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Molecular dynamics simulation of the human U2B" protein complex with U2 snRNA hairpin IV in aqueous solution.

Guo , J X; Gmeiner, W H
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /08/2001 EN
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A 2200-ps molecular dynamics (MD) simulation of the U2 snRNA hairpin IV/U2B" complex was performed in aqueous solution using the particle mesh Ewald method to consider long-range electrostatic interactions. To investigate the interaction and recognition process between the RNA and protein, the free energy contributions resulting from individual amino acids of the protein component of the RNA/protein complex were calculated using the recently developed glycine-scanning method. The results revealed that the loop region of the U2 snRNA hairpin IV interacted mainly with three regions of the U2B" protein: 1) beta 1-helix A, 2) beta 2-beta 3, and 3) beta 4-helix C. U2 snRNA hairpin IV bound U2B" in a similar orientation as that previously described for U1 snRNA with the U1A' protein; however, the details of the interaction differed in several aspects. In particular, beta 1-helix A and beta 4-helix C in U2B" were not observed to interact with RNA in the U1A' protein complex. Most of the polar and charged residues in the interacting regions had larger mutant free energies than the nonpolar residues, indicating that electrostatic interactions were important for stabilizing the RNA/protein complex. The interaction was further stabilized by a network of hydrogen bonds and salt bridges formed between RNA and protein that was maintained throughout the MD trajectory. In addition to the direct interactions between RNA and the protein...

Three-dimensional structure of the complexes of ribonuclease A with 2',5'-CpA and 3',5'-d(CpA) in aqueous solution, as obtained by NMR and restrained molecular dynamics.

Toiron, C.; González, C.; Bruix, M.; Rico, M.
Fonte: Cold Spring Harbor Laboratory Press Publicador: Cold Spring Harbor Laboratory Press
Tipo: Artigo de Revista Científica
Publicado em /08/1996 EN
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The three-dimensional structure of the complexes of ribonuclease A with cytidyl-2',5'-adenosine (2',5'-CpA) and deoxycytidyl-3',5'-deoxyadenosine [3',5'-d(CpA)] in aqueous solution has been determined by 1H NMR methods in combination with restrained molecular dynamics calculations. Twenty-three intermolecular NOE cross-corrections for the 3',5'-d(CpA) complex and 19 for the 2',5'-CpA, together with about 1,000 intramolecular NOEs assigned for each complex, were translated into distance constraints and used in the calculation. No significant changes in the global structure of the enzyme occur upon complex formation. The side chains of His 12, Thr 45, His 119, and the amide backbone group of Phe 120 are involved directly in the binding of the ligands at the active site. The conformation of the two bases is anti in the two complexes, but differs from the crystal structure in the conformation of the two sugar rings in 3',5'-d(CpA), shown to be in the S-type region, as deduced from an analysis of couplings between the ribose protons. His 119 is found in the two complexes in only one conformation, corresponding to position A in the free protein. Side chains of Asn 67, Gln 69, Asn 71, and Glu 111 from transient hydrogen bonds with the adenine base...

Genetic control of immune response. The dose of antigen given in aqueous solution is critical in determining which mouse strain is high responder to poly(LTyr, LGlu)-poly(LPro)--poly(LLys)

Fonte: The Rockefeller University Press Publicador: The Rockefeller University Press
Tipo: Artigo de Revista Científica
Publicado em 01/05/1975 EN
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Antibody response to different doses of (T,G)-Pro--L, given in aqueous solution, was investigated in the high responder SJL and low responder DBA/1 strains by measuring hemolytic plaque-forming cells (PFC) in the spleens as well as hemagglutination titers in the sera. The gene responsible for the difference between the two strains in the response to this antigen, given in complete Freund's adjuvant, has been previously denoted Ir-3. This gene is not linked to the major histocompatibility locus. In the response to the optimal dose (1 mug) of antigen, no difference could be shown between the strains. The peak of the response and the numbers of direct and indirect PFC were similar in both strains in the primary and secondary response. After injection of higher doses (10-100 mug) of antigen, both the direct and indirect PFC responses were lower in the low responder than in the high responder strain. Moreover, the peak of the response occurred earlier in the high responder strain in the primary response to the 10 mu dose of antigen. After administration of a suboptimal dose (0.02 mug) of antigen, the low responder strain produced in the primary response 4-20 times more indirect plaques than the high responder strain. Also the number of direct plaques was higher in the low responder than in the high responder strain. The serum antibody responses to the optimal and higher doses of antigen were parallel to the PFC responses. From inhibition of PFC with free antigen...

N,N'-(Hexane-1,6-diyl)bis(4-methyl-N-(oxiran-2-ylmethyl)benzenesulfonamide): Synthesis via cyclodextrin mediated N-alkylation in aqueous solution and further Prilezhaev epoxidation

Fischer, Julian; Millan, Simon; Ritter, Helmut
Fonte: Beilstein-Institut Publicador: Beilstein-Institut
Tipo: Artigo de Revista Científica
Publicado em 09/12/2013 EN
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N-alkylation of N,N'-(hexane-1,6-diyl)bis(4-methylbenzenesulfonamide) with allyl bromide and subsequent Prilezhaev reaction with m-chloroperbenzoic acid to give N,N'-(hexane-1,6-diyl)bis(4-methyl-N-(oxiran-2-ylmethyl)benzenesulfonamide) is described. This twofold alkylation was performed in aqueous solution, whereby α-, and randomly methylated β-cyclodextrin were used as adequate phase transfer catalysts and the cyclodextrin–guest complexes were characterized by 1H NMR and 2D NMR ROESY spectroscopy. Finally, the curing properties of the diepoxide with lysine-based α-amino-ε-caprolactam were analyzed by rheological measurements.

Blinking and nonradiant dark fraction of water-soluble quantum dots in aqueous solution

Yao, Jie; Larson, Daniel R.; Vishwasrao, Harshad D.; Zipfel, Warren R.; Webb, Watt W.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
EN
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Water-soluble quantum dots (qdots) are now being used in life sciences research to take advantage of their bright, easily excited fluorescence and high photostability. Although the frequent erratic blinking and substantial dark (never radiant) fractions that occur in all available qdots may interfere with many applications, these properties of individual particles in biological environments had not been fully evaluated. By labeling Qdot-streptavidin with organic dyes, we were able to distinguish individual dark and bright qdots and to observe blinking events as qdots freely diffused in aqueous solution. Bright fractions were measured by confocal fluorescence coincidence analysis (CFCA) and two-photon cross-correlation fluorescence correlation spectroscopy (FCS). The observed bright fractions of various preparations were proportional to the ensemble quantum yields (QYs), but the intrinsic brightness of individual qdots was found to be constant across samples with different QYs but the same emission wavelengths. Increasing qdots' illuminated dwell time by 10-fold during FCS did not change the fraction of apparently dark qdots but did increase the detected fraction of blinking qdots, suggesting that the dark population does not arise from millisecond blinking. Combining CFCA with wide-field imaging of arrays of qdots localized in dilute agarose gel...

Kinetics of pramlintide degradation in aqueous solution as a function of temperature and pH

Kenley, Richard A.; Tracht, Scott; Stepanenko, Anna; Townsend, Michael; L'Italien, James
Fonte: Springer-Verlag Publicador: Springer-Verlag
Tipo: Artigo de Revista Científica
Publicado em 15/03/2000 EN
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The stability of the 37-amino acid peptide pramlintide, in aqueous solution, was studied as a function of pH and temperature. Samples of pramlintide formulated as a parenteral product were exposed to elevated temperatures and to realistic storage conditions for as long as 30 months. Pramlintide degradation was monitored by three high-performance liquid chromatography (HPLC) methods: a reversedphase (RP-HPLC) and a strong-cation exchange (SCX-HPLC) method for percentage purity determination by area normalization, plus a second RP-HPLC method for potency determinationversus external standards. The pH-rate profile for pramlintide shows increasing degradation rate constants with increasing pH over the range pH=3.5 to 5.0. The Arrhenius expression for pramlintide degradation at pH=4.0 over the temperature range 5°C to 50°C is In(k0)=37.39−21.900/RT, where k0 is the zero-order rate constant (in %/mo) for pramlintide degradation. The pramlintide parenteral product formulated at pH=4.0 is extremely stable, with percentage purity and percentage potency loss of only approximately 2% over 30 months at 5°C. The formulated pramlintide drug product has acceptable shelf life for long-term storage at 5°C and up to a 30-day patient use when stored at ambient temperature.

Surface cellulose modification with 2-aminomethylpyridine for copper, cobalt, nickel and zinc removal from aqueous solution

Silva Filho,Edson Cavalcanti; Santos Júnior,Luiz Sousa; Silva,Marcia Maria Fernandes; Fonseca,Maria Gardênnia; Santana,Sirlane Aparecida Abreu; Airoldi,Claudio
Fonte: ABM, ABC, ABPol Publicador: ABM, ABC, ABPol
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/02/2013 EN
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Cellulose was first modified with thionyl chloride, followed by reaction with 2-aminomethylpyridine to yield 6-(2'-aminomethylpyridine)-6-deoxycellulose. The resulting chemically-immobilized surface was characterized by elemental analysis, FTIR, 13C NMR and thermogravimetry. From 0.28% of nitrogen incorporated in the polysaccharide backbone, the amount of 0.10 ± 0.01 mmol of the proposed molecule was anchored per gram of the chemically modified cellulose. The available basic nitrogen centers attached to the covalent pendant chain bonded to the biopolymer skeleton were investigated for copper, cobalt, nickel and zinc adsorption from aqueous solution at room temperature. The newly synthesized biopolymer gave maximum sorption capacities of 0.100 ± 0.012, 0.093 ± 0.021, 0.074 ± 0.011 and 0.071 ± 0.019 mmol.g-1 for copper, cobalt, nickel and zinc cations, respectively, using the batchwise method, whose data was fitted to different sorption models, the best fit being obtained with the Langmuir model. The results suggested the use of this anchored biopolymer for cation removal from the environment.

SELF-ASSEMBLY OF TRIBLOCK COPOLYMERS IN AQUEOUS SOLUTION

Olea, Andrés F.; Martínez, Francisco; Fuentes, Irma; Silva, Patricio; Urbano, Bruno
Fonte: Sociedad Chilena de Química Publicador: Sociedad Chilena de Química
Tipo: Artículo de revista
EN
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The aggregation of PE4VP-b-PS-b-PE4VP block copolymers was studied in aqueous solution. Triblock copolymers P4VP-b-PS-b-P4VP were synthesized by sequential anionic polymerization of poly(styrene) and poly(4-vinylpirydine) using sodium naphthalene as a bifunctional initiator. Subsequently, the 4- vinylpyridine units were quaternized with ethyl bromide to obtain cationic PE4VP-b-PS-b-PE4VP block copolymers. Both star and crew-cut micelles were formed. The concentrations at which micelles are formed cmc were determined, by steady-state and time-resolved fluorescence probing methods, as a function of quaternization degree. The results indicate that cmc of crew-cut micelles increases with increasing charge density of the PE4VP blocks. For star micelles there is not a clear dependency of cmc with the percentage of quaternization. The lifetime of pyrene fluorescence and the ratio I1/I3 were determined at concentrations of copolymers well above the cmc, and the results show that the location of pyrene into the micelle changes with the charge density of the micelle corona. The micropolarity sensed by pyrene decreases with increasing quaternization degree. The presence of aggregates was confirmed by transmission electronic microscopy.; This work was supported by FONDECYT 1070371...

Experimental and Theoretical Studies of Redox Reactions of o -Chloranil in Aqueous Solution.

Zare, Hamid; Eslami, Marzieh; Namazian, Mansoor; Coote, Michelle
Fonte: American Chemical Society Publicador: American Chemical Society
Tipo: Artigo de Revista Científica
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The electrochemical reduction of o-chloranil (OCA) in aqueous solution has been studied experimentally and theoretically. The effects of temperature and pH on various thermodynamic parameters were studied by means of cyclic voltammetry. The pH dependence

The effects of salts and ionic surfactants on the micellar structure of tri-block copolymer PEO-PPO-PEO in aqueous solution

Bharatiya, Bhavesh; Ghosh, Goutam; Bahadur, P; Jitendrakumar, Mata
Fonte: Marcel Dekker Inc. Publicador: Marcel Dekker Inc.
Tipo: Artigo de Revista Científica
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The micelles of two poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) block copolymers, P123 and F127 (same mol wt of PPO but different % PEO) in aqueous solution in the absence and presence of salts as well as ionic surfactant

Effect of phenol on the aggregation characteristics of an ethylene oxide-propylene oxide triblock copolymer P65 in aqueous solution

Jitendrakumar, Mata; Majhi, P R; Kubota, O; Khanal, A; Nakashima, K; Bahadur, P
Fonte: Academic Press Publicador: Academic Press
Tipo: Artigo de Revista Científica
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The effects of phenol on the micellization, micellar growth, and phase separation of a poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) (PEO-PPO-PEO) amphiphilic copolymer (Pluronic P65: EO19PO30EO19) in aqueous solution have be

Theoretical Study of the Oxidation Mechanism of Hematoxylin in Aqueous Solution

Namazian, Mansoor; Zare, Hamid; Coote, Michelle
Fonte: CSIRO Publishing Publicador: CSIRO Publishing
Tipo: Artigo de Revista Científica
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The oxidation of the two catechol rings A and B in the chemical structure of hematoxylin in aqueous solution has been studied theoretically in order to identify the mechanism of oxidation. In a recent experimental study, the oxidation mechanism of hematox

The nature of species derived from [Pt(bipy) 2 ] 2+ in aqueous solution: X-ray structural, mass spectral, NMR, and computational studies

Cavigliasso, German; Stranger, Robert; Lo, Warrick K.C.; Crowley, James D.; Blackman, Allan G.
Fonte: Pergamon-Elsevier Ltd Publicador: Pergamon-Elsevier Ltd
Tipo: Artigo de Revista Científica
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The reaction of [Pt(bipy)2]2+ with a variety of organic and inorganic ligands in aqueous solution has been studied by 195Pt, 1H and 13C NMR, X-ray crystallography, UV-Vis spectroscopy and high-resolution mass spectrometry. 195Pt NMR spectra of D2O solutio

Calculation of two-electron reduction potentials for some quinone derivatives in aqueous solution using Møller-Plesset perturbation theory

Namazian, Mansoor; Siahrostami, Samira; Noorbala, Mohammad; Coote, Michelle
Fonte: Elsevier Publicador: Elsevier
Tipo: Artigo de Revista Científica
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Møller-Plesset perturbation theory at the level of third order (MP3) is used to compute two-electron reduction potentials for some substituted benzoquinones in aqueous solution. The calculations are carried out at the MP2 and MP3 levels with the use of c

A swollen phase observed between the liquid-crystalline phase and the interdigitated phase induced by pressure and/or adding ethanol in DPPC aqueous solution

Seto, H.; Hishida, M.; Nobutou, H.; Yamada, N. L.; Nagao, M.; Takeda, T.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 21/02/2006
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A swollen phase, in which the mean repeat distance of lipid bilayers is larger than the other phases, is found between the liquid-crystalline phase and the interdigitated gel phase in DPPC aqueous solution. Temperature, pressure and ethanol concentration dependences of the structure were investigated by small-angle neutron scattering, and a bending rigidity of lipid bilayers was by neutron spin echo. The nature of the swollen phase is similar to the anomalous swelling reported previously. However, the temperature dependence of the mean repeat distance and the bending rigidity of lipid bilayers are different. This phase could be a precursor to the interdigitated gel phase induced by pressure and/or adding ethanol.; Comment: 7 pages, 6 figures

Inverse swelling of a hydrophobic polymer in aqueous solution

Pretti, Marco
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 29/05/2006
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We address the problem of inverse polymer swelling. This phenomenon, in which a collapsed polymer chain swells upon decreasing temperature, can be observed experimentally in so-called thermoreversible homopolymers in aqueous solution, and is believed to be related to the role of hydrophobicity in protein folding. We consider a lattice-fluid model of water, defined on a body-centered cubic lattice, which has been previously shown to account for most thermodynamic anomalies of water and of hydrophobic solvation for monomeric solutes. We represent the polymer as a self-avoiding walk on the same lattice, and investigate the resulting model at a first order approximation level, equivalent to the exact calculation on a Husimi lattice. Depending on interaction parameters and applied pressure, the model exhibits first and/or second order swelling transitions upon decreasing temperature.; Comment: 10 pages, 8 figures, 1 table

Self-assembly of liquid crystal block copolymer PEG-b-smectic polymer in pure state and in dilute aqueous solution

Xu, B.; Pinol, R.; Nono-Djamen, M.; Pensec, S.; Keller, P.; Albouy, P. -A.; Levy, D.; Li, M. -H.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 03/09/2009
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A series of amphiphilic LC block copolymers, in which the hydrophobic block is a smectic polymer poly(4-methoxyphenyl 4-(6-acryloyloxy-hexyloxy)-benzoate) (PA6ester1) and the hydrophilic block is polyethyleneglycol (PEG), were synthesized and characterized. The self-assembly of one of them in both the pure state and the dilute aqueous solution was investigated in detail. Nano-structures in the pure state were studied by SAXS and WAXS on samples aligned by a magnetic field. A hexagonal cylindrical micro-segregation phase was observed with a lattice distance of 11.2 nm. The PEG blocks are in the cylinder, while the smectic polymer blocks form a matrix with layer spacing 2.4 nm and layer normal parallel to the long axis of the cylinders. Faceted unilamellar polymer vesicles, polymersomes, were formed in water, as revealed by cryo-TEM. In the lyotropic bilayer membrane of these polymersomes, the thermotropic smectic order in the hydrophobic block is clearly visible with layer normal parallel to the membrane surface.

Low-Temperature and High-Pressure Induced Swelling of a Hydrophobic Polymer-Chain in Aqueous Solution

Paschek, Dietmar; Nonn, Sascha; Geiger, Alfons
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 21/03/2005
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We report molecular dynamics simulations of a hydrophobic polymer-chain in aqueous solution between $260 {K}$ and $420 {K}$ at pressures of $1 {bar}$, $3000 {bar}$, and $4500 {bar}$. The simulations reveal a hydrophobically collapsed state at low pressures and high temperatures. At $3000 {bar}$ and about $260 {K}$ and at $4500 {bar}$ and about $260 {K}$, however, a transition to a swelled state is observed. The transition is driven by a smaller volume and a remarkably strong lower enthalpy of the swelled state, indicating a steep positive slope of the corresponding transition line. The swelling is stabilized almost completely by the energetically favorable state of water in the polymers hydrophobic first hydration shell at low temperatures. Although surprising, this finding is consistent with the observation of a positive heat capacity of hydrophobic solvation. Moreover, the slope and location of the observed swelling transition for the collapsed hydrophobic chain coincides remarkably well with the cold denaturation transition of proteins.; Comment: 9 pages, 9 figures, twocolumn revtex

Use of an activated carbon from antibiotic waste for the removal of Hg(II) from aqueous solution

Budinova, Temenuzhka; Petrov, Nartzislav; Parra Soto, José Bernardo; Baloutzov, Venelin
Fonte: Elsevier Publicador: Elsevier
Tipo: Artículo Formato: 22195 bytes; application/pdf
ENG
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8 pages, 6 figures, 4 tables.-- PMID: 17428604 [PubMed].-- Available online Apr 10, 2007.; Porous carbon has been prepared from waste antibiotic material by a chemical activation method using K2CO3 as an activating reagent. Carbon was studied systematically by the adsorption of nitrogen and iodine. It was found that the process parameters such as activation temperature and activation time are crucial for preparing high-quality activated carbon. The proper choice of the preparation conditions allows to produce microporous activated carbon with a micropore volume up to 0.492 cm3/g and a BET surface area of 1260 m2/g. Adsorption of mercury(II) from an aqueous solution on antibiotic carbon was investigated under the varying conditions of agitation time, metal ion concentration and pH. The adsorption capacity of the carbon is 129 mg/g.; Financial support from The Ministry of Education and Science (project CC-1401) is gratefully acknowledged.; Peer reviewed

Spontaneous CO Release from RuII(CO)2?Protein Complexes in Aqueous Solution, Cells, and Mice

Chaves-Ferreira, Miguel; Albuquerque, In?s S.; Matak-Vinkovic, Dijana; Coelho, Ana C.; Carvalho, Sandra M.; Saraiva, L?gia M.; Rom?o, Carlos C.; Bernardes, Gon?alo J. L.
Fonte: Wiley Publicador: Wiley
Tipo: Article; published version
EN
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This is the final published version. It first appeared at http://onlinelibrary.wiley.com/doi/10.1002/anie.201409344/abstract.; We demonstrate that RuII(CO)2?protein complexes, formed by the reaction of the hydrolytic decomposition products of [fac-RuCl(?2-H2NCH2CO2)(CO)3] (CORM-3) with histidine residues exposed on the surface of proteins, spontaneously release CO in aqueous solution, cells, and mice. CO release was detected by mass spectrometry (MS) and confocal microscopy using a CO-responsive turn-on fluorescent probe. These findings support our hypothesis that plasma proteins act as CO carriers after in?vivo administration of CORM-3. CO released from a synthetic bovine serum albumin (BSA)?RuII(CO)2 complex leads to downregulation of the cytokines interleukin (IL)-6, IL-10, and tumor necrosis factor (TNF)-? in cancer cells. Finally, administration of BSA?RuII(CO)2 in mice bearing a colon carcinoma tumor results in enhanced CO accumulation at the tumor. Our data suggest the use of RuII(CO)2?protein complexes as viable alternatives for the safe and spatially controlled delivery of therapeutic CO in?vivo.; We thank the FCT, the EU, and the EPSRC for funding. G.J.L.B. is a Royal Society University Research Fellow.