, and employed to analyze 103 non-homologous membrane proteins with 3 to 14 TM helices...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432345/distant-phe345-mutation-compromises-the-stability-and-activity-of-mycobacterium-tuberculosis-isocitrate-lyase-by-modulating-its-structural-flexibility
#11
Harish Shukla, Rohit Shukla, Amit Sonkar, Tripti Pandey, Timir Tripathi
Isocitrate lyase (ICL), a potential anti-tubercular drug target, catalyzes the first step of the glyoxylate shunt. In the present investigation, we studied the conformational flexibility of MtbICL to better understand its stability and catalytic activity. Our biochemical results showed that a point mutation at Phe345, which is topologically distant (>10 Å) to the active site signature sequence ((189)KKCGH(193)), completely abolishes the activity of the enzyme. In depth computational analyses were carried out for understanding the structural alterations using molecular dynamics, time-dependent secondary structure and principal component analysis...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432329/affinity-biosensors-using-recombinant-native-membrane-proteins-displayed-on-exosomes-application-to-botulinum-neurotoxin-b-receptor
#12
Richard Desplantes, Christian Lévêque, Benjamin Muller, Manuela Lotierzo, Géraldine Ferracci, Michel Popoff, Michael Seagar, Robert Mamoun, Oussama El Far
The development of simple molecular assays with membrane protein receptors in a native conformation still represents a challenging task. Exosomes are extracellular vesicles which, due to their stability and small size, are suited for analysis in various assay formats. Here, we describe a novel approach to sort recombinant fully native and functional membrane proteins to exosomes using a targeting peptide. Specific binding of high affinity ligands to the potassium channel Kv1.2, the G-protein coupled receptor CXCR4, and the botulinum neurotoxin type B (BoNT/B) receptor, indicated their correct assembly and outside out orientation in exosomes...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432259/probing-native-metal-ion-association-sites-through-quenching-of-fluorophores-in-the-nucleotide-binding-domains-of-the-abc-transporter-msba
#13
Daiki Tatsumi, Kei Nanatani, Yuto Koike, Kiyoto Kamagata, Satoshi Takahashi, Ayumu Konno, Tadaomi Furuta, Minoru Sakurai, Nobuyuki Uozumi
ATP binding cassette (ABC) transporters are ubiquitously present in prokaryotic and eukaryotic cells. Binding of ATP to the nucleotide binding domains (NBDs) elicits major conformational changes of the transporters resulting in the transport of the substrate across the membrane. The availability of a crystal structure of the NBDs enabled us to elucidate the local structure and small-scale dynamics in the NBDs. Here, we labeled the ABC transporter MsbA, a homodimeric flippase from E. coli , with a fluorescent probe, Alexa532, within the NBDs...
April 21, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28432020/surface-modification-of-acetaminophen-particles-by-atomic-layer-deposition
#14
Tommi O Kääriäinen, Marianna Kemell, Marko Vehkamäki, Marja-Leena Kääriäinen, Alexandra Correia, Hélder A Santos, Luis M Bimbo, Jouni Hirvonen, Pekka Hoppu, Steven M George, David C Cameron, Mikko Ritala, Markku Leskelä
Active pharmaceutical ingredients (APIs) are predominantly organic solid powders. Due to their bulk properties many APIs require processing to improve pharmaceutical formulation and manufacturing in the preparation for various drug dosage forms. Improved powder flow and protection of the APIs are often anticipated characteristics in pharmaceutical manufacturing. In this work, we have modified acetaminophen particles with atomic layer deposition (ALD) by conformal nanometer scale coatings in a one-step coating process...
April 18, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28431927/membrane-insertion-of-f0-c-subunit-of-f0f1-atpase-depends-on-glycolipozyme-mpiase-and-is-stimulated-by-yidc
#15
Hanako Nishikawa, Masaru Sasaki, Ken-Ichi Nishiyama
The F0 c subunit of F0F1 ATPase (F0-c) possesses two membrane-spanning stretches with N- and C-termini exposed to the periplasmic (extracellular) side of the cytoplasmic membrane of E. coli. Although F0-c insertion has been extensively analyzed in vitro by means of protease protection assaying, it is unclear whether such assays allow elucidation of the insertion process faithfully, since the membrane-protected fragment, an index of membrane insertion, is a full-length polypeptide of F0-c, which is the same as the protease-resistant conformation without membrane insertion...
April 18, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28431576/enhanced-neuroinvasion-by-smaller-soluble-prions
#16
Cyrus Bett, Jessica Lawrence, Timothy D Kurt, Christina Orru, Patricia Aguilar-Calvo, Anthony E Kincaid, Witold K Surewicz, Byron Caughey, Chengbiao Wu, Christina J Sigurdson
Infectious prion aggregates can propagate from extraneural sites into the brain with remarkable efficiency, likely transported via peripheral nerves. Yet not all prions spread into the brain, and the physical properties of a prion that is capable of transit within neurons remain unclear. We hypothesized that small, diffusible aggregates spread into the CNS via peripheral nerves. Here we used a structurally diverse panel of prion strains to analyze how the prion conformation impacts transit into the brain. Two prion strains form fibrils visible ultrastructurally in the brain in situ, whereas three strains form diffuse, subfibrillar prion deposits and no visible fibrils...
April 21, 2017: Acta Neuropathologica Communications
https://www.readbyqxmd.com/read/28431243/cryo-em-structure-of-the-open-human-ether-%C3%A3-go-go-related-k-channel-herg
#17
Weiwei Wang, Roderick MacKinnon
The human ether-à-go-go-related potassium channel (hERG, Kv11.1) is a voltage-dependent channel known for its role in repolarizing the cardiac action potential. hERG alteration by mutation or pharmacological inhibition produces Long QT syndrome and the lethal cardiac arrhythmia torsade de pointes. We have determined the molecular structure of hERG to 3.8 Å using cryo-electron microscopy. In this structure, the voltage sensors adopt a depolarized conformation, and the pore is open. The central cavity has an atypically small central volume surrounded by four deep hydrophobic pockets, which may explain hERG's unusual sensitivity to many drugs...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28431242/structural-and-functional-analysis-of-a-%C3%AE-2-adrenergic-receptor-complex-with-grk5
#18
Konstantin E Komolov, Yang Du, Nguyen Minh Duc, Robin M Betz, João P G L M Rodrigues, Ryan D Leib, Dhabaleswar Patra, Georgios Skiniotis, Christopher M Adams, Ron O Dror, Ka Young Chung, Brian K Kobilka, Jeffrey L Benovic
The phosphorylation of agonist-occupied G-protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) functions to turn off G-protein signaling and turn on arrestin-mediated signaling. While a structural understanding of GPCR/G-protein and GPCR/arrestin complexes has emerged in recent years, the molecular architecture of a GPCR/GRK complex remains poorly defined. We used a comprehensive integrated approach of cross-linking, hydrogen-deuterium exchange mass spectrometry (MS), electron microscopy, mutagenesis, molecular dynamics simulations, and computational docking to analyze GRK5 interaction with the β2-adrenergic receptor (β2AR)...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28431169/spa-ln-a-scoring-function-of-ligand-nucleic-acid-interactions-via-optimizing-both-specificity-and-affinity
#19
Zhiqiang Yan, Jin Wang
Nucleic acids have been widely recognized as potential targets in drug discovery and aptamer selection. Quantifying the interactions between small molecules and nucleic acids is critical to discover lead compounds and design novel aptamers. Scoring function is normally employed to quantify the interactions in structure-based virtual screening. However, the predictive power of nucleic acid-ligand scoring functions is still a challenge compared to other types of biomolecular recognition. With the rapid growth of experimentally determined nucleic acid-ligand complex structures, in this work, we develop a knowledge-based scoring function of nucleic acid-ligand interactions, namely SPA-LN...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28431137/trapp-webserver-predicting-protein-binding-site-flexibility-and-detecting-transient-binding-pockets
#20
Antonia Stank, Daria B Kokh, Max Horn, Elena Sizikova, Rebecca Neil, Joanna Panecka, Stefan Richter, Rebecca C Wade
The TRAnsient Pockets in Proteins (TRAPP) webserver provides an automated workflow that allows users to explore the dynamics of a protein binding site and to detect pockets or sub-pockets that may transiently open due to protein internal motion. These transient or cryptic sub-pockets may be of interest in the design and optimization of small molecular inhibitors for a protein target of interest. The TRAPP workflow consists of the following three modules: (i) TRAPP structure- generation of an ensemble of structures using one or more of four possible molecular simulation methods; (ii) TRAPP analysis-superposition and clustering of the binding site conformations either in an ensemble of structures generated in step (i) or in PDB structures or trajectories uploaded by the user; and (iii) TRAPP pocket-detection, analysis, and visualization of the binding pocket dynamics and characteristics, such as volume, solvent-exposed area or properties of surrounding residues...
April 20, 2017: Nucleic Acids Research
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