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https://www.readbyqxmd.com/read/28088110/highly-sensitive-detection-of-cysteine-over-glutathione-and-homo-cysteine-new-insight-into-the-michael-addition-of-mercapto-group-to-maleimide
#1
Zhaoyang Chen, Qian Sun, Yuhua Yao, Xiaoxiang Fan, Weibing Zhang, Junhong Qian
A fluorescence "off-on" probe CMP for thiols was designed with coumarin as the fluorophore and maleimide as the receptor. The fluorescence of the coumarin was quenched through photoinduced electron transfer (PET) from the fluorophore to maleimide group. The Michael addition of the mercapto group toward maleimide formed a thioether with relatively weak fluorescence. The intramolecular nucleophilic substitution of amino group in cysteine (Cys) to alkylthio produced a much stronger fluorescent amino adduct, which was supported by UPLC-MS and NMR titration...
January 7, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28088012/new-4-4-chlorophenyl-2-2-6-2%C3%A2-terpyridine-ruthenium-ii-complexes-synthesis-characterization-interaction-with-dna-bsa-and-cytotoxicity-studies
#2
Milan M Milutinović, Ana Rilak, Ioannis Bratsos, Olivera Klisurić, Milan Vraneš, Nevenka Gligorijević, Siniša Radulović, Živadin D Bugarčić
In this study, we have developed a series of new monofunctional Ru(II) complexes of the general formula mer-[Ru(Cl-Ph-tpy)(N-N)Cl]Cl in which Cl-Ph-tpy is 4'-(4-chlorophenyl)-2,2':6',2″-terpyridine, N-N is a bidentate chelating ligand (1,2-diaminoethane (en, 1), 1,2-diaminocyclohexane (dach, 2) or 2,2'-bipyridine (bpy, 3)). All complexes were fully characterized by elemental analysis and spectroscopic techniques (IR, UV-Vis, 1D and 2D NMR). Their chemical behavior in aqueous solution was studied by UV-Vis and NMR spectroscopy showing that all compounds are relatively labile leading to the formation of the corresponding aqua species 1aq-3aq...
October 14, 2016: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28087830/recognition-of-the-magnaporthe-oryzae-effector-avr-pia-by-the-decoy-domain-of-the-rice-nlr-immune-receptor-rga5
#3
Diana Ortiz, Karine De Guillen, Stella Cesari, Véronique Chalvon, Jérome Gracy, André Padilla, Thomas Kroj
Nucleotide-binding domain and leucine-rich repeat proteins (NLRs) are important receptors in plant immunity that allow recognition of pathogen effectors. The rice NLR RGA5 recognizes the Magnaporthe oryzae effector AVR-Pia through direct interaction. Here, we gained detailed insights into the molecular and structural bases of AVR-Pia-RGA5 interaction and the role of the RATX1 decoy domain of RGA5. NMR titration combined with in vitro and in vivo protein-protein interaction analyses identified the AVR-Pia interaction surface that binds to the RATX1 domain...
January 13, 2017: Plant Cell
https://www.readbyqxmd.com/read/28080040/insights-into-thiol-aromatic-interactions-a-stereoelectronic-basis-for-s-h-%C3%AF-interactions
#4
Christina R Forbes, Sudipta Kumar Sinha, Himal Kanti Ganguly, Shi Bai, Glenn P A Yap, Sandeep Patel, Neal J Zondlo
Thiols can engage favorably with aromatic rings in S-H/π interactions, within abiological systems and within proteins. However, the underlying bases for S-H/π interactions are not well understood. The crystal structure of Boc-L-4-thiolphenylalanine tert-butyl ester revealed crystal organization centered on the interaction of the thiol S-H with the aromatic ring of an adjacent molecule, with a through-space Hthiol...Caromatic distance of 2.71 Å, below the 2.90 Å sum of the van der Waals radii of H and C...
January 12, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28078416/poly-ethylene-glycol-functionalization-of-monolithic-poly-divinyl-benzene-for-improved-miniaturized-solid-phase-extraction-of-protein-rich-samples
#5
Esme Candish, Aminreza Khodabandeh, Marianne Gaborieau, Thomas Rodemann, Robert A Shellie, Andrew A Gooley, Emily F Hilder
Non-specific protein adsorption on hydrophobic solid phase extraction (SPE) adsorbents can reduce the efficacy of purification. To improve sample clean-up, poly(divinyl benzene) (PDVB) monoliths grafted with hydrophilic polyethylene glycol methacrylate (PEGMA) were developed. Residual vinyl groups (RVGs) of the PDVB were employed as anchor points for PEGMA grafting. Two PEGMA monomers, M n 360 and 950, were compared for graft solutions containing 5-20% monomer. Protein binding was qualitatively screened using fluorescently labeled human serum albumin (HSA) to determine optimal PEGMA concentration...
January 11, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28078344/kinetic-analysis-of-copper-transfer-from-a-chaperone-to-its-target-protein-mediated-by-complex-formation
#6
Kristine L Kay, Liang Zhou, Leonardo Tenori, Justin M Bradley, Chloe Singleton, Margaret A Kihlken, Simone Ciofi-Baffoni, Nick E Le Brun
Chaperone proteins that traffic copper around the cell minimise its toxicity by maintaining it in a tightly bound form. The transfer of copper from chaperones to target proteins is promoted by complex formation, but the kinetic characteristics of transfer have yet to be demonstrated for any chaperone-target protein pair. Here we report studies of copper transfer between the Atx1-type chaperone CopZ from Bacillus subtilis and the soluble domains of its cognate P-type ATPase transporter, CopAab. Transfer of copper from CopZ to CopAab was found to occur rapidly, with a rate constant at 25 °C of ∼267 s(-1), many orders of magnitude higher than that for Cu(i) dissociation from CopZ in the absence of CopAab...
January 12, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28077807/folding-of-apomyoglobin-analysis-of-transient-intermediate-structure-during-refolding-using-quick-hydrogen-deuterium-exchange-and-nmr
#7
Chiaki Nishimura
The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28076999/iridoids-and-anti-inflammatory-properties-of-n-butanol-extract-of-linaria-tingitana-boiss-reut
#8
Mourad Hanfer, Thamere Cheriet, Souad Ameddah, Ines Mancini, Ramdane Seghiri, Ahmed Menad, Samir Benayache, Fadila Benayache
The analysis of the n-butanol extract of Linaria tingitana (BELT) by HPLC-DAD-ESI/MS allowed the identification of four iridoids structurally confirmed by NMR and ESI-MS/MS extensive experiments data. The subjection of BELT to the anti-inflammatory activity showed that it exhibited a concentration dependent stabilisation of HRBC membrane, inhibition of protein denaturation and nitric oxide scavenging effect in the in vitro process. These results were confirmed in the in vivo experiments which showed that BELT was found to be most pronounced at 200 mg/kg after carrageenan injection which significantly reduced the swelling in both early and late phases of carrageenan-evoked oedema, as well as a significant reduce at the accumulation of infiltrating cells, inhibition of the myeloperoxidase activity and suppressed the lipid peroxidation...
January 11, 2017: Natural Product Research
https://www.readbyqxmd.com/read/28075555/familial-mutations-may-switch-conformational-preferences-in-%C3%AE-synuclein-fibrils
#9
Liang Xu, Buyong Ma, Ruth Nussinov, Damien Thompson
The pathogenesis of Parkinson's disease is closely associated with the aggregation of the α-synuclein protein. Several familial mutants have been identified and shown to affect the aggregation kinetics of α-synuclein through distinct molecular mechanisms. Quantitative evaluation of the relative stabilities of the wild type and mutant fibrils is crucial for understanding the aggregation process and identifying the key component steps. In this work, we examined two topologically different α-synuclein fibril structures that are either determined by solid-state NMR method or modelled based on solid-state NMR data, and characterized their conformational properties and thermodynamic stabilities using molecular dynamics simulations...
January 11, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28074361/partially-deuterated-samples-of-het-s-218-289-fibrils-assignment-and-deuterium-isotope-effect
#10
Albert A Smith, Francesco Ravotti, Emilie Testori, Riccardo Cadalbert, Matthias Ernst, Anja Böckmann, Beat H Meier
Fast magic-angle spinning and partial sample deuteration allows direct detection of (1)H in solid-state NMR, yielding significant gains in mass sensitivity. In order to further analyze the spectra, (1)H detection requires assignment of the (1)H resonances. In this work, resonance assignments of backbone H(N) and Hα are presented for HET-s(218-289) fibrils, based on the existing assignment of Cα, Cβ, C', and N resonances. The samples used are partially deuterated for higher spectral resolution, and the shifts in resonance frequencies of Cα and Cβ due to the deuterium isotope effect are investigated...
January 10, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28070494/pure-myopathy-with-enlarged-mitochondria-associated-to-a-new-mutation-in-mtnd2-gene
#11
Alice Zanolini, Ana Potic, Franco Carrara, Eleonora Lamantea, Daria Diodato, Flavia Blasevich, Silvia Marchet, Marina Mora, Francesco Pallotti, Lucia Morandi, Massimo Zeviani, Costanza Lamperti
To date, only few mutations in the mitochondrial DNA (mtDNA)-encoded ND2 subunit of Complex I have been reported, usually presenting a severe phenotype characterized by early onset encephalomyopathy and early death. In this report, we describe a new mutation in the MTND2 gene in a 21-year-old man with a mild myopathic phenotype characterized by exercise intolerance and increased plasma lactate at rest. Electromyography and brain NMR were normal, and no cardiac involvement was present. Muscle biopsy showed a massive presence of ragged red - COX-positive fibres, with enlarged mitochondria containing osmiophilic inclusions...
March 2017: Molecular Genetics and Metabolism Reports
https://www.readbyqxmd.com/read/28069813/residues-in-the-recq-c-terminal-domain-of-the-human-werner-syndrome-helicase-are-involved-in-unwinding-g-quadruplex-dna
#12
Amit Ketkar, Markus Voehler, Tresor Mukiza, Robert L Eoff
The structural and biophysical properties typically associated with G-quadruplex (G4) structures renders them a significant block for DNA replication, which must be overcome for cell division to occur. The Werner syndrome protein (WRN) is a RecQ-family helicase that has been implicated in the efficient processing of G4 DNA structures. The aim of the current study was to identify the residues of WRN involved in the binding and ATPase-driven unwinding of G4 DNA. Using a c-Myc G4 DNA model sequence and recombinant WRN, we have determined that the RecQ-C-terminal (RQC) domain of WRN imparts a 2-fold preference for binding to G4 DNA relative to non-G4 DNA substrates...
January 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28069412/influence-of-glutamic-acid-residues-and-ph-on-the-properties-of-transmembrane-helices
#13
Venkatesan Rajagopalan, Denise V Greathouse, Roger E Koeppe
Negatively charged side chains are important for the function of particular ion channels and certain other membrane proteins. To investigate the influence of single glutamic acid side chains on helices that span lipid-bilayer membranes, we have employed GWALP23 (acetyl-GGALW(5)LALALALALALALW(19)LAGA-amide) as a favorable host peptide framework. We substituted individual Leu residues with Glu residues (L12E or L14E or L16E) and incorporated specific (2)H-labeled alanine residues within the core helical region or near the ends of the sequence...
January 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28067528/urinary-1-h-nmr-metabolomic-fingerprinting-reveals-biomarkers-of-pulse-consumption-related-to-energy-metabolism-modulation-in-a-subcohort-from-the-predimed-study
#14
Francisco Madrid-Gambin, Rafael Llorach, Rosa Vázquez-Fresno, Mireia Urpi-Sarda, Enrique Almanza-Aguilera, Mar Garcia-Aloy, Ramón Estruch, Dolores Corella, Cristina Andres-Lacueva
Little is known about the metabolome fingerprint of pulse consumption. The study of robust and accurate biomarkers for pulse dietary assessment has great value for nutritional epidemiology regarding health benefits and their mechanisms. To characterize the fingerprinting of dietary pulses (chickpeas, lentils and beans), spot urine samples from a subcohort from the PREDIMED study were stratified, using a validated food frequency questionnaire. Non-pulse consumers (≤ 4 g/day of pulse intake) and habitual pulse consumers (≥ 25 g/day of pulse intake) were analysed using a 1H-NMR metabolomics approach combined with multi- and univariate data analysis...
January 9, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28067496/probing-conformational-exchange-dynamics-in-a-short-lived-protein-folding-intermediate-by-real-time-relaxation-dispersion-nmr
#15
Rémi Franco, Sergio Gil-Caballero, Isabel Ayala, Adrien Favier, Bernhard Brutscher
NMR spectroscopy is a powerful tool for studying molecular dynamics at atomic resolution simultaneously for a large number of nuclear sites. In this communication, we combine two powerful NMR techniques, relaxation-dispersion NMR and real-time NMR, in order to obtain unprecedented information on the conformational exchange dynamics present in short-lived excited protein states, such as those transiently accumulated during protein folding. We demonstrate the feasibility of the approach for the amyloidogenic protein β2-microglobulin that folds via an intermediate state which is believed to be responsible for the onset of the aggregation process leading to amyloid formation...
January 11, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28067358/simultaneous-nmr-characterisation-of-multiple-minima-in-the-free-energy-landscape-of-an-rna-uucg-tetraloop
#16
Aditi N Borkar, Pramodh Vallurupalli, Carlo Camilloni, Lewis E Kay, Michele Vendruscolo
RNA molecules in solution tend to undergo structural fluctuations of relatively large amplitude and to populate a range of different conformations some of which with low populations. It is still very challenging, however, to characterise the structures of these low populated states and to understand their functional roles. In the present study, we address this problem by using NMR residual dipolar couplings (RDCs) as structural restraints in replica-averaged metadynamics (RAM) simulations. By applying this approach to a 14-mer RNA hairpin containing the prototypical UUCG tetraloop motif, we show that it is possible to construct the free energy landscape of this RNA molecule...
January 9, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28066974/hydrogen-mobility-and-protein-water-interaction-in-proteins-of-solid-state
#17
Kalman Tompa, Monika Bokor, Dorina Ágner, Dávid Iván, Denes Kovacs, Tamas Verebélyi, Peter Tompa
In this work we lay the groundwork of characterizing the mobility of hydrogen-hydrogen pairs (proton-proton radial vectors) in proteins in the solid state that contains only residual water. In this novel approach we introduce new ways of analyzing and interpreting data, by: i) representing hydrogen mobility (HM) and melting diagram (MD) data recorded by wide-line 1H-NMR as a function of fundamental temperature (thermal excitation energy); ii) suggesting novel mode of interpretation of these parameters that sheds light on details of protein-water interaction such as the exact amount of water molecules and the distribution of barrier potentials pertaining to their rotational and surface translational mobility; iii) relying on directly determined physical observables...
January 8, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28065984/the-possible-role-of-nonbilayer-structures-in-regulating-atp-synthase-activity-in-mitochondrial-membranes
#18
S E Gasanov, A A Kim, R K Dagda
The effects of temperature and of the membrane-active protein CTII on the formation of nonbilayer structures in mitochondrial membranes were studied by (31)P-NMR. Increasing the temperature of isolated mitochondrial fractions correlated with an increase in ATP synthase activity and the formation of nonbilayer packed phospholipids with immobilized molecular mobility. Computer modeling was employed for analyzing the interaction of mitochondrial membrane phospholipids with the molecular surface of CTII, which behaves like a dicyclohexylcarbodiimide-binding protein (DCCD-BP) of the F0 group in a lipid phase...
July 2016: Biophysics
https://www.readbyqxmd.com/read/28063412/spectral-characterisation-antiviral-activities-in-silico-admet-and-molecular-docking-of-the-compounds-isolated-from-tectona-grandis-to-chikungunya-virus
#19
Sangeetha K, Indu Purushothaman, Rajarajan S
Chikungunya infection is treated symptomatically with antipyretics and anti-inflammatory drugs without any specific antiviral drug till date. The lack of an approved antiviral drug and the emergence of virulent strains after 2006 epidemics emphasize the need for the development of potential antiviral drugs to Chikungunya virus. Hence, we studied the antiviral activity of the extracts and compounds isolated from Tectona grandis leaves to both the Asian and East central South African strains of Chikungunya virus...
January 4, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28062839/redox-and-ph-linked-conformational-changes-in-triheme-cytochrome-ppca-from-geobacter-sulfurreducens
#20
Leonor Morgado, Marta Bruix, P Raj Pokkuluri, Carlos A Salgueiro, David L Turner
The periplasmic triheme cytochrome PpcA from Geobacter sulfurreducens is highly abundant; it is the likely reservoir of electrons to the outer surface to assist the reduction of extracellular terminal acceptors; these include insoluble metal oxides in natural habitats and electrode surfaces from which electricity can be harvested. A detailed thermodynamic characterization of PpcA showed that it has an important redox-Bohr effect that might implicate the protein in e(-)/H(+) coupling mechanisms to sustain cellular growth...
January 15, 2017: Biochemical Journal
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